Regulating the regulators: Serine/arginine‐rich proteins under scrutiny

Risso, Guillermo; Pelisch, Federico; Quaglino, Ana; Pozzi, Berta; Srebrow, Anabella

doi:10.1002/iub.1075

Cited by 30 publications

(31 citation statements)

References 64 publications

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“…Last but not least, posttranslational modifications may also play a key role in ABA regulation of plant SR proteins. Indeed, aside from the well-established phosphorylation of RS domains to regulate protein-protein interactions and subcellular localization of SR proteins [100], several other modifications such as lysine acetylation, arginine methylation, ubiquitination or SUMO conjugation have been reported in animal systems to regulate SR protein degradation, stability and localization [101]. The regulation of SR gene expression is thus a decidedly complex affair involving multiple levels of control, and the mechanisms underlying ABA-regulated expression of plant SR/SR-like proteins, as well as their involvement in the ABA pathway, await further study.…”

Section: Discussionmentioning

confidence: 99%

Abscisic Acid (ABA) Regulation of Arabidopsis SR Protein Gene Expression

Cruz

Carvalho

Richardson

et al. 2014

IJMS

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Serine/arginine-rich (SR) proteins are major modulators of alternative splicing, a key generator of proteomic diversity and flexible means of regulating gene expression likely to be crucial in plant environmental responses. Indeed, mounting evidence implicates splicing factors in signal transduction of the abscisic acid (ABA) phytohormone, which plays pivotal roles in the response to various abiotic stresses. Using real-time RT-qPCR, we analyzed total steady-state transcript levels of the 18 SR and two SR-like genes from Arabidopsis thaliana in seedlings treated with ABA and in genetic backgrounds with altered expression of the ABA-biosynthesis ABA2 and the ABA-signaling ABI1 and ABI4 genes. We also searched for ABA-responsive cis elements in the upstream regions of the 20 genes. We found that members of the plant-specific SC35-Like (SCL) Arabidopsis SR protein subfamily are distinctively responsive to exogenous ABA, while the expression of seven SR and SR-related genes is affected by alterations in key components of the ABA pathway. Finally, despite pervasiveness of established ABA-responsive promoter elements in Arabidopsis SR and SR-like genes, their expression is likely governed by additional, yet unidentified cis-acting elements. Overall, this study pinpoints SR34, SR34b, SCL30a, SCL28, SCL33, RS40, SR45 and SR45a as promising candidates for involvement in ABA-mediated stress responses.

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Section: Discussionmentioning

confidence: 99%

Abscisic Acid (ABA) Regulation of Arabidopsis SR Protein Gene Expression

Cruz

Carvalho

Richardson

et al. 2014

IJMS

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“…In plants, SR proteins have been investigated for their function in splicing (Lopato et al, 1999a(Lopato et al, , 1999b. In animal systems, SR proteins, apart from their role in pre-mRNA splicing, function in diverse processes associated with RNA metabolism and gene regulation, including mRNA export, stability and translation, chromatin binding, transcription elongation, subcellular localization of transcripts, genome stability and formation of cellular RNA granules, and miRNA processing structures (stress granules and processing bodies) (Long and Caceres, 2009;Shepard and Hertel, 2009;Risso et al, 2012;Yoon et al, 2013). Whether plant SR proteins, like their animal counterparts, have wide-ranging roles in other aspects of RNA metabolism remains to be seen.…”

Section: Trans-acting Factorsmentioning

confidence: 99%

Complexity of the Alternative Splicing Landscape in Plants

et al. 2013

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Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.

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“…Recent studies support the role of SR proteins not only as splicing regulators, but also implicate these proteins in genome stability, chromatin binding, transcription elongation, mRNA stability, mRNA export, and translation (see review 23 ). The function of SR proteins is regulated by phosphorylation and de-phosphorylation.…”

mentioning

confidence: 99%

“…Indeed, SR proteins undergo acetylation, methylation, and also ubiquitinylation (Ub), as well as modification by the small Ubiquitin-like modifier (SUMO). 23 Ub conjugation to SR proteins was suggested to serve as regulatory signal, rather than to direct the protein for degradation.…”

mentioning

confidence: 99%

Two splicing factors carrying serine-arginine motifs, TSR1 and TSR1IP, regulate splicing, mRNA stability, and rRNA processing inTrypanosoma brucei

Gupta¹,

Chikne²,

Eliaz³

et al. 2014

RNA Biology

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In trypanosomes, mRNas are processed by trans-splicing; in this process, a common exon, the spliced leader, is added to all mRNas from a small RNa donor, the spliced leader RNa (sL RNa). however, little is known regarding how this process is regulated. In this study, we investigated the function of two serine-arginine-rich proteins, TsR1 and TsR1IP, implicated in trans-splicing in Trypanosoma brucei. Depletion of these factors by RNai suggested their role in both cisand trans-splicing. Microarray was used to examine the transcriptome of the silenced cells. The level of hundreds of mRNas was changed, suggesting that these proteins have a role in regulating only a subset of T. brucei mRNas. Massspectrometry analyses of complexes associated with these proteins suggest that these factors function in mRNa stability, translation, and rRNa processing. We further demonstrate changes in the stability of mRNa as a result of depletion of the two TsR proteins. In addition, rRNa defects were observed under the depletion of U2aF35, TsR1, and TsR1IP, but not sF1, suggesting involvement of sR proteins in rRNa processing. ©2014 Landes Bioscience. Do not distribute 716RNa Biology Volume 11 Issue 6 among the hundreds of proteins present in the RNA polymerase II transcription complex, and are often loaded co-transcriptionally and accompany the fully spliced mRNA to the cytoplasm. 19 Since splice site consensus sequences are not sufficient to direct assembly of the spliceosome, sequences present in exons or introns such as exonic and intronic splicing enhancers (ESE and ISE), or exonic and intronic splicing silencers (ESS or ISS), are used to bind factors that regulate spliceosome assembly. SR proteins stabilize interactions between the U1 snRNP at the 5′ splice site and U2AF65 at the 3′ splice site. SR proteins are also known to bind to ESE and antagonize the activity of hnRNP proteins recognizing ESS. 20 In metazoa such as C. elegans, several SR proteins are essential, but others are not. 21 In mouse, many SR proteins are essential for life. 22 SR proteins have other functions in addition to their role in splicing, such as nuclear export, non-sense-mediated decay, and translation. SR proteins affect translation directly and indirectly. SF2/ASF was shown to associate with polyribosomes and to enhance translation, probably via release of 4E-BP, a competitive inhibitor of cap-dependent translation. 17 Recent studies support the role of SR proteins not only as splicing regulators, but also implicate these proteins in genome stability, chromatin binding, transcription elongation, mRNA stability, mRNA export, and translation (see review 23 ).The function of SR proteins is regulated by phosphorylation and de-phosphorylation. The RS domain is extensively phosphorylated on serine residues and this modification controls the localization of the protein. Mammalian SR proteins become dephosphorylated during the course of pre-mRNA processing, and promote mRNP transit through the nuclear pore complex. 24 SR proteins associate with the exon-junct...

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Regulating the regulators: Serine/arginine‐rich proteins under scrutiny

Cited by 30 publications

References 64 publications

Abscisic Acid (ABA) Regulation of Arabidopsis SR Protein Gene Expression

Abscisic Acid (ABA) Regulation of Arabidopsis SR Protein Gene Expression

Complexity of the Alternative Splicing Landscape in Plants

Two splicing factors carrying serine-arginine motifs, TSR1 and TSR1IP, regulate splicing, mRNA stability, and rRNA processing inTrypanosoma brucei

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