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Evolução viral e o uso de ferramentas de bioinformática Atila Iamarino [email protected] http://scienceblogs.com.br/rainha/

Filogenia evolucao 2012

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Palestra sobre evolução moleular de vírus ministrada na disciplina de Microbiologia Ambiental de 2012 - ICB USP.

Text of Filogenia evolucao 2012

  • 1. Evoluo viral e o uso de ferramentasde bioinformtica [email protected] Atila Iamarino http://scienceblogs.com.br/rainha/
  • 2. O que evoluo molecularIntegrao entre biologia molecular, biologiaevolutiva e gentica de populaes
  • 3. Resumo Evoluo Mecanismos Evolutivos Mutao Migrao Recombinao Deriva Gentica Seleo Natural Evoluo viral Vrus de dsDNA: grandes genomas e grandes possibilidades Vrus de RNA: pequenos e furiosos Evoluo do hospedeiro Ferramentas de estudo
  • 4. A informao est contida no DNA/RNAA_Arizona_01_2009_112_2009.307 ATG AAT CCA AAC CAA AAG ATA ATA ACC ATT GGT TCG GTCA_Arizona_01_2009_112_2009.307 AUG AAU CCA AAC CAA AAG AUA AUA ACC AUU GGU UCG GUCA_Arizona_01_2009_112_2009.307 Met Asn Pro Asn Gln Lys Ile Ile Thr Ile Gly Ser Val
  • 5. O que evoluo Conceito: Variao na frequncia allica entre uma gerao e outraGerao 1 Gerao 2 Gerao 3 Gerao 4
  • 6. Mecanismos evolutivos: MutaoGerao 1 Gerao 2 Gerao 3 Gerao 4 Mutao
  • 7. Mecanismos evolutivos: Migrao Populao 1 Populao 2Gerao 1 Gerao 2 Gerao 3 Gerao 4
  • 8. Mecanismos evolutivos: RecombinaoSimon-Loriere, E., & Holmes, E. C. (2011). Whydo RNA viruses recombine? Nature reviews.Microbiology, 9(8), 617-626.
  • 9. Mecanismos evolutivos: DerivaOrigem do alelo Tempo para fixao(1 gerao) ~4N geraes
  • 10. Mecanismos evolutivos: Deriva Populao Gargalo (reduo Sobreviventes Prxima parental drstica na gerao populao)
  • 11. Mecanismos evolutivos: Seleo Organismos diferem em sua habilidade de sobreviver e sereproduzir, devido principalmente a diferenas genticas entre osindivduos. A cada gerao os indivduos que sobrevivem e sereplicam/reproduzem mais eficientemente, contribuem mais naformao da proxima gerao. A seleo atua somente em caracteres herdveis.
  • 12. Mecanismos evolutivos: Seleo FitnessFentipo
  • 13. Mecanismos evolutivos: Seleo Positiva Comparao da taxa de substituio sinnima (dS) e no sinnima (dN)por stio (dN/dS = ): Ser Met Leu Gly GlySeq 1: TCA ATG TTA GGG GGA * **Seq 2: TCG ATA CTA GGT ATA Ser Ile Leu Gly Ilesubstituio sinnima *substituio no sinnima dN/dS < 1.0 = seleo purificadora dN/dS ~ 1.0 = seleo neutra dN/dS > 1.0 = seleo positiva
  • 14. Evoluo viral: Taxa de mutao Taxa de mutao (mutaes/stio/replicao) Taxa de substituio (mutaes/stio/ano) Eucariotos: ~ 0.01 mutaes por genoma, por replicao ~10-8 a 10-9 substituies/stio/ano Bactrias: ~ 0.003 mutaes por genoma, por replicao ~10-7 a 10-9 substituies/stio/anoDuffy, S., Shackelton, L. a, & Holmes, E. C. (2008). Rates of evolutionary change in viruses: patterns anddeterminants. Nature reviews. Genetics, 9(4), 267-76. doi:10.1038/nrg2323
