Skip to main content Accessibility help
×
Hostname: page-component-76fb5796d-qxdb6 Total loading time: 0 Render date: 2024-04-25T11:38:39.260Z Has data issue: false hasContentIssue false

12 - Metabolic regulation

Published online by Cambridge University Press:  05 September 2012

Byung Hong Kim
Affiliation:
Korea Institute of Science and Technology, Seoul
Geoffrey Michael Gadd
Affiliation:
University of Dundee
Get access

Summary

Life processes transform materials available from the environment into cell components. Organic materials are converted to carbon skeletons for monomer and polymer synthesis, as well as being used to supply energy. Microbes synthesize monomers in the proportions needed for growth. This is possible through the regulation of the reactions of anabolism and catabolism. With a few exceptions, microbial ecosystems are oligotrophic with a limited availability of nutrients, the raw materials used for biosynthesis. Furthermore, nutrients are not usually found in balanced concentrations while the organisms have to compete with each other for available nutrients.

Unlike animals and plants, unicellular microbial cells are more directly coupled to their environment, which changes continuously. Many of these changes are stressful so organisms have evolved to cope with this situation. They regulate their metabolism to adapt to the ever-changing environment.

Since almost all biological reactions are catalyzed by enzymes, metabolism is regulated by controlling the synthesis of enzymes and their activity (Table 12.1). Metabolic regulation through the dynamic interactions between DNA or RNA and the regulatory apparatus employed determine major characteristics of organisms. In this chapter, different mechanisms of metabolic regulation are discussed in terms of enzyme synthesis through transcription and translation and enzyme activity modulation.

Mechanisms regulating enzyme synthesis

The rate of biological reactions catalyzed by enzymes is determined by the concentration and activity of the enzymes. Various mechanisms regulating the synthesis of individual enzymes are discussed here before multigene regulation is considered.

Type
Chapter
Information
Publisher: Cambridge University Press
Print publication year: 2008

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Ades, S. E. (2004). Control of the alternative sigma factor σE in Escherichia coli. Current Opinion in Microbiology 7, 157–162.CrossRefGoogle ScholarPubMed
Barnard, A., Wolfe, A. & Busby, S. (2004). Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes. Current Opinion in Microbiology 7, 102–108.CrossRefGoogle ScholarPubMed
Bell, S. D. (2005). Archaeal transcriptional regulation – variation on a bacterial theme?Trends in Microbiology 13, 262–265.CrossRefGoogle ScholarPubMed
Borukhov, S. & Severinov, K. (2002). Role of the RNA polymerase sigma subunit in transcription initiation. Research in Microbiology 153, 557–562.CrossRefGoogle ScholarPubMed
Dove, S. L., Darst, S. A. & Hochschild, A. (2003). Region 4 of σ as a target for transcription regulation. Molecular Microbiology 48, 863–874.CrossRefGoogle ScholarPubMed
Geiduschek, E. P. & Ouhammouch, M. (2005). Archaeal transcription and its regulators. Molecular Microbiology 56, 1397–1407.CrossRefGoogle ScholarPubMed
Gourse, R. L., Ross, W. & Rutherford, S. T. (2006). General pathway for turning on promoters transcribed by RNA polymerases containing alternative σ factors. Journal of Bacteriology 188, 4589–4591.CrossRefGoogle ScholarPubMed
Gruber, T. M. & Gross, C. A. (2003). Multiple sigma subunits and the partitioning of bacterial transcription space. Annual Review of Microbiology 57, 441–466.CrossRefGoogle ScholarPubMed
Helmann, J. D. (2002). The extracytoplasmic function (ECF) sigma factors. Advances in Microbial Physiology 46, 47–110.CrossRefGoogle ScholarPubMed
Hinton, D. M. (2005). Molecular gymnastics: distortion of an RNA polymerase σ-factor. Trends in Microbiology 13, 140–143.CrossRefGoogle ScholarPubMed
Hughes, K. T. & Mathee, K. (1998). The anti-sigma factors. Annual Review of Microbiology 52, 231–286.CrossRefGoogle ScholarPubMed
Kazmierczak, M. J., Wiedmann, M. & Boor, K. J. (2005). Alternative sigma factors and their roles in bacterial virulence. Microbiology and Molecular Biology Reviews 69, 527–543.CrossRefGoogle ScholarPubMed
Geiduschek, E. P. & Ouhammouch, M. (2005). Archaeal transcription and its regulators. Molecular Microbiology 56, 1397–1407.CrossRefGoogle ScholarPubMed
Mullerhill, B. (1998). Some repressors of bacterial transcription. Current Opinion in Microbiology 1, 145–151.CrossRefGoogle Scholar
Pittard, J., Camakaris, H. & Yang, J. (2005). The TyrR regulon. Molecular Microbiology 55, 16–26.CrossRefGoogle ScholarPubMed
Rhodius, V. A. & Busby, S. J. W. (1998). Positive activation of gene expression. Current Opinion in Microbiology 1, 152–159.CrossRefGoogle ScholarPubMed
Rojo, F. (1999). Repression of transcription initiation in bacteria. Journal of Bacteriology 181, 2987–2991.Google ScholarPubMed
Roy, S., Garges, S. & Adhya, S. (1998). Activation and repression of transcription by differential contact: two sides of a coin. Journal of Biological Chemistry 273, 14059–14062.CrossRefGoogle ScholarPubMed
Xu, H. & Hoover, T. R. (2001). Transcriptional regulation at a distance in bacteria. Current Opinion in Microbiology 4, 138–144.CrossRefGoogle Scholar
Alifano, P., Fani, R., Lio, P., Lazcano, A., Bazzicalupo, M., Carlomagno, M. S. & Bruni, C. B. (1996). Histidine biosynthetic pathway and genes: structure, regulation, and evolution. Microbiological Reviews 60, 44.Google ScholarPubMed
Babitzke, P. (2004). Regulation of transcription attenuation and translation initiation by allosteric control of an RNA-binding protein: the Bacillus subtilis TRAP protein. Current Opinion in Microbiology 7, 132–139.CrossRefGoogle ScholarPubMed
Gollnick, P., Babitzke, P., Antson, A. & Yanofsky, C. (2005). Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. Annual Review of Genetics 39, 47–68.CrossRefGoogle ScholarPubMed
Mullerhill, B. (1998). Some repressors of bacterial transcription. Current Opinion in Microbiology 1, 145–151.CrossRefGoogle Scholar
Rojo, F. (1999). Repression of transcription initiation in bacteria. Journal of Bacteriology 181, 2987–2991.Google ScholarPubMed
Yanofsky, C. (2004). The different roles of tryptophan transfer RNA in regulating trp operon expression in E. coli versus B. subtilis. Trends in Genetics 20, 367–374.CrossRefGoogle Scholar
Amster-Choder, O. (2005). The bgl sensory system: a transmembrane signaling pathway controlling transcriptional antitermination. Current Opinion in Microbiology 8, 127–134.CrossRefGoogle ScholarPubMed
Condon, C., Squires, C. & Squires, C. L. (1995). Control of rRNA transcription in Escherichia coli. Microbiological Reviews 59, 623.Google ScholarPubMed
Gollnick, P. & Babitzke, P. (2002). Transcription attenuation. Biochimica et Biophysica Acta – Gene Structure and Expression 1577, 240–250.CrossRefGoogle ScholarPubMed
Santangelo, T. J. & Roberts, J. W. (2002). RfaH, a bacterial transcription antiterminator. Molecular Cell 9, 698–700.CrossRefGoogle ScholarPubMed
Shu, C. J. & Zhulin, I. B. (2002). ANTAR: an RNA-binding domain in transcription antitermination regulatory proteins. Trends in Biochemical Sciences 27, 3–5.CrossRefGoogle ScholarPubMed
Weisberg, R. A. & Gottesman, M. E. (1999). Processive antitermination. Journal of Bacteriology 181, 359–367.Google ScholarPubMed
Alexandre, G. & Zhulin, I. B. (2001). More than one way to sense chemicals [Review]. Journal of Bacteriology 183, 4681–4686.CrossRefGoogle Scholar
Backert, S. & Selbach, M. (2005). Tyrosine-phosphorylated bacterial effector proteins: the enemies within. Trends in Microbiology 13, 476–484.CrossRefGoogle Scholar
Beier, D. & Gross, R. (2006). Regulation of bacterial virulence by two-component systems. Current Opinion in Microbiology 9, 143–152.CrossRefGoogle ScholarPubMed
Buckler, D. R., Anand, G. S. & Stock, A. M. (2000). Response-regulator phosphorylation and activation: a two-way street?Trends in Microbiology 8, 153–156.CrossRefGoogle ScholarPubMed
Dunny, G. M. & Leonard, B. A. B. (1997). Cell-cell communication in Gram-positive bacteria. Annual Review of Microbiology 51, 527–564.CrossRefGoogle ScholarPubMed
Fabret, C., Feher, V. A. & Hoch, J. A. (1999). Two-component signal transduction in Bacillus subtilis: how one organism sees its world. Journal of Bacteriology 181, 1975–1983.Google ScholarPubMed
Galperin, M. Y. (2004). Bacterial signal transduction network in a genomic perspective. Environmental Microbiology 6, 552–567.CrossRefGoogle Scholar
Hancock, L. & Perego, M. (2002). Two-component signal transduction in Enterococcus faecalis. Journal of Bacteriology 184, 5819–5825.CrossRefGoogle ScholarPubMed
Hoch, J. A. & Varughese, K. I. (2001). Keeping signals straight in phosphorelay signal transduction. Journal of Bacteriology 183, 4941–4949.CrossRefGoogle ScholarPubMed
Hoskisson, P. A. & Hutchings, M. I. (2006). MtrAB-LpqB: a conserved three-component system in actinobacteria?Trends in Microbiology 14, 444–449.CrossRefGoogle ScholarPubMed
Hutchings, M. I., Hoskisson, P. A., Chandra, G. & Chandra, G. (2004). Sensing and responding to diverse extracellular signals? Analysis of the sensor kinases and response regulators of Streptomyces coelicolor A3(2). Microbiology-UK 150, 2795–2806.CrossRefGoogle Scholar
Lux, R. & Shi, W. (2005). A novel bacterial signalling system with a combination of a Ser/Thr kinase cascade and a His/Asp two-component system. Molecular Microbiology 58, 345–348.CrossRefGoogle Scholar
Novick, R. P. (2003). Autoinduction and signal transduction in the regulation of staphylococcal virulence. Molecular Microbiology 48, 1429–1449.CrossRefGoogle ScholarPubMed
Ruiz, N. & Silhavy, T. J. (2005). Sensing external stress: watchdogs of the Escherichia coli cell envelope. Current Opinion in Microbiology 8, 122–126.CrossRefGoogle ScholarPubMed
Stock, A. M. & Guhaniyogi, J. (2006). A new perspective on response regulator activation. Journal of Bacteriology 188, 7328–7330.CrossRefGoogle ScholarPubMed
Stock, A. M., Robinson, V. L. & Goudreau, P. N. (2000). Two-component signal transduction. Annual Review of Biochemistry 69, 183–215.CrossRefGoogle ScholarPubMed
Varughese, K. (2002). Molecular recognition of bacterial phosphorelay proteins. Current Opinion in Microbiology 5, 142–148.CrossRefGoogle ScholarPubMed
West, A. H. & Stock, A. M. (2001). Histidine kinases and response regulator proteins in two-component signaling systems. Trends in Biochemical Sciences 26, 369–376.CrossRefGoogle ScholarPubMed
Lindner, C., Hecker, M., Coq, D. & Deutscher, J. (2002). Bacillus subtilis mutant LicT antiterminators exhibiting enzyme I- and HPr-independent antitermination affect catabolite repression of the bglPH operon. Journal of Bacteriology 184, 4819–4828.CrossRefGoogle ScholarPubMed
Schneider, D. A., Ross, W. & Gourse, R. L. (2003). Control of rRNA expression in Escherichia coli. Current Opinion in Microbiology 6, 151–156.CrossRefGoogle ScholarPubMed
Agrawal, N., Dasaradhi, P. V. N., Mohmmed, A., Malhotra, P., Bhatnagar, R. K. & Mukherjee, S. K. (2003). RNA interference: biology, mechanism, and applications. Microbiology and Molecular Biology Reviews 67, 657–685.CrossRefGoogle ScholarPubMed
Altuvia, S. (2004). Regulatory small RNAs: the key to coordinating global regulatory circuits. Journal of Bacteriology 186, 6679–6680.CrossRefGoogle ScholarPubMed
