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Transcriptional regulation of central amino acid metabolism in Lactococcus lactisLarsen, Rasmus

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References

Chapter 7

180

1. Abdelal, A. T. 1979. Arginine catabolism by microorganisms. Annu.Rev.Microbiol. 33:139-168.

2. Andersson, U. and P. Radstrom. 2002. Physiological function of the maltose operon regulator, MalR, in Lactococcus lactis. BMC.Microbiol. 2:28.

3. Araya, T., N. Ishibashi, S. Shimamura, K. Tanaka, and H. Takahashi. 1993. Genetic and molecular analysis of the rpoD gene from Lactococcus lactis. Biosci.Biotechnol.Biochem. 57:88-92.

4. Archibald, R. M. 1944. Determination of citrulline and allantoin and demonstration of citrulline in blood plasma. J.Biol.Chem. 156:121-142.

5. Arcondeguy, T., R. Jack, and M. Merrick. 2001. P(II) signal transduction proteins, pivotal players in microbial nitrogen control. Microbiol.Mol.Biol.Rev. 65:80-105.

6. Atkinson, M. R. and S. H. Fisher. 1991. Identification of genes and gene products whose exxpression is activated during nitrogen-limited growth in Bacillus subtilis. J.Bacteriol. 173:23-27.

7. Atkinson, M. R. and A. J. Ninfa. 1998. Role of the GlnK signal transduction protein in the regulation of nitrogen assimilation in Escherichia coli. Mol.Microbiol. 29:431-447.

8. Auerbach, D., S. Thaminy, M. O. Hottinger, and I. Stagljar. 2002. The post-genomic era of interactive proteomics: Facts and perspectives. Proteomics 2:611-623.

9. Babu, M. M. and S. A. Teichmann. 2003. Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res. 31:1234-1244.

10. Baerends, R. J. S., W. K. Smits, A. de Jong, L. W. Hamoen, J. Kok, and O. P. Kuipers. 2004. Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data. Genome Biol. 5:R37.

11. Barcelona-Andres, B., A. Marina, and V. Rubio. 2002. Gene structure, organization, expression, and potential regulatory mechanisms of arginine catabolism in Enterococcus faecalis. J.Bacteriol. 184:6289-6300.

12. Bardowski, J., S. D. Ehrlich, and A. Chopin. 1994. BglR protein, which belongs to the BglG family of transcriptional antiterminators, is involved in beta-glucoside utilization in Lactococcus lactis. J.Bacteriol. 176:5681-5685.

13. Bateman, A., L. Coin, R. Durbin, R. D. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, S. Moxon, E. L. L. Sonnhammer, D. J. Studholme, C. Yeats, and S. R. Eddy. 2004. The Pfam protein families database. Nucleic Acids Res. 32:D141.

14. Belitsky, B. R. 2002. Biosynthesis of amino acids of the glutamate and aspartate families, alanine and polyamines., p. 203-231. In A. L. Sonenshein, J. A. Hoch, and R. Losick (eds.), Bacillus subtilis and its closest relatives: From genes to cells. ASM Press, Washington D.C.

15. Belitsky, B. R., P. J. Janssen, and A. L. Sonenshein. 1995. Sites required for GltC-dependent regulation of Bacillus subtilis glutamate synthase expression. J.Bacteriol. 177:5686-5695.

16. Belitsky, B. R., H.-J. Kim, and A. L. Sonenshein. 2004. CcpA-dependent regulation of Bacillus subtilis glutamate dehydrogenase gene expression. J.Bacteriol. 186:3392-3398.

17. Belitsky, B. R. and A. L. Sonenshein. 1995. Mutations in GltC that increase Bacillus subtilis gltA expression. J.Bacteriol. 177:5696-5700.

References

181

18. Belitsky, B. R. and A. L. Sonenshein. 1997. Altered transcription activation specificity of a mutant form of Bacillus subtilis GltR, a LysR family member. J.Bacteriol. 179:1035-1043.

19. Belitsky, B. R. and A. L. Sonenshein. 1998. Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J.Bacteriol. 180:6298-6305.

20. Belitsky, B. R. and A. L. Sonenshein. 2004. Modulation of activity of Bacillus subtilis regulatory proteins GltC and TnrA by glutamate dehydrogenase. J.Bacteriol. 186:3399-3407.

21. Belitsky, B. R., L. V. Wray, Jr., S. H. Fisher, D. E. Bohannon, and A. L. Sonenshein. 2000. Role of TnrA in nitrogen source-dependent repression of Bacillus subtilis glutamate synthase gene expression. J.Bacteriol. 182:5939-5947.

22. Birnboim, H. C. 1983. A rapid alkaline extraction method for the isolation of plasmid DNA. Methods Enzymol. 100:243-255.

23. Blauwkamp, T. A. and A. J. Ninfa. 2002. Physiological role of the GlnK signal transduction protein of Escherichia coli: survival of nitrogen starvation. Mol.Microbiol. 46:203-214.

24. Bolotin, A., P. Wincker, S. Mauger, O. Jaillon, K. Malarme, J. Weissenbach, S. D. Ehrlich, and A. Sorokin. 2001. The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res. 11:731-753.

25. Boys, C. W., L. G. Czaplewski, S. E. Phillips, S. Baumberg, and P. G. Stockley. 1990. Crystallization of the arginine-dependent repressor/activator AhrC from Bacillus subtilis. J.Mol.Biol. 213:227-228.

26. Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein using the principle of protein-dye binding. Anal.Biochem. 72:248-254.

27. Brandenburg, J. L., L. V. Wray, Jr., L. Beier, H. Jarmer, H. H. Saxild, and S. H. Fisher. 2002. Roles of PucR, GlnR, and TnrA in regulating expression of the Bacillus subtilis ure P3 promoter. J.Bacteriol. 184:6060-6064.

28. Bringel, F., L. Frey, S. Boivin, and J. C. Hubert. 1997. Arginine biosynthesis and regulation in Lactobacillus plantarum: the carA gene and the argCJBDF cluster are divergently transcribed. J.Bacteriol. 179:2697-2706.

29. Bringel, F., H. Nicoloff, F. Arsene-Ploetze, and J. C. Hubert. 2002. Phylogenetic analysis and gene linkage of ArgR/AhrC orthologs revealed groups of synteny in Gram-positive bacteria. Sci.Aliments 22:133-142.

30. Brown, N. L., J. V. Stoyanov, S. P. Kidd, and J. L. Hobman. 2003. The MerR family of transcriptional regulators. FEMS Microbiol.Rev. 27:145-163.

31. Brown, S. W. and A. L. Sonenshein. 1996. Autogenous regulation of the Bacillus subtilis glnRA operon. J.Bacteriol. 178:2450-2454.

32. Bueno, R., G. Pahel, and B. Magasanik. 1985. Role of glnB and glnD gene products in regulation of the glnALG operon of Escherichia coli. J.Bacteriol. 164:816-822.

33. Burke, M., A. F. Merican, and D. J. Sherratt. 1994. Mutant Escherichia coli arginine repressor proteins that fail to bind L- arginine, yet retain the ability to bind their normal DNA-binding sites. Mol.Microbiol. 13:609-618.

34. Burkovski, A. 2003. Ammonium assimilation and nitrogen control in Corynebacterium glutamicum and its relatives: an example for new regulatory mechanisms in actinomycetes. FEMS Microbiol.Rev. 27:617-628.

Chapter 7

182

35. Burkovski, A. 2003. I do it my way: regulation of ammonium uptake and ammonium assimilation in Corynebacterium glutamicum. Arch.Microbiol. 179:83-88.

36. Calogero, S., R. Gardan, P. Glaser, J. Schweizer, G. Rapoport, and M. Debarbouille. 1994. RocR, a novel regulatory protein controlling arginine utilization in Bacillus subtilis, belongs to the NtrC/NifA family of transcriptional activators. J.Bacteriol. 176:1234-1241.

37. Cases, I., V. de Lorenzo, and C. A. Ouzounis. 2003. Transcription regulation and environmental adaptation in bacteria. Trends Microbiol. 11:248-253.

