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11 - Horizontal gene transfer and bacterial genomic legacies

Published online by Cambridge University Press:  06 August 2009

By
James R. Brown
Edited by
Peter Mullany
James R. Brown
Affiliation:
Bioinformatics Division, Genetics Research
Peter Mullany
Affiliation:
University College London
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Summary

Molecular biologists have long used viruses, plasmids, transposons, and other “vectors” as tools to directly manipulate the genetic makeup of experimental organisms. In nature, these tool vectors originated in species, usually bacteria, as facilitators of horizontal (also known as lateral) gene transfer (HGT). In contrast to vertical inheritance, where the transmission of genetic material occurs vertically from parent to offspring, HGT refers to the horizontal exchange of genes between distantly related strains and species. As described in this volume, there are many examples of HGT between species of bacteria, such as that mediated by plasmids and phages, which bear genes responsible for pathogenicity and antibiotic resistance. HGT is also known to occur in eukaryotes; for example, DNA transposons have been suggested as being horizontally transferred between different species of the fruitfly Drosophila (Bushman, 2002). These are examples of HGT on a relatively recent evolutionary timescale. However, HGT might have had a pivotal evolutionary role in more ancient times. Comparative analyses of molecular data that are exploding from genome sequencing projects indicates that HGT might have been the main driving force behind the evolution of cellular life (Brown, 2003).

The reason for believing the occurrence of ancient HGT is relatively simple. In an evolutionary context, genes are not found where they are expected to be. The most fundamental subdivisions of living organisms are the three urkingdoms or domains of life: the Archea (traditionally called “archaebacteria”), Bacteria (traditionally called “eubacteria”), and Eucarya (interchangeable here and elsewhere with the term “eukaryote”; Woese, Kandler, and Wheelis, 1990).

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The Dynamic Bacterial Genome , pp. 385 - 414
Publisher: Cambridge University Press
Print publication year: 2005

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References

Altschul, S. F.. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402CrossRefGoogle ScholarPubMed
Andersson, S. G.. (1998) The genome sequence of Rickettsia prowzekii and the origin of mitochondria. Nature 396, 133–140CrossRefGoogle ScholarPubMed
Aravind, L., Tatusov, R. L., Wolf, Y. I., Walker, D. R., and Koonin, E. V. (1998) Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genetics 14, 442–444CrossRefGoogle ScholarPubMed
Baldauf, S. L., Palmer, J. D., and Doolittle, W. F. (1996) The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc. Natl. Acad. Sci. U S A 93, 7749–7754CrossRefGoogle ScholarPubMed
Baldauf, S. L., Roger, A. J., Wenk-Siefert, I., and Doolittle, W. F. (2001) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290, 972–977CrossRefGoogle Scholar
Benachenhou-Lahfa, N., Forterre, P., and Labedan, B. (1993) Evolution of glutamate dehydrogenase genes: Evidence for paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life. J. Mol. Evol. 36, 335–346CrossRefGoogle ScholarPubMed
Berg, O. G., and Kurland, C. G. (2000) Why mitochondrial genes are most often found in nuclei. Mol. Biol. Evol. 17, 951–961CrossRefGoogle ScholarPubMed
Blanchard, J. L., and Lynch, M. (2000) Organellar genes: Why do they end up in the nucleus?Trends Genetics 16, 315–320CrossRefGoogle ScholarPubMed
