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Anil AT, Pandian R, Mishra SK. Introns with branchpoint-distant 3' splice sites: Splicing mechanism and regulatory roles. Biophys Chem 2024; 314:107307. [PMID: 39173313 DOI: 10.1016/j.bpc.2024.107307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 07/26/2024] [Accepted: 08/07/2024] [Indexed: 08/24/2024]
Abstract
The two transesterification reactions of pre-mRNA splicing require highly complex yet well-controlled rearrangements of small nuclear RNAs and proteins (snRNP) in the spliceosome. The efficiency and accuracy of these reactions are critical for gene expression, as almost all human genes pass through pre-mRNA splicing. Key parameters that determine the splicing outcome are the length of the intron, the strengths of its splicing signals and gaps between them, and the presence of splicing controlling elements. In particular, the gap between the branchpoint (BP) and the 3' splice site (ss) of introns is a major determinant of the splicing efficiency. This distance falls within a small range across the introns of an organism. The constraints exist possibly because BP and 3'ss are recognized by BP-binding proteins, U2 snRNP and U2 accessory factors (U2AF) in a coordinated manner. Furthermore, varying distances between the two signals may also affect the second transesterification reaction since the intervening RNA needs to be accurately positioned within the complex RNP machinery. Splicing such pre-mRNAs requires cis-acting elements in the RNA and many trans-acting splicing regulators. Regulated pre-mRNA splicing with BP-distant 3'ss adds another layer of control to gene expression and promotes alternative splicing.
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Affiliation(s)
- Anupa T Anil
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306, Punjab, India
| | - Rakesh Pandian
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306, Punjab, India
| | - Shravan Kumar Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306, Punjab, India.
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2
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García Morato J, Gloeckner CJ, Kahle PJ. Proteomics elucidating physiological and pathological functions of TDP-43. Proteomics 2023; 23:e2200410. [PMID: 37671599 DOI: 10.1002/pmic.202200410] [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: 05/19/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
Trans-activation response DNA binding protein of 43 kDa (TDP-43) regulates a great variety of cellular processes in the nucleus and cytosol. In addition, a defined subset of neurodegenerative diseases is characterized by nuclear depletion of TDP-43 as well as cytosolic mislocalization and aggregation. To perform its diverse functions TDP-43 can associate with different ribonucleoprotein complexes. Combined with transcriptomics, MS interactome studies have unveiled associations between TDP-43 and the spliceosome machinery, polysomes and RNA granules. Moreover, the highly dynamic, low-valency interactions regulated by its low-complexity domain calls for innovative proximity labeling methodologies. In addition to protein partners, the analysis of post-translational modifications showed that they may play a role in the nucleocytoplasmic shuttling, RNA binding, liquid-liquid phase separation and protein aggregation of TDP-43. Here we review the various TDP-43 ribonucleoprotein complexes characterized so far, how they contribute to the diverse functions of TDP-43, and roles of post-translational modifications. Further understanding of the fluid dynamic properties of TDP-43 in ribonucleoprotein complexes, RNA granules, and self-assemblies will advance the understanding of RNA processing in cells and perhaps help to develop novel therapeutic approaches for TDPopathies.
