ORCID Profile
0000-0001-6624-636X
Current Organisation
University of Adelaide
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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 | Crop and pasture production | Crop and pasture biomass and bioproducts | Space maritime and aviation law | Crop and pasture improvement (incl. selection and breeding) | Crop and Pasture Biochemistry and Physiology | Plant cell and molecular biology | Plant Biology | Industrial biotechnology not elsewhere classified | Agricultural molecular engineering of nucleic acids and proteins | Plant biology | Food engineering | Sociology and Social Studies of Science and Technology |
ANZSRC Socio-Economic Objective (SEO)
Winter Grains and Oilseeds not elsewhere classified | Resourcing of Education and Training Systems | Expanding Knowledge in Technology
Related Links
Publications
NADPH oxidase involvement in cellular integrity
Publisher: Springer Science and Business Media LLC
Date: 04-03-2008
DOI: 10.1007/S00425-008-0716-2
Abstract: NADPH oxidase activity is involved in plant adaptation and development. The reactive oxygen species sourced by NADPH oxidase activity may contribute to wall strength and protoplast volume adjustment. Root hair bulge apices of the NADPH oxidase mutant rhd2/Atrbohc were more robust than the kjk cellulose synthase mutant, but burst more readily than the wild type (WT). Root epidermal wall appeared impaired in rhd2/Atrbohc, as revealed by the number of protoplasts released by wall-degrading enzymes. Root hair bulges of rhd2/Atrbohc burst more than the WT when challenged in situ with hypo-osmotic low ionic strength medium. Inhibition of NADPH oxidase activity with diphenylene iodonium caused WT to phenocopy the rhd2/Atrbohc bursting in response to hypo-osmotic shock. This implicates RHD2/AtRBOHC in softening the cell wall to permit protoplast expansion. Overall, the results point to a role for RHD2/AtRBOHC in contributing to wall strength.
Approaches for More Efficient Biological Conversion of Lignocellulosic Feedstocks to Biofuels and Bioproducts
Publisher: American Chemical Society (ACS)
Date: 29-04-2019
The Golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of Arabidopsis
Publisher: Proceedings of the National Academy of Sciences
Date: 22-07-2014
Abstract: Delivery of nucleotide sugar substrates into the Golgi apparatus and endoplasmic reticulum for processes such as cell wall biosynthesis and protein glycosylation is critical for plant growth and development. Plant genomes encode large families of uncharacterized nucleotide sugar transporters that are specifically presumed to deliver the erse array of nucleotide sugars found in plants. This study has developed a novel approach that enabled functional characterization of six bifunctional UDP-rhamnose (Rha)/UDP-galactose (Gal) transporters from Arabidopsis . An analysis of loss-of-function and overexpression lines for two of these transporters identified biochemical alterations supporting their roles in the biosynthesis of Rha- and Gal-containing polysaccharides. Thus, cell wall polysaccharide biosynthesis in the Golgi apparatus of plants is likely also regulated by substrate transport mechanisms.
A grass-specific cellulose–xylan interaction dominates in sorghum secondary cell walls
Publisher: Springer Science and Business Media LLC
Date: 27-11-2020
DOI: 10.1038/S41467-020-19837-Z
Abstract: Sorghum ( Sorghum bicolor L. Moench) is a promising source of lignocellulosic biomass for the production of renewable fuels and chemicals, as well as for forage. Understanding secondary cell wall architecture is key to understanding recalcitrance i.e. identifying features which prevent the efficient conversion of complex biomass to simple carbon units. Here, we use multi-dimensional magic angle spinning solid-state NMR to characterize the sorghum secondary cell wall. We show that xylan is mainly in a three-fold screw conformation due to dense arabinosyl substitutions, with close proximity to cellulose. We also show that sorghum secondary cell walls present a high ratio of amorphous to crystalline cellulose as compared to dicots. We propose a model of sorghum cell wall architecture which is dominated by interactions between three-fold screw xylan and amorphous cellulose. This work will aid the design of low-recalcitrance biomass crops, a requirement for a sustainable bioeconomy.
Solid-State Nuclear Magnetic Resonance as a Tool to Probe the Impact of Mechanical Preprocessing on the Structure and Arrangement of Plant Cell Wall Polymers
Publisher: Frontiers Media SA
Date: 12-01-2022
Abstract: Efficient separation of the plant cell wall polymers during lignocellulose processing has been historically challenging due to insolubility of the polymers and their propensity for recalcitrant reassembly. Methods, such as “lignin first” extraction techniques, have advanced efficient biomass use, but the molecular mechanisms for recalcitrance remain enigmatic. Here, we discuss how solid-state Nuclear Magnetic Resonance (NMR) approaches report on the 3D organization of cellulose, xylan, and lignin in the plant cell wall. Recent results illustrate that the organization of these polymers varies across biomass sources and s le preparation methods, with even minimal physical processing causing significant effects. These structural differences contribute to variable extraction efficiencies for bioproducts after downstream processing. We propose that solid-state NMR methods can be applied to follow biomass processing, providing an understanding of the polymer rearrangements that can lead to poor yields for the desired bioproducts. The utility of the technique is illustrated for mechanical processing using lab-scale vibratory ball milling of Sorghum bicolor .
Extensive plant use of exometabolites
Publisher: Cold Spring Harbor Laboratory
Date: 30-07-2022
DOI: 10.1101/2022.07.29.496484
Abstract: Root exudation has been extensively studied due to its importance in soil carbon cycling and in supporting growth of soil microbes. However, the extent and dynamics of plant uptake of exogenous metabolites is poorly understood. To gain new insights into these processes we used 13 C-tracing to characterize plant uptake of exometabolites across a panel of erse plant species ( Arabidopsis thaliana, Brachypodium distachyon, Lotus japonicus, Panicum virgatum , and Kalanchoe fedtschenkoi ) grown in sterile hydroponic cultures. The uptake of exometabolites accounted for 23% of the overall B. distachyon carbon budget, and we identified 33 metabolites that were taken up by plants. Counterintuitively, many metabolites had higher uptake rates during the day vs. night. Thirteen of the metabolites from root exudates were found to promote root growth in A. thaliana , including hydroxybenzoate, threonate, N -acetyl-glucosamine, and uracil. Together these results indicate that the root uptake of organics can account for a significant portion of the plant carbon budget and that exogenous small molecules used by plants alter root growth with implications for plant nutrition, organic farming, soil nutrient cycling, and rhizosphere community dynamics.
Nanotechnology to advance CRISPR-Cas genetic engineering of plants
Publisher: Springer Science and Business Media LLC
Date: 03-2021
DOI: 10.1038/S41565-021-00854-Y
Abstract: CRISPR-Cas genetic engineering of plants holds tremendous potential for providing food security, battling biotic and abiotic crop stresses caused by climate change, and for environmental remediation and sustainability. Since the discovery of CRISPR-Cas technology, its usefulness has been demonstrated widely, including for genome editing in plants. Despite the revolutionary nature of genome-editing tools and the notable progress that these tools have enabled in plant genetic engineering, there remain many challenges for CRISPR applications in plant biotechnology. Nanomaterials could address some of the most critical challenges of CRISPR genome editing in plants through improvements in cargo delivery, species independence, germline transformation and gene editing efficiency. This Perspective identifies major barriers preventing CRISPR-mediated plant genetic engineering from reaching its full potential, and discusses ways that nanoparticle technologies can lower or eliminate these barriers. We also describe advances that are needed in nanotechnology to facilitate and accelerate plant genome editing. Timely advancement of the application of CRISPR technologies in plant engineering is crucial for our ability to feed and sustain the growing human population under a changing global climate.
GLUCOSAMINE INOSITOLPHOSPHORYLCERAMIDE TRANSFERASE1 (GINT1) Is a GlcNAc-Containing Glycosylinositol Phosphorylceramide Glycosyltransferase
Publisher: Oxford University Press (OUP)
Date: 14-05-2018
DOI: 10.1104/PP.18.00396
Supply Cost and Life-Cycle Greenhouse Gas Footprint of Dry and Ensiled Biomass Sorghum for Biofuel Production
Publisher: American Chemical Society (ACS)
Date: 30-09-2020
Transcriptional and metabolic changes associated with internode development and reduced cinnamyl alcohol dehydrogenase activity in sorghum
Publisher: Oxford University Press (OUP)
Date: 05-07-2022
DOI: 10.1093/JXB/ERAC300
Abstract: The molecular mechanisms associated with secondary cell wall (SCW) deposition in sorghum remain largely uncharacterized. Here, we employed untargeted metabolomics and large-scale transcriptomics to correlate changes in SCW deposition with variation in global gene expression profiles and metabolite abundance along an elongating internode of sorghum, with a major focus on lignin and phenolic metabolism. To gain deeper insight into the metabolic and transcriptional changes associated with pathway perturbations, a bmr6 mutant [with reduced cinnamyl alcohol dehydrogenase (CAD) activity] was analyzed. In the wild type, internode development was accompanied by an increase in the content of oligolignols, p-hydroxybenzaldehyde, hydroxycinnamate esters, and flavonoid glucosides, including tricin derivatives. We further identified modules of genes whose expression pattern correlated with SCW deposition and the accumulation of these target metabolites. Reduced CAD activity resulted in the accumulation of hexosylated forms of hydroxycinnamates (and their derivatives), hydroxycinnamaldehydes, and benzenoids. The expression of genes belonging to one specific module in our co-expression analysis correlated with the differential accumulation of these compounds and contributed to explaining this metabolic phenotype. Metabolomics and transcriptomics data further suggested that CAD perturbation activates distinct detoxification routes in sorghum internodes. Our systems biology approach provides a landscape of the metabolic and transcriptional changes associated with internode development and with reduced CAD activity in sorghum.