  • 15. Vrus de dsDNA: grandes genomas e grandes possibilidades Imunomoduladores Enzimas chave de vias metablicas Capacidade de permutar e evoluir genes capturados gene Bo17 de BoHV-4 20 a 30 vezes mais rpidoMarkine-Goriaynoff, N., Georgin, J.-P., Goltz, M., Zimmermann, W., Broll, H., Wamwayi, H. M., Pastoret, P.-P.,et al. (2003). The Core 2 -1,6-N-Acetylglucosaminyltransferase-Mucin Encoded by Bovine Herpesvirus 4Was Acquired from an Ancestor of the African Buffalo. Journal of Virology, 77(3), 1784-1792.doi:10.1128/JVI.77.3.1784-1792.2003
  • 16. Vrus de dsDNA: grandes genomas e grandes possibilidades EGT - ecdisonaHoover, K., Grove, M., Gardner, M., Hughes, D. P., McNeil, J., & Slavicek, J. (2011). A gene for an extendedphenotype. Science, 333(6048), 1401. doi:10.1126/science.1209199
  • 17. Vrus de RNA: pequenos e furiososHIV:Genoma de 9,8 kb~10-3 substituies/stio/replicao~ 1 mutaes por genoma, porreplicao~10-10 partculas por diaAD101, CCR5 e CXCR4Trkola, A., Kuhmann, S. E., Strizki, J. M., Maxwell, E., Ketas, T., Morgan, T., Pugach, P., et al. (2002). HIV-1escape from a small molecule, CCR5-specific entry inhibitor does not involve CXCR4 use. PNAS, 99(1), 395-400. doi:10.1073/pnas.012519099
  • 18. Vrus de RNA: pequenos e furiosos Sironen et al. (2001): Taxa de substituio ~1x10-7!!Smith, G. J. D., Vijaykrishna, D., Bahl, J., Lycett, S. J., Worobey, M., Pybus, O. G., Ma, S. K., et al. (2009).Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature, 459(7250),1122-5.
  • 19. Vrus de RNA: pequenos e furiosos Icosaedro: bornavirus Tringulo: filovirus Sironen et al. (2001): Taxa de substituio ~1x10-7!!Belyi, V. a, Levine, A.J. & Skalka, A.M., 2010. Unexpected inheritance: multiple integrations of ancientbornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes. PLoS pathogens, 6(7),p.e1001030.
  • 20. Evoluo viral: ResumoDuffy, S., Shackelton, L. a, & Holmes, E. C. (2008). Rates of evolutionary change in viruses: patterns anddeterminants. Nature reviews. Genetics, 9(4), 267-76. doi:10.1038/nrg2323
  • 21. Evoluo do Hospedeiro: Imunidade inata Meyerson, N. R., & Sawyer, S. L. (2011). Two- stepping through time: mammals and viruses. Trends in microbiology, 19(6), 286-94. Elsevier Ltd. doi:10.1016/j.tim.2011.03.006
  • 22. Evoluo do Hospedeiro: Sincitina HERVs formam 8% do genoma Placenta Fusognica e imunossupressoraLee YN, Bieniasz PD (2007) Reconstitution of an Infectious Human Endogenous Retrovirus. PLoS Pathog 3(1):e10. doi:10.1371/journal.ppat.0030010Mi, S., Lee, X., Li, X.-ping, Veldman, G. M., Finnerty, H., Racie, L., Lavallie, E., et al. (2000). Syncytin is a captiveretroviral envelope protein involved. Nature, 403(February), 785-789.
