Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota

Current Biology

Volumn 27, Issue 9, 2017, Pages 1362-1368

  Philosof, Alon ^a   Yutin, Natalya ^b   Flores Uribe, José ^a   Sharon, Itai ^c,d   Koonin, Eugene V ^b   Béjà, Oded ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c MIGAL Galilee Technology Center Kiryat   (Israel)

^d TEL HAI COLLEGE   (Israel)

Author keywords

archaea; DNA polymerase; marine; phage; replication; virus

Indexed keywords

DNA DIRECTED DNA POLYMERASE; VIRAL PROTEIN;

ARCHAEAL VIRUS; CLASSIFICATION; EURYARCHAEOTA; GENETICS; METABOLISM; METAGENOMICS; PHYLOGENY; PHYSIOLOGY; SEA; VIROLOGY; VIRUS DNA CELL DNA INTERACTION; VIRUS GENOME; VIRUS REPLICATION;

ARCHAEAL VIRUSES; DNA-DIRECTED DNA POLYMERASE; EURYARCHAEOTA; GENOME, VIRAL; METAGENOMICS; OCEANS AND SEAS; PHYLOGENY; VIRAL PROTEINS; VIRUS INTEGRATION; VIRUS REPLICATION;

EID: 85018179010     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2017.03.052     Document Type: Article

References (41)

