Abstract
The processing of the Sindbis virus nonstructural polyprotein translated in vitro has been studied. When Sindbis virus genomic RNA was translated in a reticulocyte lysate, polyprotein P123 was cleaved efficiently to produce nsP1, nsP2, and nsP3. Inhibition of this processing by anti-nsP2 antibodies, but not by antibodies specific for nsP1, nsP3, or nsP4, suggested that the viral proteinase was present in nsP2. To localize the proteolytic activity more precisely, deletions were made in a full-length cDNA clone of Sindbis virus, and RNA was transcribed from these constructs with SP6 RNA polymerase and translated in vitro. Although virtually all of the nsP1, nsP3, and nsP4 sequences could be deleted without affecting processing, deletions in the N-terminal half of nsP2 led to aberrant processing, and deletions in the C-terminal half abolished proteolysis. However, inactive polyproteins containing the nsP2 deletions could be processed by exogenously supplied proteins translated from virion RNA, demonstrating that cleavage was virus specific and not due to a protease present in the reticulocyte lysate and that the deleted polyproteins still served as substrates for the enzyme. From these results and from experiments in which processing was studied at increasingly higher dilution, we have concluded the following: (i) the viral nonstructural proteinase is located in the C-terminal half of nsP2; (ii) in the P123 precursor the cleavage between nsP2 and nsP3 occurs efficiently as a bimolecular reaction (in trans) to remove nsP3, while the bond between nsP1 and nsP2 is cleaved inefficiently, but detectably, in trans, but no autoproteolysis of P123 was detected; (iii) once nsP3 has been removed, the bond between nsP1 and nsP2 in the P12 precursor is cleaved efficiently by autoproteolysis (in cis). This mode of processing leads to a slow rate of cleavage, particularly early in infection, suggesting that the polyproteins might play roles in virus RNA replication distinct from those of the cleaved products. A hypothesis is presented that the proteinase is a thiol protease related to papain.
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Selected References
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- Ahlquist P., Strauss E. G., Rice C. M., Strauss J. H., Haseloff J., Zimmern D. Sindbis virus proteins nsP1 and nsP2 contain homology to nonstructural proteins from several RNA plant viruses. J Virol. 1985 Feb;53(2):536–542. doi: 10.1128/jvi.53.2.536-542.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Aliperti G., Schlesinger M. J. Evidence for an autoprotease activity of sindbis virus capsid protein. Virology. 1978 Oct 15;90(2):366–369. doi: 10.1016/0042-6822(78)90321-5. [DOI] [PubMed] [Google Scholar]
- Bazan J. F., Fletterick R. J. Viral cysteine proteases are homologous to the trypsin-like family of serine proteases: structural and functional implications. Proc Natl Acad Sci U S A. 1988 Nov;85(21):7872–7876. doi: 10.1073/pnas.85.21.7872. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Boege U., Wengler G., Wengler G., Wittmann-Liebold B. Primary structures of the core proteins of the alphaviruses Semliki Forest virus and Sindbis virus. Virology. 1981 Aug;113(1):293–303. doi: 10.1016/0042-6822(81)90156-2. [DOI] [PubMed] [Google Scholar]
- Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1016/0003-2697(76)90527-3. [DOI] [PubMed] [Google Scholar]
- Brzeski H., Kennedy S. I. Synthesis of Sindbis virus nonstructural polypeptides in chicken embryo fibroblasts. J Virol. 1977 May;22(2):420–429. doi: 10.1128/jvi.22.2.420-429.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Burge B. W., Pfefferkorn E. R. Isolation and characterization of conditional-lethal mutants of Sindbis virus. Virology. 1966 Oct;30(2):204–213. doi: 10.1016/0042-6822(66)90096-1. [DOI] [PubMed] [Google Scholar]
- Butterworth B. E., Korant B. D. Characterization of the large picornaviral polypeptides produced in the presence of zinc ion. J Virol. 1974 Aug;14(2):282–291. doi: 10.1128/jvi.14.2.282-291.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Carrington J. C., Dougherty W. G. Small nuclear inclusion protein encoded by a plant potyvirus genome is a protease. J Virol. 1987 Aug;61(8):2540–2548. doi: 10.1128/jvi.61.8.2540-2548.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Clarke B. E., Sangar D. V. Processing and assembly of foot-and-mouth disease virus proteins using subgenomic RNA. J Gen Virol. 1988 Sep;69(Pt 9):2313–2325. doi: 10.1099/0022-1317-69-9-2313. [DOI] [PubMed] [Google Scholar]
