LFQ proteomics of Streptomyces albus phosoablative CslA mutant strain
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ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Streptomyces Albus J1074
TISSUE(S): Cell Culture, Cell Line Cell
SUBMITTER: 
Michał Tracz
LAB HEAD: dr Michal Tracz
PROVIDER: PXD071342 | Pride | 2026-06-17
REPOSITORIES: Pride
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Project description:Streptomyces coelicolor A3(2) is a model organism for antibiotic production at high potency. Its chromosome contains over 20 gene clusters responsible for secondary metabolite biosynthesis. This complexity of putatively competing regulatory and biosynthetic pathways can however negatively impact the yield of desired metabolite biosynthesis. Hence, a better understanding of these pathways is crucial for design of high-scale bioengineering processes. For this study proteome changes of certain S. coelicolor biosynthesis mutants were monitored. These were a double mutant with scbA protein deletion and atrA protein overexpression (∆scbA-atrAOE), as well as, an atrA protein deletion mutant (ΔatrA). These two mutants were relatively assessed against, respectively, a single mutant with scbA protein deletion (∆scbA-atrAOE vs ∆scbA-Φ) and a wild-type strain (ΔatrA vs M145).
2026-04-02 | PXD066756 | Pride
Project description:Bacteria can detect, transmit and react to signals from the outside world by using two-component systems an serine-threonine kinases and phosphatases. Streptococcus mutans contains one serine-threonine kinase, encoded by pknB. A gene encoding a serine-threonine phosphatase, pppL, is located downstream of pknB. In this study, the phenotypes of single mutants in pknB and pppL and a pknBpppL double mutant were characterized. All mutants exhibited a reduction in genetic transformability and biofilm formation, showed abnormal cell shapes, grew slower than the wild type strain in several complex media and had lost acid tolerance. The mutants had reduced cariogenic capacity, but no defects in colonization in a rat caries model. Whole genome transcriptome analysis revealed that pknB mutant showed reduced expression of genes involved in bacteriocin production and genetic competence. Among the genes that were diferentially regulated in the pknB mutant, severeal were likely to be involved in cell wall metabolism. One such gene, SMU.2146c and two genes encoding bacteriocins, were showed to be also down-regulated in vicK, which encodes a sensor kinase involved in response to oxidative stress. Collectively, the results suggest that PknB can modulate the activity of the two-component signal transduction systems vicKR and comDE. Real-time PCR showed that the genes down-regulated in the pknB mutant were up-regulated in the pppL mutant, indicating that PppL served to counteract PknB.
2010-03-05 | GSE18355 | GEO
Project description:Bacteria can detect, transmit and react to signals from the outside world by using two-component systems an serine-threonine kinases and phosphatases. Streptococcus mutans contains one serine-threonine kinase, encoded by pknB. A gene encoding a serine-threonine phosphatase, pppL, is located downstream of pknB. In this study, the phenotypes of single mutants in pknB and pppL and a pknBpppL double mutant were characterized. All mutants exhibited a reduction in genetic transformability and biofilm formation, showed abnormal cell shapes, grew slower than the wild type strain in several complex media and had lost acid tolerance. The mutants had reduced cariogenic capacity, but no defects in colonization in a rat caries model. Whole genome transcriptome analysis revealed that pknB mutant showed reduced expression of genes involved in bacteriocin production and genetic competence. Among the genes that were diferentially regulated in the pknB mutant, severeal were likely to be involved in cell wall metabolism. One such gene, SMU.2146c and two genes encoding bacteriocins, were showed to be also down-regulated in vicK, which encodes a sensor kinase involved in response to oxidative stress. Collectively, the results suggest that PknB can modulate the activity of the two-component signal transduction systems vicKR and comDE. Real-time PCR showed that the genes down-regulated in the pknB mutant were up-regulated in the pppL mutant, indicating that PppL served to counteract PknB. Wild-type strain UA159 and a pknB mutant derivative were grown planktonically until OD600nm was 0.3. RNA was extracted, converted to cDNA, labelled and hybridized on S. mutans microarrays. The experiment was done in triplicate including one dye swap.
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Project description:The Mycobacterium tuberculosis eukaryotic-like serine/threonine protein kinase (STPKs) PknA and PknB regulate several processes required for cell growth, both kinase have been found to be and can be investigated by using the conditional mutant. In the present study, we created the M. tuberculosis kinase PknA/ PknB depletion mutant and performed the phosphoproteomics to uncover phosphorylation substrates changes when PknA/ PknB depletion.
2020-05-27 | PXD015197 | Pride
Project description:To evaluate the DNA binding of FscRI in Streptomyces albus S4 in vivo ChIP-Seq experiments were carried out on dusing anti-FLAG antibodies against 3xFLAG-FscRI protein using two biological replicates. The wild type strain was used as a control in experiments using the anti-FLAG antibodies as well as a DNA only control.