Iron Supplementation Eliminates Antagonistic Interactions Between Root-Associated Bacteria
Publisher: Frontiers Media SA
Date: 22-07-2020
Identification of an additional protein involved in mannan biosynthesis
Publisher: Wiley
Date: 19-10-2012
DOI: 10.1111/TPJ.12019
Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants
Publisher: American Chemical Society (ACS)
Date: 08-02-2017
DOI: 10.1021/ACSSYNBIO.6B00295
Abstract: Tight control and multifactorial regulation of gene expression are important challenges in genetic engineering and are critical for the development of regulatory circuits. Meeting these challenges will facilitate transgene expression regulation and support the fine-tuning of metabolic pathways to avoid the accumulation of undesired intermediates. By employing the endoribonuclease Csy4 and its recognition sequence from Pseudomonas aeruginosa and manipulating 5'UTR of mRNA, we developed a two-component expression-repression system to tightly control synthesis of transgene products. We demonstrated that this regulatory device was functional in monocotyledonous and dicotyledonous plant species, and showed that it can be used to repress transgene expression by >400-fold and to synchronize transgene repression. In addition to tissue-specific transgene repression, this system offers stimuli-dependent expression control. Using a bioinformatics approach, we identified 54 orthologous systems from various bacteria, and then validated in planta the activity for a few of those systems, demonstrating the potential ersity of such a two-component repressor system.
Lignin biosynthesis perturbations affect secondary cell wall composition and saccharification yield in Arabidopsis thaliana
Publisher: Springer Science and Business Media LLC
Date: 26-04-2013
Abstract: Second-generation biofuels are generally produced from the polysaccharides in the lignocellulosic plant biomass, mainly cellulose. However, because cellulose is embedded in a matrix of other polysaccharides and lignin, its hydrolysis into the fermentable glucose is h ered. The senesced inflorescence stems of a set of 20 Arabidopsis thaliana mutants in 10 different genes of the lignin biosynthetic pathway were analyzed for cell wall composition and saccharification yield. Saccharification models were built to elucidate which cell wall parameters played a role in cell wall recalcitrance. Although lignin is a key polymer providing the strength necessary for the plant’s ability to grow upward, a reduction in lignin content down to 64% of the wild-type level in Arabidopsis was tolerated without any obvious growth penalty. In contrast to common perception, we found that a reduction in lignin was not compensated for by an increase in cellulose, but rather by an increase in matrix polysaccharides. In most lignin mutants, the saccharification yield was improved by up to 88% cellulose conversion for the cinnamoyl-coenzyme A reductase1 mutants under pretreatment conditions, whereas the wild-type cellulose conversion only reached 18%. The saccharification models and Pearson correlation matrix revealed that the lignin content was the main factor determining the saccharification yield. However, also lignin composition, matrix polysaccharide content and composition, and, especially, the xylose, galactose, and arabinose contents influenced the saccharification yield. Strikingly, cellulose content did not significantly affect saccharification yield. Although the lignin content had the main effect on saccharification, also other cell wall factors could be engineered to potentially increase the cell wall processability, such as the galactose content. Our results contribute to a better understanding of the effect of lignin perturbations on plant cell wall composition and its influence on saccharification yield, and provide new potential targets for genetic improvement.
An unusual xylan in Arabidopsis primary cell walls is synthesised by GUX 3, IRX 9L, IRX 10L and IRX 14
Publisher: Wiley
Date: 25-06-2015
DOI: 10.1111/TPJ.12898
Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE
Publisher: MyJove Corporation
Date: 16-10-2017
DOI: 10.3791/56424
Bifunctional glycosyltransferases catalyze both extension and termination of pectic galactan oligosaccharides
Publisher: Wiley
Date: 22-03-2018
DOI: 10.1111/TPJ.13860
Abstract: Pectins are the most complex polysaccharides of the plant cell wall. Based on the number of methylations, acetylations and glycosidic linkages present in their structures, it is estimated that up to 67 transferase activities are involved in pectin biosynthesis. Pectic galactans constitute a major part of pectin in the form of side-chains of rhamnogalacturonan-I. In Arabidopsis, galactan synthase 1 (GALS1) catalyzes the addition of galactose units from UDP-Gal to growing β-1,4-galactan chains. However, the mechanisms for obtaining varying degrees of polymerization remain poorly understood. In this study, we show that AtGALS1 is bifunctional, catalyzing both the transfer of galactose from UDP-α-d-Gal and the transfer of an arabinopyranose from UDP-β-l-Ara
GUX 1 and GUX 2 glucuronyltransferases decorate distinct domains of glucuronoxylan with different substitution patterns
Publisher: Wiley
Date: 25-03-2013
DOI: 10.1111/TPJ.12135
Abstract: Xylan comprises up to one-third of plant cell walls, and it influences the properties and processing of biomass. Glucuronoxylan in Arabidopsis is characterized by a linear β-(1,4)-linked backbone of xylosyl residues substituted by glucuronic acid and 4-O-methylglucuronic acid (collectively termed [Me]GlcA). The role of these substitutions remains unclear. GUX1 (glucuronic acid substitution of xylan 1) and GUX2, recently identified as glucuronyltransferases, are both required for substitution of the xylan backbone with [Me]GlcA. Here, we demonstrate clear differences in the pattern of [Me]GlcA substitution generated by each of these glucuronyltransferases. GUX1 decorates xylan with a preference for addition of [Me]GlcA at evenly spaced xylosyl residues. Intervals of eight or 10 residues dominate, but larger intervals are observed. GUX2, in contrast, produces more tightly clustered decorations with most frequent spacing of five, six or seven xylosyl residues, with no preference for odd or even spacing. Moreover, each of these GUX transferases substitutes a distinct domain of secondary cell wall xylan, which we call the major and minor domains. These major and minor xylan domains were not separable from each other by size or charge, a finding that suggests that they are tightly associated. The presence of both differently [Me]GlcA decorated domains may produce a xylan molecule that is heterogeneous in its properties. We speculate that the major and minor domains of xylan may be specialised, such as for interaction with cellulose or lignin. These findings have substantial implications for our understanding of xylan synthesis and structure, and for models of the molecular architecture of the lignocellulosic matrix of plant cell walls.
Abnormal Glycosphingolipid Mannosylation Triggers Salicylic Acid–Mediated Responses inArabidopsis
Publisher: Oxford University Press (OUP)
Date: 05-2013
Abstract: The Arabidopsis thaliana protein GOLGI-LOCALIZED NUCLEOTIDE SUGAR TRANSPORTER (GONST1) has been previously identified as a GDP-d-mannose transporter. It has been hypothesized that GONST1 provides precursors for the synthesis of cell wall polysaccharides, such as glucomannan. Here, we show that in vitro GONST1 can transport all four plant GDP-sugars. However, gonst1 mutants have no reduction in glucomannan quantity and show no detectable alterations in other cell wall polysaccharides. By contrast, we show that a class of glycosylated sphingolipids (glycosylinositol phosphoceramides [GIPCs]) contains Man and that this mannosylation is affected in gonst1. GONST1 therefore is a Golgi GDP-sugar transporter that specifically supplies GDP-Man to the Golgi lumen for GIPC synthesis. gonst1 plants have a dwarfed phenotype and a constitutive hypersensitive response with elevated salicylic acid levels. This suggests an unexpected role for GIPC sugar decorations in sphingolipid function and plant defense signaling. Additionally, we discuss these data in the context of substrate channeling within the Golgi.
Annexin 1 regulates the H2O2-induced calcium signature in Arabidopsis thaliana roots
Publisher: Wiley
Date: 29-11-2014
DOI: 10.1111/TPJ.12372
Abstract: Hydrogen peroxide is the most stable of the reactive oxygen species (ROS) and is a regulator of development, immunity and adaptation to stress. It frequently acts by elevating cytosolic free Ca(2+) ([Ca(2+) ]cyt ) as a second messenger, with activation of plasma membrane Ca(2+) -permeable influx channels as a fundamental part of this process. At the genetic level, to date only the Ca(2) (+) -permeable Stelar K(+) Outward Rectifier (SKOR) channel has been identified as being responsive to hydrogen peroxide. We show here that the ROS-regulated Ca(2+) transport protein Annexin 1 in Arabidopsis thaliana (AtANN1) is involved in regulating the root epidermal [Ca(2+) ]cyt response to stress levels of extracellular hydrogen peroxide. Peroxide-stimulated [Ca(2+) ]cyt elevation (determined using aequorin luminometry) was aberrant in roots and root epidermal protoplasts of the Atann1 knockout mutant. Similarly, peroxide-stimulated net Ca(2+) influx and K(+) efflux were aberrant in Atann1 root mature epidermis, determined using extracellular vibrating ion-selective microelectrodes. Peroxide induction of GSTU1 (Glutathione-S-Transferase1 Tau 1), which is known to be [Ca(2+) ]cyt -dependent was impaired in mutant roots, consistent with a lesion in signalling. Expression of AtANN1 in roots was suppressed by peroxide, consistent with the need to restrict further Ca(2+) influx. Differential regulation of annexin expression was evident, with AtANN2 down-regulation but up-regulation of AtANN3 and AtANN4. Overall the results point to involvement of AtANN1 in shaping the root peroxide-induced [Ca(2+) ]cyt signature and downstream signalling.
