@article {3149, title = {The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features.}, journal = {BMC Genomics}, volume = {13}, year = {2012}, month = {2012 Dec 10}, pages = {690}, abstract = {

BACKGROUND: The bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. The genome of P. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing Geobacter species.

RESULTS: Pathways were predicted for catabolism of known substrates: 2,3-butanediol, acetoin, glycerol, 1,2-ethanediol, ethanolamine, choline and ethanol. Multiple isozymes of 2,3-butanediol dehydrogenase, ATP synthase and [FeFe]-hydrogenase were differentiated and assigned roles according to their structural properties and genomic contexts. The absence of asparagine synthetase and the presence of a mutant tRNA for asparagine encoded among RNA-active enzymes suggest that P. carbinolicus may make asparaginyl-tRNA in a novel way. Catabolic glutamate dehydrogenases were discovered, implying that the tricarboxylic acid (TCA) cycle can function catabolically. A phosphotransferase system for uptake of sugars was discovered, along with enzymes that function in 2,3-butanediol production. Pyruvate:ferredoxin/flavodoxin oxidoreductase was identified as a potential bottleneck in both the supply of oxaloacetate for oxidation of acetate by the TCA cycle and the connection of glycolysis to production of ethanol. The P. carbinolicus genome was found to encode autotransporters and various appendages, including three proteins with similarity to the geopilin of electroconductive nanowires.

CONCLUSIONS: Several surprising metabolic capabilities and physiological features were predicted from the genome of P. carbinolicus, suggesting that it is more versatile than anticipated.

}, keywords = {Base Pairing, Base Sequence, Butylene Glycols, Choline, Deltaproteobacteria, Ethanolamine, Ethylene Glycol, Genome, Bacterial, Glycerol, Metabolic Networks and Pathways, Molecular Sequence Annotation, Molecular Sequence Data, Mutation, Oxidation-Reduction, Oxidoreductases, Propylene Glycols, RNA, Transfer, Asn, Sequence Analysis, DNA}, issn = {1471-2164}, doi = {10.1186/1471-2164-13-690}, author = {Aklujkar, Muktak and Haveman, Shelley A and DiDonato, Raymond and Chertkov, Olga and Han, Cliff S and Land, Miriam L and Brown, Peter and Lovley, Derek R} } @article {411, title = {Role of the NiFe hydrogenase Hya in oxidative stress defense in Geobacter sulfurreducens.}, journal = {J Bacteriol}, volume = {194}, year = {2012}, month = {2012 May}, pages = {2248-53}, abstract = {Geobacter sulfurreducens, an Fe(III)-reducing deltaproteobacterium found in anoxic subsurface environments, contains 4 NiFe hydrogenases. Hyb, a periplasmically oriented membrane-bound NiFe hydrogenase, is essential for hydrogen-dependent growth. The functions of the three other hydrogenases are unknown. We show here that the other periplasmically oriented membrane-bound NiFe hydrogenase, Hya, is necessary for growth after exposure to oxidative stress when hydrogen or a highly limiting concentration of acetate is the electron source. The beneficial impact of Hya on growth was dependent on the presence of H(2) in the atmosphere. Moreover, the Hya-deficient strain was more sensitive to the presence of superoxide or hydrogen peroxide. Hya was also required to safeguard Hyb hydrogen oxidation activity after exposure to O(2). Overexpression studies demonstrated that Hya was more resistant to oxidative stress than Hyb. Overexpression of Hya also resulted in the creation of a recombinant strain better fitted for exposure to oxidative stress than wild-type G. sulfurreducens. These results demonstrate that one of the physiological roles of the O(2)-resistant Hya is to participate in the oxidative stress defense of G. sulfurreducens.}, keywords = {Bacterial Proteins, Gene Expression Regulation, Bacterial, Geobacter, Hydrogen Peroxide, Hydrogenase, Mutation, Oxidative Stress, Oxygen, Reactive Oxygen Species, Reverse Transcriptase Polymerase Chain Reaction, Xanthine Oxidase}, issn = {1098-5530}, doi = {10.1128/JB.00044-12}, author = {Tremblay, Pier-Luc 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 {431, title = {Direct exchange of electrons within aggregates of an evolved syntrophic coculture of anaerobic bacteria.