2016-11-14 | E-MTAB-5122 | biostudies-arrayexpress
Project description:Tuberculosis claims nearly 2 million lives annually and its causative agent Mycobacterium tuberculosis is a highly successful pathogen which explores multiple signalling mechanisms to grow and survive in humans for decades. Well-studied protein kinase B (PknB), one of the 11 serine/threonine kinases present in M. tuberculosis, is critical for growth in vitro and in vivo. Here we demonstrate that PknB-depleted mycobacteria can normally replicate and synthesise peptidoglycan in osmoprotective medium. Comparative phosphoproteomics of PknB-producing and PknB-depleted mycobacteria identifies CwlM as a major PknB substrate. Complementation studies of cwlM mutant further support CwlM phosphorylation as the molecular basis for the PknB essentiality. We demonstrate that in growing mycobacteria CwlM is produced in two forms with distinct functions which are essential for growth: a non-phosphorylated membrane-associated CwlM and a PknB-phosphorylated cytoplasmic CwlM. Immunoprecipitation and mycobacterial two hybrid assays reveal partner proteins for phosphorylated and non-phosphorylated CwlM forms, as FhaA, a forkhead-associated domain protein, and MurJ (MviN), a predicted Lipid II flippase, respectively. We propose that PknB is not required for mycobacterial division but coordinates peptidoglycan polymerization and cross-linking by a novel CwlM-mediated mechanism
2018-09-24 | PXD009239 | Pride
Project description:To evaluate the DNA binding of AntA in Streptomyces albus S4, in vivo ChIP-Seq experiments were performed 3xFLAG-AntA and anti-FLAG antibodies using two biological replicates. The wild type strain was used as a control in experiments using the anti-FLAG antibodies as well as a DNA only control (which were published previously, E-MTAB-5122).
2019-02-28 | E-MTAB-7700 | biostudies-arrayexpress
Project description:Streptomyces albus S12, TK and Tet30Chl25 are the parental strain , low-yield and high-yield of salinomycin mutant obtained by ARTP and ribosome engineering ,respectively. There are total 1602 differentially expressed genes (DEGs) show differences in expression between the mutant strain TK, Tet30Chl25 and the initial strain S12. KEGG pathway analysis of differentially expressed genes (DEGs) between the mutant strain TK, Tet30Chl25 and the initial strain S12 show that the relevant differential pathways affecting salinomycin production were mainly related to butanoate metabolism, starch and sucrose metabolism, glyoxylate metabolism. Besides , the transcription of genes in the salinomycin biosynthesis gene cluster and the transcription level of related genes in the precursors biosynthesis pathway were more active in the high-yield salinomycin production strain Tet30Chl25. Furthermore, the transcription level ribosomal protein, string response, two component system and sigma factors are more active in high-yield of salinomycin mutants and that may involve in regulation of salinomycin biosynthesis and may account for the high-yield of salinomycin.
2019-10-01 | GSE133580 | GEO
Project description:To elucidate the effect of the rational ribosomal engineering on the changes in the expression of the endogenious biosynthetic gene clusters the transcriptome analysis was performed. The Streptomyces albus strains carrying mutations in rpsL gene (encode for ribosomal protein S12) and the deletion of the rsmG gene (16S rRNA methyltransferase G), as well as their combination were used for the experiment. The list of the strains with mutations is next: S. albus K88E, S. albus GI92, S. albus K88E-GI92, S. albus P91S, S. albus K88E-P91S, S. albus del rsmG, S. albus K88E-GI92 del rsmG, S. albus K88E-P91S del rsmG. Abovementioned strains along with S. albus native strain were grown in NL-19 production medium. Samples were harvested by centrifugation after 48 and 72 hours of cultivation. For total RNA isolation, S. albus cells were grown in SG medium (for ara expression) or NL19 medium (for indigenous BGC expression). Then, 2 ml of 2-day and 3-day cultures was spun down for 20 s at 14,000 × rpm, and the pellets were immediately frozen in liquid nitrogen and stored at ?80 °C. Total RNA extraction was performed using an RNeasy Kit (Qiagen, Hilden, Germany) as previously described (Huser et al. 2003). An RNase-Free DNase set (Qiagen) was used two times for on-column DNA digestion, and an additional DNase treatment was then performed with a DNase I kit (Roche Diagnostics, Mannheim, Germany) to ensure that all DNA was completely removed. To check the RNA samples for DNA contamination, PCR was performed using oligonucleotides designed to create two different products approximately 150 bp and 500 bp in size. Initially, RNA quality was checked with Trinean Xpose (Gentbrugge, Belgium) and Agilent RNA Nano 6000 kits on an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). A Ribo-Zero rRNA Removal Kit for bacteria was obtained from Illumina (San Diego, CA, USA) and used to remove ribosomal RNA molecules from isolated total RNA. rRNA removal was checked using an Agilent RNA Pico 6000 kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). A TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) was used to prepare cDNA libraries (Koepff et al. 2017). The resulting cDNAs were pair-end sequenced on an Illumina HiSeq 1500 system (San Diego, CA, USA) using a 70 bp read length. Short read alignments and differential gene expression were illustrated using ReadXplorer 2.2.0 (Hilker et al. 2014) and DEseq (Anders and Huber 2010), respectively.
2019-05-01 | E-MTAB-7715 | biostudies-arrayexpress
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2010-05-05 | E-GEOD-15346 | biostudies-arrayexpress