LESS IS MORE: SELECTIVE ADVANTAGES CAN EXPLAIN THE PREVALENT LOSS OF BIOSYNTHETIC GENES IN BACTERIA
暂无分享,去创建一个
Silvio Waschina | Christoph Kaleta | Katrin Bohl | Samay Pande | Christian Kost | C. Kaleta | C. Kost | Samay Pande | Katrin Bohl | S. Waschina | Glen D'souza | Glen D'Souza | Christian Kost | Silvio Waschina
[1] Susumu Goto,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..
[2] A. Danchin,et al. Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths , 2009, PLoS genetics.
[3] F. Taddei,et al. Costs and Benefits of High Mutation Rates: Adaptive Evolution of Bacteria in the Mouse Gut , 2001, Science.
[4] Stefan Engelen,et al. MicroScope: a platform for microbial genome annotation and comparative genomics , 2009, Database J. Biol. Databases Curation.
[5] R. Milo,et al. Glycolytic strategy as a tradeoff between energy yield and protein cost , 2013, Proceedings of the National Academy of Sciences.
[6] Reinhard Guthke,et al. Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs , 2011, Molecular Systems Biology.
[7] Tomer Shlomi,et al. Computational Design of Auxotrophy-Dependent Microbial Biosensors for Combinatorial Metabolic Engineering Experiments , 2011, PloS one.
[8] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[9] T. Hwa,et al. Interdependence of Cell Growth and Gene Expression: Origins and Consequences , 2010, Science.
[10] U. Alon,et al. Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth. , 2010, Molecular cell.
[11] N. Moran,et al. Genomic changes following host restriction in bacteria. , 2004, Current opinion in genetics & development.
[12] Ming-Chun Lee,et al. Repeated, Selection-Driven Genome Reduction of Accessory Genes in Experimental Populations , 2012, PLoS genetics.
[13] Andrew R. Joyce,et al. Experimental and Computational Assessment of Conditionally Essential Genes in Escherichia coli , 2006, Journal of bacteriology.
[14] S. Eriksson,et al. Bacterial genome size reduction by experimental evolution. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[15] W. Maas,et al. Feedback inhibition of acetylglutamate synthetase by arginine in Escherichia coli. , 1963, Archives of biochemistry and biophysics.
[16] N. Costantino,et al. E. coli genome manipulation by P1 transduction. , 2007, Current protocols in molecular biology.
[17] Hiroyuki Ogata,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..
[18] I-Min A. Chen,et al. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..
[19] Jeffrey E. Barrick,et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli , 2009, Nature.
[20] P. Gajer,et al. The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates , 2008, Journal of bacteriology.
[21] R. Lenski,et al. Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population , 2011, Science.
[22] James J. Davis,et al. Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome , 2011, Proceedings of the National Academy of Sciences.
[23] J. Gibrat,et al. The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[24] Philip Hugenholtz,et al. Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity , 1998, Journal of bacteriology.
[25] N. Moran,et al. Parallel genomic evolution and metabolic interdependence in an ancient symbiosis , 2007, Proceedings of the National Academy of Sciences.
[26] M. Noordewier,et al. Genome Streamlining in a Cosmopolitan Oceanic Bacterium , 2005, Science.
[27] R. Somerville,et al. Feedback regulation in the anthranilate aggregate from wild type and mutant strains of Escherichia coli. , 1973, The Journal of biological chemistry.
[28] Vincent Schächter,et al. A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1 , 2008, Molecular systems biology.
[29] C. Kurland,et al. Reductive evolution of resident genomes. , 1998, Trends in microbiology.
[30] M. Hattori,et al. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS , 2000, Nature.
[31] N. Moran,et al. Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution , 2010, Genome biology and evolution.
[32] S. Zamenhof,et al. Study of Microbial Evolution through Loss of Biosynthetic Functions: Establishment of “Defective” Mutants , 1967, Nature.