38. Casiano-Colon, A. and R. E. Marquis. 1988. Role of the arginine deiminase system in protecting oral bacteria and an enzymatic basis for acid tolerance. Appl.Environ.Microbiol. 54:1318-1324.

39. Chambellon, E. and M. Yvon. 2003. CodY-regulated aminotransferases AraT and BcaT play a major role in the growth of Lactococcus lactis in milk by regulating the intracellular pool of amino acids. Appl.Environ.Microbiol. 69:3061-3068.

40. Champomier Verges, M. C., M. Zuñiga, F. Morel-Deville, G. Perez-Martinez, M. Zagorec, and S. D. Ehrlich. 1999. Relationships between arginine degradation, pH and survival in Lactobacillus sakei. FEMS Microbiol.Lett. 180:297-304.

41. Charlier, D. 2004. Arginine regulation in Thermotoga neapolitana and Thermotoga maritima. Biochem.Soc.Trans. 32:310-313.

42. Charlier, D., M. Roovers, F. Van Vliet, A. Boyen, R. Cunin, Y. Nakamura, N. Glansdorff, and A. Pierard. 1992. Arginine regulon of Escherichia coli K-12. A study of repressor- operator interactions and of in vitro binding affinities versus in vivo repression. J.Mol.Biol. 226:367-386.

43. Chen, S. H., A. F. Merican, and D. J. Sherratt. 1997. DNA binding of Escherichia coli arginine repressor mutants altered in oligomeric state. Mol.Microbiol. 24:1143-1156.

44. Chopin, A. 1993. Organization and regulation of genes for amino acid biosynthesis in lactic acid bacteria. FEMS Microbiol.Rev. 12:21-37.

45. Christensen, J. E., E. G. Dudley, J. A. Pederson, and J. L. Steele. 1999. Peptidases and amino acid catabolism in lactic acid bacteria. Antonie van Leeuwenhoek 76:217-246.

46. Cotter, P. D. and C. Hill. 2003. Surviving the acid test: responses of Gram-positive bacteria to low pH. Microbiol.Mol.Biol.Rev. 67:429-453.

47. Coutts, G., G. Thomas, D. Blakey, and M. Merrick. 2002. Membrane sequestration of the signal transduction protein GlnK by the ammonium transporter AmtB. EMBO J. 21:536-545.

48. Crooks, G. E., G. Hon, J.-M. Chandonia, and S. E. Brenner. 2004. WebLogo: a sequence logo generator. Genome Res. 14:1188-1190.

49. Crow, V. L. and T. D. Thomas. 1982. Arginine metabolism in lactic streptococci. J.Bacteriol. 150:1024-1032.

50. Cruz Ramos, H. C., P. Glaser, L. V. Wray, Jr., and S. H. Fisher. 1997. The Bacillus subtilis ureABC operon. J.Bacteriol. 179:3371-3373.

51. Cunin, R., T. Eckhardt, J. Piette, A. Boyen, A. Pierard, and N. Glansdorff. 1983. Molecular basis for modulated regulation of gene expression in the arginine regulon of Escherichia coli K-12. Nucleic Acids Res. 11:5007-5019.

References

183

52. Cunin, R., N. Glansdorff, A. Pierard, and V. Stalon. 1986. Biosynthesis and metabolism of arginine in bacteria. Microbiol.Rev. 50:314-352.

53. Czaplewski, L. G., A. K. North, M. C. Smith, S. Baumberg, and P. G. Stockley. 1992. Purification and initial characterization of AhrC: the regulator of arginine metabolism genes in Bacillus subtilis. Mol.Microbiol. 6:267-275.

54. De Angelis, M., L. Mariotti, J. Rossi, M. Servili, P. F. Fox, G. Rollan, and M. Gobbetti. 2002. Arginine catabolism by sourdough lactic acid bacteria: purification and characterization of the arginine deiminase pathway enzymes from Lactobacillus sanfranciscensis CB1. Appl.Environ.Microbiol. 68:6193-6201.

55. de Vos, W. M. and G. F. M. Simons. 1994. Gene cloning and expression systems in lactococci., p. 52-105. In M. J. Gasson and W. M. de Vos (eds.), Genetics and biotechnology of lactic acid bacteria.

56. Dean, D. R., Hoch, and A. I. Aronson. 1977. Alteration of the Bacillus subtilis glutamine synthetase results in overexpression of the enzyme. J.Bacteriol. 131:981-987.

57. Degnan, B. A., M. C. Fontaine, A. H. Doebereiner, J. J. Lee, P. Mastroeni, G. Dougan, J. A. Goodacre, and M. A. Kehoe. 2000. Characterization of an isogenic mutant of Streptococcus pyogenes Manfredo lacking the ability to make streptococcal acid glycoprotein. Infect.Immun. 68:2441-2448.

58. Degnan, B. A., J. M. Palmer, T. Robson, C. E. Jones, M. Fischer, M. Glanville, G. D. Mellor, A. G. Diamond, M. A. Kehoe, and J. A. Goodacre. 1998. Inhibition of human peripheral blood mononuclear cell proliferation by Streptococcus pyogenes cell extracts is associated with arginine deiminase activity. Infect.Immun. 66:3050-3058.

59. Deguchi, Y. and T. Morishita. 1992. Nutritional requirements in multiple auxotrophic lactic acid bacteria: genetic lesions affecting amino acid biosynthesis pathways in Lactococcus lactis, Enterococcus faecium and Pediococcus acidilactici. Biosci.Biotechnol.Biochem. 56:913-918.

60. Delorme, C., S. D. Ehrlich, and P. Renault. 1999. Regulation of expression of the Lactococcus lactis histidine operon. J.Bacteriol. 181:2026-2037.

61. Delorme, C., J. J. Godon, S. D. Ehrlich, and P. Renault. 1993. Gene inactivation in Lactococcus lactis: histidine biosynthesis. J.Bacteriol. 175:4391-4399.

62. den Hengst, C. D., P. Curley, R. Larsen, G. Buist, A. Nauta, D. van Sinderen, O. P. Kuipers, and J. Kok. 2005. Probing direct interactions between CodY and the oppD promoter of Lactococcus lactis. J.Bacteriol. 187:512-521.

63. Dennis, C. C., N. M. Glykos, M. R. Parsons, and S. E. Phillips. 2002. The structure of AhrC, the arginine repressor/activator protein from Bacillus subtilis. Acta Crystallogr.D.Biol.Crystallogr. 58:421-430.

64. Detsch, C. and J. Stulke. 2003. Ammonium utilization in Bacillus subtilis: transport and regulatory functions of NrgA and NrgB. Microbiology 149:3289-3297.

65. Deuel, T. F. and S. Prusiner. 1974. Regulation of glutamine synthetase from Bacillus subtilis by divalent cations, feedback inhibitors, and L-glutamine. J.Biol.Chem. 249:257-264.

66. Deuel, T. F. and E. R. Stadtman. 1970. Some kinetic properties of Bacillus subtilis glutamine synthetase. Nature (London) 323:304-309.

67. Dimova, D., P. Weigel, M. Takahashi, F. Marc, G. D. Van Duyne, and V. Sakanyan. 2000. Thermostability, oligomerization and DNA-binding properties of the regulatory protein

Chapter 7

184

ArgR from the hyperthermophilic bacterium Thermotoga neapolitana. Mol.Gen.Genet. 263:119-130.

68. Dion, M., D. Charlier, H. Wang, D. Gigot, A. Savchenko, J. N. Hallet, N. Glansdorff, and V. Sakanyan. 1997. The highly thermostable arginine repressor of Bacillus stearothermophilus: gene cloning and repressor-operator interactions. Mol.Microbiol. 25:385-398.

69. Dodd, I. B. and J. B. Egan. 1990. Improved detection of helix-turn-helix DNA-binding motifs in protein sequences. Nucleic Acids Res. 18:5019-5026.

70. Dong, Y., Y. Y. Chen, J. A. Snyder, and R. A. Burne. 2002. Isolation and molecular analysis of the gene cluster for the arginine deiminase system from Streptococcus gordonii DL1. Appl.Environ.Microbiol. 68:5549-5553.

