ORCID Profile
0000-0002-6668-1326
Current Organisation
Australian National University
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Publisher: Springer New York
Date: 2019
DOI: 10.1007/978-1-4939-9042-9_17
Abstract: The study of gene function is best achieved through the generation of loss-of-function mutants. However, for many plant microRNAs (miRNAs), this has proven challenging, as they often belong to sequence-related families, which are encoded by multiple genes that are functionally redundant. To overcome this issue, transgenic methods have been developed that express miRNA decoys, which can sequester and inhibit families of sequence-related miRNAs. This includes miRNA MIMICs, SHORT TANDEM TARGET MIMICs, and miRNA SPONGEs. Here, we describe the methods to generate transgenic Arabidopsis that express these miRNA decoys in order to determine miRNA function.
Publisher: Informa UK Limited
Date: 26-12-2019
Publisher: Informa UK Limited
Date: 06-2009
DOI: 10.4161/PSB.4.6.8316
Publisher: Oxford University Press (OUP)
Date: 17-05-2017
DOI: 10.1104/PP.16.01898
Publisher: Wiley
Date: 09-10-2015
DOI: 10.1002/HEC.3272
Abstract: This study uses data from the 2004-2006 Australian National Survey of Adult Oral Health and a simultaneous equation framework to investigate the interrelationships between dental health, private dental insurance and the use of dental services. The results show that insurance participation is influenced by social and demographic factors, health and health behaviours. In turn, these factors affect the use of dental services, both directly and through insurance participation. Our findings confirm that affordability is a major barrier to visiting the dentist for oral health maintenance and treatment. Our results suggest that having supplementary insurance is associated with some 56 percentage points higher probability of seeing the dentist in the general population. For those who did not have private insurance cover, we predict that conditional on them facing the same insurance conditions, on average, having insurance would increase their visits to the dentist by 43 percentage points. The uninsured in the survey have lower income, worse oral health and lower rates of preventive and treatment visits. Copyright © 2015 John Wiley & Sons, Ltd.
Publisher: Oxford University Press (OUP)
Date: 10-08-2010
Abstract: The microRNA159 (miR159) family represses the conserved GAMYB-like genes that encode R2R3 MYB domain transcription factors that have been implicated in gibberellin (GA) signaling in anthers and germinating seeds. In Arabidopsis (Arabidopsis thaliana), the two major miR159 family members, miR159a and miR159b, are functionally specific for two GAMYB-like genes, MYB33 and MYB65. These transcription factors have been shown to be involved in anther development, but there are differing reports about their role in the promotion of flowering and little is known about their function in seed germination. To understand the function of this pathway, we identified the genes and processes controlled by these GAMYB-like genes. First, we demonstrate that miR159 completely represses MYB33 and MYB65 in vegetative tissues. We show that GA does not release this repression and that these transcription factors are not required for flowering or growth. By contrast, in the absence of miR159, the deregulation of MYB33 and MYB65 in vegetative tissues up-regulates genes that are highly expressed in the aleurone and GA induced during seed germination. Confirming that these genes are GAMYB-like regulated, their expression was reduced in myb33.myb65.myb101 seeds. Aleurone vacuolation, a GA-mediated programmed cell death process required for germination, was impaired in these seeds. Finally, the deregulation of MYB33 and MYB65 in vegetative tissues inhibits growth by reducing cell proliferation. Therefore, we conclude that miR159 acts as a molecular switch, only permitting the expression of GAMYB-like genes in anthers and seeds. In seeds, these transcription factors participate in GA-induced pathways required for aleurone development and death.
Publisher: Wiley
Date: 02-2010
Publisher: Public Library of Science (PLoS)
Date: 09-03-2011
Publisher: MDPI AG
Date: 30-07-2019
Abstract: MicroR159 (miR159) is ancient, being present in the majority of land plants where it targets a class of regulatory genes called GAMYB or GAMYB-like via highly conserved miR159-binding sites. These GAMYB genes encode R2R3 MYB domain transcription factors that transduce the gibberellin (GA) signal in the seed aleurone and the anther tapetum. Here, GAMYB plays a conserved role in promoting the programmed cell death of these tissues, where miR159 function appears weak. By contrast, GAMYB is not involved in GA-signaling in vegetative tissues, but rather its expression is deleterious, leading to the inhibition of growth and development. Here, the major function of miR159 is to mediate strong silencing of GAMYB to enable normal growth. Highlighting this requirement of strong silencing are conserved RNA secondary structures associated with the miR159-binding site in GAMYB mRNA that promotes miR159-mediated repression. Although the miR159-GAMYB pathway in vegetative tissues has been implicated in a number of different functions, presently no conserved role for this pathway has emerged. We will review the current knowledge of the different proposed functions of miR159, and how this ancient pathway has been used as a model to help form our understanding of miRNA biology in plants.
