ppGpp Signaling

Bacterial Signaling

Volumn , Issue , 2010, Pages 395-414

  Wagner, Rolf ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

(p)ppGpp; Global regulator; Macromolecular synthesis; RNA polymerase; Transcription

Indexed keywords

EID: 78649391519     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527629237.ch22     Document Type: Chapter

References (112)

1. Potrykus, K. Cashel, M. (2008) (p)ppGpp: still magical? Annu. Rev. Microbiol., 62, 35-51.
2. Srivatsan, A. Wang, J.D. (2008) Control of bacterial transcription, translation and replication by (p)ppGpp. Curr. Opin. Microbiol., 11, 100-105.
3. Szalewska-Palasz, A., Wegrzyn, G., Wegrzyn, A. (2007) Mechanisms of physiological regulation of RNA synthesis in bacteria: new discoveries breaking old schemes. J. Appl. Genet., 48, 281-294.
4. Jain, V., Kumar, M., Chatterji, D. (2006) ppGpp: stringent response and survival. J. Microbiol., 44, 1-10.
5. Braeken, K., Moris, M., Daniels, R., Vanderleyden, J., Michiels, J. (2006) New horizons for (p)ppGpp in bacterial and plant physiology. Trends Microbiol., 14, 45-54.
6. Magnusson, L.U., Farewell, A., Nystrom, T. (2005) ppGpp: a global regulator in Escherichia coli. Trends Microbiol., 13, 236-242.
7. Wagner, R. (2002) Regulation of ribosomal RNA synthesis inE. coli: effects of the global regulator guanosine tetraphosphate (ppGpp). J. Mol. Microbiol. Biotechnol., 4, 331-340.
8. Ryals, J., Little, R., Bremer, H. (1982) Temperature dependence of RNA synthesis parameters in Escherichia coli. J. Bacteriol., 151, 879-887.
9. Battesti, A. Bouveret, E. (2006) Acyl carrier protein/SpoT interaction, the switch linking SpoT-dependent stress response to fatty acid metabolism. Mol. Microbiol., 62, 1048-1063.
10. Raskin, D.M., Judson, N., Mekalanos, J.J. (2007) Regulation of thestringent response is the essential function of the conserved bacterial G protein CgtA in Vibrio cholerae. Proc. Natl. Acad. Sci. USA, 104, 4636-4641.
11. Jiang, M., Sullivan, S.M., Wout, P.K., Maddock, J.R. (2007) G-protein control of the ribosome-associated stress response protein SpoT. J. Bacteriol., 189, 6140-6147.
12. Lemos, J.A., Lin, V.K., Nascimento, M.M., Abranches, J., Burne, R.A. (2007) Three gene products govern (p)ppGpp production by Streptococcus mutans. Mol. Microbiol., 65, 1568-1581.
13. Nanamiya, H., Kasai, K., Nozawa, A., Yun, C.S., Narisawa, T., Murakami, K., Natori, Y., Kawamura, F., Tozawa, Y. (2008) Identification and functional analysis of novel (p)ppGpp synthetase genes in Bacillus subtilis. Mol. Microbiol., 67, 291-304.
14. Chang, D.-E., Smalley, D.J., Conway, T. (2002) Gene expression profiling of Escherichia coli growth transitions: an expanded stringent control model. Mol. Microbiol., 45, 289-306.
15. Traxler, M.F., Summers, S.M., Nguyen, H.T., Zacharia, V.M., Hightower, G.A., Smith, J.T., Conway, T. (2008) The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli. Mol. Microbiol., 68, 1128-1148.
16. Durfee, T., Hansen, A.M., Zhi, H., Blattner, F.R., Jin, D.J. (2008) Transcription profiling of the stringent response in Escherichia coli. J. Bacteriol., 190, 1084-1096.
17. Eymann, C., Homuth, G., Scharf, C., Hecker, M. (2002) Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis. J. Bacteriol., 184, 2500-2520.
18. Brockmann-Gretza, O. Kalinowski, J. (2006) Global gene expression during stringent response in Corynebacterium glutamicum in presence and absence of the rel gene encoding (p)ppGpp synthase. BMC Genomics, 7, 230.
19. Hesketh, A., Chen, W.J., Ryding, J., Chang, S., Bibb, M. (2007) The global role of ppGpp synthesis in morphological differentiation and antibiotic production in Streptomyces coelicolor A3(2). Genome Biol., 8, R161.