}, journal = {Science}, volume = {330}, year = {2010}, month = {2010 Dec 3}, pages = {1413-5}, abstract = {Microbial consortia that cooperatively exchange electrons play a key role in the anaerobic processing of organic matter. Interspecies hydrogen transfer is a well-documented strategy for electron exchange in dispersed laboratory cultures, but cooperative partners in natural environments often form multispecies aggregates. We found that laboratory evolution of a coculture of Geobacter metallireducens and Geobacter sulfurreducens metabolizing ethanol favored the formation of aggregates that were electrically conductive. Sequencing aggregate DNA revealed selection for a mutation that enhances the production of a c-type cytochrome involved in extracellular electron transfer and accelerates the formation of aggregates. Aggregate formation was also much faster in mutants that were deficient in interspecies hydrogen transfer, further suggesting direct interspecies electron transfer.}, keywords = {Anaerobiosis, Bacterial Proteins, Biological Evolution, Culture Media, Cytochrome c Group, Electron Transport, Electrons, Ethanol, Fimbriae Proteins, Geobacter, Hydrogen, Microbial Consortia, Microbial Interactions, Mutation, Oxidation-Reduction, Selection, Genetic}, issn = {1095-9203}, doi = {10.1126/science.1196526}, author = {Summers, Zarath M and Fogarty, Heather E and Leang, Ching and Franks, Ashley E and Malvankar, Nikhil S and Lovley, Derek R} } @article {473, title = {Diversity of promoter elements in a Geobacter sulfurreducens mutant adapted to disruption in electron transfer.}, journal = {Funct Integr Genomics}, volume = {9}, year = {2009}, month = {2009 Feb}, pages = {15-25}, abstract = {The delta-proteobacterium, Geobacter sulfurreducens, can obtain energy by coupling the oxidation of organic matter to the reduction of insoluble Fe(III) or the anode of a microbial fuel cell. Because Fe(III) oxide or the anode surface, in contrast to oxygen, nitrate, or sulfate, is not soluble nor can it be reduced readily, Geobacter species have developed mechanisms which allow electrons to be delivered across outer membrane to the cell surface. OmcB is an outer-membrane c-type cytochrome important for G. sulfurreducens Fe(III) respiration. In the absence of OmcB, cells lost the ability to reduce soluble or insoluble Fe(III). However, the omcB deletion mutant can slowly adapt to growth on soluble Fe(III) over prolonged incubation in the medium with acetate as the electron donor. We discuss available information about predicted or experimentally validated promoters and transcription regulatory sites identified upstream of operons with transcriptional expression significantly changed in the adapted omcB mutant. DNA sequences of upstream regions of coregulated operons in the adapted mutant are divergent, suggesting the presence of recognition sites for different transcriptional regulators and indicating that adaptation of the omcB mutant to growth on soluble Fe(III) has shifted the relevant expression networks involved to a more diverse molecular basis.}, keywords = {Adaptation, Physiological, Electron Transport, Genetic Variation, Geobacter, Mutation, Promoter Regions, Genetic}, issn = {1438-7948}, doi = {10.1007/s10142-008-0094-7}, author = {Krushkal, Julia and Leang, Ching and Barbe, Jose F and Qu, Yanhua and Yan, Bin and Puljic, Marko and Adkins, Ronald M and Lovley, Derek R} } @article {466, title = {Genome-scale constraint-based modeling of Geobacter metallireducens.}, journal = {BMC Syst Biol}, volume = {3}, year = {2009}, month = {2009}, pages = {15}, abstract = {BACKGROUND: Geobacter metallireducens was the first organism that can be grown in pure culture to completely oxidize organic compounds with Fe(III) oxide serving as electron acceptor. Geobacter species, including G. sulfurreducens and G. metallireducens, are used for bioremediation and electricity generation from waste organic matter and renewable biomass. The constraint-based modeling approach enables the development of genome-scale in silico models that can predict the behavior of complex biological systems and their responses to the environments. Such a modeling approach was applied to provide physiological and ecological insights on the metabolism of G. metallireducens. RESULTS: The genome-scale metabolic model of G. metallireducens was constructed to include 747 genes and 697 reactions. Compared to the G. sulfurreducens model, the G. metallireducens metabolic model contains 118 unique reactions that reflect many of G. metallireducens{\textquoteright} specific metabolic capabilities. Detailed examination of the G. metallireducens model suggests that its central metabolism contains several energy-inefficient reactions that are not present in the