Transcriptome analysis of Crp-dependent catabolite control of gene expression in Escherichia coli

Journal of Bacteriology

Volumn 186, Issue 11, 2004, Pages 3516-3524

  Gosset, Guillermo ^a,b   Zhang, Zhongge ^a   Nayyar, Samir ^a   Cuevas, William A ^c   Saier Jr , Milton H ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b INSTITUTO DE BIOTECNOLOGÍA   (Mexico)

^c GENENCOR INTERNATIONAL INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; CARBON; CHAPERONE; CYCLIC AMP BINDING PROTEIN; GLUCOSE; HEAT SHOCK PROTEIN; RIBOSOME PROTEIN; TRANSFER RNA;

ARTICLE; BACTERIAL GENE; BACTERIAL METABOLISM; CARBON METABOLISM; CATABOLITE REPRESSION; CITRIC ACID CYCLE; COMPLEX FORMATION; ESCHERICHIA COLI; GENE CONTROL; GENE EXPRESSION REGULATION; GENE FUSION; GENETIC ANALYSIS; GENETIC CODE; GENETIC TRANSCRIPTION; NONHUMAN; OPERON; PHENOTYPE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REGULON; REPORTER GENE;

CYCLIC AMP RECEPTOR PROTEIN; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GLUCOSE; HEAT-SHOCK PROTEINS; PHENOTYPE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 2442655332     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.186.11.3516-3524.2004     Document Type: Article

References (43)

