Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bacillus subtilis acetylome and succinylome

ABSTRACT: The two major acyl-modifications on lysine residues, acetylation and succinylation, were analyzed in the gram-positive model bacterium Bacillus subtilis. To identify and quantify the changes in acetylation and succinylation in response to the carbon source, a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomic analysis of cells grown on glucose or citrate was performed.

INSTRUMENT(S): Q Exactive

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

TISSUE(S): Cell Lysate

SUBMITTER: Saori Kosono

LAB HEAD: Saori Kosono

PROVIDER: PXD001615 | Pride | 2015-07-02

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	131128_QE_509_Kosono_1_GlcH_Ac.raw	Raw
	131128_QE_509_Kosono_1_GlcH_Ac_miss2.pep.xml	Pepxml
	131128_QE_509_Kosono_2_GlcH_Sc.raw	Raw
	131128_QE_509_Kosono_2_GlcH_Sc_miss2.pep.xml	Pepxml
	140218_QE_641_Kosono_1_Ac.raw	Raw

Items per page:

1 - 5 of 14

Publications

Changes in the Acetylome and Succinylome of Bacillus subtilis in Response to Carbon Source.

Kosono Saori S Tamura Masaru M Suzuki Shota S Kawamura Yumi Y Yoshida Ayako A Nishiyama Makoto M Yoshida Minoru M

PloS one 20150622 6

Lysine residues can be post-translationally modified by various acyl modifications in bacteria and eukarya. Here, we showed that two major acyl modifications, acetylation and succinylation, were changed in response to the carbon source in the Gram-positive model bacterium Bacillus subtilis. Acetylation was more common when the cells were grown on glucose, glycerol, or pyruvate, whereas succinylation was upregulated when the cells were grown on citrate, reflecting the metabolic states that prefer ...[more]

PMID: 26098117

Similar Datasets

Comparative assessment of quantification methods for tumor tissue phosphoproteomics

Project description:The choice of quantification method is critical for study design and comparison of cancer phosphoproteomes. We comparatively assessed label-free quantification (LFQ), spike-in-SILAC (stable isotope labeling of amino acids in cell culture) and tandem mass tag (TMT) labeling techniques for quantitative phosphoproteome analysis in tumor tissues. Using ovarian cancer tissue as an example, our study establishes a resource for the design and analysis of quantitative phosphoproteomics studies in cancer research and diagnosis. TMT provided the lowest accuracy and the highest precision and robustness across different phosphosite abundances and matrices (cell culture versus tumor tissue). Spike-in-SILAC offered the best compromise between these features, but was limited by low phosphosite coverage. LFQ provided the lowest precision, but the highest number of phosphosite identifications. Spike-in-SILAC and LFQ were susceptible to matrix effects arising from different sample types. Analysis based on match between run (MBR) improved phosphosite coverage across technical replicates in LFQ and spike-in-SILAC, but further reduced the precision and robustness of quantification.

2022-08-09 | PXD030450 | Pride

Transcription profiling of yeast mutants Gal-YAH1, Gal-ATM1 and Gal-NBP35 to investigate responses to defects in cellular Fe-S protein maturation

Project description:The biogenesis of iron-sulfur proteins in eukaryotes is an essential process involving the mitochondrial iron-sulfur cluster (ISC) assembly and export machineries and the cytosolic Fe/S protein assembly (CIA) apparatus. To define the integration of Fe/S protein biogenesis into cellular homeostasis, we compared the global transcriptional responses to defects in the three biogenesis systems in S. cerevisiae using DNA microarrays. Microarray analyses were carried out with regulatable yeast mutants in which representatives of each of the three biosynthetic systems could be depleted. In particular, we used the mutants Gal-YAH1, Gal-ATM1 and Gal-NBP35.

2007-12-14 | E-MEXP-1215 | biostudies-arrayexpress

Functional analysis of BipA in E. coli reveals the plasticity of 50S ribosome assembly

Project description:BipA is a conserved translational GTPase that resembles elongation factor EF-G and 30S assembly factor LepA. Recent evidence suggests that BipA functions in 50S subunit assembly, but the precise role of the factor remains unclear. Here, we use stable isotope labeling of amino acids in culture and mass spectrometry (SILAC / MS) to examine the function of BipA in ribosome biogenesis. During growth at suboptimal temperature, loss of BipA leads to accumulation of immature large subunit particles (~40S) that lack several proteins. These include L2, L7/12, L10, L14, L16, L17, L19, L27, L28 and L32. Parallel analysis of the control (wild-type) strain shows accumulation of virtually identical intermediate particles, although at much lower levels. Further analysis showed that the main path of 50S assembly differs depending on media in which the cells are grown, demonstrating the robust and flexible nature of the assembly process.

