Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response
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Erin A. Becker | Phillip M Seitzer | M. Facciotti | J. Eisen | Dongying Wu | A. Darling | D. Madern | A. Tritt | David J. Larsen | Megan L. Krusor | Andrew I. Yao | Phillip M. Seitzer | Andrew J. Tritt
[1] 张静,et al. Banana Ovate family protein MaOFP1 and MADS-box protein MuMADS1 antagonistically regulated banana fruit ripening , 2015 .
[2] Idris A. Eckley,et al. changepoint: An R Package for Changepoint Analysis , 2014 .
[3] N. Youssef,et al. Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales , 2013, The ISME Journal.
[4] E. Girard,et al. An experimental point of view on hydration/solvation in halophilic proteins , 2014, Front. Microbiol..
[5] Frederick Albert Matsen IV,et al. PhyloSift: phylogenetic analysis of genomes and metagenomes , 2014, PeerJ.
[6] J. Eisen,et al. Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups , 2013, PloS one.
[7] J. Hinton,et al. ProP Is Required for the Survival of Desiccated Salmonella enterica Serovar Typhimurium Cells on a Stainless Steel Surface , 2013, Applied and Environmental Microbiology.
[8] Pierre M. Durand,et al. A Role for Programmed Cell Death in the Microbial Loop , 2013, PloS one.
[9] G. Zaccai. Hydration shells with a pinch of salt. , 2013, Biopolymers.
[10] L. Tran,et al. Systems biology-based approaches toward understanding drought tolerance in food crops , 2013, Critical reviews in biotechnology.
[11] Marc T. Facciotti,et al. JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison , 2013, BMC Bioinformatics.
[12] A. Janssen,et al. Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea , 2012, Proceedings of the National Academy of Sciences.
[13] Douglas W. Raiford,et al. An Extremely Halophilic Proteobacterium Combines a Highly Acidic Proteome with a Low Cytoplasmic Potassium Content* , 2012, The Journal of Biological Chemistry.
[14] M. Facciotti,et al. An Integrated Pipeline for de Novo Assembly of Microbial Genomes , 2012, PloS one.
[15] Songnian Hu,et al. Complete Genome Sequence of the Metabolically Versatile Halophilic Archaeon Haloferax mediterranei, a Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate) Producer , 2012, Journal of bacteriology.
[16] Marc T. Facciotti,et al. Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux , 2012, PloS one.
[17] O. Nureki,et al. Structural basis for translation termination by archaeal RF1 and GTP-bound EF1α complex , 2012, Nucleic acids research.
[18] C. Dutta,et al. Microbial Lifestyle and Genome Signatures , 2012, Current genomics.
[19] Genome Sequence of the Halophilic Archaeon Halococcus hamelinensis , 2012, Journal of bacteriology.
[20] C. Stefanadis,et al. Significance of Hyponatremia in Heart Failure , 2012 .
[21] J. Banfield,et al. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities , 2011, The ISME Journal.
[22] Lynne A. Goodwin,et al. A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T , 2012, BMC Genomics.
[23] J. Soppa. Functional Genomic and Advanced Genetic Studies Reveal Novel Insights into the Metabolism, Regulation, and Biology of Haloferax volcanii , 2011, Archaea.
[24] Peixiang Ni,et al. Genome Sequence of Halobiforma lacisalsi AJ5, an Extremely Halophilic Archaeon Which Harbors a bop Gene , 2011, Journal of bacteriology.
[25] David J. Reiss,et al. Niche adaptation by expansion and reprogramming of general transcription factors , 2011, Molecular systems biology.
[26] H. Gohlke,et al. Arg149 is involved in switching the low affinity, open state of the binding protein AfProX into its high affinity, closed state. , 2011, Journal of molecular biology.
[27] Y. Jeon,et al. Osmoadaptive strategies of the archaeon Halococcus hamelinensis isolated from a hypersaline stromatolite environment. , 2011, Astrobiology.
[28] E. Duan,et al. Aquaporins in sperm osmoadaptation: an emerging role for volume regulation , 2011, Acta Pharmacologica Sinica.
[29] Peer Bork,et al. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy , 2011, Nucleic Acids Res..
[30] Ramón Doallo,et al. ProtTest 3: fast selection of best-fit models of protein evolution , 2011, Bioinform..
[31] J. Wiegel,et al. Temperature and pH optima of extremely halophilic archaea: a mini-review , 2011, Extremophiles.
[32] Andrew C. Adey,et al. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition , 2010, Genome Biology.
[33] R. Usami,et al. Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene. , 2010, International journal of systematic and evolutionary microbiology.
[34] E. Koonin,et al. Evolution of diverse cell division and vesicle formation systems in Archaea , 2010, Nature Reviews Microbiology.
