Learning how to live together: genomic insights into prokaryote–animal symbioses (original) (raw)

• Hypsa, V. & Dale, C. In vitro culture and phylogenetic analysis of 'Candidatus Arsenophonus triatominarum', an intracellular bacterium from the triatomine bug, Triatoma infestans. Int. J. Syst. Bacteriol. 47, 1140–1144 (1997).
  Article CAS PubMed Google Scholar
• Dale, C. & Maudlin, I. Sodalis gen. nov. and Sodalis glossinidius sp. nov., a microaerophilic secondary endosymbiont of the tsetse fly Glossina morsitans morsitans. Int. J. Syst. Bacteriol. 49, 267–275 (1999).
  Article CAS PubMed Google Scholar
• Dale, C., Beeton, M., Harbison, C., Jones, T. & Pontes, M. Isolation, pure culture, and characterization of 'Candidatus Arsenophonus arthropodicus', an intracellular secondary endosymbiont from the hippoboscid louse fly Pseudolynchia canariensis. Appl. Environ. Microbiol. 72, 2997–3004 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Darby, A. C., Chandler, S. M., Welburn, S. C. & Douglas, A. E. Aphid-symbiotic bacteria cultured in insect cell lines. Appl. Environ. Microbiol. 71, 4833–4839 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Sagan, L. On the origin of mitosing cells. J. Theor. Biol. 14, 255–274 (1967).
  Article CAS PubMed Google Scholar
• Sapp, J. Evolution by Association. A History of Symbiosis (Oxford University Press, New York, 1994). This book is the first historical report on the symbiosis concept and its central role in shaping contemporary evolutionary ideas about the origin and diversification of life.
• de Duve, C. The origin of eukaryotes: a reappraisal. Nature Rev. Genet. 8, 395–403 (2007).
  Article CAS PubMed Google Scholar
• Margulis, L. Symbiosis in Cell Evolution. Microbial Communities in the Archaean and Proterozoic Eons (W. H. Freeman and Co., New York, 1993).
• Shigenobu, S., Watanabe, H., Hattori, M., Sakaki, Y. & Ishikawa, H. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407, 81–86 (2000).
  Article CAS PubMed Google Scholar
• Tamas, I. et al. 50 million years of genomic stasis in endosymbiotic bacteria. Science 296, 2376–2379 (2002).
  Article CAS PubMed Google Scholar
• Akman, L. et al. Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nature Genet. 32, 402–407 (2002).
  Article CAS PubMed Google Scholar
• van Ham, R. C. et al. Reductive genome evolution in Buchnera aphidicola. Proc. Natl Acad. Sci. USA 100, 581–586 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Gil, R. et al. The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes. Proc. Natl Acad. Sci. USA 100, 9388–9393 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Degnan, P. H., Lazarus, A. B. & Wernegreen, J. J. Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects. Genome Res. 15, 1023–1033 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Wu, D. et al. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS Biol. 4, e188 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Nakabachi, A. et al. The 160-kilobase genome of the bacterial endosymbiont. Carsonella Science 314, 267 (2006).
  CAS PubMed Google Scholar
• Newton, I. L. et al. The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315, 998–1000 (2007).
  Article CAS PubMed Google Scholar
• Kuwahara, H. et al. Reduced genome of the thioautotrophic intracellular symbiont in a deep-sea clam, Calyptogena okutanii. Curr. Biol. 17, 881–886 (2007).
  Article CAS PubMed Google Scholar
• Foster, J. et al. The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol. 3, e121 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Nakagawa, S. et al. Deep-sea vent ε-proteobacterial genomes provide insights into emergence of pathogens. Proc. Natl Acad. Sci. USA 104, 12146–12150 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Pérez-Brocal, V. et al. A small microbial genome: the end of a long symbiotic relationship? Science 314, 312–313 (2006). This paper, together with reference 16, shows that the genomes of B. aphidicola BCc and C. ruddii represent the lower limits of genome size in insect endosymbionts. Further research in these systems might shed light on the evolutionary fate of endosymbionts.
