@article {408,
	title = {Real-time spatial gene expression analysis within current-producing biofilms.},
	journal = {ChemSusChem},
	volume = {5},
	year = {2012},
	month = {2012 Jun},
	pages = {1092-8},
	abstract = {<p>The expression of genes involved in central metabolism and extracellular electron transfer was examined in real-time in current-producing anode biofilms of Geobacter sulfurreducens. Strains of G. sulfurreducens were generated, in which the expression of the gene for a short half-life fluorescent protein was placed under control of the promoter of the genes of interest. Anode biofilms were grown in a chamber that permitted direct examination of the cell fluorescence with confocal scanning laser microscopy. Studies on nifD and citrate synthase expression in response to environmental changes demonstrated that the reporter system revealed initiation and termination of gene transcription. Uniform expression throughout the biofilms was noted for the genes for citrate synthase; PilA, the structural protein of the conductive pili; and OmcZ, a c-type cytochrome essential for optimal current production, which was localized at the anode-biofilm interface. These results demonstrate that even cells at great distance from the anode, or within expected low-pH zones, are metabolically active and likely to contribute to current production and that there are factors other than gene expression differences influencing the distribution of OmcZ. This real-time reporter approach is likely to be a useful tool in optimizing the design of technologies relying on microbe-electrode interactions.</p>},
	keywords = {Bacterial Proteins, Bioelectric Energy Sources, Biofilms, Citrate (si)-Synthase, Cytochrome c Group, Fimbriae Proteins, Fimbriae, Bacterial, Gene Expression Regulation, Bacterial, Geobacter, Quaternary Ammonium Compounds},
	issn = {1864-564X},
	doi = {10.1002/cssc.201100714},
	author = {Franks, Ashley E and Glaven, Richard H and Lovley, Derek R}
}
@article {441,
	title = {A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution.},
	journal = {Environ Microbiol},
	volume = {13},
	year = {2011},
	month = {2011 Jan},
	pages = {13-23},
	abstract = {The stimulation of subsurface microbial metabolism often associated with engineered bioremediation of groundwater contaminants presents subsurface microorganisms, which are adapted for slow growth and metabolism in the subsurface, with new selective pressures. In order to better understand how Geobacter species might adapt to selective pressure for faster metal reduction in the subsurface, Geobacter sulfurreducens was put under selective pressure for rapid Fe(III) oxide reduction. The genomes of two resultant strains with rates of Fe(III) oxide reduction that were 10-fold higher than those of the parent strain were resequenced. Both strains contain either a single base-pair change or a 1 nucleotide insertion in a GEMM riboswitch upstream of GSU1761, a gene coding for the periplasmic c-type cytochrome designated PgcA. GSU1771, a gene coding for a SARP regulator, was also mutated in both strains. Introduction of either of the GEMM riboswitch mutations upstream of pgcA in the wild-type increased the abundance of pgcA transcripts, consistent with increased expression of pgcA in the adapted strains. One of the mutations doubled the rate of Fe(III) oxide reduction. Interruption of GSU1771 doubled the Fe(III) oxide reduction rate. This was associated with an increased in expression of pilA, the gene encoding the structural protein for the pili thought to function as microbial nanowires. The combination of the GSU1771 interruption with either of the pgcA mutations resulted in a strain that reduced Fe(III) as fast as the comparable adapted strain. These results suggest that the accumulation of a small number of beneficial mutations under selective pressure, similar to that potentially present during bioremediation, can greatly enhance the capacity for Fe(III) oxide reduction in G. sulfurreducens. Furthermore, the results emphasize the importance of the c-type cytochrome PgcA and pili in Fe(III) oxide reduction and demonstrate how adaptive evolution studies can aid in the elucidation of complex mechanisms, such as extracellular electron transfer.},
	keywords = {Adaptation, Physiological, Biodegradation, Environmental, Cytochrome c Group, DNA, Bacterial, Electron Transport, Evolution, Molecular, Ferric Compounds, Gene Expression Profiling, Genes, Bacterial, Genome, Bacterial, Geobacter, Mutagenesis, Insertional, Mutation, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, Riboswitch, Sequence Analysis, DNA},
	issn = {1462-2920},
	doi = {10.1111/j.1462-2920.2010.02302.x},
