Regulation of expression of bacterial genes in the absence of active cell growth

Russian Journal of Genetics

Volumn 41, Issue 9, 2005, Pages 968-984

  Khmel, I A ^a  

^a INSTITUTE OF MOLECULAR GENETICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 26444598544     PISSN: 10227954     EISSN: 16083369     Source Type: Journal    
DOI: 10.1007/s11177-005-0188-4     Document Type: Review

References (139)

1. Kolter, R., Siegele, D.A., and Tormo, A., The Stationary Phase of the Bacterial Life Cycle, Annu. Rev. Microbiol., 1993, vol. 47, pp. 855-874.
2. Hengge-Aronis, R., Regulation of Gene Expression during Entry into Stationary Phase, Escherichia coli and Salmonella: Cellular and Molecular Biology, Neidhardt, F.C., Curtiss, R. III, Ingraham, J.L., et al., Eds., Washington: Am. Soc. Microbiol., 1996, pp. 1497-1512.
3. Huisman, G.V., Siegele, D.A., Zambrano, M.M., and Kolter, R., Morphological and Physiological Changes during Stationary Phase, in Escherichia coli and Salmonella: Cellular and Molecular Biology, Neidhardt, F.C., Curtiss, R. III, Ingraham, J.L., et al., Eds., Washington: Am. Soc. Microbiol., 1996, pp. 1672-1682.
4. Velkov, V.V., How Environmental Factors Regulate Mutagenesis and Gene Transfer in Microorganisms, J. Biosci., 1999, vol. 24, pp. 529-559.
5. Nilsson, L., Oliver, J.D., and Kjelleberg, S., Resuscitation of Vibrio vulnificus from the Viable but Nonculturable State, J. Bacteriol., 1991, vol. 173, pp. 5054-5059.
6. Duncan, S., Glover, L.A., Killham, K., and Prosser, J.I., Luminescence-Based Detection of Activity of Starved and Viable but Nonculturable Bacteria, Appl. Environ. Microbiol., 1994, vol. 60, pp. 1308-1316.
7. Nystrom, T., Nonculturable Bacteria: Programmed Survival Forms or Cells at Death's Door?, BioEssays, 2003, vol. 25, pp. 204-211.
8. Groat, R.G., Schultz, E., Zychlinski, E., et al., Starvation Proteins in Escherichia coli: Kinetics of Synthesis and Role in Starvation Survival, J. Bacteriol., 1986, vol. 168, pp. 486-493.
9. Matin, A., The Molecular Basis of Carbon Starvation-Induced General Resistance in Escherichia coli, Mol. Microbiol., 1991, vol. 5, pp. 3-10.
10. S-Regulated Gene in Escherichia coli Which Is Required for Stationary-Phase Resistance to Ethanol, J. Bacteriol., 1998, vol. 180, pp. 6140-6147.
11. Kvint, K., Nachin, L., Diez, A., and Nystrom, T., The Bacterial Universal Stress Protein: Function and Regulation, Curr. Opin. Microbiol., 2003, vol. 6, pp. 140-145.
12. S (RpoS) Subunit of RNA Polymerase, Microbiol. Mol. Biol. Rev., 2002, vol. 66, pp. 373-395.
13. Ishihama, A., Modulation of the Nucleoid, the Transcription Apparatus, and the Translation Machinery in Bacteria for Stationary Phase Survival, Genes Cells, 1999, vol. 4, pp. 135-143.
14. Ishihama, A., Functional Modulation of Escherichia coli RNA Polymerase, Annu. Rev. Microbiol., 2000, vol. 54, pp. 499-518.
15. S, J. Bacteriol, 1991, vol. 173, pp. 4474-4481.
16. Makinoshima, H., Aizawa, S., Hayashi, H., et al., Growth Phase-Coupled Alterations in Cell Structure and Function of Escherichia coli, J. Bacteriol., 2003, vol. 185, pp. 1338-1345.
17. Deutscher, M.P., Degradation of Stable RNA in Bacteria, J. Biol. Chem., 2003, vol. 278, pp. 45 041-45 044.
18. Drlika, K. and Rouviere-Janiv, J., Histone-Like Proteins of Bacteria, Microbiol. Rev., 1987, vol. 51, pp. 301-319.
19. Pettijohn, D., Histone-Like Proteins and Bacterial Chromosome Structure, J. Biol. Chem., 1988, vol. 263, pp. 12 793-12 796.