G. sulfurreducens model. Experimental biomass yield of G. metallireducens growing on pyruvate was lower than the predicted optimal biomass yield. Microarray data of G. metallireducens growing with benzoate and acetate indicated that genes encoding these energy-inefficient reactions were up-regulated by benzoate. These results suggested that the energy-inefficient reactions were likely turned off during G. metallireducens growth with acetate for optimal biomass yield, but were up-regulated during growth with complex electron donors such as benzoate for rapid energy generation. Furthermore, several computational modeling approaches were applied to accelerate G. metallireducens research. For example, growth of G. metallireducens with different electron donors and electron acceptors were studied using the genome-scale metabolic model, which provided a fast and cost-effective way to understand the metabolism of G. metallireducens. CONCLUSION: We have developed a genome-scale metabolic model for G. metallireducens that features both metabolic similarities and differences to the published model for its close relative, G. sulfurreducens. Together these metabolic models provide an important resource for improving strategies on bioremediation and bioenergy generation.}, keywords = {Biodegradation, Environmental, Biomass, Computer Simulation, Ecosystem, Electron Transport, Energy Metabolism, Genome, Bacterial, Geobacter, Iron, Metabolic Networks and Pathways, Models, Biological, Models, Genetic, Mutation, Phenotype, Species Specificity, Systems Biology}, issn = {1752-0509}, doi = {10.1186/1752-0509-3-15}, author = {Sun, Jun and Sayyar, Bahareh and Butler, Jessica E and Pharkya, Priti and Fahland, Tom R and Famili, Iman and Schilling, Christophe H and Lovley, Derek R and Mahadevan, Radhakrishnan} } @article {480, title = {Insights into genes involved in electricity generation in Geobacter sulfurreducens via whole genome microarray analysis of the OmcF-deficient mutant.}, journal = {Bioelectrochemistry}, volume = {73}, year = {2008}, month = {2008 Jun}, pages = {70-5}, abstract = {Geobacter sulfurreducens effectively produces electricity in microbial fuel cells by oxidizing acetate with an electrode serving as the sole electron acceptor. Deletion of the gene encoding OmcF, a monoheme outer membrane c-type cytochrome, substantially decreased current production. Previous studies demonstrated that inhibition of Fe(III) reduction in the OmcF-deficient mutant could be attributed to poor transcription of the gene for OmcB, an outer membrane c-type cytochrome that is required for Fe(III) reduction. However, a mutant in which omcB was deleted produced electricity as well as wild type. Microarray analysis of the OmcF-deficient mutant versus the wild type revealed that many of the genes with the greatest decreases in transcript levels were genes whose expression was previously reported to be upregulated in cells grown with an electrode as the sole electron acceptor. These included genes with putative functions related to metal efflux and/or type I secretion and two hypothetical proteins. The outer membrane cytochromes, OmcS and OmcE, which previous studies have demonstrated are required for optimal current generation, were not detected on the outer surface of the OmcF-deficient mutant even though the omcS and omcE genes were still transcribed, suggesting that the putative secretion system could be involved in the export of outer membrane proteins necessary for electron transfer to the fuel cell anode. These results suggest that the requirement for OmcF for optimal current production is not because OmcF is directly involved in extracellular electron transfer but because OmcF is required for the appropriate transcription of other genes either directly or indirectly involved in electricity production.}, keywords = {Bacterial Outer Membrane Proteins, Cytochromes c, Down-Regulation, Electricity, Gene Expression Regulation, Bacterial, Genome, Bacterial, Geobacter, Mutation, Oligonucleotide Array Sequence Analysis, Transcription, Genetic}, issn = {1567-5394}, doi = {10.1016/j.bioelechem.2008.04.023}, author = {Kim, Byoung-Chan and Postier, Bradley L and Didonato, Raymond J and Chaudhuri, Swades K and Nevin, Kelly P and Lovley, Derek R} } @article {503, title = {Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a relGsu mutant.