The minimal genome concept.

Complete genome sequences are becoming available for a large number of diverse species. Quantification of gene content, of gene family expansion, of orthologous gene conservation, as well as their displacement, are now possible - laying the ground for the estimation of the minimal set of proteins sufficient for cellular life. The consensus of computational results suggests a set close to 300 genes. These predictions will be evaluated by engineering of small bacterial genomes.

[1]  T. Traut,et al.  A minimal gene set for cellular life derived by comparison of complete bacterial genomes , 1998 .

[2]  Michael Y. Galperin,et al.  Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea , 1997, Molecular microbiology.

[3]  Ronald W. Davis,et al.  Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. , 1999, Science.

[4]  G. Gonnet,et al.  Exhaustive matching of the entire protein sequence database. , 1992, Science.

[5]  J. Maniloff.  Nannobacteria: size limits and evidence. , 1997, Science.

[6]  ECOLI SODF,et al.  Analogous Enzymes : Independent Inventions in Enzyme Evolution , 1998 .

[7]  Michael Y. Galperin,et al.  A superfamily of metalloenzymes unifies phosphopentomutase and cofactor‐independent phosphoglycerate mutase with alkaline phosphatases and sulfatases , 1998, Protein science : a publication of the Protein Society.

[8]  M. Kates.  Archaebacterial lipids: structure, biosynthesis and function. , 1992, Biochemical Society symposium.

[9]  Nikos Kyrpides,et al.  Universal Protein Families and the Functional Content of the Last Universal Common Ancestor , 1999, Journal of Molecular Evolution.

[10]  P. Bork,et al.  Variation and evolution of the citric-acid cycle: a genomic perspective. , 1999, Trends in microbiology.

[11]  T. Gojobori,et al.  Identification of a ribonuclease H gene in both Mycoplasma genitalium and Mycoplasma pneumoniae by a new method for exhaustive identification of ORFs in the complete genome sequences , 1999, FEBS letters.

[12]  E. Koonin,et al.  Conserved domains in DNA repair proteins and evolution of repair systems. , 1999, Nucleic acids research.

[13]  R. Psenner,et al.  Nannobacteria: size limits and evidence. , 1997, Science.

[14]  M. Itaya,et al.  Fate of unstable Bacillus subtilis subgenome: re‐integration and amplification in the main genome , 1999, FEBS letters.

[15]  Mitsuhiro Itaya,et al.  An estimation of minimal genome size required for life , 1995, FEBS letters.

[16]  Manuel Peitsch,et al.  A genome-based approach for the identification of essential bacterial genes , 1998, Nature Biotechnology.

[17]  A. Godzik,et al.  Fold and function predictions for Mycoplasma genitalium proteins. , 1998, Folding & design.

[18]  D. Söll,et al.  Glu-tRNAGln amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[19]  P. Bork,et al.  Measuring genome evolution. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Detlef D. Leipe,et al.  Did DNA replication evolve twice independently? , 1999, Nucleic acids research.

[21]  M. Levy,et al.  The Prebiotic Synthesis of Modified Purines and Their Potential Role in the RNA World , 1999, Journal of Molecular Evolution.

[22]  M. Levy,et al.  The stability of the RNA bases: implications for the origin of life. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Detlef D. Leipe,et al.  SURVEY AND SUMMARY Did DNA replication evolve twice independently ? , 1999 .

[24]  P. Bork,et al.  Non-orthologous gene displacement. , 1996, Trends in genetics : TIG.

[25]  V. Ramakrishnan,et al.  Ribosomal protein structures: insights into the architecture, machinery and evolution of the ribosome. , 1998, Trends in biochemical sciences.

[26]  J. Heinemann.  Genetic evidence of protein transfer during bacterial conjugation. , 1999, Plasmid.

[27]  M. Tomita,et al.  Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination. , 1998, Nucleic acids research.

[28]  W. Fitch.  Distinguishing homologous from analogous proteins. , 1970, Systematic zoology.

[29]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[30]  S E Brenner,et al.  Distribution of protein folds in the three superkingdoms of life. , 1999, Genome research.

[31]  P. Forterre.  Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins , 1999, Molecular microbiology.

[32]  Yan P. Yuan,et al.  Predicting function: from genes to genomes and back. , 1998, Journal of molecular biology.

[33]  L E Orgel,et al.  The origin of life--a review of facts and speculations. , 1998, Trends in biochemical sciences.

[34]  G. Gonnet,et al.  2 Reading the Palimpsest: Contemporary Biochemical Data and the RNA World , 1993 .

[35]  R. Herrmann,et al.  Mycoplasma pneumoniae and Mycoplasma genitalium: a comparison of two closely related bacterial species. , 1998, Current opinion in microbiology.

[36]  P Bork,et al.  Homology-based fold predictions for Mycoplasma genitalium proteins. , 1998, Journal of molecular biology.

[37]  P. Bork,et al.  Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli , 1996, Current Biology.