71. Dong, Y., Y.-Y. M. Chen, and R. A. Burne. 2004. Control of expression of the arginine deiminase operon of Streptococcus gordonii by CcpA and Flp. J.Bacteriol. 186:2511-2514.

72. Driessen, A. J., B. Poolman, R. Kiewiet, and W. Konings. 1987. Arginine transport in Streptococcus lactis is catalyzed by a cationic exchanger. Proc.Natl.Acad.Sci.U.S.A 84:6093-6097.

73. Ebbole, D. J. and H. Zalkin. 1989. Interaction of a putative repressor protein with an extended control region of the Bacillus subtilis pur operon. J.Biol.Chem. 264:3553-3561.

74. Erlandson, K. A., J.-H. Park, W. E. Khal, H.-H. Kao, P. Basaran, S. Brydges, and C. A. Batt. 2000. Dissolution of xylose metabolism in Lactococcus lactis. Appl.Environ.Microbiol. 66:3974-3980.

75. Faires, N., S. Tobisch, S. Bachem, I. Martin-Verstraete, M. Hecker, and J. Stulke. 1999. The catabolite control protein CcpA controls ammonium assimilation in Bacillus subtilis. J.Mol.Microbiol.Biotechnol. 1:141-148.

76. Fernández, C. and G. Wider. 2003. TROSY in NMR studies of the structure and function of large biological macromolecules. Curr.Opin.Struct.Biol. 13:570-580.

77. Fernandez, M., M. Kleerebezem, O. P. Kuipers, R. J. Siezen, and R. van Kranenburg. 2002. Regulation of the metC-cysK operon, involved in sulfur metabolism in Lactococcus lactis. J.Bacteriol. 184:82-90.

78. Ferson, A. E., L. V. Wray, Jr., and S. H. Fisher. 1996. Expression of the Bacillus subtilis gabP gene is regulated independently in response to nitrogen and amino acid availability. Mol.Microbiol. 22:693-701.

79. Fierro-Monti, I. P., S. J. Reid, and D. R. Woods. 1992. Differential expression of a Clostridium acetobutylicum antisense RNA: implications for regulation of glutamine synthetase. J.Bacteriol. 174:7642-7647.

80. Fink, D., D. Falke, W. Wohlleben, and A. Engels. 1999. Nitrogen metabolism in Streptomyces coelicolor A3(2): modification of glutamine synthetase I by adenylylation. Microbiology 145:2313-2322.

81. Fink, D., N. Weissschuh, J. Reuther, W. Wohlleben, and A. Engels. 2002. Two transcriptional regulators GlnR and GlnRII are involved in regulation of nitrogen metabolism in Streptomyces coelicolor A3(2). Mol.Microbiol. 46:331-347.

82. Fisher, S. H. 1999. Regulation of nitrogen metabolism in Bacillus subtilis: vive la difference! Mol.Microbiol. 32:223-232.

References

185

83. Fisher, S. H., J. L. Brandenburg, and L. V. Wray, Jr. 2002. Mutations in Bacillus subtilis glutamine synthetase that block its interaction with transcription factor TnrA. Mol.Microbiol. 45:627-635.

84. Fisher, S. H. and M. Debarbouille. 2002. Nitrogen source utilization and its regulation., p. 181-191. In A. L. Sonenshein, J. A. Hoch, and R. Losick (eds.), Bacillus subtilis and its closest relatives: from genes to cells. ASM Press, Washington, D.C.

85. Fisher, S. H. and A. L. Sonenshein. 1984. Bacillus subtilis glutamine synthetase mutants pleiotropically altered in glucose catabolite repression. J.Bacteriol. 157:612-621.

86. Fisher, S. H. and L. V. Wray, Jr. 2002. Bacillus subtilis 168 contains two differentially regulated genes encoding L-asparaginase. J.Bacteriol. 184:2148-2154.

87. Fisher, S. H. and L. V. Wray, Jr. 2002. Mutations in the Bacillus subtilis glnRA operon that cause nitrogen source-dependent defects in regulation of TnrA activity. J.Bacteriol. 184:4636-4639.

88. Galimand, M., M. Gamper, A. Zimmermann, and D. Haas. 1991. Positive FNR-like control of anaerobic arginine degradation and nitrate respiration in Pseudomonas aeruginosa. J.Bacteriol. 173:1598-1606.

89. Gamper, M., B. Ganter, M. R. Polito, and D. Haas. 1992. RNA processing modulates the expression of the arcDABC operon in Pseudomonas aeruginosa. J.Mol.Biol. 226:943-957.

90. Gamper, M. and D. Haas. 1993. Processing of the Pseudomonas arcDABC mRNA requires functional RNase E in Escherichia coli. Gene 129:119-122.

91. Gardan, R., G. Rapoport, and M. Debarbouille. 1995. Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis. J.Mol.Biol. 249:843-856.

92. Gardan, R., G. Rapoport, and M. Debarbouille. 1997. Role of the transcriptional activator RocR in the arginine-degradation pathway of Bacillus subtilis. Mol.Microbiol. 24:825-837.

93. Gasson, M. J. 1983. Plasmid complements of Streptococcus lactis NCDO 712 and other lactic streptococci after protoplast-induced curing. J.Bacteriol. 154:1-9.

94. Glansdorff, N. 1996. Biosynthesis of arginine and polyamines., p. 408-433. In F. C. Neidhardt, R. Curtiss, III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (eds.), Escherichia coli and Salmonella: cellular and molecular biology. American Society for Microbiology, Washington, D.C.

95. Godon, J. J., C. Delorme, J. Bardowski, M. C. Chopin, S. D. Ehrlich, and P. Renault. 1993. Gene inactivation in Lactococcus lactis: branched-chain amino acid biosynthesis. J.Bacteriol. 175:4383-4390.

96. Gostick, D. O., H. G. Griffin, C. A. Shearman, C. Scott, J. Green, M. J. Gasson, and J. R. Guest. 1999. Two operons that encode FNR-like proteins in Lactococcus lactis. Mol.Microbiol. 31:1523-1535.

97. Goupil-Feuillerat, N., M. Cocaign-Bousquet, J. J. Godon, S. D. Ehrlich, and P. Renault. 1997. Dual role of alpha-acetolactate decarboxylase in Lactococcus lactis subsp. lactis. J.Bacteriol. 179:6285-6293.

98. Grandori, R., T. A. Lavoie, M. Pflumm, G. Tian, H. Niersbach, W. K. Maas, R. Fairman, and J. Carey. 1995. The DNA-binding domain of the hexameric arginine repressor. J.Mol.Biol. 254:150-162.

Chapter 7

186

99. Griswold, A., Y.-Y. M. Chen, J. A. Snyder, and R. A. Burne. 2004. Characterization of the arginine deiminase operon of Streptococcus rattus FA-1. Appl.Environ.Microbiol. 70:1321-1327.

100. Guédon, E., E. Jamet, and P. Renault. 2002. Gene regulation in Lactococcus lactis: the gap between predicted and and characterized regulators. Antonie Van Leeuwenhoek 82:93-112.

101. Guédon, E., P. Serror, S. D. Ehrlich, P. Renault, and C. Delorme. 2001. Pleiotropic transcriptional repressor CodY senses the intracellular pool of branched-chain amino acids in Lactococcus lactis. Mol.Microbiol. 40:1227-1239.

102. Gustafson, J., A. Strassle, H. Hachler, F. H. Kayser, and B. Berger-Bachi. 1994. The femC locus of Staphylococcus aureus required for methicillin resistance includes the glutamine synthetase operon. J.Bacteriol. 176:1460-1467.

103. Gutowski, J. C. and H. J. Schreier. 1992. Interaction of the Bacillus subtilis glnRA repressor with operator and promoter sequences in vivo. J.Bacteriol. 174:671-681.

104. Haas, D., B. W. Holloway, A. Schambock, and T. Leisinger. 1977. The genetic organization of arginine biosynthesis in Pseudomonas aeruginosa. Mol.Gen.Genet. 154:7-22.