Biophysical analysis of the plant-specific GIPC sphingolipids reveals multiple modes of membrane regulation
Publisher: Elsevier BV
Date: 2021
Publisher Correction: Sphingolipid biosynthesis modulates plasmodesmal ultrastructure and phloem unloading
Publisher: Springer Science and Business Media LLC
Date: 16-08-2019
DOI: 10.1038/S41477-019-0513-X
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
No evidence for transient transformation via pollen magnetofection in several monocot species
Publisher: Cold Spring Harbor Laboratory
Date: 03-05-2020
DOI: 10.1101/2020.05.01.071266
Abstract: The development of rapid and efficient transformation methods for many plant species remains an obstacle in both the basic and applied plant sciences. A novel method described by Zhao et al. (2017) used magnetic nanoparticles to deliver DNA into pollen grains of several dicot species, and one monocot (lily), to achieve transformation (“pollen magnetofection”). Using the published protocol, extensive trials by two independent research groups showed no indication of transient transformation success with pollen from two monocots, maize and sorghum. To further address the feasibility of magnetofection, lily pollen was used for side-by-side trials of magnetofection with a proven methodology for transient transformation, biolistics. Using a Green Fluorescent Protein reporter plasmid, transformation efficiency with the biolistic approach averaged 0.7% over three trials. However, the same plasmid produced no recognizable transformants via magnetofection, despite screening in idual pollen grains. We conclude that pollen magnetofection is not effective for transient transformation of pollen for at least three species of monocots, and suggest that efforts to replicate the magnetofection protocol in dicot species would be useful to fully assess its potential. ARISING FROM Zhao et al. Nature Plants 0.1038/s41477-017-0063-z (2017)
Zea mays Annexins Modulate Cytosolic Free Ca2+ and Generate a Ca2+-Permeable Conductance
Publisher: Oxford University Press (OUP)
Date: 02-2009
Abstract: Regulation of reactive oxygen species and cytosolic free calcium ([Ca2+]cyt) is central to plant function. Annexins are small proteins capable of Ca2+-dependent membrane binding or membrane insertion. They possess structural motifs that could support both peroxidase activity and calcium transport. Here, a Zea mays annexin preparation caused increases in [Ca2+]cyt when added to protoplasts of Arabidopsis thaliana roots expressing aequorin. The pharmacological profile was consistent with annexin activation (at the extracellular plasma membrane face) of Arabidopsis Ca2+-permeable nonselective cation channels. Secreted annexins could therefore modulate Ca2+ influx. As maize annexins occur in the cytosol and plasma membrane, they were incorporated at the intracellular face of lipid bilayers designed to mimic the plasma membrane. Here, they generated an instantaneously activating Ca2+-permeable conductance at mildly acidic pH that was sensitive to verapamil and Gd3+ and had a Ca2+-to-K+ permeability ratio of 0.36. These results suggest that cytosolic annexins create a Ca2+ influx pathway directly, particularly during stress responses involving acidosis. A maize annexin preparation also demonstrated in vitro peroxidase activity that appeared independent of heme association. In conclusion, this study has demonstrated that plant annexins create Ca2+-permeable transport pathways, regulate [Ca2+]cyt, and may function as peroxidases in vitro.
Folding of xylan onto cellulose fibrils in plant cell walls revealed by solid-state NMR
Publisher: Springer Science and Business Media LLC
Date: 21-12-2016
DOI: 10.1038/NCOMMS13902
Abstract: Exploitation of plant lignocellulosic biomass is h ered by our ignorance of the molecular basis for its properties such as strength and digestibility. Xylan, the most prevalent non-cellulosic polysaccharide, binds to cellulose microfibrils. The nature of this interaction remains unclear, despite its importance. Here we show that the majority of xylan, which forms a threefold helical screw in solution, flattens into a twofold helical screw ribbon to bind intimately to cellulose microfibrils in the cell wall. 13 C solid-state magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy, supported by in silico predictions of chemical shifts, shows both two- and threefold screw xylan conformations are present in fresh Arabidopsis stems. The twofold screw xylan is spatially close to cellulose, and has similar rigidity to the cellulose microfibrils, but reverts to the threefold screw conformation in the cellulose-deficient irx3 mutant. The discovery that induced polysaccharide conformation underlies cell wall assembly provides new principles to understand biomass properties.
Production of clovamide and its analogues inSaccharomyces cerevisiaeandLactococcus lactis
Publisher: Oxford University Press (OUP)
Date: 16-07-2019
DOI: 10.1111/LAM.13190
Abstract: Clovamide and its analogues are N-hydroxycinnamoyl-L-amino acids (HAA) that exhibit antioxidant activities. For environmental and economic reasons, biological synthesis of these plant-derived metabolites has garnered interest. In this study, we exploited HDT1, a BAHD acyltransferase recently isolated from red clover, for the production of clovamide and derivatives in S. cerevisiae and L. lactis. HDT1 catalyses the transfer of hydroxycinnamoyl-coenzyme A (CoA) onto aromatic amino acids. Therefore, by heterologously co-expressing HDT1 with 4-coumarate:CoA ligase (4CL), we succeeded in the biological production of clovamide and more than 20 other HAA, including halogenated ones, upon feeding the engineered micro-organisms with various combinations of cinnamates and amino acids. To the best of our knowledge, this is the first report on the biological synthesis of HAA and, more generally, on the synthesis of plant-derived antioxidant phenolic compounds in L. lactis. The production of these health beneficial metabolites in Generally Recognized As Safe (GRAS) micro-organisms such as S. cerevisiae and L. lactis provides new options for their delivery as therapeutics. SIGNIFICANCE AND IMPACT OF THE STUDY: N-hydroxycinnamoyl-L-amino acids such as clovamide are bioactive plant-derived phenolic compounds with health beneficial effects. Relying on chemical synthesis or direct extraction from plant sources for the supply of these valuable molecules poses challenges to environmental sustainability. As an alternative route, this work demonstrates the potential for biological synthesis of N-hydroxycinnamoyl-L-amino acids using engineered microbial hosts such as Saccharomyces cerevisiae and Lactococcus lactis. Besides being more eco-friendly, this approach should also provide more structurally erse compounds and offer new methods for their delivery to the human body.
Oligosaccharide relative quantitation using isotope tagging and normal‐phase liquid chromatography/mass spectrometry
Publisher: Wiley
Date: 08-2008
DOI: 10.1002/RCM.3665
Abstract: The growing interest in the conversion of plant biomass into biofuels has recently highlighted the lack of analytical techniques that are able to profile the fine structures of plant cell-wall polysaccharides. Here we present a new liquid chromatography/electrospray ionisation mass spectrometry (LC/ESI-MS) platform called Oligosaccharide Quantitation using Isotope Tagging (OliQuIT) developed for profiling the oligosaccharides derived from glycosyl hydrolase digestion of polysaccharides. The method is demonstrated using different arabinoxylan-derived oligosaccharide s les, which are reductively aminated with either the light (12C6) or heavy (13C6) form of aniline. The complex oligosaccharide mixtures are analysed by capillary normal-phase (NP)-LC and ESI-MS. Importantly, arabinoxylan oligosaccharide isomers are separated by NP-LC and their relative abundance in different s les can be determined from the intensities of ions labeled with the different isotopes. OliQuIT will be of use in multiple applications, including screening for plant varieties with improved saccharification properties, characterizing glycosyl hydrolase specificities and analysing plant glycosyl transferase mutants.
Arabidopsis Annexin1 Mediates the Radical-Activated Plasma Membrane Ca2+- and K+-Permeable Conductance in Root Cells
Publisher: Oxford University Press (OUP)
Date: 04-2012
Identifying transcription factors that reduce wood recalcitrance and improve enzymatic degradation of xylem cell wall in Populus
Publisher: Springer Science and Business Media LLC
Date: 16-05-2002
DOI: 10.1038/S41598-020-78781-6
Abstract: Developing an efficient deconstruction step of woody biomass for biorefinery has been drawing considerable attention since its xylem cell walls display highly recalcitrance nature. Here, we explored transcriptional factors (TFs) that reduce wood recalcitrance and improve saccharification efficiency in Populus species. First, 33 TF genes up-regulated during poplar wood formation were selected as potential regulators of xylem cell wall structure. The transgenic hybrid aspens ( Populus tremula × Populus tremuloides ) overexpressing each selected TF gene were screened for in vitro enzymatic saccharification. Of these, four transgenic seedlings overexpressing previously uncharacterized TF genes increased total glucan hydrolysis on average compared to control. The best performing lines overexpressing Pt × tERF123 and Pt × tZHD14 were further grown to form mature xylem in the greenhouse. Notably, the xylem cell walls exhibited significantly increased total xylan hydrolysis as well as initial hydrolysis rates of glucan. The increased saccharification of Pt × tERF123 -overexpressing lines could reflect the improved balance of cell wall components, i.e., high cellulose and low xylan and lignin content, which could be caused by upregulation of cellulose synthase genes upon the expression of Pt × tERF123 . Overall, we successfully identified Pt × tERF123 and Pt × tZHD14 as effective targets for reducing cell wall recalcitrance and improving the enzymatic degradation of woody plant biomass.
The TaCslA12 gene expressed in the wheat grain endosperm synthesizes wheat-like mannan when expressed in yeast and Arabidopsis.
