Browsing by Subject "Arabidopsis thaliana"

Now showing 1 - 7 of 7
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    Open Access
    A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1
    (2017) Yocgo, Rosita E; Geza, Ephifania; Chimusa, Emile R; Mazandu, Gaston K
    Advances in forward and reverse genetic techniques have enabled the discovery and identification of several plant defence genes based on quantifiable disease phenotypes in mutant populations. Existing models for testing the effect of gene inactivation or genes causing these phenotypes do not take into account eventual uncertainty of these datasets and potential noise inherent in the biological experiment used, which may mask downstream analysis and limit the use of these datasets. Moreover, elucidating biological mechanisms driving the induced disease resistance and influencing these observable disease phenotypes has never been systematically tackled, eliciting the need for an efficient model to characterize completely the gene target under consideration.
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    Open Access
    A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1
    (BioMed Central, 2017-11-23) Yocgo, Rosita E; Geza, Ephifania; Chimusa, Emile R; Mazandu, Gaston K
    Background: Advances in forward and reverse genetic techniques have enabled the discovery and identification of several plant defence genes based on quantifiable disease phenotypes in mutant populations. Existing models for testing the effect of gene inactivation or genes causing these phenotypes do not take into account eventual uncertainty of these datasets and potential noise inherent in the biological experiment used, which may mask downstream analysis and limit the use of these datasets. Moreover, elucidating biological mechanisms driving the induced disease resistance and influencing these observable disease phenotypes has never been systematically tackled, eliciting the need for an efficient model to characterize completely the gene target under consideration. Results: We developed a post-gene silencing bioinformatics (post-GSB) protocol which accounts for potential biases related to the disease phenotype datasets in assessing the contribution of the gene target to the plant defence response. The post-GSB protocol uses Gene Ontology semantic similarity and pathway dataset to generate enriched process regulatory network based on the functional degeneracy of the plant proteome to help understand the induced plant defence response. We applied this protocol to investigate the effect of the NPR1 gene silencing to changes in Arabidopsis thaliana plants following Pseudomonas syringae pathovar tomato strain DC3000 infection. Results indicated that the presence of a functionally active NPR1 reduced the plant’s susceptibility to the infection, with about 99% of variability in Pseudomonas spore growth between npr1 mutant and wild-type samples. Moreover, the post-GSB protocol has revealed the coordinate action of target-associated genes and pathways through an enriched process regulatory network, summarizing the potential target-based induced disease resistance mechanism. Conclusions: This protocol can improve the characterization of the gene target and, potentially, elucidate induced defence response by more effectively utilizing available phenotype information and plant proteome functional knowledge.
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    Open Access
    Defence responses of Arabidopsis thaliana to infection by Pseudomonas syringae are regulated by the circadian clock
    (Public Library of Science, 2011) Bhardwaj, Vaibhav; Meier, Stuart; Petersen, Lindsay N; Ingle, Robert A; Roden, Laura C
    The circadian clock allows plants to anticipate predictable daily changes in abiotic stimuli, such as light; however, whether the clock similarly allows plants to anticipate interactions with other organisms is unknown. Here we show that Arabidopsis thaliana (Arabidopsis) has circadian clock-mediated variation in resistance to the virulent bacterial pathogen Pseudomonas syringae pv. tomato DC3000 ( Pst DC3000), with plants being least susceptible to infection in the subjective morning. We suggest that the increased resistance to Pst DC3000 observed in the morning in Col-0 plants results from clock-mediated modulation of pathogen associated molecular pattern (PAMP)-triggered immunity. Analysis of publicly available microarray data revealed that a large number of Arabidopsis defence-related genes showed both diurnal- and circadian-regulation, including genes involved in the perception of the PAMP flagellin which exhibit a peak in expression in the morning. Accordingly, we observed that PAMP-triggered callose deposition was significantly higher in wild-type plants inoculated with Pst DC3000 hrpA in the subjective morning than in the evening, while no such temporal difference was evident in arrhythmic plants. Our results suggest that PAMP-triggered immune responses are modulated by the circadian clock and that temporal regulation allows plants to anticipate and respond more effectively to pathogen challenges in the daytime.
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    Open Access
    Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction
    (Public Library of Science, 2005) Seoighe, Cathal; Gehring, Chris; Hurst, Laurence D
    Why do highly expressed genes have small introns? This is an important issue, not least because it provides a testing ground to compare selectionist and neutralist models of genome evolution. Some argue that small introns are selectively favoured to reduce the costs of transcription. Alternatively, large introns might permit complex regulation, not needed for highly expressed genes. This "genome design" hypothesis evokes a regionalized model of control of expression and hence can explain why intron size covaries with intergene distance, a feature also consistent with the hypothesis that highly expressed genes cluster in genomic regions with high deletion rates. As some genes are expressed in the haploid stage and hence subject to especially strong purifying selection, the evolution of genes in Arabidopsis provides a novel testing ground to discriminate between these possibilities. Importantly, controlling for expression level, genes that are expressed in pollen have shorter introns than genes that are expressed in the sporophyte. That genes flanking pollen-expressed genes have average-sized introns and intergene distances argues against regional mutational biases and genomic design. These observations thus support the view that selection for efficiency contributes to the reduction in intron length and provide the first report of a molecular signature of strong gametophytic selection.
