About this Journal Submit a Manuscript Table of Contents
ISRN Biochemistry
Volume 2013 (2013), Article ID 645983, 47 pages
http://dx.doi.org/10.1155/2013/645983
Review Article

Metabolic Regulation of a Bacterial Cell System with Emphasis on Escherichia coli Metabolism

1Kyushu Institute of Technology, Fukuoka, Iizuka 820-8502, Japan
2Institute of Advanced Bioscience, Keio University, Yamagata, Tsuruoka 997-0017, Japan

Received 11 September 2012; Accepted 25 October 2012

Academic Editors: W. Antonin, C. F. S. Bonafe, and T. B. Ng

Copyright © 2013 Kazuyuki Shimizu. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. G. Caetano-Anollés, L. S. Yafremava, H. Gee, D. Caetano-Anollés, H. S. Kim, and J. E. Mittenthal, “The origin and evolution of modern metabolism,” International Journal of Biochemistry and Cell Biology, vol. 41, no. 2, pp. 285–297, 2009. View at Publisher · View at Google Scholar · View at Scopus
  2. S. C. Janga, H. Salgado, A. Martínez-Antonio, and J. Collado-Vides, “Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli,” Nucleic Acids Research, vol. 35, no. 20, pp. 6963–6972, 2007. View at Publisher · View at Google Scholar · View at Scopus
  3. S. Gama-Castro, V. Jiménez-Jacinto, M. Peralta-Gil et al., “RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation,” Nucleic Acids Research, vol. 36, no. 1, pp. D120–D124, 2008. View at Publisher · View at Google Scholar · View at Scopus
  4. M. Heinemann and U. Sauer, “Systems biology of microbial metabolism,” Current Opinion in Microbiology, vol. 13, no. 3, pp. 337–343, 2010. View at Publisher · View at Google Scholar · View at Scopus
  5. A. M. Feist and B. Ø. Palsson, “The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli,” Nature Biotechnology, vol. 26, no. 6, pp. 659–667, 2008. View at Publisher · View at Google Scholar · View at Scopus
  6. B. Palsson, “Metabolic systems biology,” FEBS Letters, vol. 583, no. 24, pp. 3900–3904, 2009. View at Publisher · View at Google Scholar · View at Scopus
  7. C. T. Harbison, D. B. Gordon, T. I. Lee et al., “Transcriptional regulatory code of a eukaryotic genome,” Nature, vol. 430, no. 7004, pp. 99–104, 2004. View at Publisher · View at Google Scholar · View at Scopus
  8. N. M. Luscombe, M. M. Babu, H. Yu, M. Snyder, S. A. Teichmann, and M. Gerstein, “Genomic analysis of regulatory network dynamics reveals large topological changes,” Nature, vol. 431, no. 7006, pp. 308–312, 2004. View at Publisher · View at Google Scholar · View at Scopus
  9. G. Balázsi, A. L. Barabási, and Z. N. Oltvai, “Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 22, pp. 7841–7846, 2005. View at Publisher · View at Google Scholar · View at Scopus
  10. J. F. Moxley, M. C. Jewett, M. R. Antoniewicz et al., “Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 16, pp. 6477–6482, 2009. View at Publisher · View at Google Scholar · View at Scopus
  11. U. Sauer, “Metabolic networks in motion: 13C-based flux analysis,” Molecular Systems Biology, vol. 2, article 62, 2006. View at Publisher · View at Google Scholar · View at Scopus
  12. B. R. B. H. van Rijsewijk, A. Nanchen, S. Nallet, R. J. Kleijn, and U. Sauer, “Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli,” Molecular Systems Biology, vol. 7, article 477, 2011. View at Publisher · View at Google Scholar · View at Scopus
  13. N. Zamboni, S.-M. Fendt, M. Ruhl, and U. Sauer, “13C-based metabolic flux analysis,” Nature Protocols, vol. 4, no. 6, pp. 878–892, 2009.
  14. C. Wittman, “Fluome analysis using GC-MS,” Microbial Cell Factories, vol. 6, pp. 1–17, 2007. View at Publisher · View at Google Scholar
  15. K. Shimizu, “Metabolic flux analysis based on 13C-labeling experiments and integration of the information with gene and protein expression patterns,” Advances in Biochemical Engineering/Biotechnology, vol. 91, pp. 1–49, 2004. View at Scopus
  16. K. Shimizu, “Toward systematic metabolic engineering based on the analysis of metabolic regulation by the integration of different levels of information,” Biochemical Engineering Journal, vol. 46, no. 3, pp. 235–251, 2009. View at Publisher · View at Google Scholar · View at Scopus
  17. K. Shimizu, Bacterial Cellular Metabolic Systems, Woodhead Publishing, Oxford, UK, 2012.
  18. S. M. Fendt, J. M. Buescher, F. Rudroff, P. Picotti, N. Zamboni, and U. Sauer, “Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity,” Molecular Systems Biology, vol. 6, article 356, 2010. View at Publisher · View at Google Scholar · View at Scopus
  19. N. Ishii, K. Nakahigashi, T. Baba et al., “Multiple high-throughput analyses monitor the response of E. coli to perturbations,” Science, vol. 316, no. 5824, pp. 593–597, 2007. View at Publisher · View at Google Scholar · View at Scopus
  20. N. Zamboni, M. Heinemann, and U. Sauer, “Getting closer to the whole picture,” Science, vol. 316, no. 5824, pp. 550–551, 2007. View at Publisher · View at Google Scholar · View at Scopus
  21. A. L. Barabasi and Z. N. Oltvai, “Network topology: understanding the cell’s functional organization,” Nature Reviews Genetics, vol. 5, pp. 101–113, 2004. View at Publisher · View at Google Scholar
  22. M. M. Babu, N. M. Luscombe, L. Aravind, M. Gerstein, and S. A. Teichmann, “Structure and evolution of transcriptional regulatory networks,” Current Opinion in Structural Biology, vol. 14, no. 3, pp. 283–291, 2004. View at Publisher · View at Google Scholar · View at Scopus
  23. H. Salgado, S. Gama-Castro, M. Peralta-Gil et al., “RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions,” Nucleic Acids Research, vol. 34, pp. D394–D397, 2006. View at Scopus
  24. A. S. Seshasayee, P. Bertone, G. M. Fraser, and N. M. Luscombe, “Transcriptional regulatory networks in bacteria: from input signals to output responses,” Current Opinion in Microbiology, vol. 9, no. 5, pp. 511–519, 2006. View at Publisher · View at Google Scholar · View at Scopus
  25. A. Martínez-Antonio, S. C. Janga, H. Salgado, and J. Collado-Vides, “Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli,” Trends in Microbiology, vol. 14, no. 1, pp. 22–27, 2006. View at Publisher · View at Google Scholar · View at Scopus
  26. M. Kanehisa, S. Goto, M. Hattori et al., “From genomics to chemical genomics: new developments in KEGG,” Nucleic Acids Research, vol. 34, pp. D354–D357, 2006. View at Scopus
  27. K. Yamamoto, K. Hirao, T. Oshima, H. Aiba, R. Utsumi, and A. Ishihama, “Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli,” The Journal of Biological Chemistry, vol. 280, no. 2, pp. 1448–1456, 2005. View at Publisher · View at Google Scholar · View at Scopus
  28. J. Timmermans and L. van Melderen, “Post-transcriptional global regulation by CsrA in bacteria,” Cellular and Molecular Life Sciences, vol. 67, no. 17, pp. 2897–2908, 2010. View at Publisher · View at Google Scholar · View at Scopus
  29. L. Kroos, “The Bacillus and Myxococcus developmental networks and their transcriptional regulators,” Annual Review of Genetics, vol. 41, pp. 13–39, 2007. View at Publisher · View at Google Scholar · View at Scopus
  30. R. Brückner and F. Titgemeyer, “Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization,” FEMS Microbiology Letters, vol. 209, no. 2, pp. 141–148, 2002. View at Publisher · View at Google Scholar · View at Scopus
  31. R. M. Gutierrez-Ríos, J. A. Freyre-Gonzalez, O. Resendis, J. Collado-Vides, M. Saier, and G. Gosset, “Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli,” BMC Microbiology, vol. 7, article 53, 2007. View at Publisher · View at Google Scholar · View at Scopus
  32. N. de Lay and S. Gottesman, “The crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior,” Journal of Bacteriology, vol. 191, no. 2, pp. 461–476, 2009. View at Publisher · View at Google Scholar · View at Scopus
  33. C. M. Müller, A. Åberg, J. Straseviçiene, L. Emody, B. E. Uhlin, and C. Balsalobre, “Type 1 fimbriae, a colonization factor of uropathogenic Escherichia coli, are controlled by the metabolic sensor CRP-cAMP,” PLoS Pathogens, vol. 5, no. 2, Article ID e1000303, 2009. View at Publisher · View at Google Scholar · View at Scopus
  34. D. Zheng, C. Constantinidou, J. L. Hobman, and S. D. Minchin, “Identification of the CRP regulon using in vitro and in vivo transcriptional profiling,” Nucleic Acids Research, vol. 32, no. 19, pp. 5874–5893, 2004. View at Publisher · View at Google Scholar · View at Scopus
  35. S. Gottesman, “Micros for microbes: non-coding regulatory RNAs in bacteria,” Trends in Genetics, vol. 21, no. 7, pp. 399–404, 2005. View at Publisher · View at Google Scholar · View at Scopus
  36. C. K. Vanderpool and S. Gottesman, “Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system,” Molecular Microbiology, vol. 54, no. 4, pp. 1076–1089, 2004. View at Publisher · View at Google Scholar · View at Scopus
  37. C. S. Wadler and C. K. Vanderpool, “A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 51, pp. 20454–20459, 2007. View at Publisher · View at Google Scholar · View at Scopus
  38. N. Majdalani, C. K. Vanderpool, and S. Gottesman, “Bacterial small RNA regulators,” Critical Reviews in Biochemistry and Molecular Biology, vol. 40, no. 2, pp. 93–113, 2005. View at Publisher · View at Google Scholar
  39. P. Babitzke and T. Romeo, “CsrB sRNA family: sequestration of RNA-binding regulatory proteins,” Current Opinion in Microbiology, vol. 10, no. 2, pp. 156–163, 2007. View at Publisher · View at Google Scholar · View at Scopus
  40. H. Nikaido and T. Nakae, “The outer membrane of gram-negative bacteria,” Advances in Microbial Physiology, vol. 20, pp. 163–250, 1980. View at Publisher · View at Google Scholar · View at Scopus
  41. M. A. de la Cruz, M. Fernández-Mora, C. Guadarrama et al., “LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1,” Molecular Microbiology, vol. 66, no. 3, pp. 727–743, 2007. View at Publisher · View at Google Scholar · View at Scopus
  42. H. Nikaido, “Molecular basis of bacterial outer membrane permeability revisited,” Microbiology and Molecular Biology Reviews, vol. 67, no. 4, pp. 593–656, 2003. View at Publisher · View at Google Scholar · View at Scopus
  43. M. H. Saier, C. V. Tran, and R. D. Barabote, “TCDB: the transporter classification database for membrane transport protein analyses and information,” Nucleic Acids Research, vol. 34, pp. D181–D186, 2006. View at Scopus
  44. M. H. Saier, M. R. Yen, K. Noto, D. G. Tamang, and C. Elkan, “The transporter classification database: recent advances,” Nucleic Acids Research, vol. 37, no. 1, pp. D274–D278, 2009. View at Publisher · View at Google Scholar · View at Scopus
  45. H. Nikaido, Outer Membrane, ASM Press, Washington, DC, USA, 1996, edited by F. C. Neidhardt.
  46. M. N. Hall and T. J. Silhavy, “The ompB locus and the regulation of the major outer membrane porin proteins of Escherichia coli K12,” Journal of Molecular Biology, vol. 146, no. 1, pp. 23–43, 1981. View at Scopus
  47. B. Lugtenberg, R. Peters, H. Bernheimer, and W. Berendsen, “Influence of cultural conditions and mutations on the composition of the outer membrane proteins of Escherichia coli,” Molecular and General Genetics, vol. 147, no. 3, pp. 251–262, 1976. View at Scopus
  48. L. A. Pratt and T. J. Silhavy, “The response regulator SprE controls the stability of RpoS,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 6, pp. 2488–2492, 1996. View at Publisher · View at Google Scholar · View at Scopus
  49. H. Nikaido and M. Vaara, “Molecular basis of bacterial outer membrane permeability,” Microbiological Reviews, vol. 49, no. 1, pp. 1–32, 1985. View at Scopus
  50. A. Death and T. Ferenci, “Between feast and famine: endogenous inducer synthesis in the adaptation of Escherichia coli to growth with limiting carbohydrates,” Journal of Bacteriology, vol. 176, no. 16, pp. 5101–5107, 1994. View at Scopus
  51. H. Nikaido and E. Y. Rosenberg, “Porin channels in Escherichia coli: studies with liposomes reconstituted from purified proteins,” Journal of Bacteriology, vol. 153, no. 1, pp. 241–252, 1983. View at Scopus
  52. K. von Meyenburg and H. Nikaido, “Outer membrane of gram-negative bacteria. XVII. Specificity of transport process catalyzed by the λ-receptor protein in Escherichia coli,” Biochemical and Biophysical Research Communications, vol. 78, no. 3, pp. 1100–1107, 1977. View at Scopus
  53. G. Gosset, “Improvement of Escherichia coli production strains by modification of the phosphoenolpyruvate:sugar phosphotransferase system,” Microbial Cell Factories, vol. 4, article 14, 2005. View at Publisher · View at Google Scholar · View at Scopus
  54. K. Brzostek, M. Brzóstkowska, I. Bukowska, E. Karwicka, and A. Raczkowska, “OmpR negatively regulates expression of invasin in Yersinia enterocolitica,” Microbiology, vol. 153, no. 8, pp. 2416–2425, 2007. View at Publisher · View at Google Scholar · View at Scopus
  55. W. M. Von Kruger, L. M. Lery, M. R. Soares et al., “The phosphate-starvation response in Vibrio cholerae O1 and phoB mutant under proteomic analysis: disclosing functions involved in adaptation, survival and virulence,” Proteomics, vol. 6, pp. 1495–1511, 2006.
  56. M. Ferrario, B. R. Ernsting, D. W. Borst, D. E. Wiese II, R. M. Blumenthal, and R. G. Matthews, “The leucine-responsive regulatory protein of Escherichia coli negatively regulates transcription of ompC and micF and positively regulates translation of ompF,” Journal of Bacteriology, vol. 177, no. 1, pp. 103–113, 1995. View at Scopus
  57. N. Delihas and S. Forst, “MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factors,” Journal of Molecular Biology, vol. 313, no. 1, pp. 1–12, 2001. View at Publisher · View at Google Scholar · View at Scopus
  58. Y. H. Lee, B. H. Kim, J. H. Kim, W. S. Yoon, S. H. Bang, and Y. K. Park, “CadC has a global translational effect during acid adaptation in Salmonella enterica serovar Typhimurium,” Journal of Bacteriology, vol. 189, pp. 2417–2425, 2007.
