Sequence analysis of L RNA of Lassa virus

Virology

Volumn 318, Issue 1, 2004, Pages 153-168

  Vieth, Simon ^a   Torda, Andrew E ^b   Asper, Marcel ^a   Schmitz, Herbert ^a   Günther, Stephan ^a  

^a BERNHARD NOCHT INSTITUTE FOR TROPICAL MEDICINE   (Germany)

^b UNIVERSITY OF HAMBURG   (Germany)

Author keywords

Arenavirus; Lassa virus; Phylogeny; RNA dependent RNA polymerase; Secondary structure prediction; Sequence

Indexed keywords

AMINO ACID; RNA POLYMERASE; VIRUS PROTEIN; VIRUS RNA;

ARENAVIRUS; ARTICLE; COTE D'IVOIRE; GHANA; LASSA VIRUS; MOLECULAR PHYLOGENY; NAIRO VIRUS; NIGERIA; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; RNA STRUCTURE; SEQUENCE ANALYSIS; SIERRA LEONE; VIRUS STRAIN;

ARENAVIRIDAE; ARENAVIRUS; LASSA VIRUS; NAIROVIRUS; RNA VIRUSES;

EID: 1242297008     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virol.2003.09.009     Document Type: Article

References (72)

1. Ago H., Adachi T., Yoshida A., Yamamoto M., Habuka N., Yatsunami K., Miyano M. Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Struct. Fold. Des. 7:1999;1417-1426.
2. Akey D.L., Malashkevich V.N., Kim P.S. Buried polar residues in coiled-coil interfaces. Biochemistry. 40:2001;6352-6360.
3. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
4. Auperin D.D., McCormick J.B. Nucleotide sequence of the Lassa virus (Josiah strain) S genome RNA and amino acid sequence comparison of the N and GPC proteins to other arenaviruses. Virology. 168:1989;421-425.
5. Bates P.A., Kelley L.A., MacCallum R.M., Sternberg M.J. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins Suppl. 5:2001;39-46.
6. Borden K.L., Campbell Dwyer E.J., Salvato M.S. An arenavirus RING (zinc-binding) protein binds the oncoprotein promyelocyte leukemia protein (PML) and relocates PML nuclear bodies to the cytoplasm. J. Virol. 72:1998;758-766.
7. Borden K.L., Campbelldwyer E.J., Carlile G.W., Djavani M., Salvato M.S. Two RING finger proteins, the oncoprotein PML and the arenavirus Z protein, colocalize with the nuclear fraction of the ribosomal P proteins. J. Virol. 72:1998;3819-3826.
8. Bowen M.D., Peters C.J., Nichol S.T. Phylogenetic analysis of the Arenaviridae: patterns of virus evolution and evidence for cospeciation between arenaviruses and their rodent hosts. Mol. Phylogenet. Evol. 8:1997;301-316.
9. Bowen M.D., Rollin P.E., Ksiazek T.G., Hustad H.L., Bausch D.G., Demby A.H., Bajani M.D., Peters C.J., Nichol S.T. Genetic diversity among Lassa virus strains. J. Virol. 74:2000;6992-7004.
10. Bressanelli S., Tomei L., Roussel A., Incitti I., Vitale R.L., Mathieu M., De Francesco R., Rey F.A. Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Proc. Natl. Acad. Sci. U. S. A. 96:1999;13034-13039.
11. Bruenn J.A. Relationships among the positive strand and double-strand RNA viruses as viewed through their RNA-dependent RNA polymerases. Nucleic Acids Res. 19:1991;217-226.
12. Campbell Dwyer E.J., Lai H., MacDonald R.C., Salvato M.S., Borden K.L. The lymphocytic choriomeningitis virus RING protein Z associates with eukaryotic initiation factor 4E and selectively represses translation in a RING-dependent manner. J. Virol. 74:2000;3293-3300.
13. Charrel R.N., Feldmann H., Fulhorst C.F., Khelifa R., de Chesse R., de Lamballerie X. Phylogeny of New World arenaviruses based on the complete coding sequences of the small genomic segment identified an evolutionary lineage produced by intrasegmental recombination. Biochem. Biophys. Res. Commun. 296:2002;1118-1124.