Altuvia, S. & Wagner, E. G. (2000). Switching on and off with RNA. Proceedings of the National Academy of Sciences, USA 97, 9824–9826.CrossRefGoogle ScholarPubMed
Babitzke, P. (2004). Regulation of transcription attenuation and translation initiation by allosteric control of an RNA-binding protein: the Bacillus subtilis TRAP protein. Current Opinion in Microbiology 7, 132–139.CrossRefGoogle ScholarPubMed
Baulcombe, D. (2005). RNA silencing. Trends in Biochemical Sciences 30, 290–293.CrossRefGoogle ScholarPubMed
Boni, I. V. (2006). Diverse molecular mechanisms of translation initiation in prokaryotes. Molecular Biology 40, 587–596.CrossRefGoogle ScholarPubMed
Brantl, S. (2002). Antisense-RNA regulation and RNA interference. Biochimica et Biophysica Acta – Gene Structure and Expression 1575, 15–25.CrossRefGoogle ScholarPubMed
Condon, C. (2003). RNA processing and degradation in Bacillus subtilis. Microbiology and Molecular Biology Reviews 67, 157–174.CrossRefGoogle ScholarPubMed
Condon, C. (2006). Shutdown decay of mRNA. Molecular Microbiology 61, 573–583.CrossRefGoogle ScholarPubMed
Delihas, N. & Forst, S. (2001). MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factors. Journal of Molecular Biology 313, 1–12.CrossRefGoogle ScholarPubMed
Denli, A. M. & Hannon, G. J. (2003). RNAi: an ever-growing puzzle. Trends in Biochemical Sciences 28, 196–201.CrossRefGoogle ScholarPubMed
Dennis, P. P., Omer, A. & Lowe, T. (2001). A guided tour: small RNA function in Archaea. Molecular Microbiology 40, 509–519.CrossRefGoogle ScholarPubMed
Eckstein, F. (2005). Small non-coding RNAs as magic bullets. Trends in Biochemical Sciences 30, 445–452.CrossRefGoogle ScholarPubMed
Filipowicz, W., Jaskiewicz, L., Kolb, F. A. & Pillai, R. S. (2005). Post-transcriptional gene silencing by siRNAs and miRNAs. Current Opinion in Structural Biology 15, 331–341.CrossRefGoogle ScholarPubMed
Franch, T. & Gerdes, K. (2000). U-turns and regulatory RNAs. Current Opinion in Microbiology 3, 159–164.CrossRefGoogle ScholarPubMed
Gelfand, M. S. (2006). Bacterial cis-regulatory RNA structures. Molecular Biology 40, 541–550.CrossRefGoogle Scholar
Gottesman, S. (2004). The small RNA regulators of Escherichia coli: roles and mechanisms. Annual Review of Microbiology 58, 303–328.CrossRefGoogle ScholarPubMed
Huttenhofer, A., Brosius, J. & Bachellerie, J. P. (2002). RNomics: identification and function of small, non-messenger RNAs. Current Opinion in Chemical Biology 6, 835–843.CrossRefGoogle ScholarPubMed
Kennell, D. (2002). Processing endoribonucleases and mRNA degradation in bacteria. Journal of Bacteriology 184, 4645–4657.CrossRefGoogle ScholarPubMed
Kushner, S. R. (2002). mRNA decay in Escherichia coli comes of age. Journal of Bacteriology 184, 4658–4665.CrossRefGoogle ScholarPubMed
Lease, R. A. & Belfort, M. (2000). Riboregulation by DsrA RNA: trans-actions for global economy. Molecular Microbiology 38, 667–672.CrossRefGoogle ScholarPubMed
Mata, J., Marguerat, S. & Bahler, J. (2005). Post-transcriptional control of gene expression: a genome-wide perspective. Trends in Biochemical Sciences 30, 506–514.CrossRefGoogle ScholarPubMed
Nair, V. & Zavolan, M. (2006). Virus-encoded microRNAs: novel regulators of gene expression. Trends in Microbiology 14, 169–175.CrossRefGoogle ScholarPubMed
Nogueira, T. & Springer, M. (2000). Post-transcriptional control by global regulators of gene expression in bacteria. Current Opinion in Microbiology 3, 154–158.CrossRefGoogle ScholarPubMed
Nudler, E. & Mironov, A. S. (2004). The riboswitch control of bacterial metabolism. Trends in Biochemical Sciences 29, 11–17.CrossRefGoogle ScholarPubMed
Rauhut, R. & Klug, G. (1999). mRNA degradation in bacteria. FEMS Microbiology Reviews 23, 353–370.CrossRefGoogle ScholarPubMed
Repoila, F., Majdalani, N. & Gottesman, S. (2003). Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm. Molecular Microbiology 48, 855–861.CrossRefGoogle ScholarPubMed
Schlax, P. J. & Worhunsky, D. J. (2003). Translational repression mechanisms in prokaryotes. Molecular Microbiology 48, 1157–1169.CrossRefGoogle ScholarPubMed
Storz, G., Opdyke, J. A. & Zhang, A. (2004). Controlling mRNA stability and translation with small, noncoding RNAs. Current Opinion in Microbiology 7, 140–144.CrossRefGoogle ScholarPubMed
Takayama, K. & Kjelleberg, S. A. (2000). The role of RNA stability during bacterial stress responses and starvation. Environmental Microbiology 2, 355–365.CrossRefGoogle ScholarPubMed
Tang, G. (2005). siRNA and miRNA: an insight into RISCs. Trends in Biochemical Sciences 30, 106–114.CrossRefGoogle ScholarPubMed
Valentin-Hansen, P., Eriksen, M. & Udesen, C. (2004). The bacterial Sm-like protein Hfq: a key player in RNA transactions. Molecular Microbiology 51, 1525–1533.CrossRefGoogle ScholarPubMed
Wang, Y., Liu, C. L., Storey, J. D., Tibshirani, R. J., Herschlag, D. & Brown, P. O. (2002). Precision and functional specificity in mRNA decay. Proceedings of the National Academy of Sciences, USA 99, 5860–5865.CrossRefGoogle ScholarPubMed
Winkler, W. C. (2005). Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Current Opinion in Chemical Biology 9, 594–602.CrossRefGoogle ScholarPubMed
Braeken, K., Moris, M., Daniels, R., Vanderleyden, J. & Michiels, J. (2006). New horizons for (p)ppGpp in bacterial and plant physiology. Trends in Microbiology 14, 45–54.CrossRefGoogle ScholarPubMed
Dennis, P. P., Ehrenberg, M. & Bremer, H. (2004). Control of rRNA synthesis in Escherichia coli: a systems biology approach. Microbiology and Molecular Biology Reviews 68, 639–668.CrossRefGoogle ScholarPubMed
Ferenci, T. (1999). Regulation by nutrient limitation. Current Opinion in Microbiology 2, 208–213.CrossRefGoogle ScholarPubMed
Ferenci, T. (2001). Hungry bacteria: definition and properties of a nutritional state. Environmental Microbiology 3, 605–611.CrossRefGoogle ScholarPubMed
Gralla, J. D. (2005). Escherichia coli ribosomal RNA transcription: regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein. Molecular Microbiology 55, 973–977.CrossRefGoogle Scholar
Hengge-Aronis, R. (1999). Interplay of global regulators and cell physiology in the general stress response of Escherichia coli. Current Opinion in Microbiology 2, 148–152.CrossRefGoogle ScholarPubMed
Hengge-Aronis, R. (2002). Signal transduction and regulatory mechanisms involved in control of the σS (RpoS) subunit of RNA polymerase. Microbiology and Molecular Biology Reviews 66, 373–395.CrossRefGoogle Scholar
Magnusson, L. U., Farewell, A. & Nystrom, T. (2005). ppGpp: a global regulator in Escherichia coli. Trends in Microbiology 13, 236–242.CrossRefGoogle ScholarPubMed
Spector, M. P. (1998). The starvation-stress response (SSR) of Salmonella. Advances in Microbial Physiology 40, 233–279.CrossRefGoogle ScholarPubMed
Venturi, V. (2003). Control of rpoS transcription in Escherichia coli and Pseudomonas: why so different?Journal of Molecular Microbiology and Biotechnology 49, 1–9.Google ScholarPubMed
Arcondeguy, T., Jack, R. & Merrick, M. (2001). P-II signal transduction proteins, pivotal players in microbial nitrogen control. Microbiology and Molecular Biology Reviews 65, 80–105.CrossRefGoogle ScholarPubMed
Burkovski, A. (2003). Ammonium assimilation and nitrogen control in Corynebacterium glutamicum and its relatives: an example for new regulatory mechanisms in actinomycetes. FEMS Microbiology Reviews 27, 617–628.CrossRefGoogle ScholarPubMed
Charbit, A. (1996). Coordination of carbon and nitrogen metabolism. Research in Microbiology 147, 513–518.CrossRefGoogle ScholarPubMed
Commichau, F. M., Forchhammer, K. & Stulke, J. (2006). Regulatory links between carbon and nitrogen metabolism. Current Opinion in Microbiology 9, 167–172.CrossRefGoogle ScholarPubMed
Fisher, S. H. (1999). Regulation of nitrogen metabolism in Bacillus subtilis: vive la difference!Molecular Microbiology 32, 223–232.CrossRefGoogle ScholarPubMed
Forchhammer, K. (2004). Global carbon/nitrogen control by PII signal transduction in cyanobacteria: from signals to targets. FEMS Microbiology Reviews 28, 319–333.CrossRefGoogle Scholar
Merrick, M. J. & Edwards, R. A. (1995). Nitrogen control in bacteria. Microbiological Reviews 59, 604–622.Google ScholarPubMed
Ninfa, A. J. & Jiang, P. (2005). PII signal transduction proteins: sensors of α-ketoglutarate that regulate nitrogen metabolism. Current Opinion in Microbiology 8, 168–173.CrossRefGoogle ScholarPubMed
Reitzer, L. (2003). Nitrogen assimilation and global regulation in Escherichia coli. Annual Review of Microbiology 57, 155–176.CrossRefGoogle ScholarPubMed
Schwarz, R. & Forchhammer, K. (2005). Acclimation of unicellular cyanobacteria to macronutrient deficiency: emergence of a complex network of cellular responses. Microbiology-UK 151, 2503–2514.CrossRefGoogle ScholarPubMed
Silberbach, M. & Burkovski, A. (2006). Application of global analysis techniques to Corynebacterium glutamicum: new insights into nitrogen regulation. Journal of Biotechnology 126, 101–110.CrossRefGoogle ScholarPubMed
Atkinson, S., Sockett, R. E., Camara, M. & Williams, P. (2006). Quorum sensing and the lifestyle of Yersinia. Current Issues in Molecular Biology 8, 1–10.Google ScholarPubMed
Bauer, W. & Robinson, J. (2002). Disruption of bacterial quorum sensing by other organisms. Current Opinion in Biotechnology 13, 234–237.CrossRefGoogle ScholarPubMed
Daniels, R., Vanderleyden, J. & Michiels, J. (2004). Quorum sensing and swarming migration in bacteria. FEMS Microbiology Reviews 28, 261–289.CrossRefGoogle ScholarPubMed
Keersmaecker, S. C. J., Sonck, K. & Vanderleyden, J. (2006). Let LuxS speak up in AI-2 signaling. Trends in Microbiology 14, 114–119.CrossRefGoogle ScholarPubMed
Fuqua, C. (2006). The QscR quorum-sensing regulon of Pseudomonas aeruginosa: an orphan claims its identity. Journal of Bacteriology 188, 3169–3171.CrossRefGoogle ScholarPubMed
Gonzalez, J. E. & Marketon, M. M. (2003). Quorum sensing in nitrogen-fixing rhizobia. Microbiology and Molecular Biology Reviews 67, 574–592.CrossRefGoogle ScholarPubMed
Jacob, E. B., Becker, I., Shapira, Y. & Levine, H. (2004). Bacterial linguistic communication and social intelligence. Trends in Microbiology 12, 366–372.CrossRefGoogle ScholarPubMed
Keller, L. & Surette, M. G. (2006). Communication in bacteria: an ecological and evolutionary perspective. Nature Reviews Microbiology 4, 249–258.CrossRefGoogle ScholarPubMed
Kjelleberg, S. & Molin, S. (2002). Is there a role for quorum sensing signals in bacterial biofilms?Current Opinion in Microbiology 5, 254–258.CrossRefGoogle Scholar
Klose, K. E. (2006). Increased chatter: cyclic dipeptides as molecules of chemical communication in Vibrio spp. Journal of Bacteriology 188, 2025–2026.CrossRefGoogle ScholarPubMed
Miller, M. B. & Bassler, B. L. (2001). Quorum sensing in bacteria. Annual Review of Microbiology 55, 165–199.CrossRefGoogle ScholarPubMed
Pappas, K. M., Weingart, C. L. & Winans, S. C. (2004). Chemical communication in proteobacteria: biochemical and structural studies of signal synthases and receptors required for intercellular signalling. Molecular Microbiology 53, 755–770.CrossRefGoogle ScholarPubMed
Parsek, M. R. & Greenberg, E. P. (2005). Sociomicrobiology: the connections between quorum sensing and biofilms. Trends in Microbiology 13, 27–33.CrossRefGoogle ScholarPubMed
Rasmussen, T. B. & Givskov, M. (2006). Quorum sensing inhibitors: a bargain of effects. Microbiology-UK 152, 895–904.CrossRefGoogle Scholar
Reading, N. C. & Sperandio, V. (2006). Quorum sensing: the many languages of bacteria. FEMS Microbiology Letters 254, 1–11.CrossRefGoogle Scholar
