ORCID Profile
0000-0001-9850-0828
Current Organisation
University of Queensland
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Plant Cell and Molecular Biology | Plant Biology | Plant Developmental and Reproductive Biology | Plant Physiology | Receptors and Membrane Biology | Crop and Pasture Biochemistry and Physiology
ANZSRC Socio-Economic Objective (SEO)
Environmentally Sustainable Plant Production not elsewhere classified | Expanding Knowledge in the Biological Sciences | Soybeans | Grain Legumes | Farmland, Arable Cropland and Permanent Cropland Soils |
Related Links
Publications
Purple Acid Phosphatases of Arabidopsis thaliana
Publisher: Elsevier BV
Date: 08-2002
A NAP-AAO3 Regulatory Module Promotes Chlorophyll Degradation via ABA Biosynthesis in Arabidopsis Leaves
Publisher: Oxford University Press (OUP)
Date: 12-2014
Isolation and analysis of a cDNA clone that encodes an alfalfa (Medicago sativa) aspartate aminotransferase
Publisher: Springer Science and Business Media LLC
Date: 12-1991
DOI: 10.1007/BF00293827
A sucrose transporter, LjSUT4, is up-regulated during Lotus japonicus nodule development
Publisher: Oxford University Press (OUP)
Date: 13-05-2003
DOI: 10.1093/JXB/ERG179
The Sulfate Transporter SST1 Is Crucial for Symbiotic Nitrogen Fixation in Lotus japonicus Root Nodules
Publisher: Oxford University Press (OUP)
Date: 04-2005
Genomic Inventory and Transcriptional Analysis of Medicago truncatula Transporters
Publisher: Oxford University Press (OUP)
Date: 18-12-2009
Abstract: Transporters move hydrophilic substrates across hydrophobic biological membranes and play key roles in plant nutrition, metabolism, and signaling and, consequently, in plant growth, development, and responses to the environment. To initiate and support systematic characterization of transporters in the model legume Medicago truncatula, we identified 3,830 transporters and classified 2,673 of these into 113 families and 146 subfamilies. Analysis of gene expression data for 2,611 of these transporters identified 129 that are expressed in an organ-specific manner, including 50 that are nodule specific and 36 specific to mycorrhizal roots. Further analysis uncovered 196 transporters that are induced at least 5-fold during nodule development and 44 in roots during arbuscular mycorrhizal symbiosis. Among the nodule- and mycorrhiza-induced transporter genes are many candidates for known transport activities in these beneficial symbioses. The data presented here are a unique resource for the selection and functional characterization of legume transporters.
Recent insights into antioxidant defenses of legume root nodules
Publisher: Wiley
Date: 29-10-2010
DOI: 10.1111/J.1469-8137.2010.03512.X
Abstract: Legume root nodules are sites of intense biochemical activity and consequently are at high risk of damage as a result of the generation of reactive oxygen species (ROS) and reactive nitrogen species (RNS). These molecules can potentially give rise to oxidative and nitrosative damage but, when their concentrations are tightly controlled by antioxidant enzymes and metabolites, they also play positive roles as critical components of signal transduction cascades during nodule development and stress. Thus, recent advances in our understanding of ascorbate and (homo)glutathione biosynthesis in plants have opened up the possibility of enhancing N 2 fixation through an increase of their concentrations in nodules. It is now evident that antioxidant proteins other than the ascorbate‐glutathione enzymes, such as some isoforms of glutathione peroxidases, thioredoxins, peroxiredoxins, and glutathione S‐ transferases, are also critical for nodule activity. To avoid cellular damage, nodules are endowed with several mechanisms for sequestration of Fenton‐active metals (nicotianamine, phytochelatins, and metallothioneins) and for controlling ROS/RNS bioactivity (hemoglobins). The use of ‘omic’ technologies has expanded the list of known antioxidants in plants and nodules that participate in ROS/RNS/antioxidant signaling networks, although aspects of developmental variation and subcellular localization of these networks remain to be elucidated. To this end, a critical point will be to define the transcriptional and post‐transcriptional regulation of antioxidant proteins. Contents Summary 960 I. Introduction 961 II. Ascorbate 961 III. Thiols 963 IV. Ascorbate–glutathione pathway 963 V. Superoxide dismutases and catalases 964 VI. Thiol peroxidases: glutathione peroxidases and peroxiredoxins 966 VII. Protein disulfide reductases: thioredoxins and glutaredoxins 967 VIII. Glutathione S‐ transferases 967 IX. Antioxidants and metal sequestration 968 X. Antioxidants of nodule bacteroids 969 XI. Other molecules with antioxidative properties in nodules 969 XII. Antioxidants and oxidative/nitrosative signaling 970 XIII. Antioxidants and oxidative/nitrosative stress 971 XIV. Conclusions and perspectives 972 Acknowledgements 973 References 973
Application of synthetic peptide CEP1 increases nutrient uptake rates along plant roots
Publisher: Wiley
Date: 21-11-2021
Functional genomics of plant transporters in legume nodules
Publisher: CSIRO Publishing
Date: 2006
DOI: 10.1071/FP06085
Abstract: Over the past few decades, a combination of physiology, biochemistry, molecular and cell biology, and genetics has given us a basic understanding of some of the key transport processes at work in nitrogen-fixing legume nodules, especially those involved in nutrient exchange between infected plant cells and their endosymbiotic rhizobia. However, our knowledge in this area remains patchy and dispersed over numerous legume species. Recent progress in the areas of genomics and functional genomics of the two model legumes, Medicago truncatula and Lotus japonicus is rapidly filling the gap in knowledge about which plant transporter genes are expressed constitutively in nodules and other organs, and which are induced or expressed specifically in nodules. The latter class in particular is the focus of current efforts to understand specialised, nodule-specific roles of transporters. This article briefly reviews past work on the biochemistry and molecular biology of plant transporters in nodules, before describing recent work in the areas of transcriptomics and bioinformatics. Finally, we consider where functional genomics together with more classical approaches are likely to lead us in this area of research in the future.
An Iron-Activated Citrate Transporter, MtMATE67, Is Required for Symbiotic Nitrogen Fixation
Publisher: Oxford University Press (OUP)
Date: 28-12-2017
DOI: 10.1104/PP.17.01538
Overexpression of AtLOV1 in Switchgrass Alters Plant Architecture, Lignin Content, and Flowering Time
Publisher: Public Library of Science (PLoS)
Date: 26-12-2012
Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing
Publisher: Springer Science and Business Media LLC
Date: 20-06-2018
Genetic and genomic analysis of legume flowers and seeds
Publisher: Elsevier BV
Date: 04-2006
DOI: 10.1016/J.PBI.2006.01.014
Abstract: New tools, such as ordered mutant libraries, microarrays and sequence based comparative maps, are available for genetic and genomic studies of legumes that are being used to shed light on seed production, the objective of most arable farming. The new information and understanding brought by these tools are revealing the biological processes that underpin and impact on seed production.
Symbiotic nitrogen fixation research in the postgenomics era
Publisher: Wiley
Date: 2002
Legume genomes and discoveries in symbiosis research.
Publisher: Springer Science and Business Media LLC
Date: 2002
DOI: 10.1186/GB-2002-3-9-REPORTS4028
Abstract: A report on the First International Conference on Legume Genomics and Genetics: Translation to Crop Improvement, Minneapolis-St. Paul, USA, 2-6 June 2002.
Inferring large-scale gene regulatory networks using a low-order constraint-based algorithm
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/B917571G
Abstract: Recently, simplified graphical modeling approaches based on low-order conditional (in-)dependence calculations have received attention because of their potential to model gene regulatory networks. Such methods are able to reconstruct large-scale gene networks with a small number of experimental measurements, at minimal computational cost. However, unlike Bayesian networks, current low-order graphical models provide no means to distinguish between cause and effect in gene regulatory relationships. To address this problem, we developed a low-order constraint-based algorithm for gene regulatory network inference. The method is capable of inferring causal directions using limited-order conditional independence tests and provides a computationally-feasible way to analyze high-dimensional datasets while maintaining high reliability. To assess the performance of our algorithm, we compared it to several existing graphical models: relevance networks graphical Gaussian models ARACNE Bayesian networks and the classical constraint-based algorithm, using realistic synthetic datasets. Furthermore, we applied our algorithm to real microarray data from Escherichia coli Affymetrix arrays and validated the results by comparison to known regulatory interactions collected in RegulonDB. The algorithm was found to be both effective and efficient at reconstructing gene regulatory networks from microarray data.
Characterization of Three Functional High-Affinity Ammonium Transporters in Lotus japonicus with Differential Transcriptional Regulation and Spatial Expression
Publisher: Oxford University Press (OUP)
Date: 04-2004
Abstract: Ammonium is a primary source of nitrogen for plants. In legume plants ammonium can also be obtained by symbiotic nitrogen fixation, and \\batchmode \\documentclass[fleqn,10pt,legalpaper]{article} \\usepackage{amssymb} \\usepackage{amsfonts} \\usepackage{amsmath} \\pagestyle{empty} \\begin{document} \\(\\mathrm{NH}_{4}^{{+}}\\) \\end{document} is also a regulator of early and late symbiotic interaction steps. Ammonium transporters are likely to play important roles in the control of nodule formation as well as in nitrogen assimilation. Two new genes, LjAMT1 and LjAMT1 , were cloned from Lotus japonicus. Both were able to complement the growth defect of a yeast (Saccharomyces cerevisiae) ammonium transport mutant. Measurement of [14C]methylammonium uptake rates and competition experiments revealed that each transporter had a high affinity for \\batchmode \\documentclass[fleqn,10pt,legalpaper]{article} \\usepackage{amssymb} \\usepackage{amsfonts} \\usepackage{amsmath} \\pagestyle{empty} \\begin{document} \\(\\mathrm{NH}_{4}^{{+}}\\) \\end{document}. The K i for ammonium was 1.7, 3, and 15 μ m for LjAMT1 , 1 , and 1 , respectively. Real-time PCR revealed higher expression of LjAMT1 , 1 , and 1 genes in leaves than in roots and nodule, with expression levels decreasing in the order LjAMT1 & 1 & 1 except in flowers, in which LjAMT1 was expressed at higher level than in leaves, and LjAMT1 showed the lowest level of expression. Expression of LjAMT1 and 1 in roots was induced by nitrogen deprivation. Expression of LjAMT1 was repressed in leaves exposed to elevated CO2 concentrations, which also suppress photorespiration. Tissue and cellular localization of LjAMT1 genes expression, using promoter-β-glucuronidase and in situ RNA hybridization approaches, revealed distinct cellular spatial localization in different organs, including nodules, suggesting differential roles in the nitrogen metabolism of these organs.
From Model to Crop: Functional Analysis of a STAY-GREEN Gene in the Model Legume Medicago truncatula and Effective Use of the Gene for Alfalfa Improvement
Publisher: Oxford University Press (OUP)
Date: 28-09-2011
Abstract: Medicago truncatula has been developed into a model legume. Its close relative alfalfa (Medicago sativa) is the most widely grown forage legume crop in the United States. By screening a large population of M. truncatula mutants tagged with the transposable element of tobacco (Nicotiana tabacum) cell type1 (Tnt1), we identified a mutant line (NF2089) that maintained green leaves and showed green anthers, central carpels, mature pods, and seeds during senescence. Genetic and molecular analyses revealed that the mutation was caused by Tnt1 insertion in a STAY-GREEN (MtSGR) gene. Transcript profiling analysis of the mutant showed that loss of the MtSGR function affected the expression of a large number of genes involved in different biological processes. Further analyses revealed that SGR is implicated in nodule development and senescence. MtSGR expression was detected across all nodule developmental zones and was higher in the senescence zone. The number of young nodules on the mutant roots was higher than in the wild type. Expression levels of several nodule senescence markers were reduced in the sgr mutant. Based on the MtSGR sequence, an alfalfa SGR gene (MsSGR) was cloned, and transgenic alfalfa lines were produced by RNA interference. Silencing of MsSGR led to the production of stay-green transgenic alfalfa. This beneficial trait offers the opportunity to produce premium alfalfa hay with a more greenish appearance. In addition, most of the transgenic alfalfa lines retained more than 50% of chlorophylls during senescence and had increased crude protein content. This study illustrates the effective use of knowledge gained from a model system for the genetic improvement of an important commercial crop.
Genome-Wide Identification of Medicago Peptides Involved in Macronutrient Responses and Nodulation
Publisher: Oxford University Press (OUP)
Date: 13-10-2017
DOI: 10.1104/PP.17.01096
Lotus japonicus karrikin receptors display divergent ligand-binding specificities and organ-dependent redundancy
Publisher: Cold Spring Harbor Laboratory
Date: 03-09-2019
DOI: 10.1101/754937
Abstract: Karrikins (KARs), smoke-derived butenolides, are perceived by the α/β-fold hydrolase KARRIKIN INSENSITIVE2 (KAI2) and are thought to mimic endogenous, yet elusive plant hormones tentatively called KAI2-ligands (KLs). The sensitivity to different karrikin types as well as the number of KAI2 paralogs varies among plant species, suggesting ersification and co-evolution of ligand-receptor relationships. In legumes, which comprise a number of important crops with protein-rich, nutritious seed, KAI2 has duplicated. We report sub-functionalization of KAI2a and KAI2b in the model legume Lotus japonicus and demonstrate that their ability to bind the synthetic ligand GR24 ent -5DS differs in vitro as well as in genetic assays in Lotus japonicus and in the heterologous Arabidopsis thaliana background. These differences can be explained by the exchange of a widely conserved phenylalanine in the binding pocket of KAI2a with a tryptophan in KAI2b, which occured independently in KAI2 proteins of several unrelated angiosperms. Furthermore, two polymorphic residues in the binding pocket are conserved across a number of legumes and may contribute to ligand binding preferences. Unexpectedly, L. japonicus responds to erse synthetic KAI2-ligands in an organ-specific manner. Hypocotyl development responds to KAR 1 , KAR 2 and rac -GR24, while root system development responds only to KAR 1 . This organ-specificity cannot be explained by receptor-ligand preferences alone, because Lj KAI2a is sufficient for karrikin responses in the hypocotyl, while Lj KAI2a and Lj KAI2b operate redundantly in roots. Our findings open novel research avenues into the evolution and ersity of butenolide ligand-receptor relationships, their ecological significance and the mechanisms controlling erse developmental responses to different KAI2 ligands.
MtSWEET11, a Nodule-Specific Sucrose Transporter of Medicago truncatula
Publisher: Oxford University Press (OUP)
Date: 28-03-2016
DOI: 10.1104/PP.15.01910
Deficiency in plastidic glutamine synthetase alters proline metabolism and transcriptomic response in Lotus japonicus under drought stress
Publisher: Wiley
Date: 26-08-2010
DOI: 10.1111/J.1469-8137.2010.03440.X
Abstract: The role of plastidic glutamine synthetase (GS2) in proline biosynthesis and drought stress responses in Lotus japonicus was investigated using the GS2 mutant, Ljgln2-2. Wild-type (WT) and mutant plants were submitted to different lengths of time of water and nutrient solution deprivation. Several biochemical markers were measured and the transcriptional response to drought was determined by both quantitative real-time polymerase chain reaction and transcriptomics. The Ljgln2-2 mutant exhibited normal sensitivity to mild water deprivation, but physiological, biochemical and massive transcriptional differences were detected in the mutant, which compromised recovery (rehydration) following re-watering after severe drought stress. Proline accumulation during drought was substantially lower in mutant than in WT plants, and significant differences in the pattern of expression of the genes involved in proline metabolism were observed. Transcriptomic analysis revealed that about three times as many genes were regulated in response to drought in Ljgln2-2 plants compared with WT. The transcriptomic and accompanying biochemical data indicate that the Ljgln2-2 mutant is subject to more intense cellular stress than WT during drought. The results presented here implicate plastidic GS2 in proline production during stress and provide interesting insights into the function of proline in response to drought.
Methods for studying nodule development and function
Publisher: Springer-Verlag
Date: 2005
Improved node culture methods for rapid vegetative propagation of switchgrass (Panicum virgatum L.)
Publisher: Springer Science and Business Media LLC
Date: 04-03-2021
DOI: 10.1186/S12870-021-02903-Z
Abstract: Switchgrass ( Panicum virgatum L.) is an important bioenergy and forage crop. The outcrossing nature of switchgrass makes it infeasible to maintain a genotype through sexual propagation. Current asexual propagation protocols in switchgrass have various limitations. An easy and highly-efficient vegetative propagation method is needed to propagate large natural collections of switchgrass genotypes for genome-wide association studies (GWAS). Micropropagation by node culture was found to be a rapid method for vegetative propagation of switchgrass. Bacterial and fungal contamination during node culture is a major cause for cultural failure. Adding the biocide, Plant Preservative Mixture (PPM, 0.2%), and the fungicide, Benomyl (5 mg/l), in the incubation solution after surface sterilization and in the culture medium significantly decreased bacterial and fungal contamination. In addition, “shoot trimming” before subculture had a positive effect on shoot multiplication for most genotypes tested. Using the optimized node culture procedure, we successfully propagated 330 genotypes from a switchgrass GWAS panel in three separate experiments. Large variations in shoot induction efficiency and shoot growth were observed among genotypes. Separately, we developed an in planta node culture method by stimulating the growth of aerial axillary buds into shoots directly on the parent plants, through which rooted plants can be generated within 6 weeks. By circumventing the tissue culture step and avoiding application of exterior hormones, the in planta node culture method is labor- and cost-efficient, easy to master, and has a high success rate. Plants generated by the in planta node culture method are similar to seedlings and can be used directly for various experiments. In this study, we optimized a switchgrass node culture protocol by minimizing bacterial and fungal contamination and increasing shoot multiplication. With this improved protocol, we successfully propagated three quarters of the genotypes in a erse switchgrass GWAS panel. Furthermore, we established a novel and high-throughput in planta node culture method. Together, these methods provide better options for researchers to accelerate vegetative propagation of switchgrass.
Lotus japonicus: legume research in the fast lane
Publisher: Elsevier BV
Date: 05-2005
DOI: 10.1016/J.TPLANTS.2005.03.008
Abstract: Legumes are of immense importance to humanity and a key to sustainable agriculture. Two model species, Lotus japonicus and Medicago truncatula, are the focus of genome sequencing and functional genomics programmes, but most researchers focus exclusively on one or the other. In spite of this, legume researchers now have a unique opportunity to integrate work on these and other legume species, including soybean, common bean and pea to create a platform for comparative genomics second to none of any other plant family. The question is: do we have the scientific fortitude and political will to achieve this?
Ammonia transport in free-living and symbiotic Rhizobium sp. ANU289
Publisher: Microbiology Society
Date: 02-1986
Analysis of Large Seeds from Three Different Medicago truncatula Ecotypes Reveals a Potential Role of Hormonal Balance in Final Size Determination of Legume Grains
Publisher: MDPI AG
Date: 08-09-2016
DOI: 10.3390/IJMS17091472
Nitrogen remobilization and conservation, and underlying senescence‐associated gene expression in the perennial switchgrass Panicum virgatum
Publisher: Wiley
Date: 03-03-2016
DOI: 10.1111/NPH.13898
Abstract: Improving nitrogen (N) remobilization from aboveground to underground organs during yearly shoot senescence is an important goal for sustainable production of switchgrass ( Panicum virgatum ) as a biofuel crop. Little is known about the genetic control of senescence and N use efficiency in perennial grasses such as switchgrass, which limits our ability to improve the process. Switchgrass aboveground organs (leaves, stems and inflorescences) and underground organs (crowns and roots) were harvested every month over a 3‐yr period. Transcriptome analysis was performed to identify genes differentially expressed in various organs during development. Total N content in aboveground organs increased from spring until the end of summer, then decreased concomitant with senescence, while N content in underground organs exhibited an increase roughly matching the decrease in shoot N during fall. Hundreds of senescence‐associated genes were identified in leaves and stems. Functional grouping indicated that regulation of transcription and protein degradation play important roles in shoot senescence. Coexpression networks predict important roles for five switchgrass NAC (NAM, ATAF1,2, CUC2) transcription factors (TFs) and other TF family members in orchestrating metabolism of carbohydrates, N and lipids, protein modification/degradation, and transport processes during senescence. This study establishes a molecular basis for understanding and enhancing N remobilization and conservation in switchgrass.
LegumeGRN: A Gene Regulatory Network Prediction Server for Functional and Comparative Studies
Publisher: Public Library of Science (PLoS)
Date: 03-07-2013
Celebrating 20 Years of Genetic Discoveries in Legume Nodulation and Symbiotic Nitrogen Fixation
Publisher: Oxford University Press (OUP)
Date: 24-10-2019
DOI: 10.1105/TPC.19.00279
Standards for plant synthetic biology: A common syntax for exchange of DNA parts
Publisher: Wiley
Date: 14-07-2015
DOI: 10.1111/NPH.13532
Abstract: Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease‐mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.
Global gene expression profiling of two switchgrass cultivars following inoculation withBurkholderia phytofirmansstrain PsJN
Publisher: Oxford University Press (OUP)
Date: 18-03-2015
DOI: 10.1093/JXB/ERV096
Abstract: Improvement and year-to-year stabilization of biomass yields are primary objectives for the development of a low-input switchgrass feedstock production system using microbial endophytes. An earlier investigation of the effect of Burkholderia phytofirmans strain PsJN on switchgrass germplasm demonstrated differential responses between genotypes. PsJN inoculation of cv. Alamo (lowland ecotype) increased the plant root system, shoot length, and biomass yields, whereas it had no beneficial effect on cv. Cave-in-Rock (upland ecotype). To understand the gene networks governing plant growth promotion responses triggered by PsJN, the gene expression profiles were analysed in these two hosts, following seedling inoculation. The Affymetrix platform switchgrass expressed sequence tag (EST) microarray chip representing 122 972 probe sets, developed by the DOE BioEnergy Science Center, was employed to assess transcript abundance at 0.5, 2, 4, and 8 DAI (days after PsJN inoculation). Approximately 20 000 switchgrass probe sets showed significant responses in either cultivar. Switchgrass identifiers were used to map 19 421 genes in MapMan software. There were apparent differences in gene expression profiling between responsive and non-responsive cultivars after PsJN inoculation. Overall, there were 14 984 and 9691 genes affected by PsJN inoculation in Alamo and Cave-in-Rock, respectively. Of these, 394 are annotated as pathogenesis-related genes. In the responsive cv. Alamo, 68 pathogenesis-related genes were affected, compared with only 10 in the non-responsive cv. Cave-in-Rock. At the very early stage at 0.5 DAI, both cultivars exhibited similar recognition and defence responses, such as genes in signalling and proteolysis, after which the defence reaction in the responsive cv. Alamo became weaker while it was sustained in non-responsive cv. Cave-in-Rock.
Integrative functional genomics of salt acclimatization in the model legume Lotus japonicus
Publisher: Wiley
Date: 30-11-2007
Corrigendum: A Plant Gene Encoding One-Heme and Two-Heme Hemoglobins With Extreme Reactivities Toward Diatomic Gases and Nitrite
Publisher: Frontiers Media SA
Date: 25-01-2021
MtMTP2-Facilitated Zinc Transport Into Intracellular Compartments Is Essential for Nodule Development in Medicago truncatula
Publisher: Frontiers Media SA
Date: 10-07-2018
Interplay between genetic predisposition, macronutrient intake and type 2 diabetes incidence: analysis within EPIC-InterAct across eight European countries
Publisher: Springer Science and Business Media LLC
Date: 17-03-2018
Mechanisms of ammonium transport, accumulation, and retention in ooyctes and yeast cells expressingArabidopsisAtAMT1;1
Publisher: Wiley
Date: 21-06-2006
DOI: 10.1016/J.FEBSLET.2006.06.026
Abstract: Ammonium is a primary source of N for plants, so knowing how it is transported, stored, and assimilated in plant cells is important for rational approaches to optimise N-use in agriculture. Electrophysiological studies of Arabidopsis AtAMT1 expressed in oocytes revealed passive, Deltapsi-driven transport of NH(4)(+) through this protein. Expression of AtAMT1 in a novel yeast mutant defective in endogenous ammonium transport and vacuolar acidification supported the above mechanism for AtAMT1 and revealed a central role for acid vacuoles in storage and retention of ammonia in cells. These results highlight the mechanistic differences between plant AMT proteins and related transporters in bacteria and animal cells, and suggest novel strategies to enhance nitrogen use efficiency in agriculture.
