Streptomyces coelicolor
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PROVIDER: PRJNA101661 | ENA |
REPOSITORIES: ENA
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Project description:The filamentous bacterium Streptomyces coelicolor differentiates by forming specialized, spore-bearing aerial hyphae that grow into the air. Using microarrays, we identified genes that are down-regulated in a mutant unable to erect aerial hyphae. Through this route, we identified a previously unknown layer of aerial mycelium surface proteins (the "chaplins"). The chaplins share a hydrophobic domain of ~40 residues (the "chaplin domain"), and all have a secretion signal. The five short chaplins (ChpD,E,F,G,H) have one chaplin domain, whereas the three long chaplins (ChpA,B,C) have two chaplin domains and a C-terminal "sorting signal" that targets them for covalent attachment to the cell wall by sortase enzyme. Expression of the two chaplin genes examined (chpE, chpH) depended on aerial hyphae formation but not sporulation, and egfp fusions showed their expression localized to aerial structures. Mass spectrometry of cell wall extracts confirmed that the short chaplins localized to the cell surface. Deletion of chaplin genes caused severe delays in aerial hyphae formation, a phenotype rescued by exogenous application of chaplin proteins. These observations implicate the chaplins in aerial mycelium formation, and suggest that coating of the envelope by the chaplins is required for aerial hyphae to grow out of the aqueous environment of the substrate mycelium into the air.
2007-06-11 | E-SMDB-4093 | biostudies-arrayexpress
Project description:Extracytoplasmic function (ECF) sigma factors are a major type of bacterial signal transducer whose biological functions remain poorly characterised in streptomycetes. In this work, we studied SCO4117, a conserved ECF sigma factor from the ECF52 family, a class of ECF sigma factors exclusive to Actinobacteria. We demonstrate that SCO4117 is a pleiotropic activator of secondary metabolism, germination, aerial mycelium differentiation and sporulation. The expression of genes encoding secondary metabolism pathways (deoxysugar synthases, actinorhodin biosynthetic genes), and genes involved in differentiation (bld, whi, rdl, chp, nepA, ssgB, scbR), was dramatically reduced (up to 300-fold) in a SCO4117 knockout strain. SCO4117 expression depends on its position in the chromosome, as the knockout mutant phenotype can only be fully complemented when the SCO4117 ORF is restored in the chromosome. A strain expressing a truncated version of SCO4117 harbouring only the ECF sigma factor domain, has an opposite phenotype to that observed in the knockout strain, consisting of overproduction of antibiotics (actinorhodin, CDA, cryptic antibiotics) and acceleration of differentiation (aerial mycelium differentiation and sporulation), suggesting a complex interaction between the SCO4117 domains that affects protein activity. Some genes from predicted secondary metabolite clusters (cryptic pathways) were up-regulated compared to the wild strain, indicating that this truncated version of the SCO4117 protein might be useful to activate cryptic pathways. Overall, in this work we demonstrate the pleiotropic effects on the regulation of secondary metabolism and differentiation of SCO4117, the first member of the ECF52 family to be characterised. SCO4117 is a conserved gene overexpressed during the substrate and aerial mycelium stages, showing complex regulation at the transcriptional and post-translational levels.
2018-03-07 | GSE107661 | GEO
Project description:The developmental life cycle of Streptomyces species includes aerial hyphae formation and spore maturation, two distinct developmental processes that are controlled, respectively, by two families of developmental regulatory genes, bld and whi. In this study, we show that the response regulator MtrA (SCO3013) is critical for normal development of aerial hyphae in S. coelicolor and related species. ΔmtrA, a deletion mutant of the response regulator gene mtrA, exhibited the bald phenotype typical of bld mutants defective in aerial mycelium formation, with formation either much delayed or absent depending on the culture medium. Transcriptional analysis indicated that MtrA activates multiple genes involved in formation of aerial mycelium, including chp, rdl, and ram genes, as well as developmental regulatory genes of the bld and whi families. However, the major regulatory gene bldD showed enhanced expression in ΔmtrA, suggesting it is repressed by MtrA. EMSAs indicated that MtrA binds upstream of several genes with altered expression in ΔmtrA, including bldD and whiI, and sequences similar to the consensus binding sequence for MtrA of another actinomycete, Mycobacterium tuberculosis, were found in the bound sites. A loosely conserved recognition sequence containing two short, direct repeats was identified for MtrA of S. coelicolor and was validated using mutational analysis. MtrA homologues are widely distributed among Streptomyces species, and as with S. coelicolor, deletion of the mtrA homologues sve_2757 from S. venezuelae and sli_3357 from S. lividans resulted in conditional bald morphology. Our study suggests a critical and conserved role for MtrA in Streptomyces development.
2017-09-27 | GSE104263 | GEO
Project description:GlnK is an important nitrogen sensor protein in Streptomyces coelicolor. Deletion of glnK results in a medium-dependent failure of aerial mycelium and spore formation and loss of antibiotic production. Thus, GlnK is not only a regulator of nitrogen metabolism but also of morphological differentiation and secondary metabolite production. Through a comparative transcriptomic approach between the S. coelicolor wild-type and a S. coelicolor glnK mutant strain, 142 genes were identified that are differentially regulated in both strains. Among these are genes of the ram and rag operon, which are involved in S. coelicolor morphogenesis, as well as, genes involved in gas vesicle biosynthesis and ectoine biosynthesis. Surprisingly, no relevant nitrogen genes were found to be differentially regulated, revealing that GlnK is not an important nitrogen sensor under the tested conditions.