  59. C. A. Santiviago, C. S. Toro, A. A. Hidalgo, P. Youderian, and G. C. Mora, “Global regulation of the Salmonella enterica serovar Typhimurium major porin, OmpD,” Journal of Bacteriology, vol. 185, no. 19, pp. 5901–5905, 2003. View at Publisher · View at Google Scholar · View at Scopus
  60. V. L. Miller and J. J. Mekalanos, “A novel suicide vector and its use in construction of insertion mutations: osmoregulation of outer membrane proteins and virulence determinants in Vibrio cholerae requires toxR,” Journal of Bacteriology, vol. 170, no. 6, pp. 2575–2583, 1988. View at Scopus
  61. P. Deighan, A. Free, and C. J. Dorman, “A role for the Escherichia coli H-NS-like protein StpA in OmpF porin expression through modulation of micF RNA stability,” Molecular Microbiology, vol. 38, no. 1, pp. 126–139, 2000. View at Publisher · View at Google Scholar · View at Scopus
  62. M. Fernández-Mora, J. L. Puente, and E. Calva, “OmpR and LeuO Positively Regulate the Salmonella enterica Serovar Typhi ompS2 porin gene,” Journal of Bacteriology, vol. 186, no. 10, pp. 2909–2920, 2004. View at Publisher · View at Google Scholar · View at Scopus
  63. C. Dorel, P. Lejeune, and A. Rodrigue, “The Cpx system of Escherichia coli, a strategic signaling pathway for confronting adverse conditions and for settling biofilm communities?” Research in Microbiology, vol. 157, no. 4, pp. 306–314, 2006. View at Publisher · View at Google Scholar · View at Scopus
  64. T. L. Raivio, “Envelope stress responses and gram-negative bacterial pathogenesis,” Molecular Microbiology, vol. 56, no. 5, pp. 1119–1128, 2005. View at Publisher · View at Google Scholar · View at Scopus
  65. B. L. Wanner, “Phosphorus assimilation and control of the phosphate regulon,” in Escherichia coli and Salmonella: Cellular and Molecular Biology, F. C. Neidhardt, I. I. I. Curtiss R, J. L. Ingraham et al., Eds., pp. 1357–1381, ASM Press, Washington, DC, USA, 1996.
  66. J. M. Calvo and R. G. Matthews, “The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli,” Microbiological Reviews, vol. 58, no. 3, pp. 466–490, 1994. View at Scopus
  67. M. T. Gallegos, R. Schleif, A. Bairoch, K. Hofmann, and J. L. Ramos, “AraC/Xyls family of transcriptional regulators,” Microbiology and Molecular Biology Reviews, vol. 61, no. 4, pp. 393–410, 1997. View at Scopus
  68. C. Balagué and E. G. Véscovi, “Activation of multiple antibiotic resistance in uropathogenic Escherichia coli strains by aryloxoalcanoic acid compounds,” Antimicrobial Agents and Chemotherapy, vol. 45, no. 6, pp. 1815–1822, 2001. View at Publisher · View at Google Scholar · View at Scopus
  69. H. Hachler, S. P. Cohen, and S. B. Levy, “marA, a regulated locus which controls expression of chromosomal multiple antibiotic resistance in Escherichia coli,” Journal of Bacteriology, vol. 173, no. 17, pp. 5532–5538, 1991. View at Scopus
  70. J. T. Oh, Y. Cajal, E. M. Skowronska et al., “Cationic peptide antimicrobials induce selective transcription of micF and osmY in Escherichia coli,” Biochimica et Biophysica Acta, vol. 1463, no. 1, pp. 43–54, 2000. View at Publisher · View at Google Scholar · View at Scopus
  71. C. Küper and K. Jung, “CadC-mediated activation of the cadBA promoter in Escherichia coli,” Journal of Molecular Microbiology and Biotechnology, vol. 10, no. 1, pp. 26–39, 2006. View at Publisher · View at Google Scholar · View at Scopus
  72. J. E. Rhee, K. S. Kim, and S. H. Choi, “CadC activates pH-dependent expression of the Vibrio vulnificus cadBA operon at a distance through direct binding to an upstream region,” Journal of Bacteriology, vol. 187, no. 22, pp. 7870–7875, 2005. View at Publisher · View at Google Scholar · View at Scopus
  73. L. Huang, P. Tsui, and M. Freundlich, “Positive and negative control of ompB transcription in Escherichia coli by cyclic AMP and the cyclic AMP receptor protein,” Journal of Bacteriology, vol. 174, no. 3, pp. 664–670, 1992. View at Scopus
  74. I. Gibert and J. Barbe, “Cyclic AMP stimulates transcription of the structural gene of the outer-membrane protein ompA of Escherichia coli,” FEMS Microbiology Letters, vol. 68, no. 3, pp. 307–311, 1990. View at Scopus
  75. K. Papenfort, V. Pfeiffer, S. Lucchini, A. Sonawane, J. C. D. Hinton, and J. Vogel, “Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis,” Molecular Microbiology, vol. 68, no. 4, pp. 890–906, 2008. View at Publisher · View at Google Scholar · View at Scopus
  76. B. Nandi, R. K. Nandy, A. Sarkar, and A. C. Ghose, “Structural features, properties and regulation of the outer-membrane protein W (OmpW) of Vibrio cholerae,” Microbiology, vol. 151, no. 9, pp. 2975–2986, 2005. View at Publisher · View at Google Scholar · View at Scopus
  77. F. Hommais, E. Krin, C. Laurent-Winter et al., “Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS,” Molecular Microbiology, vol. 40, no. 1, pp. 20–36, 2001. View at Publisher · View at Google Scholar · View at Scopus
  78. W. W. Navarre, S. Porwollik, Y. Wang et al., “Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella,” Science, vol. 313, no. 5784, pp. 236–238, 2006. View at Publisher · View at Google Scholar · View at Scopus
  79. J. Johansson, B. Dagberg, E. Richet, and B. E. Uhlin, “H-NS and StpA proteins stimulate expression of the maltose regulon in Escherichia coli,” Journal of Bacteriology, vol. 180, no. 23, pp. 6117–6125, 1998. View at Scopus
  80. L. Huang, P. Tsui, and M. Freundlich, “Integration host factor is a negative effector of in vivo and in vitro expression of ompC in Escherichia coli,” Journal of Bacteriology, vol. 172, no. 9, pp. 5293–5298, 1990. View at Scopus
  81. M. A. Flores-Valdez, J. L. Puente, and E. Calva, “Negative osmoregulation of the Salmonella ompS1 porin gene independently of OmpR in an hns background,” Journal of Bacteriology, vol. 185, no. 22, pp. 6497–6506, 2003. View at Publisher · View at Google Scholar · View at Scopus
  82. P. Romby, F. Vandenesch, and E. G. H. Wagner, “The role of RNAs in the regulation of virulence-gene expression,” Current Opinion in Microbiology, vol. 9, no. 2, pp. 229–236, 2006. View at Publisher · View at Google Scholar · View at Scopus
  83. G. Storz, S. Altuvia, and K. M. Wassarman, “An abundance of RNA regulators,” Annual Review of Biochemistry, vol. 74, pp. 199–217, 2005. View at Publisher · View at Google Scholar · View at Scopus
  84. J. Vogel and K. Papenfort, “Small non-coding RNAs and the bacterial outer membrane,” Current Opinion in Microbiology, vol. 9, no. 6, pp. 605–611, 2006. View at Publisher · View at Google Scholar · View at Scopus
  85. M. G. W. Gunnewijk, P. T. C. van den Bogaard, L. M. Veenhoff et al., “Hierarchical control versus autoregulation of carbohydrate utilization in bacteria,” Journal of Molecular Microbiology and Biotechnology, vol. 3, no. 3, pp. 401–413, 2001. View at Scopus
  86. B. Poolman and W. N. Konings, “Secondary solute transport in bacteria,” Biochimica et Biophysica Acta, vol. 1183, no. 1, pp. 5–39, 1993. View at Publisher · View at Google Scholar · View at Scopus
  87. P. W. Postma, J. W. Lengeler, and G. R. Jacobson, “Phosphoenolpyruvate: carbohydrate phosphotransferase systems,” in Escherichia coli and Salmonella: Cellular and Molecular Biology, F. C. Neidhardt, Ed., pp. 1149–1174, ASM Press, Washington, DC, USA, 1996.
  88. J. H. Tchieu, V. Norris, J. S. Edwards, and M. H. Saier Jr., “The complete phosphotransferase system in Escherichia coli,” Journal of Molecular Microbiology and Biotechnology, vol. 3, no. 3, pp. 329–346, 2001. View at Scopus
  89. S. J. Curtis and W. Epstein, “Phosphorylation of D glucose in Escherichia coli mutants defective in glucosephosphotransferase, mannosephosphotransferase, and glucokinase,” Journal of Bacteriology, vol. 122, no. 3, pp. 1189–1199, 1975. View at Scopus
  90. C. H. Chou, G. N. Bennett, and K. Y. San, “Effect of modulated glucose uptake on high-level recombinant protein production in a dense Escherichia coli culture,” Biotechnology Progress, vol. 10, no. 6, pp. 644–647, 1994. View at Scopus
  91. N. Flores, S. Flores, A. Escalante et al., “Adaptation for fast growth on glucose by differential expression of central carbon metabolism and gal regulon genes in an Escherichia coli strain lacking the phosphoenolpyruvate:carbohydrate phosphotransferase system,” Metabolic Engineering, vol. 7, no. 2, pp. 70–87, 2005. View at Publisher · View at Google Scholar · View at Scopus
  92. A. Death and T. Ferenci, “Between feast and famine: Endogenous inducer synthesis in the adaptation of Escherichia coli to growth with limiting carbohydrates,” Journal of Bacteriology, vol. 176, pp. 5101–5107, 1994.
  93. V. V. Lunin, Y. Li, J. D. Schrag, P. Iannuzzi, M. Cygler, and A. Matte, “Crystal structures of Escherichia coli ATP-dependent glucokinase and its complex with glucose,” Journal of Bacteriology, vol. 186, no. 20, pp. 6915–6927, 2004. View at Publisher · View at Google Scholar · View at Scopus
  94. J. Monod, Recherches sur la Croissance de cultures Bacteriennes [thesis], Hermann et Cie, Paris, France, 1942.
  95. B. Magasanik, “Catabolite repression,” Cold Spring Harbor Symposia on Quantitative Biology, vol. 26, pp. 249–256, 1961. View at Scopus
  96. B. Bowien and B. Kusian, “Genetics and control of CO2 assimilation in the chemoautotroph Ralstonia eutropha,” Archives of Microbiology, vol. 178, no. 2, pp. 85–93, 2002. View at Publisher · View at Google Scholar · View at Scopus
  97. T. L. Nicholson, K. Chiu, and R. S. Stephens, “Chlamydia trachomatis lacks an adaptive response to changes in carbon source availability,” Infection and Immunity, vol. 72, no. 7, pp. 4286–4289, 2004. View at Publisher · View at Google Scholar · View at Scopus
  98. S. Halbedel, H. Eilers, B. Jonas et al., “Transcription in Mycoplasma pneumoniae: analysis of the promoters of the ackA and ldh genes,” Journal of Molecular Biology, vol. 371, no. 3, pp. 596–607, 2007. View at Publisher · View at Google Scholar · View at Scopus
  99. J. Frunzke, V. Engels, S. Hasenbein, C. Gätgens, and M. Bott, “Co-ordinated regulation of gluconate catabolism and glucose uptake in Corynebacterium glutamicum by two functionally equivalent transcriptional regulators, GntR1 and GntR2,” Molecular Microbiology, vol. 67, no. 2, pp. 305–322, 2008. View at Publisher · View at Google Scholar · View at Scopus
  100. V. F. Wendisch, A. A. de Graaf, H. Sahm, and B. J. Eikmanns, “Quantitative determination of metabolic fluxes during coutilization of two carbon sources: comparative analyses with Corynebacterium glutamicum during growth on acetate and/or glucose,” Journal of Bacteriology, vol. 182, no. 11, pp. 3088–3096, 2000. View at Publisher · View at Google Scholar · View at Scopus
  101. P. T. C. Van den Bogaard, M. Kleerebezem, O. P. Kuipers, and W. M. Vos, “Control of lactose transport, β-galactosidase activity, and glycolysis by CcpA in Streptococcus thermophilus: evidence for carbon catabolite repression by a non-phosphoenolpyryvate-dependent phosphotransferase system sugar,” Journal of Bacteriology, vol. 182, pp. 5982–5989, 2000.
  102. S. Parche, M. Beleut, E. Rezzonico et al., “Lactose-over-glucose preference in Bifidobacterium longum NCC2705: glcP, encoding a glucose transporter, is subject to lactose repression,” Journal of Bacteriology, vol. 188, pp. 1260–1265, 2006.
  103. D. N. Collier, P. W. Hager, and P. V. Phibbs Jr., “Catabolite repression control in the Pseudomonads,” Research in Microbiology, vol. 147, no. 6-7, pp. 551–561, 1996. View at Publisher · View at Google Scholar · View at Scopus
  104. M. Liu, T. Durfee, J. E. Cabrera, K. Zhao, D. J. Jin, and F. R. Blattner, “Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli,” The Journal of Biological Chemistry, vol. 280, no. 16, pp. 15921–15927, 2005. View at Publisher · View at Google Scholar · View at Scopus
  105. H. M. Blencke, G. Homuth, H. Ludwig, U. Mäder, M. Hecker, and J. Stülke, “Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways,” Metabolic Engineering, vol. 5, no. 2, pp. 133–149, 2003. View at Publisher · View at Google Scholar · View at Scopus
  106. M. S. Moreno, B. L. Schneider, R. R. Maile, W. Weyler, and M. H. Saier Jr., “Catabolite repression mediated by the CcpA protein in Bacillus subtilis: novel modes of regulation revealed by whole-genome analyses,” Molecular Microbiology, vol. 39, no. 5, pp. 1366–1381, 2001. View at Scopus
  107. B. Görke and J. Stülke, “Carbon catabolite repression in bacteria: many ways to make the most out of nutrients,” Nature Reviews Microbiology, vol. 6, no. 8, pp. 613–624, 2008. View at Publisher · View at Google Scholar · View at Scopus
  108. H. H. Winkler and T. H. Wilson, “Inhibition of β-galactoside transport by substrates of the glucose transport system in Escherichia coli,” Biochimica et Biophysica Acta, vol. 135, no. 5, pp. 1030–1051, 1967. View at Scopus
  109. B. M. Hogema, J. C. Arents, R. Bader, and P. W. Postma, “Autoregulation of lactose uptake through the LacY permease by enzyme IIAGlc of the PTS in Escherichia coli K-12,” Molecular Microbiology, vol. 31, no. 6, pp. 1825–1833, 1999. View at Publisher · View at Google Scholar · View at Scopus
  110. S. O. Nelson, J. K. Wright, and P. W. Postma, “The mechanism of inducer exclusion. Direct interaction between purified IIIGlc of the phosphoenolpyruvate:sugar phosphotransferase system and the lactose carrier of Escherichia coli,” The EMBO Journal, vol. 2, pp. 715–720, 1983.
  111. I. Smirnova, V. Kasho, J. Y. Choe, C. Altenbach, W. L. Hubbell, and H. R. Kaback, “Sugar binding induces an outward facing conformation of LacY,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 42, pp. 16504–16509, 2007. View at Publisher · View at Google Scholar · View at Scopus
  112. F. Titgemeyer, R. E. Mason, and M. H. Saier Jr., “Regulation of the raffinose permease of Escherichia coli by the glucose-specific enzyme IIA of the phosphoenolpyruvate:sugar phosphotransferase system,” Journal of Bacteriology, vol. 176, no. 2, pp. 543–546, 1994. View at Scopus
  113. T. P. Misko, W. J. Mitchell, N. D. Meadow, and S. Roseman, “Sugar transport by the bacterial phosphotransferase system. Reconstitution of inducer exclusion in Salmonella typhimurium membrane vesicles,” The Journal of Biological Chemistry, vol. 262, no. 33, pp. 16261–16266, 1987. View at Scopus
  114. G. M. Djordjevic, J. H. Tchieu, and M. H. Saier Jr., “Genes involved in control of galactose uptake in Lactobacillus brevis and reconstitution of the regulatory system in Bacillus subtilis,” Journal of Bacteriology, vol. 183, no. 10, pp. 3224–3236, 2001. View at Publisher · View at Google Scholar · View at Scopus
  115. B. Poolman, J. Knol, B. Mollet, B. Nieuwenhuis, and G. Sulter, “Regulation of bacterial sugar-H+ symport by phosphoenolpyruvate-dependent enzyme I/HPr-mediated phosphorylation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 92, no. 3, pp. 778–782, 1995. View at Publisher · View at Google Scholar · View at Scopus
  116. M. G. W. Gunnewijk and B. Poolman, “Phosphorylation state of Hpr determines the level of expression and the extent of phosphorylation of the lactose transport protein of Streptococcus thermophilus,” The Journal of Biological Chemistry, vol. 275, no. 44, pp. 34073–34079, 2000. View at Scopus
  117. J. Plumbridge, “Expression of ptsG, the gene for the major glucose PTS transporter in Escherichia coli, is repressed by Mlc and induced by growth on glucose,” Molecular Microbiology, vol. 29, no. 4, pp. 1053–1063, 1998. View at Publisher · View at Google Scholar · View at Scopus
  118. H. de Reuse and A. Danchin, “The ptsH, ptsI, and crr genes of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system: a complex operon with several modes of transcription,” Journal of Bacteriology, vol. 170, no. 9, pp. 3827–3837, 1988. View at Scopus
  119. K. Bettenbrock, S. Fischer, A. Kremling, K. Jahreis, T. Sauter, and E. D. Gilles, “A quantitative approach to catabolite repression in Escherichia coli,” The Journal of Biological Chemistry, vol. 281, no. 5, pp. 2578–2584, 2006. View at Publisher · View at Google Scholar · View at Scopus
  120. G. Boris, “Carbon catabolite repression in bacteria: many ways to make the most out of nutrients,” Nature Reviews Microbiology, vol. 6, no. 8, pp. 613–624, 2008.
