Horizontal gene transfer in osmotrophs: playing with public goods (original) (raw)
Morris, J. J., Lenski, R. E. & Zinser, E. R. The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. mBio3, e00036–12 (2012). ArticlePubMedPubMed Central Google Scholar
Cordero, O. X., Ventouras, L. A., DeLong, E. F. & Polz, M. F. Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations. Proc. Natl Acad. Sci. USA109, 20059–20064 (2012). ArticleCASPubMedPubMed Central Google Scholar
Lee, W., van Baalen, M. & Jansen, V. A. An evolutionary mechanism for diversity in siderophore-producing bacteria. Ecol. Lett.15, 119–125 (2012). ArticlePubMed Google Scholar
Nogueira, T. et al. Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Curr. Biol.19, 1683–1691 (2009). ArticleCASPubMedPubMed Central Google Scholar
Berbee, M. L. & Taylor, J. W. Dating the molecular clock in fungi – how close are we? Fungal Biol. Rev.24, 1–16 (2011). Article Google Scholar
Selosse, M. A. & Le Tacon, F. The land flora: a phototroph–fungus partnership? Trends Ecol. Evol.13, 15–20 (1998). ArticleCASPubMed Google Scholar
Taylor, J. W. & Berbee, M. L. Dating divergences in the fungal tree of life: review and new analyses. Mycologia98, 838–849 (2006). ArticlePubMed Google Scholar
Pirozynski, K. A. & Malloch, D. W. The origin of land plants: a matter of mycotrophism. Biosystems5, 153–164 (1975). Article Google Scholar
Fisher, M. C. et al. Emerging fungal threats to animal, plant and ecosystem health. Nature484, 186–194 (2012). ArticleCASPubMed Google Scholar
Hawksworth, D. L. The fungal dimension of biodiversity: magnitude, significance and conservation. Mycol. Res.95, 641–655 (1991). Article Google Scholar
Hibbett, D. S. et al. A higher-level phylogenetic classification of the Fungi. Mycol. Res.111, 509–547 (2007). ArticlePubMed Google Scholar
James, T. Y. et al. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature443, 818–822 (2006). ArticleCASPubMed Google Scholar
Richards, T. A., Jones, M. D. M., Leonard, G. & Bass, D. Marine fungi: their ecology and molecular diversity. Annu. Rev. Mar. Sci.4, 495–522 (2012). Article Google Scholar
Buée, M. et al. 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol.184, 449–456 (2009). ArticlePubMedCAS Google Scholar
Jumpponen, A. & Jones, K. L. Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol.184, 438–448 (2009). ArticleCASPubMed Google Scholar
O'brien, H. E., Parrent, J. L., Jackson, J. A., Moncalvo, J.-M. & Vilgalys, R. Fungal community analysis by large-scale sequencing of environmental samples. Appl. Environ. Microbiol.71, 5544–5550 (2005). ArticleCASPubMedPubMed Central Google Scholar
Keller, N. P., Turner, G. & Bennett, J. W. Fungal secondary metabolism — from biochemistry to genomics. Nature Rev. Microbiol.3, 937–947 (2005). ArticleCAS Google Scholar
Soanes, D. M. et al. Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis. PLoS ONE3, e2300 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Cornell, M. J. et al. Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi. Genome Res.17, 1809–1822 (2007). ArticleCASPubMedPubMed Central Google Scholar
Chiang, Y. M., Lee, K. H., Sanchez, J. F., Keller, N. P. & Wang, C. C. Unlocking fungal cryptic natural products. Nat. Prod. Commun.4, 1505–1510 (2009). CASPubMedPubMed Central Google Scholar
Bushley, K. E. & Turgeon, B. G. Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships. BMC Evol. Biol.10, 26 (2010). ArticlePubMedPubMed CentralCAS Google Scholar
