Metabolic Context and Possible Physiological Themes of ς⁵⁴-Dependent Genes inEscherichia coli

Abstract

SUMMARY ς54 has several features that distinguish it from other sigma factors in Escherichia coli: it is not homologous to other ς subunits, ς54-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 ς54-dependent genes. Surveys of ς54-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 ς54-dependent genes from a potentially coherent metabolic context. To address this concern, we consider the function and metabolic context of ς54-dependent genes primarily from a single organism, Escherichia coli, in which a reasonably complete list of ς54-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 ς54-dependent operons, and about half are involved in nitrogen assimilation and metabolism. A possible physiological relationship between ς54-dependent genes may be based on the fact that nitrogen assimilation consumes energy and intermediates of central metabolism. The products of the ς54-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 ς54-dependent genes within a single organism and may partially account for the unique features of ς54 and ς54-dependent gene expression.

Phosphorylation-independent Dimer-Dimer Interactions by the Enhancer-binding Activator NtrC of Escherichia coli

“…glnHPQ codes for components of a high affinity glutamine transport system (43,44); nac for a regulator of several Ntr genes (44); and ygjG for putrescine transaminase (45,46). The promoters for these operons, except for glnA-ntrBC, were fused to lacZ and expressed on the chromosome.…”

Expression of the six chromate ion transporter homologues of Burkholderia xenovorans LB400

“…However, the homologues with the lowest expression levels (chrA1a and chr1NCa), both from chromosome 1, were predicted to possess promoters regulated by s 54 factors. The fact that s 54 controls the transcription of genes devoted to a variety of functions (Reitzer & Schneider, 2001) suggests that these chr genes might express under conditions distinct from those tested in this work. This proposal is supported by the finding that chrA1a and chr1NCa genes conferred clear chromate resistance phenotypes when assayed in E. coli.…”

A σ 54-dependent promoter in the regulatory region of the Escherichia coli rpoH gene

“…In a paper by Reitzer & Schneider (2001), the authors mentioned unpublished results of experiments in which it was not possible to demonstrate the existence of a transcript from the P6 promoter in nitrogen-limited cells, which meant NtrC was not the activator of this transcription. We confirm this opinion.…”

“…Analysis of the upstream sequence of the rpoH gene by a BLAST search showed that the s 54 promoter was correctly situated according to the rules proposed by Reitzer & Schneider (2001) for active s 54 promoters. Moreover, an IHF-binding site homologous to the consensus sequence was found at the position 2349 to 2362 (Fig.…”

“…Functional s 54 promoters are rare in the E. coli genome: their number was estimated to be about 30, though sequences resembling canonical s 54 promoters are abundant (Reitzer & Schneider, 2001). The s 54 subunit is not essential for E. coli growth under laboratory conditions; however, it is necessary for expression of genes involved in diverse processes like nitrogen metabolism, transport of dicarboxylic acids, pilus formation, formate dehydrogenase synthesis, metabolism of aromatic compounds (xylene, toluene), and expression of the pspA-E operon and of the ibpB gene encoding a small heat shock protein.…”