1
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Bai R, Yuan M, Zhang P, Luo T, Shi Y, Wan R. Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome. Science 2024; 383:1245-1252. [PMID: 38484052 DOI: 10.1126/science.adn7272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 02/09/2024] [Indexed: 03/19/2024]
Abstract
The minor spliceosome, which is responsible for the splicing of U12-type introns, comprises five small nuclear RNAs (snRNAs), of which only one is shared with the major spliceosome. In this work, we report the 3.3-angstrom cryo-electron microscopy structure of the fully assembled human minor spliceosome pre-B complex. The atomic model includes U11 small nuclear ribonucleoprotein (snRNP), U12 snRNP, and U4atac/U6atac.U5 tri-snRNP. U11 snRNA is recognized by five U11-specific proteins (20K, 25K, 35K, 48K, and 59K) and the heptameric Sm ring. The 3' half of the 5'-splice site forms a duplex with U11 snRNA; the 5' half is recognized by U11-35K, U11-48K, and U11 snRNA. Two proteins, CENATAC and DIM2/TXNL4B, specifically associate with the minor tri-snRNP. A structural analysis uncovered how two conformationally similar tri-snRNPs are differentiated by the minor and major prespliceosomes for assembly.
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Affiliation(s)
- Rui Bai
- Research Center for Industries of the Future, Key Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Meng Yuan
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pu Zhang
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ting Luo
- Research Center for Industries of the Future, Key Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Yigong Shi
- Research Center for Industries of the Future, Key Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ruixue Wan
- Research Center for Industries of the Future, Key Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China
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2
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Wang Z, Xu X, Li X, Fang J, Huang Z, Zhang M, Liu J, Qiu X. Investigations of Single-Subunit tRNA Methyltransferases from Yeast. J Fungi (Basel) 2023; 9:1030. [PMID: 37888286 PMCID: PMC10608323 DOI: 10.3390/jof9101030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
tRNA methylations, including base modification and 2'-O-methylation of ribose moiety, play critical roles in the structural stabilization of tRNAs and the fidelity and efficiency of protein translation. These modifications are catalyzed by tRNA methyltransferases (TRMs). Some of the TRMs from yeast can fully function only by a single subunit. In this study, after performing the primary bioinformatic analyses, the progress of the studies of yeast single-subunit TRMs, as well as the studies of their homologues from yeast and other types of eukaryotes and the corresponding TRMs from other types of organisms was systematically reviewed, which will facilitate the understanding of the evolutionary origin of functional diversity of eukaryotic single-subunit TRM.
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Affiliation(s)
- Zhongyuan Wang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xiangbin Xu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xinhai Li
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Jiaqi Fang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Zhenkuai Huang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Mengli Zhang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Jiameng Liu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xiaoting Qiu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
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3
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Ding Z, Meng YR, Fan YJ, Xu YZ. Roles of minor spliceosome in intron recognition and the convergence with the better understood major spliceosome. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1761. [PMID: 36056453 DOI: 10.1002/wrna.1761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/06/2022] [Accepted: 08/06/2022] [Indexed: 01/31/2023]
Abstract
Catalyzed by spliceosomes in the nucleus, RNA splicing removes intronic sequences from precursor RNAs in eukaryotes to generate mature RNA, which also significantly increases proteome complexity and fine-tunes gene expression. Most metazoans have two coexisting spliceosomes; the major spliceosome, which removes >99.5% of introns, and the minor spliceosome, which removes far fewer introns (only 770 at present have been predicted in the human genome). Both spliceosomes are large and dynamic machineries, each consisting of five small nuclear RNAs (snRNAs) and more than 100 proteins. However, the dynamic assembly, catalysis, and protein composition of the minor spliceosome are still poorly understood. With different splicing signals, minor introns are rare and usually distributed alone and flanked by major introns in genes, raising questions of how they are recognized by the minor spliceosome and how their processing deals with the splicing of neighboring major introns. Due to large numbers of introns and close similarities between the two machinery, cooperative, and competitive recognition by the two spliceosomes has been investigated. Functionally, many minor-intron-containing genes are evolutionarily conserved and essential. Mutations in the minor spliceosome exhibit a variety of developmental defects in plants and animals and are linked to numerous human diseases. Here, we review recent progress in the understanding of minor splicing, compare currently known components of the two spliceosomes, survey minor introns in a wide range of organisms, discuss cooperation and competition of the two spliceosomes in splicing of minor-intron-containing genes, and contributions of minor splicing mutations in development and diseases. This article is categorized under: RNA Processing > Processing of Small RNAs RNA Processing > Splicing Mechanisms RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
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Affiliation(s)
- Zhan Ding
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan-Ran Meng
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
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4
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Gao C, Lu S, Zhou R, Ding J, Fan J, Han B, Chen M, Wang B, Cao Y. Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family. BMC Genomics 2022; 23:744. [DOI: 10.1186/s12864-022-08956-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Alternative splicing (AS) is an important channel for gene expression regulation and protein diversification, in addition to a major reason for the considerable differences in the number of genes and proteins in eukaryotes. In plants, U2 small nuclear ribonucleoprotein B″ (U2B″), a component of splicing complex U2 snRNP, plays an important role in AS. Currently, few studies have investigated plant U2B″, and its mechanism remains unclear.