Publisher: Elsevier BV
Date: 2020
Voltage, reactive oxygen species and the influx of calcium
Publisher: Informa UK Limited
Date: 09-2008
DOI: 10.4161/PSB.3.9.6405
Unlocking the architecture of native plant cell walls via solid-state nuclear magnetic resonance
Publisher: Elsevier
Date: 2020
Reimagining Lignin for the Biorefinery
Publisher: Oxford University Press (OUP)
Date: 12-04-2022
DOI: 10.1093/PCP/PCAC051
Elongated galactan side chains mediate cellulose–pectin interactions in engineered Arabidopsis secondary cell walls
Publisher: Wiley
Date: 26-04-2023
DOI: 10.1111/TPJ.16242
Abstract: The plant secondary cell wall is a thickened matrix of polysaccharides and lignin deposited at the cessation of growth in some cells. It forms the majority of carbon in lignocellulosic biomass, and it is an abundant and renewable source for forage, fiber, materials, fuels, and bioproducts. The complex structure and arrangement of the cell wall polymers mean that the carbon is difficult to access in an economical and sustainable way. One solution is to alter the cell wall polymer structure so that it is more suited to downstream processing. However, it remains difficult to predict what the effects of this engineering will be on the assembly, architecture, and properties of the cell wall. Here, we make use of Arabidopsis plants expressing a suite of genes to increase pectic galactan chain length in the secondary cell wall. Using multi‐dimensional solid‐state nuclear magnetic resonance, we show that increasing galactan chain length enhances pectin–cellulose spatial contacts and increases cellulose crystallinity. We also found that the increased galactan content leads to fewer spatial contacts of cellulose with xyloglucan and the backbone of pectin. Hence, we propose that the elongated galactan side chains compete with xyloglucan and the pectic backbone for cellulose interactions. Due to the galactan topology, this may result in comparatively weak interactions and disrupt the cell wall architecture. Therefore, introduction of this strategy into trees or other bioenergy crops would benefit from cell‐specific expression strategies to avoid negative effects on plant growth.
Annexins: multifunctional components of growth and adaptation
Publisher: Oxford University Press (OUP)
Date: 02-2008
DOI: 10.1093/JXB/ERM344
Abstract: Plant annexins are ubiquitous, soluble proteins capable of Ca(2+)-dependent and Ca(2+)-independent binding to endomembranes and the plasma membrane. Some members of this multigene family are capable of binding to F-actin, hydrolysing ATP and GTP, acting as peroxidases or cation channels. These multifunctional proteins are distributed throughout the plant and throughout the life cycle. Their expression and intracellular localization are under developmental and environmental control. The in vitro properties of annexins and their known, dynamic distribution patterns suggest that they could be central regulators or effectors of plant growth and stress signalling. Potentially, they could operate in signalling pathways involving cytosolic free calcium and reactive oxygen species.
The Arabidopsis thaliana nucleotide sugar transporter GONST2 is a functional homolog of GONST1
Publisher: Wiley
Date: 03-2021
DOI: 10.1002/PLD3.309
GONST2 transports GDP-Mannose for sphingolipid glycosylation in the Golgi apparatus of Arabidopsis
Publisher: Cold Spring Harbor Laboratory
Date: 14-06-2018
DOI: 10.1101/346775
Abstract: The Golgi lumen is the site of many different glycosylation events, including cell wall polysaccharide biosynthesis and lipid glycosylation. Transporters are necessary for the import of the substrates required for glycosylation (nucleotide sugars) from the cytosol where they are synthesized. Plants use four GDP-linked sugars to glycosylate macromolecules: GDP-L-Fucose, GDP-D-Mannose, GDP-L-Galactose and GDP-D-Glucose. Of the predicted fifty-one members of the nucleotide sugar transporter/triose phosphate transporter family in Arabidopsis, only four appear to contain the conserved motif needed for the transport of GDP-linked sugars, GOLGI LOCALIZED NUCLEOTIDE SUGAR TRANSPORTER (GONST) 1-4. Previously, we have demonstrated that GONST1 provides GDP-D-Mannose for glycosylation of a class of sphingolipids, the glycosylinositolphosphorylceramides (GIPCs). Here, we characterize its closest homologue, GONST2, and conclude that it also specifically provides substrate for GIPC glycosylation. Expression of GONST2 driven by the GONST1 promoter is able to rescue the severe growth phenotype of gonst1 . Loss of GONST2 exacerbates the gonst1 constitutive hypersensitive response, as well as the reduced cell wall cellulose content. The gonst2 mutant grows normally under standard conditions, but has enhanced resistance to the powdery mildew-causing fungus Golovinomyces orontii .
Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification
Publisher: Springer Science and Business Media LLC
Date: 04-09-2018
Reprogramming sphingolipid glycosylation is required for endosymbiont persistence in Medicago truncatula
Publisher: Elsevier BV
Date: 06-2021
DOI: 10.1016/J.CUB.2021.03.067
Abstract: Plant endosymbiosis relies on the development of specialized membranes that encapsulate the endosymbiont and facilitate nutrient exchange. However, the identity and function of lipids within these membrane interfaces is largely unknown. Here, we identify GLUCOSAMINE INOSITOL PHOSPHORYLCERAMIDE TRANSFERASE1 (GINT1) as a sphingolipid glycosyltransferase highly expressed in Medicago truncatula root nodules and roots colonized by arbuscular mycorrhizal (AM) fungi and further demonstrate that this enzyme functions in the synthesis of N-acetyl-glucosamine-decorated glycosyl inositol phosphoryl ceramides (GIPCs) in planta. MtGINT1 expression was developmentally regulated in symbiotic tissues associated with the development of symbiosome and periarbuscular membranes. RNAi silencing of MtGINT1 did not affect overall root growth but strongly impaired nodulation and AM symbiosis, resulting in the senescence of symbiosomes and arbuscules. Our results indicate that, although M. truncatula root sphingolipidome predominantly consists of hexose-decorated GIPCs, local reprogramming of GIPC glycosylation by MtGINT1 is required for the persistence of endosymbionts within the plant cell.
Plant single-cell solutions for energy and the environment
Publisher: Springer Science and Business Media LLC
Date: 12-08-2021
DOI: 10.1038/S42003-021-02477-4
Abstract: Progress in sequencing, microfluidics, and analysis strategies has revolutionized the granularity at which multicellular organisms can be studied. In particular, single-cell transcriptomics has led to fundamental new insights into animal biology, such as the discovery of new cell types and cell type-specific disease processes. However, the application of single-cell approaches to plants, fungi, algae, or bacteria (environmental organisms) has been far more limited, largely due to the challenges posed by polysaccharide walls surrounding these species’ cells. In this perspective, we discuss opportunities afforded by single-cell technologies for energy and environmental science and grand challenges that must be tackled to apply these approaches to plants, fungi and algae. We highlight the need to develop better and more comprehensive single-cell technologies, analysis and visualization tools, and tissue preparation methods. We advocate for the creation of a centralized, open-access database to house plant single-cell data. Finally, we consider how such efforts should balance the need for deep characterization of select model species while still capturing the ersity in the plant kingdom. Investments into the development of methods, their application to relevant species, and the creation of resources to support data dissemination will enable groundbreaking insights to propel energy and environmental science forward.
Plant synthetic biology could drive a revolution in biofuels and medicine
Publisher: SAGE Publications
Date: 24-09-2019
Abstract: Population growth, climate change, and dwindling finite resources are amongst the major challenges which are facing the planet. Requirements for food, materials, water, and energy will soon exceed capacity. Green biotechnology, fueled by recent plant synthetic biology breakthroughs, may offer solutions. This review summarizes current progress towards robust and predictable engineering of plants. I then discuss applications from the lab and field, with a focus on bioenergy, biomaterials, and medicine. The plant synthetic biology field has exploded in the last five years, in part driven by techniques such as CRISPR and cheap DNA synthesis. This review summarizes the current state of research in plant synthetic biology, and how it is being applied to two topics: renewable fuels and chemicals, and medicine.
Synthesis and Function of Complex Sphingolipid Glycosylation
Publisher: Elsevier BV
Date: 06-2020
Agrobacterium-mediated transient transformation of sorghum leaves for accelerating functional genomics and genome editing studies
Publisher: Cold Spring Harbor Laboratory
Date: 24-09-2019
DOI: 10.1101/779918
Abstract: Sorghum is one of the most recalcitrant species for transformation. Considering the time and effort required for stable transformation in sorghum, establishing a transient system to screen the efficiency and full functionality of vector constructs is highly desirable. Here, we report an Agrobacterium -mediated transient transformation assay with intact sorghum leaves using green fluorescent protein as marker. It also provides a good monocot alternative to tobacco and protoplast assays with a direct, native and more reliable system for testing single guide RNA (sgRNA) expression construct efficiency. Given the simplicity and ease of transformation, high reproducibility, and ability to test large constructs, this method can be widely adopted to speed up functional genomic and genome editing studies.
Sphingolipid biosynthesis modulates plasmodesmal ultrastructure and phloem unloading
Publisher: Springer Science and Business Media LLC
Date: 10-06-2019
Secondary cell wall characterization in a BY-2 inductive system
Publisher: Springer Science and Business Media LLC
Date: 20-07-2013
Development and application of a high throughput carbohydrate profiling technique for analyzing plant cell wall polysaccharides and carbohydrate active enzymes
Publisher: Springer Science and Business Media LLC
Date: 03-07-2013
Abstract: Plant cell wall polysaccharide composition varies substantially between species, organs and genotypes. Knowledge of the structure and composition of these polysaccharides, accompanied by a suite of well characterised glycosyl hydrolases will be important for the success of lignocellulosic biofuels. Current methods used to characterise enzymatically released plant oligosaccharides are relatively slow. A method and software was developed allowing the use of a DNA sequencer to profile oligosaccharides derived from plant cell wall polysaccharides (DNA sequencer-Assisted Saccharide analysis in High throughput, DASH). An ABI 3730xl, which can analyse 96 s les simultaneously by capillary electrophoresis, was used to separate fluorophore derivatised reducing mono- and oligo-saccharides from plant cell walls. Using electrophoresis mobility markers, oligosaccharide mobilities were standardised between experiments to enable reproducible oligosaccharide identification. These mobility markers can be flexibly designed to span the mobilities of oligosaccharides under investigation, and they have a fluorescence emission that is distinct from that of the saccharide labelling. Methods for relative and absolute quantitation of oligosaccharides are described. Analysis of a large number of s les is facilitated by the DASHboard software which was developed in parallel. Use of this method was exemplified by comparing xylan structure and content in Arabidopsis thaliana mutants affected in xylan synthesis. The product profiles of specific xylanases were also compared in order to identify enzymes with unusual oligosaccharide products. The DASH method and DASHboard software can be used to carry out large-scale analyses of the compositional variation of plant cell walls and biomass, to compare plants with mutations in plant cell wall synthesis pathways, and to characterise novel carbohydrate active enzymes.