[35] S. Kelly,et al. Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes , 2010, Proceedings of the Royal Society B: Biological Sciences.
[36] R. Tjian,et al. Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation , 2010, Nature Reviews Genetics.
[37] Seong-Hyeuk Nam,et al. Complete Genome Sequence of Halalkalicoccus jeotgali B3T, an Extremely Halophilic Archaeon , 2010, Journal of bacteriology.
[38] L. Gram,et al. The survival of Listeria monocytogenes during long term desiccation is facilitated by sodium chloride and organic material. , 2010, International journal of food microbiology.
[39] Natalia N. Ivanova,et al. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes , 2010, Nature Methods.
[40] O. Gascuel,et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.
[41] C. Fizames,et al. Potassium and sodium transport in non-animal cells: the Trk/Ktr/HKT transporter family , 2010, Cellular and Molecular Life Sciences.
[42] Jeffrey R. Robinson,et al. The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon , 2010, PloS one.
[43] K. Murakami,et al. Functional Analysis of the Three TATA Binding Protein Homologs in Methanosarcina acetivorans , 2010, Journal of bacteriology.
[44] Sean R Eddy,et al. A new generation of homology search tools based on probabilistic inference. , 2009, Genome informatics. International Conference on Genome Informatics.
[45] Lynne A. Goodwin,et al. Complete genome sequence of Halogeometricum borinquense type strain (PR3T) , 2009, Standards in genomic sciences.
[46] Adam P. Arkin,et al. FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix , 2009, Molecular biology and evolution.
[47] R. Dutzler,et al. X-ray structure of the C-terminal domain of a prokaryotic cation-chloride cotransporter. , 2009, Structure.
[48] A. Oren,et al. Emended descriptions of genera of the family Halobacteriaceae. , 2009, International journal of systematic and evolutionary microbiology.
[49] S. Pongor,et al. The quest for orthologs: finding the corresponding gene across genomes. , 2008, Trends in genetics : TIG.
[50] Andreas Prlic,et al. Sequence analysis , 2003 .
[51] F. Pfeifer,et al. Variations in the multiple tbp genes in different Halobacterium salinarum strains and their expression during growth , 2008, Archives of Microbiology.
[52] C. Lange,et al. Genomics and functional genomics with haloarchaea , 2008, Archives of Microbiology.
[53] J. Lachuer,et al. Gene expression profiling in brain following acute systemic hypertonicity: novel genes possibly involved in osmoadaptation , 2008, Journal of neurochemistry.
[54] Volker Müller,et al. The molecular basis of salt adaptation in Methanosarcina mazei Gö1 , 2008, Archives of Microbiology.
[55] P. Forterre,et al. Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota , 2008, Nature Reviews Microbiology.
[56] Orland R. Gonzalez,et al. Metabolism of halophilic archaea , 2008, Extremophiles.
[57] Gabriel Moreno-Hagelsieb,et al. Choosing BLAST options for better detection of orthologs as reciprocal best hits , 2008, Bioinform..
[58] Rick L. Stevens,et al. The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.
[59] Shiladitya DasSarma,et al. Genetic and transcriptomic analysis of transcription factor genes in the model halophilic Archaeon: coordinate action of TbpD and TfbA , 2007, BMC Genetics.
[60] Richard Bonneau,et al. General transcription factor specified global gene regulation in archaea , 2007, Proceedings of the National Academy of Sciences.
[61] Peer Bork,et al. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation , 2007, Bioinform..
[62] Friedhelm Pfeiffer,et al. The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity , 2006, BMC Genomics.
[63] Jakob Fredslund,et al. PHY·FI: fast and easy online creation and manipulation of phylogeny color figures , 2006, BMC Bioinformatics.
[64] J. Soppa. From genomes to function: haloarchaea as model organisms. , 2006, Microbiology.
[65] Torsten Schwede,et al. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling , 2006, Bioinform..
[66] T. Vallaeys,et al. LadR, a new PadR-related transcriptional regulator from Listeria monocytogenes, negatively regulates the expression of the multidrug efflux pump MdrL. , 2006, FEMS microbiology letters.
[67] J. Townsend,et al. Horizontal gene transfer, genome innovation and evolution , 2005, Nature Reviews Microbiology.
[68] David Posada,et al. ProtTest: selection of best-fit models of protein evolution , 2005, Bioinform..
[69] Eric Bapteste,et al. Evolution of the RNA polymerase B' subunit gene (rpoB') in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. , 2004, Molecular biology and evolution.
[70] Robert C. Edgar,et al. MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.
[71] E. Bremer,et al. Thermoprotection of Bacillus subtilis by Exogenously Provided Glycine Betaine and Structurally Related Compatible Solutes: Involvement of Opu Transporters , 2004, Journal of bacteriology.