Boucher, Y., and Doolittle, W. F. (2000) The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways. Mol Microbiol 37, 703–716CrossRefGoogle ScholarPubMed
Brinkman, F. S. L.. (2002) Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, Cyanobacteria, and the chloroplast. Genome Res. 12, 1159–1167CrossRefGoogle ScholarPubMed
Brinkman, H., and Philippe, H. (1999) Archaea sister group of bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol. Biol. Evol. 16, 817–825CrossRefGoogle Scholar
Brochier, C., Philippe, H., and Moreira, D. (2000) The evolutionary history of ribosomal protein RpS14: Horizontal gene transfer at the heart of the ribosome. Trends Genetics 16, 529–533CrossRefGoogle ScholarPubMed
Brown, J. R. (2001) Genomic and phylogenetic perspectives on the evolution of prokaryotes. Syst. Biol. 50, 497–512CrossRefGoogle ScholarPubMed
Brown, J. R. (2003) Ancient horizontal gene transfer. Nat. Rev. Genetics 4, 121–132CrossRefGoogle ScholarPubMed
Brown, J. R., and Doolittle, W. F. (1995) Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc. Natl. Acad. Sci. U S A 92, 2441–2445CrossRefGoogle ScholarPubMed
Brown, J. R., and Doolittle, W. F. (1997) Archaea and the prokaryote to eukaryote transition. Microbiol. Mol. Biol. Rev. 61, 456–502Google ScholarPubMed
Brown, J. R., and Doolittle, W. F. (1999) Gene descent, duplication, and horizontal transfer in the evolution of glutamyl- and glutaminyl-tRNA synthetases. J. Mol. Evol. 49, 485–495CrossRefGoogle ScholarPubMed
Brown, J. R., Douady, C. J., Italia, M. J., Marshall, W. E., and Stanhope, M. J. (2001) Universal trees based on large combined protein sequence datasets. Nature Genetics 28, 281–285CrossRefGoogle Scholar
Brown, J. R., Gentry, D. R., Becker, J. A., Ingraham, K., Holmes, D. J., and Stanhope, M. J. (2003) Horizontal transfer of drug resistant aminoacyl-tRNA synthetases of anthrax and Gram-positive pathogens. EMBO Rep. 4, 692–698CrossRefGoogle ScholarPubMed
Brown, J. R., Masuchi, Y., Robb, F. T., and Doolittle, W. F. (1994) Evolutionary relationships of bacterial and archaeal glutamine synthetase genes. J. Mol. Evol. 38, 566–576CrossRefGoogle ScholarPubMed
Brown, J. R., Zhang, J., and Hodgson, J. E. (1998) A bacterial antibiotic resistance gene with eukaryotic origins. Curr. Biol. 8, R365–R367CrossRefGoogle ScholarPubMed
Bushman, F. (2002) Lateral DNA transfer. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory PressGoogle Scholar
Canback, B., Andersson, S. G. E., and Kurland, C. G. (2002) The global phylogeny of glycolytic enzymes. Proc. Natl. Acad. Sci. U S A 99, 6097–6102CrossRefGoogle ScholarPubMed
Cavalier-Smith, T. (1993) Kingdom protozoa and its 18 phyla. Microbiol. Rev. 57, 953–994Google ScholarPubMed
Chihade, J., Brown, J. R., Schimmel, P., and Ribas de Pouplana, L. (2000) Origin of mitochondria in relation to evolutionary history of eukaryotic alanyl-tRNA synthetase. Proc. Natl. Acad. Sci. U S A 97, 12153–12157CrossRefGoogle ScholarPubMed
Clark, C. G., and Roger, A. J. (1995) Direct evidence for secondary loss of mitochondria in Entamoeba histolytica. Proc. Natl. Acad. Sci. U S A 92, 6518–6521CrossRefGoogle ScholarPubMed
Courvalin, P., Goussard, S., and Grillot-Courvalin, C. (1995) Gene transfer from bacteria to mammalian cells. C. R. Acad. Sci. Paris, Life Sciences 318, 1207–1212Google ScholarPubMed
Dehal, P.. (2002) The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science 298, 2157–2167CrossRefGoogle ScholarPubMed
Deppenmeier, U.. (2002) The genome of Methanosacrina mazei: Evidence for lateral gene transfer between bacteria and archaea. J. Mol. Microbiol. Biotechnol. 4, 453–461Google ScholarPubMed
