Global gene expression profiling in Escherichia coli K12: The effects of oxygen availability and FNR

Journal of Biological Chemistry

Volumn 278, Issue 32, 2003, Pages 29837-29855

  Salmon, Kirsty ^a   Hung, She pin ^b,d   Mekjian, Kathy ^a   Baldi, Pierre ^c,d   Hatfield, G Wesley ^b,d   Gunsalus, Robert P ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Ringgold Standard Institution Informatics   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARRAYS; DNA; ESCHERICHIA COLI; GENES; METABOLISM; OXYGEN;

GENE EXPRESSION PROFILING;

BIOCHEMISTRY;

FUMARATE REDUCTASE; FUMARIC ACID DERIVATIVE; LEUCINE; LEUCINE RESPONSIVE REGULATORY PROTEIN; NITRIC ACID DERIVATIVE; REGULATOR PROTEIN; UNCLASSIFIED DRUG;

AEROBIC METABOLISM; ANAEROBIC METABOLISM; ANALYTIC METHOD; ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; CONTROLLED STUDY; DNA MICROARRAY; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; NONHUMAN; PRIORITY JOURNAL; REDUCTION; REGULATORY MECHANISM;

CELL DIVISION; DNA, COMPLEMENTARY; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OPEN READING FRAMES; OXYGEN; PROMOTER REGIONS (GENETICS);

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0043032584     PISSN: 00219258     EISSN: None     Source Type: Journal    
DOI: 10.1074/jbc.M213060200     Document Type: Article

References (54)

