Dynamic gene expression profiling of Escherichia coli in carbon source transition from glucose to acetate

Journal of Microbiology and Biotechnology

Volumn 16, Issue 4, 2006, Pages 543-549

  Oh, Min Kyu ^a   Cha, Mee Jeong ^a   Lee, Sun Gu ^b   Rohlin, Lars ^c   Liao, James C ^c  

^a Korea University   (South Korea)

^b Pusan National University   (South Korea)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Acetate; Carbon source; DNA microarray; Escherichia coli; Gene expression profiling; Glucose

Indexed keywords

ACETIC ACID; BACTERIAL ENZYME; CARBON; CYCLIC AMP BINDING PROTEIN; DNA; GLUCOSE; GLYOXYLIC ACID; MALATE DEHYDROGENASE (DECARBOXYLATING); PENTOSE PHOSPHATE; PHOSPHOTRANSFERASE;

ADAPTATION; ANIMAL CELL; ARTICLE; BACTERIAL GENETICS; BACTERIAL GROWTH; CARBON SOURCE; CONTROLLED STUDY; CULTURE MEDIUM; DNA MICROARRAY; ESCHERICHIA COLI; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE REPRESSION; GLUCONEOGENESIS; GLYCOLYSIS; MONITORING; NONHUMAN; REGULON; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TIME;

ANIMALIA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 33646590248     PISSN: 10177825     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (27)

1. Arfin, S. M., A. D. Long, E. T. Ito, L. Tolleri, M. M. Riehle, E. S. Paegle, and G. W. Hatfield. 2000. Global gene expression profiling in Escherichia coli K12. The effects of integration host factor. J. Biol. Chem. 275: 29672-29684.
2. Balazsi, G., A. L. Barabasi, and Z. N. Oltvai. 2005. Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc. Natl. Acad. Sci. USA 102: 7841-7846.
3. Cakir, T., B. Kirdar, and K. O. Ulgen. 2004. Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks. Biotechnol. Bioeng. 86: 251-260.
4. Cozzone, A. J. 1998. Regulation of acetate metabolism by protein phosphorylation in enteric bacteria. Annu. Rev. Microbiol. 52: 127-164.
5. DeRisi, J. L., V. R. Iyer, and P. O. Brown. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686.
6. Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95: 14863-14868.
7. Gonzalez, R., H. Tao, K. T. Shanmugam, S. W. York, and L. O. Ingram. 2002. Global gene expression differences 6associated with changes in glycolytic flux and growth rate in Escherichia coli during the fermentation of glucose and xylose. Biotechnol. Prog. 18: 6-20.
8. Gosset, G., Z. Zhang, S. Nayyar, W. A. Cuevas, and M. H. Saier, Jr. 2004. Transcriptome analysis of Crp-dependent catabolite control of gene expression in Escherichia coli. J. Bacteriol. 186: 3516-3524.
9. Hua, Q., C. Yang, T. Oshima, H. Mori, and K. Shimizu. 2004. Analysis of gene expression in Escherichia coli in response to changes of growth-limiting nutrient in chemostat cultures. Appl. Environ. Microbiol. 70: 2354-2366.
10. Kang, M. J., S. H. Yoon, Y. M. Lee, S. H. Lee, J. E. Kim, K. H. Jung, Y. C. Shin, and S. W. Kim. 2005. Enhancement of lycopene production in Escherichia coli by optimization of the lycopene synthetic pathway. J. Microbiol. Biotechnol. 15: 880-886.
11. Kao, K. C., Y. L. Yang, R. Boscolo, C. Sabatti, V. Roychowdhury, and J. C. Liao. 2004. Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis. Proc. Natl. Acad. Sci. USA 101: 641-646.
12. Khodursky, A. B., B. J. Peter, N. R. Cozzarelli, D. Botstein, P. O. Brown, and C. Yanofsky. 2000. DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proc. Natl. Acad. Sci. USA 97: 12170-12175.
13. Lee, S. G., K. S. Hwang, and C. M. Kim. 2005. Dynamic behavior of regulatory elements in the hierarchical regulatory network of various carbon sources-grown Escherichia coli. J. Microbiol. Biotechnol. 15: 551-559.
14. Liao, J. C., R. Boscolo, Y. L. Yang, L. M. Tran, C. Sabatti, and V. P. Roychowdhury. 2003. Network component analysis: Reconstruction of regulatory signals in biological systems. Proc. Natl. Acad. Sci. USA 100: 15522-15527.
15. Liu, M., T. Durfee, J. E. Cabrera, K. Zhao, D. J. Jin, and F. R. Blattner. 2005. Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J. Biol. Chem. 280: 15921-15927.
16. Oh, K. S., O. Kwon, Y. W. Oh, M. J. Shon, S. G. Jung, Y. K. Kim, M. G. Kim, S. K. Rhee, G. Gellissen, and H. A. Kang. 2004. Fabrication of a partial genome microarray of the methylotrophic yeast Hansenula polymorpha: Optimization and evaluation of transcript profiling. J. Microbiol. Biotechnol. 14: 1239-1248.
17. Oh, M. K. and J. C. Liao. 2000. Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli. Biotechnol. Prog. 16: 278-286.
18. Oh, M. K., L. Rohlin, K. C. Kao, and J. C. Liao. 2002. Global expression profiling of acetate-grown Escherichia coli. J. Biol. Chem. 277: 13175-13183.
19. Park, S. J., J. I. Choi, and S. Y. Lee. 2005. Short-chain-length polyhydroxyalkanoates: Synthesis in metabolically engineered Escherichia coli and medical applications. J. Microbiol. Biotechnol. 15: 206-215.
20. Patten, C. L., M. G. Kirchhof, M. R. Schertzberg, R. A. Morton, and H. E. Schellhorn. 2004. Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12. Mol. Genet. Genomics 272: 580-591.
21. Polen, T., D. Rittmann, V. F. Wendisch, and H. Sahm. 2003. DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate. Appl. Environ. Microbiol. 69: 1759-1774.
22. Stelling, J., S. Klamt, K. Bettenbrock, S. Schuster, and E. D. Gilles. 2002. Metabolic network structure determines key aspects of functionality and regulation. Nature 420: 190-193.
23. Tani, T. H., A. Khodursky, R. M. Blumenthal, P. O. Brown, and R. G. Matthews. 2002. Adaptation to famine: A family of stationary-phase genes revealed by microarray analysis. Proc. Natl. Acad. Sci. USA 99: 13471-13476.
24. Tao, H., C. Bausch, C. Richmond, F. R. Blattner, and T. Conway. 1999. Functional genomics: Expression analysis of Escherichia coli growing on minimal and rich media. J. Bacteriol. 181: 6425-6440.
25. Tseng, G. C., M. K. Oh, L. Rohlin, J. C. Liao, and W. H. Wong. 2001. Issues in cDNA microarray analysis: Quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res. 29: 2549-2557.
26. Weber, H., T. Polen, J. Heuveling, V. F. Wendisch, and R. Hengge. 2005. Genome-wide analysis of the general stress response network in Escherichia coli: SigmaS-dependent genes, promoters, and sigma factor selectivity. J. Bacteriol. 187: 1591-1603.
27. Zheng, D., C. Constantinidou, J. L. Hobman, and S. D. Minchin. 2004. Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic Acids Res. 32: 5874-5893.