  • 23. Evoluo do Hospedeiro: Vespas parasitidesIchneumonidae IchnovrusBraconidae Bracovrus Manduca sexta+ Cotesia congregata + PolydnavirusBzier, A., Annaheim, M., Herbinire, J., Wetterwald, C., Gyapay, G., Bernard-Samain, S., Wincker, P., et al.(2009). Polydnaviruses of braconid wasps derive from an ancestral nudivirus. Science .323(5916), 926-30.doi:10.1126/science.1166788Burke, G.R. and Strand, M.R. (2012). Deep Sequencing Identifies Viral and Wasp Genes with Potential Rolesin Replication of Microplitis demolitor Bracovirus. J. Virol. 86:3293-3306 doi:10.1128/JVI.06434-11
  • 24. Evoluo do Hospedeiro: Cianfagos e fotossistemas Fagos de Prochlorococcus e Synechococcus Fotossistemas turbinados psbA - 60% pertencem a fagos ~10% da fotossnteseMann, N. H., Cook, A., Millard, A., Bailey, S. &Clokie,M. Bacterial photosynthesis genes in a virus. Nature424, 741 (2003).Sharon, I., Alperovitch, A., Rohwer, F., Haynes, M.,Glaser, F., Atamna-Ismaeel, N., Pinter, R. Y., et al.(2009). Photosystem I gene cassettes are present in Sironen et al. (2001):marine virus genomes. Nature, 461(7261), 258-62.doi:10.1038/nature08284 Taxa de substituio ~1x10-7!!Rohwer, F., & Thurber, R. V. (2009). Viruses manipulatethe marine environment. Nature, 459(7244), 207-12.doi:10.1038/nature08060
  • 25. Mimivrus e a origem... 600 nm Mamavrus Legionella sp. sem 16S 1,2 Mb RNAt: ArgRS, CysRS, MetRS e TyrRS 4 Domnio da vida? SputnikLa Scola, B., Audic, S., Robert, C., Jungang, L., Lamballerie, X. de, Drancourt, M., et al. (2003). A giant virus inamoebae. Science, 299(5615), 2033 et al. (2001): Sironen Taxa de substituio ~1x10-7!!La Scola, B., Desnues, C., Pagnier, I., Robert, C., Barrassi, L., Fournous, G., et al. (2008). The virophage as aunique parasite of the giant mimivirus. Nature, 455(7209), 100-4. doi: 10.1038/nature07218.
  • 26. Raoult, D. et al. (2004). The 1.2-megabase genome sequence of Mimivirus.Science 306, 13441350.Moreira, D., & Lpez-Garca, P. (2009). Ten reasons to exclude viruses from thetree of life. Nature reviews. Microbiology, 7(4), 306-11Hegde, N. R., Maddur, M. S., Kaveri, S. V., & Bayry, J. (2009). Reasons to includeviruses in the tree of life. Nature reviews. Microbiology, 7(8), 615Navas-Castillo, J. (2009). Six comments on the ten reasons for the demotion ofviruses. Nature reviews. Microbiology, 7(8), 615Claverie, J.-M., & Ogata, H. (2009). Ten good reasons not to exclude giruses fromthe evolutionary picture. Nature reviews. Microbiology, 7(8), 615Ludmir, E. B., & Enquist, L. W. (2009). Viral genomes are part of the phylogenetictree of life. Nature reviews. Microbiology, 7(8), 615Koonin, E. V., Senkevich, T. G., & Dolja, V. V. (2009). Compelling reasons whyviruses are relevant for the origin of cells. Nature reviews. Microbiology, 7(8), 615Lpez-Garca, P., & Moreira, D. (2009). Yet viruses cannot be included in the treeof life. Nature Reviews Microbiology, 7(8), 615-617.Raoult, D. (2009). There is no such thing as a tree of life (and of course viruses areout!). Nature reviews. Microbiology, 7(8), 615
  • 27. Mimivrus e a origem... Cafeteria roenbergensis virus - CroV 730 kb Mavirus ~ transposons Maverick polimerase integrase organizao genmica Demais genes parecidos com SputnikYau, S., Lauro, F. M., DeMaere, M. Z., Brown, M. V., Thomas, T., Raftery, M. J., Andrews-Pfannkoch, C., et al. Sironen et al. (2001):(2011). Virophage control of antarctic algal host-virus dynamics. Proceedings of the National Academy ofSciences of the United States of America, 108(15), 6163-8. doi:10.1073/pnas.1018221108La Scola, B., Taxa de substituio ~1x10-7!!Fischer, M. G., & Suttle, C. a. (2011). A virophage at the origin of large DNA transposons. Science (New York,N.Y.), 332(6026), 231-4. doi:10.1126/science.1199412
  • 28. Mimivrus e a origem... Megavirus chilensis 1,26 Mb 594 genes compartilhados 50% de resduos idnticos RNAt ArgRS, CysRS, MetRS e TyrRS + IleRS, TrpRS, e AsnRS Sironen et al. (2001): Taxa de substituio ~1x10-7!!Arslan, D., Legendre, M., Seltzer, V., Abergel, C., & Claverie, J.-M. (2011). Distant Mimivirus relative with alarger genome highlights the fundamental features of Megaviridae. Proceedings of the National Academy ofSciences, 108(42). doi:10.1073/pnas.1110889108
  • 29. Ferramentas Sironen et al. (2001): Taxa de substituio ~1x10-7!!
