Main Factors Shaping Amino Acid Usage Across Evolution

[1]  H. Musto How Many Factors Influence Genomic GC Content Among Prokaryotes? , 2022, Journal of Molecular Evolution.

[2]  D. Niu,et al.  A positive correlation between GC content and growth temperature in prokaryotes , 2022, bioRxiv.

[3]  H. Musto,et al.  Codon Usage Bias: An Endless Tale , 2021, Journal of Molecular Evolution.

[4]  H. Musto,et al.  Nucleotide Composition and Codon Usage Across Viruses and Their Respective Hosts , 2021, Frontiers in Microbiology.

[5]  I. Roterman,et al.  Solubility and Aggregation of Selected Proteins Interpreted on the Basis of Hydrophobicity Distribution , 2021, International journal of molecular sciences.

[6]  R. Singer,et al.  Intracellular mRNA transport and localized translation , 2021, Nature Reviews Molecular Cell Biology.

[7]  I. Roterman,et al.  Model of Environmental Membrane Field for Transmembrane Proteins , 2021, International journal of molecular sciences.

[8]  Amish J. Patel,et al.  Identifying hydrophobic protein patches to inform protein interaction interfaces , 2021, Proceedings of the National Academy of Sciences.

[9]  M. Meyer Revisiting the Relationships Between Genomic G + C Content, RNA Secondary Structures, and Optimal Growth Temperature , 2020, Journal of Molecular Evolution.

[10]  M. Davies,et al.  Detection, identification, and quantification of oxidative protein modifications , 2019, The Journal of Biological Chemistry.

[11]  D. Barrick,et al.  A second backbone: the contribution of a buried asparagine ladder to the global and local stability of a leucine-rich repeat protein. , 2019, Biochemistry.

[12]  L. Hurst A century of bias in genetics and evolution , 2019, Heredity.

[13]  G. Bernardi,et al.  The short-sequence design of DNA and its involvement in the 3-D structure of the genome , 2018, Scientific Reports.

[14]  Jeffrey A. Hussmann,et al.  Ribosome Profiling: Global Views of Translation. , 2018, Cold Spring Harbor perspectives in biology.

[15]  A. Lazcano,et al.  Evolutionary convergence in the biosyntheses of the imidazole moieties of histidine and purines , 2018, PloS one.

[16]  Pablo Mier,et al.  Proteome-wide comparison between the amino acid composition of domains and linkers , 2018, BMC Research Notes.

[17]  Sergey V. Venev,et al.  Thermophilic Adaptation in Prokaryotes Is Constrained by Metabolic Costs of Proteostasis , 2017, Molecular biology and evolution.

[18]  W. Hoff,et al.  In defence of the three-domains of life paradigm , 2017, BMC Evolutionary Biology.

[19]  R. Goldstein,et al.  Sequence entropy of folding and the absolute rate of amino acid substitutions , 2017, Nature Ecology & Evolution.

[20]  Frédéric Barras,et al.  Oxidative stress, protein damage and repair in bacteria , 2017, Nature Reviews Microbiology.

[21]  H. Musto,et al.  The Isochores as a Fundamental Level of Genome Structure and Organization: A General Overview , 2017, Journal of Molecular Evolution.

[22]  Kamel Jabbari,et al.  An Isochore Framework Underlies Chromatin Architecture , 2016, bioRxiv.

[23]  Patrick Forterre,et al.  The universal tree of life: an update , 2015, Front. Microbiol..

[24]  E. Koonin Carl Woese's vision of cellular evolution and the domains of life , 2014, RNA biology.

[25]  L. Diana,et al.  Trends in amino acid usage across the class Mollicutes , 2014, Journal of biomolecular structure & dynamics.

[26]  D. Tieleman,et al.  Hydrophobicity scales: a thermodynamic looking glass into lipid-protein interactions. , 2011, Trends in biochemical sciences.

[27]  V. Gladyshev,et al.  Cysteine function governs its conservation and degeneration and restricts its utilization on protein surfaces. , 2010, Journal of molecular biology.

