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PMID: 11528004 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. Review

Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli.

Microbiology and molecular biology reviews : MMBR ·Vol. 65 ·No. 3 ·2001-09-00 ·Pages 422-44, table of contents

Reitzer L, Schneider BL

Abstract

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.

MeSH Terms
DNA-Binding Proteins DNA-Directed RNA Polymerases/chemistry,physiology Escherichia coli/genetics,metabolism,physiology Escherichia coli Proteins Gene Expression Genes, Bacterial Nitrogen/metabolism Promoter Regions, Genetic RNA Polymerase Sigma 54 Sigma Factor/chemistry,physiology Transcription, Genetic
Chemicals
DNA-Binding Proteins Escherichia coli Proteins Sigma Factor rpoN protein, E coli DNA-Directed RNA Polymerases RNA Polymerase Sigma 54 Nitrogen
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Reitzer L
Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, TX 75083-0688, USA. [email protected]
Schneider B L
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Article Info
Journal
Microbiology and molecular biology reviews : MMBR
Abbr.
Microbiol Mol Biol Rev
ISSN
1092-2172
DOI
10.1128/MMBR.65.3.422-444.2001
Email
[email protected]
Published
2001-09-00
Pages
422-44, table of contents
Language
English
Region
United States
NLM ID
9706653
PMCID
PMC99035
Subset
IM
Grants
NIGMS NIH HHS · GM47965 · United States
External Links
PubMed source DOI: 10.1128/MMBR.65.3.422-444.2001 PMC Full Text View journal details
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