Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture - Archives of Virology
- ️Gorbalenya, Alexander E.
- ️Fri Feb 22 2008
References
Adams MJ, Antoniw JF, Bar-Joseph M, Brunt AA, Candresse T, Foster GD, Martelli GP, Milne RG, Zavriev SK, Fauquet CM (2004) The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch Virol 149:1045–1060
Allaire M, Chernaia MM, Malcolm BA, James MN (1994) Picornaviral 3C cysteine proteinases have a fold similar to chymotrypsin-like serine proteinases. Nature 369:72–76
Argos P, Kamer G, Nicklin MJ, Wimmer E (1984) Similarity in gene organization and homology between proteins of animal picornaviruses and a plant comovirus suggest common ancestry of these virus families. Nucleic Acids Res 12:7251–7267
Arnold E, Luo M, Vriend G, Rossmann MG, Palmenberg AC, Parks GD, Nicklin MJ, Wimmer E (1987) Implications of the picornavirus capsid structure for polyprotein processing. Proc Natl Acad Sci USA 84:21–25
Atkins JF, Wills NM, Loughran G, Wu CY, Parsawar K, Ryan MD, Wang CH, Nelson CC (2007) A case for “StopGo”: reprogramming translation to augment codon meaning of GGN by promoting unconventional termination (Stop) after addition of glycine and then allowing continued translation (Go). RNA 13:803–810
Bazan JF, Fletterick RJ (1988) Viral cysteine proteases are homologous to the trypsin-like family of serine proteases: structural and functional implications. Proc Natl Acad Sci USA 85:7872–7876
Berger PH, Adams MJ, Barnett OW, Brunt AA, Hammond J, Hill JH, Jordan CV, Kashiwazaki S, Rybicki E, Spence N, Stenger DC, Ohki ST, Uyeda I, van Zaayen A, Valkonen JP, Vetten HJ (2005) Potyviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London, pp 819–841
Bishop NE, Anderson DA (1993) RNA-dependent cleavage of VP0 capsid protein in provirions of hepatitis A virus. Virology 197:616–623
Blair WS, Semler BL (1991) Role for the P4 amino acid residue in substrate utilization by the poliovirus 3CD proteinase. J Virol 65:6111–6123
Buck KW, Esteban R, Hillman BI (2005) Narnaviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London, pp 751–756
Candresse T, Svanella-Dumas L, Le Gall O (2006) Characterization and partial genome sequence of stocky prune virus, a new member of the genus Cheravirus. Arch Virol 151:1179–1188
Carrington JC, Cary SM, Dougherty WG (1988) Mutational analysis of tobacco etch virus polyprotein processing: cis and trans proteolytic activities of polyproteins containing the 49-kilodalton proteinase. J Virol 62:2313–2320
Chandrasekar V, Johnson JE (1998) The structure of tobacco ringspot virus: a link in the evolution of icosahedral capsids in the picornavirus superfamily. Structure 6:157–171
Cheah KC, Leong LE, Porter AG (1990) Site-directed mutagenesis suggests close functional relationship between a human rhinovirus 3C cysteine protease and cellular trypsin-like serine proteases. J Biol Chem 265:7180–7187
Chen ZG, Stauffacher C, Li Y, Schmidt T, Bomu W, Kamer G, Shanks M, Lomonossoff G, Johnson JE (1989) Protein-RNA interactions in an icosahedral virus at 3.0 Å resolution. Science 245:154–159
Christian P, Carstens E, Domier L, Johnson J, Johnson K, Nakashima N, Scotti P, van der Wilk F (2005) Dicistroviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 783–788
Christian P, Carstens E, Domier L, Johnson J, Johnson K, Nakashima N, Scotti P, van der Wilk F (2005) Iflavirus. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 779–782
Culley AI, Lang AS, Suttle CA (2003) High diversity of unknown picorna-like viruses in the sea. Nature 424:1054–1057
Culley AI, Lang AS, Suttle CA (2005) Marnaviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London, pp 789–792
Culley AI, Lang AS, Suttle CA (2007) The complete genomes of three viruses assembled from shotgun libraries of marine RNA virus communities. Virol J (electronic resource) 4:69