20. Schmid, M.B., More Than Just "Histone-Like" Proteins, Cell (Cambridge, Mass.), 1990, vol. 63, pp. 451-453.
21. Williams, R. and Rimsky, S., Molecular Aspects of the Escherichia coli Nucleoid Protein H-NS, a Central Controller of Gene Regulatory Networks, FEMS Microbiol. Lett., 1997, vol. 156, pp. 175-185.
22. Dorman, C.J. and Deighan, P., Regulation of Gene Expression by Histone-Like Proteins in Bacteria, Curr. Opin. Genet. Dev., 2003, vol. 13, pp. 179-184.
23. Tendeng, C. and Bertin, P.N., H-NS in Gram-Negative Bacteria: A Family of Multifaceted Proteins, Trends Microbiol., 2003, vol. 11, pp. 511-518.
24. Brinkman, A.B., Ettema, T.J.G., de Vos, W.M., and van der Oost, J., The Lrp Family of Transcriptional Regulators, Mol. Microbiol., 2003, vol. 48, pp. 287-294.
25. Rimsky, S., Structure of the Histone-Like Protein H-NS and Its Role in Regulation and Genome Superstructure, Curr. Opin. Microbiol., 2004, vol. 7, pp. 109-114.
26. Balke, V.L. and Gralla, J.D., Changes in the Linking Number of Supercoiled DNA Accompany Growth Transitions in Escherichia coli, J. Bacteriol., 1987, vol. 169, pp. 4499-4506.
27. Almiron, M., Link, A.J., Furlong, D., and Kolter, R., A Novel DNA-Binding Protein with Regulatory and Protective Roles in Starved Escherichia coli, Genes Dev., 1992, vol. 6, pp. 2646-2654.
28. Azam, T.A. and Ishihama, A., Twelve Species of the Nucleoid-Associated Protein from Escherichia coli: Sequence Recognition Specificity and DNA Binding Affinity, J. Biol. Chem., 1999, vol. 274, pp. 33 105-33 113.
29. Azam, A.T., Iwata, A., Nishimura, A., et al., Growth Phase-Dependent Variation in Protein Composition of the Escherichia coli Nucleoid, J. Bacteriol., 1999, vol. 181, pp. 6361-6370.
30. Frenkiel-Krispin, D., Ben-Avraham, I., Englander, J., et al., Nucleoid Restructuring in Stationary-State Bacteria, Mol. Microbiol., 2004, vol. 51, pp. 395-405.
31. Nair, S. and Finkel, S.E., Dps Protects Cells against Multiple Stresses during Stationary Phase, J. Bacteriol., 2004, vol. 186, pp. 4192-4198.
32. Nikiforov, V.G., Structural and Functional Studies of RNA Polymerase (1962-2002), Mol. Biol. (Moscow), 2002, vol. 36, pp. 197-207.
33. Dove, S.L. and Hochschild, A., Conversion of the ω Subunit of Escherichia coli RNA Polymerase into a Transcriptional Activator or an Activation Target, Genes Dev., 1998, vol. 12, pp. 745-754.
34. Ghosh, P., Ishihama, A., and Chatterji, D., Escherichia coli RNA Polymerase Subunit ω and Its Terminal Domain Bind Full-length β to Facilitate Incorporation into α2β Subassembly, Eur. J. Biochem., 2001, vol. 268, pp. 4621-4627.
35. Helmann, J.D. and Chamberlin, M.J., Structure and Function of Bacterial σ Factors, Annu. Rev. Biochem., 1988, vol. 57, pp. 839-872.
36. 70 Family: Sequence Conservation and Evolutionary Relationship, J. Bacteriol., 1992, vol. 174, pp. 3843-3849.
37. Maeda, H., Fugita, N., and Ishihama, A., Competition among Seven Escherichia coli σ-Subunits: Relative Binding Affinities to the Core RNA Polymerase, Nucleic Acids Res., 2000, vol. 28, pp. 3497-3503.
38. FecI, of Escherichia coli: Promoter Selectivity and Intracellular Levels, J. Bacteriol., 2000, vol. 182, pp. 1181-1184.