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    Leaf tensile properties of resurrection plants differ among species in their response to drying
    (2009) Hedderson, N.; Balsamo, R. A.; Cooper, K.; Farrant, J. M.
    Previous studies report that leaf tensile strength (TS) of the desiccation tolerant (resurrection) grass Eragrostis nindensis does not change on drying, but increases in dried desiccation sensitive Eragrostis species. In this paper we tested whether unchanging TS on dehydration is a common feature among 4 resurrection species, Craterostigma wilmsii, Sporobolus stapfianus, Xerophyta humilis and Xerophyta schlecteri, and how this might relate to leaf structure and mechanisms of protection against mechanical stress of drying. Desiccation sensitive controls were Zea mays and Arabidopsis thaliana. Light and transmission electron microscopy of leaves was performed to determine lignification and the nature of subcellular mechanical stabilization. There was a positive correlation between % lignin/unit cross-sectional area and TS of hydrated leaves. Only the grass, S. stapfianus, did not change TS when naturally dried. All others increased in TS when naturally dried, but there was variation among them when flash dried. In S. stapfianus, mechanical stabilization was by both wall folding (mesophyll) and vacuole packaging (bundle sheath) as reported for E. nindensis. This combination may account, in part, for unchanging TS during drying and may be a feature of resurrection grasses. We conclude that leaf tensile properties differ among resurrection plants and are not necessarily affected by protection mechanisms associated with mechanical stress.
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    Leaf tensile properties of resurrection plants differ among species in their response to drying.
    (Elsevier, 2009) Hedderson, N; Balsamo, R; Farrant, J; Cooper, K
    Previous studies report that leaf tensile strength (TS) of the desiccation tolerant (resurrection) grass Eragrostis nindensis does not change on drying, but increases in dried desiccation sensitive Eragrostis species. In this paper we tested whether unchanging TS on dehydration is a common feature among 4 resurrection species, Craterostigma wilmsii, Sporobolus stapfianus, Xerophyta humilis and Xerophyta schlecteri, and how this might relate to leaf structure and mechanisms of protection against mechanical stress of drying. Desiccation sensitive controls were Zea mays and Arabidopsis thaliana. Light and transmission electron microscopy of leaves was performed to determine lignification and the nature of subcellular mechanical stabilization. There was a positive correlation between % lignin/unit cross-sectional area and TS of hydrated leaves. Only the grass, S. stapfianus, did not change TS when naturally dried. All others increased in TS when naturally dried, but there was variation among them when flash dried. In S. stapfianus, mechanical stabilization was by both wall folding (mesophyll) and vacuole packaging (bundle sheath) as reported for E. nindensis. This combination may account, in part, for unchanging TS during drying and may be a feature of resurrection grasses. We conclude that leaf tensile properties differ among resurrection plants and are not necessarily affected by protection mechanisms associated with mechanical stress.
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    Open Access
    The window of desiccation tolerance shown by early-stage germinating seedlings remains open in the resurrection plant, Xerophyta viscosa
    (Public Library of Science, 2014) Lyall, Rafe; Ingle, Robert A; Illing, Nicola
    Resurrection plants are renowned for their vegetative desiccation tolerance (DT). While DT in vegetative tissues is rare in angiosperms, it is ubiquitous in mature orthodox seeds. During germination, seedlings gradually lose DT until they pass a point of no return, after which they can no longer survive dehydration. Here we investigate whether seedlings of the resurrection plant Xerophyta viscosa ever lose the capacity to establish DT. Seedlings from different stages of germination were dehydrated for 48 hours and assessed for their ability to recover upon rehydration. While a transient decline in the ability of X. viscosa seedlings to survive dehydration was observed, at no point during germination was the ability to re-establish DT completely lost in all seedlings. Pre-treatment of seedlings with PEG or sucrose reduced this transient decline, and improved the survival rate at all stages of germination. Additionally, we observed that the trait of poikilochlorophylly (or loss of chlorophyll) observed in adult X. viscosa leaves can be induced throughout seedling development. These results suggest that the window of DT seen in germinating orthodox seeds remains open in X. viscosa seedlings and that vegetative DT in Xerophyta species may have evolved from the ability to retain this program through to adulthood.