Systems biology of S.aureus adaptation under Ser/Thr kinase wild type and mutations of kinase (pknB) or phosphatase (stp)
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ABSTRACT:
PROVIDER: PRJNA504786 | ENA |
REPOSITORIES: ENA
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Project description:Different transcriptome, metabolome, and phosphoproteome studies have already indicated a regulatory role of Ser/Thr phosphorylation in the central metabolism of S. aureus. However, it remains still unknown how this exactly tunes its metabolism. For that reason, Extreme Pathway Analysis was used to understand metabolic flux regulation by Ser/Thr phosphorylation. YANAsquare software and YANAvergence routine were chosen to calculate pathway activities of WT, ΔpknB, Δstp, and double mutant S. aureus NewmanHG strains. Gene expression data of S. aureus NewmanHG were collected taking the wild type and mutations of kinase (pknB), phosphatase (stp) or both (pknB/stp) phenotypes. The resulting flux changes were modelled with YANAvergence taking the different gene expression data and an established genome scale model of S. aureus metabolic modes as basis. The fluxes of the different strains were next calculated, taking the gene expression data into account. A concerted metabolic change of fluxes was observed. In particular the pathways for peptidoglycan, nucleotide, and aromatic amino acid synthesis as well as catabolism involving aspartate transaminase (GOT) changed significantly compared to the wild type. Single mutations of pknB and stp were compared to illustrate their different contribution to the phenotype, e.g. pyrimidine synthesis is dramatically impaired by pknB deletion but much less by loss of stp. In the double knock out strain, there is higher activity of peptidoglycan, purine, and aromatic amino acids synthesis from glucose, but lower activity of pyrimidine synthesis from glucose compared to WT. The results suggest a probable regulatory role of Ser/Thr phosphorylation in amino acid catabolism and the glycolysis/gluconeogenesis switch to provide the cell with sufficient cell wall components, nucleotides, and aromatic amino acids. Yvck is suggested to serve as regulatory protein linking Ser/Thr phosphorylation to the previous results of S. aureus metabolism. Moreover, Yvck seems in particular to be involved in the switch between glycolysis and gluconeogenesis. However, further studies based on experimental approaches are needed to demonstrate that Ser/Thr phosphorylation and Yvck are necessary for a correct cell growth under gluconeogenic conditions. The metabolic model allows not only a comprehensive representation of these changes for all involved pathways in the four strains, it further points out the function of the previously unannotated ycvk operon.. The relevance of these specific metabolic pathway adaptations regarding the pathogenicity of S.aureus and their contributions to the infection process will be analyzed and discussed.
2019-11-11 | GSE122362 | GEO
Project description:To understand the functional network of Human Ser/Thr phosphatse regulatory subunits in the cell, we performed a systematic proteomic analysis of nine human Ser/Thr phosphatase regulatory subunits using tandem affinity purification coupled with mass spectrometry (TAP-MS).
2019-08-16 | PXD014772 | Pride
Project description:We report the mRNA expression profile of Streptococcus pneumoniae Type 2 D39 strain-derived mutant lacking the phpP gene encoding eukaryote-type ser/thr phosphatase and the stkP gene encoding Ser/Thr protein kinase.
2019-04-13 | GSE113337 | GEO
Project description:The PPP2R5D encodes for a Protein phosphatase 2A (PP2A), one of the four major Ser/Thr phosphatases negatively controlling cell growth and division. PP2A is consisting of a common heteromeric core enzyme with a catalytic subunit and a B regulatory subunit that might control the substrate selectivity and catalytic activity. We investigated the potential role of Ppp2r5d for the cardiomyocyte (cultured mouse cardiomyocytes).
2024-09-30 | GSE238141 | GEO
Project description:Protein Ser/Thr kinases are post-translational regulators of key molecular processes in bacteria, such as cell division and antibiotic tolerance. Here we characterize the E. coli toxin YjjJ (HipH), a putative protein kinase annotated as a member of the family of HipA-like Ser/Thr kinases which are involved in antibiotic tolerance. Using SILAC-based phosphoproteomics we provide experimental evidence that YjjJ is a Ser/Thr protein kinase and its primary protein substrates are the ribosomal protein RpmE (L31) and the carbon storage regulator CsrA. YjjJ activity impacts ribosome assembly, cell division and central carbon metabolism but it does not increase antibiotic tolerance as does its homologue HipA. Intriguingly, overproduction of YjjJ and its kinase-deficient variant can activate HipA and other kinases, pointing to a crosstalk between Ser/Thr kinases in E. coli.
