UBB pseudogene 4 encodes functional ubiquitin variants

Marie-Line Dubois, Anna Meller, Sondos Samandi, Mylène Brunelle, Julie Frion, Marie A. Brunet, Amanda Toupin, Maxime C. Beaudoin, Jean-François Jacques, Dominique Lévesque, Michelle S. Scott, Pierre Lavigne, Xavier Roucou () and François-Michel Boisvert ()
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Marie-Line Dubois: Department of Immunology and Cell Biology
Anna Meller: Department of Immunology and Cell Biology
Sondos Samandi: Department of Biochemistry and Functional Genomics
Mylène Brunelle: Department of Biochemistry and Functional Genomics
Julie Frion: Department of Immunology and Cell Biology
Marie A. Brunet: Department of Biochemistry and Functional Genomics
Amanda Toupin: Department of Biochemistry and Functional Genomics
Maxime C. Beaudoin: Department of Biochemistry and Functional Genomics
Jean-François Jacques: Department of Biochemistry and Functional Genomics
Dominique Lévesque: Department of Immunology and Cell Biology
Michelle S. Scott: Department of Biochemistry and Functional Genomics
Pierre Lavigne: Department of Biochemistry and Functional Genomics
Xavier Roucou: Department of Biochemistry and Functional Genomics
François-Michel Boisvert: Department of Immunology and Cell Biology

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: Abstract Pseudogenes are mutated copies of protein-coding genes that cannot be translated into proteins, but a small subset of pseudogenes has been detected at the protein level. Although ubiquitin pseudogenes represent one of the most abundant pseudogene families in many organisms, little is known about their expression and signaling potential. By re-analyzing public RNA-sequencing and proteomics datasets, we here provide evidence for the expression of several ubiquitin pseudogenes including UBB pseudogene 4 (UBBP4), which encodes UbKEKS (Q2K, K33E, Q49K, N60S). The functional consequences of UbKEKS conjugation appear to differ from canonical ubiquitylation. Quantitative proteomics shows that UbKEKS modifies specific proteins including lamins. Knockout of UBBP4 results in slower cell division, and accumulation of lamin A within the nucleolus. Our work suggests that a subset of proteins reported as ubiquitin targets may instead be modified by ubiquitin variants that are the products of wrongly annotated pseudogenes and induce different functional effects.

Date: 2020
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DOI: 10.1038/s41467-020-15090-6

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