@article {422,
	title = {Genome diversity of the TetR family of transcriptional regulators in a metal-reducing bacterial family Geobacteraceae and other microbial species.},
	journal = {OMICS},
	volume = {15},
	year = {2011},
	month = {2011 Jul-Aug},
	pages = {495-506},
	abstract = {Members of the TetR family of bacterial transcriptional regulators affect expression of genes whose products are involved in a variety of important functions, including osmotic stress, catabolic pathways, homeostasis, biosynthesis of antibiotics, expression of efflux pumps, multidrug resistance, and virulence of pathogenic bacteria. We used genome sequence information to carry out phylogenetic classification of 864 TetR family members with a special focus on TetR regulators in Geobacteraceae, an environmentally important family of delta-Proteobacteria. The genome of Geobacter sulfurreducens, a model representative of Geobacteraceae, contains nine genes from the tetR family. Several of these genes are located immediately upstream of operons encoding functionally important c-type cytochromes. Computational analyses identified the presence of conserved promoters and other regulatory binding sites upstream of several G. sulfurreducens tetR genes. This suggests the possibility of an intermediary role of TetR family proteins in Geobacteraceae in regulatory cascades involving a variety of sigma factors. In order to understand the role of the TetR regulatory family in Geobacteraceae, we have inferred phylogenetic relationships among the Geobacteraceae TetR proteins and their homologs in other microbial species.},
	keywords = {Bacterial Proteins, Binding Sites, Gram-Negative Bacteria, Metals, Oxidation-Reduction, Phylogeny, Promoter Regions, Genetic, Sigma Factor},
	issn = {1557-8100},
	doi = {10.1089/omi.2010.0117},
	author = {Krushkal, Julia and Sontineni, Sreedhar and Leang, Ching and Qu, Yanhua and Adkins, Ronald M and Lovley, Derek R}
}
@article {436,
	title = {Genome-wide survey for PilR recognition sites of the metal-reducing prokaryote Geobacter sulfurreducens.},
	journal = {Gene},
	volume = {469},
	year = {2010},
	month = {2010 Dec 1},
	pages = {31-44},
	abstract = {Geobacter sulfurreducens is a species from the bacterial family Geobacteraceae, members of which participate in bioenergy production and in environmental bioremediation. G. sulfurreducens pili are electrically conductive and are required for Fe(III) oxide reduction and for optimal current production in microbial fuel cells. PilR is an enhancer binding protein, which is an activator acting together with the alternative sigma factor, RpoN, in transcriptional regulation. Both RpoN and PilR are involved in regulation of expression of the pilA gene, whose product is pilin, a structural component of a pilus. Using bioinformatic approaches, we predicted G. sulfurreducens sequence elements that are likely to be regulated by PilR. The functional importance of the genome region containing a PilR binding site predicted upstream of the pilA gene was experimentally validated. The predicted G. sulfurreducens PilR binding sites are similar to PilR binding sites of Pseudomonas and Moraxella. While the number of predicted PilR-regulated sites did not deviate from that expected by chance, multiple sites were predicted upstream of genes with roles in biosynthesis and function of pili and flagella, in secretory pathways, and in cell wall biogenesis, suggesting the possible involvement of G. sulfurreducens PilR in regulation of production and assembly of pili and flagella.},
	keywords = {Bacterial Proteins, Base Sequence, Binding Sites, Conserved Sequence, Ferric Compounds, Fimbriae Proteins, Gene Expression Regulation, Bacterial, Genome, Bacterial, Geobacter, Molecular Sequence Data, Promoter Regions, Genetic, Transcription Factors, Transcription, Genetic},
	issn = {1879-0038},
	doi = {10.1016/j.gene.2010.08.005},
	author = {Krushkal, Julia and Ju{\'a}rez, Katy and Barbe, Jose F and Qu, Yanhua and Andrade, Angel and Puljic, Marko and Adkins, Ronald M and Lovley, Derek R and Ueki, Toshiyuki}
}
@article {440,
	title = {Novel regulatory cascades controlling expression of nitrogen-fixation genes in Geobacter sulfurreducens.},
	journal = {Nucleic Acids Res},
	volume = {38},
	year = {2010},