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Affiliation(s)
- Jorge García Morato
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Christian Johannes Gloeckner
- Research Group Functional Neuroproteomics, German Center of Neurodegenerative Diseases, Tübingen, Germany
- Core Facility for Medical Bioanalytics, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Philipp J Kahle
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Department of Biochemistry, University of Tübingen, Tübingen, Germany
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3
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Street L, Rothamel K, Brannan K, Jin W, Bokor B, Dong K, Rhine K, Madrigal A, Al-Azzam N, Kim JK, Ma Y, Abdou A, Wolin E, Doron-Mandel E, Ahdout J, Mujumdar M, Jovanovic M, Yeo GW. Large-scale map of RNA binding protein interactomes across the mRNA life-cycle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544225. [PMID: 37333282 PMCID: PMC10274859 DOI: 10.1101/2023.06.08.544225] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Messenger RNAs (mRNAs) interact with RNA-binding proteins (RBPs) in diverse ribonucleoprotein complexes (RNPs) during distinct life-cycle stages for their processing and maturation. While substantial attention has focused on understanding RNA regulation by assigning proteins, particularly RBPs, to specific RNA substrates, there has been considerably less exploration leveraging protein-protein interaction (PPI) methodologies to identify and study the role of proteins in mRNA life-cycle stages. To address this gap, we generated an RNA-aware RBP-centric PPI map across the mRNA life-cycle by immunopurification (IP-MS) of ~100 endogenous RBPs across the life-cycle in the presence or absence of RNase, augmented by size exclusion chromatography (SEC-MS). Aside from confirming 8,700 known and discovering 20,359 novel interactions between 1125 proteins, we determined that 73% of our IP interactions are regulated by the presence of RNA. Our PPI data enables us to link proteins to life-cycle stage functions, highlighting that nearly half of the proteins participate in at least two distinct stages. We show that one of the most highly interconnected proteins, ERH, engages in multiple RNA processes, including via interactions with nuclear speckles and the mRNA export machinery. We also demonstrate that the spliceosomal protein SNRNP200 participates in distinct stress granule-associated RNPs and occupies different RNA target regions in the cytoplasm during stress. Our comprehensive RBP-focused PPI network is a novel resource for identifying multi-stage RBPs and exploring RBP complexes in RNA maturation.
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Affiliation(s)
- Lena Street
- These authors contributed equally
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Katherine Rothamel
- These authors contributed equally
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kristopher Brannan
- These authors contributed equally
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Bokor
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Kevin Dong
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kevin Rhine
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Assael Madrigal
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Norah Al-Azzam
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jenny Kim Kim
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Yanzhe Ma
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Ahmed Abdou
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Erica Wolin
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Ella Doron-Mandel
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Joshua Ahdout
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mayuresh Mujumdar
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
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4
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Jia J, Hilal T, Bohnsack KE, Chernev A, Tsao N, Bethmann J, Arumugam A, Parmely L, Holton N, Loll B, Mosammaparast N, Bohnsack MT, Urlaub H, Wahl MC. Extended DNA threading through a dual-engine motor module of the activating signal co-integrator 1 complex. Nat Commun 2023; 14:1886. [PMID: 37019967 PMCID: PMC10076317 DOI: 10.1038/s41467-023-37528-3] [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: 08/28/2022] [Accepted: 03/21/2023] [Indexed: 04/07/2023] Open
Abstract
Activating signal co-integrator 1 complex (ASCC) subunit 3 (ASCC3) supports diverse genome maintenance and gene expression processes, and contains tandem Ski2-like NTPase/helicase cassettes crucial for these functions. Presently, the molecular mechanisms underlying ASCC3 helicase activity and regulation remain unresolved. We present cryogenic electron microscopy, DNA-protein cross-linking/mass spectrometry as well as in vitro and cellular functional analyses of the ASCC3-TRIP4 sub-module of ASCC. Unlike the related spliceosomal SNRNP200 RNA helicase, ASCC3 can thread substrates through both helicase cassettes. TRIP4 docks on ASCC3 via a zinc finger domain and stimulates the helicase by positioning an ASC-1 homology domain next to the C-terminal helicase cassette of ASCC3, likely supporting substrate engagement and assisting the DNA exit. TRIP4 binds ASCC3 mutually exclusively with the DNA/RNA dealkylase, ALKBH3, directing ASCC3 for specific processes. Our findings define ASCC3-TRIP4 as a tunable motor module of ASCC that encompasses two cooperating NTPase/helicase units functionally expanded by TRIP4.
