Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6T adapted to coastal planktonic lifestyle

[1]  A. Parte.  LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. , 2018, International journal of systematic and evolutionary microbiology.

[2]  Robert D. Finn,et al.  Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families , 2017, Nucleic Acids Res..

[3]  Hyun-Hee Lee,et al.  Comparative Genome Analysis of Rathayibacter tritici NCPPB 1953 with Rathayibacter toxicus Strains Can Facilitate Studies on Mechanisms of Nematode Association and Host Infection , 2017, The plant pathology journal.

[4]  Matthew R. Laird,et al.  IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets , 2017, Nucleic Acids Res..

[5]  J. Tambong.  Comparative genomics of Clavibacter michiganensis subspecies, pathogens of important agricultural crops , 2017, PloS one.

[6]  Henrik Nielsen,et al.  Predicting Secretory Proteins with SignalP. , 2017, Methods in molecular biology.

[7]  Sheng Yang,et al.  Comparative analysis of Corynebacterium glutamicum genomes: a new perspective for the industrial production of amino acids , 2017, BMC Genomics.

[8]  E. Bamberg,et al.  Functional Green-Tuned Proteorhodopsin from Modern Stromatolites , 2016, PloS one.

[9]  A. Romero-Rodríguez,et al.  Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor , 2016, BMC Microbiology.

[10]  Michel-Yves Mistou,et al.  Bacterial glycobiology: rhamnose-containing cell wall polysaccharides in Gram-positive bacteria , 2016, FEMS microbiology reviews.

[11]  Tohru Kobayashi,et al.  Complete genome sequence of the xylan-degrading subseafloor bacterium Microcella alkaliphila JAM-AC0309. , 2016, Journal of biotechnology.

[12]  Robert D. Finn,et al.  The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..

[13]  Andreas Wilke,et al.  The MG-RAST metagenomics database and portal in 2015 , 2015, Nucleic Acids Res..

[14]  Milton H. Saier,et al.  The Transporter Classification Database (TCDB): recent advances , 2015, Nucleic Acids Res..

[15]  W. Whitman.  Bergey's Manual of Systematics of Archaea and Bacteria , 2016 .

[16]  W. Bitter,et al.  Type VII Secretion: A Highly Versatile Secretion System. , 2016, Microbiology spectrum.

[17]  Alice C. McHardy,et al.  Functional overlap of the Arabidopsis leaf and root microbiota , 2015, Nature.

[18]  Haiwei Luo,et al.  How do divergent ecological strategies emerge among marine bacterioplankton lineages? , 2015, Trends in microbiology.

[19]  Christophe Caron,et al.  MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution , 2015, Database J. Biol. Databases Curation.

[20]  Luis Pedro Coelho,et al.  Structure and function of the global ocean microbiome , 2015, Science.

[21]  F. Rodríguez-Valera,et al.  Genomes of Planktonic Acidimicrobiales: Widening Horizons for Marine Actinobacteria by Metagenomics , 2015, mBio.

[22]  J. M. Dow,et al.  Targeting cyclic di-GMP signalling: a strategy to control biofilm formation? , 2014, Current pharmaceutical design.

[23]  Michael Y. Galperin,et al.  Expanded microbial genome coverage and improved protein family annotation in the COG database , 2014, Nucleic Acids Res..

[24]  Narmada Thanki,et al.  CDD: NCBI's conserved domain database , 2014, Nucleic Acids Res..

[25]  A. Groisillier,et al.  The Mannitol Utilization System of the Marine Bacterium Zobellia galactanivorans , 2014, Applied and Environmental Microbiology.

[26]  F. Rodríguez-Valera,et al.  Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing , 2014, Molecular ecology.

[27]  A. Mark,et al.  Effect of methyl-branched fatty acids on the structure of lipid bilayers. , 2014, The journal of physical chemistry. B.

[28]  W. Doolittle,et al.  Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome , 2014, International journal of systematic and evolutionary microbiology.

[29]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[30]  A. Steyn,et al.  The Physiology and Genetics of Oxidative Stress in Mycobacteria , 2014, Microbiology spectrum.

[31]  S. Giovannoni,et al.  Implications of streamlining theory for microbial ecology , 2014, The ISME Journal.

[32]  P. Genevaux,et al.  Multiple Toxin-Antitoxin Systems in Mycobacterium tuberculosis , 2014, Toxins.

[33]  T. Parish.  Two-Component Regulatory Systems of Mycobacteria. , 2014, Microbiology spectrum.