Real-time RT-PCR profiling of over 1400Arabidopsistranscription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes
Publisher: Wiley
Date: 04-2004
The peptide GOLVEN10 controls nodule and lateral root organogenesis and positioning along the longitudinal root axis
Publisher: Cold Spring Harbor Laboratory
Date: 06-05-2022
DOI: 10.1101/2022.05.06.490929
Abstract: GLV/RGF peptide encoding genes can be identified in genomes of all plants that can form roots or root-like structures suggesting they were essential for transition of plants to land. In Medicago truncatula , five of fifteen GOLVEN(GLV)/ROOT MERISTEM GROWTH FACTOR (RGF) peptide coding genes were induced during nodule organogenesis and to a varying extent under nitrogen deficiency and auxin treatment. Expression of MtGLV9 and MtGLV10 at nodule initiation sites was dependent on the transcription factor NODULE INCEPTION. Overexpression of all five nodule-induced GLV genes in M. truncatula hairy roots as well as application of the corresponding synthetic peptides resulted in a 25-50% reduction in nodule number indicating GOLVENs are negative regulators of nodule organogenesis. The peptide GOLVEN10 shifted the position of the first formed lateral root (rhizotaxis) as well as the first formed nodule along the longitudinal primary root axis, a phenomenon we term ‘nodulotaxis’, thereby reducing the absolute length of the zone of lateral organ formation on roots. Application of synthetic GOLVEN10 peptide caused an increase in cell number but not cell length in each root cortical cell layer causing an increase in root length and a consequent spatiotemporal delay in formation of the first lateral organ. Nodule positioning is an understudied trait, yet it determines the length of the root that can support nodule formation and consequently the total number of functional nodules formed. We identify for the first time, genetic factors called GOLVEN peptides that alter nodule and lateral root positioning on the primary root along with several other traits including nodule organ initiation and root architecture.
Characterization of two novel nodule-enhanced α-type carbonic anhydrases from Lotus japonicus
Publisher: Elsevier BV
Date: 04-2011
DOI: 10.1016/J.BBAPAP.2011.01.007
Abstract: Two cDNA clones coding for α-type carbonic anhydrases (CA EC 4.2.1.1) in the nitrogen-fixing nodules of the model legume Lotus japonicus were identified. Functionality of the full-length proteins was confirmed by heterologous expression in Escherichia coli and purification of the encoded polypeptides. The developmental expression pattern of LjCAA1 and LjCAA2 revealed that both genes code for nodule enhanced carbonic anhydrase isoforms, which are induced early during nodule development. The genes were slightly to moderately down-regulated in ineffective nodules formed by mutant Mesorhizobium loti strains, indicating that these genes may also be involved in biochemical and physiological processes not directly linked to nitrogen fixation/assimilation. The spatial expression profiling revealed that both genes were expressed in nodule inner cortical cells, vascular bundles and central tissue. These results are discussed in the context of the possible roles of CA in nodule carbon dioxide (CO(2)) metabolism.
Lignin Modification Leads to Increased Nodule Numbers in Alfalfa
Publisher: Oxford University Press (OUP)
Date: 09-01-2014
Abstract: Reduction of lignin levels in the forage legume alfalfa (Medicago sativa) by down-regulation of the monolignol biosynthetic enzyme hydroxycinnamoyl coenzyme A:shikimate hydroxycinnamoyl transferase (HCT) results in strongly increased digestibility and processing ability of lignocellulose. However, these modifications are often also associated with dwarfing and other changes in plant growth. Given the importance of nitrogen fixation for legume growth, we evaluated the impact of constitutively targeted lignin modification on the belowground organs (roots and nodules) of alfalfa plants. HCT down-regulated alfalfa plants exhibit a striking reduction in root growth accompanied by an unexpected increase in nodule numbers when grown in the greenhouse or in the field. This phenotype is associated with increased levels of gibberellins and certain flavonoid compounds in roots. Although HCT down-regulation reduced biomass yields in both the greenhouse and field experiments, the impact on the allocation of nitrogen to shoots or roots was minimal. It is unlikely, therefore, that the altered growth phenotype of reduced-lignin alfalfa is a direct result of changes in nodulation or nitrogen fixation efficiency. Furthermore, HCT down-regulation has no measurable effect on carbon allocation to roots in either greenhouse or 3-year field trials.
Specificity and regulation of the dicarboxylate carrier on the peribacteroid membrane of soybean nodules
Publisher: Springer Science and Business Media LLC
Date: 10-1990
DOI: 10.1007/BF02411397
A DICARBOXYLATE TRANSPORTER ON THE PERIBACTEROID MEMBRANE OF SOYBEAN NODULES
Publisher: Wiley
Date: 11-04-1988
The Integral Membrane Protein SEN1 is Required for Symbiotic Nitrogen Fixation in Lotus japonicus Nodules
Publisher: Oxford University Press (OUP)
Date: 28-11-2011
DOI: 10.1093/PCP/PCR167
Abstract: Legume plants establish a symbiotic association with bacteria called rhizobia, resulting in the formation of nitrogen-fixing root nodules. A Lotus japonicus symbiotic mutant, sen1, forms nodules that are infected by rhizobia but that do not fix nitrogen. Here, we report molecular identification of the causal gene, SEN1, by map-based cloning. The SEN1 gene encodes an integral membrane protein homologous to Glycine max nodulin-21, and also to CCC1, a vacuolar iron/manganese transporter of Saccharomyces cerevisiae, and VIT1, a vacuolar iron transporter of Arabidopsis thaliana. Expression of the SEN1 gene was detected exclusively in nodule-infected cells and increased during nodule development. Nif gene expression as well as the presence of nitrogenase proteins was detected in rhizobia from sen1 nodules, although the levels of expression were low compared with those from wild-type nodules. Microscopic observations revealed that symbiosome and/or bacteroid differentiation are impaired in the sen1 nodules even at a very early stage of nodule development. Phylogenetic analysis indicated that SEN1 belongs to a protein clade specific to legumes. These results indicate that SEN1 is essential for nitrogen fixation activity and symbiosome/bacteroid differentiation in legume nodules.
Symbiotic Leghemoglobins Are Crucial for Nitrogen Fixation in Legume Root Nodules but Not for General Plant Growth and Development
Publisher: Elsevier BV
Date: 03-2005
DOI: 10.1016/J.CUB.2005.01.042
Abstract: Hemoglobins are ubiquitous in nature and among the best-characterized proteins. Genetics has revealed crucial roles for human hemoglobins, but similar data are lacking for plants. Plants contain symbiotic and nonsymbiotic hemoglobins the former are thought to be important for symbiotic nitrogen fixation (SNF). In legumes, SNF occurs in specialized organs, called nodules, which contain millions of nitrogen-fixing rhizobia, called bacteroids. The induction of nodule-specific plant genes, including those encoding symbiotic leghemoglobins (Lb), accompanies nodule development. Leghemoglobins accumulate to millimolar concentrations in the cytoplasm of infected plant cells prior to nitrogen fixation and are thought to buffer free oxygen in the nanomolar range, avoiding inactivation of oxygen-labile nitrogenase while maintaining high oxygen flux for respiration. Although widely accepted, this hypothesis has never been tested in planta. Using RNAi, we abolished symbiotic leghemoglobin synthesis in nodules of the model legume Lotus japonicus. This caused an increase in nodule free oxygen, a decrease in the ATP/ADP ratio, loss of bacterial nitrogenase protein, and absence of SNF. However, LbRNAi plants grew normally when fertilized with mineral nitrogen. These data indicate roles for leghemoglobins in oxygen transport and buffering and prove for the first time that plant hemoglobins are crucial for symbiotic nitrogen fixation.
The Medicago truncatula Gene Expression Atlas (MtGEA): A Tool for Legume Seed Biology and Biotechnology
Publisher: Springer Netherlands
Date: 2012
The Galactolipid Digalactosyldiacylglycerol Accumulates in the Peribacteroid Membrane of Nitrogen-fixing Nodules of Soybean and Lotus
Publisher: Elsevier BV
Date: 08-2004
Functional genomics: tools of the trade
Publisher: Wiley
Date: 11-01-2002
Isolation and characterization of a ntrC mutant of Bradyrhizobium (Parasponia) sp. ANU289
Publisher: Microbiology Society
Date: 05-1992
DOI: 10.1099/00221287-138-5-1019
Abstract: A mutant of Bradyrhizobium (Parasponia) sp. ANU289 affected in the regulation of nitrogen metabolism was isolated. The mutant, designated ANU293, was unable to induce ammonium transport (Amt), nitrate reductase (NR) or glutamine synthetase II (GSII) activities under conditions that induce these activities in the wild-type. However, glutamine synthetase I (GSI), which is expressed constitutively in the wild-type, was present at normal levels in the mutant. The mutant also retained the ability to fix nitrogen in vitro and in planta, although nodule development on siratro (Macroptilium atropurpureum) was retarded. Southern blot analysis showed that ntrC, the product of which is involved in regulation of nitrogen metabolism, is the site of pSUP1021 insertion in ANU293. These results indicate that the transcriptional activator NtrC is required for the expression of Amt, NR and GSII, but not GSI or nitrogenase in Bradyrhizobium (Parasponia) sp. ANU289.
Silencing Folylpolyglutamate Synthetase1 (FPGS1) in Switchgrass (Panicum virgatum L.) Improves Lignocellulosic Biofuel Production
Publisher: Frontiers Media SA
Date: 19-06-2020
ELECTROGENIC ATPASE ACTIVITY ON THE PERIBACTEROID MEMBRANE OF SOYBEAN (GLYCINE-MAX L) ROOT-NODULES
Publisher: Oxford University Press (OUP)
Date: 07-1989
DOI: 10.1104/PP.90.3.982
The SoybeanGmN6LGene Encodes a Late Nodulin Expressed in the Infected Zone of Nitrogen-Fixing Nodules
Publisher: Scientific Societies
Date: 07-2002
DOI: 10.1094/MPMI.2002.15.7.630
Abstract: Previously, we determined the N-terminal amino acid sequences of a number of putative peribacteroid membrane proteins from soybean. Here, we report the cloning of a gene, GmN6L, that encodes one of these proteins. The protein encoded by GmN6L is similar in sequence to MtN6, an early nodulin expressed in Medicago truncatula roots in response to infection by Sinorhizobium meliloti. The GmN6L gene was strongly expressed in mature nodules but not in other plant organs. GmN6L protein was first detected 2 weeks after inoculation with Bradyrhizobium japonicum and was limited to the infected zone of nodules. GmN6L protein was found in symbiosomes isolated from mature soybean nodules, both as a soluble protein and as a peripheral membrane protein bound to the peribacteroid membrane. These data indicate that GmN6L is a late nodulin, which is not involved in the infection process. Homology between GmN6L and FluG, a protein involved in signaling in Aspergillus nidulans, suggests that GmN6L may play a role in communication between the host and microsymbionts during symbiotic nitrogen fixation.
Cessation of photosynthesis in Lotus japonicus leaves leads to reprogramming of nodule metabolism
Publisher: Oxford University Press (OUP)
Date: 11-02-2013
DOI: 10.1093/JXB/ERT015
The Development of Bacteriophage Resistance in Vibrio alginolyticus Depends on a Complex Metabolic Adaptation Strategy
Publisher: MDPI AG
Date: 10-04-2021
DOI: 10.3390/V13040656
Abstract: Lytic bacteriophages have been well documented to play a pivotal role in microbial ecology due to their complex interactions with bacterial species, especially in aquatic habitats. Although the use of phages as antimicrobial agents, known as phage therapy, in the aquatic environment has been increasing, recent research has revealed drawbacks due to the development of phage-resistant strains among Gram-negative species. Acquired phage resistance in marine Vibrios has been proven to be a very complicated process utilizing biochemical, metabolic, and molecular adaptation strategies. The results of our multi-omics approach, incorporating transcriptome and metabolome analyses of Vibrio alginolyticus phage-resistant strains, corroborate this prospect. Our results provide insights into phage-tolerant strains diminishing the expression of phage receptors ompF, lamB, and btuB. The same pattern was observed for genes encoding natural nutrient channels, such as rbsA, ptsG, tryP, livH, lysE, and hisp, meaning that the cell needs to readjust its biochemistry to achieve phage resistance. The results showed reprogramming of bacterial metabolism by transcript regulations in key-metabolic pathways, such as the tricarboxylic acid cycle (TCA) and lysine biosynthesis, as well as the content of intracellular metabolites belonging to processes that could also significantly affect the cell physiology. Finally, SNP analysis in resistant strains revealed no evidence of amino acid alterations in the studied putative bacterial phage receptors, but several SNPs were detected in genes involved in transcriptional regulation. This phenomenon appears to be a phage-specific, fine-tuned metabolic engineering, imposed by the different phage genera the bacteria have interacted with, updating the role of lytic phages in microbial marine ecology.
Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes
Publisher: American Society for Microbiology
Date: 07-2016
DOI: 10.1128/AEM.01055-16
Abstract: Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N 2 to NH 3 , a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater ersity of crop plants through synthetic biology.
Plant metabolomics reveals conserved and divergent metabolic responses to salinity
Publisher: Wiley
Date: 08-11-2007
DOI: 10.1111/J.1399-3054.2007.00993.X
Abstract: New metabolic profiling technologies provide data on a wider range of metabolites than traditional targeted approaches. Metabolomic technologies currently facilitate acquisition of multivariate metabolic data using erse, mostly hyphenated, chromatographic detection systems, such as GC-MS or liquid chromatography coupled to mass spectrometry, Fourier-transformed infrared spectroscopy or NMR-based methods. Analysis of the resulting data can be performed through a combination of non-supervised and supervised statistical methods, such as independent component analysis and analysis of variance, respectively. These methods reduce the complex data sets to information, which is relevant for the discovery of metabolic markers or for hypothesis-driven, pathway-based analysis. Plant responses to salinity involve changes in the activity of genes and proteins, which invariably lead to changes in plant metabolism. Here, we highlight a selection of recent publications in the salt stress field, and use gas chromatography time-of-flight mass spectrometry profiles of polar fractions from the plant models, Arabidopsis thaliana, Lotus japonicus and Oryza sativa to demonstrate the power of metabolite profiling. We present evidence for conserved and ergent metabolic responses among these three species and conclude that a change in the balance between amino acids and organic acids may be a conserved metabolic response of plants to salt stress.
MtSSPdb: The Medicago truncatula Small Secreted Peptide Database
Publisher: Oxford University Press (OUP)
Date: 20-02-2020
DOI: 10.1104/PP.19.01088
Physiological and biochemical adaptive traits support the specific breeding of alfalfa (Medicago sativa ) for severely drought‐stressed or moisture‐favourable environments
Publisher: Wiley
Date: 16-05-2022
DOI: 10.1111/JAC.12600
Abstract: The adaptation of alfalfa to moisture‐favourable and drought‐prone environments and its underlying mechanisms have not been thoroughly investigated despite their crucial importance to maximize the crop breeding progress. The main aim of this study was to support breeding strategies by exploring the relationship of leaf morphophysiological traits assessed in three growth chamber experiments with the adaptive response of five cultivars (Mamuntanas Demnat 203 Erfoud 1 Prosementi SARDI 10) that showed large genotype × environment interaction (GEI) across 10 drought‐prone to moisture‐favourable Mediterranean environments. Changes in shoot and root metabolite profiles across moisture‐contrasting conditions were assessed for two cultivars with contrasting adaptation pattern. The cultivar specifically adapted to drought‐prone environments (Mamuntanas), compared with that specifically adapted to moisture‐favourable environments (Demnat 203), displayed: (i) lower leaf wilting under drought stress (ii) delayed leaf senescence under stress, assessed as limited chlorophyll reduction either in vivo from upper to central leaves or in vitro from control to polyethylene glycol‐treated leaflets, (iii) greater leaf tolerance to desiccation, measured in vitro as less pronounced reduction of leaf dry weight from control to polyethylene glycol‐treated leaflets, (iv) smaller leaves, (v) lower early root and shoot growth and (vi) lower leaf stomata density. The other cultivars exhibited different combinations and/or intermediate values of these traits. The metabolite profiles of Mamuntanas and Demnat 203 differed more in shoots than in roots. Mamuntanas accumulated more amino acids than Demnat 203 under moisture‐favourable and drought conditions. The distinct and partly incompatible combination of traits featuring the cultivars that maximized the crop yield in favourable or drought‐prone conditions (Mamuntanas and Demnat 203) improves our understanding of traits contributing to large GEI across moisture‐contrasting environments and support the breeding for specific adaptation to either condition. We identified a few inexpensive morphophysiological traits that could be used for early selection targeting drought‐prone environments.
The Medicago genome provides insight into the evolution of rhizobial symbioses
Publisher: Springer Science and Business Media LLC
Date: 16-11-2011
DOI: 10.1038/NATURE10625
Metabolome-ionome-biomass interactions
Publisher: Informa UK Limited
Date: 08-2008
DOI: 10.4161/PSB.3.8.6347
Legume Transcription Factors: Global Regulators of Plant Development and Response to the Environment
Publisher: Oxford University Press (OUP)
Date: 06-2007
Comparative ionomics and metabolomics in extremophile and glycophytic Lotus species under salt stress challenge the metabolic pre-adaptation hypothesis
Publisher: Wiley
Date: 21-01-2011
DOI: 10.1111/J.1365-3040.2010.02266.X
Abstract: The legume genus Lotus includes glycophytic forage crops and other species adapted to extreme environments, such as saline soils. Understanding salt tolerance mechanisms will contribute to the discovery of new traits which may enhance the breeding efforts towards improved performance of legumes in marginal agricultural environments. Here, we used a combination of ionomic and gas chromatography-mass spectrometry (GC-MS)-based metabolite profilings of complete shoots (pooling leaves, petioles and stems) to compare the extremophile Lotus creticus, adapted to highly saline coastal regions, and two cultivated glycophytic grassland forage species, Lotus corniculatus and Lotus tenuis. L. creticus exhibited better survival after exposure to long-term lethal salinity and was more efficient at excluding Cl⁻ from the shoots than the glycophytes. In contrast, Na+ levels were higher in the extremophile under both control and salt stress, a trait often observed in halophytes. Ionomics demonstrated a differential rearrangement of shoot nutrient levels in the extremophile upon salt exposure. Metabolite profiling showed that responses to NaCl in L. creticus shoots were globally similar to those of the glycophytes, providing little evidence for metabolic pre-adaptation to salinity. This study is the first comparing salt acclimation responses between extremophile and non-extremophile legumes, and challenges the generalization of the metabolic salt pre-adaptation hypothesis.
Gene expression profiling of M. truncatula transcription factors identifies putative regulators of grain legume seed filling
Publisher: Springer Science and Business Media LLC
Date: 05-06-2008
DOI: 10.1007/S11103-008-9320-X
Abstract: Legume seeds represent a major source of proteins for human and livestock diets. The model legume Medicago truncatula is characterized by a process of seed development very similar to that of other legumes, involving the interplay of sets of transcription factors (TFs). Here, we report the first expression profiling of over 700 M. truncatula genes encoding putative TFs throughout seven stages of seed development, obtained using real-time quantitative RT-PCR. A total of 169 TFs were selected which were expressed at late embryogenesis, seed filling or desiccation. The site of expression within the seed was examined for 41 highly expressed transcription factors out of the 169. To identify possible target genes for these TFs, the data were combined with a microarray-derived transcriptome dataset. This study identified 17 TFs preferentially expressed in in idual seed tissues and 135 corresponding co-expressed genes, including possible targets. Certain of the TFs co-expressed with storage protein mRNAs correspond to those already known to regulate seed storage protein synthesis in Arabidopsis, whereas the timing of expression of others may be more specifically related to the delayed expression of the legumin-class storage proteins observed in legumes.
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass
Publisher: Springer Science and Business Media LLC
Date: 27-01-2021
DOI: 10.1038/S41586-020-03127-1
Abstract: Long-term climate change and periodic environmental extremes threaten food and fuel security 1 and global crop productivity 2–4 . Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience 5 , these approaches require sufficient knowledge of the genes that underlie productivity and adaptation 6 —knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass ( Panicum virgatum ). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate–gene–biomass associations were abundant but varied considerably among deeply erged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic ersity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene–trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.
Differentiation of plant cells during symbiotic nitrogen fixation
Publisher: Hindawi Limited
Date: 2002
DOI: 10.1002/CFG.155
Abstract: Nitrogen-fixing symbioses between legumes and bacteria of the family Rhizobiaceae involve differentiation of both plant and bacterial cells. Differentiation of plant root cells is required to build an organ, the nodule, which can feed and accommodate a large population of bacteria under conditions conducive to nitrogen fixation. An efficient vascular system is built to connect the nodule to the root, which delivers sugars and other nutrients to the nodule and removes the products of nitrogen fixation for use in the rest of the plant. Cells in the outer cortex differentiate to form a barrier to oxygen diffusion into nodules, which helps to produce the micro-aerobic environment necessary for bacterial nitrogenase activity. Cells of the central, infected zone of nodules undergo multiple rounds of endoreduplication, which may be necessary for colonisation by rhizobia and may enable enlargement and greater metabolic activity of these cells. Infected cells of the nodule contain rhizobia within a unique plant membrane called the peribacteroid or symbiosome membrane, which separates the bacteria from the host cell cytoplasm and mediates nutrient and signal exchanges between the partners. Rhizobia also undergo differentiation during nodule development. Not surprisingly, perhaps, differentiation of each partner is dependent upon interactions with the other. High-throughput methods to assay gene transcripts, proteins, and metabolites are now being used to explore further the different aspects of plant and bacterial differentiation. In this review, we highlight recent advances in our understanding of plant cell differentiation during nodulation that have been made, at least in part, using high-throughput methods.
Characterization of an ammonium transport protein from the peribacteroid membrane of soybean nodules
Publisher: American Association for the Advancement of Science (AAAS)
Date: 21-08-1998
DOI: 10.1126/SCIENCE.281.5380.1202
Abstract: Nitrogen-fixing bacteroids in legume root nodules are surrounded by the plant-derived peribacteroid membrane, which controls nutrient transfer between the symbionts. A nodule complementary DNA ( GmSAT1 ) encoding an ammonium transporter has been isolated from soybean. GmSAT1 is preferentially transcribed in nodules and immunoblotting indicates that GmSAT1 is located on the peribacteroid membrane. [ 14 C]methylammonium uptake and patch-cl analysis of yeast expressing GmSAT1 demonstrated that it shares properties with a soybean peribacteroid membrane NH 4 + channel described elsewhere. GmSAT1 is likely to be involved in the transfer of fixed nitrogen from the bacteroid to the host.
Molecular and cell biology of a family of voltage-dependent anion channel porins in Lotus japonicus
Publisher: Oxford University Press (OUP)
Date: 2004
Abstract: Voltage-dependent anion channels (VDACs) are generally considered as the main pathway for metabolite transport across the mitochondrial outer membrane. Recent proteomic studies on isolated symbiosome membranes from legume nodules indicated that VDACs might also be involved in transport of nutrients between plants and rhizobia. In an attempt to substantiate this, we carried out a detailed molecular and cellular characterization of VDACs in Lotus japonicus and soybean (Glycine max). Database searches revealed at least five genes encoding putative VDACs in each of the legumes L. japonicus, Medicago truncatula, and soybean. We obtained and sequenced cDNA clones from L. japonicus encoding five full-length VDAC proteins (LjVDAC1.1–1.3, LjVDAC2.1, and LjVDAC3.1). Complementation of a yeast (Saccharomyces cerevisiae) mutant impaired in VDAC1, a porin of the mitochondrial outer membrane, showed that LjVDAC1.1, LjVDAC1.2, LjVDAC2.1, and LjVDAC3.1, but not LjVDAC1.3, are functional and targeted to the mitochondrial outer membrane in yeast. Studies of the expression pattern of the five L. japonicus VDAC genes revealed largely constitutive expression of each throughout the plant, including nodules. Antibodies to LjVDAC1.1 of L. japonicus and the related POM36 protein of potato (Solanum tuberosum) recognized several proteins between 30 and 36 kD on western blots, including LjVDAC1.1, LjVDAC1.2, LjVDAC1.3, and LjVDAC2.1. Immunolocalization of VDACs in L. japonicus and soybean root nodules demonstrated their presence on not only mitochondria but also on numerous, small vesicles at the cell periphery. No evidence was found for the presence of VDACs on the symbiosome membrane. Nonetheless, the data indicate that VDACs may play more erse roles in plants than suspected previously.
Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatumL.)
