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Identifying protein acetylation

ABSTRACT: Five proteins, YdeH, Era, YegE, YeaJ and YihK were mixed and performed the Q Exactive MS analysis to identify the protien acetylation sites.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Escherichia Coli

SUBMITTER: Zhaowei Xu

LAB HEAD: Zhaowei Xu

PROVIDER: PXD007651 | Pride | 2019-06-17

REPOSITORIES: Pride

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			Action	DRS
	20161202_ZHN_AC-01.msf	Msf
	20161202_ZHN_AC.raw	Raw

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Publications

Interplay between the bacterial protein deacetylase CobB and the second messenger c-di-GMP.

Xu Zhaowei Z Zhang Hainan H Zhang Xingrun X Jiang Hewei H Liu Chengxi C Wu Fanlin F Qian Lili L Hao Bingbing B Czajkowsky Daniel M DM Guo Shujuan S Xu Zhijing Z Bi Lijun L Wang Shihua S Li Haitao H Tan Minjia M Yan Wei W Feng Lei L Hou Jingli J Tao Sheng-Ce SC

The EMBO journal 20190816 18

As a ubiquitous bacterial secondary messenger, c-di-GMP plays key regulatory roles in processes such as bacterial motility and transcription regulation. CobB is the Sir2 family protein deacetylase that controls energy metabolism, chemotaxis, and DNA supercoiling in many bacteria. Using an Escherichia coli proteome microarray, we found that c-di-GMP strongly binds to CobB. Further, protein deacetylation assays showed that c-di-GMP inhibits the activity of CobB and thereby modulates the biogenesis ...[more]

PMID: 31418899

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Identifing YdeH acetylation sites

Project description:we found the E. coli major DGC, YdeH, is endogenously acetylated and CobB promotes YdeH activity through deacetylation of YdeH. This experiment will identify the sites that can be acetylated by CobB on YdeH.

2019-06-17 | PXD008113 | Pride

Monitoring of the spatial and temporal dynamics of BER/SSBR pathway proteins, including MYH, UNG2, MPG, NTH1 and NEIL1-3, during DNA replication, Batch 1

Project description:Base lesions in DNA can stall the replication machinery or induce mutations if bypassed. Consequently, lesions must be repaired before replication or in a post-replicative process to maintain genomic stability. Base excision repair (BER) is the main pathway for repair of base lesions, but how BER is organized during DNA replication is unclear. Here we refined the iPOND (isolation of proteins on nascent DNA) technique with targeted mass-spectrometry analysis, which enabled us to detect all proteins required for BER on nascent DNA and to monitor their spatiotemporal orchestration at replication forks. We demonstrate that XRCC1 and other BER/single-strand break repair (SSBR) proteins are enriched in replisomes in unstressed cells, supporting a cellular capacity of post-replicative BER/SSBR. Importantly, the DNA glycosylases MYH, UNG2, MPG, NTH1, NEIL1 and NEIL3 were also detected on nascent DNA. Thus our findings reveal that a broad spectrum of DNA base lesions are recognized and repaired by BER in a post-replicative process.

2017-11-23 | PXD004288 | Pride

Monitoring of the spatial and temporal dynamics of BER/SSBR pathway proteins, including MYH, UNG2, MPG, NTH1 and NEIL1-3, during DNA replication, Batch 2

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Identification of BER/SSBR proteins and the DNA glycosylases MPG, UNG2, MYH, NTH1, NEIL1 and NEIL3 in replisomes Batch 3

2024-06-07 | PXD004324 | Pride

Compounds activating VCP D1 ATPase enhance both autophagic and proteasomal neurotoxic protein clearance

Project description:Enhancing the removal of aggregate-prone toxic proteins is a rational therapeutic strategy for a number of neurodegenerative diseases, especially Huntington’s disease and various spinocerebellar ataxias. Ideally, such approaches should preferentially clear the mutant/misfolded species, while having minimal impact on the stability of wild-type/normally-folded proteins. Furthermore, activation of both ubiquitin-proteasome and autophagy-lysosome routes may be advantageous, as this would allow effective clearance of both monomeric and oligomeric species, the latter which are inaccessible to the proteasome. Here we find that compounds that activate the D1 ATPase activity of VCP/p97 fulfill these requirements. Such effects are seen with small molecule VCP activators like SMER28, which activate autophagosome biogenesis by enhancing interactions of PI3K complex components to increase PI(3)P production, and also accelerate VCP-dependent proteasomal clearance of such substrates. Thus, this mode of VCP activation may be a very attractive target for many neurodegenerative diseases.

2022-07-15 | PXD034712 | Pride

THE PROTEOME SPECIATION OF AN IMMORTALIZED CYSTIC FIBROSIS CELL LINE: NEW PERSPECTIVES ON THE PATHOPHYSIOLOGY OF THE DISEASE.

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2022-03-01 | PXD006933 | Pride

MHC immunopeptidome of JY cells analysed by EThcD at Orbitrap Fusion after mild acid elution

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2020-11-11 | PXD012498 | Pride

Proteomic analysis of Rhodopsedomonas palustris longevity

Project description:Proteomics analysis of Rhodopseudomonas palustris 6 and 20 days after growth arrest.

2019-10-02 | PXD013729 | Pride

Parallel G-quadruplexes recruit the HSV-1 transcription factor ICP4 to promote viral transcription in herpes virus-infected human cells

Project description:G-quadruplexes (G4s) are four-stranded nucleic acid structures abundant at gene promoters. They can adopt several distinctive conformations. G4s have been shown to form in the herpes simplex virus-1 (HSV-1) genome during its viral cycle. Here by cross-linking/pull-down assay we identified ICP4, the major HSV-1 transcription factor, as the protein that most efficiently interacts with viral G4s during infection. ICP4 specific and direct binding and unfolding of parallel G4s, including those present in HSV-1 immediate early gene promoters, induced transcription in vitro and in infected cells. This mechanism was also exploited by ICP4 to promote its own transcription. Proximity ligation assay allowed visualization of G4-protein interaction at the single selected G4 in cells. G4 ligands inhibited ICP4 binding to G4s. Our results indicate the existence of a well-defined G4-viral protein network that regulates the productive HSV-1 cycle. They also point to G4s as elements that recruit transcription factors to activate transcription in cells.

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Depletion of the RNA binding protein HNRNPD impairs homologous recombination by inhibiting DNA-end resection and inducing R-loop accumulation

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