  Article CAS PubMed Google Scholar
• Toh, H. et al. Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host. Genome Res. 16, 149–156 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• McCutcheon, J. P. & Moran, N. A. Parallel genomic evolution and metabolic interdependence in an ancient symbiosis. Proc. Natl Acad. Sci. USA 104, 19392–19397 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Dale, C. & Moran, N. A. Molecular interactions between bacterial symbionts and their hosts. Cell 126, 453–465 (2006).
  Article CAS PubMed Google Scholar
• Baumann, P. Biology of bacteriocyte-associated endosymbionts of plant sap-sucking insects. Annu. Rev. Microbiol. 59, 155–189 (2005).
  Article CAS PubMed Google Scholar
• Russell, J. A., Latorre, A., Sabater-Munoz, B., Moya, A. & Moran, N. A. Side-stepping secondary symbionts: widespread horizontal transfer across and beyond the Aphidoidea. Mol. Ecol. 12, 1061–1075 (2003).
  Article CAS PubMed Google Scholar
• Chen, D.-Q., Montllor, C. B. & Purcell, A. H. Fitness effects of two facultative endosymbiotic bacteria on the pea aphid, Acyrthosiphon pisum, and the blue alfalfa aphid, A. kondoi. Entomol. Exp. Appl. 95, 315–323 (2000).
  Article Google Scholar
• Montllor, C. B., Maxmen, A. & Purcell, A. H. Facultative bacterial endosymbionts benefit pea aphids Acyrthosiphon pisum under heat stress. Ecol. Entomol. 27, 189–195 (2002).
  Article Google Scholar
• Russell, J. A. & Moran, N. A. Costs and benefits of symbiont infection in aphids: variation among symbionts and across temperatures. Proc. Biol. Sci. 273, 603–610 (2006).
  Article PubMed Google Scholar
• Oliver, K. M., Moran, N. A. & Hunter, M. S. Variation in resistance to parasitism in aphids is due to symbionts not host genotype. Proc. Natl Acad. Sci. USA 102, 12795–12800 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Oliver, K. M., Russell, J. A., Moran, N. A. & Hunter, M. S. Facultative bacterial symbionts in aphids confer resistance to parasitic wasps. Proc. Natl Acad. Sci. USA 100, 1803–1807 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Scarborough, C. L., Ferrari, J. & Godfray, H. C. Aphid protected from pathogen by endosymbiont. Science 310, 1781 (2005).
  Article CAS PubMed Google Scholar
• Tsuchida, T., Koga, R. & Fukatsu, T. Host plant specialization governed by facultative symbiont. Science 303, 1989 (2004).
  Article CAS PubMed Google Scholar
• Simon, J. C. et al. Host-based divergence in populations of the pea aphid: insights from nuclear markers and the prevalence of facultative symbionts. Proc. Biol. Sci. 270, 1703–1712 (2003).
  Article PubMed PubMed Central Google Scholar
• Leonardo, T. E. & Muiru, G. T. Facultative symbionts are associated with host plant specialization in pea aphid populations. Proc. Biol. Sci. 270 (Suppl 2), S209–S212 (2003).
  PubMed PubMed Central Google Scholar
• Leonardo, T. E. & Mondor, E. B. Symbiont modifies host life-history traits that affect gene flow. Proc. Biol. Sci. 273, 1079–1084 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• McGraw, E. A. & O'Neill, S. L. Wolbachia pipientis: intracellular infection and pathogenesis in Drosophila. Curr. Opin. Microbiol. 7, 67–70 (2004).
  Article CAS PubMed Google Scholar
• Welburn, S. C. & Maudlin, I. Tsetse–trypanosome interactions: rites of passage. Parasitol. Today 15, 399–403 (1999).
