A Meta-Analysis Reveals Opposite Effects of Biotic and Abiotic Stresses on Transcript Levels of Arabidopsis Intracellular Immune Receptor Genes

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.

Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice

“…Despite the findings of the differences in the number of yield-related genes among the different N-responsive transcriptomic data sets generated under different growth and treatment conditions, taking them together, we identified 1,064 genes as both N-responsive and yield-related. Meta-analysis allows such identification from diverse data sets as reported earlier for Arabidopsis (Zhang et al, 2020a ; Yang et al, 2021 ) and rice (de Abreu-Neto and Frei, 2016 ; Muthuramalingam et al, 2017 ; Cohen and Leach, 2019 ; Kong et al, 2019 ). In order to minimize variations in data processing, we used uniform selection criteria (Log 2 FC ≥ 1, value of p ≤ 0.05) with a default redundancy removal setting for all the microarray data sets.…”

Plant autoimmunity—fresh insights into an old phenomenon

“…Only few exceptions such as the zed1-D mutant behave differently, possibly due to specific characteristics of the involved guardees. A recent meta-analysis of whole-genome shotgun (RNA-sequencing) data sets revealed that generally the expression of NLR genes is increased upon biotic stress (or treatment with SA) while their expression is mostly reduced under abiotic stress such as heat, but also drought or treatment with the phytohormone abscisic acid ( Yang et al, 2021 ). This could explain why NLR-dependent autoimmune phenotypes are generally reduced at higher temperatures and often depend on the availability of light.…”

Meta-Analysis of Common and Differential Transcriptomic Responses to Biotic and Abiotic Stresses in Arabidopsis thaliana

“…They are faced with various biotic stresses, including bacteria, fungi, viruses, herbivorous insects, and nematodes [1]. Moreover, abiotic stresses, such as salinity, drought, and extreme temperature, affect many physiological processes in plants [2]. The regulation of proper responses is crucial to reduce the damage caused by these stresses [3].…”