Barley susceptibility factor RACB modulates transcript levels of signalling protein genes in compatible interaction with Blumeria graminis f.sp hordei.

RHO (rat sarcoma homologue) GTPases (guanosine triphosphatases) are regulators of downstream transcriptional responses of eukaryotes to intracellular and extracellular stimuli. For plants, little is known about the function of Rho-like GTPases [called RACs (rat sarcoma-related C botulinum substrate) or ROPs (RHO of plants)] in transcriptional reprogramming of cells. However, in plant hormone response and innate immunity, RAC/ROP proteins influence gene expression patterns. The barley RAC/ROP RACB is required for full susceptibility of barley to the powdery mildew fungus Blumeria graminis f.sp. hordei (Bgh). We compared the transcriptomes of barley plants either silenced for RACB or over-expressing constitutively activated RACB with and without inoculation with Bgh. This revealed a large overlap of the barley transcriptome during the early response to Bgh and during the over-expression of constitutively activated RACB. Global pathway analyses and stringent analyses of differentially expressed genes suggested that RACB influences, amongst others, the expression of signalling receptor kinases. Transient induced gene silencing of RACB-regulated signalling genes (a leucine-rich repeat protein, a leucine-rich repeat receptor-like kinase and an S-domain SD1-receptor-like kinase) suggested that they might be involved in RACB-modulated susceptibility to powdery mildew. We discuss the function of RACB in regulating the transcriptional responses of susceptible barley to Bgh

RNASeqExpressionBrowser - a web interface to browse and visualize high-throughput expression data.

MOTIVATION: RNA-seq techniques generate massive amounts of expression data. Several pipelines (e.g. Tophat and Cufflinks) are broadly applied to analyse these data sets. However, accessing and handling the analytical output remains challenging for non-experts. RESULTS: We present the RNASeqExpressionBrowser, an open-source web interface that can be used to access the output from RNA-seq expression analysis packages in different ways as it allows browsing for genes by identifiers, annotations or sequence similarity. Gene expression information can be loaded as long as it is represented in a matrix like format. Additionally, data can be made available by setting up the tool on a public server. For demonstration purposes, we have set up a version providing expression information from the barley genome. AVAILABILITY: The source code and a show case are accessible at: http://mips.helmholtz-muenchen.de/plant/RNASeqExpressionBrowser/

TopKLists: A comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists.

High-throughput sequencing techniques are increasingly affordable and produce massive amounts of data. Together with other high-throughput technologies, such as microarrays, there are an enormous amount of resources in databases. The collection of these valuable data has been routine for more than a decade. Despite different technologies, many experiments share the same goal. For instance, the aims of RNA-seq studies often coincide with those of differential gene expression experiments based on microarrays. As such, it would be logical to utilize all available data. However, there is a lack of biostatistical tools for the integration of results obtained from different technologies. Although diverse technological platforms produce different raw data, one commonality for experiments with the same goal is that all the outcomes can be transformed into a platform-independent data format - rankings - for the same set of items. Here we present the R package TopKLists, which allows for statistical inference on the lengths of informative (top-k) partial lists, for stochastic aggregation of full or partial lists, and for graphical exploration of the input and consolidated output. A graphical user interface has also been implemented for providing access to the underlying algorithms. To illustrate the applicability and usefulness of the package, we integrated microRNA data of non-small cell lung cancer across different measurement techniques and draw conclusions. The package can be obtained from CRAN under a LGPL-3 license

Brassinosteroids are master regulators of gibberellin biosynthesis in arabidopsis.

Plant growth and development are highly regulated processes that are coordinated by hormones including the brassinosteroids (BRs), a group of steroids with structural similarity to steroid hormones of mammals. Although it is well understood how BRs are produced and how their signals are transduced, BR targets, which directly confer the hormone's growth-promoting effects, have remained largely elusive. Here, we show that BRs regulate the biosynthesis of gibberellins (GAs), another class of growth-promoting hormones, in Arabidopsis thaliana. We reveal that Arabidopsis mutants deficient in BR signaling are severely impaired in the production of bioactive GA, which is correlated with defective GA biosynthetic gene expression. Expression of the key GA biosynthesis gene GA20ox1 in the BR signaling mutant bri1-301 rescues many of its developmental defects. We provide evidence that supports a model in which the BR-regulated transcription factor BES1 binds to a regulatory element in promoters of GA biosynthesis genes in a BR-induced manner to control their expression. In summary, our study underscores a role of BRs as master regulators of GA biosynthesis and shows that this function is of major relevance for the growth and development of vascular plants

chromoWIZ: A web tool to query and visualize chromosome-anchored genes from cereal and model genomes.

