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Jia ZC, Das D, Zhang Y, Fernie AR, Liu YG, Chen M, Zhang J. Plant serine/arginine-rich proteins: versatile players in RNA processing. PLANTA 2023; 257:109. [PMID: 37145304 DOI: 10.1007/s00425-023-04132-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/05/2023] [Indexed: 05/06/2023]
Abstract
MAIN CONCLUSION Serine/arginine-rich (SR) proteins participate in RNA processing by interacting with precursor mRNAs or other splicing factors to maintain plant growth and stress responses. Alternative splicing is an important mechanism involved in mRNA processing and regulation of gene expression at the posttranscriptional level, which is the main reason for the diversity of genes and proteins. The process of alternative splicing requires the participation of many specific splicing factors. The SR protein family is a splicing factor in eukaryotes. The vast majority of SR proteins' existence is an essential survival factor. Through its RS domain and other unique domains, SR proteins can interact with specific sequences of precursor mRNA or other splicing factors and cooperate to complete the correct selection of splicing sites or promote the formation of spliceosomes. They play essential roles in the composition and alternative splicing of precursor mRNAs, providing pivotal functions to maintain growth and stress responses in animals and plants. Although SR proteins have been identified in plants for three decades, their evolutionary trajectory, molecular function, and regulatory network remain largely unknown compared to their animal counterparts. This article reviews the current understanding of this gene family in eukaryotes and proposes potential key research priorities for future functional studies.
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Affiliation(s)
- Zi-Chang Jia
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences and Technology, 52 Agricultural Building, University of Missouri, Columbia, MO, 65201, USA
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Youjun Zhang
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
- Max-Planck-Institut Für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
- Max-Planck-Institut Für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Moxian Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
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De Nova-Ocampo M, Soliman MC, Espinosa-Hernández W, Velez-Del Valle C, Salas-Benito J, Valdés-Flores J, García-Morales L. Human astroviruses: in silico analysis of the untranslated region and putative binding sites of cellular proteins. Mol Biol Rep 2018; 46:1413-1424. [PMID: 30448895 PMCID: PMC7089336 DOI: 10.1007/s11033-018-4498-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/12/2018] [Indexed: 12/21/2022]
Abstract
Human astrovirus (HAstV) constitutes a major cause of acute gastroenteritis in children. The viral 5' and 3' untranslated regions (UTR) have been involved in the regulation of several molecular mechanisms. However, in astrovirues have been less characterized. Here, we analyzed the secondary structures of the 5' and 3' UTR of HAstV, as well as their putative target sites that might be recognized by cellular factors. To our knowledge, this is the first bioinformatic analysis that predicts the HAstV 5' UTR secondary structure. The analysis showed that both the UTR sequence and secondary structure are highly conserved in all HAstVs analyzed, suggesting their regulatory role of viral activities. Notably, the UTRs of HAstVs contain putative binding sites for the serine/arginine-rich factors SRSF2, SRSF5, SRSF6, SRSF3, and the multifunctional hnRNPE2 protein. More importantly, putative binding sites for PTB were localized in single-stranded RNA sequences, while hnRNPE2 sites were localized in double-stranded sequence of the HAstV 5' and 3' UTR structures. These analyses suggest that the combination of SRSF proteins, hnRNPE2 and PTB described here could be involved in the maintenance of the secondary structure of the HAstVs, possibly allowing the recruitment of the replication complex that selects and recruits viral RNA replication templates.