Doolittle, R. F., Feng, D. F., Anderson, K. L., and Alberro, M. R. (1990) A naturally occurring horizontal gene transfer from a eukaryote to prokaryote. J. Mol. Evol. 31, 383–388CrossRefGoogle Scholar
Doolittle, W. F. (1998) You are what you eat: A gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genetics 14, 307–311CrossRefGoogle ScholarPubMed
Doolittle, W. F. (1999a) Lateral gene transfer, genome surveys and the phylogeny of prokaryotes. Technical Comments. Science 286, 1443aGoogle Scholar
Doolittle, W. F. (1999b) Phylogenetic classification and the universal tree. Science 284, 2124–2128CrossRefGoogle Scholar
Dröge, M., Pühler, A., and Selbitschka, W. (1998) Horizontal gene transfer as a biosafety issue: A natural phenomenon of public concern. J. Biotechnol. 64, 75–90CrossRefGoogle ScholarPubMed
Eisen, J. A. (2000) Horizontal gene transfer among microbial genomes: New insights from complete genome analysis. Curr. Opin. Genetics Dev. 10, 606–611CrossRefGoogle ScholarPubMed
Faguy, D. M., and Doolittle, W. F. (2000) Horizontal transfer of catalase-peroxidase genes between Archaea and pathogenic bacteria. Trends Genetics 16, 196–197CrossRefGoogle ScholarPubMed
Felmingham, D., and Washington, J. (1999) Trends in the antimicrobial suspectibility of bacterial respiratory tract pathogens — findings of the Alexander Project 1992–1996. J. Chemother. 11, 5–21CrossRefGoogle Scholar
Felsenstein, J. (1993) PHYLIP (Phylogeny Inference Package) version 3.57c. Department of Genetics, University of Washington, Seattle. Available at: http://evolution.genetics.washington.edu/phylip.html
Feng, D.-F., Cho, G., and Doolittle, W. F. (1997) Determining divergence times with a protein clock: update and reevaluation. Proc. Natl. Acad. Sci. U S A 94, 13028–13033CrossRefGoogle ScholarPubMed
Fitz-Gibbon, S. T., and House, C. H. (1999) Whole genome-based phylogenetic analysis of free-living organisms. Nucleic Acids Res. 27, 4218–4222CrossRefGoogle Scholar
Fleischmann, R. D.. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512CrossRefGoogle ScholarPubMed
Forterre, P., Bouthier de la Tour, C., Philippe, H., and Duguet, M. (2000) Reverse gyrase from thermophiles: Probable transfer of a thermoadaptation trait from Archaea to Bacteria. Trends Genetics 16, 152–154CrossRefGoogle Scholar
Forterre, P., and Philippe, H. (1999) Where is the root of the universal tree of life?BioEssays 21, 871–8793.0.CO;2-Q>CrossRefGoogle ScholarPubMed
Fox, G. E.. (1977) Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proc. Natl. Acad. Sci. U S A 74, 4537–4541CrossRefGoogle ScholarPubMed
Garcia-Vallvé, S., Romeu, A., and Palau, J. (2000) Horizontal gene transfer in bacterial and archaea complete genomes. Genome Res. 10, 1719–1725CrossRefGoogle ScholarPubMed
Gentry, D. R., Ingraham, K. A., Stanhope, M. J., Rittenhouse, S., Jarvest, R. L., O'Hanlon, P. J., Brown, J. R.. (2003) Variable sensitivity to bacterial methionyl-tRNA synthetase inhibitors reveals sub populations of Streptococcus pneumoniae with two distinct methionyl tRNA synthetase genes. Antimicrob. Agents Chemother. 47, 1784–1789CrossRefGoogle Scholar
Germot, A., Philippe, H., and Guyader, H. (1996) Presence of a mitochondrial-type 70-kDa heat shock protein in Trichomonas vaginalis suggests a very early mitochondrial endosymbiosis in eukaryotes. Proc. Natl. Acad. Sci. U S A 93, 14614–14617CrossRefGoogle ScholarPubMed
Gogarten, J. P.. (1989) Evolution of the vacuolar H+-ATPase: Implications for the origin of eukaryotes. Proc. Natl. Acad. Sci. U S A 86, 6661–6665CrossRefGoogle ScholarPubMed
