Growth Temperature and Genome Size in Bacteria Are Negatively Correlated, Suggesting Genomic Streamlining During Thermal Adaptation
暂无分享,去创建一个
Andreas Wagner | Evandro Ferrada | Aditya Barve | A. Wagner | Aditya Barve | N. Sabath | E. Ferrada | Niv Sabath | Niv Sabath
[1] R. Jaenicke,et al. Stability and stabilization of globular proteins in solution. , 2000, Journal of biotechnology.
[2] Frédéric Partensky,et al. Accelerated evolution associated with genome reduction in a free-living prokaryote , 2005, Genome Biology.
[3] N. Moran,et al. Comment on "The Origins of Genome Complexity" , 2004, Science.
[4] N. Moran,et al. Lifestyle evolution in symbiotic bacteria: insights from genomics. , 2000, Trends in ecology & evolution.
[5] E. Koonin,et al. Potential genomic determinants of hyperthermophily. , 2003, Trends in genetics : TIG.
[6] R. Nussinov,et al. How do thermophilic proteins deal with heat? , 2001, Cellular and Molecular Life Sciences CMLS.
[7] N. Lartillot,et al. A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters. , 2011, Molecular biology and evolution.
[8] Eduardo P. C. Rocha,et al. The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics , 2010, PLoS genetics.
[9] J. Felsenstein. Comparative Methods with Sampling Error and Within‐Species Variation: Contrasts Revisited and Revised , 2008, The American Naturalist.
[10] Igor N. Berezovsky,et al. Protein and DNA Sequence Determinants of Thermophilic Adaptation , 2006, PLoS Comput. Biol..
[11] M. Noordewier,et al. Genome Streamlining in a Cosmopolitan Oceanic Bacterium , 2005, Science.
[12] M. Lynch. Streamlining and simplification of microbial genome architecture. , 2006, Annual review of microbiology.
[13] N. Goldman,et al. A codon-based model of nucleotide substitution for protein-coding DNA sequences. , 1994, Molecular biology and evolution.
[14] Eduardo P C Rocha,et al. Causes of insertion sequences abundance in prokaryotic genomes. , 2007, Molecular biology and evolution.
[15] N. Moran,et al. Estimating Population Size and Transmission Bottlenecks in Maternally Transmitted Endosymbiotic Bacteria , 2002, Microbial Ecology.
[16] F. Crick,et al. Selfish DNA: the ultimate parasite , 1980, Nature.
[17] R. Lenski,et al. Microbial genetics: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation , 2003, Nature Reviews Genetics.
[18] N. Moran,et al. The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria , 2009, Science.
[19] P. Mitchell. Chemiosmotic coupling in oxidative and photosynthetic phosphorylation. 1966. , 2011, Biochimica et biophysica acta.
[20] Janet M. Thornton,et al. Microeconomic Principles Explain an Optimal Genome Size in Bacteria , 2004, Spanish Bioinformatics Conference.
[21] D. Tempest,et al. Metabolic and energetic aspects of the growth of Bacillus stearothermophilus in glucose-limited and glucose-sufficient chemostat culture , 1988, Archives of Microbiology.
[22] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..
[23] J. Lobry,et al. Relationships Between Genomic G+C Content, RNA Secondary Structures, and Optimal Growth Temperature in Prokaryotes , 1997, Journal of Molecular Evolution.
[24] L. Holm,et al. The Pfam protein families database , 2005, Nucleic Acids Res..
[25] R. D. Crotty,et al. Seasonal variation in cell volume of epilimnetic bacteria , 1988, Microbial Ecology.
[26] Andrés Moya,et al. Toward minimal bacterial cells: evolution vs. design , 2008, FEMS microbiology reviews.
[27] J. Drake,et al. Genome-Wide Patterns of Nucleotide Substitution Reveal Stringent Functional Constraints on the Protein Sequences of Thermophiles , 2004, Genetics.
[28] Bernhard Sonnleitner,et al. Biotechnology of Thermophilic Bacteria — Growth, Products, and Application , 1983, Microbial Activities.
[29] N. Moran,et al. Deletional bias and the evolution of bacterial genomes. , 2001, Trends in genetics : TIG.
[30] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[31] Howard Ochman,et al. The consequences of genetic drift for bacterial genome complexity. , 2009, Genome research.
[32] W. Doolittle,et al. Selfish genes, the phenotype paradigm and genome evolution , 1980, Nature.
[33] P. Mitchell. CHEMIOSMOTIC COUPLING IN OXIDATIVE AND PHOTOSYNTHETIC PHOSPHORYLATION , 1966, Biological reviews of the Cambridge Philosophical Society.
[34] Patrick Forterre,et al. A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. , 2002, Trends in genetics : TIG.
[35] Inna Dubchak,et al. Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes , 2008, Journal of bacteriology.
[36] R. Nussinov,et al. How do thermophilic proteins deal with heat? Cell Mol Life Sci , 2001 .
[37] Effect of Growth Temperature on Fatty Acid Composition of Ten Thermus Strains , 1992, Applied and environmental microbiology.
[38] E. Koonin,et al. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world , 2008, Nucleic acids research.
[39] T. Coultate,et al. Energetics of Bacillus stearothermophilus growth: molar growth yield and temperature effects on growth efficiency , 1975, Journal of bacteriology.
[40] Shibu Yooseph,et al. Genomic and functional adaptation in surface ocean planktonic prokaryotes , 2010, Nature.
[41] J. Drake,et al. The Rate and Character of Spontaneous Mutation in Thermus thermophilus , 2008, Genetics.
[42] K. Dill,et al. Physical limits of cells and proteomes , 2011, Proceedings of the National Academy of Sciences.
[43] K. Katoh,et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.
[44] William D. Taylor,et al. Phenotypic Correlates of Genomic DNA Content in Unicellular Eukaryotes and Other Cells , 1983, The American Naturalist.
[45] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[46] U. Alon,et al. Environmental variability and modularity of bacterial metabolic networks , 2007, BMC Evolutionary Biology.
[47] D. Hartl,et al. Principles of population genetics , 1981 .
[48] Andreas Wagner,et al. Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks , 2009, PLoS Comput. Biol..
[49] R. Varadarajan,et al. Elucidation of determinants of protein stability through genome sequence analysis , 2000, FEBS letters.
[50] John W. Drake,et al. Avoiding Dangerous Missense: Thermophiles Display Especially Low Mutation Rates , 2009, PLoS genetics.
[51] D Eisenberg,et al. Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability. , 1999, Journal of molecular biology.
[52] Andreas Wagner,et al. Energy constraints on the evolution of gene expression. , 2005, Molecular biology and evolution.
[53] P. Tompa,et al. Reduction in Structural Disorder and Functional Complexity in the Thermal Adaptation of Prokaryotes , 2010, PloS one.
[54] H. Kuhn,et al. Effects of growth temperature on maximal specific growth rate, yield, maintenance, and death rate in glucose-limited continuous culture of the thermophilic Bacillus caldotenax , 1980, European journal of applied microbiology and biotechnology.
[55] C. Jones,et al. Energy conservation in the extreme thermophile Thermus thermophilus HB8 , 1982, Archives of Microbiology.