Modelling the evolution of the archeal tryptophan synthase

[1]  R. Sterner,et al.  Evolution of multi-enzyme complexes: the case of tryptophan synthase. , 2006, Biochemistry.

[2]  Eric J Alm,et al.  Correction: The Life-Cycle of Operons , 2006, PLoS Genetics.

[3]  S. Gribaldo,et al.  The origin and evolution of Archaea: a state of the art , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[4]  A. Arkin,et al.  The Life-Cycle of Operons , 2006, PLoS genetics.

[5]  Iain M. Wallace,et al.  M-Coffee: combining multiple sequence alignment methods with T-Coffee , 2006, Nucleic acids research.

[6]  B. Snel,et al.  Toward Automatic Reconstruction of a Highly Resolved Tree of Life , 2006, Science.

[7]  R. Sterner,et al.  Catalytic Versatility, Stability, and Evolution of the (βα)8‐Barrel Enzyme‐Fold , 2006 .

[8]  D. Huson,et al.  Application of phylogenetic networks in evolutionary studies. , 2006, Molecular biology and evolution.

[9]  Birte Höcker,et al.  Catalytic versatility, stability, and evolution of the (betaalpha)8-barrel enzyme fold. , 2005, Chemical reviews.

[10]  Kim Henrick,et al.  Detection of Protein Assemblies in Crystals , 2005, CompLife.

[11]  J. Reeve,et al.  Regulation of Tryptophan Operon Expression in the Archaeon Methanothermobacter thermautotrophicus , 2005, Journal of bacteriology.

[12]  T. Tsukihara,et al.  Conformational changes in the tryptophan synthase from a hyperthermophile upon α2β2 complex formation : Crystal structure of the complex , 2005 .

[13]  C. Yanofsky,et al.  New insights into regulation of the tryptophan biosynthetic operon in Gram-positive bacteria. , 2005, Trends in genetics : TIG.

[14]  Michael A Savageau,et al.  Evidence of selection for low cognate amino acid bias in amino acid biosynthetic enzymes , 2005, Molecular microbiology.

[15]  Janet M. Thornton,et al.  PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids , 2004, Nucleic Acids Res..

[16]  Christian von Mering,et al.  STRING: known and predicted protein–protein associations, integrated and transferred across organisms , 2004, Nucleic Acids Res..

[17]  C. Yanofsky,et al.  The different roles of tryptophan transfer RNA in regulating trp operon expression in E. coli versus B. subtilis. , 2004, Trends in genetics : TIG.

[18]  Mikhail S. Gelfand,et al.  SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins , 2004, Nucleic Acids Res..

[19]  M. Ota,et al.  The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors. , 2004, European journal of biochemistry.

[20]  C. Bonner,et al.  Inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy , 2004, BMC Biology.

[21]  Rainer Merkl,et al.  SIGI: score-based identification of genomic islands , 2004, BMC Bioinformatics.

[22]  J A Eisen,et al.  Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments , 2003, Science.

[23]  M. Giulio.  The Universal Ancestor and the Ancestor of Bacteria Were Hyperthermophiles , 2003, Journal of Molecular Evolution.

[24]  Q. Teng,et al.  Detection of Open and Closed Conformations of Tryptophan Synthase by 15N-Heteronuclear Single-Quantum Coherence Nuclear Magnetic Resonance of Bound 1-15N-L-Tryptophan* , 2003, Journal of Biological Chemistry.

[25]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[26]  Nemat O. Keyhani,et al.  Ancient Origin of the Tryptophan Operon and the Dynamics of Evolutionary Change , 2003, Microbiology and Molecular Biology Reviews.

[27]  E. Koonin,et al.  Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ , 2003, Genome Biology.

[28]  K. Stetter,et al.  The phylum Nanoarchaeota: present knowledge and future perspectives of a unique form of life. , 2003, Research in microbiology.

[29]  C. Yanofsky.  Using Studies on Tryptophan Metabolism to Answer Basic Biological Questions , 2003, The Journal of Biological Chemistry.

[30]  R. Sterner,et al.  A novel tryptophan synthase beta-subunit from the hyperthermophile Thermotoga maritima. Quaternary structure, steady-state kinetics, and putative physiological role. , 2002, The Journal of biological chemistry.

