This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Reitzer, L.
Right arrow Articles by Schneider, B. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Reitzer, L.
Right arrow Articles by Schneider, B. L.

 Previous Article  |  Next Article 

Microbiology and Molecular Biology Reviews, September 2001, p. 422-444, Vol. 65, No. 3
1092-2172/01/$04.00+0   DOI: 10.1128/MMBR.65.3.422-444.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Metabolic Context and Possible Physiological Themes of sigma 54-Dependent Genes in Escherichia coli

Larry Reitzer* and Barbara L. Schneider

Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75083-0688

sigma 54 has several features that distinguish it from other sigma factors in Escherichia coli: it is not homologous to other sigma  subunits, sigma 54-dependent expression absolutely requires an activator, and the activator binding sites can be far from the transcription start site. A rationale for these properties has not been readily apparent, in part because of an inability to assign a common physiological function for sigma 54-dependent genes. Surveys of sigma 54-dependent genes from a variety of organisms suggest that the products of these genes are often involved in nitrogen assimilation; however, many are not. Such broad surveys inevitably remove the sigma 54-dependent genes from a potentially coherent metabolic context. To address this concern, we consider the function and metabolic context of sigma 54-dependent genes primarily from a single organism, Escherichia coli, in which a reasonably complete list of sigma 54-dependent genes has been identified by computer analysis combined with a DNA microarray analysis of nitrogen limitation-induced genes. E. coli appears to have approximately 30 sigma 54-dependent operons, and about half are involved in nitrogen assimilation and metabolism. A possible physiological relationship between sigma 54-dependent genes may be based on the fact that nitrogen assimilation consumes energy and intermediates of central metabolism. The products of the sigma 54-dependent genes that are not involved in nitrogen metabolism may prevent depletion of metabolites and energy resources in certain environments or partially neutralize adverse conditions. Such a relationship may limit the number of physiological themes of sigma 54-dependent genes within a single organism and may partially account for the unique features of sigma 54 and sigma 54-dependent gene expression.

* Corresponding author. Mailing address: Department of Molecular and Cell Biology, Mail Station FO 31, The University of Texas at Dallas, P.O. Box 830688, Richardson, TX 75083-0688. Phone: (972) 883-2502/2523. Fax: (972) 883-2409. E-mail: reitzer{at}utdallas.edu.

Microbiology and Molecular Biology Reviews, September 2001, p. 422-444, Vol. 65, No. 3
1092-2172/01/$04.00+0   DOI: 10.1128/MMBR.65.3.422-444.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


This article has been cited by other articles:

