The conserved ubiquitin-like protein Hub1 plays a critical role in splicing in human cells

Abstract

Different from canonical ubiquitin-like proteins, Hub1 does not form covalent conjugates with substrates but binds proteins non-covalently. In Saccharomyces cerevisiae, Hub1 associates with spliceosomes and mediates alternative splicing of SRC1, without affecting pre-mRNA splicing generally. Human Hub1 is highly similar to its yeast homolog, but its cellular function remains largely unexplored. Here, we show that human Hub1 binds to the spliceosomal protein Snu66 as in yeast; however, unlike its S. cerevisiae homolog, human Hub1 is essential for viability. Prolonged in vivo depletion of human Hub1 leads to various cellular defects, including splicing speckle abnormalities, partial nuclear retention of mRNAs, mitotic catastrophe, and consequently cell death by apoptosis. Early consequences of Hub1 depletion are severe splicing defects, however, only for specific splice sites leading to exon skipping and intron retention. Thus, the ubiquitin-like protein Hub1 is not a canonical spliceosomal factor needed generally for splicing, but rather a modulator of spliceosome performance and facilitator of alternative splicing.

An Rtf2 Domain-Containing Protein Influences Pre-mRNA Splicing and Is Essential for Embryonic Development in Arabidopsis thaliana

“…(C) Quantitative RT-PCR showing accumulation of long and short GFP transcripts in the indicated genotypes. Stably expressed At5g60390 was used for normalization (Wang et al 2014). acetylation, methylation, and phosphorylation, ubiquitination is increasingly recognized for its role in regulating the spliceosomal cycle (Bellare et al 2008;Song et al 2010;Mishra et al 2011;Korneta et al 2012;Ammon et al 2014;Chen and Moore 2014;Oka et al 2014). Notably, PRP8, which can bind ubiquitin through its conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) domain, was detected as an ubiquitin conjugate in affinity-purified particles in budding yeast, suggesting a means to reversibly modulate the activity of this protein (Bellare et al 2008).…”

Sde2 is an intron‐specific pre‐ mRNA splicing regulator activated by ubiquitin‐like processing

“…Hub1 thereby promotes alternative splicing of the SRC1 pre-mRNA in Saccharomyces cerevisiae (Mishra et al, 2011). Specific roles of Hub1 in pre-mRNA splicing have also been reported in both Schizosaccharomyces pombe and mammalian cells (Wilkinson et al, 2004;Mishra et al, 2011;Ammon et al, 2014). Whereas HUB1 is a non-essential gene in S. cerevisiae, its orthologs in S. pombe and mammalian cells are essential for viability, perhaps because of the increased prevalence of introns and alternative splicing in S. pombe and humans.…”

“…We have previously reported the role of the UBL Hub1 in alternative RNA splicing through usage of non-canonical 5 0 splice sites in the budding yeast S. cerevisiae (Mishra et al, 2011). Orthologs of Hub1 in S. pombe and humans are essential for viability and play specific roles in pre-mRNA splicing (Mishra et al, 2011;Ammon et al, 2014). To identify spliceosomal regulators in an intron prevalent organism, we screened for genetic interactors of hub1 by combining S. pombe hub1-1 mutant (Yashiroda & Tanaka, 2004) with the haploid deletion library of non-essential genes (Kim et al, 2010).…”

Human MFAP1 is a cryptic ortholog of the Saccharomyces cerevisiae Spp381 splicing factor

“…Homo sapiens ( hs ) Prp38 has acquired a veritable, C-terminal arginine-serine-rich (RS) domain, a hallmark of the splicing regulatory serine-arginine-rich (SR) proteins that are largely lacking in yeast [21]. UBL5, also called Hub1, was the first splicing factor that was found to be involved in alterative splicing in human [22] as well as in a rare case of alternative splicing in yeast [23]. In contrast, MFAP1, Smu1, RED, FBP21, NPW38 and NPW38BP lack obvious orthologs in yeast, where alternative splicing is essentially absent.…”