ArticleGenome biology2009
Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 40 citations in OpenAlex.
- Insights into the Orchestration of Gene Transcription Regulators inInternational journal of molecular sciences · 2022Review
- Genome-wide analysis of the role of the antibiotic biosynthesis regulator AbsA2 in Streptomyces coelicolor A3(2).PloS one · 2019Article
- Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor.Nucleic acids research · 2018Article
- The Interplay between Two Transcriptional Repressors and Chaperones OrchestratesInternational journal of molecular sciences · 2018Review
- Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor.BMC microbiology · 2016Article
- A terD domain-encoding gene (SCO2368) is involved in calcium homeostasis and participates in calcium regulation of a DosR-like regulon in Streptomyces coelicolor.Journal of bacteriology · 2015Article
- Genome-wide analysis of in vivo binding of the master regulator DasR in Streptomyces coelicolor identifies novel non-canonical targets.PloS one · 2015Article
- A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing.Molecular microbiology · 2014Article
- Deciphering the regulon of Streptomyces coelicolor AbrC3, a positive response regulator of antibiotic production.Applied and environmental microbiology · 2014Article
- Activating secondary metabolism with stress and chemicals.Journal of industrial microbiology & biotechnology · 2014Review
- Inference of sigma factor controlled networks by using numerical modeling applied to microarray time series data of the germinating prokaryote.Nucleic acids research · 2014Article
- The actinobacterial transcription factor RbpA binds to the principal sigma subunit of RNA polymerase.Nucleic acids research · 2013Article
- The ROK family regulator Rok7B7 pleiotropically affects xylose utilization, carbon catabolite repression, and antibiotic production in streptomyces coelicolor.Journal of bacteriology · 2013Article
- Article
- Diverse control of metabolism and other cellular processes in Streptomyces coelicolor by the PhoP transcription factor: genome-wide identification of in vivo targets.Nucleic acids research · 2012Article
- The -omics Era- Toward a Systems-Level Understanding of Streptomyces.Current genomics · 2011Article
- Genome-wide identification of in vivo binding sites of GlxR, a cyclic AMP receptor protein-type regulator in Corynebacterium glutamicum.Journal of bacteriology · 2011Article
- Genome-wide dynamics of a bacterial response to antibiotics that target the cell envelope.BMC genomics · 2011Article
- Article
- ChIP on Chip: surprising results are often artifacts.BMC genomics · 2010Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundDNA 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 probes were experimentally tested for sensitivity and specificity to enable selection of optimal probe sets for the genome microarrays. The heat-shock HspR regulatory system of S. coelicolor, a well-characterized repressor with a small number of known targets, was exploited to test and validate the arrays for use in global chromatin immunoprecipitation-on-chip (ChIP-chip) and gene expression analysis.
resultsIn addition to confirming dnaK, clpB and lon as in vivo targets of HspR, it was revealed, using a novel ChIP-chip data clustering method, that HspR also apparently interacts with ribosomal RNA (rrnD operon) and specific transfer RNA genes (the tRNAGln/tRNAGlu cluster). It is suggested that enhanced synthesis of Glu-tRNAGlu may reflect increased demand for tetrapyrrole biosynthesis following heat-shock. Moreover, it was found that heat-shock-induced genes are significantly enriched for Gln/Glu codons relative to the whole genome, a finding that would be consistent with HspR-mediated control of the tRNA species.
conclusionsThis study suggests that HspR fulfils a broader, unprecedented role in adaptation to stresses than previously recognized -- influencing expression of key components of the translational apparatus in addition to molecular chaperone and protease-encoding genes. It is envisaged that these experimentally optimized arrays will provide a key resource for systems level studies of Streptomyces biology.
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