  • Ishida, Y., Kori, A., Ishihama, A. (2009). Participation of Regulator AscG of the {beta}-Glucoside Utilization Operon in Regulation of the Propionate Catabolism Operon. J. Bacteriol. 191: 6136-6144 [Abstract] [Full Text]  
  • Sanchez-Torres, V., Maeda, T., Wood, T. K. (2009). Protein Engineering of the Transcriptional Activator FhlA To Enhance Hydrogen Production in Escherichia coli. Appl. Environ. Microbiol. 75: 5639-5646 [Abstract] [Full Text]  
  • Bergholz, T. M., Vanaja, S. K., Whittam, T. S. (2009). Gene Expression Induced in Escherichia coli O157:H7 upon Exposure to Model Apple Juice. Appl. Environ. Microbiol. 75: 3542-3553 [Abstract] [Full Text]  
  • Yang, T.-C., Leu, Y.-W., Chang-Chien, H.-C., Hu, R.-M. (2009). Flagellar Biogenesis of Xanthomonas campestris Requires the Alternative Sigma Factors RpoN2 and FliA and Is Temporally Regulated by FlhA, FlhB, and FlgM. J. Bacteriol. 191: 2266-2275 [Abstract] [Full Text]  
  • Ali, H., Murrell, J. C. (2009). Development and validation of promoter-probe vectors for the study of methane monooxygenase gene expression in Methylococcus capsulatus Bath. Microbiology 155: 761-771 [Abstract] [Full Text]  
  • Raberg, M., Reinecke, F., Reichelt, R., Malkus, U., Konig, S., Potter, M., Fricke, W. F., Pohlmann, A., Voigt, B., Hecker, M., Friedrich, B., Bowien, B., Steinbuchel, A. (2008). Ralstonia eutropha H16 Flagellation Changes According to Nutrient Supply and State of Poly(3-Hydroxybutyrate) Accumulation. Appl. Environ. Microbiol. 74: 4477-4490 [Abstract] [Full Text]  
  • Zaini, P. A., Fogaca, A. C., Lupo, F. G. N., Nakaya, H. I., Vencio, R. Z. N., da Silva, A. M. (2008). The Iron Stimulon of Xylella fastidiosa Includes Genes for Type IV Pilus and Colicin V-Like Bacteriocins. J. Bacteriol. 190: 2368-2378 [Abstract] [Full Text]  
  • Saldias, M. S., Lamothe, J., Wu, R., Valvano, M. A. (2008). Burkholderia cenocepacia Requires the RpoN Sigma Factor for Biofilm Formation and Intracellular Trafficking within Macrophages. Infect. Immun. 76: 1059-1067 [Abstract] [Full Text]  
  • Zhang, X.-X., Rainey, P. B. (2008). Dual Involvement of CbrAB and NtrBC in the Regulation of Histidine Utilization in Pseudomonas fluorescens SBW25. Genetics 178: 185-195 [Abstract] [Full Text]  
  • Habe, H., Kouzuma, A., Endoh, T., Omori, T., Yamane, H., Nojiri, H. (2007). Transcriptional regulation of the sulfate-starvation-induced gene sfnA by a {sigma}54-dependent activator of Pseudomonas putida. Microbiology 153: 3091-3098 [Abstract] [Full Text]  
  • Matta, M. K., Lioliou, E. E., Panagiotidis, C. H., Kyriakidis, D. A., Panagiotidis, C. A. (2007). Interactions of the Antizyme AtoC with Regulatory Elements of the Escherichia coli atoDAEB Operon. J. Bacteriol. 189: 6324-6332 [Abstract] [Full Text]  
  • Zhang, X.-X., Rainey, P. B. (2007). Genetic Analysis of the Histidine Utilization (hut) Genes in Pseudomonas fluorescens SBW25. Genetics 176: 2165-2176 [Abstract] [Full Text]  
  • Janaszak, A., Majczak, W., Nadratowska, B., Szalewska-Palasz, A., Konopa, G., Taylor, A. (2007). A {sigma}54-dependent promoter in the regulatory region of the Escherichia coli rpoH gene. Microbiology 153: 111-123 [Abstract] [Full Text]  
  • Deutscher, J., Francke, C., Postma, P. W. (2006). How Phosphotransferase System-Related Protein Phosphorylation Regulates Carbohydrate Metabolism in Bacteria. Microbiol. Mol. Biol. Rev. 70: 939-1031 [Abstract] [Full Text]  
