1887

Abstract

Representative amino acid sequences of the RNA-dependent RNA polymerases of all groups of positive-strand RNA viruses were aligned hierarchically, starting with the most closely related ones. This resulted in delineation of three large supergroups. Within each of the supergroups, the sequences of segments of approximately 300 amino acid residues originating from the central and/or C-terminal portions of the polymerases could be aligned with statistically significant scores. Specific consensus patterns of conserved amino acid residues were derived for each of the supergroups. The composition of the polymerase supergroups was as follows. I. Picorna-, noda-, como-, nepo-, poty-, bymo-, sobemoviruses, and a subset of luteoviruses (beet western yellows virus and potato leafroll virus). II. Carmo-, tombus-, dianthoviruses, another subset of luteoviruses (barley yellow dwarf virus), pestiviruses, hepatitis C virus (HCV), flaviviruses and, unexpectedly, single-stranded RNA bacteriophages. III. Tobamo-, tobra-, hordei-, tricornaviruses, beet yellows virus, alpha-, rubi-, furoviruses, hepatitis E virus (HEV), potex-, carla-, tymoviruses, and apple chlorotic leaf spot virus. An unusual organization was shown for corona- and torovirus polymerases whose N-terminal regions were found to be related to the respective domains of supergroup I, and the C-terminal regions to those of the supergroup III polymerases. The alignments of the three polymerase supergroups were superimposed to produce a comprehensive final alignment encompassing eight distinct conserved motifs. Phylogenetic analysis using three independent methods of tree construction confirmed the separation of the positive-strand RNA viral polymerases into three supergroups and revealed some unexpected clusters within the supergroups. These included the grouping of HCV and the pestiviruses with carmoviruses and related plant viruses in supergroup II, and the grouping of HEV and rubiviruses with furoviruses in supergroup III.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-72-9-2197
1991-09-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/jgv/72/9/JV0720092197.html?itemId=/content/journal/jgv/10.1099/0022-1317-72-9-2197&mimeType=html&fmt=ahah

References

  1. Agranovsky A. A., Boyko V. P., Karasev A. V., Lunina N. A., Koonin E. V., Dolja V. V. 1991a; Nucleotide sequence of the 3′-terminal half of beet yellows closterovirus RNA genome: unique arrangement of eight virus genes. Journal of General Virology 72:15–23
    [Google Scholar]
  2. Agranovsky A. A., Boyko V. P., Karasev A. V., Koonin E. V., Dolja V. V. 1991b; The putative 65K protein of beet yellows closterovirus is a homologue of HSP70 heat shock proteins. Journal of Molecular Biology 217:603–610
    [Google Scholar]
  3. Bandziulis R. J., Swanson M. S., Dreyfuss G. 1989; RNA-binding proteins as developmental regulators. Genes and Development 3:431–437
    [Google Scholar]
  4. Blumenthal T. 1979; Q β replicase and protein synthesis elongation factors EF-Tu and EF-Ts. Methods in Enzymology 60:628–638
    [Google Scholar]
  5. Bredenbeek P. J., Pachuk C. J., Noten A. F. H., Charite J., Luytjes W., Weiss S. R., Spaan W. J. M. 1990; The primary structure and expression of the second open reading frame of the polymerase gene of the coronavirus MHV-A59; a highly conserved polymerase is expressed by an efficient ribosome frameshifting mechanism. Nucleic Acids Research 18:1825–1832
    [Google Scholar]
  6. Brodsky L. I., Drachev A. L., Tatuzov R. L., Chumakov K. M. 1991; GENEBEE: a package of computer programs for bio-polymer sequence analysis.. Biopolimery i Kletka (in press)
    [Google Scholar]
  7. Bruenn J. A. 1991; Relationships among the positive-strand and double-strand RNA viruses as viewed through their RNA-dependent RNA polymerases. Nucleic Acids Research 19:217–226
    [Google Scholar]