Roche, D. M., Byers, J. T., Smith, D. S., Glansdorp, F. G., Spring, D. R. & Welch, M. (2004). Communications blackout? Do N-acylhomoserine-lactone-degrading enzymes have any role in quorum sensing?Microbiology-UK 150, 2023–2028.CrossRefGoogle ScholarPubMed
Sturme, M. H., Kleerebezem, M., Nakayama, J., Akkermans, A. D., Vaugha, E. E. & Vos, W. M. (2002). Cell to cell communication by autoinducing peptides in Gram-positive bacteria. Antonie van Leeuwenhoek 81, 233–243.CrossRefGoogle ScholarPubMed
Suntharalingam, P. & Cvitkovitch, D. G. (2005). Quorum sensing in streptococcal biofilm formation. Trends in Microbiology 13, 3–6.CrossRefGoogle ScholarPubMed
Venturi, V. (2006). Regulation of quorum sensing in Pseudomonas. FEMS Microbiology Reviews 30, 274–291.CrossRefGoogle ScholarPubMed
Whitehead, N. A., Barnard, A. M. L., Slater, H., Simpson, N. J. L. & Salmond, G. P. C. (2001). Quorum-sensing in Gram-negative bacteria. FEMS Microbiology Reviews 25, 365–404.CrossRefGoogle ScholarPubMed
Withers, H., Swift, S. & Williams, P. (2001). Quorum sensing as an integral component of gene regulatory networks in Gram-negative bacteria. Current Opinion in Microbiology 4, 186–193.CrossRefGoogle ScholarPubMed
Zhang, L. H. & Dong, Y. H. (2004). Quorum sensing and signal interference: diverse implications. Molecular Microbiology 53, 1563–1571.CrossRefGoogle ScholarPubMed
Bauer, C. E., Elsen, S. & Bird, T. H. (1999). Mechanisms for redox control of gene expression. Annual Review of Microbiology 53, 495–523.CrossRefGoogle ScholarPubMed
Beinert, H. & Kiley, P. (1996). Redox control of gene expression involving iron-sulfur proteins. Change of oxidation-state or assembly/disassembly of Fe-S clusters?FEBS Letters 382, 218–219.CrossRefGoogle ScholarPubMed
Elsen, S., Swem, L. R., Swem, D. L. & Bauer, C. E. (2004). RegB/RegA, a highly conserved redox-responding global two-component regulatory system. Microbiology and Molecular Biology Reviews 68, 263–279.CrossRefGoogle ScholarPubMed
Green, J. & Paget, M. S. (2004). Bacterial redox sensors. Nature Reviews Microbiology 2, 954–966.CrossRefGoogle ScholarPubMed
Imlay, J. A. (2006). Iron-sulphur clusters and the problem with oxygen. Molecular Microbiology 59, 1073–1082.CrossRefGoogle ScholarPubMed
Kiley, P. J. & Beinert, H. (1999). Oxygen sensing by the global regulator, FNR, the role of the iron-sulfur cluster. FEMS Microbiology Reviews 22, 341–352.CrossRefGoogle Scholar
Kiley, P. J. & Beinert, H. (2003). The role of Fe-S proteins in sensing and regulation in bacteria. Current Opinion in Microbiology 6, 181–185.CrossRefGoogle ScholarPubMed
Nakano, M. M. & Zuber, P. (1998). Anaerobic growth of a ‘strict aerobe’ (Bacillus subtilis). Annual Review of Microbiology 52, 165–190.CrossRefGoogle Scholar
Sawers, G. (2001). A novel mechanism controls anaerobic and catabolite regulation of the Escherichia coli tdc operon. Molecular Microbiology 39, 1285–1298.CrossRefGoogle ScholarPubMed
Taylor, B. L., Zhulin, I. B. & Johnson, M. S. (1999). Aerotaxis and other energy-sensing behavior in bacteria. Annual Review of Microbiology 53, 103–128.CrossRefGoogle ScholarPubMed
Unden, G. (1998). Transcriptional regulation and energetics of alternative respiratory pathways in facultatively anaerobic bacteria. Biochimica et Biophysica Acta – Bioenergetics 1365, 220–224.CrossRefGoogle Scholar
Unden, G. & Schirawski, J. (1997). The oxygen-responsive transcriptional regulator FNR of Escherichia coli: the search for signals and reactions. Molecular Microbiology 25, 205–210.CrossRefGoogle ScholarPubMed
Groisman, E. A. (2001). The pleiotropic two-component regulatory system PhoP-PhoQ. Journal of Bacteriology 183, 1835–1842.CrossRefGoogle ScholarPubMed
Hulett, F. M. (1996). The signal-transduction network for Pho regulation in Bacillus subtilis. Molecular Microbiology 19, 933–939.CrossRefGoogle ScholarPubMed
Lenburg, M. E. & Oshea, E. K. (1996). Signaling phosphate starvation. Trends in Biochemical Sciences 21, 383–387.CrossRefGoogle ScholarPubMed
Martin, J. F. (2004). Phosphate control of the biosynthesis of antibiotics and other secondary metabolites is mediated by the PhoR-PhoP system: an unfinished story. Journal of Bacteriology 186, 5197–5201.CrossRefGoogle Scholar
Vershinina, O. A. & Znamenskaya, L. V. (2002). The pho regulons of bacteria. Microbiology-Moscow 71, 497–511.CrossRefGoogle Scholar
Aertsen, A., Vanoirbeek, K., Spiegeleer, P., Sermon, J., Hauben, K., Farewell, A., Nystrom, T. & Michiels, C. W. (2004). Heat shock protein-mediated resistance to high hydrostatic pressure in Escherichia coli. Applied and Environmental Microbiology 70, 2660–2666.CrossRefGoogle ScholarPubMed
Chhabra, S. R., He, Q., Huang, K. H., Gaucher, S. P., Alm, E. J., He, Z., Hadi, M. Z., Hazen, T. C., Wall, J. D., Zhou, J., Arkin, A. P. & Singh, A. K. (2006). Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology 188, 1817–1828.CrossRefGoogle ScholarPubMed
Crapoulet, N., Barbry, P., Raoult, D. & Renesto, P. (2006). Global transcriptome analysis of Tropheryma whipplei in response to temperature stresses. Journal of Bacteriology 188, 5228–5239.CrossRefGoogle ScholarPubMed
Dubern, J. F., Lagendijk, E. L., Lugtenberg, B. J. J. & Bloemberg, G. V. (2005). The heat shock genes dnaK, dnaJ, and grpE are involved in regulation of putisolvin biosynthesis in Pseudomonas putida PCL1445. Journal of Bacteriology 187, 5967–5976.CrossRefGoogle ScholarPubMed
Engels, S., Schweitzer, J. E., Ludwig, C., Bott, M. & Schaffer, S. (2004). clpC and clpP1P2 gene expression in Corynebacterium glutamicum is controlled by a regulatory network involving the transcriptional regulators ClgR and HspR as well as the ECF sigma factor σH. Molecular Microbiology 52, 285–302.CrossRefGoogle ScholarPubMed
Helmann, J. D., Wu, M. F. W., Kobel, P. A., Gamo, F. J., Wilson, M., Morshedi, M. M., Navre, M. & Paddon, C. (2001). Global transcriptional response of Bacillus subtilis to heat shock. Journal of Bacteriology 183, 7318–7328.CrossRefGoogle ScholarPubMed
Hillmann, F., Fischer, R. J. & Bahl, H. (2006). The rubrerythrin-like protein Hsp21 of Clostridium acetobutylicum is a general stress protein. Archives of Microbiology 185, 270–276.CrossRefGoogle ScholarPubMed
Kourennaia, O. V., Tsujikawa, L. & Haseth, P. L. (2005). Mutational analysis of Escherichia coli heat shock transcription factor sigma 32 reveals similarities with sigma 70 in recognition of the − 35 promoter element and differences in promoter DNA melting and − 10 recognition. Journal of Bacteriology 187, 6762–6769.CrossRefGoogle ScholarPubMed
Laksanalamai, P., Maeder, D. L. & Robb, F. T. (2001). Regulation and mechanism of action of the small heat shock protein from the hyperthermophilic archaeon Pyrococcus furiosus. Journal of Bacteriology 183, 5198–5202.CrossRefGoogle ScholarPubMed
Musatovova, O., Dhandayuthapani, S. & Baseman, J. B. (2006). Transcriptional heat shock response in the smallest known self-replicating cell, Mycoplasma genitalium. Journal of Bacteriology 188, 2845–2855.CrossRefGoogle ScholarPubMed
Schmid, A. K., Howell, H. A., Battista, Jo R., Peterson, S. N. & Lidstrom, M. E. (2005). HspR is a global negative regulator of heat shock gene expression in Deinococcus radiodurans. Molecular Microbiology 55, 1579–1590.CrossRefGoogle ScholarPubMed
Senn, M. M., Giachino, P., Homerova, D., Steinhuber, A., Strassner, J., Kormanec, J., Fluckiger, U., Berger-Bachi, B. & Bischoff, M. (2005). Molecular analysis and organization of the σB operon in Staphylococcus aureus. Journal of Bacteriology 187, 8006–8019.CrossRefGoogle ScholarPubMed
Servant, P. & Mazodier, P. (2001). Negative regulation of the heat shock response in Streptomyces. Archives of Microbiology 176, 237–242.CrossRefGoogle ScholarPubMed
Tachdjian, S. & Kelly, R. M. (2006). Dynamic metabolic adjustments and genome plasticity are implicated in the heat shock response of the extremely thermoacidophilic archaeon Sulfolobus solfataricus. Journal of Bacteriology 188, 4553–4559.CrossRefGoogle ScholarPubMed
Beckering, C. L., Steil, L., Weber, M. H. W., Volker, U. & Marahiel, M. A. (2002). Genomewide transcriptional analysis of the cold shock response in Bacillus subtilis. Journal of Bacteriology 184, 6395–6402.CrossRefGoogle ScholarPubMed
Beran, R. K. & Simons, R. W. (2001). Cold-temperature induction of Escherichia coli polynucleotide phosphorylase occurs by reversal of its autoregulation. Molecular Microbiology 39, 112–125.CrossRefGoogle ScholarPubMed
Cairrao, F., Cruz, A., Mori, H. & Arraiano, C. M. (2003). Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA. Molecular Microbiology 50, 1349–1360.CrossRefGoogle ScholarPubMed
Cavicchioli, R., Thomas, T. & Curmi, P. M. G. (2000). Cold stress response in Archaea. Extremophiles 4, 321–331.CrossRefGoogle ScholarPubMed
Datta, P. P. & Bhadra, R. K. (2003). Cold shock response and major cold shock proteins of Vibrio cholerae. Applied and Environmental Microbiology 69, 6361–6369.CrossRefGoogle ScholarPubMed
Fang, L., Hou, Y. & Inouye, M. (1998). Role of the cold-box region in the 5′ untranslated region of the cspA mRNA in its transient expression at low temperature inEscherichia coli. Journal of Bacteriology 180, 90–95.Google ScholarPubMed
Gao, H., Yang, Z. K., Wu, L., Thompson, D. K. & Zhou, J. (2006). Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins. Journal of Bacteriology 188, 4560–4569.CrossRefGoogle ScholarPubMed
Gerday, C., Aittaleb, M., Bentahir, M., Chessa, J. P., Claverie, P., Collins, T., D'Amico, S., Dumont, J., Garsoux, G., Georlette, D., Hoyoux, A., Lonhienne, T., Meuwis, M. A. & Feller, G. (2000). Cold-adapted enzymes: from fundamentals to biotechnology. Trends in Biotechnology 18, 103–107.CrossRefGoogle ScholarPubMed
Giangrossi, M., Exley, R. M., Hegarat, F. & Pon, C. L. (2001). Different in vivo localization of the Escherichia coli proteins CspD and CspA. FEMS Microbiology Letters 202, 171–176.CrossRefGoogle ScholarPubMed
Graumann, P. & Marahiel, M. A. (1996). Some like it cold: response of microorganisms to cold shock. Archives of Microbiology 166, 293–300.CrossRefGoogle ScholarPubMed
Graumann, P. L. & Marahiel, M. A. (1998). A superfamily of proteins that contain the cold-shock domain. Trends in Biochemical Sciences 23, 286–290.CrossRefGoogle ScholarPubMed
Hunger, K., Beckering, C. L., Wiegeshoff, F., Graumann, P. L. & Marahiel, M. A. (2006). Cold-induced putative DEAD box RNA helicases CshA and CshB are essential for cold adaptation and interact with cold shock protein B in Bacillus subtilis. Journal of Bacteriology 188, 240–248.CrossRefGoogle ScholarPubMed
Katzif, S., Lee, E. H., Law, A. B., Tzeng, Y. L. & Shafer, W. M. (2005). CspA regulates pigment production in Staphylococcus aureus through a SigB-dependent mechanism. Journal of Bacteriology 187, 8181–8184.CrossRefGoogle ScholarPubMed
Lopez, M. M., Yutani, K. & Makhatadze, G. I. (2001). Interactions of the cold shock protein CspB from Bacillus subtilis with single-stranded DNA: importance of the T base content and position within the template. Journal of Biological Chemistry 276, 15511–15518.CrossRefGoogle Scholar
Magg, C., Kubelka, J., Holtermann, G., Haas, E. & Schmid, F. X. (2006). Specificity of the initial collapse in the folding of the cold shock protein. Journal of Molecular Biology 360, 1067–1080.CrossRefGoogle ScholarPubMed
Martinez-Costa, O. H., Zalacain, M., Holmes, D. J. & Malpartida, F. (2003). The promoter of a cold-shock-like gene has pleiotropic effects on Streptomyces antibiotic biosynthesis. FEMS Microbiology Letters 220, 215–221.CrossRefGoogle ScholarPubMed