  • Roh, J.-B., Lee, M.-A., Lee, H.-J., Kim, S.-M., Cho, Y., Kim, Y.-J., Seok, Y.-J., Park, S.-J., Lee, K.-H. (2006). Transcriptional Regulatory Cascade for Elastase Production in Vibrio vulnificus: LuxO ACTIVATES luxT EXPRESSION AND LuxT REPRESSES smcR EXPRESSION. J. Biol. Chem. 281: 34775-34784 [Abstract] [Full Text]  
  • Anfora, A. T., Welch, R. A. (2006). DsdX Is the Second D-Serine Transporter in Uropathogenic Escherichia coli Clinical Isolate CFT073.. J. Bacteriol. 188: 6622-6628 [Abstract] [Full Text]  
  • Doughty, D. M., Sayavedra-Soto, L. A., Arp, D. J., Bottomley, P. J. (2006). Product Repression of Alkane Monooxygenase Expression in Pseudomonas butanovora.. J. Bacteriol. 188: 2586-2592 [Abstract] [Full Text]  
  • Choi, S.-K., Saier, M. H. Jr. (2005). Regulation of sigL Expression by the Catabolite Control Protein CcpA Involves a Roadblock Mechanism in Bacillus subtilis: Potential Connection between Carbon and Nitrogen Metabolism. J. Bacteriol. 187: 6856-6861 [Abstract] [Full Text]  
  • Lee, S. K., Newman, J. D., Keasling, J. D. (2005). Catabolite Repression of the Propionate Catabolic Genes in Escherichia coli and Salmonella enterica: Evidence for Involvement of the Cyclic AMP Receptor Protein. J. Bacteriol. 187: 2793-2800 [Abstract] [Full Text]  
  • Zhang, Z., Gosset, G., Barabote, R., Gonzalez, C. S., Cuevas, W. A., Saier, M. H. Jr. (2005). Functional Interactions between the Carbon and Iron Utilization Regulators, Crp and Fur, in Escherichia coli. J. Bacteriol. 187: 980-990 [Abstract] [Full Text]  
  • Nandineni, M. R., Laishram, R. S., Gowrishankar, J. (2004). Osmosensitivity Associated with Insertions in argP (iciA) or glnE in Glutamate Synthase-Deficient Mutants of Escherichia coli. J. Bacteriol. 186: 6391-6399 [Abstract] [Full Text]  
  • Yang, X. F., Ji, Y., Schneider, B. L., Reitzer, L. (2004). Phosphorylation-independent Dimer-Dimer Interactions by the Enhancer-binding Activator NtrC of Escherichia coli: A THIRD FUNCTION FOR THE C-TERMINAL DOMAIN. J. Biol. Chem. 279: 36708-36714 [Abstract] [Full Text]  
  • Lopez-Marques, R. L., Perez-Castineira, J. R., Losada, M., Serrano, A. (2004). Differential Regulation of Soluble and Membrane-Bound Inorganic Pyrophosphatases in the Photosynthetic Bacterium Rhodospirillum rubrum Provides Insights into Pyrophosphate-Based Stress Bioenergetics. J. Bacteriol. 186: 5418-5426 [Abstract] [Full Text]  
  • Green, R. C., Darwin, A. J. (2004). PspG, a New Member of the Yersinia enterocolitica Phage Shock Protein Regulon. J. Bacteriol. 186: 4910-4920 [Abstract] [Full Text]  
  • Kabir, Md. S., Sagara, T., Oshima, T., Kawagoe, Y., Mori, H., Tsunedomi, R., Yamada, M. (2004). Effects of mutations in the rpoS gene on cell viability and global gene expression under nitrogen starvation in Escherichia coli. Microbiology 150: 2543-2553 [Abstract] [Full Text]  
  • Nandineni, M. R., Gowrishankar, J. (2004). Evidence for an Arginine Exporter Encoded by yggA (argO) That Is Regulated by the LysR-Type Transcriptional Regulator ArgP in Escherichia coli. J. Bacteriol. 186: 3539-3546 [Abstract] [Full Text]  
  • Wolfe, A. J., Millikan, D. S., Campbell, J. M., Visick, K. L. (2004). Vibrio fischeri {sigma}54 Controls Motility, Biofilm Formation, Luminescence, and Colonization. Appl. Environ. Microbiol. 70: 2520-2524 [Abstract] [Full Text]  
