[Frontiers in Bioscience 8, d143-155, January 1, 2003]
RETROVIRAL RECOMBINATION: REVIEW OF GENETIC ANALYSES
Wei-Shau Hu1, Terence Rhodes1,2, Que Dang1,2, and Vinay Pathak1
1
FIGURES
Figure 1.Minus- and plus-strand DNA synthesis and proposed models of retroviral recombination. Light lines: viral RNA, dashed lines: degraded vRNA from the RNA/DNA hybrid, heavy lines: synthesized DNA, arrows: direction of DNA synthesis. (A) Minus- and plus-strand DNA synthesis. Viral RNA is used as a template for minus-strand DNA synthesis, then minus-strand DNA is used as template for plus-strand DNA synthesis. Plus-strand DNA is synthesized in a discontinuous manner. (B) Forced copy-choice model for recombination. Minus-strand DNA synthesis uses one of the copackaged viral RNA as a template (strand "a"). When encountering a break in the strand "a" RNA, RT switches to use the copackaged strand "b" RNA as a template, and the resulting DNA is a recombinant. (C) DNA strand displacement-assimilation model for recombination. The two copackaged RNA molecules are both copied and two molecules of minus-strand DNA are synthesized (shown as "a" and "b"). Plus-strand DNA synthesis occurs in a discontinuous manner. One short stretch of plus-strand DNA from the "a" molecule is displaced by the growing point of the 5' DNA. The displaced "a" DNA fragment anneals to the minus-strand DNA "b". After repair by the host machinery a recombinant could be formed.
Figure 2. Dynamic copy-choice model for retroviral recombination. Bold arrows and lines: DNA synthesis, black boxes: viral RNA, white boxes: RNase H cleaved RNA, and vertical lines: hydrogen bonds between base pairs. (A) Recombination during reverse transcription using wild-type RT. Wild-type RT is efficient in both DNA polymerization and RNA degradation. RNase H removes the RNA from the DNA:RNA hybrid and exposes the newly synthesized DNA 3' to the RT. This single-stranded DNA can anneal to the copackaged RNA, thereby promoting RT to switch templates, which leads to recombination. (B) Recombination during reverse transcription with altered rate of either DNA polymerization or RNA degradation. When DNA polymerization slows down and RNA degradation remains at the normal rate, DNA 3' to the RT becomes more available to anneal to the other RNA and promotes recombination. When DNA polymerization occurs at normal rate and RNA degradation slows down, much of the DNA 3' to the RT remains in the RNA:DNA hybrid and is less available to anneal to the other RNA, which leads to a lower rate of recombination.