Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources

Wong, Edith D.; Miyasato, Stuart R.; Aleksander, Suzi; Karra, Kalpana; Nash, Robert S.; Skrzypek, Marek S.; Weng, Shuai; Engel, Stacia R.; Cherry, J. Michael

doi:10.1093/genetics/iyac191

Cited by 24 publications

(27 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Gene ontology (GO) term analysis was performed using the upregulated transmembrane standard names. They were mapped against the generic component terms using the GoSLIM mapper of the Saccharomyces genome database 91 . GO terms with only one hit were removed and hits from the term ‘cytoplasmic vesicles’ were fused either with the plasma membrane or with endosomes according to their localization in the yeast GFP database 92 .…”

Section: Methodsmentioning

confidence: 99%

The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi

Weyer,

Schwabl,

Tang

et al. 2024

Preprint

View full text Add to dashboard Cite

The Golgi apparatus is essential for protein sorting, yet its quality control mechanisms are poorly understood. Here we show that the Dsc ubiquitin ligase complex, particularly the rhomboid pseudo-protease subunit, Dsc2, assesses the hydrophobic length of α-helical transmembrane domains (TMDs) at the Golgi. Thereby the Dsc complex interacts with orphaned ER and Golgi proteins that have shorter TMDs and ubiquitinates them for targeted degradation. Some Dsc substrates will be K63 polyubiquitinated for ESCRT dependent vacuolar degradation or K48 polyubiquitinated for endosome and Golgi associated proteasomal degradation (EGAD). Other Dsc substrates are exclusively extracted by Cdc48 for EGAD. The accumulation of Dsc substrates entails a specific increase in glycerophospholipids with shorter and asymmetric fatty acyl chains. Hence, the Dsc complex mediates the selective degradation of orphaned proteins at the sorting center of cells, which prevents their spreading across other organelles and thus preserves cellular membrane protein and lipid composition.

show abstract

Section: Methodsmentioning

confidence: 99%

The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi

Weyer,

Schwabl,

Tang

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…We used the list of URI interactors in human HEK 293T cells identified by AP-MS [5]. The list of yeast URI/Bud27 interactors, identified by various experimental approaches, was obtained from the Saccharomyces Genome Database [44]. URI had 142 and 117 partners in humans and yeast, respectively (Table S1) [5,44], suggesting that both are promiscuous proteins.…”

Section: Aturi Has An Extensive Interactomementioning

confidence: 99%

“…The list of yeast URI/Bud27 interactors, identified by various experimental approaches, was obtained from the Saccharomyces Genome Database [44]. URI had 142 and 117 partners in humans and yeast, respectively (Table S1) [5,44], suggesting that both are promiscuous proteins. The number of interactors, however, was smaller for the AtURI partner UXT (Fig.…”

Section: Aturi Has An Extensive Interactomementioning

confidence: 99%

The prefoldin‐like protein AtURI exhibits characteristics of intrinsically disordered proteins

Gómez‐Mínguez,

Palacios‐Abella,

Costigliolo‐Rojas

et al. 2024

FEBS Letters

View full text Add to dashboard Cite

The prefoldin‐like protein UNCONVENTIONAL PREFOLDIN RPB5 INTERACTOR (URI) participates in diverse cellular functions, including protein homeostasis, transcription, translation, and signal transduction. Thus, URI is a highly versatile protein, although the molecular basis of this versatility remains unknown. In this work, we show that Arabidopsis thaliana (Arabidopsis) URI (AtURI) possesses a large intrinsically disordered region (IDR) spanning most of the C‐terminal part of the protein, a feature conserved in yeast and human orthologs. Our findings reveal two key characteristics of disordered proteins in AtURI: promiscuity in interacting with partners and protein instability. We propose that these two features contribute to providing AtURI with functional versatility.

show abstract

“…We used GO Slim Mapper (https://www.yeastgenome.org/goSlimMapper) which is available through the Saacharomyces Genome Database (SGD) 128 . We searched query genes for all Yeast GO-Slim processes.…”

Section: Go Term Analysismentioning

confidence: 99%

A protein condensation network contextualises cell fate decisions

Peskett,

Lee,

Barral

2024

Preprint

View full text Add to dashboard Cite

For cells to thrive, they must make appropriate fate decisions based on a myriad of internal and external stimuli. But how do they integrate these different forms of information to contextualise their decisions? Old yeast cells showed an ability to dampen their proliferation as they entered senescence. Conversely, they had an enhanced ability to promote proliferation during escape from pheromone stimulation. A network of nucleoprotein condensation states involving processing bodies (P-bodies) and the prion-like RNA-binding protein, Whi3, controlled these opposing fate decisions. In old but not in young cells, condensation of Whi3 was both necessary and sufficient for senescence entry. In old cells, Whi3 localised to age-dependent P-bodies. Preventing their formation stopped Whi3 condensation from driving senescence entry. Challenging old cells with an external stimulus, pheromone, revealed that the condensates had a second function: potentiating the cell's ability to trigger escape from the mating pheromone response. These findings identify biomolecular condensation as an integrator of contextual information as cells make decisions, enabling them to navigate overlapping life events.

show abstract

Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources

Cited by 24 publications

References 15 publications

The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi

The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi

The prefoldin‐like protein AtURI exhibits characteristics of intrinsically disordered proteins

A protein condensation network contextualises cell fate decisions

Contact Info

Product

Resources

About