[72] Christopher Miller,et al. Secondary active transport mediated by a prokaryotic homologue of ClC Cl- channels , 2004, Nature.
[73] Korbinian Strimmer,et al. APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..
[74] J. Verbalis,et al. Disorders of body water homeostasis. , 2003, Best practice & research. Clinical endocrinology & metabolism.
[75] T. Steitz,et al. Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit. , 2003, RNA.
[76] B. Tindall. Taxonomic problems arising in the genera Haloterrigena and Natrinema. , 2003, International journal of systematic and evolutionary microbiology.
[77] G. Perrière,et al. The source of laterally transferred genes in bacterial genomes , 2003, Genome Biology.
[78] A. Oren,et al. Metabolism of chloride in halophilic prokaryotes , 2003, Extremophiles.
[79] H. Santos,et al. Compatible solutes of organisms that live in hot saline environments. , 2002, Environmental microbiology.
[80] K. Katoh,et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.
[81] Dieter Oesterhelt,et al. A novel mode of sensory transduction in archaea: binding protein‐mediated chemotaxis towards osmoprotectants and amino acids , 2002, The EMBO journal.
[82] Anton J. Enright,et al. An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.
[83] Christopher Miller,et al. A biological role for prokaryotic ClC chloride channels , 2002, Nature.
[84] W. Delano. The PyMOL Molecular Graphics System , 2002 .
[85] B. Poolman,et al. Osmosensing and osmoregulatory compatible solute accumulation by bacteria. , 2001, Comparative biochemistry and physiology. Part A, Molecular & integrative physiology.
[86] W. Guder,et al. Influence of dehydratation on glycerophosphorylcholine and choline distribution along the rat nephron , 2001, Pflügers Archiv.
[87] B. Tindall,et al. Transfer of Natrialba asiatica B1T to Natrialba taiwanensis sp. nov. and description of Natrialba aegyptiaca sp. nov., a novel extremely halophilic, aerobic, non-pigmented member of the Archaea from Egypt that produces extracellular poly(glutamic acid). , 2001, International journal of systematic and evolutionary microbiology.
[88] R. Schwartz,et al. Whole proteome pI values correlate with subcellular localizations of proteins for organisms within the three domains of life. , 2001, Genome research.
[89] L. Barthelmebs,et al. Inducible Metabolism of Phenolic Acids inPediococcus pentosaceus Is Encoded by an Autoregulated Operon Which Involves a New Class of Negative Transcriptional Regulator , 2000, Journal of bacteriology.
[90] V. Thorsson,et al. Genome sequence of Halobacterium species NRC-1. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[91] F. Schluenzen,et al. Structure of Functionally Activated Small Ribosomal Subunit at 3.3 Å Resolution , 2000, Cell.
[92] D. Madern,et al. Halophilic adaptation of enzymes , 2000, Extremophiles.
[93] Michael Y. Galperin,et al. The COG database: a tool for genome-scale analysis of protein functions and evolution , 2000, Nucleic Acids Res..
[94] P B Sigler,et al. The structural basis for the oriented assembly of a TBP/TFB/promoter complex. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[95] Aharon Oren,et al. Bioenergetic Aspects of Halophilism , 1999, Microbiology and Molecular Biology Reviews.
[96] I. Booth,et al. Protection of Escherichia coli cells against extreme turgor by activation of MscS and MscL mechanosensitive channels: identification of genes required for MscS activity , 1999, The EMBO journal.
[97] J. Soppa,et al. Transcription initiation in Archaea: facts, factors and future aspects , 1999, Molecular microbiology.
[98] D. Botstein,et al. Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[99] E. Bremer,et al. Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolality environments , 1998, Archives of Microbiology.
[100] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[101] J. Boch,et al. Synthesis of the osmoprotectant glycine betaine in Bacillus subtilis: characterization of the gbsAB genes , 1996, Journal of bacteriology.
[102] K. Yamauchi,et al. Archaebacterial lipids: highly proton-impermeable membranes from 1,2-diphytanyl-sn-glycero-3-phosphocholine. , 1993, Biochimica et biophysica acta.
[103] T. Lamark,et al. DNA sequence and analysis of the bet genes encoding the osmoregulatory choline—glycine betaine pathway of Escherichia coli , 1991, Molecular microbiology.
[104] M. Rosa,et al. The lipids of archaebacteria. , 1988, Progress in lipid research.
[105] A. Duschl,et al. Primary and secondary chloride transport in Halobacterium halobium , 1986, Journal of bacteriology.
[106] W. Doolittle,et al. Archaebacterial heat‐shock proteins , 1984, The EMBO journal.