Publisher: Wiley
Date: 18-02-2013
DOI: 10.1111/TPJ.12104
Abstract: Switchgrass (Panicum virgatum L.) is a perennial C4 grass with the potential to become a major bioenergy crop. To help realize this potential, a set of RNA-based resources were developed. Expressed sequence tags (ESTs) were generated from two tetraploid switchgrass genotypes, Alamo AP13 and Summer VS16. Over 11.5 million high-quality ESTs were generated with 454 sequencing technology, and an additional 169 079 Sanger sequences were obtained from the 5' and 3' ends of 93 312 clones from normalized, full-length-enriched cDNA libraries. AP13 and VS16 ESTs were assembled into 77 854 and 30 524 unique transcripts (unitranscripts), respectively, using the Newbler and pave programs. Published Sanger-ESTs (544 225) from Alamo, Kanlow, and 15 other cultivars were integrated with the AP13 and VS16 assemblies to create a universal switchgrass gene index (PviUT1.2) with 128 058 unitranscripts, which were annotated for function. An Affymetrix cDNA microarray chip (Pvi_cDNAa520831) containing 122 973 probe sets was designed from PviUT1.2 sequences, and used to develop a Gene Expression Atlas for switchgrass (PviGEA). The PviGEA contains quantitative transcript data for all major organ systems of switchgrass throughout development. We developed a web server that enables flexible, multifaceted analyses of PviGEA transcript data. The PviGEA was used to identify representatives of all known genes in the phenylpropanoid-monolignol biosynthesis pathway.
Spatial and Temporal Organization of Sucrose Metabolism in Lotus japonicus Nitrogen-Fixing Nodules Suggests a Role for the Elusive Alkaline/Neutral Invertase
Publisher: Springer Science and Business Media LLC
Date: 08-2006
DOI: 10.1007/S11103-006-9003-4
Abstract: Symbiotic nitrogen fixation (SNF) in legume nodules is a highly energy demanding process, fuelled by plant-supplied carbohydrates mainly in the form of sucrose. In this study, we have combined molecular and biochemical approaches in order to study the spatial and temporal organisation of sucrose metabolism in nitrogen-fixing nodules of the model legume Lotus japonicus, with an emphasis on the neglected role of alkaline/neutral invertase. For this purpose, a full-length cDNA clone coding for an alkaline/neutral invertase isoform, termed LjInv1, was identified in a L. japonicus mature nodule cDNA libraries. Alkaline/neutral invertase activity was also found to be the predominant invertase activity in mature nodules. Real-time reverse-transcription polymerase chain reaction analysis was used in order to study the temporal expression patterns of LjInv1 in parallel with genes encoding acid invertase and sucrose synthase (SuSy) isoforms, and enzymes involved in the subsequent hexose partitioning including hexokinase, phosphoglucomutase (PGM) and phosphoglucose isomerase (PGI). The spatial organisation of sucrose metabolism was studied by in situ localisation of LjInv1 transcripts and alkaline/neutral invertase activity, and SuSy protein during nodule development. Furthermore, the spatial organisation of hexose metabolism was investigated by histochemical localisation of hexokinase, PGM and PGI activities in mature nodules. The results considered together indicate that alkaline/neutral invertase could contribute to both the Glc-1-P and Glc-6-P pools in nodules, fuelling both biosynthetic processes and SNF. Furthermore, transcript profiling analysis revealed that genes coding for hexokinase and putative plastidic PGM and PGI isoforms are upregulated during the early stages of nodule development, while the levels of transcripts corresponding to cytosolic PGM and PGI isoforms remained similar to uninfected roots, indicating a possible role of LjInv1 in producing hexoses for starch production and other biosynthetic processes in developing nodules.
Medicago truncatulacopper transporter 1 (MtCOPT1) delivers copper for symbiotic nitrogen fixation
Publisher: Cold Spring Harbor Laboratory
Date: 31-01-2017
DOI: 10.1101/104554
Abstract: • Copper is an essential nutrient for symbiotic nitrogen fixation. This element is delivered by the host plant to the nodule, where membrane copper transporter would introduce it into the cell to synthesize cupro-proteins. • COPT family members in model legume Medicago truncatula were identified and their expression determined. Yeast complementation assays, confocal microscopy, and phenotypical characterization of a Tnt1 insertional mutant line were carried out in the nodule-specific M.truncatula COPT family member. • Medicago truncatula genome encodes eight COPT transporters. MtCOPT1 ( Medtr4g019870 ) is the only nodule-specific COPT gene. It is located in the plasma membrane of the differentiation, interzone and early fixation zones. Loss of MtCOPT1 function results in a copper-mitigated reduction of biomass production when the plant obtains its nitrogen exclusively from symbiotic nitrogen fixation. Mutation of MtCOPT1 results in diminished nitrogenase activity in nodules, likely an indirect effect from the loss of a copper-dependent function, such as cytochrome oxidase activity in copt1-1 bacteroids. • These data are consistent with a model in which MtCOPT1 transports copper from the apoplast into nodule cells to provide copper for essential metabolic processes associated with symbiotic nitrogen fixation.
Nodulation enhances dark CO2 fixation and recycling in the model legume Lotus japonicus
Publisher: Oxford University Press (OUP)
Date: 09-02-2011
DOI: 10.1093/JXB/ERR009
Abstract: During symbiotic nitrogen fixation (SNF), the nodule becomes a strong sink for photosynthetic carbon. Here, it was studied whether nodule dark CO(2) fixation could participate in a mechanism for CO(2) recycling through C(4)-type photosynthesis. Differences in the natural δ(13)C abundance between Lotus japonicus inoculated or not with the N-fixing Mesorhizobium loti were assessed. (13)C labelling and gene expression of key enzymes of CO(2) metabolism were applied in plants inoculated with wild-type or mutant fix(-) (deficient in N fixation) strains of M. loti, and in non-inoculated plants. Compared with non-inoculated legumes, inoculated legumes had higher natural δ(13)C abundance and total C in their hypergeous organs and nodules. In stems, (13)C accumulation and expression of genes coding for enzymes of malate metabolism were greater in inoculated compared with non-inoculated plants. Malate-oxidizing activity was localized in stem xylem parenchyma, sieve tubes, and photosynthetic outer cortex parenchyma of inoculated plants. In stems of plants inoculated with fix(-) M. loti strains, (13)C accumulation remained high, while accumulation of transcripts coding for malic enzyme isoforms increased. A potential mechanism is proposed for reducing carbon losses during SNF by the direct reincorporation of CO(2) respired by nodules and the transport and metabolism of C-containing metabolites in hypergeous organs.
Induction and Spatial Organization of Polyamine Biosynthesis During Nodule Development in Lotus japonicus
Publisher: Scientific Societies
Date: 12-2004
DOI: 10.1094/MPMI.2004.17.12.1283
Abstract: Putrescine and other polyamines are produced by two alternative pathways in plants. One pathway starts with the enzyme arginine decarboxylase (ADC EC 4.1.1.19), the other with ornithine decarboxylase (ODC EC 4.1.1.17). Metabolite profiling of nitrogen-fixing Lotus japonicus nodules, using gas chromatography coupled to mass spectrometry, revealed a two- to sixfold increase in putrescine levels in mature nodules compared with other organs. Genes involved in polyamine biosynthesis in L. japonicus nodules were identified by isolating cDNA clones encoding ADC (LjADC1) and ODC (LjODC) from a nodule library. Searches of the public expressed sequence tag databases revealed the presence of a second gene encoding ADC (LjADC2). Real-time reverse-transcription-polymerase chain reaction analysis showed that LjADC1 and LjADC2 were expressed throughout the plant, while LjODC transcripts were detected only in nodules and roots. Induction of LjODC and LjADC gene expression during nodule development preceded symbiotic nitrogen fixation. Transcripts accumulation was maximal at 10 days postinfection, when a 6.5-fold increase in the transcript levels of LjODC was observed in comparison with the uninfected roots, while a twofold increase in the transcript levels of LjADC1 and LjADC2 was detected. At later stages of nodule development, transcripts for ADC drastically declined, while in the case of ODC, transcript accumulation was higher than that in roots until after 21 days postinfection. The expression profile of genes involved in putrescine biosynthesis correlated well with the expression patterns of genes involved in cell ision and expansion, including a L. japonicus Cyclin D3 and an α-expansin gene. Spatial localization of LjODC and LjADC1 gene transcripts in developing nodules revealed that both transcripts were expressed in nodule inner cortical cells and in the central tissue. High levels of LjADC1 transcripts were also observed in both nodule and connecting root vascular tissue, suggesting that putrescine and other polyamines may be subject to long-distance transport. Our results indicate that polyamines are primarily involved in physiological and cellular processes involved in nodule development, rather than in processes that support directly symbiotic nitrogen fixation and assimilation.
The Medicago truncatula gene expression atlas web server
Publisher: Springer Science and Business Media LLC
Date: 12-2009
AhNGE: A Database for Arachis hypogaea Nodule Developmental Gene Expression
Publisher: Cold Spring Harbor Laboratory
Date: 02-2021
DOI: 10.1101/2021.01.30.428929
Abstract: Symbiotic nitrogen fixation (SNF) inside root-nodules is a primary and sustainable source of soil nitrogen. Understanding nodule development and metabolism in crop legumes may lead to more effective SNF in agriculture. Peanut ( Arachis hypogaea ) is an economically important allotetraploid legume with non-canonical nodule developmental features. Recent genome sequencing of peanut has opened the possibility of making peanut a model for studying atypical nodule development. To help the community of nodule biologists, we have developed a database called AhNGE ( Arachis hypogaea Nodule Developmental Gene Expression: nipgr.ac.in/AhNGE/index.php ). AhNGE contains RNAseq data from six data points of nodule development in A. hypogagea cv. Tifrunner . This data represents a dynamic view of gene expression during peanut nodule development. Research in model legumes has generated a huge knowledgebase in the last twenty years. To streamline comparative genomics among legumes, we performed ortholog analysis among four legumes (Cicer, Glycine, Lotus, and Medicago) and one non-legume (Arabidopsis). This will facilitate the integration of existing knowledge in nodule development with the Arachis transcriptome. The available data can be retrieved using a single or batch query or searching using gene ID, from above mentioned five species. The output displays the gene expression pattern in graphical as well as tabular form, along with further options to download the sequence data. The database is linked with PeanutBase, the main genomic resource of peanut. Additionally, the expression level of different splicing variants can be retrieved from the database. In summary, AhNGE serves as an important resource for the scientific community working on nodule development.
Mining for robust transcriptional and metabolic responses to long-term salt stress: a case study on the model legumeLotus japonicus
Publisher: Wiley
Date: 04-2010
DOI: 10.1111/J.1365-3040.2009.02047.X
Abstract: Translational genomics, the use of model species to generate knowledge about biological processes and the functions of genes, offers great promise to biotechnologists. Few studies have sought robust responses of model plants to environmental stresses, such as salinity, by altering the stress dosage or by repeating experiments in consecutive years and/or different seasons. We mined our published and unpublished data on legume salt acclimation for robust system features at the ionomic, transcriptomic and metabolomic levels. We analysed data from the model legume Lotus japonicus, obtained through six independent, long-term, non-lethal salt stress experiments which were carried out over two consecutive years. Best possible controlled greenhouse conditions were applied and two main questions asked: how reproducible are results obtained from physiologically meaningful salinity experiments, and what degree of bias may be expected if conclusions are drawn from less well-repeated s ling? A surprisingly large fraction of the transcriptional and metabolic responses to salt stress were not reproducible between experiments. A core set of robust changes was found that was shared between experiments. Many of these robust responses were qualitatively and quantitatively conserved between different accessions of the same species, indicating that the robust responses may be a sound starting point for translational genomics.
Diversity of Nitrogen-Fixing Bacteria Associated with Switchgrass in the Native Tallgrass Prairie of Northern Oklahoma
Publisher: American Society for Microbiology
Date: 15-09-2014
DOI: 10.1128/AEM.02091-14
Abstract: Switchgrass ( Panicum virgatum L.) is a perennial C 4 grass native to North America that is being developed as a feedstock for cellulosic ethanol production. Industrial nitrogen fertilizers enhance switchgrass biomass production but add to production and environmental costs. A potential sustainable alternative source of nitrogen is biological nitrogen fixation. As a step in this direction, we studied the ersity of nitrogen-fixing bacteria (NFB) associated with native switchgrass plants from the tallgrass prairie of northern Oklahoma (United States), using a culture-independent approach. DNA sequences from the nitrogenase structural gene, nifH , revealed over 20 putative diazotrophs from the alpha-, beta-, delta-, and gammaproteobacteria and the firmicutes associated with roots and shoots of switchgrass. Alphaproteobacteria, especially rhizobia, predominated. Sequences derived from nifH RNA indicated expression of this gene in several bacteria of the alpha-, beta-, delta-, and gammaproteobacterial groups associated with roots. Prominent among these were Rhizobium and Methylobacterium species of the alphaproteobacteria, Burkholderia and Azoarcus species of the betaproteobacteria, and Desulfuromonas and Geobacter species of the deltaproteobacteria.
Nitrogen Fertilization Reduces Nitrogen Fixation Activity of Diverse Diazotrophs in Switchgrass Roots
Publisher: Scientific Societies
Date: 2021
DOI: 10.1094/PBIOMES-09-19-0050-FI
Abstract: The use of synthetic nitrogen fertilizers to grow biofuel crops adds to the economic and environmental costs of biomass production. Biological nitrogen fixation provides an alternative, eco-friendly source of nitrogen for leguminous plants and some nonlegumes. With the objective of characterizing and eventually harnessing nitrogen-fixing bacteria in switchgrass roots, we assayed nitrogenase activity and surveyed nifH-expressing bacteria in roots of switchgrass grown under agricultural conditions. Plants were cultivated at two separate locations in Oklahoma in different soil types for 5 years with three nitrogen fertilizer regimes (0, 90, and 180 kg of N ha −1 year −1 ). Nitrogenase activity associated with roots cleaned of soil was found to be highest in plants grown with no N fertilizer and lowest or not detectable for plants grown at the highest level of N fertilizer. A total of 454 abundant nifH operational taxonomic units (OTUs) were identified in the switchgrass roots. Diversity analysis of active nifH-expressing bacteria showed that the most common orders were Burkholderiales (171 OTUs), Desulfovibrionales (55 OTUs), and Rhizobiales (44 OTUs). OTUs belonging to Azonexus, Pseudacidovorax, Desulfovibrio, Dechloromonas, and Bradyrhizobium were enriched in roots of plants grown under low nitrogen conditions. Analysis of significant OTUs showed distinct nifH-expressing microbial communities at the two field locations, as well as a unique community in roots of unfertilized soil at Frederick that exhibited the highest rates of nitrogen fixation. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Medicago truncatula Natural Resistance-Associated Macrophage Protein1 Is Required for Iron Uptake by Rhizobia-Infected Nodule Cells
Publisher: Oxford University Press (OUP)
Date: 27-03-2015
Abstract: Iron is critical for symbiotic nitrogen fixation (SNF) as a key component of multiple ferroproteins involved in this biological process. In the model legume Medicago truncatula, iron is delivered by the vasculature to the infection/maturation zone (zone II) of the nodule, where it is released to the apoplast. From there, plasma membrane iron transporters move it into rhizobia-containing cells, where iron is used as the cofactor of multiple plant and rhizobial proteins (e.g. plant leghemoglobin and bacterial nitrogenase). MtNr 1 (Medtr3g088460) is the M. truncatula Natural Resistance-Associated Macrophage Protein family member, with the highest expression levels in roots and nodules. Immunolocalization studies indicate that MtNr 1 is mainly targeted to the plasma membrane. A loss-of-function nr 1 mutant exhibited reduced growth compared with the wild type under symbiotic conditions, but not when fertilized with mineral nitrogen. Nitrogenase activity was low in the mutant, whereas exogenous iron and expression of wild-type MtNr 1 in mutant nodules increased nitrogen fixation to normal levels. These data are consistent with a model in which MtNr 1 is the main transporter responsible for apoplastic iron uptake by rhizobia-infected cells in zone II.
Global regulation of reactive oxygen species scavenging genes in alfalfa root and shoot under gradual drought stress and recovery
Publisher: Informa UK Limited
Date: 05-2012
DOI: 10.4161/PSB.19780
Cloning and Sequencing of a Full-Length cDNA from Thlaspi arvense L. That Encodes a Cytochrome P-450
Publisher: Oxford University Press (OUP)
Date: 06-1994
DOI: 10.1104/PP.105.2.755
Spectroscopic analysis reveals that soil phosphorus availability and plant allocation strategies impact feedstock quality of nutrient-limited switchgrass
Publisher: Springer Science and Business Media LLC
Date: 11-03-2022
DOI: 10.1038/S42003-022-03157-7
Abstract: The perennial native switchgrass adapts better than other plant species do to marginal soils with low plant-available nutrients, including those with low phosphorus (P) content. Switchgrass roots and their associated microorganisms can alter the pools of available P throughout the whole soil profile making predictions of P availability in situ challenging. Plant P homeostasis makes monitoring of P limitation via measurements of plant P content alone difficult to interpret. To address these challenges, we developed a machine-learning model trained with high accuracy using the leaf tissue chemical profile, rather than P content. By applying this learned model in field trials across two sites with contrasting extractable soil P, we observed that actual plant available P in soil was more similar than expected, suggesting that adaptations occurred to alleviate the apparent P constraint. These adaptations come at a metabolic cost to the plant that have consequences for feedstock chemical components and quality. We observed that other biochemical signatures of P limitation, such as decreased cellulose-to-lignin ratios, were apparent, indicating re-allocation of carbon resources may have contributed to increased P acquisition. Plant P allocation strategies also differed across sites, and these differences were correlated with the subsequent year’s biomass yields.
Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis
Publisher: Oxford University Press (OUP)
Date: 09-2005
Abstract: Gene transcripts with invariant abundance during development and in the face of environmental stimuli are essential reference points for accurate gene expression analyses, such as RNA gel-blot analysis or quantitative reverse transcription-polymerase chain reaction (PCR). An exceptionally large set of data from Affymetrix ATH1 whole-genome GeneChip studies provided the means to identify a new generation of reference genes with very stable expression levels in the model plant species Arabidopsis (Arabidopsis thaliana). Hundreds of Arabidopsis genes were found that outperform traditional reference genes in terms of expression stability throughout development and under a range of environmental conditions. Most of these were expressed at much lower levels than traditional reference genes, making them very suitable for normalization of gene expression over a wide range of transcript levels. Specific and efficient primers were developed for 22 genes and tested on a erse set of 20 cDNA s les. Quantitative reverse transcription-PCR confirmed superior expression stability and lower absolute expression levels for many of these genes, including genes encoding a protein phosphatase 2A subunit, a coatomer subunit, and an ubiquitin-conjugating enzyme. The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future.
Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation inLotus japonicus
Publisher: Wiley
Date: 08-2004
Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation
Publisher: Wiley
Date: 07-10-2020
DOI: 10.1111/PCE.13872
Draft Genome Sequences of Switchgrass Diazotrophs
Publisher: American Society for Microbiology
Date: 27-05-2021
DOI: 10.1128/MRA.00284-21
Abstract: We report the draft genome sequences of five native nitrogen-fixing bacteria associated with roots of switchgrass isolated from the Tallgrass Prairies of Oklahoma. Nitrogen-fixing genes, including the nif cluster, are conserved across the Klebsiella and Kosakonia strains.
Functional Analysis of Cellulose Synthase CesA4 and CesA6 Genes in Switchgrass (Panicum virgatum) by Overexpression and RNAi-Mediated Gene Silencing
Publisher: Frontiers Media SA
Date: 03-08-2018
AtMyb41 Regulates Transcriptional and Metabolic Responses to Osmotic Stress in Arabidopsis
Publisher: Oxford University Press (OUP)
Date: 11-02-2009
Abstract: Myb transcription factors have been implicated in a wide variety of plant-specific processes, including secondary metabolism, cell shape determination, cell differentiation, and stress responses. Very recently, AtMyb41 from Arabidopsis (Arabidopsis thaliana) was described as a gene transcriptionally regulated in response to salinity, desiccation, cold, and abscisic acid. The corresponding transcription factor was suggested to control stress responses linked to cell wall modifications. In this work, we have characterized AtMyb41 further by subjecting independent AtMyb41-overexpressing lines to detailed transcriptome and metabolome analysis. Our molecular data indicate that AtMyb41 is involved in distinct cellular processes, including control of primary metabolism and negative regulation of short-term transcriptional responses to osmotic stress.
Comparative Functional Genomics of Salt Stress in Related Model and Cultivated Plants Identifies and Overcomes Limitations to Translational Genomics
Publisher: Public Library of Science (PLoS)
Date: 14-02-2011
Comparative metabolomics of drought acclimation in model and forage legumes
Publisher: Wiley
Date: 12-10-2011
DOI: 10.1111/J.1365-3040.2011.02423.X
Abstract: Water limitation has become a major concern for agriculture. Such constraints reinforce the urgent need to understand mechanisms by which plants cope with water deprivation. We used a non-targeted metabolomic approach to explore plastic systems responses to non-lethal drought in model and forage legume species of the Lotus genus. In the model legume Lotus. japonicus, increased water stress caused gradual increases of most of the soluble small molecules profiled, reflecting a global and progressive reprogramming of metabolic pathways. The comparative metabolomic approach between Lotus species revealed conserved and unique metabolic responses to drought stress. Importantly, only few drought-responsive metabolites were conserved among all species. Thus we highlight a potential impediment to translational approaches that aim to engineer traits linked to the accumulation of compatible solutes. Finally, a broad comparison of the metabolic changes elicited by drought and salt acclimation revealed partial conservation of these metabolic stress responses within each of the Lotus species, but only few salt- and drought-responsive metabolites were shared between all. The implications of these results are discussed with regard to the current insights into legume water stress physiology.
A Nonconservative Lagrangian Framework for Statistical Fluid Registration-SAFIRA
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 02-2011
Rhizobial Infection Is Associated with the Development of Peripheral Vasculature in Nodules ofMedicago truncatula
Publisher: Oxford University Press (OUP)
Date: 27-03-2013
Abstract: Nodulation in legumes involves the coordination of epidermal infection by rhizobia with cell isions in the underlying cortex. During nodulation, rhizobia are entrapped within curled root hairs to form an infection pocket. Transcellular tubes called infection threads then develop from the pocket and become colonized by rhizobia. The infection thread grows toward the developing nodule primordia and rhizobia are taken up into the nodule cells, where they eventually fix nitrogen. The epidermal and cortical developmental programs are synchronized by a yet-to-be-identified signal that is transmitted from the outer to the inner cell layers of the root. Using a new allele of the Medicago truncatula mutant Lumpy Infections, lin-4, which forms normal infection pockets but cannot initiate infection threads, we show that infection thread initiation is required for normal nodule development. lin-4 forms nodules with centrally located vascular bundles similar to that found in lateral roots rather than the peripheral vasculature characteristic of legume nodules. The same phenomenon was observed in M. truncatula plants inoculated with the Sinorhizobium meliloti exoY mutant, and the M. truncatula vapyrin-2 mutant, all cases where infections arrest. Nodules on lin-4 have reduced expression of the nodule meristem marker MtCRE1 and do not express root-tip markers. In addition, these mutant nodules have altered patterns of gene expression for the cytokinin and auxin markers CRE1 and DR5. Our work highlights the coordinating role that bacterial infection exerts on the developing nodule and allows us to draw comparisons with primitive actinorhizal nodules and rhizobia-induced nodules on the nonlegume Parasponia andersonii.
