Microbiol Mol Biol Rev 69(1): 12-50

The Acetate Switch

Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois

^{Mailing address: Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153. Phone: (708) 216-5814. Fax: (708) 216-9574. E-mail:}ude.cmul@eflowa.

Abstract

To succeed, many cells must alternate between life-styles that permit rapid growth in the presence of abundant nutrients and ones that enhance survival in the absence of those nutrients. One such change in life-style, the “acetate switch,” occurs as cells deplete their environment of acetate-producing carbon sources and begin to rely on their ability to scavenge for acetate. This review explains why, when, and how cells excrete or dissimilate acetate. The central components of the “switch” (phosphotransacetylase [PTA], acetate kinase [ACK], and AMP-forming acetyl coenzyme A synthetase [AMP-ACS]) and the behavior of cells that lack these components are introduced. Acetyl phosphate (acetyl∼P), the high-energy intermediate of acetate dissimilation, is discussed, and conditions that influence its intracellular concentration are described. Evidence is provided that acetyl∼P influences cellular processes from organelle biogenesis to cell cycle regulation and from biofilm development to pathogenesis. The merits of each mechanism proposed to explain the interaction of acetyl∼P with two-component signal transduction pathways are addressed. A short list of enzymes that generate acetyl∼P by PTA-ACKA-independent mechanisms is introduced and discussed briefly. Attention is then directed to the mechanisms used by cells to “flip the switch,” the induction and activation of the acetate-scavenging AMP-ACS. First, evidence is presented that nucleoid proteins orchestrate a progression of distinct nucleoprotein complexes to ensure proper transcription of its gene. Next, the way in which cells regulate AMP-ACS activity through reversible acetylation is described. Finally, the “acetate switch” as it exists in selected eubacteria, archaea, and eukaryotes, including humans, is described.

Abstract

Acknowledgments

The work performed in the Wolfe laboratory has been supported by grants from the National Institutes of Health, the National Science Foundation, and Loyola University Chicago.

I thank all my collaborators, all the individuals who provided me with access to their unpublished results, and anyone with whom I have spent hours discussing various aspects of the “acetate switch.” I specifically want to emphasize the intellectual and technical efforts of four postdoctoral fellows, Christine M. Beatty, Douglas F. Browning, Suman Kumari, and Birgit M. Prüβ.

Acknowledgments

REFERENCES

References

1. Abaibou, H., J. Pommier, S. Benoit, G. Giordano, and M. Mandrand-Berthelot. 1995. Expression and characterization of the Escherichia coli fdo locus and a possible physiological role for aerobic formate dehydrogenase. J. Bacteriol.177:7141-7149.
2. Abdel-Hamid, A. M., M. M. Attwood, and J. R. Guest. 2001. Pyruvate oxidase contributes to the aerobic growth efficiency of Escherichia coli. Microbiology147:1483-1498. [[PubMed]
3. Alam, K. Y., and D. P. Clark. 1989. Anaerobic fermentation balance of Escherichia coli as observed by in vivo nuclear magnetic resonance spectroscopy. J. Bacteriol.171:6213-6217.
4. 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.
5. Allen, A. 1984. The structure and function of gastrointestinal mucus, p. 3-11. In I. E. C. Boedeker (ed.), Attachment of organisms to the gut mucosa, vol. II. CRC Press, Inc., Boca Raton, Fla. [PubMed]
6. Amarasingham, C. D., and B. D. Davis. 1965. Regulation of delta-ketoglutarate dehydrogenase formation in Escherichia coli. J. Biol. Chem.240:3664-3668. [[PubMed]
7. Amemura, M., K. Makino, H. Shinagawa, and A. Nakata. 1990. Cross talk to the phosphate regulon of Escherichia coli by PhoM protein: PhoM is a histidine protein kinase and catalyzes phosphorylation of PhoB and PhoM opon reading frame 2. J. Bacteriol.172:6300-6307.
8. Ames, G. F., and A. K. Joshi. 1990. Energy coupling in bacterial periplasmic permeases. J. Bacteriol.172:4133-4137.
9. Amsler, C. D., M. Cho, and P. Matsumura. 1993. Multiple factors underlying the maximum motility of Escherichia coli as cultures enter post-exponential growth. J. Bacteriol.175:6238-6244.
10. Anderson, G. G., J. J. Palermo, J. D. Schilling, R. Roth, J. Heuser, and S. J. Hultgren. 2003. Intracellular bacterial biofilm-like pods in urinary tract infections. Science301:105-107. [[PubMed]
11. Andreesen, JR. 1994. Glycine metabolism in anaerobes. Antonie Leeuwenhoek66:223-237. [[PubMed][Google Scholar]
12. Andreesen, J. R., M. Wagner, D. Sonntag, M. Kohlstock, C. Harms, T. Gursinsky, J. Jager, T. Parther, U. Kabisch, A. Grantzdorffer, A. Pich, and B. Sohling. 1999. Various functions of selenols and thiols in anaerobic gram-positive, amino acids-utilizing bacteria. Biofactors10:263-270. [[PubMed]
13. Antelmann, H., J. Bernhardt, R. Schmid, H. Mach, U. Volker, and M. Hecker. 1997. First steps from a two-dimensional protein index towards a response-regulation map for Bacillus subtilis. Electrophoresis18:1451-1463. [[PubMed]
14. Argenzio, R. A., and M. Southworth. 1974. Sites of organic acid production and absorption in gastrointestinal tract of the pig. Am. J. Physiol. Endocrinol. Metab.228:454-460. [[PubMed]
15. Aristidou, A. A., K.-Y. San, and G. N. Bennett. 1994. Modification of central pathway in Escherichia coli to reduce acetate accumulation by heterologous expression of the Bacillus subtilis acetolactate synthase gene. Biotechnol. Bioeng.44:944-951. [[PubMed]
16. Arkowitz, R., and RAbeles. 1989. Identification of acetyl phosphate as the product of clostridial glycine reductase: evidence for an acetyl enzyme intermediate. Biochemistry28:4639-4644. [[PubMed][Google Scholar]
17. Arkowitz, R., and RAbeles. 1991. Mechanism of action of clostridial glycine reductase: isolation and characterization of a covalent acetyl enzyme intermediate. Biochemistry30:4090-4097. [[PubMed][Google Scholar]
18. Arthur, M., F. Depardieu, G. Gerbaud, M. Galimand, R. Leclercq, and P. Courvalin. 1997. The VanS sensor negatively controls VanR-mediated transcriptional activation of glycopeptide resistance genes of Tn1546 and related elements in the absence of induction. J. Bacteriol.179:97-106.
19. Asada, Y., Miyake, M., Miyake, J., Kurane, R., and Tokiwa, Y. 1999. Photosynthetic accumulation of poly-(hydroxybutyrate) by cyanobacteria—the metabolism and potential for CO2 recycling. Int. J. Biol. Macromol.25:37-42. [[PubMed]
20. Atkinson, M. R., and A. J. Ninfa. 1998. Role of the GlnK signal transduction protein in the regulation of nitrogen assimilation in Escherichia coli. Mol. Microbiol.29:431-447. [[PubMed]
21. Azam, T. A., and A. Ishihama. 1999. Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J. Biol. Chem.274:33105-33113. [[PubMed]
22. Azam, T. A., A. Iwata, A. Nishimura, S. Ueda, and A. Ishihama. 1999. Growth phase- dependent variation in protein composition of the Escherichia coli nucleoid. J. Bacteriol.181:6361-6370.
23. Ball, C. A., R. Osuna, K. C. Ferguson, and R. C. Johnson. 1992. Dramatic changes in FIS levels upon nutrient upshift in Escherichia coli. J. Bacteriol.174:8043-8056.
24. Bang, I., B. Kim, J. Foster, and Y. Park. 2000. OmpR regulates the stationary-phase acid tolerance response of Salmonella enterica serovar Typhimurium. J. Bacteriol.182:2245-2252.
25. Bang, I. S., J. P. Audia, Y. K. Park, and J. W. Foster. 2002. Autoinduction of the ompR response regulator by acid shock and control of the Salmonella enterica acid tolerance response. Mol. Microbiol.44:1235-1250. [[PubMed]
26. Barak, R., W. N. Abouhamad, and M. Eisenbach. 1998. Both acetate kinase and acetyl coenzyme A synthetase are involved in acetate-stimulated chnage in the direction of flagellar rotation in Escherichia coli. J. Bacteriol.180:985-988.
27. Barak, R., and MEisenbach. 2001. Acetylation of the response regulator, CheY, is involved in bacterial chemotaxis. Mol. Microbiol.40:731-743. [[PubMed][Google Scholar]
28. Barak, R., and MEisenbach. 1999. Chemotactic-like response of Escherichia coli cells lacking the known chemotaxis machinery but containing overexpressed CheY. Mol. Microbiol.31:1125-1137. [[PubMed][Google Scholar]
29. Barak, R., and MEisenbach. 2004. Co-regulation of acetylation and phosphorylation of CheY, a response regulator in chemotaxis of Escherichia coli. J. Mol. Biol.342:375-381. [[PubMed][Google Scholar]
30. Barak, R., K. Prasad, A. Shainskaya, A. J. Wolfe, and M. Eisenbach. 2004. Acetylation of the chemotaxis response regulator CheY by acetyl-CoA synthetase purified from Escherichia coli. J. Mol. Biol.342:383-401. [[PubMed]
31. 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. Biochemistry31:10099-10107. [[PubMed]
32. Barker, HA. 1992. The path from acetylphosphate to acetyl CoA. FASEB J.6:3014-3015. [[PubMed][Google Scholar]
33. Barnard, A., A. Wolfe, and S. Busby. 2004. Regulation at complex bacterial promoters: how bacteria use different promoter organisations to produce different regulatory outcomes. Curr. Opin. Microbiol.7:102-108. [[PubMed]
34. Baronofsky, J. J., W. J. A. Schreurs, and E. R. Kashket. 1984. Uncoupling by acetic acid limits growth of and acetogenesis by Clostridium thermoaceticum. Appl. Environ. Microbiol.48:1134-1139.
35. Baskett, R. C., and D. J. Hentges. 1973. Shigella flexneri inhibition by acetic acid. Infect. Immun.8:91-97.
36. Basson, M. D., N. J. Emenaker, and F. Hong. 1998. Differential modulation of human (Caco-2) colon cancer cell line phenotype by short chain fatty acids. Proc. Soc. Exp. Biol. Med.217:476-483. [[PubMed]
37. Batt, R. M., H. C. Rutgers, and A. A. Sancak. 1996. Enteric bacteria: friend or foe? J. Small Anim. Pract.37:261-267. [[PubMed]
38. Bauer, D. A., A. Ben-Basst, M. Dawson, V. T. Dela Peunte, and J. O. Neway. 1990. Improved expression of human interleukin-2 in high-cell-density fermentor cultures of Escherichia coli K-12 by a phosphotransacetylase mutant. Appl. Environ. Microbiol.56:1296-1302.
39. Bearson, B. L., L. Wilson, and J. W. Foster. 1998. A low pH-inducible, PhoPQ-dependent acid tolerance response protects Salmonella typhimurium against inorganic acid stress. J. Bacteriol.180:2409-2417.
40. Beatty, C. M., D. F. Browning, S. J. W. Busby, and A. J. Wolfe. 2003. CRP-dependent activation of the Escherichia coli acsP2 promoter by a synergistic class III mechanism. J. Bacteriol.185:5148-5157.
41. Begley, T. P., C. Kinsland, and E. Strauss. 2001. The biosynthesis of coenzyme A in bacteria. Vitam. Horm.61:157-171. [[PubMed]
42. Behrens, M., and PDurre. 2000. KdpE of Clostridium acetobutylicum is a highly specific response regulator controlling only the expression of the kdp operon. J. Mol. Microbiol. Biotechnol.2:45-52. [[PubMed][Google Scholar]
43. Belaich, A., and J. P. Belaich. 1976. Microcalorimetric study of the anaerobic growth of Escherichia coli: growth thermograms in a synthetic medium. J. Bacteriol.125:14-18.
44. Bennett, P. M., and W. H. Holms. 1975. Reversible inactivation of the isocitrate dehydrogenase of Escherichia coli ML308 during growth on acetate. J. Gen. Microbiol.87:37-51. [[PubMed]
45. Bentley, R. 2000. From ′reactive C2 units' to acetyl coenzyme A: a long trail with an acetyl phosphate detour. Trends Biochem. Sci.25:302-305. [[PubMed]
46. Berg, P. 1956. Acyl adenylates: an enzymatic mechanism of acetate activation. J. Biol. Chem.222:991-1013. [[PubMed]
47. Bernish, B., and Ivan de Rijn. 1999. Characterization of a two-component system in Streptococcus pyogenes which is involved in regulation of hyaluronic acid production. J. Biol. Chem.274:4786-4793. [[PubMed][Google Scholar]
48. Bertagnolli, B. L., and L. P. Hager. 1991. Activation of Escherichia coli pyruvate oxidase enhances the oxidation of hydroxyethylthiamin pyrophosphate. J. Biol. Chem.266:10168-10173. [[PubMed]
49. Bertagnolli, B. L., and L. P. Hager. 1993. Role of flavin in acetoin production by two bacterial pyruvate oxidases. Arch. Biochem. Biophys.300:364-371. [[PubMed]
50. 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.
51. Bleves, S., M.-N. Marenne, G. Detry, and G. R. Cornelis. 2002. Up-regulation of the Yersinia enterocolitica yop regulon by deletion of the flagellum master operon flhDC. J. Bacteriol.184:3214-3223.
52. Bobik, T. A., G. D. Havemann, R. J. Busch, D. S. Williams, and H. C. Aldrich. 1999. The propanediol utilization (pdu) operon of Salmonella enterica serovar Typhimurium LT2 includes genes necessary for formation of polyhedral organelles involved in coenzyme B12-dependent 1,2-propanediol degradation. J. Bacteriol.181:5967-5975.
