Retroviral DNA integration

Abstract

DNA integration is a unique enzymatic process shared by all retroviruses and retrotransposons. During integration, double-stranded linear viral DNA is inserted into the host genome in a process catalyzed by the virus-encoded integrase (IN). The mechanism involves a series of nucleophilic attacks, the first of which removes the terminal 2 bases from the 3' ends of the long terminal repeats and of the second which inserts the viral DNA into the host genome. IN specifically recognizes the DNA sequences at the termini of the viral DNA, juxtaposing both ends in an enzyme complex that inserts the viral DNA into a single site in a concerted manner. Small duplications of the host DNA, characteristic of the viral IN, are found at the sites of insertion. At least two host proteins, HMG-I(Y) and BAF, have been shown to increase the efficiency of the integration reaction.

FIG. 1

Ribbon diagrams of the structures of HIV-1 IN fragments. The N-terminal domain of HIV IN is shown on the left. It is based upon PDB file 1WJA (11), coordinating a single zinc cation (black sphere) by using the HHCC motif. This motif consists of residues His12, His16, Cys40, and Cys43, depicted as black sticks. The core domain, center, is based upon 1B14 (68), showing the active form of the HIV IN catalytic domain. The active site has a D,D(35)E motif. Residues Asp116, Asp64, and Glu152 are depicted as black sticks, in order from left to right. Side chains of the two Asp residues bind a single magnesium cation, shown here as a black sphere. The C-terminal DNA binding domain is based upon coordinates in PDB file 1IHV (65). The N- and C-terminal domains were solved by NMR; the catalytic core domain was solved by X-ray diffraction.

FIG. 2

Diagrammatic representation of the mechanism of integration. (A) End-processing reaction. A viral DNA is depicted with the U3 LTR sequence on the left. Magnified below is the 20-bp sequence of the terminal HIV-1 U3 LTR. In an initial reaction, there is a loss of 2 bases from the 3′ strand, adjacent to a highly conserved CA dinucleotide (underlined), via a nucleophilic attack by a water molecule. (B) Joining reaction. The processed LTR DNA ends are brought together into a complex with the target DNA. Insertion of the donor into the target DNA involves a nucleophilic attack by using the 3′ hydroxyl groups on the exposed 3′ strand. The result is a gapped DNA with 5′ 2-base overhangs. Overhang removal, gap, and nick repair would complete the integration reaction.