Dolja VV, Boyko VP, Agranovsky AA, Koonin EV (1991) Phylogeny of capsid proteins of rod-shaped and filamentous RNA plant viruses: two families with distinct patterns of sequence and probably structure conservation. Virology 184:79–86
Dolja VV, Carrington JC (1992) Evolution of positive-strand RNA viruses. Semin Virol 3:315–326
Dunham DM, Jiang X, Berke T, Smith AW, Matson DO (1998) Genomic mapping of a calicivirus VPg. Arch Virol 143:2421–2430
Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (2005) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Fenner F, Gibbs AJ (eds) (1988) Portraits of viruses: a history of virology. Karger, Basel
Franssen H, Leunissen J, Goldbach R, Lomonossoff GP, Zimmern D (1984) Homologous sequences in nonstructural proteins from cowpea mosaic virus and picornaviruses. EMBO J 3:855–861
Goldbach R (1986) Molecular evolution of plant RNA viruses. Annu Rev Phytopathol 24:289–310
Goldbach R (1987) Genome similarities between plant and animal RNA viruses. Microbiol Sci 4:197–202
Goldbach R, Wellink J (1988) Evolution of plus-strand RNA viruses. Intervirology 29:260–267
Gorbalenya AE, Koonin EV (1993) Comparative analysis of amino acid sequences of key enzymes of replication and expression of positive-strand RNA viruses. Validity of approach and functional and evolutionary implications. Sov Sci Rev D Physicochem Biol 11:1–84
Gorbalenya AE, Koonin EV (1993) Helicases: amino acid sequence comparisons and structure-function relationships. Curr Opin Struct Biol 3:419–429
Gorbalenya AE, Blinov VM, Donchenko AP (1986) Poliovirus-encoded proteinase 3C: a possible evolutionary link between cellular serine and cysteine proteinase families. FEBS Lett 194:253–257
Gorbalenya AE, Donchenko AP, Blinov VM, Koonin EV (1989) Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases: a distinct protein superfamily with a common structural fold. FEBS Lett 243:103–114
Gorbalenya AE, Koonin EV, Wolf YI (1990) A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses. FEBS Lett 262:145–148
Gorbalenya AE, Pringle FM, Zeddam JL, Luke BT, Cameron CE, Kalmakoff J, Hanzlik TN, Gordon KH, Ward VK (2002) The palm subdomain-based active site is internally permuted in viral RNA-dependent RNA polymerases of an ancient lineage. J Mol Biol 324:47–62
Gromeier M, Wimmer E, Gorbalenya AE (1999) Genetics, pathogenesis and evolution of picornaviruses. In: Domingo E, Webster RG, Holland JJ (eds) Academic Press, pp 287–343
Habayeb MS, Ekengren SK, Hultmark D (2006) Nora virus, a persistent virus in Drosophila, defines a new picorna-like virus family. J Gen Virol 87:3045–3051
Hansen JL, Long AM, Schultz SC (1997) Structure of the RNA-dependent RNA polymerase of poliovirus. Structure 5:1109–1122
Harber JJ, Bradley J, Anderson CW, Wimmer E (1991) Catalysis of poliovirus VP0 maturation cleavage is not mediated by serine 10 of VP2. J Virol 65:326–334
Hemmer O, Greif C, Dufourcq P, Reinbolt J, Fritsch C (1995) Functional characterization of the proteolytic activity of the tomato black ring nepovirus RNA-1-encoded polyprotein. Virology 206:362–371
Higaki JN, Evnin LB, Craik CS (1989) Introduction of a cysteine protease active site into trypsin. Biochemistry (Mosc) 28:9256–9263
Hogle JM, Chow M, Filman DJ (1985) Three-dimensional structure of poliovirus at 2.9 Å resolution. Science 229:1358–1365
Ikegami M, Iwanami T, Jones AT, Karasev AV, Le Gall O, Lehto K, Sanfacon H, Wellink J, Wetzel T (2002) Taxonomy of recognized and putative species in the family Comoviridae. In: XIIth IUMS Virology meeting, Paris, France, 27th July–12th August 2002
Iwanami T, Kondo Y, Karasev AV (1999) Nucleotide sequences and taxonomy of Satsuma dwarf virus. J Gen Virol 80:793–797
Kamer G, Argos P (1984) Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res 12:7269–7282
