Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous

Virology Journal

Volumn 9, Issue , 2012, Pages

  Baeza, Marcelo ^a   Bravo, Natalia ^a   Sanhueza, Mario ^a   Flores, Oriana ^a   Villarreal, Pablo ^a   Cifuentes, Victor ^a  

^a UNIVERSITY OF CHILE   (Chile)

Author keywords

dsRNA; Mycovirus; Totivirus; X. dendrorhous

Indexed keywords

DOUBLE STRANDED RNA; HYBRID PROTEIN; RIBONUCLEASE; RNA DIRECTED RNA POLYMERASE;

AMINO ACID SEQUENCE; ARTICLE; GENE STRUCTURE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RIBOSOMAL FRAMESHIFTING; TOTIVIRUS; VIRUS CAPSID; VIRUS CHARACTERIZATION; XANTHOPHYLLOMYCES DENDRORHOUS; YEAST;

AMINO ACID SEQUENCE; BASE SEQUENCE; BASIDIOMYCOTA; CLUSTER ANALYSIS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; RNA, DOUBLE-STRANDED; RNA, VIRAL; SATELLITE VIRUSES; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; TOTIVIRUS;

MIRIDAE; MYCOVIRUS; SATELLITE VIRUSES; TOTIVIRIDAE; TOTIVIRUS; XANTHOPHYLLOMYCES DENDRORHOUS;

EID: 84864227275     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-9-140     Document Type: Article

References (59)