Golding, G. B., and Gupta, R. S. (1995) Protein-based phylogenies support a chimeric origin for the eukaryotic genome. Mol. Evol. Biol. 12, 1–6CrossRefGoogle ScholarPubMed
Graham, D. E., Overbeek, R., Olsen, G. J., and Woese, C. R. (2000) An archaeal genomic signature. Proc. Natl. Acad. Sci. U S A 97, 3304–3308CrossRefGoogle ScholarPubMed
Grauer, D., and Li, W. H. (2000) Fundamentals of molecular evolution, 2nd ed. Sunderland, MA: Sinauer AssociatesGoogle Scholar
Gribaldo, S., Lumia, V., Creti, R., Conway de Macario, E., Sanangelantoni, A., and Cammarano, P. (1999) Discontinuous occurrence of the hsp70 (dnaK) gene among Archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein. J Bacteriol 181, 434–443Google ScholarPubMed
Gupta, R. H. (1998) Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria and eukaryotes. Microbiol. Mol. Biol. Rev. 62, 1435–1491Google ScholarPubMed
Gupta, R. S., and Golding, G. B. (1996) The origin of the eukaryotic cell. Trends Biochem. Sci. 21, 166–171CrossRefGoogle ScholarPubMed
Hansmann, S., and Martin, W. (2000) Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: Influence of excluding poorly alignable sites from analysis. Int. J. Syst. Evol. Microbiol. 50, 1655–1663CrossRefGoogle Scholar
Hartman, H., and Fedorov, A. (2002) The origin of the eukaryotic cell: A genomic investigation. Proc. Natl. Acad. Sci. U S A 99, 1420–1425CrossRefGoogle ScholarPubMed
Hashimoto, T., Sánchez, L. B., Shirakura, T., Müller, M., and Hasegawa, M. (1998) Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny. Proc. Natl. Acad. Sci. U S A 95, 6860–6865CrossRefGoogle ScholarPubMed
Henze, K. A., Badr, A., Wettern, M., Cerff, R., and Martin, W. (1995) A nuclear gene of eubacterial origin in Euglena gracilis reflects cryptic endosymbioses during protist evolution. Proc. Natl. Acad. Sci. U S A 92, 9122–9126CrossRefGoogle ScholarPubMed
Hilario, E., and Gogarten, J. P. (1993) Horizontal transfer of ATPase genes — the tree of life becomes the net of life. BioSystems 31, 111–119CrossRefGoogle ScholarPubMed
Horiike, T., Hamada, K., Kanaya, S., and Shinozawa, T. (2002) Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis. Nature Cell Biol. 3, 210–214CrossRefGoogle Scholar
Horner, D. S., Heil, B., Happe, T., and Embley, T. M. (2002) Iron hydrogenases — ancient enzymes in modern eukaryotes. Trends Biochem. Sci. 27, 148–153CrossRefGoogle ScholarPubMed
Horner, D. S., Hirt, R. P., and Embley, T. M. (1999) A single eubacterial origin of eukaryotic pyruvate:ferredoxin oxidoreductase genes: Implications for the evolution of anaerobic eukaryotes. Mol. Biol. Evol. 16, 1280–1291CrossRefGoogle ScholarPubMed
Huang, P., and Oliff, A. (2001) Signaling pathways in apoptosis as potential targets for cancer therapy. Trend Cell Biol. 11, 343–348CrossRefGoogle ScholarPubMed
Huber, H.. (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63–67CrossRefGoogle ScholarPubMed
Huynen, M., Snel, B., and Bork, P. (1999) Lateral gene transfer, genome surveys and the phylogeny of prokaryotes. Technical Comments. Science 286, 1443aCrossRefGoogle Scholar
International Human Genome Sequencing Consortium. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860–892CrossRef
Iwabe, N., Kuma, K.-I., Hasegawa, M., Osawa, S., and Miyata, T. (1989) Evolutionary relationship of Archaea, Bacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. U S A 86, 9355–9359CrossRefGoogle ScholarPubMed
Jain, R., Rivera, M. C., and Lake, J. A. (1999) Horizontal gene transfer among genomes: The complexity hypothesis. Proc. Natl. Acad. Sci. U S A 96, 3801–3806CrossRefGoogle ScholarPubMed