Publisher: Springer Science and Business Media LLC
Date: 06-2003
Publisher: Wiley
Date: 30-03-2010
DOI: 10.1111/J.1467-7652.2010.00513.X
Abstract: Wheat streak mosaic virus (WSMV), vectored by Wheat curl mite, has been of great economic importance in the Great Plains of the United States and Canada. Recently, the virus has been identified in Australia, where it has spread quickly to all major wheat growing areas. The difficulties in finding adequate natural resistance in wheat prompted us to develop transgenic resistance based on RNA interference (RNAi). An RNAi construct was designed to target the nuclear inclusion protein 'a' (NIa) gene of WSMV. Wheat was stably cotransformed with two plasmids: pStargate-NIa expressing hairpin RNA (hpRNA) including WSMV sequence and pCMneoSTLS2 with the nptII selectable marker. When T(1) progeny were assayed against WSMV, ten of sixteen families showed complete resistance in transgenic segregants. The resistance was classified as immunity by four criteria: no disease symptoms were produced ELISA readings were as in uninoculated plants viral sequences could not be detected by RT-PCR from leaf extracts and leaf extracts failed to give infections in susceptible plants when used in test-inoculation experiments. Southern blot hybridization analysis indicated hpRNA transgene integrated into the wheat genome. Moreover, accumulation of small RNAs derived from the hpRNA transgene sequence positively correlated with immunity. We also showed that the selectable marker gene nptII segregated independently of the hpRNA transgene in some transgenics, and therefore demonstrated that it is possible using these techniques, to produce marker-free WSMV immune transgenic plants. This is the first report of immunity in wheat to WSMV using a spliceable intron hpRNA strategy.
Publisher: Frontiers Media SA
Date: 2013
Publisher: MDPI AG
Date: 05-02-2020
Abstract: MicroRNAs (miRNAs) are a class of small RNAs (sRNAs) that repress gene expression via high complementary binding sites in target mRNAs (messenger RNAs). Many miRNAs are ancient, and their intricate integration into gene expression programs have been fundamental for plant life, controlling developmental programs and executing responses to biotic/abiotic cues. Additionally, there are many less conserved miRNAs in each plant species, raising the possibility that the functional impact of miRNAs extends into virtually every aspect of plant biology. This Special Issue of Plants presents papers that investigate the function and mechanism of miRNAs in controlling development and abiotic stress response. This includes how miRNAs adapt plants to nutrient availability, and the silencing machinery that is responsible for this. Several papers profile changes in miRNA abundances during stress, and another study raises the possibility of circular RNAs acting as endogenous decoys to sequester and inhibit plant miRNA function. These papers act as foundational studies for the more difficult task ahead of determining the functional significance of these changes to miRNA abundances, or the presence of these circular RNAs. Finally, how miRNAs trigger the production of secondary sRNAs is reviewed, along with the potential agricultural impact of miRNAs and these secondary sRNA in the exemplar crop maize.