[28]  Tapio Salakoski,et al.  Accuracy of protein hydropathy predictions , 2010, Int. J. Data Min. Bioinform..

[29]  Theodore J. Perkins,et al.  A General Model of Codon Bias Due to GC Mutational Bias , 2010, PloS one.

[30]  Guang-Zhong Wang,et al.  Amino acid composition in endothermic vertebrates is biased in the same direction as in thermophilic prokaryotes , 2010, BMC Evolutionary Biology.

[31]  Laurent Duret,et al.  Biased gene conversion and the evolution of mammalian genomic landscapes. , 2009, Annual review of genomics and human genetics.

[32]  Xuhua Xia,et al.  GC skew in protein-coding genes between the leading and lagging strands in bacterial genomes: new substitution models incorporating strand bias. , 2008, Journal of theoretical biology.

[33]  Michail Yu. Lobanov,et al.  Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms , 2007, Bioinform..

[34]  Hugo Naya,et al.  Trends of Amino Acid Usage in the Proteins from the Human Genome , 2007, Journal of biomolecular structure & dynamics.

[35]  H. Ellegren Molecular evolutionary genomics of birds , 2007, Cytogenetic and Genome Research.

[36]  G. Bernardi The neoselectionist theory of genome evolution , 2007, Proceedings of the National Academy of Sciences.

[37]  Richard Wolfenden,et al.  Experimental Measures of Amino Acid Hydrophobicity and the Topology of Transmembrane and Globular Proteins , 2007, The Journal of general physiology.

[38]  Laurent Duret,et al.  A new perspective on isochore evolution. , 2006, Gene.

[39]  S. Trivedi,et al.  Protein thermostability in Archaea and Eubacteria. , 2006, Genetics and molecular research : GMR.

[40]  E. Yeramian,et al.  Evolution of proteomes: fundamental signatures and global trends in amino acid compositions , 2006, BMC Genomics.

[41]  G. Bernardi,et al.  Genomic GC level, optimal growth temperature, and genome size in prokaryotes. , 2006, Biochemical and biophysical research communications.

[42]  Igor N. Berezovsky,et al.  Protein and DNA Sequence Determinants of Thermophilic Adaptation , 2006, PLoS Comput. Biol..

[43]  Giorgio Bernardi,et al.  An isochore map of human chromosomes. , 2006, Genome research.

[44]  Hugo Naya,et al.  Genomic GC content prediction in prokaryotes from a sample of genes. , 2005, Gene.

[45]  G. Bernardi,et al.  The correlation between genomic G+C and optimal growth temperature of prokaryotes is robust: a reply to Marashi and Ghalanbor. , 2005, Biochemical and biophysical research communications.

[46]  Hugo Naya,et al.  Correspondence analysis of amino acid usage within the family Bacillaceae. , 2004, Biochemical and biophysical research communications.

[47]  S. Marashi,et al.  Correlations between genomic GC levels and optimal growth temperatures are not 'robust'. , 2004, Biochemical and biophysical research communications.

[48]  G. Singer,et al.  Genomic and proteomic adaptations to growth at high temperature , 2004, Genome Biology.

[49]  G. Bernardi,et al.  Correlations between genomic GC levels and optimal growth temperatures in prokaryotes , 2004, FEBS letters.

[50]  E. Nevo,et al.  Adaptive role of increased frequency of polypurine tracts in mRNA sequences of thermophilic prokaryotes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[51]  M. Bonato,et al.  Preferred amino acids and thermostability. , 2003, Genetics and molecular research : GMR.

[52]  G. Singer,et al.  Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. , 2003, Gene.

[53]  B. Silverman,et al.  Hydrophobicity of transmembrane proteins: Spatially profiling the distribution , 2003, Protein science : a publication of the Protein Society.

[54]  Hugo Naya,et al.  Aerobiosis Increases the Genomic Guanine Plus Cytosine Content (GC%) in Prokaryotes , 2002, Journal of Molecular Evolution.

[55]  Takashi Gojobori,et al.  Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[56]  A. R. Merchant,et al.  High guanine–cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes , 2001, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[57]  H. Musto,et al.  Trends of amino acid usage in the proteins from the unicellular parasite Giardia lamblia. , 2000, Biochemical and biophysical research communications.