14. Cheney I.W., Naim S., Lai V.C., Dempsey S., Bellows D., Walker M.P., Shim J.H., Horscroft N., Hong Z., Zhong W. Mutations in NS5B polymerase of hepatitis C virus: impacts on in vitro enzymatic activity and viral RNA replication in the subgenomic replicon cell culture. Virology. 297:2002;298-306.
15. Chizhikov V.E., Spiropoulou C.F., Morzunov S.P., Monroe M.C., Peters C.J., Nichol S.T. Complete genetic characterization and analysis of isolation of Sin Nombre virus. J. Virol. 69:1995;8132-8136.
16. Clegg J.C., Wilson S.M., Oram J.D. Nucleotide sequence of the S RNA of Lassa virus (Nigerian strain) and comparative analysis of arenavirus gene products. Virus Res. 18:1991;151-164.
17. Cuff J.A., Barton G.J. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins. 40:2000;502-511.
18. Dayhoff M.O., Schwartz R.M., Orcutt B.C. A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure. vol. 5:1978;345-352 National Biomedical Research Foundation, Washington, DC.
19. Dhillon J., Cowley J.A., Wang Y., Walker P.J. RNA polymerase (L) gene and genome terminal sequences of ephemeroviruses bovine ephemeral fever virus and Adelaide River virus indicate a close relationship to vesiculoviruses. Virus Res. 70:2000;87-95.
20. Djavani M., Lukashevich I.S., Sanchez A., Nichol S.T., Salvato M.S. Completion of the Lassa fever virus sequence and identification of a RING finger open reading frame at the L RNA 5′ end. Virology. 235:1997;414-418.
21. Djavani M., Lukashevich I.S., Salvato M.S. Sequence comparison of the large genomic RNA segments of two strains of lymphocytic choriomeningitis virus differing in pathogenic potential for guinea pigs. Virus Genes. 17:1998;151-155.
22. Felsenstein, J., 1995. PHYLIP (Phylogeny Inference Package) Version 3.57c. [Online] Department of Genetics, University of Washington, Washington, D.C. Available from: URL: http://evolution.genetics.washington.edu/phylip.html [28 January 2000, last date accessed].
23. Fuller-Pace F.V., Southern P.J. Detection of virus-specific RNA-dependent RNA polymerase activity in extracts from cells infected with lymphocytic choriomeningitis virus: in vitro synthesis of full-length viral RNA species. J. Virol. 63:1989;1938-1944.
24. Garcia J.B., Morzunov S.P., Levis S., Rowe J., Calderon G., Enria D., Sabattini M., Buchmeier M.J., Bowen M.D., Jeor S.C.S. Genetic diversity of the Junin virus in Argentina: geographic and temporal patterns. Virology. 272:2000;127-136.
25. Guex N., Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 18:1997;2714-2723.
26. Günther S., Emmerich P., Laue T., Kühle O., Asper M., Jung A., Grewing T., ter Meulen J., Schmitz H. Imported lassa fever in Germany: molecular characterization of a new lassa virus strain. Emerg. Infect. Dis. 6:2000;466-476.
27. Günther S., Weisner B., Roth A., Grewing T., Asper M., Drosten C., Emmerich P., Petersen J., Wilczek M., Schmitz H. Lassa fever encephalopathy: Lassa virus in cerebrospinal fluid but not in serum. J. Infect. Dis. 184:2001;345-349.
28. Hansen J.L., Long A.M., Schultz S.C. Structure of the RNA-dependent RNA polymerase of poliovirus. Structure. 5:1997;1109-1122.
29. Henderson W.W., Monroe M.C., St. Jeor S.C., Thayer W.P., Rowe J.E., Peters C.J., Nichol S.T. Naturally occurring Sin Nombre virus genetic reassortants. Virology. 214:1995;602-610.
30. Hong Z., Cameron C.E., Walker M.P., Castro C., Yao N., Lau J.Y., Zhong W. A novel mechanism to ensure terminal initiation by hepatitis C virus NS5B polymerase. Virology. 285:2001;6-11.
31. Hooft R.W., Vriend G., Sander C., Abola E.E. Errors in protein structures. Nature. 381:1996;272.