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Affiliation(s)
- Junqiao Jia
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195, Berlin, Germany
- Harvard Medical School, Department of Cell Biology, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Tarek Hilal
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195, Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy, Fabeckstr. 36a, D-14195, Berlin, Germany
| | - Katherine E Bohnsack
- Universitätsmedizin Göttingen, Department of Molecular Biology, Humboldallee 23, D-37073, Göttingen, Germany
| | - Aleksandar Chernev
- Max-Planck-Institut für Multidisziplinäre Naturwissenschaften, Bioanalytical Mass Spectrometry, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Ning Tsao
- Washington University School of Medicine, Department of Pathology & Immunology and Center for Genome Integrity, 660 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Juliane Bethmann
- Max-Planck-Institut für Multidisziplinäre Naturwissenschaften, Bioanalytical Mass Spectrometry, Am Fassberg 11, D-37077, Göttingen, Germany
- Universitätsmedizin Göttingen, Institut für Klinische Chemie, Bioanalytik, Robert-Koch-Straße 40, D-35075, Göttingen, Germany
| | - Aruna Arumugam
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195, Berlin, Germany
| | - Lane Parmely
- Washington University School of Medicine, Department of Pathology & Immunology and Center for Genome Integrity, 660 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Nicole Holton
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195, Berlin, Germany
| | - Bernhard Loll
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195, Berlin, Germany
| | - Nima Mosammaparast
- Washington University School of Medicine, Department of Pathology & Immunology and Center for Genome Integrity, 660 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Markus T Bohnsack
- Universitätsmedizin Göttingen, Department of Molecular Biology, Humboldallee 23, D-37073, Göttingen, Germany
- Georg-August-Universität, Göttingen Center for Molecular Biosciences, Justus-von-Liebig-Weg 11, D-37077, Göttingen, Germany
- Max-Planck-Institut für Multidisziplinäre Naturwissenschaften, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Henning Urlaub
- Max-Planck-Institut für Multidisziplinäre Naturwissenschaften, Bioanalytical Mass Spectrometry, Am Fassberg 11, D-37077, Göttingen, Germany
- Universitätsmedizin Göttingen, Institut für Klinische Chemie, Bioanalytik, Robert-Koch-Straße 40, D-35075, Göttingen, Germany
| | - Markus C Wahl
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195, Berlin, Germany.
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Str. 15, D-12489, Berlin, Germany.
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Dybkov O, Preußner M, El Ayoubi L, Feng VY, Harnisch C, Merz K, Leupold P, Yudichev P, Agafonov DE, Will CL, Girard C, Dienemann C, Urlaub H, Kastner B, Heyd F, Lührmann R. Regulation of 3' splice site selection after step 1 of splicing by spliceosomal C* proteins. SCIENCE ADVANCES 2023; 9:eadf1785. [PMID: 36867703 PMCID: PMC9984181 DOI: 10.1126/sciadv.adf1785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Alternative precursor messenger RNA splicing is instrumental in expanding the proteome of higher eukaryotes, and changes in 3' splice site (3'ss) usage contribute to human disease. We demonstrate by small interfering RNA-mediated knockdowns, followed by RNA sequencing, that many proteins first recruited to human C* spliceosomes, which catalyze step 2 of splicing, regulate alternative splicing, including the selection of alternatively spliced NAGNAG 3'ss. Cryo-electron microscopy and protein cross-linking reveal the molecular architecture of these proteins in C* spliceosomes, providing mechanistic and structural insights into how they influence 3'ss usage. They further elucidate the path of the 3' region of the intron, allowing a structure-based model for how the C* spliceosome potentially scans for the proximal 3'ss. By combining biochemical and structural approaches with genome-wide functional analyses, our studies reveal widespread regulation of alternative 3'ss usage after step 1 of splicing and the likely mechanisms whereby C* proteins influence NAGNAG 3'ss choices.