Phadtare, S. & Inouye, M. (2004). Genome-wide transcriptional analysis of the cold shock response in wild-type and cold-sensitive, quadruple-csp-deletion strains of Escherichia coli. Journal of Bacteriology 186, 7007–7014.CrossRefGoogle ScholarPubMed
Polissi, A., Laurentis, W., Zangrossi, S., Briani, F., Longhi, V., Pesole, G. & Deho, G. (2003). Changes in Escherichia coli transcriptome during acclimatization at low temperature. Research in Microbiology 154, 573–580.CrossRefGoogle ScholarPubMed
Prud'homme-Genereux, A., Beran, R. K., Iost, I., Ramey, C. S., Mackie, G. A. & Simons, R. W. (2004). Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a ‘cold shock degradosome’. Molecular Microbiology 54, 1409–1421.CrossRefGoogle ScholarPubMed
Sakamoto, T. & Murata, N. (2002). Regulation of the desaturation of fatty acids and its role in tolerance to cold and salt stress. Current Opinion in Microbiology 5, 206–210.CrossRefGoogle ScholarPubMed
Smirnova, G. V. & Zakirova, O. N. (2001). The role of antioxidant systems in the cold stress response of Escherichia coli. Microbiology-Moscow 70, 45–50.CrossRefGoogle Scholar
Weber, M. H. W., Klein, W., Muller, L., Niess, U. M. & Marahiel, M. A. (2001). Role of the Bacillus subtilis fatty acid desaturase in membrane adaptation during cold shock. Molecular Microbiology 39, 1321–1329.CrossRefGoogle ScholarPubMed
Wiegeshoff, F., Beckering, C. L., Debarbouille, M. & Marahiel, M. A. (2006). Sigma L is important for cold shock adaptation of Bacillus subtilis. Journal of Bacteriology 188, 3130–3133.CrossRefGoogle Scholar
Wouters, J. A., Rombouts, F. M., Kuipers, O. P., Vos, W. M. & Abee, T. (2000). The role of cold-shock proteins in low-temperature adaptation of food-related bacteria. Systematic and Applied Microbiology 23, 165–173.CrossRefGoogle ScholarPubMed
Xia, B., Ke, H., Jiang, W. & Inouye, M. (2002). The Cold Box stem-loop proximal to the 5′-end of the Escherichia coli cspA gene stabilizes its mRNA at low temperature. Journal of Biological Chemistry 277, 6005–6011.CrossRefGoogle ScholarPubMed
Yamanaka, K. & Inouye, M. (2001). Selective mRNA degradation by polynucleotide phosphorylase in cold shock adaptation in Escherichia coli. Journal of Bacteriology 183, 2808–2816.CrossRefGoogle ScholarPubMed
Brioukhanov, A. L., Netrusov, A. I. & Eggen, R. I. L. (2006). The catalase and superoxide dismutase genes are transcriptionally up-regulated upon oxidative stress in the strictly anaerobic archaeon Methanosarcina barkeri. Microbiology-UK 152, 1671–1677.CrossRefGoogle ScholarPubMed
Gaudu, P., Dubrac, S. & Touati, D. (2000). Activation of SoxR by overproduction of desulfoferrodoxin: multiple ways to induce the soxRS regulon. Journal of Bacteriology 182, 1761–1763.CrossRefGoogle ScholarPubMed
Giro, M., Carrillo, N. & Krapp, A. R. (2006). Glucose-6-phosphate dehydrogenase and ferredoxin-NADP(H) reductase contribute to damage repair during the soxRS response of Escherichia coli. Microbiology-UK 152, 1119–1128.CrossRefGoogle ScholarPubMed
Gonzalez-Flecha, B. & Demple, B. (1999). Role for the oxyS gene in regulation of intracellular hydrogen peroxide in Escherichia coli. Journal of Bacteriology 181, 3833–3836.Google ScholarPubMed
Hassett, D. J., Ma, J. F., Elkins, J. G., McDermott, T. R., Ochsner, U. A., West, S. E. H., Huang, C-T., Fredericks, J., Burnett, S., Stewart, P. S., McFeters, G., Passador, L. and Iglewski, B. H. (1999). Quorum sensing in Pseudomonas aeruginosa controls expression of catalase and superoxide dismutase genes and mediates biofilm susceptibility to hydrogen peroxide. Molecular Microbiology 34, 1082–1093.CrossRefGoogle ScholarPubMed
Imlay, J. A. (2003). Pathways of oxidative damage. Annual Review of Microbiology 57, 395–418.CrossRefGoogle ScholarPubMed
Manchado, M., Michan, C. & Pueyo, C. (2000). Hydrogen peroxide activates the SoxRS regulon in vivo. Journal of Bacteriology 182, 6842–6844.CrossRefGoogle ScholarPubMed
Ohara, N., Kikuchi, Y., Shoji, M., Naito, M. & Nakayama, K. (2006). Superoxide dismutase-encoding gene of the obligate anaerobe Porphyromonas gingivalis is regulated by the redox-sensing transcription activator OxyR. Microbiology-UK 152, 955–966.CrossRefGoogle ScholarPubMed
Rocha, E. R., Owens, G. & Smith, C. J. (2000). The redox-sensitive transcriptional activator OxyR regulates the peroxide response regulon in the obligate anaerobe Bacteroides fragilis. Journal of Bacteriology 182, 5059–5069.CrossRefGoogle ScholarPubMed
Toledano, M. B., Delaunay, A., Monceau, L. & Tacnet, F. (2004). Microbial H2O2 sensors as archetypical redox signaling modules. Trends in Biochemical Sciences 29, 351–357.CrossRefGoogle ScholarPubMed
Bohin, J. P. (2000). Osmoregulated periplasmic glucans in Proteobacteria. FEMS Microbiology Letters 186, 11–19.CrossRefGoogle ScholarPubMed
Kramer, R. & Morbach, S. (2004). BetP of Corynebacterium glutamicum, a transporter with three different functions: betaine transport, osmosensing, and osmoregulation. Biochimica et Biophysica Acta – Bioenergetics 1658, 31–36.CrossRefGoogle ScholarPubMed
Leonardo, M. R. & Forst, S. (1996). Re-examination of the role of the periplasmic domain of EnvZ in sensing of osmolarity signals in Escherichia coli. Molecular Microbiology 22, 405–413.CrossRefGoogle ScholarPubMed
Poolman, B., Spitzer, J. J. & Wood, J. M. (2004). Bacterial osmosensing: roles of membrane structure and electrostatics in lipid-protein and protein-protein interactions. Biochimica et Biophysica Acta – Biomembranes 1666, 88–104.CrossRefGoogle ScholarPubMed
Sleator, R. D. & Hill, C. (2002). Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence. FEMS Microbiology Reviews 26, 49–71.CrossRefGoogle ScholarPubMed
Wood, J. M. (1999). Osmosensing by bacteria: signals and membrane-based sensors. Microbiology and Molecular Biology Reviews 63, 230–262.Google ScholarPubMed
Aizawa, S., Harwood, C. S. & Kadner, R. J. (2000). Signaling components in bacterial locomotion and sensory reception. Journal of Bacteriology 182, 1459–1471.CrossRefGoogle ScholarPubMed
Alexandre, G., Greer-Phillips, S. & Zhulin, I. B. (2004). Ecological role of energy taxis in microorganisms. FEMS Microbiology Reviews 28, 113–126.CrossRefGoogle ScholarPubMed
Blair, D. F. (1995). How bacteria sense and swim. Annual Review of Microbiology 49, 489–522.CrossRefGoogle ScholarPubMed
Bren, A. & Eisenbach, M. (2000). How signals are heard during bacterial chemotaxis: protein-protein interactions in sensory signal propagation. Journal of Bacteriology 182, 6865–6873.CrossRefGoogle ScholarPubMed
Chilcott, G. S. & Hughes, K. T. (2000). Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli. Microbiology and Molecular Biology Reviews 64, 694–708.CrossRefGoogle ScholarPubMed
Levit, M. N., Liu, Y. & Stock, J. B. (1998). Stimulus response coupling in bacterial chemotaxis: receptor dimers in signalling arrays. Molecular Microbiology 30, 459–466.CrossRefGoogle ScholarPubMed
Macnab, R. M. (1999). The bacterial flagellum: reversible rotary propeller and type III export apparatus. Journal of Bacteriology 181, 7149–7153.Google Scholar
Manson, M. D., Armitage, J. P., Hoch, J. A. & Macnab, R. M. (1998). Bacterial locomotion and signal transduction. Journal of Bacteriology 180, 1009–1022.Google ScholarPubMed
Mitchell, J. G. & Kogure, K. (2006). Bacterial motility: links to the environment and a driving force for microbial physics. FEMS Microbiology Ecology 55, 3–16.CrossRefGoogle Scholar
Parkinson, J. S. (2003). Bacterial chemotaxis: a new player in response regulator dephosphorylation. Journal of Bacteriology 185, 1492–1494.CrossRefGoogle ScholarPubMed
Parkinson, J. S., Ames, P. & Studdert, C. A. (2005). Collaborative signaling by bacterial chemoreceptors. Current Opinion in Microbiology 8, 116–121.CrossRefGoogle ScholarPubMed
Sourjik, V. (2004). Receptor clustering and signal processing in E. coli chemotaxis. Trends in Microbiology 12, 569–576.CrossRefGoogle ScholarPubMed
Szurmant, H. & Ordal, G. W. (2004). Diversity in chemotaxis mechanisms among the bacteria and archaea. Microbiology and Molecular Biology Reviews 68, 301–319.CrossRefGoogle ScholarPubMed
Taylor, B. L., Zhulin, I. B. & Johnson, M. S. (1999). Aerotaxis and other energy-sensing behavior in bacteria. Annual Review of Microbiology 53, 103–128.CrossRefGoogle ScholarPubMed
Aertsen, A. & Michiels, C. W. (2005). Diversify or die: generation of diversity in response to stress. Critical Reviews in Microbiology 31, 69–78.CrossRefGoogle ScholarPubMed
Amzallag, G. N. (2004). Adaptive changes in bacteria: a consequence of nonlinear transitions in chromosome topology?Journal of Theoretical Biology 229, 361–369.CrossRefGoogle ScholarPubMed
Dubnau, D. & Losick, R. (2006). Bistability in bacteria. Molecular Microbiology 61, 564–572.CrossRefGoogle ScholarPubMed
Foster, P. L. (1993). Adaptive mutation: the uses of adversity. Annual Review of Microbiology 47, 467–504.CrossRefGoogle ScholarPubMed
Foster, P. L. (2005). Stress responses and genetic variation in bacteria. Mutation Research–Fundamental and Molecular Mechanisms of Mutagenesis 569, 3–11.CrossRefGoogle ScholarPubMed
Goudreau, P. N. & Stock, A. M. (1998). Signal transduction in bacteria: molecular mechanisms of stimulus-response coupling. Current Opinion in Microbiology 1, 160–169.CrossRefGoogle ScholarPubMed
Igoshin, O. A., Price, C. W. & Savageau, M. A. (2006). Signalling network with a bistable hysteretic switch controls developmental activation of the sigmaF transcription factor in Bacillus subtilis. Molecular Microbiology 61, 165–184.CrossRefGoogle ScholarPubMed
Martin, B., Quentin, Y., Fichant, G. & Claverys, J. P. (2006). Independent evolution of competence regulatory cascades in streptococci?Trends in Microbiology 14, 339–345.CrossRefGoogle ScholarPubMed
Osorio, G. & Jerez, C. A. (1996). Adaptive response of the archaeon Sulfolobus acidocaldarius BC65 to phosphate starvation. Microbiology-UK 142, 1531–1536.CrossRefGoogle ScholarPubMed
Rosenberg, S. M. (1994). In pursuit of a molecular mechanism for adaptive mutation. Genome 37, 893–899.CrossRefGoogle ScholarPubMed
Sniegowski, P. D. & Lenski, R. E. (1995). Mutation and adaptation: the directed mutation controversy in evolutionary perspective. Annual Review of Ecology and Systematics 26, 553–578.CrossRefGoogle Scholar
Wright, B. E. (2004). Stress-directed adaptive mutations and evolution. Molecular Microbiology 52, 643–650.CrossRefGoogle ScholarPubMed
Arcondeguy, T., Jack, R. & Merrick, M. (2001). P-II signal transduction proteins, pivotal players in microbial nitrogen control. Microbiology Molecular Biology Reviews 65, 80–105.CrossRefGoogle ScholarPubMed
Commichau, F. M., Forchhammer, K. & Stulke, J. (2006). Regulatory links between carbon and nitrogen metabolism. Current Opinion in Microbiology 9, 167–172.CrossRefGoogle ScholarPubMed
Edwards, J. S., Covert, M. & Palsson, B. (2002). Metabolic modelling of microbes: the flux-balance approach. Environmental Microbiology 4, 133–140.CrossRefGoogle ScholarPubMed
Ehrmann, M. & Clausen, T. (2004). Proteolysis as a regulatory mechanism. Annual Review of Genetics 38, 709–724.CrossRefGoogle ScholarPubMed
El-Mansi, M., Cozzone, A. J., Shiloach, J. & Eikmanns, B. J. (2006). Control of carbon flux through enzymes of central and intermediary metabolism during growth of Escherichia coli on acetate. Current Opinion in Microbiology 9, 173–179.CrossRefGoogle Scholar
Forchhammer, K. (2004). Global carbon/nitrogen control by PII signal transduction in cyanobacteria: from signals to targets. FEMS Microbiology Reviews 28, 319–333.CrossRefGoogle Scholar
