Summary
The sequence of the 3′-terminal 2597 nucleotides of potato virus A (PVA) genome has been determined from cDNA clones. An open reading frame was identified and potentially encodes a large polyprotein containing 789 amino acid residues. This large open reading frame was found to have a high similarity to the nuclear inclusion protein (NIb) and the capsid protein (CP) genes of several potyviruses. The data suggest that the PVA NIb and CP are products arising from the maturation of the large polyprotein as observed for other potyviruses. Putative cleavage sites corresponded to consensus sequences NIa/NIb and NIb/CP, respectively, of other potyviruses. The NIb (putative RNA polymerase) and CP are expected to be 516 and 269 amino acid residues (Mr of 58,939 and 30,094), respectively. The non-coding region is 227 nucleotides long, rich in A and U and unlike other viruses. Furthermore, there are two AUG codons in frame in front of the capsid protein gene suggesting an alternative mode for the capsid protein expression.
References
AbouHaidar MG (1988) Nucleotide sequence of the capsid protein gene and 3′ non-coding region of papaya mosaic virus RNA. J Gen Virol 69: 219–226
AbouHaidar MG, Bancroft JB (1978) The initiation of papaya mosaic virus assembly. Virology 90: 54–59
Allison RF, Johnston RE, Dougherty WG (1986) The nucleotide sequence of the coding region of tobacco etch virus genomic RNA: evidence for the synthesis of a single polyprotein. Virology 154: 9–29
Allison RF, Dougherty WG, Parks TD, Willis L, Johnston RE, Kelly ME, Armstrong FB (1985) Biochemical analysis of the capsid protein gene and capsid protein of tobacco etch virus: N-terminal amino acids are located on the virion's surface. Virology 147: 309:x1316
Bartels R (1971) Potato virus A. CAB/AAB Descriptions of plant viruses no 54.
Biggin MD, Gibson TJ, Hong GF (1983) Buffer gradient gels and [35S] label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci USA 80: 3963–3965
Domier LL, Shaw JG, Rhoads RE (1987) Potyviral proteins share amino acid sequence homology with picorna-, como-, and caulimoviral proteins. Virology 158: 20–27
Domier LL, Franklin KM, Shahabuddin M, Hellman GM, Overmeyer JH, Hiremath ST, Siaw MFE, Lomonossoff GP, Shaw JG, Rhoads RE (1986) The nucleotide sequence of tobacco vein mottling virus RNA. Nucleic Acids Res 14: 5430–5417
Dougherty WG, Allison RF, Parks TD, Johnston RE, Field MJ, Armstrong FB (1985) Nucleotide sequence at the 3′ terminus of pepper mottle virus genomic RNA: evidence for an alternative mode of potyvirus capsid protein gene organization. Virology 146: 282–291
Dougherty WG, Hiebert E (1985) Genome structure and gene expression by plant RNA viruses. In: Davies JW (ed) Molecular plant virology, vol 2. CRC Press, Boca Raton, pp 23–28
Francki RIB, Milne RG, Hatta T (1985) Atlas of plant viruses, vol 2. CRC Press, Boca Raton
Frenkel MJ, Ward CW, Shukla DD (1989) The use of 3′ non-coding nucleotide sequences in the taxonomy of potyviruses: application to watermelon mosaic virus 2 and soybean mosaic virus-N. J Gen Virol 70: 2775–2783
Gough KH, Azad AA, Hanna PJ, Shukla DD (1987) Nucleotide sequence of the capsid and nuclear inclusion protein genes from the Johnsongrass strain of sugarcane mosaic virus RNA. J Gen Virol 68: 297–304
Gubler U, Hoffman BJ (1983) A simple and very efficient method for generating cDNA libraries. Gene 25: 263–269
Kong L-J, Fang R-X, Chen Z-H, Mang K-Q (1990) Molecular cloning and nucleotide sequence of coat protein gene of turnip mosaic virus. Nucleic Acids Res 18: 5555
Lain S, Reichmann JL, Mendez E, Garcia JA (1988) Plum pox potyvirus (PPV) capsid protein and RNA polymerase genes. Virus Res 10: 325–342
Lipman DJ, Pearson WR (1985) Rapid and sensitive protein similarity searches. Science 227: 1435–1441
Lütcke HA, Chow KC, Mickel FS, Moss KA, Kern HF, Scheele GA (1987) Selection of AUG initiation codons differs in plants and animals. EMBO J 6: 43–48
Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, New York
McKern NM, Edskes HK, Ward CW, Strike PM, Barnett OW, Shukla DD (1991) Coat protein of potyviruses 7. Amino acid sequence of peanut stripe virus. Arch Virol 119: 25–35
Pelletier J, Sonenberg N (1988) Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Nature 334: 320–325
Robaglia C, Durand-Tardif M, Tronchet M, Boudanzin G, Astier-Manifacier S, Casse-Delbart F (1989) Nucleotide sequence of potato virus Y (N strain) genomic RNA. J Gen Virol 70: 935–947
Roy BP, AbouHaidar MG, Sit TL, Alexander A (1988) Construction and use of cloned cDNA bioton and32P-labelled probes for the detection of papaya mosaic potexvirus RNA in plants. Phytopathology 78: 1425–1429
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with Chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5463–5467
Shukla DD, Strike PM, Tracy SL, Gough KH, Ward CW (1988) The N and C termini of the coat proteins of potyviruses are surface-located and the N terminus contains the major virus-specific epitopes. J Gen Virol 69: 1497–1508
Tabor S, Richardson CC (1987) DNA sequence analysis with modified bacteriophage T 7 DNA polymerase. Proc Natl Acad Sci USA 84: 4767–4771
Thomas AAM, Haar E, Wellink J, Voorma HO (1991) Cowpea mosaic virus middle component RNA contains a sequence that allows internal binding of ribosomes and that requires eukaryotic initiation factor 4 F for optimal translation. J Virol 65: 2953–2959
Tremblay M-F, Nicolas O, Sinha RC, Lazure C, Laliberte J-F (1990) Sequence of the 3′-terminal region of turnip mosaic virus RNA and the capsid protein gene. J Gen Virol 71: 2769–2771
Wefels E, Sommer H, Salamini F, Rhode W (1989) Cloning of the potato virus Y genes encoding the capsid protein CP and the nuclear inclusion protein NIb. Arch Virol 107: 123–134
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Collins, R.F., Leclerc, D. & AbouHaidar, M.G. Cloning and nucleotide sequence of the capsid protein and the nuclear inclusion protein (NIb) of potato virus A. Archives of Virology 128, 135–142 (1993). https://doi.org/10.1007/BF01309794
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DOI: https://doi.org/10.1007/BF01309794