20. Nascimento, M.M., Lemos, J.A., Abranches, J., Lin, V.K., Burne, R.A. (2008) Role of RelA of Streptococcus mutans in global control of gene expression. J. Bacteriol., 190, 28-36.
21. Traxler, M.F., Chang, D.E., Conway, T. (2006) Guanosine 30,50-bispyrophosphate coordinates global gene expression during glucose-lactose diauxie in Escherichia coli. Proc. Natl. Acad. Sci. USA, 103, 2374-2379.
22. Ouellette, S.P.,Hatch,T.P.,AbdelRahman, Y.M., Rose, L.A., Belland, R.J., Byrne, G.I. (2006) Global transcriptional upregulation in the absence of increased translation in Chlamydia during IFNgamma-mediated host cell tryptophan starvation. Mol. Microbiol., 62, 1387-1401.
23. Cellini, A., Scoarughi, G.L., Poggiali, P., Santino, I., Sessa, R., Donini, P., Cimmino, C. (2004) Stringent control in the archaeal genus Sulfolobus. Res. Microbiol., 155, 98-104.
24. Cimmino, C., Scoarughi, G.L., Donini, P. (1993) Stringency and relaxation among the halobacteria. J. Bacteriol., 175, 6659-6662.
25. Scoarughi, G.L., Cimmino, C., Donini, P. (1995) Lack of production of (p) ppGpp in Halobacterium volcanii under conditions that are effective in the eubacteria. J. Bacteriol., 177, 82-85.
26. van der Biezen, E.A., Sun, J., Coleman, M.J., Bibb, M.J., Jones, J.D. (2000) Arabidopsis RelA/SpoT homologs implicate (p)ppGpp in plant signalling. Proc. Natl. Acad. Sci. USA, 97, 3747-3752.
27. Givens, R.M., Lin, M.H., Taylor, D.J., Mechold, U., Berry, J.O., Hernandez, V.J. (2004) Inducible expression, enzymatic activity, and origin of higher plant homologues of bacterial RelA/SpoT stress proteins in Nicotiana tabacum. J. Biol. Chem., 279, 7495-7504.
28. Takahashi, K., Kasai, K., Ochi, K. (2004) Identification of the bacterial alarmone guanosine 50-diphosphate30-diphosphate (ppGpp) in plants. Proc. Natl. Acad. Sci. USA, 101, 4320-4324.
29. Kasai, K., Kanno, T., Endo, Y.,Wakasa, K., Tozawa, Y. (2004) Guanosine tetraand pentaphosphate synthase activity in chloroplasts of a higher plant: association with 70S ribosomes and inhibition by tetracycline. Nucleic Acids Res., 32, 5732-5741.
30. Kasai, K., Usami, S., Yamada, T., Endo, Y., Ochi, K., Tozawa, Y. (2002) A RelA-SpoT homolog (Cr-RSH) identified in Chlamydomonas reinhardtii generates stringent factor in vivo and localizes to chloroplasts in vitro. Nucleic Acids Res., 30, 4985-4992.
31. Tozawa, Y., Nozawa, A., Kanno, T., Narisawa, T., Masuda, S., Kasai, K., Nanamiya, H. (2007) Calcium-activated (p)ppGpp synthetase in chloroplasts of land plants. J. Biol. Chem., 282, 35536-35545.
32. Masuda, S., Mizusawa, K., Narisawa, T., Tozawa, Y., Ohta, H., Takamiya, K. (2008) The bacterial stringent response, conserved in chloroplasts, controls plant fertilization. Plant Cell Physiol., 49, 135-141.
33. Bassler, B.L. (1999) How bacteria talk to each other: regulation of gene expression by quorum sensing. Curr. Opin. Microbiol., 2, 582-587.
34. Lazazzera, B.A. (2000) Quorum sensing and starvation: signals for entry into stationary phase. Curr. Opin. Microbiol., 3, 177-182.
35. van Delden, C., Comte, R., Bally, A.M. (2001) Stringent response activates quorum sensing and modulates cell density-dependent gene expression in Pseudomonas aeruginosa. J. Bacteriol., 183, 5376-5384.
36. Balzer, G.J. McLean, R.J. (2002) The stringent response genes relA and spoT are important for Escherichia coli biofilms under slow-growth conditions. Can. J. Microbiol., 48, 675-680.
