- Volume 71, Issue 7, 1990
Volume 71, Issue 7, 1990
- Animal
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An unusual retrovirus-like sequence identified in human DNA
More LessThe human genome contains many different types of endogenous proviruses and retrovirus-like elements. An unusual element of this kind has been isolated from human DNA on the basis of its relatedness to the integrase-coding domain of the pol gene of feline leukaemia virus (FeLV). The element, termed Hs5, is related to FeLV only over a short region of 81 nucleotides predicted to encode the carboxyl terminus of the FeLV integrase protein, p46pol. The region of relatedness between Hs5 and FeLV identifies a short conserved amino acid stretch which is shared among distantly related retroviruses. The conservation of this sequence, its position, and predicted secondary structure suggest that it may represent a conserved substrate binding site or active site of the integrase enzyme. Nucleotide sequence analysis of Hs5 reveals that it is not an intact retrovirus, but contains only the 3′ terminus of pol and a defective env gene without apparent long terminal repeat; Hs5 is unusual among human endogenous retrovirus-like elements in this respect.
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- Plant
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Ambisense segment 4 of rice stripe virus: possible evolutionary relationship with phleboviruses and uukuviruses (Bunyaviridae)
More LessThe complete nucleotide sequence of segment 4 of the rice stripe virus (RSV) genome was determined from overlapping cDNA clones and by direct RNA sequencing. The segment has two long open reading frames (ORFs). One of the ORFs (534 bases) is in the 5′ region of the viral sequence, and the other (858 bases) is in the viral complementary sequence of the viral 3′ region. Such ambisense genome organizations have been seen previously in RNAs of phleboviruses, uukuviruses and arenaviruses. The ORF in the viral sequence encodes the major non-structural protein, but the product of the ORF in the viral complementary sequence (M r 32407) has not yet been identified. The first 18 bases of each of the 5′ and 3′ ends of segment 4 are complementary in sequence. Among the 3′-terminal 16 bases, 14 were identical between RSV genome segments 3 and 4. These terminal sequences are very similar to those of RNAs of phleboviruses and uukuviruses. These and other characteristics indicate a possible evolutionary relationship between RSV and phleboviruses and/or uukuviruses.
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RNA2 of grapevine fanleaf virus: sequence analysis and coat protein cistron location
More LessThe nucleotide sequence of the genomic RNA2 (3774 nucleotides) of grapevine fanleaf virus strain FI 3 was determined from overlapping cDNA clones and its genetic organization was deduced. Two rapid and efficient methods were used for cDNA cloning of the 5′ region of RNA2. The complete sequence contained only one long open reading frame of 3555 nucleotides (1184 codons, 13IK product). The analysis of the N- terminal sequence of purified coat protein (CP) and identification of its C-terminal residue have allowed the CP cistron to be precisely positioned within the polyprotein. The CP produced by proteolytic cleavage at the Arg/Gly site between residues 680 and 681 contains 504 amino acids (M r 56019) and has hydrophobic properties. The Arg/Gly cleavage site deduced by N-terminal amino acid sequence analysis is the first for a nepovirus coat protein and for plant viruses expressing their genomic RNAs by polyprotein synthesis. Comparison of GFLV RNA2 with M RNA of cowpea mosaic comovirus and with RNA2 of two closely related nepoviruses, tomato black ring virus and Hungarian grapevine chrome mosaic virus, showed strong similarities among the 3′ non-coding regions but less similarity among the 5′ end non-coding sequences than reported among other nepovirus RNAs.
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Cucumber mosaic virus satellite RNA (strain Y): analysis of sequences which affect systemic necrosis on tomato
More LessThe location of a sequence within the Y satellite RNA of cucumber mosaic virus (CMV) that confers the ability to induce necrosis on tomato plants has been analysed using chimeric satellite RNAs. These recombinant RNA molecules contained parts of the Y (necrogenic) and Ra (benign) satellite RNAs and were inoculated into tomato plants together with CMV helper virus. From the composition of the recombinant satellite RNAs that induced necrosis it was concluded that, of the nucleotides which differ between Y and Ra satellite RNAs, those affecting necrosis are on the 3′ side of nucleotide 259. The composition of satellite RNAs that failed to induce necrosis implies that at least some of the necrogenic positions are on the 3′ side of nucleotide 311. The symptoms induced by mutated forms of Y and Ra satellite RNAs showed that nucleotide spacing between positions 322 and 323 and sequence identity at one or more of nucleotides 318, 323 or 325 affects the necrogenic potential of Y satellite RNA. The effect of a frameshifting mutation in Y satellite RNA and the location of the necrogenic sites relative to open reading frames in other satellite RNAs suggested that necrosis is not caused by polypeptides encoded in satellite RNA.
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Watermelon mosaic virus II and zucchini yellow mosaic virus: cloning of 3′-terminal regions, nucleotide sequences, and phylogenetic comparisons
More LessThe 3′-terminal genomic regions of an isolate of watermelon mosaic virus II (WMVII) and a Florida isolate of zucchini yellow mosaic virus (ZYMV-F) have been cloned. The nucleotide sequence of the WMVII cDNA clone shows the presence of the large nuclear inclusion protein gene, the coat protein gene and 3′ untranslated region. The nucleotide sequence of a ZYMV-F cDNA clone shows the presence of the coat protein gene and 3′ untranslated region. Comparisons of the nucleotide and deduced amino acid sequences of these clones with those from other potyviruses show that WMVII and the soybean mosaic virus N strain are closely related, thus supporting their classification as different strains of the same virus. Our comparisons also indicate that ZYMV-F is a distinct potyvirus type and that its closest relative is WMVII. Phylogenetic analysis using the most-parsimonious branching arrangement derived from the alignment of coat protein gene sequences suggests the existence of two major potyvirus groupings.
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cDNA cloning and sequence analysis of the 3′-terminal region of zucchini yellow mosaic virus RNA
More LessThe 3′ half of the RNA of the cucurbit potyvirus zucchini yellow mosaic virus (ZYMV) was genetically cloned and the cDNA sequence of a portion of the putative RNA polymerase gene, the complete coat protein gene and the 3′ untranslated region was determined. The coat protein and putative polymerase genes are both part of a continuous open reading frame as is the case for other potyviruses whose genomes are expressed as polyproteins. The Q/S protease cleavage site for the N terminus of the coat protein was deduced by alignment of the coat protein and polymerase genes with other potyviral sequences. The resulting protein has 279 amino acids and a calculated M r of 31214. The predicted amino acid sequence indicates a ZYMV- unique N-terminal region and potyvirus-characteristic central and C-terminal regions. These data also verify that ZYMV is distinct from the cucurbit potyvirus watermelon mosaic virus 2.
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Detection of the trans activity of the plum pox virus NIa-like protease in infected plants
The Nla-like protein of plum pox virus is a protease with high sequence specificity that is autocatalytically released from the viral polyprotein. In order to determine whether the protease is active in trans we constructed a fusion protein consisting of the C-terminal region of the plum pox virus polyprotein and the staphylococcal Protein A. The authentic protease recognition sequence Asn-Val-Val-Val-His- Gln-Ala occurs in the centre of this protein fusion. This protein was cleaved specifically by extracts of plum pox virus-infected plants due to the strong activity of the viral protease making it a useful tool for diagnostic purposes.
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- Corrigendum
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