39. Reitzer, L. and Schneider, B.L., Metabolic Context and Possible Physiological Themes of σ(54)-Dependent Genes in Escherichia coli, Microbiol. Mol. Biol. Rev., 2001, vol. 65, pp. 422-444.
40. 38, J. Bacteriol., 1995, vol. 177, pp. 6832-6835.
41. Jishage, M., Iwata, A., Ueda, S., and Ishihama, A., Regulation of RNA Polymerase σ Subunit Synthesis in Escherichia coli: Intracellular Levels of Four Species of σ Subunit under Various Growth Conditions, J. Bacteriol., 1996, vol. 178, pp. 5447-5451.
42. E Factor in Escherichia coli, Curr. Opin. Microbiol., 2004, vol. 7, pp. 157-162.
43. Santos, J.M., Freire, P., Vicente, M., and Arraiano, C.M., The Stationary-Phase Morphogene bolA from Escherichia coli Is Induced by Stress during Early Stages of Growth, Mol. Microbiol., 1999, vol. 32, pp. 789-798.
44. S and Requires Activation by cAMP-CRP, J. Mol. Biol., 1998, vol. 276, pp. 339-353.
45. S in Stationary Phase, Mol. Microbiol., 1994, vol. 13, pp. 265-272.
46. Fomenko, D., Veselovskii, A., and Khmel, I., Regulation of Microcin C51 Operon Expression: The Role of Global Regulators of Transcription, Res. Microbiol., 2001, vol. 152, pp. 469-479.
47. 70 Subunits of RNA Polymerase and the CRP Protein in the Regulation of Microcin C51 Operon Expression, Rus. J. Genet., 2004, vol. 40, no. 11, pp. 1199-1209.
48. Moreno, F., Gonzalez-Pastor, J.E., Baquero, M.-R., and Bravo, D., The Regulation of Microcin B, C, and J Operons, Biochimie, 2002, vol. 84, pp. 521-529.
49. Bouvier, J., Gordia, S., Kampmann, G., et al., Interplay between Global Regulators of Escherichia coli: Effect of RpoS, H-NS and Lrp on Transcription of the Gene osmC, Mol. Microbiol., 1998, vol. 28, pp. 971-980.
50. 70 RNA Polymerase Holoenzymes in Growth Phase Regulation of the Escherichia coli osmE Promoter, Mol. Microbiol., 2000, vol. 35, pp. 845-853.
51. Conter, A., Menchon, C., and Gutierrez, C., Role of DNA Supercoiling and RpoS σ Factor in the Osmotic and Growth Phase-Dependent Induction of the Gene osmE of Escherichia coli K12, J. Mol. Biol., 1997, vol. 273, pp. 75-83.
52. Colland, F., Barth, M., Hengge-Aronis, R., and Kolb, A., σ Factor Selectivity of Escherichia coli RNA Polymerase: Role for CRP, IHF, and Lrp Transcription Factors, EMBO J., 2000, vol. 19, pp. 3028-3037.
53. Ruiz, N., Petersen, C.N., and Silhavy, T.J., RpoS-Dependent Transcriptional Control of sprE: Regulatory Feedback Loop, J. Bacteriol., 2001, vol. 183, pp. 5974-5981.
54. Farewell, A., Kvint, K., and Nystrom, T., Negative Regulation by RpoS: A Case of σ Factor Competition, Mol. Microbiol., 1998, vol. 29, pp. 1039-1051.
55. Khmel, I.A., Microcins, Peptide Antibiotics of Enterobacteria: Genetic Control of Synthesis, Structure, and Mode of Action, Rus. J. Genet., 1999, vol. 35, no. 1, pp. 5-16.
56. Yamagishi, M., Matsushima, H., Wada, A., et al., Regulation of the Escherichia coli rmf Gene Encoding the Ribosome Modulation Factor: Growth Phase- and Growth Rate-Dependent Control, EMBO J., 1993, vol. 12, pp. 625-630.
57. Wada, A., Growth Phase Coupled Modulation of Escherichia coli Ribosomes, Genes Cells, 1998, vol. 3, pp. 203-208.
58. Lange, R. and Hengge-Aronis, R., Identification of a Central Regulator of Stationary-Phase Gene Expression in Escherichia coli, Mol. Microbiol., 1991, vol. 5, pp. 49-59.
