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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Streptomyces coelicolor hspR mutant compared to wild-type strain

ABSTRACT: Global gene expression patterns of S. coelicolor MT1151 and MT1153 (two independent MT1110 hspR disruption mutants ) cultures compared to MT1152 and MT1154 (two independent isolates of hspR+ integrants), grown on SMMS agar medium for 36 h .

ORGANISM(S): Streptomyces coelicolor

SUBMITTER: Emma Laing

PROVIDER: E-MAXD-44 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon.

Bucca Giselda G Laing Emma E Mersinias Vassilis V Allenby Nicholas N Hurd Douglas D Holdstock Jolyon J Brenner Volker V Harrison Marcus M Smith Colin P CP

Genome biology 20090116 1

<h4>Background</h4>DNA microarrays are a key resource for global analysis of genome content, gene expression and the distribution of transcription factor binding sites. We describe the development and application of versatile high density ink-jet in situ-synthesized DNA arrays for the G+C rich bacterium Streptomyces coelicolor. High G+C content DNA probes often perform poorly on arrays, yielding either weak hybridization or non-specific signals. Thus, more than one million 60-mer oligonucleotide ...[more]

PMID: 19146703

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Transcription profiling of Streptomyces coelicolor hspR+integrants of MT1110 after heat shock

Project description:Global gene expression patterns of MT1152 and MT1154 (two hspR+integrants of MT1110) grown on SMMS agar medium for 36 h and heat shocked at 42oC for 15 min. RNA was harvested from heat-shocked cultures and control cultures grown at 30oC and hybridized onto high density IJISS arrays to identify which genes are induced following heat shock in S.coelicolor

2009-02-07 | E-MAXD-46 | biostudies-arrayexpress

Transcription profiling of S. coelicolor grown in liquid culture and heat shock stimulated

Project description:Global gene expression patterns of two biological replicate cultures of S.coelicolor MT1110 grown on YEME plus 10% sucrose up to early stationary phase ( the culture conditions were the same used for obtaining ChIP-chip data with anti HspR antibodies). RNA was harvested from heat-shocked cultures (42oC) and control cultures grown at 30oC and hybridized onto high density IJISS arrays to identify which genes are induced following heat shock in S. coelicolor

2009-02-07 | E-MAXD-49 | biostudies-arrayexpress

Transcription profiling of Streptomyces coelicolor wild type and zur deletion strains

Project description:Description: In Streptomyces coelicolor the Zur repressor controls genes involved in zinc uptake and alternative ribosomal proteins that lack structural zinc. This experiment provides global gene expression patterns of M145 and S121 (zur deletion) grown in NMMP plus glucose medium to mid-log phase. The data reveal that Zur also controls genes involved in production of a non-ribosomally encoded siderophore-related peptide designated coelibactin.

2010-10-13 | E-MAXD-56 | biostudies-arrayexpress

Transcription profiling of Streptomyces coelicolor wild type and phP-null mutants at different time points during phosphate starvation

Project description:S. coelicolor was grown in low-phosphate concentration R5 liquid medium which facilitated the transition to a phosphate starvation induced stationary phase and the subsequent induction of the PhoP regulon. Global gene expression profiling of a wild-type and a phoP-null mutant was performed using samples isolated, respectively, at 24, 30, 35 and 45 h of growth. RNA was extracted and the resulting cDNA was hybridised to S. coelicolor high density DNA microarrays.

2012-08-30 | E-MAXD-51 | biostudies-arrayexpress

Transcription profiling of Streptomyces ceolicolor M600 and J2139 (sigR deletion) strains

Project description:In Streptomyces coelicolor the SigR sigma factor controls genes involved in coping with the deleterious formation of disulphide bonds in cellular proteins. This experiment provides global gene expression patterns of M600 and J2139 (sigR deletion) grown in NMMP plus glucose medium to mid-log phase then treated with diamide. The data reveal that sigR activates, directly or indirectly, more than 65 transcription units, encoding functions that include thiol-disulphide oxidoreductases, thiol buffers, and ATP-dependent proteases. The sigR regulon partially overlaps the ClgR and HspR regulons, that include functions for protein degradation and protein refolding. Diamide also leads to the transient down-regulation of central metabolic gene expression, in particular ribosomal protein expression.

2010-12-21 | E-MAXD-57 | biostudies-arrayexpress

Chromatin immunoprecipitation of Streptomyces coelicolor HspR binding sites

Project description:Global ChIP-chip analysis of HspR repressor binding sites in Streptomyces coelicolor MT1110 cultures grown in YEME plus 10% sucrose at 30?C up to early stationary phase. Chromatin extracted from formaldehyde treated cultures was incubated with anti HspR polyclonal antibodies and the DNA purified from anti HspR IP and mock IP samples was labelled with either Cy3 or Cy5- dCTP and hybridized in an indirect and direct type of microarray experiment onto SCO-Chip2-v1 and SCO-Chip2-v2 High Density IJISS arrays, developed in collaboration with Oxford Gene Technology.

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Transcription profiling of Corynebacterium glutamicum shows a differential response to moderate or severe heat shock of the HrcA- and HspR-dependent systems

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2008-12-10 | E-MTAB-66 | biostudies-arrayexpress

Chromatin immunoprecipitation of Streptomyces coelicolor wild type and phP-null mutants during phosphate starvation to determine binding locations of PhoP

Project description:S. coelicolor was grown in low-phosphate concentration R5 liquid medium which facilitated the transition to a phosphate starvation induced stationary phase and the subsequent induction of the PhoP regulon. The genome wide binding locations of PhoP during phosphate starvation were determined by chromatin-immunopreciptiation followed by hybridisation to high density S. coelicolor DNA microarrays. The use of both wild-type S. coelicolor and phoP-null mutant strains allowed the identification of specific PhoP binding locations.

2012-08-30 | E-MAXD-50 | biostudies-arrayexpress

Proteomic analysis of Rhizoctonia solani

Project description:Rhizoctonia solani is an important root infecting pathogen of a range of food staples worldwide including wheat, rice, maize, soybean, potato and others. Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues however, little is known about how R. solani causes disease. This study capitalises on recent genomic studies by applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Many of the proteins found in the culture filtrate had predicted functions relating to modification of the plant cell wall, a major activity required for pathogenesis on the plant host, including a number found only under infection conditions. Other infection related proteins included a high proportion of proteins with redox associated functions and many novel proteins without functional classification.

2016-01-28 | PXD002806 | Pride

Combined transcriptome analysis and polysome profiling of Streptomyces coelicolor MT1110 in SMMS

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