1. Origin, adaptation and evolutionary pathways of fungal viruses. Ghabrial SA, Virus Genes 1998 16 119 131 10.1023/A:1007966229595 9562896 (Pubitemid 28110830)
2. Viruses of plant pathogenic fungi. Ghabrial SA, Suzuki N, Annu Rev Phytopathol 2009 47 353 384 10.1146/annurev-phyto-080508-081932 19400634
3. The effects of dsRNA mycoviruses on growth and murine virulence of Aspergillus fumigatus. Bhatti MF, Jamal A, Petrou MA, Cairns TC, Bignell EM, Coutts RH, Fungal Genet Biol 2011
4. Dynamics of dsRNA mycoviruses in black Aspergillus populations. van Diepeningen AD, Debets AJ, Hoekstra RF, Fungal Genet Biol 2006 43 446 452 10.1016/j.fgb.2006.01.014 16546419 (Pubitemid 43668996)
5. Mycoviruses of filamentous fungi and their relevance to plant pathology. Pearson MN, Beever RE, Boine B, Arthur K, Mol Plant Pathol 2009 10 115 128 10.1111/j.1364-3703.2008.00503.x 19161358
6. Yeast killer systems. Magliani W, Conti S, Gerloni M, Bertolotti D, Polonelli L, Clin Microbiol Rev 1997 10 369 400 9227858 (Pubitemid 27359257)
7. Bruenn J, The double-stranded RNA viruses of Ustilago maydis and their killer toxins. dsRNA genetic elements: concepts and applications in agriculture, forestry, and medicine CRC Press Boca Raton, Florida 2002 109 124
8. The H1 double-stranded RNA genome of Ustilago maydis virus-H1 encodes a polyprotein that contains structural motifs for capsid polypeptide, papain-like protease, and RNA-dependent RNA polymerase. Kang J, Wu J, Bruenn JA, Park C, Virus Res 2001 76 183 189 10.1016/S0168-1702(01)00250-7 11410317 (Pubitemid 32532106)
9. Yeast viral killer toxins: lethality and self-protection. Schmitt MJ, Breinig F, Nat Rev Microbiol 2006 4 212 221 10.1038/nrmicro1347 16489348
10. Yeast dsRNA viruses: replication and killer phenotypes. Tipper DJ, Schmitt MJ, Mol Microbiol 1991 5 2331 2338 10.1111/j.1365-2958.1991.tb02078.x 1665194 (Pubitemid 21895963)
11. Family Totiviridae. Wickner RB, Wang CC, Patterson JL, Virus taxonomy: classification and nomenclature of viruses: eighth report of the International Committee on the Taxonomy of Viruses Elsevier Academic Press, San Diego, CA, Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA, 2005 571 580
12. Presence of double-stranded RNA and virus-like particles in Phaffia rhodozyma. Castillo A, Cifuentes V, Curr Genet 1994 26 364 368 10.1007/BF00310502 7882432 (Pubitemid 24297663)
13. Variability and inheritance of double-stranded RNA viruses in Phaffia rhodozyma. Pfeiffer I, Kucsera J, Varga J, Parducz A, Ferenczy L, Curr Genet 1996 30 294 297 10.1007/s002940050135 8781171 (Pubitemid 26381624)
14. Effects of double-stranded rna viruses on the reproduction of Phaffia rhodozyma. Pfeiffer I, Litter J, Kucsera J, Acta Biol Hung 2001 52 299 306 10.1556/ABiol.52.2001.2-3.14 11426864 (Pubitemid 32540347)
15. Polymorphism of viral dsRNA in Xanthophyllomyces dendrorhous strains isolated from different geographic areas. Baeza M, Sanhueza M, Flores O, Oviedo V, Libkind D, Cifuentes V, Virol J 2009 6 160 10.1186/1743-422X-6-160 19814805
16. Phaffia, a New Yeast Genus in the Deuteromycotina (Blastomycetes). Miller MW, Yoneyama MMS, Int J Syst Bacteriol 1976 26 6
17. Perfect state of Rhodomyces dendrorhous (Phaffia rhodozyma). Golubev WI, Yeast 1995 11 101 110 7732720
18. A microbial consortium involving the astaxanthin producer Xanthophyllomyces dendrorhous on freshly cut birch stumps in Germany. Weber RWS, Davoli P, Anke H, Mycologist 2006 20 57 61 10.1016/j.mycol.2006.03.010 (Pubitemid 43963664)
19. Characterization of a novel South American population of the astaxanthin producing yeast Xanthophyllomyces dendrorhous (Phaffia rhodozyma). Libkind D, Moline M, de Garcia V, Fontenla S, van Broock M, J Ind Microbiol Biotechnol 2008 35 151 158 10.1007/s10295-007-0275-8 18000694
20. Biogeography, host specificity, and molecular phylogeny of the basidiomycetous yeast Phaffia rhodozyma and its sexual form, Xanthophyllomyces dendrorhous. Libkind D, Ruffini A, van Broock M, Alves L, Sampaio JP, Appl Environ Microbiol 2007 73 1120 1125 10.1128/AEM.01432-06 17189439
21. Potential health-promoting effects of astaxanthin: A high-value carotenoid mostly from microalgae. Yuan JP, Peng J, Yin K, Wang JH, Mol Nutr Food Res 2011 55 150 165 10.1002/mnfr.201000414 21207519
22. Astaxanthin: a review of its chemistry and applications. Higuera-Ciapara I, Felix-Valenzuela L, Goycoolea FM, Crit Rev Food Sci Nutr 2006 46 185 196 10.1080/10408690590957188 16431409
23. Mycocin production in Cryptococcus aquaticus. Pfeiffer I, Golubev WI, Kucsera J, Golubev N, Antonie Van Leeuwenhoek 2004 369 375 15702390 (Pubitemid 40260298)
24. Cloning of noncultivatable human rotavirus by single primer amplification. Lambden PR, Cooke SJ, Caul EO, Clarke IN, J Virol 1992 66 1817 1822 1371174
25. Cloning of complete genome sets of six dsRNA viruses using an improved cloning method for large dsRNA genes. Potgieter AC, Steele AD, van Dijk AA, J Gen Virol 2002 83 2215 2223 12185276 (Pubitemid 34993728)
26. Brierley I, Gilbert RJC, Pennell S, Pseudoknot-Dependent Programmed ?1 Ribosomal Frameshifting: Structures, Mechanisms and Models Springer New York, New York, NY, Atkins JF, Gesteland RF, 2010 149 174
27. RNA pseudoknots: Translational frameshifting and readthrough on viral RNAs. Ten Dam EB, Pleij CW, Bosch L, Virus Genes 1990 4 121 10.1007/BF00678404 2402881
28. Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses. Firth AE, Blitvich BJ, Wills NM, Miller CL, Atkins JF, Virology 2010 399 153 166 10.1016/j.virol.2009.12.033 20097399
29. Identification and analysis of the site of 1 ribosomal frameshifting in red clover necrotic mosaic virus. Kim KH, Lommel SA, Virology 1994 200 574 582 10.1006/viro.1994.1220 8178444 (Pubitemid 24146533)