53. Bochner, B. R., and B. N. Ames. 1982. Selective precipitation orthophosphate from mixtures containing labile phosphorylated metabolites. Anal. Biochem.122:100-107. [[PubMed]
54. Bock, A., and GSawers. 1996. Fermentation, p. 262-282. 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.
55. Bohnhoff, M., C. P. Miller, and W. R. Martin. 1964. Resistance of the mouse's intestinal tract to experimental Salmonella infection. I. Factors which interfere with the initiation of infection by oral inoculation. J. Exp. Med.120:805-816.
56. Booth, IR. 1985. Regulation of cytoplasmic pH in bacteria. Microbiol. Rev.49:359-378. [Google Scholar]
57. Bouche, S., E. Klauck, D. Fischer, M. Lucassen, K. Jung, and R. Hengge-Aronis. 1998. Regulation of RssB-dependent proteolysis in Escherichia coli: a role for acetyl phosphate in a response regulator-controlled process. Mol. Microbiol.27:787-795. [[PubMed]
58. Boucher, P. E., F. D. Menozzi, and C. Locht. 1994. The modular architecture of bacterial response regulators. Insights into the activation mechanism of the BvgA transactivator of Bordetella pertussis. J. Mol. Biol.241:363-377. [[PubMed]
59. Brasen, C., and PSchonheit. 2001. Mechanisms of acetate formation and acetate activation in halophilic archaea. Arch. Microbiol.175:360-368. [[PubMed][Google Scholar]
60. Brillard, J., C. Ribeiro, N. Boemare, M. Brehelin, and A. Givaudan. 2001. Two distinct hemolytic activities in Xenorhabdus nematophila are active against immunocompetent insect cells. Appl. Environ. Microbiol.67:2515-2525.
61. 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. [[PubMed]
62. Browning, D. F., C. M. Beatty, E. A. Sanstad, K. A. Gunn, S. J. W. Busby, and A. J. Wolfe. 2004. Modulation of CRP-dependent transcription at the Eschericheria coli acsP2 promoter by a nucleoprotein complex: anti-activation by the nucleoid proteins FIS and IHF. Mol Microbiol.51:241-254 [[PubMed]
63. Browning, D. F., C. M. Beatty, A. J. Wolfe, J. A. Cole, and S. J. W. Busby. 2002. Independent regulation of the divergent Escherichia coli nrfA and acsP1 promoters by a nucleoprotein assembly at a shared regulatory region. Mol. Microbiol.43:687-701. [[PubMed]
64. Browning, D. F., and S. J. W. Busby. 2004. The regulation of bacterial transcription initiation. Nat. Rev. Microbiol.2:1-5. [[PubMed]
65. Bruggemann, C., K. Denger, A. M. Cook, and J. Ruff. 2004. Enzymes and genes of taurine and isethionate dissimilation in Paracoccus denitrificans. Microbiology150:805-816. [[PubMed]
66. Buckley, B. M., and D. H. Williamson. 1977. Origins of blood acetate in the rat. Biochem. J.166:539-545.
67. Bulter, T., S. G. Lee, W. W. Wong, E. Fung, M. R. Connor, and J. C. Liao. 2004. Design of artificial cell-cell communication using gene and metabolic networks. Proc. Natl. Acad. Sci. USA101:2299-2304.
68. Bunch, P. K., F. Mat-Jan, N. Lee, and D. P. Clark. 1997. The ldhA gene encoding the fermentative lactate dehydrogenase of Escherichia coli. Microbiology143:187-195. [[PubMed]
69. Busby, S., and REbright. 1999. Transcription activation by catabolite activator protein (CAP). J. Mol. Biol.293:199-213. [[PubMed][Google Scholar]
70. Buss, K. A., D. R. Cooper, C. Ingram-Smith, J. G. Ferry, D. A. Sanders, and M. S. Hasson. 2001. Urkinase: structure of acetate kinase, a member of the ASKHA superfamily of phosphotransferases. J. Bacteriol.183:680-686.
71. Buss, K. A., C. Ingram-Smith, J. G. Ferry, D. A. Sanders, and M. S. Hasson. 1997. Crystallization of acetate kinase from Methanosarcina thermophila and prediction of its fold. Protein Sci.6:2659-2662.
72. Butow, R. A., and N. G. Avadhani. 2004. Mitochondrial signaling: the retrograde response. Mol. Cell14:1-15. [[PubMed]
73. Cai, S. J., and M. Inouye. 2002. EnvZ-OmpR interaction and osmoregulation in Escherichia coli. J. Biol. Chem.277:24155-24161. [[PubMed]
74. Carmany, D. O., K. Hollingsworth, and W. R. McCleary. 2003. Genetic and biochemical studies of phosphatase activity of PhoR. J. Bacteriol.185:1112-1115.
75. Carroll, PT. 1997. Evidence to suggest that extracellular acetate is accumulated by rat hippocampal cholinergic nerve terminals for acetylcholine formation and release. Brain Res.753:47-55. [[PubMed][Google Scholar]
76. Chamnongpol, S., M. Cromie, and E. A. Groisman. 2003. Mg^{sensing by the Mg}^{sensor PhoQ of}Salmonella enterica. J. Mol. Biol.325:795-807. [[PubMed]
77. Chamnongpol, S., and E. A. Groisman. 2000. Acetyl phosphate-dependent activation of a mutant PhoP response regulator that functions independently of its cognate sensor kinase. J. Mol. Biol.300:291-305. [[PubMed]
78. 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-CoA flux for the growth and survival. J. Bacteriol.181:6656-6663.
79. Chang, Y. Y., and J. E. J. Cronan. 1983. Genetic and biochemical analyses of Escherichia coli strains having a mutation in the structural gene (poxB) for pyruvate oxidase. J. Bacteriol.154:756-762.
80. Chang, Y. Y., A. Y. Wang, and J. Cronan, J. E. 1994. Expression of Escherichia coli pyruvate oxidase (PoxB) depends on the sigma factor encoded by the rpoS (katF)gene. Mol. Microbiol.11:1019-1028. [[PubMed]
81. Chatterjee, R., C. S. Millard, K. Champion, D. P. Clark, and M. I. Donnelly. 2001. Mutation of the ptsG gene results in increased production of succinate in fermentation of glucose by Escherichia coli. Appl. Environ. Microbiol.67:148-154.
82. Chen, R., V. Hatzimanikatis, W. M. Yap, P. W. Postma, and J. E. Bailey. 1997. Metabolic consequences of phosphotransferase (PTS) mutation in a phenylalanine- producing recombinant Escherichia coli. Biotechnol. Prog.13:768-775. [[PubMed]
83. Chiang, S. L., and J. J. Mekalanos. 1998. Use of signature-tagged transposon mutagenesis to identify Vibrio cholerae genes critical for colonization. Mol. Microbiol.27:797-805. [[PubMed]
84. Chohnan, S., H. Furukawa, T. Fujio, H. Nishihara, and Y. Takamura. 1997. Changes in the size and composition of intracellular pools of nonesterified coenzyme A and coenzyme A thioesters in aerobic and facultatively anaerobic bacteria. Appl. Environ. Microbiol.63:553-560.
85. Chohnan, S., H. Izawa, H. Nishihara, and Y. Takamura. 1998. Changes in size of intracellular pools of coenzyme A and its thioesters in Escherichia coli K-12 cells to various carbon sources and stresses. Biosci. Biotechnol. Biochem.62:1122-1128. [[PubMed]
86. Chohnan, S., and YTakamura. 1991. A simple micromethod for measurement of CoASH and its use in measuring intracellular levels of CoASH and short chain acyl- CoAs in Escherichia coli K12 cells. Agric. Biol. Chem.55:87-94. [PubMed][Google Scholar]
87. Chou, T. C., and F. Lipmann. 1952. Separation of acetyl transfer enzymes in pigeon liver extract. J. Biol. Chem.196:89-103. [[PubMed]
88. Claes, W. A., A. Puhler, and J. Kalinowski. 2002. Identification of two prpdbc gene clusters in Corynebacterium glutamicum and their involvement in propionate degradation via the 2-methylcitrate cycle. J. Bacteriol.184:2728-2739.
89. Clark, DP. 1989. The fermentation pathways of Escherichia coli. FEMS Microbiol. Rev.5:223-234. [[PubMed][Google Scholar]
90. Clark, D. P., and J. E. Cronan, Jr. 1996. Two-carbon compounds and fatty acids as carbon sources, p. 343-357. 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.
91. Clegg, S., and K. T. Hughes. 2002. FimZ is a molecular link between sticking and swimming in Salmonella enterica serovar Typhimurium. J. Bacteriol.184:1209-1213.
92. Comolli, J. C., A. J., Carl, C. Hall, and T. Donohue. 2002. Transcriptional activation of the Rhodobacter sphaeroides cytochrome c₂ gene promoter by the response regulator PrrA. J. Bacteriol.184:390-399.
93. Contiero, J., C. M. Beatty, S. Kumari, C. L. DeSanti, W. R. Strohl, and A. J. Wolfe. 2000. Effects of mutations in acetate metabolism on high-cell-density growth of Escherichia coli. J. Ind. Microbiol. Biotechnol.24:421-430. [PubMed]
94. Cook, A. M., and K. Denger. 2002. Dissimilation of the C2 sulfonates. Arch. Microbiol.179:1-6. [[PubMed]
95. Cozzone, AJ. 1998. Regulation of acetate metabolism by protein phosphorylation in enteric bacteria. Annu. Rev. Microbiol.52:127-164. [[PubMed][Google Scholar]
96. Crabtree, B., M. J. Gordon, and S. L. Christie. 1990. Measurement of the rates of acetyl-CoA hydrolysis and synthesis from acetate in rat hepatocytes and the role of these fluxes in substrate cycling. Biochem. J.270:219-225.
97. Crabtree, B., M. J. Souter, and S. E. Anderson. 1989. Evidence that the production of acetate in rat hepatocytes is a predominantly cytoplasmic process. Biochem. J.257:673-678.
98. Crabtree, HG. 1929. Observations on the carbohydrate metabolism of tumours. Biochem. J.23:536-545. [Google Scholar]
99. Cronan, J., Jr. 1997. In vivo evidence that acyl coenzyme A regulates DNA binding by the Escherichia coli FadR global transcription factor. J. Bacteriol.179:1819-1823.
100. Cronan, J. E., Jr., and D. LaPorte. 1996. Tricarboxylic acid cycle and gloxylate bypass, p. 206-216. 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.
101. Cummings, J. H., and G. T. Macfarlane. 1997. Role of intestinal bacteria in nutrient metabolism. J. Parenter Enteral. Nutr.21:357-365. [[PubMed]
102. Cummings, J. H., E. W. Pomare, W. J. Branch, C. P. Naylor, and G. T. Macfarlane. 1987. Short chain fatty acids in human large intestine, portal, hepatic and venous blood. Gut28:1221-1227.
103. Cunning, C., and TElliott. 1999. RpoS synthesis is growth rate regulated in Salmonella typhimurium, but its turnover is not dependent on acetyl phosphate synthesis or PTS function. J Bacteriol.181:4853-4862. [Google Scholar]
104. Cunningham, L., D. Georgellis, J. Green, and J. R. Guest. 1998. Co-regulation of lipoamide dehydrogenase and 2-oxoglutarate dehydrogenase synthesis in Escherichia coli: characterisation of an ArcA binding site in the lpd promoter. FEMS Microbiol. Lett.169:403-408. [[PubMed]
105. Cunningham, L., and J. R. Guest. 1998. Transcription and transcript processing in the sdhCDAB-sucABCD operon of Escherichia coli. Microbiology144:2113-2123. [[PubMed]
106. Dailey, F. E., and H. C. Berg. 1993. Change in direction of flagellar rotation in Escherichia coli mediated by acetate kinase. J. Bacteriol.175:3236-3239.
107. Danese, P. N., and T. J. Silhavy. 1998. CpxP, a stress-combative member of the Cpx regulon. J. Bacteriol.180:831-839.
108. Danese, P. N., Snyder, W. B., Cosma, C. L., Davis, L. J. & Silhavy, T. J. 1995. The Cpx two-component signal transduction pathway of Escherichia coli regulates transcription of the gene specifying the stress-inducible periplasmic protease, DegP. Genes Dev.9:387-398. [[PubMed]
109. Da Re, S. S., D. Deville-Bonne, T. Tolstykh, M. Veron, and J. B. Stock. 1999. Kinetics of CheY phosphorylation by small molecule phosphodonors. FEBS Lett.457:323-326. [[PubMed]
110. Dartigalongue, C., and SRaina. 1998. A new heat-shock gene, ppiD, encodes a peptidyl-prolyl isomerase required for folding of outer membrane proteins in Escherichia coli. EMBO J.17:3968-3980. [Google Scholar]
111. Darwin, A., H. Hussain, L. Griffiths, J. Grove, Y. Sambongi, S. Busby, and J. Cole. 1993. Regulation and sequence of the structural gene for cytochrome c552 from Escherichia coli: not a hexahaem but a 50 kDa tetrahaem nitrite reductase. Mol. Microbiol.9:1255-1265. [[PubMed]
112. Davalos-Garcia, M., A. Conter, I. Toesca, C. Gutierrez, and K. Cam. 2001. Regulation of osmC gene expression by the two-component system rcsB-rcsC in Escherichia coli. J. Bacteriol.183:5870-5876.
113. de Graef, M. R., S. Alexeeva, J. L. Snoep, and M. J. Teixeira de Mattos. 1999. The steady-state internal redox state (NADH/NAD) reflects the external redox state and is correlated with catabolic adaptation in Escherichia coli. J. Bacteriol.181:2351-2357.
114. Denger, K., J. Ruff, D. Schleheck, and A. M. Cook. 2004. Rhodococcus opacus expresses the xsc gene to utilize taurine as a carbon source or as a nitrogen source but not as a sulfur source. Microbiology150:1859-1867. [[PubMed]
115. Deretic, V., J. H. J. Leveau, C. D. Mohr, and N. S. Hibler. 1992. In vitro phosphorylation of AlgR, a regulator of mucoidy in Pseudomonas aeruginosa, by a histidine protein kinase and effects of small phospho-donor molecules. Mol. Microbiol.6:2761-2767. [[PubMed]
116. Deutscher, J., E. Kuster, U. Bergstedt, U. Charrier, and W. Hillen. 1995. Protein kinase-dependent HPr/CcpA interaction links glycolytic activity to carbon catabolite repression in Gram-positive bacteria. Mol. Microbiol.15:1049-1053. [[PubMed]
117. Deutscher, J., J. Reizer, C. Fischer, A. Galinier, M. H. Saier, Jr., and M. Steinmetz. 1994. Loss of protein kinase-catalyzed phosphorylation of HPr, a phosphocarrier protein of the phosphotransferase system, by mutation of the ptsHI gene confers catabolite repression resistance to several catabolic genes of Bacillus subtilis. J. Bacteriol.176:3336-3344.