The Three Members of the Arabidopsis thaliana Glycosyltransferase Family 92 are Functional β-1,4-Galactan Synthases.
Publisher: Oxford University Press (OUP)
Date: 09-2018
DOI: 10.1093/PCP/PCY180
Abstract: Pectin is a major component of primary cell walls and performs a plethora of functions crucial for plant growth, development and plant-defense responses. Despite the importance of pectic polysaccharides their biosynthesis is poorly understood. Several genes have been implicated in pectin biosynthesis by mutant analysis, but biochemical activity has been shown for very few. We used reverse genetics and biochemical analysis to study members of Glycosyltransferase Family 92 (GT92) in Arabidopsis thaliana. Biochemical analysis gave detailed insight into the properties of GALS1 (Galactan synthase 1) and showed galactan synthase activity of GALS2 and GALS3. All proteins are responsible for adding galactose onto existing galactose residues attached to the rhamnogalacturonan-I (RG-I) backbone. Significant GALS activity was observed with galactopentaose as acceptor but longer acceptors are favored. Overexpression of the GALS proteins in Arabidopsis resulted in accumulation of unbranched β-1, 4-galactan. Plants in which all three genes were inactivated had no detectable β-1, 4-galactan, and surprisingly these plants exhibited no obvious developmental phenotypes under standard growth conditions. RG-I in the triple mutants retained branching indicating that the initial Gal substitutions on the RG-I backbone are added by enzymes different from GALS.
Cell wall O-acetyl and methyl esterification patterns of leaves reflected in atmospheric emission signatures of acetic acid and methanol
Publisher: Cold Spring Harbor Laboratory
Date: 24-12-2019
DOI: 10.1101/2019.12.24.887844
Abstract: Plants emit high rates of methanol (meOH), generally assumed to derive from pectin demethylation, and this increases during abiotic stress. In contrast, less is known about the emission and source of acetic acid (AA). In this study, Populus trichocarpa (California poplar) leaves in different developmental stages were desiccated and quantified for total meOH and AA emissions together with bulk cell wall acetylation and methylation content. While young leaves showed high emissions of meOH (140 μmol m −2 ) and AA (42 μmol m −2 ), emissions were reduced in mature (meOH: 69%, AA: 60%) and old (meOH: 83%, AA: 76%) leaves. In contrast, the ratio of AA/meOH emissions increased with leaf development (young: 35%, mature: 43%, old: 82%), mimicking the pattern of O -acetyl/methyl ester ratios of leaf bulk cell walls (young: 35%, mature: 38%, old: 51%), which is driven by an increase in O -acetyl and decrease in methyl ester content with age. The results are consistent with meOH and AA emission sources from cell wall de-esterification, with young expanding tissues producing highly methylated pectin that is progressively demethyl-esterified. We highlight the quantification of AA/meOH emission ratios as a potential tool for rapid phenotype screening of structural carbohydrate esterification patterns.
Impact of abiotic stress on the regulation of cell wall biosynthesis in <i>Populus trichocarpa</i>
Publisher: Japanese Society for Plant Cell and Molecular Biology
Date: 25-09-2020
Glycan complexity dictates microbial resource allocation in the large intestine
Publisher: Springer Science and Business Media LLC
Date: 26-06-2015
DOI: 10.1038/NCOMMS8481
Abstract: The structure of the human gut microbiota is controlled primarily through the degradation of complex dietary carbohydrates, but the extent to which carbohydrate breakdown products are shared between members of the microbiota is unclear. We show here, using xylan as a model, that sharing the breakdown products of complex carbohydrates by key members of the microbiota, such as Bacteroides ovatus , is dependent on the complexity of the target glycan. Characterization of the extensive xylan degrading apparatus expressed by B. ovatus reveals that the breakdown of the polysaccharide by the human gut microbiota is significantly more complex than previous models suggested, which were based on the deconstruction of xylans containing limited monosaccharide side chains. Our report presents a highly complex and dynamic xylan degrading apparatus that is fine-tuned to recognize the different forms of the polysaccharide presented to the human gut microbiota.
Loss of Inositol Phosphorylceramide Sphingolipid Mannosylation Induces Plant Immune Responses and Reduces Cellulose Content in Arabidopsis
Publisher: Oxford University Press (OUP)
Date: 28-11-2016
DOI: 10.1105/TPC.16.00186
Rhizobacteria Mediate the Phytotoxicity of a Range of Biorefinery‐Relevant Compounds
Publisher: Wiley
Date: 26-07-2019
DOI: 10.1002/ETC.4501
Abstract: Advances in engineering biology have expanded the list of renewable compounds that can be produced at scale via biological routes from plant biomass. In most cases, these chemical products have not been evaluated for effects on biological systems, defined in the present study as bioactivity, that may be relevant to their manufacture. For sustainable chemical and fuel production, the industry needs to transition from fossil to renewable carbon sources, resulting in unprecedented expansion in the production and environmental distribution of chemicals used in biomanufacturing. Further, although some chemicals have been assessed for mammalian toxicity, environmental and agricultural hazards are largely unknown. We assessed 6 compounds that are representative of the emerging biofuel and bioproduct manufacturing process for their effect on model plants ( Arabidopsis thaliana , Sorghum bicolor ) and show that several alter plant seedling physiology at submillimolar concentrations. However, these responses change in the presence of in idual bacterial species from the A. thaliana root microbiome. We identified 2 in idual microbes that change the effect of chemical treatment on root architecture and a pooled microbial community with different effects relative to its constituents in idually. The present study indicates that screening industrial chemicals for bioactivity on model organisms in the presence of their microbiomes is important for biologically and ecologically relevant risk analyses. Environ Toxicol Chem 2019 :1911–1922. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.
Suppression of Arabidopsis GGLT1 affects growth by reducing the L-galactose content and borate cross-linking of rhamnogalacturonan-II
Publisher: Wiley
Date: 20-10-2018
DOI: 10.1111/TPJ.14088
Cell wall O-acetyl and methyl esterification patterns of leaves reflected in atmospheric emission signatures of acetic acid and methanol
Publisher: Public Library of Science (PLoS)
Date: 20-05-2020
Glycosyl transferases in family 61 mediate arabinofuranosyl transfer onto xylan in grasses
Publisher: Proceedings of the National Academy of Sciences
Date: 03-01-2012
Abstract: Xylan, a hemicellulosic component of the plant cell wall, is one of the most abundant polysaccharides in nature. In contrast to dicots, xylan in grasses is extensively modified by α-(1,2)– and α-(1,3)–linked arabinofuranose. Despite the importance of grass arabinoxylan in human and animal nutrition and for bioenergy, the enzymes adding the arabinosyl substitutions are unknown. Here we demonstrate that knocking-down glycosyltransferase (GT) 61 expression in wheat endosperm strongly decreases α-(1,3)–linked arabinosyl substitution of xylan. Moreover, heterologous expression of wheat and rice GT61s in Arabidopsis leads to arabinosylation of the xylan, and therefore provides gain-of-function evidence for α-(1,3)-arabinosyltransferase activity. Thus, GT61 proteins play a key role in arabinoxylan biosynthesis and therefore in the evolutionary ergence of grass cell walls.
Cell wall glucomannan in Arabidopsis is synthesised by CSLA glycosyltransferases, and influences the progression of embryogenesis
Publisher: Wiley
Date: 28-10-2009
Iron Supplementation Eliminates Antagonistic Interactions Between Root Associated Bacteria
Publisher: Cold Spring Harbor Laboratory
Date: 05-06-2020
DOI: 10.1101/2020.06.05.132704
Abstract: The rhizosphere microbiome (rhizobiome) plays a critical role in plant health and development. However the processes by which the constituent microbes interact to form and maintain a community are not well understood. To investigate these molecular processes, we examined pairwise interactions between 11 different microbial isolates under selected nutrient-rich and nutrient-limited conditions. We observed that when grown with media supplemented with 56 mM glucose, 2 microbial isolates were able to inhibit the growth of 6 out of 11 other microbes tested. The interaction between microbes persisted even after the antagonistic microbe was removed, upon exposure to spent media. To probe the genetic basis for these antagonistic interactions, we used a barcoded transposon library in a proxy bacterium, Pseudomonas putida , to identify genes which showed enhanced sensitivity to the antagonistic factor(s) secreted by Acinetobacter sp. 02. Iron metabolism-related gene clusters in P. putida were implicated by this systems-level analysis. The supplementation of iron prevented the antagonistic interaction in the original microbial pair supporting the hypothesis that iron limitation drives antagonistic microbial interactions between rhizobionts. We conclude that rhizobiome community composition is influenced by competition for limiting nutrients with implications for growth and development of the plant.