59. Hengge-Aronis, R., Survival of Hunger and Stress: The Role of RpoS in Stationary Phase Gene Regulation in Escherichia coli, Cell (Cambridge, Mass.), 1993, vol. 72, pp. 165-168.
60. S (KatF) in Bacterial Global Regulation, Annu. Rev. Microbiol., 1994, vol. 48, pp. 53-80.
61. Bishop, R.E., Leskiw, B.K., Hodges, R.S., et al., The Entericidin Locus of Escherichia coli and Its Implications for Programmed Bacterial Cell Death, J. Mol. Biol., 1998, vol. 280, pp. 583-596.
62. S Subunit of RNA Polymerase in Escherichia coli Is Controlled at the Levels of Transcription, Translation and Protein Stability, Genes Dev., 1994, vol. 8, pp. 1600-1612.
63. Venturi, V., Control of rpoS Transcription in Escherichia coli and Pseudomonas: Why So Different?, Mol. Microbiol., 2003, vol. 49, pp. 1-9.
64. Mulvey, M.R., Switala, J., Borys, A., and Loewen, P.C., Regulation of Transcription of katE and katF in Escherichia coli, J. Bacteriol., 1990, vol. 172, pp. 6713-6720.
65. S Subunit of RNA Polymerase in Escherichia coli, J. Bacteriol., 1995, vol. 177, pp. 4676-4680.
66. Takayanagi, Y., Tanaka, K., and Takahashi, H., Structure of 5′-Upstream Region and the Regulation of the rpoS Gene of Escherichia coli, Mol. Gen. Genet., 1994, vol. 243, pp. 525-531.
67. Cashel, M., Gentry, D.R., Hernandez, V.J., and Vinella, D., The Stringent Response, Escherichia coli and Salmonella: Cellular and Molecular Biology, Neidhardt, F.C., Curtiss, R. III, Ingraham, J.L., et al., Eds., Washington: Am. Soc. Microbiol., 1996, pp. 1458-1496.
68. S Is Positively Regulated by ppGpp, J. Bacteriol., 1993, vol. 175, pp. 7982-7989.
69. Hirsch, M. and Elliott, T., Role of ppGpp in rpoS Stationary-Phase Regulation in Escherichia coli, J. Bacteriol., 2002, vol. 184, pp. 5077-5087.
70. Shiba, T., Tsutsumi, K., Yano, H., et al., Inorganic Polyphosphate and the Induction of rpoS Expression, Proc. Natl. Acad. Sci. USA, 1997, vol. 94, pp. 11 210-11 215.
71. S Subunit of RNA Polymerase in Escherichia coli, J. Bacteriol., 1996, vol. 178, pp. 1607-1613.
72. S) by ClpXP Protease, J. Bacteriol., 1996, vol. 178, pp. 470-476.
73. Becker, G., Klauck, E., and Hengge-Aronis, R., Regulation of RpoS Proteolysis in Escherichia coli: The Response Regulator RssB Is a Recognition Factor That Interacts with the Turnover Element in RpoS, Proc. Natl. Acad. Sci. USA, 1999, vol. 96, pp. 6439-6444.
74. Balandina, A., Claret, I., Hengge-Aronis, R., and Rouviere-Yaniv, J., The Escherichia coli Histone-Like Protein HU Regulates rpoS Translation, Mol. Microbiol., 2001, vol. 39, pp. 1069-1079.
75. Kamashev, D., Baladina, A., and Rouivere-Yaniv, J., The Binding Motif Recognized by HU on Both Nicked and Cruciform DNA, EMBO J., 1999, vol. 18, pp. 5434-5444.
76. S-Dependent Genes in Escherichia coli, J. Bacteriol., 1995, vol. 177, pp. 3455-3464.
77. S in Escherichia coli: Involvement of the Nucleoid Protein H-NS, EMBO J., 1995, vol. 14, pp. 594-602.
78. Sledjeski, D.D., Gupta, A., and Gottesman, S., The Small RNA, DsrA, Is Essential for the Low Temperature Expression of rpoS during Exponential Growth in Escherichia coli, EMBO J., 1996, vol. 15, pp. 3993-4000.
79. Zhou, Y. and Gottesman, S., Regulation of Proteolysis of the Stationary-Phase σ Factor RpoS, J. Bacteriol., 1998, vol. 180, pp. 1154-1158.