[34]  R. Manganelli.  Sigma Factors: Key Molecules in Mycobacterium tuberculosis Physiology and Virulence. , 2014, Microbiology spectrum.

[35]  I-Min A. Chen,et al.  IMG 4 version of the integrated microbial genomes comparative analysis system , 2013, Nucleic Acids Res..

[36]  M. Van Sluys,et al.  Complete Genome Sequence of Leifsonia xyli subsp. cynodontis Strain DSM46306, a Gram-Positive Bacterial Pathogen of Grasses , 2013, Genome Announcements.

[37]  Cuiqing Ma,et al.  Escherichia coli transcription termination factor NusA: heat-induced oligomerization and chaperone activity , 2013, Scientific Reports.

[38]  Dongqing Xu,et al.  Isolation of proteorhodopsin-bearing bacterium JL-3 from fresh water and characterization of the proteorhodopsin. , 2013, FEMS microbiology letters.

[39]  B. Cho,et al.  Pontimonas salivibrio gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a seawater reservoir of a solar saltern. , 2013, International journal of systematic and evolutionary microbiology.

[40]  D. Schrag,et al.  Dynamics of a Snowball Earth ocean , 2013, Nature.

[41]  M. Bennett,et al.  Adenylylation of mycobacterial Glnk (PII) protein is induced by nitrogen limitation , 2013, Tuberculosis.

[42]  Hugo Beraldi-Campesi,et al.  Early life on land and the first terrestrial ecosystems , 2013, Ecological Processes.

[43]  T. Schmidt,et al.  Shallow breathing: bacterial life at low O2 , 2013, Nature Reviews Microbiology.

[44]  K. Sarva,et al.  Septal Localization of the Mycobacterium tuberculosis MtrB Sensor Kinase Promotes MtrA Regulon Expression* , 2012, The Journal of Biological Chemistry.

[45]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[46]  Shane S. Sturrock,et al.  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..

[47]  Maxim Teslenko,et al.  MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space , 2012, Systematic biology.

[48]  J. Poulain,et al.  Complete Genome Sequence of Streptomyces cattleya NRRL 8057, a Producer of Antibiotics and Fluorometabolites , 2011, Journal of bacteriology.

[49]  Richard E. Lenski,et al.  Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli , 2011, G3: Genes | Genomes | Genetics.

[50]  N. Someya,et al.  Genome Sequence of Microbacterium testaceum StLB037, an N-Acylhomoserine Lactone-Degrading Bacterium Isolated from Potato Leaves , 2011, Journal of bacteriology.

[51]  J. Collins,et al.  How antibiotics kill bacteria: from targets to networks , 2010, Nature Reviews Microbiology.

[52]  Yi-Ju Hsieh,et al.  Global regulation by the seven-component Pi signaling system. , 2010, Current opinion in microbiology.

[53]  F. Partensky,et al.  Prochlorococcus: advantages and limits of minimalism. , 2010, Annual review of marine science.

[54]  I. Paulsen,et al.  Computational prediction of the osmoregulation network in Synechococcus sp. WH8102 , 2010, BMC Genomics.

[55]  L. Levin,et al.  Effects of natural and human-induced hypoxia on coastal benthos , 2009 .

[56]  Sean R Eddy,et al.  A new generation of homology search tools based on probabilistic inference. , 2009, Genome informatics. International Conference on Genome Informatics.

[57]  C. Hertweck,et al.  The biosynthetic logic of polyketide diversity. , 2009, Angewandte Chemie.

[58]  Karl Kaiser,et al.  Biochemical Composition and Size Distribution of Organic Matter at the Pacific and Atlantic Time-Series Stations , 2009 .

[59]  Sonja Hansen,et al.  Molecular Mechanisms of HipA-Mediated Multidrug Tolerance and Its Neutralization by HipB , 2009, Science.

[60]  M. Taga,et al.  Sinorhizobium meliloti, a bacterium lacking the autoinducer‐2 (AI‐2) synthase, responds to AI‐2 supplied by other bacteria , 2008, Molecular microbiology.

[61]  Ruth Hershberg,et al.  Selection on codon bias. , 2008, Annual review of genetics.

[62]  K. Jahreis,et al.  Ins and outs of glucose transport systems in eubacteria. , 2008, FEMS microbiology reviews.

[63]  D. Choi,et al.  Nocardioides salarius sp. nov., isolated from seawater enriched with zooplankton. , 2008, International journal of systematic and evolutionary microbiology.

[64]  Daniel N. Wilson,et al.  Structural aspects of RbfA action during small ribosomal subunit assembly. , 2007, Molecular cell.

