GrowthInvolved in Aerobic and Anoxic Shewanella oneidensis MR-1 Sensory Box

[1]  G. Sawers,et al.  Characterization of Transcriptional Regulation of Shewanella frigidimarina Fe(III)-Induced Flavocytochrome c Reveals a Novel Iron-Responsive Gene Regulation System , 2003, Journal of bacteriology.

[2]  K. Lund,et al.  Association-dissociation behavior and subunit structure of heat-released nitrate reductase from Escherichia coli. , 1976, The Journal of biological chemistry.

[3]  Gordon A Anderson,et al.  Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Dorothea K. Thompson,et al.  Transcriptome Analysis of Shewanella oneidensis MR-1 in Response to Elevated Salt Conditions , 2005, Journal of bacteriology.

[5]  D. Roop,et al.  Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. , 1995, Gene.

[6]  L. M. Markillie,et al.  Overexpression of multi-heme C-type cytochromes. , 2005, BioTechniques.

[7]  B. Giese,et al.  Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. , 2004, Genes & development.

[8]  Andreas Möglich,et al.  Structure and signaling mechanism of Per-ARNT-Sim domains. , 2009, Structure.

[9]  Michael E. Taveirne,et al.  The Dual-Functioning Fumarate Reductase Is the Sole Succinate:Quinone Reductase in Campylobacter jejuni and Is Required for Full Host Colonization , 2009, Journal of bacteriology.

[10]  Grigoriy E. Pinchuk,et al.  Involvement of a Membrane-Bound Class III Adenylate Cyclase in Regulation of Anaerobic Respiration in Shewanella oneidensis MR-1 , 2009, Journal of bacteriology.

[11]  Robert D. Finn,et al.  Pfam: clans, web tools and services , 2005, Nucleic Acids Res..

[12]  Inna Dubchak,et al.  MicrobesOnline: an integrated portal for comparative and functional genomics , 2009, Nucleic Acids Res..

[13]  Michael Y. Galperin,et al.  Bacterial signal transduction network in a genomic perspective. , 2004, Environmental microbiology.

[14]  C. Myers,et al.  Replication of plasmids with the p15A origin in Shewanella putrefaciens MR‐1 , 1997, Letters in applied microbiology.

[15]  S. Chapman,et al.  Sequence of the gene encoding flavocytochrome c from Shewanella putrefaciens: a tetraheme flavoenzyme that is a soluble fumarate reductase related to the membrane-bound enzymes from other bacteria. , 1992, Biochemistry.

[16]  Correlation of PAS domains with electron transport-associated proteins in completely sequenced microbial genomes. , 1998, Molecular microbiology.

[17]  P. Salinas,et al.  Quaternary structure changes in a second Per‐Arnt‐Sim domain mediate intramolecular redox signal relay in the NifL regulatory protein , 2010, Molecular microbiology.

[18]  Andrew J. Schmidt,et al.  The Ubiquitous Protein Domain EAL Is a Cyclic Diguanylate-Specific Phosphodiesterase: Enzymatically Active and Inactive EAL Domains , 2005, Journal of bacteriology.

[19]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[20]  D. Newman,et al.  Genetic identification of a respiratory arsenate reductase , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Markus Meuwly,et al.  Allosteric Control of Cyclic di-GMP Signaling* , 2006, Journal of Biological Chemistry.

[22]  A. Osterman,et al.  Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization , 2009, Proceedings of the National Academy of Sciences.

[23]  O. White,et al.  Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis , 2002, Nature Biotechnology.

[24]  S. Austin,et al.  Azotobacter vinelandii NIFL is a flavoprotein that modulates transcriptional activation of nitrogen-fixation genes via a redox-sensitive switch. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[25]  A. Rosenzweig,et al.  Structure of the redox sensor domain of Methylococcus capsulatus (Bath) MmoS. , 2009, Biochemistry.

[26]  M. Sternberg,et al.  Protein structure prediction on the Web: a case study using the Phyre server , 2009, Nature Protocols.

[27]  J. Blatny,et al.  Construction and use of a versatile set of broad-host-range cloning and expression vectors based on the RK2 replicon , 1997, Applied and environmental microbiology.

[28]  S. Mesa,et al.  NifA is required for maximal expression of denitrification genes in Bradyrhizobium japonicum. , 2010, Environmental microbiology.

[29]  S. Mongkolsuk,et al.  Construction and characterization of regulated L-arabinose-inducible broad host range expression vectors in Xanthomonas. , 1999, FEMS microbiology letters.