  121. Y. H. Park, B. R. Lee, Y. J. Seok, and A. Peterkofsky, “In vitro reconstitution of catabolite repression in Escherichia coli,” The Journal of Biological Chemistry, vol. 281, no. 10, pp. 6448–6454, 2006. View at Publisher · View at Google Scholar · View at Scopus
  122. Y. Tanaka, K. Kimata, and H. Aiba, “A novel regulatory role of glucose transporter of Escherichia coli: membrane sequestration of a global repressor Mlc,” The EMBO Journal, vol. 19, no. 20, pp. 5344–5352, 2000. View at Scopus
  123. S. J. Lee, W. Boos, J. P. Bouché, and J. Plumbridge, “Signal transduction between a membrane-bound transporter, PtsG, and a soluble transcription factor, Mlc of Escherichia coli,” The EMBO Journal, vol. 19, no. 20, pp. 5353–5361, 2000. View at Scopus
  124. K. Bettenbrock, T. Sauter, K. Jahreis, A. Kremling, J. W. Lengeler, and E. D. Gilles, “Correlation between growth rates, EIIACrr phosphorylation, and intracellular cyclic AMP levels in Escherichia coli K-12,” Journal of Bacteriology, vol. 189, no. 19, pp. 6891–6900, 2007. View at Publisher · View at Google Scholar · View at Scopus
  125. B. M. Hogema, J. C. Arents, R. Bader et al., “Inducer exclusion in Escherichia coli by non-PTS substrates: the role of the PEP to pyruvate ratio in determining the phosphorylation state of enzyme IIAGlc,” Molecular Microbiology, vol. 30, no. 3, pp. 487–498, 1998. View at Publisher · View at Google Scholar · View at Scopus
  126. T. Inada, K. Kimata, and H. Aiba, “Mechanism responsible for glucose-lactose diauxie in Escherichia coli: challenge to the cAMP model,” Genes to Cells, vol. 1, no. 3, pp. 293–301, 1996. View at Scopus
  127. K. Kimata, H. Takahashi, T. Inada, P. Postma, and H. Aiba, “cAMP receptor protein-cAMP plays a crucial role in glucose-lactose diauxie by activating the major glucose transporter gene in Escherichia coli,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 24, pp. 12914–12919, 1997. View at Publisher · View at Google Scholar · View at Scopus
  128. J. Deutscher, C. Francke, and P. W. Postma, “How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria,” Microbiology and Molecular Biology Reviews, vol. 70, no. 4, pp. 939–1031, 2006. View at Publisher · View at Google Scholar · View at Scopus
  129. P. Aulkemeyer, R. Ebner, G. Heilenmann et al., “Molecular analysis of two fructokinases involved in sucrose metabolism of enteric bacteria,” Molecular Microbiology, vol. 5, no. 12, pp. 2913–2922, 1991. View at Scopus
  130. H. L. Kornberg, “Fructose transport by Escherichia coli,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 326, no. 1236, pp. 505–513, 1990.
  131. H. L. Kornberg, “Routes for fructose utilization by Escherichia coli,” Journal of Molecular Microbiology and Biotechnology, vol. 3, no. 3, pp. 355–359, 2001. View at Scopus
  132. F. Titgemeyer and W. Hillen, “Global control of sugar metabolism: a gram-positive solution,” Antonie van Leeuwenhoek, vol. 82, no. 1-4, pp. 59–71, 2002. View at Publisher · View at Google Scholar · View at Scopus
  133. J. B. Warner and J. S. Lolkema, “A Crh-specific function in carbon catabolite repression in Bacillus subtilis,” FEMS Microbiology Letters, vol. 220, no. 2, pp. 277–280, 2003. View at Publisher · View at Google Scholar · View at Scopus
  134. T. M. Henkin, F. J. Grundy, W. L. Nicholson, and G. H. Chambliss, “Catabolite repression of α-amylase gene expression in Bacillus subtilis involves a trans-acting gene product homologous to the Escherichia coli lacI and galR repressors,” Molecular Microbiology, vol. 5, no. 3, pp. 575–584, 1991. View at Scopus
  135. A. Galinier, M. Kravanja, R. Engelmann et al., “New protein kinase and protein phosphatase families mediate signal transduction in bacterial catabolite repression,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 4, pp. 1823–1828, 1998. View at Publisher · View at Google Scholar · View at Scopus
  136. J. Reizer, C. Hoischen, F. Titgemeyer et al., “A novel protein kinase that controls carbon catabolite repression in bacteria,” Molecular Microbiology, vol. 27, no. 6, pp. 1157–1169, 1998. View at Publisher · View at Google Scholar · View at Scopus
  137. J. M. Jault, S. Fieulaine, S. Nessler et al., “The HPr kinase from Bacillus subtilis is a homo-oligomeric enzyme which exhibits strong positive cooperativity for nucleotide and fructose 1,6-bisphosphate binding,” The Journal of Biological Chemistry, vol. 275, no. 3, pp. 1773–1780, 2000. View at Publisher · View at Google Scholar · View at Scopus
  138. I. Mijakovic, S. Poncet, A. Galinier et al., “Pyrophosphate-producing protein dephosphorylation by HPr kinase/phosphorylase: a relic of early life?” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 21, pp. 13442–13447, 2002. View at Publisher · View at Google Scholar · View at Scopus
  139. G. Seidel, M. Diel, N. Fuchsbauer, and W. Hillen, “Quantitative interdependence of coeffectors, CcpA and cre in carbon catabolite regulation of Bacillus subtilis,” FEBS Journal, vol. 272, no. 10, pp. 2566–2577, 2005. View at Publisher · View at Google Scholar · View at Scopus
  140. M. A. Schumacher, G. Seidel, W. Hillen, and R. G. Brennan, “Structural mechanism for the fine-tuning of CcpA function by the small molecule effectors glucose 6-phosphate and fructose 1,6-bisphosphate,” Journal of Molecular Biology, vol. 368, no. 4, pp. 1042–1050, 2007. View at Publisher · View at Google Scholar · View at Scopus
  141. G. P. van Wezel, M. König, K. Mahr et al., “A new piece of an old jigsaw: glucose kinase is activated posttranslationally in a glucose transport-dependent manner in Streptomyces coelicolor A3(2),” Journal of Molecular Microbiology and Biotechnology, vol. 12, no. 1-2, pp. 67–74, 2006. View at Publisher · View at Google Scholar · View at Scopus
  142. A. Arndt and B. J. Eikmanns, “The alcohol dehydrogenase gene adhA in Corynebacterium glutamicum is subject to carbon catabolite repression,” Journal of Bacteriology, vol. 189, no. 20, pp. 7408–7416, 2007. View at Publisher · View at Google Scholar · View at Scopus
  143. R. Gerstmeir, A. Cramer, P. Dangel, S. Schaffer, and B. J. Eikmanns, “RamB, a novel transcriptional regulator of genes involved in acetate metabolism of Corynebacterium glutamicum,” Journal of Bacteriology, vol. 186, no. 9, pp. 2798–2809, 2004. View at Publisher · View at Google Scholar · View at Scopus
  144. M. Bott and M. Brocker, “Two-component signal transduction in Corynebacterium glutamicum and other corynebacteria: on the way towards stimuli and targets,” Applied Microbiology and Biotechnology, vol. 94, no. 5, pp. 1131–1150, 2012. View at Publisher · View at Google Scholar
  145. C. Müller, L. Petruschka, H. Cuypers, G. Burchhardt, and H. Herrmann, “Carbon catabolite repression of phenol degradation in Pseudomonas putida is mediated by the inhibition of the activator protein PhIR,” Journal of Bacteriology, vol. 178, no. 7, pp. 2030–2036, 1996. View at Scopus
  146. R. Moreno, A. Ruiz-Manzano, L. Yuste, and F. Rojo, “The Pseudomonas putida Crc global regulator is an RNA binding protein that inhibits translation of the AlkS transcriptional regulator,” Molecular Microbiology, vol. 64, no. 3, pp. 665–675, 2007. View at Publisher · View at Google Scholar · View at Scopus
  147. R. Moreno and F. Rojo, “The target for the Pseudomonas putida Crc global regulator in the benzoate degradation pathway is the BenR transcriptional regulator,” Journal of Bacteriology, vol. 190, no. 5, pp. 1539–1545, 2008. View at Publisher · View at Google Scholar · View at Scopus
  148. S. Petersen and G. M. Young, “Essential role for cyclic AMP and its receptor protein in Yersinia enterocolitica virulence,” Infection and Immunity, vol. 70, no. 7, pp. 3665–3672, 2002. View at Publisher · View at Google Scholar · View at Scopus
  149. H. Ramström, M. Bourotte, C. Philippe, M. Schmitt, J. Haiech, and J. J. Bourguignon, “Heterocyclic bis-cations as starting hits for design of inhibitors of the bifunctional enzyme histidine-containing protein kinase/phosphatase from Bacillus subtilis,” Journal of Medicinal Chemistry, vol. 47, no. 9, pp. 2264–2275, 2004. View at Publisher · View at Google Scholar · View at Scopus
  150. R. Curtiss and S. M. Kelly, “Salmonella typhimurium deletion mutants lacking adenylate cyclase and cyclic AMP receptor protein are avirulent and immunogenic,” Infection and Immunity, vol. 55, no. 12, pp. 3035–3043, 1987. View at Scopus
  151. T. Romeo, “Global regulation by the small RNA-binding protein CsrA and the non- coding RNA molecule CsrB,” Molecular Microbiology, vol. 29, no. 6, pp. 1321–1330, 1998. View at Publisher · View at Google Scholar · View at Scopus
  152. K. Jonas, A. N. Edwards, I. Ahmad, T. Romeo, U. Römling, and O. Melefors, “Complex regulatory network encompassing the Csr, c-di-GMP and motility systems of Salmonella typhimurium,” Environmental Microbiology, vol. 12, no. 2, pp. 524–540, 2010. View at Publisher · View at Google Scholar · View at Scopus
  153. H. Yakhnin, P. Pandit, T. J. Petty, C. S. Baker, T. Romeo, and P. Babitzke, “CsrA of Bacillus subtilis regulates translation initiation of the gene encoding the flagellin protein (hag) by blocking ribosome binding,” Molecular Microbiology, vol. 64, no. 6, pp. 1605–1620, 2007. View at Publisher · View at Google Scholar · View at Scopus
  154. T. Romeo and M. Gong, “Genetic and physical mapping of the regulatory gene csrA on the Escherichia coli K-12 chromosome,” Journal of Bacteriology, vol. 175, no. 17, pp. 5740–5741, 1993. View at Scopus
  155. T. Romeo, M. Gong, M. Y. Liu, and A. M. Brun-Zinkernagel, “Identification and molecular characterization of csrA, a pleiotropic gene from Escherichia coli that affects glycogen biosynthesis, gluconeogenesis, cell size, and surface properties,” Journal of Bacteriology, vol. 175, no. 15, pp. 4744–4755, 1993. View at Scopus
  156. T. Romeo, “Post-transcriptional regulation of bacterial carbohydrate metabolism: evidence that the gene product CsrA is global mRNA decay factor,” Research in Microbiology, vol. 147, no. 6-7, pp. 505–512, 1996. View at Publisher · View at Google Scholar · View at Scopus
  157. C. S. Baker, L. A. Eöry, H. Yakhnin, J. Mercante, T. Romeo, and P. Babitzke, “CsrA inhibits translation initiation of Escherichia coli hfq by binding to a single site overlapping the Shine-Dalgarno sequence,” Journal of Bacteriology, vol. 189, no. 15, pp. 5472–5481, 2007. View at Publisher · View at Google Scholar · View at Scopus
  158. A. K. Dubey, C. S. Baker, T. Romeo, and P. Babitzke, “RNA sequence and secondary structure participate in high-affinity CsrA-RNA interaction,” RNA, vol. 11, no. 10, pp. 1579–1587, 2005. View at Publisher · View at Google Scholar · View at Scopus
  159. K. Suzuki, X. Wang, T. Weilbacher et al., “Regulatory circuitry of the CsrA/CsrB and BarA/UvrY systems of Escherichia coli,” Journal of Bacteriology, vol. 184, no. 18, pp. 5130–5140, 2002. View at Publisher · View at Google Scholar · View at Scopus
  160. T. Weilbacher, K. Suzuki, A. K. Dubey et al., “A novel sRNA component of the carbon storage regulatory system of Escherichia coli,” Molecular Microbiology, vol. 48, no. 3, pp. 657–670, 2003. View at Publisher · View at Google Scholar · View at Scopus
  161. C. S. Baker, I. Morozov, K. Suzuki, T. Romeo, and P. Babitzke, “CsrA regulates glycogen biosynthesis by preventing translation of glgC in Escherichia coli,” Molecular Microbiology, vol. 44, no. 6, pp. 1599–1610, 2002. View at Publisher · View at Google Scholar · View at Scopus
  162. A. E. Mckee, B. J. Rutherford, D. C. Chivian et al., Microbial Cell Factories.
  163. N. Yakandawala, T. Romeo, A. D. Friesen, and S. Madhyastha, “Metabolic engineering of Escherichia coli to enhance phenylalanine production,” Applied Microbiology and Biotechnology, vol. 78, no. 2, pp. 283–291, 2008. View at Publisher · View at Google Scholar · View at Scopus
  164. A. G. Moat, J. W. Foster, and M. P. Spector, Microbiology, Wiley-Liss, New York, NY, USA, 4th edition, 2002.
  165. M. H. Saier Jr., T. M. Ramseier, and J. Reizer, “Regulation of carbon utilization,” in Escherichia coli and Salmonella: Cellular and Molecular Biology, C. Neidhardt, R. Curtiss III, J. L. Ingraham et al., Eds., pp. 1325–1343, ASM Press, Washington, DC, USA, 1996.
  166. M. H. Saier Jr. and T. M. Ramseier, “The catabolite repressor/activator (Cra) protein of enteric bacteria,” Journal of Bacteriology, vol. 178, no. 12, pp. 3411–3417, 1996. View at Scopus
  167. A. M. Chin, D. A. Feldheim, and M. H. Saier Jr., “Altered transcriptional patterns affecting several metabolic pathways in strains of Salmonella typhimurium which overexpress the fructose regulon,” Journal of Bacteriology, vol. 171, no. 5, pp. 2424–2434, 1989. View at Scopus
  168. J. H. Lee, D. E. Lee, B. U. Lee, and H. S. Kim, “Global analyses of transcriptomes and proteomes of a parent strain and an l-threonine-overproducing mutant strain,” Journal of Bacteriology, vol. 185, no. 18, pp. 5442–5451, 2003. View at Publisher · View at Google Scholar
  169. T. M. Ramseier, S. Bledig, V. Michotey, R. Feghali, and M. H. Saier Jr., “The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli,” Molecular Microbiology, vol. 16, no. 6, pp. 1157–1169, 1995. View at Publisher · View at Google Scholar · View at Scopus
  170. T. M. Ramseier, S. Y. Chien, and M. H. Saier Jr., “Cooperative interaction between Cra and Fnr in the regulation of the cydAB operon of Escherichia coli,” Current Microbiology, vol. 33, no. 4, pp. 270–274, 1996. View at Publisher · View at Google Scholar · View at Scopus
  171. H. M. Saier Jr., T. Ramseier, and J. Reizer, “Regulation of carbon utilization,” in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, F. C. Neidhardt, Ed., ASM Press, Washington, DC, USA, 1997.