Result
Phylogenetic analysis, including gene and protein structures, revealed that U2B″ is highly conserved in plants and typically contains two RNA recognition motifs. Subcellular localisation showed that OsU2B″ is located in the nucleus and cytoplasm, indicating that it has broad functions throughout the cell. Elemental analysis of the promoter region showed that it responded to numerous external stimuli, including hormones, stress, and light. Subsequent qPCR experiments examining response to stress (cold, salt, drought, and heavy metal cadmium) corroborated the findings. The prediction results of protein–protein interactions showed that its function is largely through a single pathway, mainly through interaction with snRNP proteins.
Conclusion
U2B″ is highly conserved in the plant kingdom, functions in the nucleus and cytoplasm, and participates in a wide range of processes in plant growth and development.
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5
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Ipsaro JJ, Joshua‐Tor L. Developmental roles and molecular mechanisms of Asterix/GTSF1. WIRES RNA 2022; 13:e1716. [PMID: 35108755 PMCID: PMC9539491 DOI: 10.1002/wrna.1716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023]
Abstract
Maintenance of germline genomic integrity is critical for the survival of animal species. Consequently, many cellular and molecular processes have evolved to ensure genetic stability during the production of gametes. Here, we describe the discovery, characterization, and emerging molecular mechanisms of the protein Asterix/Gametocyte‐specific factor 1 (GTSF1), an essential gametogenesis factor that is conserved from insects to humans. Beyond its broad importance for healthy germline development, Asterix/GTSF1 has more specific functions in the Piwi‐interacting RNA (piRNA)–RNA interference pathway. There, it contributes to the repression of otherwise deleterious transposons, helping to ensure faithful transmission of genetic information to the next generation. This article is categorized under:Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > RNA‐Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein‐RNA Interactions: Functional Implications
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Affiliation(s)
- Jonathan J. Ipsaro
- Howard Hughes Medical Institute W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory Cold Spring Harbor New York USA
| | - Leemor Joshua‐Tor
- Howard Hughes Medical Institute W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory Cold Spring Harbor New York USA
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6
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Li H, Dong H, Xu B, Xiong QP, Li CT, Yang WQ, Li J, Huang ZX, Zeng QY, Wang ED, Liu RJ. A dual role of human tRNA methyltransferase hTrmt13 in regulating translation and transcription. EMBO J 2021; 41:e108544. [PMID: 34850409 PMCID: PMC8922252 DOI: 10.15252/embj.2021108544] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 10/19/2021] [Accepted: 10/29/2021] [Indexed: 12/15/2022] Open
Abstract
Since numerous RNAs and RBPs prevalently localize to active chromatin regions, many RNA-binding proteins (RBPs) may be potential transcriptional regulators. RBPs are generally thought to regulate transcription via noncoding RNAs. Here, we describe a distinct, dual mechanism of transcriptional regulation by the previously uncharacterized tRNA-modifying enzyme, hTrmt13. On one hand, hTrmt13 acts in the cytoplasm to catalyze 2'-O-methylation of tRNAs, thus regulating translation in a manner depending on its tRNA-modification activity. On the other hand, nucleus-localized hTrmt13 directly binds DNA as a transcriptional co-activator of key epithelial-mesenchymal transition factors, thereby promoting cell migration independent of tRNA-modification activity. These dual functions of hTrmt13 are mutually exclusive, as it can bind either DNA or tRNA through its CHHC zinc finger domain. Finally, we find that hTrmt13 expression is tightly associated with poor prognosis and survival in diverse cancer patients. Our discovery of the noncatalytic roles of an RNA-modifying enzyme provides a new perspective for understanding epitranscriptomic regulation.
