Plant serine/arginine-rich proteins: versatile players in RNA processing

Jia, Zichang; Das, Debatosh; Zhang, Youjun; Fernie, Alisdair R.; Liu, Yinggao; Chen, Moxian; Zhang, Jianhua

doi:10.1007/s00425-023-04132-0

Cited by 5 publications

(2 citation statements)

References 95 publications

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“…Splicing factors are usually rich in serine/arginine (SR) residues and recognize the cis ‐regulatory elements of their targets to facilitate pre‐mRNA splicing. Typically, the SR proteins have the N‐terminal RNA recognition motifs (RRMs) for RNA‐binding and the C‐terminal arginine/serine (RS) domains for protein–protein interactions (Barta et al ., 2010; Sahebi et al ., 2016; Jia et al ., 2023). The first functionally characterized plant splicing factor is SR1 showing its ability to promote splice site switching in mammalian nuclear extracts (Lazar et al ., 1995).…”

Section: Introductionmentioning

confidence: 99%

Regulation of plant resistance to salt stress by the SnRK1‐dependent splicing factor SRRM1L

Sun,

Liu

et al. 2024

New Phytologist

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Summary Most splicing factors are extensively phosphorylated but their physiological functions in plant salt resistance are still elusive. We found that phosphorylation by SnRK1 kinase is essential for SRRM1L nuclear speckle formation and its splicing factor activity in plant cells. In Arabidopsis, loss‐of‐function of SRRM1L leads to the occurrence of alternative pre‐mRNA splicing events and compromises plant resistance to salt stress. In Arabidopsis srrm1l mutant line, we identified an intron‐retention Nuclear factor Y subunit A 10 (NFYA10) mRNA variant by RNA‐Seq and found phosphorylation‐dependent RNA‐binding of SRRM1L is indispensable for its alternative splicing activity. In the wild‐type Arabidopsis, salt stress can activate SnRK1 to phosphorylate SRRM1L, triggering enrichment of functional NFYA10.1 variant to enhance plant salt resistance. By contrast, the Arabidopsis srrm1l mutant accumulates nonfunctional NFYA10.3 variant, sensitizing plants to salt stress. In summary, this work deciphered the molecular mechanisms and physiological functions of SnRK1‐SRRM1L‐NFYA10 module, shedding light on a regulatory pathway to fine‐tune plant adaptation to abiotic stress at the post‐transcriptional and post‐translational levels.

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Section: Introductionmentioning

confidence: 99%

Regulation of plant resistance to salt stress by the SnRK1‐dependent splicing factor SRRM1L

Sun,

Liu

et al. 2024

New Phytologist

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“…Splicing of precursor mRNA is catalysed by the spliceosome, a large complex in the nucleus consisting of five small nuclear ribonucleoprotein (snRNP) complexes and various splicing factors. Among them, evolutionarily conserved serine/arginine-rich (SR) proteins govern splice-site selection by the recognition of cis-regulatory elements within the pre-mRNA sequence, thereby regulating both constitutive and alternative splicing (21). SR proteins consist of one or two N-terminal RNA-binding domains and a C-terminal RS domain, which contains multiple arginine/serine dipeptide repeats (22).…”

Section: Introductionmentioning

confidence: 99%

AFC kinases function as thermosensors that regulate warm temperature-responsive growth inArabidopsis

Dimos-Röhl,

Ostwaldt,

Bäsmann

et al. 2024

Preprint

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Plants respond to elevated temperatures with enhanced elongation growth and an upward movement of their leaves. These adaptive growth responses depend on a rapid transcriptional, post-transcriptional and post-translational reprogramming. It is unclear, however, how temperature information is sensed and integrated with the cellular splicing machinery to establish warm-temperature dependent splicing patterns. In animals, CDC2-LIKE KINASES (CLKs) function as body temperature sensors that control temperature-dependent alternative splicing through the phosphorylation of serine/arginine-rich (SR) proteins. Here, we demonstrate that the CLK-homologous ARABIDOPSIS FUS3-COMPLEMENTING (AFC) kinases function as temperature sensors that regulate post-transcriptional RNA processing to control warm temperature-dependent growth responses in Arabidopsis. We show that the contrasting temperature-activity profiles of the three Arabidopsis AFCs depend on specific structural elements including a conserved activation segment within the kinase domain. By combining protein structure prediction with site-directed mutagenesis, we provide insights into structural features that determine different temperature-activity profiles of the three AFC paralogs. Subsequent analyses ofafcmutant plants demonstrate their requirement for hypocotyl elongation growth and thermonastic leaf movement at elevated temperature. Impaired hypocotyl elongation ofafctriple mutant seedlings was accompanied by defects in temperature-dependent splicing especially affecting the post-transcriptional regulation of transcripts encoding splicing factors. Finally, based on transcriptomics, immunodetection and mutant analyses our data indicate SR34 and SR34a as phosphorylation targets that mediate temperature-dependent post-transcriptional RNA processing downstream of AFCs. In conclusion, the characterisation of Arabidopsis AFC kinases as thermosensors provides compelling evidence that temperature-controlled AFC activity is evolutionarily conserved between plants and animals.

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Importance of pre-mRNA splicing and its study tools in plants

Liu,

Do,

Huynh

et al. 2024

Adv. Biotechnol.

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Alternative splicing (AS) significantly enriches the diversity of transcriptomes and proteomes, playing a pivotal role in the physiology and development of eukaryotic organisms. With the continuous advancement of high-throughput sequencing technologies, an increasing number of novel transcript isoforms, along with factors related to splicing and their associated functions, are being unveiled. In this review, we succinctly summarize and compare the different splicing mechanisms across prokaryotes and eukaryotes. Furthermore, we provide an extensive overview of the recent progress in various studies on AS covering different developmental stages in diverse plant species and in response to various abiotic stresses. Additionally, we discuss modern techniques for studying the functions and quantification of AS transcripts, as well as their protein products. By integrating genetic studies, quantitative methods, and high-throughput omics techniques, we can discover novel transcript isoforms and functional splicing factors, thereby enhancing our understanding of the roles of various splicing modes in different plant species.

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Plant serine/arginine-rich proteins: versatile players in RNA processing

Cited by 5 publications

References 95 publications

Regulation of plant resistance to salt stress by the SnRK1‐dependent splicing factor SRRM1L

Regulation of plant resistance to salt stress by the SnRK1‐dependent splicing factor SRRM1L

AFC kinases function as thermosensors that regulate warm temperature-responsive growth inArabidopsis

Importance of pre-mRNA splicing and its study tools in plants

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