PMID- 36542656 OWN - NLM STAT- MEDLINE DCOM- 20230109 LR - 20230727 IS - 1545-7885 (Electronic) IS - 1544-9173 (Print) IS - 1544-9173 (Linking) VI - 20 IP - 12 DP - 2022 Dec TI - Alternative splicing liberates a cryptic cytoplasmic isoform of mitochondrial MECR that antagonizes influenza virus. PG - e3001934 LID - 10.1371/journal.pbio.3001934 [doi] LID - e3001934 AB - Viruses must balance their reliance on host cell machinery for replication while avoiding host defense. Influenza A viruses are zoonotic agents that frequently switch hosts, causing localized outbreaks with the potential for larger pandemics. The host range of influenza virus is limited by the need for successful interactions between the virus and cellular partners. Here we used immunocompetitive capture-mass spectrometry to identify cellular proteins that interact with human- and avian-style viral polymerases. We focused on the proviral activity of heterogenous nuclear ribonuclear protein U-like 1 (hnRNP UL1) and the antiviral activity of mitochondrial enoyl CoA-reductase (MECR). MECR is localized to mitochondria where it functions in mitochondrial fatty acid synthesis (mtFAS). While a small fraction of the polymerase subunit PB2 localizes to the mitochondria, PB2 did not interact with full-length MECR. By contrast, a minor splice variant produces cytoplasmic MECR (cMECR). Ectopic expression of cMECR shows that it binds the viral polymerase and suppresses viral replication by blocking assembly of viral ribonucleoprotein complexes (RNPs). MECR ablation through genome editing or drug treatment is detrimental for cell health, creating a generic block to virus replication. Using the yeast homolog Etr1 to supply the metabolic functions of MECR in MECR-null cells, we showed that specific antiviral activity is independent of mtFAS and is reconstituted by expressing cMECR. Thus, we propose a strategy where alternative splicing produces a cryptic antiviral protein that is embedded within a key metabolic enzyme. CI - Copyright: (c) 2022 Baker et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. FAU - Baker, Steven F AU - Baker SF AUID- ORCID: 0000-0001-8379-283X AD - Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America. FAU - Meistermann, Helene AU - Meistermann H AD - Roche Pharma Research and Early Development, Pharmaceutical Sciences-Biomarkers, Bioinformatics and Omics & Pathology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland. FAU - Tzouros, Manuel AU - Tzouros M AD - Roche Pharma Research and Early Development, Pharmaceutical Sciences-Biomarkers, Bioinformatics and Omics & Pathology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland. FAU - Baker, Aaron AU - Baker A AUID- ORCID: 0000-0002-2815-9932 AD - Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America. AD - Morgridge Institute for Research, Madison, Wisconsin, United States of America. FAU - Golling, Sabrina AU - Golling S AD - Roche Pharma Research and Early Development, Pharmaceutical Sciences-Biomarkers, Bioinformatics and Omics & Pathology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland. FAU - Polster, Juliane Siebourg AU - Polster JS AD - Roche Pharma Research and Early Development, Pharmaceutical Sciences-Biomarkers, Bioinformatics and Omics & Pathology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland. FAU - Ledwith, Mitchell P AU - Ledwith MP AD - Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America. FAU - Gitter, Anthony AU - Gitter A AUID- ORCID: 0000-0002-5324-9833 AD - Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America. AD - Morgridge Institute for Research, Madison, Wisconsin, United States of America. AD - Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America. FAU - Augustin, Angelique AU - Augustin A AD - Roche Pharma Research and Early Development, Pharmaceutical Sciences-Biomarkers, Bioinformatics and Omics & Pathology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland. FAU - Javanbakht, Hassan AU - Javanbakht H AD - Roche Pharma Research and Early Development, Infectious Diseases, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland. FAU - Mehle, Andrew AU - Mehle A AUID- ORCID: 0000-0001-6060-4330 AD - Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America. LA - eng GR - R01 AI164690/AI/NIAID NIH HHS/United States GR - R21 AI125897/AI/NIAID NIH HHS/United States GR - T32 AI055397/AI/NIAID NIH HHS/United States GR - T32 LM012413/LM/NLM NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20221221 PL - United States TA - PLoS Biol JT - PLoS biology JID - 101183755 RN - EC 1.14.19.- (Fatty Acid Desaturases) RN - 0 (Protein Isoforms) SB - IM MH - Humans MH - *Fatty Acid Desaturases/metabolism MH - Alternative Splicing/genetics MH - Mitochondria/metabolism MH - *Influenza A virus/genetics MH - Protein Isoforms/metabolism MH - Virus Replication PMC - PMC9815647 COIS- I have read the journal's policy and the authors of this manuscript have the following competing interests: AM is an editorial board member for PLoS Biology and PLoS Pathogens. HM, MT, SG, JSP, AA and HJ were employees of F. Hoffmann-La Roche when performing this work. No other authors declare a competing interest. EDAT- 2022/12/22 06:00 MHDA- 2023/01/10 06:00 PMCR- 2022/12/21 CRDT- 2022/12/21 13:42 PHST- 2022/10/12 00:00 [received] PHST- 2022/11/29 00:00 [accepted] PHST- 2023/01/05 00:00 [revised] PHST- 2022/12/22 06:00 [pubmed] PHST- 2023/01/10 06:00 [medline] PHST- 2022/12/21 13:42 [entrez] PHST- 2022/12/21 00:00 [pmc-release] AID - PBIOLOGY-D-22-02267 [pii] AID - 10.1371/journal.pbio.3001934 [doi] PST - epublish SO - PLoS Biol. 2022 Dec 21;20(12):e3001934. doi: 10.1371/journal.pbio.3001934. eCollection 2022 Dec.