80. S Subunit of RNA Polymerase in Escherichia coli, EMBO J., 1996, vol. 15, pp. 1333-1339.
81. S for Degradation by ClpXP, Genes Dev., 2001, vol. 15, pp. 627-637.
82. 38 (the rpoS Gene Product), Nucleic Acids Res., 1995, vol. 23, pp. 827-834.
83. S Holoenzymes, Mol. Microbiol., 1995, vol. 16, pp. 649-656.
84. S-Dependent? Role of the -13/-14 Nucleotide Promoter Positions and Region 2.5 of E. coli, J. Mol. Biol., 2001, vol. 39, pp. 1153-1165.
85. S-Dependent Promoters, Mol. Microbiol., 1996, vol. 21, pp. 657-659.
86. Hengge-Aronis, R., Interplay of Global Regulators and Cell Physiology in the General Stress Response of Escherichia coli, Curr. Opin. Microbiol., 1999, vol. 2, pp. 148-152.
87. S-Selective?, Curr. Opin. Microbiol., 2002, vol. 5, pp. 591-595.
88. Busby, S. and Elbright, R., Promoter Structure, Promoter Recognition and Transcription Activation in Prokaryotes, Cell (Cambridge, Mass.), 1994, vol. 79, pp. 743-746.
89. Ross, W., Gosink, K.K., Salomon, J., et al., A Third Recognition Element in Bacterial Promoters: DNA Binding by the α Subunits of RNA Polymerase, Science, 1993, vol. 262, pp. 1407-1413.
90. Estrem, S.T., Gaal, T., Ross, W., and Course, R.L., Identification of an UP Element Consensus Sequence for Bacterial Promoters, Proc. Natl. Acad. Sci. USA, 1998, vol. 95, pp. 9761-9766.
91. 70 Is Inessential for Initiation of Transcription at an "Extended Minus 10" Promoter, J. Mol. Biol., 1993, vol. 232, pp. 406-418.
92. 70 Subunit Is Responsible for the Recognition of the "Extended -10" Motif at Promoters, EMBO J., 1997, vol. 16, pp. 4034-4040.
93. Burr, T., Mitchell, J., Kolb, A., et al., DNA Sequence Elements Located Immediately Upstream of the -10 Hexamer in Escherichia coli Promoters: A Systematic Study, Nucleic Acids Res., 2000, vol. 28, pp. 1864-1870.
94. 38 (RpoS) RNA Polymerase Promoter Engagement via -10 Region Nucleotides, J. Biol. Chem., 2001, vol. 276, pp. 30 064-30 071.
95. S RNA Polymerase, Mol. Microbiol., 2001, vol. 42, pp. 939-954.
96. Colland, F., Fujita, N., Kotlarz, D., et al., Positioning of the Stationary Phase σ Factor in Escherichia coli RNA Polymerase-Promoter Open Complex, EMBO J., 1999, vol. 18, pp. 4049-4059.
97. S-Dependent Stationary Phase-Induced and Osmotically Regulated osmJ Gene Suggests Novel Roles for Lrp, cAMP, cAMP-CRP and IHF in the Stationary Phase Response of Escherichia coli, J. Bacteriol., 1993, vol. 175, pp. 7910-7917.
98. S, J. Biol. Chem., 2000, vol. 275, pp. 14 795-14 798.
99. S-Dependent Promoter in Escherichia coli, Mol. Microbiol., 2001, vol. 41, pp. 705-716.
100. 70 of Escherichia coli to Utilize Promoters Containing Half or Full UP-Element Sites, Mol. Microbiol., 2005, vol. 55, pp. 250-260.
101. S-Dependent Growth-Phase Induction of the CsgBA Promoter in Escherichia coli Can Be Achieved in Vivo by Sigma 70 in the Absence of the Nucleoid-Associated Protein H-NS, Mol. Microbiol., 1994, vol. 13, pp. 1021-1032.
102. 38 Holoenzymes: Effect of DNA Supercoiling, J. Biol. Chem., 1996, vol. 271, pp. 1998-2004.
103. S- Dependent Transcription in Escherichia coli, Mol. Microbiol., 2003, vol. 48, pp. 561-571.
104. Jishage, M. and Ishihama, A., A Stationary Phase Protein in Escherichia coli with Binding Activity to the Major σ Subunit of RNA Polymerase, Proc. Natl. Acad. Sci. USA, 1998, vol. 95, pp. 4953-4958.