2021-09-09 | PXD017917 | Pride

Saccharomyces cerevisiae mutant strain with R1158 strain background: Fold change after doxycycline treatment

Project description:To understand the extent that Heat shock protein 90 (Hsp90) regulated its target proteins at the transcription level, transcriptomic change was profiled in yeast cells upon Hsp90 compromising. We genetically modified the R1158 strain (resulting genotype of mutant strain: TETp-HSC82 hsp82Δ arg4Δ lys5Δ car2Δ::URA3) and then reduced the Hsp90 amount with doxycycline treatment. Fold change of mRNA from untreated to treated cells indicated the transcriptomic change. Totally, we identified 1104 genes mis-regulated with a fold change of no less than 1.5 (P <0.05) upon Hsp90 compromising. Two-condition experiment, treated vs. untreated cells. Biological duplicates, independently grown and harvested. Technical triplicates for RNA isolation.

2014-03-26 | E-GEOD-56186 | biostudies-arrayexpress

Succinylome analysis of pCAR1-free and pCAR1-harbouring Pseudomonas putida KT2440.

Project description:The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis. This dataset is related to PXD007089.

2018-11-21 | PXD007133 | Pride

Succinylome analysis of pCAR1-free and pCAR1-harbouring Pseudomonas putida KT2440 (2).

2018-11-21 | PXD007722 | Pride

Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane treated human breast epithelial cells

Project description:Sulforaphane (SFN), an isothiocyanate found in cruciferous vegetables, is a potent inhibitor of experimental mammary carcinogenesis and may be an effective, safe chemopreventive agent for use in humans. SFN acts in part on the Keap1/Nrf2 pathway to regulate a battery of cytoprotective genes. In this study transcriptomic and proteomic changes in the estrogen receptor negative, non tumorigenic human breast epithelial MCF10A cell line were analyzed following SFN treatment or KEAP1 knockdown with siRNA using microarray and stable isotopic labeling with amino acids in culture (SILAC), respectively. Changes in selected transcripts and proteins were confirmed by PCR and Western blot in MCF10A and MCF12A cells. There was strong correlation between the transcriptomic and proteomic responses in both the SFN treatment (R=0.679, P<0.05) and KEAP1 knockdown (R=0.853, P<0.05) experiments. Common pathways for SFN treatment and KEAP1 knockdown were xenobiotic metabolism and antioxidants, glutathione metabolism, carbohydrate metabolism and NADH/NADPH regeneration. Moreover, these pathways were most prominent in both the transcriptomic and proteomic analyses. The aldo-keto reductase family members, AKR1B10, AKR1C1, AKR1C2 and AKR1C3, as well as NQO1 and ALDH3A1, were highly upregulated at both the transcriptomic and proteomic level. Collectively, these studies served to identify potential biomarkers that can be used in clinical trials to investigate the initial pharmacodynamic action of SFN in the breast. MCF10A cells were treated with SFN or had KEAP1 knocked down by siRNA.

2011-04-22 | E-GEOD-28813 | biostudies-arrayexpress

MS2-Deisotoper: A tool for deisotoping high-resolution MS/MS spectra in normal and heavy isotope-labelled samples

Project description:High-resolution MS/MS spectra of peptides can be deisotoped to identify monoisotopic masses of peptide fragments. The use of such masses should improve protein identification rates. However, deisotoping is not universally used and its benefits have not been fully explored. Here, we developed MS2-Deisotoper, a tool for use prior to database search, to identify monoisotopic peaks in centroided MS/MS spectra. MS2-Deisotoper works by comparing the mass and relative intensity of each peptide fragment peak to every other peak of greater mass, and by applying a set of rules concerning mass and intensity differences. After comprehensive parameter optimisation, we show that MS2-Deisotoper could improve the number of peptide spectrum matches (PSMs) identified by up to 8.2% and proteins by up to 2.8%. It was effective with SILAC and non-SILAC MS/MS data. The identification of unique peptide sequences was also improved, increasing the number of human proteoforms by 3.7%. Detailed investigation of results showed that deisotoping increases Mascot ion scores, improves FDR estimation for PSMs and leads to greater protein sequence coverage. At a peptide level, we found that the efficacy of deisotoping was affected by peptide mass and charge. MS2-Deisotoper can be used via a user interface or as a command-line tool.

2019-08-05 | PXD010587 | Pride

Proteome, acetylome and succinylome analysis of pCAR1-free and pCAR1-harbouring Pseudomonas putida KT2440 (2)

Project description:The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the proteome, acetylome, and succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis.

2018-11-22 | PXD007090 | Pride

Proteome, acetylome and succinylome analysis of pCAR1-free and pCAR1-harbouring Pseudomonas putida KT2440

2018-09-24 | PXD007089 | Pride