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Lysine acetylation of the housekeeping sigma factor enhances the activity of RNA polymerase holoenzyme

ABSTRACT: Protein lysine acetylation is one of the abundant post-translational modifications in eukaryotes, but found in prokaryotes as well. Despite the evidence of the lysine acetylation in the prokaryotic RNA polymerases (RNAPs), its function remains unrevealed. We revealed that the housekeeping sigma factor (HrdB) was acetylated throughout the growth of Streptomyces venezuelae. The 259th lysine (K259) located between 1.2 and 2 regions was determined as the acetylated residue of HrdB in vivo by LC-MS/MS analyses

INSTRUMENT(S): Q Exactive

ORGANISM(S): Streptomyces Venezuelae

SUBMITTER: Ji-Eun Kim

LAB HEAD: Jung-Hye Roe

PROVIDER: PXD015174 | Pride | 2020-05-27

REPOSITORIES: Pride

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			Action	DRS
	Early_KJE01_NCP1_J100_0129_1.raw	Raw
	Early_KJE03_NAQ454_J100_1210.raw	Raw
	Early_KJE03_NCP1_J100_0129_1.raw	Raw
	Early_KJE05_NCP1_J100_0129_1.raw	Raw
	KJE_exp_1_NAQ448_J100_180420.raw	Raw

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Lysine acetylation of the housekeeping sigma factor enhances the activity of the RNA polymerase holoenzyme.

Kim Ji-Eun JE Choi Joon-Sun JS Kim Jong-Seo JS Cho You-Hee YH Roe Jung-Hye JH

Nucleic acids research 20200301 5

Protein lysine acetylation, one of the most abundant post-translational modifications in eukaryotes, occurs in prokaryotes as well. Despite the evidence of lysine acetylation in bacterial RNA polymerases (RNAPs), its function remains unknown. We found that the housekeeping sigma factor (HrdB) was acetylated throughout the growth of an actinobacterium, Streptomyces venezuelae, and the acetylated HrdB was enriched in the RNAP holoenzyme complex. The lysine (K259) located between 1.2 and 2 regions ...[more]

PMID: 31970401

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S. venezuelae HupS protein acetylated lysine mapping via bottom-up LC-MS

Project description:Nucleoid-associated proteins (NAPs) are critical during the process of chromatin compaction in Streptomyces soil bacteria. HupS is one of the two NAPs encoded in the Streptomyces genome. Its unique C-terminal domain, rich in lysine repeats (LR domain), is alike to the H2B histone found in eukaryotic cells or the HupB protein found in Mycobacterium. Project study aim was to identify post-translationally acetylated lysine residues of HupS via bottom-up LC-MS. Two approaches were uptaken. One was based on HupS enrichment from a strain expressing a recombinant HupS with a C-terminal FLAG tag (TM015) via an antiFLAG pull-down, and the other relied on a proteome-wide search of acetylated peptides in a WT strain lysate. Controls for spectral false-positives were also carried out in parallel, which were an antiFLAG pull-down with a WT strain, and a proteome-wide search of acetylated peptides in a HupS deletion mutant strain (ΔhupS) lysate. 5 lysine acetylation sites were confidently determined for the HupS protein within this study, them being Lys51, Lys85, Lys104, Lys119, and either Lys193 or Lys194.

2024-06-03 | PXD050776 | Pride

Histone H3K4 Demethylation is Negatively Regulated by Histone H3 Acetylation in S. cerevisiae

Project description:Histone H3 lysine 4 tri-methylation (H3K4me3) is a hallmark of transcription initiation, but how H3K4me3 is demethylated during gene repression is poorly understood. Jhd2, a JmjC domain protein, was recently identified as the major H3K4me3 histone demethylase (HDM) in S. cerevisiae. While JHD2 is required for removal of methylation upon gene repression, deletion of JHD2 does not result in increased levels of H3K4me3 in bulk histones, indicating that this HDM is unable to demethylate histones during steady state conditions. In this study, we showed that this was due to the negative regulation of Jhd2 activity by histone H3 lysine 14 acetylation, which co-localizes with H3K4me3 across the yeast genome. We demonstrated that loss of the histone H3-specific acetyltransferases (HATs) resulted in genome-wide-depletion of H3K4me3, and this was not due to a transcription defect. Moreover, H3K4me3 levels were reestablished in HAT mutants following loss of JHD2, which suggested that H3-specific HATs and Jhd2 served opposing functions in regulating H3K4me3 levels. We revealed the molecular basis for this suppression by demonstrating that histone H3K14 acetylation negatively regulated Jhd2 demethylase activity on an acetylated peptide in vitro. These results revealed the existence of a general mechanism for removal of H3K4me3 following gene repression. Examination of H3K4me3 in WT, ada2sas3, ada2sas3jhd2, and jhd2 strains.