2022-11-28 | PXD033071 | Pride
Project description:RNA-seq analysis of a Streptococcus pyogenes mutant lacking the eukaryote-type ser/thr phosphatase (SP-STP)
| PRJNA300672 | ENA
Project description:We report the mRNA expression profile of Streptococcus pneumoniae Type 2 D39 strain-derived mutant lacking the phpP gene encoding eukaryote-type ser/thr phosphatase .
2016-10-27 | GSE74421 | GEO
Project description:Huarat2016 -Starvation-induced Ser/Thr
protein kinase ArnS (Saci_1181) (Model 14)
This model is described in the article:
ArnS, a kinase involved in
starvation-induced archaellum expression.
Haurat MF, Figueiredo AS, Hoffmann
L, Li L, Herr K, J Wilson A, Beeby M, Schaber J, Albers SV.
Mol. Microbiol. 2016 Oct; :
Abstract:
Organisms have evolved motility organelles that allow them
to move to favourable habitats. Cells integrate environmental
stimuli into intracellular signals to motility machineries to
direct this migration. Many motility organelles are complex
surface appendages that have evolved a tight, hierarchical
regulation of expression. In the crenearchaeon Sulfolobus
acidocaldarius, biosynthesis of the archaellum is regulated by
regulatory network proteins that control expression of
archaellum components in a phosphorylation-dependent manner. A
major trigger for archaellum expression is nutrient starvation,
but although some components are known, the regulatory cascade
triggered by starvation is poorly understood. In this work, the
starvation-induced Ser/Thr protein kinase ArnS (Saci_1181)
which is located proximally to the archaellum operon was
identified. Deletion of arnS results in reduced motility,
though the archaellum is properly assembled. Therefore, our
experimental and modelling results indicate that ArnS plays an
essential role in the precisely controlled expression of
archaellum components during starvation-induced motility in
Sulfolobus acidocaldarius. Furthermore they combined in vivo
experiments and mathematical models to describe for the first
time in archaea the dynamics of key regulators of archaellum
expression.
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MODEL1607210000.
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2016-12-05 | MODEL1607210000 | BioModels
Project description:Vibrio alginolyticus is a Gram-negative marine bacterium. A limited population of the organisms causes acute gastroenteritis in humans. In this study, Vibrio alginolyticus wild type strain EPGS is compared with the mutants of Ser-Thr kinase PpkA and phosphatase PppA, after cultured for 7h, in Luria-Bertani containing medium 3 % NaCl at 30 C. Our goal is to determine the ppkA and pppA regulon.
2011-12-31 | GSE24319 | GEO
Project description:Like eukaryotes, different bacterial species express one or more Ser/Thr kinases and phosphatases that operate in various signaling networks by catalyzing phosphorylation and dephosphorylation of proteins that can immediately regulate biochemical pathways by altering protein function. The human pathogen Streptococcus pneumoniae encodes a single Ser/Thr kinase-phosphatase couple known as StkP-PhpP, which has shown to be crucial in the regulation of cell wall synthesis and cell division. In this study, we applied proteomics to further understand the physiological role of pneumococcal PhpP and StkP with an emphasis on phosphorylation events on Ser and Thr residues. Therefore, the proteome of the non-encapsulated D39 strain (WT), a kinase (ΔstkP) and phosphatase mutant (ΔphpP) were compared in a mass spectrometry based label-free quantification experiment. Results show that a loss of function of PhpP causes an increased abundance of proteins in the phosphate uptake system Pst. Quantitative proteomic data demonstrated an effect of StkP and PhpP on the two-component systems ComDE, LiaRS, CiaRH and VicRK. To obtain further information on the function, targets and target sites of PhpP and StkP we combined the advantages of phosphopeptide enrichment using titan dioxide and spectral library based data evaluation for sensitive detection of changes in the phosphoproteome of the wild type and the mutant strains. According to the role of StkP in cell division we identified several proteins involved in cell wall synthesis and cell division that are apparently phosphorylated by StkP. Unlike StkP, the physiological function of the co-expressed PhpP is poorly understood. For the first time we were able to provide a list of previously unknown putative targets of PhpP. Under these new putative targets of PhpP are, among others, five proteins with direct involvement in cell division (DivIVA, GpsB) and peptidoglycan biosynthesis (MltG, MreC, MacP).
2020-01-22 | PXD015268 | Pride