Hengge, R. & Gourse, R. L. (2004). Cell regulation: tying together the cellular regulatory network. Current Opinion in Microbiology 7, 99–101.CrossRefGoogle Scholar
Herrero, A. (2004). New targets of the PII signal transduction protein identified in cyanobacteria. Molecular Microbiology 52, 1225–1228.CrossRefGoogle ScholarPubMed
Jenal, U. & Hengge-Aronis, R. (2003). Regulation by proteolysis in bacterial cells. Current Opinion in Microbiology 6, 163–172.CrossRefGoogle ScholarPubMed
Ninfa, A. J. & Jiang, P. (2005). PII signal transduction proteins: sensors of α-ketoglutarate that regulate nitrogen metabolism. Current Opinion in Microbiology 8, 168–173.CrossRefGoogle ScholarPubMed
Noirot, P. & Noirot-Gros, M. F. (2004). Protein interaction networks in bacteria. Current Opinion in Microbiology 7, 505–512.CrossRefGoogle ScholarPubMed
Russell, R. B., Alber, F., Aloy, P., Davis, F. P., Korkin, D., Pichaud, M., Topf, M. & Sali, A. (2004). A structural perspective on protein-protein interactions. Current Opinion in Structural Biology 14, 313–324.CrossRefGoogle ScholarPubMed
Ades, S. E. (2004). Control of the alternative sigma factor σE in Escherichia coli. Current Opinion in Microbiology 7, 157–162.CrossRefGoogle ScholarPubMed
Barnard, A., Wolfe, A. & Busby, S. (2004). Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes. Current Opinion in Microbiology 7, 102–108.CrossRefGoogle ScholarPubMed
Bell, S. D. (2005). Archaeal transcriptional regulation – variation on a bacterial theme?Trends in Microbiology 13, 262–265.CrossRefGoogle ScholarPubMed
Borukhov, S. & Severinov, K. (2002). Role of the RNA polymerase sigma subunit in transcription initiation. Research in Microbiology 153, 557–562.CrossRefGoogle ScholarPubMed
Dove, S. L., Darst, S. A. & Hochschild, A. (2003). Region 4 of σ as a target for transcription regulation. Molecular Microbiology 48, 863–874.CrossRefGoogle ScholarPubMed
Geiduschek, E. P. & Ouhammouch, M. (2005). Archaeal transcription and its regulators. Molecular Microbiology 56, 1397–1407.CrossRefGoogle ScholarPubMed
Gourse, R. L., Ross, W. & Rutherford, S. T. (2006). General pathway for turning on promoters transcribed by RNA polymerases containing alternative σ factors. Journal of Bacteriology 188, 4589–4591.CrossRefGoogle ScholarPubMed
Gruber, T. M. & Gross, C. A. (2003). Multiple sigma subunits and the partitioning of bacterial transcription space. Annual Review of Microbiology 57, 441–466.CrossRefGoogle ScholarPubMed
Helmann, J. D. (2002). The extracytoplasmic function (ECF) sigma factors. Advances in Microbial Physiology 46, 47–110.CrossRefGoogle ScholarPubMed
Hinton, D. M. (2005). Molecular gymnastics: distortion of an RNA polymerase σ-factor. Trends in Microbiology 13, 140–143.CrossRefGoogle ScholarPubMed
Hughes, K. T. & Mathee, K. (1998). The anti-sigma factors. Annual Review of Microbiology 52, 231–286.CrossRefGoogle ScholarPubMed
Kazmierczak, M. J., Wiedmann, M. & Boor, K. J. (2005). Alternative sigma factors and their roles in bacterial virulence. Microbiology and Molecular Biology Reviews 69, 527–543.CrossRefGoogle ScholarPubMed
Geiduschek, E. P. & Ouhammouch, M. (2005). Archaeal transcription and its regulators. Molecular Microbiology 56, 1397–1407.CrossRefGoogle ScholarPubMed
Mullerhill, B. (1998). Some repressors of bacterial transcription. Current Opinion in Microbiology 1, 145–151.CrossRefGoogle Scholar
Pittard, J., Camakaris, H. & Yang, J. (2005). The TyrR regulon. Molecular Microbiology 55, 16–26.CrossRefGoogle ScholarPubMed
Rhodius, V. A. & Busby, S. J. W. (1998). Positive activation of gene expression. Current Opinion in Microbiology 1, 152–159.CrossRefGoogle ScholarPubMed
Rojo, F. (1999). Repression of transcription initiation in bacteria. Journal of Bacteriology 181, 2987–2991.Google ScholarPubMed
Roy, S., Garges, S. & Adhya, S. (1998). Activation and repression of transcription by differential contact: two sides of a coin. Journal of Biological Chemistry 273, 14059–14062.CrossRefGoogle ScholarPubMed
Xu, H. & Hoover, T. R. (2001). Transcriptional regulation at a distance in bacteria. Current Opinion in Microbiology 4, 138–144.CrossRefGoogle Scholar
Alifano, P., Fani, R., Lio, P., Lazcano, A., Bazzicalupo, M., Carlomagno, M. S. & Bruni, C. B. (1996). Histidine biosynthetic pathway and genes: structure, regulation, and evolution. Microbiological Reviews 60, 44.Google ScholarPubMed
Babitzke, P. (2004). Regulation of transcription attenuation and translation initiation by allosteric control of an RNA-binding protein: the Bacillus subtilis TRAP protein. Current Opinion in Microbiology 7, 132–139.CrossRefGoogle ScholarPubMed
Gollnick, P., Babitzke, P., Antson, A. & Yanofsky, C. (2005). Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. Annual Review of Genetics 39, 47–68.CrossRefGoogle ScholarPubMed
Mullerhill, B. (1998). Some repressors of bacterial transcription. Current Opinion in Microbiology 1, 145–151.CrossRefGoogle Scholar
Rojo, F. (1999). Repression of transcription initiation in bacteria. Journal of Bacteriology 181, 2987–2991.Google ScholarPubMed
Yanofsky, C. (2004). The different roles of tryptophan transfer RNA in regulating trp operon expression in E. coli versus B. subtilis. Trends in Genetics 20, 367–374.CrossRefGoogle Scholar
Amster-Choder, O. (2005). The bgl sensory system: a transmembrane signaling pathway controlling transcriptional antitermination. Current Opinion in Microbiology 8, 127–134.CrossRefGoogle ScholarPubMed
Condon, C., Squires, C. & Squires, C. L. (1995). Control of rRNA transcription in Escherichia coli. Microbiological Reviews 59, 623.Google ScholarPubMed
Gollnick, P. & Babitzke, P. (2002). Transcription attenuation. Biochimica et Biophysica Acta – Gene Structure and Expression 1577, 240–250.CrossRefGoogle ScholarPubMed
Santangelo, T. J. & Roberts, J. W. (2002). RfaH, a bacterial transcription antiterminator. Molecular Cell 9, 698–700.CrossRefGoogle ScholarPubMed
Shu, C. J. & Zhulin, I. B. (2002). ANTAR: an RNA-binding domain in transcription antitermination regulatory proteins. Trends in Biochemical Sciences 27, 3–5.CrossRefGoogle ScholarPubMed
Weisberg, R. A. & Gottesman, M. E. (1999). Processive antitermination. Journal of Bacteriology 181, 359–367.Google ScholarPubMed
Alexandre, G. & Zhulin, I. B. (2001). More than one way to sense chemicals [Review]. Journal of Bacteriology 183, 4681–4686.CrossRefGoogle Scholar
Backert, S. & Selbach, M. (2005). Tyrosine-phosphorylated bacterial effector proteins: the enemies within. Trends in Microbiology 13, 476–484.CrossRefGoogle Scholar
Beier, D. & Gross, R. (2006). Regulation of bacterial virulence by two-component systems. Current Opinion in Microbiology 9, 143–152.CrossRefGoogle ScholarPubMed
Buckler, D. R., Anand, G. S. & Stock, A. M. (2000). Response-regulator phosphorylation and activation: a two-way street?Trends in Microbiology 8, 153–156.CrossRefGoogle ScholarPubMed
Dunny, G. M. & Leonard, B. A. B. (1997). Cell-cell communication in Gram-positive bacteria. Annual Review of Microbiology 51, 527–564.CrossRefGoogle ScholarPubMed
Fabret, C., Feher, V. A. & Hoch, J. A. (1999). Two-component signal transduction in Bacillus subtilis: how one organism sees its world. Journal of Bacteriology 181, 1975–1983.Google ScholarPubMed
Galperin, M. Y. (2004). Bacterial signal transduction network in a genomic perspective. Environmental Microbiology 6, 552–567.CrossRefGoogle Scholar
Hancock, L. & Perego, M. (2002). Two-component signal transduction in Enterococcus faecalis. Journal of Bacteriology 184, 5819–5825.CrossRefGoogle ScholarPubMed
Hoch, J. A. & Varughese, K. I. (2001). Keeping signals straight in phosphorelay signal transduction. Journal of Bacteriology 183, 4941–4949.CrossRefGoogle ScholarPubMed
Hoskisson, P. A. & Hutchings, M. I. (2006). MtrAB-LpqB: a conserved three-component system in actinobacteria?Trends in Microbiology 14, 444–449.CrossRefGoogle ScholarPubMed
Hutchings, M. I., Hoskisson, P. A., Chandra, G. & Chandra, G. (2004). Sensing and responding to diverse extracellular signals? Analysis of the sensor kinases and response regulators of Streptomyces coelicolor A3(2). Microbiology-UK 150, 2795–2806.CrossRefGoogle Scholar
Lux, R. & Shi, W. (2005). A novel bacterial signalling system with a combination of a Ser/Thr kinase cascade and a His/Asp two-component system. Molecular Microbiology 58, 345–348.CrossRefGoogle Scholar
Novick, R. P. (2003). Autoinduction and signal transduction in the regulation of staphylococcal virulence. Molecular Microbiology 48, 1429–1449.CrossRefGoogle ScholarPubMed
Ruiz, N. & Silhavy, T. J. (2005). Sensing external stress: watchdogs of the Escherichia coli cell envelope. Current Opinion in Microbiology 8, 122–126.CrossRefGoogle ScholarPubMed
Stock, A. M. & Guhaniyogi, J. (2006). A new perspective on response regulator activation. Journal of Bacteriology 188, 7328–7330.CrossRefGoogle ScholarPubMed
Stock, A. M., Robinson, V. L. & Goudreau, P. N. (2000). Two-component signal transduction. Annual Review of Biochemistry 69, 183–215.CrossRefGoogle ScholarPubMed
Varughese, K. (2002). Molecular recognition of bacterial phosphorelay proteins. Current Opinion in Microbiology 5, 142–148.CrossRefGoogle ScholarPubMed
West, A. H. & Stock, A. M. (2001). Histidine kinases and response regulator proteins in two-component signaling systems. Trends in Biochemical Sciences 26, 369–376.CrossRefGoogle ScholarPubMed
Lindner, C., Hecker, M., Coq, D. & Deutscher, J. (2002). Bacillus subtilis mutant LicT antiterminators exhibiting enzyme I- and HPr-independent antitermination affect catabolite repression of the bglPH operon. Journal of Bacteriology 184, 4819–4828.CrossRefGoogle ScholarPubMed
Schneider, D. A., Ross, W. & Gourse, R. L. (2003). Control of rRNA expression in Escherichia coli. Current Opinion in Microbiology 6, 151–156.CrossRefGoogle ScholarPubMed
Agrawal, N., Dasaradhi, P. V. N., Mohmmed, A., Malhotra, P., Bhatnagar, R. K. & Mukherjee, S. K. (2003). RNA interference: biology, mechanism, and applications. Microbiology and Molecular Biology Reviews 67, 657–685.CrossRefGoogle ScholarPubMed
Altuvia, S. (2004). Regulatory small RNAs: the key to coordinating global regulatory circuits. Journal of Bacteriology 186, 6679–6680.CrossRefGoogle ScholarPubMed
Altuvia, S. & Wagner, E. G. (2000). Switching on and off with RNA. Proceedings of the National Academy of Sciences, USA 97, 9824–9826.CrossRefGoogle ScholarPubMed
Babitzke, P. (2004). Regulation of transcription attenuation and translation initiation by allosteric control of an RNA-binding protein: the Bacillus subtilis TRAP protein. Current Opinion in Microbiology 7, 132–139.CrossRefGoogle ScholarPubMed
Baulcombe, D. (2005). RNA silencing. Trends in Biochemical Sciences 30, 290–293.CrossRefGoogle ScholarPubMed
Boni, I. V. (2006). Diverse molecular mechanisms of translation initiation in prokaryotes. Molecular Biology 40, 587–596.CrossRefGoogle ScholarPubMed
Brantl, S. (2002). Antisense-RNA regulation and RNA interference. Biochimica et Biophysica Acta – Gene Structure and Expression 1575, 15–25.CrossRefGoogle ScholarPubMed
Condon, C. (2003). RNA processing and degradation in Bacillus subtilis. Microbiology and Molecular Biology Reviews 67, 157–174.CrossRefGoogle ScholarPubMed
Condon, C. (2006). Shutdown decay of mRNA. Molecular Microbiology 61, 573–583.CrossRefGoogle ScholarPubMed
Delihas, N. & Forst, S. (2001). MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factors. Journal of Molecular Biology 313, 1–12.CrossRefGoogle ScholarPubMed
