Physiological studies of Escherichia coli strain MG1655: Growth defects and apparent cross-regulation of gene expression

Journal of Bacteriology

Volumn 185, Issue 18, 2003, Pages 5611-5626

  Soupene, Eric ^a   Van Heeswijk, Wally C ^a,d   Plumbridge, Jacqueline ^b   Stewart, Valley ^c   Bertenthal, Daniel ^a,e   Lee, Haidy ^a,f   Prasad, Gyaneshwar ^a   Paliy, Oleg ^a   Charernnoppakul, Parinya ^a   Kustu, Sydney ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF AMSTERDAM   (Netherlands)

^e SAN FRANCISCO VETERANS AFFAIRS MEDICAL CENTER   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GALACTOSE; LACTOSE;

ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATE; CARBOHYDRATE METABOLISM; DNA MICROARRAY; ESCHERICHIA COLI; GENE DELETION; GENE EXPRESSION REGULATION; NONHUMAN; PRIORITY JOURNAL; REGULATOR GENE; REGULATORY MECHANISM;

ACETYLGLUCOSAMINE; CELL DIVISION; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; ETHANOLAMINE; GALACTOSE; GENE EXPRESSION REGULATION, BACTERIAL; GLUCOSE; HUMANS; LACTOSE; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OPERON; REGULON;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; MAMMALIA; NEGIBACTERIA; PROKARYOTA;

EID: 0041335300     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.18.5611-5626.2003     Document Type: Article

References (60)