105. D, J. Bacteriol., 1999, vol. 181, pp. 3768-3776.
106. 70 Complex, J. Mol. Biol., 2004, vol. 335, pp. 685-692.
107. Wassarman, K. and Storz, G., 6S RNA Regulates Escherichia coli RNA Polymerase Activity, Cell (Cambridge, Mass.), 2000, vol. 101, pp. 613-623.
108. Trotochaud, A.E. and Wassarman, K.M., 6S RNA Function Enhances Long-Term Cell Survival, J. Bacteriol., 2004, vol. 186, pp. 4978-4985.
109. Bougdour, A., Lelong, C., and Geiselmann, J., Crl, a Low Temperature-Induced Protein in Escherichia coli That Binds Directly to the Stationary Phase σ Subunit of RNA Polymerase, J. Biol. Chem., 2004, vol. 279, pp. 19 540-19 550.
110. Miller, M.B. and Bassler, B.L., Quorum Sensing in Bacteria, Annu. Rev. Microbiol., 2001, vol. 55, pp. 169-199.
111. Zavilgelsky, G.B. and Manukhov, I.V., Quorum Sensing, or How Bacteria "Talk" to Each Other, Mol. Biol., 2001, vol. 35, pp. 268-277.
112. Gintsburg, A.L., Il'ina, T.S., and Romanova, Yu.M., Quorum Sensing, or Social Behavior of Bacteria, Zh. Mikrobiol., Epidemiol., Immunobiol., 2003, no. 5, pp. 86-93.
113. Henke, J.M. and Bassler, B.L., Bacterial Social Engagements, Trends Cell Biol., 2004, vol. 14, pp. 648-656.
114. Wei, Y., Lee, J.M., Smulski, D.R., and LaRossa, R.A., Global Impact of sdiA Amplification Revealed by Comprehensive Gene Expression Profiling of Escherichia coli, J. Bacteriol., 2001, vol. 183, pp. 2265-2272.
115. Ahmer, B.M.M., Cell-to-Cell Signaling in Escherichia coli and Salmonella enterica, Mol. Microbiol., 2004, vol. 52, pp. 933-945.
116. Surette, M.G., Miller, M., and Bassler, B., Quorum Sensing in Escherichia coli, Salmonella typhimuium, and Vibrio harveyi: A New Family of Genes Responsible for Autoinducer Production, Proc. Natl. Acad. Sci. USA, 1999, vol. 96, pp. 1639-1644.
117. Chen, X., Schauder, S., Potler, N., et al., Structural Identification of a Bacterial Quorum-Sensing Signal Containing Boron, Nature, 2002, vol. 415, pp. 545-549.
118. Schauder, S., Shokat, K., Surette, M.G., and Bassler, B.L., The LuxS Family of Bacterial Autoinducers: Biosynthesis of a Novel Quorum-Sensing Signal Molecule, Mol. Microbiol., 2001, vol. 41, pp. 463-476.
119. Schauder, S. and Bassler, B.L., The Languages of Bacteria, Genes Dev., 2001, vol. 15, pp. 1468-1480.
120. DeLisa, M.P., Wu, C.F., Wang, L., et al., DNA Microarray-Based Identification of Genes Controlled by Autoinducer 2-Stimulated Quorum Sensing in Escherichia coli, J. Bacteriol., 2001, vol. 183, pp. 5239-5247.
121. Sircili, M.P., Walters, M., Trabulsi, L.R., and Sperandio, V., Modulation of Enteropathogenic Escherichia coli Virulence by Quorum Sensing, Infect. Immunol., 2004, vol. 72, pp. 2329-2337.
122. Withers, H.L. and Nordstrom, K., Quorum Sensing Acts at Initiation of Chromosomal Replication in Escherichia coli, Proc. Natl. Acad. Sci. USA, 1998, vol. 95, pp. 15 694-15 699.
123. Baca-DeLancey, R.R., South, M.M., Ding, X., and Rather, P.N., Escherichia coli Genes Regulated by Cell-to-Cell Signaling, Proc. Natl. Acad. Sci. USA, 1999, vol. 96, pp. 4610-4614.