}, journal = {Funct Integr Genomics}, volume = {7}, year = {2007}, month = {2007 Jul}, pages = {229-55}, abstract = {Rel(Gsu) is the single Geobacter sulfurreducens homolog of RelA and SpoT proteins found in many organisms. These proteins are involved in the regulation of levels of guanosine 3{\textquoteright}, 5{\textquoteright} bispyrophosphate, ppGpp, a molecule that signals slow growth and stress response under nutrient limitation in bacteria. We used information obtained from genome-wide expression profiling of the rel(Gsu) deletion mutant to identify putative regulatory sites involved in transcription networks modulated by Rel(Gsu) or ppGpp. Differential gene expression in the rel(Gsu) deletion mutant, as compared to the wild type, was available from two growth conditions, steady state chemostat cultures and stationary phase batch cultures. Hierarchical clustering analysis of these two datasets identified several groups of operons that are likely co-regulated. Using a search for conserved motifs in the upstream regions of these co-regulated operons, we identified sequences similar to Fur- and RpoS-regulated sites. These findings suggest that Fur- and RpoS-dependent gene expression in G. sulfurreducens is affected by Rel(Gsu)-mediated signaling.}, keywords = {Bacterial Proteins, Base Sequence, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genes, Bacterial, Genome, Bacterial, Geobacter, Ligases, Mutation, Operon, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid, Repressor Proteins, Sigma Factor, Transcription, Genetic}, issn = {1438-793X}, doi = {10.1007/s10142-007-0048-5}, author = {Krushkal, Julia and Yan, Bin and DiDonato, Laurie N and Puljic, Marko and Nevin, Kelly P and Woodard, Trevor L and Adkins, Ronald M and Meth{\'e}, Barbara A and Lovley, Derek R} } @article {505, title = {Importance of c-Type cytochromes for U(VI) reduction by Geobacter sulfurreducens.}, journal = {BMC Microbiol}, volume = {7}, year = {2007}, month = {2007}, pages = {16}, abstract = {BACKGROUND: In order to study the mechanism of U(VI) reduction, the effect of deleting c-type cytochrome genes on the capacity of Geobacter sulfurreducens to reduce U(VI) with acetate serving as the electron donor was investigated. RESULTS: The ability of several c-type cytochrome deficient mutants to reduce U(VI) was lower than that of the wild type strain. Elimination of two confirmed outer membrane cytochromes and two putative outer membrane cytochromes significantly decreased (ca. 50-60\%) the ability of G. sulfurreducens to reduce U(VI). Involvement in U(VI) reduction did not appear to be a general property of outer membrane cytochromes, as elimination of two other confirmed outer membrane cytochromes, OmcB and OmcC, had very little impact on U(VI) reduction. Among the periplasmic cytochromes, only MacA, proposed to transfer electrons from the inner membrane to the periplasm, appeared to play a significant role in U(VI) reduction. A subpopulation of both wild type and U(VI) reduction-impaired cells, 24-30\%, accumulated amorphous uranium in the periplasm. Comparison of uranium-accumulating cells demonstrated a similar amount of periplasmic uranium accumulation in U(VI) reduction-impaired and wild type G. sulfurreducens. Assessment of the ability of the various suspensions to reduce Fe(III) revealed no correlation between the impact of cytochrome deletion on U(VI) reduction and reduction of Fe(III) hydroxide and chelated Fe(III). CONCLUSION: This study indicates that c-type cytochromes are involved in U(VI) reduction by Geobacter sulfurreducens. The data provide new evidence for extracellular uranium reduction by G. sulfurreducens but do not rule out the possibility of periplasmic uranium reduction. Occurrence of U(VI) reduction at the cell surface is supported by the significant impact of elimination of outer membrane cytochromes on U(VI) reduction and the lack of correlation between periplasmic uranium accumulation and the capacity for uranium reduction. Periplasmic uranium accumulation may reflect the ability of uranium to penetrate the outer membrane rather than the occurrence of enzymatic U(VI) reduction. Elimination of cytochromes rarely had a similar impact on both Fe(III) and U(VI) reduction, suggesting that there are differences in the routes of electron transfer to U(VI) and Fe(III). Further studies are required to clarify the pathways leading to U(VI) reduction in G. sulfurreducens.