SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23

Segovia, Danilo, Adams, Dexter W, Hoffman, Nickolas, Safaric Tepes, Polona, Wee, Tse-Luen, Cifani, Paolo, Joshua-Tor, Leemor, Krainer, Adrian R (May 2024) SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23. Proceedings of the National Academy of Sciences of the United States of America, 121 (21). e2322974121. ISSN 0027-8424 (Public Dataset)

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URL: https://www.ncbi.nlm.nih.gov/pubmed/38743621
DOI: 10.1073/pnas.2322974121

Abstract

SRSF1 is the founding member of the SR protein family. It is required-interchangeably with other SR proteins-for pre-mRNA splicing in vitro, and it regulates various alternative splicing events. Dysregulation of SRSF1 expression contributes to cancer and other pathologies. Here, we characterized SRSF1's interactome using proximity labeling and mass spectrometry. This approach yielded 190 proteins enriched in the SRSF1 samples, independently of the N- or C-terminal location of the biotin-labeling domain. The detected proteins reflect established functions of SRSF1 in pre-mRNA splicing and reveal additional connections to spliceosome proteins, in addition to other recently identified functions. We validated a robust interaction with the spliceosomal RNA helicase DDX23/PRP28 using bimolecular fluorescence complementation and in vitro binding assays. The interaction is mediated by the N-terminal RS-like domain of DDX23 and both RRM1 and the RS domain of SRSF1. During pre-mRNA splicing, DDX23's ATPase activity is essential for the pre-B to B spliceosome complex transition and for release of U1 snRNP from the 5' splice site. We show that the RS-like region of DDX23's N-terminal domain is important for spliceosome incorporation, while larger deletions in this domain alter subnuclear localization. We discuss how the identified interaction of DDX23 with SRSF1 and other SR proteins may be involved in the regulation of these processes.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification
organism description > animal
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > enzymes
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > enzymes > helicase
organism description > animal > mammal > primates > hominids
organism description > animal > mammal > primates > hominids > human
organism description > animal > mammal
organism description > animal > mammal > primates
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > RNA splicing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > spliceosome complex
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > splicing factor
CSHL Authors:
Communities: CSHL Cancer Center Program > Cellular Communication in Cancer Program
CSHL Cancer Center Program > Gene Regulation and Inheritance Program
CSHL labs > Joshua-Tor lab
CSHL labs > Krainer lab
CSHL labs > Sordella lab
CSHL labs > Spector lab
CSHL Cancer Center Program
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 21 May 2024
Date Deposited: 20 May 2024 13:35
Last Modified: 20 May 2024 13:35
Related URLs:
Dataset ID:
  • 10.6019/PXD048180
URI: https://repository.cshl.edu/id/eprint/41553

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