1. 1 Massana, R., Murray, A.E., Preston, C.M., DeLong, E.F., Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl. Environ. Microbiol. 63 (1997), 50–56.
2. 2 Massana, R., DeLong, E.F., Pedrós-Alió, C., A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl. Environ. Microbiol. 66 (2000), 1777–1787.
3. 3 Galand, P.E., Casamayor, E.O., Kirchman, D.L., Potvin, M., Lovejoy, C., Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing. ISME J. 3 (2009), 860–869.
4. 4 Lincoln, S.A., Wai, B., Eppley, J.M., Church, M.J., Summons, R.E., DeLong, E.F., Planktonic Euryarchaeota are a significant source of archaeal tetraether lipids in the ocean. Proc. Natl. Acad. Sci. USA 111 (2014), 9858–9863.
5. 5 Zhang, C.L., Xie, W., Martin-Cuadrado, A.-B., Rodriguez-Valera, F., Marine Group II Archaea, potentially important players in the global ocean carbon cycle. Front. Microbiol., 6, 2015, 1108.
6. 6 Murray, A.E., Blakis, A., Massana, R., Strawzewiski, S., Passow, U., Alldredge, A., DeLong, E.F., A timeseries assessment of planktonic archaeal variability in the Santa Barbara Channel. Aquat. Microb. Ecol. 20 (1999), 129–145.
7. 7 Pernthaler, A., Preston, C.M., Pernthaler, J., DeLong, E.F., Amann, R., Comparison of fluorescently labeled oligonucleotide and polynucleotide probes for the detection of pelagic marine bacteria and archaea. Appl. Environ. Microbiol. 68 (2002), 661–667.
8. 8 Ottesen, E.A., Young, C.R., Eppley, J.M., Ryan, J.P., Chavez, F.P., Scholin, C.A., DeLong, E.F., Pattern and synchrony of gene expression among sympatric marine microbial populations. Proc. Natl. Acad. Sci. USA 110 (2013), E488–E497.
9. 9 Aylward, F.O., Eppley, J.M., Smith, J.M., Chavez, F.P., Scholin, C.A., DeLong, E.F., Microbial community transcriptional networks are conserved in three domains at ocean basin scales. Proc. Natl. Acad. Sci. USA 112 (2015), 5443–5448.
10. 10 Iverson, V., Morris, R.M., Frazar, C.D., Berthiaume, C.T., Morales, R.L., Armbrust, E.V., Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335 (2012), 587–590.
11. 11 Martin-Cuadrado, A.-B., Garcia-Heredia, I., Moltó, A.G., López-Úbeda, R., Kimes, N., López-García, P., Moreira, D., Rodriguez-Valera, F., A new class of marine Euryarchaeota group II from the Mediterranean deep chlorophyll maximum. ISME J. 9 (2015), 1619–1634.
12. 12 Prangishvili, D., The wonderful world of archaeal viruses. Annu. Rev. Microbiol. 67 (2013), 565–585.
13. 13 Krupovic, M., Prangishvili, D., Hendrix, R.W., Bamford, D.H., Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol. Mol. Biol. Rev. 75 (2011), 610–635.
14. 14 Porter, K., Russ, B.E., Dyall-Smith, M.L., Virus-host interactions in salt lakes. Curr. Opin. Microbiol. 10 (2007), 418–424.
15. 15 Pina, M., Bize, A., Forterre, P., Prangishvili, D., The archeoviruses. FEMS Microbiol. Rev. 35 (2011), 1035–1054.
16. 16 Atanasova, N.S., Roine, E., Oren, A., Bamford, D.H., Oksanen, H.M., Global network of specific virus-host interactions in hypersaline environments. Environ. Microbiol. 14 (2012), 426–440.
17. 17 Pietilä, M.K., Laurinmäki, P., Russell, D.A., Ko, C.C., Jacobs-Sera, D., Butcher, S.J., Bamford, D.H., Hendrix, R.W., Insights into head-tailed viruses infecting extremely halophilic archaea. J. Virol. 87 (2013), 3248–3260.
18. 18 Brum, J.R., Ignacio-Espinoza, J.C., Roux, S., Doulcier, G., Acinas, S.G., Alberti, A., Chaffron, S., Cruaud, C., de Vargas, C., Gasol, J.M., et al., Tara Oceans Coordinators. Ocean plankton. Patterns and ecological drivers of ocean viral communities. Science, 348, 2015, 1261498.
19. 19 Paez-Espino, D., Eloe-Fadrosh, E.A., Pavlopoulos, G.A., Thomas, A.D., Huntemann, M., Mikhailova, N., Rubin, E., Ivanova, N.N., Kyrpides, N.C., Uncovering Earth's virome. Nature 536 (2016), 425–430.
20. 20 Pesant, S., Not, F., Picheral, M., Kandels-Lewis, S., Le Bescot, N., Gorsky, G., Iudicone, D., Karsenti, E., Speich, S., Troublé, R., et al., Tara Oceans Consortium Coordinators. Open science resources for the discovery and analysis of Tara Oceans data. Sci. Data, 2, 2015, 150023.