Microscopic and Transcriptomic Analyses of Dalbergoid Legume Peanut Reveal a Divergent Evolution Leading to Nod-Factor-Dependent Epidermal Crack-Entry and Terminal Bacteroid Differentiation
Publisher: Scientific Societies
Date: 02-2022
DOI: 10.1094/MPMI-05-21-0122-R
Abstract: Root nodule symbiosis (RNS) is the pillar behind sustainable agriculture and plays a pivotal role in the environmental nitrogen cycle. Most of the genetic, molecular, and cell-biological knowledge on RNS comes from model legumes that exhibit a root-hair mode of bacterial infection, in contrast to the Dalbergoid legumes exhibiting crack-entry of rhizobia. As a step toward understanding this important group of legumes, we have combined microscopic analysis and temporal transcriptome to obtain a dynamic view of plant gene expression during Arachis hypogaea (peanut) nodule development. We generated comprehensive transcriptome data by mapping the reads to A. hypogaea, and two diploid progenitor genomes. Additionally, we performed BLAST searches to identify nodule-induced yet-to-be annotated peanut genes. Comparison between peanut, Medicago truncatula, Lotus japonicus, and Glycine max showed upregulation of 61 peanut orthologs among 111 tested known RNS-related genes, indicating conservation in mechanisms of nodule development among members of the Papilionoid family. Unlike model legumes, recruitment of class 1 phytoglobin-derived symbiotic hemoglobin (SymH) in peanut indicates ersification of oxygen-scavenging mechanisms in the Papilionoid family. Finally, the absence of cysteine-rich motif-1-containing nodule-specific cysteine-rich peptide (NCR) genes but the recruitment of defensin-like NCRs suggest a erse molecular mechanism of terminal bacteroid differentiation. In summary, our work describes genetic conservation and ersification in legume–rhizobia symbiosis in the Papilionoid family, as well as among members of the Dalbergoid legumes. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Transcriptional Programs and Regulators Underlying Age-Dependent and Dark-Induced Senescence in Medicago truncatula
Publisher: MDPI AG
Date: 06-05-2022
Abstract: In forage crops, age-dependent and stress-induced senescence reduces forage yield and quality. Therefore, delaying leaf senescence may be a way to improve forage yield and quality as well as plant resilience to stresses. Here, we used RNA-sequencing to determine the molecular bases of age-dependent and dark-induced leaf senescence in Medicago truncatula. We identified 6845 differentially expressed genes (DEGs) in M3 leaves associated with age-dependent leaf senescence. An even larger number (14219) of DEGs were associated with dark-induced senescence. Upregulated genes identified during age-dependent and dark-induced senescence were over-represented in oxidation–reduction processes and amino acid, carboxylic acid and chlorophyll catabolic processes. Dark-specific upregulated genes also over-represented autophagy, senescence and cell death. Mitochondrial functions were strongly inhibited by dark-treatment while these remained active during age-dependent senescence. Additionally, 391 DE transcription factors (TFs) belonging to various TF families were identified, including a core set of 74 TFs during age-dependent senescence while 759 DE TFs including a core set of 338 TFs were identified during dark-induced senescence. The heterologous expression of several senescence-induced TFs belonging to NAC, WKRY, bZIP, MYB and HD-zip TF families promoted senescence in tobacco leaves. This study revealed the dynamics of transcriptomic responses to age- and dark-induced senescence in M. truncatula and identified senescence-associated TFs that are attractive targets for future work to control senescence in forage legumes.
GWASpro: a high-performance genome-wide association analysis server
Publisher: Oxford University Press (OUP)
Date: 03-12-2018
DOI: 10.1093/BIOINFORMATICS/BTY989
Abstract: We present GWASpro, a high-performance web server for the analyses of large-scale genome-wide association studies (GWAS). GWASpro was developed to provide data analyses for large-scale molecular genetic data, coupled with complex replicated experimental designs such as found in plant science investigations and to overcome the steep learning curves of existing GWAS software tools. GWASpro supports building complex design matrices, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted for in the linear mixed model. GWASpro is optimized to handle GWAS data that may consist of up to 10 million markers and 10 000 s les from replicable lines or hybrids. GWASpro provides an interface that significantly reduces the learning curve for new GWAS investigators. GWASpro is freely available at bioinfo.noble.org/GWASPRO. Supplementary data are available at Bioinformatics online.
GRAS Genes and the Symbiotic Green Revolution
Publisher: American Association for the Advancement of Science (AAAS)
Date: 17-06-2005
AffyTrees: Facilitating Comparative Analysis of Affymetrix Plant Microarray Chips
Publisher: Oxford University Press (OUP)
Date: 07-12-2007
Identification with Proteomics of Novel Proteins Associated with the Peribacteroid Membrane of Soybean Root Nodules
Publisher: Scientific Societies
Date: 03-2000
DOI: 10.1094/MPMI.2000.13.3.325
Abstract: Soybean peribacteroid membrane (PBM) proteins were isolated from nitrogen-fixing root nodules and subjected to N-terminal sequencing. Sequence data from 17 putative PBM proteins were obtained. Six of these proteins are homologous to proteins of known function. These include three chaperones (HSP60, BiP [HSP70], and PDI) and two proteases (a serine and a thiol protease), all of which are involved in some aspect of protein processing in plants. The PBM homologs of these proteins may play roles in protein translocation, folding, maturation, or degradation in symbiosomes. Two proteins are homologous to known, nodule-specific proteins from soybean, nodulin 53b and nodulin 26B. Although the function of these nodulins is unknown, nodulin 53b has independently been shown to be associated with the PBM. All of the eight proteins with identifiable homologs are likely to be peripheral rather than integral membrane proteins. Possible reasons for this apparent bias are discussed. The identification of homologs of HSP70 and HSP60 associated with the PBM is the first evidence that the molecular machinery for co- or post-translational import of cytoplasmic proteins is present in symbiosomes. This has important implications for the biogenesis of this unique, nitrogen-fixing organelle.
Presymbiotic factors released by the arbuscular mycorrhizal fungus Gigaspora margarita induce starch accumulation in Lotus japonicus roots
Publisher: Wiley
Date: 03-06-2009
DOI: 10.1111/J.1469-8137.2009.02871.X
Abstract: * Nutrient exchange is the key symbiotic feature of arbuscular mycorrhiza (AM). As evidence is accumulating that plants sense presymbiotic factors from AM fungi and prepare for colonization, we investigated whether modifications in plant sugar metabolism might be part of the precolonization program. * Inoculation of Lotus japonicus roots in a double Millipore sandwich with the AM fungus Gigaspora margarita prevented contact between the symbionts but allowed exchange of signal molecules. Starch content was used as a marker for root carbohydrate status. * Mycorrhizal colonization of L. japonicus roots led to a decrease in starch concentration. In roots inoculated in the double sandwich, the polysaccharide accumulated after 1 wk and persisted for at least 4 wk. The response was absent in the castor myc(-) mutant, sym4-2, while transcript levels of both CASTOR and POLLUX were slightly enhanced in the wild-type L. japonicus roots, suggesting a requirement of the corresponding proteins for the starch-accumulation response. Exudates obtained from fungal spores germinated in the absence of the plant also induced starch accumulation in wild-type L. japonicus roots. * We conclude that factors released from germinating AM fungal spores induce changes in the root carbon status, possibly by enhancing sugar import, which leads to starch accumulation when colonization is prevented.
The Nodule-Specific PLAT Domain Protein NPD1 Is Required for Nitrogen-Fixing Symbiosis
Publisher: Oxford University Press (OUP)
Date: 06-05-2019
DOI: 10.1104/PP.18.01613
Medicago truncatula and Glomus intraradices gene expression in cortical cells harboring arbuscules in the arbuscular mycorrhizal symbiosis
Publisher: Springer Science and Business Media LLC
Date: 22-01-2009
Abstract: Most vascular flowering plants have the capacity to form symbiotic associations with arbuscular mycorrhizal (AM) fungi. The symbiosis develops in the roots where AM fungi colonize the root cortex and form arbuscules within the cortical cells. Arbuscules are enveloped in a novel plant membrane and their establishment requires the coordinated cellular activities of both symbiotic partners. The arbuscule-cortical cell interface is the primary functional interface of the symbiosis and is of central importance in nutrient exchange. To determine the molecular events the underlie arbuscule development and function, it is first necessary to identify genes that may play a role in this process. Toward this goal we used the Affymetrix GeneChip ® Medicago Genome Array to document the M. truncatula transcript profiles associated with AM symbiosis, and then developed laser microdissection (LM) of M. truncatula root cortical cells to enable analyses of gene expression in in idual cell types by RT-PCR. This approach led to the identification of novel M. truncatula and G. intraradices genes expressed in colonized cortical cells and in arbuscules. Within the arbuscule, expression of genes associated with the urea cycle, amino acid biosynthesis and cellular autophagy was detected. Analysis of gene expression in the colonized cortical cell revealed up-regulation of a lysine motif (LysM)-receptor like kinase, members of the GRAS transcription factor family and a symbiosis-specific ammonium transporter that is a likely candidate for mediating ammonium transport in the AM symbiosis. Transcript profiling using the Affymetrix GeneChip ® Medicago Genome Array provided new insights into gene expression in M. truncatula roots during AM symbiosis and revealed the existence of several G. intraradices genes on the M. truncatula GeneChip ® . A laser microdissection protocol that incorporates low-melting temperature Steedman's wax, was developed to enable laser microdissection of M. truncatula root cortical cells. LM coupled with RT-PCR provided spatial gene expression information for both symbionts and expanded current information available for gene expression in cortical cells containing arbuscules.
SARS-CoV-2 vaccination modelling for safe surgery to save lives: data from an international prospective cohort study
Publisher: Oxford University Press (OUP)
Date: 24-03-2021
DOI: 10.1093/BJS/ZNAB101
Abstract: Preoperative SARS-CoV-2 vaccination could support safer elective surgery. Vaccine numbers are limited so this study aimed to inform their prioritization by modelling. The primary outcome was the number needed to vaccinate (NNV) to prevent one COVID-19-related death in 1 year. NNVs were based on postoperative SARS-CoV-2 rates and mortality in an international cohort study (surgical patients), and community SARS-CoV-2 incidence and case fatality data (general population). NNV estimates were stratified by age (18–49, 50–69, 70 or more years) and type of surgery. Best- and worst-case scenarios were used to describe uncertainty. NNVs were more favourable in surgical patients than the general population. The most favourable NNVs were in patients aged 70 years or more needing cancer surgery (351 best case 196, worst case 816) or non-cancer surgery (733 best case 407, worst case 1664). Both exceeded the NNV in the general population (1840 best case 1196, worst case 3066). NNVs for surgical patients remained favourable at a range of SARS-CoV-2 incidence rates in sensitivity analysis modelling. Globally, prioritizing preoperative vaccination of patients needing elective surgery ahead of the general population could prevent an additional 58 687 (best case 115 007, worst case 20 177) COVID-19-related deaths in 1 year. As global roll out of SARS-CoV-2 vaccination proceeds, patients needing elective surgery should be prioritized ahead of the general population.
Effects of pre‐operative isolation on postoperative pulmonary complications after elective surgery: an international prospective cohort study
Publisher: Wiley
Date: 09-08-2021
DOI: 10.1111/ANAE.15560
Abstract: We aimed to determine the impact of pre‐operative isolation on postoperative pulmonary complications after elective surgery during the global SARS‐CoV‐2 pandemic. We performed an international prospective cohort study including patients undergoing elective surgery in October 2020. Isolation was defined as the period before surgery during which patients did not leave their house or receive visitors from outside their household. The primary outcome was postoperative pulmonary complications, adjusted in multivariable models for measured confounders. Pre‐defined sub‐group analyses were performed for the primary outcome. A total of 96,454 patients from 114 countries were included and overall, 26,948 (27.9%) patients isolated before surgery. Postoperative pulmonary complications were recorded in 1947 (2.0%) patients of which 227 (11.7%) were associated with SARS‐CoV‐2 infection. Patients who isolated pre‐operatively were older, had more respiratory comorbidities and were more commonly from areas of high SARS‐CoV‐2 incidence and high‐income countries. Although the overall rates of postoperative pulmonary complications were similar in those that isolated and those that did not (2.1% vs 2.0%, respectively), isolation was associated with higher rates of postoperative pulmonary complications after adjustment (adjusted OR 1.20, 95%CI 1.05–1.36, p = 0.005). Sensitivity analyses revealed no further differences when patients were categorised by: pre‐operative testing use of COVID‐19‐free pathways or community SARS‐CoV‐2 prevalence. The rate of postoperative pulmonary complications increased with periods of isolation longer than 3 days, with an OR (95%CI) at 4–7 days or ≥ 8 days of 1.25 (1.04–1.48), p = 0.015 and 1.31 (1.11–1.55), p = 0.001, respectively. Isolation before elective surgery might be associated with a small but clinically important increased risk of postoperative pulmonary complications. Longer periods of isolation showed no reduction in the risk of postoperative pulmonary complications. These findings have significant implications for global provision of elective surgical care.
Medicago truncatula
copper transporter 1 (Mt
COPT
1) delivers copper for symbiotic nitrogen fixation
Publisher: Wiley
Date: 19-01-2018
DOI: 10.1111/NPH.14992
Abstract: Copper is an essential nutrient for symbiotic nitrogen fixation. This element is delivered by the host plant to the nodule, where membrane copper (Cu) transporter would introduce it into the cell to synthesize cupro-proteins. COPT family members in the model legume Medicago truncatula were identified and their expression determined. Yeast complementation assays, confocal microscopy and phenotypical characterization of a Tnt1 insertional mutant line were carried out in the nodule-specific M. truncatula COPT family member. Medicago truncatula genome encodes eight COPT transporters. MtCOPT1 (Medtr4g019870) is the only nodule-specific COPT gene. It is located in the plasma membrane of the differentiation, interzone and early fixation zones. Loss of MtCOPT1 function results in a Cu-mitigated reduction of biomass production when the plant obtains its nitrogen exclusively from symbiotic nitrogen fixation. Mutation of MtCOPT1 results in diminished nitrogenase activity in nodules, likely an indirect effect from the loss of a Cu-dependent function, such as cytochrome oxidase activity in copt1-1 bacteroids. These data are consistent with a model in which MtCOPT1 transports Cu from the apoplast into nodule cells to provide Cu for essential metabolic processes associated with symbiotic nitrogen fixation.
Characterization of Arabidopsis AtAMT2, a novel ammonium transporter in plants.
Publisher: Wiley
Date: 07-02-2000
DOI: 10.1016/S0014-5793(00)01153-4
Abstract: We have cloned and characterized the first member of a novel family of ammonium transporters in plants: AtAMT2 from Arabidopsis thaliana. AtAMT2 is more closely related to bacterial ammonium transporters than to plant transporters of the AMT1 family. The protein was expressed and functionally characterized in yeast. AtAMT2 transported ammonium in an energy-dependent manner. In contrast to transporters of the AMT1 family, however, AtAMT2 did not transport the ammonium analogue, methylammonium. AtAMT2 was expressed more highly in shoots than roots and was subject to nitrogen regulation.
Keel petal incision: a simple and efficient method for genetic crossing in Medicago truncatula
Publisher: Springer Science and Business Media LLC
Date: 16-05-2014
Identification and Overexpression of a Knotted1-Like Transcription Factor in Switchgrass (Panicum virgatum L.) for Lignocellulosic Feedstock Improvement
Publisher: Frontiers Media SA
Date: 28-04-2016
Repressor- and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of Arabidopsis transcription factor gene expression
Publisher: Oxford University Press (OUP)
Date: 23-09-2005
Abstract: To identify transcription factors (TFs) involved in jasmonate (JA) signaling and plant defense, we screened 1,534 Arabidopsis (Arabidopsis thaliana) TFs by real-time quantitative reverse transcription-PCR for their altered transcript at 6 h following either methyl JA treatment or inoculation with the incompatible pathogen Alternaria brassicicola. We identified 134 TFs that showed a significant change in expression, including many APETALA2/ethylene response factor (AP2/ERF), MYB, WRKY, and NAC TF genes with unknown functions. Twenty TF genes were induced by both the pathogen and methyl JA and these included 10 members of the AP2/ERF TF family, primarily from the B1a and B3 subclusters. Functional analysis of the B1a TF AtERF4 revealed that AtERF4 acts as a novel negative regulator of JA-responsive defense gene expression and resistance to the necrotrophic fungal pathogen Fusarium oxysporum and antagonizes JA inhibition of root elongation. In contrast, functional analysis of the B3 TF AtERF2 showed that AtERF2 is a positive regulator of JA-responsive defense genes and resistance to F. oxysporum and enhances JA inhibition of root elongation. Our results suggest that plants coordinately express multiple repressor- and activator-type AP2/ERFs during pathogen challenge to modulate defense gene expression and disease resistance.
SARS‐CoV‐2 infection and venous thromboembolism after surgery: an international prospective cohort study
Publisher: Wiley
Date: 24-08-2021
DOI: 10.1111/ANAE.15563
Abstract: SARS‐CoV‐2 has been associated with an increased rate of venous thromboembolism in critically ill patients. Since surgical patients are already at higher risk of venous thromboembolism than general populations, this study aimed to determine if patients with peri‐operative or prior SARS‐CoV‐2 were at further increased risk of venous thromboembolism. We conducted a planned sub‐study and analysis from an international, multicentre, prospective cohort study of elective and emergency patients undergoing surgery during October 2020. Patients from all surgical specialties were included. The primary outcome measure was venous thromboembolism (pulmonary embolism or deep vein thrombosis) within 30 days of surgery. SARS‐CoV‐2 diagnosis was defined as peri‐operative (7 days before to 30 days after surgery) recent (1–6 weeks before surgery) previous (≥7 weeks before surgery) or none. Information on prophylaxis regimens or pre‐operative anti‐coagulation for baseline comorbidities was not available. Postoperative venous thromboembolism rate was 0.5% (666/123,591) in patients without SARS‐CoV‐2 2.2% (50/2317) in patients with peri‐operative SARS‐CoV‐2 1.6% (15/953) in patients with recent SARS‐CoV‐2 and 1.0% (11/1148) in patients with previous SARS‐CoV‐2. After adjustment for confounding factors, patients with peri‐operative (adjusted odds ratio 1.5 (95%CI 1.1–2.0)) and recent SARS‐CoV‐2 (1.9 (95%CI 1.2–3.3)) remained at higher risk of venous thromboembolism, with a borderline finding in previous SARS‐CoV‐2 (1.7 (95%CI 0.9–3.0)). Overall, venous thromboembolism was independently associated with 30‐day mortality (5.4 (95%CI 4.3–6.7)). In patients with SARS‐CoV‐2, mortality without venous thromboembolism was 7.4% (319/4342) and with venous thromboembolism was 40.8% (31/76). Patients undergoing surgery with peri‐operative or recent SARS‐CoV‐2 appear to be at increased risk of postoperative venous thromboembolism compared with patients with no history of SARS‐CoV‐2 infection. Optimal venous thromboembolism prophylaxis and treatment are unknown in this cohort of patients, and these data should be interpreted accordingly.
A gene expression atlas of the model legumeMedicago truncatula
Publisher: Wiley
Date: 08-2008
Application of synthetic peptide CEP1 increases nutrient uptake rates along plant roots
Publisher: Cold Spring Harbor Laboratory
Date: 12-10-2021
DOI: 10.1101/2021.10.11.463963
Abstract: The root system of a plant provides vital functions including resource uptake, storage, and anchorage in soil. Uptake from the soil of macro-nutrients like nitrogen (N), phosphorus (P), potassium (K), and sulphur (S) is critical for plant growth and development. Small signaling peptide (SSP) hormones are best known as potent regulators of plant growth and development with a few also known to have specialized roles in macronutrient utilization. Here we describe a high-throughput screen of SSP effects on root uptake of multiple nutrients. The SSP, MtCEP1 enhanced nitrate uptake rate per unit root length in Medicago truncatula plants deprived of N. MtCEP1 and AtCEP1 enhanced uptake not only of nitrate, but also phosphate and sulfate in both Medicago and Arabidopsis. Transcriptome analysis of Medicago roots treated with different MtCEP1 encoded peptide domains revealed that hundreds of genes respond to these peptides, including several nitrate transporters and a sulfate transporter that may mediate the uptake of these macronutrients downstream of CEP1 signaling. Likewise, several putative signaling pathway genes were induced in roots by CEP1 treatment. Thus, a scalable method has been developed for screening synthetic peptides of potential use in agriculture, with CEP1 shown to be one such peptide.
Characterization of Arabidopsis AtAMT2, a High-Affinity Ammonium Transporter of the Plasma Membrane
Publisher: Oxford University Press (OUP)
Date: 12-2002
DOI: 10.1104/PP.008599
Abstract: AtAMT2 is an ammonium transporter that is only distantly related to the five members of the AtAMT1 family of high-affinity ammonium transporters in Arabidopsis. The short-lived radioactive ion13NH4 + was used to show that AtAMT2, expressed in yeast (Saccharomyces cerevisiae), is a high-affinity transporter with a K m for ammonium of about 20 μm. Changes in external pH between 5.0 and 7.5 had little effect on the K m for ammonium, indicating that NH4 +, not NH3, is the substrate for AtAMT2. TheAtAMT2 gene was expressed in all organs of Arabidopsis and was subject to nitrogen (N) regulation, at least in roots where expression was partially repressed by high concentrations of ammonium nitrate and derepressed in the absence of external N. Although expression of AtAMT2 in shoots responded little to changes in root N status, transcript levels in leaves declined under high CO2 conditions. Transient expression of an AtAMT2-green fluorescent protein fusion protein in Arabidopsis leaf epidermal cells indicated a plasma membrane location for the AtAMT2 protein. Thus, AtAMT2 is likely to play a significant role in moving ammonium between the apoplast and symplast of cells throughout the plant. However, a dramatic reduction in the level ofAtAMT2 transcript brought about by dsRNA interference with gene expression had no obvious effect on plant growth or development, under the conditions tested.
Senescence and nitrogen use efficiency in perennial grasses for forage and biofuel production
Publisher: Oxford University Press (OUP)
Date: 07-08-2017
DOI: 10.1093/JXB/ERX241
Abstract: Organ senescence is an important developmental process in plants that enables recycling of nutrients, such as nitrogen, to maximize reproductive success. Nitrogen is the mineral nutrient required in greatest amount by plants, although soil-N limits plant productivity in many natural and agricultural systems, especially systems that receive little or no fertilizer-N. Use of industrial N-fertilizers in agriculture increased crop yields several fold over the past century, although at substantial cost to fossil energy reserves and the environment. Therefore, it is important to optimize nitrogen use efficiency (NUE) in agricultural systems. Organ senescence contributes to NUE in plants and manipulation of senescence in plant breeding programs is a promising approach to improve NUE in agriculture. Much of what we know about plant senescence comes from research on annual plants, which provide most of the food for humans. Relatively little work has been done on senescence in perennial plants, especially perennial grasses, which provide much of the forage for grazing animals and promise to supply much of the biomass required by the future biofuel industry. Here, we review briefly what is known about senescence from studies of annual plants, before presenting current knowledge about senescence in perennial grasses and its relationship to yield, quality, and NUE. While higher yield is a common target, desired N-content erges between forage and biofuel crops. We discuss how senescence programs might be altered to produce high-yielding, stress-tolerant perennial grasses with high-N (protein) for forage or low-N for biofuels in systems optimized for NUE.
Functional Genomics of Symbiotic Nitrogen Fixation in Legumes with a Focus on Transcription Factors and Membrane Transporters
Publisher: Wiley
Date: 14-07-2015
Retrotransposon ( Tnt1 )‐Insertion Mutagenesis in Medicago as a Tool for Genetic Dissection of Symbiosis in Legumes
Publisher: Wiley
Date: 25-02-0002
An efficient reverse genetics platform in the model legume M edicago truncatula
Publisher: Wiley
Date: 11-11-2013
DOI: 10.1111/NPH.12575
Abstract: M edicago truncatula is one of the model species for legume studies. In an effort to develop legume genetics resources, 21 700 T nt1 retrotransposon insertion lines have been generated. To facilitate fast‐growing needs in functional genomics, two reverse genetics approaches have been established: web‐based database searching and PCR ‐based reverse screening. More than 840 genes have been reverse screened using the PCR ‐based approach over the past 6 yr to identify mutants in these genes. Overall, c . 84% (705 genes) success rate was achieved in identifying mutants with at least one T nt1 insertion, of which c . 50% (358 genes) had three or more alleles. To demonstrate the utility of the two reverse genetics platforms, two mutant alleles were isolated for each of the two floral homeotic MADS ‐box genes, M t PISTILATA and M t AGAMOUS . Molecular and genetic analyses indicate that T nt1 insertions in exons of both genes are responsible for the defects in floral organ development. In summary, we have developed two efficient reverse genetics platforms to facilitate functional characterization of M . truncatula genes.