Amselem, J. et al. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet.7, e1002230 (2011). ArticleCASPubMedPubMed Central Google Scholar
de Boer, W., Folman, L. B., Summerbell, R. C. & Boddy, L. Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiol. Rev.29, 795–811 (2005). ArticleCAS Google Scholar
Cavalier-Smith, T. in Evolutionary Biology of the Fungi (British Mycological Society Symposia) 339–353 (eds Rayer, A. D. M., Brasier, C. M. & Moore, D., 1987). Google Scholar
Cavalier-Smith, T. & Chao, E. E. Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista). J. Mol. Evol.62, 388–420 (2006). ArticleCASPubMed Google Scholar
Bermudez Moretti, M., Perullini, A. M., Batlle, A. & Correa Garcia, S. Expression of the UGA4 gene encoding the δ-aminolevulinic and γ-aminobutyric acids permease in Saccharomyces cerevisiae is controlled by amino acid-sensing systems. Arch. Microbiol.184, 137–140 (2005). ArticleCASPubMed Google Scholar
Boles, E. & Hollenberg, C. P. The molecular genetics of hexose transport in yeasts. FEMS Microbiol. Rev.21, 85–111 (1997). ArticleCASPubMed Google Scholar
Heymann, P., Ernst, J. F. & Winkelmann, G. Identification of a fungal triacetylfusarinine C siderophore transport gene (TAF1) in Saccharomyces cerevisiae as a member of the major facilitator superfamily. Biometals12, 301–306 (1999). ArticleCASPubMed Google Scholar
Greig, D. & Travisano, M. The Prisoner's Dilemma and polymorphism in yeast SUC genes. Proc. Biol. Sci.271 (Suppl. 3), S25–S26 (2004). CASPubMedPubMed Central Google Scholar
Crespi, B. J. The evolution of social behavior in microorganisms. Trends. Ecol. Evol.16, 178–183 (2001). ArticlePubMed Google Scholar
West, S. A., Diggle, S. P., Buckling, A., Gardner, A. & Griffin, A. S. The social lives of microbes. Annu. Rev. Ecol. Evol. Syst.38, 53–77 (2007). Article Google Scholar
Inglis, R. F., Brown, S. P. & Buckling, A. Spite versus cheats: competition among social strategies shapes virulence in Pseudomonas aeruginosa. Evolution66, 3472–3484 (2012). ArticlePubMedPubMed Central Google Scholar
Riley, M. A. & Wertz, J. E. Bacteriocins: evolution, ecology, and application. Annu. Rev. Microbiol.56, 117–137 (2002). ArticleCASPubMed Google Scholar
West, S. A., Griffin, A. S. & Gardner, A. Social semantics: altruism, cooperation, mutualism, strong reciprocity and group selection. J. Evol. Biol.20, 415–432 (2007). ArticleCASPubMed Google Scholar
MaClean, R. C., Fuentes-Hernandez, A., Greig, D., Hurst, L. D. & Gudelj, I. A mixture of “cheats” and “co-operators” can enable maximal group benefit. PLoS Biol.8, e1000486 (2010). ArticlePubMedPubMed CentralCAS Google Scholar
Galeote, V. et al. FSY1, a horizontally transferred gene in the Saccharomyces cerevisiae EC1118 wine yeast strain, encodes a high-affinity fructose/H+ symporter. Microbiology156, 3754–3761 (2011). ArticleCAS Google Scholar
Slot, J. C. & Hibbett, D. S. Horizontal transfer of a nitrate assimilation gene cluster and ecological transitions in fungi: a phylogenetic study. PLoS ONE2, e1097 (2007). ArticlePubMedPubMed CentralCAS Google Scholar
Brown, C. J., Todd, K. M. & Rosenzweig, R. F. Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment. Mol. Biol. Evol.15, 931–942 (1998). ArticleCASPubMed Google Scholar
Wei, H. et al. A putative high affinity hexose transporter, hxtA, of Aspergillus nidulans is induced in vegetative hyphae upon starvation and in ascogenous hyphae during cleistothecium formation. Fungal Genet. Biol.41, 148–156 (2004). ArticleCASPubMed Google Scholar