KONJAC1 and 2 Are Key Factors for GDP-Mannose Generation and Affect L-Ascorbic Acid and Glucomannan Biosynthesis in Arabidopsis
Publisher: Oxford University Press (OUP)
Date: 12-2015
DOI: 10.1105/TPC.15.00379
The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains
Publisher: Elsevier BV
Date: 2022
Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism
Publisher: Elsevier BV
Date: 09-2019
DOI: 10.1016/J.CUB.2019.07.086
Abstract: Parasitic plants in the genus Striga, commonly known as witchweeds, cause major crop losses in sub-Saharan Africa and pose a threat to agriculture worldwide. An understanding of Striga parasite biology, which could lead to agricultural solutions, has been h ered by the lack of genome information. Here, we report the draft genome sequence of Striga asiatica with 34,577 predicted protein-coding genes, which reflects gene family contractions and expansions that are consistent with a three-phase model of parasitic plant genome evolution. Striga seeds germinate in response to host-derived strigolactones (SLs) and then develop a specialized penetration structure, the haustorium, to invade the host root. A family of SL receptors has undergone a striking expansion, suggesting a molecular basis for the evolution of broad host range among Striga spp. We found that genes involved in lateral root development in non-parasitic model species are coordinately induced during haustorium development in Striga, suggesting a pathway that was partly co-opted during the evolution of the haustorium. In addition, we found evidence for horizontal transfer of host genes as well as retrotransposons, indicating gene flow to S. asiatica from hosts. Our results provide valuable insights into the evolution of parasitism and a key resource for the future development of Striga control strategies.
Agrobacterium-mediated transient transformation of sorghum leaves for accelerating functional genomics and genome editing studies
Publisher: Springer Science and Business Media LLC
Date: 27-02-2020
DOI: 10.1186/S13104-020-04968-9
Abstract: Sorghum is one of the most recalcitrant species for transformation. Considering the time and effort required for stable transformation in sorghum, establishing a transient system to screen the efficiency and full functionality of vector constructs is highly desirable. Here, we report an Agrobacterium -mediated transient transformation assay with intact sorghum leaves using green fluorescent protein as marker. It also provides a good monocot alternative to tobacco and protoplast assays with a direct, native and more reliable system for testing single guide RNA (sgRNA) expression construct efficiency. Given the simplicity and ease of transformation, high reproducibility, and ability to test large constructs, this method can be widely adopted to speed up functional genomic and genome editing studies.
No evidence for transient transformation via pollen magnetofection in several monocot species
Publisher: Springer Science and Business Media LLC
Date: 02-11-2020
Genome editing of a rice CDP-DAG synthase confers multipathogen resistance
Publisher: Springer Science and Business Media LLC
Date: 14-06-2023
A Transcriptomic Analysis of Xylan Mutants Does Not Support the Existence of a Secondary Cell Wall Integrity System in Arabidopsis
Publisher: Frontiers Media SA
Date: 27-03-2018
Eudicot plant-specific sphingolipids determine host selectivity of microbial NLP cytolysins
Publisher: American Association for the Advancement of Science (AAAS)
Date: 15-12-2017
Abstract: Many microbial pathogens produce proteins that are toxic to the cells that they are targeting. Broad-leaved plants are susceptible to NLP (necrosis and ethylene-inducing peptide 1–like protein) toxins. Lenarčič et al. identified the receptors for NLP toxins to be GIPC (glycosylinositol phosphorylceramide) sphingolipids (see the Perspective by Van den Ackerveken). Their findings reveal why these toxins only attack broad-leaved plants (so-called eudicots): If the sphingolipid carries just two hexoses, as is the case for eudicots, the toxin binds and causes cell lysis. But in monocots with sphingolipids that have three hexoses, the toxin is ineffective. Science , this issue p. 1431 see also p. 1383
Complete Genome Sequence of Agrobacterium sp. Strain 33MFTa1.1, Isolated from Thlaspi arvense Roots
Publisher: American Society for Microbiology
Date: 12-09-2019
DOI: 10.1128/MRA.00432-19
Abstract: Agrobacterium sp. strain 33MFTa1.1 was isolated for functional host-microbe interaction studies from the Thlaspi arvense root-associated microbiome. The complete genome is comprised of a circular chromosome of 2,771,937 bp, a linear chromosome of 2,068,443 bp, and a plasmid of 496,948 bp, with G+C contents of 59%, 59%, and 58%, respectively.
Structural Analysis of Cell Wall Polysaccharides Using PACE
Publisher: Springer New York
Date: 2017
DOI: 10.1007/978-1-4939-6722-3_16
Abstract: The plant cell wall is composed of many complex polysaccharides. The composition and structure of the polysaccharides affect various cell properties including cell shape, cell function and cell adhesion. PACE (Polysaccharide Analysis using Carbohydrate gel Electrophoresis) uses a simple, rapid technique to analyze polysaccharide quantity and structure (Goubet et al., Anal Biochem 300:53-68, 2002).
Are Methanol-Derived Foliar Methyl Acetate Emissions a Tracer of Acetate-Mediated Drought Survival in Plants?
Publisher: MDPI AG
Date: 23-02-2021
Abstract: Upregulation of acetate fermentation in plants has recently been described as an evolutionarily conserved drought survival strategy, with the amount of acetate produced directly correlating to survival. However, destructive measurements are required to evaluate acetate-linked drought responses, limiting the temporal and spatial scales that can be studied. Here, 13C-labeling studies with poplar (Populus trichocarpa) branches confirmed that methyl acetate is produced in plants from the acetate-linked acetylation of methanol. Methyl acetate emissions from detached leaves were strongly stimulated during desiccation, with total emissions decreasing with the leaf developmental stage. In addition, diurnal methyl acetate emissions from whole physiologically active poplar branches increased as a function of temperature, and light-dark transitions resulted in significant emission bursts lasting several hours. During experimental drought treatments of potted poplar saplings, light-dark methyl acetate emission bursts were eliminated while strong enhancements in methyl acetate emissions lasting 6 days were observed with their initiation coinciding with the suppression of transpiration and photosynthesis. The results suggest that methyl acetate emissions represent a novel non-invasive tracer of acetate-mediated temperature and drought survival response in plants. The findings may have important implications for the future understanding of acetate-mediated drought responses to transcription, cellular metabolism, and hormone signaling, as well as its associated changes in carbon cycling and water use from in idual plants to whole ecosystems.
Accumulation of high-value bioproducts in planta can improve the economics of advanced biofuels (vol 117, pg 8639, 2020)
Publisher: Proceedings of the National Academy of Sciences
Date: 12-10-2020
Heme-independent soluble and membrane-associated peroxidase activity of aZea maysannexin preparation
Publisher: Informa UK Limited
Date: 05-2009
DOI: 10.4161/PSB.4.5.8297
VASCULAR-RELATED NAC-DOMAIN6 and VASCULAR-RELATED NAC-DOMAIN7 Effectively Induce Transdifferentiation into Xylem Vessel Elements under Control of an Induction System
Publisher: Oxford University Press (OUP)
Date: 20-05-2010
Abstract: We previously showed that the VASCULAR-RELATED NAC-DOMAIN6 (VND6) and VND7 genes, which encode NAM/ATAF/CUC domain protein transcription factors, act as key regulators of xylem vessel differentiation. Here, we report a glucocorticoid-mediated posttranslational induction system of VND6 and VND7. In this system, VND6 or VND7 is expressed as a fused protein with the activation domain of the herpes virus VP16 protein and hormone-binding domain of the animal glucocorticoid receptor, and the protein's activity is induced by treatment with dexamethasone (DEX), a glucocorticoid derivative. Upon DEX treatment, transgenic Arabidopsis (Arabidopsis thaliana) plants carrying the chimeric gene exhibited transdifferentiation of various types of cells into xylem vessel elements, and the plants died. Many genes involved in xylem vessel differentiation, such as secondary wall biosynthesis and programmed cell death, were up-regulated in these plants after DEX treatment. Chemical analysis showed that xylan, a major hemicellulose component of the dicot secondary cell wall, was increased in the transgenic plants after DEX treatment. This induction system worked in poplar (Populus tremula × tremuloides) trees and in suspension cultures of cells from Arabidopsis and tobacco (Nicotiana tabacum) more than 90% of the tobacco BY-2 cells expressing VND7-VP16-GR transdifferentiated into xylem vessel elements after DEX treatment. These data demonstrate that the induction systems controlling VND6 and VND7 activities can be used as powerful tools for understanding xylem cell differentiation.
Golgi-localized STELLO proteins regulate the assembly and trafficking of cellulose synthase complexes in Arabidopsis
Publisher: Springer Science and Business Media LLC
Date: 09-06-2016
DOI: 10.1038/NCOMMS11656
Abstract: As the most abundant biopolymer on Earth, cellulose is a key structural component of the plant cell wall. Cellulose is produced at the plasma membrane by cellulose synthase (CesA) complexes (CSCs), which are assembled in the endomembrane system and trafficked to the plasma membrane. While several proteins that affect CesA activity have been identified, components that regulate CSC assembly and trafficking remain unknown. Here we show that STELLO1 and 2 are Golgi-localized proteins that can interact with CesAs and control cellulose quantity. In the absence of STELLO function, the spatial distribution within the Golgi, secretion and activity of the CSCs are impaired indicating a central role of the STELLO proteins in CSC assembly. Point mutations in the predicted catalytic domains of the STELLO proteins indicate that they are glycosyltransferases facing the Golgi lumen. Hence, we have uncovered proteins that regulate CSC assembly in the plant Golgi apparatus.