Publisher: Wiley
Date: 05-09-2012
DOI: 10.1111/J.1467-7652.2011.00647.X
Abstract: Wheat streak mosaic virus (WSMV) is a persistent threat to wheat production, necessitating novel approaches for protection. We developed an artificial miRNA strategy against WSMV, incorporating five amiRNAs within one polycistronic amiRNA precursor. Using miRNA sequence and folding rules, we chose five amiRNAs targeting conserved regions of WSMV but avoiding off-targets in wheat. These replaced the natural miRNA in each of five arms of the polycistronic rice miR395, producing amiRNA precursor, FanGuard (FGmiR395), which was transformed into wheat behind a constitutive promoter. Splinted ligation detected all five amiRNAs being processed in transgenic leaves. Resistance was assessed over two generations. Three types of response were observed in T(1) plants of different transgenic families: completely immune initially resistant with resistance breaking down over time and initially susceptible followed by plant recovery. Deep sequencing of small RNAs from inoculated leaves allowed the virus sequence to be assembled from an immune transgenic, susceptible transgenic, and susceptible non-transgenic plant the amiRNA targets were fully conserved in all three isolates, indicating virus replication on some transgenics was not a result of mutational escape by the virus. For resistant families, the resistance segregated with the transgene. Analysis in the T(2) generation confirmed the inheritance of immunity and gave further insights into the other phenotypes. Stable resistant lines developed no symptoms and no virus by ELISA this resistance was classified as immunity when extracts failed to transmit from inoculated leaves to test plants. This study demonstrates the utility of a polycistronic amiRNA strategy in wheat against WSMV.
Publisher: Oxford University Press (OUP)
Date: 11-1998
Abstract: Transgenic Arabidopsis plants overexpressing the Arabidopsis FATTY ACID ELONGATION1 gene under the control of the 35S promoter from cauliflower mosaic virus accumulated very-long-chain fatty acids (VLCFAs) throughout the plant. In some transformants, C20 and C22 VLCFAs accounted for >30% of the total fatty acids, accumulating at the expense of C16 and C18 fatty acids. These C20 and C22 fatty acids were incorporated into all of the major membrane glycerolipid classes. Plants with a high VLCFA content displayed a dramatically altered morphology, which included the failure of flowering shoots to elongate, a modified spatial pattern of siliques, an altered floral phenotype, and a large accumulation of anthocyanins. In addition, these plants also exhibited a unique alteration of the chloroplast membrane structure. We discuss a possible role for VLCFAs in establishing the shape/curvature of the membranes, which in turn may affect the shape of the cell and ultimately that of the whole plant.
Publisher: Wiley
Date: 13-02-2006
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 02-2011
Publisher: Informa UK Limited
Date: 19-06-2019
Publisher: Elsevier BV
Date: 10-2020
Publisher: Cold Spring Harbor Laboratory
Date: 10-09-2022
DOI: 10.1101/2022.09.07.507021
Abstract: In plants, high complementarity between microRNAs (miRNAs) and their target genes is a prerequisite for a miRNA-target interaction (MTI). However, evidence suggests there are complexities beyond complementarity that impacts the strength of the MTI. To explore this, the bioinformatic pipeline TRUEE (Targets Ranked Using Experimental Evidence) was applied to strongly conserved miRNAs to identity their high evidence (HE) targets across species. For each miRNA family, HE targets predominantly consisted of homologues from one conserved target gene family (primary family). If an additional HE target family(s) was identified (secondary family), it was likely functionally related to the primary family. Many primary target families contained highly conserved nucleotide sequences flanking their miRNA binding-sites that were enriched in HE homologues across species, suggesting these sequences facilitate miRNA-mediated regulation. A subset of these flanking sequences are predicted to form conserved RNA secondary structures that preferentially base-pair with the miRNA binding-site, implying that these sites are highly structured. Functional testing of the conserved flanking sequences of the miR160 target, AUXIN RESPONSE FACTOR 10 ( ARF10 ), found that mutations within these flanking sequences resulted in attenuated ARF10 silencing. Our findings support the notion that features beyond complementarity at highly conserved miRNA binding-sites underpin these ancient MTIs.
Publisher: Frontiers Media SA
Date: 2013
Publisher: Elsevier BV
Date: 03-2000
DOI: 10.1016/S1360-1385(00)01566-1
Abstract: Plant membrane lipids are primarily composed of 16-carbon and 18-carbon fatty acids containing up to three double bonds. By contrast, the seed oils of many plant species contain fatty acids with significantly different structures. These unusual fatty acids sometimes accumulate to >90% of the total fatty acid content in the seed triacylglycerols, but are generally excluded from the membrane lipids of the plant, including those of the seed. The reasons for their exclusion and the mechanisms by which this is achieved are not completely understood. Here we discuss recent research that has given new insights into how plants prevent the accumulation of unusual fatty acids in membrane lipids, and how strict this censorship of membrane composition is. We also describe a transgenic experiment that resulted in an excessive buildup of unusual fatty acids in cellular membranes, and clearly illustrated that the control of membrane lipid composition is essential for normal plant growth and development.
