DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate

Applied and Environmental Microbiology

Volumn 69, Issue 3, 2003, Pages 1759-1774

  Polen, T ^a   Rittmann, D ^a   Wendisch, V F ^a   Sahm, H ^a  

^a FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; DNA; GENES; PH EFFECTS;

OSMOTIC EFFECTS;

BACTERIA;

ACETIC ACID; PROPIONATE SODIUM; PROPIONIC ACID; PROPIONIC ACID DERIVATIVE; RNA; UNCLASSIFIED DRUG;

BACTERIUM;

ARTICLE; BACTERIAL CHROMOSOME; BIOSYNTHESIS; CHEMOTAXIS; CONTROLLED STUDY; DEFENSE MECHANISM; DNA MICROARRAY; ESCHERICHIA COLI; GENE EXPRESSION; NONHUMAN; OSMOSIS; PH; PROTEIN EXPRESSION;

ACETATES; ADAPTATION, PHYSIOLOGICAL; CARBONYL CYANIDE M-CHLOROPHENYL HYDRAZONE; CULTURE MEDIA; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; HYDROGEN-ION CONCENTRATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROPIONATES; TIME FACTORS; UNCOUPLING AGENTS;

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

EID: 0037338332     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.69.3.1759-1774.2003     Document Type: Article

References (76)