[30]  Kenneth H. Nealson,et al.  Microarray Transcription Profiling of a Shewanella oneidensis etrA Mutant , 2002, Journal of bacteriology.

[31]  A. Beliaev,et al.  Involvement of Cyclic AMP (cAMP) and cAMP Receptor Protein in Anaerobic Respiration of Shewanella oneidensis , 2003, Journal of bacteriology.

[32]  S. Brunak,et al.  Locating proteins in the cell using TargetP, SignalP and related tools , 2007, Nature Protocols.

[33]  Yang Zhang,et al.  I-TASSER: a unified platform for automated protein structure and function prediction , 2010, Nature Protocols.

[34]  Peer Bork,et al.  SMART 6: recent updates and new developments , 2008, Nucleic Acids Res..

[35]  K. Moffat,et al.  Structure of the redox sensor domain of Azotobacter vinelandii NifL at atomic resolution: signaling, dimerization, and mechanism. , 2007, Biochemistry.

[36]  M. Gilles-Gonzalez,et al.  Dos, a heme-binding PAS protein from Escherichia coli, is a direct oxygen sensor. , 2000, Biochemistry.

[37]  A. G. Bobrov,et al.  HmsP, a putative phosphodiesterase, and HmsT, a putative diguanylate cyclase, control Hms‐dependent biofilm formation in Yersinia pestis , 2004, Molecular microbiology.

[38]  Dan Coursolle,et al.  Modularity of the Mtr respiratory pathway of Shewanella oneidensis strain MR‐1 , 2010, Molecular microbiology.

[39]  D. Newman,et al.  Anaerobic regulation by an atypical Arc system in Shewanella oneidensis , 2005, Molecular microbiology.

[40]  Birgit Eisenhaber,et al.  On filtering false positive transmembrane protein predictions. , 2002, Protein engineering.

[41]  A. Spormann,et al.  Periplasmic Electron Transfer via the c-Type Cytochromes MtrA and FccA of Shewanella oneidensis MR-1 , 2009, Applied and Environmental Microbiology.

[42]  H. Sondermann,et al.  Vibrio cholerae VpsT Regulates Matrix Production and Motility by Directly Sensing Cyclic di-GMP , 2010, Science.

[43]  Kay Hofmann,et al.  Tmbase-A database of membrane spanning protein segments , 1993 .

[44]  S. Hall,et al.  Growth of Campylobacter jejuni Supported by Respiration of Fumarate, Nitrate, Nitrite, Trimethylamine-N-Oxide, or Dimethyl Sulfoxide Requires Oxygen , 2002, Journal of bacteriology.

[45]  Søren Brunak,et al.  Prediction of twin-arginine signal peptides , 2005, BMC Bioinformatics.

[46]  Rolf Apweiler,et al.  Evaluation of methods for the prediction of membrane spanning regions , 2001, Bioinform..

[47]  Dorothea K. Thompson,et al.  Transcriptomic and Proteomic Characterization of the Fur Modulon in the Metal-Reducing Bacterium Shewanella oneidensis , 2004, Journal of bacteriology.

[48]  Jack Snoeyink,et al.  Nucleic Acids Research Advance Access published April 22, 2007 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids , 2007 .

[49]  Alyssa M. Redding,et al.  Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation , 2009, Nucleic acids research.

[50]  U. Jenal Cyclic di-guanosine-monophosphate comes of age: a novel secondary messenger involved in modulating cell surface structures in bacteria? , 2004, Current opinion in microbiology.

[51]  Pascal Benkert,et al.  QMEAN server for protein model quality estimation , 2009, Nucleic Acids Res..

[52]  A. Spormann,et al.  Control of Formation and Cellular Detachment from Shewanella oneidensis MR-1 Biofilms by Cyclic di-GMP , 2006, Journal of bacteriology.

[53]  Liisa Holm,et al.  Searching protein structure databases with DaliLite v.3 , 2008, Bioinform..

[54]  R. Samudrala,et al.  Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix , 2010, Molecular microbiology.

[55]  I. Zhulin,et al.  PAS Domains: Internal Sensors of Oxygen, Redox Potential, and Light , 1999, Microbiology and Molecular Biology Reviews.

[56]  Morten Nielsen,et al.  CPHmodels-3.0—remote homology modeling using structure-guided sequence profiles , 2010, Nucleic Acids Res..

[57]  Manfred J. Sippl,et al.  Thirty years of environmental health research--and growing. , 1996, Nucleic Acids Res..

[58]  C. Ponting,et al.  PAS: a multifunctional domain family comes to light , 1997, Current Biology.