Nutrient exchange across the peribacteroid membrane of isolated symbiosomes
Publisher: Springer US
Date: 1990
Localization of H+ -ATPase in soybean root nodules
Publisher: Springer Science and Business Media LLC
Date: 19-07-1999
Abstract: The localization of H(+)-ATPases in soybean (Glycine max L. cv. Stevens) nodules was investigated using antibodies against both P-type and V-type enzymes. Immunoblots of peribacteroid membrane (PBM) proteins using antibodies against tobacco and Arabidopsis H(+)-ATPases detected a single immunoreactive band at approximately 100 kDa. These antibodies recognized a protein of similar relative molecular mass in the crude microsomal fraction from soybean nodules and uninoculated roots. The amount of this protein was greater in PBM from mature nodules than in younger nodules. Immunolocalization of P-type ATPases using silver enhancement of colloidal-gold labelling at the light-microscopy level showed signal distributed around the periphery of non-infected cells in both the nodule cortex and nodule parenchyma. In the central nitrogen-fixing zone of the nodule, staining was present in both the infected and uninfected cells. Examination of nodule sections using confocal microscopy and fluorescence staining showed an immunofluorescent signal clearly visible around the periphery of in idual symbiosomes which appeared as vesicles distributed throughout the infected cells of the central zone. Electron-microscopic examination of immunogold-labelled sections shows that P-type ATPase antigens were present on the PBM of both newly formed, single-bacteroid symbiosomes just released from infection threads, and on the PBM of mature symbiosomes containing two to four bacteroids. Immunogold labelling using antibody against the B-subunit of V-type ATPase from oat failed to detect this protein on symbiosome membranes. Only a very faint signal with this antibody was detected on Western blots of purified PBM. During nodule development, fusion of small symbiosomes to form larger ones containing multiple bacteroids was observed. Fusion was preceded by the formation of cone-like extensions of the PBM, allowing the membrane to make contact with the adjoining membrane of another symbiosome. We conclude that the major H(+)-ATPase on the PBM of soybean is a P-type enzyme with homology to other such enzymes in plants. In vivo, this enzyme is likely to play a critical role in the regulation of nutrient exchange between legume and bacteroids.
Stimulation of respiration and nitrogenase in bacteroids of Siratro (Macroptilium atropurpureum) by plant nodule cytosol
Publisher: Springer Science and Business Media LLC
Date: 06-1986
DOI: 10.1007/BF00269120
Global reprogramming of transcription and metabolism in
M
edicago truncatula
during progressive drought and aft
Publisher: Wiley
Date: 11-05-2014
DOI: 10.1111/PCE.12328
PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool
Publisher: Springer Science and Business Media LLC
Date: 12-11-2013
Abstract: Plants regulate intrinsic gene expression through transcription factors (TFs), transcriptional regulators (TRs), chromatin regulators (CRs), and the basal transcription machinery. An understanding of plant gene regulatory mechanisms at a systems level requires the identification of these regulatory elements on a genomic scale. Here, we present PlantTFcat, a high-performance web-based analysis tool that is designed to identify and categorize plant TF/TR/CR genes from genome-scale protein and nucleic acid sequences by systematically analyzing InterProScan domain patterns in protein sequences. The comprehensive prediction logics that are included in PlantTFcat are based on relationships between gene families and conserved domains from 108 published plant TF/TR/CR families. These prediction logics effectively distinguish TF/TR/CR families with common conserved domains. Our systematic performance evaluations indicate that PlantTFcat annotates known TF/TR/CR families with high coverage and sensitivity. PlantTFcat provides an analysis tool to identify and categorize plant TF/TR/CR genes on a genomic scale. PlantTFcat is freely available to the public at plantgrn.noble.org/PlantTFcat/ .
Dissection of Symbiosis and Organ Development by Integrated Transcriptome Analysis of Lotus japonicus Mutant and Wild-Type Plants
Publisher: Public Library of Science (PLoS)
Date: 07-08-2009
Establishment of theLotus japonicusGene Expression Atlas (LjGEA) and its use to explore legume seed maturation
Publisher: Wiley
Date: 04-03-2013
DOI: 10.1111/TPJ.12119
Abstract: Lotus japonicus is a model species for legume genomics. To accelerate legume functional genomics, we developed a Lotus japonicus Gene Expression Atlas (LjGEA), which provides a global view of gene expression in all organ systems of this species, including roots, nodules, stems, petioles, leaves, flowers, pods and seeds. Time-series data covering multiple stages of developing pod and seed are included in the LjGEA. In addition, previously published L. japonicus Affymetrix data are included in the database, making it a 'one-stop shop' for transcriptome analysis of this species. The LjGEA web server (ljgea.noble.org/) enables flexible, multi-faceted analyses of the transcriptome. Transcript data may be accessed using the Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, and GO and KEGG annotation terms. Genes may be discovered through co-expression or differential expression analysis. Users may select a subset of experiments and visualize and compare expression profiles of multiple genes simultaneously. Data may be downloaded in a tabular form compatible with common analytical and visualization software. To illustrate the power of LjGEA, we explored the transcriptome of developing seeds. Genes represented by 36 474 probe sets were expressed at some stage during seed development, and almost half of these genes displayed differential expression during development. Among the latter were 624 transcription factor genes, some of which are orthologs of transcription factor genes that are known to regulate seed development in other species, while most are novel and represent attractive targets for reverse genetics approaches to determine their roles in this important organ.
Suppression of Arbuscule Degeneration in Medicago truncatula phosphate transporter4 Mutants Is Dependent on the Ammonium Transporter 2 Family Protein AMT2;3
Publisher: Oxford University Press (OUP)
Date: 04-2015
Abstract: During arbuscular mycorrhizal (AM) symbiosis, the plant gains access to phosphate (Pi) and nitrogen delivered by its fungal symbiont. Transfer of mineral nutrients occurs at the interface between branched hyphae called arbuscules and root cortical cells. In Medicago truncatula, a Pi transporter, PT4, is required for symbiotic Pi transport, and in pt4, symbiotic Pi transport fails, arbuscules degenerate prematurely, and the symbiosis is not maintained. Premature arbuscule degeneration (PAD) is suppressed when pt4 mutants are nitrogen-deprived, possibly the result of compensation by PT8, a second AM-induced Pi transporter. However, PAD is also suppressed in nitrogen-starved pt4 pt8 double mutants, negating this hypothesis and furthermore indicating that in this condition, neither of these symbiotic Pi transporters is required for symbiosis. In M. truncatula, three AMT2 family ammonium transporters are induced during AM symbiosis. To test the hypothesis that suppression of PAD involves AMT2 transporters, we analyzed double and triple Pi and ammonium transporter mutants. ATM2 but not AMT2 was required for suppression of PAD in pt4, while AMT2 , but not AMT2 , complemented growth of a yeast ammonium transporter mutant. In summary, arbuscule life span is influenced by PT4 and ATM2 , and their relative importance varies with the nitrogen status of the plant.
Timing of surgery following SARS‐CoV‐2 infection: an international prospective cohort study
Publisher: Wiley
Date: 09-03-2021
DOI: 10.1111/ANAE.15458
Abstract: Peri‐operative SARS‐CoV‐2 infection increases postoperative mortality. The aim of this study was to determine the optimal duration of planned delay before surgery in patients who have had SARS‐CoV‐2 infection. This international, multicentre, prospective cohort study included patients undergoing elective or emergency surgery during October 2020. Surgical patients with pre‐operative SARS‐CoV‐2 infection were compared with those without previous SARS‐CoV‐2 infection. The primary outcome measure was 30‐day postoperative mortality. Logistic regression models were used to calculate adjusted 30‐day mortality rates stratified by time from diagnosis of SARS‐CoV‐2 infection to surgery. Among 140,231 patients (116 countries), 3127 patients (2.2%) had a pre‐operative SARS‐CoV‐2 diagnosis. Adjusted 30‐day mortality in patients without SARS‐CoV‐2 infection was 1.5% (95%CI 1.4–1.5). In patients with a pre‐operative SARS‐CoV‐2 diagnosis, mortality was increased in patients having surgery within 0–2 weeks, 3–4 weeks and 5–6 weeks of the diagnosis (odds ratio (95%CI) 4.1 (3.3–4.8), 3.9 (2.6–5.1) and 3.6 (2.0–5.2), respectively). Surgery performed ≥ 7 weeks after SARS‐CoV‐2 diagnosis was associated with a similar mortality risk to baseline (odds ratio (95%CI) 1.5 (0.9–2.1)). After a ≥ 7 week delay in undertaking surgery following SARS‐CoV‐2 infection, patients with ongoing symptoms had a higher mortality than patients whose symptoms had resolved or who had been asymptomatic (6.0% (95%CI 3.2–8.7) vs. 2.4% (95%CI 1.4–3.4) vs. 1.3% (95%CI 0.6–2.0), respectively). Where possible, surgery should be delayed for at least 7 weeks following SARS‐CoV‐2 infection. Patients with ongoing symptoms ≥ 7 weeks from diagnosis may benefit from further delay.
A Research Road Map for Responsible Use of Agricultural Nitrogen
Publisher: Frontiers Media SA
Date: 31-05-2021
DOI: 10.3389/FSUFS.2021.660155
Abstract: Nitrogen (N) is an essential but generally limiting nutrient for biological systems. Development of the Haber-Bosch industrial process for ammonia synthesis helped to relieve N limitation of agricultural production, fueling the Green Revolution and reducing hunger. However, the massive use of industrial N fertilizer has doubled the N moving through the global N cycle with dramatic environmental consequences that threaten planetary health. Thus, there is an urgent need to reduce losses of reactive N from agriculture, while ensuring sufficient N inputs for food security. Here we review current knowledge related to N use efficiency (NUE) in agriculture and identify research opportunities in the areas of agronomy, plant breeding, biological N fixation (BNF), soil N cycling, and modeling to achieve responsible, sustainable use of N in agriculture. Amongst these opportunities, improved agricultural practices that synchronize crop N demand with soil N availability are low-hanging fruit. Crop breeding that targets root and shoot physiological processes will likely increase N uptake and utilization of soil N, while breeding for BNF effectiveness in legumes will enhance overall system NUE. Likewise, engineering of novel N-fixing symbioses in non-legumes could reduce the need for chemical fertilizers in agroecosystems but is a much longer-term goal. The use of simulation modeling to conceptualize the complex, interwoven processes that affect agroecosystem NUE, along with multi-objective optimization, will also accelerate NUE gains.
Translating Medicago truncatula genomics to crop legumes
Publisher: Elsevier BV
Date: 04-2009
DOI: 10.1016/J.PBI.2008.11.005
Abstract: Genomic resources developed in the model legume, Medicago truncatula, have the potential to accelerate practical advances in crop legumes. M. truncatula is closely related to many economically important legumes, frequently displaying genome-scale synteny. Translating genome data from M. truncatula should be highly effective in marker development, gene discovery, and positional cloning in crop legumes. The M. truncatula genome sequence also provides valuable insights about gene families of practical importance, especially those that are legume-specific. The M. truncatula genome sequence should also simplify the assembly of next-generation sequence data in closely related taxa, especially alfalfa. Genomic resources, such as whole-genome arrays, make it possible to pursue detailed questions about gene expression in both M. truncatula and related crop species, while tagged mutant populations simplify the process of determining gene function.
Cloning and functional characterization ofLjPLT4, a plasma membrane xylitol H+- symporter fromLotus japonicus
Publisher: Informa UK Limited
Date: 2011
DOI: 10.3109/09687688.2010.500626
Abstract: Polyols are compounds that play various physiological roles in plants. Here we present the identification of four cDNA clones of the model legume Lotus japonicus, encoding proteins of the monosaccharide transporter-like (MST) superfamily that share significant homology with previously characterized polyol transporters (PLTs). One of the transporters, named LjPLT4, was characterized functionally after expression in yeast. Transport assays revealed that LjPLT4 is a xylitol-specific H(+)-symporter (K (m), 0.34 mM). In contrast to the previously characterized homologues, LjPLT4 was unable to transport other polyols, including mannitol, sorbitol, myo-inositol and galactitol, or any of the monosaccharides tested. Interestingly, some monosaccharides, including fructose and xylose, inhibited xylitol uptake, although no significant uptake of these compounds was detected in the LjPLT4 transformed yeast cells, suggesting interactions with the xylitol binding site. Subcellular localization of LjPLT4-eYFP fusions expressed in Arabidopsis leaf epidermal cells indicated that LjPLT4 is localized in the plasma membrane. Real-time RT-PCR revealed that LjPLT4 is expressed in all major plant organs, with maximum transcript accumulation in leaves correlating with maximum xylitol levels there, as determined by GC-MS. Thus, LjPLT4 is the first plasma membrane xylitol-specific H(+)-symporter to be characterized in plants.
MtPAR MYB transcription factor acts as an on switch for proanthocyanidin biosynthesis in Medicago truncatula
Publisher: Proceedings of the National Academy of Sciences
Date: 17-01-2012
Abstract: MtPAR ( Medicago truncatula proanthocyanidin regulator) is an MYB family transcription factor that functions as a key regulator of proanthocyanidin (PA) biosynthesis in the model legume Medicago truncatula . MtPAR expression is confined to the seed coat, the site of PA accumulation. Loss-of-function par mutants contained substantially less PA in the seed coat than the wild type, whereas levels of anthocyanin and other specialized metabolites were normal in the mutants. In contrast, massive accumulation of PAs occurred when MtPAR was expressed ectopically in transformed hairy roots of Medicago . Transcriptome analysis of par mutants and MtPAR -expressing hairy roots, coupled with yeast one-hybrid analysis, revealed that MtPAR positively regulates genes encoding enzymes of the flavonoid–PA pathway via a probable activation of WD40-1 . Expression of MtPAR in the forage legume alfalfa ( Medicago sativa ) resulted in detectable levels of PA in shoots, highlighting the potential of this gene for biotechnological strategies to increase PAs in forage legumes for reduction of pasture bloat in ruminant animals.
Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis
Publisher: Springer Science and Business Media LLC
Date: 06-07-2011
Abstract: Single nucleotide polymorphisms (SNPs) are the most common type of sequence variation among plants and are often functionally important. We describe the use of 454 technology and high resolution melting analysis (HRM) for high throughput SNP discovery in tetraploid alfalfa ( Medicago sativa L.), a species with high economic value but limited genomic resources. The alfalfa genotypes selected from M. sativa subsp. sativa var. 'Chilean' and M. sativa subsp. falcata var. 'Wisfal', which differ in water stress sensitivity, were used to prepare cDNA from tissue of clonally-propagated plants grown under either well-watered or water-stressed conditions, and then pooled for 454 sequencing. Based on 125.2 Mb of raw sequence, a total of 54,216 unique sequences were obtained including 24,144 tentative consensus (TCs) sequences and 30,072 singletons, ranging from 100 bp to 6,662 bp in length, with an average length of 541 bp. We identified 40,661 candidate SNPs distributed throughout the genome. A s le of candidate SNPs were evaluated and validated using high resolution melting (HRM) analysis. A total of 3,491 TCs harboring 20,270 candidate SNPs were located on the M. truncatula (MT 3.5.1) chromosomes. Gene Ontology assignments indicate that sequences obtained cover a broad range of GO categories. We describe an efficient method to identify thousands of SNPs distributed throughout the alfalfa genome covering a broad range of GO categories. Validated SNPs represent valuable molecular marker resources that can be used to enhance marker density in linkage maps, identify potential factors involved in heterosis and genetic variation, and as tools for association mapping and genomic selection in alfalfa.
Lotus japonicus LjKUP Is Induced Late During Nodule Development and Encodes a Potassium Transporter of the Plasma Membrane
Publisher: Scientific Societies
Date: 07-2004
DOI: 10.1094/MPMI.2004.17.7.789
Abstract: The KUP family of potassium transporters in plants is large but poorly characterized. We isolated and characterized the first KUP transporter from a legume, LjKUP of Lotus japonicus. Although expressed throughout plants, LjKUP transcript levels were highest in nodules. Induction of LjKUP expression occurred late during nodule development, at a time of rapid organ expansion. A high level of LjKUP expression was maintained in mature, full-sized nodules. However, induction of LjKUP expression was independent of symbiotic nitrogen fixation (SNF), and occurred in ineffective nodules resulting from mutations in either the plant or its microsymbiont, Mesorhizobium loti. Heterologous expression of LjKUP in Escherichia coli showed that the protein is able to transport potassium. Transient expression of a GFP-LjKUP fusion protein in Arabidopsis cells indicated a plasma membrane location for the transporter. Taken together, the results indicate that LjKUP is a potassium transporter of the plasma membrane, which may play roles in cell expansion during nodule development and in ion homeostasis during SNF.
Priming of plant innate immunity by rhizobacteria and β‐aminobutyric acid: differences and similarities in regulation
Publisher: Wiley
Date: 29-04-2009
DOI: 10.1111/J.1469-8137.2009.02851.X
Abstract: Pseudomonas fluorescens WCS417r bacteria and beta-aminobutyric acid can induce disease resistance in Arabidopsis, which is based on priming of defence. In this study, we examined the differences and similarities of WCS417r- and beta-aminobutyric acid-induced priming. Both WCS417r and beta-aminobutyric acid prime for enhanced deposition of callose-rich papillae after infection by the oomycete Hyaloperonospora arabidopsis. This priming is regulated by convergent pathways, which depend on phosphoinositide- and ABA-dependent signalling components. Conversely, induced resistance by WCS417r and beta-aminobutyric acid against the bacterial pathogen Pseudomonas syringae are controlled by distinct NPR1-dependent signalling pathways. As WCS417r and beta-aminobutyric acid prime jasmonate- and salicylate-inducible genes, respectively, we subsequently investigated the role of transcription factors. A quantitative PCR-based genome-wide screen for putative WCS417r- and beta-aminobutyric acid-responsive transcription factor genes revealed distinct sets of priming-responsive genes. Transcriptional analysis of a selection of these genes showed that they can serve as specific markers for priming. Promoter analysis of WRKY genes identified a putative cis-element that is strongly over-represented in promoters of 21 NPR1-dependent, beta-aminobutyric acid-inducible WRKY genes. Our study shows that priming of defence is regulated by different pathways, depending on the inducing agent and the challenging pathogen. Furthermore, we demonstrated that priming is associated with the enhanced expression of transcription factors.
A Lotus japonicus β-type carbonic anhydrase gene expression pattern suggests distinct physiological roles during nodule development
Publisher: Elsevier BV
Date: 08-2003
DOI: 10.1016/S0167-4781(03)00142-8
Abstract: A full-length cDNA clone, designated Ljca1, coding for a beta-type carbonic anhydrase (CA EC: 4.2.1.1) was isolated from a Lotus japonicus nodule cDNA library. Semi-quantitative RT-PCR analysis revealed that Ljca1 codes for a nodule-specific CA, transcripts of which accumulate at maximum levels in young nodules at 14 days post-infection (d.p.i.). In situ hybridization and immunolocalization revealed that Ljca1 transcripts and LjCA1 polypeptides were present at high levels in all cell types of young nodules. In contrast, in mature nodules both transcripts and polypeptides were confined in a few cell layers of the nodules inner cortex. However, the central infected tissue of both young and mature nodules exhibited high CA activity, indicating the presence of additional CA isoforms of plant and/or microbial origin. This was supported by the finding that a putative Mesorhizobium loti CA gene was transiently expressed during nodule development. In addition, the temporal and spatial accumulation of phosphoenolpyruvate carboxylase (PEPC EC: 4.1.1.31) was determined by semi-quantitative RT-PCR and immunolocalization. The results suggest that LjCA1 might fulfill different physiological needs during L. japonicus nodule development.
Three Common Symbiotic ABC Subfamily B Transporters in Medicago truncatula Are Regulated by a NIN-Independent Branch of the Symbiosis Signaling Pathway
Publisher: Scientific Societies
Date: 08-2021
DOI: 10.1094/MPMI-02-21-0036-R
Abstract: Several ATP-binding cassette (ABC) transporters involved in the arbuscular mycorrhizal symbiosis and nodulation have been identified. We describe three previously unreported ABC subfamily B transporters, named AMN1, AMN2, and AMN3 (ABCB for mycorrhization and nodulation), that are expressed early during infection by rhizobia and arbuscular mycorrhizal fungi. These ABCB transporters are strongly expressed in symbiotically infected tissues, including in root-hair cells with rhizobial infection threads and arbusculated cells. During nodulation, the expression of these genes is highly induced by rhizobia and purified Nod factors and is dependent on DMI3 but is not dependent on other known major regulators of infection, such as NIN, NSP1, or NSP2. During mycorrhization their expression is dependent on DMI3 and RAM1 but not on NSP1 and NSP2. Therefore, they may be commonly regulated through a distinct branch of the common symbiotic pathway. Mutants with exonic Tnt1-transposon insertions were isolated for all three genes. None of the single or double mutants showed any differences in colonization by either rhizobia or mycorrhizal fungi, but the triple amn1 amn2 amn3 mutant showed an increase in nodule number. Further studies are needed to identify potential substrates of these transporters and understand their roles in these beneficial symbioses. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Arabidopsis ammonium transporters, atAMT1;1 and atAMT1;2, have different biochemical properties and functional roles
Publisher: Springer Science and Business Media LLC
Date: 2001
Nutrient transport across symbiotic membranes from legume nodules
Publisher: CSIRO Publishing
Date: 2001
DOI: 10.1071/PP01028
A remorin protein interacts with symbiotic receptors and regulates bacterial infection
Publisher: Proceedings of the National Academy of Sciences
Date: 19-01-2010
Abstract: Remorin proteins have been hypothesized to play important roles during cellular signal transduction processes. Induction of some members of this multigene family has been reported during biotic interactions. However, no roles during host-bacteria interactions have been assigned to remorin proteins until now. We used root nodule symbiosis between Medicago truncatula and Sinorhizobium meliloti to study the roles of a remorin that is specifically induced during nodulation. Here we show that this oligomeric remorin protein attaches to the host plasma membrane surrounding the bacteria and controls infection and release of rhizobia into the host cytoplasm. It interacts with the core set of symbiotic receptors that are essential for perception of bacterial signaling molecules, and thus might represent a plant-specific scaffolding protein.
SUGAR AND AMINO-ACID-TRANSPORT ACROSS SYMBIOTIC MEMBRANES FROM SOYBEAN NODULES
Publisher: Scientific Societies
Date: 1990
DOI: 10.1094/MPMI-3-334
GmVTL1 is an iron transporter on the symbiosome membrane of soybean with an important role in nitrogen fixation
Publisher: Cold Spring Harbor Laboratory
Date: 05-03-2020
DOI: 10.1101/2020.03.03.975805
Abstract: Legumes establish symbiotic relationships with soil bacteria (rhizobia), housed in nodules on plant roots. The plant supplies carbon substrates and other nutrients to the bacteria in exchange for fixed nitrogen. The exchange occurs across a plant-derived symbiosome membrane (SM), which encloses rhizobia to form a symbiosome. Iron supplied by the plant is crucial for the rhizobial enzyme nitrogenase that catalyses N 2 fixation, but the SM iron transporter has not been identified. We use complementation of yeast and plant mutants, real-time PCR, hairy root transformation, microscopy and proteomics to demonstrate the role of soybean GmVTL1 and 2. Both are members of the vacuolar iron transporter family and homologous to Lotus japonicus SEN1 (LjSEN1), previously shown to be essential for N 2 fixation. GmVTL1 expression is enhanced in nodule infected cells and both proteins are localised to the SM. GmVTL1 and 2 transport iron in yeast and GmVTL1 restores N 2 fixation when expressed in the Ljsen1 mutant. Three GmVTL1 amino acid substitutions that reduce iron transport in yeast also block N 2 fixation in Ljsen1 plants. We conclude GmVTL1 is responsible for transport of iron across the SM to bacteroids and plays a crucial role in the N 2 -fixing symbiosis.
Evolutionary History of the phl Gene Cluster in the Plant-Associated Bacterium Pseudomonas fluorescens
Publisher: American Society for Microbiology
Date: 04-2009
DOI: 10.1128/AEM.02052-08
Abstract: Pseudomonas fluorescens is of agricultural and economic importance as a biological control agent largely because of its plant association and production of secondary metabolites, in particular 2,4-diacetylphloroglucinol (2,4-DAPG). This polyketide, which is encoded by the eight-gene phl cluster, has antimicrobial effects on phytopathogens, promotes amino acid exudation from plant roots, and induces systemic resistance in plants. Despite its importance, 2,4-DAPG production is limited to a subset of P. fluorescens strains. Determination of the evolution of the phl cluster and understanding the selective pressures promoting its retention or loss in lineages of P. fluorescens will help in the development of P. fluorescens as a viable and effective inoculant for application in agriculture. In this study, genomic and sequence-based approaches were integrated to reconstruct the phylogeny of P. fluorescens and the phl cluster. It was determined that 2,4-DAPG production is an ancestral trait in the species P. fluorescens but that most lineages have lost this capacity through evolution. Furthermore, intragenomic recombination has relocated the phl cluster within the P. fluorescens genome at least three times, but the integrity of the cluster has always been maintained. The possible evolutionary and functional implications for retention of the phl cluster and 2,4-DAPG production in some lineages of P. fluorescens are discussed.