Publisher: Oxford University Press (OUP)
Date: 20-03-2023
DOI: 10.1093/PCP/PCAD019
Publisher: Springer Science and Business Media LLC
Date: 28-10-2010
Abstract: A current challenge of microRNA (miRNA) research is the identification of biologically relevant miRNA:target gene relationships. In plants, high miRNA:target gene complementarity has enabled accurate target predictions, and slicing of target mRNAs has facilitated target validation through rapid lification of 5' cDNA ends (5'-RACE) analysis. Together, these approaches have identified more than 20 targets potentially regulated by the deeply conserved miR159 family in Arabidopsis , including eight MYB genes with highly conserved miR159 target sites. However, genetic analysis has revealed the functional specificity of the major family members, miR159a and miR159b is limited to only two targets, MYB33 and MYB65 . Here, we examine the functional role of miR159 regulation for the other potential MYB target genes. For these target genes, functional analysis failed to identify miR159 regulation that resulted in any major phenotypic impact, either at the morphological or molecular level. This appears to be mainly due to the quiescent nature of the remaining family member, MIR159c . Although its expression overlaps in a temporal and spatial cell-specific manner with a subset of these targets in anthers, the abundance of miR159c is extremely low and concomitantly a mir159c mutant displays no anther defects. Examination of potential miR159c targets with conserved miR159 binding sites found neither their spatial or temporal expression domains appeared miR159 regulated, despite the detection of miR159-guided cleavage products by 5'-RACE. Moreover, expression of a miR159-resistant target ( mMYB101 ) resulted predominantly in plants that are indistinguishable from wild type. Plants that displayed altered morphological phenotypes were found to be ectopically expressing the mMYB101 transgene, and hence were misrepresentative of the in vivo functional role of miR159. This study presents a novel explanation for a paradox common to plant and animal miRNA systems, where among many potential miRNA-target relationships usually only a few appear physiologically relevant. The identification of a quiescent miR159c:target gene regulatory module in anthers provides a likely rationale for the presence of conserved miR159 binding sites in many targets for which miR159 regulation has no obvious functional role. Remnants from the demise of such modules may lead to an overestimation of miRNA regulatory complexity when investigated using bioinformatic, 5'-RACE or transgenic approaches.
Publisher: Wiley
Date: 14-09-2017
DOI: 10.1111/NPH.14717
Abstract: Root knot nematodes (RKN) are root parasites that induce the genetic reprogramming of vascular cells into giant feeding cells and the development of root galls. MicroRNAs (miRNAs) regulate gene expression during development and plant responses to various stresses. Disruption of post-transcriptional gene silencing in Arabidopsis ago1 or ago2 mutants decrease the infection rate of RKN suggesting a role for this mechanism in the plant-nematode interaction. By sequencing small RNAs from uninfected Arabidopsis roots and from galls 7 and 14 d post infection with Meloidogyne incognita, we identified 24 miRNAs differentially expressed in gall as putative regulators of gall development. Moreover, strong activity within galls was detected for five miRNA promoters. Analyses of nematode development in an Arabidopsis miR159abc mutant had a lower susceptibility to RKN, suggesting a role for the miR159 family in the plant response to M. incognita. Localization of mature miR159 within the giant and surrounding cells suggested a role in giant cell and gall. Finally, overexpression of miR159 in galls at 14 d post inoculation was associated with the repression of the miR159 target MYB33 which expression is restricted to the early stages of infection. Overall, these results implicate the miR159 in plant responses to RKN.
Publisher: Springer Science and Business Media LLC
Date: 20-04-2020
DOI: 10.1038/S41591-020-0807-6
Abstract: A double burden of malnutrition occurs when in iduals, household members or communities experience both undernutrition and overweight. Here, we show geospatial estimates of overweight and wasting prevalence among children under 5 years of age in 105 low- and middle-income countries (LMICs) from 2000 to 2017 and aggregate these to policy-relevant administrative units. Wasting decreased overall across LMICs between 2000 and 2017, from 8.4% (62.3 (55.1–70.8) million) to 6.4% (58.3 (47.6–70.7) million), but is predicted to remain above the World Health Organization’s Global Nutrition Target of % in over half of LMICs by 2025. Prevalence of overweight increased from 5.2% (30 (22.8–38.5) million) in 2000 to 6.0% (55.5 (44.8–67.9) million) children aged under 5 years in 2017. Areas most affected by double burden of malnutrition were located in Indonesia, Thailand, southeastern China, Botswana, Cameroon and central Nigeria. Our estimates provide a new perspective to researchers, policy makers and public health agencies in their efforts to address this global childhood syndemic.