Editorial Feature: Meet the PCP Editor—Jenny Mortimer
Publisher: Oxford University Press (OUP)
Date: 13-01-2021
DOI: 10.1093/PCP/PCAA178
Glycosylation of inositol phosphorylceramide sphingolipids is required for normal growth and reproduction in Arabidopsis
Publisher: Wiley
Date: 2017
DOI: 10.1111/TPJ.13382
Abstract: Sphingolipids are a major component of plant plasma membranes and endomembranes, and mediate a erse range of biological processes. Study of the highly glycosylated glycosyl inositol phosphorylceramide ( GIPC ) sphingolipids has been slow as a result of challenges associated with the extractability of GIPC s, and their functions in the plant remain poorly characterized. We recently discovered an Arabidopsis GIPC glucuronosyltransferase, INOSITOL PHOSPHORYLCERAMIDE GLUCURONOSYLTRANSFERASE 1 ( IPUT 1), which is the first enzyme in the GIPC glycosylation pathway. Plants homozygous for the iput1 loss‐of‐function mutation were unobtainable, and so the developmental effects of reduced GIPC glucuronosylation could not be analyzed in planta . Using a pollen‐specific rescue construct, we have here isolated homozygous iput1 mutants. The iput1 mutants show severe dwarfism, compromised pollen tube guidance, and constitutive activation of salicyclic acid‐mediated defense pathways. The mutants also possess reduced GIPC s, increased ceramides, and an increased incorporation of short‐chain fatty acids and dihydroxylated bases into inositol phosphorylceramides and GIPC s. The assignment of a direct role for GIPC glycan head groups in the impaired processes in iput1 mutants is complicated by the vast compensatory changes in the sphingolipidome however, our results reveal that the glycosylation steps of GIPC biosynthesis are important regulated components of sphingolipid metabolism. This study corroborates previously suggested roles for GIPC glycans in plant growth and defense, suggests important roles for them in reproduction and demonstrates that the entire sphingolipidome is sensitive to their status.
Do Cell Wall Esters Facilitate Forest Response to Climate?
Publisher: Elsevier BV
Date: 08-2020
Variation in sugarcane biomass composition and enzymatic saccharification of leaves, internodes and roots
Publisher: Springer Science and Business Media LLC
Date: 12-2020
DOI: 10.1186/S13068-020-01837-2
Abstract: The composition of biomass determines its suitability for different applications within a biorefinery system. The proportion of the major biomass fractions (sugar, cellulose, hemicellulose and lignin) may vary in different sugarcane genotypes and growth environments and different parts of the plant. This study investigated the composition of mature and immature internodes, roots and mature leaves of sugarcane. Internodes were found to have a significantly larger alcohol-soluble component than leaves and roots. The primary difference between the immature and mature internodes was the ratio of soluble sugars. In mature tissues, sucrose content was significantly higher, whereas in immature internodal tissues there was lower sucrose and heightened concentrations of reducing sugars. Carbon (C) partitioning in leaf tissues was characterised by low levels of soluble components and high “other” and cell wall fractions. Root tissue had low ratios of soluble fractions relative to their cell wall contents, indicating a lack of storage of soluble carbon. There was no significant difference in the ratio of the major cell wall fractions between the major organ types. Characterisation of in idual non-cellulosic monomers indicated leaf and root tissues had significantly higher arabinose and galactose fractions. Significantly larger proportions of syringyl lignin compounds and the hydroxycinnamic compound, p- coumaric acid were observed in mature internodal tissues compared to the other tissue types. Tissue-specific differences in composition were shown to greatly affect the recalcitrance of the cell wall to enzymatic saccharification. Overall, this study displayed clear evidence of the differential partitioning of C throughout the sugarcane plant in specific organs. These organ-specific differences have major implications in their utility as a bioproduct feedstock. For ex le, the inclusion of trash (leaves) with the culms (internodes) may alter processing efficiency.
COG-imposed Golgi functional integrity determines the onset of dark-induced senescence
Publisher: Springer Science and Business Media LLC
Date: 26-10-2023
A screening method to identify efficient sgRNAs in Arabidopsis, used in conjunction with cell-specific lignin reduction
Publisher: Springer Science and Business Media LLC
Date: 23-05-2019
Two members of the DUF 579 family are responsible for arabinogalactan methylation in Arabidopsis
Publisher: Wiley
Date: 02-2019
DOI: 10.1002/PLD3.117
Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction
Publisher: Springer Science and Business Media LLC
Date: 25-10-2022
DOI: 10.1186/S40168-022-01377-X
Abstract: Plant cell walls are interwoven structures recalcitrant to degradation. Native and adapted microbiomes can be particularly effective at plant cell wall deconstruction. Although most understanding of biological cell wall deconstruction has been obtained from isolates, cultivated microbiomes that break down cell walls have emerged as new sources for biotechnologically relevant microbes and enzymes. These microbiomes provide a unique resource to identify key interacting functional microbial groups and to guide the design of specialized synthetic microbial communities. To establish a system assessing comparative microbiome performance, parallel microbiomes were cultivated on sorghum ( Sorghum bicolor L. Moench) from compost inocula. Biomass loss and biochemical assays indicated that these microbiomes erged in their ability to deconstruct biomass. Network reconstructions from gene expression dynamics identified key groups and potential interactions within the adapted sorghum-degrading communities, including Actinotalea , Filomicrobium , and Gemmatimonadetes populations. Functional analysis demonstrated that the microbiomes proceeded through successive stages that are linked to enzymes that deconstruct plant cell wall polymers. The combination of network and functional analysis highlighted the importance of cellulose-degrading Actinobacteria in differentiating the performance of these microbiomes. The two-tier cultivation of compost-derived microbiomes on sorghum led to the establishment of microbiomes for which community structure and performance could be assessed. The work reinforces the observation that subtle differences in community composition and the genomic content of strains may lead to significant differences in community performance.
Progress and challenges in sorghum biotechnology, a multipurpose feedstock for the bioeconomy
Publisher: Oxford University Press (OUP)
Date: 13-10-2021
DOI: 10.1093/JXB/ERAB450
Abstract: Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop globally by harvested area and production. Its drought and heat tolerance allow high yields with minimal input. It is a promising biomass crop for the production of biofuels and bioproducts. In addition, as an annual diploid with a relatively small genome compared with other C4 grasses, and excellent germplasm ersity, sorghum is an excellent research species for other C4 crops such as maize. As a result, an increasing number of researchers are looking to test the transferability of findings from other organisms such as Arabidopsis thaliana and Brachypodium distachyon to sorghum, as well as to engineer new biomass sorghum varieties. Here, we provide an overview of sorghum as a multipurpose feedstock crop which can support the growing bioeconomy, and as a monocot research model system. We review what makes sorghum such a successful crop and identify some key traits for future improvement. We assess recent progress in sorghum transformation and highlight how transformation limitations still restrict its widespread adoption. Finally, we summarize available sorghum genetic, genomic, and bioinformatics resources. This review is intended for researchers new to sorghum research, as well as those wishing to include non-food and forage applications in their research.
Salt stress signalling involves ATP release and Arabidopsis annexin 1
Publisher: Elsevier BV
Date: 06-2009
High Temperature Acclimation of Leaf Gas Exchange, Photochemistry, and Metabolomic Profiles in Populus trichocarpa
Publisher: American Chemical Society (ACS)
Date: 03-08-2021
Expression of S-adenosylmethionine Hydrolase in Tissues Synthesizing Secondary Cell Walls Alters Specific Methylated Cell Wall Fractions and Improves Biomass Digestibility
Publisher: Frontiers Media SA
Date: 19-07-2016
Plant extracellular ATP signalling by plasma membrane NADPH oxidase and Ca2+ channels
Publisher: Wiley
Date: 06-2009
Enrichment of the Plant Cytosolic Fraction
Publisher: Springer New York
Date: 12-10-2017
DOI: 10.1007/978-1-4939-6533-5_17
Abstract: The cytosol is at the core of cellular metabolism and contains many important metabolic pathways, including glycolysis, gluconeogenesis, and the pentose phosphate pathway. Despite the importance of this matrix, few attempts have sought to specifically enrich this compartment from plants. Although a variety of biochemical pathways and signaling cascades pass through the cytosol, much of the focus has usually been targeted at the reactions that occur within membrane-bound organelles of the plant cell. In this chapter, we outline a method for the enrichment of the cytosol from rice suspension cell cultures which includes s le preparation and enrichment as well as validation using immunoblotting and fluorescence-tagged proteins.
Correction: Corrigendum: Glycan complexity dictates microbial resource allocation in the large intestine
Publisher: Springer Science and Business Media LLC
Date: 05-02-2016
DOI: 10.1038/NCOMMS10705
Abstract: Nature Communications 6 Article number: 7481 (2015) Published 26 June 2015 Updated 5 February 2016 The financial support for the work described in this Article was not fully acknowledged. The Acknowledgements should have included the following: This work was supported in part by a grant to H.J.G.,B.
Accumulation of high-value bioproducts in planta can improve the economics of advanced biofuels
Publisher: Proceedings of the National Academy of Sciences
Date: 27-03-2020
Abstract: Cellulosic biofuels have not yet reached cost parity with conventional petroleum fuels. One strategy to address this challenge is to generate valuable coproducts alongside biofuels. Engineering bioenergy crops to generate value-added bioproducts in planta can reduce input requirements relative to microbial chassis and skip costly deconstruction and conversion steps. Although rapid progress has been made in plant metabolic engineering, there has been no systematic analysis devoted to quantifying the impact of such engineered bioenergy crops on biorefinery economics. Here, we provide new insights into how bioproduct accumulation in planta affects biofuel selling prices. We present the range of bioproduct selling prices and accumulation rates needed to compensate for additional extraction steps and reach a target $2.50/gal minimum biofuel selling price.