Denli, A. M. & Hannon, G. J. (2003). RNAi: an ever-growing puzzle. Trends in Biochemical Sciences 28, 196–201.CrossRefGoogle ScholarPubMed
Dennis, P. P., Omer, A. & Lowe, T. (2001). A guided tour: small RNA function in Archaea. Molecular Microbiology 40, 509–519.CrossRefGoogle ScholarPubMed
Eckstein, F. (2005). Small non-coding RNAs as magic bullets. Trends in Biochemical Sciences 30, 445–452.CrossRefGoogle ScholarPubMed
Filipowicz, W., Jaskiewicz, L., Kolb, F. A. & Pillai, R. S. (2005). Post-transcriptional gene silencing by siRNAs and miRNAs. Current Opinion in Structural Biology 15, 331–341.CrossRefGoogle ScholarPubMed
Franch, T. & Gerdes, K. (2000). U-turns and regulatory RNAs. Current Opinion in Microbiology 3, 159–164.CrossRefGoogle ScholarPubMed
Gelfand, M. S. (2006). Bacterial cis-regulatory RNA structures. Molecular Biology 40, 541–550.CrossRefGoogle Scholar
Gottesman, S. (2004). The small RNA regulators of Escherichia coli: roles and mechanisms. Annual Review of Microbiology 58, 303–328.CrossRefGoogle ScholarPubMed
Huttenhofer, A., Brosius, J. & Bachellerie, J. P. (2002). RNomics: identification and function of small, non-messenger RNAs. Current Opinion in Chemical Biology 6, 835–843.CrossRefGoogle ScholarPubMed
Kennell, D. (2002). Processing endoribonucleases and mRNA degradation in bacteria. Journal of Bacteriology 184, 4645–4657.CrossRefGoogle ScholarPubMed
Kushner, S. R. (2002). mRNA decay in Escherichia coli comes of age. Journal of Bacteriology 184, 4658–4665.CrossRefGoogle ScholarPubMed
Lease, R. A. & Belfort, M. (2000). Riboregulation by DsrA RNA: trans-actions for global economy. Molecular Microbiology 38, 667–672.CrossRefGoogle ScholarPubMed
Mata, J., Marguerat, S. & Bahler, J. (2005). Post-transcriptional control of gene expression: a genome-wide perspective. Trends in Biochemical Sciences 30, 506–514.CrossRefGoogle ScholarPubMed
Nair, V. & Zavolan, M. (2006). Virus-encoded microRNAs: novel regulators of gene expression. Trends in Microbiology 14, 169–175.CrossRefGoogle ScholarPubMed
Nogueira, T. & Springer, M. (2000). Post-transcriptional control by global regulators of gene expression in bacteria. Current Opinion in Microbiology 3, 154–158.CrossRefGoogle ScholarPubMed
Nudler, E. & Mironov, A. S. (2004). The riboswitch control of bacterial metabolism. Trends in Biochemical Sciences 29, 11–17.CrossRefGoogle ScholarPubMed
Rauhut, R. & Klug, G. (1999). mRNA degradation in bacteria. FEMS Microbiology Reviews 23, 353–370.CrossRefGoogle ScholarPubMed
Repoila, F., Majdalani, N. & Gottesman, S. (2003). Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm. Molecular Microbiology 48, 855–861.CrossRefGoogle ScholarPubMed
Schlax, P. J. & Worhunsky, D. J. (2003). Translational repression mechanisms in prokaryotes. Molecular Microbiology 48, 1157–1169.CrossRefGoogle ScholarPubMed
Storz, G., Opdyke, J. A. & Zhang, A. (2004). Controlling mRNA stability and translation with small, noncoding RNAs. Current Opinion in Microbiology 7, 140–144.CrossRefGoogle ScholarPubMed
Takayama, K. & Kjelleberg, S. A. (2000). The role of RNA stability during bacterial stress responses and starvation. Environmental Microbiology 2, 355–365.CrossRefGoogle ScholarPubMed
Tang, G. (2005). siRNA and miRNA: an insight into RISCs. Trends in Biochemical Sciences 30, 106–114.CrossRefGoogle ScholarPubMed
Valentin-Hansen, P., Eriksen, M. & Udesen, C. (2004). The bacterial Sm-like protein Hfq: a key player in RNA transactions. Molecular Microbiology 51, 1525–1533.CrossRefGoogle ScholarPubMed
Wang, Y., Liu, C. L., Storey, J. D., Tibshirani, R. J., Herschlag, D. & Brown, P. O. (2002). Precision and functional specificity in mRNA decay. Proceedings of the National Academy of Sciences, USA 99, 5860–5865.CrossRefGoogle ScholarPubMed
Winkler, W. C. (2005). Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Current Opinion in Chemical Biology 9, 594–602.CrossRefGoogle ScholarPubMed
Braeken, K., Moris, M., Daniels, R., Vanderleyden, J. & Michiels, J. (2006). New horizons for (p)ppGpp in bacterial and plant physiology. Trends in Microbiology 14, 45–54.CrossRefGoogle ScholarPubMed
Dennis, P. P., Ehrenberg, M. & Bremer, H. (2004). Control of rRNA synthesis in Escherichia coli: a systems biology approach. Microbiology and Molecular Biology Reviews 68, 639–668.CrossRefGoogle ScholarPubMed
Ferenci, T. (1999). Regulation by nutrient limitation. Current Opinion in Microbiology 2, 208–213.CrossRefGoogle ScholarPubMed
Ferenci, T. (2001). Hungry bacteria: definition and properties of a nutritional state. Environmental Microbiology 3, 605–611.CrossRefGoogle ScholarPubMed
Gralla, J. D. (2005). Escherichia coli ribosomal RNA transcription: regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein. Molecular Microbiology 55, 973–977.CrossRefGoogle Scholar
Hengge-Aronis, R. (1999). Interplay of global regulators and cell physiology in the general stress response of Escherichia coli. Current Opinion in Microbiology 2, 148–152.CrossRefGoogle ScholarPubMed
Hengge-Aronis, R. (2002). Signal transduction and regulatory mechanisms involved in control of the σS (RpoS) subunit of RNA polymerase. Microbiology and Molecular Biology Reviews 66, 373–395.CrossRefGoogle Scholar
Magnusson, L. U., Farewell, A. & Nystrom, T. (2005). ppGpp: a global regulator in Escherichia coli. Trends in Microbiology 13, 236–242.CrossRefGoogle ScholarPubMed
Spector, M. P. (1998). The starvation-stress response (SSR) of Salmonella. Advances in Microbial Physiology 40, 233–279.CrossRefGoogle ScholarPubMed
Venturi, V. (2003). Control of rpoS transcription in Escherichia coli and Pseudomonas: why so different?Journal of Molecular Microbiology and Biotechnology 49, 1–9.Google ScholarPubMed
Arcondeguy, T., Jack, R. & Merrick, M. (2001). P-II signal transduction proteins, pivotal players in microbial nitrogen control. Microbiology and Molecular Biology Reviews 65, 80–105.CrossRefGoogle ScholarPubMed
Burkovski, A. (2003). Ammonium assimilation and nitrogen control in Corynebacterium glutamicum and its relatives: an example for new regulatory mechanisms in actinomycetes. FEMS Microbiology Reviews 27, 617–628.CrossRefGoogle ScholarPubMed
Charbit, A. (1996). Coordination of carbon and nitrogen metabolism. Research in Microbiology 147, 513–518.CrossRefGoogle ScholarPubMed
Commichau, F. M., Forchhammer, K. & Stulke, J. (2006). Regulatory links between carbon and nitrogen metabolism. Current Opinion in Microbiology 9, 167–172.CrossRefGoogle ScholarPubMed
Fisher, S. H. (1999). Regulation of nitrogen metabolism in Bacillus subtilis: vive la difference!Molecular Microbiology 32, 223–232.CrossRefGoogle ScholarPubMed
Forchhammer, K. (2004). Global carbon/nitrogen control by PII signal transduction in cyanobacteria: from signals to targets. FEMS Microbiology Reviews 28, 319–333.CrossRefGoogle Scholar
Merrick, M. J. & Edwards, R. A. (1995). Nitrogen control in bacteria. Microbiological Reviews 59, 604–622.Google ScholarPubMed
Ninfa, A. J. & Jiang, P. (2005). PII signal transduction proteins: sensors of α-ketoglutarate that regulate nitrogen metabolism. Current Opinion in Microbiology 8, 168–173.CrossRefGoogle ScholarPubMed
Reitzer, L. (2003). Nitrogen assimilation and global regulation in Escherichia coli. Annual Review of Microbiology 57, 155–176.CrossRefGoogle ScholarPubMed
Schwarz, R. & Forchhammer, K. (2005). Acclimation of unicellular cyanobacteria to macronutrient deficiency: emergence of a complex network of cellular responses. Microbiology-UK 151, 2503–2514.CrossRefGoogle ScholarPubMed
Silberbach, M. & Burkovski, A. (2006). Application of global analysis techniques to Corynebacterium glutamicum: new insights into nitrogen regulation. Journal of Biotechnology 126, 101–110.CrossRefGoogle ScholarPubMed
Atkinson, S., Sockett, R. E., Camara, M. & Williams, P. (2006). Quorum sensing and the lifestyle of Yersinia. Current Issues in Molecular Biology 8, 1–10.Google ScholarPubMed
Bauer, W. & Robinson, J. (2002). Disruption of bacterial quorum sensing by other organisms. Current Opinion in Biotechnology 13, 234–237.CrossRefGoogle ScholarPubMed
Daniels, R., Vanderleyden, J. & Michiels, J. (2004). Quorum sensing and swarming migration in bacteria. FEMS Microbiology Reviews 28, 261–289.CrossRefGoogle ScholarPubMed
Keersmaecker, S. C. J., Sonck, K. & Vanderleyden, J. (2006). Let LuxS speak up in AI-2 signaling. Trends in Microbiology 14, 114–119.CrossRefGoogle ScholarPubMed
Fuqua, C. (2006). The QscR quorum-sensing regulon of Pseudomonas aeruginosa: an orphan claims its identity. Journal of Bacteriology 188, 3169–3171.CrossRefGoogle ScholarPubMed
Gonzalez, J. E. & Marketon, M. M. (2003). Quorum sensing in nitrogen-fixing rhizobia. Microbiology and Molecular Biology Reviews 67, 574–592.CrossRefGoogle ScholarPubMed
Jacob, E. B., Becker, I., Shapira, Y. & Levine, H. (2004). Bacterial linguistic communication and social intelligence. Trends in Microbiology 12, 366–372.CrossRefGoogle ScholarPubMed
Keller, L. & Surette, M. G. (2006). Communication in bacteria: an ecological and evolutionary perspective. Nature Reviews Microbiology 4, 249–258.CrossRefGoogle ScholarPubMed
Kjelleberg, S. & Molin, S. (2002). Is there a role for quorum sensing signals in bacterial biofilms?Current Opinion in Microbiology 5, 254–258.CrossRefGoogle Scholar
Klose, K. E. (2006). Increased chatter: cyclic dipeptides as molecules of chemical communication in Vibrio spp. Journal of Bacteriology 188, 2025–2026.CrossRefGoogle ScholarPubMed
Miller, M. B. & Bassler, B. L. (2001). Quorum sensing in bacteria. Annual Review of Microbiology 55, 165–199.CrossRefGoogle ScholarPubMed
Pappas, K. M., Weingart, C. L. & Winans, S. C. (2004). Chemical communication in proteobacteria: biochemical and structural studies of signal synthases and receptors required for intercellular signalling. Molecular Microbiology 53, 755–770.CrossRefGoogle ScholarPubMed
Parsek, M. R. & Greenberg, E. P. (2005). Sociomicrobiology: the connections between quorum sensing and biofilms. Trends in Microbiology 13, 27–33.CrossRefGoogle ScholarPubMed
Rasmussen, T. B. & Givskov, M. (2006). Quorum sensing inhibitors: a bargain of effects. Microbiology-UK 152, 895–904.CrossRefGoogle Scholar
Reading, N. C. & Sperandio, V. (2006). Quorum sensing: the many languages of bacteria. FEMS Microbiology Letters 254, 1–11.CrossRefGoogle Scholar
Roche, D. M., Byers, J. T., Smith, D. S., Glansdorp, F. G., Spring, D. R. & Welch, M. (2004). Communications blackout? Do N-acylhomoserine-lactone-degrading enzymes have any role in quorum sensing?Microbiology-UK 150, 2023–2028.CrossRefGoogle ScholarPubMed
Sturme, M. H., Kleerebezem, M., Nakayama, J., Akkermans, A. D., Vaugha, E. E. & Vos, W. M. (2002). Cell to cell communication by autoinducing peptides in Gram-positive bacteria. Antonie van Leeuwenhoek 81, 233–243.CrossRefGoogle ScholarPubMed
Suntharalingam, P. & Cvitkovitch, D. G. (2005). Quorum sensing in streptococcal biofilm formation. Trends in Microbiology 13, 3–6.CrossRefGoogle ScholarPubMed
Venturi, V. (2006). Regulation of quorum sensing in Pseudomonas. FEMS Microbiology Reviews 30, 274–291.CrossRefGoogle ScholarPubMed
Whitehead, N. A., Barnard, A. M. L., Slater, H., Simpson, N. J. L. & Salmond, G. P. C. (2001). Quorum-sensing in Gram-negative bacteria. FEMS Microbiology Reviews 25, 365–404.CrossRefGoogle ScholarPubMed
Withers, H., Swift, S. & Williams, P. (2001). Quorum sensing as an integral component of gene regulatory networks in Gram-negative bacteria. Current Opinion in Microbiology 4, 186–193.CrossRefGoogle ScholarPubMed