2012-11-05 | E-GEOD-41424 | biostudies-arrayexpress

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

The global acetylome of the human pathogen Vibrio cholerae V52 reveals lysine acetylation of major transcriptional regulators

Project description:Protein lysine acetylation is recognized as an important reversible post translational modification in all domains of life. While its primary roles appear to reside in metabolic processes, lysine acetylation has also been implicated in regulating pathogenesis in bacteria. By now, several global lysine acetylome analyses have been carried out in various bacteria, but thus far there have been no reports of lysine acetylation taking place in the important human pathogen Vibrio cholerae. In this study, we analyzed the lysine acetylproteome of the human pathogen V. cholerae V52. By applying a combination of immuno-enrichment of acetylated peptides and high resolution mass spectrometry, we identified 3402 acetylation sites on 1240 proteins. Of the acetylated proteins, more than half were acetylated on two or more sites. As reported for other bacteria, we observed that many of the acetylated proteins were involved in metabolic and cellular processes and there was an over-representation of acetylated proteins involved in protein synthesis. Of interest, we demonstrated that many global transcription factors such as CRP, H-NS, IHF, Lrp and RpoN as well as transcription factors AphB, TcpP, PhoB, and ToxR, involved in direct regulation of virulence in V. cholerae were acetylated. In addition VAS effector proteins involved in type VI secretion were acetylated. The overall level of acetylation increased during growth and was higher in stationary phase. In conclusion, this is the first global protein lysine acetylome analysis of V. cholerae and should constitute a valuable resource for in-depth studies of the impact of lysine acetylation in pathogenesis and other cellular processes.

2018-01-02 | PXD008055 | Pride

Nε- and O-Acetylation in Mycobacterium tuberculosis Lineage 7 is Biased Towards Proteins Involved in Growth, Virulence and Antimicrobial Resistance

Project description:Protein acetylation is one of the post-translational modifications (PTMs) involved in regulating a myriad of cellular processes in bacteria. Increasing evidence demonstrates that lysine acetylation is involved in Mycobacterium tuberculosis (Mtb) virulence and pathogenesis. However, previous reports have detected acetylation at lysine residues using only reference strains. Here, we analyzed the global Nε- and O-acetylation of Mtb lineage 7 clinical isolates and H37Rv. Quantitative acetylome analysis resulted in identification of 2577 class-I acetylation sites derived from 987 proteins. These proteins were found to be involved in central metabolism, translation, stress responses and drug resistance. Interestingly, 261 acetylation sites on 164 proteins were differentially regulated between the two virulent strains. A total of 257 acetylation sites on 160 proteins were hypoacetylated in lineage 7. These proteins are involved in Mtb growth, virulence, energy metabolism, host-pathogen interaction and stress responses. Furthermore, Gene Ontology (GO) analysis of exclusively acetylated proteins identified revealed strain-specific enrichment of selected biological processes. Taken together, this study provides the first global analysis of O-acetylated proteins in Mtb. This quantitative acetylome data presents the abundance and diversity of acetylated proteins in Mtb and opens a new avenue of research in exploring the role of protein acetylation in fine-tuning Mtb physiology.

2018-05-02 | PXD006630 | Pride

The acetylome analysis of lysine acetylation in the plant pathogenic bacterium Brenneria nigrifluens

Project description:Protein lysine acetylation, a dynamic and reversible posttranslational modification, plays a crucial role in several cellular processes including cell cycle regulation, metabolic pathways, enzymatic activities and protein interactions. Brenneria nigrifluens is the pathogen of shallow bark canker of walnut trees and can cause serious disease on walnut trees. Up to now, it is little known about the roles of lysine acetylation in the plant pathogenic bacteria. In the present study, the lysine acetylome of B. nigrifluens was determined by high-resolution LC-MS/MS analysis. In total, we identified 1,866 lysine acetylation sites distributed in 737 acetylated proteins. Bioinformatics results indicate that acetylated proteins participate in many different biological functions in B. nigrifluens. Four conserved motifs, namely, LKac, Kac*F, I*Kac and L*Kac, were identified in this bacterium. Protein interaction network analysis indicates that all kinds of interactions are modulated by protein lysine acetylation. Overall, 14 acetylated proteins are related to the virulence of B. nigrifluens.

2019-09-30 | PXD014046 | Pride

Systematic analysis of the lysine acetylome in Beauveria bassiana

Project description:Lysine acetylation emerging as a ubiquitous and conserved posttranslational modification plays an important regulatory role in almost every aspect of eukaryotes and prokaryotes. To gain insight into the nature, extent and biological function of lysine acetylation in Beauveria bassiana, a filamentous entomopathogenic fungus, we used immunoaffinity-based acetyl-lysine peptide enrichment integrated with high resolution mass spectrometry to comprehensively characterize lysine acetylated proteins in this fungus. Here we identified a total of 283 proteins with 464 acetylated sites, representing the first acetylproteome reported to date in filamentous fungi. Bioinformatics analysis of this acetylome showed that the acetylated proteins are involved in a wide range of cellular functions, such as metabolism, transcription, and exhibit diverse subcellular localizations. Enrichment of molecular function, biological process, and KEGG pathway implied that identified acetylated proteins of B. bassiana were very important in chromatin organization, ribosome, nucleosome assembly, carbon metabolism, and biosynthesis of secondary metabolites. Moreover, we matched five conserved lysine acetylated motifs containing of KacY, KacH, KacF, FxKac, KacxxxxK and one specific motif KacW in B. bassiana. Taken together, our acetylome analysis revealed a surprising breadth of cellular processes affected by lysine acetylation and also furnishes some fresh intervention nodes for the rational improvement of the friednly entomopathogenic fungus.

