1. Evoluo viral e o uso de ferramentasde bioinformtica atila@usp.br 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/