118. Diaz-Ricci, J. C., L. Regan, and J. E. Bailey. 1991. Effect of alteration of the acetic acid synthesis pathway on the fermentation pattern of Escherichia coli. Biotechnol. Bioeng.38:1318-1324. [[PubMed]
119. Doelle, H. W., K. N. Ewings, and N. W. Hollywood. 1982. Regulation of glucose metabolism in bacterial systems. Adv. Biochem. Eng.23:1-35. [PubMed]
120. Dominguez, H., C. Nezondet, N. D. Lindley, and M. Cocaign. 1993. Modified carbon flux during oxygen limited growth of Corynebacterium glutamicum and the consequences for amino acid overproduction. Biotechnol. Lett.15:449-454. [PubMed]
121. Drake, S., R. Bourret, L. Luck, M. Simon, and J. Falke. 1993. Activation of the phosphosignaling protein Che Y. I. Analysis of the phosphorylated conformation by 19F NMR and protein engineering. J. Biol. Chem.268:13081-13088.
122. Durant, J. A., V. K. Lowry, D. J. Nisbet, L. H. Stanker, D. E. Corrier, and S. C. Ricke. 1999. Short-chain fatty acids affect cell-association and invasion of HEp-2 cells by Salmonella typhimurium. J. Environ. Sci. Health Ser. B34:1083-1099. [[PubMed]
123. el-Mansi, E. M., and W. H. Holms. 1989. Control of carbon flux to acetate excretion during growth of Escherichia coli in batch and continuous cultures. J. Gen. Microbiol.135:2875-2883. [[PubMed]
124. El-Mansi, M. 2004. Flux to acetate and lactate excretions in industrial fermentations: physiological and biochemical implications. J. Ind. Microbiol. Biotechnol.31:295-300. [[PubMed]
125. Farewell, A., K. Kvint, and T. Nystrom. 1998. Negative regulation by RpoS: a case of sigma factor competition. Mol. Microbiol.29:1039-1051. [[PubMed]
126. Farmer, W. R., and J. C. Liao. 1997. Reduction of aerobic acetate production by Escherichia coli. Appl. Environ. Microbiol.63:3205-3210.
127. Feng, J., M. R. Atkinson, W. McCleary, J. B. Stock, B. L. Wanner, and A. J. Ninfa. 1992. Role of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli. J. Bacteriol.174:6061-6070.
128. Ferre, A., J. de la Mora, T. Ballado, L. Camarena, and G. Dreyfus. 2004. Biochemical study of multiple chey response regulators of the chemotactic pathway of Rhodobacter sphaeroides. J. Bacteriol.186:5172-5177.
129. Ferrieres, L., and D. J. Clarke. 2003. The RcsC sensor kinase is required for normal biofilm formation in Escherichia coli K-12 and controls the expression of a regulon in response to growth on a solid surface. Mol. Microbiol.50:1665-1682. [[PubMed]
130. Field, J., B. Rosenthal, and J. Samuelson. 2000. Early lateral transfer of genes encoding malic enzyme, acetyl-CoA synthetase and alcohol dehydrogenases from anaerobic prokaryotes to Entamoeba histolytica. Mol. Microbiol.38:446-455. [[PubMed]
131. Fisher, SH. 1999. Regulation of nitrogen metabolism in Bacillus subtilis: vive la difference! Mol. Microbiol.32:223-232. [[PubMed][Google Scholar]
132. Forst, S., and BBoylan. 2002. Characterization of the pleiotropic phenotype of an ompR strain of Xenorhabdus nematophila. Antonie Leeuwenhoek81:43-49. [[PubMed][Google Scholar]
133. Forst, S., J. Delgado, G. Ramakrishnan, and M. Inouye. 1988. Regulation of ompC and ompF expression in Escherichia coli in the absence of envZ. J. Bacteriol.170:5080-5085.
134. Forst, S., J. Gelgado, A. Rampersaud, and M. Inouye. 1990. In vivo phosphorylation of OmpR, the transcription activator of the ompF and ompC genes in Escherichia coli. J. Bacteriol.172:3473-3477.
135. Fox, D. K., N. D. Meadow, and S. Roseman. 1986. Phosphate transfer between acetate kinase and enzyme I of the bacterial phosphotransferase system. J. Biol. Chem.261:13498-13503. [[PubMed]
136. Fox, D. K., and S. Roseman. 1986. Isolation and characterization of homogeous acetate kinase from Salmonella typhimurium and Escherichia coli. J. Biol. Chem.261:13487-13497. [[PubMed]
137. Fraenkel, DG. 1996. Glycolysis, p. 189-198. 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. ASM Press, Washington, D.C.
138. Francez-Charlot, A., B. Laugel, A. Van Gemert, N. Dubarry, F. Wiorowski, M.-P. Castanie-Cornet, C. Gutierrez, and K. Cam. 2003. RcsCDB His-Asp phosphorelay system negatively regulates the flhDC operon in Escherichia coli. Mol. Microbiol.49:823-832. [[PubMed]
139. Fraser, C. M., J. D. Gocayne, O. White, M. D. Adams, R. A. Clayton, R. D. Fleischmann, C. J. Bult, A. R. Kerlavage, G. Sutton, J. M. Kelley, et al. 1995. The minimal gene complement of Mycoplasma genitalium. Science270:397-403. [[PubMed]
140. Fraser, G. M., L. Claret, R. Furness, S. Gupta, and C. Hughes. 2002. Swarming- coupled expression of the Proteus mirabilis hpmBA haemolysin operon. Microbiology148:2191-2201.
141. Freestone, P., S. Grant, M. Trinei, T. Onoda, and V. Norris. 1998. Protein phosphorylation in Escherichia coli L. form NC-7. Microbiology144:3289-3295. [[PubMed]
142. Freter, R. 1988. Mechanisms of bacterial colonization of the mucosal surfaces of the gut, p. 45-60, Virulence mechanisms of bacterial pathogens. American Society for Microbiology, Washington, D.C.
143. Freter, R. 1983. Mechanisms that control the microflora in the large intestine, p. 33-54. In D. J. Hentges (ed.), Human intestinal microflora in health and disease. Academic Press, Inc., New York, N.Y.
144. Fujino, T., J. Kondo, M. Ishikawa, K. Morikawa, and T. T. Yamamoto. 2001. Acetyl-CoA Synthetase 2, a mitochondrial matrix enzyme involved in the oxidation of acetate. J. Biol. Chem.276:11420-11426. [[PubMed]
145. Galinier, A., J. Haiech, M. Kilhoffer, M. Jaquinod, J. Stulke, J. Deutscher, and I. Martin-Verstraete. 1997. The Bacillus subtilis crh gene encodes a HPr-like protein involved in carbon catabolite repression. Proc. Natl. Acad. Sci. USA94:8439-8444.
146. Galinier, A., M. Kranaja, R. Engelmann, W. Hengstenber, M.-C. Kilhoffer, J. Deutscher, and J. Haiech. 1998. New protein kinase and protein phosphatase families mediate signal transduction in bacterial catabolite repression. Proc. Natl. Acad. Sci. USA95:1823-1828.
147. Galperin, M. Y., and N. V. Grishin. 2000. The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase. Proteins41:238-247. [[PubMed]
148. Galperin, M. Y., A. N. Nikolskaya, and E. V. Koonin. 2001. Novel domains of the prokaryotic two-component signal transduction systems. FEMS Microbiol. Lett.11:11-21. [[PubMed]
149. Garnak, M., and H. C. Reeves. 1979. Phosphorylation of isocitrate dehydrogenase of Escherichia coli. Science203:1111-1112. [[PubMed]
150. Gennis, R. B., and L. P. Hager. 1976. Pyrvuate oxidase, p. 493-504. In A. N. Martonosi (ed.), The enzymes and biological membranes, vol. 2. Plenum, New York, N.Y. [PubMed]
151. Gerstmeir, R., A. Cramer, P. Dangel, S. Schaffer, and B. J. Eikmanns. 2004. RamB, a novel transcriptional regulator of genes involved in acetate metabolism of Corynebacterium glutamicum. J. Bacteriol.186:2798-2809.
152. Gerstmeir, R., V. F. Wendisch, S. Schnicke, H. Ruan, M. Farwick, D. Reinscheid, and B. J. Eikmanns. 2003. Acetate metabolism and its regulation in Corynebacterium glutamicum. J. Biotechnol.104:99-122. [[PubMed]
153. Gimenez, R., M. F. Nunez, J. Badia, J. Aguilar, and L. Baldoma. 2003. The gene yjcG, cotranscribed with the gene acs, encodes an acetate permease in Escherichia coli. J. Bacteriol.185:6448-6455.
154. Glasemacher, J., A. K. Bock, R. Schmid, and P. Schonheit. 1997. Purification and properties of acetyl-CoA synthetase (ADP-forming), an archaeal enzyme of acetate formation and ATP synthesis, from the hyperthermophile Pyrococcus furiosus. Eur. J. Biochem.244:561-567. [[PubMed]
155. Gonzalez-Gil, G., R. Kahmann, and G. Muskhelishvili. 1998. Regulation of crp transcription by oscillation between distinct nucleoprotein complexes. EMBO J.17:2877-2885.
156. Goodier, R. I., and B. M. Ahmer. 2001. SirA orthologs affect both motility and virulence. J. Bacteriol.183:2249-2258.
157. Gottschalk, G. 1985. Bacterial metabolism, 2nd ed. Springer-Verlag, New York, N.Y.
158. Gourse, R. L., W. Ross, and T. Gaal. 2000. UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol. Microbiol.37:687-695. [[PubMed]
159. Grabau, C., and J. E. J. Cronan. 1984. Molecular cloning of the gene (poxB) encoding the pyruvate oxidase of Escherichia coli, a lipid-activated enzyme. J. Bacteriol.160:1088-1092.
160. Gray, C. T., J. W. T. Wimpenny, and W. R. Mossman. 1966. Regulation of metabolism in facultative bacteria. II. Effects of aerobiosis, anaerobiosis and nutrition on the formation of Kreb's cycle enzymes in Escherichia coli. Biochim. Biophys. Acta117:33-41. [[PubMed]
161. Green, J., and MBaldwin. 1997. HlyX, the FNR homologue of Actinobacillus pleuropneumoniae, is a [4Fe-4S]-containing oxygen-responsive transcription regulator that anaerobically activates FNR-dependent class I promoters via an enhanced AR1 contact. Mol. Microbiol.24:593-605. [[PubMed][Google Scholar]
162. Grozinger, C. M., and S. L. Schreiber. 2002. Deacetylase enzymes: biological functions and the use of small-molecule inhibitors. Chem. Biol.9:3-16. [[PubMed]
163. Grundy, F. H., D. A. Waters, S. H. G. Allen, and T. M. Henkin. 1993. Identification of genes involved in utilization of acetate and acetoin in Bacillus subtilis. Mol. Microbiol.10:259-271. [[PubMed]
164. Grundy, F. H., D. A. Waters, S. H. G. Allen, and T. M. Henkin. 1993. Regulation of the Bacillus subtilis acetate kinase gene by CcpA. J. Bacteriol.175:7348-7355.
165. Grundy, F. J., A. J. Turinsky, and T. M. Henkin. 1994. Catabolite regulation of Bacillus subtilis acetate and acetoin utilization genes by CcpA. J. Bacteriol.176:4527-4533.
166. Guarente, L. 2000. Sir2 links chromatin silencing, metabolism, and aging. Genes Dev.14:1021-1026. [[PubMed]
167. Guest, J. R., S. J. Angier, and G. C. Russell. 1989. Structure, expression, and protein engineering of the pyruvate dehydrogenase complex of Escherichia coli. Ann. N. Y. Acad. Sci.573:76-99. [[PubMed]
168. Guest, J. R., and G. C. Russell. 1992. Complexes and complexities of the citric acid cycle in Escherichia coli. Curr. Top. Cell. Regul.33:231-247. [[PubMed]
169. Gulick, A. M., V. J. Starai, A. R. Horswill, K. M. Homick, and J. C. Escalante- Semerena. 2003. The 1.75 A crystal structure of acetyl-CoA synthetase bound to adenosine-5′-propylphosphate and coenzyme A. Biochemistry42:2866-2873. [[PubMed]
170. Gunsalus, R. P., and S. J. Park. 1994. Aerobic-anaerobic gene regulation in Escherichia coli: control by the ArcAB and Fnr regulons. Res. Microbiol.145:437-450. [[PubMed]
171. Gupta, S., and D. P. Clark. 1989. Escherichia coli derivatives lacking both alcohol dehydrogenase and phosphotransacetylase grow anaerobically by lactate fermentation. J. Bacteriol.171:3650-3655.
172. Hahm, D. H., J. Pan, and J. S. Rhee. 1994. Characterization and evaluation of a pta (phosphotransacetylase) negative mutant of Escherichia coli HB101 as production host of foreign lipase. Appl. Microbiol. Biotechnol.42:100-107. [[PubMed]
173. Haldimann, A., S. Fisher, L. Daniels, C. Walsh, and B. Wanner. 1997. Transcriptional regulation of the Enterococcus faecium BM4147 vancomycin resistance gene cluster by the VanS-VanR two-component regulatory system in Escherichia coli K- 12. J. Bacteriol.179:5903-5913.
174. Han, K., H. C. Lim, and J. Hong. 1992. Acetic acid formation in Escherichia coli fermentation. Biotechnol. Bioeng.39:663-671. [[PubMed]
175. Han, M.-J., S. S. Yoon, and S. Y. Lee. 2001. Proteome analysis of metabolically engineered Escherichia coli producing poly(3-hydroxybutyrate). J. Bacteriol.183:301-308.