Publisher: Oxford University Press (OUP)
Date: 08-2002
DOI: 10.1104/PP.003707
Abstract: To learn more about the role of the CER6 condensing enzyme in Arabidopsis surface wax production, we determinedCER6 transcription domains and the timing ofCER6 transcription in vegetative and reproductive structures from juvenile, mature, and senescing tissues. We found thatCER6 is highly transcribed throughout development, exclusively in the epidermal cells in all tissues examined. The only exception to the epidermal expression was observed in anthers nearing maturity, in which CER6 mRNA was localized in the tapetum. To determine if environmental factors such as light and water deficit, which are known to stimulate wax accumulation, induceCER6 transcription, we examined the effects of these factors on CER6 transcript abundance. Our results demonstrate that light is essential for CER6transcription, and that osmotic stress and the presence of abscisic acid enhance CER6 transcript accumulation.CER6 promoter-directed expression of the β-glucuronidase reporter gene in transgenic plants demonstrated that the CER6 promoter was highly effective in directing epidermis-specific expression in Arabidopsis and tobacco (Nicotiana tabacum). Furthermore, CER6promoter-driven CER6 overexpression resulted in increased wax deposition in Arabidopsis stems. These experiments indicate that the expression level of CER6 in the epidermis is one of the factors controlling wax accumulation on Arabidopsis stems.
Publisher: Oxford University Press (OUP)
Date: 05-1999
DOI: 10.1105/TPC.11.5.825
Abstract: Land plants secrete a layer of wax onto their aerial surfaces that is essential for survival in a terrestrial environment. This wax is composed of long-chain, aliphatic hydrocarbons derived from very-long-chain fatty acids (VLCFAs). Using the Arabidopsis expressed sequence tag database, we have identified a gene, designated CUT1, that encodes a VLCFA condensing enzyme required for cuticular wax production. Sense suppression of CUT1 in transgenic Arabidopsis plants results in waxless (eceriferum) stems and siliques as well as conditional male sterility. Scanning electron microscopy revealed that this was a severe waxless phenotype, because stems of CUT1-suppressed plants were completely devoid of wax crystals. Furthermore, chemical analyses of waxless plants demonstrated that the stem wax load was reduced to 6 to 7% of wild-type levels. This value is lower than that reported for any of the known eceriferum mutants. The severe waxless phenotype resulted from the downregulation of both the decarbonylation and acyl reduction wax biosynthetic pathways. This result indicates that CUT1 is involved in the production of VLCFA precursors used for the synthesis of all stem wax components in Arabidopsis. In CUT1-suppressed plants, the C24 chain-length wax components predominate, suggesting that CUT1 is required for elongation of C24 VLCFAs. The unique wax composition of CUT1-suppressed plants together with the fact that the location of CUT1 on the genetic map did not coincide with any of the known ECERIFERUM loci suggest that we have identified a novel gene involved in wax biosynthesis. CUT1 is currently the only known gene with a clearly established function in wax production.
Publisher: Elsevier BV
Date: 10-2020
Publisher: Elsevier BV
Date: 10-2020
Publisher: Elsevier BV
Date: 11-1999
DOI: 10.1016/S0031-9422(99)00403-3
Abstract: The fatty-acyl composition of the seed oil was determined for 100 ecotypes of Arabidopsis thaliana. Despite coming from erse geographical locations, seed fatty-acyl profiles of all ecotypes were remarkably similar. They contained identical fatty acids, including the characteristic C20 and C22 very-long-chain fatty acids (VLCFAs). The total proportions of seed VLCFA varied between 22% and 35% w/w of the total seed fatty acid content.
