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Silencing Defective 2 (SDE2), an essential human protein, plays important roles in mRNA splicing, DNA repair and ribosomal biogenesis. Cleavage of SDE2 downstream to its N-terminal ubiquitin-like domain (SDE2\n                    <jats:sub>UBL<\/jats:sub>\n                    ) releases the biologically functional C-terminal domain (SDE2\n                    <jats:sub>CT<\/jats:sub>\n                    ), highlighting the importance of this proteolytic event. However, the protease responsible for this cleavage in human cells has remained undefined. Here, we identify deubiquitinating enzyme, ubiquitin-specific protease 5 (USP5), as the\u00a0selectively primary effector of SDE2 cleavage both in vitro and in cell. Biophysical and structural analysis suggests that SDE2\n                    <jats:sub>UBL<\/jats:sub>\n                    engages with USP5 through a two-site interaction that mirrors key features of ubiquitin recognition, supporting a mechanism of substrate mimicry. Functionally, depletion of USP5 increases intron retention in previously reported SDE2-dependent transcripts, linking the removal of SDE2\n                    <jats:sub>UBL<\/jats:sub>\n                    domain by USP5 to the role of SDE2 in mRNA splicing. Together, these findings reveal a non-canonical proteolytic function of USP5, uncovering a previously unrecognised regulatory axis linking deubiquitinating enzymes to protein maturation, expanding the substrate repertoire for USP5 and providing a framework for identifying protease\u2013substrate relationships in post-translational regulation.\n                  <\/jats:p>","DOI":"10.1038\/s41467-026-76751-6","type":"journal-article","created":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T11:54:57Z","timestamp":1786708497000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["USP5 acts as a proteolytic switch to control SDE2 function via UBL-directed cleavage"],"prefix":"10.1038","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-7870-2671","authenticated-orcid":false,"given":"Liam T.","family":"Hales","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-8000-5341","authenticated-orcid":false,"given":"Paul M.","family":"Tammiste","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-3563-1809","authenticated-orcid":false,"given":"Adam J.","family":"Walker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca","family":"Bryce","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-2015-2737","authenticated-orcid":false,"given":"Andrew","family":"Sugden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Axel","family":"Knebel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1337-0612","authenticated-orcid":false,"given":"Rachel","family":"Toth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Lamoliatte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2211-6189","authenticated-orcid":false,"given":"Marian","family":"P\u00e9teri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7471-3685","authenticated-orcid":false,"given":"Oliwia","family":"Curry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1386-4719","authenticated-orcid":false,"given":"Glenn R.","family":"Masson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2640-6389","authenticated-orcid":false,"given":"Virginia","family":"De Cesare","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7887-7388","authenticated-orcid":false,"given":"Chiara","family":"Maniaci","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,14]]},"reference":[{"key":"76751_CR1","doi-asserted-by":"publisher","first-page":"e261","DOI":"10.1002\/mco2.261","volume":"4","author":"Q Zhong","year":"2023","unstructured":"Zhong, Q. et al. 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