title: 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.
  
  
  RESULTS
  An 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.
  
  
  CONCLUSIONS
  The G. sulfurreducens RpoN is an essential sigma factor and a global regulator involved in a complex transcriptional network controlling a variety of cellular processes.
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA. leang@microbio.umass.edu
authors.forename: Ching
authors.initials: C
authors.lastname: Leang
authors.forename: Julia
authors.initials: J
authors.lastname: Krushkal
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Ueki
authors.forename: Marko
authors.initials: M
authors.lastname: Puljic
authors.forename: Jun
authors.initials: J
authors.lastname: Sun
authors.forename: Katy
authors.initials: K
authors.lastname: Juárez
authors.forename: Cinthia
authors.initials: C
authors.lastname: Núñez
authors.forename: Gemma
authors.initials: G
authors.lastname: Reguera
authors.forename: Raymond
authors.initials: R
authors.lastname: DiDonato
authors.forename: Bradley
authors.initials: B
authors.lastname: Postier
authors.forename: Ronald M
authors.initials: RM
authors.lastname: Adkins
authors.forename: Derek R
authors.initials: DR
authors.lastname: Lovley
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D055106:Genome-Wide Association Study; D045302:Geobacter / Q000235:genetics*; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D051877:RNA Polymerase Sigma 54 / Q000235:genetics*; D018085:Regulon
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D051877:RNA Polymerase Sigma 54