30. A structural and primary sequence comparison of the viral RNA-dependent RNA polymerases. Bruenn JA, Nucleic Acids Res 2003 31 1821 1829 10.1093/nar/gkg277 12654997 (Pubitemid 36432688)
31. Evidence for common ancestry of a chestnut blight hypovirulence- associated double-stranded RNA and a group of positive-strand RNA plant viruses. Koonin EV, Choi GH, Nuss DL, Shapira R, Carrington JC, Proc Natl Acad Sci USA 1991 88 10647 10651 10.1073/pnas.88.23.10647 1961731 (Pubitemid 21915894)
32. RNA-dependent RNA polymerase consensus sequence of the LA double-stranded RNA virus: definition of essential domains. Ribas JC, Wickner RB, Proc Natl Acad Sci USA 1992 89 2185 10.1073/pnas.89.6.2185 1549580
33. Functions of conserved motifs in the RNA-dependent RNA polymerase of a yeast double-stranded RNA virus. Routhier E, Bruenn JA, J Virol 1998 72 4427 9557735
34. Characterization of debilitation-associated mycovirus infecting the plant-pathogenic fungus Sclerotinia sclerotiorum. Xie J, Wei D, Jiang D, Fu Y, Li G, Ghabrial S, Peng Y, J Gen Virol 2006 87 241 249 10.1099/vir.0.81522-0 16361437 (Pubitemid 43056963)
35. A novel mycovirus that is related to the human pathogen hepatitis E virus and rubi-like viruses. Liu H, Fu Y, Jiang D, Li G, Xie J, Peng Y, Yi X, Ghabrial SA, J Virol 2009 83 1981 1991 10.1128/JVI.01897-08 19073734
36. Ghabrial SA, A transmissible disease of Helminthosporium victoriae: Evidence for a viral etiology CRC Press, Boca Raton, FL 1986 163 176
37. Molecular genetics of the viruses infecting the plant pathogenic fungus Helminthosporium victoriae. Ghabrial SA, Soldevila AI, Havens WM, Molecular Biology of Double-stranded RNA: Concepts and Applications in Agriculture, Forestry and Medicine 2002 213 236
38. Coinfection of a fungal pathogen by two distinct double-stranded RNA viruses. Preisig O, Wingfield BD, Wingfield MJ, Virology 1998 252 399 406 10.1006/viro.1998.9480 9878619 (Pubitemid 29013422)
39. The double-stranded RNA viruses of Saccharomyces cerevisiae. Wickner R, Ribas J, Searfoss A, dsRNA genetic elements. Concepts and applicaiotns in agriculture, forestry, and medicine CRC Press, Boca Raton, SM T, 2002 67 108
40. Genome organization and expression of the Penicillium stoloniferum virus F. Kim JW, Choi EY, Lee JI, Virus Genes 2005 31 175 183 10.1007/s11262-005-1793- y 16025243 (Pubitemid 41126211)
41. Genome organization and expression of the Penicillium stoloniferum virus S. Kim JW, Kim SY, Kim KM, Virus Genes 2003 27 249 256 10.1023/A:1026343831909 14618085 (Pubitemid 37500712)
42. Characterization of double-stranded RNA elements in the violet root rot fungus Helicobasidium mompa. Osaki H, Nomura K, Matsumoto N, Ohtsu Y, Mycol Res 2004 108 635 640 10.1017/S095375620400005X 15323245 (Pubitemid 38893588)
43. Co-infection by two distinct totivirus-like double-stranded RNA elements in Chalara elegans (Thielaviopsis basicola). Park Y, James D, Punja ZK, Virus Res 2005 109 71 85 10.1016/j.virusres.2004.10.011 15826915 (Pubitemid 40249360)
44. Mycoviruses infecting the endophytic and entomopathogenic fungus Tolypocladium cylindrosporum. Herrero N, Zabalgogeazcoa I, Virus Res 2011 160 409 413 10.1016/j.virusres.2011.06.015 21736906
45. Complexity of dsRNA mycovirus isolated from Fusarium graminearum. Chu YM, Lim WS, Yea SJ, Cho JD, Lee YW, Kim KH, Virus Genes 2004 28 135 143 14739658
46. An inexpensive alternative to glassmilk for DNA purification. Boyle JS, Lew AM, Trends Genet 1995 11 8 10.1016/S0168-9525(00)88977-5 7900196
47. A Rapid Method for Sequencing the 5'- and 3'-Termini of Double-Stranded RNA Viral Templates using RLM-RACE. Coutts R, Livieratos C, J Phytopathology 2003 527 525 527 (Pubitemid 39615729)
48. Mapping the 5 and 3 ends of Tetrahymena thermophila mRNAs using RNA ligase mediated amplification of cDNA ends (RLM-RACE). Liu X, Gorovsky MA, Nucleic Acids Res 1993 21 4954 10.1093/nar/21.21.4954 8177745
49. A new mathematical model for relative quantification in real-time RT-PCR. Pfaffl MW, Nucleic Acids Res 2001 29 45 10.1093/nar/29.9.e45 11328886
50. Analysis of relative gene expression data using real-time quantitative PCR and the 2- CT method. Livak KJ, Schmittgen TD, Methods 2001 25 402 408 10.1006/meth.2001.1262 11846609 (Pubitemid 34164012)
51. Rapid affinity immunochromatography column-based tests for sensitive detection of Clostridium botulinum neurotoxins and Escherichia coli O157. Brunt J, Webb MD, Peck MW, Appl Environ Microbiol 2010 76 4143 4150 10.1128/AEM.03059-09 20435757
52. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, Mol Biol Evol 2011 28 2731 2739 10.1093/molbev/msr121 21546353
53. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Saitou N, Nei M, Mol Biol Evol 1987 4 406 425 3447015
54. Evolutionary divergence and convergence in proteins. Zuckerkandl E, Pauling L, Evolving genes and proteins 1965 97 166
55. Confidence limits on phylogenies: an approach using the bootstrap. Felsenstein J, Evolution 1985 39 783 791 10.2307/2408678
56. DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model. Sperschneider J, Datta A, Nucleic Acids Res 2010 38 103 10.1093/nar/gkq021 20123730
57. Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins. Sperschneider J, Datta A, Wise MJ, RNA 2011 17 27 38 10.1261/rna.2394511 21098139
58. Predicting structures and stabilities for H-type pseudoknots with interhelix loops. Cao S, Chen SJ, RNA 2009 15 696 706 10.1261/rna.1429009 19237463
59. Predicting RNA pseudoknot folding thermodynamics. Cao S, Chen SJ, Nucleic Acids Res 2006 34 2634 2652 10.1093/nar/gkl346 16709732 (Pubitemid 43985627)