Zhang, L. H. & Dong, Y. H. (2004). Quorum sensing and signal interference: diverse implications. Molecular Microbiology 53, 1563–1571.CrossRefGoogle ScholarPubMed
Bauer, C. E., Elsen, S. & Bird, T. H. (1999). Mechanisms for redox control of gene expression. Annual Review of Microbiology 53, 495–523.CrossRefGoogle ScholarPubMed
Beinert, H. & Kiley, P. (1996). Redox control of gene expression involving iron-sulfur proteins. Change of oxidation-state or assembly/disassembly of Fe-S clusters?FEBS Letters 382, 218–219.CrossRefGoogle ScholarPubMed
Elsen, S., Swem, L. R., Swem, D. L. & Bauer, C. E. (2004). RegB/RegA, a highly conserved redox-responding global two-component regulatory system. Microbiology and Molecular Biology Reviews 68, 263–279.CrossRefGoogle ScholarPubMed
Green, J. & Paget, M. S. (2004). Bacterial redox sensors. Nature Reviews Microbiology 2, 954–966.CrossRefGoogle ScholarPubMed
Imlay, J. A. (2006). Iron-sulphur clusters and the problem with oxygen. Molecular Microbiology 59, 1073–1082.CrossRefGoogle ScholarPubMed
Kiley, P. J. & Beinert, H. (1999). Oxygen sensing by the global regulator, FNR, the role of the iron-sulfur cluster. FEMS Microbiology Reviews 22, 341–352.CrossRefGoogle Scholar
Kiley, P. J. & Beinert, H. (2003). The role of Fe-S proteins in sensing and regulation in bacteria. Current Opinion in Microbiology 6, 181–185.CrossRefGoogle ScholarPubMed
Nakano, M. M. & Zuber, P. (1998). Anaerobic growth of a ‘strict aerobe’ (Bacillus subtilis). Annual Review of Microbiology 52, 165–190.CrossRefGoogle Scholar
Sawers, G. (2001). A novel mechanism controls anaerobic and catabolite regulation of the Escherichia coli tdc operon. Molecular Microbiology 39, 1285–1298.CrossRefGoogle ScholarPubMed
Taylor, B. L., Zhulin, I. B. & Johnson, M. S. (1999). Aerotaxis and other energy-sensing behavior in bacteria. Annual Review of Microbiology 53, 103–128.CrossRefGoogle ScholarPubMed
Unden, G. (1998). Transcriptional regulation and energetics of alternative respiratory pathways in facultatively anaerobic bacteria. Biochimica et Biophysica Acta – Bioenergetics 1365, 220–224.CrossRefGoogle Scholar
Unden, G. & Schirawski, J. (1997). The oxygen-responsive transcriptional regulator FNR of Escherichia coli: the search for signals and reactions. Molecular Microbiology 25, 205–210.CrossRefGoogle ScholarPubMed
Groisman, E. A. (2001). The pleiotropic two-component regulatory system PhoP-PhoQ. Journal of Bacteriology 183, 1835–1842.CrossRefGoogle ScholarPubMed
Hulett, F. M. (1996). The signal-transduction network for Pho regulation in Bacillus subtilis. Molecular Microbiology 19, 933–939.CrossRefGoogle ScholarPubMed
Lenburg, M. E. & Oshea, E. K. (1996). Signaling phosphate starvation. Trends in Biochemical Sciences 21, 383–387.CrossRefGoogle ScholarPubMed
Martin, J. F. (2004). Phosphate control of the biosynthesis of antibiotics and other secondary metabolites is mediated by the PhoR-PhoP system: an unfinished story. Journal of Bacteriology 186, 5197–5201.CrossRefGoogle Scholar
Vershinina, O. A. & Znamenskaya, L. V. (2002). The pho regulons of bacteria. Microbiology-Moscow 71, 497–511.CrossRefGoogle Scholar
Aertsen, A., Vanoirbeek, K., Spiegeleer, P., Sermon, J., Hauben, K., Farewell, A., Nystrom, T. & Michiels, C. W. (2004). Heat shock protein-mediated resistance to high hydrostatic pressure in Escherichia coli. Applied and Environmental Microbiology 70, 2660–2666.CrossRefGoogle ScholarPubMed
Chhabra, S. R., He, Q., Huang, K. H., Gaucher, S. P., Alm, E. J., He, Z., Hadi, M. Z., Hazen, T. C., Wall, J. D., Zhou, J., Arkin, A. P. & Singh, A. K. (2006). Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology 188, 1817–1828.CrossRefGoogle ScholarPubMed
Crapoulet, N., Barbry, P., Raoult, D. & Renesto, P. (2006). Global transcriptome analysis of Tropheryma whipplei in response to temperature stresses. Journal of Bacteriology 188, 5228–5239.CrossRefGoogle ScholarPubMed
Dubern, J. F., Lagendijk, E. L., Lugtenberg, B. J. J. & Bloemberg, G. V. (2005). The heat shock genes dnaK, dnaJ, and grpE are involved in regulation of putisolvin biosynthesis in Pseudomonas putida PCL1445. Journal of Bacteriology 187, 5967–5976.CrossRefGoogle ScholarPubMed
Engels, S., Schweitzer, J. E., Ludwig, C., Bott, M. & Schaffer, S. (2004). clpC and clpP1P2 gene expression in Corynebacterium glutamicum is controlled by a regulatory network involving the transcriptional regulators ClgR and HspR as well as the ECF sigma factor σH. Molecular Microbiology 52, 285–302.CrossRefGoogle ScholarPubMed
Helmann, J. D., Wu, M. F. W., Kobel, P. A., Gamo, F. J., Wilson, M., Morshedi, M. M., Navre, M. & Paddon, C. (2001). Global transcriptional response of Bacillus subtilis to heat shock. Journal of Bacteriology 183, 7318–7328.CrossRefGoogle ScholarPubMed
Hillmann, F., Fischer, R. J. & Bahl, H. (2006). The rubrerythrin-like protein Hsp21 of Clostridium acetobutylicum is a general stress protein. Archives of Microbiology 185, 270–276.CrossRefGoogle ScholarPubMed
Kourennaia, O. V., Tsujikawa, L. & Haseth, P. L. (2005). Mutational analysis of Escherichia coli heat shock transcription factor sigma 32 reveals similarities with sigma 70 in recognition of the − 35 promoter element and differences in promoter DNA melting and − 10 recognition. Journal of Bacteriology 187, 6762–6769.CrossRefGoogle ScholarPubMed
Laksanalamai, P., Maeder, D. L. & Robb, F. T. (2001). Regulation and mechanism of action of the small heat shock protein from the hyperthermophilic archaeon Pyrococcus furiosus. Journal of Bacteriology 183, 5198–5202.CrossRefGoogle ScholarPubMed
Musatovova, O., Dhandayuthapani, S. & Baseman, J. B. (2006). Transcriptional heat shock response in the smallest known self-replicating cell, Mycoplasma genitalium. Journal of Bacteriology 188, 2845–2855.CrossRefGoogle ScholarPubMed
Schmid, A. K., Howell, H. A., Battista, Jo R., Peterson, S. N. & Lidstrom, M. E. (2005). HspR is a global negative regulator of heat shock gene expression in Deinococcus radiodurans. Molecular Microbiology 55, 1579–1590.CrossRefGoogle ScholarPubMed
Senn, M. M., Giachino, P., Homerova, D., Steinhuber, A., Strassner, J., Kormanec, J., Fluckiger, U., Berger-Bachi, B. & Bischoff, M. (2005). Molecular analysis and organization of the σB operon in Staphylococcus aureus. Journal of Bacteriology 187, 8006–8019.CrossRefGoogle ScholarPubMed
Servant, P. & Mazodier, P. (2001). Negative regulation of the heat shock response in Streptomyces. Archives of Microbiology 176, 237–242.CrossRefGoogle ScholarPubMed
Tachdjian, S. & Kelly, R. M. (2006). Dynamic metabolic adjustments and genome plasticity are implicated in the heat shock response of the extremely thermoacidophilic archaeon Sulfolobus solfataricus. Journal of Bacteriology 188, 4553–4559.CrossRefGoogle ScholarPubMed
Beckering, C. L., Steil, L., Weber, M. H. W., Volker, U. & Marahiel, M. A. (2002). Genomewide transcriptional analysis of the cold shock response in Bacillus subtilis. Journal of Bacteriology 184, 6395–6402.CrossRefGoogle ScholarPubMed
Beran, R. K. & Simons, R. W. (2001). Cold-temperature induction of Escherichia coli polynucleotide phosphorylase occurs by reversal of its autoregulation. Molecular Microbiology 39, 112–125.CrossRefGoogle ScholarPubMed
Cairrao, F., Cruz, A., Mori, H. & Arraiano, C. M. (2003). Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA. Molecular Microbiology 50, 1349–1360.CrossRefGoogle ScholarPubMed
Cavicchioli, R., Thomas, T. & Curmi, P. M. G. (2000). Cold stress response in Archaea. Extremophiles 4, 321–331.CrossRefGoogle ScholarPubMed
Datta, P. P. & Bhadra, R. K. (2003). Cold shock response and major cold shock proteins of Vibrio cholerae. Applied and Environmental Microbiology 69, 6361–6369.CrossRefGoogle ScholarPubMed
Fang, L., Hou, Y. & Inouye, M. (1998). Role of the cold-box region in the 5′ untranslated region of the cspA mRNA in its transient expression at low temperature inEscherichia coli. Journal of Bacteriology 180, 90–95.Google ScholarPubMed
Gao, H., Yang, Z. K., Wu, L., Thompson, D. K. & Zhou, J. (2006). Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins. Journal of Bacteriology 188, 4560–4569.CrossRefGoogle ScholarPubMed
Gerday, C., Aittaleb, M., Bentahir, M., Chessa, J. P., Claverie, P., Collins, T., D'Amico, S., Dumont, J., Garsoux, G., Georlette, D., Hoyoux, A., Lonhienne, T., Meuwis, M. A. & Feller, G. (2000). Cold-adapted enzymes: from fundamentals to biotechnology. Trends in Biotechnology 18, 103–107.CrossRefGoogle ScholarPubMed
Giangrossi, M., Exley, R. M., Hegarat, F. & Pon, C. L. (2001). Different in vivo localization of the Escherichia coli proteins CspD and CspA. FEMS Microbiology Letters 202, 171–176.CrossRefGoogle ScholarPubMed
Graumann, P. & Marahiel, M. A. (1996). Some like it cold: response of microorganisms to cold shock. Archives of Microbiology 166, 293–300.CrossRefGoogle ScholarPubMed
Graumann, P. L. & Marahiel, M. A. (1998). A superfamily of proteins that contain the cold-shock domain. Trends in Biochemical Sciences 23, 286–290.CrossRefGoogle ScholarPubMed
Hunger, K., Beckering, C. L., Wiegeshoff, F., Graumann, P. L. & Marahiel, M. A. (2006). Cold-induced putative DEAD box RNA helicases CshA and CshB are essential for cold adaptation and interact with cold shock protein B in Bacillus subtilis. Journal of Bacteriology 188, 240–248.CrossRefGoogle ScholarPubMed
Katzif, S., Lee, E. H., Law, A. B., Tzeng, Y. L. & Shafer, W. M. (2005). CspA regulates pigment production in Staphylococcus aureus through a SigB-dependent mechanism. Journal of Bacteriology 187, 8181–8184.CrossRefGoogle ScholarPubMed
Lopez, M. M., Yutani, K. & Makhatadze, G. I. (2001). Interactions of the cold shock protein CspB from Bacillus subtilis with single-stranded DNA: importance of the T base content and position within the template. Journal of Biological Chemistry 276, 15511–15518.CrossRefGoogle Scholar
Magg, C., Kubelka, J., Holtermann, G., Haas, E. & Schmid, F. X. (2006). Specificity of the initial collapse in the folding of the cold shock protein. Journal of Molecular Biology 360, 1067–1080.CrossRefGoogle ScholarPubMed
Martinez-Costa, O. H., Zalacain, M., Holmes, D. J. & Malpartida, F. (2003). The promoter of a cold-shock-like gene has pleiotropic effects on Streptomyces antibiotic biosynthesis. FEMS Microbiology Letters 220, 215–221.CrossRefGoogle ScholarPubMed
Phadtare, S. & Inouye, M. (2004). Genome-wide transcriptional analysis of the cold shock response in wild-type and cold-sensitive, quadruple-csp-deletion strains of Escherichia coli. Journal of Bacteriology 186, 7007–7014.CrossRefGoogle ScholarPubMed
Polissi, A., Laurentis, W., Zangrossi, S., Briani, F., Longhi, V., Pesole, G. & Deho, G. (2003). Changes in Escherichia coli transcriptome during acclimatization at low temperature. Research in Microbiology 154, 573–580.CrossRefGoogle ScholarPubMed
Prud'homme-Genereux, A., Beran, R. K., Iost, I., Ramey, C. S., Mackie, G. A. & Simons, R. W. (2004). Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a ‘cold shock degradosome’. Molecular Microbiology 54, 1409–1421.CrossRefGoogle ScholarPubMed
Sakamoto, T. & Murata, N. (2002). Regulation of the desaturation of fatty acids and its role in tolerance to cold and salt stress. Current Opinion in Microbiology 5, 206–210.CrossRefGoogle ScholarPubMed
Smirnova, G. V. & Zakirova, O. N. (2001). The role of antioxidant systems in the cold stress response of Escherichia coli. Microbiology-Moscow 70, 45–50.CrossRefGoogle Scholar