Publisher: Wiley
Date: 10-2018
DOI: 10.1002/PLD3.88
Publisher: Wiley
Date: 25-04-2022
DOI: 10.1111/TPJ.15751
Abstract: Central to plant microRNA (miRNA) biology is the identification of functional miRNA‐target interactions (MTIs). However, the complementarity basis of bioinformatic target prediction results in mostly false positives, and the degree of complementarity does not equate with regulation. Here, we develop a bioinformatic workflow named TRUEE (Targets Ranked Using Experimental Evidence) that ranks MTIs on the extent to which they are subjected to miRNA‐mediated cleavage. It sorts predicted targets into high (HE) and low evidence (LE) groupings based on the frequency and strength of miRNA‐guided cleavage degradome signals across multiple degradome experiments. From this, each target is assigned a numerical value, termed a Category Score , ranking the extent to which it is subjected to miRNA‐mediated cleavage. As a proof‐of‐concept, the 428 Arabidopsis miRNAs annotated in miRBase were processed through the TRUEE pipeline to determine the miRNA ‘targetome’. The majority of high‐ranking Category Score targets corresponded to highly conserved MTIs, validating the workflow. Very few Arabidopsis ‐ specific , Brassicaceae ‐ specific , or Conserved‐passenger miRNAs had HE targets with high Category Score s. In total, only several hundred MTIs were found to have Category Score s characteristic of currently known physiologically significance MTIs. Although non‐exhaustive, clearly the number of functional MTIs is much narrower than many studies claim. Therefore, using TRUEE to numerically rank targets directly on experimental evidence has given insights into the scope of the functional miRNA targetome of Arabidopsis.
Publisher: Proceedings of the National Academy of Sciences
Date: 09-10-2007
Abstract: Currently, there are very few loss-of-function mutations in micro-RNA genes. Here, we characterize two members of the Arabidopsis MIR159 family, miR159a and miR159b, that are predicted to regulate the expression of a family of seven transcription factors that includes the two redundant GAMYB-like genes, MYB33 and MYB65 . Using transfer DNA (T-DNA) insertional mutants, we show that a mir159ab double mutant has pleiotropic morphological defects, including altered growth habit, curled leaves, small siliques, and small seeds. Neither mir159a nor mir159b single mutants displayed any of these traits, indicating functional redundancy. By using reporter-gene constructs, it appears that MIR159a and MIR159b are transcribed almost exclusively in the cells in which MYB33 is repressed, as had been previously determined by comparison of MYB33 and mMYB33 (an miR159-resistant allele of MYB33 ) expression patterns. Consistent with these overlapping transcriptional domains, MYB33 and MYB65 expression levels were elevated throughout mir159ab plants. By contrast, the other five GAMYB-like family members are transcribed predominantly in tissues where miR159a and miR159b are absent, and consequently their expression levels are not markedly elevated in mir159ab . Additionally, mMYB33 transgenic plants can phenocopy the mir159ab phenotype, suggesting that its phenotype is explained by deregulated expression of the redundant gene pair MYB33 and MYB65 . This prediction was confirmed the pleiotropic developmental defects of mir159ab are suppressed through the combined mutations of MYB33 and MYB65 , demonstrating the narrow and specific target range of miR159a and miR159b.
Publisher: Oxford University Press (OUP)
Date: 10-2016
DOI: 10.1105/TPC.16.00562
Publisher: Oxford University Press (OUP)
Date: 18-02-2005
Publisher: Humana Press
Date: 2012
DOI: 10.1007/978-1-61779-882-5_2
Abstract: Given the widespread impact of RNA silencing on the Arabidopsis thaliana genome, it is indeed remarkable that this means of gene regulation went undiscovered for so long. Since the publication of landmark papers in 1998 (Fire et al., Nature 391:806-811, 1998 Waterhouse et al., Proc Natl Acad Sci U S A 95:13959-13964, 1998), intense research efforts have resulted in much progress from the speculation of Mello and colleagues that "the mechanisms underlying RNA interference probably exist for a biological purpose" (Fire et al., Nature 391:806-811, 1998). Across the eukaryotic kingdom, with the notable exception of Saccharomyces cerevisiae (Moazed, Science 326:544-550, 2009), the importance of small RNA-driven gene regulation has been recognized and implicated in central developmental processes as well as in aberrant and diseased states. Plants have by far the most complex RNA-based control of gene expression (Wang et al., Floriculture, ornamental and plant biotechnology, vol. III, 2006). Four distinct RNA silencing pathways have been recognized in plants, albeit with considerable conservation of the molecular components. These pathways are directed by various small RNA species, including microRNAs (miRNAs), trans-acting small interfering RNAs (siRNA) (ta-siRNAs), repeat-associated siRNAs (ra-siRNAs), and natural antisense transcript siRNAs (nat-siRNAs). The effective functionality of each of these pathways appear to be fundamental to the integrity of A. thaliana. Furthermore, in response to viral invasion, plants synthesize viral sRNAs as a means of defense. This process may in fact reflect the ancient origins of RNA silencing: plants may have evolved RNA silencing pathways as a defense mechanism against foreign nucleic acid species in the absence of an immune system (Wang and Metzlaff, Curr Opin Plant Biol 8:216-222, 2005). The generation of viral siRNAs is a particularly interesting illustration of RNA silencing as it provides a context to explore the potential to harness a naturally occurring system to the end goal of artificially engineering viral resistance.