1. Alexeeva, S., B. de Kort, G. Sawers, K. J. Hellingwerf, and M. J. de Mattos. 2000. Effects of limited aeration and of the ArcAB system on intermediary pyruvate catabolism in Escherichia coli. J. Bacteriol. 182:4934-4940.
2. 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.
3. Aristidou, A. A., K. Y. San, and G. N. Bennett. 1995. Metabolic engineering of Escherichia coli to enhance recombinant protein production through acetate reduction. Biotechnol. Prog. 11:475-478.
4. 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.
5. Axe, D. D., and J. E. Bailey. 1995. Transport of lactate and acetate through the energized cytoplasmic membrane of Escherichia coli. Biotechnol. Bioeng. 47:8-19.
6. Barak, R., and M. Eisenbach. 2001. Acetylation of the response regulator, CheY, is involved in bacterial chemotaxis. Mol. Microbiol. 40:731-743.
7. Barak, R., M. Welch, A. Yanovsky, K. Oosawa, and M. Eisenbach. 1992. Acetyladenylate or its derivative acetylates the chemotaxis protein CheY in vitro and increases its activity at the flagellar switch. Biochemistry 31:10099-10107.
8. Bermejo, L. L., N. E. Welker, and E. T. Papoutsakis. 1998. Expression of Clostridium acetobutylicum ATCC 824 genes in Escherichia coli for acetone production and acetate detoxification. Appl. Environ. Microbiol. 64:1079-1085.
9. Bertin, P., E. Terao, E. H. Lee, P. Lejeune, C. Colson, A. Danchin, and E. Collatz. 1994. The H-NS protein is involved in the biogenesis of flagella in Escherichia coli. J. Bacteriol. 176:5537-5540.
10. Blank, L., J. Green, and J. R. Guest. 2002. AcnC of Escherichia coli is a 2-methylcitrate dehydratase (PrpD) that can use citrate and isocitrate as substrates. Microbiology 148:133-146.
11. Blankenhorn, D., J. Phillips, and J. L. Slonczewski. 1999. Acid- and base-induced proteins during aerobic and anaerobic growth of Escherichia coli revealed by two-dimensional gel electrophoresis. J. Bacteriol. 181:2209 -2216.
12. Böck, A., and G. Sawers. 1996. Fermentation, p. 262-282. In F. C. Neidhardt et al. (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. ASM Press, Washington. D.C.
13. Brown, T. D. K., M. C. Jones-Mortimer, and H. L. Kornberg. 1977. The enzymic interconversion of acetate and acetyl-coenzyme A in Escherichia coli. J. Gen. Microbiol. 102:327-336.
14. Bunch, P. K., F. Mat-Jan, N. Lee, and D. P. Clark. 1997. The IdhA gene encoding the fermentative lactate dehydrogenase of Escherichia coli. Microbiology 143:187-195.
15. Chang, D. E., S. Shin, J. S. Rhee, and J. G. Pan. 1999. Acetate metabolism in a pta mutant of Escherichia coli W3110: importance of maintaining acetyl coenzyme A flux for growth and survival. J. Bacteriol. 181:6656-6663.
16. Clark, D. P., and J. E. Cronan. 1996. Two-carbon compounds and fatty acids as carbon sources, p. 343-357. In F. C. Neidhardt et al. (ed.), Escherichia coli and Salmonella: cellular and molecular biology. 2nd ed. ASM Press, Washington, D.C.
17. De Biase, D., A. Tramonti, R. A. John, and F. Bossa. 1996. Isolation, overexpression, and biochemical characterization of the two isoforms of glutamic acid decarboxylase from Escherichia coli. Protein Expr. Purif. 8:430-438.
18. 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.
19. Eppler, T., P. Postma, A. Schutz, U. Volker, and W. Boos. 2002. Glycerol-3-phosphate-induced catabolite repression in Escherichia coli. J. Bacteriol. 184:3044-3052.
20. Farmer, W. R., and J. C. Liao. 1997. Reduction of aerobic acetate production by Escherichia coli. Appl. Environ. Microbiol. 63:3205-3210.
21. Gestwicki, J. E., and L. L. Kiessling. 2002. Inter-receptor communication through arrays of bacterial chemoreceptors. Nature 415:81-84.
22. Gokarn, R. R., M. A. Eiteman, and E. Altman. 2000. Metabolic analysis of Escherichia coli in the presence and absence of the carboxylating enzymes phosphoenolpyruvate carboxylase and pyruvate carboxylase. Appl. Environ. Microbiol. 66:1844-1850.
23. Hengge-Aronis, R. 2002. Recent insights into the general stress response regulatory network in Escherichia coli. J. Mol. Microbiol. Biotechnol. 4:341-346.
24. Hengge-Aronis, R. 2000. A role for the sigma S subunit of RNA polymerase in the regulation of bacterial virulence. Adv. Exp. Med. Biol. 485:85-93.
25. Hesslinger, C., S. A. Fairhurst, and G. Sawers. 1998. Novel keto acid formate lyase and propionate kinase enzymes are components of an anaerobic pathway in Escherichia coli that degrades L-threonine to propionate. Mol. Microbiol. 27:477-492.
