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Aeromonas hydrophila CobQ is a new type of NAD+/Zn2+ independent protein lysine deacetylase in prokaryote

ABSTRACT: Protein NƐ-lysine acetylation (Kac) modification plays crucial roles on diverse physiological and pathological functions in cell.

ORGANISM(S): Aeromonas Hydrophila Subsp. Hydrophila Atcc 7966

SUBMITTER: Xiangmin Lin

PROVIDER: PXD038735 | iProX | Fri Dec 09 00:00:00 GMT 2022

REPOSITORIES: iProX

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Aeromonas hydrophila CobQ is a new type of NAD+- and Zn2+-independent protein lysine deacetylase.

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| S-EPMC11856932 | biostudies-literature

Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification

Project description:We report the identification of 67 previously undescribed histone modifications, increasing the current number of known histone marks by about 70%. We further investigated one of the marks, lysine crotonylation (Kcr), confirming that it represents an evolutionarily-conserved histone posttranslational modification. The unique structure and genomic localization of histone Kcr suggest that it is mechanistically and functionally different from histone lysine acetylation (Kac). Specifically, in both human somatic and mouse male germ cell genomes, histone Kcr marks either active promoters or potential enhancers. In male germinal cells immediately following meiosis, Kcr is enriched on sex chromosomes and specifically marks testis-specific genes, including a significant proportion of X-linked genes that escape sex chromosome inactivation in haploid cells. These results therefore dramatically extend the repertoire of histone PTM sites and designate Kcr as a specific mark of active sex chromosome-linked genes in postmeiotic male germ cells. 2 histone marks (pan-lysine acetylation and pan-lysine crotonylation) were studied in 1 human cell type and 2 mouse cell types using ChIP-Seq. Input was sequenced for each cell type as a control. Pan-anti_Kac and pan-anti_Kcr antibodies were custom developed with PTM BioLab, Co., Ltd (Chicago, IL).

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Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification

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Identification of a new effector-immunity pair of Aeromonas hydrophila type VI secretion system.

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Deep, quantitative coverage of the lysine acetylome using novel anti-acetyl-lysine antibodies

Project description:Svinkina T, Gu H, Silva JC, Mertins P, Qiao J, Fereshetian S, Jaffe JD, Kuhn E, Udeshi ND,Carr SA. Mol Cell Proteomics, 2015. Introduction of antibodies specific for acetylated lysine has significantly improved the detection of endogenous acetylation sites by mass spectrometry. Here, we describe a new, commercially available mixture of anti-Kac antibodies and show its utility for in-depth profiling of the acetylome. Specifically, seven complementary monoclones with high specificity for Kac were combined into a final anti-Kac reagent which results in at least a 2-fold increase in identification of Kac peptides over a commonly used Kac antibody. We outline optimal antibody usage conditions, effective offline bRP separation, and use of state-of-the art LC-MS technology for achieving unprecedented coverage of the acetylome. The methods presented in this study enabled the quantification of over 10,000 Kac peptides from over 3000 Kac proteins from a single SILAC labeled sample using 7.5 mg of peptide input per state. These methods result in the deepest coverage of acetylation sites from SAHA treated Jurkat cells. The approach was also applied to breast tumor xenograft samples using isobaric mass tag labeling of peptides (iTRAQ4-plex, TMT6 and TMT10-plex reagents) for quantification. Greater than 6,700 Kac peptides from over 2,300 Kac proteins were quantified using 1 mg of tumor per iTRAQ 4-plex channel.

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Rice (Oryza sativa) lysine-acetylation LC-MS/MS

Project description:Lysine acetylation is a dynamic and reversible post-translational modification that plays an imporant role in the gene transcription regulation. Here, we report high quality proteome-scale data for lysine-acetylation sites and proteins in rice (Oryza sativa). A total of 1337 Kac sites in 716 Kac proteins with diverse biological functions and subcellular localizations were identified in rice seedlings.

2016-02-24 | PXD002291 | Pride

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