Variable repeats in the eukaryotic polyubiquitin gene ubi4 modulate proteostasis and stress survival

Abstract

Ubiquitin conjugation signals for selective protein degradation by the proteasome. In eukaryotes, ubiquitin is encoded both as a monomeric ubiquitin unit fused to a ribosomal gene and as multiple ubiquitin units in tandem. The polyubiquitin gene is a unique, highly conserved open reading frame composed solely of tandem repeats, yet it is still unclear why cells utilize this unusual gene structure. Using the Saccharomyces cerevisiae UBI4 gene, we show that this multi-unit structure allows cells to rapidly produce large amounts of ubiquitin needed to respond to sudden stress. The number of ubiquitin units encoded by UBI4 influences cellular survival and the rate of ubiquitin-proteasome system (UPS)-mediated proteolysis following heat stress. Interestingly, the optimal number of repeats varies under different types of stress indicating that natural variation in repeat numbers may optimize the chance for survival. Our results demonstrate how a variable polycistronic transcript provides an evolutionary alternative for gene copy number variation.

Pleiotropic effects of Ubi4, a polyubiquitin precursor required for ubiquitin accumulation, conidiation and pathogenicity of a fungal insect pathogen

“…A Ub molecule can be fused to the C‐terminal ribosomal proteins (r‐proteins) Rpl40A/B of Ubi1/2 and the C‐terminal protein Rps31 of Ubi3 or self‐fused to form a pentamer of Ubi4 (Ozkaynak et al ., ; Finley et al ., ). Ubi4 is a polyUb precursor consisting of variable Ub repeats organized in a head‐to‐tail manner (Zhao et al ., ), and the numbers of the repeats are crucial for cellular proteostasis and stress response (Gemayel et al ., ). The diversity of the Ub signalling stems from a Ub ability to form polyUb chains through covalent linkage between the εNH 2 group of a specific Lys (K6, K11, K27, K29, K33, K48 or K63) or the αNH 2 group of the first Met residue (M1) on one Ub molecule and the C‐terminus of another Ub molecule (Castaneda et al ., ).…”

Tandem repeats drive variation of intrinsically disordered regions in budding yeast

“…We and others have proposed that variation in repetitive regions is an important driver of protein diversification (Fuchs, 2013, Gemayel, Yang et al, 2017, Morrill et al, 2016, Rogers, McConnell et al, 2017, Verstrepen, Jansen et al, 2005, Zhao, Strope et al, 2014. However, it is also possible that some or many of these repeats have randomly risen within the genome and thus are unlikely to contribute to protein function.…”

A broad mutational target explains a fast rate of phenotypic evolution

“…Such highly mutable repeats may lie in a coding region (Verstrepen et al, 2005) or within regulatory sequences of a gene (Vinces et al, 2009, Chan et al, 2010. Their variation has been shown to affect various phenotypes in different organisms (Levdansky et al, 2007, Undurraga et al, 2012, Gemayel et al, 2017, Dai and Holland, 2019 and in humans to lead to diseases such as Huntington and fragile X syndromes (Budworth and McMurray, 2013). Consequently, the high mutability of some DNA regions may accelerate the evolution of specific traits.…”