The determination of the total 5,224 base-pair DNA sequence of the virus SV40 has enabled us to locate precisely the known genes on the genome. At least 15.2% of the genome is presumably not translated into polypeptides. Particular points of interest revealed by the complete sequence are the initiation of the early t and T antigens at the same position and the fact that the T antigen is coded by two non-contiguous regions of the genome; the T antigen mRNA is spliced in the coding region. In the late region the gene for the major protein VP1 overlaps those for proteins VP2 and VP3 over 122 nucleotides but is read in a different frame. The almost complete amino acid sequences of the two early proteins as well as those of the late proteins have been deduced from the nucleotide sequence. The mRNAs for the latter three proteins are presumably spliced out of a common primary RNA transcript. The use of degenerate codons is decidedly non-random, but is similar for the early and late regions. Codons of the type NUC, NCG and CGN are absent or very rare.
"Therefore, from each group 1 genome (SV40 reference genome and strain SV40-RI257 genome) was included here. The final collection comprised 31 genomes, 14 from 3 great ape species, 13 from 8 old world monkey (OWM) species, and 4 from 3 new world monkey (NWM) species (Cantalupo et al., 2005; Deuzing et al., 2010; Fagrouch et al., 2011; Fiers et al., 1978; Furuno et al., 1986; Groenewoud et al., 2010; Pawlita et al., 1985; Scuda et al., 2011, 2013; Verschoor et al., 2008; Yamaguchi et al., 2013). They are listed with their hosts, accession numbers and general Fig. 1. "
[Show abstract][Hide abstract] ABSTRACT: Polyomaviruses have so far only been isolated from mammals and birds. Typical for all members of this family is their double-stranded genome of approximately 5,000 base-pairs which can be divided into an early region encoding at least two functional proteins, the large and small tumor antigens, and a late region encompassing genes for the capsid proteins VP1 and VP2. During the last 10 years several novel polyomaviruses have been described in non-human primates and man. This review compares the non-human primate polyomavirus genomes that have been completely sequenced with each other and with the genomes of human polyomaviruses. We predict the presence of protein- and microRNA-encoding sequences. Our analyses demonstrate that several genetically distinct groups of non-human primate polyomaviruses exist, that different polyomaviruses can infect the same non-human primate species but that most of their proteins display highly similar domains and motifs, indicating conservation of key functions.
Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 06/2014; 26. DOI:10.1016/j.meegid.2014.05.030 · 3.02 Impact Factor
"In the sixties, the monkey polyomavirus simian virus 40 (SV40) was isolated and became the first polyomavirus whose complete genome was sequenced (Fiers et al., 1978). Sequence analyses of other polyomavirus genomes confirmed that they all have a similar functional organization encoding the large (LT-ag) and small tumor antigen (st-ag) proteins and the capsid proteins VP1, VP2 and VP3. "
[Show abstract][Hide abstract] ABSTRACT: Polyomaviruses are naked viruses with an icosahedral capsid that surrounds a circular double-stranded DNA molecule of about 5000 base-pairs. Their genome encodes at least five proteins: large and small tumor antigens and the capsid proteins VP1, VP2 and VP3. The tumor antigens are expressed during early stages of the viral life cycle and are implicated in the regulation of viral transcription and DNA replication, while the capsid proteins are produced later during infection. Members of the Polyomaviridae family have been isolated in birds (Avipolyomavirus) and mammals (Orthopolyomavirus and Wukipolyomavirus). Some mammalian polyomaviruses encode an additional protein, referred to as agnoprotein, which is a relatively small polypeptide that exerts multiple functions. This review discusses the structure, post-translational modifications, and functions of agnoprotein, and speculates why not all polyomaviruses express this protein.
"junctions are close to one end of the wild type SV40 21 bp repeat in strain 776 (residues 62–82/83–103)( Fiers et al., 1978; Reddy et al., 1978). In another case, the SV40 junctions with monkey α-satellite DNA in ev-1110 and with monkey chromosome 5 DNA in ev-2102 occur just 2 bp apart at, respectively, SV40 residues 285 and 283 (Figs. "
[Show abstract][Hide abstract] ABSTRACT: The available monkey genomic data banks were examined in order to determine the chromosomal locations of the host DNA inserts in 8 host-substituted SV40 variant DNAs. Five of the 8 variants contained more than one linked monkey DNA insert per tandem repeat unit and in all cases but one, the 19 monkey DNA inserts in the 8 variants mapped to different locations in the monkey genome. The 50 parental DNAs (32 monkey and 18 SV40 DNA segments) which spanned the crossover and flanking regions that participated in monkey/monkey and monkey/SV40 recombinations were characterized by substantial levels of microhomology of up to 8 nucleotides in length; the parental DNAs also exhibited direct and inverted repeats at or adjacent to the crossover sequences. We discuss how the host-substituted SV40 variants arose and the nature of the recombination mechanisms involved.
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