UBB Pseudogene 4 encodes novel ubiquitin variants

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.