Karlberg, O., Canbäck, B., Kurland, C. G., and Andersson, S. G. E. (2000) The dual origin of the yeast mitochondrial proteome. Yeast Comp. Funct. Genomics 17, 170–187Google ScholarPubMed
Keeling, P. J., and Doolittle, W. F. (1997) Evidence that eukaryotic triosephosphate isomerase is of alpha-proteobacterial origin. Proc. Natl. Acad. Sci. U S A 94, 1270–1275CrossRefGoogle ScholarPubMed
Keeling, P. J., and McFadden, G. I. (1998) Origins of microsporidia. Trends Microbiol. 6, 19–23CrossRefGoogle ScholarPubMed
Kondo, N., Nikoh, N., Ijichi, N., Shimada, M., and Fukatsu, T. (2002) Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect. Proc. Natl. Acad. Sci. U S A 99, 14280–14285CrossRefGoogle Scholar
Koonin, E. V., and Aravind, L. (2002) Origin and evolution of eukaryotic apoptosis: The bacterial connection. Cell Death Differ. 9, 394–404CrossRefGoogle ScholarPubMed
Koonin, E. V., Aravind, L., and Kondrashov, A. S. (2000) The impact of comparative genomics on our understanding of evolution. Cell 101, 573–576CrossRefGoogle ScholarPubMed
Koonin, E. V., Makarova, K. S., and Aravind, L. (2001) Horizontal gene transfer in prokaryotes: Quantification and classification. Annu. Rev. Microbiol. 55, 709–742CrossRefGoogle ScholarPubMed
Koretke, K. K., Lupas, A. N., Warren, P. V., Rosenberg, M., and Brown, J. R. (2000) Evolution of two-component signal transduction. Mol. Biol. Evol. 17, 1956–1970CrossRefGoogle ScholarPubMed
Koski, L. B., and Golding, B. (2001) The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52, 540–542CrossRefGoogle Scholar
Kunik, T., Tzfira, T., Kapulnik, Y., Gafni, Y., Dingwall, C., and Citovsky, V. (2001) Genetic transformation of HeLa cells by Agrobacterium. Proc. Natl. Acad. Sci. U S A 98, 1871–1876CrossRefGoogle ScholarPubMed
Kurland, C., and Andersson, S. G. E. (2000) Origin and evolution of the mitochondrial proteome. Mol. Biol. Rev. 64, 786–820CrossRefGoogle ScholarPubMed
Kurland, C. G. (2000) Something for everyone: Horizontal gene transfer in evolution. EMBO Rep. 1, 92–95CrossRefGoogle Scholar
Kyrpides, N. C., and Olsen, G. J. (1999) Archaeal and bacterial hyperthermophiles: Horizontal gene exchange or common ancestry?Trends Genetics 15, 298–299CrossRefGoogle ScholarPubMed
Lamour, V., Quevillon, S., Diriong, S., N'Guyen, V. C., Lipinski, M., and Mirande, M. (1994) Evolution of the Glx-tRNA synthetase family: The glutaminyl enzyme as a case for horizontal gene transfer. Proc. Natl. Acad. Sci. U S A 91, 8670–8674CrossRefGoogle ScholarPubMed
Lathe, W. C., Snel, B., and Bork, P. (2000) Gene context conservation of a higher order than operons. Trends Biochem. Sci. 25, 474–479CrossRefGoogle ScholarPubMed
Lawrence, J. G., and Ochman, H. (1998) Molecular archaeology of the Escherichia coli “genome”. Proc. Natl. Acad. Sci. U S A 95, 9413–9417CrossRefGoogle ScholarPubMed
Lawrence, J. G., and Ochman, H. (2002) Reconciling the many faces of lateral gene transfer. Trends Microbiol. 10, 1–3CrossRefGoogle ScholarPubMed
Logsdon, J. M. Jr., and Faguy, D. M. (1999) Evolutionary genomics: Thermotoga heats up lateral gene transfer. Current Biol. 9, R747–R751CrossRefGoogle Scholar
Lopez, P., Forterre, P., and Philippe, H. (1999) The root of the tree of life in the light of the covarion model. J. Mol. Evol. 49, 496–508CrossRefGoogle ScholarPubMed
Margulis, L. (1970) Origin of eukaryotic cells. New Haven CT: Yale University PressGoogle Scholar
Martin, W. (1996) Is something wrong with the tree of life?BioEssays 18, 523–527CrossRefGoogle Scholar
Martin, W. (1999) Mosaic bacterial chromosomes: A challenge en route to a tree of genomes. BioEssays 21, 99–1043.0.CO;2-B>CrossRefGoogle ScholarPubMed
