Alternative splicing regulation by plant SR proteins: Molecular mechanisms, biological functions, and implications for crop improvement

Serine/arginine-rich (SR) proteins are conserved RNA-binding proteins essential for pre-mRNA splicing in plants. As core regulators of alternative splicing (AS), these proteins mediate constitutive splicing (CS) and alternative splicing (AS) primarily via two well-characterized key domains: RNA recognition motifs (RRMs), which bind to exonic/intronic splicing enhancers (ESEs/ISEs), and arginine-serine (RS) domains, which facilitate spliceosome assembly. It is worth noting that many SR proteins contain additional accessory domains, and the specific regulatory roles of individual domains in the splicing process remain incompletely understood. Beyond splicing, plant SR proteins participate in mRNA nuclear export, nonsense-mediated mRNA decay (NMD), and translation, thereby regulating plant growth, development, and stress adaptation. This review summarizes the molecular mechanisms of plant SR proteins in AS regulation—with a focus on plant-specific subfamilies (RS, SCL, RS2Z)—and their roles in embryonic development, seed germination, flowering, and stress responses. We also discuss bioinformatic tools and sequencing technologies for analyzing SR protein-associated AS events and propose future directions to resolve the functional redundancy of plant SR proteins. This work provides insights into AS regulation in plants and supports crop breeding for stress resistance. • Systematic elucidation of domain-specific functions, AS regulatory mechanisms, and plant-unique roles of plant-specific SR subfamilies (RS, SCL, RS2Z), distinguishing from animal homologs. • Integrating the regulatory roles of plant SR proteins across the entire mRNA lifecycle for the first time, including transcription, splicing, nuclear export, translation, and nonsense-mediated mRNA decay. Breaking the limitation of previous reviews that only focused on the "SR-AS-stress" single pathway. • Incorporating cutting-edge advances (2021–2025) including CRISPR-mediated SR gene editing for crop stress resistance, liquid-liquid phase separation of SR proteins in nuclear speckles, and single-cell/long-read sequencing applications in SR-related AS analysis. • Establishing a functional model linking SR proteins to plant growth/development and stress responses, providing a theoretical framework for stress-resistant crop breeding.