  172. S. Ryu, T. M. Ramseier, V. Michotey, M. H. Saier Jr., and S. Garges, “Effect of the FruR regulator on transcription of the pts operon in Escherichia coli,” The Journal of Biological Chemistry, vol. 270, no. 6, pp. 2489–2496, 1995. View at Publisher · View at Google Scholar · View at Scopus
  173. A. Mikulskis, A. Aristarkhov, and E. C. C. Lin, “Regulation of expression of the ethanol dehydrogenase gene (adhE) in Escherichia coli by catabolite repressor activator protein Cra,” Journal of Bacteriology, vol. 179, no. 22, pp. 7129–7134, 1997. View at Scopus
  174. J. F. Prost, D. Nègre, C. Oudot et al., “Cra-dependent transcriptional activation of the icd gene of Escherichia coli,” Journal of Bacteriology, vol. 181, no. 3, pp. 893–898, 1999. View at Scopus
  175. J.-C. Cortay, D. Negre, M. Scarabel et al., “In vitro asymmetric binding of the pleiotropic regulatory protein , FruR, to the ace operator controlling glyoxylate shunt enzyme synthesis,” Journal of Biological Chemictry, vol. 269, pp. 14885–14891, 1994.
  176. D. Sarkar and K. Shimizu, “Effect of cra gene knockout together with other genes knockouts on the improvement of substrate consumption rate in Escherichia coli under microaerobic condition,” Biochemical Engineering Journal, vol. 42, no. 3, pp. 224–228, 2008. View at Publisher · View at Google Scholar · View at Scopus
  177. D. Sarkar, K. A. Z. Siddiquee, M. J. Araúzo-Bravo, T. Oba, and K. Shimizu, “Effect of cra gene knockout together with edd and iclR genes knockout on the metabolism in Escherichia coli,” Archives of Microbiology, vol. 190, no. 5, pp. 559–571, 2008. View at Publisher · View at Google Scholar · View at Scopus
  178. J. N. Phue, S. B. Noronha, R. Hattacharyya, A. J. Wolfe, and J. Shiloach, “Glucose metabolism at high density growth of E. coli B and E. coli K: differences in metabolic pathways are responsible for efficient glucose utilization in E. coli B as determined by microarrays and Northern blot analyses,” Biotechnology and Bioengineering, vol. 90, no. 7, pp. 805–820, 2005. View at Publisher · View at Google Scholar · View at Scopus
  179. R. Yao, Y. Hirose, D. Sarkar, K. Nakahigashi, Q. Ye, and K. Shimizu, “Catabolic regulation analysis of Escherichia coli and its crp, mlc, mgsA, pgi and ptsG mutants,” Microbial Cell Factories, vol. 10, article 67, 2011. View at Publisher · View at Google Scholar
  180. D. Yan, “Protection of the glutamate pool concentration in enteric bacteria,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 22, pp. 9475–9480, 2007. View at Publisher · View at Google Scholar · View at Scopus
  181. A. J. Ninfa, P. Jiang, M. R. Atkinson, and J. A. Peliska, “Integration of antagonistic signals in the regulation of nitrogen assimilation in Escherichia coli,” Current Topics in Cellular Regulation, vol. 36, pp. 31–75, 2000.
  182. L. Reitzer, “Nitrogen assimilation and global regulation in Escherichia coli,” Annual Reviews in Microbiology, vol. 57, pp. 155–176, 2003.
  183. E. Fischer and U. Sauer, “Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS,” European Journal of Biochemistry, vol. 270, no. 5, pp. 880–891, 2003. View at Publisher · View at Google Scholar · View at Scopus
  184. X. Zhang, K. Jantama, J. C. Moore, K. T. Shanmugam, and L. O. Ingram, “Production of L-alanine by metabolically engineered Escherichia coli,” Applied Microbiology and Biotechnology, vol. 77, no. 2, pp. 355–366, 2007. View at Publisher · View at Google Scholar · View at Scopus
  185. F. M. Commichau, K. Forchhammer, and J. Stülke, “Regulatory links between carbon and nitrogen metabolism,” Current Opinion in Microbiology, vol. 9, no. 2, pp. 167–172, 2006. View at Publisher · View at Google Scholar
  186. X. J. Mao, Y. X. Huo, M. Buck, A. Kolb, and Y. P. Wang, “Interplay between CRP-cAMP and PII-Ntr systems forms novel regulatory network between carbon metabolism and nitrogen assimilation in Escherichia coli,” Nucleic Acids Research, vol. 35, no. 5, pp. 1432–1440, 2007. View at Publisher · View at Google Scholar · View at Scopus
  187. U. Sauer and B. J. Eikmanns, “The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria,” FEMS Microbiology Reviews, vol. 29, no. 4, pp. 765–794, 2005. View at Publisher · View at Google Scholar · View at Scopus
  188. Q. Hua, C. Yang, T. Baba, H. Mori, and K. Shimizu, “Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts,” Journal of Bacteriology, vol. 185, no. 24, pp. 7053–7067, 2003. View at Publisher · View at Google Scholar · View at Scopus
  189. Q. Hua, C. Yang, T. Oshima, H. Mori, and K. Shimizu, “Analysis of gene expression in Escherichia coli in response to changes of growth-limiting nutrient in chemostat cultures,” Applied and Environmental Microbiology, vol. 70, no. 4, pp. 2354–2366, 2004. View at Publisher · View at Google Scholar · View at Scopus
  190. A. Nanchen, A. Schicker, O. Revelles, and U. Sauer, “Cyclic AMP-dependent catabolite repression is the dominant control mechanism of metabolic fluxes under glucose limitation in Escherichia coli,” Journal of Bacteriology, vol. 190, no. 7, pp. 2323–2330, 2008. View at Publisher · View at Google Scholar · View at Scopus
  191. R. Kumar and K. Shimizu, “Metabolic regulation of Escherichia coli and its gdhA, glnL, gltB, D mutants under different carbon and nitrogen limitations in the continuous culture,” Microbial Cell Factories, vol. 9, 8 pages, 2010.
  192. P. Jiang and A. J. Ninfa, “Escherichia coli PII signal transduction protein controlling nitrogen assimilation acts as a sensor of adenylate energy charge in vitro,” Biochemistry, vol. 46, no. 45, pp. 12979–12996, 2007. View at Publisher · View at Google Scholar · View at Scopus
  193. A. J. Ninfa and P. Jiang, “PII signal transduction proteins: sensors of α-ketoglutarate that regulate nitrogen metabolism,” Current Opinion in Microbiology, vol. 8, no. 2, pp. 168–173, 2005. View at Publisher · View at Google Scholar · View at Scopus
  194. G. Gosset, Z. Zhang, S. Nayyar, W. A. Cuevas, and M. H. Saier Jr., “Transcriptome analysis of Crp-dependent catabolite control of gene expression in Escherichia coli,” Journal of Bacteriology, vol. 186, no. 11, pp. 3516–3524, 2004. View at Publisher · View at Google Scholar · View at Scopus
  195. M. Rahman, M. R. Hasan, and K. Shimizu, “Growth phase-dependent changes in the expression of global regulatory genes and associated metabolic pathways in Escherichia coli,” Biotechnology Letters, vol. 30, no. 5, pp. 853–860, 2008. View at Publisher · View at Google Scholar · View at Scopus
  196. R. B. Helling, “Pathway choice in glutamate synthesis in Escherichia coli,” Journal of Bacteriology, vol. 180, no. 17, pp. 4571–4575, 1998. View at Scopus
  197. A. Liang and L. Houghton, “Coregulation of oxidized nicotinamide adenine dinucleotide (phosphate) transhydrogenase and glutamate dehydrogenase activities in enteric bacteria during nitrogen limitation,” Journal of Bacteriology, vol. 146, no. 3, pp. 997–1002, 1981. View at Scopus
  198. R. C. Willis, K. K. Iwata, and C. E. Furlong, “Regulation of glutamine transport in Escherichia coli,” Journal of Bacteriology, vol. 122, no. 3, pp. 1032–1037, 1975. View at Scopus
  199. F. Claverie-Martin and B. Magasanik, “Role of integration host factor in the regulation of the glnHp2 promoter of Escherichia coli,” Proceedings of the National Academy of Sciences of the United States of America, vol. 88, no. 5, pp. 1631–1635, 1991. View at Scopus
  200. T. A. Blauwkamp and A. J. Ninfa, “Physiological role of the GlnK signal transduction protein of Escherichia coli: survival of nitrogen starvation,” Molecular Microbiology, vol. 46, no. 1, pp. 203–214, 2002. View at Publisher · View at Google Scholar · View at Scopus
  201. B. Magasanik, “Regulation of nitrogen utilization,” in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, F. C. Neidhardt, Ed., pp. 1344–1356, ASM Press, Washington, DC, USA, 1996.
  202. L. Riba, B. Becerril, L. Servin-Gonzalez, F. Valle, and F. Bolivar, “Identification of a functional promoter for the Escherichia coli gdhA gene and its regulation,” Gene, vol. 71, no. 2, pp. 233–246, 1988. View at Scopus
  203. L. Camarena, S. Poggio, N. García, and A. Osorio, “Transcriptional repression of gdhA in Escherichia coli is mediated by the Nac protein,” FEMS Microbiology Letters, vol. 167, no. 1, pp. 51–56, 1998. View at Publisher · View at Google Scholar · View at Scopus
  204. L. J. Reitzer and B. Magasanik, “Expression of glnA in Escherichia coli is regulated at tandem promoters,” Proceedings of the National Academy of Sciences of the United States of America, vol. 82, no. 7, pp. 1979–1983, 1985. View at Scopus
  205. M. R. Atkinson and A. J. Ninfa, “Mutational analysis of the bacterial signal-transducing protein kinase/phosphatase nitrogen regulator II (NR(II) or NtrB),” Journal of Bacteriology, vol. 175, no. 21, pp. 7016–7023, 1993. View at Scopus
  206. M. R. Atkinson, T. A. Blauwkamp, and A. J. Ninfa, “Context-dependent functions of the PII and GlnK signal transduction proteins in Escherichia coli,” Journal of Bacteriology, vol. 184, no. 19, pp. 5364–5375, 2002. View at Publisher · View at Google Scholar · View at Scopus
  207. W. C. van Heeswijk, S. Hoving, D. Molenaar, B. Stegeman, D. Kahn, and H. V. Westerhoff, “An alternative P(II) protein in the regulation of glutamine synthetase in Escherichia coli,” Molecular Microbiology, vol. 21, no. 1, pp. 133–146, 1996. View at Scopus
  208. G. Pahel, D. M. Rothstein, and B. Magasanik, “Complex glnA-glnL-glnG operon of Escherichia coli,” Journal of Bacteriology, vol. 150, no. 1, pp. 202–213, 1982. View at Scopus
  209. L. Paul, P. K. Mishra, R. M. Blumenthal, and R. G. Matthews, “Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR,” BMC Microbiology, vol. 7, article 2, 2007. View at Publisher · View at Google Scholar · View at Scopus
  210. B. M. Shapiro and E. R. Stadtman, “Glutamine synthetase deadenylylating enzyme,” Biochemical and Biophysical Research Communications, vol. 30, no. 1, pp. 32–37, 1968. View at Scopus
  211. E. R. Stadtman, “Discovery of glutamine synthetase cascade,” Methods in Enzymology, vol. 182, pp. 793–809, 1990. View at Publisher · View at Google Scholar · View at Scopus
  212. R. Jaggi, W. C. van Heeswijk, H. V. Westerhoff, D. L. Ollis, and S. G. Vasudevan, “The two opposing activities of adenylyl transferase reside in distinct homologous domains, with intramolecular signal transduction,” The EMBO Journal, vol. 16, no. 18, pp. 5562–5571, 1997. View at Publisher · View at Google Scholar · View at Scopus
  213. M. Maheswaran and K. Forchhammer, “Carbon-source-dependent nitrogen regulation in Escherichia coli is mediated through glutamine-dependent GlnB signalling,” Microbiology, vol. 149, no. 8, pp. 2163–2172, 2003. View at Scopus
  214. M. J. Merrick and R. A. Edwards, “Nitrogen control in bacteria,” Microbiological Reviews, vol. 59, no. 4, pp. 604–622, 1995. View at Scopus
  215. A. J. Ninfa and M. R. Atkinson, “PII signal transduction proteins,” Trends in Microbiology, vol. 8, no. 4, pp. 172–179, 2000. View at Publisher · View at Google Scholar · View at Scopus
  216. P. Jiang, J. A. Peliska, and A. J. Ninfa, “The regulation of Escherichia coli glutamine synthetase revisited: role of 2-ketoglutarate in the regulation of glutamine synthetase adenylylation state,” Biochemistry, vol. 37, no. 37, pp. 12802–12810, 1998. View at Publisher · View at Google Scholar · View at Scopus
  217. S. Kustu, E. Santero, J. Keener, D. Popham, and D. Weiss, “Expression of sigma 54 (ntrA)-dependent genes is probably united by a common mechanism,” Microbiological Reviews, vol. 53, no. 3, pp. 367–376, 1989. View at Scopus
  218. M. G. Lamarche, B. L. Wanner, S. Crépin, and J. Harel, “The phosphate regulon and bacterial virulence: a regulatory network connecting phosphate homeostasis and pathogenesis,” FEMS Microbiology Reviews, vol. 32, no. 3, pp. 461–473, 2008. View at Publisher · View at Google Scholar · View at Scopus
  219. T. Ishige, M. Krause, M. Bott, V. F. Wendisch, and H. Sahm, “The phosphate starvation stimulon of Corynebacterium glutamicum determined by DNA microarray analyses,” Journal of Bacteriology, vol. 185, no. 15, pp. 4519–4529, 2003. View at Publisher · View at Google Scholar · View at Scopus
  220. J. H. Baek and S. Y. Lee, “Novel gene members in the Pho regulon of Escherichia coli,” FEMS Microbiology Letters, vol. 264, no. 1, pp. 104–109, 2006. View at Publisher · View at Google Scholar · View at Scopus
  221. V. F. Wendisch, “Genetic regulation of Corynebacterium glutamicum metabolism,” Journal of Microbiology and Biotechnology, vol. 16, no. 7, pp. 999–1009, 2006. View at Scopus
  222. A. P. Damoglou and E. A. Dawes, “Studies on the lipid content and phosphate requirement of glucose-and acetate-grown Escherichia coli,” Biochemical Journal, vol. 110, no. 4, pp. 775–781, 1968. View at Scopus
  223. B. L. Wanner, “Gene regulation by phosphate in enteric bacteria,” Journal of Cellular Biochemistry, vol. 51, no. 1, pp. 47–54, 1993. View at Publisher · View at Google Scholar · View at Scopus
  224. J. B. Stock, A. J. Ninfa, and A. M. Stock, “Protein phosphorylation and regulation of adaptive responses in bacteria,” Microbiological Reviews, vol. 53, no. 4, pp. 450–490, 1989. View at Scopus
  225. J. S. Parkinson, “Signal transduction schemes of bacteria,” Cell, vol. 73, no. 5, pp. 857–871, 1993. View at Publisher · View at Google Scholar · View at Scopus
  226. J. H. Baek and S. Y. Lee, “Transcriptome analysis of phosphate starvation response in Escherichia coli,” Journal of Microbiology and Biotechnology, vol. 17, no. 2, pp. 244–252, 2007. View at Scopus
  227. R. M. Harris, D. C. Webb, S. M. Howitt, and G. B. Cox, “Characterization of PitA and PitB from Escherichia coli,” Journal of Bacteriology, vol. 183, no. 17, pp. 5008–5014, 2001. View at Publisher · View at Google Scholar · View at Scopus
  228. A. G. Blanco, M. Sola, F. X. Gomis-Rüth, and M. Coll, “Tandem DNA recognition by PhoB, a two-component signal transduction transcriptional activator,” Structure, vol. 10, no. 5, pp. 701–713, 2002. View at Publisher · View at Google Scholar · View at Scopus
  229. A. Torriani and D. N. Ludke, “The pho regulon of Escherichia coli,” in The Molecular Biology of Bacterial Growth, M. Schaechter, F. C. Neidhardt, J. Ingraham, and N. O. Kjeldgaard, Eds., Jones and Bartlett, Boston, Mass, USA, 1985.