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Affiliation(s)
- Hao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Han Dong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qing-Ping Xiong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Cai-Tao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Wen-Qing Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jing Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhi-Xuan Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Qi-Yu Zeng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - En-Duo Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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7
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Lu S, Gao C, Wang Y, He Y, Du J, Chen M, Zhao H, Fang H, Wang B, Cao Y. Phylogenetic Analysis of the Plant U2 snRNP Auxiliary Factor Large Subunit A Gene Family in Response to Developmental Cues and Environmental Stimuli. FRONTIERS IN PLANT SCIENCE 2021; 12:739671. [PMID: 34868124 PMCID: PMC8635922 DOI: 10.3389/fpls.2021.739671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
In all organisms, splicing occurs through the formation of spliceosome complexes, and splicing auxiliary factors are essential during splicing. U2AF65 is a crucial splicing cofactor, and the two typical RNA-recognition motifs at its center recognize and bind the polypyrimidine sequence located between the intron branch site and the 3'-splice site. U2AF65A is a member of the U2AF65 gene family, with pivotal roles in diseases in mammals, specifically humans; however, few studies have investigated plant U2AF65A, and its specific functions are poorly understood. Therefore, in the present study, we systematically identified U2AF65A in plant species from algae to angiosperms. Based on 113 putative U2AF65A sequences from 33 plant species, phylogenetic analyses were performed, followed by basic bioinformatics, including the comparisons of gene structure, protein domains, promoter motifs, and gene expression levels. In addition, using rice as the model crop, we demonstrated that the OsU2AF65A protein is localized to the nucleus and cytoplasm, and it is involved in responses to various stresses, such as drought, high salinity, low temperature, and heavy metal exposure (e.g., cadmium). Using Arabidopsis thaliana and rice mutants, we demonstrated that U2AF65A is involved in the accumulation of plant biomass, growth of hypocotyl upon thermal stimulation, and reduction of tolerance of high temperature stress. These findings offer an overview of the U2AF65 gene family and its stress response functions, serving as the reference for further comprehensive functional studies of the essential specific splicing cofactor U2AF65A in the plant kingdom.
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Affiliation(s)
- Shuai Lu
- School of Life Sciences, Nantong University, Nantong, China
| | - Cong Gao
- School of Life Sciences, Nantong University, Nantong, China
| | - Yongzhou Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Yingying He
- School of Life Sciences, Nantong University, Nantong, China
| | - Junrong Du
- School of Life Sciences, Nantong University, Nantong, China
| | - Moxian Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hua Zhao
- School of Life Sciences, Nantong University, Nantong, China
| | - Hui Fang
- School of Life Sciences, Nantong University, Nantong, China
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Yunying Cao
- School of Life Sciences, Nantong University, Nantong, China
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8
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Ipsaro JJ, O'Brien PA, Bhattacharya S, Palmer AG, Joshua-Tor L. Asterix/Gtsf1 links tRNAs and piRNA silencing of retrotransposons. Cell Rep 2021; 34:108914. [PMID: 33789107 DOI: 10.1016/j.celrep.2021.108914] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/15/2021] [Accepted: 03/05/2021] [Indexed: 02/05/2023] Open
Abstract
The Piwi-interacting RNA (piRNA) pathway safeguards genomic integrity by silencing transposable elements (transposons) in the germline. While Piwi is the central piRNA factor, others including Asterix/Gtsf1 have also been demonstrated to be critical for effective silencing. Here, using enhanced crosslinking and immunoprecipitation (eCLIP) with a custom informatic pipeline, we show that Asterix/Gtsf1 specifically binds tRNAs in cellular contexts. We determined the structure of mouse Gtsf1 by NMR spectroscopy and identified the RNA-binding interface on the protein's first zinc finger, which was corroborated by biochemical analysis as well as cryo-EM structures of Gtsf1 in complex with co-purifying tRNA. Consistent with the known dependence of long terminal repeat (LTR) retrotransposons on tRNA primers, we demonstrate that LTR retrotransposons are, in fact, preferentially de-repressed in Asterix mutants. Together, these findings link Asterix/Gtsf1, tRNAs, and LTR retrotransposon silencing and suggest that Asterix exploits tRNA dependence to identify transposon transcripts and promote piRNA silencing.