  8. Candresse T., Morch M. D., Dunez J. 1990; Multiple alignment and hierarchical clustering of conserved amino acid sequences in the replication-associated proteins of plant RNA viruses. Research in Virology 141:315–329
    [Google Scholar]
  9. Chumakov K. M., Yushmanov S. Yu. 1988; Maximum topological similarity principle in molecular taxonomy. Molekularnaya Genetika, Mikrobiologija i Virusologija 3:3–9 (in Russian)
    [Google Scholar]
  10. Collett M. S., Larson R., Gold C., Strick D., Anderson D. K., Purchio A. F. 1988; Molecular cloning and nucleotide sequence of the pestivirus bovine viral diarrhea virus. Virology 165:191–199
    [Google Scholar]
  11. Corpet F. 1988; Multiple sequence alignment with hierarchical clustering. Nucleic Acids Research 16:10881–10890
    [Google Scholar]
  12. Dayhoff M. O., Barker W. C., Hunt L. T. 1983; Establishing homologies in protein sequences. Methods in Enzymology 91:524–549
    [Google Scholar]
  13. Delarue M., Poch O., Tordo N., Moras D., Argos P. 1990; An attempt to unify the structure of polymerases. Protein Engineering 3:461–467
    [Google Scholar]
  14. Doolittle R. F. 1986 Of URFs and ORFs. A Primer on How to Analyze Derived Amino Acid Sequences Mill Valley: University Science Books;
    [Google Scholar]
  15. Dominguez G., Wang C.-Y., Frey T. K. 1990; Sequence of the rubella virus genome: evidence for genetic rearrangement during togavirus evolution. Virology 177:225–238
    [Google Scholar]
  16. Felsenstein J. 1988; Phylogenies from molecular sequences: inference and reliability. Annual Review of Genetics 22:521–565
    [Google Scholar]
  17. Felsenstein J. 1989 Phylip 3.2 Manual. Berkeley: University of California Herbarium.:
    [Google Scholar]
  18. Feng D. F., Johnson M. S., Doolittle R. F. 1985; Aligning amino acid sequences: comparison of commonly used methods. Journal of Molecular Evolution 21:112–125
    [Google Scholar]
  19. Fry D. C., Kuby S. A., Mildvan A. S. 1986; ATP-binding site of adenylate kinase: mechanistic implications of its homology with ras- encoded p21, F1-ATPase, and other nucleotide-binding proteins. Proceedings of the National Academy of Sciences, U.S.A. 83:907–911
    [Google Scholar]
  20. German S., Candresse T., Lanneau M., Huet J. C., Pernolet J. C., Dunez J. 1990; Nucleotide sequence and genomic organization of apple chlorotic leaf spot virus. Virology 178:104–112
    [Google Scholar]
  21. Goldbach R. 1986; Molecular evolution of plant RNA viruses. Annual Review of Phytopathology 24:289–310
    [Google Scholar]
  22. Goldbach R. 1987; Genome similarities between plant and animal RNA viruses. Microbiological Sciences 4:197–202
    [Google Scholar]
  23. Goldbach R., Wellink J. 1988; Evolution of plus-strand RNA viruses. Intervirology 29:260–267
    [Google Scholar]
  24. Goldbach R., Le Gall O., Wellink J. 1991; Alpha-like viruses in plants. Seminars in Virology (in press)
    [Google Scholar]
  25. Gorbalenya A. E., Koonin E. V. 1989; Virus proteins containing the purine nucleotide-binding proteins. Nucleic Acids Research 17:8413–8440
    [Google Scholar]
  26. Gorbalenya A. E., Blinov V. M., Donchenko A. P., Koonin E. V. 1989a; An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive-strand RNA viral replication. Journal of Molecular Evolution 28:256–268
    [Google Scholar]
  27. Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. 1989b; Coronavirus genome: tentative functional mapping of the non-structural polyprotein by theoretical analysis of the amino acid sequence. Nucleic Acids Research 17:4456–4469
    [Google Scholar]
  28. Haseloff J., Goelet P., Zimmern D., Ahlquist P., Dasgupta R., Kaesberg P. 1984; Striking similarities in amino acid sequence among nonstructural proteins encoded by RNA viruses that have dissimilar genomic organization. Proceedings of the National Academy of Sciences, U.S.A 81:4358–4362
    [Google Scholar]