King AF, Sangar DV, Harris TJ, Brown F (1980) Heterogeneity of the genome-linked protein of foot-and-mouth disease virus. J Virol 34:627–634
Koonin EV (1991) The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J Gen Virol 72:2197–2206
Koonin EV, Dolja VV (1993) Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit Rev Biochem Mol Biol 28:375–430
Koonin EV, Choi GH, Nuss DL, Shapira R, Carrington JC (1991) Evidence for common ancestry of a chestnut blight hypovirulence-associated double-stranded RNA and a group of positive-strand RNA plant viruses. Proc Natl Acad Sci USA 88:10647–10651
Koopmans MK, Green KY, Ando T, Clarke IN, Estes MK, Matson DO, Nakata S, Neill JD, Smith AW, Studdert MJ, Thiel HJ (2005) Caliciviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London, pp 843–851
Lain S, Riechmann JL, Garcia JA (1990) RNA helicase: a novel activity associated with a protein encoded by a positive strand RNA virus. Nucleic Acids Res 18:7003–7006
Laine P, Savolainen C, Blomqvist S, Hovi T (2005) Phylogenetic analysis of human rhinovirus capsid protein VP1 and 2A protease coding sequences confirms shared genus-like relationships with human enteroviruses. J Gen Virol 86:697–706
Lang AS, Culley AI, Suttle CA (2004) Genome sequence and characterization of a virus (HaRNAV) related to picorna-like viruses that infects the marine toxic bloom-forming alga Heterosigma akashiwo. Virology 320:206–217
Lawson MA, Semler BL (1991) Poliovirus thiol proteinase 3C can utilize a serine nucleophile within the putative catalytic triad. Proc Natl Acad Sci USA 88:9919–9923
Le Gall O, Iwanami T, Jones AT, Lehto K, Sanfacon H, Wellink J, Wetzel T, Yoshikawa N (2005) Cheravirus. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 803–805
Le Gall O, Iwanami T, Jones AT, Lehto K, Sanfacon H, Wellink J, Wetzel T, Yoshikawa N (2005) Sequiviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 793–798
Le Gall O, Iwanami T, Jones AT, Lehto K, Sanfacon H, Wellink J, Wetzel T, Yoshikawa N (2005) Comoviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 807–818
Le Gall O, Iwanami T, Jones AT, Lehto K, Sanfacon H, Wellink J, Wetzel T, Yoshikawa N (2005) Sadwavirus. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 799–802
Le Gall O, Sanfaçon H, Ikegami M, Iwanami T, Jones T, Karasev A, Lehto K, Wellink J, Wetzel T, Yoshikawa N (2007) Cheravirus and Sadwavirus : two unassigned genera of plant positive-sense single-stranded RNA viruses formerly considered atypical members of the genus Nepovirus (family Comoviridae). Arch Virol 152:1767–1774
Liljas L, Tate J, Lin T, Christian P, Johnson JE (2002) Evolutionary and taxonomic implications of conserved structural motifs between picornaviruses and insect picorna-like viruses. Arch Virol 147:59–84
Margis R, Pinck L (1992) Effects of site-directed mutagenesis on the presumed catalytic triad and substrate-binding pocket of grapevine fanleaf nepovirus 24-kDa proteinase. Virology 190:884–888
Martin A, Benichou D, Chao SF, Cohen LM, Lemon SM (1999) Maturation of the hepatitis A virus capsid protein VP1 is not dependent on processing by the 3Cpro proteinase. J Virol 73:6220–6227
Matthews DA, Smith WW, Ferre RA, Condon B, Budahazi G, Sisson W, Villafranca JE, Janson CA, McElroy HE, Gribskov CL, et al (1994) Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein. Cell 77:761–771
Mayo MA, Fritsch C (1994) A possible consensus sequence for VPg of viruses in the family Comoviridae. FEBS Lett 354:129–130
Mayo MA, Ball LA (2006) ICTV in San Francisco: a report from the Plenary Session. Arch Virol 151:413–422
Meyers G, Wirblich C, Thiel HJ (1991) Genomic and subgenomic RNAs of rabbit hemorrhagic disease virus are both protein-linked and packaged into particles. Virology 184:677–686
Mirzayan C, Wimmer E (1994) Biochemical studies on poliovirus polypeptide 2C: evidence for ATPase activity. Virology 199:176–187