  • Harrod, A. C., Yang, X., Junker, M., Reitzer, L. (2004). Evidence for a Second Interaction between the Regulatory Amino-terminal and Central Output Domains of the Response Regulator NtrC (Nitrogen Regulator I) in Escherichia coli. J. Biol. Chem. 279: 2350-2359 [Abstract] [Full Text]  
  • Farrell, M. J., Finkel, S. E. (2003). The Growth Advantage in Stationary-Phase Phenotype Conferred by rpoS Mutations Is Dependent on the pH and Nutrient Environment. J. Bacteriol. 185: 7044-7052 [Abstract] [Full Text]  
  • Rediers, H., Bonnecarrere, V., Rainey, P. B., Hamonts, K., Vanderleyden, J., De Mot, R. (2003). Development and Application of a dapB-Based In Vivo Expression Technology System To Study Colonization of Rice by the Endophytic Nitrogen-Fixing Bacterium Pseudomonas stutzeri A15. Appl. Environ. Microbiol. 69: 6864-6874 [Abstract] [Full Text]  
  • Magasanik, B. (2003). Ammonia Assimilation by Saccharomyces cerevisiae. Eukaryot Cell 2: 827-829 [Full Text]  
  • Yang, X. F., Alani, S. M., Norgard, M. V. (2003). The response regulator Rrp2 is essential for the expression of major membrane lipoproteins in Borrelia burgdorferi. Proc. Natl. Acad. Sci. USA 100: 11001-11006 [Abstract] [Full Text]  
  • Stewart, B. J., McCarter, L. L. (2003). Lateral Flagellar Gene System of Vibrio parahaemolyticus. J. Bacteriol. 185: 4508-4518 [Abstract] [Full Text]  
  • Stafford, G. P., Scanlan, J., McDonald, I. R., Murrell, J. C. (2003). rpoN, mmoR and mmoG, genes involved in regulating the expression of soluble methane monooxygenase in Methylosinus trichosporium OB3b. Microbiology 149: 1771-1784 [Abstract] [Full Text]  
  • Csaki, R., Bodrossy, L., Klem, J., Murrell, J. C., Kovacs, K. L. (2003). Genes involved in the copper-dependent regulation of soluble methane monooxygenase of Methylococcus capsulatus (Bath): cloning, sequencing and mutational analysis. Microbiology 149: 1785-1795 [Abstract] [Full Text]  
  • Heurlier, K., Denervaud, V., Pessi, G., Reimmann, C., Haas, D. (2003). Negative Control of Quorum Sensing by RpoN ({sigma}54) in Pseudomonas aeruginosa PAO1. J. Bacteriol. 185: 2227-2235 [Abstract] [Full Text]  
  • Endoh, T., Habe, H., Yoshida, T., Nojiri, H., Omori, T. (2003). A CysB-regulated and {sigma}54-dependent regulator, SfnR, is essential for dimethyl sulfone metabolism of Pseudomonas putida strain DS1. Microbiology 149: 991-1000 [Abstract] [Full Text]  
  • Studholme, D. J., Dixon, R. (2003). Domain Architectures of {sigma}54-Dependent Transcriptional Activators. J. Bacteriol. 185: 1757-1767 [Full Text]  
  • Gardner, A. M., Gessner, C. R., Gardner, P. R. (2003). Regulation of the Nitric Oxide Reduction Operon (norRVW) in Escherichia coli. ROLE OF NorR AND sigma 54 IN THE NITRIC OXIDE STRESS RESPONSE. J. Biol. Chem. 278: 10081-10086 [Abstract] [Full Text]  
  • Adams, H., Teertstra, W., Demmers, J., Boesten, R., Tommassen, J. (2003). Interactions between Phage-Shock Proteins in Escherichia coli. J. Bacteriol. 185: 1174-1180 [Abstract] [Full Text]  
  • Schneider, B. L., Ruback, S., Kiupakis, A. K., Kasbarian, H., Pybus, C., Reitzer, L. (2002). The Escherichia coli gabDTPC Operon: Specific {gamma}-Aminobutyrate Catabolism and Nonspecific Induction. J. Bacteriol. 184: 6976-6986 [Abstract] [Full Text]  
  • Atkinson, M. R., Blauwkamp, T. A., Bondarenko, V., Studitsky, V., Ninfa, A. J. (2002). Activation of the glnA, glnK, and nac Promoters as Escherichia coli Undergoes the Transition from Nitrogen Excess Growth to Nitrogen Starvation. J. Bacteriol. 184: 5358-5363 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»