- Collins P. L., Fuller F. J., Marcus P. I., Hightower L. E., Ball L. A. Synthesis and processing of Sindbis virus nonstructural proteins in vitro. Virology. 1982 Apr 30;118(2):363–379. doi: 10.1016/0042-6822(82)90356-7. [DOI] [PubMed] [Google Scholar]
- Ding M. X., Schlesinger M. J. Evidence that Sindbis virus NSP2 is an autoprotease which processes the virus nonstructural polyprotein. Virology. 1989 Jul;171(1):280–284. doi: 10.1016/0042-6822(89)90539-4. [DOI] [PubMed] [Google Scholar]
- Faragher S. G., Meek A. D., Rice C. M., Dalgarno L. Genome sequences of a mouse-avirulent and a mouse-virulent strain of Ross River virus. Virology. 1988 Apr;163(2):509–526. doi: 10.1016/0042-6822(88)90292-9. [DOI] [PubMed] [Google Scholar]
- Gorbalenya A. E., Donchenko A. P., Blinov V. M., Koonin E. V. Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases. A distinct protein superfamily with a common structural fold. FEBS Lett. 1989 Jan 30;243(2):103–114. doi: 10.1016/0014-5793(89)80109-7. [DOI] [PubMed] [Google Scholar]
- Goto K., Takahashi N., Murachi T. Structural studies on stem bromelain. Cyanogen bromide cleavage and amino acid sequence of carboxyl-terminal half of the molecule. Int J Pept Protein Res. 1980 Apr;15(4):335–341. [PubMed] [Google Scholar]
- Hahn C. S., Strauss E. G., Strauss J. H. Sequence analysis of three Sindbis virus mutants temperature-sensitive in the capsid protein autoprotease. Proc Natl Acad Sci U S A. 1985 Jul;82(14):4648–4652. doi: 10.1073/pnas.82.14.4648. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hahn Y. S., Grakoui A., Rice C. M., Strauss E. G., Strauss J. H. Mapping of RNA- temperature-sensitive mutants of Sindbis virus: complementation group F mutants have lesions in nsP4. J Virol. 1989 Mar;63(3):1194–1202. doi: 10.1128/jvi.63.3.1194-1202.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hahn Y. S., Strauss E. G., Strauss J. H. Mapping of RNA- temperature-sensitive mutants of Sindbis virus: assignment of complementation groups A, B, and G to nonstructural proteins. J Virol. 1989 Jul;63(7):3142–3150. doi: 10.1128/jvi.63.7.3142-3150.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hanecak R., Semler B. L., Anderson C. W., Wimmer E. Proteolytic processing of poliovirus polypeptides: antibodies to polypeptide P3-7c inhibit cleavage at glutamine-glycine pairs. Proc Natl Acad Sci U S A. 1982 Jul;79(13):3973–3977. doi: 10.1073/pnas.79.13.3973. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hardy W. R., Strauss J. H. Processing the nonstructural polyproteins of Sindbis virus: study of the kinetics in vivo by using monospecific antibodies. J Virol. 1988 Mar;62(3):998–1007. doi: 10.1128/jvi.62.3.998-1007.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Haseloff J., Goelet P., Zimmern D., Ahlquist P., Dasgupta R., Kaesberg P. Striking similarities in amino acid sequence among nonstructural proteins encoded by RNA viruses that have dissimilar genomic organization. Proc Natl Acad Sci U S A. 1984 Jul;81(14):4358–4362. doi: 10.1073/pnas.81.14.4358. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kelley P. M., Schlesinger M. J. Antibodies to two major chicken heat shock proteins cross-react with similar proteins in widely divergent species. Mol Cell Biol. 1982 Mar;2(3):267–274. doi: 10.1128/mcb.2.3.267. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kinney R. M., Johnson B. J., Welch J. B., Tsuchiya K. R., Trent D. W. The full-length nucleotide sequences of the virulent Trinidad donkey strain of Venezuelan equine encephalitis virus and its attenuated vaccine derivative, strain TC-83. Virology. 1989 May;170(1):19–30. doi: 10.1016/0042-6822(89)90347-4. [DOI] [PubMed] [Google Scholar]
- Kräusslich H. G., Wimmer E. Viral proteinases. Annu Rev Biochem. 1988;57:701–754. doi: 10.1146/annurev.bi.57.070188.003413. [DOI] [PubMed] [Google Scholar]
