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The cucumovirus 2b gene drives selection of inter-viral recombinants affecting the crossover site, the acceptor RNA and the rate of selection.

Shi BJ, Symons RH, Palukaitis P - Nucleic Acids Res. (2007)

Bottom Line: The source of the 2b also determined the selection of the acceptor RNA and the crossover site, as well as affecting the rate of selection of the recombinant RNAs.A 163-nt tandem repeat in RNA 3 significantly affected the rate of selection of the recombinant RNA, while a single nucleotide within the repeat affected the crossover site.The recombination occurred in a non-random manner, involved no intermediates and probably was generated via a copy-choice mechanism during (+) strand RNA synthesis.

View Article: PubMed Central - PubMed

Affiliation: Australian Centre for Plant Functional Genomics, University of Adelaide, School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA 5064, Australia. bujun.shi@acpfg.com.au

ABSTRACT
RNA-RNA recombination is an important pathway in virus evolution and has been described for many viruses. However, the factors driving recombination or promoting the selection of recombinants are still unclear. Here, we show that the small movement protein (2b) was able to promote selection of RNA 1/2-RNA 3 recombinants within a chimeric virus having RNAs 1 and 2 from cucumber mosaic virus, and RNA 3 from the related tomato aspermy virus, along with heterologous 2b genes. The source of the 2b also determined the selection of the acceptor RNA and the crossover site, as well as affecting the rate of selection of the recombinant RNAs. The nature of the RNA 3 also influenced the selection of the recombinant RNAs. A 163-nt tandem repeat in RNA 3 significantly affected the rate of selection of the recombinant RNA, while a single nucleotide within the repeat affected the crossover site. The recombination occurred in a non-random manner, involved no intermediates and probably was generated via a copy-choice mechanism during (+) strand RNA synthesis.

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Genome organization of C1C2T2BT3, C1C2W2BT3 and their derived recombinant viruses. The genomic RNAs or 2b genes of each virus are indicated by different pattern fills. The short black bars on the RNAs represent the 23 nt of sequence identity. The arrows on RNA 3 represent the tandem repeats (first repeat, A, or second repeat, G). The junction site of each RNA 3 recombinant is indicated. The nucleotide sequence in the junction site of the RNA 3 recombinant derived from C1C2W2BT3 is indicated. The sequence in italics is from TAV RNA 3. The sequences underlined represent the imperfect 19-nt repeats. The single nucleotide difference in the repeats is indicated by an asterisk.
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Figure 3: Genome organization of C1C2T2BT3, C1C2W2BT3 and their derived recombinant viruses. The genomic RNAs or 2b genes of each virus are indicated by different pattern fills. The short black bars on the RNAs represent the 23 nt of sequence identity. The arrows on RNA 3 represent the tandem repeats (first repeat, A, or second repeat, G). The junction site of each RNA 3 recombinant is indicated. The nucleotide sequence in the junction site of the RNA 3 recombinant derived from C1C2W2BT3 is indicated. The sequence in italics is from TAV RNA 3. The sequences underlined represent the imperfect 19-nt repeats. The single nucleotide difference in the repeats is indicated by an asterisk.

Mentions: To determine the nature of the recombinant RNAs derived from C1C2T2BT3, the recombinant RNAs derived from this virus were purified from infected plants, subjected to RT-PCR and the RT-PCR products were then cloned into the pBluescript SK+ vector for sequencing. The sequencing results from five independent clones showed that there was one type of RNA 3 recombinant derived from C1C2T2BT3, containing 2370 nt, of which the 5′ terminal 2060 nt was derived from the 5′ terminal 2060 nt of TAV RNA 3 (Figure 3A right, open bar), while the 3′ terminal 310 nt was identical to the 3′ terminal 310 nt of Q-CMV RNA 1 (Figure 3A right, stippled bar). The crossover site on the TAV RNA 3 sequence was 7 nt 5′ of a homologous sequence of 23 nt conserved in all three genomic RNAs, and 3 nt 5′ of this conserved 23 nt sequence in the Q-CMV RNA 1 sequence.Figure 3.