	month = {2010 Nov},
	pages = {7485-99},
	abstract = {Geobacter species often play an important role in bioremediation of environments contaminated with metals or organics and show promise for harvesting electricity from waste organic matter in microbial fuel cells. The ability of Geobacter species to fix atmospheric nitrogen is an important metabolic feature for these applications. We identified novel regulatory cascades controlling nitrogen-fixation gene expression in Geobacter sulfurreducens. Unlike the regulatory mechanisms known in other nitrogen-fixing microorganisms, nitrogen-fixation gene regulation in G. sulfurreducens is controlled by two two-component His-Asp phosphorelay systems. One of these systems appears to be the master regulatory system that activates transcription of the majority of nitrogen-fixation genes and represses a gene encoding glutamate dehydrogenase during nitrogen fixation. The other system whose expression is directly activated by the master regulatory system appears to control by antitermination the expression of a subset of the nitrogen-fixation genes whose transcription is activated by the master regulatory system and whose promoter contains transcription termination signals. This study provides a new paradigm for nitrogen-fixation gene regulation.},
	keywords = {Bacterial Proteins, Binding Sites, DNA-Binding Proteins, Gene Expression Regulation, Bacterial, Geobacter, Nitrogen Fixation, Promoter Regions, Genetic, Protein Kinases, RNA-Binding Proteins, Transcription, Genetic},
	issn = {1362-4962},
	doi = {10.1093/nar/gkq652},
	author = {Ueki, Toshiyuki and Lovley, Derek R}
}
@article {445,
	title = {Purification and characterization of OmcZ, an outer-surface, octaheme c-type cytochrome essential for optimal current production by Geobacter sulfurreducens.},
	journal = {Appl Environ Microbiol},
	volume = {76},
	year = {2010},
	month = {2010 Jun},
	pages = {3999-4007},
	abstract = {Previous studies have demonstrated that Geobacter sulfurreducens requires the c-type cytochrome OmcZ, which is present in large (OmcZ(L); 50-kDa) and small (OmcZ(S); 30-kDa) forms, for optimal current production in microbial fuel cells. This protein was further characterized to aid in understanding its role in current production. Subcellular-localization studies suggested that OmcZ(S) was the predominant extracellular form of OmcZ. N- and C-terminal amino acid sequence analysis of purified OmcZ(S) and molecular weight measurements indicated that OmcZ(S) is a cleaved product of OmcZ(L) retaining all 8 hemes, including 1 heme with the unusual c-type heme-binding motif CX(14)CH. The purified OmcZ(S) was remarkably thermally stable (thermal-denaturing temperature, 94.2 degrees C). Redox titration analysis revealed that the midpoint reduction potential of OmcZ(S) is approximately -220 mV (versus the standard hydrogen electrode [SHE]) with nonequivalent heme groups that cover a large reduction potential range (-420 to -60 mV). OmcZ(S) transferred electrons in vitro to a diversity of potential extracellular electron acceptors, such as Fe(III) citrate, U(VI), Cr(VI), Au(III), Mn(IV) oxide, and the humic substance analogue anthraquinone-2,6-disulfonate, but not Fe(III) oxide. The biochemical properties and extracellular localization of OmcZ suggest that it is well suited for promoting electron transfer in current-producing biofilms of G. sulfurreducens.},
	keywords = {Binding Sites, Bioelectric Energy Sources, Cytochromes c, Electricity, Electron Transport, Geobacter, Heme, Hot Temperature, Molecular Sequence Data, Molecular Weight, Oxidation-Reduction, Protein Binding, Protein Stability, Sequence Alignment, Sequence Analysis, Protein},
	issn = {1098-5336},
	doi = {10.1128/AEM.00027-10},
	author = {Inoue, Kengo and Qian, Xinlei and Morgado, Leonor and Kim, Byoung-Chan and Mester, T{\"u}nde and Izallalen, Mounir and Salgueiro, Carlos A and Lovley, Derek R}
}
@article {509,
	title = {Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens.},
	journal = {Biosystems},
	volume = {90},
	year = {2007},
	month = {2007 Sep-Oct},
	pages = {421-41},