[58]  G. Singer,et al.  Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. , 2000, Molecular biology and evolution.

[59]  H. Romero,et al.  Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. , 2000, Nucleic acids research.

[60]  A. Szilágyi,et al.  Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. , 2000, Structure.

[61]  G Bernardi,et al.  Isochores and the evolutionary genomics of vertebrates. , 2000, Gene.

[62]  G Bernardi,et al.  The correlation of protein hydropathy with the base composition of coding sequences. , 1999, Gene.

[63]  G. Bernardi,et al.  Compositional Correlations in the Chicken Genome , 1999, Journal of Molecular Evolution.

[64]  A. Eyre-Walker,et al.  Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA. , 1999, Genetics.

[65]  A. Danchin,et al.  Universal replication biases in bacteria , 1999, Molecular microbiology.

[66]  M. Nishizawa,et al.  Biased Usages of Arginines and Lysines in Proteins Are Correlated with Local-Scale Fluctuations of the G + C Content of DNA Sequences , 1998, Journal of Molecular Evolution.

[67]  J O McInerney,et al.  Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[68]  L. Hurst,et al.  The Genetic Code Is One in a Million , 1998, Journal of Molecular Evolution.

[69]  E. Mayr Two empires or three? , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[70]  J. Lobry,et al.  Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species. , 1997, Gene.

[71]  J. Oliver,et al.  A relationship between GC content and coding-sequence length , 1996, Journal of Molecular Evolution.

[72]  G Bernardi,et al.  Compositional properties of nuclear genes from Plasmodium falciparum. , 1995, Gene.

[73]  M. Williamson,et al.  The structure and function of proline-rich regions in proteins. , 1994, The Biochemical journal.

[74]  Giorgio Bernardi,et al.  Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins , 1991, Journal of Molecular Evolution.

[75]  O. Kandler,et al.  Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[76]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[77]  C R Woese,et al.  Evolution of the genetic code , 1973, The Science of Nature.

[78]  N. Sueoka,et al.  CORRELATION BETWEEN BASE COMPOSITION OF DEOXYRIBONUCLEIC ACID AND AMINO ACID COMPOSITION OF PROTEIN. , 1961, Proceedings of the National Academy of Sciences of the United States of America.

[79]  Bijoyita Roy Effects of mRNA Modifications on Translation: An Overview. , 2021, Methods in molecular biology.

[80]  Nikola Štambuk,et al.  Determining amino acid scores of the genetic code table: Complementarity, structure, function and evolution , 2020, Biosyst..

[81]  I. Roterman,et al.  Secondary and Supersecondary Structure of Proteins in Light of the Structure of Hydrophobic Cores. , 2019, Methods in molecular biology.

[82]  A. Link,et al.  Identification and quantification of protein posttranslational modifications. , 2009, Methods in Enzymology.

[83]  D. Gianola,et al.  Inferring parameters shaping amino acid usage in prokaryotic genomes via Bayesian MCMC methods. , 2006, Molecular biology and evolution.

[84]  D. Forsdyke,et al.  Amino Acids as Placeholders , 2005 .

[85]  G. Bernardi,et al.  Codon usage and genome composition , 2005, Journal of Molecular Evolution.

[86]  D. Forsdyke,et al.  Amino acids as placeholders: base-composition pressures on protein length in malaria parasites and prokaryotes. , 2005, Applied Bioinformatics.

[87]  G. Bernardi,et al.  Compositional constraints and genome evolution , 2005, Journal of Molecular Evolution.

[88]  Laurence D. Hurst,et al.  A Quantitative Measure of Error Minimization in the Genetic Code , 1999, Journal of Molecular Evolution.

[89]  J. Lobry,et al.  A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. , 1996, Biochimie.

[90]  G. Bernardi,et al.  The vertebrate genome: isochores and evolution. , 1993, Molecular biology and evolution.

[91]  S. Osawa,et al.  The guanine and cytosine content of genomic DNA and bacterial evolution. , 1987, Proceedings of the National Academy of Sciences of the United States of America.