@article {3111, title = {Structural basis for metallic-like conductivity in microbial nanowires.}, journal = {mBio}, volume = {6}, year = {2015}, month = {2015 Mar 03}, pages = {e00084}, abstract = {

UNLABELLED: Direct measurement of multiple physical properties of Geobacter sulfurreducens pili have demonstrated that they possess metallic-like conductivity, but several studies have suggested that metallic-like conductivity is unlikely based on the structures of the G.~sulfurreducens pilus predicted from homology models. In order to further evaluate this discrepancy, pili were examined with synchrotron X-ray microdiffraction and rocking-curve X-ray diffraction. Both techniques revealed a periodic 3.2-{\r A} spacing in conductive, wild-type G.~sulfurreducens pili that was missing in the nonconductive pili of strain Aro5, which lack key aromatic acids required for conductivity. The intensity of the 3.2-{\r A} peak increased 100-fold when the pH was shifted from 10.5 to 2, corresponding with a previously reported 100-fold increase in pilus conductivity with this pH change. These results suggest a clear structure-function correlation for metallic-like conductivity that can be attributed to overlapping π-orbitals of aromatic amino acids. A homology model of the G.~sulfurreducens pilus was constructed with a Pseudomonas aeruginosa pilus model as a template as an alternative to previous models, which were based on a Neisseria gonorrhoeae pilus structure. This alternative model predicted that aromatic amino acids in G.~sulfurreducens pili are packed within 3 to 4~{\r A}, consistent with the experimental results. Thus, the predictions of homology modeling are highly sensitive to assumptions inherent in the model construction. The experimental results reported here further support the concept that the pili of G.~sulfurreducens represent a novel class of electronically functional proteins in which aromatic amino acids promote long-distance electron transport.

IMPORTANCE: The mechanism for long-range electron transport along the conductive pili of Geobacter sulfurreducens is of interest because these "microbial nanowires" are important in biogeochemical cycling as well as applications in bioenergy and bioelectronics. Although proteins are typically insulators, G.~sulfurreducens pilus proteins possess metallic-like conductivity. The studies reported here provide important structural insights into the mechanism of the metallic-like conductivity of G.~sulfurreducens pili. This information is expected to be useful in the design of novel bioelectronic materials.

}, keywords = {Amino Acids, Aromatic, Chemical Phenomena, Electrophysiological Phenomena, Fimbriae, Bacterial, Geobacter, Hydrogen-Ion Concentration, Models, Molecular, Nanowires, X-Ray Diffraction}, issn = {2150-7511}, doi = {10.1128/mBio.00084-15}, author = {Malvankar, Nikhil S and Vargas, Madeline and Nevin, Kelly and Tremblay, Pier-Luc and Evans-Lutterodt, Kenneth and Nykypanchuk, Dmytro and Martz, Eric and Tuominen, Mark T and Lovley, Derek R} } @article {404, title = {Interspecies electron transfer via hydrogen and formate rather than direct electrical connections in cocultures of Pelobacter carbinolicus and Geobacter sulfurreducens.}, journal = {Appl Environ Microbiol}, volume = {78}, year = {2012}, month = {2012 Nov}, pages = {7645-51}, abstract = {

Direct interspecies electron transfer (DIET) is an alternative to interspecies H(2)/formate transfer as a mechanism for microbial species to cooperatively exchange electrons during syntrophic metabolism. To understand what specific properties contribute to DIET, studies were conducted with Pelobacter carbinolicus, a close relative of Geobacter metallireducens, which is capable of DIET. P. carbinolicus grew in coculture with Geobacter sulfurreducens with ethanol as the electron donor and fumarate as the electron acceptor, conditions under which G. sulfurreducens formed direct electrical connections with G. metallireducens. In contrast to the cell aggregation associated with DIET, P. carbinolicus and G. sulfurreducens did not aggregate. Attempts to initiate cocultures with a genetically modified strain of G. sulfurreducens incapable of both H(2) and formate utilization were unsuccessful, whereas cocultures readily grew with mutant strains capable of formate but not H(2) uptake or vice versa. The hydrogenase mutant of G. sulfurreducens compensated, in cocultures, with significantly increased formate dehydrogenase gene expression. In contrast, the transcript abundance of a hydrogenase gene was comparable in cocultures with that for the formate dehydrogenase mutant of G. sulfurreducens or the wild type, suggesting that H(2) was the primary electron carrier in the wild-type cocultures. Cocultures were also initiated with strains of G. sulfurreducens that could not produce pili or OmcS, two essential components for DIET. The finding that P. carbinolicus exchanged electrons with G. sulfurreducens via interspecies transfer of H(2)/formate rather than DIET demonstrates that not all microorganisms that can grow syntrophically are capable of DIET and that closely related microorganisms may use significantly different strategies for interspecies electron exchange.