  Article CAS PubMed Google Scholar
• Moran, N. A. Symbiosis as an adaptive process and source of phenotypic complexity. Proc. Natl Acad. Sci. USA 104 (Suppl 1), 8627–8633 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Gomez-Valero, L. et al. Coexistence of Wolbachia with Buchnera aphidicola and a secondary symbiont in the aphid Cinara cedri. J. Bacteriol. 186, 6626–6633 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Takiya, D. M., Tran, P. L., Dietrich, C. H. & Moran, N. A. Co-cladogenesis spanning three phyla: leafhoppers (Insecta: Hemiptera: Cicadellidae) and their dual bacterial symbionts. Mol. Ecol. 15, 4175–4191 (2006).
  Article CAS PubMed Google Scholar
• Woyke, T. et al. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443, 950–955 (2006). This paper and reference 15 are two pioneering works on the application of genomic analysis to uncultivable microbial consortia, which opened up a new field of research on symbiosis.
  Article CAS PubMed Google Scholar
• Giere, O. & Erséus, C. Taxonomy and new bacterial symbioses of gutless marine Tubificidae (Annelida, Oligochaeta) from the island of Elba (Italy). Org. Divers. Evol. 2, 289–297 (2002).
  Article Google Scholar
• Wernegreen, J. J. Genome evolution in bacterial endosymbionts of insects. Nature Rev. Genet. 3, 850–861 (2002).
  Article CAS PubMed Google Scholar
• Moran, N. A. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc. Natl Acad. Sci. USA 93, 2873–2878 (1996).
  Article CAS PubMed PubMed Central Google Scholar
• Itoh, T., Martin, W. & Nei, M. Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts. Proc. Natl Acad. Sci. USA 99, 12944–12948 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Wernegreen, J. J. For better or worse: genomic consequences of intracellular mutualism and parasitism. Curr. Opin. Genet. Dev. 15, 572–583 (2005).
  Article CAS PubMed Google Scholar
• Rocha, E. P. & Danchin, A. Base composition bias might result from competition for metabolic resources. Trends Genet. 18, 291–294 (2002).
  Article CAS PubMed Google Scholar
• Fares, M. A., Ruiz-Gonzalez, M. X., Moya, A., Elena, S. F. & Barrio, E. Endosymbiotic bacteria: GroEL buffers against deleterious mutations. Nature 417, 398 (2002).
  Article CAS PubMed Google Scholar
• Moya, A., Latorre, A., Sabater-Munoz, B. & Silva, F. J. Comparative molecular evolution of primary (Buchnera) and secondary symbionts of aphids based on two protein-coding genes. J. Mol. Evol. 55, 127–137 (2002).
  Article CAS PubMed Google Scholar
• Rispe, C., Delmotte, F., van Ham, R. C. & Moya, A. Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids. Genome Res. 14, 44–53 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Moran, N. A. & Mira, A. The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Genome Biol. 2, RESEARCH0054 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Moran, N. A. & Plague, G. R. Genomic changes following host restriction in bacteria. Curr. Opin. Genet. Dev. 14, 627–633 (2004).
  Article CAS PubMed Google Scholar
• Plague, G. R., Dunbar, H. E., Tran, P. L. & Moran, N. A. Extensive proliferation of transposable elements in heritable bacterial symbionts. J. Bacteriol. 190, 777–779 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Heddi, A., Charles, H., Khatchadourian, C., Bonnot, G. & Nardon, P. Molecular characterization of the principal symbiotic bacteria of the weevil Sitophilus oryzae: a peculiar G+C content of an endocytobiotic DNA. J. Mol. Evol. 47, 52–61 (1998).
  Article CAS PubMed Google Scholar
• Lefevre, C. et al. Endosymbiont phylogenesis in the Dryophthoridae weevils: evidence for bacterial replacement. Mol. Biol. Evol. 21, 965–973 (2004).
  Article CAS PubMed Google Scholar
• Wu, M. et al. Phylogenomics of the reproductive parasite _Wolbachia pipientis w_Mel: a streamlined genome overrun by mobile genetic elements. PLoS Biol. 2, e69 (2004).