  29. Houghton M., Choo Q. L., Kuo G. 1989 European Patent Application #88310922.5, 5/31/89, Bulletin 89/22.
    [Google Scholar]
  30. Inokuchi Y., Hirashima A. 1987; Interference with viral infection by defective RNA replicase. Journal of Virology 61:3946–3949
    [Google Scholar]
  31. Kamer G., Argos P. 1984; Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Research 12:7269–7282
    [Google Scholar]
  32. Kashiwazaki S., Minobe Y., Omura T., Hibino H. 1990; Nucleotide sequence of barley yellow mosaic virus RNA 1: a close evolutionary relationship with potyviruses. Journal of General Virology 71:2781–2790
    [Google Scholar]
  33. Koonin E. V., Gorbalenya A. E., Chumakov K. M., Donchenko A. P., Blinov V. M. 1987; Evolution of RNA-dependent RNA polymerases of positive-strand RNA viruses. Molekularnaya Genetika, Mikrobiologija i Virusologija 7:27–39 (in Russian)
    [Google Scholar]
  34. Koonin E. V., Chumakov K. M. Yushmanov S. Yu, Gorbalenya A. E. 1988; Evolution of RNA-dependent RNA polymerases of positive-strand RNA viruses: a comparison of phylogenetic trees generated by different methods. Molekularnaya Genetika, Mikrobiologija i Virusologija 3:16–19 (in Russian)
    [Google Scholar]
  35. Koonin E. V., Chumakov K. M., Gorbalenya A. E. 1989; Tentative identification of the RNA-dependent RNA polymerases of dsRNA viruses. FEBS Letters 252:42–46
    [Google Scholar]
  36. Kroner P., Richards D., Traynor P., Ahlquist P. 1989; Defined mutations in a small region of the brome mosaic virus 2a gene cause diverse temperature-sensitive RNA replication phenotypes. Journal of Virology 63:5302–5309
    [Google Scholar]
  37. Leontovich A. M., Gorbalenya A. E., Brodsky L. I. 1990; Generation of a complete local similarity map for two biopolymer sequences (DOTHELIX program of the GENEBEE package). Biopolimery i Kletka 6:12–19 (in Russian)
    [Google Scholar]
  38. Miller R. M., Purcell R. M. 1990; Hepatitis C virus shares amino acid similarity with pestiviruses and flaviviruses as well as members of two plant virus supergroups. Proceedings of the National Academy of Sciences, U.S.A 87:2057–2061
    [Google Scholar]
  39. Morozov S. Yu., Kanyuka K. V., Levay K. E., Zavriev S. K. 1990; The putative RNA replicase of potato virus M: obvious sequence similarity with potex- and tymoviruses. Virology 179:911–914
    [Google Scholar]
  40. Pletnev A. G., Yamschikov V. F., Blinov V. M. 1989; Nucleotide sequence of the genome and complete amino acid sequence of the polyprotein of tick-borne encephalitis virus. Virology 174:250–263
    [Google Scholar]
  41. Poch O., Sauvageut I., Delarue M., Tordo N. 1989; Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. EMBO Journal 8:3867–3874
    [Google Scholar]
  42. Quadt R., Jaspars E. M. J. 1989; RNA polymerases of plus-strand RNA viruses of plants. Molecular Plant-Microbe Interactions 2:219–223
    [Google Scholar]
  43. Reyes G. R., Purdy M. A., Kim J. P., Luk K.-C., Young L. M., Fry K. E., Bradley D. W. 1990; Isolation of a cDNA from the virus responsible for enterically transmitted non-A, non-B hepatitis. Science 247:1335–1339
    [Google Scholar]
  44. Rozanov M. N., Morozov S. Yu., Skryabin K. G. 1990; Unexpected close relationship between the large non-virion proteins of filamentous potexviruses and spherical tymoviruses. Virus Genes 3:373–379
    [Google Scholar]
  45. Sneath P., Sokal R. 1973 Principles of Numerical Taxonomy. San Francisco: Freeman.:
    [Google Scholar]
  46. Snijder E. J., den Boon J. A., Bredenbeek P. J., Horzinek M. C., Rijnbrand R., Spaan W. J. M. 1990; The carboxyl-terminal part of the putative Berne virus polymerase is expressed by ribosomal frameshifting and contains sequence motifs which indicate that toro- and coronaviruses are evolutionarily related. Nucleic Acids Research 18:4535–4542
    [Google Scholar]
  47. Wimmer E., Kuhn R. J., Pincus S., Yang C. F., Toyoda H., Nicklin M. J. H., Takeda N. 1987; Molecular events leading to picornavirus genome replication. Journal of Cell Science supplement 7:1–26
    [Google Scholar]
  48. Xiong Y., Eickbusch T. H. 1990; Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO Journal 9:3353–3362
    [Google Scholar]
  49. Xiong Z., Lommel S. A. 1989; The complete nucleotide sequence and genome organization of red clover necrotic mosaic virus RNA 1. Virology 171:543–554
    [Google Scholar]
  50. Yushmanov S. Yu., Chumakov K. M. 1988; Algorithms for construction of maximum topological similarity phylogenetic trees.. Molekularnaya Genetika, Mikrobiologija i Virusologija 3:3–9 (in Russian)
    [Google Scholar]
  51. Zimmern D. 1988; Evolution of RNA viruses. In RNA Genetics pp 211–240 Edited by Holland J. J., Domingo E., Ahlquist P. Boca Raton: CRC Press;
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-72-9-2197
Loading
/content/journal/jgv/10.1099/0022-1317-72-9-2197
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error