Gene Acquisition Convergence between Entomopoxviruses and Baculoviruses
Abstract
:1. Introduction
2. Materials and Methods
2.1. Viral Orthologous Clustering
2.2. Phylogenetic Analyses
3. Results
3.3. Convergence between Viruses Infecting Different Hosts
4. Discussion
Supplementary Files
Supplementary File 1Acknowledgments
Author Contributions
Conflicts of Interest
References
- Eckburg, P.B.; Bik, E.M.; Bernstein, C.N.; Purdom, E.; Dethlefsen, L.; Sargent, M.; Gill, S.R.; Nelson, K.E.; Relman, D.A. Diversity of the human intestinal microbial flora. Science 2005, 308, 1635–1638. [Google Scholar]
- Cox, F.E.G. Concomitant infections, parasites and immune responses. Parasitology 2011, 122, S23–S38. [Google Scholar] [CrossRef]
- Tenaillon, O.; Rodríguez-Verdugo, A.; Gaut, R.L.; McDonald, P.; Bennett, A.F.; Long, A.D.; Gaut, B.S. The molecular diversity of adaptive convergence. Science 2012, 335, 457–461. [Google Scholar] [CrossRef] [PubMed]
- Smillie, C.S.; Smith, M.B.; Friedman, J.; Cordero, O.X.; David, L.A.; Alm, E.J. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 2011, 480, 241–244. [Google Scholar] [CrossRef] [PubMed]
- Parker, J.; Tsagkogeorga, G.; Cotton, J.A.; Liu, Y.; Provero, P.; Stupka, E.; Rossiter, S.J. Genome-wide signatures of convergent evolution in echolocating mammals. Nature 2013, 502, 228–231. [Google Scholar] [CrossRef] [PubMed]
- Herniou, E.A.; Huguet, E.; Thézé, J.; Bézier, A.; Periquet, G.; Drezen, J.-M. When parasitic wasps hijacked viruses: Genomic and functional evolution of polydnaviruses. Phil. Trans. R. Soc. B 2013, 368, e20130051. [Google Scholar] [CrossRef]
- Combes, C. Parasitism: The Ecology and Evolution of Intimate Interactions; University of Chicago Press: Chicago, IL, USA, 2001. [Google Scholar]
- Shackelton, L.A.; Holmes, E.C. The evolution of large DNA viruses: Combining genomic information of viruses and their hosts. Trends Microbiol. 2004, 12, 458–465. [Google Scholar] [CrossRef] [PubMed]
- Sabehi, G.; Shaulov, L.; Silver, D.H.; Yanai, I.; Harel, A.; Lindell, D. A novel lineage of myoviruses infecting cyanobacteria is widespread in the oceans. Proc. Natl. Acad. Sci. USA 2012, 109, 2037–2042. [Google Scholar] [CrossRef] [PubMed]
- Anantharaman, K.; Duhaime, M.B.; Breier, J.A.; Wendt, K.A.; Toner, B.M.; Dick, G.J. Sulfur oxidation genes in diverse deep-sea viruses. Science 2014, 344, 757–760. [Google Scholar] [CrossRef] [PubMed]
- May, R.M. How many species are there on earth? Science 1988, 241, 1441. [Google Scholar] [CrossRef] [PubMed]
- Cory, J. Use of baculoviruses as biological insecticides. Mol. Biotechnol. 1997, 7, 303–313. [Google Scholar] [CrossRef] [PubMed]
- King, A.M.; Lefkowitz, E.; Adams, M.J.; Carstens, E.B. Virus Taxonomy: Ninth Report of the International Committee of Taxonomy of Viruses; Elsevier: Amsterdam, The Netherlands, 2011. [Google Scholar]
- Thézé, J.; Takatsuka, J.; Li, Z.; Gallais, J.; Doucet, D.; Arif, B.; Nakai, M.; Herniou, E.A. New insights into the evolution of Entomopoxvirinae from the complete genome sequences of four entomopoxviruses infecting Adoxophyes honmai, Choristoneura biennis, Choristoneura rosaceana, and Mythimna separata. J. Virol. 2013, 87, 7992–8003. [Google Scholar] [CrossRef] [PubMed]
- Forterre, P.; Prangishvili, D. The origin of viruses. Res. Microbiol. 2009, 160, 466–472. [Google Scholar] [CrossRef] [PubMed]
- Upton, C.; Slack, S.; Hunter, A.L.; Ehlers, A.; Roper, R.L. Poxvirus orthologous clusters: Toward defining the minimum essential poxvirus genome. J. Virol. 2003, 77, 7590–7600. [Google Scholar] [CrossRef] [PubMed]
- Garavaglia, M.J.; Miele, S.A.B.; Iserte, J.A.; Belaich, M.N.; Ghiringhelli, P.D. The ac53, ac78, ac101, and ac103 genes are newly discovered core genes in the family Baculoviridae. J. Virol. 2012, 86, 12069–12079. [Google Scholar] [CrossRef] [PubMed]