32. Huber T., Russell A.J., Ayers D., Torda A.E. SAUSAGE: protein threading with flexible force fields. Bioinformatics. 15:1999;1064-1065.
33. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17:2001;754-755.
34. Iapalucci S., Lopez N., Rey O., Zakin M.M., Cohen G.N., Franze-Fernandez M.T. The 5′ region of Tacaribe virus L RNA encodes a protein with a potential metal binding domain. Virology. 173:1989;357-361.
35. Iapalucci S., Lopez R., Rey O., Lopez N., Franze-Fernandez M.T., Cohen G.N., Lucero M., Ochoa A., Zakin M.M. Tacaribe virus L gene encodes a protein of 2210 amino acid residues. Virology. 170:1989;40-47.
36. Jones D.T., Taylor W.R., Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:1992;275-282.
37. Kadare G., Haenni A.L. Virus-encoded RNA helicases. J. Virol. 71:1997;2583-2590.
38. Koonin E.V. The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J. Gen. Virol. 72:1991;2197-2206.
39. Koonin E.V., Dolja V.V. Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit. Rev. Biochem. Mol. Biol. 28:1993;375-430.
40. Kumar S., Tamura K., Jakobsen I.B., Nei M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics. 17:2001;1244-1245.
41. Lee K.J., Novella I.S., Teng M.N., Oldstone M.B., de La Torre J.C. NP and L proteins of lymphocytic choriomeningitis virus (LCMV) are sufficient for efficient transcription and replication of LCMV genomic RNA analogs. J. Virol. 74:2000;3470-3477.
42. Lenz O., ter Meulen J., Klenk H.D., Seidah N.G., Garten W. The Lassa virus glycoprotein precursor GP-C is proteolytically processed by subtilase SKI-1/S1P. Proc. Natl. Acad. Sci. U. S. A. 98:2001;12701-12715.
43. Lesburg C.A., Cable M.B., Ferrari E., Hong Z., Mannarino A.F., Weber P.C. Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site. Nat. Struct. Biol. 6:1999;937-943.
44. Lopez N., Jacamo R., Franze-Fernandez M.T. Transcription and RNA replication of tacaribe virus genome and antigenome analogs require N and L proteins: Z protein is an inhibitor of these processes. J. Virol. 75:2001;12241-12251.
45. Lukashevich I.S. Generation of reassortants between African arenaviruses. Virology. 188:1992;600-605.
46. Lukashevich I.S., Djavani M., Shapiro K., Sanchez A., Ravkov E., Nichol S.T., Salvato M.S. The Lassa fever virus L gene: nucleotide sequence, comparison, and precipitation of a predicted 250 kDa protein with monospecific antiserum. J. Gen. Virol. 78:1997;547-551.
47. Lupas A., Van Dyke M., Stock J. Predicting coiled coils from protein sequences. Science. 252:1991;1162-1164.
48. Marriott A.C., Nuttall P.A. Large RNA segment of Dugbe nairovirus encodes the putative RNA polymerase. J. Gen. Virol. 77:1996;1775-1780.
49. Martin D., Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics. 16:2000;562-563.
50. Mirny L.A., Shakhnovich E.I. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J. Mol. Biol. 291:1999;177-196.
51. Müller R., Poch O., Delarue M., Bishop D.H., Bouloy M. Rift Valley fever virus L segment: correction of the sequence and possible functional role of newly identified regions conserved in RNA-dependent polymerases. J. Gen. Virol. 75:1994;1345-1352.
52. Ng K.K., Cherney M.M., Vazquez A.L., Machin A., Alonso J.M., Parra F., James M.N. Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase. J. Biol. Chem. 277:2002;1381-1387.
53. Peitsch M.C. ProMod and Swiss-Model: internet-based tools for automated comparative protein modelling. Biochem. Soc. Trans. 24:1996;274-279.