- LIGHT A., FRATER R., KIMMEL J. R., SMITH E. L. CURRENT STATUS OF THE STRUCTURE OF PAPAIN: THE LINEAR SEQUENCE, ACTIVE SULFHYDRYL GROUP, AND THE DISULFIDE BRIDGES. Proc Natl Acad Sci U S A. 1964 Nov;52:1276–1283. doi: 10.1073/pnas.52.5.1276. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Li G. P., Rice C. M. Mutagenesis of the in-frame opal termination codon preceding nsP4 of Sindbis virus: studies of translational readthrough and its effect on virus replication. J Virol. 1989 Mar;63(3):1326–1337. doi: 10.1128/jvi.63.3.1326-1337.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lutz C. T., Hollifield W. C., Seed B., Davie J. M., Huang H. V. Syrinx 2A: an improved lambda phage vector designed for screening DNA libraries by recombination in vivo. Proc Natl Acad Sci U S A. 1987 Jul;84(13):4379–4383. doi: 10.1073/pnas.84.13.4379. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
- Melancon P., Garoff H. Processing of the Semliki Forest virus structural polyprotein: role of the capsid protease. J Virol. 1987 May;61(5):1301–1309. doi: 10.1128/jvi.61.5.1301-1309.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ohno S., Emori Y., Imajoh S., Kawasaki H., Kisaragi M., Suzuki K. Evolutionary origin of a calcium-dependent protease by fusion of genes for a thiol protease and a calcium-binding protein? Nature. 1984 Dec 6;312(5994):566–570. doi: 10.1038/312566a0. [DOI] [PubMed] [Google Scholar]
- Ou J. H., Strauss E. G., Strauss J. H. Comparative studies of the 3'-terminal sequences of several alpha virus RNAs. Virology. 1981 Mar;109(2):281–289. doi: 10.1016/0042-6822(81)90499-2. [DOI] [PubMed] [Google Scholar]
- Palmenberg A. C., Rueckert R. R. Evidence for intramolecular self-cleavage of picornaviral replicase precursors. J Virol. 1982 Jan;41(1):244–249. doi: 10.1128/jvi.41.1.244-249.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Polgár L., Halász P. Current problems in mechanistic studies of serine and cysteine proteinases. Biochem J. 1982 Oct 1;207(1):1–10. doi: 10.1042/bj2070001. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rice C. M., Levis R., Strauss J. H., Huang H. V. Production of infectious RNA transcripts from Sindbis virus cDNA clones: mapping of lethal mutations, rescue of a temperature-sensitive marker, and in vitro mutagenesis to generate defined mutants. J Virol. 1987 Dec;61(12):3809–3819. doi: 10.1128/jvi.61.12.3809-3819.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rice C. M., Strauss J. H. Nucleotide sequence of the 26S mRNA of Sindbis virus and deduced sequence of the encoded virus structural proteins. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2062–2066. doi: 10.1073/pnas.78.4.2062. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ritonja A., Popovic T., Turk V., Wiedenmann K., Machleidt W. Amino acid sequence of human liver cathepsin B. FEBS Lett. 1985 Feb 11;181(1):169–172. doi: 10.1016/0014-5793(85)81136-4. [DOI] [PubMed] [Google Scholar]
- Simmons D. T., Strauss J. H. Translation of Sindbis virus 26 S RNA and 49 S RNA in lysates of rabbit reticulocytes. J Mol Biol. 1974 Jun 25;86(2):397–409. doi: 10.1016/0022-2836(74)90027-8. [DOI] [PubMed] [Google Scholar]
- Strauss E. G., Levinson R., Rice C. M., Dalrymple J., Strauss J. H. Nonstructural proteins nsP3 and nsP4 of Ross River and O'Nyong-nyong viruses: sequence and comparison with those of other alphaviruses. Virology. 1988 May;164(1):265–274. doi: 10.1016/0042-6822(88)90644-7. [DOI] [PubMed] [Google Scholar]
- Strauss E. G., Rice C. M., Strauss J. H. Complete nucleotide sequence of the genomic RNA of Sindbis virus. Virology. 1984 Feb;133(1):92–110. doi: 10.1016/0042-6822(84)90428-8. [DOI] [PubMed] [Google Scholar]
- Tabor S., Richardson C. C. DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc Natl Acad Sci U S A. 1987 Jul;84(14):4767–4771. doi: 10.1073/pnas.84.14.4767. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Takio K., Towatari T., Katunuma N., Teller D. C., Titani K. Homology of amino acid sequences of rat liver cathepsins B and H with that of papain. Proc Natl Acad Sci U S A. 1983 Jun;80(12):3666–3670. doi: 10.1073/pnas.80.12.3666. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Takkinen K. Complete nucleotide sequence of the nonstructural protein genes of Semliki Forest virus. Nucleic Acids Res. 1986 Jul 25;14(14):5667–5682. doi: 10.1093/nar/14.14.5667. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wieslander L. A simple method to recover intact high molecular weight RNA and DNA after electrophoretic separation in low gelling temperature agarose gels. Anal Biochem. 1979 Oct 1;98(2):305–309. doi: 10.1016/0003-2697(79)90145-3. [DOI] [PubMed] [Google Scholar]