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Prokaryotic Genomics pp 131–144Cite as

Transcriptional Profiling in Bacteria Using Microarrays

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Part of the book series: Methods and Tools in Biosciences and Medicine ((MTBM))

Abstract

Recent advances in robotics and computer science now make possible the acquisition and processing of immense amounts of genetic data. Because of their small size and relative simplicity, microbial genomes were the proving grounds for technologies that accelerated the Human Genome Project [1–4]. The present state of these technologies is such that it is feasible to completely sequence a microbial genome in days rather than years. As of the time this volume went to press, more than 60 microbial genomes had been sequenced and provisionally annotated (http://www.tigr.org/tigr-scripts/CMR2/CMRHome-Page.spl).

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References

  1. Bult CJ, Whit O, Olsen GJ, Zhou L, et al (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273: 1058–1073

    CAS  Google Scholar 

  2. Fraser CM, Gocayne JD, White O, Adams MD, et al (1995) The minimal gene complement of Mycoplasma genitalium. Science 270: 397–403

    Article  CAS  Google Scholar 

  3. Goffeau, A et al. (1997) The yeast genome directory. Nature 387: suppl. 5–6.

    CAS  Google Scholar 

  4. International Human Genome Mapping Consortium. 2001. A physical map of the human genome. Nature 409: 934–941

    Article  Google Scholar 

  5. Fodor SP, Rava RP, Huang XC, Pease AC, et al (1993) Multiplexed biochemical assays with biological chips. Nature 364: 555–556

    Article  CAS  Google Scholar 

  6. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467–470

    Article  CAS  Google Scholar 

  7. DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680–686

    Article  CAS  Google Scholar 

  8. Ming Zheng XW, Templeton LJ, Smulski DR, LaRossa RA et al (2001) DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. J Bacteriol 183: 4562–4570

    Article  Google Scholar 

  9. Zimmer DP, Soupene E, Lee HL, Wendisch VF (2000) Nitrogen regulatory protein C-controlled genes of Escherichia coli: Scavenging as a defense against nitrogen limitation. Proc Nat Acad Sci (USA) 97 (26): 14674–14679

    Article  CAS  Google Scholar 

  10. Blattner FR, Richmond CS, Glasner JD, Mau R et al (1999) Genome-wide expression profiling in Escherichia coli K-12. Nuc Acids Res 27 (19): 3821–3835

    Article  Google Scholar 

  11. Tao Han CB, Richmond C, Blattner FR, Conway T (1999) Functional genomics: Expression Analysis of Escherichia coli growing on minimal and rich media. J Bacteriol 181: 6425–6440

    Google Scholar 

  12. Wei Y, Lee J, Smulski DR, LaRossa RA (2001) Global impact of sdiA amplification revealed by comprehensive gene expression profiling of Escherichia coli. J Bacteriol 183: 2265–2272

    CAS  Google Scholar 

  13. Greenberg EP, Whiteley M, Bangera MG, Bumgarner RE et al (2001) Gene expression in Pseudomonas aeruginosa bio-films. Nature 413 (6858): 860–864

    Article  Google Scholar 

  14. Tanaka T, Ogura M, Yamaguchi H, Yoshida K et al (2001) DNA microarray analysis of Bacillus subtilis DegU, ComA and PhoP regulons: An approach to comprehensive analysis of B. subtilis two-component regulatory systems. Nuc Acids Res 29 (18): 3804–3813

    Article  Google Scholar 

  15. Hoch JA, and M Perego (2001) Functional Genomics of Gram-Positive Microorganisms: Review of the Meeting, San Diego, California, 24 to 28 June 2001. J Bacteriol 183: 6973–6978

    Article  Google Scholar 

  16. Kobayashi K, Ogura M, Yamaguchi H, Yoshida K, Ogasawara N, Tanaka T, Fujita Y (2001) Comprehensive DNA micro-array analysis of Bacillus subtilis two-component regulatory systems. J Bacteriol 183: 7365–7370

    Article  CAS  Google Scholar 

  17. Ye RW, Tao W, L Bedzyk L, Young T, Chen M, Li L (2000) Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions. J Bacteriol 182: 4458–4465

    Article  CAS  Google Scholar 

  18. Dunman PM, Murphy E, Haney S, Palacios D et al (2001) Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/or sarA loci. J Bacteriol 183 (24): 7341–7353

    Article  CAS  Google Scholar 

  19. Hughes TR, Marton MJ, Jones AR, Roberts CJ et al (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109–126

    Article  CAS  Google Scholar 

  20. Schut GJ, Zhou J, Adams MW (2001) DNA microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus: Evidence for a New type of sulfur-reducing enzyme complex. J Bacteriol 183: 7027–7036

    Article  CAS  Google Scholar 

  21. Singh AK, Sherman LA (2000) Identification of iron-responsive, differential gene expression in the cyanobacterium Synechocystis sp. Strain PCC 6803 with a customized amplification library. J Bacteriol 182: 3536–3543

    Article  CAS  Google Scholar 

  22. Laub MT, McAdams HH, Feldblyum T, Fraser CM et al (2000) Global analysis of the genetic network controlling a bacterial cell cycle. Science 290: 2144–8

    Article  CAS  Google Scholar 

  23. Ang S, Lee ZC, Peck K, Sindici M et al (2001) Acid-induced gene expression in Helicobacter pylori: study in genomic scale by microarray. Infect Immun 69: 1679–76.