- De Andrade Zanotto, P.M.; Krakauer, D.C. Complete genome viral phylogenies suggests the concerted evolution of regulatory cores and accessory satellites. PLoS ONE 2008, 3, e3500. [Google Scholar] [CrossRef] [PubMed]
- Dall, D.; Luque, T.; O’Reilly, D. Insect-virus relationships: Sifting by informatics. Bioessays 2001, 23, 184–193. [Google Scholar] [PubMed]
- Hughes, A.L.; Friedman, R. Genome-wide survey for genes horizontally transferred from cellular organisms to baculoviruses. Mol. Biol. Evol. 2003, 20, 979–987. [Google Scholar] [CrossRef] [PubMed]
- McLysaght, A.; Baldi, P.F.; Gaut, B.S. Extensive gene gain associated with adaptive evolution of poxviruses. Proc. Natl. Acad. Sci. USA 2003, 100, 15655–15660. [Google Scholar] [CrossRef] [PubMed]
- Hughes, A.L.; Friedman, R. Poxvirus genome evolution by gene gain and loss. Mol. Phylogenet. Evol. 2005, 35, 186–195. [Google Scholar] [CrossRef] [PubMed]
- Bratke, K.A.; McLysaght, A. Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach. BMC Evol. Biol. 2008, 8, e67. [Google Scholar] [CrossRef]
- Insect Virology; Asgari, S.; Johnson, K.N. (Eds.) Caister Academic Press: Norfolk, UK, 2010.
- Eddy, S.R. Profile hidden Markov models. Bioinformatics 1998, 14, 755–763. [Google Scholar] [CrossRef] [PubMed]
- Sievers, F.; Wilm, A.; Dineen, D.; Gibson, T.J.; Karplus, K.; Li, W.; Lopez, R.; McWilliam, H.; Remmert, M.; Söding, J.; et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 2011, 7, e539. [Google Scholar] [CrossRef]
- Hyatt, D.; Chen, G.-L.; Locascio, P.F.; Land, M.L.; Larimer, F.W.; Hauser, L.J. Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 2010, 11, 119. [Google Scholar] [CrossRef]
- Stamatakis, A. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22, 2688–2690. [Google Scholar] [CrossRef] [PubMed]
- Mukawa, S.; Goto, C. In vivo characterization of two granuloviruses in larvae of Mythimna separata (Lepidoptera: Noctuidae). J. Gen. Virol. 2008, 89, 915–921. [Google Scholar] [CrossRef] [PubMed]
- Boc, A.; Philippe, H.; Makarenkov, V. Inferring and validating horizontal gene transfer events using bipartition dissimilarity. Syst. Biol. 2010, 59, 195–211. [Google Scholar] [CrossRef] [PubMed]
- Thézé, J.; Bézier, A.; Periquet, G.; Drezen, J.-M.; Herniou, E.A. Paleozoic origin of insect large dsDNA viruses. Proc. Natl. Acad. Sci. USA 2011, 108, 15931–15935. [Google Scholar] [CrossRef] [PubMed]
- Brüssow, H. The not so universal tree of life or the place of viruses in the living world. Phil. Trans. R. Soc. B 2009, 364, 2263–2274. [Google Scholar] [CrossRef] [PubMed]
- Filée, J.; Pouget, N.; Chandler, M. Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses. BMC Evol. Biol. 2008, 8, e320. [Google Scholar] [CrossRef]
- Possee, R.D.; Rohrmann, G.F. Baculovirus genome organization and evolution. In The Baculoviruses (The Viruses); Miller, L.K., Ed.; Springer: Berlin, Germany, 1997; pp. 109–134. [Google Scholar]
- Xu, J.; Hukuhara, T. Enhanced infection of a nuclear polyhedrosis virus in larvae of the armyworm, Pseudaletia separata, by a factor in the spheroids of an entomopoxvirus. J. Invertebr. Pathol. 1992, 60, 259–264. [Google Scholar] [CrossRef]
- Mitsuhashi, W.; Kawakita, H.; Murakami, R.; Takemoto, Y.; Saiki, T.; Miyamoto, K.; Wada, S. Spindles of an entomopoxvirus facilitate its infection of the host insect by disrupting the peritrophic membrane. J. Virol. 2007, 81, 4235–4243. [Google Scholar] [CrossRef] [PubMed]
- Takatsuka, J.; Okuno, S.; Ishii, T.; Nakai, M.; Kunimi, Y. Fitness-related traits of entomopoxviruses isolated from Adoxophyes honmai (Lepidoptera: Tortricidae) at three localities in Japan. J. Invertebr. Pathol. 2010, 105, 121–131. [Google Scholar] [CrossRef] [PubMed]