Weber, M. H. W., Klein, W., Muller, L., Niess, U. M. & Marahiel, M. A. (2001). Role of the Bacillus subtilis fatty acid desaturase in membrane adaptation during cold shock. Molecular Microbiology 39, 1321–1329.CrossRefGoogle ScholarPubMed
Wiegeshoff, F., Beckering, C. L., Debarbouille, M. & Marahiel, M. A. (2006). Sigma L is important for cold shock adaptation of Bacillus subtilis. Journal of Bacteriology 188, 3130–3133.CrossRefGoogle Scholar
Wouters, J. A., Rombouts, F. M., Kuipers, O. P., Vos, W. M. & Abee, T. (2000). The role of cold-shock proteins in low-temperature adaptation of food-related bacteria. Systematic and Applied Microbiology 23, 165–173.CrossRefGoogle ScholarPubMed
Xia, B., Ke, H., Jiang, W. & Inouye, M. (2002). The Cold Box stem-loop proximal to the 5′-end of the Escherichia coli cspA gene stabilizes its mRNA at low temperature. Journal of Biological Chemistry 277, 6005–6011.CrossRefGoogle ScholarPubMed
Yamanaka, K. & Inouye, M. (2001). Selective mRNA degradation by polynucleotide phosphorylase in cold shock adaptation in Escherichia coli. Journal of Bacteriology 183, 2808–2816.CrossRefGoogle ScholarPubMed
Brioukhanov, A. L., Netrusov, A. I. & Eggen, R. I. L. (2006). The catalase and superoxide dismutase genes are transcriptionally up-regulated upon oxidative stress in the strictly anaerobic archaeon Methanosarcina barkeri. Microbiology-UK 152, 1671–1677.CrossRefGoogle ScholarPubMed
Gaudu, P., Dubrac, S. & Touati, D. (2000). Activation of SoxR by overproduction of desulfoferrodoxin: multiple ways to induce the soxRS regulon. Journal of Bacteriology 182, 1761–1763.CrossRefGoogle ScholarPubMed
Giro, M., Carrillo, N. & Krapp, A. R. (2006). Glucose-6-phosphate dehydrogenase and ferredoxin-NADP(H) reductase contribute to damage repair during the soxRS response of Escherichia coli. Microbiology-UK 152, 1119–1128.CrossRefGoogle ScholarPubMed
Gonzalez-Flecha, B. & Demple, B. (1999). Role for the oxyS gene in regulation of intracellular hydrogen peroxide in Escherichia coli. Journal of Bacteriology 181, 3833–3836.Google ScholarPubMed
Hassett, D. J., Ma, J. F., Elkins, J. G., McDermott, T. R., Ochsner, U. A., West, S. E. H., Huang, C-T., Fredericks, J., Burnett, S., Stewart, P. S., McFeters, G., Passador, L. and Iglewski, B. H. (1999). Quorum sensing in Pseudomonas aeruginosa controls expression of catalase and superoxide dismutase genes and mediates biofilm susceptibility to hydrogen peroxide. Molecular Microbiology 34, 1082–1093.CrossRefGoogle ScholarPubMed
Imlay, J. A. (2003). Pathways of oxidative damage. Annual Review of Microbiology 57, 395–418.CrossRefGoogle ScholarPubMed
Manchado, M., Michan, C. & Pueyo, C. (2000). Hydrogen peroxide activates the SoxRS regulon in vivo. Journal of Bacteriology 182, 6842–6844.CrossRefGoogle ScholarPubMed
Ohara, N., Kikuchi, Y., Shoji, M., Naito, M. & Nakayama, K. (2006). Superoxide dismutase-encoding gene of the obligate anaerobe Porphyromonas gingivalis is regulated by the redox-sensing transcription activator OxyR. Microbiology-UK 152, 955–966.CrossRefGoogle ScholarPubMed
Rocha, E. R., Owens, G. & Smith, C. J. (2000). The redox-sensitive transcriptional activator OxyR regulates the peroxide response regulon in the obligate anaerobe Bacteroides fragilis. Journal of Bacteriology 182, 5059–5069.CrossRefGoogle ScholarPubMed
Toledano, M. B., Delaunay, A., Monceau, L. & Tacnet, F. (2004). Microbial H2O2 sensors as archetypical redox signaling modules. Trends in Biochemical Sciences 29, 351–357.CrossRefGoogle ScholarPubMed
Bohin, J. P. (2000). Osmoregulated periplasmic glucans in Proteobacteria. FEMS Microbiology Letters 186, 11–19.CrossRefGoogle ScholarPubMed
Kramer, R. & Morbach, S. (2004). BetP of Corynebacterium glutamicum, a transporter with three different functions: betaine transport, osmosensing, and osmoregulation. Biochimica et Biophysica Acta – Bioenergetics 1658, 31–36.CrossRefGoogle ScholarPubMed
Leonardo, M. R. & Forst, S. (1996). Re-examination of the role of the periplasmic domain of EnvZ in sensing of osmolarity signals in Escherichia coli. Molecular Microbiology 22, 405–413.CrossRefGoogle ScholarPubMed
Poolman, B., Spitzer, J. J. & Wood, J. M. (2004). Bacterial osmosensing: roles of membrane structure and electrostatics in lipid-protein and protein-protein interactions. Biochimica et Biophysica Acta – Biomembranes 1666, 88–104.CrossRefGoogle ScholarPubMed
Sleator, R. D. & Hill, C. (2002). Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence. FEMS Microbiology Reviews 26, 49–71.CrossRefGoogle ScholarPubMed
Wood, J. M. (1999). Osmosensing by bacteria: signals and membrane-based sensors. Microbiology and Molecular Biology Reviews 63, 230–262.Google ScholarPubMed
Aizawa, S., Harwood, C. S. & Kadner, R. J. (2000). Signaling components in bacterial locomotion and sensory reception. Journal of Bacteriology 182, 1459–1471.CrossRefGoogle ScholarPubMed
Alexandre, G., Greer-Phillips, S. & Zhulin, I. B. (2004). Ecological role of energy taxis in microorganisms. FEMS Microbiology Reviews 28, 113–126.CrossRefGoogle ScholarPubMed
Blair, D. F. (1995). How bacteria sense and swim. Annual Review of Microbiology 49, 489–522.CrossRefGoogle ScholarPubMed
Bren, A. & Eisenbach, M. (2000). How signals are heard during bacterial chemotaxis: protein-protein interactions in sensory signal propagation. Journal of Bacteriology 182, 6865–6873.CrossRefGoogle ScholarPubMed
Chilcott, G. S. & Hughes, K. T. (2000). Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli. Microbiology and Molecular Biology Reviews 64, 694–708.CrossRefGoogle ScholarPubMed
Levit, M. N., Liu, Y. & Stock, J. B. (1998). Stimulus response coupling in bacterial chemotaxis: receptor dimers in signalling arrays. Molecular Microbiology 30, 459–466.CrossRefGoogle ScholarPubMed
Macnab, R. M. (1999). The bacterial flagellum: reversible rotary propeller and type III export apparatus. Journal of Bacteriology 181, 7149–7153.Google Scholar
Manson, M. D., Armitage, J. P., Hoch, J. A. & Macnab, R. M. (1998). Bacterial locomotion and signal transduction. Journal of Bacteriology 180, 1009–1022.Google ScholarPubMed
Mitchell, J. G. & Kogure, K. (2006). Bacterial motility: links to the environment and a driving force for microbial physics. FEMS Microbiology Ecology 55, 3–16.CrossRefGoogle Scholar
Parkinson, J. S. (2003). Bacterial chemotaxis: a new player in response regulator dephosphorylation. Journal of Bacteriology 185, 1492–1494.CrossRefGoogle ScholarPubMed
Parkinson, J. S., Ames, P. & Studdert, C. A. (2005). Collaborative signaling by bacterial chemoreceptors. Current Opinion in Microbiology 8, 116–121.CrossRefGoogle ScholarPubMed
Sourjik, V. (2004). Receptor clustering and signal processing in E. coli chemotaxis. Trends in Microbiology 12, 569–576.CrossRefGoogle ScholarPubMed
Szurmant, H. & Ordal, G. W. (2004). Diversity in chemotaxis mechanisms among the bacteria and archaea. Microbiology and Molecular Biology Reviews 68, 301–319.CrossRefGoogle ScholarPubMed
Taylor, B. L., Zhulin, I. B. & Johnson, M. S. (1999). Aerotaxis and other energy-sensing behavior in bacteria. Annual Review of Microbiology 53, 103–128.CrossRefGoogle ScholarPubMed
Aertsen, A. & Michiels, C. W. (2005). Diversify or die: generation of diversity in response to stress. Critical Reviews in Microbiology 31, 69–78.CrossRefGoogle ScholarPubMed
Amzallag, G. N. (2004). Adaptive changes in bacteria: a consequence of nonlinear transitions in chromosome topology?Journal of Theoretical Biology 229, 361–369.CrossRefGoogle ScholarPubMed
Dubnau, D. & Losick, R. (2006). Bistability in bacteria. Molecular Microbiology 61, 564–572.CrossRefGoogle ScholarPubMed
Foster, P. L. (1993). Adaptive mutation: the uses of adversity. Annual Review of Microbiology 47, 467–504.CrossRefGoogle ScholarPubMed
Foster, P. L. (2005). Stress responses and genetic variation in bacteria. Mutation Research–Fundamental and Molecular Mechanisms of Mutagenesis 569, 3–11.CrossRefGoogle ScholarPubMed
Goudreau, P. N. & Stock, A. M. (1998). Signal transduction in bacteria: molecular mechanisms of stimulus-response coupling. Current Opinion in Microbiology 1, 160–169.CrossRefGoogle ScholarPubMed
Igoshin, O. A., Price, C. W. & Savageau, M. A. (2006). Signalling network with a bistable hysteretic switch controls developmental activation of the sigmaF transcription factor in Bacillus subtilis. Molecular Microbiology 61, 165–184.CrossRefGoogle ScholarPubMed
Martin, B., Quentin, Y., Fichant, G. & Claverys, J. P. (2006). Independent evolution of competence regulatory cascades in streptococci?Trends in Microbiology 14, 339–345.CrossRefGoogle ScholarPubMed
Osorio, G. & Jerez, C. A. (1996). Adaptive response of the archaeon Sulfolobus acidocaldarius BC65 to phosphate starvation. Microbiology-UK 142, 1531–1536.CrossRefGoogle ScholarPubMed
Rosenberg, S. M. (1994). In pursuit of a molecular mechanism for adaptive mutation. Genome 37, 893–899.CrossRefGoogle ScholarPubMed
Sniegowski, P. D. & Lenski, R. E. (1995). Mutation and adaptation: the directed mutation controversy in evolutionary perspective. Annual Review of Ecology and Systematics 26, 553–578.CrossRefGoogle Scholar
Wright, B. E. (2004). Stress-directed adaptive mutations and evolution. Molecular Microbiology 52, 643–650.CrossRefGoogle ScholarPubMed
Arcondeguy, T., Jack, R. & Merrick, M. (2001). P-II signal transduction proteins, pivotal players in microbial nitrogen control. Microbiology Molecular Biology Reviews 65, 80–105.CrossRefGoogle ScholarPubMed
Commichau, F. M., Forchhammer, K. & Stulke, J. (2006). Regulatory links between carbon and nitrogen metabolism. Current Opinion in Microbiology 9, 167–172.CrossRefGoogle ScholarPubMed
Edwards, J. S., Covert, M. & Palsson, B. (2002). Metabolic modelling of microbes: the flux-balance approach. Environmental Microbiology 4, 133–140.CrossRefGoogle ScholarPubMed
Ehrmann, M. & Clausen, T. (2004). Proteolysis as a regulatory mechanism. Annual Review of Genetics 38, 709–724.CrossRefGoogle ScholarPubMed
El-Mansi, M., Cozzone, A. J., Shiloach, J. & Eikmanns, B. J. (2006). Control of carbon flux through enzymes of central and intermediary metabolism during growth of Escherichia coli on acetate. Current Opinion in Microbiology 9, 173–179.CrossRefGoogle Scholar
Forchhammer, K. (2004). Global carbon/nitrogen control by PII signal transduction in cyanobacteria: from signals to targets. FEMS Microbiology Reviews 28, 319–333.CrossRefGoogle Scholar
Hengge, R. & Gourse, R. L. (2004). Cell regulation: tying together the cellular regulatory network. Current Opinion in Microbiology 7, 99–101.CrossRefGoogle Scholar
Herrero, A. (2004). New targets of the PII signal transduction protein identified in cyanobacteria. Molecular Microbiology 52, 1225–1228.CrossRefGoogle ScholarPubMed
Jenal, U. & Hengge-Aronis, R. (2003). Regulation by proteolysis in bacterial cells. Current Opinion in Microbiology 6, 163–172.CrossRefGoogle ScholarPubMed
Ninfa, A. J. & Jiang, P. (2005). PII signal transduction proteins: sensors of α-ketoglutarate that regulate nitrogen metabolism. Current Opinion in Microbiology 8, 168–173.CrossRefGoogle ScholarPubMed
Noirot, P. & Noirot-Gros, M. F. (2004). Protein interaction networks in bacteria. Current Opinion in Microbiology 7, 505–512.CrossRefGoogle ScholarPubMed
Russell, R. B., Alber, F., Aloy, P., Davis, F. P., Korkin, D., Pichaud, M., Topf, M. & Sali, A. (2004). A structural perspective on protein-protein interactions. Current Opinion in Structural Biology 14, 313–324.CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×