  230. K. Makino, H. Shinagawa, and A. Nakata, “Regulation of the phosphate regulon of Escherichia coli K-12: regulation and role of the regulatory gene phoR,” Journal of Molecular Biology, vol. 184, no. 2, pp. 231–240, 1985. View at Scopus
  231. K. Makino, H. Shinagawa, M. Amemura, S. Kimura, A. Nakata, and A. Ishihama, “Regulation of the phosphate regulon of Escherichia coli. Activation of pstS transcription by PhoB protein in vitro,” Journal of Molecular Biology, vol. 203, no. 1, pp. 85–95, 1988. View at Scopus
  232. K. Makino, H. Shinagawa, M. Amemura, T. Kawamoto, M. Yamada, and A. Nakata, “Signal transduction in the phosphate regulon of Escherichia coli involves phosphotransfer between PhoR and PhoB proteins,” Journal of Molecular Biology, vol. 210, no. 3, pp. 551–559, 1989. View at Publisher · View at Google Scholar · View at Scopus
  233. H. Shinagawa, K. Makino, M. Amemura, and A. Nakata, “Structure and function of the regulatory gene for the phosphate regulon in Escherichia coli,” in Phosphate Metabolism and Cellular Regulation in Microorganisms, A. Torriani-Gorini, F. G. Rothman, S. Silver, A. Wright, and E. Yagil, Eds., pp. 20–25, American Society for Microbiology, Washington, DC, USA, 1987.
  234. B. L. Wanner, “Phosphate regulon of gene expression in Escherichia coli,” in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, F. C. Neidhardt, J. L. lngraham, K. B. Low, M. Schaechter, and H. E. Umbarger, Eds., pp. 1326–1333, American Society for Microbiology, Washington, DC, USA, 1987.
  235. M. Amemura, K. Makino, H. Shinagawa, and A. Nakata, “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-open reading frame 2,” Journal of Bacteriology, vol. 172, no. 11, pp. 6300–6307, 1990. View at Scopus
  236. Y. J. Hsieh and B. L. Wanner, “Global regulation by the seven-component Pi signaling system,” Current Opinion in Microbiology, vol. 13, no. 2, pp. 198–203, 2010. View at Publisher · View at Google Scholar · View at Scopus
  237. S. J. van Dien and J. D. Keasling, “A dynamic model of the Escherichia coli phosphate-starvation response,” Journal of Theoretical Biology, vol. 190, no. 1, pp. 37–49, 1998. View at Publisher · View at Google Scholar · View at Scopus
  238. B. L. Wanner, “Phosphate signaling and the control of gene expression in Escherichia coli,” in Metal Ions in Gene Regulation, S. Silver and W. William, Eds., pp. 104–128, Chapman & Hall, New York, NY, USA, 1997.
  239. V. Oganesyan, N. Oganesyan, P. D. Adams et al., “Crystal structure of the “PhoU-like” phosphate uptake regulator from Aquifex aeolicus,” Journal of Bacteriology, vol. 187, no. 12, pp. 4238–4244, 2005. View at Publisher · View at Google Scholar
  240. M. A. Nesmeianova, S. A. Gonina, and I. S. Kulaev, “Biosynthesis of Escherichia coli polyphosphatases under control of the regulatory genes usual for alkaline phosphatase,” Doklady Akademii Nauk SSSR, vol. 224, no. 3, pp. 710–712, 1975. View at Scopus
  241. C. Pratt and A. Torriani, “Complementation test between alkaline phosphatase regulatory mutations phoB and phoRc in Escherichia coli,” Genetics, vol. 85, no. 2, pp. 203–208, 1977. View at Scopus
  242. G. Zuckier, E. Ingenito, and A. Torriani, “Pleiotropic effects of alkaline phosphatase regulatory mutations phoB and phoT on anaerobic growth of and polyphosphate synthesis in Escherichia coli,” Journal of Bacteriology, vol. 143, no. 2, pp. 934–941, 1980. View at Scopus
  243. C. D. Guan, B. Wanner, and H. Inouye, “Analysis of regulation of phoB expression using a phoB-cat fusion,” Journal of Bacteriology, vol. 156, no. 2, pp. 710–717, 1983. View at Scopus
  244. M. Yamada, K. Makino, M. Amemura, H. Shinagawa, and A. Nakata, “Regulation of the phosphate regulon of Escherichia coli: analysis of mutant phoB and phoR genes causing different phenotypes,” Journal of Bacteriology, vol. 171, no. 10, pp. 5601–5606, 1989. View at Scopus
  245. S. Kimura, K. Makino, H. Shinagawa, M. Amemura, and A. Nakata, “Regulation of the phosphate regulon of Escherichia coli: characterization of the promoter of the pstS gene,” Molecular and General Genetics, vol. 215, no. 3, pp. 374–380, 1989. View at Scopus
  246. A. Nakata, M. Amemura, and H. Shinagawa, “Regulation of the phosphate regulon in Escherichia coli K-12: regulation of the negative regulatory gene phoU and identification of the gene product,” Journal of Bacteriology, vol. 159, no. 3, pp. 979–985, 1984. View at Scopus
  247. I. M. Tsfasman and M. A. Nesmeyanova, “Membrane proteins in Escherichia coli: effect of orthophosphate and mutations on regulatory genes of secreted alkaline phosphatase,” Molekulyarnaya Biologiya, vol. 15, no. 2, pp. 298–309, 1981. View at Scopus
  248. D. Ault-Riché, C. D. Fraley, C. M. Tzeng, and A. Kornberg, “Novel assay reveals multiple pathways regulating stress-induced accumulations of inorganic polyphosphate in Escherichia coli,” Journal of Bacteriology, vol. 180, no. 7, pp. 1841–1847, 1998. View at Scopus
  249. J. C. Lazzaroni and R. C. Portalier, “Regulation of the lkyB gene expression in Escherichia coli K-12 strains carrying an lkyB-lacZ gene fusion,” Molecular and General Genetics, vol. 201, no. 2, pp. 323–328, 1985. View at Scopus
  250. P. K. Shin and J. H. Seo, “Analysis of E. coliphoA-lacZ fusion gene expression inserted into a multicopy plasmid and host cell's chromosome,” Biotechnology and Bioengineering, vol. 36, no. 11, pp. 1097–1104, 1990. View at Publisher · View at Google Scholar · View at Scopus
  251. L. W. Marzan and K. Shimizu, “Metabolic regulation of Escherichia coli and its phoB and phoR genes knockout mutants under phosphate and nitrogen limitations as well as at acidic condition,” Microbial Cell Factories, vol. 10, 39 pages, 2011.
  252. K. Makino, M. Amemura, S. K. Kim, A. Nakata, and H. Shinagawa, “Role of the σ70 subunit of RNA polymerase in transcriptional activation by activator protein PhoB in Escherichia coli,” Genes and Development, vol. 7, no. 1, pp. 149–160, 1993. View at Scopus
  253. D. R. Gentry, V. J. Hernandez, L. H. Nguyen, D. B. Jensen, and M. Cashel, “Synthesis of the stationary-phase sigma factor σs is positively regulated by ppGpp,” Journal of Bacteriology, vol. 175, no. 24, pp. 7982–7989, 1993. View at Scopus
  254. N. Ruiz and T. J. Silhavy, “Constitutive activation of the Escherichia coli Pho regulon upregulates rpoS translation in an Hfq-dependent fashion,” Journal of Bacteriology, vol. 185, no. 20, pp. 5984–5992, 2003. View at Publisher · View at Google Scholar · View at Scopus
  255. N. P. Taschner, E. Yagil, and B. Spira, “A differential effect of σs on the expression of the PHO regulon genes of Escherichia coli,” Microbiology, vol. 150, no. 9, pp. 2985–2992, 2004. View at Publisher · View at Google Scholar · View at Scopus
  256. B. Spira, N. Silberstein, and E. Yagil, “Guanosine 3′,5′-bispyrophosphate (ppGpp) synthesis in cells of Escherichia coli starved for Pi,” Journal of Bacteriology, vol. 177, no. 14, pp. 4053–4058, 1995. View at Scopus
  257. B. Spira and E. Yagil, “The integration host factor (IHF) affects the expression of the phosphate-binding protein and of alkaline phosphatase in Escherichia coli,” Current Microbiology, vol. 38, no. 2, pp. 80–85, 1999. View at Publisher · View at Google Scholar · View at Scopus
  258. N. P. Taschner, E. Yagil, and B. Spira, “The effect of IHF on σs selectivity of the phoA and pst promoters of Escherichia coli,” Archives of Microbiology, vol. 185, no. 3, pp. 234–237, 2006. View at Publisher · View at Google Scholar · View at Scopus
  259. M. S. Schurdell, G. M. Woodbury, and W. R. McCleary, “Genetic evidence suggests that the intergenic region between pstA and pstB plays a role in the regulation of rpoS translation during phosphate limitation,” Journal of Bacteriology, vol. 189, no. 3, pp. 1150–1153, 2007. View at Publisher · View at Google Scholar · View at Scopus
  260. B. L. Wanner, M. R. Wilmes, and D. C. Young, “Control of bacterial alkaline phosphatase synthesis and variation in an Escherichia coli K-12 phoR mutant by adenyl cyclase, the cyclic AMP receptor protein, and the phoM operon,” Journal of Bacteriology, vol. 170, no. 3, pp. 1092–1102, 1988. View at Scopus
  261. Y. Kang, K. D. Weber, Y. Qiu, P. J. Kiley, and F. R. Blattner, “Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function,” Journal of Bacteriology, vol. 187, no. 3, pp. 1135–1160, 2005. View at Publisher · View at Google Scholar · View at Scopus
  262. R. P. Gunsalus, “Control of electron flow in Escherichia coli: coordinated transcription of respiratory pathway genes,” Journal of Bacteriology, vol. 174, no. 22, pp. 7069–7074, 1992. View at Scopus
  263. S. Alexeeva, K. J. Hellingwerf, and M. J. T. de Mattos, “Requirement of ArcA for redox regulation in Escherichia coli under microaerobic but not anaerobic or aerobic conditions,” Journal of Bacteriology, vol. 185, no. 1, pp. 204–209, 2003. View at Publisher · View at Google Scholar · View at Scopus
  264. J. Zhu, S. Shalel-Levanon, G. Bennett, and K. Y. San, “Effect of the global redox sensing/regulation networks on Escherichia coli and metabolic flux distribution based on C-13 labeling experiments,” Metabolic Engineering, vol. 8, no. 6, pp. 619–627, 2006. View at Publisher · View at Google Scholar · View at Scopus
  265. S. Shalel-Levanon, K. Y. San, and G. N. Bennett, “Effect of oxygen, and ArcA and FNR regulators on the expression of genes related to the electron transfer chain and the TCA cycle in Escherichia coli,” Metabolic Engineering, vol. 7, no. 5-6, pp. 364–374, 2005. View at Publisher · View at Google Scholar · View at Scopus
  266. J. Zhu and K. Shimizu, “The effect of pfl gene knockout on the metabolism for optically pure D-lactate production by Escherichia coli,” Applied Microbiology and Biotechnology, vol. 64, no. 3, pp. 367–375, 2004. View at Publisher · View at Google Scholar · View at Scopus
  267. J. Zhu and K. Shimizu, “Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition,” Metabolic Engineering, vol. 7, no. 2, pp. 104–115, 2005. View at Publisher · View at Google Scholar · View at Scopus
  268. S. Alexeeva, B. de Kort, G. Sawers, K. J. Hellingwerf, and M. J. T. de Mattos, “Effects of limited aeration and of the ArcAB system on intermediary pyruvate catabolism in Escherichia coli,” Journal of Bacteriology, vol. 182, no. 17, pp. 4934–4940, 2000. View at Publisher · View at Google Scholar · View at Scopus
  269. D. Kessler and J. Knappe, “Anaerobic dissimilation of pyruvate,” in E. Coli and Salmonella: Cellular and Molecular Biology, F. C. Neidhardt, R. Curtiss, J. I. Ingraham et al., Eds., vol. 1, pp. 199–205, ASM Press, Washington, DC, USA, 2nd edition, 1996.
  270. G. Sawers and G. Watson, “A glycyl radical solution: oxygen-dependent interconversion of pyruvate formate-lyase,” Molecular Microbiology, vol. 29, no. 4, pp. 945–954, 1998. View at Publisher · View at Google Scholar · View at Scopus
  271. A. F. V. Wagner, S. Schultz, J. Bomke, T. Pils, W. D. Lehmann, and J. Knappe, “YfiD of Escherichia coli and Y061 of bacteriophage T4 as autonomous glycyl radical cofactors reconstituting the catalytic center of oxygen-fragmented pyruvate formate-lyase,” Biochemical and Biophysical Research Communications, vol. 285, no. 2, pp. 456–462, 2001. View at Publisher · View at Google Scholar · View at Scopus
  272. M. Kato, T. Mizuno, T. Shimizu, and T. Hakoshima, “Insights into multistep phosphorelay from the crystal structure of the C-terminal HPt domain of ArcB,” Cell, vol. 88, no. 5, pp. 717–723, 1997. View at Publisher · View at Google Scholar · View at Scopus
  273. K. Ishige, S. Nagasawa, S. I. Tokishita, and T. Mizuno, “A novel device of bacterial signal transducers,” The EMBO Journal, vol. 13, no. 21, pp. 5195–5202, 1994. View at Scopus
  274. S. Iuchi and E. C. C. Lin, “Mutational analysis of signal transduction by ArcB, a membrane sensor protein responsible for anaerobic repression of operons involved in the central aerobic pathways in Escherichia coli,” Journal of Bacteriology, vol. 174, no. 12, pp. 3972–3980, 1992. View at Scopus
  275. M. Tsuzuki, K. Ishige, and T. Mizuno, “Phosphotransfer circuitry of the putative multi-signal transducer, ArcB, of Escherichia coli: in vitro studies with mutants,” Molecular Microbiology, vol. 18, no. 5, pp. 953–962, 1995. View at Scopus
  276. D. Georgellis, A. S. Lynch, and E. C. C. Lin, “In vitro phosphorylation study of the Arc two-component signal transduction system of Escherichia coli,” Journal of Bacteriology, vol. 179, no. 17, pp. 5429–5435, 1997. View at Scopus
  277. S. Iuchi, “Phosphorylation/dephosphorylation of the receiver module at the conserved aspartate residue controls transphosphorylation activity of histidine kinase in sensor protein ArcB of Escherichia coli,” The Journal of Biological Chemistry, vol. 268, no. 32, pp. 23972–23980, 1993. View at Scopus
  278. A. Matsushika and T. Mizuno, “A dual-signaling mechanism mediated by the ArcB hybrid sensor kinase containing the histidine-containing phosphotransfer domain in Escherichia coli,” Journal of Bacteriology, vol. 180, no. 15, pp. 3973–3977, 1998. View at Scopus
  279. D. Georgellis, O. Kwon, and E. C. C. Lin, “Amplification of signaling activity of the Arc two-component system of Escherichia coli by anaerobic metabolites. An in vitro study with different protein modules,” The Journal of Biological Chemistry, vol. 274, no. 50, pp. 35950–35954, 1999. View at Publisher · View at Google Scholar · View at Scopus
  280. S. Iuchi and E. C. C. Lin, “arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways,” Proceedings of the National Academy of Sciences of the United States of America, vol. 85, no. 6, pp. 1888–1892, 1988. View at Publisher · View at Google Scholar · View at Scopus
  281. A. S. Lynch and E. C. C. Lin, “Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters,” Journal of Bacteriology, vol. 178, no. 21, pp. 6238–6249, 1996. View at Scopus
  282. S. J. Park, J. McCabe, J. Turna, and R. P. Gunsalus, “Regulation of the citrate synthase (gltA) gene of Escherichia coli in response to anaerobiosis and carbon supply: role of the arcA gene product,” Journal of Bacteriology, vol. 176, no. 16, pp. 5086–5092, 1994. View at Scopus
  283. S. J. Park, C. P. Tseng, and R. P. Gunsalus, “Regulation of succinate dehydrogenase (sdhCDAB) operon expression in Escherichia coli in response to carbon supply and anaerobiosis: role of ArcA and Fnr,” Molecular Microbiology, vol. 15, no. 3, pp. 473–482, 1995. View at Publisher · View at Google Scholar · View at Scopus
  284. S. J. Park and R. P. Gunsalus, “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,” Journal of Bacteriology, vol. 177, no. 21, pp. 6255–6262, 1995. View at Scopus
  285. S. J. Park, G. Chao, and R. P. Gunsalus, “Aerobic regulation of the sucABCD genes of Escherichia coli, which encode α-ketoglutarate dehydrogenase and succinyl coenzyme A synthetase: roles of ArcA, Fnr, and the upstream sdhCDAB promoter,” Journal of Bacteriology, vol. 179, no. 13, pp. 4138–4142, 1997. View at Scopus
  286. S. Iuchi, V. Chepuri, H. A. Fu, R. B. Gennis, and E. C. C. Lin, “Requirement for terminal cytochromes in generation of the aerobic signal for the arc regulatory system in Escherichia coli: study utilizing deletions and lac fusions of cyo and cyd,” Journal of Bacteriology, vol. 172, no. 10, pp. 6020–6025, 1990. View at Scopus
  287. A. S. Lynch and E. C. C. Lin, “Responses to molecular oxygen,” in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, F. C. Neidhardt, Ed., pp. 1526–1538, ASM press, Washington, DC, USA, 2nd edition, 1996.