    Article  CAS  Google Scholar 

  24. Peterson S, Cline RT, Tettelin H, Sharov V, et al (2000) Gene expression analysis of the Streptococcus pneumoniae competence regulons by use of DNA micro-arrays. J Bacteriol 182: 6192–6202

    Article  CAS  Google Scholar 

  25. de Saizieu A, Gardes C, Flint N, Wagner C et al (2000) Microarray-based identification of a novel Streptococcus pneumoniae regulon controlled by an autoinduced peptide. J Bacteriol 182: 4696–4703

    Article  Google Scholar 

  26. Heimann JD, Wu MF, Kobel PA, Gamo FJ et al (2001) Global transcriptional response of Bacillus subtilis to heat shock. J Bacteriol 183: 7318–7328

    Article  Google Scholar 

  27. Smoot LM, Smoot JC, Graham MR, Somerville GA et al (2001) Global differential gene expression in response to growth temperature alteration in group A Streptococcus. Proc Natl Acad Sci (USA) 98: 10416–21

    Article  CAS  Google Scholar 

  28. Paustian ML, May BJ, Kapur V (2001) Pasteurella multocida gene expression in response to iron limitation. Infect Immun 69: 4109–15

    Article  CAS  Google Scholar 

  29. Fitzgerald JR, Musser JM (2001) Evolutionary genomics of pathogenic bacteria. Trends Microbiol 9: 547–553

    Article  CAS  Google Scholar 

  30. Kato-Maeda M, Rhee JT, Gingeras TR, Salamon H, et al (2001) Comparing genomes within the species Mycobacterium tuberculosis. Genome Res 11: 547–54

    CAS  Google Scholar 

  31. Malloff CA, Fernandez RC, Lam WL (2001) Bacterial comparative genomic hybridization: a method for directly identifying lateral gene transfer. J Mol Biol 312: 1–5

    Article  CAS  Google Scholar 

  32. Day WA Jr, Maurelli AT (2001) Pathoadaptive mutations that enhance virulence: Genetic organization of the cadA regions of Shigella spp. Infect Immun 69: 7471–7480

    Article  CAS  Google Scholar 

  33. Salama N, Guillemin K, McDaniel TK, Sherlock G et al (2000) A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains Proc Natl Acad Sci (USA) 97: 14668–14773

    Article  CAS  Google Scholar 

  34. Hakenbeck R, Balmelle N, Weber B, Gardes C et al (2001) Mosaic genes and mosaic chromosomes: intra-and inter-species genomic variation of Streptococcus pneumoniae. Infec Immun 69: 2477–2486

    Article  CAS  Google Scholar 

  35. McClelland M, Sanderson KE, Spieth J, Clifton SW et al (2001) Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413: 852–856

    Article  CAS  Google Scholar 

  36. Ferea T, Botstein D, Brown PO, Rosenzweig RF (1999) Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci (USA) 96: 9721–9726

    Article  CAS  Google Scholar 

  37. Laub MT, Chen SL, Shapiro L, McAdams HH (2002) Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle. Proc Natl Acad Sci (USA) 99: 4632–4637

    Article  CAS  Google Scholar 

  38. Khodursky AB, Peter BJ, Schmid MD, DeRisi J et al (2000) Analysis of topoisomerase function in bacterial replication fork movement: use of DNA micro-arrays. Proc Natl Acad Sci (USA) 97: 9419–9424

    Article  CAS  Google Scholar 

  39. Behr MA, Wilson MA, Gill WP, Salamon H et al (1999) Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284: 1520–1523

    Article  CAS  Google Scholar 

  40. Ramdas L, Wang J, Hu L, Cogdell D (2001) Comparative evaluation of laser-based microarray scanners. Biotechniques 31: 546, 548, 550, passim

    Google Scholar 

  41. Eberwine J, Yeh H, Miyashiro K, Cao Y et al (1992) Analysis of gene statement in single live neurons. Proc Natl Acad Sci (USA) 89: 3010–3014

    Article  CAS  Google Scholar 

  42. Phillips J, Eberwine JH (1996) Antisense RNA amplification: A linear amplification method for analyzing the mRNA population from single living cells. Methods Enzymology 10: 283–288

    Article  CAS  Google Scholar 

  43. Talaat AM, Hunter P, Johnston SA (2000) Genome-directed primers for selective labeling of bacterial transcripts for DNA microarray analysis. Nat Biotechnol 18: 679–682

    Article  CAS  Google Scholar 

  44. Sherlock G (2000) Analysis of large-scale gene expression data. Curr Opinion Immun 12: 201–205

    Article  CAS  Google Scholar 

  45. Quackenbush J (2001) Computational genetics and computational analysis of microarray data. Nat Rev Genet 2: 418–427

    Article  CAS  Google Scholar 

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Authors
  1. Michael T. Laub
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  2. R. Frank Rosenzweig
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Editor information

Editors and Affiliations

  1. Université Joseph Fourier, 460 rue de la piscine, 38400, St Martin d’Hères, France

    Michel Blot

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© 2003 Birkhäuser Verlag Basel/Switzerland

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Laub, M.T., Rosenzweig, R.F. (2003). Transcriptional Profiling in Bacteria Using Microarrays. In: Blot, M. (eds) Prokaryotic Genomics. Methods and Tools in Biosciences and Medicine. Birkhäuser Basel. https://doi.org/10.1007/978-3-0348-8963-6_11

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  • DOI: https://doi.org/10.1007/978-3-0348-8963-6_11

  • Publisher Name: Birkhäuser Basel

  • Print ISBN: 978-3-7643-6596-7

  • Online ISBN: 978-3-0348-8963-6

  • eBook Packages: Springer Book Archive

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