The Mechanics and Biology of Plant Cell Walls: Resilience and Sustainability for Our Future Society
Publisher: Oxford University Press (OUP)
Date: 12-2021
DOI: 10.1093/PCP/PCAB168
Cell wall ester modifications and volatile emission signatures of plant response to abiotic stress
Publisher: Wiley
Date: 20-10-2022
DOI: 10.1111/PCE.14464
Abstract: Growth suppression and defence signalling are simultaneous strategies that plants invoke to respond to abiotic stress. Here, we show that the drought stress response of poplar trees ( Populus trichocarpa ) is initiated by a suppression in cell wall derived methanol (MeOH) emissions and activation of acetic acid (AA) fermentation defences. Temperature sensitive emissions dominated by MeOH (AA/MeOH %) were observed from physiologically active leaves, branches, detached stems, leaf cell wall isolations and whole ecosystems. In contrast, drought treatment resulted in a suppression of MeOH emissions and strong enhancement in AA emissions together with volatiles acetaldehyde, ethanol, and acetone. These drought‐induced changes coincided with a reduction in stomatal conductance, photosynthesis, transpiration, and leaf water potential. The strong enhancement in AA/MeOH emission ratios during drought (400%–3500%) was associated with an increase in acetate content of whole leaf cell walls, which became significantly 13 C 2 ‐labelled following the delivery of 13 C 2 ‐acetate via the transpiration stream. The results are consistent with both enzymatic and nonenzymatic MeOH and AA production at high temperature in hydrated tissues associated with accelerated primary cell wall growth processes, which are downregulated during drought. While the metabolic source(s) require further investigation, the observations are consistent with drought‐induced activation of aerobic fermentation driving high rates of foliar AA emissions and enhancements in leaf cell wall O ‐acetylation. We suggest that atmospheric AA/MeOH emission ratios could be useful as a highly sensitive signal in studies investigating environmental and biological factors influencing growth‐defence trade‐offs in plants and ecosystems.
Xyloglucan endotransglucosylase-hydrolase30 negatively affects salt tolerance in Arabidopsis
Publisher: Oxford University Press (OUP)
Date: 29-06-2019
DOI: 10.1093/JXB/ERZ311
Abstract: Plants have evolved various strategies to sense and respond to saline environments, which severely reduce plant growth and limit agricultural productivity. Alteration to the cell wall is one strategy that helps plants adapt to salt stress. However, the physiological mechanism of how the cell wall components respond to salt stress is not fully understood. Here, we show that expression of XTH30, encoding xyloglucan endotransglucosylase-hydrolase30, is strongly up-regulated in response to salt stress in Arabidopsis. Loss-of-function of XTH30 leads to increased salt tolerance and overexpression of XTH30 results in salt hypersensitivity. XTH30 is located in the plasma membrane and is highly expressed in the root, flower, stem, and etiolated hypocotyl. The NaCl-induced increase in xyloglucan (XyG)-derived oligosaccharide (XLFG) of the wild type is partly blocked in xth30 mutants. Loss-of-function of XTH30 slows down the decrease of crystalline cellulose content and the depolymerization of microtubules caused by salt stress. Moreover, lower Na+ accumulation in shoot and lower H2O2 content are found in xth30 mutants in response to salt stress. Taken together, these results indicate that XTH30 modulates XyG side chains, altered abundance of XLFG, cellulose synthesis, and cortical microtubule stability, and negatively affecting salt tolerance.
SpaceHort: redesigning plants to support space exploration and on-earth sustainability
Publisher: Elsevier BV
Date: 02-2022
DOI: 10.1016/J.COPBIO.2021.08.018
Abstract: Crewed missions to Mars are planned within the next twenty years. Production of food and materials in situ will eventually be necessary for mission success. This will require the development of crops which can thrive in environments we can sustain in Space. Here, we discuss the challenges we must solve to provide adequate nutrition to support long term Space habitation. Further, we propose that plants are an ideal biomanufacturing platform for producing pharmaceuticals and biomaterials on demand. Designing Space plants requires advances in our ability to engineer plant biology in a predictive manner. Parallel development of suitable tightly controlled growth environments, including extensive monitoring and sensing, will also be a key enabler. Collectively, such research promises to deliver solutions for progressing sustainable closed environment agriculture on Earth.
Purification, characterization and influence on membrane properties of the plant-specific sphingolipids GIPC
Publisher: Cold Spring Harbor Laboratory
Date: 02-10-2020
DOI: 10.1101/2020.10.01.313304
Abstract: The plant plasma membrane (PM) is an essential barrier between the cell and the external environment. The PM is crucial for signal perception and transmission. It consists of an asymmetrical lipid bilayer made up of three different lipid classes: sphingolipids, sterols and phospholipids. The most abundant sphingolipids in the plant PM are the Glycosyl Inositol Phosphoryl Ceramides (GIPCs), representing up to 40% of total sphingolipids, assumed to be almost exclusively in the outer leaflet of the PM. In this study, we investigated the structure of GIPCs and their role in membrane organization. Since GIPCs are not commercially available, we developed a protocol to extract and isolate GIPC-enriched fractions from eudicots (cauliflower and tobacco) and monocots (leek and rice). Lipidomic analysis confirmed the presence of different long chain bases and fatty acids. The glycan head groups of the different GIPC series from monocots and dicots were analysed by GC-MS showing different sugar moieties. Multiple biophysics tools namely Langmuir monolayer, ζ-Potential, light scattering, neutron reflectivity, solid state 2 H-NMR and molecular modelling were used to investigate the physical properties of the GIPCs, as well as their interaction with free and conjugated phytosterols. We showed that GIPCs increase the thickness and electronegativity of model membranes, interact differentially with the phytosterols species and regulate the gel-to-fluid phase transition during temperature variations.
Evidence That GH115 α-Glucuronidase Activity, Which Is Required to Degrade Plant Biomass, Is Dependent on Conformational Flexibility
Publisher: Elsevier BV
Date: 2014
Potential abiotic stress targets for modern genetic manipulation
Publisher: Oxford University Press (OUP)
Date: 15-11-2023
Abstract: Research into crop yield and resilience has underpinned global food security, evident in yields tripling in the past 5 decades. The challenges that global agriculture now faces are not just to feed 10+ billion people within a generation, but to do so under a harsher, more variable, and less predictable climate, and in many cases with less water, more expensive inputs, and declining soil quality. The challenges of climate change are not simply to breed for a “hotter drier climate,” but to enable resilience to floods and droughts and frosts and heat waves, possibly even within a single growing season. How well we prepare for the coming decades of climate variability will depend on our ability to modify current practices, innovate with novel breeding methods, and communicate and work with farming communities to ensure viability and profitability. Here we define how future climates will impact farming systems and growing seasons, thereby identifying the traits and practices needed and including exemplars being implemented and developed. Critically, this review will also consider societal perspectives and public engagement about emerging technologies for climate resilience, with participatory approaches presented as the best approach.
Lignin deconstruction by anaerobic fungi
Publisher: Springer Science and Business Media LLC
Date: 09-03-2023
DOI: 10.1038/S41564-023-01336-8
Abstract: Lignocellulose forms plant cell walls, and its three constituent polymers, cellulose, hemicellulose and lignin, represent the largest renewable organic carbon pool in the terrestrial biosphere. Insights into biological lignocellulose deconstruction inform understandings of global carbon sequestration dynamics and provide inspiration for biotechnologies seeking to address the current climate crisis by producing renewable chemicals from plant biomass. Organisms in erse environments disassemble lignocellulose, and carbohydrate degradation processes are well defined, but biological lignin deconstruction is described only in aerobic systems. It is currently unclear whether anaerobic lignin deconstruction is impossible because of biochemical constraints or, alternatively, has not yet been measured. We applied whole cell-wall nuclear magnetic resonance, gel-permeation chromatography and transcriptome sequencing to interrogate the apparent paradox that anaerobic fungi (Neocallimastigomycetes), well-documented lignocellulose degradation specialists, are unable to modify lignin. We find that Neocallimastigomycetes anaerobically break chemical bonds in grass and hardwood lignins, and we further associate upregulated gene products with the observed lignocellulose deconstruction. These findings alter perceptions of lignin deconstruction by anaerobes and provide opportunities to advance decarbonization biotechnologies that depend on depolymerizing lignocellulose.
Agrobacterium-mediated transient transformation of sorghum leaves for accelerating functional genomics and genome editing studies.
Publisher: Research Square Platform LLC
Date: 26-07-2019
Abstract: Objectives Sorghum is one of the most recalcitrant species for transformation. Considering the time and effort required for stable transformation in sorghum, establishing a transient system to screen the efficiency and full functionality of vector constructs is highly desirable. Results Here, we report an Agrobacterium-mediated transient transformation assay with intact sorghum leaves using green fluorescent protein as marker. It also provides a good monocot alternative to tobacco and protoplast assays with a direct, native and more reliable system for testing single guide RNA (sgRNA) expression construct efficiency. Given the simplicity and ease of transformation, high reproducibility, and ability to test large constructs, this method can be widely adopted to speed up functional genomic and genome editing studies.
Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem
Publisher: Cold Spring Harbor Laboratory
Date: 14-06-2023
DOI: 10.1101/2023.06.13.544848
Abstract: Studying plant-microbe-soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacteria inoculation practices and plant harvesting time points affect the reproducibility of a microbial synthetic community (SynCom) in association with the model grass Brachypodium distachyon . We tested three microbial inoculation practices: seed inoculation, transplant inoculation, and seedling inoculation and two harvesting points: early (14-day-old plants) and late (21 days post-inoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community only when harvesting at an early time point but not at the late stage. As the SynCom showed a persistent association with B. distachyon at 21 days post-inoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacteria inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB- B. distachyon -SynCom fabricated ecosystem and recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems.
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