Tissue-specific down-regulation of LjAMT1;1 compromises nodule function and enhances nodulation in Lotus japonicus
Publisher: Springer Science and Business Media LLC
Date: 10-09-2008
DOI: 10.1007/S11103-008-9394-5
Abstract: Plant ammonium transporters of the AMT1 family are involved in N-uptake from the soil and ammonium transport, and recycling within the plant. Although AMT1 genes are known to be expressed in nitrogen-fixing nodules of legumes, their precise roles in this specialized organ remain unknown. We have taken a reverse-genetic approach to decipher the physiological role of LjAMT1 in Lotus japonicus nodules. LjAMT1 is normally expressed in both the infected zone and the vascular tissue of Lotus nodules. Inhibition of LjAMT1 gene expression, using an antisense gene construct driven by a leghemoglobin promoter resulted in a substantial reduction of LjAMT1 transcript in the infected tissue but not the vascular bundles of transgenic plants. As a result, the nitrogen-fixing activity of nodules was partially impaired and nodule number increased compared to control plants. Expression of LjAMT1 -GFP fusion protein in plant cells indicated a plasma-membrane location for the LjAMT1 protein. Taken together, the results are consistent with a role of LjAMT1 in retaining ammonium derived from symbiotic nitrogen fixation in plant cells prior to its assimilation.
Soil, seed or the tiller: why do trainees leave?
Publisher: Wiley
Date: 05-2018
DOI: 10.1111/ANS.14423
Metabolite transport across symbiotic membranes of legume nodules
Publisher: Annual Reviews
Date: 06-1997
DOI: 10.1146/ANNUREV.ARPLANT.48.1.493
Abstract: ▪ Abstract Infection of legume roots or stems with soil bacteria of the Rhizobiaceae results in the formation of nodules that become symbiotic nitrogen-fixing organs. Within the infected cells of these nodules, bacteria are enveloped in a membrane of plant origin, called the peribacteroid membrane (PBM), and ide and differentiate to form nitrogen-fixing bacteroids. The organelle-like structure comprised of PBM and bacteroids is termed the symbiosome, and is the basic nitrogen-fixing unit of the nodule. The major exchange of nutrients between the symbiotic partners is reduced carbon from the plant, to fuel nitrogenase activity in the bacteroid, and fixed nitrogen from the bacteroid, which is assimilated in the plant cytoplasm. However, many other metabolites are also exchanged. The metabolic interaction between the plant and the bacteroids is regulated by a series of transporters and channels on the PBM and the bacteroid membrane, and these form the focus of this review.
Eleven Golden Rules of Quantitative RT-PCR
Publisher: Oxford University Press (OUP)
Date: 07-2008
Lotus japonicus NF-YA1 Plays an Essential Role During Nodule Differentiation and Targets Members of the SHI/STY Gene Family
Publisher: Scientific Societies
Date: 12-2016
DOI: 10.1094/MPMI-10-16-0206-R
Abstract: Legume plants engage in intimate relationships with rhizobial bacteria to form nitrogen-fixing nodules, root-derived organs that accommodate the microsymbiont. Members of the Nuclear Factor Y (NF-Y) gene family, which have undergone significant expansion and functional ersification during plant evolution, are essential for this symbiotic liaison. Acting in a partially redundant manner, NF-Y proteins were shown, previously, to regulate bacterial infection, including selection of a superior rhizobial strain, and to mediate nodule structure formation. However, the exact mechanism by which these transcriptional factors exert their symbiotic functions has remained elusive. By carrying out detailed functional analyses of Lotus japonicus mutants, we demonstrate that LjNF-YA1 becomes indispensable downstream from the initial cortical cell isions but prior to nodule differentiation, including cell enlargement and vascular bundle formation. Three affiliates of the SHORT INTERNODES/STYLISH transcription factor gene family, called STY1, STY2, and STY3, are demonstrated to be among likely direct targets of LjNF-YA1, and our results point to their involvement in nodule formation.
A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula
Publisher: Springer Science and Business Media LLC
Date: 08-07-2008
Abstract: Medicago truncatula is a model legume species that is currently the focus of an international genome sequencing effort. Although several different oligonucleotide and cDNA arrays have been produced for genome-wide transcript analysis of this species, intrinsic limitations in the sensitivity of hybridization-based technologies mean that transcripts of genes expressed at low-levels cannot be measured accurately with these tools. Amongst such genes are many encoding transcription factors (TFs), which are arguably the most important class of regulatory proteins. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is the most sensitive method currently available for transcript quantification, and one that can be scaled up to analyze transcripts of thousands of genes in parallel. Thus, qRT-PCR is an ideal method to tackle the problem of TF transcript quantification in Medicago and other plants. We established a bioinformatics pipeline to identify putative TF genes in Medicago truncatula and to design gene-specific oligonucleotide primers for qRT-PCR analysis of TF transcripts. We validated the efficacy and gene-specificity of over 1000 TF primer pairs and utilized these to identify sets of organ-enhanced TF genes that may play important roles in organ development or differentiation in this species. This community resource will be developed further as more genome sequence becomes available, with the ultimate goal of producing validated, gene-specific primers for all Medicago TF genes. High-throughput qRT-PCR using a 384-well plate format enables rapid, flexible, and sensitive quantification of all predicted Medicago transcription factor mRNAs. This resource has been utilized recently by several groups in Europe, Australia, and the USA, and we expect that it will become the 'gold-standard' for TF transcript profiling in Medicago truncatula .
Molecular and Biochemical Characterization of the Parvulin-Type PPIases in Lotus japonicus
Publisher: Oxford University Press (OUP)
Date: 29-04-2009
Abstract: The cis/trans isomerization of the peptide bond preceding proline is an intrinsically slow process, although important in many biological processes in both prokaryotes and eukaryotes. In vivo, this isomerization is catalyzed by peptidyl-prolyl cis/trans-isomerases (PPIases). Here, we present the molecular and biochemical characterization of parvulin-type PPIase family members of the model legume Lotus japonicus, annotated as LjPar1, LjPar2, and LjPar3. Although LjPar1 and LjPar2 were found to be homologous to PIN1 (Protein Interacting with NIMA)-type parvulins and hPar14 from human, respectively, LjPar3 represents a novel multidomain parvulin, apparently present only in plants, that contains an active carboxyl-terminal sulfurtransferase domain. All Lotus parvulins were heterologously expressed and purified from Escherichia coli, and purified protein verification measurements used a liquid chromatography-mass spectrometry-based proteomic method. The biochemical characterization of the recombinant Lotus parvulins revealed that they possess PPIase activity toward synthetic tetrapeptides, although they exhibited different substrate specificities depending on the amino acid amino terminal to proline. These differences were also studied in a structural context using molecular modeling of the encoded polypeptides. Real-time reverse transcription-polymerase chain reaction revealed that the three parvulin genes of Lotus are ubiquitously expressed in all plant organs. LjPar1 was found to be up-regulated during the later stages of nodule development. Subcellular localization of LjPar-enhanced Yellow Fluorescence Protein (eYFP) fusions expressed in Arabidopsis (Arabidopsis thaliana) leaf epidermal cells revealed that LjPar1- and LjPar2-eYFP fusions were localized in the cytoplasm and in the nucleus, in contrast to LjPar3-eYFP, which was clearly localized in plastids. Divergent substrate specificities, expression profiles, and subcellular localization indicate that plant parvulin-type PPIases are probably involved in a wide range of biochemical and physiological processes.
PvNAC1 and PvNAC2 Are Associated with Leaf Senescence and Nitrogen Use Efficiency in Switchgrass
Publisher: Springer Science and Business Media LLC
Date: 13-12-2014
A prolonged cold treatment-induced cytochrome P450 gene from Arabidopsis thaliana
Publisher: Wiley
Date: 07-1999
Transcriptomic and Metabolic Changes Associated with Photorespiratory Ammonium Accumulation in the Model Legume Lotus japonicus
Publisher: Oxford University Press (OUP)
Date: 06-06-2013
Abstract: The transcriptomic and metabolic consequences of the lack of plastidic glutamine (Gln) synthetase in the model legume Lotus japonicus were investigated. Wild-type and mutant plants lacking the plastidic isoform of Gln synthetase were grown in conditions that suppress photorespiration and then transferred for different lengths of time to photorespiratory conditions. Transcript and metabolite levels were determined at the different time points considered. Under photorespiratory active conditions, the mutant accumulated high levels of ammonium, followed by its subsequent decline. A coordinate repression of the photorespiratory genes was observed in the mutant background. This was part of a greater modulation of the transcriptome, especially in the mutant, that was paralleled by changes in the levels of several key metabolites. The data obtained for the mutant represent the first direct experimental evidence for a coordinate regulation of photorespiratory genes over time. Metabolomic analysis demonstrated that mutant plants under active photorespiratory conditions accumulated high levels of several amino acids and organic acids, including intermediates of the Krebs cycle. An increase in Gln levels was also detected in the mutant, which was paralleled by an increase in cytosolic Gln synthetase1 gene transcription and enzyme activity levels. The global panoramic of the transcripts and metabolites that changed in L. japonicus plants during the transfer from photorespiration-suppressed to photorespiration-active conditions highlighted the link between photorespiration and several other cellular processes, including central carbon metabolism, amino acid metabolism, and secondary metabolism.
Isolation and characterization of a cDNA encoding NADP+-specific isocitrate dehydrogenase from soybean (Glycine max)
Publisher: Springer Science and Business Media LLC
Date: 03-1993
DOI: 10.1007/BF00027108
Targeted Switchgrass BAC Library Screening and Sequence Analysis Identifies Predicted Biomass and Stress Response-Related Genes
Publisher: Springer Science and Business Media LLC
Date: 30-08-2015
Global Changes in the Transcript and Metabolic Profiles during Symbiotic Nitrogen Fixation in Phosphorus-Stressed Common Bean Plants
Publisher: Oxford University Press (OUP)
Date: 15-09-2009
Abstract: Phosphorus (P) deficiency is widespread in regions where the common bean (Phaseolus vulgaris), the most important legume for human consumption, is produced, and it is perhaps the factor that most limits nitrogen fixation. Global gene expression and metabolome approaches were used to investigate the responses of nodules from common bean plants inoculated with Rhizobium tropici CIAT899 grown under P-deficient and P-sufficient conditions. P-deficient inoculated plants showed drastic reduction in nodulation and nitrogenase activity as determined by acetylene reduction assay. Nodule transcript profiling was performed through hybridization of nylon filter arrays spotted with cDNAs, approximately 4,000 unigene set, from the nodule and P-deficient root library. A total of 459 genes, representing different biological processes according to updated annotation using the UniProt Knowledgebase database, showed significant differential expression in response to P: 59% of these were induced in P-deficient nodules. The expression platform for transcription factor genes based in quantitative reverse transcriptase-polymerase chain reaction revealed that 37 transcription factor genes were differentially expressed in P-deficient nodules and only one gene was repressed. Data from nontargeted metabolic profiles indicated that amino acids and other nitrogen metabolites were decreased, while organic and polyhydroxy acids were accumulated, in P-deficient nodules. Bioinformatics analyses using MapMan and PathExpress software tools, customized to common bean, were utilized for the analysis of global changes in gene expression that affected overall metabolism. Glycolysis and glycerolipid metabolism, and starch and Suc metabolism, were identified among the pathways significantly induced or repressed in P-deficient nodules, respectively.
Increased Ascorbate Biosynthesis Does Not Improve Nitrogen Fixation Nor Alleviate the Effect of Drought Stress in Nodulated Medicago truncatula Plants
Publisher: Frontiers Media SA
Date: 28-06-2021
Abstract: Legume plants are able to establish nitrogen-fixing symbiotic relations with Rhizobium bacteria. This symbiosis is, however, affected by a number of abiotic constraints, particularly drought. One of the consequences of drought stress is the overproduction of reactive oxygen (ROS) and nitrogen species (RNS), leading to cellular damage and, ultimately, cell death. Ascorbic acid (AsA), also known as vitamin C, is one of the antioxidant compounds that plants synthesize to counteract this oxidative damage. One promising strategy for the improvement of plant growth and symbiotic performance under drought stress is the overproduction of AsA via the overexpression of enzymes in the Smirnoff-Wheeler biosynthesis pathway. In the current work, we generated Medicago truncatula plants with increased AsA biosynthesis by overexpressing MtVTC2 , a gene coding for GDP-L-galactose phosphorylase. We characterized the growth and physiological responses of symbiotic plants both under well-watered conditions and during a progressive water deficit. Results show that increased AsA availability did not provide an advantage in terms of plant growth or symbiotic performance either under well-watered conditions or in response to drought.
JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional gene descriptions across the plant kingdom
Publisher: Cold Spring Harbor Laboratory
Date: 03-10-2022
DOI: 10.1101/2022.09.30.510380
Abstract: Gene functional descriptions, which are typically derived from sequence similarity to experimentally validated genes in a handful of model species, offer a crucial line of evidence when searching for candidate genes that underlie trait variation. Plant responses to environmental cues, including gene expression regulatory variation, represent important resources for understanding gene function and crucial targets for plant improvement through gene editing and other biotechnologies. However, even after years of effort and numerous large-scale functional characterization studies, biological roles of large proportions of protein coding genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, a public and updateable data resource consisting of transcript abundance assays from 2,090 s les derived from 604 tissues or conditions across 18 erse species. We integrated across these erse conditions and genotypes by analyzing expression profiles, building gene clusters that exhibited tissue/condition specific expression, and testing for transcriptional modulation in response to environmental queues. For ex le, we discovered extensive phylogenetically constrained and condition-specific expression profiles across many gene families and genes without any functional annotation. Such conserved expression patterns and other tightly co-expressed gene clusters let us assign expression derived functional descriptions to 64,620 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas ( plantgeneatlas.jgi.doe.gov ) and Phytozome ( phytozome-next.jgi.doe.gov ), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.
Extreme specificity of NCR gene expression in Medicago truncatula
Publisher: Springer Science and Business Media LLC
Date: 25-08-2014
Molecular and cellular characterisation of LjAMT2 ; 1, an ammonium transporter from the model legume Lotus japonicus
Publisher: Springer Science and Business Media LLC
Date: 2003
Abstract: Two related families of ammonium transporters have been identified and partially characterised in plants in the past the AMT1 and AMT2 families. Most attention has focused on the larger of the two families, the AMT1 family, which contains members that are likely to fulfil different, possibly overlapping physiological roles in plants, including uptake of ammonium from the soil. The possible physiological functions of AMT2 proteins are less clear. Lack of data on cellular and tissue location of gene expression, and the intracellular location of proteins limit our understanding of the physiological role of all AMT proteins. We have cloned the first AMT2 family member from a legume, LjAMT2 of Lotus japonicus, and demonstrated that it functions as an ammonium transporter by complementing a yeast mutant defective in ammonium uptake. However, like AtAMT2 from Arabidopsis, and unlike AMT1 transporters from several plant species, LjAMT2 was unable to transport methylammonium. The LjAMT2 gene was found to be expressed constitutively throughout Lotus plants. In situ RNA hybridisation revealed LjAMT2 expression in all major tissues of nodules. Transient expression of LjAMT2 -GFP fusion protein in plant cells indicated that the transporter is located on the plasma membrane. In view of the fact that nodules derive ammonium internally, rather than from the soil, the results implicate LjAMT2 in the recovery of ammonium lost from nodule cells by efflux. A similar role may be fulfilled in other organs, especially leaves, which liberate ammonium during normal metabolism.
Siderophore-bound iron in the peribacteroid space of soybean root nodules
Publisher: Springer Science and Business Media LLC
Date: 1996
DOI: 10.1007/BF00011579
Genome‐wide association analysis of salinity responsive traits in
Medicago truncatula
Publisher: Wiley
Date: 27-02-2019
DOI: 10.1111/PCE.13508
TransportTP: A two-phase classification approach for membrane transporter prediction and characterization
Publisher: Springer Science and Business Media LLC
Date: 12-2009
Abstract: Membrane transporters play crucial roles in living cells. Experimental characterization of transporters is costly and time-consuming. Current computational methods for transporter characterization still require extensive curation efforts, especially for eukaryotic organisms. We developed a novel genome-scale transporter prediction and characterization system called TransportTP that combined homology-based and machine learning methods in a two-phase classification approach. First, traditional homology methods were employed to predict novel transporters based on sequence similarity to known classified proteins in the Transporter Classification Database (TCDB). Second, machine learning methods were used to integrate a variety of features to refine the initial predictions. A set of rules based on transporter features was developed by machine learning using well-curated proteomes as guides. In a cross-validation using the yeast proteome for training and the proteomes of ten other organisms for testing, TransportTP achieved an equivalent recall and precision of 81.8%, based on TransportDB, a manually annotated transporter database. In an independent test using the Arabidopsis proteome for training and four recently sequenced plant proteomes for testing, it achieved a recall of 74.6% and a precision of 73.4%, according to our manual curation. TransportTP is the most effective tool for eukaryotic transporter characterization up to date.
Genome‐wide reprogramming of regulatory networks, transport, cell wall and membrane biogenesis during arbuscular mycorrhizal symbiosis in Lotus japonicus
Publisher: Wiley
Date: 15-01-2009
DOI: 10.1111/J.1469-8137.2008.02725.X
Abstract: * Arbuscular mycorrhizas (AMs) contribute significantly to soil nutrient uptake in plants. As a consequence of the fungal colonization and of the deep reorganization shown by arbusculated cells, important impacts on root transcriptome are expected. * An Affymetrix GeneChip with 50,000 probe-sets and real-time RT-PCR allowed us to detect transcriptional changes triggered in Lotus japonicus by the AM fungus Gigaspora margarita, when arbuscules are at their maximum (28 d postinoculation (dpi)). An early time (4 dpi) was selected to differentiate genes potentially involved in signaling and/or in colonization of outer tissues. * A large number (75 out of 558) of mycorrhiza-induced genes code for proteins involved in protein turnover, membrane dynamics and cell wall synthesis, while many others are involved in transport (47) or transcription (24). Induction of a subset (24 genes) of these was tested and confirmed by qRT-PCR, and transcript location in arbusculated cells was demonstrated for seven genes using laser-dissected cells. * When compared with previously published papers, the transcript profiles indicate the presence of a core set of responsive genes (25) that seem to be conserved irrespective of the symbiotic partner identity.
Legume Models Strut Their Stuff
Publisher: Scientific Societies
Date: 2001
Characterization of spermidine and spermine synthases in Lotus japonicus: induction and spatial organization of polyamine biosynthesis in nitrogen fixing nodules
Publisher: Springer Science and Business Media LLC
Date: 05-03-2008
DOI: 10.1007/S00425-008-0717-1
Abstract: The biosynthesis of the polyamines spermidine (Spd) and spermine (Spm) from putrescine (Put) is catalysed by the consequent action of two aminopropyltransferases, spermidine synthase (SPDS EC: 2.5.1.16) and spermine synthase (SPMS EC: 2.5.1.22). Two cDNA clones coding for SPDS and SPMS homologues in the nitrogen-fixing nodules of the model legume Lotus japonicus were identified. Functionality of the encoded polypeptides was confirmed by their ability to complement spermidine and spermine deficiencies in yeast. The temporal and spatial expression pattern of the respective genes was correlated with the accumulation of total polyamines in symbiotic and non-symbiotic organs. Expression of both genes was maximal at early stages of nodule development, while at later stages the levels of both transcripts declined. Both genes were expressed in nodule inner cortical cells, vascular bundles, and central tissue. In contrast to gene expression, increasing amounts of Put, Spd, and Spm were found to accumulate during nodule development and after maturity. Interestingly, nodulated plants exhibited systemic changes in both LjSPDS and LjSPMS transcript levels and polyamine content in roots, stem and leaves, in comparison to uninoculated plants. These results give new insights into the neglected role of polyamines during nodule development and symbiotic nitrogen fixation (SNF).
Transcriptomic and metabolomic adaptation of Nannochloropsis gaditana grown under different light regimes
Publisher: Elsevier BV
Date: 2020
Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus
Publisher: Wiley
Date: 2007
DOI: 10.1111/J.1365-3040.2006.01608.X
Abstract: Affymetrix ATH1 arrays, large-scale real-time reverse transcription PCR of approximately 2200 transcription factor genes and other gene families, and analyses of metabolites and enzyme activities were used to investigate the response of Arabidopsis to phosphate (Pi) deprivation and re-supply. Transcript data were analysed with MapMan software to identify coordinated, system-wide changes in metabolism and other cellular processes. Phosphorus (P) deprivation led to induction or repression of > 1000 genes involved in many processes. A subset, including the induction of genes involved in P uptake, the mobilization of organic Pi, the conversion of phosphorylated glycolytic intermediates to carbohydrates and organic acids, the replacement of P-containing phospholipids with galactolipids and the repression of genes involved in nucleotide/nucleic acid synthesis, was reversed within 3 h after Pi re-supply. Analyses of 22 enzyme activities revealed that changes in transcript levels often, but not always, led to changes in the activities of the encoded enzymes in P-deprived plants. Analyses of metabolites confirmed that P deprivation leads to a shift towards the accumulation of carbohydrates, organic acids and amino acids, and that Pi re-supply leads to use of the latter. P-deprived plants also showed large changes in the expression of many genes involved in, for ex le, secondary metabolism and photosynthesis. These changes were not reversed rapidly upon Pi re-supply and were probably secondary in origin. Differentially expressed and highly P-specific putative regulator genes were identified that presumably play central roles in coordinating the complex responses of plants to changes in P nutrition. The specific responses to Pi differ markedly from those found for nitrate, whereas the long-term responses during P and N deprivation share common and non-specific features.
A protein complex required for polar growth of rhizobial infection threads
Publisher: Springer Science and Business Media LLC
Date: 28-06-2019
DOI: 10.1038/S41467-019-10029-Y
Abstract: During root nodule symbiosis, intracellular accommodation of rhizobia by legumes is a prerequisite for nitrogen fixation. For many legumes, rhizobial colonization initiates in root hairs through transcellular infection threads. In Medicago truncatula , VAPYRIN (VPY) and a putative E3 ligase LUMPY INFECTIONS (LIN) are required for infection thread development but their cellular and molecular roles are obscure. Here we show that LIN and its homolog LIN-LIKE interact with VPY and VPY-LIKE in a subcellular complex localized to puncta both at the tip of the growing infection thread and at the nuclear periphery in root hairs and that the punctate accumulation of VPY is positively regulated by LIN. We also show that an otherwise nuclear and cytoplasmic exocyst subunit, EXO70H4, systematically co-localizes with VPY and LIN during rhizobial infection. Genetic analysis shows that defective rhizobial infection in exo70h4 is similar to that in vpy and lin . Our results indicate that VPY, LIN and EXO70H4 are part of the symbiosis-specific machinery required for polar growth of infection threads.
Novel Aspects of Symbiotic Nitrogen Fixation Uncovered by Transcript Profiling with cDNA Arrays
Publisher: Scientific Societies
Date: 05-2002
DOI: 10.1094/MPMI.2002.15.5.411
Abstract: An array of 2,304 cDNA clones derived from nitrogen-fixing nodules of Lotus japonicus was produced and used to detect differences in relative gene transcript abundance between nodules and uninfected roots. Transcripts of 83 different genes were found to be more abundant in nodules than in roots. More than 50 of these have never before been identified as nodule-induced in any species. Expression of 36 genes was detected in nodules but not in roots. Several known nodulin genes were included among the nodule-induced genes. Also included were genes involved in sucrose breakdown and glycolysis, CO 2 recycling, and amino acid synthesis, processes that are known to be accelerated in nodules compared with roots. Genes involved in membrane transport, hormone metabolism, cell wall and protein synthesis, and signal transduction and regulation of transcription were also induced in nodules. Genes that may subvert normal plant defense responses, including two encoding enzymes involved in detoxification of active oxygen species and one that may prohibit phytoalexin synthesis, were also identified. The data represent a rich source of information for hypothesis building and future exploration of symbiotic nitrogen fixation.