Miyashita K, Utsumi R, Utsumi T, Komano T, Satoh N (1995) Mutational analysis of the putative substrate-binding site of 3C proteinase of coxsackievirus B3. Biosci Biotechnol Biochem 59:121–122
Murphy JF, Rhoads RE, Hunt AG, Shaw JG (1990) The VPg of tobacco etch virus RNA is the 49-kDa proteinase or the N-terminal 24-kDa part of the proteinase. Virology 178:285–288
Nakashima N, Shibuya N (2006) Multiple coding sequences for the genome-linked virus protein (VPg) in dicistroviruses. J Invertebr Pathol 92:100–104
Nuss DL, Hillman BI, Rigling D, Suzuki N (2005) Hypoviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 597–601
Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358
Palmenberg AC, Kirby EM, Janda MR, Drake NL, Duke GM, Potratz KF, Collett MS (1984) The nucleotide and deduced amino acid sequences of the encephalomyocarditis viral polyprotein coding region. Nucl Acids Res 12:2969–2985
Pfister T, Wimmer E (2001) Polypeptide p41 of a Norwalk-Like Virus Is a Nucleic Acid-Independent Nucleoside Triphosphatase. J Virol 75:1611–1619
Prasad BV, Hardy ME, Dokland T, Bella J, Rossmann MG, Estes MK (1999) X-ray crystallographic structure of the Norwalk virus capsid. Science 286:287–290
Rossmann MG, Johnson JE (1987) Icosahedral RNA virus structure. Annu Rev Biochem 58:533–573
Rossmann MG, Arnold E, Erickson JW, Frankenberger EA, Griffith JP, Hecht HJ, Johnson JE, Kamer G, Luo M, Mosser AG et al (1985) Structure of a human common cold virus and functional relationship to other picornaviruses. Nature 317:145–153
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Shukla DD, Ward CW, Brunt AA (1994) The Potyviridae. CAB International, Wallingford
Spaan WJM, Cavanagh D, de Groot RJ, Enjuanes L, Gorbalenya AE, Snijder EJ, Walker PJ (2005) Nidovirales. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 937–945
Stanway G, Brown F, Christian P, Hovi T, Hyypiä T, King AMQ, Knowles NJ, Lemon SM, Minor PD, Pallansch MA, Palmenberg AC, Skern T (2005) Picornaviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 757–778
Takao Y, Mise K, Nagasaki K, Okuno T, Honda D (2006) Complete nucleotide sequence and genome organization of a single-stranded RNA virus infecting the marine fungoid protist Schizochytrium sp. J Gen Virol 87:723–733
Tanner NK, Linder P (2001) DExD/H box helicases: from generic motors to specific dissociation functions. Mol Cell 8:251–262
Tate J, Liljas L, Scotti P, Christian P, Lin T, Johnson JE (1999) The crystal structure of cricket paralysis virus: the first view of a new virus family. Nat Struct Biol 6:765–774
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876–4882
Turnbull-Ross AD, Mayo MA, Reavy B, Murant AF (1993) Sequence analysis of the parsnip yellow fleck virus polyprotein: evidence of affinities with picornaviruses. J Gen Virol 74:555–561
Tzanetakis IE, Postman JD, Gergerich RC, Martin RR (2006) A virus between families: nucleotide sequence and evolution of Strawberry latent ringspot virus. Virus Res 121:199–204
Verbeek M, Dullemans AM, van den Heuvel JF, Maris PC, van der Vlugt RA (2007) Identification and characterisation of tomato torrado virus, a new plant picorna-like virus from tomato. Arch Virol 152: 881–890
Wetzel T, Ebel R, Moury B, Le Gall O, Endisch S, Reustle GM, Krczal G (2006) Sequence analysis of grapevine isolates of Raspberry ringspot nepovirus. Arch Virol 151:599–606
Wildy P (1971) Classification and nomenclature of viruses. First report of the International Committee on Nomenclature of Viruses. Monogr Virol 5:1–65
Wilson JE, Powell MJ, Hoover SE, Sarnow P (2000) Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites. Mol Cell Biol 20:4990–4999
Ypma-Wong MF, Filman DJ, Hogle JM, Semler BL (1988) Structural domains of the poliovirus polyprotein are major determinants for proteolytic cleavage at Gln-Gly pairs. J Biol Chem 263:17846–17856