Browse
Submit Data
Databases
API
Help

Dataset Information

274 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Growth-phase regulated acetylation in B. subtilis

ABSTRACT: To uncover potential regulatory roles for acetylation, we analyzed how acetylation patterns and abundances change between logarithmic and stationary phase growth in Bacillus subtilis. Using acetyllysine peptide enrichment followed by label-free mass spectrometry-based proteomics, we identified over 2,300 unique acetylation sites on proteins that function in many essential pathways. By comparing the changes in acetylation with total cell protein abundances, we discover a subset of specific acetylation events that are stoichiometrically regulated under different growth conditions.

INSTRUMENT(S): LTQ Orbitrap, LTQ Orbitrap Velos

ORGANISM(S): Bacillus Subtilis Subsp. Subtilis Str. 168

SUBMITTER: Todd Greco

LAB HEAD: Ileana Cristea

PROVIDER: PXD003272 | Pride | 2016-07-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	2013_07_19_ac_1x_CID.raw	Raw
	2013_07_19_ac_1x_HCD.raw	Raw
	2014-08-01-acetyl-MIN-log_CID.raw	Raw
	2014-08-01-acetyl-MIN-log_HCD.raw	Raw
	2014-08-21-acetyl-MIN-log_CID.raw	Raw

Items per page:

1 - 5 of 32

Publications

Temporal Regulation of the Bacillus subtilis Acetylome and Evidence for a Role of MreB Acetylation in Cell Wall Growth.

Carabetta Valerie J VJ Greco Todd M TM Tanner Andrew W AW Cristea Ileana M IM Dubnau David D

mSystems 20160531 3

Nε-Lysine acetylation has been recognized as a ubiquitous regulatory posttranslational modification that influences a variety of important biological processes in eukaryotic cells. Recently, it has been realized that acetylation is also prevalent in bacteria. Bacteria contain hundreds of acetylated proteins, with functions affecting diverse cellular pathways. Still, little is known about the regulation or biological relevance of nearly all of these modifications. Here we charac ...[more]

PMID: 27376153

Similar Datasets

A synthetic non-histone substrate to study substrate targeting by the Gcn5 HAT and sirtuin HDACs

Project description:Gcn5 and sirtuins are conserved HAT and HDAC enzymes that were first characterised as regulators of gene expression via histone acetylation. Although histone tails are important substrates of these enzymes, they also target non-histone proteins in diverse processes. Previously, we used SILAC-based mass spectrometry to identify novel non-histone substrates of Gcn5 and sirtuins in yeast. We found a shared target consensus sequence. In our latest work we used a synthetic biology approach to demonstrate that this consensus sequence can direct acetylation and deacetylation targeting by these enzymes in vivo. We used the synthetic substrate as a tool to prioritize SILAC-based acetylome analyses of SAGA mutants. Presented here are analyses of ada3∆ mutants analyzed in this work versus wild-type control. The strains and labels used are described in the BioRxiv report linked in the methods sections below.

2019-02-25 | PXD012608 | Pride

Genome-wide analysis reveals determinants of redundant and specific binding within a transcription factor family

Project description:A central question in transcription factor biology is how a specific member of a transcription factor family occupies a promoter in vivo, when all family members bind the same consensus site in vitro. To uncover the mechanisms regulating DNA binding specificity within transcription factor families, we have used the techniques of chromatin immunoprecipitation coupled with genome-wide microarray analysis to query the occupancy of three members of the ETS transcription factor family in a human T-cell line. Unexpectedly, redundant occupancy was frequently detected while specific occupancy was less likely. An unbiased bioinformatics approach correlated redundant binding with consensus ETS binding sequences near transcription start sites, whereas specific binding sites diverged dramatically from the consensus, were coupled with a site for a cooperative binding partner, and were found further from transcription start sites. The specific and redundant DNA binding modes illustrate the regulation of transcription factor specificity in vivo and suggest two distinct roles for members of the ETS transcription factor family. Keywords: ChIP-chip Chromatin IP from uninduced asynchronous Jurkat T cells, or HT29 colon cells using antibodies to three ETS transcription factors (ETS1, ELF1, and GABPa) or the transcription factors RUNX1 or E2F4. IP and whole input DNAs are amplified (WGA2 kit sigma) and labeled and compared by promoter microarrays (Agilent). Each experiment requires 2 microarrays to cover the genome. Proximal promoter arrays assay 1kb surrounding transcription start sites, extended promoter arrays assay 7kb surrounding transcription start sites. Each microarray is performed as two biological replicates with the exception of ETS1 in HT29 proximal promoter array which were done once, and ETS1 in Jurkat proximal promoter array which was done three times.