2017-11-02 | PXD003682 | Pride

ChIP-Seq of H4K5acK8ac and BRD2 in H23 NSCLC cell line treated with 500 nM JQ1 for 24h

Project description:Changes in acetylation of histone H4 are a common hallmark of cancer cells. In leukemia cells, histone H4 is characterized by loss of K16 mono-acetylation. Bromodomain proteins specifically recognize acetylated lysines and have been used as a target for anti cancer drug, JQ1 and iBET. Although acetylation and de-acetylation of histone H4 have been shown to have big impact in cancer cells, little attention has been focused on histone H4-acetylation at a genome level. To uncover potential epigenetic role of hyper-acetylated histone H4 at a genome-wide level in cancer cell, we generated a novel monoclonal antibody specifically recognizing histone H4 with at least two acetylated lysine residues (H4K5ac+K8ac). At the genome-wide level, hyper-acetylated histone H4 is associated with promoter and regulatory element (active enhancer, eRNA and super enhancer). We show that diacetylation at K5 and K8 of histone H4 co-localizes H3K27ac and BRD2 in the majority of active enhancer and promoters. However BRD2 has a stronger association with H4K5acK8ac. Furthermore we identified two specific chromatin states, which separately contain either H3K27ac or acetylated histone H4. Although JQ1 led to global reduction of BRD2 binding on the chromatin, only local changes of histone H4 multi-acetylation were observed upon BET inhibition by JQ1

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Integrated lysine acetylation stoichiometry and proteomics analysis in human cells

Project description:Lysine acetylation is a widespread posttranslational modification that targets a large number of biological pathways. Recent studies reveal that lysine acetylation sites exhibit mainly low stoichiometry. Here we explored three sample preparation methods, the use of detergents for the chemical acetylation reaction in combination with stable and efficient alkylating reagent, to analyze the stoichiometry of acetylation in three human cell lines. We identified and determined the acetylation occupancy in about 1500 protein in each cell line. Lysine acetylation is highly dynamic, we determined variations in the acetylation stoichiometry when nearby residues are phosphorylated. The stoichiometric analysis in combination with quantitative proteomics allowed us to better understand the role of this PTM in different cells. We found that high abundance of the deacetylase SIRT1 correlates with less acetylation occupancy and abundance of ribosomes, proteins involved in ribosome biogenesis, rRNA processing, among others. We confirmed through the inhibition of SIRT1 with EX-527, followed by quantitative proteomics and acetylation stoichiometry analyzes, the negative role of this deacetylase on transcription and translation pathways. In addition, we found that SIRT1 positively regulates several metabolic pathways.

2017-09-12 | PXD005903 | Pride

Comparative histone modification profiling revealed developmentally regulated acetylation on upstream promoters of C4 genes and potential C4 regulators

Project description:We analysed genome-wide histone H3 lysine 4 trimethylation and histone H3 lysine 9 acetylation, two modifications typically associated with active genes, in meristematic cells at the base and expanding cells in the maturing zone of the maize (Zea mays) leaf. These data were compared to transcript levels of associated genes. Our data revealed that for individual genes fold-changes in histone modification and transcript abundance were much better correlated than absolute intensities. When focusing on regulated modification sites, we identified secondary upstream H3 lysine 9 acetylation peaks (SUPs) on upstream promoter regions of approximately 6% of all acetylated genes. SUPs showed stronger regulation than the previously described acetylation peaks at transcription initiation sites, were more often found on genes that were upregulated towards the maturing zone than on downregulated genes, and were significantly enriched on photosynthetic genes. We identified SUPs on all genes encoding enzymes of the C4 cycle. Moreover, SUPs were enriched in four lists of candidate C4-associated genes that were derived from previous transcriptomic studies. Based on these data, we used highly regulated SUPs as an epigenetic mark to identify new genes potentially involved in C4 metabolism. This approach also allowed the identification of ethylene response elements as highly enriched cis-acting elements in SUP regions. Our data suggest co-evolution of epigenetic promoter elements during the establishment of C4 photosynthesis. Comparative analysis of H3K9ac, H3K4me3 and the transcription between two developmental zones within one maize leaf.

2015-09-03 | E-GEOD-67551 | biostudies-arrayexpress

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