105. Haas, D., V. Kurer, and T. Leisinger. 1972. N-acetylglutamate synthetase of Pseudomonas aeruginosa. An assay in vitro and feedback inhibition by arginine. Eur.J.Biochem. 31:290-295.

106. Haldenwang, W. G. 1995. The sigma factors of Bacillus subtilis. Microbiol.Rev. 59:1-30.

107. Hamoen, L. W., A. F. van Werkhoven, J. J. Bijlsma, D. Dubnau, and G. Venema. 1998. The competence transcription factor of Bacillus subtilis recognizes short A/T-rich sequences arranged in a unique, flexible pattern along the DNA helix. Genes Dev. 12:1539-1550.

108. Hanson, T. E., K. Forchhammer, N. Tandeau de Marsac, and J. C. Meeks. 1998. Characterization of the glnB gene product of Nostoc punctiforme strain ATCC 29133: glnB or the PII protein may be essential. Microbiology 144:1537-1547.

109. Hashim, S., D. H. Kwon, A. Abdelal, and C. D. Lu. 2004. The arginine regulatory protein mediates repression by arginine of the operons encoding glutamate synthase and anabolic glutamate dehydrogenase in Pseudomonas aeruginosa. J.Bacteriol. 186:3848-3854.

110. Herrgard, M. J., M. W. Covert, and B. O. Palsson. 2004. Reconstruction of microbial transcriptional regulatory networks. Curr.Opin.Biotechnol. 15:70-77.

111. Hesketh, A., D. Fink, B. Gust, H. U. Rexer, B. Scheel, K. Chater, W. Wohlleben, and A. Engels. 2002. The GlnD and GlnK homologues of Streptomyces coelicolor A3(2) are functionally dissimilar to their nitrogen regulatory system counterparts from enteric bacteria. Mol.Microbiol. 46:319-330.

112. Hindle, Z., R. Callis, S. Dowden, B. A. Rudd, and S. Baumberg. 1994. Cloning and expression in Escherichia coli of a Streptomyces coelicolor A3(2) argCJB gene cluster. Microbiology 140:311-320.

113. Hodgman, T. C., H. Griffiths, and D. K. Summers. 1998. Nucleoprotein architecture and ColE1 dimer resolution: a hypothesis. Mol.Microbiol. 29:545-558.

114. Holo, H. and I. F. Nes. 1995. Transformation of Lactococcus by electroporation. Methods Mol.Biol. 47:195-199.

References

187

115. Holtham, C. A., K. Jumel, C. M. Miller, S. E. Harding, S. Baumberg, and P. G. Stockley. 1999. Probing activation of the prokaryotic arginine transcriptional regulator using chimeric proteins. J.Mol.Biol. 289:707-727.

116. Huffman, J. L. and R. G. Brennan. 2002. Prokaryotic transcription regulators: more than just the helix-turn-helix. Curr.Opin.Struct.Biol. 12:98-106.

117. Israelsen, H., S. M. Madsen, A. Vrang, E. B. Hansen, and E. Johansen. 1995. Cloning and partial characterization of regulated promoters from Lactococcus lactis Tn917-lacZ integrants with the new promoter probe vector, pAK80. Appl.Environ.Microbiol. 61:2540-2547.

118. Jakoby, M., R. Kramer, and A. Burkovski. 1999. Nitrogen regulation in Corynebacterium glutamicum: isolation of genes involved and biochemical characterization of corresponding proteins. FEMS Microbiol.Lett. 173:303-310.

119. Jakoby, M., L. Nolden, J. Meier-Wagner, R. Kramer, and A. Burkovski. 2000. AmtR, a global repressor in the nitrogen regulation system of Corynebacterium glutamicum. Mol.Microbiol. 37:964-977.

120. Jakoby, M., M. Tesch, H. Sahm, R. Krämer, and A. Burkovski. 1997. Isolation of the Corynebacterium glutamicum glnA gene encoding glutamine synthetase I. FEMS Microbiol.Lett. 154:81-88.

121. Janssen, P. J., W. A. Jones, D. T. Jones, and D. R. Woods. 1988. Molecular analysis and regulation of the glnA gene of the gram-positive anaerobe Clostridium acetobutylicum. J.Bacteriol. 170:400-408.

122. Jarmer, H. 2002. PhD. thesis. Techical University of Denmark. Regulation of transcription in Bacillus subtilis.

123. Javelle, A., E. Severi, J. Thornton, and M. Merrick. 2004. Ammonium sensing in Escherichia coli. J.Biol.Chem. 279:8530-8538.

124. Johansen, E. and A. Kibenich. 1992. Isolation and characterization of IS1165, an insertion sequence of Leuconostoc mesenteroides subsp. cremoris and other lactic acid bacteria. Plasmid 27:200-206.

125. Juillard, V., D. Le Bars, E. R. Kunji, W. N. Konings, J. C. Gripon, and J. Richard. 1995. Oligopeptides are the main source of nitrogen for Lactococcus lactis during growth in milk. Appl.Environ.Microbiol. 61:3024-3030.

126. Karaivanova, I. M., P. Weigel, M. Takahashi, C. Fort, A. Versavaud, G. Van Duyne, D. Charlier, J. N. Hallet, N. Glansdorff, and V. Sakanyan. 1999. Mutational analysis of the thermostable arginine repressor from Bacillus stearothermophilus: dissecting residues involved in DNA binding properties. J.Mol.Biol. 291:843-855.

127. Khunajakr, N., C. Q. Liu, P. Charoenchai, and N. W. Dunn. 1999. A plasmid-encoded two-component system involved in copper-inducible transcription in Lactococcus lactis. Gene 229:229-235.

128. Kilstrup, M. and J. Martinussen. 1998. A transcriptional activator, homologous to the Bacillus subtilis PurR repressor, is required for expression of purine biosynthetic genes in Lactococcus lactis. J.Bacteriol. 180:3907-3916.

129. Klaenhammer, T. R., E. Altermann, F. Arigoni, A. Bolotin, F. Breidt, J. Broadbent, R. Cano, S. Chaillou, J. Deutscher, M. J. Gasson, M. van de Guchte, J. Guzzo, A. Hartke, T. Hawkins, P. Hols, R. Hutkins, M. Kleerebezem, J. Kok, O. P. Kuipers, M. W. Lubbers, E. Maguin, L. L. McKay, D. Mills, A. Nauta, R. Overbeek, H. Pel, D. Pridmore, M. Saier, D. van Sinderen, A. Sorokin, J. Steele, D. O'Sullivan, W. M. de Vos, B. Weimer,

Chapter 7

188

M. Zagorec, and R. Siezen. 2002. Discovering lactic acid bacteria by genomics. Antonie van Leeuwenhoek 82:29-58.

130. Kleerebezem, M. and J. Hugenholtz. 2003. Metabolic pathway engineering in lactic acid bacteria. Curr.Opin.Biotechnol. 14:232-237.

131. Klingel, U., C. M. Miller, A. K. North, P. G. Stockley, and S. Baumberg. 1995. A binding site for activation by the Bacillus subtilis AhrC protein, a repressor/activator of arginine metabolism. Mol.Gen.Genet. 248:329-340.

132. Kok, J. 1990. Genetics of the proteolytic system of lactic acid bacteria. FEMS Microbiol.Rev. 7:15-42.

133. Konings, W. N. 2002. The cell membrane and the struggle for life of lactic acid bacteria. Antonie van Leeuwenhoek 82:3-27.

134. Kuipers, O. P., M. M. Beerthuyzen, P. G. G. de Ruyter, E. J. Luesink, and W. M. de Vos. 1995. Autoregulation of nisin biosynthesis in Lactococcus lactis by signal transduction. J.Biol.Chem. 270:27299-27304.

135. Kuipers, O. P., A. de Jong, R. J. S. Baerends, S. A. F. T. van Hijum, A. L. Zomer, H. A. Karsens, C. D. den Hengst, N. E. Kramer, G. Buist, and J. Kok. 2002. Transcriptome analysis and related databases of Lactococcus lactis. Antonie van Leeuwenhoek 82:113-122.