2007-07-27 | E-GEOD-7449 | biostudies-arrayexpress

Genomic analyses of Loc1, Puf6, and Khd1 binding patterns and transcriptional effects

Project description:We performed ChIP-chip of Loc1, Puf6, and Khd1 in order to determine the genetic loci they bind. We repeated these experiments with lighter fixation in the presence and absence of RNase to determine whether these associations are via DNA or RNA (analysis shows that they associate with the loci via the RNA). We also performed transcriptional profiling of knd1- and puf6- cells to determine if the binding of each factor has significant effects on the mRNA abundances of its targets (no significant transcriptional effects were observed). Each analyzed dataset comes from independently-produced triplicate samples, with one dye-swap performed for each dataset.

2014-01-01 | E-GEOD-34245 | biostudies-arrayexpress

Acetylome of Acinetobacter baumannii SK17 reveals a highly-conserved modification of histone-like protein HU

Project description:Lysine acetylation is a prevalent post-translational modification in both eukaryotes and prokaryotes. Whereas this modification is known to play pivotal roles in eukaryotes, the function and extent of this modification in prokaryotic cells remain largely unexplored. Here we report the acetylome of a pair of antibiotic-sensitive and -resistant nosocomial pathogen Acinetobacter baumannii SK17-S and SK17-R. A total of 145 lysine acetylation sites on 125 proteins was identified, and there are 23 acetylated proteins found in both strains, including histone-like protein HU which was found to be acetylated at Lys13. HU is a dimeric DNA-binding protein critical for maintaining chromosomal architecture and other DNA-dependent functions. To analyze the effects of site-specific acetylation, homogenously Lys13-acetylated HU protein, HU(K13ac) was prepared by genetic code expansion. Whilst not exerting an obvious effect on the oligomeric state, Lys13 acetylation alters both the thermal stability and DNA binding kinetics of HU. Accordingly, this modification likely destabilizes the chromosome structure and regulates bacterial gene transcription. By preparing and characterizing site-specifically acetylated bacterial protein for the first time, this work indicates that acetyllysine plays an important role in bacterial epigenetics and presents a promising target against bacterial infections.

2018-10-24 | PXD007289 | Pride

Characterization of the acetylome associated with rapamycin-induced autophagy in HeLa cells

Project description:Autophagy is a lysosomal-mediated catabolic process that degrades cytoplasmic components to help maintain cellular homeostasis and cell survival during exposure to stress. Lysine acetylation is a reversible post-translational modification that plays an important role in the regulation of diverse cellular processes. In this study, by using stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics analysis, we explored lysine acetylomics in response to rapamycin-induced autophagy in HeLa cells. In total, we identified 1,808 acetylation sites on 944 proteins, among which, significant changes of lysine acetylation on 533 sites on 397 proteins were observed. The identified lysine acetylated proteins were mainly distributed in the cytoplasm, nucleus and mitochondria. FxK*, K*xxxxK and KxxxxK* were shown to be potential autophagy-related lysine acetylated motifs. Gene Ontology enrichment analysis showed that all of the significantly acetylated proteins were involved in diverse transcription-dependent and independent pathways. Further analysis found that acetylation was significantly enriched in three major metabolic processes. Moreover, Several protein complexes, such as ribosomes, RNA spliceosomes and the ubiquitin-proteasome complex, were also significantly acetylated. Moreover, as expected, significant changes of variations were observed in the acetylation levels of lysine acetylation in acetyltransferases and deacetylases, such as KAT7 and p300, were observed in response to rapamycin-induced autophagy. Taken together, our data are the first to these data reveal that the lysine acetylation associates acetylome associated with autophagy, and therefore to provide new insights into exploring the mechanism of autophagy.