Publisher: Springer Science and Business Media LLC
Date: 08-1994
DOI: 10.1007/BF00555831
Publisher: Cold Spring Harbor Laboratory
Date: 05-09-2019
DOI: 10.1101/758946
Abstract: RNA-binding proteins (RBPs) are critical regulators of gene expression, but have been poorly studied relative to other classes of gene regulators. Recently, mRNA-interactome capture identified many Arabidopsis RBPs of unknown function, including a family of ALBA domain containing proteins. Arabidopsis has three short-form ALBA homologues ( ALBA1-3 ) and three long-form ALBA homologues ( ALBA4-6 ), both of which are conserved throughout the plant kingdom. Despite this ancient origin, ALBA-GUS translational fusions of ALBA1, ALBA2, ALBA4 , and ALBA5 had indistinguishable expression patterns, all being preferentially expressed in young, rapidly iding tissues. Likewise, all four ALBA proteins had indistinguishable ALBA-GFP subcellular localizations in roots, all being preferentially located to the cytoplasm, consistent with being mRNA-binding. Genetic analysis demonstrated redundancy within the long-form ALBA family members in contrast to single alba mutants that all appeared wild-type, a triple alba456 mutant had slower rosette growth and a strong delay in flowering-time. RNA-sequencing found most differentially expressed genes in alba456 were related to metabolism, not development. Additionally, changes to the alba456 transcriptome were subtle, suggesting ALBA4-6 participates in a process that does not strongly affect transcriptome composition. Together, our findings demonstrate that ALBA protein function is highly redundant, and is essential for proper growth and flowering in Arabidopsis. The RNA-binding ALBA proteins have indistinguishable expression patterns and subcellular localizations in Arabidopsis, acting redundantly to promote growth and flowering via a mechanism that does not strongly affect transcriptome composition.
Publisher: Oxford University Press (OUP)
Date: 09-10-2018
DOI: 10.1104/PP.18.00758
Publisher: Springer Science and Business Media LLC
Date: 04-03-2015
DOI: 10.1186/S12284-015-0046-5
Abstract: The genetic ersity of six starch biosynthetic genes ( Wx , SSI , SSIIa , SBEI , SBEIIa and SBEIIb ) in indica and japonica rices opens an opportunity to produce a new variety with more favourable grain starch quality. However, there is limited information about the effects of these six gene allele combinations on starch structure and properties. A recombinant inbred line population from a cross between indica and japonica varieties offers opportunities to combine specific alleles of the six genes. The allelic ( indica vs japonica ) effects of six starch biosynthetic genes on starch structure, functional properties, and abundance of granule bound proteins in rice grains were investigated in a common genetic background using a recombinant inbred line population. The indica Wx ( Wxi ) allele played a major role while indica SSI ( SSIi ), japonica SSIIa ( SSIIaj ) and indica SBEI ( SBEIi ) alleles had minor roles on the increase of amylose content. SSIIaj and japonica SBEIIb ( SBEIIbj ) alleles had a major and a minor role on high ratio of ∑DP ≤ 10 to ∑DP ≤ 24 fractions (R CL10/24 ), respectively. Both major alleles ( Wxi and SSIIaj ) reduced peak viscosity (PV), onset, peak and end gelatinization temperatures (GTs) of amylopectin, and increased amylose-lipid complex dissociation enthalpy compared with their counterpart-alleles, respectively. SBEIIai and SBEIIbj decreased PV, whereas SSIi and SBEIIbj decreased FV. SBEIi reduced setback viscosity and gelatinization enthalpy. R CL10/24 of chain length distribution in amylopectin is negatively correlated with PV and BD of paste property and GTs of thermal properties. We also report RILs with superior starch properties combining Wxi , SSIj , SSIIaj , SBEIi and SBEIIbj alleles. Additionally, a clear relation is drawn to starch biosynthetic gene alleles, starch structure, properties, and abundance of granule bound starch biosynthetic enzymes inside starch granules. Rice Wxi and SSIIaj alleles play major roles, while SSIi , SBEIi , SBEIIai and SBEIIbj alleles have minor roles in the determination of starch properties between indica and japonica rice through starch structural modification. The combination of these alleles is a key factor for starch quality improvement in rice breeding programs. R CL10/24 value is critical for starch structure and property determination.