[33] J. McCutcheon,et al. An Interdependent Metabolic Patchwork in the Nested Symbiosis of Mealybugs , 2011, Current Biology.
[34] P. François,et al. Comparative genomic hybridization and physiological characterization of environmental isolates indicate that significant (eco-)physiological properties are highly conserved in the species Escherichia coli. , 2007, Microbiology.
[35] Y. Benjamini,et al. Adaptive linear step-up procedures that control the false discovery rate , 2006 .
[36] Eduardo P C Rocha,et al. Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction. , 2007, Genome research.
[37] Hans C. Bernstein,et al. Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity. , 2012, Journal of biotechnology.
[38] R. Lenski,et al. The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss , 2012, mBio.
[39] N. Moran,et al. Microbial Minimalism Genome Reduction in Bacterial Pathogens , 2002, Cell.
[40] E. Kiers,et al. Ecological interactions drive evolutionary loss of traits. , 2012, Ecology letters.
[41] D. Dykhuizen. SELECTION FOR TRYPTOPHAN AUXOTROPHS OF ESCHERICHIA COLI IN GLUCOSE‐LIMITED CHEMOSTATS AS A TEST OF THE ENERGY CONSERVATION HYPOTHESIS OF EVOLUTION , 1978, Evolution; international journal of organic evolution.
[42] D. Ussery,et al. Comparison of 61 Sequenced Escherichia coli Genomes , 2010, Microbial Ecology.
[43] Blaise R. Boles,et al. Self-generated diversity produces "insurance effects" in biofilm communities. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[44] U. Alon,et al. Optimality and evolutionary tuning of the expression level of a protein , 2005, Nature.
[45] H. Mori,et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.
[46] Joshua A. Lerman,et al. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments , 2013, Proceedings of the National Academy of Sciences.
[47] K. Schleifer,et al. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.
[48] I-Min A. Chen,et al. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata , 2011, Nucleic Acids Res..
[49] Joanna Masel,et al. THE POPULATION GENETICS OF PHENOTYPIC DETERIORATION IN EXPERIMENTAL POPULATIONS OF BACILLUS SUBTILIS , 2006, Evolution; international journal of organic evolution.
[50] N. Moran,et al. Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis , 2001, Science.
[51] O. Berg,et al. Selection-Driven Gene Loss in Bacteria , 2012, PLoS genetics.
[52] U. Münster. Concentrations and fluxes of organic carbon substrates in the aquatic environment , 2004, Antonie van Leeuwenhoek.
[53] R. Fleischmann,et al. The Minimal Gene Complement of Mycoplasma genitalium , 1995, Science.
[54] Jaideep P. Sundaram,et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[55] Frédéric Partensky,et al. Accelerated evolution associated with genome reduction in a free-living prokaryote , 2005, Genome Biology.
[56] J. Vanderleyden,et al. Transposon Mutagenesis of Azospirillum brasilense and Azospirillum lipoferum: Physical Analysis of Tn5 and Tn5-Mob Insertion Mutants , 1987, Applied and environmental microbiology.
[57] N. Moran,et al. Genomics and evolution of heritable bacterial symbionts. , 2008, Annual review of genetics.
[58] Peter L. Freddolino,et al. Bacterial Adaptation through Loss of Function , 2013, PLoS genetics.
[59] Stefan Schuster,et al. Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria , 2013, The ISME Journal.
[60] R. Isberg,et al. Experimental Evolution of Legionella pneumophila in Mouse Macrophages Leads to Strains with Altered Determinants of Environmental Survival , 2012, PLoS pathogens.
[61] R. Lenski,et al. Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations , 1991, The American Naturalist.
[62] Peter D. Karp,et al. EcoCyc: a comprehensive database of Escherichia coli biology , 2010, Nucleic Acids Res..
[63] Howard Ochman,et al. The consequences of genetic drift for bacterial genome complexity. , 2009, Genome research.