2022-03-03 | PXD004582 | Pride

Characterization of the acetylome associated with rapamycin-induced autophagy in HeLa cells

2019-01-02 | PXD005793 | Pride

Time-resolved analysis reveals rapid dynamics and broad scope of the CBP/p300 acetylome

Project description:The acetyltransferases CBP and p300 are multifunctional transcriptional co-activators; however, their acetylation targets, site-specific acetylation kinetics, and function in proteome regulation are incompletely understood. We combined quantitative proteomics with novel CBP/p300-specific catalytic inhibitors, bromodomain inhibitor, and gene knockout to show that CBP/p300 acetylates thousands of sites, including signature histone sites, as well as a multitude of sites on signaling effectors and enhancer-associated transcriptional regulators. Kinetic analysis identified a subset of CBP/p300-regulated sites with very rapid (<30min) acetylation turnover, revealing a dynamic balance between acetylation and deacetylation. Quantification of acetylation, mRNA, and protein abundance after CBP/p300 inhibition reveals a kinetically competent network of gene expression that strictly depends on CBP/p300-catalyzed rapid acetylation. Collectively, our in-depth acetylome analyses reveal systems attributes of CBP/p300 targets, and the resource dataset provides a framework for investigating CBP/p300 functions, as well as for understanding the impact of small molecule inhibitors targeting its catalytic and bromodomain activities.

2018-06-10 | PXD005252 | Pride

Acetylome and succinylome of Corynebacterium glutamicum

Project description:Profiles of two major acyl-modifications, lysine acetylation and succinylation, under L-glutamate-producting and non-producing conditions in Corynebacterium glutamicum, which is industrially utilized for amino acid fermentation, was analyzed. During glutamate overproduction induced by Tween 40, global lysine acetylation was decreased, while lysine succinylation was increased. A label-free semi-quantitative proteomic analysis identified 591 acetylated proteins with 1,509 unique acetylation sites and 297 succinylated proteins with 790 unique succinylation sites. Lysine acetylation and succinylation targeted most enzymes in the central carbon metabolic pathways that are directly related to glutamate production, including the 2-oxoglutarate dehydrogenase complex (ODHC), a key enzyme for glutamate overproduction.

2015-12-21 | PXD001662 | Pride

Quantitative analysis of acetylation in Vero cells infected with Peste des petits ruminants virus

Project description:Peste des petits ruminants virus (PPRV) is a negative-stranded RNA virus belonging to the Paramyxoviridae family and causes acute, highly contagious disease in small ruminants. Lysine acetylation plays central role in regulating gene expression. However, the extent and function of lysine acetylation in host cells during PPRV infection remains unknown. In this study, intensive proteomic quantification analysis of the proteome and acetylome of PPRV-infected Vero cells was performed using dimethylation labeling-based quantitative proteomics. As results, we identified 4729 proteins and 1068 acetylated proteins with 2641 quantified modification sites detected by mass spectrometry, of which 304 acetylated proteins with 410 acetylation sites were significantly acetylated in response to PPRV infection. Bioinformatics analyses revealed that the differentially acetylated proteins participated in carbohydrate catabolic and DNA metabolic process, and were associated with multifarious functions, suggesting that intracellular activities were extensively changed after PPRV infection. Protein-protein interaction network of the identified proteins further indicated that a variety of chaperone and ribosome processes were modulated by acetylation. To our knowledge, this is the first study on acetylome in host cell infected with PPRV. It provides an important point for future studies on the acetylated proteins involved in the host response to PPRV replication.

2023-10-24 | PXD025081 | Pride

Accurate quantification of site-specific acetylation stoichiometry reveals the impact of sirtuin deacetylase CobB on the E. coli acetylome

Project description:We applied SD-SILAC to determine absolute acetylation stoichiometry in exponentially-growing and stationary-phase wild type and sirtuin deacetylase CobB-deficient E. coli. We further assayed stoichiometry in phophotransacetylase (pta) and acetate kinase (ackA) mutant strains in the presence and absence of the sirtuin inhibitor nicotinamide. Comparison to relative quantification under the same conditions validated our stoichiometry estimates at hundreds of sites, demonstrating the accuracy of our method. We measured acetylation stoichiometry at 3,669 unique sites and found that the vast majority of acetylation occurs at very low stoichiometry (median 0.04%). Manipulations that cause increased nonenzymatic acetylation by acetyl-phosphate (AcP), such stationary-phase arrest and deletion of ackA, resulted in globally increased acetylation stoichiometry. Similar to sirtuin deacetylase 3 (SIRT3) in mitochondria, CobB suppressed acetylation to lower than median stoichiometry at hundreds of sites in WT, pta, and ackA cells. These results suggest an evolutionarily conserved function of sirtuin deacetylases in suppressing low stoichiometry acetylation.

2017-03-07 | PXD005757 | Pride