  288. L. Cunningham, D. Georgellis, J. Green, and J. R. Guest, “Co-regulation of lipoamide dehydrogenase and 2-oxoglutarate dehydrogenase synthesis in Escherichia coli: characterisation of an ArcA binding site in the lpd promoter,” FEMS Microbiology Letters, vol. 169, no. 2, pp. 403–408, 1998. View at Publisher · View at Google Scholar · View at Scopus
  289. P. A. Cotter and R. P. Gunsalus, “Contribution of the fnr and arcA gene products in coordinate regulation of cytochrome o and d oxidase (cyoABCDE and cydAB) genes in Escherichia coli,” FEMS Microbiology Letters, vol. 91, no. 1, pp. 31–36, 1992. View at Publisher · View at Google Scholar · View at Scopus
  290. N. Drapal and G. Sawers, “Promoter 7 of the Escherichia coli pfl operon is a major determinant in the anaerobic regulation of expression by ArcA,” Journal of Bacteriology, vol. 177, no. 18, pp. 5338–5341, 1995. View at Scopus
  291. C. P. Tseng, J. Albrecht, and R. P. Gunsalus, “Effect of microaerophilic cell growth conditions on expression of the aerobic (cyoABCDE and cydAB) and anaerobic (narGHJI, frdABCD, and dmsABC) respiratory pathway genes in Escherichia coli,” Journal of Bacteriology, vol. 178, no. 4, pp. 1094–1098, 1996. View at Scopus
  292. T. M. Ramseier, S. Y. Chien, and M. H. Saier Jr., “Cooperative interaction between Cra and Fnr in the regulation of the cydAB operon of Escherichia coli,” Current Microbiology, vol. 33, pp. 270–274, 1996.
  293. D. Georgellis, O. Kwon, and E. C. C. Lin, “Quinones as the redox signal for the arc two-component system of bacteria,” Science, vol. 292, no. 5525, pp. 2314–2316, 2001. View at Publisher · View at Google Scholar · View at Scopus
  294. R. Malpica, B. Franco, C. Rodriguez, O. Kwon, and D. Georgellis, “Identification of a quinone-sensitive redox switch in the ArcB sensor kinase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 36, pp. 13318–13323, 2004. View at Publisher · View at Google Scholar · View at Scopus
  295. S. A. Nizam, J. Zhu, P. Y. Ho, and K. Shimizu, “Effects of arcA and arcB genes knockout on the metabolism in Escherichia coli under aerobic condition,” Biochemical Engineering Journal, vol. 44, no. 2-3, pp. 240–250, 2009. View at Publisher · View at Google Scholar · View at Scopus
  296. G. N. Vemuri, M. A. Eiteman, and E. Altman, “Increased recombinant protein production in Escherichia coli strains with overexpressed water-forming NADH oxidase and a deleted ArcA regulatory protein,” Biotechnology and Bioengineering, vol. 94, no. 3, pp. 538–542, 2006. View at Publisher · View at Google Scholar · View at Scopus
  297. G. N. Vemuri, E. Altman, D. P. Sangurdekar, A. B. Khodursky, and M. A. Eiteman, “Overflow metabolism in Escherichia coli during steady-state growth: transcriptional regulation and effect of the redox ratio,” Applied and Environmental Microbiology, vol. 72, no. 5, pp. 3653–3661, 2006. View at Publisher · View at Google Scholar · View at Scopus
  298. S. A. Nizam and K. Shimizu, “Effects of arc A and arc B genes knockout on the metabolism in Escherichia coli under anaerobic and microaerobic conditions,” Biochemical Engineering Journal, vol. 42, pp. 229–236, 2008.
  299. L. Peng and K. Shimizu, “Effect of fadR gene knockout on the metabolism of Escherichia coli based on analyses of protein expressions, enzyme activities and intracellular metabolite concentrations,” Enzyme and Microbial Technology, vol. 38, pp. 512–520, 2006.
  300. R. Schuetz, L. Kuepfer, and U. Sauer, “Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli,” Molecular Systems Biology, vol. 3, no. 119, 2007.
  301. J. C. Crack, N. E. Le Brun, A. J. Thomson, J. Green, and A. J. Jervis, “Reactions of Nitric Oxide and Oxygen with the Regulator of Fumarate and Nitrate Reduction, a Global Transcriptional Regulator, during Anaerobic Growth of Escherichia coli,” Methods in Enzymology, vol. 437, pp. 191–209, 2008.
  302. S. Spiro and J. R. Guest, “Adaptive responses to oxygen limitation in Escherichia coli,” Trends in Biochemical Sciences, vol. 16, pp. 310–314, 1991.
  303. J. Green and J. R. Guest, “Activation of FNR-dependent transcription by iron: an in vitro switch for FNR,” FEMS Microbiology Letters, vol. 113, no. 2, pp. 219–222, 1993. View at Publisher · View at Google Scholar · View at Scopus
  304. P. J. Kiley and W. S. Reznikoff, “fnr mutants that activate gene expression in the presence of oxygen,” Journal of Bacteriology, vol. 173, no. 1, pp. 16–22, 1991. View at Scopus
  305. K. Salmon, S. P. Hung, K. Mekjian, P. Baldi, G. W. Hatfield, and R. P. Gunsalus, “Global gene expression profiling in Escherichia coli K12: The effects of oxygen availability and FNR,” The Journal of Biological Chemistry, vol. 278, no. 32, pp. 29837–29855, 2003. View at Publisher · View at Google Scholar · View at Scopus
  306. R. Williams, A. Bell, G. Sims, and S. Busby, “The role of two surface exposed loops in transcription activation by the Escherichia coli CRP and FNR proteins,” Nucleic Acids Research, vol. 19, no. 24, pp. 6705–6712, 1991. View at Scopus
  307. E. C. Ziegelhoffer and P. J. Kiley, “In vitro analysis of a constitutively active mutant form of the Escherichia coli global transcription factor FNR,” Journal of Molecular Biology, vol. 245, no. 4, pp. 351–361, 1995. View at Publisher · View at Google Scholar · View at Scopus
  308. A. I. Bell, K. L. Gaston, J. A. Cole, and S. J. W. Busby, “Cloning of binding sequences for the Escherichia coli transcription activators, FNR and CRP: location of bases involved in discrimination between FNR and CRP,” Nucleic Acids Research, vol. 17, no. 10, pp. 3865–3874, 1989. View at Scopus
  309. B. Li, H. Wing, D. Lee, H. C. Wu, and S. Busby, “Transcription activation by Escherichia coli FNR protein: similarities to, and differences from, the CRP paradigm,” Nucleic Acids Research, vol. 26, no. 9, pp. 2075–2081, 1998. View at Publisher · View at Google Scholar · View at Scopus
  310. G. Unden, S. Achebach, G. Holighaus, H. Q. Tran, B. Wackwitz, and Y. Zeuner, “Control of Fnr function of Escherichia coli by O2 and reducing conditions,” Journal of Molecular Microbiology and Biotechnology, vol. 4, no. 3, pp. 263–268, 2002. View at Scopus
  311. L. W. Marzan, K. A. Z. Siddiquee, and K. Shimizu, “Metabolic regulation of fnr gene knockout Escherichia coli under oxygen limitation,” Bioengineered Bugs, vol. 2, no. 6, pp. 331–337, 2011. View at Publisher · View at Google Scholar
  312. J. T. Greenberg and B. Demple, “A global response induced in Escherichia coli by redox-cycling agents overlaps with that induced by peroxide stress,” Journal of Bacteriology, vol. 171, no. 7, pp. 3933–3939, 1989. View at Scopus
  313. P. J. Pomposiello and B. Demple, “Redox-operated genetic switches: the SoxR and OxyR transcription factors,” Trends in Biotechnology, vol. 19, no. 3, pp. 109–114, 2001. View at Publisher · View at Google Scholar · View at Scopus
  314. P. Gaudu and B. Weiss, “SoxR, a [2Fe–2S] transcription factor, is active only in its oxidized form,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 19, pp. 10094–10098, 1996. View at Publisher · View at Google Scholar
  315. C. F. Amabile-Cuevas and B. Demple, “Molecular characterization of the soxRS genes of Escherichia coli: two genes control a superoxide stress regulon,” Nucleic Acids Research, vol. 19, no. 16, pp. 4479–4490, 1991. View at Scopus
  316. W. P. Fawcett and R. E. Wolf, “Genetic definition of the Escherichia coli zwf “soxbox”, the DNA binding site for SoxS-mediated induction of glucose 6-phosphate dehydrogenase in response to superoxide,” Journal of Bacteriology, vol. 177, no. 7, pp. 1742–1750, 1995. View at Scopus
  317. P. Gaudu and B. Weiss, “Flavodoxin mutants of Escherichia coli K-12,” Journal of Bacteriology, vol. 182, no. 7, pp. 1788–1793, 2000. View at Publisher · View at Google Scholar · View at Scopus
  318. S. I. Liochev and I. Fridovich, “Fumarase C, the stable fumarase of Escherichia coli, is controlled by the soxRS regulon,” Proceedings of the National Academy of Sciences of the United States of America, vol. 89, no. 13, pp. 5892–5896, 1992. View at Publisher · View at Google Scholar · View at Scopus
  319. M. J. Gruer and J. R. Guest, “Two genetically-distinct and differentially-regulated aconitases (AcnA and AcnB) in Escherichia coli,” Microbiology, vol. 140, no. 10, pp. 2531–2541, 1994. View at Scopus
  320. S. I. Liochev, A. Hausladen, and I. Fridovich, “Nitroreductase A is regulated as a member of the soxRS regulon of Escherichia coli,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 7, pp. 3537–3539, 1999. View at Publisher · View at Google Scholar · View at Scopus
  321. D. H. Flint, J. F. Tuminello, and M. H. Emptage, “The inactivation of Fe–S cluster containing hydro-lyases by superoxide,” The Journal of Biological Chemistry, vol. 268, no. 30, pp. 22369–22376, 1993. View at Scopus
  322. S. I. Liochev and I. Fridovich, “The role of O2. in the production of HO.: in vitro and in vivo,” Free Radical Biology and Medicine, vol. 16, no. 1, pp. 29–33, 1994. View at Publisher · View at Google Scholar · View at Scopus
  323. J. T. Greenberg, P. Monach, J. H. Chou, P. D. Josephy, and B. Demple, “Positive control of a global antioxidant defense regulon activated by superoxide-generating agents in Escherichia coli,” Proceedings of the National Academy of Sciences of the United States of America, vol. 87, no. 16, pp. 6181–6185, 1990. View at Publisher · View at Google Scholar
  324. G. Storz, L. A. Tartaglia, and B. N. Ames, “Transcriptional regulator of oxidative stress-inducible genes: direct activation by oxidation,” Science, vol. 248, no. 4952, pp. 189–194, 1990. View at Scopus
  325. M. M. Kabir and K. Shimizu, “Investigation into the effect of soxR and soxS genes deletion on the central metabolism of Escherichia coli based on gene expressions and enzyme activities,” Biochemical Engineering Journal, vol. 30, no. 1, pp. 39–47, 2006. View at Publisher · View at Google Scholar · View at Scopus
  326. R. E. Wolf, D. M. Prather, and F. M. Shea, “Growth-ratedependent alteration of 6-phosphogluconate dehydrogenase and glucose 6-phosphate dehydrogenase levels in Escherichia coli K-12,” Journal of Bacteriology, vol. 139, pp. 1093–1096, 1979.
  327. I. R. Tsaneva and B. Weiss, “soxR, a locus governing a superoxide response regulon in Escherichia coli K-12,” Journal of Bacteriology, vol. 172, pp. 4197–4205, 1990.
  328. R. L. Hanson and C. Rose, “Effects of an insertion mutation in a locus affecting pyridine nucleotide transhydrogenase (pnt::Tn5) on the growth of Escherichia coli,” Journal of Bacteriology, vol. 141, no. 1, pp. 401–404, 1980. View at Scopus
  329. J. L. Smith, “The role of gastric acid in preventing foodborne disease and how bacteria overcome acid conditions,” Journal of Food Protection, vol. 66, no. 7, pp. 1292–1303, 2003. View at Scopus
  330. M. P. Castanie-Cornet, T. A. Penfound, D. Smith, J. F. Elliott, and J. W. Foster, “Control of acid resistance in Escherichia coli,” Journal of Bacteriology, vol. 181, no. 11, pp. 3525–3535, 1999. View at Scopus
  331. J. Lin, I. S. Lee, J. Frey, J. L. Slonczewski, and J. W. Foster, “Comparative analysis of extreme acid survival in Salmonella typhimurium, Shigella flexneri, and Escherichia coli,” Journal of Bacteriology, vol. 177, no. 14, pp. 4097–4104, 1995. View at Scopus
  332. M. Rektorschek, A. Buhmann, D. Weeks et al., “Acid resistance of Helicobacter pylori depends on the UreI membrane protein and an inner membrane proton barrier,” Molecular Microbiology, vol. 36, no. 1, pp. 141–152, 2000. View at Publisher · View at Google Scholar · View at Scopus
  333. J. W. Foster, “Escherichia coli acid resistance: tales of an amateur acidophile,” Nature Reviews Microbiology, vol. 2, no. 11, pp. 898–907, 2004. View at Publisher · View at Google Scholar · View at Scopus
  334. A. Stincone, N. Daudi, A. S. Rahman et al., “A systems biology approach sheds new light on Escherichia coli acid resistance,” Nucleic Acids Research, vol. 39, no. 17, pp. 7512–7528, 2011. View at Publisher · View at Google Scholar
  335. H. T. Richard and J. W. Foster, “Acid resistance in Escherichia coli,” Advances in Applied Microbiology, vol. 52, pp. 167–186, 2003. View at Publisher · View at Google Scholar
  336. H. T. Richard and J. W. Foster, “Escherichia coli glutamate- and arginine-dependent acid resistance systems increase internal pH and reverse transmembrane potential,” Journal of Bacteriology, vol. 86, no. 18, pp. 6032–6041, 2004.
  337. S. Gong, H. Richard, and J. W. Foster, “YjdE (AdiC) is the arginine:agmatine antiporter essential for arginine-dependent acid resistance in Escherichia coli,” Journal of Bacteriology, vol. 185, no. 15, pp. 4402–4409, 2003. View at Publisher · View at Google Scholar · View at Scopus
  338. R. Iyer, C. Williams, and C. Miller, “Arginin-agmatine antiporter in extreme acid resistance in Escherichia coli,” Journal of Bacteriology, vol. 185, pp. 6556–6561, 2003.