BackgroundOver the last years reference genome sequences of several economically and scientifically important cereals and model plants became available. Despite the agricultural significance of these crops only a small number of tools exist that allow users to inspect and visualize the genomic position of genes of interest in an interactive manner.DescriptionWe present chromoWIZ, a web tool that allows visualizing the genomic positions of relevant genes and comparing these data between different plant genomes. Genes can be queried using gene identifiers, functional annotations, or sequence homology in four grass species (Triticum aestivum, Hordeum vulgare, Brachypodium distachyon, Oryza sativa). The distribution of the anchored genes is visualized along the chromosomes by using heat maps. Custom gene expression measurements, differential expression information, and gene-to-group mappings can be uploaded and can be used for further filtering.ConclusionsThis tool is mainly designed for breeders and plant researchers, who are interested in the location and the distribution of candidate genes as well as in the syntenic relationships between different grass species. chromoWIZ is freely available and online accessible at http://mips.helmholtz-muenchen.de/plant/chromoWIZ/index.jsp

Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (<em>Triticum aestivum</em> L.).

BACKGROUND: Fusarium head blight (FHB) caused by Fusarium graminearum Schwabe is one of the most prevalent diseases of wheat (Triticum aestivum L.) and other small grain cereals. Resistance against the fungus is quantitative and more than 100 quantitative trait loci (QTL) have been described. Two well-validated and highly reproducible QTL, Fhb1 and Qfhs.ifa-5A have been widely investigated, but to date the underlying genes have not been identified. RESULTS: We have investigated a gene co-expression network activated in response to F. graminearum using RNA-seq data from near-isogenic lines, harboring either the resistant or the susceptible allele for Fhb1 and Qfhs.ifa-5A. The network identified pathogen-responsive modules, which were enriched for differentially expressed genes between genotypes or different time points after inoculation with the pathogen. Central gene analysis identified transcripts associated with either QTL within the network. Moreover, we present a detailed gene expression analysis of four gene families (glucanases, NBS-LRR, WRKY transcription factors and UDP-glycosyltransferases), which take prominent roles in the pathogen response. CONCLUSIONS: A combination of a network-driven approach and differential gene expression analysis identified genes and pathways associated with Fhb1 and Qfhs.ifa-5A. We find G-protein coupled receptor kinases and biosynthesis genes for jasmonate and ethylene earlier induced for Fhb1. Similarly, we find genes involved in the biosynthesis and metabolism of riboflavin more abundant for Qfhs.ifa-5A. &nbsp

Ribosome quality control is a central protection mechanism for yeast exposed to deoxynivalenol and trichothecin.

BACKGROUND: The trichothecene mycotoxins deoxynivalenol (DON) and trichothecin (TTC) are inhibitors of eukaryotic protein synthesis. Their effect on cellular homeostasis is poorly understood. We report a systematic functional investigation of the effect of DON and TTC on the yeast Saccharomyces cerevisiae using genetic array, network and microarray analysis. To focus the genetic analysis on intracellular consequences of toxin action we eliminated the PDR5 gene coding for a potent pleiotropic drug efflux protein potentially confounding results. We therefore used a knockout library with a pdr5&Delta; strain background. RESULTS: DON or TTC treatment creates a fitness bottleneck connected to ribosome efficiency. Genes isolated by systematic genetic array analysis as contributing to toxin resistance function in ribosome quality control, translation fidelity, and in transcription. Mutants in the E3 ligase Hel2, involved in ribosome quality control, and several members of the Rpd3 histone deacetylase complex were highly sensitive to DON. DON and TTC have similar genetic profiles despite their different toxic potency. Network analysis shows a coherent and tight network of genetic interactions among the DON and TTC resistance conferring gene products. The networks exhibited topological properties commonly associated with efficient processing of information. Many sensitive mutants have a &quot;slow growth&quot; gene expression signature. DON-exposed yeast cells increase transcripts of ribosomal protein and histone genes indicating an internal signal for growth enhancement. CONCLUSIONS: The combination of gene expression profiling and analysis of mutants reveals cellular pathways which become bottlenecks under DON and TTC stress. These are generally directly or indirectly connected to ribosome biosynthesis such as the general secretory pathway, cytoskeleton, cell cycle delay, ribosome synthesis and translation quality control. Gene expression profiling points to an increased demand of ribosomal components and does not reveal activation of stress pathways. Our analysis highlights ribosome quality control and a contribution of a histone deacetylase complex as main sources of resistance against DON and TTC

Genetic analysis of DEK1 loop function in three-dimensional body patterning in physcomitrella patens.