37. Moris, M., Braeken, K., Schoeters, E., Verreth, C., Beullens, S.,Vanderleyden, J., Michiels, J. (2005) Effective symbiosis between Rhizobium etli and Phaseolus vulgaris requires the alarmone ppGpp. J. Bacteriol., 187, 5460-5469.
38. Thompson, A., Rolfe, M.D., Lucchini, S., Schwerk, P., Hinton, J.C., Tedin, K. (2006) The bacterial signal molecule, ppGpp, mediates the environmental regulation of both the invasion and intracellular virulence gene programs of Salmonella. J. Biol. Chem., 281, 30112-30121.
39. Pizarro-Cerda, J. Tedin, K. (2004) The bacterial signal molecule, ppGpp, regulates Salmonella virulence gene expression. Mol. Microbiol., 52, 1827-1844.
40. Na, H.S., Kim, H.J., Lee, H.C., Hong, Y., Rhee, J.H., Choy, H.E. (2006) Immune response induced by Salmonella typhimurium defective in ppGpp synthesis. Vaccine, 24, 2027-2034.
41. Song, M., Kim, H.J., Kim, E.Y., Shin, M., Lee, H.C., Hong, Y., Rhee, J.H., Yoon, H., Ryu, S., Lim, S. et al. (2004) ppGppdependent stationary phase induction of genes on Salmonella pathogenicity island 1. J. Biol. Chem., 279, 34183-34190.
42. Nakanishi, N., Abe, H., Ogura, Y., Hayashi, T., Tashiro, K., Kuhara, S., Sugimoto, N., Tobe, T. (2006) ppGpp with DksA controls gene expression in the locus of enterocyte effacement (LEE) pathogenicity island of enterohaemorrhagic Escherichia coli through activation of two virulence regulatory genes. Mol. Microbiol., 61, 194-205.
43. Godfrey, H.P., Bugrysheva, J.V., Cabello, F.C. (2002) The role of the stringent response in the pathogenesis of bacterial infections. Trends Microbiol., 10, 349-351.
44. Engelberg-Kulka, H. Glaser, G. (1999) Addiction modules and programmed cell death and antideath in bacterial cultures. Annu. Rev. Microbiol., 53, 43-70.
45. Aizenman, E., Engelberg-Kulka, H., Glaser, G. (1996) An Escherichia coli chromosomal.addiction module. regulated by guanosine [corrected] 30,50-bispyrophosphate: a model for programmed bacterial cell death. Proc. Natl. Acad. Sci. USA, 93, 6059-6063.
46. Hazan, R. Engelberg-Kulka, H. (2004) Escherichia coli mazEF-mediated cell death as a defense mechanism thatinhibits the spread of phage P1. Mol. Genet. Genomics, 272, 227-234.
47. Gross, M.,Marianovsky, I., Glaser, G. (2006)MazG - a regulator of programmed cell death in Escherichia coli. Mol. Microbiol., 59, 590-601.
48. Hansen, S., Lewis, K., Vulic, M. (2008) The role of global regulators and nucleotide metabolism in antibiotic tolerance in Escherichia coli. Antimicrob. Agents Chemother., 52, 2718-2726.
49. Lewis, K. (2007) Persister cells, dormancy and infectious disease. Nat. Rev. Microbiol., 5, 48-56.
50. Gardner, A., West, S.A., Griffin, A.S. (2007) Is bacterial persistence a social trait? PLoS ONE, 2, e752.
51. Korch, S.B., Henderson, T.A., Hill, T.M. (2003) Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis. Mol. Microbiol., 50, 1199-1213.
52. Wright, B.E. (2004) Stress-directed adaptive mutations and evolution. Mol. Microbiol., 52, 643-650.
53. Zyskind, J.W. Smith, D.W. (1992) DNA replication, the bacterial cell cycle, and cell growth. Cell, 69, 5-8.
54. Autret, S., Levine, A., Vannier, F., Fujita, Y., Seror, S.J. (1999) The replication checkpoint control in Bacillus subtilis: identification of a novel RTP-binding sequence essential for the replication fork arrest after induction of the stringent response. Mol. Microbiol., 31, 1665-1679.
55. Levine, A., Autret, S., Seror, S.J. (1995) A checkpoint involving RTP, the replication terminator protein, arrests replication downstream of the origin during the Stringent Response in Bacillus subtilis. Mol. Microbiol., 15, 287-295.