136. Kuipers, O. P., P. G. de Ruyter, M. Kleerebezem, and W. M. de Vos. 1998. Quorum sensing controlled gene expression in lactic acid bacteria. Biotechnol. 64:15-21.

137. Kunji, E. R., I. Mierau, A. Hagting, B. Poolman, and W. N. Konings. 1996. The proteolytic systems of lactic acid bacteria. Antonie van Leeuwenhoek 70:187-221.

138. Kunji, E. R., I. Mierau, B. Poolman, W. N. Konings, G. Venema, and J. Kok. 1996. Fate of peptides in peptidase mutants of Lactococcus lactis. Mol.Microbiol. 21:123-131.

139. Kunji, E. R., E. J. Smid, R. Plapp, B. Poolman, and W. N. Konings. 1993. Di-tripeptides and oligopeptides are taken up via distict transport mechanisms in Lactococcus lactis. J.Bacteriol. 175:2052-2059.

140. Kunji, E. R. S., T. Ubbink, A. Matin, B. Poolman, and W. N. Konings. 1993. Physiological responses of Lactococcus lactis ML3 to alternating conditions of growth and starvation. Arch.Microbiol. 159:372-379.

141. Kunst, F. e. al. 1997. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390:249-256.

142. Larsen, R., G. Buist, O. P. Kuipers, and J. Kok. 2004. ArgR and AhrC are both required for regulation of arginine metabolism in Lactococcus lactis. J.Bacteriol. 186:1147-1157.

143. Law, B. A., E. Sezgin, and M. E. Sharpe. 1976. Amino acid nutrition of some commercial cheese starters in relation to their growth in peptone-supplemented whey media. J.Dairy Res. 43:291-300.

144. Lazazzera, B. A., I. G. Kurtser, R. S. McQuade, and A. D. Grossman. 1999. An autoregulatory circuit affecting peptide signaling in Bacillus subtilis. J.Bacteriol. 181:5193-5200.

145. Leenhouts, K., A. Bolhuis, G. Venema, and J. Kok. 1998. Construction of a food-grade multiple-copy integration system for Lactococcus lactis. Appl.Microbiol.Biotechnol. 49:417-423.

References

189

146. Leenhouts, K., G. Buist, A. Bolhuis, A. ten Berge, J. Kiel, I. Mierau, M. Dabrowska, G. Venema, and J. Kok. 1996. A general system for generating unlabelled gene replacements in bacterial chromosomes. Mol.Gen.Genet. 253:217-224.

147. Li, H., V. Rhodius, C. Gross, and E. D. Siggia. 2002. Identification of the binding sites of regulatory proteins in bacterial genomes. Proc.Natl.Acad.Sci.U.S.A 99:11772-11777.

148. Lim, D. B., J. D. Oppenheim, T. Eckhardt, and W. K. Maas. 1987. Nucleotide sequence of the argR gene of Escherichia coli K-12 and isolation of its product, the arginine repressor. Proc.Natl.Acad.Sci.U.S.A 84:6697-6701.

149. Lin, J., M. P. Smith, K. C. Chapin, H. S. Baik, G. N. Bennett, and J. W. Foster. 1996. Mechanisms of acid resistance in enterohemorrhagic Escherichia coli. Appl.Environ.Microbiol. 62:3094-3100.

150. Long, A. D., H. J. Mangalam, B. Y. Chan, L. Tolleri, G. W. Hatfield, and P. Baldi. 2001. Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in E.coli K12. J.Biol.Chem. 276:19937-19944.

151. Lu, C. D., J. E. Houghton, and A. T. Abdelal. 1992. Characterization of the arginine repressor from Salmonella typhimurium and its interactions with the carAB operator. J.Mol.Biol. 225:11-24.

152. Lu, C. D., H. Winteler, A. Abdelal, and D. Haas. 1999. The ArgR regulatory protein, a helper to the anaerobic regulator ANR during transcriptional activation of the arcD promoter in Pseudomonas aeruginosa. J.Bacteriol. 181:2459-2464.

153. Lu, C. D., Z. Yang, and W. Li. 2004. Transcriptome analysis of the ArgR regulon in Pseudomonas aeruginosa. J.Bacteriol. 186:3855-3861.

154. Ludovice, M., J. F. Martin, P. Carrachas, and P. Liras. 1992. Characterization of the Streptomyces clavuligerus argC gene encoding N-acetylglutamyl-phosphate reductase: expression in Streptomyces lividans and effect on clavulanic acid production. J.Bacteriol. 174:4606-4613.

155. Luesink, E. J., R. E. Herpen, B. P. Grossiord, O. P. Kuipers, and W. M. de Vos. 1998. Transcriptional activation of the glycolytic las operon and catabolite repression of the gal operon in Lactococcus lactis are mediated by the catabolite control protein CcpA. Mol.Microbiol. 30:789-798.

156. Luesink, E. J., J. D. Marugg, O. P. Kuipers, and W. M. de Vos. 1999. Characterization of the divergent sacBK and sacAR operons, involved in sucrose utilization by Lactococcus lactis. J.Bacteriol. 181:1924-1926.

157. Maas, W. K. 1994. The arginine repressor of Escherichia coli. Microbiol.Rev. 58:631-640.

158. Madsen, S. M., B. Albrechtsen, E. B. Hansen, and H. Israelsen. 1996. Cloning and transcriptional analysis of two threonine biosynthetic genes from Lactococcus lactis MG1614. J.Bacteriol. 178:3689-3694.

159. Magasanik, B. 1996. Regulation of nitrogen utilization., p. 1344-1356. In F. C. Neidhardt, R. Curtiss, III, J. L. Ingraham, E. C. C. Lin, B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (eds.), Escherichia coli and Salmonella: Cellular and Molecular Biology. American Society for Microbiology, Washington, D.C.

160. Maghnouj, A., A. A. Abu-Bakr, S. Baumberg, V. Stalon, and W. C. Vander. 2000. Regulation of anaerobic arginine catabolism in Bacillus licheniformis by a protein of the Crp/Fnr family. FEMS Microbiol.Lett. 191:227-234.

Chapter 7

190

161. Maguin, E., P. Duwat, T. Hege, D. Ehrlich, and A. Gruss. 1992. New thermosensitive plasmid for gram-positive bacteria. J.Bacteriol. 174:5633-5638.

162. Maguin, E., H. Prevost, S. D. Ehrlich, and A. Gruss. 1996. Efficient insertional mutagenesis in lactococci and other gram-positive bacteria. J.Bacteriol. 178:931-935.

163. Makarova, K. S., A. A. Mironov, and M. S. Gelfand. 2001. Conservation of the binding site for the arginine repressor in all bacterial lineages. Genome Biol. 2:RESEARCH0013.

164. Martinussen, J. and K. Hammer. 1998. The carB gene encoding the large subunit of carbamoylphosphate synthetase from Lactococcus lactis is transcribed monocistronically. J.Bacteriol. 180:4380-4386.

165. Martinussen, J., J. Schallert, B. Andersen, and K. Hammer. 2001. The pyrimidine operon pyrRPB-carA from Lactococcus lactis. J.Bacteriol. 183:2785-2794.

166. McAdams, H. H., B. Srinivasan, and A. P. Arkin. 2004. The evolution of genetic regulatory systems in bacteria. Nature Rev. 5:169-178.

167. Mechold, U., M. Cashel, K. Steiner, D. Gentry, and H. Malke. 1996. Functional analysis of a relA/spoT gene homolog from Streptococcus equisimilis. J.Bacteriol. 178:1401-1411.

168. Mechold, U. and H. Malke. 1997. Characterization of the stringent and relaxed responses of Streptococcus equisimilis. J.Bacteriol. 179:2658-2667.

169. Meier-Wagner, J., L. Nolden, M. Jakoby, R. Siewe, R. Krämer, and A. Burkovski. 2001. Multiplicity of ammonium uptake systems in Corynebacterium glutamicum: role of Amt and AmtB. Microbiology 147:135-143.

170. Meletzus, D., P. Rudnick, N. Doetsch, A. Green, and C. Kennedy. 1998. Characterization of the glnK-amtB operon of Azotobacter vinelandii. J.Bacteriol. 180:3260-3264.