1. Agashe, V. R., and F.-U. Hartl. 2000. Roles of molecular chaperones in cytoplasm protein folding. Semin. Cell Dev. Biol. 11:15-25.
2. Blattner, F. R., G. Plunkett III, C. A. Bloch, N. T. Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1474.
3. Bochner, B. R. 2003. New technologies to assess genotype-phenotype relationships. Nat. Rev. Genet. 4:309-314.
4. Bukau, B., T. Hesterkamp, and J. Luirink. 1996. Growing up in a dangerous environment: a network of multiple targeting and folding pathways for nascent polypeptides in the cytosol. Trends Cell Biol. 6:480-486.
5. Busby, S., and R. H. Ebright. 1999. Transcription activation by catabolite activator protein (CAP). J. Mol. Biol. 293:199-213.
6. Caldwell, R., R. Sapolsky, W. Weyler, R. R. Maile, S. C. Causey, and E. Ferrari. 2001. Correlation between Bacillus subtilis scoC phenotype and gene expression determined using microarrays for transcriptome analysis. J. Bacteriol. 183:7329-7340.
7. Cho, R. J., and M. J. Campbell. 2000. Transcription, genomes, function. Trends Genet. 16:409-415.
8. de Saizieu, A., C. Gardes, N. Flint, C. Wagner, M. Kamber, T. J. Mitchell, W. Keck, K. E. Amrein, and R. Lange. 2000. Microarray-based identification of a novel Streptococcus pneumoniae regulon controlled by an autoinduced peptide. J. Bacteriol. 182:4696-4703.
9. Dougan, D. A., A. Mogk, and B. Bukau. 2002. Protein folding and degradation in bacteria: to degrade or not to degrade? That is the question. Cell Mol. Life Sci. 59:1607-1616.
10. Gonzalez, R., H. Tao, K. T. Shanmugam, S. W. York, and L. O. Ingram. 2002. Global gene expression differences associated with changes in glycolytic flux and growth rate in Escherichia coli during the fermentation of glucose and xylose. Biotechnol. Prog. 18:6-20.
11. Hengge, R., and B. Bukau. 2003. Proteolysis in prokaryotes: protein quality control and regulatory principles. Mol. Microbiol. 49:1451-1462.
12. Inouye, M. 1999. Cold-shock response and adaptation. J. Mol. Microbiol. Biotechnol. 1:191.
13. Isaacs, H., Jr., D. Chao, C. Yanofsky, and M. H. Saier, Jr. 1994. Mechanism of catabolite repression of tryptophanase synthesis in Escherichia coli. Microbiology 140:2125-2134.
14. Jinks-Robertson, S., and M. Nomura. 1987. Ribosomes and tRNA, p. 1358-1385. In F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: cellular and molecular biology. American Society for Microbiology, Washington, D.C.
15. Kolb, A., S. Busby, H. Buc, S. Garges, and S. Adhya. 1993. Transcriptional regulation by cAMP and its receptor protein. Annu. Rev. Biochem. 62:749-795.
16. Lee, S.-J., W. Boos, J.-P. Bouché, and J. Plumbridge. 2000. Signal transduction between a membrane-bound transporter, PtsG, and a soluble transcription factor, Mlc, of Escherichia coli. EMBO J. 19:5353-5361.
17. Magasanik, B., and F. C. Neidhardt. 1987. Regulation of carbon and nitrogen utilization, p. 1318-1325. In F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: cellular and molecular biology. American Society for Microbiology, Washington, D.C.
18. Matin, A. 1991. The molecular basis of carbon-starvation-induced general resistance in Escherichia coli. Mol. Microbiol. 5:3-10.
19. Matin, A., M. Baetens, S. Pandza, C. H. Park, and S. Waggoner. 1999. Survival strategies in the stationary phase, p. 30-48. In E. Rosenberg (ed.), Microbial ecology and infectious disease. American Society for Microbiology, Washington, D.C.
20. Matouschek, A. 2003. Protein unfolding-an important process in vivo? Curr. Opin. Struct. Biol. 13:98-109.
21. Moreno, M. S., B. L. Schneider, R. R. Maile, W. Weyler, and M. H. Saier, Jr. 2001. Catabolite repression mediated by the CcpA protein in Bacillus subtilis: novel modes of regulation revealed by whole-genome analyses. Mol. Microbiol. 39:1366-1381.
22. Nasser, W., R. Schneider, A. Travers, and G. Muskhelishvili. 2001. CRP modulates fis transcription by alternate formation of activating and repressing nucleoprotein complexes. J. Biol. Chem. 276:17878-17886.
23. Park, S. J., G. Chao, and R. P. Gunsalus. 1997, Aerobic regulation of the sucABCD genes of Escherichia coli, which encode α-ketoglutarate dehydrogenase and succinyl coenzyme A synthetase: roles of ArcA, Fnr, and the upstream sdhCDAB promoter. J. Bacteriol. 179:4138-4142.
24. Park, S. J., P. A. Cotter, and R. P. Gunsalus. 1995. Regulation of malate dehydrogenase (mdh) gene expression in Escherichia coli in response to oxygen, carbon and heme availability. J. Bacteriol. 177:6652-6656.
25. Park, S. J., and R. P. Gunsalus. 1995. Oxygen, iron, carbon, and superoxide control of the fumarase fumA and fumC genes of Escherichia coli: role of the arcA, fnr, and soxR gene products. J. Bacteriol. 177:6255-6262.
26. Park, S. J., J. McCabe, J. Turna, and R. P. Gunsalus. 1994. Regulation of the citrate synthase (gltA) gene of Escherichia coli in response to anaerobiosis and carbon supply: role of the arcA gene product. J. Bacteriol. 176:5086-5092.
27. Pessi, G., C. Blumer, and D. Haas. 2001. lacZ fusions report gene expression, don't they? Microbiology 147:1993-1995.
28. Plumbridge, J. 1998. Expression of ptsG, the gene for the major glucose PTS transporter in Escherichia coli, is repressed by Mlc and induced by growth on glucose. Mol. Microbiol. 29:1053-1063.
29. Plumbridge, J. 1999. Expression of the phosphotransferase system both mediates and is mediated by Mlc regulation in Escherichia coli. Mol. Microbiol. 33:260-273.
30. Plumbridge, J. 2001. Regulation of PTS gene expression by the homologous transcriptional regulators, Mlc and NagC, in Escherichia coli. J. Mol. Microbiol. Biotechnol. 3:371-380.
31. Polissi, A., W. De Laurentis, S. Zangrossi, F. Briani, V. Longhi, G. Pesole, and G. Deho. 2003. Changes in Escherichia coli transcriptome during acclimatization at low temperature. Res. Microbiol. 154:573-580.
32. Ramseier, T. M., S. Bledig, V. Michotey, R. Feghali, and M. H. Saier, Jr. 1995. The global regulatory protein, FruR, modulates the direction of carbon flow in enteric bacteria. Mol. Microbiol. 16:1157-1169.
33. Ramseier, T. M., D. Nègre, J.-C. Cortay, M. Scarabel, A. J. Cozzone, and M. H. Saier, Jr. 1993. In vitro binding of the pleiotropic transcriptional regulatory protein, FruR, to the fru, pps, pts, icd and ace operons of Escherichia coli and Salmonella typhimurium. J. Mol. Biol. 234:28-44.
34. Saier, M. H., Jr., S. Chauvaux, J. Deutscher, J. Reizer, and J.-J. Ye. 1995. Protein phosphorylation and the regulation of carbon metabolism: comparisons in gram-negative versus gram-positive bacteria. Trends Biochem. Sci. 20:267-271.
35. Saier, M. H., Jr., T. M. Ramseier, and J. Reizer. 1996. Regulation of carbon utilization, p. 1325-1343. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. ASM Press, Washington, D.C.
36. Schilling, C. H., L. Held, M. Torre, and M. H. Saier, Jr. 2000. GRASP-DNA: a web application to screen prokaryotic genomes for specific DNA-binding sites and repeat motifs. J. Mol. Microbiol. Biotechnol. 2:495-500.
37. Selinger, D. W., K. J. Cheung, R. Mei, E. M. Johansson, C. S. Richmond, F. R. Blattner, D. J. Lockhart, and G. M. Church. 2000. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat. Biotechnol. 18:1262-1268.
38. Shinde, U., and M. Inouye. 2000. Intramolecular chaperones: polypeptide extensions that modulate protein folding. Semin. Cell Dev. Biol. 11:35-44.
39. Snapyan, M., M. Lecocq, L. Guevel, M. C. Arnaud, A. Ghochikyan, and V. Sakanyan. 2003. Dissecting DNA-protein and protein-protein interactions involved in bacterial transcriptional regulation by a sensitive protein array method combining a near-infrared fluorescence detection. Proteomics 3:647-657.
40. Weber, M. H., and M. A. Marahiel. 2003. Bacterial cold shock responses. Sci. Prog. 86:9-72.
41. Xu, J., and C. Johnson. 1997. Cyclic AMP receptor protein functions as a repressor of the osmotically inducible promoter proP P1 in Escherichia coli. J. Bacteriol. 179:2410-2417.
42. Yamanaka, K., and M. Inouye, 1997. Growth-phase-dependent expression of cspD, encoding a member of the CspA family in Escherichia coli. J. Bacteriol. 179:5126-5130.
43. Zhang, Z., M. Aboulwafa, M. H. Smith, and M. H. Saier, Jr. 2003. The ascorbate transporter of Escherichia coli. J. Bacteriol. 185:2443-2450.