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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.


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