title: Regulation of Gene Expression in Shewanella oneidensis MR-1 during Electron Acceptor Limitation and Bacterial Nanowire Formation.
abstract: In limiting oxygen as an electron acceptor, the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 rapidly forms nanowires, extensions of its outer membrane containing the cytochromes MtrC and OmcA needed for extracellular electron transfer. RNA sequencing (RNA-Seq) analysis was employed to determine differential gene expression over time from triplicate chemostat cultures that were limited for oxygen. We identified 465 genes with decreased expression and 677 genes with increased expression. The coordinated increased expression of heme biosynthesis, cytochrome maturation, and transport pathways indicates that S. oneidensis MR-1 increases cytochrome production, including the transcription of genes encoding MtrA, MtrC, and OmcA, and transports these decaheme cytochromes across the cytoplasmic membrane during electron acceptor limitation and nanowire formation. In contrast, the expression of the mtrA and mtrC homologs mtrF and mtrD either remains unaffected or decreases under these conditions. The ompW gene, encoding a small outer membrane porin, has 40-fold higher expression during oxygen limitation, and it is proposed that OmpW plays a role in cation transport to maintain electrical neutrality during electron transfer. The genes encoding the anaerobic respiration regulator cyclic AMP receptor protein (CRP) and the extracytoplasmic function sigma factor RpoE are among the transcription factor genes with increased expression. RpoE might function by signaling the initial response to oxygen limitation. Our results show that RpoE activates transcription from promoters upstream of mtrC and omcA The transcriptome and mutant analyses of S. oneidensis MR-1 nanowire production are consistent with independent regulatory mechanisms for extending the outer membrane into tubular structures and for ensuring the electron transfer function of the nanowires.
  
  
  
  Shewanella oneidensis MR-1 has the capacity to transfer electrons to its external surface using extensions of the outer membrane called bacterial nanowires. These bacterial nanowires link the cell's respiratory chain to external surfaces, including oxidized metals important in bioremediation, and explain why S. oneidensis can be utilized as a component of microbial fuel cells, a form of renewable energy. In this work, we use differential gene expression analysis to focus on which genes function to produce the nanowires and promote extracellular electron transfer during oxygen limitation. Among the genes that are expressed at high levels are those encoding cytochrome proteins necessary for electron transfer. Shewanella coordinates the increased expression of regulators, metabolic pathways, and transport pathways to ensure that cytochromes efficiently transfer electrons along the nanowires.
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.
authors.forename: Sarah E
authors.initials: SE
authors.lastname: Barchinger
authors.affiliation: Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA.
authors.forename: Sahand
authors.initials: S
authors.lastname: Pirbadian
authors.affiliation: School of Biosciences, University of Exeter, Exeter, United Kingdom.
authors.forename: Christine
authors.identifier: 0000-0002-7219-0398
authors.initials: C
authors.lastname: Sambles
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.
authors.forename: Carol S
authors.initials: CS
authors.lastname: Baker
authors.affiliation: Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA.
authors.forename: Kar Man
authors.initials: KM
authors.lastname: Leung
authors.affiliation: Warwick Systems Biology Centre and Mathematics Institute, University of Warwick, Coventry, United Kingdom.
authors.forename: Nigel J
authors.initials: NJ
authors.lastname: Burroughs
authors.affiliation: Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA Molecular and Computational Biology Section, Department of Biological Sciences and Department of Chemistry, University of Southern California, Los Angeles, California, USA.
authors.forename: Mohamed Y
authors.initials: MY
authors.lastname: El-Naggar
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA jhg5@psu.edu.
authors.forename: John H
authors.initials: JH
authors.lastname: Golbeck
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001674:Bioelectric Energy Sources; D002373:Cyclic AMP Receptor Protein / Q000235:genetics / Q000378:metabolism; D004579:Electron Transport; D015964:Gene Expression Regulation, Bacterial; D053770:Nanowires / Q000737:chemistry*; D010084:Oxidation-Reduction; D020592:Shewanella / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*
chemical_list: D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D002373:Cyclic AMP Receptor Protein