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Affiliation(s)
- Jonathan J Ipsaro
- Howard Hughes Medical Institute, W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Paul A O'Brien
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 650 West 168th Street, New York, NY 10032, USA
| | | | - Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 650 West 168th Street, New York, NY 10032, USA
| | - Leemor Joshua-Tor
- Howard Hughes Medical Institute, W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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9
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Almeida MV, Dietz S, Redl S, Karaulanov E, Hildebrandt A, Renz C, Ulrich HD, König J, Butter F, Ketting RF. GTSF-1 is required for formation of a functional RNA-dependent RNA Polymerase complex in Caenorhabditis elegans. EMBO J 2018; 37:embj.201899325. [PMID: 29769402 DOI: 10.15252/embj.201899325] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/22/2018] [Accepted: 03/24/2018] [Indexed: 11/09/2022] Open
Abstract
Argonaute proteins and their associated small RNAs (sRNAs) are evolutionarily conserved regulators of gene expression. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured C-terminal tail, are conserved in animals and have been shown to interact with Piwi clade Argonautes, thereby assisting their activity. We identified the Caenorhabditis elegans Gtsf1 homolog, named it gtsf-1 and characterized it in the context of the sRNA pathways of C. elegans We report that GTSF-1 is not required for Piwi-mediated gene silencing. Instead, gtsf-1 mutants show a striking depletion of 26G-RNAs, a class of endogenous sRNAs, fully phenocopying rrf-3 mutants. We show, both in vivo and in vitro, that GTSF-1 interacts with RRF-3 via its CHHC zinc fingers. Furthermore, we demonstrate that GTSF-1 is required for the assembly of a larger RRF-3 and DCR-1-containing complex (ERIC), thereby allowing for 26G-RNA generation. We propose that GTSF-1 homologs may act to drive the assembly of larger complexes that act in sRNA production and/or in imposing sRNA-mediated silencing activities.
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Affiliation(s)
| | - Sabrina Dietz
- Quantitative Proteomics Group, Institute of Molecular Biology, Mainz, Germany
| | - Stefan Redl
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
| | - Emil Karaulanov
- Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany
| | - Andrea Hildebrandt
- Genomic Views of Splicing Regulation Group, Institute of Molecular Biology, Mainz, Germany
| | - Christian Renz
- Maintenance of Genome Stability Group, Institute of Molecular Biology, Mainz, Germany
| | - Helle D Ulrich
- Maintenance of Genome Stability Group, Institute of Molecular Biology, Mainz, Germany
| | - Julian König
- Genomic Views of Splicing Regulation Group, Institute of Molecular Biology, Mainz, Germany
| | - Falk Butter
- Quantitative Proteomics Group, Institute of Molecular Biology, Mainz, Germany
| | - René F Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
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10
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Norppa AJ, Kauppala TM, Heikkinen HA, Verma B, Iwaï H, Frilander MJ. Mutations in the U11/U12-65K protein associated with isolated growth hormone deficiency lead to structural destabilization and impaired binding of U12 snRNA. RNA (NEW YORK, N.Y.) 2018; 24:396-409. [PMID: 29255062 PMCID: PMC5824358 DOI: 10.1261/rna.062844.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/12/2017] [Indexed: 05/09/2023]
Abstract
Mutations in the components of the minor spliceosome underlie several human diseases. A subset of patients with isolated growth hormone deficiency (IGHD) harbors mutations in the RNPC3 gene, which encodes the minor spliceosome-specific U11/U12-65K protein. Although a previous study showed that IGHD patient cells have defects in U12-type intron recognition, the biochemical effects of these mutations on the 65K protein have not been characterized. Here, we show that a proline-to-threonine missense mutation (P474T) and a nonsense mutation (R502X) in the C-terminal RNA recognition motif (C-RRM) of the 65K protein impair the binding of 65K to U12 and U6atac snRNAs. We further show that the nonsense allele is targeted to the nonsense-mediated decay (NMD) pathway, but in an isoform-specific manner, with the nuclear-retained 65K long-3'UTR isoform escaping the NMD pathway. In contrast, the missense P474T mutation leads, in addition to the RNA-binding defect, to a partial defect in the folding of the C-RRM and reduced stability of the full-length protein, thus reducing the formation of U11/U12 di-snRNP complexes. We propose that both the C-RRM folding defect and NMD-mediated decrease in the levels of the U11/U12-65K protein reduce formation of the U12-type intron recognition complex and missplicing of a subset of minor introns leading to pituitary hypoplasia and a subsequent defect in growth hormone secretion.