}, keywords = {Biodegradation, Environmental, Cytochrome c Group, Ferric Compounds, Geobacter, Microscopy, Electron, Transmission, Mutation, Oxidation-Reduction, Periplasm, Uranium}, issn = {1471-2180}, doi = {10.1186/1471-2180-7-16}, author = {Shelobolina, Evgenya S and Coppi, Maddalena V and Korenevsky, Anton A and DiDonato, Laurie N and Sullivan, Sara A and Konishi, Hiromi and Xu, Huifang and Leang, Ching and Butler, Jessica E and Kim, Byoung-Chan and Lovley, Derek R} } @article {514, title = {Biofilm and nanowire production leads to increased current in Geobacter sulfurreducens fuel cells.}, journal = {Appl Environ Microbiol}, volume = {72}, year = {2006}, month = {2006 Nov}, pages = {7345-8}, abstract = {Geobacter sulfurreducens developed highly structured, multilayer biofilms on the anode surface of a microbial fuel cell converting acetate to electricity. Cells at a distance from the anode remained viable, and there was no decrease in the efficiency of current production as the thickness of the biofilm increased. Genetic studies demonstrated that efficient electron transfer through the biofilm required the presence of electrically conductive pili. These pili may represent an electronic network permeating the biofilm that can promote long-range electrical transfer in an energy-efficient manner, increasing electricity production more than 10-fold.}, keywords = {Acetates, Bioelectric Energy Sources, Biofilms, Electricity, Electrodes, Electron Transport, Fimbriae, Bacterial, Geobacter, Microscopy, Confocal, Mutation, Nanowires}, issn = {0099-2240}, doi = {10.1128/AEM.01444-06}, author = {Reguera, Gemma and Nevin, Kelly P and Nicoll, Julie S and Covalla, Sean F and Woodard, Trevor L and Lovley, Derek R} } @article {517, title = {A putative multicopper protein secreted by an atypical type II secretion system involved in the reduction of insoluble electron acceptors in Geobacter sulfurreducens.}, journal = {Microbiology}, volume = {152}, year = {2006}, month = {2006 Aug}, pages = {2257-64}, abstract = {Extracellular electron transfer onto Fe(III) oxides in Geobacter sulfurreducens is considered to require proteins that must be exported to the outer surface of the cell. In order to investigate this, the putative gene for OxpG, the pseudopilin involved in a type II general secretion pathway of Gram-negative bacteria, was deleted. The mutant was unable to grow with insoluble Fe(III) oxide as the electron acceptor. Growth on soluble Fe(III) was not affected. An analysis of proteins that accumulated in the periplasm of the oxpG mutant, but not in the wild-type, led to the identification of a secreted protein, OmpB. OmpB is predicted to be a multicopper protein, with highest homology to the manganese oxidase, MofA, from Leptothrix discophora. OmpB contains a potential Fe(III)-binding site and a fibronectin type III domain, suggesting a possible role for this protein in accessing Fe(III) oxides. OmpB was localized to the membrane fraction of G. sulfurreducens and in the supernatant of growing cultures, consistent with the type II secretion system exporting OmpB. A mutant in which ompB was deleted had the same phenotype as the oxpG mutant, suggesting that the failure to export OmpB was responsible for the inability of the oxpG-deficient mutant to reduce Fe(III) oxide. This is the first report that proposes a role for a multicopper oxidase-like protein in an anaerobic organism. These results further emphasize the importance of outer-membrane proteins in Fe(III) oxide reduction and suggest that outer-membrane proteins other than c-type cytochromes are required for Fe(III) oxide reduction in Geobacter species.}, keywords = {Bacterial Outer Membrane Proteins, Electron Transport, Ferric Compounds, Fimbriae Proteins, Geobacter, Manganese Compounds, Mutation, Oxidation-Reduction, Oxides}, issn = {1350-0872}, doi = {10.1099/mic.0.28864-0}, author = {Mehta, Teena and Childers, Susan E and Glaven, Richard and Lovley, Derek R and Mester, T{\"u}nde} } @article {511, title = {Role of RelGsu in stress response and Fe(III) reduction in Geobacter sulfurreducens.