1. Adhya, S., and M. Schwartz. 1971. Phosphoglucomutase mutants of Escherichia coli K-12. J. Bacteriol. 108:621-626.
2. Arnold, C. N., J. McElhanon, A. Lee, R. Leonhart, and D. A. Siegele. 2001. Global analysis of Escherichia coli gene expression during the acetate-induced acid tolerance response. J. Bacteriol. 183:2178-2186.
3. Bachman, B. J. 1996. Derivations and genotypes of some mutant derivatives of Escherichia coli K-12, p. 2460-2488. In F. C. Neidhardt et al. (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2. ASM Press, Washington, D.C.
4. Blattner, F. R., G. Plunkett, 3rd, 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.
5. Blomfield, I. C., V. Vaughn, R. F. Rest, and B. I. Eisenstein. 1991. Allelic exchange in Escherichia coli with the Bacillus subtilis sacB gene and a temperature-sensitive pSC101 replicon. Mol. Microbiol. 5:1447-1458.
6. Boos, W., and H. Shuman. 1998. Maltose/maltodextrin system of Escherichia coli: transport, metabolism, and regulation. Microbiol. Mol. Biol. Rev. 62:204-229.
7. Broach, J., C. Neumann, and S. Kustu. 1976. Mutant strains (nit) of Salmonella typhimurium with a pleiotropic defect in nitrogen metabolism. J. Bacteriol. 128:86-98.
8. Cook, A. L. J. 1962. Recombination studies of lactose nonfermenting mutants of Escherichia coli K-12. Genetics 47:1335-1353.
9. Decker, K., R. Peist, J. Reidl, M. Kossmann, B. Brand, and W. Boos. 1993. Maltose and maltotriose can be formed endogenously in Escherichia coli from glucose and glucose-1-phosphate independently of enzymes of the maltose system. J. Bacteriol. 175:5655-5665.
10. Ehrmann, M. A., and R. F. Vogel. 1998. Maltose metabolism of Lactobacillus sanfranciscensis: cloning and heterologous expression of the key enzymes, maltose phosphorylase and phosphoglucomutase. FEMS Microbiol. Lett. 169:81-86.
11. Elliott, T. 1992. A method for constructing single-copy lac fusions in Salmonella typhimurium and its application to the hemA-prfA operon. J. Bacteriol. 174:245-253.
12. Freundlieb, S., and W. Boos. 1986. α-amylase of Escherichia coli, mapping and cloning of the structural gene, malS, and identification of its product as a periplasmic protein. J. Biol. Chem. 261:2946-2953.
13. Freundlieb, S., U. Ehmann, and W. Boos. 1988. Facilitated diffusion of p-nitrophenyl-α-D-maltohexaoside through the outer membrane of Escherichia coli. Characterization of LamB as a specific and saturable channel for maltooligosaccharides. J. Biol. Chem. 253:314-320.
14. Gaal, T., M. S. Bartlett, W. Ross, C. L. Turnbough, Jr., and R. L. Gourse. 1997. Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria. Science 278:2092-2097.
15. Ganesan, A. K., and B. Rotman. 1966. Transport systems for galactose and galactosides in Escherichia coli. I. Genetic determination and regulation of the methylgalactoside permease. J. Mol. Biol. 16:42-50.
16. Geanacopoulos, M., and S. Adhya. 1997. Functional characterization of roles of Ga1R and Ga1S as regulators of the gal regulon. J. Bacteriol. 179:228-234.
17. Gustavsson, N., A. A. Diez, and T. Nystrom. 2002. The universal stress protein paralogues of Escherichia coli are coordinately regulated and cooperate in the defence against DNA damage. Mol. Microbiol. 43:107-117.
18. Gutnick, D., J. M. Calvo, T. Klopotowski, and B. N. Ames. 1969. Compounds which serve as the sole source of carbon or nitrogen for Salmonella typhimurium LT-2. J. Bacteriol. 100:215-219.
19. Guyer, M. S., R. R. Reed, J. A. Steitz, and K. B. Low. 1981. Identification of a sex-factor-affinity site in E. coli as γδ. Cold Spring Harb. Symp. Quant. Biol. 45:135-140.
20. Hamilton, C. M., M. Aldea, B. K. Washburn, P. Babitzke, and S. R. Kushner. 1989. New method for generating deletions and gene replacements in Escherichia coli. J. Bacteriol. 171:4617-4622.
21. He, L., E. Soupene, A. Ninfa, and S. Kustu. 1998. Physiological role for the GInK protein of enteric bacteria: relief of NifL inhibition under nitrogen-limiting conditions. J. Bacteriol. 180:6661-6667.
22. Glc. Mol. Microbiol. 30:487-498.
23. Hussein, M. J., J. M. Green, and B. P. Nichols. 1998. Characterization of mutations that allow p-aminobenzoyl-glutamate utilization. J. Bacteriol. 180:6260-6268.
24. Ibarra, R. U., J. S. Edwards, and B. O. Palsson. 2002. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420:186-189.
25. Ingraham, J. L., O. Maaløe, and F. C. Neidhardt. 1953. Growth of the bacterial cell. Sinauer Associates, Sunderland, Mass.
26. Jacob, F., and J. Monod. 1961. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3:318-356.
27. Jensen, K. F. 1993. The Escherichia coli K-12 "wild-types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J. Bacteriol. 175:3401-3407.
28. Kiley, P. J., and H. Beinert. 1998. Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster. FEMS Microbiol. Rev. 22:341-352.
29. Kofoid, E., C. Rappleye, I. Stojiljkovic, and J. Roth. 1999. The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. J. Bacteriol. 181:5317-5329.
30. Kubitschek, H. E. 1970. Introduction to research with continuous cultures. Prentice-Hall, Englewood Cliffs, N.J.
31. Lawther, R. P., D. H. Calhoun, C. W. Adams, C. A. Hauser, J. Gray, and G. W. Hatfield. 1981. Molecular basis of valine resistance in Escherichia coli K-12. Proc. Natl. Acad. Sci. USA 78:922-925.
