The SR Splicing Factors: Providing Perspectives on Their Evolution, Expression, Alternative Splicing, and Function in Populus trichocarpa.

Xijuan Zhao,Shenkui Liu,Yirong Shen,Liangyu Guo,Ying Feng,Wenwu Wu,Shuo Wang,Lingling Tan,Xiaoxue Ye

doi:10.3390/ijms222111369

Abstract

Serine/arginine-rich (SR) proteins are important splicing factors in plant development and abiotic/hormone-related stresses. However, evidence that SR proteins contribute to the process in woody plants has been lacking. Using phylogenetics, gene synteny, transgenic experiments, and RNA-seq analysis, we identified 24 PtSR genes and explored their evolution, expression, and function in Popolus trichocarpa. The PtSR genes were divided into six subfamilies, generated by at least two events of genome triplication and duplication. Notably, they were constitutively expressed in roots, stems, and leaves, demonstrating their fundamental role in P. trichocarpa. Additionally, most PtSR genes (~83%) responded to at least one stress (cold, drought, salt, SA, MeJA, or ABA), and, especially, cold stress induced a dramatic perturbation in the expression and/or alternative splicing (AS) of 18 PtSR genes (~75%). Evidentially, the overexpression of PtSCL30 in Arabidopsis decreased freezing tolerance, which probably resulted from AS changes of the genes (e.g., ICE2 and COR15A) critical for cold tolerance. Moreover, the transgenic plants were salt-hypersensitive at the germination stage. These indicate that PtSCL30 may act as a negative regulator under cold and salt stress. Altogether, this study sheds light on the evolution, expression, and AS of PtSR genes, and the functional mechanisms of PtSCL30 in woody plants.

Highlights

Alternative splicing (AS) is an important mechanism in the regulation of gene expression in eukaryotes, which enhances transcriptome and proteome diversity [1,2]
We identified 24 PtSR genes and their evolutionary history in P. trichocarpa, revealed their conservation and divergence of expression and AS in tissues and under abiotic/hormone stresses, and exemplified a cold-affected gene, PtSCL30, to explore its molecular mechanism and functions
The PtSR genes were divided into six subgroups, and they were distributed unequally on P. trichocarpa chromosomes with 16 collinearity gene blocks, which were generated by two expansion events of genome triplication and duplication before and after the divergence of P. trichocarpa from Arabidopsis

Summary

Introduction

Alternative splicing (AS) is an important mechanism in the regulation of gene expression in eukaryotes, which enhances transcriptome and proteome diversity [1,2]. About 83% and 73% of intron-containing genes undergo AS in Arabidopsis thaliana and Oryza sativa, respectively [5,6]. There are mainly five different types of AS events, including exon-skipping (ES), intron retention (IR), mutually exclusive exons (MXE), alternative 5 splice site (A5SS) and 3 splice site selection (A3SS) [7]. IR is a major mode of AS in plants, whereas ES is a predominant mode in animals [8,9,10]. The importance of AS has been clearly manifested by the genetic hereditary diseases caused by splicing defects [11,12]

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Discussion

Conclusion