26. Hommais, F., E. Krin, C. Laurent-Winter, O. Soutourina, A. Malpertuy, J. P. Le Caer, A. Danchin, and P. Bertin. 2001. Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-assoelated protein, H-NS. Mol. Microbiol. 40:20-36.
27. Horswill, A. R., and J. C. Escalante-Semerena. 1999. The prpE gene of Salmonella typhimurium LT2 encodes propionyl-CoA synthetase. Microbiology 145:1381-1388.
28. Hosono, K., H. Kakuda, and S. Ichihara. 1995. Decreasing accumulation of acetate in a rich medium by Escherichia coli on introduction of genes on a multicopy plasmid. Biosci. Biotechnol. Biochem. 59:256-261.
29. Hughes, K. T., K. L. Gillen, M. J. Semon, and J. E. Karlinsey. 1993. Sensing structural intermediates in bacterial flagellar assembly by export of a negative regulator. Science 262:1277-1280.
30. Jiang, G. R., S. Nikolova, and D. P. Clark. 2001. Regulation of the Idha gene, encoding the fermentative lactate dehydrogenase of Escherichia coli. Microbiology 147:2437-2446.
31. Kalir, S., J. McClure, K. Pabbaraju, C. Southward, M. Ronen, S. Leibler, M. G. Surette, and U. Alon. 2001. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science 292:2080-2083.
32. Kessler, D., and J. Knappe. 1996. Anaerobic dissimilation of pyruvate, p. 199-204. In F. C. Neidhardt et al. (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. ASM Press, Washington, D.C.
33. 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.
34. Kihara, M., and R. M. Macnab. 1981. Cytoplasmic pH mediates pH taxis and weak-acid repellent taxis of bacteria. J. Bacteriol. 145:1209-1221.
35. Kirkpatrick, C., L. M. Maurer, N. E. Oyelakin, Y. N. Yoncheva, R. Maurer, and J. L. Slonczewski. 2001. Acetate and formate stress: opposite responses in the proteome of Escherichia coli. J. Bacteriol. 183:6466-6477.
36. Kumari, S., C. M. Beatty, D. F. Browning, S. J. Busby, E. J. Simel, G. Hovel-Miner, and A. J. Wolfe. 2000. Regulation of acetyl coenzyme A synthetase in Escherichia coli. J. Bacteriol. 182:4173-4179.
37. Kutsukake, K. 1997. Autogenous and global control of the flagellar master operon, flhD, in Salmonella typhimurium. Mol. Gen. Genet. 254:440-448.
38. Lambert, L. A., K. Abshire, D. Blankenhorn, and J. L. Slonczewski. 1997. Proteins induced in Escherichia coli by benzoic acid. J. Bacteriol. 179:7595-7599.
39. Lasko, D. R., N. Zamboni, and U. Sauer. 2000. Bacterial response to acetate challenge: a comparison of tolerance among species. Appl. Microbiol. Biotechnol. 54:243-247.
40. Lee, J., A. Goel, M. M. Ataai, and M. M. Domach. 1994. Flux adaptations of citrate synthase-deficient Escherichia coli. Ann. N. Y. Acad. Sci. 745:35-50.
41. Lee, S. J., W. Boos, J. P. Bouche, 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.
42. Lee, S. Y. 1996. High cell-density culture of Escherichia coli. Trends Biotechnol. 14:98-105.
43. 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.
44. Levit, M. N., Y. Liu, and J. B. Stock. 1998. Stimulus response coupling in bacterial chemotaxis: receptor dimers in signalling arrays. Mol. Microbiol. 30:459-466.
45. Liu, X., and P. Matsumura. 1994. The FlhD-FlhC complex, a transcriptional activator of the Escherichia coli flagellar class II operons. J. Bacteriol. 176:7345-7351.
46. Macnab, R. M. 1996. Flagella and motility, p. 123-145. In F. C. Neidhardt et al. (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. ASM Press, Washington, D.C.
47. Miller, J. H. 1992. A short course in bacterial genetics, p. 72-74. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
48. Nam, T. W., S. H. Cho, D. Shin, J. H. Kim, J. Y. Jeong, J. H. Lee, J. H. Roe, A. Peterkofsky, S. O. Kang, S. Ryu, and Y. J. Seok. 2001. The Escherichia coli glucose transporter enzyme IICB(Glc) recruits the global repressor Mlc. EMBO J. 20:491-498.
49. Noronha, S. B., H. J. Yeh, T. F. Spande, and J. Shiloach. 2000. Investigation of the TCA cycle and the glyoxylate shunt in Escherichia coli BL21 and JM109 using (13)C-NMR/MS. Biotechnol. Bioeng. 68:316-327.
50. 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.
51. Palacios, S., and J. C. Escalante-Semerena. 2000. prpR, ntrA, and ihf functions are required for expression of the prpBCDE operon, encoding enzymes that catabolize propionate in Salmonella enterica serovar Typhimurium LT2. J. Bacteriol. 182:905-910.
52. Pomposiello, P. J., M. H. Bennik, and B. Demple. 2001. Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate. J. Bacteriol. 183:3890-3902.