}, journal = {J Bacteriol}, volume = {188}, year = {2006}, month = {2006 Dec}, pages = {8469-78}, abstract = {Geobacter species are key members of the microbial community in many subsurface environments in which dissimilatory metal reduction is an important process. The genome of Geobacter sulfurreducens contains a gene designated rel(Gsu), which encodes a RelA homolog predicted to catalyze both the synthesis and the degradation of guanosine 3{\textquoteright},5{\textquoteright}-bispyrophosphate (ppGpp), a regulatory molecule that signals slow growth in response to nutrient limitation in bacteria. To evaluate the physiological role of Rel(Gsu) in G. sulfurreducens, a rel(Gsu) mutant was constructed and characterized, and ppGpp levels were monitored under various conditions in both the wild-type and rel(Gsu) mutant strains. In the wild-type strain, ppGpp and ppGp were produced in response to acetate and nitrogen deprivation, whereas exposure to oxygen resulted in an accumulation of ppGpp alone. Neither ppGpp nor ppGp could be detected in the rel(Gsu) mutant. The rel(Gsu) mutant consistently grew to a higher cell density than the wild type in acetate-fumarate medium and was less tolerant of oxidative stress than the wild type. The capacity for Fe(III) reduction was substantially diminished in the mutant. Microarray and quantitative reverse transcription-PCR analyses indicated that during stationary-phase growth, protein synthesis genes were up-regulated in the rel(Gsu) mutant and genes involved in stress responses and electron transport, including several implicated in Fe(III) reduction, were down-regulated in the mutant. The results are consistent with a role for Rel(Gsu) in regulating growth, stress responses, and Fe(III) reduction in G. sulfurreducens under conditions likely to be prevalent in subsurface environments.}, keywords = {Bacterial Proteins, Culture Media, Ferric Compounds, Gene Expression Regulation, Bacterial, Geobacter, Guanosine Tetraphosphate, Heat-Shock Response, Ligases, Mutation, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, Reverse Transcriptase Polymerase Chain Reaction, Sulfur}, issn = {0021-9193}, doi = {10.1128/JB.01278-06}, author = {DiDonato, Laurie N and Sullivan, Sara A and Meth{\'e}, Barbara A and Nevin, Kelly P and England, Reg and Lovley, Derek R} } @article {535, title = {Extracellular electron transfer via microbial nanowires.}, journal = {Nature}, volume = {435}, year = {2005}, month = {2005 Jun 23}, pages = {1098-101}, abstract = {Microbes that can transfer electrons to extracellular electron acceptors, such as Fe(iii) oxides, are important in organic matter degradation and nutrient cycling in soils and sediments. Previous investigations on electron transfer to Fe(iii) have focused on the role of outer-membrane c-type cytochromes. However, some Fe(iii) reducers lack c-cytochromes. Geobacter species, which are the predominant Fe(iii) reducers in many environments, must directly contact Fe(iii) oxides to reduce them, and produce monolateral pili that were proposed, on the basis of the role of pili in other organisms, to aid in establishing contact with the Fe(iii) oxides. Here we report that a pilus-deficient mutant of Geobacter sulfurreducens could not reduce Fe(iii) oxides but could attach to them. Conducting-probe atomic force microscopy revealed that the pili were highly conductive. These results indicate that the pili of G. sulfurreducens might serve as biological nanowires, transferring electrons from the cell surface to the surface of Fe(iii) oxides. Electron transfer through pili indicates possibilities for other unique cell-surface and cell-cell interactions, and for bioengineering of novel conductive materials.}, keywords = {Biotechnology, Electric Conductivity, Electron Transport, Ferric Compounds, Fimbriae Proteins, Fimbriae, Bacterial, Genes, Bacterial, Geobacter, Microscopy, Atomic Force, Microscopy, Electron, Transmission, Mutation, Nanostructures, Phylogeny}, issn = {1476-4687}, doi = {10.1038/nature03661}, author = {Reguera, Gemma and McCarthy, Kevin D and Mehta, Teena and Nicoll, Julie S and Tuominen, Mark T and Lovley, Derek R} } @article {549, title = {The RpoS sigma factor in the dissimilatory Fe(III)-reducing bacterium Geobacter sulfurreducens.}, journal = {J Bacteriol}, volume = {186}, year = {2004}, month = {2004 Aug}, pages = {5543-6}, abstract = {Geobacter sulfurreducens RpoS sigma factor was shown to contribute to survival in stationary phase and upon oxygen exposure. Furthermore, a mutation in rpoS decreased the rate of reduction of insoluble Fe(III) but not of soluble forms of iron. This study suggests that RpoS plays a role in regulating metabolism of Geobacter under suboptimal conditions in subsurface environments.}, keywords = {Adaptation, Physiological, Bacterial Proteins, Base Sequence, Ferric Compounds, Gene Expression Regulation, Bacterial, Genes, Bacterial, Geobacter, Molecular Sequence Data, Mutation, Oxidation-Reduction, Oxidative Stress, Sigma Factor, Transcription Initiation Site}, issn = {0021-9193}, doi = {10.1128/JB.186.16.5543-5546.2004}, author = {N{\'u}{\~n}ez, Cinthia and Adams, Lorrie and Childers, Susan and Lovley, Derek R} }