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Ares M, Igel H, Katzman S, Donohue JP. Intron lariat spliceosomes convert lariats to true circles: implications for intron transposition. Genes Dev 2024; 38:322-335. [PMID: 38724209 PMCID: PMC11146597 DOI: 10.1101/gad.351764.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
Rare, full-length circular intron RNAs distinct from lariats have been reported in several species, but their biogenesis is not understood. We envisioned and tested a hypothesis for their formation using Saccharomyces cerevisiae, documenting full-length and novel processed circular RNAs from multiple introns. Evidence implicates a previously undescribed catalytic activity of the intron lariat spliceosome (ILS) in which the 3'-OH of the lariat tail (with optional trimming and adenylation by the nuclear 3' processing machinery) attacks the branch, joining the intron 3' end to the 5' splice site in a 3'-5' linked circle. Human U2 and U12 spliceosomes produce analogous full-length and processed circles. Postsplicing catalytic activity of the spliceosome may promote intron transposition during eukaryotic genome evolution.
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Affiliation(s)
- Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA;
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Sol Katzman
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - John P Donohue
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
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Ares M, Igel H, Katzman S, Donohue JP. Intron-lariat spliceosomes convert lariats to true circles: implications for intron transposition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586863. [PMID: 38585890 PMCID: PMC10996645 DOI: 10.1101/2024.03.26.586863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Rare, full length circular intron RNAs distinct from lariats have been reported in several species, but their biogenesis is not understood. We envision and test a hypothesis for their formation using Saccharomyces cerevisiae, documenting full length and novel processed circular RNAs from multiple introns. Evidence implicates a previously undescribed catalytic activity of the intron-lariat spliceosome (ILS) in which the 3'-OH of the lariat tail (with optional trimming and adenylation by the nuclear 3' processing machinery) attacks the branch, joining the intron 3' end to the 5' splice site in a 3'-5' linked circle. Human U2 and U12 spliceosomes produce analogous full length and processed circles. Post-splicing catalytic activity of the spliceosome may promote intron transposition during eukaryotic genome evolution.
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Affiliation(s)
- Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz
- Genomics Institute, Santa Cruz, CA 95064 USA
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz
| | - Sol Katzman
- Center for Molecular Biology of RNA, University of California, Santa Cruz
- Genomics Institute, Santa Cruz, CA 95064 USA
| | - John P. Donohue
- Center for Molecular Biology of RNA, University of California, Santa Cruz
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Tseng CK, Cheng SC. Arresting Spliceosome Intermediates at Various Stages of the Splicing Pathway. Methods Mol Biol 2023; 2666:193-211. [PMID: 37166667 DOI: 10.1007/978-1-0716-3191-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The spliceosome is a dynamic ribonucleoprotein particle and is assembled via sequential binding of five snRNAs and numerous protein factors. To understand the molecular mechanism of the splicing reaction, it is necessary to dissect the spliceosome pathway and isolate spliceosome intermediates in various stages of the pathway for biochemical and structural analysis. Here, we describe protocols for preparing intron-containing transcripts, cell-free splicing extracts, and in vitro splicing reactions, as well as procedures to arrest the spliceosome at different stages of the pathway for characterization of specific splicing complexes from the budding yeast Saccharomyces cerevisiae. Methods for arresting spliceosomes at specific stages include depletion with antibodies against factors required for specific steps of the pathway, use of extracts prepared from temperature-sensitive mutants, use of dominant negative mutants of DExD/H-box proteins, and use of mutant substrates.
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Affiliation(s)
- Chi-Kang Tseng
- Graduate Institute of Microbiology, National Taiwan University, College of Medicine, Taipei, Taiwan, Republic of China
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China.
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Mechanisms of germ cell survival and plasticity in Caenorhabditis elegans. Biochem Soc Trans 2022; 50:1517-1526. [PMID: 36196981 PMCID: PMC9704514 DOI: 10.1042/bst20220878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022]
Abstract
Animals constantly encounter environmental and physiological stressors that threaten survival and fertility. Somatic stress responses and germ cell arrest/repair mechanisms are employed to withstand such challenges. The Caenorhabditis elegans germline combats stress by initiating mitotic germ cell quiescence to preserve genome integrity, and by removing meiotic germ cells to prevent inheritance of damaged DNA or to tolerate lack of germline nutrient supply. Here, we review examples of germline recovery from distinct stressors - acute starvation and defective splicing - where quiescent mitotic germ cells resume proliferation to repopulate a germ line following apoptotic removal of meiotic germ cells. These protective mechanisms reveal the plastic nature of germline stem cells.