124. Ren, D., Bedzyk, L.A., Ye, R.W., et al., Stationary-Phase Quorum-Sensing Signals Affect Autoinducer-2 and Gene Expression in Escherichia coli, Appl. Environ. Microbiol., 2004, vol. 70, pp. 2038-2043.
125. Wang, D., Ding, X., and Rather, P.N., Indole Can Act As an Extracellular Signal in Escherichia coli, J. Bacteriol., 2001, vol. 183, pp. 4210-4216.
126. Gallio, M., Sturgill, G., Rather, P., and Kylsten, P., A Conserved Mechanism for Extracellular Signaling in Eukaryotes and Prokaryotes, Proc. Natl. Acad. Sci. USA, 2002, vol. 99, pp. 12 208-12 213.
127. Bremer, H. and Dennis, P.P., Modulation of Chemical Composition and Other Parameters of the Cell by Growth Rate, Escherichia coli and Salmonella: Cellular and Molecular Biology, Neidhardt, F.C., Ingraham, J.L., Low, K.B., et al., Eds., Washington: Am. Soc. Microbiol., 1987, pp. 1527-1542.
128. Jinks-Robertson, S. and Nomura, M., Ribosomes and tRNA, Escherichia coli and Salmonella: Cellular and Molecular Biology, Neidhardt, F.C., Ingraham, J.L., Low, K.B., et al., Eds., Washington: Am. Soc. Microbiol., 1987, pp. 1358-1385.
129. Wada, A., Yamazaki, Y., Fujita, N., and Ishihama, A., Structure and Probable Genetic Location of a "Ribosome Modulation Factor" Associated with 100S Ribosomes in Stationary-Phase Escherichia coli Cells, Proc. Natl. Acad. Sci. USA, 1990, vol. 87, pp. 2657-2661.
130. Wada, A., Igarashi, K., Yoshimura, S., et al., Ribosome Modulation Factor: Stationary Growth Phase-Specific Inhibitor of Ribosome Functions from Escherichia coli, Biochem. Biophys. Res. Commun., 1995, vol. 214, pp. 410-417.
131. Yoshida, H., Maki, Y., Kato, H., et al., The Ribosome Modulation Factor (RMF) Binding Site on the 100S Ribosome of Escherichia coli, J. Biochem. (Tokyo), 2002, vol. 132, pp. 983-989.
132. Yoshida, H., Yamamoto, H., Uchiumi, T., and Wada, A., RMF Inactivates Ribosomes by Covering the Peptidyl Transferase Center and Entrance of Peptide Exit Tunnel, Genes Cells, 2004, vol. 9, pp. 271-278.
133. Wada, A., Mikkola, R., Kurland, C.G., and Ishihama, A., Growth Phase-Coupled Changes of the Ribosome Profile in Natural Isolates and Laboratory Strains of Escherichia coli, J. Bacteriol., 2000, vol. 182, pp. 2893-2899.
134. Ramagopal, S., Metabolic Changes in Ribosomes of Escherichia coli during Prolonged Culture in Different Media, Eur. J. Biochem., 1984, vol. 140, pp. 353-361.
135. Ramagopal, S. and Subramanian, A.R., Growth-Dependent Regulation in Production and Utilization of Acetylated Ribosomal Protein L7, J. Mol.Biol., 1975, vol. 94, pp. 633-641.
136. Agafonov, D.E., Kolb, V.A., Nazimov, I.V., and Spirin, A.S., A Protein Residing at the Subunit Interface of Bacterial Ribosome, Proc. Natl. Acad. Sci. USA, 1999, vol. 96, pp. 12 345-12 349.
137. Maki, Y., Yoshida, H., and Wada, A., Two Proteins, YfiA and YhbH, Associated with Resting Ribosomes in Stationary Phase Escherichia coli, Genes Cells, 2000, vol. 5, pp. 965-974.
138. Agafonov, D.E., Kolb, V.A., and Spirin, A.S., Ribosome-Associated Protein That Inhibits Translation at the Aminoacyl-tRNA Binding Stage, EMBO Rep., 2001, vol. 2, pp. 399-402.
139. Vicente, M., Chater, K., and de Lorenzo, V., Bacterial Transcription Factors Involved in Global Regulation, Mol. Microbiol., 1999, vol. 33, pp. 8-17.