171. Merrick, M. J. and R. A. Edwards. 1995. Nitrogen control in bacteria. Microbiol.Rev. 59:604-622.

172. Mierau, I., A. J. Haandrikman, O. Velterop, P. S. Tan, K. L. Leenhouts, W. N. Konings, G. Venema, and J. Kok. 1994. Tripeptidase gene (pepT) of Lactococcus lactis: molecular cloning and nucleotide sequencing of pepT and construction of a chromosomal deletion mutant. J.Bacteriol. 176:2854-2861.

173. Miller, C. M., S. Baumberg, and P. G. Stockley. 1997. Operator interactions by the Bacillus subtilis arginine repressor/activator, AhrC: novel positioning and DNA-mediated assembly of a transcriptional activator at catabolic sites. Mol.Microbiol. 26:37-48.

174. Mills, O. E. and T. D. Thomas. 1981. Nitrogen sources for growth of lactic streptococci in milk. N.Z.J.Dairy Sci.Technol. 15:43-55.

175. Mirel, D. B., W. F. Estacio, M. Mathieu, E. Olmsted, J. Ramirez, and L. M. Marquez-Magana. 2000. Environmental regulation of Bacillus subtilis sigma(D)-dependent gene expression. J.Bacteriol. 182:3055-3062.

176. Mironov, A. A., E. V. Koonin, M. A. Roytberg, and M. S. Gelfand. 1999. Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res. 27:2981-2989.

177. Molle, V., Y. Nakaura, R. P. Shivers, H. Yamaguchi, R. Losick, Y. Fujita, and A. L. Sonenshein. 2003. Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J.Bacteriol. 185:1911-1922.

References

191

178. Montel, M. C. and M. C. Champomier. 1987. Arginine catabolism in Lactobacillus sake isolated from meat. Appl.Environ.Microbiol. 53:2683-2685.

179. Morin, A., N. Huysveld, F. Braun, D. Dimova, V. Sakanyan, and D. Charlier. 2003. Hyperthermophilic Thermotoga arginine repressor binding to full-length cognate and heterologous arginine operators and to half-site targets. J.Mol.Biol. 332:537-553.

180. Nakano, M. M., T. Hoffmann, Y. Zhu, and D. Jahn. 1998. Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE. J.Bacteriol. 180:5344-5350.

181. Nakano, M. M., F. Yang, P. Hardin, and P. Zuber. 1995. Nitrogen regulation of nasA and the nasB operon, which encode genes required for nitrate assimilation in Bacillus subtilis. J.Bacteriol. 177:573-579.

182. Nakano, Y. and K. Kimura. 1991. Purification and characterization of a repressor for the Bacillus cereus glnRA operon. J.Biochem. 109:223-228.

183. Ni, J., V. Sakanyan, D. Charlier, N. Glansdorff, and G. D. Van Duyne. 1999. Structure of the arginine repressor from Bacillus stearothermophilus. Nat.Struct.Biol. 6:427-432.

184. Nicoloff, H., F. Arsene-Ploetze, C. Malandain, M. Kleerebezem, and F. Bringel. 2004. Two arginine repressors regulate arginine biosynthesis in Lactobacillus plantarum. J.Bacteriol. 186:6059-6069.

185. Nicoloff, H., J. C. Hubert, and F. Bringel. 2000. In Lactobacillus plantarum, carbamoyl phosphate is synthesized by two carbamoyl-phosphate synthetases (CPS): carbon dioxide differentiates the arginine-repressed from the pyrimidine-regulated CPS. J.Bacteriol. 182:3416-3422.

186. Niersbach, H., R. Lin, G. D. Van Duyne, and W. K. Maas. 1998. A superrepressor mutant of the arginine repressor with a correctly predicted alteration of ligand binding specificity. J.Mol.Biol. 279:753-760.

187. Nilsson, D. and E. Johansen. 1994. A conserved sequence in tRNA and rRNA promoters of Lactococcus lactis. Biochim.Biophys.Acta 1219:141-144.

188. North, A. K., M. C. Smith, and S. Baumberg. 1989. Nucleotide sequence of a Bacillus subtilis arginine regulatory gene and homology of its product to the Escherichia coli arginine repressor. Gene 80:29-38.

189. Nygaard, P., S. M. Bested, K. A. Andersen, and H. H. Saxild. 2000. Bacillus subtilis guanine deaminase is encoded by the yknA gene and is induced during growth with purines as the nitrogen source. Microbiology 146:3061-3069.

190. O'Connell-Motherway, M., G. F. Fitzgerald, and D. van Sinderen. 1997. Cloning and sequence analysis of putative histidine protein kinases isolated from Lactococcus lactis MG1363. Appl.Environ.Microbiol. 63:2454-2459.

191. O'Connell-Motherway, M., D. van Sinderen, F. Morel-Deville, G. F. Fitzgerald, S. D. Ehrlich, and P. Morel. 2000. Six putative two-component regulatory systems isolated from Lactococcus lactis subsp. cremoris MG1363. Microbiology 146:935-947.

192. O'Sullivan, E. and S. Condon. 1997. Intracellular pH is a major factor in the induction of tolerance to acid and other stresses in Lactococcus lactis. Appl.Environ.Microbiol. 63:4210-4215.

193. Park, S. M., C. D. Lu, and A. T. Abdelal. 1997. Cloning and characterization of argR, a gene that participates in regulation of arginine biosynthesis and catabolism in Pseudomonas aeruginosa PAO1. J.Bacteriol. 179:5300-5308.

Chapter 7

192

194. Park, S. M., C. D. Lu, and A. T. Abdelal. 1997. Purification and characterization of an arginine regulatory protein, ArgR, from Pseudomonas aeruginosa and its interactions with the control regions for the car, argF, and aru operons. J.Bacteriol. 179:5309-5317.

195. Pesole, G., C. Gissi, C. Lanave, and C. Saccone. 1995. Glutamine synthetase gene evolution in bacteria. Mol.Biol.Evol. 12:189-197.

196. Petranovic, D., E. Guédon, B. Sperandio, C. Delorme, D. Ehrlich, and P. Renault. 2004. Intracellular effectors regulating the activity of the Lactococcus lactis CodY pleiotropic transcription regulator. Mol.Microbiol. 53:613-621.

197. Poolman, B., A. J. Driessen, and W. N. Konings. 1987. Regulation of arginine-ornithine exchange and the arginine deiminase pathway in Streptococcus lactis. J.Bacteriol. 169:5597-5604.

198. Rallu, F., A. Gruss, S. D. Ehrlich, and E. Maguin. 2000. Acid- and multistress-resistant mutants of Lactococcus lactis: identification of intracellular stress signals. Mol.Microbiol. 35:517-528.

199. Rallu, F., A. Gruss, and E. Maguin. 1996. Lactococcus lactis and stress. Antonie van Leeuwenhoek 70:243-251.

200. Ratnayake-Lecamwasam, M., P. Serror, K.-W. Wong, and A. L. Sonenshein. 2001. Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels. Genes Dev. 15:1093-1103.

201. Ravn, P., J. Arnau, S. M. Madsen, A. Vrang, and H. Israelsen. 2000. The development of TnNuc and its use for the isolation of novel secretion signals in Lactococcus lactis. Gene 242:347-356.

202. Raya, R., J. Bardowski, P. S. Andersen, S. D. Ehrlich, and A. Chopin. 1998. Multiple transcriptional control of the Lactococcus lactis trp operon. J.Bacteriol. 180:3174-3180.

203. Reiter, B. and J. D. Oram. 1962. Nutritional studies on cheese starters. J.Dairy Res. 29:63.

204. Reitzer, L. 2003. Nitrogen assimilation and global regulation in Escherichia coli. Annu.Rev.Microbiol. 57:155-176.

205. Renault, P., C. Gaillardin, and H. Heslot. 1989. Product of the Lactococcus lactis gene required for malolactic fermentation is homologous to a family of positive regulators. J.Bacteriol. 171:3108-3114.