54. Poch O., Sauvaget I., Delarue M., Tordo N. Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. EMBO J. 8:1989;3867-3874.
55. Posada D., Crandall K.A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl. Acad. Sci. U. S. A. 98:2001;13757-13762.
56. Roberts A., Rossier C., Kolakofsky D., Nathanson N., Gonzalez-Scarano F. Completion of the La Crosse virus genome sequence and genetic comparisons of the L proteins of the Bunyaviridae. Virology. 206:1995;742-745.
57. Salvato M.S., Shimomaye E.M. The completed sequence of lymphocytic choriomeningitis virus reveals a unique RNA structure and a gene for a zinc finger protein. Virology. 173:1989;1-10.
58. Salvato M., Shimomaye E., Oldstone M.B. The primary structure of the lymphocytic choriomeningitis virus L gene encodes a putative RNA polymerase. Virology. 169:1989;377-384.
59. Salvato M.S., Schweighofer K.J., Burns J., Shimomaye E.M. Biochemical and immunological evidence that the 11 kDa zinc-binding protein of lymphocytic choriomeningitis virus is a structural component of the virus. Virus Res. 22:1992;185-198.
60. Sawyer, S.A., 1999. GENECONV: a computer package for the statistical detection of gene conversion. Distributed by the author, Department of Mathematics, Washington University in St. Louis, available at http://www.math.wustl.edu/~sawyer .
61. Schmitz H., Köhler B., Laue T., Drosten C., Veldkamp P.J., Günther S., Emmerich P., Geisen H.P., Fleischer K., Beersma M.F., Hoerauf A. Monitoring of clinical and laboratory data in two cases of imported Lassa fever. Microbes Infect. 4:2002;43-50.
62. Sibold C., Meisel H., Krüger D.H., Labuda M., Lysy J., Kozuch O., Pejcoch M., Vaheri A., Plyusnin A. Recombination in Tula hantavirus evolution: analysis of genetic lineages from Slovakia. J. Virol. 73:1999;667-675.
63. Singh M.K., Fuller-Pace F.V., Buchmeier M.J., Southern P.J. Analysis of the genomic L RNA segment from lymphocytic choriomeningitis virus. Virology. 161:1987;448-456.
64. Strimmer K., von Haeseler A. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:1996;964-969.
65. Strimmer K., von Haeseler A. Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc. Natl. Acad. Sci. U. S. A. 94:1997;6815-6819.
66. Vincent M.J., Sanchez A.J., Erickson B.R., Basak A., Chretien M., Seidah N.G., Nichol S.T. Crimean-Congo hemorrhagic fever virus glycoprotein proteolytic processing by subtilase SKI-1. J. Virol. 77:2003;8640-8649.
67. Vriend G. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8(52-6):1990;29.
68. Weaver S.C., Salas R.A., de Manzione N., Fulhorst C.F., Duno G., Utrera A., Mills J.N., Ksiazek T.G., Tovar D., Tesh R.B. Guanarito virus (Arenaviridae) isolates from endemic and outlying localities in Venezuela: sequence comparisons among and within strains isolated from Venezuelan hemorrhagic fever patients and rodents. Virology. 266:2000;189-195.
69. Whelan S., Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18:2001;691-699.
70. Zanotto P.M., Gibbs M.J., Gould E.A., Holmes E.C. A reevaluation of the higher taxonomy of viruses based on RNA polymerases. J. Virol. 70:1996;6083-6096.
71. Zhong W., Ferrari E., Lesburg C.A., Maag D., Ghosh S.K., Cameron C.E., Lau J.Y., Hong Z. Template/primer requirements and single nucleotide incorporation by hepatitis C virus nonstructural protein 5B polymerase. J. Virol. 74:2000;9134-9143.
72. Zhou N.N., Senne D.A., Landgraf J.S., Swenson S.L., Erickson G., Rossow K., Liu L., Yoon K., Krauss S., Webster R.G. Genetic reassortment of avian, swine, and human influenza A viruses in American pigs. J. Virol. 73:1999;8851-8856.