176. Hansen, R. G., and U. Henning. 1966. Regulation of pyruvate dehydrogenase activity in Escherichia coli K12. Biochim. Biophys. Acta122:355-358. [[PubMed]
177. Hansen, T., and PSchonheit. 2000. Purification and properties of the first-identified, archaeal, ATP-dependent 6-phosphofructokinase, an extremely thermophilic non- allosteric enzyme, from the hyperthermophile Desulfurococcus amylolyticus. Arch. Microbiol.173:103-109. [[PubMed][Google Scholar]
178. Hanson, T. S., V. R. Srinivasan, and H. O. Halvorson. 1963. Biochemistry of sporulation. I. Metabolism of acetate by vegetative and sporulating cells. J. Bacteriol.85:451-460.
179. Harms, C., U. Ludwig, and J. R. Andreesen. 1998. Sarcosine reductase of Tissierella creatinophila: purification and characterization of its components. Arch. Microbiol.170:442-450. [[PubMed]
180. Hasty, P. 2001. The impact energy metabolism and genome maintenance have on longevity and senescence: lessons from yeast to mammals. Mech. Ageing Dev.122:1651-1662. [[PubMed]
181. Head, C. G., A. Tardy, and L. J. Kenney. 1998. Relative binding affinities of OmpR and OmpR-phosphate at the ompF and ompC regulatory sites. J. Mol. Biol.281:857-870. [[PubMed]
182. Heermann, R., K. Altendorf, and K. Jung. 2003. The N-terminal input domain of the sensor kinase KdpD of Escherichia coli stabilizes the interaction between the cognate response regulator KdpE and the corresponding DNA-binding site. J. Biol. Chem.278:51277-51284. [[PubMed]
183. Hengge-Aronis, R. 2002. Signal transduction and regulatory mechanisms involved in control of the sigmaS (RpoS) subunit of RNA polymerase. Microbiol. Mol. Biol. Rev.66:373-395.
184. Henkin, TM. 1996. The role of CcpA transcriptional regulator in carbon metabolism in Bacillus subtilis. FEMS Microbiol. Lett.135:9-15. [[PubMed][Google Scholar]
185. Henkin, T. M., F. J. Grundy, W. L. Nicholson, and G. H. Chambliss. 1991. Catabolite repression of the α-amylase gene expression in Bacillus subtilis involves a trans-acting gene product homologous to the Escherichia coli lacI and galR repressors. Mol. Microbiol.5:575-584. [[PubMed]
186. 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. [[PubMed]
187. Heyde, M., P. Laloi, and R. Portalier. 2000. Involvement of carbon source and acetyl phosphate in the external-pH-dependent expression of porin genes in Escherichia coli. J. Bacteriol.182:198-202.
188. Hickey, M. W., A. J. Hillier, and G. R. Jago. 1983. Metabolism of pyruvate and citrate in lactobacilli. Aust. J. Biol. Sci.36:487-496. [[PubMed]
189. Hiesinger, M., C. Wagner, and H.-J. Schuller. 1997. The acetyl-CoA synthetase gene ACS2 of the yeast Saccharomyces cerevisiae is coregulated with structural genes of fatty acid biosynthesis by the transcriptional activators Ino2p and Ino4p. FEBS Lett.415:16-20. [[PubMed]
190. Hiratsu, K., A. Nakata, H. Shinagawa, and K. Makino. 1995. Autophosphorylation and activation of transcriptional activator PhoB of Escherichia coli by acetyl phosphate in vitro. Gene161:7-10. [[PubMed]
191. Hoch, J. A., and Silhavy, T. J. 1995. Two-component signal transduction. ASM Press, Washington, D.C.
192. Hoffman, T., N. Frankenberg, M. Marino, and D. Jahn. 1998. Ammonification in Bacillus subtilis utilizing dissimilatory nitrite reductase is dependent on resDE. J. Bacteriol.180:186-189.
193. Hollywood, N., and H. W. Doelle. 1976. Effect of specific growth rate and glucose concentration on growth and glucose metabolism of Escherichia coli K-12. Microbios17:23-33. [[PubMed]
194. Holman, T. R., Wu, Z., Wanner, B. L., and Walsh, C. T. 1994. Identification of the DNA-binding site for the phosphorylated VanR protein required for vancomycin resistance in Enterococcus faecium. Biochemistry33:4625-4631. [[PubMed]
195. Holms, H. 1996. Flux analysis and control of the central metabolic pathways in Escherichia coli. FEMS Microbiol. Rev.19:85-116. [[PubMed]
196. Holms, WH. 1986. The central metabolic pathways of Escherichia coli: relationship between flux and control at a branch point, efficiency of conversion to biomass, and excretion of acetate. Curr. Top. Cell. Regul.28:59-105. [[PubMed][Google Scholar]
197. Hong, J.-S., and A. G. Hunt. 1980. The role of acetylphosphate in active transport. J. Supramol. Struct.4:77. [PubMed]
198. Hong, J. S., A. G. Hunt, P. S. Masters, and M. A. Lieberman. 1979. Requirements of acetyl phosphate for the binding protein-dependent transport systems in Escherichia coli. Proc. Natl. Acad. Sci. USA76:1213-1217.
199. Hormann, K., and J. R. Andereesen. 1989. Reductive cleavage of sarcosine and betaine by Eubacterium acidaminophilum via enzyme systems different from glycine reductase. Arch. Microbiol.153:50-59. [PubMed]
200. Horswill, A. R., and J. C. Escalante-Semerena. 2002. Characterization of the propionyl-CoA synthetase (PrpE) enzyme of Salmonella enterica: residue Lys592 is required for propionyl-AMP synthesis. Biochemistry41:2379-2387. [[PubMed]
201. Horswill, A. R., and J. C. Escalante-Semerena. 1999. The prpE gene of Salmonella typhimurium LT2 encodes propionyl-CoA synthetase. Microbiology145:1381-1388. [[PubMed]
202. Horton, J. D., J. L. Goldstein, and M. S. Brown. 2002. SREBPs: transcriptional mediators of lipid homeostasis. Cold Spring Harbor Symp. Quant. Biol.67:491-498. [[PubMed]
203. Hoyt, J., and HReeves. 1988. In vivo phosphorylation of isocitrate lyase from Escherichia coli. Biochem. Biophys. Res. Commun.153:875-880. [[PubMed][Google Scholar]
204. Huang, M., F. B. Oppermann-Sanio, and A. Steinbuchel. 1999. Biochemical and molecular characterization of the Bacillus subtilis acetoin catabolic pathway. J. Bacteriol.181:3837-3841.
205. Hubschmann, T., H. J. M. M. Jorissen, T. Borner, W. Gartner, and N. Tandeau de Marsac. 2001. Phosphorylation of proteins in the light-dependent signalling pathway of a filamentous cyanobacterium. Eur. J. Biochem.268:3383-3389. [[PubMed]
206. Hueck, C. J., and W. Hillen. 1995. Catabolite repression in Bacillus subtilis: a global mechanism for the gram-positive bacteria? Mol. Microbiol.15:395-401. [[PubMed]
207. Hueck, C. J., W. Hillen, and M. H. Saier, Jr. 1994. Analysis of a cis-active sequence mediating catabolite repression in gram-positive bacteria. Res. Microbiol.145:503-518. [[PubMed]
208. Hunt, AG. 1982. The energetics of osmotic shock-sensitive active transport in Escherichia coli: studies in whole cells and isolated membrane vesicles. PhD thesis. Brandeis, Waltham, Mass.
209. Hunt, A. G., and J.-S. Hong. 1983. Properties and characterization of binding protein dependent active transport of glutamine in isolated membrane vesicles of Escherichia coli. Biochemistry22:844-850. [[PubMed]
210. Ikeda, Y., J. Yamamoto, M. Okamura, T. Fujino, S. Takahashi, K. Takeuchi, T. F. Osborne, T. T. Yamamoto, S. Ito, and J. Sakai. 2001. Transcriptional regulation of the murine acetyl-CoA synthetase 1 gene through multiple clustered binding sites for sterol regulatory element-binding proteins and a single neighboring site for Sp1. J. Biol. Chem.276:34259-34269. [[PubMed]
211. Inouye, M., R. Dutta, and Y. Zhu. 2002. Regulation of porins in Escherichia coli by the osmosensing histidine kinase/phosphatase EnvZ, p. 25-46. In M. Inouye and R. Dutta (ed.), Histidine kinases in signal transduction. Academic Press, Ltd., London, United Kingdom.
212. Iuchi, S., and E. C. Lin. 1988. arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. Proc. Natl. Acad. Sci. USA85:1888-1892.
213. Jackowski, S. 1996. Biosynthesis of pantothenic acid and coenzyme A, p. 687-694. 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. American ASM Press, Washington, D.C.
214. Jackowski, S., and C. O. Rock. 1986. Consequences of reduced intracellular coenzyme A content in Escherichia coli. J. Bacteriol.166:866-871.
215. Jackowski, S., and C. O. Rock. 1984. Metabolism of 4′-phosphopantetheine in Escherichia coli. J. Bacteriol.158:115-120.
216. Jackowski, S., and C. O. Rock. 1981. Regulation of coenzyme A biosynthesis. J. Bacteriol.148:926-932.
217. Janausch, I. G., I. Garcia-Moreno, D. Lehnen, Y. Zeuner, and G. Unden. 2004. Phosphorylation and DNA binding of the regulator DcuR of the fumarate-responsive two-component system DcuSR of Escherichia coli. Microbiology150:877-883. [[PubMed]
218. Janiak-Spens, F., J. M. Sparling, M. Gurfinkel, and A. H. West. 1999. Differential stabilities of phosphorylated response regulator domains reflect functional roles of the yeast osmoregulatory SLN1 and SSK1 proteins. J. Bacteriol.181:411-417.
219. Jensen, E. B., and S. Carlsen. 1990. Production of recombinant human growth hormone in Escherichia coli. Expression of different precursors and physiological effects of glucose, acetate and salts. Biotechnol. Bioeng.36:1-11. [[PubMed]
220. Johannes, E., D. M. Barnhart, and J. L. Slonczewski. 2004. pH-dependent catabolic protein expression during anaerobic growth of Escherichia coli. J. Bacteriol.186:192-199.
221. Jolly, C. A., H. Chao, A. B. Kier, J. T. Billheimer, and F. Schroeder. 2000. Sterol carrier protein-2 suppresses microsomal acyl-CoA hydrolysis. Mol. Cell. Biochem.205:83-90. [[PubMed]
222. Jones, B. E., V. Dossonnet, E. Kuster, W. Hillen, J. Deutscher, and R. E. Klevit. 1997. Binding of the catabolite repressor protein CcpA to its DNA target is regulated by phosphorylation of its corepressor HPr. J. Biol. Chem.272:26530-26535. [[PubMed]
223. Kaiser, M., and GSawers. 1994. Pyruvate formate-lyase is not essential for nitrate respiration by Escherichia coli. FEMS Microbiol. Lett.117:163-168. [[PubMed][Google Scholar]
224. Kakuda, H., K. Hosono, K. Shiroishi, and S. Ichihara. 1994. Identification and characterization of the ackA (acetate kinase A)-pta (phosphotransacetylase) operon and complementation analysis of acetate utilization by an ackA-pta deletion mutant of Escherichia coli. J. Biochem.116:916-922. [[PubMed]
225. Kakuda, H., K. Shiroishi, K. Hosono, and S. Ichihara. 1994. Construction of Pta-Ack pathway deletion mutants of Escherichia coli and characteristic growth profiles of the mutants in a rich medium. Biosci. Biotechnol. Biochem.58:2232-2235. [[PubMed]
226. 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. USA101:641-646.
227. Karan, D., J. R. David, and P. Capy. 2001. Molecular evolution of the AMP-forming Acetyl-CoA synthetase. Gene265:95-101. [[PubMed]
228. Kasahara, M., and MOhmori. 1999. Activation of a cyanobacterial adenylate cyclase, CyaC, by autophosphorylation and a subsequent phosphotransfer reaction. J. Biol. Chem.274:15167-15172. [[PubMed][Google Scholar]
229. Kaya, S., T. Yokoyama, Y. Hayashi, K. Taniguchi, and T. Tsuda. 1998. ATP and acetyl phosphate induces molecular events near the ATP binding site and the membrane domain of Na^,K^{-ATPase. The tetrameric nature of the enzyme.}J. Biol. Chem.273:24334-24338. [[PubMed]
230. Ke, J., R. H. Behal, S. L. Back, B. J. Nikolau, E. S. Wurtele, and D. J. Oliver. 2000. The role of pyruvate dehydrogenase and acetyl-coenzyme a synthetase in fatty acid synthesis in developing arabidopsis seeds. Plant Physiol.123:497-508.
231. Kennedy, EP. 2001. Hitler's gift and the era of biosynthesis. J. Biol. Chem.276:42619-42631. [[PubMed][Google Scholar]
232. Kessler, D., and JKnappe. 1996. Anaerobic dissimilation of pyruvate, p. 199-204. 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.
233. Kihara, M., and R. M. Macnab. 1981. Cytoplasmic pH mediates pH taxis and weak- acid repellent taxis of bacteria. J. Bacteriol.145:1209-1221.
234. Kim, C. C., and S. Falkow. 2004. Delineation of upstream signaling events in the salmonella pathogenicity island 2 transcriptional activation pathway. J. Bacteriol.186:4694-4704.
235. Kim, D.-J., B. Boylan, N. George, and S. Forst. 2003. Inactivation of ompR promotes precocious swarming and flhDC expression in Xenorhabdus nematophila. J. Bacteriol.185:5290-5294.
236. Kim, J. H., Z. T. Guvener, J. Y. Cho, K. Chung, and G. H. Chambliss. 1995. Specificity of DNA binding activity of the Bacillus subtilis catabolite control protein CcpA. J. Bacteriol.177:5129-5134.
