New interacting partners of the F‐box protein Ufo1 of yeast

Transcriptome analyses indicate that a core 10%–15% of the yeast genome is modulated by a variety of different stresses. However, not all the induced genes undergo translation, and null mutants of many induced genes do not show elevated sensitivity to the particular stress. Elucidation of the RNA lifecycle reveals accumulation of non-translating mRNAs in cytoplasmic granules, P-bodies, and stress granules for future regulation. P-bodies contain enzymes for mRNA degradation; under stress conditions mRNAs may be transferred to stress granules for storage and return to translation. Protein degradation by the ubiquitin-proteasome system is elevated by stress; and here we analyzed the steady state levels, decay, and subcellular localization of the mRNA of the gene encoding the F-box protein, UFO1, that is induced by stress. Using the MS2L mRNA reporter system UFO1 mRNA was observed in granules that colocalized with P-bodies and stress granules. These P-bodies stored diverse mRNAs. Granules of two mRNAs transported prior to translation, ASH1-MS2L and OXA1-MS2L, docked with P-bodies. HSP12 mRNA that gave rise to highly elevated protein levels was not observed in granules under these stress conditions. ecd3, pat1 double mutants that are defective in P-body formation were sensitive to mRNAs expressed ectopically from strong promoters. These highly expressed mRNAs showed elevated translation compared with wild-type cells, and the viability of the mutants was strongly reduced. ecd3, pat1 mutants also exhibited increased sensitivity to different stresses. Our interpretation is that sequestration of highly expressed mRNAs in P-bodies is essential for viability. Storage of mRNAs for future regulation may contribute to the discrepancy between the steady state levels of many stress-induced mRNAs and their proteins. Sorting of mRNAs for future translation or decay by individual cells could generate potentially different phenotypes in a genetically identical population and enhance its ability to withstand stress.

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“…Next morning the cells were diluted to A 600 = 0.1 and regrown to A 600 = 0.5 for TCA precipitation [77] and Western blotting [78].…”

Section: Methodsmentioning

confidence: 99%

Sequestration of Highly Expressed mRNAs in Cytoplasmic Granules, P-Bodies, and Stress Granules Enhances Cell Viability

Lavut

Raveh

2012

PLoS Genet

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“…Notably, Ubc4/5 work with SUMO-targeted ubiquitin ligases (STUbLs) that target poly-SUMOylated substrates (Sriramachandran and Dohmen, 2014;Uzunova et al, 2007). SUMO also modified five ubiquitin E3 ligases, Ubr1, Ufo1, Uls1, Gid7 and Ufd4, involved in a variety processes including the N-end rule, catabolite-degradation of fructose-1,6-bisphosphatase, transcription, cell cycle and genome maintenance (Bao et al, 2015;Baranes-Bachar et al, 2008;Finley et al, 2012;Kramarz et al, 2017;Lin et al, 2015;Sriramachandran and Dohmen, 2014;Varshavsky, 1997). Notable is Uls1, a putative STUbL that is thought to compete with a second STUbL, Slx5-Slx8, to displace from DNA poly-SUMOylated proteins that have been rendered defective or inactive (Sriramachandran and Dohmen, 2014;Tan et al, 2013;Wei et al, 2017).…”

Section: Ups Targets Included Ubc4 and Ubc5mentioning

confidence: 99%

SUMO is a pervasive regulator of meiosis

Bhagwat

Owens

Ito

et al. 2021

eLife

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Protein modification by SUMO helps orchestrate the elaborate events of meiosis to faithfully produce haploid gametes. To date, only a handful of meiotic SUMO targets have been identified. Here we delineate a multidimensional SUMO-modified meiotic proteome in budding yeast, identifying 2747 conjugation sites in 775 targets, and defining their relative levels and dynamics. Modified sites cluster in disordered regions and only a minority match consensus motifs. Target identities and modification dynamics imply that SUMOylation regulates all levels of chromosome organization and each step of meiotic prophase I. Execution-point analysis confirms these inferences, revealing functions for SUMO in S-phase, the initiation of recombination, chromosome synapsis and crossing over. K15-linked SUMO chains become prominent as chromosomes synapse and recombine, consistent with roles in these processes. SUMO also modifies ubiquitin, forming hybrid oligomers with potential to modulate ubiquitin signaling. We conclude that SUMO plays diverse and unanticipated roles in regulating meiotic chromosome metabolism.

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“…Ho endonuclease is recruited by Ufo1 to the SCF ubiquitin ligase complex for ubiquitination and subsequently transferred by Ddi1 to the 26S proteasome for degradation (Kaplun et al, 2003; Kaplun et al, 2000). Ufo1 is a unique F-box protein, which in addition to the F-box and a protein-protein interaction domain contains three u biquitin- i nteracting m otifs (UIM) that are important for Ufo1 autoubiquitination (Baranes-Bachar et al, 2008). Interestingly, it was suggested that turnover of Ufo1 depends on the presence of Ufo1UIMs and the UBL domain of Ddi1 (Ivantsiv et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

DNA-Damage-Inducible 1 Protein (Ddi1) Contains an Uncharacteristic Ubiquitin-like Domain that Binds Ubiquitin

et al. 2015

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SUMMARY Ddi1 belongs to a family of shuttle proteins targeting polyubiquitinated substrates for proteasomal degradation. Unlike the other proteasomal shuttles, Rad23 and Dsk2, Ddi1 remains an enigma: its function is not fully understood and structural properties are poorly characterized. We determined the structure and binding properties of the ubiquitin-like (UBL) and ubiquitin-associated (UBA) domains of Ddi1 from Saccharomyces cerevisiae. We found that, while Ddi1UBA forms a characteristic UBA:ubiquitin complex, Ddi1UBL has entirely uncharacteristic binding preferences. Despite having a ubiquitin-like fold, Ddi1UBL does not interact with typical UBL-receptors but, unexpectedly, binds ubiquitin, forming a unique interface mediated by hydrophobic contacts and by salt-bridges between oppositely-charged residues of Ddi1UBL and ubiquitin. In stark contrast with ubiquitin and other UBLs, the β-sheet surface of Ddi1UBL is negatively charged and, therefore, is recognized in a completely different way. The dual functionality of Ddi1UBL, capable of binding both ubiquitin and proteasome, suggests a novel mechanism for Ddi1 as a proteasomal shuttle.

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New interacting partners of the F‐box protein Ufo1 of yeast

Cited by 7 publications

References 60 publications

Sequestration of Highly Expressed mRNAs in Cytoplasmic Granules, P-Bodies, and Stress Granules Enhances Cell Viability

Sequestration of Highly Expressed mRNAs in Cytoplasmic Granules, P-Bodies, and Stress Granules Enhances Cell Viability

SUMO is a pervasive regulator of meiosis

DNA-Damage-Inducible 1 Protein (Ddi1) Contains an Uncharacteristic Ubiquitin-like Domain that Binds Ubiquitin

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