Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens

Abstract

Background: The role of the RNA polymerase sigma factor RpoN in regulation of gene expression in Geobacter sulfurreducens was investigated to better understand transcriptional regulatory networks as part of an effort to develop regulatory modules for genome-scale in silico models, which can predict the physiological responses of Geobacter species during groundwater bioremediation or electricity production.

Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks

“…For example, the gene GSU1745 that encodes the essential outer membrane porin OmpA 24 was only associated with a s N -dependent promoter. This observation is consistent with the previously failed attempts to generate viable rpoN (s N ) knock-out strains for G. sulfurreducens under multiple growth conditions 14 .…”

“…We confirmed many genes previously described to be regulated by s H , such as heat-inducible chaperones (for example, hspA) 13 , or by s N , such as the nitrogenase molybdenum-iron cofactor biosynthesis protein (nifEN) 14 . In addition to nifEN being transcribed from a s N -specific promoter, s N was the only s factor controlling this essential gene for nitrogen fixation.…”

“…Binding profiles of s D , s N and s S were obtained from cells grown with acetate as electron donor either planktonically with fumarate or as a biofilm on an electrode serving as the terminal electron acceptor. Furthermore, s factor binding profiles were obtained under the specific conditions, where their activity has been previously documented 13,14 . Specifically, binding profiles of s H and s N were obtained from cells under heat shock stress and nitrogen limitation, respectively.…”

“…This indicates that the change in promoter occupancy of s factors is usually not modulated through the transcription levels of the s factors, but by other mechanisms. For example, the expression changes of genes for nitrogen fixation under nitrogen limitation conditions are due to the expression of specific s N dependent regulators 14 . However, the heat shock s factor (s H ) was highly induced upon temperature upshift, suggesting that regulation of gene expression upon heat shock resulted from higher expression of the rpoH gene.…”

Identification of Multicomponent Histidine-Aspartate Phosphorelay System Controlling Flagellar and Motility Gene Expression in Geobacter Species

“…FleQ and FlrA activate flagellar genes whose expression is RpoN-dependent, consistent with the fact that EBPs generally promote transcription of RpoN-dependent genes (22,23). It has previously been suggested that the expression of some flagellar genes in G. sulfurreducens may be RpoN-dependent (25,26).…”