237. Kim, S. B., B. S. Shin, S. K. Choi, C. K. Kim, and S. H. Park. 2001. Involvement of acetyl phosphate in the in vivo activation of the response regulator ComA in Bacillus subtilis. FEMS Microbiol. Lett.195:179-183. [[PubMed]
238. Kim, S. K., M. R. Wilmes-Riesenberg, and B. L. Wanner. 1996. Involvement of the sensor kinase EnvZ in the in vivo activation of the response-regulator PhoB by acetyl phosphate. Mol. Microbiol.22:135-147. [[PubMed]
239. Kimata, K., H. Takahashi, T. Inada, P. Postma, and H. Aiba. 1997. cAMP receptor protein-cAMP plays a crucial role in glucose-lactose diauxie by activating the major glucose transporter gene in Escherichia coli. Proc. Natl. Acad. Sci. USA94:12914-12919.
240. 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.
241. Kleman, G. L., and W. R. Strohl. 1994. Acetate metabolism by Escherichia coli in high-cell-density fermentation. Appl. Environ. Microbiol.60:3952-3958.
242. Knappe, J., and GSawers. 1990. A radical-chemical route to acetyl-CoA: the anerobically induced pyruvate formate-lyase system of Escherichia coli. FEMS Microbiol. Rev.75:383-398. [[PubMed][Google Scholar]
243. Knorr, R., M. A. Ehrmann, and R. F. Vogel. 2001. Cloning of the phosphotransacetylase gene from Lactobacillus sanfranciscensis and characterization of its gene product. J. Basic Microbiol.41:339-349. [[PubMed]
244. Knorr, R., M. A. Ehrmann, and R. F. Vogel. 2001. Cloning, expression, and characterization of acetate kinase from Lactobacillus sanfranciscensis. Microbiol. Res.156:267-277. [[PubMed]
245. Knudsen, J., M. V. Jensen, J. K. Hansen, N. J. Faergeman, T. B. Neergaard, and B. Gaigg. 1999. Role of acylCoA binding protein in acylCoA transport, metabolism and cell signaling. Mol. Cell. Biochem.192:95-103. [[PubMed]
246. Kornberg, HL. 1966. The role and control of the glyoxylate cycle in Escherichia coli. Biochem. J.99:1-11. [Google Scholar]
247. Kouzarides, T. 2000. Acetylation: a regulatory modification to rival phosphorylation? EMBO J.19:1176-1179.
248. Kravanja, M., R. Engelmann, V. Dossonnet, M. Bluggel, H. E. Meyer, R. Frank, A. Galinier, J. Deutscher, N. Schnell, and W. Hengstenberg. 1999. The hprK gene of Enterococcus faecalis encodes a novel bifunctional enzyme: the HPr kinase/phosphatase. Mol. Microbiol.31:59-66. [[PubMed]
249. 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.
250. Kumari, S., E. Simel, and A. J. Wolfe. 2000. Sigma70 is the principal sigma factor responsible for the transcription of acs, which encodes acetyl-CoA synthetase in Escherichia coli. J. Bacteriol.182:551-554.
251. Kumari, S., R. Tishel, M. Eisenbach, and A. J. Wolfe. 1995. Cloning, characterization, and functional expression of acs, the gene which encodes acetyl coenzyme A synthetase in Escherichia coli. J. Bacteriol.177:2878-2886.
252. Kunst, F., N. Ogasawara, I. Moszer, A. M. Albertini, G. Alloni, V. Azevedo, M. G. Bertero, et al. 1998. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature390:249-256. [[PubMed]
253. Kuster, S., E. J. Luesink, W. M. de Vos, and W. Hillen. 1996. Immunological crossreactivity to catabolite control protein CcpA from Bacillus megaterium is found in many gram-positive bacteria. FEMS Microbiol. Lett.139:109-115. [[PubMed]
254. Kwan, H. S., H. W. Chui, and K. K. Wong. 1988. ack::Mu d1-8 (Aplac) operon fusions of Salmonella typhimurium LT-2. Mol. Gen. Genet.211:183-185. [[PubMed]
255. Kwon, Y. M., and S. C. Ricke. 1998. Induction of acid resistance of Salmonella typhimurium by exposure to short-chain fatty acids. Appl. Environ. Microbiol.64:3458-3463.
256. Lambert, L., K. Abshire, D. Blankenhorn, and J. Slonczewski. 1997. Proteins induced in Escherichia coli by benzoic acid. J. Bacteriol.179:7595-7599.
257. LaPorte, D., P. Thorness, and D. Koshland, Jr. 1985. Compensatory phosphorylation of isocitrate dehydrogenase, a mechanism for adaption to the intracellular environment. J. Biol. Chem.260:10563-10568. [[PubMed]
258. LaPorte, D. C., and D. E. Koshland, Jr. 1983. Phosphorylation of isocitrate dehydrogenase as a demonstration of enhanced sensitivity in covalent regulation. Nature305:286-290. [[PubMed]
259. Latimer, M. T., and J. G. Ferry. 1993. Cloning, sequence analysis, and hyperexpression of the genes encoding phosphotransacetylase and acetate kinase from Methanosarcina thermophila. J. Bacteriol.175:6822-6829.
260. Lawhon, S. D., R. Maurer, M. Suyemoto, and C. Altier. 2002. Intestinal short-chain fatty acids alter Salmonella typhimurium invasion gene expression and virulence through BarA/SirA. Mol. Microbiol.46:451-464. [[PubMed]
261. Lee, A. K., C. S. Detweiler, and S. Falkow. 2000. Ompr regulates the two-component system SsrA-SsrB in Salmonella pathogenicity island 2. J. Bacteriol.182:771-781.
262. Lee, J.-H., D.-E. Lee, B.-U. Lee, and H.-S. Kim. 2003. Global analyses of transcriptomes and proteomes of a parent strain and an l-threonine-overproducing mutant strain. J. Bacteriol.185:5442-5451.
263. Lee, SY. 1996. High cell density culture of Escherichia coli. Trends Biotechnol.14:98-105. [[PubMed][Google Scholar]
264. Lee, T.-Y., K. Makino, H. Shinagawa, and A. Nakata. 1990. Overproduction of acetate kinase activates the phosphate regulon in the absence of the phoR and phoM functions in Escherichia coli. J. Bacteriol.172:2245-2249.
265. Lehninger, AL. 1975. Biochemistry, 2nd ed. Worth Publishers, Inc., New York, N.Y.
266. Lesley, J. A., and C. D. Waldburger. 2003. Repression of Escherichia coli PhoP-PhoQ signaling by acetate reveals a regulatory role for acetyl coenzyme A. J. Bacteriol.185:2563-2570.
267. Leuchtenberger, W. 1996. Amino acids—technical production and use, p. 465-502. In H. J. Rehm, G. Reed, A. Puhler, P. Stadler, and M. Roehr (ed.), Biotechnology, vol. 6. VCH Verlagsgesellschaft, Weinheim, Germany. [PubMed]
268. Li, J., S. Kustu, and V. Stewart. 1994. In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12. J. Mol. Biol.241:150-165. [[PubMed]
269. Liao, J. D., S.-Y. Hou, and Y.-P. Chao. 1996. Pathway analysis, engineering, and physiological considerations for redirecting central metabolism. Biotechnol. Bioeng.52:129-140. [[PubMed]
270. Lin, J., I. S. Lee, J. Frey, J. L. Slonczewski, and J. W. Foster. 1995. Comparative analysis of extreme acid survival in Salmonella typhimurium, Shigella flexneri, and Escherichia coli. J. Bacteriol.177:4097-4104.
271. Lipmann, F. 1941. Metabolic generation and utilization of phosphate bond energy. Adv. Enzymol. 1:99-162.
272. Liu, J. H., M. J. Lai, S. Ang, J. C. Shu, P. C. Soo, Y. T. Horng, W. C. Yi, H. C. Lai, K. T. Luh, S. W. Ho, and S. Swift. 2000. Role of flhDC in the expression of the nuclease gene nucA, cell division and flagellar synthesis in Serratia marcescens. J. Biomed. Sci.7:475-483. [[PubMed]
273. Liu, X., and TFerenci. 2001. An analysis of multifactorial influences on the transcriptional control of ompF and ompC porin expression under nutrient limitation. Microbiology147:2981-2989. [[PubMed][Google Scholar]
274. Liu, X., and TFerenci. 1998. Regulation of porin-mediated outer membrane permeability by nutrient limitation in Escherichia coli. J. Bacteriol.180:3917-3922. [Google Scholar]
275. Loh, J., M. Garcia, and G. Stacey. 1997. NodV and NodW, a second flavonoid recognition system regulating nod gene expression in Bradyrhizobium japonicum. J. Bacteriol.179:3013-3020.
276. Loikkanen, I., S. Haghighi, S. Vainio, and A. Pajunen. 2002. Expression of cytosolic acetyl-CoA synthetase gene is developmentally regulated. Mech. Dev.115:139-141. [[PubMed]
277. Luby-Phelps, K. 2000. Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area. Int. Rev. Cytol.192:189-221. [[PubMed]
278. Luby-Phelps, K. 1994. Physical properties of cytoplasm. Curr. Opin. Cell Biol.6:3-9. [[PubMed]
279. Lukat, G. S., W. R. McCleary, A. M. Stock, and J. B. Stock. 1992. Phosphorylation of bacterial response regulator proteins by low molecular weight phospho-donors. Proc. Natl. Acad. Sci. USA89:718-722.
280. Luli, G. W., and W. R. Strohl. 1990. Comparison of growth, acetate production, and acetate inhibition of Escherichia coli strains in batch and fed-batch fermentations. Appl. Environ. Microbiol.56:1004-1011.
281. Luong, A., V. C. Hannah, M. S. Brown, and J. L. Goldstein. 2000. Molecular characterization of human acetyl-CoA synthetase, an enzyme regulated by sterol regulatory element-binding proteins. J. Biol. Chem.275:26458-26466. [[PubMed]
282. Lynch, A. S., and Lin, E. C. C. 1996. Responses to molecular oxygen, p. 1526-1538. 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.
283. Macfarlane, S., A. J. McBain, and G. T. Macfarlane. 1997. Consequences of biofilm and sessile growth in the large intestine. Adv. Dent. Res.11:59-68. [[PubMed]
284. Mackie, R., A. Sghir, and H. R. Gaskins. 1999. Developmental microbial ecology of the neonatal gastrointestinal tract. Am. J. Clin. Nutr.69:1035S-1045S. [[PubMed]
285. Mai, X., and MAdams. 1996. Purification and characterization of two reversible and ADP-dependent acetyl coenzyme A synthetases from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol.178:5897-5903. [Google Scholar]
286. Majewski, R. A., and M. M. Domach. 1990. Simple constrained optimization view of acetate overflow in E. coli. Biotechnol. Bioeng.35:732-738. [[PubMed]
287. Makino, K., M. Amemura, S.-K. Kim, H. Shinagawa, and A. Hakata. 1992. Signal transduction of the phosphate regulon in Escherichia coli mediated by phosphorylation. p. 191-200. In S. Papa, A. Azzi, and J. M. Tager (ed.), Adenine nucleotides in cellular energy transfer and signal transduction. Birkhaeuser Verlag, Basel, Switzerland.
288. Makino, K., H. Shinagawa, M. Amemura, S. Kimura, A. Nakata, and A. Ishihama. 1988. Regulation of the phosphate regulon of Escherichia coli: activation of pstS transcription by PhoB protein in vitro. J. Mol. Biol.203:85-95. [[PubMed]
289. Marino, M., H. C. Ramos, T. Hoffmann, P. Glaser, and D. Jahn. 2001. Modulation of anaerobic energy metabolism of Bacillus subtilis by arfM (ywiD). J. Bacteriol.183:6815-6821.
290. Marshall, F. A., S. L. Messenger, N. R. Wyborn, J. R. Guest, H. Wing, S. J. Busby, and J. Green. 2001. A novel promoter architecture for microaerobic activation by the anaerobic transcription factor FNR. Mol. Microbiol.39:747-753. [[PubMed]
291. Matsubara, M., and TMizuno. 1999. EnvZ-independent phosphotransfer signaling pathway of the OmpR-mediated osmoregulatory expression of OmpC and OmpF in Escherichia coli. Biosci. Biotechnol. Biochem.63:408-414. [[PubMed][Google Scholar]
292. Matsubara, M., and TMizuno. 2000. The SixA phospho-histidine phosphatase modulates the ArcB phosphorelay signal transduction in Escherichia coli. FEBS Lett.470:118-124. [[PubMed][Google Scholar]
293. Matsushika, A., and TMizuno. 1998. A dual-signaling mechanism mediated by the ArcB hybrid sensor kinase containing the histidine-containing phosphotransfer domain in Escherichia coli. J. Bacteriol.180:3973-3977. [Google Scholar]
294. Matsuyama, A., H. Yamamoto-Otake, J. Hewitt, R. T. A. MacGillivray, and E. Nakano. 1994. Nucleotide sequence of the phosphotransacetylase gene of Escherichia coli strain K12. Biochim. Biophys. Acta1219:559-562. [[PubMed]
295. Mayover, T. L., C. J. Halkides, and R. C. Stewart. 1999. Kinetic characterization of CheY phosphorylation reactions: comparison of P-CheA and small-molecule phosphodonors. Biochemistry38:2259-2271. [[PubMed]
296. McCleary, WR. 1996. The activation of PhoB by acetylphosphate. Mol. Microbiol.20:1155-1163. [[PubMed][Google Scholar]
297. McCleary, W. R., and J. B. Stock. 1994. Acetyl phosphate and the activation of two- component response regulators. J. Biol. Chem.269:31567-31572. [[PubMed]
298. McCleary, W. R., J. B. Stock, and A. J. Ninfa. 1993. Is acetyl phosphate a global signal in Escherichia coli? J. Bacteriol.175:2793-2798.
299. McLeod, S. M., and R. C. Johnson. 2001. Control of transcription by nucleoid proteins. Curr. Opin. Microbiol.4:152-159. [[PubMed]
300. McNeil, NI. 1984. The contribution of the large intestine to energy supplies in man. Am. J. Clin. Nutr.39:338-342. [[PubMed][Google Scholar]
301. Meile, L., L. M. Rohr, T. A. Geissmann, M. Herensperger, and M. Teuber. 2001. Characterization of the d-xylulose 5-phosphate/d-fructose 6-phosphate phosphoketolase gene (xfp) from Bifidobacterium lactis. J. Bacteriol.183:2929-2936.