  Article PubMed PubMed Central Google Scholar
• Silva, F. J., Latorre, A. & Moya, A. Genome size reduction through multiple events of gene disintegration in Buchnera APS. Trends Genet. 17, 615–618 (2001).
  Article CAS PubMed Google Scholar
• Gomez-Valero, L., Silva, F. J., Simon, J. C. & Latorre, A. Genome reduction of the aphid endosymbiont Buchnera aphidicola in a recent evolutionary time scale. Gene 389, 87–95 (2007).
  Article CAS PubMed Google Scholar
• Gomez-Valero, L., Latorre, A. & Silva, F. J. The evolutionary fate of nonfunctional DNA in the bacterial endosymbiont Buchnera aphidicola. Mol. Biol. Evol. 21, 2172–2181 (2004).
  Article CAS PubMed Google Scholar
• Tamames, J. et al. The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii. BMC Evol. Biol. 7, 181 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Wilson, A. C. et al. A dual-genome microarray for the pea aphid, Acyrthosiphon pisum, and its obligate bacterial symbiont, Buchnera aphidicola. BMC Genomics 7, 50 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Wilcox, J. L., Dunbar, H. E., Wolfinger, R. D. & Moran, N. A. Consequences of reductive evolution for gene expression in an obligate endosymbiont. Mol. Microbiol. 48, 1491–1500 (2003).
  Article CAS PubMed Google Scholar
• Koga, R., Tsuchida, T. & Fukatsu, T. Changing partners in an obligate symbiosis: a facultative endosymbiont can compensate for loss of the essential endosymbiont Buchnera in an aphid. Proc. Biol. Sci. 270, 2543–2550 (2003).
  Article PubMed PubMed Central Google Scholar
• Ren, Q. & Paulsen, I. T. Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. PLoS Comput. Biol. 1, e27 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Fiala- Médioni, A. & Métivier, C. Ultrastructure of the gill of the hydrothermal vent bivalve Calyptogena magnifica, with a discussion of its nutrition. Mar. Biol. 90, 215–222 (1986).
  Article Google Scholar
• Baumann, P., Moran, N. A. & Baumann, L. in The Prokaryotes (ed. Dworkin, M.) 1–67 (Springer, New York, 2000).
  Google Scholar
• Fiala-Médioni, A., Michalski, J. C., Jollès, J., Alonso, C. & Montreuil, J. Lysosomic and lysozyme activities in gills of bivalves from deep hydrothermal vents. C. R. Acad. Sci. Paris 317, 239–244 (1994).
  Google Scholar
• Nakabachi, A. et al. Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera. Proc. Natl Acad. Sci. USA 102, 5477–5482 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Dale, C., Young, S. A., Haydon, D. T. & Welburn, S. C. The insect endosymbiont Sodalis glossinidius utilizes a type III secretion system for cell invasion. Proc. Natl Acad. Sci. USA 98, 1883–1888 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Young, G. M., Schmiel, D. H. & Miller, V. L. A new pathway for the secretion of virulence factors by bacteria: The flagellar export apparatus functions as a protein-secretion system. Proc. Natl Acad. Sci. USA 96, 6456–6461 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Maezawa, K. et al. Hundreds of flagellar basal bodies cover the cell surface of the endosymbiotic bacterium Buchnera aphidicola sp. strain APS. J. Bacteriol. 188, 6539–6543 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• McFall-Ngai, M. Adaptive immunity: care for the community. Nature 445, 153 (2007).
  Article CAS PubMed Google Scholar
• Hoffmann, J. A. The immune response of Drosophila. Nature 426, 33–38 (2003).
  Article CAS PubMed Google Scholar
• Heddi, A. et al. Molecular and cellular profiles of insect bacteriocytes: mutualism and harm at the initial evolutionary step of symbiogenesis. Cell. Microbiol. 7, 293–305 (2005).
