Resources for Escherichia coli Systems Biology

  • Hirotada Mori
  • Natsuko Yamamoto
  • Hitomi Dose
  • Kenji Nakahigashi
  • Kirill A. Datsenko
  • Barry L. Wanner
Chapter

Abstract

Since genomic sequencing project launched, during in 1990s, biological research environments has been dramatically changed by developments of inter-disciplinary fields between biology and others such as chemistry, physics, information science, mathematics and engineering. Many high-throughput systems to obtain comprehensive analysis results have become available. As the result, accumulation of experimental data is now growing exponentially like sequence data in public databases. Experimental resources, such as plasmid clone and deletion mutant libraries, are the products of such high-throughput systems, and at the same time, motive force to generate further comprehensive information from xperimental analyses. In this manuscript, we summarize the situation about the experimental resources and how they have contributed in biology fields, especially in the 21st new generation of biology, such as systems biology.

Keywords

Essential Gene Entry Clone Single Gene Deletion Experimental Resource Keio Collection 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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References

  1. Aiba H, Baba T, Hayashi K et al. (1996) A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0–40.1 min region on the linkage map. DNA Res 3(6):363–77PubMedCrossRefGoogle Scholar
  2. Arifuzzaman M, Maeda M, Itoh A et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res 16(5):686–91PubMedCrossRefGoogle Scholar
  3. Baba T, Ara T, Hasegawa M et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2:2006 0008Google Scholar
  4. Baba T, Huan HC, Datsenko K et al. (2008) The applications of systematic in-frame, single-gene knockout mutant collection of Escherichia coli K-12. Methods Mol Biol 416:183–94PubMedCrossRefGoogle Scholar
  5. Baba T, Mori H (2008) The construction of systematic in-frame, single-gene knockout mutant collection in Escherichia coli K-12. Methods Mol Biol 416:171–81PubMedCrossRefGoogle Scholar
  6. Blattner FR, Plunkett G, 3rd, Bloch CA et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277(5331):1453–74PubMedCrossRefGoogle Scholar
  7. Butland G, Babu M, Diaz-Mejia JJ et al. (2008) eSGA: E. coli synthetic genetic array analysis. Nat MethodsGoogle Scholar
  8. Butland G, Peregrin-Alvarez JM, Li J et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433(7025):531–7PubMedCrossRefGoogle Scholar
  9. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97(12):6640–5PubMedCrossRefGoogle Scholar
  10. Dose H, Nakamichi T, Yoshino M et al. (2008) in preparationGoogle Scholar
  11. Gerdes SY, Scholle MD, Campbell JW et al. (2003) Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 185(19):5673–84PubMedCrossRefGoogle Scholar
  12. Giaever G, Chu AM, Ni L et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418(6896):387–91PubMedCrossRefGoogle Scholar
  13. Goryshin IY, Naumann TA, Apodaca J et al. (2003) Chromosomal deletion formation system based on Tn5 double transposition: use for making minimal genomes and essential gene analysis. Genome Res 13(4):644–53PubMedCrossRefGoogle Scholar
  14. Hashimoto M, Ichimura T, Mizoguchi H et al. (2005) Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol Microbiol 55(1):137–49PubMedCrossRefGoogle Scholar
  15. Hayashi K, Morooka N, Yamamoto Y et al. (2006) Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol 2:2006 0007, http://www.invitrogen.com/http://www.shigen.nig.ac.jp/ecoli/strain/top/top.jspGoogle Scholar
  16. Itoh T, Aiba H, Baba T et al. (1996) A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1–50.0 min region on the linkage map. DNA Res 3(6):379–92PubMedCrossRefGoogle Scholar
  17. Kato J, Hashimoto M (2007) Construction of consecutive deletions of the Escherichia coli chromosome. Mol Syst Biol 3:132PubMedCrossRefGoogle Scholar
  18. Kitagawa M, Ara T, Arifuzzaman M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research. DNA Res 12:291–99PubMedCrossRefGoogle Scholar
  19. Kobayashi K, Ehrlich SD, Albertini A et al. (2003) Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A 100(8):4678–83PubMedCrossRefGoogle Scholar
  20. Kohara Y, Akiyama K, Isono K (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50(3):495–508PubMedCrossRefGoogle Scholar
  21. Kolisnychenko V, Plunkett G, 3rd, Herring CD et al. (2002) Engineering a reduced Escherichia coli genome. Genome Res 12(4):640–7PubMedCrossRefGoogle Scholar
  22. Miki T, Yamamoto Y, Matsuda H (2008) A novel, simple, high-throughput method for isolation of genome-wide transposon insertion mutants of Escherichia coli K-12. Methods Mol Biol 416:195–204PubMedCrossRefGoogle Scholar
  23. Nagai T, Ibata K, Park ES et al. (2002) A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications. Nat Biotechnol 20(1):87–90PubMedCrossRefGoogle Scholar
  24. Niki H (in preparation)Google Scholar
  25. Oshima T, Aiba H, Baba T et al. (1996) A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7–28.0 min region on the linkage map. DNA Res 3(3):137–55PubMedCrossRefGoogle Scholar
  26. Posfai G, Plunkett G, 3rd, Feher T et al. (2006) Emergent properties of reduced-genome Escherichia coli. Science 312(5776):1044–6PubMedCrossRefGoogle Scholar
  27. Riley M, Abe T, Arnaud MB et al. (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot–2005. Nucleic Acids Res 34(1):1–9PubMedCrossRefGoogle Scholar
  28. Saka K, Tadenuma M, Nakade S et al. (2005) A complete set of Escherichia coli open reading frames in mobile plasmids facilitating genetic studies. DNA Res 12(1):63–8PubMedCrossRefGoogle Scholar
  29. Typas A, Nichols RJ, Siegele DA et al. (2008) High-throughput, quantitative analyses of genetic interactions in E. coli. Nat MethodsGoogle Scholar
  30. Van Dyk TK, Wei Y, Hanafey MK et al. (2001) A genomic approach to gene fusion technology. Proc Natl Acad Sci U S A 98(5):2555–60PubMedCrossRefGoogle Scholar
  31. Yamamoto N, Nakamichi T, Yoshino M et al. (2008a) unpublishedGoogle Scholar
  32. Yamamoto N, Nakamichi T, Yoshino M et al. (2008b) in preparationGoogle Scholar
  33. Yamamoto Y, Aiba H, Baba T et al. (1997) Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0–68.8 min on the linkage map and analysis of its sequence features. DNA Res 4(2):91–113PubMedCrossRefGoogle Scholar
  34. Yu BJ, Sung BH, Koob MD et al. (2002) Minimization of the Escherichia coli genome using a Tn5-targeted Cre/loxP excision system. Nat Biotechnol 20(10):1018–23PubMedCrossRefGoogle Scholar
  35. Zaslaver A, Bren A, Ronen M et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3(8):623–8PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Hirotada Mori
    • 1
    • 2
  • Natsuko Yamamoto
    • 1
  • Hitomi Dose
    • 1
  • Kenji Nakahigashi
    • 2
  • Kirill A. Datsenko
    • 3
  • Barry L. Wanner
    • 3
  1. 1.Graduate School of Biological SciencesNara Institute of Science and TechnologyIkomaJapan
  2. 2.Advanced Institute of BiosciencesKeio UniversityTsuruokaJapan
  3. 3.Department of Biological SciencesPurdue UniversityWest LafayetteUSA

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