A Putative RNA-Binding Protein Positively Regulates Salicylic Acid–Mediated Immunity in <i>Arabidopsis</i>

Qi, Yiping; Tsuda, Kazuhiko; Joe, Anna; Sato, Mitsuru; Nguyen, Le V.; Glazebrook, Jane; Alfano, James R.; Cohen, Jerry D.; Katagiri, Fumiaki

doi:10.1094/mpmi-05-10-0106

Cited by 49 publications

(46 citation statements)

References 59 publications

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“…In addition, the expression of 15 transcripts encoded by genes associated with the UPR that were present in the early and middle maturation super-cluster was highly correlated with the expression of another SF, RBP-DR1, a cytoplasmic protein, encoded by At4g03110, which, to date has been associated only with the salicylic acid signaling pathway and responses to pathogens [40], and the regulation of flowering [41]. The inferred network for RBP-DR1 is available in Additional file 17: Table S14.…”

Section: Resultsmentioning

confidence: 99%

CoSpliceNet: a framework for co-splicing network inference from transcriptomics data

Aghamirzaie

Collakova

et al. 2016

BMC Genomics

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BackgroundAlternative splicing has been proposed to increase transcript diversity and protein plasticity in eukaryotic organisms, but the extent to which this is the case is currently unclear, especially with regard to the diversification of molecular function. Eukaryotic splicing involves complex interactions of splicing factors and their targets. Inference of co-splicing networks capturing these types of interactions is important for understanding this crucial, highly regulated post-transcriptional process at the systems level.ResultsFirst, several transcript and protein attributes, including coding potential of transcripts and differences in functional domains of proteins, were compared between splice variants and protein isoforms to assess transcript and protein diversity in a biological system. Alternative splicing was shown to increase transcript and function-related protein diversity in developing Arabidopsis embryos. Second, CoSpliceNet, which integrates co-expression and motif discovery at splicing regulatory regions to infer co-splicing networks, was developed. CoSpliceNet was applied to temporal RNA sequencing data to identify candidate regulators of splicing events and predict RNA-binding motifs, some of which are supported by prior experimental evidence. Analysis of inferred splicing factor targets revealed an unexpected role for the unfolded protein response in embryo development.ConclusionsThe methods presented here can be used in any biological system to assess transcript diversity and protein plasticity and to predict candidate regulators, their targets, and RNA-binding motifs for splicing factors. CoSpliceNet is freely available at http://delasa.github.io/co-spliceNet/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3172-6) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

CoSpliceNet: a framework for co-splicing network inference from transcriptomics data

Aghamirzaie

Collakova

et al. 2016

BMC Genomics

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“…For instance, AtRBP-DR1, a putative component of the resistance protein RPS2 complex, positively regulates defense responses mediated by SA in A. thaliana [61]. The conserved MOS2 protein, a putative RBP with both G-patch and KWO domains, is required for resistance against P. syringae pv.…”

Section: Discussionmentioning

confidence: 99%

The hnRNP-Q Protein LIF2 Participates in the Plant Immune Response

et al. 2014

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Eukaryotes have evolved complex defense pathways to combat invading pathogens. Here, we investigated the role of the Arabidopsis thaliana heterogeneous nuclear ribonucleoprotein (hnRNP-Q) LIF2 in the plant innate immune response. We show that LIF2 loss-of-function in A. thaliana leads to changes in the basal expression of the salicylic acid (SA)- and jasmonic acid (JA)- dependent defense marker genes PR1 and PDF1.2, respectively. Whereas the expression of genes involved in SA and JA biosynthesis and signaling was also affected in the lif2-1 mutant, no change in SA and JA hormonal contents was detected. In addition, the composition of glucosinolates, a class of defense-related secondary metabolites, was altered in the lif2-1 mutant in the absence of pathogen challenge. The lif2-1 mutant exhibited reduced susceptibility to the hemi-biotrophic pathogen Pseudomonas syringae and the necrotrophic ascomycete Botrytis cinerea. Furthermore, the lif2-1 sid2-2 double mutant was less susceptible than the wild type to P. syringae infection, suggesting that the lif2 response to pathogens was independent of SA accumulation. Together, our data suggest that lif2-1 exhibits a basal primed defense state, resulting from complex deregulation of gene expression, which leads to increased resistance to pathogens with various infection strategies. Therefore, LIF2 may function as a suppressor of cell-autonomous immunity. Similar to its human homolog, NSAP1/SYNCRIP, a trans-acting factor involved in both cellular processes and the viral life cycle, LIF2 may regulate the conflicting aspects of development and defense programs, suggesting that a conserved evolutionary trade-off between growth and defense pathways exists in eukaryotes.

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“…5D). The regulation of this defense-related splicing factor in drought-stressed ears may represent a splicing-related response to increased disease pressure under more stressful conditions (Qi et al, 2010).…”

Section: Seed Embryo and Endosperm Undergo Hundreds Of Developmentamentioning

confidence: 99%

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

et al. 2015

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Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage-or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition.After transcription, the majority of eukaryotic premRNA is subjected to a series of posttranscriptional modifications, including the removal of introns to form a mature mRNA (Stamm et al., 2005). Although some introns are removed constitutively, many can be processed in a variety of alternative ways, including exon skipping, intron retention, alternative acceptor, alternative donor, and alternative position (change in both acceptor and donor positions; Lorkovic et al., 2000). These alternative splicing events form a crucial regulatory level and have the ability to alter an mRNA's stability, localization, and protein products. Alternative splicing events are controlled by a variety of cis-elements, including the presence of consensus splice sequences at the intron-exon border and intronic and exonic splicing enhancer sequences (Pertea et al., 2007). Trans-acting factors also exert a strong effect on splicing and are mostly composed of Ser/Arg-rich proteins, which typically promote intron removal, and heterogenous nuclear ribonucleoproteins, which typically inhibit it (Erkelenz et al., 2013). A host of other indirect factors can affect splicing, including transcription rate, methylation status, and any cellular conditions that alter RNA secondary structure (Kornblihtt et al

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A Putative RNA-Binding Protein Positively Regulates Salicylic Acid–Mediated Immunity in Arabidopsis

Cited by 49 publications

References 59 publications

CoSpliceNet: a framework for co-splicing network inference from transcriptomics data

CoSpliceNet: a framework for co-splicing network inference from transcriptomics data

The hnRNP-Q Protein LIF2 Participates in the Plant Immune Response

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

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