Dataset Information

Phospho-regulation of Cdc48/p97 cofactor protein Shp1/p47 in budding yeast

ABSTRACT: Shp1/p47 is a cofactor of the Cdc48/p97 complex involved in the energy-dependent segregation of intracellular aggregates and multiprotein complexes. We identified two serine residues (S108 and S315) in the S. Cerevisiae protein Shp1 which increase in phosphorylation upon various cell stresses such as heat shock, TORC1 inhibition, ER stress and oxidative stress. To identify binding partners of phosphorylated vs non-phosphorylated Shp1, we generated endogenous C-terminal 5xFLAG-tagged Shp1 yeast strains either harbouring either WT shp1 or CRISPR-modified S108A + S315A (2SA) shp1. These were cultured with 200 nM rapamycin treatment for 2 h to induce phosphorylation, prior to lysis, FLAG immunoprecipitation, peptide digestion and processing for LC-MS/MS.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

TISSUE(S): Cell Culture

SUBMITTER: Frederic Lamoliatte

LAB HEAD: Adrien Rousseau

PROVIDER: PXD035819 | Pride | 2023-01-30

REPOSITORIES: Pride

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Publications

Multiple phosphorylation of the Cdc48/p97 cofactor protein Shp1/p47 occurs upon cell stress in budding yeast.

Agrotis Alexander A Lamoliatte Frederic F Williams Thomas D TD Black Ailsa A Horberry Rhuari R Rousseau Adrien A

Life science alliance 20230124 4

The homohexameric p97 complex, composed of Cdc48 subunits in yeast, is a crucial component of protein quality control pathways including ER-associated degradation. The complex acts to segregate protein complexes in an ATP-dependent manner, requiring the engagement of cofactor proteins that determine substrate specificity. The function of different Cdc48 cofactors and how they are regulated remains relatively poorly understood. In this study, we assess the phosphorylation of Cdc48 adaptor protein ...[more]

PMID: 36693698

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Project description:Transposable elements have the potential to act as controlling elements to influence the expression of genes. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of the transposable element and influence the chromatin state of neighboring low-copy sequences. This would allow transposable elements to condition obligatory or facilitated epialleles and act as controlling elements. The maize genome contains numerous families of class I transposable elements (retrotransposons) that are present in moderate to high copy numbers and many are found in regions near genes which provides an opportunity to test whether the spreading of heterochromatin from retrotransposons is prevalent. We have investigated the extent of heterochromatin spreading into flanking DNA around each family of retrotransposons through profiling of DNA methylation and di-methylation of lysine 9 of histone 3 (H3K9me2) in low-copy regions of the maize genome. The effects of different retrotransposon families on local chromatin are highly variable. Some LTR families exhibit enrichment of heterochromatic marks within 800-1200 base pairs of the insertion site while other families have very little evidence for spreading of heterochromatic marks. The analysis of chromatin state in genotypes that lack specific insertions suggests that the adjacent heterochromatin results from spreading of silencing rather than insertion-site preferences. Genes that are located near elements that exhibit spreading of heterochromatin tend to be expressed at lower levels than other genes. Our findings suggest that a subset of LTR retrotransposon families may act as controlling elements influencing neighboring sequences while the majority of elements have little effect on flanking sequences Transposable elements comprise a substantial portion of many eukaryotic genomes. These mobile fragments of DNA can result in mutations through insertions into genes but may also affect the regulation of genes they insert near. There is evidence that the majority of transposable elements are epigenetically silenced and in some cases this silencing may affect neighboring sequences. However, evolutionary theory would predict that there would be selective pressures for transposable elements to limit their effects on neighboring genes. The maize genome has a complex organization with many genes flanked by retrotransposons. We profiled the spread of heterochromatin from the retrotransposons into nearby low copy sequences for 150 high copy retrotransposon families. While the manymajority of retrotransposons exhibit little to no spreading of heterochromatin there are a small number ofsome retrotransposon families that influence the chromatin state of surrounding regions. The families may represent bad “neighbors” that spread heterochromatin and influence nearby genes. 6 total samples: 3 replicates of B73 H3k9 and 3 replicates of Mo17 H3k9 3 total samples: mop1 mutant, b73.zmet2 (zmet2.m1 mutant in B73 background) and mo17.zmet2 (zmet2.m1 mutant in Mo17 background)

Dataset Information

Phospho-regulation of Cdc48/p97 cofactor protein Shp1/p47 in budding yeast

Publications

Multiple phosphorylation of the Cdc48/p97 cofactor protein Shp1/p47 occurs upon cell stress in budding yeast.

Similar Datasets

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