Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens

Ching Leang,Gemma Reguera,Cinthia Núñez,Marko Puljic,Derek R Lovley,Bradley Postier,Raymond Didonato,Toshiyuki Ueki,Julia Krushkal,Katy Juárez,Ronald M Adkins,Jun Sun

doi:10.1186/1471-2164-10-331

Abstract

BackgroundThe 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.ResultsAn rpoN deletion mutant could not be obtained under all conditions tested. In order to investigate the regulon of the G. sulfurreducens RpoN, an RpoN over-expression strain was made in which an extra copy of the rpoN gene was under the control of a taclac promoter. Combining both the microarray transcriptome analysis and the computational prediction revealed that the G. sulfurreducens RpoN controls genes involved in a wide range of cellular functions. Most importantly, RpoN controls the expression of the dcuB gene encoding the fumarate/succinate exchanger, which is essential for cell growth with fumarate as the terminal electron acceptor in G. sulfurreducens. RpoN also controls genes, which encode enzymes for both pathways of ammonia assimilation that is predicted to be essential under all growth conditions in G. sulfurreducens. Other genes that were identified as part of the RpoN regulon using either the computational prediction or the microarray transcriptome analysis included genes involved in flagella biosynthesis, pili biosynthesis and genes involved in central metabolism enzymes and cytochromes involved in extracellular electron transfer to Fe(III), which are known to be important for growth in subsurface environment or electricity production in microbial fuel cells. The consensus sequence for the predicted RpoN-regulated promoter elements is TTGGCACGGTTTTTGCT.ConclusionThe G. sulfurreducens RpoN is an essential sigma factor and a global regulator involved in a complex transcriptional network controlling a variety of cellular processes.

Highlights

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
Analysis of the chromosomal region surrounding the G. sulfurreducens rpoN gene revealed that its downstream genes encode a homolog of a ribosomal subunit interface protein (GSU1886) whose N-terminal domain is homologous to the RpoN modulation protein found in Klebsiella pneumoniae [26] and a homolog of Hpr (Ser) kinase/phosphorylase (GSU1885)
The results presented here demonstrate that G. sulfurreducens has an RpoN ortholog, which exhibits typical structural characteristics shared by the RpoN family

Summary

Introduction

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. RpoN (σ54 or sigma 54) is a subunit of the RNA polymerase and plays a critical role in the regulation of gene expression by recognizing specific promoter elements and initiating transcription. RpoN-dependent promoters do not have conserved -35 and -10 elements typically found in the promoters recognized by sigma factors in the σ70 family. In contrast to σ70 family sigma factors, RpoN is able to bind to a promoter without the core RNA polymerase (RNAP) [1]. RpoN homologs have been identified in bacteria from different phylogenetic origins and are involved in regulation of genes related to a diverse functional categories [5], including genes for pili and flagella biosynthesis and quorum sensing in Pseudomonas aeruginosa [6,7,8], C4dicarboxylate transport in Mesorhizobium ciceri [9] and carbon metabolism in Gram positive bacteria, Bacillus subtilis and Listeria monocytogenes [10,11,12,13]

Methods

Results

Discussion

Conclusion