Publisher: Elsevier BV
Date: 04-2005
DOI: 10.1016/J.PBI.2005.01.011
Abstract: Seed dormancy is an adaptive trait that enables the seeds of many species to remain quiescent until conditions become favorable for germination. Dormancy is normally initiated during seed maturation and maintained to seed maturity. In mature seeds, the loss of dormancy may be gradual (after-ripening) or can be terminated by chilling and other environmental triggers. Dormancy is an important trait for many important crop species: it inhibits pre-harvest spouting or vivipary, a widespread problem in many regions of the world. Too much dormancy, however, can lead to non-uniform germination in the field. Recent progress has been made in understanding the role of abscisic acid metabolism and dormancy release in both model plants and crop species. Advances in our understanding of the molecular mechanisms that are involved in dormancy, along with approaches using quantitative genetics, will provide new strategies through which the desired level of dormancy can be introduced into crop species.
Publisher: Springer Science and Business Media LLC
Date: 05-05-2005
DOI: 10.1007/S10142-005-0145-2
Abstract: Plant and animal microRNAs (miRNAs) are evolutionarily ancient small RNAs, approximately 19-24 nucleotides in length, that are generated by cleavage from larger highly structured precursor molecules. In both plants and animals, miRNAs posttranscriptionally regulate gene expression through interactions with their target mRNAs, and these targets are often genes involved with regulating key developmental events. Despite these similarities, plant and animal miRNAs exert their control in fundamentally different ways. Generally, animal miRNAs repress gene expression by mediating translational attenuation through (multiple) miRNA-binding sites located within the 3' untranslated region of the target gene. In contrast, almost all plant miRNAs regulate their targets by directing mRNA cleavage at single sites in the coding regions. These and other differences suggest that the two systems may have originated independently, possibly as a prerequisite to the development of complex body plans.
Publisher: Oxford University Press (OUP)
Date: 10-02-2020
DOI: 10.1104/PP.19.00786
Publisher: Springer Science and Business Media LLC
Date: 19-08-2016
Publisher: Springer International Publishing
Date: 2021
Publisher: Wiley
Date: 05-10-2013
DOI: 10.1016/J.FEBSLET.2013.09.037
Abstract: In plants, the silencing efficacy of microRNAs (miRNAs) is thought to be predominantly determined by the degree of complementarity to their target genes. Here, silencing efficacy was determined for Arabidopsis miR159 and four artificial miRNAs (amiRNAs) that all target MYB33/MYB65 with analogous complementarities. As determined through complementation of a loss-of-function mir159 mutant, the amiRNAs displayed highly variable efficacies, none of which was as strong as endogenous miR159. This was despite amiRNA expression levels being many fold-higher than miR159 in wild-type. The results highlight the variable nature of miRNA silencing efficacy in plants, where it appears that factors additional to complementarity strongly impact silencing.
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.
Publisher: Elsevier BV
Date: 03-2013
DOI: 10.1093/MP/SSS136
Publisher: Springer Science and Business Media LLC
Date: 02-07-2020
DOI: 10.1038/S41591-020-0972-7
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
No related grants have been discovered for Anthony Millar.