The cucumovirus 2b gene drives selection of inter-viral recombinants affecting the crossover site, the acceptor RNA and the rate of selection.

Shi BJ, Symons RH, Palukaitis P - Nucleic Acids Res. (2007)

Genome organization of C1C2T2BT3, C1C2W2BT3 and their derived recombinant viruses. The genomic RNAs or 2b genes of each virus are indicated by different pattern fills. The short black bars on the RNAs represent the 23 nt of sequence identity. The arrows on RNA 3 represent the tandem repeats (first repeat, A, or second repeat, G). The junction site of each RNA 3 recombinant is indicated. The nucleotide sequence in the junction site of the RNA 3 recombinant derived from C1C2W2BT3 is indicated. The sequence in italics is from TAV RNA 3. The sequences underlined represent the imperfect 19-nt repeats. The single nucleotide difference in the repeats is indicated by an asterisk.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2275080&req=5

Figure 3: Genome organization of C1C2T2BT3, C1C2W2BT3 and their derived recombinant viruses. The genomic RNAs or 2b genes of each virus are indicated by different pattern fills. The short black bars on the RNAs represent the 23 nt of sequence identity. The arrows on RNA 3 represent the tandem repeats (first repeat, A, or second repeat, G). The junction site of each RNA 3 recombinant is indicated. The nucleotide sequence in the junction site of the RNA 3 recombinant derived from C1C2W2BT3 is indicated. The sequence in italics is from TAV RNA 3. The sequences underlined represent the imperfect 19-nt repeats. The single nucleotide difference in the repeats is indicated by an asterisk.
Mentions: To determine the nature of the recombinant RNAs derived from C1C2T2BT3, the recombinant RNAs derived from this virus were purified from infected plants, subjected to RT-PCR and the RT-PCR products were then cloned into the pBluescript SK+ vector for sequencing. The sequencing results from five independent clones showed that there was one type of RNA 3 recombinant derived from C1C2T2BT3, containing 2370 nt, of which the 5′ terminal 2060 nt was derived from the 5′ terminal 2060 nt of TAV RNA 3 (Figure 3A right, open bar), while the 3′ terminal 310 nt was identical to the 3′ terminal 310 nt of Q-CMV RNA 1 (Figure 3A right, stippled bar). The crossover site on the TAV RNA 3 sequence was 7 nt 5′ of a homologous sequence of 23 nt conserved in all three genomic RNAs, and 3 nt 5′ of this conserved 23 nt sequence in the Q-CMV RNA 1 sequence.Figure 3.

Bottom Line: The source of the 2b also determined the selection of the acceptor RNA and the crossover site, as well as affecting the rate of selection of the recombinant RNAs.A 163-nt tandem repeat in RNA 3 significantly affected the rate of selection of the recombinant RNA, while a single nucleotide within the repeat affected the crossover site.The recombination occurred in a non-random manner, involved no intermediates and probably was generated via a copy-choice mechanism during (+) strand RNA synthesis.

View Article: PubMed Central - PubMed

Affiliation: Australian Centre for Plant Functional Genomics, University of Adelaide, School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA 5064, Australia. bujun.shi@acpfg.com.au

ABSTRACT
RNA-RNA recombination is an important pathway in virus evolution and has been described for many viruses. However, the factors driving recombination or promoting the selection of recombinants are still unclear. Here, we show that the small movement protein (2b) was able to promote selection of RNA 1/2-RNA 3 recombinants within a chimeric virus having RNAs 1 and 2 from cucumber mosaic virus, and RNA 3 from the related tomato aspermy virus, along with heterologous 2b genes. The source of the 2b also determined the selection of the acceptor RNA and the crossover site, as well as affecting the rate of selection of the recombinant RNAs. The nature of the RNA 3 also influenced the selection of the recombinant RNAs. A 163-nt tandem repeat in RNA 3 significantly affected the rate of selection of the recombinant RNA, while a single nucleotide within the repeat affected the crossover site. The recombination occurred in a non-random manner, involved no intermediates and probably was generated via a copy-choice mechanism during (+) strand RNA synthesis.

Show MeSH
Related in: MedlinePlus