206. Renault, P., J. J. Godon, N. Goupil, C. Delorme, G. Corthier, and S. D. Ehrlich. 1995. Metabolic operons in Lactococci. Dev.Biol.Stand. 85:431-441.

207. Robichon, D., M. Arnaud, R. Gardan, Z. Pragai, M. O'Reilly, G. Rapoport, and M. Debarbouille. 2000. Expression of a new operon from Bacillus subtilis, ykzB-ykoL, under the control of the TnrA and PhoP-phoR global regulators. J.Bacteriol. 182:1226-1231.

208. Rodriguez-Garcia, A., F. A. de la, R. Perez-Redondo, J. F. Martin, and P. Liras. 2000. Characterization and expression of the arginine biosynthesis gene cluster of Streptomyces clavuligerus. J.Mol.Microbiol.Biotechnol. 2:543-550.

209. Rodriguez-Garcia, A., M. Ludovice, J. F. Martin, and P. Liras. 1997. Arginine boxes and the argR gene in Streptomyces clavuligerus: evidence for a clear regulation of the arginine pathway. Mol.Microbiol. 25:219-228.

References

193

210. Romeo, Y., D. Obis, J. Bouvier, A. Guillot, A. Fourcans, I. Bouvier, C. Gutierrez, and M. Y. Mistou. 2003. Osmoregulation in Lactococcus lactis: BusR, a transcriptional repressor of the glycine betaine uptake system BusA. Mol.Microbiol. 47:1135-1147.

211. Sakanyan, V., P. Petrosyan, M. Lecocq, A. Boyen, C. Legrain, M. Demarez, J. N. Hallet, and N. Glansdorff. 1996. Genes and enzymes of the acetyl cycle of arginine biosynthesis in Corynebacterium glutamicum: enzyme evolution in the early steps of the arginine pathway. Microbiology 142:99-108.

212. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor laboratory Press, Cold Spring Harbor, N.Y.

213. Sanders, J. W., K. Leenhouts, J. Burghoorn, J. R. Brands, G. Venema, and J. Kok. 1998. A chloride-inducible acid resistance mechanism in Lactococcus lactis and its regulation. Mol.Microbiol. 27:299-310.

214. Sanders, J. W., G. Venema, J. Kok, and K. Leenhouts. 1998. Identification of a sodium chloride-regulated promoter in Lactococcus lactis by single-copy chromosomal fusion with a reporter gene. Mol.Gen.Genet. 257:681-685.

215. Savchenko, A., D. Charlier, M. Dion, P. Weigel, J. N. Hallet, C. Holtham, S. Baumberg, N. Glansdorff, and V. Sakanyan. 1996. The arginine operon of Bacillus stearothermophilus: characterization of the control region and its interaction with the heterologous B. subtilis arginine repressor. Mol.Gen.Genet. 252:69-78.

216. Savchenko, A., P. Weigel, D. Dimova, M. Lecocq, and V. Sakanyan. 1998. The Bacillus stearothermophilus argCJBD operon harbours a strong promoter as evaluated in Escherichia coli cells. Gene 212:167-177.

217. Schneider, T. D. and R. M. Stephens. 1990. Sequence Logos: a new way to display consensus sequences. Nucleic Acids Res. 18:6097-6100.

218. Schreier, H. J., S. W. Brown, K. D. Hirschi, J. F. Nomellini, and A. L. Sonenshein. 1989. Regulation of Bacillus subtilis glutamine synthetase gene expression by the product of the glnR gene. J.Mol.Biol. 210:51-63.

219. Schreier, H. J., S. M. Caruso, and K. C. Maier. 2000. Control of Bacillus subtilis glutamine synthetase expression by glnR from Staphylococcus aureus. Curr.Microbiol. 41:425-429.

220. Schreier, H. J. and C. A. Rostkowski. 1995. Bacillus subtilis glnR mutants defective in regulation. Gene 161:51-56.

221. Schreier, H. J., C. A. Rostkowski, J. F. Nomellini, and K. D. Hirschi. 1991. Identification of DNA sequences involved in regulating Bacillus subtilis glnRA expression by the nitrogen source. J.Mol.Biol. 220:241-253.

222. Schreier, H. J. and A. L. Sonenshein. 1986. Altered regulation of the glnA gene in glutamine synthetase mutants of Bacillus subtilis. J.Bacteriol. 167:35-43.

223. Schultz, A. C., P. Nygaard, and H. H. Saxild. 2001. Functional analysis of 14 genes that constitute the purine catabolic pathway in Bacillus subtilis and evidence for a novel regulon controlled by the PucR transcription activator. J.Bacteriol. 183:3293-3302.

224. Scott, C., J. R. Guest, and J. Green. 2000. Characterization of the Lactococcus lactis transcription factor FlpA and demonstration of an in vitro switch. Mol.Microbiol. 35:1383-1393.

225. Serror, P. and A. L. Sonenshein. 1996. CodY is required for nutritional repression of Bacillus subtilis genetic comptetence. J.Bacteriol. 178:5910-5915.

Chapter 7

194

226. Shivers, R. P. and A. L. Sonenshein. 2004. Activation of the Bacillus subtilis global regulator CodY by direct interaction with branched-chain amino acids. Mol.Microbiol. 53:599-611.

227. Simon, D. and A. Chopin. 1988. Construction of a vector plasmid family and its use for molecular cloning in Streptococcus lactis. Biochimie 70:559-566.

228. Slack, F. J., P. Serror, E. Joyce, and A. L. Sonenshein. 1995. A gene required for nutritional repression of the Bacillus subtilis dipeptide permease operon. Mol.Microbiol. 15:689-702.

229. Smith, M. C., L. Czaplewski, A. K. North, S. Baumberg, and P. G. Stockley. 1989. Sequences required for regulation of arginine biosynthesis promoters are conserved between Bacillus subtilis and Escherichia coli. Mol.Microbiol. 3:23-28.

230. Smith, M. C., A. Mountain, and S. Baumberg. 1986. Cloning in Escherichia coli of a Bacillus subtilis arginine repressor gene through its ability to confer structural stability on a fragment carrying genes of arginine biosynthesis. Mol.Gen.Genet. 205:176-182.

231. Song, H., H. Wang, D. Gigot, D. Dimova, V. Sakanyan, N. Glansdorff, and D. Charlier. 2002. Transcription regulation in thermophilic bacteria: high resolution contact probing of Bacillus stearothermophilus and Thermotoga neapolitana arginine repressor-operator interactions. J.Mol.Biol. 315:255-274.

232. Soutar, A. and S. Baumberg. 1996. Implication of a repression system, homologous to those of other bacteria, in the control of arginine biosynthesis genes in Streptomyces coelicolor. Mol.Gen.Genet. 251:245-251.

233. Stirling, C. J., G. Szatmari, G. Stewart, M. C. Smith, and D. J. Sherratt. 1988. The arginine repressor is essential for plasmid-stabilizing site- specific recombination at the ColE1 cer locus. EMBO J. 7:4389-4395.

234. Strösser, J., A. Lüdke, S. Schaffer, R. Krämer, and A. Burkovski. 2004. Regulation of GlnK activity: modification, membrane sequestration and proteolysis as regulatory principles in the network of nitrogen control in Corynebacterium glutamicum. Mol.Microbiol. 54:132-147.

235. Stuart, M. R., L. S. Chou, and B. C. Weimer. 1999. Influence of carbohydrate starvation and arginine on culturability and amino acid utilization of Lactococcus lactis subsp. lactis. Appl.Environ.Microbiol. 65:665-673.

236. Sunnerhagen, M., M. Nilges, G. Otting, and J. Carey. 1997. Solution structure of the DNA-binding domain and model for the complex of multifunctional hexameric arginine repressor with DNA. Nat.Struct.Biol. 4:819-826.

237. Takahashi, N. and T. Yamada. 1999. Acid-induced acid tolerance and acidogenicity of non-mutans streptococci. Oral.Microbiol.Immunol. 14:43-48.

238. Terzaghi, B. E. and W. E. Sandine. 1975. Improved medium for lactic streptococci and their bacteriophages. Appl.Microbiol. 29:807-813.