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Affiliation(s)
- Antto J Norppa
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Tuuli M Kauppala
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Harri A Heikkinen
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Bhupendra Verma
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Hideo Iwaï
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Mikko J Frilander
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
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Jutzi D, Akinyi MV, Mechtersheimer J, Frilander MJ, Ruepp MD. The emerging role of minor intron splicing in neurological disorders. Cell Stress 2018; 2:40-54. [PMID: 31225466 PMCID: PMC6558932 DOI: 10.15698/cst2018.03.126] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pre-mRNA splicing is an essential step in eukaryotic gene expression. Mutations in cis-acting sequence elements within pre-mRNA molecules or trans-acting factors involved in pre-mRNA processing have both been linked to splicing dysfunction that give rise to a large number of human diseases. These mutations typically affect the major splicing pathway, which excises more than 99% of all introns in humans. However, approximately 700-800 human introns feature divergent intron consensus sequences at their 5' and 3' ends and are recognized by a separate pre-mRNA processing machinery denoted as the minor spliceosome. This spliceosome has been studied less than its major counterpart, but has received increasing attention during the last few years as a novel pathomechanistic player on the stage in neurodevelopmental and neurodegenerative diseases. Here, we review the current knowledge on minor spliceosome function and discuss its potential pathomechanistic role and impact in neurodegeneration.
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Affiliation(s)
- Daniel Jutzi
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Maureen V Akinyi
- Institute of Biotechnology, University of Helsinki, FI-00014, Finland
| | - Jonas Mechtersheimer
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Mikko J Frilander
- Institute of Biotechnology, University of Helsinki, FI-00014, Finland
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 9NU London, UK
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Verbeeren J, Verma B, Niemelä EH, Yap K, Makeyev EV, Frilander MJ. Alternative exon definition events control the choice between nuclear retention and cytoplasmic export of U11/U12-65K mRNA. PLoS Genet 2017; 13:e1006824. [PMID: 28549066 PMCID: PMC5473595 DOI: 10.1371/journal.pgen.1006824] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 06/16/2017] [Accepted: 05/16/2017] [Indexed: 12/20/2022] Open
Abstract
Cellular homeostasis of the minor spliceosome is regulated by a negative feed-back loop that targets U11-48K and U11/U12-65K mRNAs encoding essential components of the U12-type intron-specific U11/U12 di-snRNP. This involves interaction of the U11 snRNP with an evolutionarily conserved splicing enhancer giving rise to unproductive mRNA isoforms. In the case of U11/U12-65K, this mechanism controls the length of the 3′ untranslated region (3′UTR). We show that this process is dynamically regulated in developing neurons and some other cell types, and involves a binary switch between translation-competent mRNAs with a short 3′UTR to non-productive isoforms with a long 3′UTR that are retained in the nucleus or/and spliced to the downstream amylase locus. Importantly, the choice between these alternatives is determined by alternative terminal exon definition events regulated by conserved U12- and U2-type 5′ splice sites as well as sequence signals used for pre-mRNA cleavage and polyadenylation. We additionally show that U11 snRNP binding to the U11/U12-65K mRNA species with a long 3′UTR is required for their nuclear retention. Together, our studies uncover an intricate molecular circuitry regulating the abundance of a key spliceosomal protein and shed new light on the mechanisms limiting the export of non-productively spliced mRNAs from the nucleus to the cytoplasm. The cellular homeostasis of many components of the eukaryotic RNA processing machinery is regulated via negative feed-back pathways that result in the formation of both productive and non-productive mRNA species. Typically, the formation of non-productive mRNAs species results from changes in alternative splicing that disrupt the reading frame of the protein coding region and leads to destabilization of the mRNA. Here, we have investigated the homeostasis regulation of the U11/U12-65K mRNA that encodes an essential protein component of the minor (U12-dependent) spliceosome intron recognition complex. We show that homeostasis is regulated at the level of nuclear mRNA export and mRNA 3′-end formation, and that it can be further regulated during neuronal differentiation. We describe a multilayered regulatory system utilizing alternative exon definition interactions that use the input from both spliceosomes and the polyadenylation machinery to decide between productive and non-productive mRNA formation. Because the 65K protein is an essential component of the minor spliceosome, this regulatory pathway can potentially affect the expression of ~700 genes containing U12-type introns.