2011-12-31 | GSE30570 | GEO
Project description:The filamentous bacterium Streptomyces coelicolor differentiates by forming specialized, spore-bearing aerial hyphae that grow into the air. Using microarrays, we identified genes that are down-regulated in a mutant unable to erect aerial hyphae. Through this route, we identified a previously unknown layer of aerial mycelium surface proteins (the "chaplins"). The chaplins share a hydrophobic domain of ~40 residues (the "chaplin domain"), and all have a secretion signal. The five short chaplins (ChpD,E,F,G,H) have one chaplin domain, whereas the three long chaplins (ChpA,B,C) have two chaplin domains and a C-terminal "sorting signal" that targets them for covalent attachment to the cell wall by sortase enzyme. Expression of the two chaplin genes examined (chpE, chpH) depended on aerial hyphae formation but not sporulation, and egfp fusions showed their expression localized to aerial structures. Mass spectrometry of cell wall extracts confirmed that the short chaplins localized to the cell surface. Deletion of chaplin genes caused severe delays in aerial hyphae formation, a phenotype rescued by exogenous application of chaplin proteins. These observations implicate the chaplins in aerial mycelium formation, and suggest that coating of the envelope by the chaplins is required for aerial hyphae to grow out of the aqueous environment of the substrate mycelium into the air. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2007-07-20 | GSE8530 | GEO
Project description:GlnK is an important nitrogen sensor protein in Streptomyces coelicolor. Deletion of glnK results in a medium-dependent failure of aerial mycelium and spore formation and loss of antibiotic production. Thus, GlnK is not only a regulator of nitrogen metabolism but also of morphological differentiation and secondary metabolite production. Through a comparative transcriptomic approach between the S. coelicolor wild-type and a S. coelicolor glnK mutant strain, 142 genes were identified that are differentially regulated in both strains. Among these are genes of the ram and rag operon, which are involved in S. coelicolor morphogenesis, as well as, genes involved in gas vesicle biosynthesis and ectoine biosynthesis. Surprisingly, no relevant nitrogen genes were found to be differentially regulated, revealing that GlnK is not an important nitrogen sensor under the tested conditions. 16 samples, no replicates; four hour resolution from 21-33h; one our resolution from 33-40 h; two hour resolution 40-50h
2011-12-31 | E-GEOD-30570 | biostudies-arrayexpress
Project description:The differentiating bacterium Streptomyces coelicolor harbours some 66 sigma factors, which support its complex life cycle. σB, a functional homologue of σS from Escherichia coli, controls both osmoprotection and differentiation in S. coelicolor A3(2). Microarray analysis revealed σB-dependent induction of more than 280 genes by 0.2 M KCl. These genes encode several sigma factors, oxidative defence proteins, chaperones, systems to provide osmolytes, cysteine, mycothiol, and gas vesicle. σB controlled induction of itself and its two paralogues (σL and σM) in a hierarchical order of σB→σL→σM, as revealed by S1 mapping and Western blot analyses. The phenotype of each sigma mutant suggested a sequential action in morphological differentiation; σB in forming aerial mycelium, σL in forming spores and σM for efficient sporulation. σB was also responsible for the increase in cysteine and mycothiol, the major thiol buffer in actinomycetes, upon osmotic shock, revealing an overlap between protections against osmotic and oxidative stresses. Proteins in sigB mutant were more oxidized (carbonylated) than the wild type. These results support a hypothesis that σB serves as a master regulator that triggers other related sigma factors in a cascade, and thus regulates differentiation and osmotic and oxidative response in S. coelicolor.
2007-06-11 | E-SMDB-4094 | biostudies-arrayexpress
Project description:The basic experiment is a comparison of gene transcript levels of Streptomyces coelicolor M145 and its wblA deletion mutant at 6 timepoints (24, 36, 48, 60, 72 and 84 hours) encompassing vegetative growth, aerial growth, and sporulation on solid medium. The wblA mutant is morphologically defective, most of its aerial hyphae failing to show any sign of sporulation-directed attributes, and also overproduces some antibiotics. The microarray analysis was aimed to reveal the major transcriptional changes underpinning or associated with this pleiotropic phenotypic change. Using a fairly stringent cut-off, 291 genes were found to be affected, including developmental genes, antibiotic biosynthetic genes, and genes for primary metabolism. Some genes were over-expressed and others under-expressed in the mutant. Although the largest effects were mostly at timepoints corresponding to aerial growth and early sporulation, some genes were most strongly influenced at earlier timepoints.
2011-01-28 | GSE24396 | GEO
Project description:The aim of this study was to expand our knowledge about the gene repertoire involved in S. coelicolor sporulation. Here we compare the global transcription patterns of the wildtype (M145) parent and two mutants lacking key regulators of aerial hyphal sporulation (whiA and whiH).
2014-01-31 | E-MTAB-1942 | biostudies-arrayexpress
Project description:BldM and WhiI are both orphan, atypical response regulators found in Streptomyces species. They have complex developmental roles in aerial mycelium formation and sporulation in these bacteria. The aim of this transcription profiling experiment was to see how the deletion of these genes affects genome wide transcript levels compared to the wild type.
2015-07-01 | E-MTAB-2716 | biostudies-arrayexpress