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Desiccation-tolerance in vegetative tissues of angiosperms has a polyphyletic origin and could be due to 1) appropriation of the seed-specific program of gene expression that protects orthodox seeds against desiccation, and/or 2) a sustainable version of the abiotic stress response. We tested these hypotheses by comparing molecular and physiological data from the development of orthodox seeds, the response of desiccation-sensitive plants to abiotic stress, and the response of desiccation-tolerant plants to extreme water loss. Analysis of publicly-available gene expression data of 35 LEA proteins and 68 anti-oxidant enzymes in the desiccation-sensitive Arabidopsis thaliana identified 13 LEAs and 4 anti-oxidants exclusively expressed in seeds. Two (a LEA6 and 1-cys-peroxiredoxin) are not expressed in vegetative tissues in A. thaliana, hut have orthologues that are specifically activated in desiccating leaves of Xerophyta humilis. A comparison of antioxidant enzyme activity in two desiccation-sensitive species of Eragrostis with the desiccation-tolerant E. nindensis showed equivalent responses upon initial dehydration, but activity was retained at low water content in E. nindensis only. We propose that these antioxidants are housekeeping enzymes and that they are protected from damage in the desiccation-tolerant species. Sucrose is considered an important protectant against desiccation in orthodox seeds, and we show that sucrose accumulates in drying leaves of E. nindensis, but not in the desiccation-sensitive Eragrostis species. The activation of "seed-specific" desiccation protection mechanisms (sucrose accumulation and expression of LEA6 and 1-cys-peroxiredoxin genes) in the vegetative tissues of desiccation-tolerant plants points towards acquisition of desiccation tolerance from seeds. [ABSTRACT FROM AUTHOR]

We report the characterization of anArabidopsis thalianamutant,ups1, isolated on the basis of reduced expression of phosphoribosylanthranilate transferase, a tryptophan biosynthetic enzyme.ups1also exhibits defects in a wide range of defence responses. After infection withPseudomonas syringaeorBotrytis cinerea, the expression of genes regulated by both the salicylic acid and jasmonic acid/ethylene pathways is reduced inups1compared with wild type. Camalexin accumulation inups1is greatly reduced after infection with these two pathogens, as well as after amino acid starvation or oxidative stress. Reactive oxygen species (ROS)-mediated gene expression is also compromised inups1indicating that this mutant is defective in signalling pathways activated in response to both biotic and abiotic stress. The fact that all three major defence signalling pathways are disrupted inups1, together with the oxidative stress phenotype, leads us to suggest that UPS1 is involved in ROS signal transduction. [ABSTRACT FROM AUTHOR]

Numerous studies have suggested that plant/pathogen interactions are partially mediated via plant secondary metabolite production and corresponding pathogen tolerance. However, there are inconsistent reports on the ability of particular compounds to provide resistance to a pathogen. Most of these studies have focused on individual isolates of a given pathogen, suggesting that pathogens vary in their sensitivity to plant-produced toxins. We tested variability in virulence among pathogen isolates, and the impact on this by plant production of, and pathogen tolerance to, secondary metabolites. Botrytis cinerea isolates showed differing sensitivity to purified camalexin, and camalexin-sensitive isolates produced larger lesions on camalexin-deficient Arabidopsis genotypes than on the wild type. In contrast, the camalexin-insensitive isolate produced lesions of similar size on wild-type and camalexin-deficient Arabidopsis. Additional analysis with Arabidopsis secondary metabolite biosynthetic mutants suggests that Botrytis also has variable sensitivity to phenylpropanoids and glucosinolates. Furthermore, Botrytis infection generates a gradient of secondary metabolite responses emanating from the developing lesion, with the Botrytis isolate used determining the accumulation pattern. Collectively, our results indicate that Arabidopsis/ Botrytis interactions are influenced at the metabolic level by variations in toxin production in the host and sensitivity in the pathogen. [ABSTRACT FROM AUTHOR]

The circadian clock, an internal time-keeping mechanism, allows plants to anticipate regular changes in the environment, such as light and dark, and biotic challenges such as pathogens and herbivores. Here, we demonstrate that the plant circadian clock influences susceptibility to the necrotrophic fungal pathogen, Botrytis cinerea. Arabidopsis plants show differential susceptibility to B. cinerea depending on the time of day of inoculation. Decreased susceptibility after inoculation at dawn compared with night persists under constant light conditions and is disrupted in dysfunctional clock mutants, demonstrating the role of the plant clock in driving time-of-day susceptibility to B. cinerea. The decreased susceptibility to B. cinerea following inoculation at subjective dawn was associated with faster transcriptional reprogramming of the defence response with gating of infection-responsive genes apparent. Direct target genes of core clock regulators were enriched among the transcription factors that responded more rapidly to infection at subjective dawn than subjective night, suggesting an influence of the clock on the defence-signalling network. In addition, jasmonate signalling plays a crucial role in the rhythmic susceptibility of Arabidopsis to B. cinerea with the enhanced susceptibility to this pathogen at subjective night lost in a jaz6 mutant. [ABSTRACT FROM AUTHOR]

A model is presented describing the gene regulatory network surrounding three similar NAC transcription factors that have roles in Arabidopsis leaf senescence and stress responses. ANAC019, ANAC055 and ANAC072 belong to the same clade of NAC domain genes and have overlapping expression patterns. A combination of promoter DNA/protein interactions identified using yeast 1-hybrid analysis and modelling using gene expression time course data has been applied to predict the regulatory network upstream of these genes. Similarities and divergence in regulation during a variety of stress responses are predicted by different combinations of upstream transcription factors binding and also by the modelling. Mutant analysis with potential upstream genes was used to test and confirm some of the predicted interactions. Gene expression analysis in mutants of ANAC019 and ANAC055 at different times during leaf senescence has revealed a distinctly different role for each of these genes. Yeast 1-hybrid analysis is shown to be a valuable tool that can distinguish clades of binding proteins and be used to test and quantify protein binding to predicted promoter motifs. [ABSTRACT FROM AUTHOR]

Motivation: Identifying regulatory modules is an important task in the exploratory analysis of gene expression time series data. Clustering algorithms are often used for this purpose. However, gene regulatory events may induce complex temporal features in a gene expression profile, including time delays, inversions and transient correlations, which are not well accounted for by current clustering methods. As the cost of microarray experiments continues to fall, the temporal resolution of time course studies is increasing. This has led to a need to take account of detailed temporal features of this kind. Thus, while standard clustering methods are both widely used and much studied, their shared shortcomings with respect to such temporal features motivates the work presented here. [ABSTRACT FROM PUBLISHER]