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Abstract
Splicing of the precursor messenger RNA, involving intron removal and exon ligation, is mediated by the spliceosome. Together with biochemical and genetic investigations of the past four decades, structural studies of the intact spliceosome at atomic resolution since 2015 have led to mechanistic delineation of RNA splicing with remarkable insights. The spliceosome is proven to be a protein-orchestrated metalloribozyme. Conserved elements of small nuclear RNA (snRNA) constitute the splicing active site with two catalytic metal ions and recognize three conserved intron elements through duplex formation, which are delivered into the splicing active site for branching and exon ligation. The protein components of the spliceosome stabilize the conformation of the snRNA, drive spliceosome remodeling, orchestrate the movement of the RNA elements, and facilitate the splicing reaction. The overall organization of the spliceosome and the configuration of the splicing active site are strictly conserved between human and yeast.
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Affiliation(s)
- Ruixue Wan
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China;,
| | - Rui Bai
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou 310024, China
| | - Xiechao Zhan
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China;,
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China;,
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou 310024, China
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6
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Toroney R, Nielsen KH, Staley JP. Termination of pre-mRNA splicing requires that the ATPase and RNA unwindase Prp43p acts on the catalytic snRNA U6. Genes Dev 2019; 33:1555-1574. [PMID: 31558568 PMCID: PMC6824469 DOI: 10.1101/gad.328294.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/03/2019] [Indexed: 11/25/2022]
Abstract
In this study, Toroney et al. set out to identify the mechanism of Prp43p action in splicing. The authors use biochemical approaches to demonstrate that the 3' end of U6 acts as the key substrate by which Prp43p promotes disassembly and intron release, thereby terminating splicing. The termination of pre-mRNA splicing functions to discard suboptimal substrates, thereby enhancing fidelity, and to release excised introns in a manner coupled to spliceosome disassembly, thereby allowing recycling. The mechanism of termination, including the RNA target of the DEAH-box ATPase Prp43p, remains ambiguous. We discovered a critical role for nucleotides at the 3′ end of the catalytic U6 small nuclear RNA in splicing termination. Although conserved sequence at the 3′ end is not required, 2′ hydroxyls are, paralleling requirements for Prp43p biochemical activities. Although the 3′ end of U6 is not required for recruiting Prp43p to the spliceosome, the 3′ end cross-links directly to Prp43p in an RNA-dependent manner. Our data indicate a mechanism of splicing termination in which Prp43p translocates along U6 from the 3′ end to disassemble the spliceosome and thereby release suboptimal substrates or excised introns. This mechanism reveals that the spliceosome becomes primed for termination at the same stage it becomes activated for catalysis, implying a requirement for stringent control of spliceosome activity within the cell.
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Affiliation(s)
- Rebecca Toroney
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637, USA
| | - Klaus H Nielsen
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637, USA
| | - Jonathan P Staley
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637, USA
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Chung CS, Tseng CK, Lai YH, Wang HF, Newman AJ, Cheng SC. Dynamic protein-RNA interactions in mediating splicing catalysis. Nucleic Acids Res 2019; 47:899-910. [PMID: 30395327 PMCID: PMC6344849 DOI: 10.1093/nar/gky1089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/19/2018] [Indexed: 11/16/2022] Open
Abstract
The spliceosome is assembled via sequential interactions of pre-mRNA with five small nuclear RNAs and many proteins. Recent determination of cryo-EM structures for several spliceosomal complexes has provided deep insights into interactions between spliceosomal components and structural changes of the spliceosome between steps, but information on how the proteins interact with pre-mRNA to mediate the reaction is scarce. By systematic analysis of proteins interacting with the splice sites (SSs), we have identified many previously unknown interactions of spliceosomal components with the pre-mRNA. Prp8 directly binds over the 5′SS and the branch site (BS) for the first catalytic step, and the 5′SS and 3′SS for the second step. Switching the Prp8 interaction from the BS to the 3′SS requires Slu7, which interacts dynamically with pre-mRNA first, and then interacts stably with the 3′-exon after Prp16-mediated spliceosome remodeling. Our results suggest that Prp8 plays a key role in positioning the 5′SS and 3′SS, facilitated by Slu7 through interactions with Prp8 and substrate RNA to advance exon ligation. We also provide evidence that Prp16 first docks on the intron 3′ tail, then translocates in the 3′ to 5′ direction on remodeling the spliceosome.
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Affiliation(s)
- Che-Sheng Chung
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Chi-Kang Tseng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Yung-Hua Lai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China.,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan 112, Republic of China
| | - Hui-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China.,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan 112, Republic of China
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
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Raut S, Yadav K, Verma AK, Tak Y, Waiker P, Sahi C. Co-evolution of spliceosomal disassembly interologs: crowning J-protein component with moonlighting RNA-binding activity. Curr Genet 2018; 65:561-573. [DOI: 10.1007/s00294-018-0906-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/30/2018] [Accepted: 11/14/2018] [Indexed: 11/28/2022]
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