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Affiliation(s)
- Mónica De Nova-Ocampo
- ENMH, Programa Institucional de Biomedicina Molecular, Instituto Politécnico Nacional, Guillermo Massieu Helguera No. 239 Col. Fracc. La Escalera-Ticomán, 07320, Ciudad de Mexico, Mexico.
| | - Mayra Cristina Soliman
- ENMH, Programa Institucional de Biomedicina Molecular, Instituto Politécnico Nacional, Guillermo Massieu Helguera No. 239 Col. Fracc. La Escalera-Ticomán, 07320, Ciudad de Mexico, Mexico
| | - Wendy Espinosa-Hernández
- ENMH, Programa Institucional de Biomedicina Molecular, Instituto Politécnico Nacional, Guillermo Massieu Helguera No. 239 Col. Fracc. La Escalera-Ticomán, 07320, Ciudad de Mexico, Mexico
| | - Cristina Velez-Del Valle
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, Avenida IPN 2508 Col. San Pedro Zacatenco, 07360, Ciudad de Mexico, Mexico
| | - Juan Salas-Benito
- ENMH, Programa Institucional de Biomedicina Molecular, Instituto Politécnico Nacional, Guillermo Massieu Helguera No. 239 Col. Fracc. La Escalera-Ticomán, 07320, Ciudad de Mexico, Mexico
| | - Jesús Valdés-Flores
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, Avenida IPN 2508 Col. San Pedro Zacatenco, 07360, Ciudad de Mexico, Mexico
| | - Lorena García-Morales
- ENMH, Programa Institucional de Biomedicina Molecular, Instituto Politécnico Nacional, Guillermo Massieu Helguera No. 239 Col. Fracc. La Escalera-Ticomán, 07320, Ciudad de Mexico, Mexico
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Expanding the SRI domain family: a common scaffold for binding the phosphorylated C-terminal domain of RNA polymerase II. FEBS Lett 2014; 588:4431-7. [PMID: 25448681 DOI: 10.1016/j.febslet.2014.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/07/2014] [Accepted: 10/12/2014] [Indexed: 11/21/2022]
Abstract
The SRI domain is a small three-helix domain originally discovered near the C-terminus of both histone methyltransferase SETD2 and helicase RECQL5. The SRI domain binds to the C-terminal repeat domain of the largest subunit of RNA polymerase II, allowing SETD2 and RECQL5 to regulate various mechanisms associated with RNA transcription. Using original tools to detect common patterns in distantly related sequences, we have identified SRI domains in several additional proteins, most of which are involved in RNA metabolism. Combining sequence analysis with structural prediction, we show that this domain family is more diverse than previously thought and we predict critical structural and functional features.
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de la Mata M, Muñoz MJ, Alló M, Fededa JP, Schor IE, Kornblihtt AR. RNA Polymerase II Elongation at the Crossroads of Transcription and Alternative Splicing. GENETICS RESEARCH INTERNATIONAL 2011; 2011:309865. [PMID: 22567350 PMCID: PMC3335476 DOI: 10.4061/2011/309865] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 06/23/2011] [Indexed: 11/20/2022]
Abstract
The elongation phase of transcription lies at the core of several simultaneous and coupled events leading to alternative splicing regulation. Although underestimated in the past, it is at this phase of the transcription cycle where complexes affecting the transcription machinery itself, chromatin structure, posttranscriptional gene regulation and pre-mRNA processing converge to regulate each other or simply to consolidate higher-order complexes and functions. This paper focuses on the multiple processes that take place during transcription elongation which ultimately regulate the outcome of alternative splicing decisions.
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Affiliation(s)
- Manuel de la Mata
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular, y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA Buenos Aires, Argentina
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Cross-talk in transcription, splicing and chromatin: who makes the first call? Biochem Soc Trans 2011; 38:1251-6. [PMID: 20863294 DOI: 10.1042/bst0381251] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The complex processes of mRNA transcription and splicing were traditionally studied in isolation. In vitro studies showed that splicing could occur independently of transcription and the perceived wisdom was that, to a large extent, it probably did. However, there is now abundant evidence for functional interactions between transcription and splicing, with important consequences for splicing regulation. In the present paper, we summarize the evidence that transcription affects splicing and vice versa, and the more recent indications of epigenetic effects on splicing, through chromatin modifications. We end by discussing the potential for a systems biology approach to obtain better insight into how these processes affect each other.