	author = {Tremblay, Pier-Luc and Summers, Zarath M and Glaven, Richard H and Nevin, Kelly P and Zengler, Karsten and Barrett, Christian L and Qiu, Yu and Palsson, Bernhard O and Lovley, Derek R}
}
@article {437,
	title = {Gene expression and deletion analysis of mechanisms for electron transfer from electrodes to Geobacter sulfurreducens.},
	journal = {Bioelectrochemistry},
	volume = {80},
	year = {2011},
	month = {2011 Feb},
	pages = {142-50},
	abstract = {Geobacter sulfurreducens is one of the few microorganisms available in pure culture known to directly accept electrons from a negatively poised electrode. Microarray analysis was used to compare gene transcript abundance in biofilms of G. sulfurreducens using a graphite electrode as the sole electron donor for fumarate reduction compared with transcript abundance in biofilms growing on the same material, but not consuming current. Surprisingly, genes for putative cell-electrode connections, such as outer-surface cytochromes and pili, which are highly expressed in current-producing biofilms, were not highly expressed in current-consuming biofilms. Microarray analysis of G. sulfurreducens gene transcript abundance in current-consuming biofilms versus current-producing biofilms gave similar results. In both comparative studies current-consuming biofilms had greater transcript abundance for a gene (GSU3274) encoding a putative monoheme, c-type cytochrome. Deletion of genes for outer-surface proteins previously shown to be essential for optimal electron transfer to electrodes had no impact on electron transfer from electrodes. Deletion of GSU3274 completely inhibited electron transfer from electrodes, but had no impact on electron transfer to electrodes. These differences in gene expression patterns and the impact of gene deletions suggest that the mechanisms for electron transfer from electrodes to G. sulfurreducens differ significantly from the mechanisms for electron transfer to electrodes.},
	keywords = {Bacterial Proteins, Biofilms, Cytochromes, Electrodes, Electron Transport, Electrons, Gene Expression, Geobacter, Graphite, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, Sequence Deletion},
	issn = {1878-562X},
	doi = {10.1016/j.bioelechem.2010.07.005},
	author = {Strycharz, Sarah M and Glaven, Richard H and Coppi, Maddalena V and Gannon, Sarah M and Perpetua, Lorrie A and Liu, Anna and Nevin, Kelly P and Lovley, Derek R}
}
@article {450,
	title = {Microtoming coupled to microarray analysis to evaluate the spatial metabolic status of Geobacter sulfurreducens biofilms.},
	journal = {ISME J},
	volume = {4},
	year = {2010},
	month = {2010 Apr},
	pages = {509-19},
	abstract = {Further insight into the metabolic status of cells within anode biofilms is essential for understanding the functioning of microbial fuel cells and developing strategies to optimize their power output. Cells throughout anode biofilms of Geobacter sulfurreducens reduced the metabolic stains: 5-cyano-2,3-ditolyl tetrazolium chloride and Redox Green, suggesting metabolic activity throughout the biofilm. To compare the metabolic status of cells growing close to the anode versus cells in the outer portion of the anode biofilm, anode biofilms were encased in resin and sectioned into inner (0-20 microm from anode surface) and outer (30-60 microm) fractions. Transcriptional analysis revealed that, at a twofold threshold, 146 genes had significant (P<0.05) differences in transcript abundance between the inner and outer biofilm sections. Only 1 gene, GSU0093, a hypothetical ATP-binding cassette transporter, had significantly higher transcript abundances in the outer biofilm. Genes with lower transcript abundance in the outer biofilm included genes for ribosomal proteins and NADH dehydrogenase, suggesting lower metabolic rates. However, differences in transcript abundance were relatively low (<threefold) and the expression of genes for the tricarboxylic acid cycle enzymes was not significantly lower. Lower expression of genes involved in stress responses in the outer biofilm may reflect the development of low pH near the surface of the anode. The results of this study suggest that cells throughout the biofilm are metabolically active and can potentially contribute to current production. The microtoming/microarray strategy described here may be useful for evaluating gene expression with depth in a diversity of microbial biofilms.},
	keywords = {Bioelectric Energy Sources, Biofilms, Electrodes, Gene Expression Profiling, Geobacter, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, Tetrazolium Salts},
	issn = {1751-7370},
	doi = {10.1038/ismej.2009.137},
	author = {Franks, Ashley E and Nevin, Kelly P and Glaven, Richard H and Lovley, Derek R}