Javelle, A., Andre, B., Marini, A.-M. & Chalot, M. High-affinity ammonium transporters and nitrogen sensing in mycorrhizas. Trends Microbiol.11, 53–55 (2003). ArticleCASPubMed Google Scholar
Smith, E. E., Sims, E. H., Spencer, D. H., Kaul, R. & Olson, M. V. Evidence for diversifying selection at the pyoverdine locus of Pseudomonas aeruginosa. J. Bacteriol.187, 2138–2147 (2005). ArticleCASPubMedPubMed Central Google Scholar
Kruckeberg, A. L. The hexose transporter family of Saccharomyces cerevisiae. Arch. Microbiol.166, 283–292 (1996). ArticleCASPubMed Google Scholar
Koschwanez, J. H., Foster, K. R. & Murray, A. W. Sucrose utilization in budding yeast as a model for the origin of undifferentiated multicellularity. PLoS Biol.9, e1001122 (2011). ArticleCASPubMed Google Scholar
Hamilton, W. D. The genetical evolution of social behaviour, I. J. Theor. Biol.7, 1–16 (1964). ArticleCASPubMed Google Scholar
Hamilton, W. D. The genetical evolution of social behaviour, II. J. Theor. Biol.7, 17–52 (1964). ArticleCASPubMed Google Scholar
Griffin, A. S., West, S. A. & Buckling, A. Cooperation and competition in pathogenic bacteria. Nature430, 1024–1027 (2004). ArticleCASPubMed Google Scholar
Nadell, C. D., Foster, K. R. & Xavier, J. B. Emergence of spatial structure in cell groups and the evolution of cooperation. PLoS Comput. Biol.6, e1000716 (2010). ArticlePubMedPubMed CentralCAS Google Scholar
Nowak, M. A. & May, R. M. Evolutionary games and spatial chaos. Nature359, 826–829 (1992). Article Google Scholar
Hauert, C. & Doebeli, M. Spatial structure often inhibits the evolution of cooperation in the snowdrift game. Nature428, 643–646 (2004). ArticleCASPubMed Google Scholar
Kummerli, R., Griffin, A. S., West, S. A., Buckling, A. & Harrison, F. Viscous medium promotes cooperation in the pathogenic bacterium Pseudomonas aeruginosa. Proc. Biol. Sci.276, 3531–3538 (2009). PubMedPubMed Central Google Scholar
Kummerli, R., Gardner, A., West, S. A. & Griffin, A. S. Limited dispersal, budding dispersal, and cooperation: an experimental study. Evolution63, 939–949 (2009). ArticlePubMed Google Scholar
Brockhurst, M. A., Buckling, A. & Gardner, A. Cooperation peaks at intermediate disturbance. Curr. Biol.17, 761–765 (2007). ArticleCASPubMed Google Scholar
Verbruggen, E. et al. Spatial structure and interspecific cooperation: theory and an empirical test using the mycorrhizal mutualism. Am. Nat.179, E133–E146 (2012). ArticlePubMed Google Scholar
Doolittle, W. F. Microbial evolution: stalking the wild bacterial species. Curr. Biol.18, R565–567 (2008). ArticleCASPubMed Google Scholar
Boenigk, J., Ereshefsky, M., Hoef-Emden, K., Mallet, J. & Bass, D. Concepts in protistology: species definitions and boundaries. Eur. J. Protistol.48, 96–102 (2012). ArticlePubMed Google Scholar
Taylor, J. W. et al. Phylogenetic species recognition and species concepts in fungi. Fungal Genet. Biol.31, 21–32 (2000). ArticleCASPubMed Google Scholar
Trivers, R. L. The evolution of reciprocal altruism. Q. Rev. Biol.46, 37–57 (1971). Article Google Scholar
Kiers, E. T. et al. Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis. Science333, 880–882 (2011). ArticleCASPubMed Google Scholar
Kiers, E. T., Rousseau, R. A., West, S. A. & Denison, R. F. Host sanctions and the legume–rhizobium mutualism. Nature425, 78–81 (2003). ArticleCASPubMed Google Scholar
Hauert, C., Holmes, M. & Doebeli, M. Evolutionary games and population dynamics: maintenance of cooperation in public goods games. Proc. Biol. Sci.273, 2565–2570 (2006). PubMedPubMed Central Google Scholar