}, keywords = {Coculture Techniques, Deltaproteobacteria, Electricity, Electron Transport, Electrons, Formates, Geobacter, Hydrogen, Microbial Interactions}, issn = {1098-5336}, doi = {10.1128/AEM.01946-12}, author = {Rotaru, Amelia-Elena and Shrestha, Pravin M and Liu, Fanghua and Ueki, Toshiyuki and Nevin, Kelly and Summers, Zarath M and Lovley, Derek R} } @article {490, title = {PilR, a transcriptional regulator for pilin and other genes required for Fe(III) reduction in Geobacter sulfurreducens.}, journal = {J Mol Microbiol Biotechnol}, volume = {16}, year = {2009}, month = {2009}, pages = {146-58}, abstract = {Growth using Fe(III) as a terminal electron acceptor is a critical physiological process in Geobacter sulfurreducens. However, the mechanisms of electron transfer during Fe(III) reduction are only now being understood. It has been demonstrated that the pili in G. sulfurreducens function as microbial nanowires conducting electrons onto Fe(III) oxides. A number of c-type cytochromes have also been shown to play important roles in Fe(III) reduction. However, the regulatory networks controlling the expression of the genes involved in such processes are not well known. Here we report that the expression of pilA, which encodes the pilistructural protein, is directly regulated by a two-component regulatory system in which PilR functions as an RpoN-dependent enhancer binding protein. Surprisingly, a deletion of the pilR gene affected not only insoluble Fe(III) reduction, which requires pili, but also soluble Fe(III) reduction, which, in contrast, does not require pili. Gene expression profiling using whole-genome DNA microarray and quantitative RT-PCR analyses obtained with a PilR-deficient mutant revealed that the expression of pilA and other pilin-related genes are downregulated, while many c-type cytochromes involved in Fe(III) reduction were differentially regulated. This is the first instance of an enhancer binding protein implicated in regulating genes involved in Fe(III) respiratory functions.}, keywords = {Bacterial Proteins, Ferric Compounds, Fimbriae Proteins, Gene Expression Regulation, Bacterial, Genes, Regulator, Geobacter, Oxidation-Reduction, Transcription, Genetic}, issn = {1660-2412}, doi = {10.1159/000115849}, author = {Ju{\'a}rez, Katy and Kim, Byoung-Chan and Nevin, Kelly and Olvera, Leticia and Reguera, Gemma and Lovley, Derek R and Meth{\'e}, Barbara A} } @article {538, title = {DNA microarray analysis of nitrogen fixation and Fe(III) reduction in Geobacter sulfurreducens.}, journal = {Appl Environ Microbiol}, volume = {71}, year = {2005}, month = {2005 May}, pages = {2530-8}, abstract = {A DNA microarray representing the genome of Geobacter sulfurreducens was constructed for use in global gene expression profiling of cells under steady-state conditions with acetate as the electron donor and Fe(III) or fumarate as the electron acceptor. Reproducible differences in transcript levels were also observed in comparisons between cells grown with ammonia and those fixing atmospheric nitrogen. There was a high correlation between changes in transcript levels determined with microarray analyses and an evaluation of a subset of the genome with quantitative PCR. As expected, cells required to fix nitrogen had higher levels of transcripts of genes associated with nitrogen fixation, further demonstrating that the microarray approach could reliably detect important physiological changes. Cells grown with Fe(III) as the electron acceptor had higher levels of transcripts for omcB, a gene coding for an outer membrane c-type cytochrome that is essential for Fe(III) reduction. Several other c-type cytochrome genes also appeared to be up-regulated. An unexpected result was significantly higher levels of transcripts for genes which have a role in metal efflux, potentially suggesting the importance of maintaining metal homeostasis during release of soluble metals when reducing Fe(III). A substantial proportion (30\%) of significantly expressed genes during Fe(III) reduction were genes of unknown function or hypothetical proteins, suggesting differences in Fe(III) reduction physiology among microorganisms which perform this metabolic process.}, keywords = {Ferric Compounds, Fumarates, Geobacter, Microarray Analysis, Nitrogen Fixation, Oxidation-Reduction, Polymerase Chain Reaction}, issn = {0099-2240}, doi = {10.1128/AEM.71.5.2530-2538.2005}, author = {Meth{\'e}, Barbara A and Webster, Jennifer and Nevin, Kelly and Butler, Jessica and Lovley, Derek R} }