}
@article {442,
	title = {Production of pilus-like filaments in Geobacter sulfurreducens in the absence of the type IV pilin protein PilA.},
	journal = {FEMS Microbiol Lett},
	volume = {310},
	year = {2010},
	month = {2010 Sep 1},
	pages = {62-8},
	abstract = {The pili of Geobacter sulfurreducens are of interest because of the apparent importance of the type IV pili in extracellular electron transfer. A strain of G. sulfurreducens, designated strain MA, produced many more pili than the previously studied DL-1 strain even though genome resequencing indicated that the MA and DL-1 genome sequences were identical. Filaments that looked similar to type IV pili in transmission electron micrographs were abundant even after the gene encoding PilA, the structural pilin protein, was deleted. The results of proteinase K treatment indicated that the filaments were proteinaceous. The simultaneous deletion of several genes encoding homologues of type II pseudopilins was required before the filaments were significantly depleted. The pilA-deficient MA strain attached to glass as well as the wild-type MA did, but strains in which three or four pseudopilin genes were deleted in addition to pilA had impaired attachment capabilities. These results demonstrate that there are several proteins that can yield pilin-like filaments in G. sulfurreducens and that some means other than microscopic observation is required before the composition of filaments can be unambiguously specified.},
	keywords = {Bacterial Adhesion, Fimbriae Proteins, Fimbriae, Bacterial, Gene Deletion, Geobacter, Glass, Microscopy, Electron, Transmission},
	issn = {1574-6968},
	doi = {10.1111/j.1574-6968.2010.02046.x},
	author = {Klimes, Anna and Franks, Ashley E and Glaven, Richard H and Tran, Hoa and Barrett, Christian L and Qiu, Yu and Zengler, Karsten and Lovley, Derek R}
}
@article {462,
	title = {Anode biofilm transcriptomics reveals outer surface components essential for high density current production in Geobacter sulfurreducens fuel cells.},
	journal = {PLoS One},
	volume = {4},
	year = {2009},
	month = {2009},
	pages = {e5628},
	abstract = {The mechanisms by which Geobacter sulfurreducens transfers electrons through relatively thick (>50 microm) biofilms to electrodes acting as a sole electron acceptor were investigated. Biofilms of Geobacter sulfurreducens were grown either in flow-through systems with graphite anodes as the electron acceptor or on the same graphite surface, but with fumarate as the sole electron acceptor. Fumarate-grown biofilms were not immediately capable of significant current production, suggesting substantial physiological differences from current-producing biofilms. Microarray analysis revealed 13 genes in current-harvesting biofilms that had significantly higher transcript levels. The greatest increases were for pilA, the gene immediately downstream of pilA, and the genes for two outer c-type membrane cytochromes, OmcB and OmcZ. Down-regulated genes included the genes for the outer-membrane c-type cytochromes, OmcS and OmcT. Results of quantitative RT-PCR of gene transcript levels during biofilm growth were consistent with microarray results. OmcZ and the outer-surface c-type cytochrome, OmcE, were more abundant and OmcS was less abundant in current-harvesting cells. Strains in which pilA, the gene immediately downstream from pilA, omcB, omcS, omcE, or omcZ was deleted demonstrated that only deletion of pilA or omcZ severely inhibited current production and biofilm formation in current-harvesting mode. In contrast, these gene deletions had no impact on biofilm formation on graphite surfaces when fumarate served as the electron acceptor. These results suggest that biofilms grown harvesting current are specifically poised for electron transfer to electrodes and that, in addition to pili, OmcZ is a key component in electron transfer through differentiated G. sulfurreducens biofilms to electrodes.},
	keywords = {Amino Acid Sequence, Bacterial Outer Membrane Proteins, Bioelectric Energy Sources, Biofilms, Cytochromes, Electrodes, Electron Transport, Fumarates, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genetic Complementation Test, Geobacter, Microscopy, Confocal, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, RNA, Messenger, Up-Regulation},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0005628},
	author = {Nevin, Kelly P and Kim, Byoung-Chan and Glaven, Richard H and Johnson, Jessica P and Woodard, Trevor L and Meth{\'e}, Barbara A and Didonato, Raymond J and Covalla, Sean F and Franks, Ashley E and Liu, Anna and Lovley, Derek R}
}
@article {525,