  Article CAS PubMed Google Scholar
• Zaidman-Remy, A. et al. The Drosophila amidase PGRP-LB modulates the immune response to bacterial infection. Immunity 24, 463–473 (2006).
  Article CAS PubMed Google Scholar
• Anselme, C., Vallier, A., Balmand, S., Fauvarque, M.-O. & Heddi, A. Host PGRP gene expression and bacterial release in endosymbiosis of the weevil Sitophilus zeamais. Appl. Environ. Microbiol. 72, 6766–6772 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Ghedin, E. et al. Draft genome of the filarial nematode parasite Brugia malayi. Science 317, 1756–1760 (2007). The complete genome sequence of the nematode B. malayi , together with the previously reported genome sequence of its Wolbachia endosymbiont, will enable a systems approach for the study of host–symbiont interactions.
  Article CAS PubMed PubMed Central Google Scholar
• Kato, Y. & Komatsu, S. ASABF, a novel cysteine-rich antibacterial peptide isolated from the nematode Ascaris suum. Purification, primary structure, and molecular cloning of cDNA. J. Biol. Chem. 271, 30493–30498 (1996).
  Article CAS PubMed Google Scholar
• Braendle, C. et al. Developmental origin and evolution of bacteriocytes in the aphid–Buchnera symbiosis. PLoS Biol. 1, e21 (2003). This paper was the first study of the development and evolution of a bacteriocyte containing endosymbiotic bacteria.
  Article PubMed PubMed Central Google Scholar
• Lwoff, A. L'évolution physiologique. Étude des pertes des fonctions chez les microorganismes (Hermann, Paris, 1944).
• Timmis, J. N., Ayliffe, M. A., Huang, C. Y. & Martin, W. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nature Rev. Genet. 5, 123–135 (2004).
  Article CAS PubMed Google Scholar
• Martin, W. Gene transfer from organelles to the nucleus: frequent and in big chunks. Proc. Natl Acad. Sci. USA 100, 8612–8614 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Hotopp, J. C. et al. Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317, 1753–1756 (2007).
  Article CAS Google Scholar
• Bhattacharya, D., Archibald, J. M., Weber, A. P. M. & Reyes-Prieto, A. How do endosymbionts become organelles? Understanding early events in plastid evolution. Bioessays 29, 1239–1246 (2007).
  Article CAS PubMed Google Scholar
• C. elegans Sequencing Consortium. Genome sequence of the nematode Caenorhabditis elegans: a platform for investigating biology. Science 282, 2012–2018 (1998).
• Myers, E. W. et al. A whole-genome assembly of Drosophila. Science 287, 2196–2204 (2000).
  Article CAS PubMed Google Scholar
• Kennedy, J., Marchesi, J. R. & Dobson, A. D. Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges. Appl. Microbiol. Biotechnol. 75, 11–20 (2007).
  Article CAS PubMed Google Scholar
• Martin, F. P. et al. A top-down systems biology view of microbiome–mammalian metabolic interactions in a mouse model. Mol. Syst. Biol. 3, 112 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Paracer, S. & Ahmadjian, V. Symbiosis. An Introduction to Biological Associations (Oxford University Press, New York, 2000).
• Kneip, C., Lockhart, P., Voss, C. & Maier, U. G. Nitrogen fixation in eukaryotes — new models for symbiosis. BMC Evol. Biol. 7, 55 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Schink, B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61, 262–280 (1997).
  CAS PubMed PubMed Central Google Scholar
• Stewart, F. J., Newton, I. L. & Cavanaugh, C. M. Chemosynthetic endosymbioses: adaptations to oxic–anoxic interfaces. Trends Microbiol. 13, 439–448 (2005).
  Article CAS PubMed Google Scholar
• Minic, Z. & Herve, G. Biochemical and enzymological aspects of the symbiosis between the deep-sea tubeworm Riftia pachyptila and its bacterial endosymbiont. Eur. J. Biochem. 271, 3093–3102 (2004).