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Affiliation(s)
- Jens Verbeeren
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Bhupendra Verma
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Elina H. Niemelä
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Karen Yap
- Centre for Developmental Neurobiology, King’s College London, London, United Kingdom
| | - Eugene V. Makeyev
- Centre for Developmental Neurobiology, King’s College London, London, United Kingdom
| | - Mikko J. Frilander
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
- * E-mail:
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Huntriss J, Lu J, Hemmings K, Bayne R, Anderson R, Rutherford A, Balen A, Elder K, Picton HM. Isolation and expression of the human gametocyte-specific factor 1 gene (GTSF1) in fetal ovary, oocytes, and preimplantation embryos. J Assist Reprod Genet 2016; 34:23-31. [PMID: 27646122 PMCID: PMC5330970 DOI: 10.1007/s10815-016-0795-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/16/2016] [Indexed: 01/23/2023] Open
Abstract
Purpose Gametocyte-specific factor 1 has been shown in other species to be required for the silencing of retrotransposons via the Piwi-interacting RNA (piRNA) pathway. In this study, we aimed to isolate and assess expression of transcripts of the gametocyte-specific factor 1 (GTSF1) gene in the human female germline and in preimplantation embryos. Methods Complementary DNA (cDNA) libraries from human fetal ovaries and testes, human oocytes and preimplantation embryos and ovarian follicles isolated from an adult ovarian cortex biopsy were used to as templates for PCR, cloning and sequencing, and real time PCR experiments of GTSF1 expression. Results GTSF1 cDNA clones that covered the entire coding region were isolated from human oocytes and preimplantation embryos. GTSF1 mRNA expression was detected in archived cDNAs from staged human ovarian follicles, germinal vesicle (GV) stage oocytes, metaphase II oocytes, and morula and blastocyst stage preimplantation embryos. Within the adult female germline, expression was highest in GV oocytes. GTSF1 mRNA expression was also assessed in human fetal ovary and was observed to increase during gestation, from 8 to 21 weeks, during which time oogonia enter meiosis and primordial follicle formation first occurs. In human fetal testis, GTSF1 expression also increased from 8 to 19 weeks. Conclusions To our knowledge, this report is the first to describe the expression of the human GTSF1 gene in human gametes and preimplantation embryos. Electronic supplementary material The online version of this article (doi:10.1007/s10815-016-0795-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John Huntriss
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK.
| | - Jianping Lu
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK
| | - Karen Hemmings
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK
| | - Rosemary Bayne
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, Edinburgh, EH16 4TJ, UK
| | - Richard Anderson
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, Edinburgh, EH16 4TJ, UK
| | - Anthony Rutherford
- Leeds Centre for Reproductive Medicine, Leeds Teaching Hospital NHS Trust, Seacroft Hospital, York Road, Leeds, LS14 6UH, UK
| | - Adam Balen
- Leeds Centre for Reproductive Medicine, Leeds Teaching Hospital NHS Trust, Seacroft Hospital, York Road, Leeds, LS14 6UH, UK
| | - Kay Elder
- Bourn Hall Clinic, Cambridge, CB23 2TN, UK
| | - Helen M Picton
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK
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Xu T, Kim BM, Kwak KJ, Jung HJ, Kang H. The Arabidopsis homolog of human minor spliceosomal protein U11-48K plays a crucial role in U12 intron splicing and plant development. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3397-406. [PMID: 27091878 PMCID: PMC4892727 DOI: 10.1093/jxb/erw158] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The minor U12 introns are removed from precursor mRNAs by the U12 intron-specific minor spliceosome. Among the seven ribonucleoproteins unique to the minor spliceosome, denoted as U11/U12-20K, U11/U12-25K, U11/U12-31K, U11/U12-65K, U11-35K, U11-48K, and U11-59K, the roles of only U11/U12-31K and U11/U12-65K have been demonstrated in U12 intron splicing and plant development. Here, the functional role of the Arabidopsis homolog of human U11-48K in U12 intron splicing and the development of Arabidopsis thaliana was examined using transgenic knockdown plants. The u11-48k mutants exhibited several defects in growth and development, such as severely arrested primary inflorescence stems, formation of serrated leaves, production of many rosette leaves after bolting, and delayed senescence. The splicing of most U12 introns analyzed was impaired in the u11-48k mutants. Comparative analysis of the splicing defects and phenotypes among the u11/u12-31k, u11-48k, and u11/12-65k mutants showed that the severity of abnormal development was closely correlated with the degree of impairment in U12 intron splicing. Taken together, these results provide compelling evidence that the Arabidopsis homolog of human U11-48K protein, as well as U11/U12-31K and U11/U12-65K proteins, is necessary for correct splicing of U12 introns and normal plant growth and development.