	title = {Genetic characterization of a single bifunctional enzyme for fumarate reduction and succinate oxidation in Geobacter sulfurreducens and engineering of fumarate reduction in Geobacter metallireducens.},
	journal = {J Bacteriol},
	volume = {188},
	year = {2006},
	month = {2006 Jan},
	pages = {450-5},
	abstract = {The mechanism of fumarate reduction in Geobacter sulfurreducens was investigated. The genome contained genes encoding a heterotrimeric fumarate reductase, FrdCAB, with homology to the fumarate reductase of Wolinella succinogenes and the succinate dehydrogenase of Bacillus subtilis. Mutation of the putative catalytic subunit of the enzyme resulted in a strain that lacked fumarate reductase activity and was unable to grow with fumarate as the terminal electron acceptor. The mutant strain also lacked succinate dehydrogenase activity and did not grow with acetate as the electron donor and Fe(III) as the electron acceptor. The mutant strain could grow with acetate as the electron donor and Fe(III) as the electron acceptor if fumarate was provided to alleviate the need for succinate dehydrogenase activity in the tricarboxylic acid cycle. The growth rate of the mutant strain under these conditions was faster and the cell yields were higher than for wild type grown under conditions requiring succinate dehydrogenase activity, suggesting that the succinate dehydrogenase reaction consumes energy. An orthologous frdCAB operon was present in Geobacter metallireducens, which cannot grow with fumarate as the terminal electron acceptor. When a putative dicarboxylic acid transporter from G. sulfurreducens was expressed in G. metallireducens, growth with fumarate as the sole electron acceptor was possible. These results demonstrate that, unlike previously described organisms, G. sulfurreducens and possibly G. metallireducens use the same enzyme for both fumarate reduction and succinate oxidation in vivo.},
	keywords = {Culture Media, Dicarboxylic Acids, Fumarates, Geobacter, Molecular Sequence Data, Operon, Oxidation-Reduction, Recombinant Proteins, Substrate Specificity, Succinate Dehydrogenase, Succinic Acid},
	issn = {0021-9193},
	doi = {10.1128/JB.188.2.450-455.2006},
	author = {Butler, Jessica E and Glaven, Richard H and Esteve-N{\'u}{\~n}ez, Abraham and N{\'u}{\~n}ez, Cinthia and Shelobolina, Evgenya S and Bond, Daniel R and Lovley, Derek R}
}
@article {536,
	title = {OmcF, a putative c-Type monoheme outer membrane cytochrome required for the expression of other outer membrane cytochromes in Geobacter sulfurreducens.},
	journal = {J Bacteriol},
	volume = {187},
	year = {2005},
	month = {2005 Jul},
	pages = {4505-13},
	abstract = {Outer membrane cytochromes are often proposed as likely agents for electron transfer to extracellular electron acceptors, such as Fe(III). The omcF gene in the dissimilatory Fe(III)-reducing microorganism Geobacter sulfurreducens is predicted to code for a small outer membrane monoheme c-type cytochrome. An OmcF-deficient strain was constructed, and its ability to reduce and grow on Fe(III) citrate was found to be impaired. Following a prolonged lag phase (150 h), the OmcF-deficient strain developed the ability to grow in Fe(III) citrate medium with doubling times and yields that were ca. 145\% and 70\% of those of the wild type, respectively. Comparison of the c-type cytochrome contents of outer membrane-enriched fractions prepared from wild-type and OmcF-deficient cultures confirmed the outer membrane association of OmcF and revealed multiple changes in the cytochrome content of the OmcF-deficient strain. These changes included loss of expression of two previously characterized outer membrane cytochromes, OmcB and OmcC, and overexpression of a third previously characterized outer membrane cytochrome, OmcS, during growth on Fe(III) citrate. The omcB and omcC transcripts could not be detected in the OmcF-deficient mutant by either reverse transcriptase PCR or Northern blot analyses. Expression of the omcF gene in trans restored both the capacity of the OmcF-deficient mutant to reduce Fe(III) and wild-type levels of omcB and omcC mRNA and protein. Thus, elimination of OmcF may impair Fe(III) reduction by influencing expression of OmcB, which has previously been demonstrated to play a critical role in Fe(III) reduction.},
	keywords = {Amino Acid Sequence, Bacterial Outer Membrane Proteins, Cytochromes c, Ferric Compounds, Gene Deletion, Gene Expression Regulation, Bacterial, Geobacter, Molecular Sequence Data, Oxidation-Reduction, Sequence Alignment},
	issn = {0021-9193},
	doi = {10.1128/JB.187.13.4505-4513.2005},
	author = {Kim, Byoung-Chan and Leang, Ching and Ding, Yan-Huai R and Glaven, Richard H and Coppi, Maddalena V and Lovley, Derek R}
}