32. Lehnen, D., C. Blumer, T. Polen, B. Wackwitz, V. F. Wendisch, and G. Unden. 2002. LrhA as a new transcriptional key regulator of flagella, motility and chemotaxis genes in Escherichia coli. Mol. Microbiol. 45:521-532.
33. Link A. J., D. Phillips, and G. M. Church. 1997. Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization. J. Bacteriol. 179:6228-6237.
34. Liu, D., and P. R. Reeves. 1994. Escherichia coli K-12 regains its O antigen. Microbiology 140:49-57.
35. Manges, A. R., J. R. Johnson, B. Foxman, T. T. O'Bryan, K. E. Fullerton, and L. W. Riley. 2001. Widespread distribution of urinary tract infections caused by a multidrug-resistant Escherichia coli clonal group. N. Engl. J. Med. 345:1007-1013.
36. Miller, J. 1972. Experiments in molecular genetics, p. 352-355. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
37. Naas, T., M. Blot, W. M. Fitch, and W. Arber. 1995. Dynamics of IS-related genetic rearrangements in resting Escherichia coli K-12. Mol. Biol. Evol. 12:198-207.
38. Newton, W. A., J. R. Beckwith, D. Zipser, and S. Brenner. 1965. Nonsense mutants and polarity in the lac operon of Escherichia coli. J. Mol. Biol. 14:290-296.
39. Nichols, B. P., O. Shafiq, and V. Meiners. 1998. Sequence of analysis of Tn10 insertion sites in a collection of Escherichia coli strains used for genetic mapping and strain construction. J. Bacteriol. 180:6408-6411.
40. Nobelmann, B., and J. W. Lengeler. 1996. Molecular analysis of the gat genes from Escherichia coli and of their roles in galactitol transport and metabolism. J. Bacteriol. 178:6790-6795.
41. Plumbridge, J. 1995. Co-ordinated regulation of amino sugar biosynthesis and degradation: the NagC repressor acts as both an activator and a repressor for the transcription of the glmUS operon and requires two separated NagC binding sites. EMBO J. 14:3958-3965.
42. Plumbridge, J. 1998. Control of the expression of the manXYZ operon in Escherichia coli: Mlc is a negative regulator of the mannose PTS. Mol. Microbiol. 27:369-380.
43. Plumbridge, J. 1996. How to achieve constitutive expression of a gene within an inducible operon: the example of the nagC gene of Escherichia coli. J. Bacteriol. 178:2629-2636.
44. Plumbridge, J. A. 1992. A dominant mutation in the gene for the Nag repressor of Escherichia coli that renders the nag regulon uninducible. J. Gen. Microbiol. 138:1011-1017.
45. Plumbridge, J. A. 1991. Repression and induction of the nag regulon of Escherichia coli K-12: the roles of nagC and nagA in maintenance of the uninduced state. Mol. Microbiol. 5:2053-2062.
46. Plumbridge, J. A., O. Cochet, J. M. Souza, M. M. Altamirano, M. L. Calcagno, and B. Badet. 1993. Coordinated regulation of amino sugar-synthesizing and -degrading enzymes in Escherichia coli K-12. J. Bacteriol. 175:4951-4956.
47. Raha, M., I. Kawagishi, V. Muller, M. Kihara, and R. M. Macnab. 1992. Escherichia coli produces a cytoplasmic α-amylase, AmyA. J. Bacteriol. 174:6644-6652.
48. Reeves, P. R., M. Hobbs, M. A. Valvano, M. Skurnik, C. Whitfield, D. Coplin, N. Kido, J. Klena, D. Maskell, C. R. H. Raetz, and P. D. Rick. 1996. Bacterial polysaccharide synthesis and gene nomenclature. Trends Microbiol. 4:495-503.
49. Reznikoff, W. S., and J. N. Abelson. 1978. The lac promoter, p. 221-243. In J. H. Miller and W. S. Reznikoff (ed.), The operon. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
50. Rosenberg, D., and A. S. Keston. 1969. Loss of "galactose permease" and galactose sensitivity of E. coli associated with mutation in lac operon. Biochem. Biophys. Res. Commun. 37:165-170.
51. Schwartz, M. 1967. Sur l'existence chez Escherichia coli K-12 d'une régulation commune à la biosynthèse des recepteurs du bacteriophage et au metabolisme du maltose. Ann. Inst. Pasteur (Paris) 113:685-704.
52. Silhavy, T., M. Berman, and L. Enquist. 1984. Experiments with gene fusions, p. 107-112. Cold Spring Harbor Laboratory Press, Plainview, N.Y.
53. Silhavy, T., M. Berman, and L. Enquist. 1984. Experiments with gene fusions, p. 271. Cold Spring Harbor Laboratory Press, Plainview, N.Y.
54. 3 bidirectionally. Proc. Natl. Acad. Sci. USA 99:3926-3931.
55. Stewart, V. 1982. Requirement of Fnr and NarL functions for nitrate reductase expression in Escherichia coli K-12. J. Bacteriol. 151:1320-1325.
56. Tapio, S., F. Yeh, H. A. Shuman, and W. Boos. 1991. The malZ gene of Escherichia coli, a member of the maltose regulon, encodes a maltodextrin glucosidase. J. Biol. Chem. 266:19450-19458.
57. Wendisch, V. F., D. P. Zimmer, A. Khodursky, B. Peter, N. Cozzarelli, and S. Kustu. 2001. Isolation of Escherichia coli mRNA and comparison of expression with mRNA and total RNA on DNA microarrays. Anal. Biochem. 290:205-213.
58. White, R. J. 1968. Control of amino sugar metabolism in Escherichia coli and isolation of mutants unable to degrade amino sugars. Biochem. J. 106:847-858.
59. Wu, H. C. P., and H. M. Kalckar. 1966. Endogenous induction of the galactose operon in Escherichia coli K-12. Proc. Natl. Acad. Sci. USA 55:622-629.
60. Zimmer, D. P., E. Soupene, H. L. Lee, V. F. Wendisch, A. B. Khodursky, B. J. Peter, R. A. Bender, and S. Kustu. 2000. Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. Proc. Natl. Acad. Sci. USA 97:14674-14679.