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Affiliation(s)
- Olexandr Dybkov
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Marco Preußner
- Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Leyla El Ayoubi
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Vivi-Yun Feng
- Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Caroline Harnisch
- Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Kilian Merz
- Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Paula Leupold
- Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Peter Yudichev
- Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Dmitry E. Agafonov
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Cindy L. Will
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Cyrille Girard
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Henning Urlaub
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
- Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, Göttingen D-37075, Germany
| | - Berthold Kastner
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Florian Heyd
- Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Reinhard Lührmann
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
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Anil AT, Choudhary K, Pandian R, Gupta P, Thakran P, Singh A, Sharma M, Mishra SK. Splicing of branchpoint-distant exons is promoted by Cactin, Tls1 and the ubiquitin-fold-activated Sde2. Nucleic Acids Res 2022; 50:10000-10014. [PMID: 36095128 PMCID: PMC9508853 DOI: 10.1093/nar/gkac769] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/22/2022] [Accepted: 08/27/2022] [Indexed: 11/13/2022] Open
Abstract
Intron diversity facilitates regulated gene expression and alternative splicing. Spliceosomes excise introns after recognizing their splicing signals: the 5'-splice site (5'ss), branchpoint (BP) and 3'-splice site (3'ss). The latter two signals are recognized by U2 small nuclear ribonucleoprotein (snRNP) and its accessory factors (U2AFs), but longer spacings between them result in weaker splicing. Here, we show that excision of introns with a BP-distant 3'ss (e.g. rap1 intron 2) requires the ubiquitin-fold-activated splicing regulator Sde2 in Schizosaccharomyces pombe. By monitoring splicing-specific ura4 reporters in a collection of S. pombe mutants, Cay1 and Tls1 were identified as additional regulators of this process. The role of Sde2, Cay1 and Tls1 was further confirmed by increasing BP-3'ss spacings in a canonical tho5 intron. We also examined BP-distant exons spliced independently of these factors and observed that RNA secondary structures possibly bridged the gap between the two signals. These proteins may guide the 3'ss towards the spliceosome's catalytic centre by folding the RNA between the BP and 3'ss. Orthologues of Sde2, Cay1 and Tls1, although missing in the intron-poor Saccharomyces cerevisiae, are present in intron-rich eukaryotes, including humans. This type of intron-specific pre-mRNA splicing appears to have evolved for regulated gene expression and alternative splicing of key heterochromatin factors.
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Affiliation(s)
- Anupa T Anil
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Karan Choudhary
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Rakesh Pandian
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Praver Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Poonam Thakran
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Arashdeep Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Shravan Kumar Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
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7
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Bergfort A, Hilal T, Kuropka B, Ilik İA, Weber G, Aktaş T, Freund C, Wahl MC. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2938-2958. [PMID: 35188580 PMCID: PMC8934646 DOI: 10.1093/nar/gkac087] [Citation(s) in RCA: 2] [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: 11/01/2021] [Revised: 01/21/2022] [Accepted: 01/26/2022] [Indexed: 11/16/2022] Open
Abstract
Biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and their recycling after splicing require numerous assembly/recycling factors whose modes of action are often poorly understood. The intrinsically disordered TSSC4 protein has been identified as a nuclear-localized U5 snRNP and U4/U6-U5 tri-snRNP assembly/recycling factor, but how TSSC4’s intrinsic disorder supports TSSC4 functions remains unknown. Using diverse interaction assays and cryogenic electron microscopy-based structural analysis, we show that TSSC4 employs four conserved, non-contiguous regions to bind the PRPF8 Jab1/MPN domain and the SNRNP200 helicase at functionally important sites. It thereby inhibits SNRNP200 helicase activity, spatially aligns the proteins, coordinates formation of a U5 sub-module and transiently blocks premature interaction of SNRNP200 with at least three other spliceosomal factors. Guided by the structure, we designed a TSSC4 variant that lacks stable binding to the PRPF8 Jab1/MPN domain or SNRNP200 in vitro. Comparative immunoprecipitation/mass spectrometry from HEK293 nuclear extract revealed distinct interaction profiles of wild type TSSC4 and the variant deficient in PRPF8/SNRNP200 binding with snRNP proteins, other spliceosomal proteins as well as snRNP assembly/recycling factors and chaperones. Our findings elucidate molecular strategies employed by an intrinsically disordered protein to promote snRNP assembly, and suggest multiple TSSC4-dependent stages during snRNP assembly/recycling.
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Affiliation(s)
- Alexandra Bergfort
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
| | - Tarek Hilal
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy, Fabeckstr. 36a, 14195 Berlin, Germany
| | - Benno Kuropka
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Thielallee 63, D-14195, Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Core Facility BioSupraMol, Thielallee 63, D-14195, Berlin, Germany
| | - İbrahim Avşar Ilik
- Max Planck Institute for Molecular Genetics, Ihnestr. 63, D-14195 Berlin, Germany
| | - Gert Weber
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Tuğçe Aktaş
- Max Planck Institute for Molecular Genetics, Ihnestr. 63, D-14195 Berlin, Germany
| | - Christian Freund
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Thielallee 63, D-14195, Berlin, Germany
| | - Markus C Wahl
- To whom correspondence should be addressed. Tel: +49 30 838 53456; Fax: +49 30 8384 53456;
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