53. Ramakrishnan, R., M. Schuster, and R. B. Bourret. 1998. Acetylation at Lys-92 enhances signaling by the chemotaxis response regulator protein CheY. Proc. Natl. Acad. Sci. USA 95:4918-4923.
54. Rashid, M. H., and A. Kornberg. 2000. Inorganic polyphosphate is needed for swimming, swarming, and twitching motilities of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. USA 97:4885-4890.
55. Roe, A. J., C. O'Byrne, D. McLaggan, and I. R. Booth. 2002. Inhibition of Escherichia coli growth by acetic acid: a problem with methionine biosynthesis and homocysteine toxicity. Microbiology 148:2215-2222.
56. Rossmann, R., G. Sawers, and A. Bock. 1991. Mechanism of regulation of the formate-hydrogenlyase pathway by oxygen, nitrate, and pH: definition of the formate regulon. Mol. Microbiol. 5:2807-2814.
57. Sambrock, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
58. Shi, W., M. Bogdanov, W. Dowhan, and D. R. Zusman. 1993. The pss and psd genes are required for motility and chemotaxis in Escherichia coli. J. Bacteriol. 175:7711-7714.
59. Shi, W., Y. Zhou, J. Wild, J. Adler, and C. A. Gross. 1992. DnaK, DnaJ, and GrpE are required for flagellum synthesis in Escherichia coli. J. Bacteriol. 174:6256-6263.
60. Shin, S., and C. Park. 1995. Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR. J. Bacteriol. 177:4696-4702.
61. Slonczewski, J. L., and J. W. Foster. 1996. pH-regulated genes and survival at extreme pH, p. 1539-1549. In F. C. Neidhardt et al. (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. ASM Press, Washington, D.C.
62. Small, P., D. Blankenhorn, D. Welty, E. Zinser, and J. L. Slonczewski. 1994. Acid and base resistance in Escherichia coli and Shigella flexneri: role of rpoS and growth pH. J. Bacteriol. 176:1729-1737.
63. Soutourina, O., A. Kolb, E. Krin, C. Laurent-Winter, S. Rimsky, A. Danchin, and P. Bertin. 1999. Multiple control of flagellum biosynthesis in Escherichia coli: role of H-NS protein and the cyclic AMP-catabolite activator protein complex in transcription of the flhDC master operon. J. Bacteriol. 181:7500-7508.
64. Soutourina, O. A., E. Krin, C. Laurent-Winter, F. Hommais, A. Danchin, and P. N. Bertin. 2002. Regulation of bacterial motility in response to low pH in Escherichia coli: the role of H-NS protein. Microbiology 148:1543-1551.
65. Sperandio, V., A. G. Torres, and J. B. Kaper. 2002. Quorum sensing Escherichia coli regulators B and C (QseBC): a novel two-component regulatory system involved in the regulation of flagella and motility by quorum sensing in E. coli. Mol. Microbiol. 43:809-821.
66. Suppmann, B., and G. Sawers. 1994. Isolation and characterization of hypophosphite-resistant mutants of Escherichia coli: identification of the FocA protein, encoded by the pfl operon, as a putative formate transporter. Mol. Microbiol. 11:965-982.
67. Tanaka, Y., K. Kimata, and H. Aiba. 2000. A novel regulatory role of glucose transporter of Escherichia coli: membrane sequestration of a global repressor Mlc. EMBO J. 19:5344-5352.
68. Textor, S., V. F. Wendisch, A. A. De Graaf, U. Muller, M. I. Linder, D. Linder, and W. Buckel. 1997. Propionate oxidation in Escherichia coli: evidence for operation of a methylcitrate cycle in bacteria. Arch. Microbiol. 168:428-436.
69. Tso, W. W., and J. Adler. 1974. Negative chemotaxis in Escherichia coli. J. Bacteriol. 118:560-576.
70. Wei, B. L., A. M. Brun-Zinkernagel, J. W. Simecka, B. M. Pruss, P. Babitzke, and T. Romeo. 2001. Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli. Mol. Microbiol. 40:245-256.
71. Wei, Y., J. M. Lee, D. R. Smulski, and R. A. LaRossa. 2001. Global impact of sdiA amplification revealed by comprehensive gene expression profiling of Escherichia coli. J. Bacteriol. 183:2265-2272.
72. 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 using mRNA and total RNA on DNA microarrays. Anal. Biochem. 290:205-213.
73. Wolfe, S. A., and J. M. Smith. 1988. Nucleotide sequence and analysis of the purA gene encoding adenylosuccinate synthetase of Escherichia coli K12. J. Biol. Chem. 263:19147-19153.
74. Yamamoto, K., R. M. Macnab, and Y. Imae. 1990. Repellent response functions of the Trg and Tap chemoreceptors of Escherichia coli. J. Bacteriol. 172:383-388.
75. Yang, Y. T., A. A. Aristidou, K. Y. San, and G. N. Bennett. 1999. Metabolic flux analysis of Escherichia coli deficient in the acetate production pathway and expressing the Bacillus subtilis acetolactate synthase. Metab. Eng. 1:26-34.
76. 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.