Ascorbate oxidase: The unexpected involvement of a ‘wasteful enzyme’ in the symbioses with nitrogen-fixing bacteria and arbuscular mycorrhizal fungi
Publisher: Elsevier BV
Date: 10-2012
DOI: 10.1016/J.PLAPHY.2012.07.006
Abstract: Ascorbate oxidase (AO, EC 1.10.3.3) catalyzes the oxidation of ascorbate (AsA) to yield water. AO over-expressing plants are prone to ozone and salt stresses, whereas lower expression apparently confers resistance to unfavorable environmental conditions. Previous studies have suggested a role for AO as a regulator of oxygen content in photosynthetic tissues. For the first time we show here that the expression of a Lotus japonicus AO gene is induced in the symbiotic interaction with both nitrogen-fixing bacteria and arbuscular mycorrhizal (AM) fungi. In this framework, high AO expression is viewed as a possible strategy to down-regulate oxygen diffusion in root nodules, and a component of AM symbiosis. A general model of AO function in plants is discussed.
GmVTL1a is an iron transporter on the symbiosome membrane of soybean with an important role in nitrogen fixation
Publisher: Wiley
Date: 12-07-2020
DOI: 10.1111/NPH.16734
Abstract: Legumes establish symbiotic relationships with soil bacteria (rhizobia), housed in nodules on roots. The plant supplies carbon substrates and other nutrients to the bacteria in exchange for fixed nitrogen. The exchange occurs across a plant‐derived symbiosome membrane (SM), which encloses rhizobia to form a symbiosome. Iron supplied by the plant is crucial for rhizobial enzyme nitrogenase that catalyses nitrogen fixation, but the SM iron transporter has not been identified. We use yeast complementation, real‐time PCR and proteomics to study putative soybean ( Glycine max ) iron transporters GmVTL1a and GmVTL1b and have characterized the role of GmVTL1a using complementation in plant mutants, hairy root transformation and microscopy. GmVTL1a and GmVTL1b are members of the vacuolar iron transporter family and homologous to Lotus japonicus SEN1 (LjSEN1), which is essential for nitrogen fixation. GmVTL1a expression is enhanced in nodule infected cells and both proteins are localized to the SM. GmVTL1a transports iron in yeast and restores nitrogen fixation when expressed in the Ljsen1 mutant. Three GmVTL1a amino acid substitutions that block nitrogen fixation in Ljsen1 plants reduce iron transport in yeast. We conclude GmVTL1a is responsible for transport of iron across the SM to bacteroids and plays a crucial role in the nitrogen‐fixing symbiosis.
Legume Transcription Factor Genes: What Makes Legumes So Special?
Publisher: Oxford University Press (OUP)
Date: 02-09-2009
Peace Talks and Trade Deals. Keys to Long-Term Harmony in Legume-Microbe Symbioses
Publisher: Oxford University Press (OUP)
Date: 04-2005
6-Hydroxydopamine but not 1-methyl-4-phenylpyridinium abolishes α-synuclein anti-apoptotic phenotype by inhibiting its proteasomal degradation and by promoting its aggregation
Publisher: Elsevier BV
Date: 04-2006
A Plant Gene Encoding One-Heme and Two-Heme Hemoglobins With Extreme Reactivities Toward Diatomic Gases and Nitrite
Publisher: Frontiers Media SA
Date: 19-11-2020
Abstract: In plants, symbiotic hemoglobins act as carriers and buffers of O 2 in nodules, whereas nonsymbiotic hemoglobins or phytoglobins (Glbs) are ubiquitous in tissues and may perform multiple, but still poorly defined, functions related to O 2 and/or nitric oxide (NO). Here, we have identified a Glb gene of the model legume Medicago truncatula with unique properties. The gene, designated MtGlb1-2 , generates four alternative splice forms encoding Glbs with one or two heme domains and 215–351 amino acid residues. This is more than double the size of any hemoglobin from plants or other organisms described so far. A combination of molecular, cellular, biochemical, and biophysical methods was used to characterize these novel proteins. RNA-sequencing showed that the four splice variants are expressed in plant tissues. MtGlb1-2 is transcriptionally activated by hypoxia and its expression is further enhanced by an NO source. The gene is preferentially expressed in the meristems and vascular bundles of roots and nodules. Two of the proteins, bearing one or two hemes, were characterized using mutants in the distal histidines of the hemes. The Glbs are extremely reactive toward the physiological ligands O 2 , NO, and nitrite. They show very high O 2 affinities, NO dioxygenase activity (in the presence of O 2 ), and nitrite reductase (NiR) activity (in the absence of O 2 ) compared with the hemoglobins from vertebrates and other plants. We propose that these Glbs act as either NO scavengers or NO producers depending on the O 2 tension in the plant tissue, being involved in the fast and fine tuning of NO concentration in the cytosol in response to sudden changes in O 2 availability.
Genome-wide association of drought-related and biomass traits with HapMap SNPs inMedicago truncatula
Publisher: Wiley
Date: 17-04-2015
DOI: 10.1111/PCE.12520
Abstract: Improving drought tolerance of crop plants is a major goal of plant breeders. In this study, we characterized biomass and drought-related traits of 220 Medicago truncatula HapMap accessions. Characterized traits included shoot biomass, maximum leaf size, specific leaf weight, stomatal density, trichome density and shoot carbon-13 isotope discrimination (δ(13) C) of well-watered M. truncatula plants, and leaf performance in vitro under dehydration stress. Genome-wide association analyses were carried out using the general linear model (GLM), the standard mixed linear model (MLM) and compressed MLM (CMLM) in TASSEL, which revealed significant overestimation of P-values by CMLM. For each trait, candidate genes and chromosome regions containing SNP markers were found that are in significant association with the trait. For plant biomass, a 0.5 Mbp region on chromosome 2 harbouring a plasma membrane intrinsic protein, PIP2, was discovered that could potentially be targeted to increase dry matter yield. A protein disulfide isomerase-like protein was found to be tightly associated with both shoot biomass and leaf size. A glutamate-cysteine ligase and an aldehyde dehydrogenase family protein with Arabidopsis homologs strongly expressed in the guard cells were two of the top genes identified by stomata density genome-wide association studies analysis.
Control of Vegetative to Reproductive Phase Transition Improves Biomass Yield and Simultaneously Reduces Lignin Content in Medicago truncatula
Publisher: Springer Science and Business Media LLC
Date: 10-12-2014
Lotus japonicus karrikin receptors display divergent ligand-binding specificities and organ-dependent redundancy
Publisher: Public Library of Science (PLoS)
Date: 28-12-2020
DOI: 10.1371/JOURNAL.PGEN.1009249
Abstract: Karrikins (KARs), smoke-derived butenolides, are perceived by the α/β-fold hydrolase KARRIKIN INSENSITIVE2 (KAI2) and thought to mimic endogenous, yet elusive plant hormones tentatively called KAI2-ligands (KLs). The sensitivity to different karrikin types as well as the number of KAI2 paralogs varies among plant species, suggesting ersification and co-evolution of ligand-receptor relationships. We found that the genomes of legumes, comprising a number of important crops with protein-rich, nutritious seed, contain two or more KAI2 copies. We uncover sub-functionalization of the two KAI2 versions in the model legume Lotus japonicus and demonstrate differences in their ability to bind the synthetic ligand GR24 ent -5DS in vitro and in genetic assays with Lotus japonicus and the heterologous Arabidopsis thaliana background. These differences can be explained by the exchange of a widely conserved phenylalanine in the binding pocket of KAI2a with a tryptophan in KAI2b, which arose independently in KAI2 proteins of several unrelated angiosperms. Furthermore, two polymorphic residues in the binding pocket are conserved across a number of legumes and may contribute to ligand binding preferences. The ersification of KAI2 binding pockets suggests the occurrence of several different KLs acting in non-fire following plants, or an escape from possible antagonistic exogenous molecules. Unexpectedly, L . japonicus responds to erse synthetic KAI2-ligands in an organ-specific manner. Hypocotyl growth responds to KAR 1 , KAR 2 and rac -GR24, while root system development responds only to KAR 1 . This differential responsiveness cannot be explained by receptor-ligand preferences alone, because Lj KAI2a is sufficient for karrikin responses in the hypocotyl, while Lj KAI2a and Lj KAI2b operate redundantly in roots. Instead, it likely reflects differences between plant organs in their ability to transport or metabolise the synthetic KLs. Our findings provide new insights into the evolution and ersity of butenolide ligand-receptor relationships, and open novel research avenues into their ecological significance and the mechanisms controlling developmental responses to ergent KLs.
Genome‐wide analysis of flanking sequences reveals that Tnt1 insertion is positively correlated with gene methylation in Medicago truncatula
Publisher: Wiley
Date: 19-03-2019
DOI: 10.1111/TPJ.14291
Abstract: From a single transgenic line harboring five Tnt1 transposon insertions, we generated a near-saturated insertion population in Medicago truncatula. Using thermal asymmetric interlaced-polymerase chain reaction followed by sequencing, we recovered 388 888 flanking sequence tags (FSTs) from 21 741 insertion lines in this population. FST recovery from 14 Tnt1 lines using the whole-genome sequencing (WGS) and/or Tnt1-capture sequencing approaches suggests an average of 80 insertions per line, which is more than the previous estimation of 25 insertions. Analysis of the distribution pattern and preference of Tnt1 insertions showed that Tnt1 is overall randomly distributed throughout the M. truncatula genome. At the chromosomal level, Tnt1 insertions occurred on both arms of all chromosomes, with insertion frequency negatively correlated with the GC content. Based on 174 546 filtered FSTs that show exact insertion locations in the M. truncatula genome version 4.0 (Mt4.0), 0.44 Tnt1 insertions occurred per kb, and 19 583 genes contained Tnt1 with an average of 3.43 insertions per gene. Pathway and gene ontology analyses revealed that Tnt1-inserted genes are significantly enriched in processes associated with 'stress', 'transport', 'signaling' and 'stimulus response'. Surprisingly, gene groups with higher methylation frequency were more frequently targeted for insertion. Analysis of 19 583 Tnt1-inserted genes revealed that 59% (1265) of 2144 transcription factors, 63% (765) of 1216 receptor kinases and 56% (343) of 616 nucleotide-binding site-leucine-rich repeat genes harbored at least one Tnt1 insertion, compared with the overall 38% of Tnt1-inserted genes out of 50 894 annotated genes in the genome.
A High-Throughput RNA Interference (RNAi)-Based Approach Using Hairy Roots for the Study of Plant–Rhizobia Interactions
Publisher: Springer New York
Date: 2015
DOI: 10.1007/978-1-4939-2453-0_12
Abstract: Legumes are major contributors to sustainable agriculture their key feature is their ability to fix atmospheric nitrogen through symbiotic nitrogen fixation. Legumes are often recalcitrant to regeneration and transformation by Agrobacterium tumefaciens however, A. rhizogenes-mediated root transformation and composite plant generation are rapid and convenient alternatives to study root biology, including root nodule symbiosis. RNA interference (RNAi), coupled with A. rhizogenes-mediated root transformation, has been very successfully used for analyses of gene function by reverse genetics. Besides being applied to model legumes (Medicago truncatula and Lotus japonicus), this method has been adopted for several other legumes due to the ease and relative speed with which transgenic roots can be generated. Several protocols for hairy root transformation have been published. Here we describe an improved hairy root transformation protocol and the methods to study nodulation in Medicago. We also highlight the major differences between our protocol and others, and key steps that need to be adjusted in order to translate this method to other legumes.
The H+-ATPase HA1 of Medicago truncatula Is Essential for Phosphate Transport and Plant Growth during Arbuscular Mycorrhizal Symbiosis
Publisher: Oxford University Press (OUP)
Date: 04-2014
Abstract: A key feature of arbuscular mycorrhizal symbiosis is improved phosphorus nutrition of the host plant via the mycorrhizal pathway, i.e., the fungal uptake of Pi from the soil and its release from arbuscules within root cells. Efficient transport of Pi from the fungus to plant cells is thought to require a proton gradient across the periarbuscular membrane (PAM) that separates fungal arbuscules from the host cell cytoplasm. Previous studies showed that the H+-ATPase gene HA1 is expressed specifically in arbuscule-containing root cells of Medicago truncatula. We isolated a ha1-2 mutant of M. truncatula and found it to be impaired in the development of arbuscules but not in root colonization by Rhizophagus irregularis hyphae. Artificial microRNA silencing of HA1 recapitulated this phenotype, resulting in small and truncated arbuscules. Unlike the wild type, the ha1-2 mutant failed to show a positive growth response to mycorrhizal colonization under Pi-limiting conditions. Uptake experiments confirmed that ha1-2 mutants are unable to take up phosphate via the mycorrhizal pathway. Increased pH in the apoplast of abnormal arbuscule-containing cells of the ha1-2 mutant compared with the wild type suggests that HA1 is crucial for building a proton gradient across the PAM and therefore is indispensible for the transfer of Pi from the fungus to the plant.
Enabling Reverse Genetics in Medicago truncatula Using High-Throughput Sequencing for Tnt1 Flanking Sequence Recovery
Publisher: Springer New York
Date: 2017
DOI: 10.1007/978-1-4939-7003-2_3
Abstract: The genome sequence of Medicago truncatula was published and released in 2011. A Tnt1 insertional mutant population with 21,700 independently regenerated lines was completed in 2012 at The Samuel Roberts Noble Foundation. With an estimated 25 insertions per line, the Tnt1 mutant population harbors more than 500,000 insertions in the M. truncatula genome. Based on the genome size, average gene length, and random insertion of Tnt1into the genome, the mutant population affects about 90% of genes in the M. truncatula genome. Therefore, the mutant population enables functional characterization of most genes in the M. truncatula genome. From 2006 to 2011, we sequenced about 33,000 flanking sequence tags (FSTs) from 2600 Tnt1 lines using TAIL-PCR followed by TA cloning, plasmid isolation, and traditional Sanger sequencing. To accelerate FST sequencing, we developed a two-dimensional DNA pooling strategy coupled with next-generation sequencing and produced about 380,000 FSTs from all 21,700 lines in a relatively short time. All FSTs are BLAST searchable in a web-based database. One can quickly search the database to find M. truncatula mutant lines with Tnt1 insertions in most genes of interest.
Defects in Rhizobial Cyclic Glucan and Lipopolysaccharide Synthesis Alter Legume Gene Expression During Nodule Development
Publisher: Scientific Societies
Date: 2008
Abstract: cDNA array technology was used to compare transcriptome profiles of Lotus japonicus roots inoculated with a Mesorhizobium loti wild-type and two mutant strains affected in cyclic β(1-2) glucan synthesis (cgs) and in lipopolysaccharide synthesis (lpsβ2). Expression of genes associated with the development of a fully functional nodule was significantly affected in plants inoculated with the cgs mutant. Array results also revealed that induction of marker genes for nodule development was delayed when plants were inoculated with the lpsβ2 mutant. Quantitative real-time reverse-transcriptase polymerase chain reaction was used to quantify gene expression of a subset of genes involved in plant defense response, redox metabolism, or genes that encode for nodulins. The majority of the genes analyzed in this study were more highly expressed in roots inoculated with the wild type compared with those inoculated with the cgs mutant strain. Some of the genes exhibited a transient increase in transcript levels during intermediate steps of normal nodule development while others displayed induced expression during the final steps of nodule development. Ineffective nodules induced by the glucan mutant showed higher expression of phenylalanine ammonia lyase than wild-type nodules. Differences in expression pattern of genes involved in early recognition and signaling were observed in plants inoculated with the M. loti mutant strain affected in the synthesis of cyclic glucan.
Lotus japonicus Metabolic Profiling. Development of Gas Chromatography-Mass Spectrometry Resources for the Study of Plant-Microbe Interactions
Publisher: Oxford University Press (OUP)
Date: 04-2005
Abstract: Symbiotic nitrogen fixation (SNF) in legume root nodules requires differentiation and integration of both plant and bacterial metabolism. Classical approaches of biochemistry, molecular biology, and genetics have revealed many aspects of primary metabolism in legume nodules that underpin SNF. Functional genomics approaches, especially transcriptomics and proteomics, are beginning to provide a more holistic picture of the metabolic potential of nodules in model legumes like Medicago truncatula and Lotus japonicus. To extend these approaches, we have established protocols for nonbiased measurement and analysis of hundreds of metabolites from L. japonicus, using gas chromatography coupled with mass spectrometry. Following creation of mass spectral tag libraries, which represent both known and unknown metabolites, we measured and compared relative metabolite levels in nodules, roots, leaves, and flowers of symbiotic plants. Principal component analysis of the data revealed distinct metabolic phenotypes for the different organs and led to the identification of marker metabolites for each. Metabolites that were enriched in nodules included: octadecanoic acid, asparagine, glutamate, homoserine, cysteine, putrescine, mannitol, threonic acid, gluconic acid, glyceric acid-3-P, and glycerol-3-P. Hierarchical cluster analysis enabled discrimination of 10 groups of metabolites, based on distribution patterns in erse Lotus organs. The resources and tools described here, together with ongoing efforts in the areas of genome sequencing, and transcriptome and proteome analysis of L. japonicus and Mesorhizobium loti, should lead to a better understanding of nodule metabolism that underpins SNF.
GmZIP1 encodes a symbiosis-specific zinc transporter in soybean
Publisher: Elsevier BV
Date: 02-2002
DASH transcription factor impacts Medicago truncatula seed size by its action on embryo morphogenesis and auxin homeostasis
Publisher: Wiley
Date: 23-01-2015
DOI: 10.1111/TPJ.12742
Distinguishing HapMap Accessions Through Recursive Set Partitioning in Hierarchical Decision Trees
Publisher: Frontiers Media SA
Date: 03-02-2021
Abstract: The HapMap (haplotype map) projects have produced valuable genetic resources in life science research communities, allowing researchers to investigate sequence variations and conduct genome-wide association study (GWAS) analyses. A typical HapMap project may require sequencing hundreds, even thousands, of in idual lines or accessions within a species. Due to limitations in current sequencing technology, the genotype values for some accessions cannot be clearly called. Additionally, allelic heterozygosity can be very high in some lines, causing genetic and sometimes phenotypic segregation in their descendants. Genetic and phenotypic segregation degrades the original accession’s specificity and makes it difficult to distinguish one accession from another. Therefore, it is vitally important to determine and validate HapMap accessions before one conducts a GWAS analysis. However, to the best of our knowledge, there are no prior methodologies or tools that can readily distinguish or validate multiple accessions in a HapMap population. We devised a bioinformatics approach to distinguish multiple HapMap accessions using only a minimum number of genetic markers. First, we assign each candidate marker with a distinguishing score (DS), which measures its capability in distinguishing accessions. The DS score prioritizes those markers with higher percentages of homozygous genotypes (allele combinations), as they can be stably passed on to offspring. Next, we apply the “set-partitioning” concept to select optimal markers by recursively partitioning accession sets. Subsequently, we build a hierarchical decision tree in which a specific path represents the selected markers and the homogenous genotypes that can be used to distinguish one accession from others in the HapMap population. Based on these algorithms, we developed a web tool named MAD-HiDTree (Multiple Accession Distinguishment-Hierarchical Decision Tree), designed to analyze a user-input genotype matrix and construct a hierarchical decision tree. Using genetic marker data extracted from the Medicago truncatula HapMap population, we successfully constructed hierarchical decision trees by which the original 262 M. truncatula accessions could be efficiently distinguished. PCR experiments verified our proposed method, confirming that MAD-HiDTree can be used for the identification of a specific accession. MAD-HiDTree was developed in C/C ++ in Linux. Both the source code and test data are publicly available at bioinfo.noble.org/MAD-HiDTree/ .
The C2H2 Transcription Factor REGULATOR OF SYMBIOSOME DIFFERENTIATION Represses Transcription of the Secretory Pathway Gene VAMP721a and Promotes Symbiosome Development in
Publisher: Oxford University Press (OUP)
Date: 09-2013
The
Vigna unguiculata
Gene Expression Atlas (Vu
GEA
) from
de novo
assembly and quantification of
Publisher: Wiley
Date: 10-2016
DOI: 10.1111/TPJ.13279
Abstract: Legume research and cultivar development are important for sustainable food production, especially of high-protein seed. Thanks to the development of deep-sequencing technologies, crop species have been taken to the front line, even without completion of their genome sequences. Black-eyed pea (Vigna unguiculata) is a legume species widely grown in semi-arid regions, which has high potential to provide stable seed protein production in a broad range of environments, including drought conditions. The black-eyed pea reference genotype has been used to generate a gene expression atlas of the major plant tissues (i.e. leaf, root, stem, flower, pod and seed), with a developmental time series for pods and seeds. From these various organs, 27 cDNA libraries were generated and sequenced, resulting in more than one billion reads. Following filtering, these reads were de novo assembled into 36 529 transcript sequences that were annotated and quantified across the different tissues. A set of 24 866 unique transcript sequences, called Unigenes, was identified. All the information related to transcript identification, annotation and quantification were stored into a gene expression atlas webserver (vugea.noble.org), providing a user-friendly interface and necessary tools to analyse transcript expression in black-eyed pea organs and to compare data with other legume species. Using this gene expression atlas, we inferred details of molecular processes that are active during seed development, and identified key putative regulators of seed maturation. Additionally, we found evidence for conservation of regulatory mechanisms involving miRNA in plant tissues subjected to drought and seeds undergoing desiccation.
Metabolome analysis using GC-MS
Publisher: Springer-Verlag
Date: 2005
Gene expression profiling identifies two regulatory genes controlling dormancy and ABA sensitivity in Arabidopsis seeds
Publisher: Wiley
Date: 02-2010
Transcriptome analysis using cDNA arrays
Publisher: Springer-Verlag
Date: 2005
RNA isolation using CsCl gradients
Publisher: Springer-Verlag
Date: 2005
Absence of Symbiotic Leghemoglobins Alters Bacteroid and Plant Cell Differentiation During Development of Lotus japonicus Root Nodules
Publisher: Scientific Societies
Date: 07-2009
Abstract: During development of legume root nodules, rhizobia and their host plant cells undergo profound differentiation, which is underpinned by massive changes in gene expression in both symbiotic partners. Oxygen concentrations in infected and surrounding uninfected cells drop precipitously during nodule development. To assess what effects this has on plant and bacterial cell differentiation and gene expression, we used a leghemoglobin-RNA-interference (LbRNAi) line of Lotus japonicus, which is devoid of leghemoglobins and has elevated levels of free-oxygen in its nodules. Bacteroids in LbRNAi nodules showed altered ultrastructure indicating changes in bacterial differentiation. Transcript analysis of 189 plant and 192 bacterial genes uncovered many genes in both the plant and bacteria that were differentially regulated during nodulation of LbRNAi plants compared with the wild type (containing Lb and able to fix nitrogen). These included fix and nif genes of the bacteria, which are involved in microaerobic respiration and nitrogen fixation, respectively, and plant genes involved in primary and secondary metabolism. Metabolite analysis revealed decreased levels of many amino acids in nodules of LbRNAi plants, consistent with the defect in symbiotic nitrogen fixation of this line.
An Efficient Brome mosaic virus-Based Gene Silencing Protocol for Hexaploid Wheat (Triticum aestivum L.)
Publisher: Frontiers Media SA
Date: 18-06-2021
Abstract: Virus-induced gene silencing (VIGS) is a rapid and powerful method to evaluate gene function, especially for species like hexaploid wheat that have large, redundant genomes and are difficult and time-consuming to transform. The Brome mosaic virus (BMV)-based VIGS vector is widely used in monocotyledonous species but not wheat. Here we report the establishment of a simple and effective VIGS procedure in bread wheat using BMVCP5, the most recently improved BMV silencing vector, and wheat genes PHYTOENE DESATURASE ( TaPDS ) and PHOSPHATE2 ( TaPHO2 ) as targets. Time-course experiments revealed that smaller inserts (~100 nucleotides, nt) were more stable in BMVCP5 and conferred higher silencing efficiency and longer silencing duration, compared with larger inserts. When using a 100-nt insert and a novel coleoptile inoculation method, BMVCP5 induced extensive silencing of TaPDS transcript and a visible bleaching phenotype in the 2nd to 5th systemically-infected leaves from nine to at least 28 days post inoculation (dpi). For TaPHO2 , the ability of BMVCP5 to simultaneously silence all three homoeologs was demonstrated. To investigate the feasibility of BMV VIGS in wheat roots, ectopically expressed enhanced GREEN FLUORESCENT PROTEIN ( eGFP ) in a transgenic wheat line was targeted for silencing. Silencing of eGFP fluorescence was observed in both the maturation and elongation zones of roots. BMVCP5 mediated significant silencing of eGFP and TaPHO2 mRNA expression in roots at 14 and 21 dpi, and TaPHO2 silencing led to the doubling of inorganic phosphate concentration in the 2nd through 4th systemic leaves. All 54 wheat cultivars screened were susceptible to BMV infection. BMVCP5-mediated TaPDS silencing resulted in the expected bleaching phenotype in all eight cultivars examined, and decreased TaPDS transcript was detected in all three cultivars examined. This BMVCP5 VIGS technology may serve as a rapid and effective functional genomics tool for high-throughput gene function studies in aerial and root tissues and in many wheat cultivars.
