Construction of Escherichia coli gene expression level perturbation collection

Metabolic Engineering

Volumn 11, Issue 1, 2009, Pages 56-63

  Kashiwagi, Akiko ^a   Sakurai, Takahiro ^a   Tsuru, Saburo ^a   Ying, Bei Wen ^a   Mori, Kotaro ^a   Yomo, Tetsuya ^a,b  

^a OSAKA UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Escherichia coli; Expression level control; Strain engineering

Indexed keywords

BIOACTIVITY; ESCHERICHIA COLI; GENE EXPRESSION;

DATA SETS; DOXYCYCLINE; EXPRESSION LEVEL CONTROL; EXPRESSION LEVELS; MRNA LEVELS; PROLIFERATION RATES; STRAIN ENGINEERING; TARGET GENE EXPRESSIONS; TARGET GENES;

STRAIN;

ANHYDROTETRACYCLINE; DOXYCYCLINE;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; ESCHERICHIA COLI; GENE CONSTRUCT; GENE CONTROL; GENE DELETION; GENE EXPRESSION; GENE INSERTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN EXPRESSION;

CLONING, MOLECULAR; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; MUTATION; PROMOTER REGIONS, GENETIC;

ESCHERICHIA COLI;

EID: 55549133238     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2008.08.002     Document Type: Article

References (28)

1. Alper H., Fischer C., Nevoigt E., and Stephanopoulos G. Tuning genetic control through promoter engineering. Proc. Natl. Acad. Sci. USA 102 (2005) 12678-12683
2. Askenazi M., Driggers E.M., Holtzman D.A., Norman T.C., Iverson S., Zimmer D.P., Boers M.E., Blomquist P.R., Martinez E.J., Monreal A.W., Feibelman T.P., Mayorga M.E., Maxon M.E., Sykes K., Tobin J.V., Cordero E., Salama S.R., Trueheart J., Royer J.C., and Madden K.T. Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains. Nat. Biotechnol. 21 (2003) 150-156
3. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K.A., Tomita, M., Wanner, B.L., Mori, H., 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006. 0008.
4. Bailey J.E., Sburlati A., Hatzimanikatis V., Lee K., Renner W.A., and Tsai P.S. Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol. Bioeng. 52 (1996) 109-121
5. Bevis B.J., and Glick B.S. Rapidly maturing variants of the Discosoma red fluorescent protein (DsRed). Nat. Biotechnol. 20 (2002) 83-87
6. Bro C., and Nielsen J. Impact of 'ome' analyses on inverse metabolic engineering. Metab. Eng. 6 (2004) 204-211
7. Datsenko K.A., and Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97 (2000) 6640-6645
8. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166 (1983) 557-580
9. Ideker T., Thorsson V., Ranish J.A., Christmas R., Buhler J., Eng J.K., Bumgarner R., Goodlett D.R., Aebersold R., and Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292 (2001) 929-934
10. Ishii N., Nakahigashi K., Baba T., Robert M., Soga T., Kanai A., Hirasawa T., Naba M., Hirai K., Hoque A., Ho P.Y., Kakazu Y., Sugawara K., Igarashi S., Harada S., Masuda T., Sugiyama N., Togashi T., Hasegawa M., Takai Y., Yugi K., Arakawa K., Iwata N., Toya Y., Nakayama Y., Nishioka T., Shimizu K., Mori H., and Tomita M. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 316 (2007) 593-597
11. Ito Y., Kawama T., Urabe I., and Yomo T. Evolution of an arbitrary sequence in solubility. J. Mol. Evol. 58 (2004) 196-202
12. Jensen P.R., and Hammer K. The sequence of spacers between the consensus sequences modulates the strength of prokaryotic promoters. Appl. Environ. Microbiol. 64 (1998) 82-87
13. Jeong K.S., Ahn J., and Khodursky A.B. Spatial patterns of transcriptional activity in the chromosome of Escherichia coli. Genome Biol. 5 (2004) R86
14. Joyce A.R., and Palsson B.O. The model organism as a system: integrating 'omics' data sets. Nat. Rev. Mol. Cell Biol. 7 (2006) 198-210
15. Kromer J.O., Sorgenfrei O., Klopprogge K., Heinzle E., and Wittmann C. In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome. J. Bacteriol. 186 (2004) 1769-1784
16. Lederer T., Kintrup M., Takahashi M., Sum P.E., Ellestad G.A., and Hillen W. Tetracycline analogs affecting binding to Tn10-Encoded Tet repressor trigger the same mechanism of induction. Biochemistry 35 (1996) 7439-7446
17. Lee J.H., Lee D.E., Lee B.U., and Kim H.S. Global analyses of transcriptomes and proteomes of a parent strain and an l-threonine-overproducing mutant strain. J. Bacteriol. 185 (2003) 5442-5451
18. Lee S.Y., Lee D.Y., and Kim T.Y. Systems biotechnology for strain improvement. Trends Biotechnol. 23 (2005) 349-358
19. Lu P., Vogel C., Wang R., Yao X., and Marcotte E.M. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 25 (2007) 117-124
20. Ooi S.L., Pan X., Peyser B.D., Ye P., Meluh P.B., Yuan D.S., Irizarry R.A., Bader J.S., Spencer F.A., and Boeke J.D. Global synthetic-lethality analysis and yeast functional profiling. Trends Genet. 22 (2006) 56-63
21. Pace C.N., Vajdos F., Fee L., Grimsley G., and Gray T. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4 (1995) 2411-2423
22. Park S.J., Lee S.Y., Cho J., Kim T.Y., Lee J.W., Park J.H., and Han M.J. Global physiological understanding and metabolic engineering of microorganisms based on omics studies. Appl. Microbiol. Biotechnol. 68 (2005) 567-579
23. Peter B.J., Arsuaga J., Breier A.M., Khodursky A.B., Brown P.O., and Cozzarelli N.R. Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol. 5 (2004) R87
24. Pir P., Kirdar B., Hayes A., Onsan Z.Y., Ulgen K.O., and Oliver S.G. Integrative investigation of metabolic and transcriptomic data. BMC Bioinformatics 7 (2006) 203
25. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual (1989), Cold Spring Harbor Laboratory Press, New York
26. Skerra A. Use of the tetracycline promoter for the tightly regulated production of a murine antibody fragment in Escherichia coli. Gene 151 (1994) 131-135
27. Sopko R., Huang D., Preston N., Chua G., Papp B., Kafadar K., Snyder M., Oliver S.G., Cyert M., Hughes T.R., Boone C., and Andrews B. Mapping pathways and phenotypes by systematic gene overexpression. Mol. Cell 21 (2006) 319-330
28. Tweeddale H., Notley-McRobb L., and Ferenci T. Effect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool ("metabolome") analysis. J. Bacteriol. 180 (1998) 5109-5116