302. Merkler, I., and JRetey. 1981. Stereochemical investigation of the phosphoketolase reaction. The formation of chiral [2H1,3H]acetyl phosphate. Eur. J. Biochem.120:593-597. [[PubMed][Google Scholar]
303. Mevissen-Verhage, E. A. E., V. H. Marcelis, M. N. De Vos, W. C. M. Harmsen-Vann Amerongen, and J. Verhoef. 1987. Bfidobacterium, Bacteroides and Clostridium spp. in fecal samples from breast-fed and bottle-fed infants with and without iron supplement. J. Clin. Microbiol.25:285-289.
304. Meyer, M., P. Dimroth, and M. Bott. 1997. In vitro binding of the response regulator CitB and of its carboxy-terminal domain to A + T-rich DNA target sequences in the control region of the divergent citC and citS operons of Klebsiella pneumoniae. J. Mol. Biol.269:719-731. [[PubMed]
305. Meyer, M., K. Granderath, and J. R. Andreesen. 1995. Purification and characterization of protein PB of betaine reductase and its relationship to the corresponding proteins glycine reductase and sarcosine reductase from Eubacterium acidaminophilum. Eur. J. Biochem.234:184-191. [[PubMed]
306. Mitsuoka, T. 1996. Intestinal flora and human health. Asia Pacific J. Clin. Nutr.5:2-9. [[PubMed]
307. Miwa, Y., M. Saikawa, and Y. Fujita. 1994. Possible function and some properties of the CcpA protein of Bacillus subtilis. Microbiology140:2567-2575. [[PubMed]
308. Miyake, M., K. Kataoka, M. Shirai, and Y. Asada. 1997. Control of poly-beta- hydroxybutyrate synthase mediated by acetyl phosphate in cyanobacteria. J. Bacteriol.179:5009-5013.
309. Miyake, M., C. Miyamoto, J. Schnackenberg, R. Kurane, and Y. Asada. 2000. Phosphotransacetylase as a key factor in biological production of polyhydroxybutyrate. Appl. Biochem. Biotechnol.84-86:1039-1044. [[PubMed]
310. Miyake, M., K. Takase, M. Narato, E. Khatipov, J. Schnackenberg, M. Shirai, R. Kurane, and Y. Asada. 2000. Polyhydroxybutyrate production from carbon dioxide by cyanobacteria. Appl. Biochem. Biotechnol.84-86:991-1002. [[PubMed]
311. Moazed, D. 2001. Common themes in mechanisms of gene silencing. Mol. Cell8:489-498. [[PubMed]
312. Moir-Blais, T. R., F. J. Grundy, and T. M. Henkin. 2001. Transcriptional activation of the Bacillus subtilis ackA promoter requires sequences upstream of the CcpA binding site. J. Bacteriol.183:2389-2393.
313. Mortensen, P. B., and M. R. Clausen. 1996. Short-chain fatty acids in the human colon: relation to gastrointestinal health and disease. Scand. J. Gastroenterol. Suppl.216:132-148. [[PubMed]
314. Muffler, A., S. Bettermann, M. Haushalter, A. Horlein, U. Neveling, M. Schramm, and O. Sorgenfrei. 2002. Genome-wide transcription profiling of Corynebacterium glutamicum after heat shock and during growth on acetate and glucose. J. Biotechnol.98:255-268. [[PubMed]
315. Murphy, M. G., L. O'Connor, D. Walsh, and S. Condon. 1985. Oxygen dependent lactate utilization by Lactobacillus plantarum. Arch. Microbiol.141:75-79. [[PubMed]
316. Musfeldt, M., M. Selig, and P. Schonheit. 1999. Acetyl coenzyme A synthetase (ADP forming) from the hyperthermophilic archaeon Pyrococcus furiosus: identification, cloning, separate expression of the encoding genes, acdAI and acdBI, in Escherichia coli, and in vitro reconstitution of the active heterotetrameric enzyme from its recombinant subunits. J. Bacteriol.181:5885-5888.
317. Nakano, M. M., Y. P. Dailly, P. Zuber, and D. P. Clark. 1997. Characterization of anaerobic fermentative growth in Bacillus subtilis: identification of fermentation end products and genes required for the growth. J. Bacteriol.179:6749-6755.
318. Nakayama, S.-I., and HWatanabe. 1998. Identification of cpxR as a positive regulator essential for expression of the Shigella sonnei virF gene. J. Bacteriol.180:3522-3528. [Google Scholar]
319. Negre, D., C. Oudot, J.-F. Prost, K. Murakami, A. Ishihama, A. J. Cozzone, and J.-C. Cortay. 1998. FruR-mediated transcriptional activation at the ppsA promoter of Escherichia coli. J. Mol. Biol.276:355-365. [[PubMed]
320. Neidhardt, F. C., J. L. Ingraham, and M. Schaechter. 1990. Physiology of the bacterial cell: a molecular approach. Sinauer Associates, Inc., Sunderland, Mass.
321. Ninfa, AJ. 1996. Regulation of gene transcription by extracellular stimuli. 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. ASM Press, Washington, D.C.
322. Ninfa, A. J., P. Jiang, M. R. Atkinson, and J. A. Peliska. 2000. Integration of antagonistic signals in the regulation of nitrogen assimilation in Escherichia coli. Curr. Top. Cell Regul.36:31-75. [[PubMed]
323. 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. [[PubMed]
324. Nyström, T. 1994. The glucose-starvation stimulon of Escherichia coli: induced and repressed synthesis of enzymes of central metabolic pathways and role of acetyl phosphate in gene expression and starvation survival. Mol. Microbiol.12:833-843. [[PubMed]
325. Nyström, T., and F. C. Neidhardt. 1993. Isolation and properties of a mutant of Escherichia coli with an insertional inactivation of the uspA gene, which encodes a universal stress protein. J. Bacteriol.175:3949-3956.
326. Ogino, T., Y. Arata, and S. Fujiwara. 1980. Proton correlation nuclear magnetic resonance study of metabolic regulations and pyruvate transport in anaerobic Escherichia coli cells. Biochemistry19:3684-3691. [[PubMed]
327. Ogino, T., M. Matsubara, N. Kato, Y. Nakamura, and T. Mizuno. 1998. An Escherichia coli protein that exhibits phosphohistidine phosphatase activity towards the HPt domain of the ArcB sensor involved in the multistep His-Asp phosphorelay. Mol. Microbiol.27:573-585. [[PubMed]
328. 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. [[PubMed]
329. 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. [[PubMed]
330. Oshima, T., H. Aiba, Y. Masuda, S. Kanaya, M. Sugiura, B. L. Wanner, H. Mori, and T. Mizuno. 2002. Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12. Mol. Microbiol.46:281-291. [[PubMed]
331. Palacios, S., V. J. Starai, and J. C. Escalante-Semerena. 2003. Propionyl coenzyme a is a common intermediate in the 1,2-propanediol and propionate catabolic pathways needed for expression of the prpBCDE operon during growth of Salmonella enterica on 1,2-Propanediol. J. Bacteriol.185:2802-2810.
332. Pan, J. G., J. S. Rhee, and J. M. Lebeault. 1987. Physiological constraints in increasing biomass concentration of Escherichia coli in fed-batch culture. Biotechnol. Lett.9:89-94. [PubMed]
333. Pantazaki, A. A., M. G. Tambaka, V. Langlois, P. Guerin, and D. A. Kyriakidis. 2004. Polyhydroxyalkanoate (PHA) biosynthesis in Thermus thermophilus: purification and biochemical properties of PHA synthase. Mol. Cell. Biochem.254:173-183. [[PubMed]
334. Pardee, A. B., and L. S. Prestidge. 1955. Induced formation of serine and threonine deaminases by Escherichia coli. J. Bacteriol.70:667-674.
335. Park, S.-J., G. Chao, and R. P. Gunsalus. 1997. Aerobic regulation of the sucABCD genes of Escherichia coli, which encode alpha-ketoglutarate dehydrogenase and succinyl coenzyme A synthetase: roles of ArcA, Fnr, and the upstream sdhCBAB promoter. J. Bacteriol.179:4138-4142.
336. 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.
337. 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.
338. 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.
339. Park, S. J., C. P. Tseng, and R. P. Gunsalus. 1995. Regulation of succinate dehydrogenase (sdhCDAB) operon expression in Escherichia coli in response to carbon supply and anaerobiosis: role of ArcA and Fnr. Mol. Microbiol.15:473-482. [[PubMed]
340. Patnaik, R., W. D. Roof, R. F. Young, and J. C. Liao. 1992. Stimulation of glucose catabolism in Escherichia coli by a potential futile cycle. J. Bacteriol.174:7527-7532.
341. Peekhaus, N., and TConway. 1998. What's for dinner? Entner-Doudoroff metabolism in Escherichia coli. J. Bacteriol.180:3495-3502. [Google Scholar]
342. Peng, L., and KShimizu. 2003. Global metabolic regulation analysis for Escherichia coli K12 based on protein expression by 2-dimensional electrophoresis and enzyme activity measurement. Appl. Microbiol. Biotechnol.61:163-178. [[PubMed][Google Scholar]
343. Pericone, C. D., S. Park, J. A. Imlay, and J. N. Weiser. 2003. Factors contributing to hydrogen peroxide resistance in Streptococcus pneumoniae include pyruvate oxidase (SpxB) and avoidance of the toxic effects of the Fenton reaction. J. Bacteriol.185:6815-6825.
344. Perrot, F., M. Hebraud, R. Charlionet, G. Junter, and T. Jouenne. 2000. Protein patterns of gel-entrapped Escherichia coli cells differ from those of free-floating organisms. Electrophoresis21:645-653. [[PubMed]
345. Pettijohn, D. 1996. The nucleoid, p. 158-166. 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.
346. Phadtare, S., and MInouye. 2001. Role of CspC and CspE in regulation of expression of RpoS and UspA, the stress response proteins in Escherichia coli. J. Bacteriol.183:1205-1214. [Google Scholar]
347. Phue, J.-N., and JShiloach. 2004. Transcription levels of key metabolic genes are the cause for different glucose utilization pathways in E. coli B (BL21) and E. coli K (JM109). J. Biotechnol.109:21-30. [[PubMed][Google Scholar]
348. Pittman, M. S., M. Goodwin, and D. J. Kelly. 2001. Chemotaxis in the human gastric pathogen Helicobacter pylori: different roles for CheW and the three CheV paralogues, and evidence for CheV2 phosphorylation. Microbiology147:2493-2504. [[PubMed]
349. Plumbridge, J. 2002. Regulation of gene expression in the PTS in Escherichia coli: the role and interactions of Mlc. Curr. Opin. Microbiol.5:187-193. [[PubMed]
350. Posthuma, C. C., R. Bader, R. Engelmann, P. W. Postma, W. Hengstenberg, and P. H. Pouwels. 2002. Expression of the xylulose 5-phosphate phosphoketolase gene, xpkA, from Lactobacillus pentosus MD363 is induced by sugars that are fermented via the phosphoketolase pathway and is repressed by glucose mediated by CcpA and the mannose phosphoenolpyruvate phosphotransferase system. Appl. Environ. Microbiol.68:831-837.
351. Postma, P. W., J. W. Lengeler, and G. R. Jacobson. 1996. Phosphoenolpyruvate:carbohydrate phosphotransferase systems, p. 1149-1174. 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.
352. Poulsen, L., T. Licht, C. Rang, K. Krogfelt, and S. Molin. 1995. Physiological state of Escherichia coli BJ4 growing in the large intestines of streptomycin-treated mice. J. Bacteriol.177:5840-5845.
353. Presecan-Siedel, E., A. Galinier, R. Longin, J. Deutscher, A. Danchin, P. Glaser, and I. Martin-Verstraete. 1999. Catabolite regulation of the pta gene as part of carbon flow pathways in Bacillus subtilis. J. Bacteriol.181:6889-6897.
354. Prohinar, P., S. A. Forst, D. Reed, I. Mandic-Mulec, and J. Weiss. 2002. OmpR- dependent and OmpR-independent responses of Escherichia coli to sublethal attack by the neutrophil bactericidal/permeability increasing protein. Mol. Microbiol.43:1493-1504. [[PubMed]
355. Prüß, BM. 1998. Acetyl phosphate and the phosphorylation of OmpR are involved in the regulation of the cell division rate in Escherichia coli. Arch. Microbiol.170:141-146. [[PubMed][Google Scholar]
356. Prüß, B. M., J. W. Campbell, T. K. Van Dyk, C. Zhu, Y. Kogan, and P. Matsumura. 2003. FlhD/FlhC Is a regulator of anaerobic respiration and the Entner-Doudoroff pathway through induction of the methyl-accepting chemotaxis protein Aer. J. Bacteriol.185:534-543.
357. Prüß, B. M., X. Liu, W. Hendrickson, and P. Matsumura. 2001. FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions. FEMS Microbiol. Lett.197:91-97. [[PubMed]
358. Prüß, B. M., and P. Matsumura. 1996. A regulator of the flagellar regulon of Escherichia coli, flhD, also affect cell division. J. Bacteriol.178:668-674.
359. Prüß, B. M., J. M. Nelms, C. Park, and A. J. Wolfe. 1994. Mutations in NADH:ubiquinone oxidoreductase of Escherichia coli affect growth on mixed amino acids. J. Bacteriol.176:2143-2150.
360. Prüß, B. M., and A. J. Wolfe. 1994. Regulation of acetyl phosphate synthesis and degradation, and the control of flagellar expression in Escherichia coli. Mol. Microbiol.12:973-984. [[PubMed]
361. Puchowicz, M. A., I. R. Bederman, B. Comte, D. Yang, F. David, E. Stone, K. Jabbour, D. H. Wasserman, and H. Brunengraber. 1999. Zonation of acetate labeling across the liver: implications for studies of lipogenesis by MIDA. Am. J. Physiol. Endocrinol. Metab.277:E1022-E1027. [[PubMed]
362. Quail, M. A., D. J. Haydon, and J. R. Guest. 1994. The pdhR-aceEF-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex. Mol. Microbiol.12:95-104. [[PubMed]
363. Rado, T. A., and J. A. Hoch. 1973. Phosphotransacetylase from Bacillus subtilis: purification and physiological studies. Biochim. Biophys. Acta321:114-125. [[PubMed]
364. Ramakrishnan, R., M. Schuster, and R. B. Bourret. 1998. Acetylation of Lys-92 enhances signaling by the chemotaxis response regulator protein CheY. Proc. Natl. Acad. Sci. USA95:4918-4923.
