Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics.

The availability of complete genome sequences of cellular life forms creates the opportunity to explore the functional content of the genomes and evolutionary relationships between them at a new qualitative level. With the advent of these sequences, the construction of a minimal gene set sufficient for sustaining cellular life and reconstruction of the genome of the last common ancestor of bacteria, eukaryotes, and archaea become realistic, albeit challenging, research projects. A version of the minimal gene set for modern-type cellular life derived by comparative analysis of two bacterial genomes, those of Haemophilus influenzae and Mycoplasma genitalium, consists of approximately 250 genes. A comparison of the protein sequences encoded in these genes with those of the proteins encoded in the complete yeast genome suggests that the last common ancestor of all extant life might have had an RNA genome.

[1]  Mitchell L Sogin.  Early evolution and the origin of eukaryotes , 1992, Current Biology.

[2]  J C Venter.  Response: More Haemophilus and Mycoplasma Genes , 1996, Science.

[3]  R. Jaussi.  Homologous nuclear-encoded mitochondrial and cytosolic isoproteins. A review of structure, biosynthesis and genes. , 1995, European journal of biochemistry.

[4]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[5]  Arcady R. Mushegian,et al.  Sequencing and analysis of bacterial genomes , 1996, Current Biology.

[6]  Peer Bork,et al.  Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology , 1995, Molecular microbiology.

[7]  Eugene V. Koonin,et al.  [18] Protein sequence comparison at genome scale , 1996 .

[8]  C. Sander,et al.  Challenging times for bioinformatics , 1995, Nature.

[9]  E V Koonin,et al.  Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[10]  W. Doolittle,et al.  Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[11]  E V Koonin,et al.  Gene order is not conserved in bacterial evolution. , 1996, Trends in genetics : TIG.

[12]  R. Overbeek,et al.  The winds of (evolutionary) change: breathing new life into microbiology , 1994 .

[13]  C Sander,et al.  Novel protein families in archaean genomes. , 1995, Nucleic acids research.

[14]  E. Koonin,et al.  A minimal gene set for cellular life derived by comparison of complete bacterial genomes. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

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

[16]  R. Fleischmann,et al.  The Minimal Gene Complement of Mycoplasma genitalium , 1995, Science.

[17]  C. Sander,et al.  Yeast chromosome III: new gene functions. , 1994, The EMBO journal.

[18]  W. Doolittle,et al.  Archaebacterial genomes: eubacterial form and eukaryotic content. , 1994, Current opinion in genetics & development.

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

[20]  R. Jaussi,et al.  Homologous nuclear-encoded mitochondrial and cytosolic isoproteins. A review of structure, biosynthesis and genes. , 1995, European journal of biochemistry.

[21]  R. Doolittle.  The origins and evolution of eukaryotic proteins. , 1995, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[22]  George M. Church,et al.  Large scale bacterial gene discovery by similarity search , 1994, Nature Genetics.

[23]  J Brosius,et al.  More haemophilus and Mycoplasma genes. , 1996, Science.

[24]  S A Benner,et al.  Modern metabolism as a palimpsest of the RNA world. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[25]  R F Doolittle,et al.  Convergent evolution: the need to be explicit. , 1994, Trends in biochemical sciences.

[26]  R. Doolittle,et al.  Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock , 1996, Science.

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

[28]  B. Dujon.  The yeast genome project: what did we learn? , 1996, Trends in genetics : TIG.

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