21. 21 Sunagawa, S., Coelho, L.P., Chaffron, S., Kultima, J.R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D.R., Alberti, A., et al., Tara Oceans coordinators. Ocean plankton. Structure and function of the global ocean microbiome. Science, 348, 2015, 1261359.
22. 22 Iranzo, J., Koonin, E.V., Prangishvili, D., Krupovic, M., Bipartite network analysis of the archaeal virosphere: evolutionary connections between viruses and capsidless mobile elements. J. Virol. 90 (2016), 11043–11055.
23. 23 Makarova, K.S., Koonin, E.V., Archaeology of eukaryotic DNA replication. Cold Spring Harb. Perspect. Biol., 5, 2013, a012963.
24. 24 Kazlauskas, D., Krupovic, M., Venclovas, Č., The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes. Nucleic Acids Res. 44 (2016), 4551–4564.
25. 25 Breitbart, M., Thompson, L.R., Suttle, C.A., Sullivan, M.B., Exploring the vast diversity of marine viruses. Oceanography (Wash. D.C.) 20 (2007), 135–139.
26. 26 Luk, A.W., Williams, T.J., Erdmann, S., Papke, R.T., Cavicchioli, R., Viruses of haloarchaea. Life (Basel) 4 (2014), 681–715.
27. 27 Makarova, K.S., Krupovic, M., Koonin, E.V., Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery. Front. Microbiol., 5, 2014, 354.
28. 28 Takemura, M., Yokobori, S., Ogata, H., Evolution of eukaryotic DNA polymerases via interaction between cells and large DNA viruses. J. Mol. Evol. 81 (2015), 24–33.
29. 29 Sullivan, M.B., Coleman, M.L., Weigele, P., Rohwer, F., Chisholm, S.W., Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol., 3, 2005, e144.
30. 30 Smith, D.R., Doucette-Stamm, L.A., Deloughery, C., Lee, H., Dubois, J., Aldredge, T., Bashirzadeh, R., Blakely, D., Cook, R., Gilbert, K., et al. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J. Bacteriol. 179 (1997), 7135–7155.
31. 31 Klenk, H.P., Clayton, R.A., Tomb, J.F., White, O., Nelson, K.E., Ketchum, K.A., Dodson, R.J., Gwinn, M., Hickey, E.K., Peterson, J.D., et al. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390 (1997), 364–370.
32. 32 Jokela, M., Eskelinen, A., Pospiech, H., Rouvinen, J., Syväoja, J.E., Characterization of the 3′ exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D. Nucleic Acids Res. 32 (2004), 2430–2440.
33. 33 Hertveldt, K., Lavigne, R., Pleteneva, E., Sernova, N., Kurochkina, L., Korchevskii, R., Robben, J., Mesyanzhinov, V., Krylov, V.N., Volckaert, G., Genome comparison of Pseudomonas aeruginosa large phages. J. Mol. Biol. 354 (2005), 536–545.
34. 34 Cornelissen, A., Hardies, S.C., Shaburova, O.V., Krylov, V.N., Mattheus, W., Kropinski, A.M., Lavigne, R., Complete genome sequence of the giant virus OBP and comparative genome analysis of the diverse ΦKZ-related phages. J. Virol. 86 (2012), 1844–1852.
35. 35 Semenyuk, P.I., Orlov, V.N., Sokolova, O.S., Kurochkina, L.P., New GroEL-like chaperonin of bacteriophage OBP Pseudomonas fluorescens suppresses thermal protein aggregation in an ATP-dependent manner. Biochem. J. 473 (2016), 2383–2393.
36. 36 Zhao, Y., Temperton, B., Thrash, J.C., Schwalbach, M.S., Vergin, K.L., Landry, Z.C., Ellisman, M., Deerinck, T., Sullivan, M.B., Giovannoni, S.J., Abundant SAR11 viruses in the ocean. Nature 494 (2013), 357–360.
37. 37 Kang, I., Oh, H.-M., Kang, D., Cho, J.-C., Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans. Proc. Natl. Acad. Sci. USA 110 (2013), 12343–12348.
38. 38 Haro-Moreno, J.M., Rodriguez-Valera, F., López-García, P., Moreira, D., Martin-Cuadrado, A.-B., New insights into marine group III Euryarchaeota, from dark to light. ISME J., 2017, 10.1038/ismej.2016.188.
39. 39 Simmonds, P., Adams, M.J., Benkő, M., Breitbart, M., Brister, J.R., Carstens, E.B., Davison, A.J., Delwart, E., Gorbalenya, A.E., Harrach, B., et al. Consensus statement: virus taxonomy in the age of metagenomics. Nat. Rev. Microbiol. 15 (2017), 161–168.
40. 40 Danovaro, R., Dell'Anno, A., Corinaldesi, C., Rastelli, E., Cavicchioli, R., Krupovic, M., Noble, R.T., Nunoura, T., Prangishvili, D., Virus-mediated archaeal hecatomb in the deep seafloor. Sci. Adv., 2, 2016, e1600492.
41. 41 Nishimura, Y., Watai, H., Honda, T., Mihara, T., Omae, K., Roux, S., Blanc-Mathieu, R., Yamamoto, K., Hingamp, P., Sako, Y., et al. Environmental viral genomes shed new light on virus-host interactions in the ocean. mSphere, 2, 2017 e00359–e16.