Dataset Information

UBB Pseudogene 4 encodes novel ubiquitin variants

ABSTRACT: Post-translational modification by ubiquitin and ubiquitin-like modifiers proteins regulate cellular processes at almost every levels. Ubiquitin itself is encoded by four different genes, either as single copy of ubiquitin fused to ribosomal proteins, or by polyubiquitin precursors3. Early studies identified several additional genes potentially coding for ubiquitin, but they were considered as pseudogenes due to differences in amino acids, or lack of apparent transcription4-6. Through analysis of large-scale proteomics and RNA sequencing experiments, we found evidence for expression at the mRNA and protein levels of several ubiquitin pseudogenes. Our results show that UBBP4, a pseudogene of the UBB subfamily, produces functional ubiquitin proteins with different amino acids composition compared to the canonical sequence. These ubiquitins variants are covalently conjugated to proteins that are different from ubiquitin, and proteins modified by UBBP4 are not targeted for proteasomal degradation. Furthermore, invalidation of UBBP4 results in slower cell division, and accumulation of lamin A within the nucleolus. This implies that a subset of proteins reported as ubiquitin targets could rather be through these variants arising from wrongly annotated pseudogenes, and that there is a specificity in the modification and differences in the functional consequence of proteins modified by these new ubiquitin variants. The identification of additional ubiquitins thus entails a new layer of complexity in protein ubiquitylation that has been unnoticed until now.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell

DISEASE(S): Cervix Carcinoma

SUBMITTER: Anonym Anonym

LAB HEAD: Anonym Ous

PROVIDER: PXD014318 | Pride | 2020-03-19

REPOSITORIES: Pride

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UBB pseudogene 4 encodes functional ubiquitin variants.

Dubois Marie-Line ML Meller Anna A Samandi Sondos S Brunelle Mylène M Frion Julie J Brunet Marie A MA Toupin Amanda A Beaudoin Maxime C MC Jacques Jean-François JF Lévesque Dominique D Scott Michelle S MS Lavigne Pierre P Roucou Xavier X Boisvert François-Michel FM

Nature communications 20200311 1

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 pseudog ...[more]

PMID: 32161257

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Project description:Measuring the properties of endogenous cell proteins, such as expression level, subcellular localization and turnover rates, on a whole proteome level remains a major challenge in the post-genome era. Quantitative methods for measuring mRNA expression do not reliably predict corresponding protein levels and provide little or no information on other protein properties. Here we describe a combined pulse-labelling, spatial proteomics and data analysis strategy to characterize the expression, localization, synthesis, degradation and turnover rates of endogenously expressed, untagged human proteins in different subcellular compartments. Using quantitative mass spectrometry and SILAC, a total of 80,098 peptides from 8,041 HeLa proteins were quantified, and their spatial distribution between the cytoplasm, nucleus and nucleolus determined and visualised using specialised software tools developed in PepTracker. Using information from ion intensities and rates of change in isotope ratios, protein abundance levels and protein synthesis, degradation and turnover rates were calculated for the whole cell and for the respective cytoplasmic, nuclear and nucleolar compartments. Expression levels of endogenous HeLa proteins varied by up to seven orders of magnitude. The average turnover rate for HeLa proteins was approximately 20 hours. Turnover rate did not correlate with either molecular weight or net charge, but did correlate with abundance, with highly abundant proteins showing longer than average half-lives. Fast turnover proteins had overall a higher frequency of PEST motifs than slow turnover proteins but no general correlation was observed between amino or carboxy terminal amino acid identities and turnover rates. A subset of proteins was identified that exist in pools with different turnover rates depending on their subcellular localization. This strongly correlated with subunits of large, multi-protein complexes, suggesting a general mechanism whereby their assembly is controlled in a different subcellular location to their main site of function.

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