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Affiliation(s)
- Tao Xu
- College of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, PR China
| | - Bo Mi Kim
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, South Korea
| | - Kyung Jin Kwak
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, South Korea
| | - Hyun Ju Jung
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, South Korea
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, South Korea
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15
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Jung HJ, Kang H. The Arabidopsis U11/U12-65K is an indispensible component of minor spliceosome and plays a crucial role in U12 intron splicing and plant development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:799-810. [PMID: 24606192 DOI: 10.1111/tpj.12498] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 02/14/2014] [Accepted: 02/19/2014] [Indexed: 05/10/2023]
Abstract
The U12-dependent introns have been identified in a wide range of eukaryotes and are removed from precursor-mRNAs by U12 intron-specific minor spliceosome. Although several proteins unique to minor spliceosome have been identified, the nature of their effect on U12 intron splicing as well as plant growth and development remain largely unknown. Here, we characterized the functional role of an U12-type spliceosomal protein, U11/U12-65K in Arabidopsis thaliana. The transgenic knockdown plants generated by artificial miRNA-mediated silencing strategy exhibited severe defect in growth and development, such as severely arrested primary inflorescence stems, serrated leaves, and the formation of many rosette leaves after bolting. RNA sequencing and reverse transcription polymerase chain reaction (RT-PCR) analyses revealed that splicing of 198 out of the 234 previously predicted U12 intron-containing genes and 32 previously unidentified U12 introns was impaired in u11/u12-65k mutant. Moreover, the U11/U12-65K mutation affected alternative splicing, as well as U12 intron splicing, of many introns. Microarray analysis revealed that the genes involved in cell wall biogenesis and function, plant development, and metabolic processes are differentially expressed in the mutant plants. U11/U12-65K protein bound specifically to U12 small nuclear RNA (snRNA), which is necessary for branch-point site recognition. Taken together, these results provide clear evidence that U11/U12-65K is an indispensible component of minor spliceosome and involved in U12 intron splicing and alternative splicing of many introns, which is crucial for plant development.
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Affiliation(s)
- Hyun Ju Jung
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju, 500-757, South Korea
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16
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Minor class splicing shapes the zebrafish transcriptome during development. Proc Natl Acad Sci U S A 2014; 111:3062-7. [PMID: 24516132 DOI: 10.1073/pnas.1305536111] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Minor class or U12-type splicing is a highly conserved process required to remove a minute fraction of introns from human pre-mRNAs. Defects in this splicing pathway have recently been linked to human disease, including a severe developmental disorder encompassing brain and skeletal abnormalities known as Taybi-Linder syndrome or microcephalic osteodysplastic primordial dwarfism 1, and a hereditary intestinal polyposis condition, Peutz-Jeghers syndrome. Although a key mechanism for regulating gene expression, the impact of impaired U12-type splicing on the transcriptome is unknown. Here, we describe a unique zebrafish mutant, caliban (clbn), with arrested development of the digestive organs caused by an ethylnitrosourea-induced recessive lethal point mutation in the rnpc3 [RNA-binding region (RNP1, RRM) containing 3] gene. rnpc3 encodes the zebrafish ortholog of human RNPC3, also known as the U11/U12 di-snRNP 65-kDa protein, a unique component of the U12-type spliceosome. The biochemical impact of the mutation in clbn is the formation of aberrant U11- and U12-containing small nuclear ribonucleoproteins that impair the efficiency of U12-type splicing. Using RNA sequencing and microarrays, we show that multiple genes involved in various steps of mRNA processing, including transcription, splicing, and nuclear export are disrupted in clbn, either through intron retention or differential gene expression. Thus, clbn provides a useful and specific model of aberrant U12-type splicing in vivo. Analysis of its transcriptome reveals efficient mRNA processing as a critical process for the growth and proliferation of cells during vertebrate development.