56. Levine, A., Vannier, F., Dehbi, M., Henckes, G., Seror, S.J. (1991) The stringent response blocks DNA replication outside the ori region in Bacillus subtilis and at the origin in Escherichia coli. J. Mol. Biol., 219, 605-613.
57. Wang, J.D., Sanders, G.M., Grossman, A.D. (2007) Nutritional control of elongation of DNA replication by (p)ppGpp. Cell, 128, 865-875.
58. Milon, P., Tischenko, E., Tomsic, J., Caserta, E., Folkers, G., La Teana, A., Rodnina,M.V., Pon, C.L., Boelens, R., Gualerzi, C.O. (2006) The nucleotidebinding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor. Proc. Natl. Acad. Sci. USA, 103, 13962-13967.
59. Chatterji, D., Fujita, N., Ishihama, A. (1998) The mediator for stringent control, ppGpp, binds to the beta-subunit of Escherichia coli RNA polymerase. Genes Cells, 3, 279-287.
60. Toulokhonov, I., Artsimovitch, I., Landick, R. (2001) Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science, 292, 730-733.
61. Reddy, P.S., Raghavan, A., Chatterji, D. (1995) Evidence for a ppGpp-binding site on Escherichia coli RNA polymerase: proximity relationship with the rifampicin-binding domain. Mol. Microbiol., 15, 255-265.
62. Artsimovitch, I., Patlan, V., Sekine, S., Vassylyeva, M.N., Hosaka, T., Ochi, K., Yokoyama, S., Vassylyev, D.G. (2004) Structural basis for transcription regulation by alarmone ppGpp. Cell, 117, 299-310.
63. Vrentas, C.E., Gaal, T., Berkmen, M.B., Rutherford, S.T., Haugen, S.P., Ross, W., Gourse, R.L. (2008) Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation. J. Mol. Biol., 377, 551-564.
64. Mathew, R. Chatterji, D. (2006) The evolving story of the omega subunit of bacterial RNA polymerase. Trends Microbiol., 14, 450-455.
65. Ghosh, P., Ishihama, A., Chatterji, D. (2001) Escherichia coli RNA polymerase subunit omega and its N-terminal domain bind full-length beta0 to facilitate incorporation into the alpha2beta subassembly. Eur. J. Biochem., 268, 4621-4627.
66. Gentry, D.R. Burgess, R.R. (1989) rpoZ, encoding the omega subunit of Escherichia coli RNA polymerase, is in the same operon as spoT. J. Bacteriol., 171, 1271-1277.
67. Igarashi, K., Fujita, N., Ishihama, A. (1989) Promoter selectivity of Escherichia coli RNA polymerase: omega factor is responsible for the ppGpp sensitivity. Nucleic Acids Res., 17, 8755-8765.
68. Gentry, D., Xiao, H., Burgess, R., Cashel, M. (1991) The omega subunit of Escherichia coli K-12 RNA polymerase is not required for stringent RNA control in vivo. J. Bacteriol., 173, 3901-3903.
69. Vrentas, C.E., Gaal, T., Ross, W., Ebright, R.H., Gourse, R.L. (2005) Response of RNA polymerase to ppGpp: requirement for the v subunit and relief of this requirement by DksA. Genes Dev., 19, 2378-2387.
70. Travers, A.A. (1980) Promoter sequence for stringent control of bacterial RNA synthesis. J. Bacteriol., 141, 973-976.
71. Mizushima-Sugano, J. Kaziro, Y. (1985) Regulation of the expression of the tufB operon: DNA sequences directly involved in the stringent control. EMBO J., 4, 1053-1058.
72. Zacharias, M., Göringer, H.U., Wagner, R. (1989) Influence of the GCGC discriminator motif introduced into the ribosomal RNA P2- and tac promoter on growth rate control and stringent sensitivity. EMBO J., 11, 3357-3363.
73. Davies, I.J. Drabble, W.T. (1996) Stringent and growth-rate-dependent control of the gua operon of Escherichia coli K-12. Microbiology, 142, 2429-2437.
74. Riggs, D.L., Muller, R.D., Kwan, H.-S., Artz, S.W. (1986) Promoter domain mediates guanosine tetraphosphate activation of the histidine operon. Proc. Natl. Acad Sci. USA, 83, 9333-9337.
75. Haugen, S.P., Berkmen, M.B., Ross, W., Gaal, T.,Ward, C., Gourse, R.L. (2006) rRNApromoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNApolymerase. Cell, 125, 1069-1082.
