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Global insights into lysine acetylome in Streptomyces coelicolor

ABSTRACT: By affinity enrichment using anti-acetyllysine antibody together with LC−MS/MS analysis, a total of 1,298 acetylation sites among 601 proteins were identified in S. coelicolor proteome

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Streptomyces Coelicolor

TISSUE(S): Cell Culture

SUBMITTER: Hong Zhang

LAB HEAD: Hong Zhang

PROVIDER: PXD019536 | Pride | 2021-09-30

REPOSITORIES: Pride

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Publications

Global Insights Into Lysine Acylomes Reveal Crosstalk Between Lysine Acetylation and Succinylation in Streptomyces coelicolor Metabolic Pathways.

Yang Yujiao Y Zhang Hong H Guo Zhenyang Z Zou Siwei S Long Fei F Wu Jiacheng J Li Peng P Zhao Guo-Ping GP Zhao Wei W

Molecular & cellular proteomics : MCP 20210914

Lysine acylations are reversible and ubiquitous post-translational modifications that play critical roles in regulating multiple cellular processes. In the current study, highly abundant and dynamic acetylation, besides succinylation, was uncovered in a soil bacterium, Streptomyces coelicolor. By affinity enrichment using anti-acetyl-lysine antibody and the following LC-MS/MS analysis, a total of 1298 acetylation sites among 601 proteins were identified. Bioinformatics analyses suggested that th ...[more]

PMID: 34530157

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Identification of desuccinylase ScCobB2 and its desuccinylation substrates in Streptomyces coelicolor

Project description:As a recently discovered protein posttranslational modification in eukaryotes, lysine succinylation has attracted increasing interest due to its ability to regulate several critical cellular processes including catabolism, β-oxidation, and ketogenesis. Nevertheless, understanding of the regulation mechanism is still at an early stage due to the lack of identified specific desuccinylases in most microorganisms.Here, in the model soil bacteria Streptomyces coelicolor, we biochemically characterized a sirtuin-like protein ScCobB2 as a divergent desuccinylase. Based on it, we identified a total of 673 unique succinylated sites, of which 470 sites in 317 proteins were quantified by combining tandem mass tag labeling, antibody affinity enrichment, and LC−MS/MS analysis. Furtheranalyses of the quantitative succinylome revealed that at least 114 proteins representing two major pathways, carbon metabolism and protein biosynthesis, are obviously hypersuccinylated in ∆ScCobB2 cells. We experimentally examined the regulatory roles of ScCobB2 on 13 hypersuccinylated proteins, including glyceraldehyde-3-phosphate dehydrogenase, aconitate hydratase, and several ribosomal proteins, the results of which suggested a high confidence in our quantitative data. This work provided the first discovery of a specificdesuccinylase in bacteria, and demonstrated it has pivotal regulatory role in multiple biological processes for S. coelicolor, laid the foundation for future research of succinylation regulation in other microorganisms.

2019-06-11 | PXD014202 | Pride

lysine acetylation and succinylation in Streptomyces coelicolor

Project description:To determine the acetylome of S. coelicolor, the wild-type S. coelicolor sample was prepared with three biological replicates and two technical replicates and analyzed. To quantify the acetylome and succinylome, three samples (wild-type, ∆SccobB1, and ∆SccobB2) with three biological replicates were prepared and analyzed. The cells were harvested, digested, and then subjected to affinity enrichment before LC-MS/MS analysis.

2021-07-13 | PXD027205 | Pride

The genome of Streptomyces rimosus shows a novel structure compared to other Streptomyces

Project description:This study compared the genome of Streptomyces rimosus rimosus against that of Streptomyces coelicolor. It also compared 4 strains with changes in oxytetracycline production and derived from G7, the type strain, against G7. Duplicate samples, each replicate may be found in the corresponding supplementary file for the Sample

2010-05-26 | E-GEOD-10126 | biostudies-arrayexpress

Global gene transcription analysis in Streptomyces coelicolor strains with modification of satKR genes.

Project description:We addressed the transcriptional changes in strains with mutations of satKR (sco3390-3389) genes to elucidate which genes are engaged in restoration of sporulation in non-sporulating Streptomyces coelicolor PS04 strain. Our experiments show that SatR can regulate growth and spore formation in Streptomyces and its activity is independent to DNA supercoiling.