365. Ramos, H. C., T. Hoffmann, M. Marino, H. Ndjari, E. Presecan-Siedel, O. Dreesen, P. Glaser, and D. Jahn. 2000. Fermentative metabolism of Bacillus subtilis: physiology and regulation of gene expression. J. Bacteriol.182:3072-3080.
366. 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 Escherichia coli. Mol. Microbiol.16:1157-1169. [[PubMed]
367. Ramseier, T. M., D. Negre, 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, ace, pts and icd operons of Escherichia coli and Salmonella typhimurium. J. Mol. Biol.234:28-44. [[PubMed]
368. Reeves, R. E., L. G. Warren, B. Susskind, and H. S. Lo. 1977. An energy-conserving pyruvate-to-acetate pathway in Entamoeba histolytica. Pyruvate synthase and a new acetate thiokinase. J. Biol. Chem.252:726-731. [[PubMed]
369. Reinscheid, D., S. Schnicke, D. Rittmann, U. Zahnow, H. Sahm, and B. Eikmanns. 1999. Cloning, sequence analysis, expression and inactivation of the Corynebacterium glutamicum pta-ack operon encoding phosphotransacetylase and acetate kinase. Microbiology145:503-513. [[PubMed]
370. Reitzer, L. 2003. Nitrogen assimilation and global regulation in Escherichia coli. Annu. Rev. Microbiol.57:155-176. [[PubMed]
371. Reitzer, L. J., and B. Magasanik. 1985. Expression of glnA in Escherichia coli is regulated at tandem promoters. Proc. Natl. Acad. Sci. USA82:1979-1983.
372. Reizer, J., J. Deutscher, and M. H. Saier, Jr. 1989. Metabolite-senstive, ATP- dependent, protein kinase catalyzed phosphorylation of HPr, a phosphocarrier protein of the phosphotransferase system in Gram-positive bacteria. Biochemie71:989-996. [[PubMed]
373. Reizer, J., C. Hoischen, F. Tigemeyer, C. Rivolta, R. Rabus, J. Stulke, D. Karamata, M. H. Saier, Jr., and W. Hillen. 1998. A novel protein kinase that controls carbon catabolite repression in bacteria. Mol. Microbiol.27:1157-1169. [[PubMed]
374. Renna, M. C., N. Najimudin, L. R. Winik, and S. A. Zahler. 1993. Regulation of the Bacillus subtilis alsS, alsD, and alsR genes involved in post-exponential-phase production of acetoin. J. Bacteriol.175:3863-3875.
375. Repaske, D. R., and J. Adler. 1981. Change in intracellular pH of Escherichia coli mediates the chemotactic response to certain attractants and repellents. J. Bacteriol.145:1196-208.
376. Reyrat, J. M., M. David, J. Batut, and P. Boistard. 1994. FixL of Rhizobium meliloti enhances the transcriptional activity of a mutant FixJD54N protein by phosphorylation of an alternate residue. J. Bacteriol.176:1969-1976.
377. Ricke, SC. 2003. The gastrointestinal tract ecology of Salmonella enteritidis colonization in molting hens. Poult. Sci.82:1003-1007. [[PubMed][Google Scholar]
378. Rigden, DJ. 2003. Unexpected catalytic site variation in phosphoprotein phosphatase homologues of cofactor-dependent phosphoglycerate mutase. FEBS Lett.536:77-84. [[PubMed][Google Scholar]
379. Rinas, U., H. Kracke-Helm, and K. Schugerl. 1989. Glucose as a substrate in recombinant strain fermentation technology. Appl. Microbiol. Biotechnol.31:163-167. [PubMed]
380. Riondet, C., R. Cachon, Y. Wache, G. Alcaraz, and C. Divies. 2000. Extracellular oxidoreduction potential modifies carbon and electron flow in Escherichia coli. J. Bacteriol.182:620-626.
381. Roe, A. J., D. McLaggan, I. Davidson, C. O'Bryne, and I. R. Booth. 1998. Perturbation of anion balance during inhibition of growth of Escherichia coli by weak acids. J. Bacteriol.180:767-772.
382. 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. Microbiology148:2215-2222. [[PubMed]
383. Roggiani, M., and DDubnau. 1993. ComA, a phosphorylated response regulator protein of Bacillus subtilis, binds to the promoter region of srfA. J. Bacteriol.175:3182-3187. [Google Scholar]
384. Romeo, T. 1998. Global regulation by the small RNA-binding protein CsrA and the non- coding RNA molecule CsrB. Mol. Microbiol.29:1321-1330. [[PubMed]
385. Rose, I. A., M. Grunsberg-Manago, S. R. Korey, and S. Ochoa. 1954. Enzymatic phosphorylation of acetate. J. Biol. Chem.211:737-756. [[PubMed]
386. Rossman, 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. [[PubMed]
387. Ruff, J., K. Denger, and A. M. Cook. 2003. Sulphoacetaldehyde acetyltransferase yields acetyl phosphate: purification from Alcaligenes defragrans and gene clusters in taurine degradation. Biochem. J.369:275-285.
388. Russell, J. B., and F. Diez-Gonzales. 1998. The effects of fermentation acids on bacterial growth. Adv. Microb. Physiol.39:205-234. [[PubMed]
389. Saier, M. H., Jr., and T. M. Ramseier. 1996. The catabolite repressor/activator (Cra) protein of enteric bacteria. J. Bacteriol.178:3411-3417.
390. Salmond, C. V., R. G. Kroll, and I. R. Booth. 1984. The effect of food preservatives on pH homeostasis in Escherichia coli. J. Gen. Microbiol.130:2845-2850. [[PubMed]
391. Sanchez, L. B., M. Y. Galperin, and M. Muller. 2000. Acetyl-CoA synthetase from the amitochondriate eukaryote Giardia lamblia belongs to the newly recognized superfamily of Acyl-CoA synthetases (nucleoside diphosphate-forming). J. Biol. Chem.275:5794-5803. [[PubMed]
392. Sanchez, L. B., and M. Muller. 1996. Purification and characterization of the acetate forming enzyme, acetyl-CoA synthetase (ADP-forming) from the amitochondriate protist, Giardia lamblia. FEBS Lett.378:240-244. [[PubMed]
393. Sanders, D. A., B. L. Gillece-Castro, A. L. Burlingame, and D. E. J. Koshland. 1992. Phosphorylation site of NtrC, a protein phosphatase whose covalent intermediate activates transcription. J. Bacteriol.174:5117-5122.
394. Sato, M., K. Machida, E. Arikado, H. Saito, T. Kakegawa, and H. Kobayashi. 2000. Expression of outer membrane proteins in Escherichia coli growing at acid pH. Appl. Environ. Microbiol.66:943-947.
395. Schafer, T., and PSchonheit. 1991. Pyruvate metabolism of the hyperthermophilic archaebacterium Pyrococcus furiosus. Acetate formation from acetyl-CoA and ATP synthesis are catalysed by an acetyl-CoA synthetase (ADP-forming). Arch. Microbiol.155:366-377. [PubMed][Google Scholar]
396. Schafer, T., M. Selig, and P. Schonheit. 1993. Acetyl-CoA synthetase (ADP-forming) in archaea, a novel enzyme involved in acetate and ATP synthesis. Arch. Microbiol.159:72-83. [PubMed]
397. Scharrer, E., and TLutz. 1990. Effects of short chain fatty acids and K on absorption of Mg and other cations by the colon and caecum. Z. Ernahrungswiss.29:162-168. [[PubMed][Google Scholar]
398. Scheppach, W., E. W. Pomare, M. Elia, and J. H. Cummings. 1991. The contribution of the large intestine to blood acetate in man. Clin. Sci. (London)80:177-182. [[PubMed]
399. Schmiel, D. H., G. M. Young, and V. L. Miller. 2000. The Yersinia enterocolitica phospholipase gene yplA is part of the flagellar regulon. J. Bacteriol.182:2314-2320.
400. Schonheit, P., and TSchafer. 1995. Metabolism of hyperthermophiles. World J. Microbiol. Biotechnol.11:26-57. [[PubMed][Google Scholar]
401. Schrader, T., and J. R. Andreesen. 1992. Purification and characterization of protein PC, a component of glycine reductase from Eubacterium acidaminophilum. Eur. J. Biochem.206:79-85. [[PubMed]
402. Sedewitz, B., K. H. Schleifer, and F. Gotz. 1984. Physiological role of pyruvate oxidase in the aerobic metabolism of Lactobacillus plantarum. J. Bacteriol.160:462-465.
403. Sedewitz, B., K. H. Schleifer, and F. Gotz. 1984. Purification and biochemical characterization of pyruvate oxidase from Lactobacillus plantarum. J. Bacteriol.160:273-278.
404. Semenza, G. 2001. Fifty years ago: the identification of ‘active acetate’ as acetyl-CoA. FEBS Lett.509:343-344. [[PubMed]
405. Seufert, C. D., M. Graf, G. Janson, A. Kuhn, and H. D. Soling. 1974. Formation of free acetate by isolated perfused livers from normal, starved and diabetic rats. Biochem. Biophys. Res. Commun.57:901-909. [[PubMed]
406. Shen, J., and R. P. Gunsalus. 1997. Role of multiple ArcA recognition sites in anaerobic regulation of succinate dehydrogenase (sdhCDAB) gene expression in Escherichia coli. Mol. Microbiol.26:223-236. [[PubMed]
407. Shin, B.-S., S.-K. Choi, and S.-H. Park. 1999. Regulation of the Bacillus subtilis phosphotransacetylase gene. J. Biochem. (Tokyo)126:333-339. [[PubMed]
408. Shin, S., and CPark. 1995. Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR. J. Bacteriol.177:4696-4702. [Google Scholar]
409. Shin, S., J. Sheen, and C. Park. 1993. Suppression of high-temperature inhibition of motility due to the change in acetate metabolism in Escherichia coli K-12. Kor. J. Microbiol.31:504-511. [PubMed]
410. Shin, S., S. G. Song, D. S. Lee, J. G. Pan, and C. Park. 1997. Involvement of iclR and rpoS in the induction of acs, the gene for acetyl coenzyme A synthetase of Escherichia coli K-12. FEMS Microbiol. Lett.146:103-108. [[PubMed]
411. Silversmith, R. E., J. L. Appleby, and R. B. Bourret. 1997. Catalytic mechanism of phosphorylation and dephosphorylation of CheY: kinetic characterization of imidazole phosphates as phosphodonors and the role of acid catalysis. Biochemistry36:14965-14974. [[PubMed]
412. Singh-Wissmann, K., and J. G. Ferry. 1995. Transcriptional regulation of the phosphotransacetylase-encoding and acetate kinase-encoding genes (pta and ack) from Methanosarcina thermophila. J. Bacteriol.177:1699-1702.
413. Smith, M. W., and F. C. Neidhardt. 1983. 2-Oxoacid dehydrogenase complexes of Escherichia coli: cellular amounts and patterns of synthesis. J. Bacteriol.156:81-88.
414. Snoep, J. L., M. J. Teixeira de Mattos, P. W. Postma, and O. M. Niejssel. 1990. Involvement of pyruvate dehydrogenase in product formation in pyruvate-limited anaerobic chemostat cultures of Enterococcus faecalis NCTC 775. Arch. Microbiol.154:50-55. [[PubMed]
415. Soler, F., M.-I. Fortea, A. Lax, and F. Fernandez-Belda. 2002. Dissecting the hydrolytic activities of sarcoplasmic reticulum ATPase in the presence of acetyl phosphate. J. Biol. Chem.277:38127-38132. [[PubMed]
416. Sone, H., H. Shimano, Y. Sakakura, N. Inoue, M. Amemiya-Kudo, N. Yahagi, M. Osawa, H. Suzuki, T. Yokoo, A. Takahashi, K. Iida, H. Toyoshima, A. Iwama, and N. Yamada. 2002. Acetyl-coenzyme A synthetase is a lipogenic enzyme controlled by SREBP-1 and energy status. Am. J. Physiol. Endocrinol. Metab.282:E222-E230. [[PubMed]
417. Sourjik, V., and RSchmitt. 1998. Phosphotransfer between CheA, CheY1, and CheY2 in the chemotaxis signal transduction chain of Rhizobium meliloti. Biochemistry37:2327-2335. [[PubMed][Google Scholar]
418. Speck, E. L., and E. Freese. 1973. Control of metabolite secretion in Bacillus subtilis. J. Gen. Microbiol.78:261-275. [[PubMed]
419. Spellerberg, B., D. R. Cundell, J. Sandros, B. J. Pearce, I. Idanpaan-Heikkila, C. Rosenow, and H. R. Masure. 1996. Pyruvate oxidase, as a determinant of virulence in Streptococcus pneumoniae. Mol. Microbiol.19:803-813. [[PubMed]
420. Spencer, M. E., and J. R. Guest. 1987. Regulation of citric acid cycle genes in facultative bacteria. Microbiol. Sci.4:164-168. [[PubMed]
421. Spencer, M. E., and J. R. Guest. 1985. Transcription analysis of the sucAB, aceEF, and lpd genes of Escherichia coli. Mol. Gen. Genet.200:145-154. [[PubMed]
422. Stadtman, T., and JDavis. 1991. Glycine reductase protein C. Properties and characterization of its role in the reductive cleavage of Se-carboxymethyl-selenoprotein A. J. Biol. Chem.266:22147-22153. [[PubMed][Google Scholar]
423. Stadtman, TC. 1989. Clostridial glycine reductase: protein C, the acetyl group acceptor, catalyzes the arsenate-dependent decomposition of acetyl phosphate. Proc. Natl. Acad. Sci. USA86:7853-7856. [Google Scholar]
424. Stancik, L. M., D. M. Stancik, B. Schmidt, D. M. Barnhart, Y. N. Yoncheva, and J. L. Slonczewski. 2002. pH-Dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli. J. Bacteriol.184:4246-4258.