Archetti, M. & Scheuring, I. Coexistence of cooperation and defection in public goods games. Evolution65, 1140–1148 (2011). ArticlePubMed Google Scholar
Raihani, N. J. & Bshary, R. The evolution of punishment in _n_-player public goods games: a volunteer's dilemma. Evolution65, 2725–2728 (2011). ArticlePubMed Google Scholar
Archetti, M. et al. Economic game theory for mutualism and cooperation. Ecol. Lett.14, 1300–1312 (2011). ArticlePubMed Google Scholar
Hauert, C., De Monte, S., Hofbauer, J. & Sigmund, K. Volunteering as Red Queen mechanism for cooperation in public goods games. Science296, 1129–1132 (2002). ArticleCASPubMed Google Scholar
Floudas, D. et al. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science336, 1715–1719 (2012). ArticleCASPubMed Google Scholar
Hastrup, A. C. S. et al. Differences in crystalline cellulose modification due to degradation by brown and white rot fungi. Fungal Biol.116, 1052–1063 (2012). ArticleCASPubMed Google Scholar
Maclean, C. R. & Brandon, C. Stable public goods cooperation and dynamic social interactions in yeast. J. Evol. Biol.21, 1836–1843 (2008). ArticleCAS Google Scholar
Garcia-Vallve, S., Romeu, A. & Palau, J. Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Mol. Biol. Evol.17, 352–361 (2000). ArticleCASPubMed Google Scholar
Gojkovic, Z. et al. Horizontal gene transfer promoted evolution of the ability to propagate under anaerobic conditions in yeasts. Mol. Genet. Genom.271, 387–393 (2004). ArticleCAS Google Scholar
Richards, T. A., Leonard, G., Soanes, D. M. & Talbot, N. J. Gene transfer into the fungi. Fungal Biol. Rev.25, 98–110 (2011). Article Google Scholar
Jain, R., Rivera, M. C., Moore, J. E. & Lake, J. A. Horizontal gene transfer accelerates genome innovation and evolution. Mol. Biol. Evol.20, 1598–1602 (2003). ArticleCASPubMed Google Scholar
Gabaldon, T. & Huynen, M. A. Reconstruction of the proto-mitochondrial metabolism. Science301, 609 (2003). ArticleCASPubMed Google Scholar
Lawrence, J. G. Microbial evolution: enforcing cooperation by partial kin selection. Curr. Biol.19, R943–R945 (2009). ArticleCASPubMed Google Scholar
Richards, T. A., Dacks, J. B., Jenkinson, J. M., Thornton, C. R. & Talbot, N. J. Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms. Curr. Biol.16, 1857–1864 (2006). ArticleCASPubMed Google Scholar
Richards, T. A. et al. Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. Plant Cell21, 1897–1911 (2009). ArticleCASPubMedPubMed Central Google Scholar
Noll, K. M. & Thirangoon, K. Interdomain transfers of sugar transporters overcome barriers to gene expression. Methods Mol. Biol.532, 309–322 (2009). ArticleCASPubMed Google Scholar
Hellborg, L., Woolfit, M., Arthursson-Hellborg, M. & Piskur, J. Complex evolution of the DAL5 transporter family. BMC Genomics9, 164 (2008). ArticlePubMedPubMed CentralCAS Google Scholar
Nesbo, C. L., Nelson, K. E. & Doolittle, W. F. Suppressive subtractive hybridization detects extensive genomic diversity in Thermotoga maritima. J. Bacteriol.184, 4475–4488 (2002). ArticleCASPubMedPubMed Central Google Scholar
Slot, J. C., Hallstrom, K. N., Matheny, P. B. & Hibbett, D. S. Diversification of NRT2 and the origin of its fungal homolog. Mol. Biol. Evol.24, 1731–1743 (2007). ArticleCASPubMed Google Scholar
McDonald, T. R., Dietrich, F. S. & Lutzoni, F. Multiple horizontal gene transfers of ammonium transporters ammonia permeases from prokaryotes to eukaryotes: towards a new functional and evolutionary classification. Mol. Biol. Evol.29, 51–60 (2012). ArticleCASPubMed Google Scholar