2021-08-21 | E-MTAB-10835 | biostudies-arrayexpress

Response of Streptomyces coelicolor to treatment with the antibiotics vancomycin bacitracin and moenomycin A

Project description:To determine the response at the transcriptional level of S. coelicolor cells to treatment with 3 antibiotics that target distinct stages of cell wall biosynthesis, biological triplicate cultures of strain M600 were treated with sub-lethal concentrations (10 µg/ml) of vancomycin, bacitracin or moenomycin A. Samples were taken 0, 30, 60, 90 minutes after addition of the antibiotic. A negative control which received no drug treatment was also performed.

2011-04-29 | E-MEXP-3032 | biostudies-arrayexpress

Functional connexion of bacterioferritin in antibiotic production and morphological differentiation in Streptomyces coelicolor

Project description:Several two-component systems of Streptomyces coelicolor, a model organism to study antibiotic production in Streptomyces, affects the expression of the bfr (SCO2113) gene, which codifies for a bacterioferritin, a protein involved in iron storage. The ∆bfr mutant has a delay in morphological differentiation and pigmented antibiotic production (actinorhodin and undecylprodigiosin) on complex media. The effect of iron in minimal medium was also tested in the wild type and the ∆bfr mutant, and we observed different production of the two pigmented antibiotics in minimal medium, with differences between strains depending on iron concentration and the medium (solid or liquid). Contrary to expected, no intracellular iron differences were detected between the two strains, but there is a higher level of reactive oxygen species in the ∆bfr mutant and a higher tolerance to oxidative stress. Proteomics analysis showed no variation in iron response proteins and a lower abundance of proteins related to actinorhodin, ribosomal proteins and others related to secondary metabolism production and differentiation. On the contrary, it revealed a higher abundance of proteins related to different kind of stresses such as respiration and hypoxia, among others. The bacterioferritin of S. coelicolor is a new element in the complex regulation of the secondary metabolism in S. coelicolor and iron acts as a signal to modulate the biosynthesis of active molecules.

2024-09-09 | PXD050869 | Pride

Evidence of a role for CutRS and actinorhodin in the secretion stress response in Streptomyces coelicolor M145

Project description:This work was carried out to elucidate the proteins that are regulated by the two-component system CutRS in Streptomyces coelicolor M145 and how this response changes in the presence of glucose. A comparison of the whole cell proteomes of Streptomyces coelicolor M145 WT and Streptomyces coelicolor M145 ∆cutRS on both DNA (no glucose) and DNAD (with glucose) was made.

2023-06-16 | PXD040579 | Pride

RNA-Seq analysis reveals a six-gene SoxR regulon in Streptomyces coelicolor

Project description:We report 6 genes that were found to be regulated by SoxR in stationary phase when the bacteria produce the antibiotic actinorhodin. Five of these genes are previously confirmed SoxR targets; the sixth is a novel SoxR-target. RNA was obtained from 1-day or 3-day old wild type or soxR null mutant strains grown on R2YE agar complex medium. Biological replicates were obtained for 3 day-old samples. RNA was sequenced in an Illumina HiSeq 2000 sequencer for single reads of 100 bp and mapped to the S. coelicolor M145 genome.

2014-08-04 | E-GEOD-57268 | biostudies-arrayexpress

Sigma E of Streptomyces coelicolor can function both as a direct activator or repressor of transcription

Project description:Sigma factors are key components of the bacterial transcriptional apparatus that are essential for promoter recognition and transcription initiation. These factors are considered as positive regulators of gene expression. Here, we reveal the opposite, inhibitory role of these proteins. We used a combination of ChIP-seq, transcriptomic time series data, promoter sequence analysis, and computational modeling of gene expression to analyze the regulatory activity of the extracytoplasmic σE factor from Streptomyces coelicolor. Kinetic modeling of gene expression then allowed to cluster respective genes into groups, based on the type of their control. Importantly, this analysis indicated that σE might act not only as an activator of gene expression but also as its repressor. The direct repressor function of σE was then demonstrated by experimental analysis of selected promoter regions in vivo, showing that σE binds to promoter-like sequences, forming roadblocks for transcription initiated upstream. Finally, the σE interactome was defined, allowing the identification of ApgA as its potential anti- factor. Taken together, the results characterize σE, its regulation, regulon, and reveal its direct inhibitory function in gene expression, a so far unknown phenomenon that may be common also to other factors and organisms.

2024-01-26 | PXD041877 | Pride

Proteomic analysis of Streptomyces coelicolor vesicles

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2021-11-02 | PXD024085 | Pride