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Turunen JJ, Niemelä EH, Verma B, Frilander MJ. The significant other: splicing by the minor spliceosome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 4:61-76. [PMID: 23074130 PMCID: PMC3584512 DOI: 10.1002/wrna.1141] [Citation(s) in RCA: 223] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The removal of non-coding sequences, introns, from the mRNA precursors is an essential step in eukaryotic gene expression. U12-type introns are a minor subgroup of introns, distinct from the major or U2-type introns. U12-type introns are present in most eukaryotes but only account for less than 0.5% of all introns in any given genome. They are processed by a specific U12-dependent spliceosome, which is similar to, but distinct from, the major spliceosome. U12-type introns are spliced somewhat less efficiently than the major introns, and it is believed that this limits the expression of the genes containing such introns. Recent findings on the role of U12-dependent splicing in development and human disease have shown that it can also affect multiple cellular processes not directly related to the functions of the host genes of U12-type introns. At the same time, advances in understanding the regulation and phylogenetic distribution of the minor spliceosome are starting to shed light on how the U12-type introns and the minor spliceosome may have evolved. © 2012 John Wiley & Sons, Ltd.
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Affiliation(s)
- Janne J Turunen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Sousounis K, Haney CE, Cao J, Sunchu B, Tsonis PA. Conservation of the three-dimensional structure in non-homologous or unrelated proteins. Hum Genomics 2012; 6:10. [PMID: 23244440 PMCID: PMC3500211 DOI: 10.1186/1479-7364-6-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 05/14/2012] [Indexed: 12/12/2022] Open
Abstract
In this review, we examine examples of conservation of protein structural motifs in unrelated or non-homologous proteins. For this, we have selected three DNA-binding motifs: the histone fold, the helix-turn-helix motif, and the zinc finger, as well as the globin-like fold. We show that indeed similar structures exist in unrelated proteins, strengthening the concept that three-dimensional conservation might be more important than the primary amino acid sequence.
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Abstract
Ribonucleoproteins (RNPs) play key roles in many cellular processes and often function as RNP enzymes. Similar to proteins, some of these RNPs exist and function as multimers, either homomeric or heteromeric. While in some cases the mechanistic function of multimerization is well understood, the functional consequences of multimerization of other RNPs remain enigmatic. In this review we will discuss the function and organization of small RNPs that exist as stable multimers, including RNPs catalyzing RNA chemical modifications, telomerase RNP, and RNPs involved in pre-mRNA splicing.
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Verbeeren J, Niemelä EH, Turunen JJ, Will CL, Ravantti JJ, Lührmann R, Frilander MJ. An ancient mechanism for splicing control: U11 snRNP as an activator of alternative splicing. Mol Cell 2010; 37:821-33. [PMID: 20347424 DOI: 10.1016/j.molcel.2010.02.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 11/03/2009] [Accepted: 12/23/2009] [Indexed: 12/15/2022]
Abstract
Alternative pre-mRNA splicing is typically regulated by specific protein factors that recognize unique sequence elements in pre-mRNA and affect, directly or indirectly, nearby splice site usage. We show that 5' splice site sequences (5'ss) of U12-type introns, when repeated in tandem, form a U11 snRNP-binding splicing enhancer, USSE. Binding of U11 to the USSE regulates alternative splicing of U2-type introns by activating an upstream 3'ss. The U12-type 5'ss-like sequences within the USSE have a regulatory role and do not function as splicing donors. USSEs, present both in animal and plant genes encoding the U11/U12 di-snRNP-specific 48K and 65K proteins, create sensitive switches that respond to intracellular levels of functional U11 snRNP and alter the stability of 48K and 65K mRNAs. We conclude that U11 functions not only in 5'ss recognition in constitutive splicing, but also as an activator of U2-dependent alternative splicing and as a regulator of the U12-dependent spliceosome.
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Affiliation(s)
- Jens Verbeeren
- Institute of Biotechnology, University of Helsinki, Helsinki FIN-00014, Finland
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Abstract
Over the last 25 years, we have learned that many structural classes of zinc-binding domains (zinc fingers, ZFs) exist and it has become clear that the molecular functions of these domains are by no means limited to the sequence-specific recognition of double-stranded DNA. For example, ZFs can act as protein recognition or RNA-binding modules, and some domains can exhibit more than one function. In this chapter we describe the progress that has been made in understanding the role of ZF domains as RNA-recognition modules, and we speculate about both the prevalence of such functions and the prospects for creating designer ZFs that target RNA.
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Affiliation(s)
- Josep Font
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
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