76. Haugen, S.P., Ross,W.,Manrique, M., Gourse, R.L. (2008) Fine structure of the promoter-s region 1.2 interaction. Proc. Natl. Acad. Sci. USA, 105, 3292-3297.
77. Figueroa-Bossi, N., Guérin, M., Rahmouni, R., Leng, M., Bossi, L. (1998) The supercoilling sensitivity of a bacterial tRNA promoter parallels its responsiveness to stringent control. EMBO J., 17, 2359-2367.
78. Krohn, M. Wagner, R. (1996) Transcriptional pausing of RNA polymerase in the presence of guanosine tetraphosphate depends on the promoter and gene sequence. J. Biol. Chem., 271, 23884-23894.
79. Vogel, U. Jensen, K.F. (1994) Effects of guanosine30,50-bisdiphosphate (ppGpp) on rate of transcription elongation in isoleucine-starved Escherichia coli. J. Biol. Chem., 269, 16236-16241.
80. Vogel, U. Jensen, K.F. (1995) Effects of the antiterminator boxA on transcription elongation kinetics and ppGpp inhibition of transcription elongation in Escherichia coli. J. Biol. Chem., 270, 18335-18340.
81. Raghavan, A. Chatterji, D. (1998) Guanosine tetraphosphate-induced dissociation of open complexes at the Escherichia coli ribosomal protein promoters rplJ and rpsA P1: nanosecond depolarization spectroscopic studies. Biophys. Chem., 75, 21-32.
82. Barker, M.M., Gaal, T., Josaitis, C.A., Gourse, R.L. (2001) Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J. Mol. Biol., 305, 673-688.
83. Paul, B.J., Barker, M.M., Ross, W., Schneider, D.A., Webb, C., Foster, J.W., Gourse, R.L. (2004) DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell, 118, 311-322.
84. Potrykus, K., Wegrzyn, G., Hernandez, V.J. (2002) Multiple mechanisms of transcription inhibition by ppGpp at the lambda PR promoter. J. Biol. Chem., 277, 43785-43791.
85. Jöres, L. Wagner, R. (2003) Essential steps in the ppGpp-dependent regulation of bacterial ribosomalRNApromoters can be explained by substrate competition. J. Biol. Chem., 278, 16834-16843.
86. Gaal, T., Bartlett, M.S., Ross, W., Turnbough, C., Gourse, R.L. (1997)Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria. Science, 278, 2092-2097.
87. Schneider, D.A. Gourse, R.L. (2003) Changes in Escherichia coli rRNA promoter activity correlate with changes in initiating nucleoside triphosphate and guanosine 50-diphosphate 30-diphosphate concentrations after induction of feedback control of ribosome synthesis. J. Bacteriol., 185, 6185-6191.
88. Krasny, L. Gourse, R.L. (2004) An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation. EMBO J, 23, 4473-4483.
89. Kasai, K., Nishizawa, T., Takahashi, K., Hosaka, T., Aoki, H., Ochi, K. (2006) Physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, Thermus thermophilus. J. Bacteriol., 188, 7111-7122.
90. Krasny, L., Tiserova, H., Jonak, J., Rejman, D., Sanderova, H. (2008) The identity of the transcription {thorn}1 position is crucial for changes in gene expression in response to amino acid starvation in Bacillus subtilis. Mol. Microbiol., 69, 42-54.
91. Perederina, A., Svetlov, V., Vassylyiva, M.N., Tahirov, T.H., Ykoyama, S., Artsimovitch, I., Vassylyev, D.G. (2004) Regulation through the secondary channel - structural framework for ppGpp-DksA synergism during transcription. Cell, 118, 297-309.
92. Paul, B.J., Berkmen, M.B., Gourse, R.L. (2005) DksA potentiates direct activation of amino acid promoters by ppGpp. Proc. Natl. Acad. Sci. USA, 102, 7823-7828.
93. Perron, K., Comte, R., van Delden, C. (2005) DksA represses ribosomal gene transcription in Pseudomonas aeruginosa by interacting with RNA polymerase on ribosomal promoters. Mol. Microbiol., 56, 1087-1102.
94. Magnusson, L.U., Gummesson, B., Joksimovic, P., Farewell, A., Nystrom, T. (2007) Identical, independent, and opposing roles of ppGpp and DksA in Escherichia coli. J. Bacteriol., 189, 5193-5202.