Martin, W., and Müller, M. (1998) The hydrogen hypothesis for the first eukaryote. Nature 392, 37–41CrossRefGoogle ScholarPubMed
Martin, W.. (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl. Acad. Sci. U S A 99, 12246–12251CrossRefGoogle ScholarPubMed
Moreira, D., and López-García, P. (1998) Symbiosis between methanogenic Archaea and δ-Proteobacteria as the origin of eukaryotes: The syntrophic hypothesis. J. Mol. Evol. 47, 517–530CrossRefGoogle ScholarPubMed
Nelson, K. E.. (1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399, 323–329CrossRefGoogle ScholarPubMed
Ochman, H., Lawrence, J. G., and Groisman, E. A. (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299–304CrossRefGoogle ScholarPubMed
Olsen, G. J., and Woese, C. R. (1997) Archaeal genomics — an overview. Cell 89, 991–994CrossRefGoogle ScholarPubMed
Olsen, G. J., Woese, C. R., and Overbeek, R. (1994) The winds of (evolutionary) change: Breathing new life into microbiology. J Bacteriol 176, 1–6CrossRefGoogle ScholarPubMed
Page, R. D. M. (1996) TREEVIEW: An application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12, 357–358Google ScholarPubMed
Palenik, B. (2002) The genomics of symbiosis: Host keep the baby and the bath water. Proc. Natl. Acad. Sci. U S A 99, 11996–11997CrossRefGoogle Scholar
Pennisi, E. (1998) Genome data shake tree of life. Science 280, 672–674CrossRefGoogle ScholarPubMed
Pennisi, E. (1999) Is it time to uproot the tree of life?Science 284, 1305–1307CrossRefGoogle ScholarPubMed
Poole, A., and Penny, D. (2001) Does endosymbiosis explain the origin of the nucleus?Nature Cell Biol. 3, E173CrossRefGoogle ScholarPubMed
Ragan, M. (2001) On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett. 201, 187–191CrossRefGoogle ScholarPubMed
Ragan, M. (2002) Reconciling the many faces of lateral gene transfer: Response. Trends Microbiol. 10, 3CrossRefGoogle Scholar
Rivera, M. C., Jain, R., Moore, J. E., and Lake, J. A. (1998) Genomic evidence for two functionally distinct gene classes. Proc. Natl. Acad. Sci. U S A 95, 6239–6244CrossRefGoogle ScholarPubMed
Rivera, M. C., and Lake, J. A. (2004) The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431, 152–155CrossRefGoogle ScholarPubMed
Roelofs, J., and Haastert, P. J. (2001) Genes lost during evolution. Nature 411, 1013–1014CrossRefGoogle ScholarPubMed
Roger, A. J., and Brown, J. R. (1996) A chimeric origin for eukaryotes re-examined. Trends Biochem. Sci. 21, 370–371CrossRefGoogle ScholarPubMed
Roger, A. J., Clark, C. G., and Doolittle, W. F. (1996) A possible mitochondrial gene in the early-branching amitochondriate protist Trichomonas vaginalis. Proc. Natl. Acad. Sci. U S A 93, 14618–14622CrossRefGoogle ScholarPubMed
Rokas, A., Williams, B. L., King, N., and Carroll, S. B. (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425, 798–804CrossRefGoogle ScholarPubMed
Rotte, C., and Martin, W. (2001) Does endosymbiosis explain the origin of the nucleus?Nature Cell Biol. 3, E173CrossRefGoogle ScholarPubMed
Rujan, T., and Martin, W. (2001) How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies. Trends Genetics 17, 113–119CrossRefGoogle ScholarPubMed
Salzberg, S. L., White, O., Peterson, J., and Eisen, J. A. (2001) Microbial genes in the human genome: Lateral transfer or gene loss?Science 292, 1903–1906CrossRefGoogle ScholarPubMed
Smith, M. W., Feng, D.-F., and Doolittle, R. F. (1992) Evolution by acquisition: The case for horizontal gene transfers. Trends Biochem. Sci. 17, 489–493CrossRefGoogle ScholarPubMed
Snel, B., Bork, P., and Huynen, M. A. (1999) Genome phylogeny based on gene content. Nature Genetics 21, 108–110CrossRefGoogle ScholarPubMed
