Home LiteratureArticle Details
PMID: 19146703 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Genome biology ·Vol. 10 ·No. 1 ·2009-00-00 ·Pages R5

Bucca G, Laing E, Mersinias V, Allenby N, Hurd D, Holdstock J, Brenner V, Harrison M, Smith CP

Abstract

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 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. In 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. This 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.

MeSH Terms
Bacterial Proteins/genetics,metabolism Chromatin/metabolism Cluster Analysis Gene Expression Profiling Genes, Bacterial Genomics/instrumentation,methods Heat-Shock Proteins/genetics,metabolism Immunoprecipitation Oligonucleotide Array Sequence Analysis/methods Protein Binding RNA, Ribosomal/metabolism RNA, Transfer/genetics Regulon/genetics Repressor Proteins/genetics,metabolism Streptomyces coelicolor/genetics
Chemicals
Bacterial Proteins Chromatin Heat-Shock Proteins HspR protein, bacteria RNA, Ribosomal Repressor Proteins RNA, Transfer
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Bucca Giselda
Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK. g.bucca@surrey.ac.uk
Laing Emma
Mersinias Vassilis
Allenby Nicholas
Hurd Douglas
Holdstock Jolyon
Brenner Volker
Harrison Marcus
Smith Colin P
References (64)
64 references, click to expand
  1. Clustal W and Clustal X version 2.0.
    Bioinformatics. 2007 Nov 1;23(21):2947-8 PMID: 17846036
  2. Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism.
    Genome Res. 2005 Jun;15(6):820-9 PMID: 15930493
  3. Clustering gene expression patterns.
    J Comput Biol. 1999 Fall-Winter;6(3-4):281-97 PMID: 10582567
  4. Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome.
    Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17693-8 PMID: 16301522
  5. A signal transduction system in Streptomyces coelicolor that activates the expression of a putative cell wall glycan operon in response to vancomycin and other cell wall-specific antibiotics.
    Mol Microbiol. 2002 Jun;44(5):1199-1211 PMID: 12068806
  6. Disruption of hspR, the repressor gene of the dnaK operon in Streptomyces albus G.
    Mol Microbiol. 1997 Jan;23(1):77-84 PMID: 9004222
  7. Heterogeneous rRNAs are differentially expressed during the morphological development of Streptomyces coelicolor.
    FEMS Microbiol Lett. 2007 Oct;275(1):146-52 PMID: 17711457
  8. The HspR regulon of Streptomyces coelicolor: a role for the DnaK chaperone as a transcriptional co-repressordagger.
    Mol Microbiol. 2000 Dec;38(5):1093-103 PMID: 11123682
  9. HspR is a global negative regulator of heat shock gene expression in Deinococcus radiodurans.
    Mol Microbiol. 2005 Mar;55(5):1579-90 PMID: 15720562
  10. RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis.
    Bioinformatics. 2006 Nov 15;22(22):2825-7 PMID: 16982708
  11. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  12. The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis.
    PLoS Biol. 2004 Oct;2(10):e328 PMID: 15383836
  13. Synthesis of ribosomal proteins during growth of Streptomyces coelicolor.
    Mol Microbiol. 1994 May;12(3):375-85 PMID: 7545948
  14. Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome.
    Nucleic Acids Res. 2006;34(16):4642-52 PMID: 16963779
  15. Regulatory sequence analysis tools.
    Nucleic Acids Res. 2003 Jul 1;31(13):3593-6 PMID: 12824373
  16. Transcription of the Escherichia coli rrnB P1 promoter by the heat shock RNA polymerase (E sigma 32) in vitro.
    J Bacteriol. 1993 Feb;175(3):661-8 PMID: 8423142
  17. New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures.
    BMC Genomics. 2007 Aug 02;8:261 PMID: 17678549
  18. Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization.
    Mol Microbiol. 2007 Jul;65(1):21-6 PMID: 17581117
  19. The dnaK operon of Streptomyces coelicolor encodes a novel heat-shock protein which binds to the promoter region of the operon.