	abstract = {The knowledge obtained from understanding individual elements involved in gene regulation is important for reconstructing gene regulatory networks, a key for understanding cellular behavior. To study gene regulatory interactions in a model microorganism, Geobacter sulfurreducens, which participates in metal reduction and energy harvesting, we investigated the presence of 59 known Escherichia coli transcription factors and predicted transcription regulatory sites in its genome. The supplementary material, available at http://www.geobacter.org/research/genomescan/, provides the results of similarity comparisons that identified regulatory proteins of G. sulfurreducens and the genome locations of the predicted regulatory sites, including the list of putative regulatory elements in the upstream regions of every predicted operon and singleton open reading frame. Regulatory sequence elements, predicted using genome similarity searches to matrices of established transcription regulatory elements from E. coli, provide an initial insight into regulation of genes and operons in G. sulfurreducens. The predicted regulatory elements were predominantly located in the upstream regions of operons and singleton open reading frames. The validity of the predictions was examined using a permutation approach. Sequence similarity searches indicate that E. coli transcription factors ArgR, CytR, DeoR, FlhCD (both FlhC and FlhD subunits), FruR, GalR, GlpR, H-NS, LacI, MetJ, PurR, TrpR, and Tus are likely missing from G. sulfurreducens. Phylogenetic analysis suggests that one HU subunit is present in G. sulfurreducens as compared to two subunits in E. coli, while each of the two E. coli IHF subunits, HimA and HimD, have two homologs in G. sulfurreducens. The closest homolog of E. coli RpoE in G. sulfurreducens may be more similar to FecI than to RpoE. These findings represent the first step in the understanding of the regulatory relationships in G. sulfurreducens on the genome scale.},
	keywords = {Bacterial Proteins, Binding Sites, False Positive Reactions, Gene Expression Regulation, Bacterial, Genome, Bacterial, Geobacter, Metals, Models, Biological, Models, Genetic, Models, Statistical, Operon, Phylogeny, Sigma Factor, Systems Biology, Transcription Factors, Transcription, Genetic},
	issn = {0303-2647},
	doi = {10.1016/j.biosystems.2006.10.006},
	author = {Yan, Bin and Lovley, Derek R and Krushkal, Julia}
}
@article {507,
	title = {Heat-shock sigma factor RpoH from Geobacter sulfurreducens.},
	journal = {Microbiology},
	volume = {153},
	year = {2007},
	month = {2007 Mar},
	pages = {838-46},
	abstract = {Recent studies with Myxococcus xanthus have suggested that homologues of the Escherichia coli heat-shock sigma factor, RpoH, may not be involved in the heat-shock response in this delta-proteobacterium. The genome of another delta-proteobacterium, Geobacter sulfurreducens, which is considered to be a representative of the Fe(III)-reducing Geobacteraceae that predominate in a diversity of subsurface environments, contains an rpoH homologue. Characterization of the G. sulfurreducens rpoH homologue revealed that it was induced by a temperature shift from 30 degrees C to 42 degrees C and that an rpoH-deficient mutant was unable to grow at 42 degrees C. The predicted heat-shock genes, hrcA, grpE, dnaK, groES and htpG, were heat-shock inducible in an rpoH-dependent manner, and comparison of promoter regions of these genes identified the consensus sequences for the -10 and -35 promoter elements. In addition, DNA elements identical to the CIRCE consensus sequence were found in promoters of rpoH, hrcA and groES, suggesting that these genes are regulated by a homologue of the repressor HrcA, which is known to bind the CIRCE element. These results suggest that the G. sulfurreducens RpoH homologue is the heat-shock sigma factor and that heat-shock response in G. sulfurreducens is regulated positively by RpoH as well as negatively by the HrcA/CIRCE system.},
	keywords = {Adaptation, Physiological, Base Sequence, Binding Sites, Consensus Sequence, DNA, Bacterial, Gene Expression Regulation, Bacterial, Genome, Bacterial, Geobacter, Heat-Shock Proteins, Hot Temperature, Molecular Sequence Data, Promoter Regions, Genetic, RNA, Bacterial, RNA, Messenger, Sigma Factor, Transcription, Genetic},
	issn = {1350-0872},
	doi = {10.1099/mic.0.2006/000638-0},
	author = {Ueki, Toshiyuki and Lovley, Derek R}
}