  • 30. Evoluo viral como marcador Biek, R., Drummond, A. J., & Poss, M. (2006). A virus reveals population structure and recent demographic history of its carnivore host. Science, 311(5760), 538-41. doi:10.1126/science.1121360 Treicker DG, Lemey P, Velasco-Villa A, Rupprecht CE (2012) Rates of Viral Evolution Are Linked to Host Geography in Bat Rabies. PLoS Pathog 8(5): e1002720. doi:10.1371/journal.ppat.1002720
  • 31. FilogeniasShackelton, L. a, & Holmes, E. C. (2004). The evolution of large DNA viruses: combining genomic informationof viruses and their hosts. Trends in microbiology, 12(10), 458-65. doi:10.1016/j.tim.2004.08.005
  • 32. Filogenias contm histria Imunidade cruzada efetiva Sironen et al. (2001): Taxa de substituio ~1x10-7!!Grenfell, B. T., Pybus, O. G., Gog, J. R., Wood, J. L. N., Daly, J. M., Mumford, J. a, & Holmes, E. C. (2004).Unifying the epidemiological and evolutionary dynamics of pathogens. Science, 303(5656), 327-32.
  • 33. Filogenias contm histria Imunidade cruzada parcial Sironen et al. (2001): Taxa de substituio ~1x10-7!!Grenfell, B. T., Pybus, O. G., Gog, J. R., Wood, J. L. N., Daly, J. M., Mumford, J. a, & Holmes, E. C. (2004).Unifying the epidemiological and evolutionary dynamics of pathogens. Science, 303(5656), 327-32.
  • 34. Filogenias contm histria Sem imunidade cruzada Sironen et al. (2001): Taxa de substituio ~1x10-7!!Grenfell, B. T., Pybus, O. G., Gog, J. R., Wood, J. L. N., Daly, J. M., Mumford, J. a, & Holmes, E. C. (2004).Unifying the epidemiological and evolutionary dynamics of pathogens. Science, 303(5656), 327-32.
  • 35. Coalescncia Atualmente Coalescncia De volta ao MRCA Most Recent Common Ancestor (MRCA)
  • 36. CoalescnciaHughes, G. J., Fearnhill, E., Dunn, D., Lycett, S. J., Rambaut, A., & Leigh Brown, A. J. (2009). Molecularphylodynamics of the heterosexual HIV epidemic in the United Kingdom. PLoS pathogens, 5(9), e1000590.
  • 37. CoalescnciaGimenes, M. V., Zanotto, P. M. D. a, Suttle, C. a, da Cunha, H. B., & Mehnert, D. U. (2012). Phylodynamics andmovement of Phycodnaviruses among aquatic environments. The ISME journal, 6(2), 237-47.doi:10.1038/ismej.2011.93
  • 38. Para MaisNot Exactly Rocket Sciencehttp://blogs.discovermagazine.com/notrocketscienceThe Loomhttp://blogs.discovermagazine.com/loom/Small Things Consideredhttp://schaechter.asmblog.org/ERVhttp://scienceblogs.com/erv/This Week in Virologyhttp://www.twiv.tv/