425. Starai, V., and JEscalante-Semerena. 2004. Identification of the protein acetyltransferase (Pat) enzyme that acetylates acetyl-CoA synthetase in Salmonella enterica. J. Mol. Biol.340:1005-1012. [[PubMed][Google Scholar]
426. Starai, V. J., I. Celic, R. N. Cole, J. D. Boeke, and J. C. Escalante-Semerena. 2002. Sir2-dependent activation of acetyl-CoA synthetase by deacetylation of active lysine. Science298:2390-2392. [[PubMed]
427. Starai, V. J., and J. C. Escalante-Semerena. 2004. Acetyl-coenzyme A synthetase (AMP forming). Cell. Mol. Life Sci.61:2020-2030. [[PubMed]
428. Starai, V. J., H. Takahashi, J. D. Boeke, and J. C. Escalante-Semerena. 2003. Short- chain fatty acid activation by acyl-coenzyme A synthetases requires SIR2 protein function in Salmonella enterica and Saccharomyces cerevisiae. Genetics163:545-555.
429. Steeg, P. S., D. Palmieri, T. Ouatas, and M. Salerno. 2003. Histidine kinases and histidine phosphorylated proteins in mammalian cell biology, signal transduction and cancer. Cancer Lett.190:1-12. [[PubMed]
430. Sterri, S. H., and F. Fonnum. 1980. Acetyl-CoA synthesizing enzymes in cholinergic nerve terminals. J. Neurochem.35:249-254. [[PubMed]
431. Stock, A. M., V. L. Robinson, and P. N. Goudreau. 2000. Two-component signal transduction. Annu. Rev. Biochem.69:183-215. [[PubMed]
432. Stokes, JL. 1949. Fermentation of glucose by suspensions of Escherichia coli. J. Bacteriol.57:147-158. [Google Scholar]
433. Stout, V. 1994. Regulation of capsule synthesis includes interactions of the RcsC/RcsB regulatory pair. Res. Microbiol.145:389-392. [[PubMed]
434. Stulke, J., and WHillen. 1999. Carbon catabolite repression in bacteria. Curr. Opin. Microbiol.2:195-201. [[PubMed][Google Scholar]
435. Summers, M. L., M. C. Denton, and T. R. McDermott. 1999. Genes coding for phosphotransacetylase and acetate kinase in Sinorhizobium meliloti are in an operon that is inducible by phosphate stress and controlled by phoB. J. Bacteriol.181:2217-2224.
436. Suzuki, K., X. Wang, T. Weilbacher, A.-K. Pernestig, O. Melefors, D. Georgellis, P. Babitzke, and T. Romeo. 2002. Regulatory circuitry of the CsrA/CsrB and BarA/UvrY systems of Escherichia coli. J. Bacteriol.184:5130-5140.
437. Suzuki, T. 1969. Phosphotransacetylase of Escherichia coli B, activation by pyruvate and inhibition by NADH and certain nucleotides. Biochim. Biophys. Acta191:559-569. [[PubMed]
438. Takamura, Y., and GNomura. 1988. Changes in the intracellular concentration of acetyl-CoA and malonyl-CoA in relation to the carbon and energy metabolism of Escherichia coli K12. J. Gen. Microbiol.134:2249-2253. [[PubMed][Google Scholar]
439. Takeda, S., A. Matsushika, and T. Mizuno. 1999. Repression of the gene encoding succinate dehydrogenase in response to glucose is mediated by the EIICB(Glc) protein in Escherichia coli. J. Biochem. (Tokyo)126:354-360. [[PubMed]
440. 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.
441. Thauer, R. K., K. Jungermann, and K. Decker. 1977. Energy conservation in chemotrophic anaerobic bacteria. Bacteriol. Rev.41:100-180.
442. Thomason, P. A., D. Traynor, J. B. Stock, and R. R. Kay. 1999. The RdeA-RegA system, a eukaryotic phospho-relay controlling cAMP breakdown. J. Biol. Chem.274:27379-27384. [[PubMed]
443. Thomason, P. A., D. Traynor, G. Cavet, W. T. Chang, A. J. Harwood, and R. R. Kay. 1998. An intersection of the cAMP/PKA and two-component signal transduction systems of Dictyostelium. EMBO J.17:2838-2845.
444. Tittmann, K., D. Proske, M. Spinka, S. Ghisla, R. Rudolph, G. Hubner, and G. Kern. 1998. Activation of thiamin diphosphate and FAD in the phosphate dependent pyruvate oxidase from Lactobacillus plantarum. J. Biol. Chem.273:12929-12934. [[PubMed]
445. Toh, H. 1990. N-terminal halves of gramicidin S synthetase 1, and tyrocidine synthetase 1 as novel members of firefly luciferase family. Protein Seq. Data Anal.3:517-521. [[PubMed]
446. Toh, H. 1991. Sequence analysis of firefly luciferase family reveals a conservative sequence motif. Protein Seq. Data Anal.4:111-117. [[PubMed]
447. Topping, D. L., and P. M. Clifton. 2001. Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol. Rev.81:1031-1064. [[PubMed]
448. Tran, V. K., R. Oropeza, and L. J. Kenney. 1999. A single amino acid substitution in the C terminus of OmpR alters DNA recognition and phosphorylation. J. Mol. Biol.299:1257-1270. [[PubMed]
449. Tsang, A., and JEscalante-Semerena. 1996. cobB function is required for catabolism of propionate in Salmonella typhimurium LT2: evidence for existence of a substitute function for CobB within the 1,2-propanediol utilization (pdu) operon. J. Bacteriol.178:7016-7019. [Google Scholar]
450. Tsang, A. W., A. R. Horswill, and J. C. Escalante-Semerena. 1998. Studies of regulation of expression of the propionate (prpBCDE) operon provide insights into how Salmonella typhimurium LT2 integrates its 1,2-propanediol and propionate catabolic pathways. J. Bacteriol.180:6511-6518.
451. 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.
452. Turinsky, A. J., F. J. Grundy, J.-H. Kim, G. H. Chambliss, and T. M. Henkin. 1998. Transcriptional activation of the Bacillus subtilis ackA gene requires sequences upstream of the promoter. J. Bacteriol.180:5961-5967.
453. Turinsky, A. J., T. R. Moir-Blais, F. J. Grundy, and T. M. Henkin. 2000. Bacillus subtilis ccpA gene mutants specifically defective in activation of acetoin biosynthesis. J. Bacteriol.182:5611-5614.
454. Vallari, D. S., and S. Jackowski. 1988. Biosynthesis and degradation both contribute to the regulation of coenzyme A content in Escherichia coli. J. Bacteriol.170:3961-3966.
455. van den Berg, M. A., P. de Jong-Gubbels, C. J. Kortland, J. P. van Dijken, J. T. Pronk, and H. Y. Steensma. 1996. The two acetyl-coenzyme A synthetases of Saccharomyces cerevisiae differ with respect to kinetic properties and transcriptional regulation. J. Biol. Chem.271:28953-28959. [[PubMed]
456. van de Walle, M., and JShiloach. 1998. Proposed mechanism of acetate accumulation in two recombinant Escherichia coli strains during high density fermentation. Biotechnol. Bioeng.57:71-78. [[PubMed][Google Scholar]
457. Van Dyk, T. K., and R. A. LaRossa. 1987. Involvement of ack-pta operon products in alpha-ketobutyrate metabolism by Salmonella typhimurium. Mol. Gen. Genet.207:435-440. [[PubMed]
458. Varma, A., and B. O. Paulson. 1994. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl. Environ. Microbiol.60:3724-3731.
459. Voet, D., and J. G. Voet. 1990. Biochemistry, John Wiley & Sons, Inc., New York, N.Y.
460. Wadolkowski, E. A., D. C. Laux, and P. S. Cohen. 1988. Colonization of the streptomycin-treated mouse large intestine by a human fecal Escherichia coli strain: role of growth in mucus. Infect. Immun.56:1030-1035.
461. Wagner, A., S. Schultz, J. Bomke, T. Pils, W. Lehmann, and J. Knappe. 2001. YfiD of Escherichia coli and Y061 of bacteriophage T4 as autonomous glycyl radical cofactors reconstituting the catalytic center of oxygen-fragmented pyruvate formate-lyase. Biochem. Biophys. Res. Commun.285:456-462. [[PubMed]
462. Wagner, M., D. Sonntag, R. Grimm, A. Pich, C. Eckerskorn, B. Sohling, and J. R. Andreesen. 1999. Substrate-specific selenoprotein B of glycine reductase from Eubacterium acidaminophilum. Biochemical and molecular analysis. Eur. J. Biochem.260:38-49. [[PubMed]
463. Wanner, BL. 1993. Gene regulation by phosphate in enteric bacteria. J. Cell. Biochem.51:47-54. [[PubMed][Google Scholar]
464. Wanner, BL. 1992. Is cross regulation by phosphorylation of two-component response regulator proteins important in bacteria? EMBO J.11:265-277. [Google Scholar]
465. Wanner, BL. 1996. Phosphorus assimilation and control of the phosphate regulon, p. 1357-1381. 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.
466. Wanner, B. L., and M. R. Wilmes-Riesenberg. 1992. Involvement of phosphotransacetylase, acetate kinase, and acetyl phosphate synthesis in control of the phosphate regulon in Escherichia coli. J. Bacteriol.174:2124-2130.
467. 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. [[PubMed]
468. Weickert, M. J., and G. H. Chambliss. 1990. Site-directed mutagenesis of a catabolite repression operator sequence in Bacillus subtilits. Proc. Natl. Acad. Sci. USA87:6238-6242.
469. Wendisch, VF. 2003. Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. J. Biotechnol.104:273-285. [[PubMed][Google Scholar]
470. Wendisch, V. F., M. Spies, D. J. Reinscheid, S. Schnicke, H. Sahm, and B. J. Eikmanns. 1997. Regulation of acetate metabolism in Corynebacterium glutamicum: transcriptional control of the isocitrate lyase and malate synthase genes. Arch. Microbiol.168:262-269. [[PubMed]
471. West, A. H., and A. M. Stock. 2001. Histidine kinases and response regulator proteins in two-component signaling systems. Trends Biochem. Sci.26:369-376. [[PubMed]
472. Wilde, R. J., and J. R. Guest. 1986. Transcript analysis of the citrate synthase and succinate dehydrogenase genes of Escherichia coli K12. J. Gen. Microbiol.132:3239-3251. [[PubMed]
473. Wolfe, A. J., D.-E. Chang, J. D. Walker, J. E. Seitz-Partridge, M. D. Vidaurri, C. F. Lange, B. M. Prüß, M. C. Henk, J. C. Larkin, and T. Conway. 2003. Evidence that acetyl phosphate functions as a global signal during biofilm development. Mol. Microbiol.48:977-988. [[PubMed]
474. Wolfe, A. J., M. P. Conley, and H. C. Berg. 1988. Acetyladenylate plays a role in controlling the direction of flagellar rotation. Proc. Natl. Acad. Sci. USA85:6711-6715.
475. Woodnutt, G., and D. S. Parker. 1986. Acetate metabolism by tissues of the rabbit. Comp. Biochem. Physiol. Ser. B.85:487-490. [[PubMed]
476. Wyborn, N. R., S. L. Messenger, R. A. Henderson, G. Sawers, R. E. Roberts, M. M. Attwood, and J. Green. 2002. Expression of the Escherichia coli yfiD gene responds to intracellular pH and reduces the accumulation of acidic metabolic end products. Microbiology148:1015-1026. [[PubMed]
477. Xu, B., M. Jahic, and S.-O. Enfors. 1999. Modeling of overflow metabolism in batch and fed-batch cultures of Escherichia coli. Biotechnol. Prog.15:81-90. [[PubMed]
478. Yamamoto, K., and AIshihama. 2003. Two different modes of transcription repression of the Escherichia coli acetate operon by IcIR. Mol. Microbiol.47:183-194. [[PubMed][Google Scholar]
479. Yamamoto-Otake, H. M., A. Matsuyama, and F. Nakano. 1990. Cloning of a gene coding for phosphotransacetylase from Escherichia coli. Appl. Microbiol. Biotechnol.33:680-682. [[PubMed]
480. Yamashita, H., A. Fukuura, T. Nakamura, T. Kaneyuki, M. Kimoto, M. Hiemori, and H. Tsuji. 2002. Purification and partial characterization of acetyl-coA synthetase in rat liver mitochondria. J. Nutr. Sci. Vitaminol. (Tokyo)48:359-364. [[PubMed]
481. Yamashita, H., T. Kaneyuki, and K. Tagawa. 2001. Production of acetate in the liver and its utilization in peripheral tissues. Biochim. Biophys. Acta1532:79-87. [[PubMed]
482. 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. [[PubMed]
483. Yang, Y. T., G. N. Bennett, and K. Y. San. 1999. Effect of inactivation of nuo and ackA-pta on redistribution of metabolic fluxes in Escherichia coli. Biotechnol. Bioeng.65:291-297. [[PubMed]
484. Zahrt, T. C., C. Wozniak, D. Jones, and A. Trevett. 2003. Functional analysis of the Mycobacterium tuberculosis MprAB two-component signal transduction system. Infect. Immun.71:6962-6970.
485. Zalieckas, J. M., J. Wray, L. V., and S. H. Fisher. 1998. Expression of the Bacillus subtilis acsA gene: position and sequence context affect cre-mediated carbon catabolite repression. J. Bacteriol.180:6649-6654.
486. Zapf, J. W., J. A. Hoch, and J. M. Whiteley. 1996. A phosphotransferase activity of the Bacillus subtilis sporulation protein Spo0F that employs phosphoramidate substrates. Biochemistry35:2926-2933. [[PubMed]
487. Zeeman, A. M., and H. Y. Steensma. 2003. The acetyl co-enzyme A synthetase genes of Kluyveromyces lactis. Yeast20:13-23. [[PubMed]
488. Zhu, P. P., and A. Peterkofsky. 1996. Sequence and organization of genes encoding enzymes involved in pyruvate metabolism in Mycoplasma capricolum. Protein Sci.5:1719-1736.