95. Potrykus, K., Vinella, D., Murphy, H., Szalewska-Palasz, A., D.Ari, R., Cashel, M. (2006) Antagonistic regulation of Escherichia coli ribosomal RNA rrnB P1 promoter activity by GreA and DksA. J. Biol. Chem., 281, 15238-15248.
96. Lamour, V., Hogan, B.P., Erie, D.A., Darst, S.A. (2006) Crystal structure of Thermus aquaticus Gfh1, a Gre-factor paralog that inhibits rather than stimulates transcript cleavage. J. Mol. Biol., 356, 179-188.
97. Blankschien, M.D., Potrykus, K., Grace, E., Choudhary, A., Vinella, D., Cashel, M.,Herman, C. (2009) TraR, a homolog of a RNAP secondary channel interactor, modulates transcription. PLoS Genet., 5, e1000345.
98. Lamour, V., Rutherford, S.T., Kuznedelov, K., Ramagopal, U.A., Gourse, R.L., Severinov, K., Darst, S.A. (2008) Crystal structure of Escherichia coli Rnk, a new RNApolymerase-interacting protein. J. Mol. Biol., 383, 367-379.
99. Choy, H.E. (2000) The study of guanosine 50-diphosphate 30-diphosphate-mediated transcription regulation in vitro using a coupled transcription- translation system. J. Biol. Chem., 275, 6783-6789.
100. Potrykus, K., Wegrzyn, G., Hernandez, V.J. (2004) Direct stimulation of the lambda paQ promoter by the transcription effector guanosine-30,50-(bis)pyrophosphate in a defined in vitro system. J. Biol. Chem., 279, 19860-19866.
101. Barker, M.M., Gaal, T., Gourse, R.L. (2001) Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP. J. Mol. Biol., 305, 689-702.
102. Kvint, K., Farewell, A., Nystrom, T. (2000) RpoS-dependent promoters require guanosine tetraphosphate for induction even in the presence of high levels of sigmaS. J. Biol. Chem., 275, 14795-14798.
103. Jishage, M., Kvint, K., Shingler, V., Nystrom, T. (2002) Regulation of sigma factor competition by the alarmone ppGpp. Genes Dev., 16, 1260-1270.
104. Laurie, A.D., Bernardo, L.M., Sze, C.C., Skarfstad, E., Szalewska-Palasz, A., Nystrom, T., Shingler, V. (2003) The role of the alarmone (p)ppGpp in sigma N competition for core RNA polymerase. J. Biol. Chem., 278, 1494-1503.
105. Costanzo, A. Ades, S.E. (2006) Growth phase-dependent regulation of the extracytoplasmic stress factor, sE, by guanosine 30,50-bispyrophosphate (ppGpp). J. Bacteriol., 188, 4627-4634.
106. Bernardo, L.M., Johansson, L.U., Solera, D., Skarfstad, E., Shingler, V. (2006) The guanosine tetraphosphate (ppGpp) alarmone, DksA and promoter affinity for RNA polymerase in regulation of sigma-dependent transcription. Mol. Microbiol., 60, 749-764.
107. Jishage, M. Ishihama, A. (1998) A stationary phase protein in Escherichia coli with binding activity to the major s subunit of RNA polymerase. Proc. Natl. Acad. Sci. USA, 95, 4953-4958.
108. Brown, L., Gentry, D., Elliot, T., Cashel, M. (2002) DksA affects ppGpp induction of RpoS at a translational level. J. Bacteriol., 184, 4455-4465.
109. Hirsch, M. Elliott, T. (2002) Role of ppGpp in rpoS stationary-phase regulation in Escherichia coli. J. Bacteriol., 184, 5077-5087.
110. Bougdour, A. Gottesman, S. (2007) ppGpp regulation of RpoS degradation via anti-adaptor protein IraP. Proc. Natl. Acad. Sci. USA, 104, 12896-12901.
111. Hernandez, V.J. Cashel, M. (1995) Changes in conserved region 3 of Escherichia coli s70 mediate ppGppdependent functions in vivo. J. Mol. Biol., 252, 536-549.
112. Costanzo, A., Nicoloff, H., Barchinger, S.E., Banta, A.B., Gourse, R.L., Ades, S.E. (2008) ppGpp and DksA likely regulate the activity of the extracytoplasmic stress factor sigmaE in Escherichia coli by both direct and indirect mechanisms. Mol. Microbiol., 67, 619-632.