    Mol Microbiol. 1995 Aug;17(4):663-74 PMID: 8801421
  20. Negative feedback regulation of dnaK, clpB and lon expression by the DnaK chaperone machine in Streptomyces coelicolor, identified by transcriptome and in vivo DnaK-depletion analysis.
    Mol Microbiol. 2003 Oct;50(1):153-66 PMID: 14507371
  21. Regulation of secondary metabolism in streptomycetes.
    Curr Opin Microbiol. 2005 Apr;8(2):208-15 PMID: 15802254
  22. clpC and clpP1P2 gene expression in Corynebacterium glutamicum is controlled by a regulatory network involving the transcriptional regulators ClgR and HspR as well as the ECF sigma factor sigmaH.
    Mol Microbiol. 2004 Apr;52(1):285-302 PMID: 15049827
  23. Molecular chaperones in the cytosol: from nascent chain to folded protein.
    Science. 2002 Mar 8;295(5561):1852-8 PMID: 11884745
  24. Molecular and evolutionary basis of the cellular stress response.
    Annu Rev Physiol. 2005;67:225-57 PMID: 15709958
  25. Gas vesicles in actinomycetes: old buoys in novel habitats?
    Trends Microbiol. 2005 Aug;13(8):350-4 PMID: 15993071
  26. The Hsp70 chaperone machines of Escherichia coli: a paradigm for the repartition of chaperone functions.
    Mol Microbiol. 2007 Nov;66(4):840-57 PMID: 17919282
  27. Partial purification of factors for differential transcription of the rrnD promoters for ribosomal RNA synthesis in Streptomyces coelicolor.
    J Microbiol. 2007 Dec;45(6):534-40 PMID: 18176537
  28. Phospholipid-binding protein Cts1 controls septation and functions coordinately with calcineurin in Cryptococcus neoformans.
    Eukaryot Cell. 2003 Oct;2(5):1025-35 PMID: 14555485
  29. Aminoacyl-tRNA synthesis by pre-translational amino acid modification.
    RNA Biol. 2004 May;1(1):16-20 PMID: 17194933
  30. Transcription factor distribution in Escherichia coli: studies with FNR protein.
    Nucleic Acids Res. 2007;35(1):269-78 PMID: 17164287
  31. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays.
    Genes Dev. 2001 Dec 1;15(23):3183-92 PMID: 11731481
  32. Molecular chaperones and protein quality control.
    Cell. 2006 May 5;125(3):443-51 PMID: 16678092
  33. Regulation of the heat-shock response in bacteria.
    Annu Rev Microbiol. 1993;47:321-50 PMID: 7504905
  34. Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species.
    Proc Natl Acad Sci U S A. 2003 Nov 25;100 Suppl 2:14555-61 PMID: 12970466
  35. Substrate induction and catabolite repression of the Streptomyces coelicolor glycerol operon are mediated through the GylR protein.
    Mol Microbiol. 1994 Jun;12(5):737-45 PMID: 8052126
  36. Glutamyl-transfer RNA: a precursor of heme and chlorophyll biosynthesis.
    Trends Biochem Sci. 1992 Jun;17(6):215-8 PMID: 1502723
  37. Ribosomal RNA synthesis in Streptomyces lividans under heat shock conditions.
    Gene. 1997 Jul 18;194(1):125-32 PMID: 9266681
  38. Diverse roles for HspR in Campylobacter jejuni revealed by the proteome, transcriptome and phenotypic characterization of an hspR mutant.
    Microbiology (Reading). 2005 Mar;151(Pt 3):905-915 PMID: 15758235
  39. A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments.
    Bioinformatics. 2008 Feb 1;24(3):374-82 PMID: 18204063
  40. A tRNA(Glu) that uncouples protein and tetrapyrrole biosynthesis.
    FEBS Lett. 2005 Nov 21;579(28):6383-7 PMID: 16271718
  41. Phosphorylated AbsA2 negatively regulates antibiotic production in Streptomyces coelicolor through interactions with pathway-specific regulatory gene promoters.