  339. M. P. Castanié-Cornet and J. W. Foster, “Escherichia coli acid resistance: cAMP receptor protein and a 20 bp cis-acting sequence control pH and stationary phase expression of the gadA and gadBC glutamate decarboxylase genes,” Microbiology, vol. 147, pp. 709–715, 2001.
  340. M. Tanabe, K. Nishio, Y. Iko et al., “Rotation of a Complex of the γ Subunit and c Ring of Escherichia coli ATP Synthase: the Rotor and Stator are Interchangeable,” Journal of Biological Chemistry, vol. 276, pp. 15269–15274, 2001.
  341. A. J. Martin-Galiano, M. J. Ferrandiz, and A. G. de La Campa, “The promoter of the operon encoding the F0F1 ATPase of Streptococcus pneumonia is inducible by pH,” Molecular Microbiology, vol. 41, pp. 327–338, 2001.
  342. M. P. Castanié-Cornet, K. Cam, B. Bastiat, A. Cros, P. Bordes, and C. Gutierrez, “Acid stress response in Escherichia coli: mechanism of regulation of gadA transcription by RcsB and GadE,” Nucleic Acids Research, vol. 38, no. 11, Article ID gkq097, pp. 3546–3554, 2010. View at Publisher · View at Google Scholar · View at Scopus
  343. L. W. Marzan, C. M. M. Hasan, and K. Shimizu, “Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant,” Microbiology. In press. View at Publisher · View at Google Scholar
  344. Y. Eguchi, J. Itou, M. Yamane et al., “B1500, a small membrane protein, connects the two-component systems EvgS/EvgA and PhoQ/ PhoP in Escherichia coli,” Proceedings of the National Academy of Sciences, vol. 104, pp. 18712–18717, 2007.
  345. M. E. Castelli, E. García Véscovi, and F. C. Soncini, “The phosphatase activity is the target for Mg2+ regulation of the sensor protein PhoQ in Salmonella,” The Journal of Biological Chemistry, vol. 275, no. 30, pp. 22948–22954, 2000. View at Publisher · View at Google Scholar · View at Scopus
  346. N. Masuda and G. M. Church, “Regulatory network of acid resistance genes in Escherichia coli,” Molecular Microbiology, vol. 48, no. 3, pp. 699–712, 2003. View at Publisher · View at Google Scholar · View at Scopus
  347. Z. Ma, S. Gong, H. Richard, D. L. Tucker, T. Conway, and J. W. Foster, “GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12,” Molecular Microbiology, vol. 49, no. 5, pp. 1309–1320, 2003. View at Publisher · View at Google Scholar · View at Scopus
  348. D. L. Tucker, N. Tucker, Z. Ma et al., “Genes of the GadX-GadW regulon in Escherichia coli,” Journal of Bacteriology, vol. 185, no. 10, pp. 3190–3201, 2003. View at Publisher · View at Google Scholar · View at Scopus
  349. M. Sato, K. Machida, E. Arikado, H. Saito, T. Kakegawa, and H. Kobayashi, “Expression of outer membrane proteins in Escherichia coli growing at acid pH,” Applied and Environmental Microbiology, vol. 66, no. 3, pp. 943–947, 2000. View at Publisher · View at Google Scholar · View at Scopus
  350. E. Sužiedeliene, K. Sužiedelis, V. Garbenčiute, and S. Normark, “The acid-inducible asr gene in Escherichia coli: transcriptional control by the phoBR operon,” Journal of Bacteriology, vol. 181, no. 7, pp. 2084–2093, 1999. View at Scopus
  351. P. K. Bunch, F. Mat-Jan, N. Lee, and D. P. Clark, “The ldhA gene encoding the fermentative lactate dehydrogenase of Escherichia coli,” Microbiology, vol. 143, pp. 1–195, 1997. View at Scopus
  352. R. C. Hockney, “Recent developments in heterologous protein production in Escherichia coli,” Trends in Biotechnology, vol. 12, no. 11, pp. 456–463, 1994. View at Publisher · View at Google Scholar · View at Scopus
  353. F. Hoffmann, J. Weber, and U. Rinas, “Metabolic adaptation of Escherichia coli during temperature-induced recombinant protein production: 1. Readjustment of metabolic enzyme synthesis,” Biotechnology and Bioengineering, vol. 80, no. 3, pp. 313–319, 2002. View at Publisher · View at Google Scholar · View at Scopus
  354. G. P. Philippidis, T. K. Smith, and C. E. Wyman, “Study of the enzymatic hydrolysis of cellulose for production of fuel ethanol by the simultaneous saccharification and fermentation process,” Biotechnology and Bioengineering, vol. 41, no. 9, pp. 846–853, 1993. View at Scopus
  355. N. Sternberg, “Properties of a mutant of Escherichia coli defective in bacteriophage λ head formation (groE). II. The propagation of phage λ,” Journal of Molecular Biology, vol. 76, no. 1, pp. 25–44, 1973. View at Scopus
  356. W. J. Chirico, M. G. Waters, and G. Blobel, “70 K heat shock related proteins stimulate protein translocation into microsomes,” Nature, vol. 332, no. 6167, pp. 805–810, 1988. View at Scopus
  357. W. E. Taylor, D. B. Straus, and A. D. Grossman, “Transcription from a heat-inducible promoter causes heat shock regulation of the sigma subunit of E. coli RNA polymerase,” Cell, vol. 38, no. 2, pp. 371–381, 1984. View at Scopus
  358. S. A. Goff, L. P. Casson, and A. L. Goldberg, “Heat shock regulatory gene htpR influences rates of protein degradation and expression of the lon gene in Escherichia coli,” Proceedings of the National Academy of Sciences of the United States of America, vol. 81, no. 21 I, pp. 6647–6651, 1984. View at Scopus
  359. R. A. VanBogelen, V. Vaughn, and F. C. Neidhardt, “Gene for heat-inducible lysyl-tRNA synthetase (lysU) maps near cadA in Escherichia coli,” Journal of Bacteriology, vol. 153, no. 2, pp. 1066–1068, 1983. View at Scopus
  360. T. Yura, H. Nagai, and H. Mori, “Regulation of the heat-shock response in bacteria,” Annual Review of Microbiology, vol. 47, pp. 321–350, 1993. View at Scopus
  361. S. E. Chuang and F. R. Blattner, “Characterization of twenty-six new heat shock genes of Escherichia coli,” Journal of Bacteriology, vol. 175, no. 16, pp. 5242–5252, 1993. View at Scopus
  362. E. A. Craig and C. A. Gross, “Is hsp70 the cellular thermometer?” Trends in Biochemical Sciences, vol. 16, no. 4, pp. 135–140, 1991. View at Scopus
  363. J. Gamer, H. Bujard, and B. Bukau, “Physical interaction between heat shock proteins DnaK, DnaJ, and GrpE and the bacterial heat shock transcription factor σ32,” Cell, vol. 69, no. 5, pp. 833–842, 1992. View at Publisher · View at Google Scholar · View at Scopus
  364. K. Liberek, T. P. Galitski, M. Zylicz, and C. Georgopoulos, “The DnaK chaperone modulates the heat shock response of Escherichia coli by binding to the σ32 transcription factor,” Proceedings of the National Academy of Sciences of the United States of America, vol. 89, no. 8, pp. 3516–3520, 1992. View at Scopus
  365. K. Tilly, N. McKittrick, M. Zylicz, and C. Georgopoulos, “The dnaK protein modulates the heat-shock response of Escherichia coli,” Cell, vol. 34, no. 2, pp. 641–646, 1983. View at Scopus
  366. A. Mogk, C. Schlieker, K. L. Friedrich, H. J. Schönfeld, E. Vierling, and B. Bukau, “Refolding of substrates bound to small Hsps relies on a disaggregation reaction mediated most efficiently by ClpB/DnaK,” The Journal of Biological Chemistry, vol. 278, no. 33, pp. 31033–31042, 2003. View at Publisher · View at Google Scholar · View at Scopus
  367. C. Schlieker, B. Bukau, and A. Mogk, “Prevention and reversion of protein aggregation by molecular chaperones in the E. coli cytosol: implications for their applicability in biotechnology,” Journal of Biotechnology, vol. 96, no. 1, pp. 13–21, 2002. View at Publisher · View at Google Scholar · View at Scopus
  368. M. Kitagawa, M. Miyakawa, Y. Matsumura, and T. Tsuchido, “Escherichia coli small heat shock proteins, IbpA and IbpB, protect enzymes from inactivation by heat and oxidants,” European Journal of Biochemistry, vol. 269, no. 12, pp. 2907–2917, 2002. View at Publisher · View at Google Scholar · View at Scopus
  369. H. P. Sørensen and K. K. Mortensen, “Soluble expression of recombinant proteins in the cytoplasm of Escherichia coli,” Microbial Cell Factories, vol. 4, article 1, 2005. View at Publisher · View at Google Scholar · View at Scopus
  370. R. Rosen and E. Z. Ron, “Proteome analysis in the study of the bacterial heat-shock response,” Mass Spectrometry Reviews, vol. 21, no. 4, pp. 244–265, 2002. View at Publisher · View at Google Scholar · View at Scopus
  371. C. S. Richmond, J. D. Glasner, R. Mau, H. Jin, and F. R. Blattner, “Genome-wide expression profiling in Escherichia coli K-12,” Nucleic Acids Research, vol. 27, no. 19, pp. 3821–3835, 1999. View at Publisher · View at Google Scholar · View at Scopus
  372. M. Gadgil, V. Kapur, and W. S. Hu, “Transcriptional response of Escherichia coli to temperature shift,” Biotechnology Progress, vol. 21, no. 3, pp. 689–699, 2005. View at Publisher · View at Google Scholar · View at Scopus
  373. C. M. Kao, “Functional genomics technologies: creating: new paradigms for fundamental and applied biology,” Biotechnology Progress, vol. 15, pp. 304–311, 1999.
  374. C. M. Hasan and K. Shimizu, “Effect of temperature up-shift on fermentation and metabolic characteristics in view of gene expressions in Escherichia coli,” Microbial Cell Factories, vol. 7, 35 pages, 2008.
  375. C. A. Gross, D. B. Straus, J. W. Erickson, and T. Yura, “The function and regulation of heat shock proteins in Escherichia coli,” in Stress Proteins in Biology and Medicine, R. I. Morimoto, A. Tissières, and Cold Spring Harbor Laboratory, Eds., pp. 167–189, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 1990.
  376. T. Yura and K. Nakahigashi, “Regulation of the heat-shock response,” Current Opinion in Microbiology, vol. 2, no. 2, pp. 153–158, 1999. View at Publisher · View at Google Scholar · View at Scopus
  377. K. Tilly, J. Erickson, S. Sharma, and C. Georgopoulos, “Heat shock regulatory gene rpoH mRNA level increases after heat shock in Escherichia coli,” Journal of Bacteriology, vol. 168, no. 3, pp. 1155–1158, 1986.
  378. S. Skelly, T. Coleman, C. F. Fu, N. Brot, and H. Weissbach, “Correlation between the 32-kDa sigma factor levels and in vitro expression of Escherichia coli heat shock genes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 84, no. 23, pp. 8365–8369, 1987. View at Scopus
  379. A. D. Grossman, J. W. Erickson, and C. A. Gross, “The htpR gene product of E. coli is a sigma factor for heat-shock promoters,” Cell, vol. 38, no. 2, pp. 383–390, 1984. View at Scopus
  380. D. W. Cowing, J. C. A. Bardwell, E. A. Craig, C. Woolford, R. W. Hendrix, and C. A. Gross, “Consensus sequence for Escherchia coli heat shock gene promoter,” Proceedings of the National Academy of Sciences of the United States of America, vol. 82, no. 9, pp. 2679–2683, 1985. View at Publisher · View at Google Scholar
  381. K. Tilly, J. Spence, and C. Georgopoulos, “Modulation of stability of the Escherichia coli heat shock regulatory factor σ32,” Journal of Bacteriology, vol. 171, no. 3, pp. 1585–1589, 1989. View at Scopus
  382. F. Arsène, T. Tomoyasu, and B. Bukau, “The heat shock response of Escherichia coli,” International Journal of Food Microbiology, vol. 55, no. 1-3, pp. 3–9, 2000. View at Publisher · View at Google Scholar · View at Scopus
  383. D. Shin, S. Lim, Y. J. Seok, and S. Ryu, “Heat shock RNA polymerase (Eσ32) is involved in the transcription of mlc and Crucial for Induction of the Mlc Regulon by Glucose in Escherichia coli,” The Journal of Biological Chemistry, vol. 276, no. 28, pp. 25871–25875, 2001. View at Publisher · View at Google Scholar · View at Scopus
  384. K. Hosono, H. Kakuda, and S. Ichihara, “Decreasing accumulation of acetate in a rich medium by Escherichia coli on introduction of genes on a multicopy plasmid,” Bioscience, Biotechnology and Biochemistry, vol. 59, no. 2, pp. 256–261, 1995. View at Scopus
  385. S. Cho, D. Shin, E. J. Geun, S. Heu, and S. Ryu, “High-level recombinant protein production by overexpression of Mlc in Escherichia coli,” Journal of Biotechnology, vol. 119, no. 2, pp. 197–203, 2005. View at Publisher · View at Google Scholar · View at Scopus
  386. J. Plumbridge, “Control of the expression of the manXYZ operon in Escherichia coli: Mlc is a negative regulator of the mannose PTS,” Molecular Microbiology, vol. 27, no. 2, pp. 369–380, 1998. View at Publisher · View at Google Scholar · View at Scopus
  387. S. Y. Kim, T. W. Nam, D. Shin, B. M. Koo, Y. J. Seok, and S. Ryu, “Purification of Mlc and analysis of its effects on the pts expression in Escherichia coli,” The Journal of Biological Chemistry, vol. 274, no. 36, pp. 25398–25402, 1999. View at Publisher · View at Google Scholar · View at Scopus
  388. K. Kimata, T. Inada, H. Tagami, and H. Aiba, “A global repressor (Mlc) is involved in glucose induction of the ptsG gene encoding major glucose transporter in Escherichia coli,” Molecular Microbiology, vol. 29, no. 6, pp. 1509–1519, 1998. View at Publisher · View at Google Scholar · View at Scopus
  389. Y. Tanaka, K. Kimata, T. Inada, H. Tagami, and H. Aiba, “Negative regulation of the pts operon by Mlc: mechanism underlying glucose induction in Escherichia coli,” Genes to Cells, vol. 4, no. 7, pp. 391–399, 1999. View at Publisher · View at Google Scholar · View at Scopus
  390. T. W. Nam, S. H. Cho, D. Shin et al., “The Escherichia coli glucose transporter enzyme IICBGlc recruits the global repressor Mlc,” The EMBO Journal, vol. 20, no. 3, pp. 491–498, 2001. View at Publisher · View at Google Scholar · View at Scopus
  391. S. Kumari, C. M. Beatty, D. F. Browning et al., “Regulation of acetyl coenzyme A synthetase in Escherichia coli,” Journal of Bacteriology, vol. 182, no. 15, pp. 4173–4179, 2000. View at Publisher · View at Google Scholar · View at Scopus
  392. H. Lin, G. N. Bennett, and K. Y. San, “Chemostat culture characterization of Escherichia coli mutant strains metabolically engineered for aerobic succinate production: a study of the modified metabolic network based on metabolite profile, enzyme activity, and gene expression profile,” Metabolic Engineering, vol. 7, no. 5-6, pp. 337–352, 2005. View at Publisher · View at Google Scholar · View at Scopus
  393. D. F. Browning, C. M. Beatty, A. J. Wolfe, J. A. Cole, and S. J. W. Busby, “Independent regulation of the divergent Escherichia coli nrfA and acsP1 promoters by a nucleoprotein assembly at a shared regulatory region,” Molecular Microbiology, vol. 43, no. 3, pp. 687–701, 2002. View at Publisher · View at Google Scholar · View at Scopus
  394. C. M. Beatty, D. F. Browning, S. J. W. Busby, and A. J. Wolfe, “Cyclic AMP receptor protein-dependent activation of the Escherichia coliacsP2 promoter by a synergistic class III mechanism,” Journal of Bacteriology, vol. 185, no. 17, pp. 5148–5157, 2003. View at Publisher · View at Google Scholar · View at Scopus
  395. D. F. Browning, C. M. Beatty, E. A. Sanstad, K. E. Gunn, S. J. W. Busby, and A. J. Wolfe, “Modulation of CRP-dependent transcription at the Escherichia coliacsP2 promoter by nucleoprotein complexes: anti-activation by the nucleoid proteins FIS and IHF,” Molecular Microbiology, vol. 51, no. 1, pp. 241–254, 2004. View at Publisher · View at Google Scholar · View at Scopus
  396. M. Rahman and K. Shimizu, “Altered acetate metabolism and biomass production in several Escherichia coli mutants lacking rpoS-dependent metabolic pathway genes,” Molecular BioSystems, vol. 4, no. 2, pp. 160–169, 2008. View at Publisher · View at Google Scholar · View at Scopus
  397. J. Soini, C. Falschlehner, C. Mayer et al., “Transient increase of ATP as a response to temperature up-shift in Escherichia coli,” Microbial Cell Factories, vol. 4, article 9, 2005. View at Publisher · View at Google Scholar · View at Scopus
  398. F. Hoffmann and U. Rinas, “Plasmid amplification in Escherichia coli after temperature upshift is impaired by induction of recombinant protein synthesis,” Biotechnology Letters, vol. 23, no. 22, pp. 1819–1825, 2001. View at Publisher · View at Google Scholar · View at Scopus
  399. J. Weber, F. Hoffmann, and U. Rinas, “Metabolic adaptation of Escherichia coli during temperature-induced recombinant protein production: 2. Redirection of metabolic fluxes,” Biotechnology and Bioengineering, vol. 80, no. 3, pp. 320–330, 2002. View at Publisher · View at Google Scholar · View at Scopus
  400. C. Wittmann, J. Weber, E. Betiku, J. Krömer, D. Böhm, and U. Rinas, “Response of fluxome and metabolome to temperature-induced recombinant protein synthesis in Escherichia coli,” Journal of Biotechnology, vol. 132, no. 4, pp. 375–384, 2007. View at Publisher · View at Google Scholar · View at Scopus
  401. C. T. Privalle and I. Fridovich, “Induction of superoxide dismutase in Escherichia coli by heat shock,” Proceedings of the National Academy of Sciences of the United States of America, vol. 84, no. 9, pp. 2723–2726, 1987. View at Scopus
  402. L. Benov and I. Fridovich, “Superoxide dismutase protects against aerobic heat shock in Escherichia coli,” Journal of Bacteriology, vol. 177, no. 11, pp. 3344–3346, 1995. View at Scopus
  403. T. S. Gunasekera, L. N. Csonka, and O. Paliy, “Genome-wide transcriptional responses of Escherichia coli K-12 to continuous osmotic and heat stresses,” Journal of Bacteriology, vol. 190, no. 10, pp. 3712–3720, 2008. View at Publisher · View at Google Scholar · View at Scopus
  404. W. R. Farmer and J. C. Liao, “Reduction of aerobic acetate production by Escherichia coli,” Applied and Environmental Microbiology, vol. 63, no. 8, pp. 3205–3210, 1997.