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Alexander RD, Innocente SA, Barrass JD, Beggs JD. Splicing-dependent RNA polymerase pausing in yeast. Mol Cell 2010; 40:582-93. [PMID: 21095588 PMCID: PMC3000496 DOI: 10.1016/j.molcel.2010.11.005] [Citation(s) in RCA: 201] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 07/20/2010] [Accepted: 09/29/2010] [Indexed: 11/19/2022]
Abstract
In eukaryotic cells, there is evidence for functional coupling between transcription and processing of pre-mRNAs. To better understand this coupling, we performed a high-resolution kinetic analysis of transcription and splicing in budding yeast. This revealed that shortly after induction of transcription, RNA polymerase accumulates transiently around the 3′ end of the intron on two reporter genes. This apparent transcriptional pause coincides with splicing factor recruitment and with the first detection of spliced mRNA and is repeated periodically thereafter. Pausing requires productive splicing, as it is lost upon mutation of the intron and restored by suppressing the splicing defect. The carboxy-terminal domain of the paused polymerase large subunit is hyperphosphorylated on serine 5, and phosphorylation of serine 2 is first detected here. Phosphorylated polymerase also accumulates around the 3′ splice sites of constitutively expressed, endogenous yeast genes. We propose that transcriptional pausing is imposed by a checkpoint associated with cotranscriptional splicing.
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Affiliation(s)
- Ross D. Alexander
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
- Edinburgh Centre for Systems Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
| | - Steven A. Innocente
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
- Edinburgh Centre for Systems Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
| | - J. David Barrass
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
- Edinburgh Centre for Systems Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
| | - Jean D. Beggs
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
- Edinburgh Centre for Systems Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
- Corresponding author
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Zhong XY, Wang P, Han J, Rosenfeld MG, Fu XD. SR proteins in vertical integration of gene expression from transcription to RNA processing to translation. Mol Cell 2009; 35:1-10. [PMID: 19595711 PMCID: PMC2744344 DOI: 10.1016/j.molcel.2009.06.016] [Citation(s) in RCA: 239] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Indexed: 12/25/2022]
Abstract
SR proteins have been studied extensively as a family of RNA-binding proteins that participate in both constitutive and regulated pre-mRNA splicing in mammalian cells. However, SR proteins were first discovered as factors that interact with transcriptionally active chromatin. Recent studies have now uncovered properties that connect these once apparently disparate functions, showing that a subset of SR proteins seem to bind directly to the histone 3 tail, play an active role in transcriptional elongation, and colocalize with genes that are engaged in specific intra- and interchromosome interactions for coordinated regulation of gene expression in the nucleus. These transcription-related activities are also coupled with a further expansion of putative functions of specific SR protein family members in RNA metabolism downstream of mRNA splicing, from RNA export to stability control to translation. These findings, therefore, highlight the broader roles of SR proteins in vertical integration of gene expression and provide mechanistic insights into their contributions to genome stability and proper cell-cycle progression in higher eukaryotic cells.
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Affiliation(s)
- Xiang-Yang Zhong
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651
| | - Pingping Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651
| | - Joonhee Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651
| | - Michael G. Rosenfeld
- Howard Hughes Medicine Institute, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651
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Abstract
The SR protein family comprises a number of phylogenetically conserved and structurally related proteins with a characteristic domain rich in arginine and serine residues, known as the RS domain. They play significant roles in constitutive pre-mRNA splicing and are also important regulators of alternative splicing. In addition they participate in post-splicing activities, such as mRNA nuclear export, nonsense-mediated mRNA decay and mRNA translation. These wide-ranging roles of SR proteins highlight their importance as pivotal regulators of mRNA metabolism, and if these functions are disrupted, developmental defects or disease may result. Furthermore, animal models have shown a highly specific, non-redundant role for individual SR proteins in the regulation of developmental processes. Here, we will review the current literature to demonstrate how SR proteins are emerging as one of the master regulators of gene expression.
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