    J Bacteriol. 2007 Jul;189(14):5284-92 PMID: 17513473
  42. Bioconductor: open software development for computational biology and bioinformatics.
    Genome Biol. 2004;5(10):R80 PMID: 15461798
  43. H-NS mediates the silencing of laterally acquired genes in bacteria.
    PLoS Pathog. 2006 Aug;2(8):e81 PMID: 16933988
  44. The autoregulatory HspR repressor protein governs chaperone gene transcription in Helicobacter pylori.
    Mol Microbiol. 1999 Nov;34(4):663-74 PMID: 10564507
  45. RheA, the repressor of hsp18 in Streptomyces albus G.
    Microbiology (Reading). 1999 Sep;145 ( Pt 9):2385-2391 PMID: 10517591
  46. WebLogo: a sequence logo generator.
    Genome Res. 2004 Jun;14(6):1188-90 PMID: 15173120
  47. Pfam: clans, web tools and services.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51 PMID: 16381856
  48. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments.
    Genomics. 2004 Mar;83(3):349-60 PMID: 14986705
  49. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).
    Nature. 2002 May 9;417(6885):141-7 PMID: 12000953
  50. Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays.
    Microbiology (Reading). 2002 Oct;148(Pt 10):3129-3138 PMID: 12368446
  51. Preferred amino acids and thermostability.
    Genet Mol Res. 2003 Dec 30;2(4):383-93 PMID: 15011142
  52. Regulation of the Escherichia coli sigma-dependent envelope stress response.
    Mol Microbiol. 2004 May;52(3):613-9 PMID: 15101969
  53. Dual control of Helicobacter pylori heat shock gene transcription by HspR and HrcA.
    J Bacteriol. 2004 May;186(10):2956-65 PMID: 15126455
  54. Analysis of gene expression in operons of Streptomyces coelicolor.
    Genome Biol. 2006;7(6):R46 PMID: 16749941
  55. Transcriptional regulation of stress response and motility functions in Helicobacter pylori is mediated by HspR and HrcA.
    J Bacteriol. 2007 Oct;189(20):7234-43 PMID: 17693507
  56. The RheA repressor is the thermosensor of the HSP18 heat shock response in Streptomyces albus.
    Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3538-43 PMID: 10716740
  57. Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays.
    J Bacteriol. 2004 Oct;186(20):6938-43 PMID: 15466047
  58. Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data.
    BMC Bioinformatics. 2006 Jul 26;7:359 PMID: 16872483
  59. Negative regulation of bacterial heat shock genes.
    Mol Microbiol. 1999 Jan;31(1):1-8 PMID: 9987104
  60. Negative regulation of the heat shock response in Streptomyces.
    Arch Microbiol. 2001 Oct;176(4):237-42 PMID: 11685367
  61. The clpB gene of Bifidobacterium breve UCC 2003: transcriptional analysis and first insights into stress induction.
    Microbiology (Reading). 2005 Sep;151(Pt 9):2861-2872 PMID: 16151199
  62. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments.
    FEBS Lett. 2004 Aug 27;573(1-3):83-92 PMID: 15327980
  63. Regulation of the dnaK operon of Streptomyces coelicolor A3(2) is governed by HspR, an autoregulatory repressor protein.
    J Bacteriol. 1997 Oct;179(19):5999-6004 PMID: 9324243
  64. Normalization of cDNA microarray data.
    Methods. 2003 Dec;31(4):265-73 PMID: 14597310
Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2009-10-1-r5
Email
g.bucca@surrey.ac.uk
Published
2009-00-00
Epub
2009-00-16
Pages
R5
Language
English
Region
England
NLM ID
100960660
PMCID
PMC2687793
Subset
IM
Grants
Biotechnology and Biological Sciences Research Council · BB/D011582/1 · United Kingdom
Biotechnology and Biological Sciences Research Council · G18886 · United Kingdom
Biotechnology and Biological Sciences Research Council · BBD0115821 · United Kingdom
External Links
PubMed source DOI: 10.1186/gb-2009-10-1-r5 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2