Stanhope, M. J.. (2001) Phylogenetic analyses of genomic and EST sequences do not support horizontal gene transfers between bacteria and vertebrates. Nature 411, 940–944CrossRefGoogle Scholar
Strimmer, K., and Haeseler, A. (1996) Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13, 964–969CrossRefGoogle Scholar
Swofford, D. L. (1999) PAUP∗. Phylogenetic Analysis Using Parsimony (∗and Other Methods). Version 4. Sunderland, MA: Sinauer AssociatesGoogle Scholar
Teichmann, S. A., and Mitchison, G. (1999) Is there a phylogenetic signal in prokaryote proteins?J. Mol. Evol. 49, 98–107CrossRefGoogle Scholar
Thorsness, P. E., and Fox, T. D. (1990) Escape of DNA from mitochondria to nucleus in Saccharomyces cerevisiae. Nature 346, 376–379CrossRefGoogle ScholarPubMed
Thorsness, P. E., and Fox, T. D. (1993) Nuclear mutations in Saccharomyces cerevisiae that affect the escape of DNA from mitochondria to the nucleus. Genetics 134, 21–28Google ScholarPubMed
Tielens, A. G. M., Rotte, C., Hellemond, J. J., and Martin, W. (2002) Mitochondria as we don't know them. Trends Biochem. Sci., 27, 564–572CrossRefGoogle Scholar
Tourmen, Y., Baris, O., Dessen, P., Jacques, C., Malthièry, Y., and Reynier, P. (2002) Structure and chromosomal distribution of human mitochondrial pseudogenes. Genomics 80, 71–77CrossRefGoogle ScholarPubMed
Tovar, J., León-Avila, G., Sánchez, L. B., Sutak, R., Tachezy, J., Giezen, M.. (2003) Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation. Nature 426, 172–176CrossRefGoogle ScholarPubMed
Ueda, K., Seki, T., Kudo, T., Yoshida, T., and Kataoka, M. (1999) Two distinct mechanisms cause heterogeneity of 16S rRNA. J Bacteriol 181, 78–82Google ScholarPubMed
Giezen, M.. (2002) Conserved properties of hydrogenosomal and mitochondrial ADP/ATP carriers: A common origin for both organelles. EMBO J. 21, 572–579CrossRefGoogle ScholarPubMed
Dohlen, C. D., Kohler, S., Alsop, S. T., and McManus, W. R. (2001) Mealybug β-proteobacterial endosymbionts contain γ-proteobacterial symbionts. Nature 412, 433–436CrossRefGoogle Scholar
Woese, C. R. (2002) On the evolution of cells. Proc. Natl. Acad. Sci. U S A 99, 8742–8747CrossRefGoogle Scholar
Woese, C. R., and Fox, G. E. (1977) Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc. Natl. Acad. Sci. U S A 51, 221–271Google Scholar
Woese, C. R., Kandler, O., and Wheelis, M. L. (1990) Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria and Eucarya. Proc. Natl. Acad. Sci. U S A 87, 4576–4579CrossRefGoogle ScholarPubMed
Woese, C. R., Olsen, G. J., Ibba, M., and Söll, D. (2000) Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64, 202–236CrossRefGoogle ScholarPubMed
Wolf, Y. I., Aravind, L., Grishin, N. V., and Koonin, E. V. (1999) Evolution of aminoacyl-tRNA synthetases — analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 9, 689–710Google ScholarPubMed
Wren, B. W. (2000) Microbial genome analysis: Insight into virulence, host adaptation and evolution. Nature Rev. Genetics 1, 30–39CrossRefGoogle Scholar
Xiong, J., Inoue, K., and Bauer, C. E. (1998) Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from Heliobacillus mobilis. Proc. Natl. Acad. Sci. U S A 95, 14851–14856CrossRefGoogle Scholar
Yap, W. H., Zhang, Z., and Wang, Y. (1999) Distinct types of rRNA operon exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J. Bacteriol. 181, 5201–5209Google ScholarPubMed
Zambryski, P., Tempe, J., and Schell, J. (1989) Transfer and function of T-DNA genes from Agrobacterium Ti and Ri plasmids. Cell 56, 193–201CrossRefGoogle ScholarPubMed

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