Medicago truncatula DNF 2 is a PI ‐PLC ‐XD ‐containing protein required for bacteroid persistence and prevention of nodule early senescence and defense‐l
Publisher: Wiley
Date: 27-12-2012
DOI: 10.1111/NPH.12091
Abstract: Medicago truncatula and Sinorhizobium meliloti form a symbiotic association resulting in the formation of nitrogen‐fixing nodules. Nodule cells contain large numbers of bacteroids which are differentiated, nitrogen‐fixing forms of the symbiotic bacteria. In the nodules, symbiotic plant cells home and maintain hundreds of viable bacteria. In order to better understand the molecular mechanism sustaining the phenomenon, we searched for new plant genes required for effective symbiosis. We used a combination of forward and reverse genetics approaches to identify a gene required for nitrogen fixation, and we used cell and molecular biology to characterize the mutant phenotype and to gain an insight into gene function. The symbiotic gene DNF 2 encodes a putative phosphatidylinositol phospholipase C‐like protein. Nodules formed by the mutant contain a zone of infected cells reduced to a few cell layers. In this zone, bacteria do not differentiate properly into bacteroids. Furthermore, mutant nodules senesce rapidly and exhibit defense‐like reactions. This atypical phenotype amongst Fix − mutants unravels dnf2 as a new actor of bacteroid persistence inside symbiotic plant cells.
Cloning and characterization of Lotus japonicus formate dehydrogenase: A possible correlation with hypoxia
Publisher: Elsevier BV
Date: 06-2009
DOI: 10.1016/J.BBAPAP.2009.02.009
Abstract: Formate dehydrogenases (FDHs, EC 1.2.1.2) comprise a group of enzymes found in both prokaryotes and eukaryotes that catalyse the oxidation of formate to CO(2). FDH1 from the model legume Lotus japonicus (LjFDH1) was cloned and expressed in E. coli BL21(DE3) as soluble active protein. The enzyme was purified using affinity chromatography on Cibacron blue 3GA-Sepharose. The enzymatic properties of the recombinant enzyme were investigated and the kinetic parameters (K(m), k(cat)) for a number of substrates were determined. Molecular modelling studies were also employed to create a model of LjFDH1, based on the known structure of the Pseudomonas sp. 101 enzyme. The molecular model was used to help interpret biochemical data concerning substrate specificity and catalytic mechanism of the enzyme. The temporal expression pattern of LjFDH1 gene was studied by real-time RT-PCR in various plant organs and during the development of nitrogen-fixing nodules. Furthermore, the spatial transcript accumulation during nodule development and in young seedpods was determined by in situ RNA-RNA hybridization. These results considered together indicate a possible role of formate oxidation by LjFDH1 in plant tissues characterized by relative hypoxia.
Genome-Wide Reprogramming of Primary and Secondary Metabolism, Protein Synthesis, Cellular Growth Processes, and the Regulatory Infrastructure of Arabidopsis in Response to Nitrogen
Publisher: Oxford University Press (OUP)
Date: 09-2004
Abstract: Transcriptome analysis, using Affymetrix ATH1 arrays and a real-time reverse transcription-PCR platform for & ,400 transcription factors, was performed to identify processes affected by long-term nitrogen-deprivation or short-term nitrate nutrition in Arabidopsis. Two days of nitrogen deprivation led to coordinate repression of the majority of the genes assigned to photosynthesis, chlorophyll synthesis, plastid protein synthesis, induction of many genes for secondary metabolism, and reprogramming of mitochondrial electron transport. Nitrate readdition led to rapid, widespread, and coordinated changes. Multiple genes for the uptake and reduction of nitrate, the generation of reducing equivalents, and organic acid skeletons were induced within 30 min, before primary metabolites changed significantly. By 3 h, most genes assigned to amino acid and nucleotide biosynthesis and scavenging were induced, while most genes assigned to amino acid and nucleotide breakdown were repressed. There was coordinate induction of many genes assigned to RNA synthesis and processing and most of the genes assigned to amino acid activation and protein synthesis. Although amino acids involved in central metabolism increased, minor amino acids decreased, providing independent evidence for the activation of protein synthesis. Specific genes encoding expansin and tonoplast intrinsic proteins were induced, indicating activation of cell expansion and growth in response to nitrate nutrition. There were rapid responses in the expression of many genes potentially involved in regulation, including genes for trehalose metabolism and hormone metabolism, protein kinases and phosphatases, receptor kinases, and transcription factors.
Phosphorus Stress in Common Bean: Root Transcript and Metabolic Responses
Publisher: Oxford University Press (OUP)
Date: 20-04-2007
Abstract: Phosphorus (P) is an essential element for plant growth. Crop production of common bean (Phaseolus vulgaris), the most important legume for human consumption, is often limited by low P in the soil. Functional genomics were used to investigate global gene expression and metabolic responses of bean plants grown under P-deficient and P-sufficient conditions. P-deficient plants showed enhanced root to shoot ratio accompanied by reduced leaf area and net photosynthesis rates. Transcript profiling was performed through hybridization of nylon filter arrays spotted with cDNAs of 2,212 unigenes from a P deficiency root cDNA library. A total of 126 genes, representing different functional categories, showed significant differential expression in response to P: 62% of these were induced in P-deficient roots. A set of 372 bean transcription factor (TF) genes, coding for proteins with Inter-Pro domains characteristic or diagnostic for TF, were identified from The Institute of Genomic Research/Dana Farber Cancer Institute Common Bean Gene Index. Using real-time reverse transcription-polymerase chain reaction analysis, 17 TF genes were differentially expressed in P-deficient roots four TF genes, including MYB TFs, were induced. Nonbiased metabolite profiling was used to assess the degree to which changes in gene expression in P-deficient roots affect overall metabolism. Stress-related metabolites such as polyols accumulated in P-deficient roots as well as sugars, which are known to be essential for P stress gene induction. Candidate genes have been identified that may contribute to root adaptation to P deficiency and be useful for improvement of common bean.
Dissection of physiological, transcriptional, and metabolic traits in two tall fescue genotypes with contrasting drought tolerance
Publisher: Wiley
Date: 22-11-2021
DOI: 10.1002/PEI3.10066
Abstract: Tall fescue ( Festuca arundinacea ) is an important cool‐season perennial forage grass that forms mutualistic symbioses with fungal endophytes. Physiological, biochemical and transcriptional comparisons were made between two tall fescue genotypes with contrasting drought tolerance (tolerant, T400, and sensitive, S279), either with or without endophyte ( Epichloë coenophiala ). Drought stress was applied by withholding watering until plants reached mild, moderate and severe stresses. Physiological characterization showed that T400 had narrower, thicker leaves, and lower leaf conductance under well‐watered conditions, compared to S279. After severe drought and recovery, endophytic T400 had greater shoot and root biomass than other plant types. Under drought, leaf osmotic pressure increased much more in T400 than S279, consistent with accumulation of metabolites/osmolytes, especially proline. Gene Ontology enrichment analysis indicated that T400 had more active organic acid metabolism than S279 under drought, and implicated the role of endophyte in stimulating protein metabolism in both genotypes. Overall T400 and S279 responded to endophyte differently in aspects of physiology, gene transcription and metabolites, indicating plant genotype‐specific reactions to endophyte infection.
A Tutorial on Lotus japonicus Transcriptomic Tools
Publisher: Springer Berlin Heidelberg
Date: 2014
Symbiosis research, technology, and education: Proceedings of the 6th International Symbiosis Society Congress held in Madison Wisconsin, USA, August 2009
Publisher: Springer Science and Business Media LLC
Date: 30-06-2010
Identification of 118 Arabidopsis Transcription Factor and 30 Ubiquitin-Ligase Genes Responding to Chitin, a Plant-Defense Elicitor
Publisher: Scientific Societies
Date: 08-2007
Abstract: Chitin, found in the cell walls of true fungi and the exoskeleton of insects and nematodes, is a well-established elicitor of plant defense responses. In this study, we analyzed the expression patterns of Arabidopsis thaliana transcription factor (TF) and ubiquitin-ligase genes in response to purified chitooctaose at different treatment times (15, 30, 60, 90, and 120 min after treatment), using both quantitative polymerase chain reaction and the Affymetrix Arabidopsis whole-genome array. A total of 118 TF genes and 30 ubiquitin-ligase genes were responsive to the chitin treatment. Among these genes, members from the following four TF families were overrepresented: APETALA2/ethylene-reponsive element binding proteins (27), C2H2 zinc finger proteins (14), MYB domain-containing proteins (11), and WRKY domain transcription factors (14). Transcript variants from a few of these genes were found to respond differentially to chitin, suggesting transcript-specific regulation of these TF genes.
Natural Variation for Nutrient Use and Remobilization Efficiencies in Switchgrass
Publisher: Springer Science and Business Media LLC
Date: 14-10-2009
Loss of the nodule-specific cysteine rich peptide, NCR169, abolishes symbiotic nitrogen fixation in the Medicago truncatula dnf7 mutant
Publisher: Proceedings of the National Academy of Sciences
Date: 23-09-2015
Abstract: In certain legume–rhizobia symbioses, the host plant is thought to control the terminal differentiation of its bacterial partner leading to nitrogen fixation. In Medicago truncatula , over 600 genes coding for nodule-specific cysteine-rich (NCR) peptides are expressed during nodule development and have been implicated in bacteroid differentiation. Up to now it was generally assumed that most of these peptides, if not all, act redundantly. By demonstrating that deletion of a single member of the NCR gene family can result in an ineffective symbiotic phenotype, we show that specific NCR peptides can have essential, non-redundant roles in controlling bacterial differentiation and symbiotic nitrogen fixation.
Metabolism of Reactive Oxygen Species Is Attenuated in Leghemoglobin-Deficient Nodules of Lotus japonicus
Publisher: Scientific Societies
Date: 12-2007
Abstract: Leghemoglobins together with high rates of respiration are believed to be major sources of reactive oxygen species (ROS) in root nodules of leguminous plants. High capacities of antioxidative systems apparently protect this organ from oxidative damage. Using leghemoglobin-RNA interference (LbRNAi) lines of Lotus japonicus, we found that loss of leghemoglobin results in significantly lower H 2 O 2 levels in nodules. Transcript levels and catalytic activities of ascorbate-glutathione cycle enzymes involved in H 2 O 2 detoxification as well as concentrations of reduced ascorbate were also altered in LbRNAi nodules. Thus, symbiotic leghemoglobins contribute significantly to ROS generation in functional nodules.
Systemic Signaling of the Plant Nitrogen Status Triggers Specific Transcriptome Responses Depending on the Nitrogen Source in Medicago truncatula
Publisher: Oxford University Press (OUP)
Date: 20-02-2008
Abstract: Legumes can acquire nitrogen (N) from NO3 −, NH4 +, and N2 (through symbiosis with Rhizobium bacteria) however, the mechanisms by which uptake and assimilation of these N forms are coordinately regulated to match the N demand of the plant are currently unknown. Here, we find by use of the split-root approach in Medicago truncatula plants that NO3 − uptake, NH4 + uptake, and N2 fixation are under general control by systemic signaling of plant N status. Indeed, irrespective of the nature of the N source, N acquisition by one side of the root system is repressed by high N supply to the other side. Transcriptome analysis facilitated the identification of over 3,000 genes that were regulated by systemic signaling of the plant N status. However, detailed scrutiny of the data revealed that the observation of differential gene expression was highly dependent on the N source. Localized N starvation results, in the unstarved roots of the same plant, in a strong compensatory up-regulation of NO3 − uptake but not of either NH4 + uptake or N2 fixation. This indicates that the three N acquisition pathways do not always respond similarly to a change in plant N status. When taken together, these data indicate that although systemic signals of N status control root N acquisition, the regulatory gene networks targeted by these signals, as well as the functional response of the N acquisition systems, are predominantly determined by the nature of the N source.
ATPASE ACTIVITY AND ANION TRANSPORT ACROSS THE PERIBACTEROID MEMBRANE OF ISOLATED SOYBEAN SYMBIOSOMES
Publisher: Springer Science and Business Media LLC
Date: 10-1991
DOI: 10.1007/BF00248711
AMMONIA (C-14-METHYLAMINE) TRANSPORT ACROSS THE BACTEROID AND PERIBACTEROID MEMBRANES OF SOYBEAN ROOT-NODULES
Publisher: Oxford University Press (OUP)
Date: 09-1990
DOI: 10.1104/PP.94.1.71
Vapyrin, a gene essential for intracellular progression of arbuscular mycorrhizal symbiosis, is also essential for infection by rhizobia in the nodule symbiosis of Medicago truncatula
Publisher: Wiley
Date: 29-11-2010
Sugar release and growth of biofuel crops are improved by downregulation of pectin biosynthesis
Publisher: Springer Science and Business Media LLC
Date: 12-02-2018
DOI: 10.1038/NBT.4067
Abstract: Cell walls in crops and trees have been engineered for production of biofuels and commodity chemicals, but engineered varieties often fail multi-year field trials and are not commercialized. We engineered reduced expression of a pectin biosynthesis gene (Galacturonosyltransferase 4, GAUT4) in switchgrass and poplar, and find that this improves biomass yields and sugar release from biomass processing. Both traits were maintained in a 3-year field trial of GAUT4-knockdown switchgrass, with up to sevenfold increased saccharification and ethanol production and sixfold increased biomass yield compared with control plants. We show that GAUT4 is an α-1,4-galacturonosyltransferase that synthesizes homogalacturonan (HG). Downregulation of GAUT4 reduces HG and rhamnogalacturonan II (RGII), reduces wall calcium and boron, and increases extractability of cell wall sugars. Decreased recalcitrance in biomass processing and increased growth are likely due to reduced HG and RGII cross-linking in the cell wall.
Nutrient-wide association study of 92 foods and nutrients and breast cancer risk
Publisher: Springer Science and Business Media LLC
Date: 13-01-2020
DOI: 10.1186/S13058-019-1244-7
Abstract: Several dietary factors have been reported to be associated with risk of breast cancer, but to date, unequivocal evidence only exists for alcohol consumption. We sought to systematically assess the association between intake of 92 foods and nutrients and breast cancer risk using a nutrient-wide association study. Using data from 272,098 women participating in the European Prospective Investigation into Cancer and Nutrition (EPIC) study, we assessed dietary intake of 92 foods and nutrients estimated by dietary questionnaires. Cox regression was used to quantify the association between each food/nutrient and risk of breast cancer. A false discovery rate (FDR) of 0.05 was used to select the set of foods and nutrients to be replicated in the independent Netherlands Cohort Study (NLCS). Six foods and nutrients were identified as associated with risk of breast cancer in the EPIC study (10,979 cases). Higher intake of alcohol overall was associated with a higher risk of breast cancer (hazard ratio (HR) for a 1 SD increment in intake = 1.05, 95% CI 1.03–1.07), as was beer/cider intake and wine intake (HRs per 1 SD increment = 1.05, 95% CI 1.03–1.06 and 1.04, 95% CI 1.02–1.06, respectively), whereas higher intakes of fibre, apple ear, and carbohydrates were associated with a lower risk of breast cancer (HRs per 1 SD increment = 0.96, 95% CI 0.94–0.98 0.96, 95% CI 0.94–0.99 and 0.96, 95% CI 0.95–0.98, respectively). When evaluated in the NLCS (2368 cases), estimates for each of these foods and nutrients were similar in magnitude and direction, with the exception of beer/cider intake, which was not associated with risk in the NLCS. Our findings confirm a positive association of alcohol consumption and suggest an inverse association of dietary fibre and possibly fruit intake with breast cancer risk.
PHO1 family members transport phosphate from infected nodule cells to bacteroids in Medicago truncatula
Publisher: Oxford University Press (OUP)
Date: 25-11-2020
Abstract: Legumes play an important role in the soil nitrogen availability via symbiotic nitrogen fixation (SNF). Phosphate (Pi) deficiency severely impacts SNF because of the high Pi requirement of symbiosis. Whereas PHT1 transporters are involved in Pi uptake into nodules, it is unknown how Pi is transferred from the plant infected cells to nitrogen-fixing bacteroids. We hypothesized that Medicago truncatula genes homologous to Arabidopsis PHO1, encoding a vascular apoplastic Pi exporter, are involved in Pi transfer to bacteroids. Among the seven MtPHO1 genes present in M. truncatula, we found that two genes, namely MtPHO1.1 and MtPHO1.2, were broadly expressed across the various nodule zones in addition to the root vascular system. Expressions of MtPHO1.1 and MtPHO1.2 in Nicotiana benthamiana mediated specific Pi export. Plants with nodule-specific downregulation of both MtPHO1.1 and MtPHO1.2 were generated by RNA interference (RNAi) to examine their roles in nodule Pi homeostasis. Nodules of RNAi plants had lower Pi content and a three-fold reduction in SNF, resulting in reduced shoot growth. Whereas the rate of 33Pi uptake into nodules of RNAi plants was similar to control, transfer of 33Pi from nodule cells into bacteroids was reduced and bacteroids activated their Pi-deficiency response. Our results implicate plant MtPHO1 genes in bacteroid Pi homeostasis and SNF via the transfer of Pi from nodule infected cells to bacteroids.
System responses to long-term drought and re-watering of two contrasting alfalfa varieties
Publisher: Wiley
Date: 04-10-2011
Identification of potential early regulators of aphid resistance in Medicago truncatula via transcription factor expression profiling
Publisher: Wiley
Date: 22-03-2010
DOI: 10.1111/J.1469-8137.2010.03229.X
Abstract: *Resistance to aphids has been identified in a number of plant species, yet the molecular mechanisms underlying aphid resistance remain largely unknown. *Using high-throughput quantitative real-time PCR technology, the transcription profiles of 752 putative Medicago truncatula transcription factor genes were analysed in a pair of susceptible and resistant closely related lines of M. truncatula following 6 and 12 h of bluegreen aphid (Acyrthosiphon kondoi) infestation. *Eighty-two transcription factor genes belonging to 30 transcription factor families were responsive to bluegreen aphid infestation. More transcription factor genes were responsive in the resistant interaction than in the susceptible interaction of the 36 genes that were induced at 6 and/or 12 h, 32 were induced only in the resistant interaction. Bluegreen aphid-induced expression of a subset of these genes was correlated with the presence of AKR, a single dominant gene conferring resistance to bluegreen aphids. Similar transcription factor expression patterns of this subset were associated with bluegreen aphid resistance in other M. truncatula genetic backgrounds, as well as with resistance to pea aphid (Acyrthosiphon pisum). *Our results suggest that these transcription factors are among the early aphid-responsive genes in resistant plants, and may play important roles in resistance to multiple aphid species.
Nitrogen-Fixing Nodules Are an Important Source of Reduced Sulfur, Which Triggers Global Changes in Sulfur Metabolism in Lotus japonicus
Publisher: Oxford University Press (OUP)
Date: 21-08-2015
DOI: 10.1105/TPC.15.00108
Small Diameter Cell-Free Tissue-Engineered Vascular Grafts: Biomaterials and Manufacture Techniques to Reach Suitable Mechanical Properties
Publisher: MDPI AG
Date: 23-08-2022
Abstract: Vascular grafts (VGs) are medical devices intended to replace the function of a blood vessel. Available VGs in the market present low patency rates for small diameter applications setting the VG failure. This event arises from the inadequate response of the cells interacting with the biomaterial in the context of operative conditions generating chronic inflammation and a lack of regenerative signals where stenosis or aneurysms can occur. Tissue Engineered Vascular grafts (TEVGs) aim to induce the regeneration of the native vessel to overcome these limitations. Besides the biochemical stimuli, the biomaterial and the particular micro and macrostructure of the graft will determine the specific behavior under pulsatile pressure. The TEVG must support blood flow withstanding the exerted pressure, allowing the proper compliance required for the biomechanical stimulation needed for regeneration. Although the international standards outline the specific requirements to evaluate vascular grafts, the challenge remains in choosing the proper biomaterial and manufacturing TEVGs with good quality features to perform satisfactorily. In this review, we aim to recognize the best strategies to reach suitable mechanical properties in cell-free TEVGs according to the reported success of different approaches in clinical trials and pre-clinical trials.
Transport and Metabolism in Legume-Rhizobia Symbioses
Publisher: Annual Reviews
Date: 29-04-2013
DOI: 10.1146/ANNUREV-ARPLANT-050312-120235
Abstract: Symbiotic nitrogen fixation by rhizobia in legume root nodules injects approximately 40 million tonnes of nitrogen into agricultural systems each year. In exchange for reduced nitrogen from the bacteria, the plant provides rhizobia with reduced carbon and all the essential nutrients required for bacterial metabolism. Symbiotic nitrogen fixation requires exquisite integration of plant and bacterial metabolism. Central to this integration are transporters of both the plant and the rhizobia, which transfer elements and compounds across various plant membranes and the two bacterial membranes. Here we review current knowledge of legume and rhizobial transport and metabolism as they relate to symbiotic nitrogen fixation. Although all legume-rhizobia symbioses have many metabolic features in common, there are also interesting differences between them, which show that evolution has solved metabolic problems in different ways to achieve effective symbiosis in different systems.
Combining ability of barley flour pasting properties
Publisher: Elsevier BV
Date: 11-2008
Structure, function and regulation of ammonium transporters in plants
Publisher: Elsevier BV
Date: 05-2000
DOI: 10.1016/S0005-2736(00)00136-X
Abstract: Ammonium is an important source of nitrogen for plants. It is taken up by plant cells via ammonium transporters in the plasma membrane and distributed to intracellular compartments such as chloroplasts, mitochondria and vacuoles probably via different transporters in each case. Ammonium is generally not used for long-distance transport of nitrogen within the plant. Instead, most of the ammonium transported into plant cells is assimilated locally via glutamine synthetases in the cytoplasm and plastids. Ammonium is also produced by plant cells during normal metabolism, and ammonium transporters enable it to be moved from intracellular sites of production to sites of consumption. Ammonium can be generated de novo from molecular nitrogen (N(2)) by nitrogen-fixing bacteria in some plant cells, such as rhizobia in legume root nodule cells, and at least one ammonium transporter is implicated in the transfer of ammonium from the bacteria to the plant cytoplasm. Plant physiologists have described many of these ammonium transport processes over the last few decades. However, the genes and proteins that underlie these processes have been isolated and studied only recently. In this review, we consider in detail the molecular structure, function and regulation of plant ammonium transporters. We also attempt to reconcile recent discoveries at the molecular level with our knowledge of ammonium transport at the whole plant level.
Over-expression of the rice OsAMT1-1 gene increases ammonium uptake and content, but impairs growth and development of plants under high ammonium nutrition
Publisher: CSIRO Publishing
Date: 2006
DOI: 10.1071/FP05165
Abstract: A transgenic approach was undertaken to investigate the role of a rice ammonium transporter (OsAMT1-1) in ammonium uptake and consequent ammonium assimilation under different nitrogen regimes. Transgenic lines overexpressing OsAMT1-1 were produced by Agrobacterium-mediated transformation of two rice cultivars, Taipei 309 and Jarrah, with an OsAMT1-1 cDNA gene construct driven by the maize ubiquitin promoter. Transcript levels of OsAMT1-1 in both Taipei 309 and Jarrah transgenic lines correlated positively with transgene copy number. Shoot and root biomass of some transgenic lines decreased during seedling and early vegetative stage compared to the wild type, especially when grown under high (2 mm) ammonium nutrition. Transgenic plants, particularly those of cv. Jarrah recovered in the mid-vegetative stage under high ammonium nutrition. Roots of the transgenic plants showed increased ammonium uptake and ammonium content. We conclude that the decreased biomass of the transgenic lines at early stages of growth might be caused by the accumulation of ammonium in the roots owing to the inability of ammonium assimilation to match the greater ammonium uptake.
Focus on climate change and plant abiotic stress biology
Publisher: Oxford University Press (OUP)
Date: 15-11-2022
The future of legume genetic data resources: Challenges, opportunities, and priorities
Publisher: Wiley
Date: 24-11-2019
DOI: 10.1002/LEG3.16
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