  Article CAS PubMed Google Scholar
• Zientz, E., Dandekar, T. & Gross, R. Metabolic interdependence of obligate intracellular bacteria and their insect hosts. Microbiol. Mol. Biol. Rev. 68, 745–770 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Croft, M. T., Lawrence, A. D., Raux-Deery, E., Warren, M. J. & Smith, A. G. Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature 438, 90–93 (2005).
  Article CAS PubMed Google Scholar
• Buchner, P. Endosymbiosis of Animals with Plant Microorganisms (Interscience, New York, 1965).
• Taylor, M. W., Radax, R., Steger, D. & Wagner, M. Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol. Mol. Biol. Rev. 71, 295–347 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Backhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A. & Gordon, J. I. Host–bacterial mutualism in the human intestine. Science 307, 1915–1920 (2005).
  Article CAS PubMed Google Scholar
• Stingl, U., Radek, R., Yang, H. & Brune, A. 'Endomicrobia': cytoplasmic symbionts of termite gut protozoa form a separate phylum of prokaryotes. Appl. Environ. Microbiol. 71, 1473–1479 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Fieseler, L., Quaiser, A., Schleper, C. & Hentschel, U. Analysis of the first genome fragment from the marine sponge-associated, novel candidate phylum Poribacteria by environmental genomics. Environ. Microbiol. 8, 612–624 (2006).
  Article CAS PubMed Google Scholar
• Moreira, D. et al. Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata. Mol. Phylogenet. Evol. 44, 255–266 (2007).
  Article CAS PubMed Google Scholar
• Rodriguez-Ezpeleta, N. et al. Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. Curr. Biol. 17, 1420–1425 (2007).
  Article CAS PubMed Google Scholar
• Lecointre, G. & Le Guyader, H. The Tree of Life. A Phylogenetic Classification (Harvard University Press Reference Library) (Belknap Press, Cambridge, 2006).
• Delsuc, F., Brinkmann, H., Chourrout, D. & Philippe, H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439, 965–968 (2006).
  Article CAS PubMed Google Scholar
• Bourlat, S. J. et al. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444, 85–88 (2006).
  Article CAS PubMed Google Scholar
• O'Malley, M., Powell, A., Davies, J. & Calvert, J. Knowledge-making distinctions in synthetic biology. Bioessays 30, 57–65 (2007).
  Article CAS Google Scholar
• Luisi, P. L. Chemical aspects of synthetic biology. Chem. Biodivers. 4, 603–621 (2007).
  Article CAS PubMed Google Scholar
• Peretó, J. & Català, J. The renaissance of synthetic biology. Biol. Theor. 2, 128–130 (2007).
  Article Google Scholar
• Mushegian, A. R. & Koonin, E. V. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl Acad. Sci. USA 93, 10268–10273 (1996).
  Article CAS PubMed PubMed Central Google Scholar
• Gil, R., Silva, F. J., Pereto, J. & Moya, A. Determination of the core of a minimal bacterial gene set. Microbiol. Mol. Biol. Rev. 68, 518–537 (2004). This Review proposes a minimal genetic repertoire for a hypothetical heterotrophic bacterium, based on comparative genomics of endosymbionts, experimentally determined gene essentiality and the functions of a coherent metabolism.
  Article CAS PubMed PubMed Central Google Scholar
• Klasson, L. & Andersson, S. G. Evolution of minimal-gene-sets in host-dependent bacteria. Trends Microbiol. 12, 37–43 (2004).
  Article CAS PubMed Google Scholar
• Gabaldon, T. et al. Structural analyses of a hypothetical minimal metabolism. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 362, 1751–1762 (2007).
  Article CAS Google Scholar
• Ruiz-Mirazo, K., Pereto, J. & Moreno, A. A universal definition of life: autonomy and open-ended evolution. Orig. Life Evol. Biosph. 34, 323–346 (2004).
  Article CAS PubMed Google Scholar