[65]  F. Kenig,et al.  A red algal bloom in the aftermath of the Marinoan Snowball Earth , 2007 .

[66]  Ibtissem Grissa,et al.  CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats , 2007, Nucleic Acids Res..

[67]  W. Jacobs,et al.  The Two-Component Regulatory System senX3-regX3 Regulates Phosphate-Dependent Gene Expression in Mycobacterium smegmatis , 2007, Journal of bacteriology.

[68]  J. Noh,et al.  Nocardioides marinus sp. nov. , 2007, International journal of systematic and evolutionary microbiology.

[69]  Benjamin J. Raphael,et al.  The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families , 2007, PLoS biology.

[70]  G. Unden,et al.  In Vitro Analysis of the Two-Component System MtrB-MtrA from Corynebacterium glutamicum , 2007, Journal of bacteriology.

[71]  Michelle G. Giglio,et al.  TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes , 2006, Nucleic Acids Res..

[72]  R. Schlitzer.  Ocean Data View , 2007 .

[73]  Alison Buchan,et al.  Bacterial Taxa That Limit Sulfur Flux from the Ocean , 2006, Science.

[74]  M. D. da Costa,et al.  Microcella alkaliphila sp. nov., a novel member of the family Microbacteriaceae isolated from a non-saline alkaline groundwater, and emended description of the genus Microcella. , 2006, International journal of systematic and evolutionary microbiology.

[75]  G. Klug,et al.  Thioredoxins in bacteria: functions in oxidative stress response and regulation of thioredoxin genes , 2006, Naturwissenschaften.

[76]  Mohamed A. Marahiel,et al.  Cold-Induced Putative DEAD Box RNA Helicases CshA and CshB Are Essential for Cold Adaptation and Interact with Cold Shock Protein B in Bacillus subtilis , 2006, Journal of bacteriology.

[77]  A. Danchin,et al.  Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. , 2005, Genome research.

[78]  M. Noordewier,et al.  Genome Streamlining in a Cosmopolitan Oceanic Bacterium , 2005, Science.

[79]  Johannes Söding,et al.  The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..

[80]  S. Hedges,et al.  A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land , 2004, BMC Evolutionary Biology.

[81]  Michael P. Cummings,et al.  PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)] , 2004 .

[82]  F. Blattner,et al.  Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.

[83]  J. Imlay,et al.  Pathways of oxidative damage. , 2003, Annual review of microbiology.

[84]  Manesh Shah,et al.  Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation , 2003, Nature.

[85]  H. Tsuda,et al.  Genes Involved in Bacitracin Resistance in Streptococcus mutans , 2002, Antimicrobial Agents and Chemotherapy.

[86]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[87]  Claudine Médigue,et al.  Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. , 2002, Microbiology.

[88]  Y. Gerchman,et al.  Na(+)/H(+) antiporters. , 2001, Biochimica et biophysica acta.

[89]  M. Marahiel,et al.  Role of the Bacillus subtilis fatty acid desaturase in membrane adaptation during cold shock , 2001, Molecular microbiology.

[90]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[91]  R. Simons,et al.  Cold‐temperature induction of Escherichia coli polynucleotide phosphorylase occurs by reversal of its autoregulation †‡ , 2001, Molecular microbiology.

[92]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[93]  M. Borodovsky,et al.  Heuristic approach to deriving models for gene finding. , 1999, Nucleic acids research.

[94]  K. Tada,et al.  Dissolved free amino acids in coastal seawater using a modified fluorometric method , 1998 .

[95]  J. Davies,et al.  Coenzyme A Disulfide Reductase, the Primary Low Molecular Weight Disulfide Reductase from Staphylococcus aureus , 1998, The Journal of Biological Chemistry.

[96]  A. Alldredge,et al.  The characteristics and transparent exopolymer particle (TEP) content of marine snow formed from thecate dinoflagellates , 1998 .

[97]  F. Azam,et al.  Abundant protein-containing particles in the sea , 1996 .

[98]  J. Davies,et al.  Distribution of thiols in microorganisms: mycothiol is a major thiol in most actinomycetes , 1996, Journal of bacteriology.

[99]  Anders Krogh,et al.  Hidden Markov models for sequence analysis: extension and analysis of the basic method , 1996, Comput. Appl. Biosci..

[100]  F. Azam,et al.  Bacterial 5-Nucleotidase in Aquatic Ecosystems: A Novel Mechanism of Phosphorus Regeneration , 1985, Science.