DEK1 of higher plants plays an essential role in position dependent signaling and consists of a large transmembrane domain (MEM) linked to a protease catalytic domain (CysPc) and a regulatory domain (C2L). Here we show that the postulated sensory Loop of the MEM domain plays an important role in the developmental regulation of DEK1 activity in the moss Physcomitrella patens. Compared with P. patens lacking DEK1 (∆dek1), the dek1∆loop mutant correctly positions the division plane in the bud apical cell. In contrast to an early developmental arrest of ∆dek1 buds, dek1∆loop develops aberrant gametophores lacking expanded phyllids resulting from mis-regulation of mitotic activity. In contrast to the highly conserved sequence of the catalytic CysPc domain, the Loop is highly variable in land plants. Functionally, the sequence from Marchantia polymorpha fully complements the dek1∆loop phenotype, whereas sequences from Zea mays and Arabidopsis thaliana give phenotypes with retarded growth and affected phyllid development. New bioinformatic analysis identifies MEM as a member of the Major Facilitator Superfamily, membrane transporters reacting to stimuli from the external environment. Transcriptome analysis comparing WT and ∆dek1 tissues identifies an effect of two groups of transcripts connected to dek1 mutant phenotypes, i.e. transcripts related to cell wall remodeling and regulation of the APB2 and APB3 transcription factors known to regulate bud initiation. Finally, new sequence data support the hypothesis that the advanced charophyte algae that evolved into ancestral land plants lost cytosolic calpains, retaining DEK1 as the sole calpain in the evolving land plant lineage

Identification and characterization of carboxylesterases from <em>Brachypodium distachyon</em> deacetylating trichothecene mycotoxins.

Increasing frequencies of 3-acetyl-deoxynivalenol (3-ADON)-producing strains of Fusarium graminearum (3-ADON chemotype) have been reported in North America and Asia. 3-ADON is nearly nontoxic at the level of the ribosomal target and has to be deacetylated to cause inhibition of protein biosynthesis. Plant cells can efficiently remove the acetyl groups of 3-ADON, but the underlying genes are yet unknown. We therefore performed a study of the family of candidate carboxylesterases (CXE) genes of the monocot model plant Brachypodium distachyon. We report the identification and characterization of the first plant enzymes responsible for deacetylation of trichothecene toxins. The product of the BdCXE29 gene efficiently deacetylates T-2 toxin to HT-2 toxin, NX-2 to NX-3, both 3-ADON and 15-acetyl-deoxynivalenol (15-ADON) into deoxynivalenol and, to a lesser degree, also fusarenon X into nivalenol. The BdCXE52 esterase showed lower activity than BdCXE29 when expressed in yeast and accepts 3-ADON, NX-2, 15-ADON and, to a limited extent, fusarenon X as substrates. Expression of these Brachypodium genes in yeast increases the toxicity of 3-ADON, suggesting that highly similar genes existing in crop plants may act as susceptibility factors in Fusarium head blight disease

Joint tanscriptomic and metabolomic analyses reveal changes in the primary metabolism and imbalances in the subgenome orchestration in the bread wheat molecular response to <em>Fusarium graminearum</em>.

Fusarium head blight is a prevalent disease of bread wheat (Triticum aestivum L. ), which leads to considerable losses in yield and quality. Quantitative resistance to the causative fungus Fusarium graminearum is yet poorly understood. We integrated transcriptomics and metabolomics data to dissect the molecular response to the fungus and its main virulence factor, the toxin deoxynivalenol in near-isogenic lines segregating for two resistance quantitative trait loci, Fhb1 and Qfhs.ifa-5A. The data sets portrait rearrangements in the primary metabolism and the translational machinery to counter the fungus and the effects of the toxin and highlight distinct changes in the metabolism of glutamate in lines carrying Qfhs.ifa-5A. These observations are possibly due to the activity of two amino acid permeases located in the QTL confidence interval, which may contribute to increased pathogen endurance. Mapping to the highly resolved region of Fhb1 reduced the list of candidates to few genes that are specifically expressed in presence of the QTL and in response to the pathogen, which include a receptor-like protein kinase, a protein kinase, and an E3 ubiquitin-protein ligase. On a genome-scale level the individual subgenomes of hexaploid wheat contribute differentially to defense: Especially the D subgenome exhibited a pronounced response to the pathogen and contributed significantly to the overall defense response