  405. M. van de Walle and J. Shiloach, “Proposed mechanism of acetate accumulation in two recombinant Escherichia coli strains during high density fermentation,” Biotechnology and Bioengineering, vol. 57, no. 1, pp. 71–78, 1998. View at Publisher · View at Google Scholar
  406. J. E. Cronan and S. Subrahmanyam, “FadR, transcriptional co-ordination of metabolic expediency,” Molecular Microbiology, vol. 29, no. 4, pp. 937–943, 1998. View at Publisher · View at Google Scholar · View at Scopus
  407. C. C. DiRusso, T. L. Heimert, and A. K. Metzger, “Characterization of FadR, a global transcriptional regulator of fatty acid metabolism in Escherichia coli,” The Journal of Biological Chemistry, vol. 267, no. 12, pp. 8685–8691, 1992. View at Scopus
  408. C. C. DiRusso and T. Nyström, “The fats of Escherichia coli during infancy and old age: regulation by global regulators, alarmones and lipid intermediates,” Molecular Microbiology, vol. 27, no. 1, pp. 1–8, 1998. View at Publisher · View at Google Scholar · View at Scopus
  409. D. G. Fraenkel, “Glycolysis,” in Escherichia coli and Salmonella: Cellular and Molecular Biology, F. C. Neidhardt, Ed., AMS, Mira Digital Publishing, Washington, DC, USA, 1999.
  410. T. Morita, W. El-Kazzaz, Y. Tanaka, T. Inada, and H. Aiba, “Accumulation of glucose 6-phosphate or fructose 6-phosphate is responsible for destabilization of glucose transporter mRNA in Escherichia coli,” The Journal of Biological Chemistry, vol. 278, no. 18, pp. 15608–15614, 2003. View at Publisher · View at Google Scholar · View at Scopus
  411. G. D'Alessio and J. Josse, “Glyceraldehyde phosphate dehydrogenase, phosphoglycerate kinase, and phosphoglyceromutase of Escherichia coli. Simultaneous purification and physical properties,” The Journal of Biological Chemistry, vol. 246, no. 13, pp. 4319–4325, 1971. View at Scopus
  412. M. M. Nakano, P. Zuber, and A. L. Sonenshein, “Anaerobic regulation of Bacillus subtilis Krebs cycle genes,” Journal of Bacteriology, vol. 180, no. 13, pp. 3304–3311, 1998. View at Scopus
  413. T. Murai, M. Tokushige, J. Nagai, and H. Katsuki, “Physiological functions of NAD- and NADP-linked malic enzymes in Escherichia coli,” Biochemical and Biophysical Research Communications, vol. 43, no. 4, pp. 875–881, 1971. View at Scopus
  414. S. H. Yoon, M. J. Han, S. Y. Lee, K. J. Jeong, and J. S. Yoo, “Combined transcriptome and proteome analysis of Escherichia coli during high cell density culture,” Biotechnology and Bioengineering, vol. 81, no. 7, pp. 753–767, 2003. View at Publisher · View at Google Scholar · View at Scopus
  415. J. W. Campbell and J. E. Cronan, “Escherichia coli fadR positively regulates transcription of the fabB fatty acid biosynthetic gene,” Journal of Bacteriology, vol. 183, no. 20, pp. 5982–5990, 2001. View at Publisher · View at Google Scholar · View at Scopus
  416. A. Farewell, A. A. Diez, C. C. DiRusso, and T. Nyström, “Role of the Escherichia coli FadR regulator in stasis survival and growth phase-dependent expression of the uspA, fad, and fab genes,” Journal of Bacteriology, vol. 178, no. 22, pp. 6443–6450, 1996. View at Scopus
  417. C. N. Arnold, J. Mcelhanon, A. Lee, R. Leonhard, and D. A. Siegele, “Global analysis of Escherichia coli gene expression during the acetate-induced acid tolerace response,” Journal of Bacteriology, vol. 183, no. 7, pp. 2178–2186, 2001. View at Publisher · View at Google Scholar
  418. C. Kirkpatrick, L. M. Maurer, N. E. Oyelakin, Y. N. Yoncheva, R. Maurer, and J. L. Slonczewski, “Acetate and formate stress: opposite responses in the proteome of Escherichia coli,” Journal of Bacteriology, vol. 183, no. 21, pp. 6466–6477, 2001. View at Publisher · View at Google Scholar · View at Scopus
  419. H. R. Aronis, “Regulation of gene expression during entry into stationary phase,” in Escherichia coli and Salmonella: Cellular and Molecular Biology, F. C. Neidhardt, R. Curtiss III, J. L. Ingram et al., Eds., pp. 1497–1512, ASM Press, Washington, DC, USA, 2nd edition, 1996.
  420. R. H. Aronis, “Signal transduction and regulatory mechanisms involved in control of the σs (RpoS) subunit of RNA polymerase,” Microbiology and Molecular Biology Reviews, vol. 66, no. 3, pp. 373–395, 2002. View at Publisher · View at Google Scholar · View at Scopus
  421. H. R. AronisAronis, “Stationary phase gene regulation: what makes an Escherichia coli promoter σs-selective?” Current Opinion in Microbiology, vol. 5, no. 6, pp. 591–595, 2002. View at Publisher · View at Google Scholar
  422. S. Lacour and P. Landini, “σS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of σs-dependent genes and identification of their promoter sequences,” Journal of Bacteriology, vol. 186, no. 21, pp. 7186–7195, 2004. View at Publisher · View at Google Scholar · View at Scopus
  423. S. R. V. Vijayakumar, M. G. Kirchhof, C. L. Patten, and H. E. Schellhorn, “RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis,” Journal of Bacteriology, vol. 186, no. 24, pp. 8499–8507, 2004. View at Publisher · View at Google Scholar · View at Scopus
  424. B. Wei, S. Shin, D. LaPorte, A. J. Wolfe, and T. Romeo, “Global regulatory mutations in csrA and rpoS cause severe central carbon stress in Escherichia coli in the presence of acetate,” Journal of Bacteriology, vol. 182, no. 6, pp. 1632–1640, 2000. View at Publisher · View at Google Scholar · View at Scopus
  425. M. Rahman, M. R. Hasan, T. Oba, and K. Shimizu, “Effect of rpoS gene knockout on the metabolism of Escherichia coli during exponential growth phase and early stationary phase based on gene expressions, enzyme activities and intracellular metabolite concentrations,” Biotechnology and Bioengineering, vol. 94, no. 3, pp. 585–595, 2006. View at Publisher · View at Google Scholar · View at Scopus
  426. I. R. Booth, “Regulation of cytoplasmic pH in bacteria,” Microbiological Reviews, vol. 49, no. 4, pp. 359–378, 1985. View at Scopus
  427. H. Weber, T. Polen, J. Heuveling, V. F. Wendisch, and R. Hengge, “Genome-wide analysis of the general stress response network in Escherichia coli: σs-dependent genes, promoters, and sigma factor selectivity,” Journal of Bacteriology, vol. 187, no. 5, pp. 1591–1603, 2005. View at Publisher · View at Google Scholar · View at Scopus
  428. H. Maeda, N. Fujita, and A. Ishihama, “Competition among seven Escherichia coliσ subunits: relative binding affinities to the core RNA polymerase,” Nucleic Acids Research, vol. 28, no. 18, pp. 3497–3503, 2000. View at Scopus
  429. S. Kusano, Q. Ding, N. Fujita, and A. Ishihama, “Promoter selectivity of Escherichia coli RNA polymerase Eσ70 and Eσ38 holoenzymes: effect of DNA supercoiling,” The Journal of Biological Chemistry, vol. 271, no. 4, pp. 1998–2004, 1996. View at Scopus
  430. P. C. Loewen, I. V. Ossowski, J. Switala, and M. R. Mulvey, “KatF (σS) synthesis in Escherichia coli is subject to posttranscriptional regulation,” Journal of Bacteriology, vol. 175, no. 7, pp. 2150–2153, 1993. View at Scopus
  431. J. C. Cortay, D. Negre, A. Galinier, B. Duclos, G. Perriere, and A. J. Cozzone, “Regulation of the acetate operon in Escherichia coli: purification and functional characterization of the IclR repressor,” The EMBO Journal, vol. 10, no. 3, pp. 675–679, 1991. View at Scopus
  432. P. A. Jordan, Y. Tang, A. J. Bradbury, A. J. Thomson, and J. R. Guest, “Biochemical and spectroscopic characterization of Escherichia coli aconitases (AcnA and AcnB),” Biochemical Journal, vol. 344, no. 3, pp. 739–746, 1999. View at Publisher · View at Google Scholar · View at Scopus
  433. C. Lu, W. E. Bentley, and G. Rao, “Comparisons of oxidative stress response genes in aerobic Escherichia coli fermentations,” Biotechnology and Bioengineering, vol. 83, no. 7, pp. 864–870, 2003. View at Publisher · View at Google Scholar · View at Scopus
  434. Y. Tang, M. A. Quail, P. J. Artymiuk, J. R. Guest, and J. Green, “Escherichia coli aconitases and oxidative stress: post-transcriptional regulation of sodA expression,” Microbiology, vol. 148, no. 4, pp. 1027–1037, 2002. View at Scopus
  435. S. Varghese, Y. Tang, and J. A. Imlay, “Contrasting sensitivities of Escherichia coli aconitases A and B to oxidation and iron depletion,” Journal of Bacteriology, vol. 185, no. 1, pp. 221–230, 2003. View at Publisher · View at Google Scholar · View at Scopus
  436. G. A. Sprenger, U. Schorken, G. Sprenger, and H. Sahm, “Transaldolase B of Escherichia coli K-12: cloning of its gene, talB, and characterization of the enzyme from recombinant strains,” Journal of Bacteriology, vol. 177, no. 20, pp. 5930–5936, 1995. View at Scopus
  437. G. Zhao and M. E. Winkler, “An Escherichia coli K-12 tktA tktB mutant deficient in transketolase activity requires pyridoxine (vitamin B6) as well as the aromatic amino acids and vitamins for growth,” Journal of Bacteriology, vol. 176, no. 19, pp. 6134–6138, 1994. View at Scopus
  438. A. G. Datta and E. Racker, “Mechanism of action of transketolase. I. Properties of the crystalline yeast enzyme,” The Journal of Biological Chemistry, vol. 236, pp. 617–623, 1961. View at Scopus
  439. I. L. Jung, K. H. Phyo, and I. G. Kim, “RpoS-mediated growth-dependent expression of the Escherichia colitkt genes encoding transketolases isoenzymes,” Current Microbiology, vol. 50, no. 6, pp. 314–318, 2005. View at Publisher · View at Google Scholar · View at Scopus
  440. L. Stryer, Biochemistry, W. H. Freeman, New York, NY, USA, 1988.
  441. C. P. Tseng, C. C. Yu, H. H. Lin, C. Y. Chang, and J. T. Kuo, “Oxygen- and growth rate-dependent regulation of Escherichia coli fumarase (FumA, FumB, and FumC) activity,” Journal of Bacteriology, vol. 183, no. 2, pp. 461–467, 2001. View at Publisher · View at Google Scholar · View at Scopus
  442. A. R. Krapp, R. E. Rodriguez, H. O. Poli, D. H. Paladini, J. F. Palatnik, and N. Carrillo, “The flavoenzyme ferredoxin (flavodoxin)-NADP(H) reductase modulates NADP(H) homeostasis during the soxRS response of Escherichia coli,” Journal of Bacteriology, vol. 184, no. 5, pp. 1474–1480, 2002. View at Scopus
  443. J. E. Cronan Jr. and D. LaPorte, “Tricarboxylic acid cycle and glyoxylate bypass,” in Escherichia coli and Salmonella: Cellular and Molecular Biology, F. C. Neidhardt, R. Curtiss III, J. L. Ingraham et al., Eds., vol. 1, pp. 206–216, American Society for Microbiology, Washington, DC, USA, 2nd edition, 1996.
  444. S. Shin, S. G. Song, D. S. Lee, J. G. Pan, and C. Park, “Involvement of iclR and rpoS in the induction of acs, the gene for acetyl coenzyme A synthetase of Escherichia coli K-12,” FEMS Microbiology Letters, vol. 146, no. 1, pp. 103–108, 1997. View at Publisher · View at Google Scholar · View at Scopus
  445. C. C. DiRusso, A. K. Metzger, and T. L. Heimert, “Regulation of transcription of genes required for fatty acid transport and unsaturated fatty acid biosynthesis in Escherichia coli by FadR,” Molecular Microbiology, vol. 7, no. 2, pp. 311–322, 1993. View at Publisher · View at Google Scholar · View at Scopus
  446. H. Marrakchi, Y. M. Zhang, and C. O. Rock, “Mechanistic diversity and regulation of type II fatty acid synthesis,” Biochemical Society Transactions, vol. 30, no. 6, pp. 1050–1055, 2002. View at Publisher · View at Google Scholar · View at Scopus
  447. S. R. Maloy and W. D. Nunn, “Genetic regulation of the glyoxylate shunt in Escherichia coli K-12,” Journal of Bacteriology, vol. 149, no. 1, pp. 173–180, 1982. View at Scopus