Journal Article

Genome-scale analysis of Arabidopsis splicing-related protein kinase families reveals roles in abiotic stress adaptation

Li, Q., Mehta, D., Uhrig, R. G., Rodriguez Gallo, M. C.

2022

Overview

Nearly 60 – 80 % of intron-containing plant genes undergo alternative splicing in response to either stress or plant developmental cues. RNA splicing is performed by a large ribonucleoprotein complex called the spliceosome in conjunction with associated subunits such as serine arginine (SR) proteins, all of which undergo extensive phosphorylation. In plants, there are three main protein kinase families suggested to phosphorylate core spliceosome subunits and related splicing factors based on orthology to human splicing-related kinases: the SERINE/ARGININE PROTEIN KINASES (SRPK), ARABIDOPSIS FUS3 COMPLEMENT (AFC), and Pre-mRNA PROCESSING FACTOR 4 (PRP4K) protein kinases. To better define the conservation and role(s) of these kinases in plants, we performed a genome-scale analysis of the three families across photosynthetic eukaryotes, followed by extensive transcriptomic and bioinformatic analysis of all Arabidopsis thaliana SRPK, AFC, and PRP4K protein kinases to elucidate their biological functions. Unexpectedly, this revealed the existence of SRPK and AFC phylogenetic groups with distinct promoter elements and patterns of transcriptional response to abiotic stress, while PRP4Ks possess no phylogenetic sub-divisions, suggestive of functional redundancy. We also reveal splicing-related kinase families are both diel and photoperiod regulated, implicating different orthologs as discrete time-of-day RNA splicing regulators. This foundational work establishes a number of new hypotheses regarding how reversible spliceosome phosphorylation contributes to both diel plant cell regulation and abiotic stress adaptation in plants.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Abiotic Stress / Adaptation / Adaptation (Physiology) / Agriculture / Alternative splicing / Alternative Splicing - genetics / Arabidopsis - metabolism / Arabidopsis Proteins - genetics / Arabidopsis Proteins - metabolism / Arabidopsis thaliana / arginine / Arginine - metabolism / bioinformatics / Biomedical and Life Sciences / Botanical research / complement / Diel cycle / Diversification / Eukaryotes / eukaryotic cells / Evolution / Gene expression / Genetic aspects / Genomes / Hardiness / humans / Insects / Kinases / Life Sciences / Metabolism / mRNA processing / mRNA splicing / Orthology / Phosphorylation / Photosynthesis / Phylogenetics / Phylogeny / Physiological aspects / Plant Sciences / Plants / Post-transcription / Protein kinase / Protein kinases / Protein Kinases - genetics / Proteins / Redundancy / Ribonucleic acid / ribonucleoproteins / Ribonucleoproteins - genetics / RNA / RNA Precursors - genetics / RNA Precursors - metabolism / RNA splicing / RNA Splicing - genetics / RNA Splicing Factors - genetics / Serine / Serine - genetics / Signal transduction / spliceosomes / Splicing / Splicing factors / Stress (Physiology) / Stress, Physiological - genetics / Time of use / transcription (genetics) / Transcriptomics / Tree Biology