Abstract
Plant intracellular immune receptor NLR (nucleotide-binding leucine-rich repeat) proteins sense the presence of pathogens and trigger strong and robust immune responses. NLR genes are known to be tightly controlled at the protein level, but little is known about their dynamics at the transcript level. In this study, we presented a meta-analysis of transcript dynamics of all 207 NLR genes in the Col-0 accession of Arabidopsis thaliana under various biotic and abiotic stresses based on 88 publicly available RNA sequencing datasets from 27 independent studies. We find that about two thirds of the NLR genes are generally induced by pathogens, immune elicitors, or salicylic acid (SA), suggesting that transcriptional induction of NLR genes might be an important mechanism in plant immunity regulation. By contrast, NLR genes induced by biotic stresses are often repressed by abscisic acid, high temperature and drought, suggesting that transcriptional regulation of NLR genes might be important for interaction between abiotic and biotic stress responses. In addition, pathogen-induced expression of some NLR genes are dependent on SA induction. Interestingly, a small group of NLR genes are repressed under certain biotic stress treatments, suggesting an unconventional function of this group of NLRs. This meta-analysis thus reveals the transcript dynamics of NLR genes under biotic and abiotic stress conditions and suggests a contribution of NLR transcript regulation to plant immunity as well as interactions between abiotic and biotic stress responses.
Highlights
Plants in nature are constantly challenged by a variety of environmental stresses including pathogen attacks
We searched literature via Google Scholar for RNAseq data of plants grown under various conditions using the keywords “transcriptome,” “RNA sequencing,” “biotic stress,” “abiotic stress,” and “autoimmunity.” The datasets used in the meta-analysis were selected based on the following criteria: datasets were performed on leaves or seedlings of Col-0 accessions; differentially expressed genes (DEGs) were listed in the publication or processed reads count for each gene (“reads count-only” datasets) were available in NCBI GEO database
NLR Genes Are in General Induced Under Biotic Stresses
Summary
Plants in nature are constantly challenged by a variety of environmental stresses including pathogen attacks. In order to fend off pathogens, plants utilize cell-surface receptors and intracellular immune receptors to sense the presence of microbes (Wang et al, 2020). The recognition of pathogens by immune receptors triggers a series of immune responses such as reactive oxygen species burst, Ca2+ influx, accumulation of salicylic acid (SA), and transcriptional reprograming (Tsuda and Katagiri, 2010; Buscaill and Rivas, 2014). Transcriptional upregulation of defense genes and reduction of growth-related genes are critical for a successful inhibition or blocking of invasion and propagation of pathogens (Lewis et al, 2015). The plant hormone SA is often induced during defense responses, and key enzymes for SA biosynthesis are regulated by a few transcription factors. SAR DEFICIENT 1 (SARD1) and its close homolog CALMODULIN BINDING PROTEIN
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