1. Gunsalus, R. P., and Park, S. J. (1994) Res. Microbiol. 145, 437-450
2. Gennis, R., and Stewart, V. (1996) in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology (Neidhartt, F. C., ed) Vol. 1, pp. 217-261, American Society for Microbiology, Washington, D. C.
3. Guest, J. R., Attwood, M. M., Machado, R. S., Matqi, K. Y., Shaw, J. E., and Turner, S. L. (1997) Microbiology 143, 457-466
4. Lynch, A. S., and Lin, E. C. C. (1996) in Regulation of Gene Expression in Escherichia coli (Lin, E. C. C., and Lynch, A. S., ed) pp. 362-381, Chapman & Hall, New York
5. Guest, J. R., Green, J., Irvine, A. S., and Spiro, S. (1996) in Regulation of Gene Expression in Escherichia coli (Lin, E. C. C., and Lynch, A. S., eds) pp. 317-342, Chapman & Hall, New York
6. Kiley, P. J., and Beinert, H. (1998) FEMS Microbiol. Lett. 22, 341-352
7. Lambden, P. R., and Guest, J. R. (1976) J. Gen. Microbiol. 97, 145-160
8. Lynch, A. S., and Lin, E. C. C. (1996) in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology (Neidhardt, F. C., ed) Vol. 1, 2nd Ed., pp. 1526-1538, American Society of Microbiology, Washington, D. C.
9. Casadaban, M. J. (1976) J. Mol. Biol. 104, 541-555
10. Cotter, P. A., and Gunsalus, R. P. (1989) J. Bacteriol. 171, 3817-3823
11. Hung, S. P., Baldi, P., and Hatfield, G. W. (2002) J. Biol. Chem. 277, 40309-40323
12. Baldi, P., and Hatfield, G. W. (2002) DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling, Cambridge University Press, Cambridge, UK
13. Hatfield, G. W., Hung, S. P., and Baldi, P. (2003) Mol. Microbiol. 47, 871-877
14. Long, A. D., Mangalam, H. J., Chan, B. Y., Tolleri, L., Hatfield, G. W., and Baldi, P. (2001) J. Biol. Chem. 276, 19937-19944
15. Baldi, P., and Long, A. D. (2001) Bioinformatics 17, 509-519
16. Allison, D. B., Gadbury, G. L., Heo, M., Fernandez, J. R., Lee, C. K., Prolla, T. A., and Weindruch, R. (2002) Comput. Statist. Data Anal. 39, 1-20
17. Baldi, P., and Hatfield, G. W. (2002) DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling, pp. 73-96, Cambridge University Press, Cambridge, UK
18. Tseng, C. P., Albrecht, J., and Gunsalus, R. P. (1996) J. Bacteriol. 178, 1094-1098
19. Iuchi, S., Chepuri, V., Fu, H. A., Gennis, R. B., and Lin, E. C. (1990) J. Bacteriol. 172, 6020-6025
20. Cotter, P. A., and Gunsalus, R. P. (1992) FEMS Microbiol. Lett, 70, 31-36
21. Cotter, P. A., Chepuri, V., Gennis, R. B., and Gunsalus, R. P. (1990) J. Bacteriol. 172, 6333-6338
22. Cotter, P. A., Melville, S. B., Albrecht, J. A., and Gunsalus, R. P. (1997) Mol. Microbiol. 25, 605-615
23. Govantes, F., Albrecht, J. A., and Gunsalus, R. P. (2000) Mol. Microbiol. 37, 1456-1469
24. Spiro, S., Roberts, R. E., and Guest, J. R. (1989) Mol. Microbiol. 3, 601-608
25. Sharrocks, A. D., Green, J., and Guest, J. R. (1991) Proc. R. Soc. Lond. Ser. B Biol. Sci. 245, 219-226
26. Green, J., and Guest, J. R. (1994) Mol. Microbiol. 12, 433-444
27. Meng, W., Green, J., and Guest, J. R. (1997) Microbiology 143, 1521-1532
28. Bongaerts, J., Zoske, S., Weidner, U., and Unden, G. (1995) Mol. Microbiol. 16, 521-534
29. Weidner, U., Geier, S., Ptock, A., Friedrich, T., Leif, H., and Weiss, H. (1993) J. Mol. Biol. 233, 109-122
30. Compan, I., and Touati, D. (1994) Mol. Microbiol. 11, 955-964
31. Quail, M. A., Haydon, D. J., and Guest, J. R. (1994) Mol. Microbiol. 12, 95-104
32. Cunningham, L., Georgellis, D., Green, J., and Guest, J. R. (1998) FEMS Microbiol. Lett. 169, 403-408
33. Birkmann, A., Sawers, R. G., and Bock, A. (1987) Mol. Gen. Genet. 210, 535-542
34. Ravnikar, P. D., and Somerville, R. L. (1987) J. Bacteriol. 169, 2611-2617
35. Ferrandez, A., Garcia, J. L., and Diaz, E. (1997) J. Bacteriol. 179, 2573-2581
36. Eichler, K., Bourgis, F., Buchet, A., Kleber, H. P., and Mandrand-Berthelot, M. A. (1994) Mol. Microbiol. 13, 775-786
37. Janausch, I. G., and Unden, G. (1999) Arch. Microbiol. 172, 219-226
38. Abaibou, H., Pommier, J., Benoit, S., Giordano, G., and Mandrand-Berthelot, M. A. (1995) J. Bacteriol. 177, 7141-7149
39. Chang, Y. Y., Wang, A. Y., and Cronan, J. E., Jr. (1994) Mol. Microbiol. 11, 1019-1028
40. Soballe, B., and Poole, R. K. (1997) FEBS Lett. 414, 373-376
41. Blankenhorn, D., Phillips, J., and Slonczewski, J. L. (1999) J. Bacteriol. 181, 2209-2216
42. Casado, C., Llagostera, M., and Barbe, J. (1991) FEMS Microbiol. Lett. 67, 153-157
43. Jones, H. M., and Gunsalus, R. P. (1987) J. Bacteriol. 169, 3340-3349
44. Bell, A. I., Cole, J. A., and Busby, S. J. (1990) Mol. Microbiol. 4, 1753-1763
45. Jayaraman, P. S., Cole, J., and Busby, S. (1989) Nucleic Acids Res. 17, 135-145
46. Woods, S. A., and Guest, J. R. (1988) Biochim. Biophys. Acta 954, 14-26
47. Tseng, C. P. (1997) FEMS Microbiol. Lett. 157, 67-72
48. Lin, R., Ernsting, B., Hirshfield, I. N., Matthews, R. G., Neidhardt, F. C., Clark, R. L., and Newman, E. B. (1992) J. Bacteriol. 174, 2779-2784
49. Leveque, F., Gazeau, M., Fromant, M., Blanquet, S., and Plateau, P. (1991) J. Bacteriol. 173, 7903-7910
50. Hirshfield, I. N., Tenreiro, R., Vanbogelen, R. A., and Neidhardt, F. C. (1984) J. Bacteriol. 158, 615-620
51. Wu, L. F., and Mandrand-Berthelot, M. A. (1986) Biochimie (Paris) 68, 167-179
52. Darwin, A. J., and Stewart, V. (1995) J. Bacteriol. 177, 3865-3869
53. Newman, E. B., Lin, R. T., and D'Ari, R. (1996) in Escherichia coli and Salmonella. Cellular and Molecular Biology (Neidhardt, F. C., Curtis, R. I., Ingraham, J. L., Lin, E. C. C., Low, K. B., Magasanik, B., Reznikoff, W. S., Riley, M., Schaechter, M., and Umbarger, H. E., eds) Vol. 1, 2nd Ed., pp. 1513-1525, American Society for Microbiology, Washington, D. C.
54. Rhee, K. Y., Parekh, B. S., and Hatfield, G. W. (1996) J. Biol. Chem. 271, 26499-26507