[31]  R. Sterner,et al.  A Novel Tryptophan Synthase β-Subunit from the HyperthermophileThermotoga maritima , 2002, Journal of Biological Chemistry.

[32]  C. Forst,et al.  Significance of two distinct types of tryptophan synthase beta chain in Bacteria, Archaea and higher plants , 2001, Genome Biology.

[33]  E. Koonin,et al.  Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins , 2001, Genome Biology.

[34]  U. Banik,et al.  Investigation of allosteric linkages in the regulation of tryptophan synthase: the roles of salt bridges and monovalent cations probed by site-directed mutation, optical spectroscopy, and kinetics. , 2001, Biochemistry.

[35]  Dmitrij Frishman,et al.  The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum , 2000, Nature.

[36]  H. Atomi,et al.  The tryptophan biosynthesis gene cluster trpCDEGFBA from Pyrococcus kodakaraensis KOD1 is regulated at the transcriptional level and expressed as a single mRNA , 1999, Molecular and General Genetics MGG.

[37]  I. Schlichting,et al.  Crystal structure of wild-type tryptophan synthase complexed with the natural substrate indole-3-glycerol phosphate. , 1999, Biochemistry.

[38]  E. W. Miles,et al.  The Molecular Basis of Substrate Channeling* , 1999, The Journal of Biological Chemistry.

[39]  R. Overbeek,et al.  The use of gene clusters to infer functional coupling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Radhey S. Gupta.  Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes , 1998, Microbiology and Molecular Biology Reviews.

[41]  I. Schlichting,et al.  Loop closure and intersubunit communication in tryptophan synthase. , 1998, Biochemistry.

[42]  James R. Brown,et al.  Archaea and the prokaryote-to-eukaryote transition. , 1997, Microbiology and molecular biology reviews : MMBR.

[43]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[44]  O Gascuel,et al.  BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. , 1997, Molecular biology and evolution.

[45]  U. Jenal,et al.  Regulation of tryptophan biosynthesis in Methanobacterium thermoautotrophicum Marburg , 1994, Journal of bacteriology.

[46]  William R. Taylor,et al.  The rapid generation of mutation data matrices from protein sequences , 1992, Comput. Appl. Biosci..

[47]  M Wilmanns,et al.  Structural conservation in parallel beta/alpha-barrel enzymes that catalyze three sequential reactions in the pathway of tryptophan biosynthesis. , 1991, Biochemistry.

[48]  A. Lane,et al.  Reciprocal communication between the lyase and synthase active sites of the tryptophan synthase bienzyme complex. , 1991, Biochemistry.

[49]  C. Sander,et al.  Database of homology‐derived protein structures and the structural meaning of sequence alignment , 1991, Proteins.

[50]  M. Roy,et al.  The tryptophan synthase bienzyme complex transfers indole between the alpha- and beta-sites via a 25-30 A long tunnel. , 1990, Biochemistry.

[51]  C. Yanofsky.  Attenuation in the control of expression of bacterial operons , 1981, Nature.

[52]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.

[53]  Rainer Merkl,et al.  AMIGOS: A Method for the Inspection of Genomic Organisation or Structure and its Application to Characterise Conserved Gene Arrangements , 2006, Silico Biol..

[54]  F. Kondrashov.  In search of the limits of evolution , 2005, Nature Genetics.

[55]  B. Snel,et al.  Genomes in flux: the evolution of archaeal and proteobacterial gene content. , 2002, Genome research.

[56]  E. W. Miles.  Tryptophan synthase: a multienzyme complex with an intramolecular tunnel. , 2001, Chemical record.

[57]  C. Yanofsky.  Advancing our knowledge in biochemistry, genetics, and microbiology through studies on tryptophan metabolism. , 2001, Annual review of biochemistry.

[58]  Geoffrey J. Barton,et al.  JPred : a consensus secondary structure prediction server , 1999 .

[59]  J. L. Smith,et al.  Enzymes utilizing glutamine as an amide donor. , 1998, Advances in enzymology and related areas of molecular biology.

[60]  R. Bentley,et al.  The shikimate pathway--a metabolic tree with many branches. , 1990, Critical reviews in biochemistry and molecular biology.

[61]  R. Jensen.  Enzyme recruitment in evolution of new function. , 1976, Annual review of microbiology.