- Nakai, M.; Shiotsuki, T.; Kunimi, Y. An entomopoxvirus and a granulovirus use different mechanisms to prevent pupation of Adoxophyes honmai. Virus Res. 2004, 101, 185–191. [Google Scholar] [CrossRef] [PubMed]
- Katzourakis, A.; Gifford, R.J. Endogenous viral elements in animal genomes. PLoS Genet. 2010, 6, e1001191. [Google Scholar] [CrossRef] [PubMed]
- Dunning Hotopp, J.C.; Clark, M.E.; Oliveira, D.C.S.G.; Foster, J.M.; Fischer, P.; Muñoz Torres, M.C.; Giebel, J.D.; Kumar, N.; Ishmael, N.; Wang, S.; et al. Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 2007, 317, 1753–1756. [Google Scholar] [CrossRef] [PubMed]
- Sharon, I.; Alperovitch, A.; Rohwer, F.; Haynes, M.; Glaser, F.; Atamna-Ismaeel, N.; Pinter, R.Y.; Partensky, F.; Koonin, E.V.; Wolf, Y.I.; et al. Photosystem I gene cassettes are present in marine virus genomes. Nature 2009, 461, 258–262. [Google Scholar] [CrossRef] [PubMed]
- Zilber-Rosenberg, I.; Rosenberg, E. Role of microorganisms in the evolution of animals and plants: The hologenome theory of evolution. FEMS Microbiol. Rev. 2008, 32, 723–735. [Google Scholar] [CrossRef] [PubMed]
- Gilbert, C.; Chateigner, A.; Ernenwein, L.; Barbe, V.; Bézier, A.; Herniou, E.A.; Cordaux, R. Population genomics supports baculoviruses as vectors of horizontal transfer of insect transposons. Nat. Commun. 2014, 5, 3348. [Google Scholar] [PubMed]
- Pace, J.K.; Gilbert, C.; Clark, M.S.; Feschotte, C. Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. Proc. Natl. Acad. Sci. USA 2008, 105, 17023–17028. [Google Scholar] [CrossRef] [PubMed]
- Feschotte, C.; Pritham, E.J. A cornucopia of Helitrons shapes the maize genome. Proc. Natl. Acad. Sci. USA 2009, 106, 19747–19748. [Google Scholar] [CrossRef] [PubMed]
- Breitbart, M.; Rohwer, F. Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 2005, 13, 278–284. [Google Scholar] [CrossRef] [PubMed]
- Elde, N.C.; Child, S.J.; Eickbush, M.T.; Kitzman, J.O.; Rogers, K.S.; Shendure, J.; Geballe, A.P.; Malik, H.S. Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses. Cell 2012, 150, 831–841. [Google Scholar] [CrossRef] [PubMed]
- Bergin, D.; Reeves, E.P.; Renwick, J.; Wientjes, F.B.; Kavanagh, K. Superoxide production in Galleria mellonella hemocytes: Identification of proteins homologous to the NADPH oxidase complex of human neutrophils. Infect. Immun. 2005, 73, 4161–4170. [Google Scholar] [CrossRef] [PubMed]
- Clem, R.J. Baculoviruses and apoptosis: A diversity of genes and responses. Curr. Drug Targets 2007, 8, 1069–1074. [Google Scholar] [CrossRef] [PubMed]
- Hughes, A.L. Evolution of inhibitors of apoptosis in baculoviruses and their insect hosts. Infect. Genet. Evol. 2002, 2, 3–10. [Google Scholar] [CrossRef] [PubMed]
© 2015 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/).
Share and Cite
Thézé, J.; Takatsuka, J.; Nakai, M.; Arif, B.; Herniou, E.A. Gene Acquisition Convergence between Entomopoxviruses and Baculoviruses. Viruses 2015, 7, 1960-1974. https://doi.org/10.3390/v7041960
Thézé J, Takatsuka J, Nakai M, Arif B, Herniou EA. Gene Acquisition Convergence between Entomopoxviruses and Baculoviruses. Viruses. 2015; 7(4):1960-1974. https://doi.org/10.3390/v7041960
Chicago/Turabian StyleThézé, Julien, Jun Takatsuka, Madoka Nakai, Basil Arif, and Elisabeth A. Herniou. 2015. "Gene Acquisition Convergence between Entomopoxviruses and Baculoviruses" Viruses 7, no. 4: 1960-1974. https://doi.org/10.3390/v7041960
APA StyleThézé, J., Takatsuka, J., Nakai, M., Arif, B., & Herniou, E. A. (2015). Gene Acquisition Convergence between Entomopoxviruses and Baculoviruses. Viruses, 7(4), 1960-1974. https://doi.org/10.3390/v7041960