Coelho, M. A., Gonçalves, C., Sampaio, J. P. & Gonçalves, P. Extensive intra-kingdom horizontal gene transfer converging on a fungal fructose transporter gene. PLoS Genet.9, e1003587 (2013). ArticleCASPubMedPubMed Central Google Scholar
Richards, T. A. et al. Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proc. Natl Acad. Sci. USA108, 15258–15263 (2011). ArticleCASPubMedPubMed Central Google Scholar
Jain, R., Rivera, M. C. & Lake, J. A. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl Acad. Sci. USA96, 3801–3806 (1999). ArticleCASPubMedPubMed Central Google Scholar
Cohen, O., Gophna, U. & Pupko, T. The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Mol. Biol. Evol.28, 1481–1489 (2011). ArticleCASPubMed Google Scholar
Uetz, P. et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature403, 623–627 (2000). ArticleCASPubMed Google Scholar
Jeong, H., Mason, S. P., Barabasi, A. L. & Oltvai, Z. N. Lethality and centrality in protein networks. Nature411, 41–42 (2001). ArticleCASPubMed Google Scholar
Stark, C. et al. BioGRID: a general repository for interaction datasets. Nucleic Acids Res.34, D535–539 (2006). ArticleCASPubMed Google Scholar
Cotton, J. A. & McInerney, J. O. Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Proc. Natl Acad. Sci. USA107, 17252–17255 (2010). ArticleCASPubMedPubMed Central Google Scholar
Belbahri, L., Calmin, G., Mauch, F. & Andersson, J. O. Evolution of the cutinase gene family: evidence for lateral gene transfer of a candidate Phytophthora virulence factor. Gene408, 1–8 (2008). ArticleCASPubMed Google Scholar
de Crecy-Lagard, V., El Yacoubi, B., de la Garza, R. D., Noiriel, A. & Hanson, A. D. Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics8, 245 (2007). ArticlePubMedPubMed CentralCAS Google Scholar
Lehmann, L., Bargum, K. & Reuter, M. An evolutionary analysis of the relationship between spite and altruism. J. Evol. Biol.19, 1507–1516 (2006). ArticleCASPubMed Google Scholar
Harrison, F. & Buckling, A. Siderophore production and biofilm formation as linked social traits. ISME J.3, 632–634 (2009). ArticleCASPubMed Google Scholar
Williams, P., Winzer, K., Chan, W. C. & Camara, M. Look who's talking: communication and quorum sensing in the bacterial world. Phil. Trans. R. Soc. B362, 1119–1134 (2007). ArticleCASPubMedPubMed Central Google Scholar
Fox, E. M. & Howlett, B. J. Secondary metabolism: regulation and role in fungal biology. Curr. Opin. Microbiol.11, 481–487 (2008). ArticleCASPubMed Google Scholar
Trejo-Estrada, S. R., Paszczynski, A. & Crawford, D. L. Antibiotics and enzymes produced by the biocontrol agent Streptomyces violaceusniger YCED-9. J. Ind. Microbiol. Biotechnol.21, 81–90 (1998). ArticleCAS Google Scholar
Friesen, T. L. et al. Emergence of a new disease as a result of interspecific virulence gene transfer. Nature Genet.38, 953–956 (2006). ArticleCASPubMed Google Scholar
Patron, N. J. et al. Origin and distribution of epipolythiodioxopiperazine (ETP) gene clusters in filamentous ascomycetes. BMC Evol. Biol.7, 174 (2007). ArticlePubMedPubMed CentralCAS Google Scholar
Slot, J. C. & Rokas, A. Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi. Curr. Biol.21, 134–139 (2011). ArticleCASPubMed Google Scholar
Powell, M. J., Letcher, P. M. & Longcore, J. E. Pseudorhizidium is a new genus with distinct zoospore ultrastructure in the order Chytridiales. Mycologia105, 496–507 (2013). ArticlePubMed Google Scholar