239. Thijs, G., M. Lescot, K. Marchal, S. Rombauts, B. de Moor, Rouze.P., and Y. Moreau. 2001. A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics. 17:1113-1122.

240. Thijs, G., K. Marchal, M. Lescot, S. Rombauts, B. de Moor, Rouze.P., and Y. Moreau. 2002. A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J.Comput.Biol. 9:447-464.

References

195

241. Thomas, G., G. Coutts, and M. Merrick. 2000. The glnKamtB operon: a conserved gene pair in prokaryotes. Trends Genet. 16:11-14.

242. Thompson, J. D., D. G. Higgins, and T. J. Gilson. 2003. Clustral W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4674-4680.

243. Tian, G., D. Lim, J. Carey, and W. K. Maas. 1992. Binding of the arginine repressor of Escherichia coli K12 to its operator sites. J.Mol.Biol. 226:387-397.

244. Tian, G., D. Lim, J. D. Oppenheim, and W. K. Maas. 1994. Explanation for different types of regulation of arginine biosynthesis in Escherichia coli B and Escherichia coli K12 caused by a difference between their arginine repressors. J.Mol.Biol. 235:221-230.

245. Tian, G. and W. K. Maas. 1994. Mutational analysis of the arginine repressor of Escherichia coli. Mol.Microbiol. 13:599-608.

246. Titgemeyer, F. and W. Hillen. 2002. Global control of sugar metabolism: a gram-positive solution. Antonie van Leeuwenhoek 82:59-71.

247. Van de Casteele, M., M. Demarez, C. Legrain, N. Glansdorff, and A. Pierard. 1990. Pathways of arginine biosynthesis in extreme thermophilic archaea and eubacteria. J.Gen.Microbiol. 136:1177-1183.

248. van de, G. M., D. S. Ehrlich, and A. Chopin. 1998. tRNATrp as a key element of antitermination in the Lactococcus lactis trp operon. Mol.Microbiol. 29:61-74.

249. van der Meer, J. R., J. Polman, M. M. Beerthuyzen, R. J. Siezen, O. P. Kuipers, and W. M. de Vos. 1993. Characterization of the Lactococcus lactis nisin A operon genes nisP, encoding a subtilisin-like serine protease involved in precursor processing, and nisR, encoding a regulatory protein involved in nisin biosynthesis. J.Bacteriol. 175:2578-2588.

250. Van Duyne, G. D., G. Ghosh, W. K. Maas, and P. B. Sigler. 1996. Structure of the oligomerization and L-arginine binding domain of the arginine repressor of Escherichia coli. J.Mol.Biol. 256:377-391.

251. van Hijum, S. A. F. T., J. Garcia de la Nava, O. Trelles, J. Kok, and O. P. Kuipers. 2003. MicroPrep: a cDNA microarray data pre-processing framework. Appl.Bioinformatics 2:241-244.

252. van Rooijen, R. J., M. J. Gasson, and W. M. de Vos. 1992. Characterization of the Lactococcus lactis lactose operon promoter: contribution of flanking sequences and LacR repressor to promoter activity. J.Bacteriol. 174:2273-2280.

253. Varmanen, P., K. Savijoki, S. Avall, A. Palva, and S. Tynkkynen. 2000. X-prolyl dipeptidyl aminopeptidase gene (pepX) is part of the glnRA operon in Lactobacillus rhamnosus. J.Bacteriol. 182:146-154.

254. Wacker, I., H. Ludwig, I. Reif, H.-M. Blencke, C. Detsch, and J. Stulke. 2003. The regulatory link between carbon and nitrogen metabolism in Bacillus subtilis: regulation of the gltAB operon by the catabolite control protein CcpA. Microbiology 149:3001-3009.

255. Winteler, H. V. and D. Haas. 1996. The homologous regulators ANR of Pseudomonas aeruginosa and FNR of Escherichia coli have overlapping but distinct specificities for anaerobically inducible promoters. Microbiology 142:685-693.

256. Woolfolk, C. A. and E. R. Stadtman. 1967. Regulation of glutamine synthetase. 3. Cumulative feedback inhibition of glutamine synthetase from Escherichia coli. Arch.Biochem.Biophys. 118:736-755.

Chapter 7

196

257. Wray, L. V., Jr., M. R. Atkinson, and S. H. Fisher. 1991. Identification and cloning of the glnR locus, which is required for transcription of the glnA gene in Streptomyces coelicolor A3(2). J.Bacteriol. 173:7351-7360.

258. Wray, L. V., Jr., A. E. Ferson, and S. H. Fisher. 1997. Expression of the Bacillus subtilis ureABC operon is controlled by multiple regulatory factors including CodY, GlnR, TnrA, and Spo0H. J.Bacteriol. 179:5494-5501.

259. Wray, L. V., Jr., A. E. Ferson, K. Rohrer, and S. H. Fisher. 1996. TnrA, a transcription factor required for global nitrogen regulation in Bacillus subtilis. Proc.Natl.Acad.Sci.U.S.A 93:8841-8845.

260. Wray, L. V., Jr. and S. H. Fisher. 1993. The Streptomyces coelicolor glnR gene encodes a protein similar to other bacterial response regulators. Gene 130:145-150.

261. Wray, L. V., Jr., J. M. Zalieckas, A. E. Ferson, and S. H. Fisher. 1998. Mutational analysis of the TnrA-binding sites in the Bacillus subtilis nrgAB and gabP promoter regions. J.Bacteriol. 180:2943-2949.

262. Wray, L. V., Jr., J. M. Zalieckas, and S. H. Fisher. 2000. Purification and in vitro activities of the Bacillus subtilis TnrA transcription factor. J.Mol.Biol. 300:29-40.

263. Wray, L. V., Jr., J. M. Zalieckas, and S. H. Fisher. 2001. Bacillus subtilis glutamine synthetase controls gene expression through a protein-protein interaction with transcription factor TnrA. Cell 107:427-435.

264. Xie, Y., L. Chou, A. Cutler, and B. Weimer. 2004. DNA macroarray profiling of Lactococcus lactis subsp. lactis IL1403 gene expression during environmental stresses. J.Bacteriol. 70:6738-6747.

265. Xu, Y., Z. Liang, C. Legrain, H. J. Ruger, and N. Glansdorff. 2000. Evolution of arginine biosynthesis in the bacterial domain: novel gene-enzyme relationships from psychrophilic Moritella strains (Vibrionaceae) and evolutionary significance of N-alpha-acetyl ornithinase. J.Bacteriol. 182:1609-1615.

266. Xu, Y., Y. Sun, N. Huysveld, D. Gigot, N. Glansdorff, and D. Charlier. 2003. Regulation of arginine biosynthesis in the psychropiezophilic bacterium Moritella profunda: in vivo repressibility and in vitro repressor-operator contact probing. J.Mol.Biol. 326:353-369.

267. Yanisch-Perron, C., J. Vieira, and J. Messing. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103-119.

268. Yanofsky, C. 1981. Attenuation in the control of expression of bacterial operons. Nature 289:751-758.

269. Yoshida, K., H. Yamaguchi, M. Kinehara, Y. Ohki, Y. Nakaura, and Y. Fujita. 2003. Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box. Mol.Microbiol. 49:157-165.

270. Zhu, H., M. Bilgin, and M. Snyder. 2003. Proteomics. Annu.Rev.Biochem. 72:783-812.

271. Zuñiga, M., M. Champomier-Verges, M. Zagorec, and G. Perez-Martinez. 1998. Structural and functional analysis of the gene cluster encoding the enzymes of the arginine deiminase pathway of Lactobacillus sake. J.Bacteriol. 180:4154-4159.

272. Zuñiga, M., M. C. Miralles Md, and G. Perez-Martinez. 2002. The product of arcR, the sixth gene of the arc operon of Lactobacillus sakei, is essential for expression of the arginine deiminase pathway. Appl.Environ.Microbiol. 68:6051-6058.

References

197

273. Zuñiga, M., G. Perez, and F. Gonzalez-Candelas. 2002. Evolution of arginine deiminase (ADI) pathway genes. Mol.Phylogenet.Evol. 25:429-444.

Chapter 7

198