<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tran, Hoa T</style></author><author><style face="normal" font="default" size="100%">Krushkal, Julia</style></author><author><style face="normal" font="default" size="100%">Antommattei, Frances M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Weis, Robert M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Chemotaxis</style></keyword><keyword><style  face="normal" font="default" size="100%">Escherichia coli</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Multigene Family</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Homology, Amino Acid</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">471</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Geobacter species are delta-Proteobacteria and are often the predominant species in a variety of sedimentary environments where Fe(III) reduction is important. Their ability to remediate contaminated environments and produce electricity makes them attractive for further study. Cell motility, biofilm formation, and type IV pili all appear important for the growth of Geobacter in changing environments and for electricity production. Recent studies in other bacteria have demonstrated that signaling pathways homologous to the paradigm established for Escherichia coli chemotaxis can regulate type IV pili-dependent motility, the synthesis of flagella and type IV pili, the production of extracellular matrix material, and biofilm formation. The classification of these pathways by comparative genomics improves the ability to understand how Geobacter thrives in natural environments and better their use in microbial fuel cells.

RESULTS: The genomes of G. sulfurreducens, G. metallireducens, and G. uraniireducens contain multiple (approximately 70) homologs of chemotaxis genes arranged in several major clusters (six, seven, and seven, respectively). Unlike the single gene cluster of E. coli, the Geobacter clusters are not all located near the flagellar genes. The probable functions of some Geobacter clusters are assignable by homology to known pathways; others appear to be unique to the Geobacter sp. and contain genes of unknown function. We identified large numbers of methyl-accepting chemotaxis protein (MCP) homologs that have diverse sensing domain architectures and generate a potential for sensing a great variety of environmental signals. We discuss mechanisms for class-specific segregation of the MCPs in the cell membrane, which serve to maintain pathway specificity and diminish crosstalk. Finally, the regulation of gene expression in Geobacter differs from E. coli. The sequences of predicted promoter elements suggest that the alternative sigma factors sigma28 and sigma54 play a role in regulating the Geobacter chemotaxis gene expression.

CONCLUSION: The numerous chemoreceptors and chemotaxis-like gene clusters of Geobacter appear to be responsible for a diverse set of signaling functions in addition to chemotaxis, including gene regulation and biofilm formation, through functionally and spatially distinct signaling pathways.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18844997?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Methé, B A</style></author><author><style face="normal" font="default" size="100%">Nelson, K E</style></author><author><style face="normal" font="default" size="100%">Eisen, J A</style></author><author><style face="normal" font="default" size="100%">Paulsen, I T</style></author><author><style face="normal" font="default" size="100%">Nelson, W</style></author><author><style face="normal" font="default" size="100%">Heidelberg, J F</style></author><author><style face="normal" font="default" size="100%">Wu, D</style></author><author><style face="normal" font="default" size="100%">Wu, M</style></author><author><style face="normal" font="default" size="100%">Ward, N</style></author><author><style face="normal" font="default" size="100%">Beanan, M J</style></author><author><style face="normal" font="default" size="100%">Dodson, R J</style></author><author><style face="normal" font="default" size="100%">Madupu, R</style></author><author><style face="normal" font="default" size="100%">Brinkac, L M</style></author><author><style face="normal" font="default" size="100%">Daugherty, S C</style></author><author><style face="normal" font="default" size="100%">DeBoy, R T</style></author><author><style face="normal" font="default" size="100%">Durkin, A S</style></author><author><style face="normal" font="default" size="100%">Gwinn, M</style></author><author><style face="normal" font="default" size="100%">Kolonay, J F</style></author><author><style face="normal" font="default" size="100%">Sullivan, S A</style></author><author><style face="normal" font="default" size="100%">Haft, D H</style></author><author><style face="normal" font="default" size="100%">Selengut, J</style></author><author><style face="normal" font="default" size="100%">Davidsen, T M</style></author><author><style face="normal" font="default" size="100%">Zafar, N</style></author><author><style face="normal" font="default" size="100%">White, O</style></author><author><style face="normal" font="default" size="100%">Tran, B</style></author><author><style face="normal" font="default" size="100%">Romero, C</style></author><author><style face="normal" font="default" size="100%">Forberger, H A</style></author><author><style face="normal" font="default" size="100%">Weidman, J</style></author><author><style face="normal" font="default" size="100%">Khouri, H</style></author><author><style face="normal" font="default" size="100%">Feldblyum, T V</style></author><author><style face="normal" font="default" size="100%">Utterback, T R</style></author><author><style face="normal" font="default" size="100%">Van Aken, S E</style></author><author><style face="normal" font="default" size="100%">Lovley, D R</style></author><author><style face="normal" font="default" size="100%">Fraser, C M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome of Geobacter sulfurreducens: metal reduction in subsurface environments.</style></title><secondary-title><style face="normal" font="default" size="100%">Science</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Science</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Acetyl Coenzyme A</style></keyword><keyword><style  face="normal" font="default" size="100%">Aerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon</style></keyword><keyword><style  face="normal" font="default" size="100%">Chemotaxis</style></keyword><keyword><style  face="normal" font="default" size="100%">Chromosomes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Energy Metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Regulator</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">Metals</style></keyword><keyword><style  face="normal" font="default" size="100%">Movement</style></keyword><keyword><style  face="normal" font="default" size="100%">Open Reading Frames</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Dec 12</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">302</style></volume><pages><style face="normal" font="default" size="100%">1967-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.</style></abstract><issue><style face="normal" font="default" size="100%">5652</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/14671304?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Childers, Susan E</style></author><author><style face="normal" font="default" size="100%">Ciufo, Stacy</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Geobacter metallireducens accesses insoluble Fe(III) oxide by chemotaxis.</style></title><secondary-title><style face="normal" font="default" size="100%">Nature</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nature</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Chemotaxis</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA-Binding Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferrous Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Flagella</style></keyword><keyword><style  face="normal" font="default" size="100%">Manganese Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Movement</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxides</style></keyword><keyword><style  face="normal" font="default" size="100%">Solubility</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Apr 18</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">416</style></volume><pages><style face="normal" font="default" size="100%">767-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Microorganisms that use insoluble Fe(III) oxide as an electron acceptor can have an important function in the carbon and nutrient cycles of aquatic sediments and in the bioremediation of organic and metal contaminants in groundwater. Although Fe(III) oxides are often abundant, Fe(III)-reducing microbes are faced with the problem of how to access effectively an electron acceptor that can not diffuse to the cell. Fe(III)-reducing microorganisms in the genus Shewanella have resolved this problem by releasing soluble quinones that can carry electrons from the cell surface to Fe(III) oxide that is at a distance from the cell. Here we report that another Fe(III)-reducer, Geobacter metallireducens, has an alternative strategy for accessing Fe(III) oxides. Geobacter metallireducens specifically expresses flagella and pili only when grown on insoluble Fe(III) or Mn(IV) oxide, and is chemotactic towards Fe(II) and Mn(II) under these conditions. These results suggest that G. metallireducens senses when soluble electron acceptors are depleted and then synthesizes the appropriate appendages to permit it to search for, and establish contact with, insoluble Fe(III) or Mn(IV) oxide. This approach to the use of an insoluble electron acceptor may explain why Geobacter species predominate over other Fe(III) oxide-reducing microorganisms in a wide variety of sedimentary environments.</style></abstract><issue><style face="normal" font="default" size="100%">6882</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11961561?dopt=Abstract</style></custom1></record></records></xml>