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Journal of Virology, August 2003, p. 8548-8554, Vol. 77, No. 15
0022-538X/03/$08.00+0 DOI: 10.1128/JVI.77.15.8548-8554.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
HIV Drug Resistance Program,1 Data Management Services, Frederick Cancer Research and Development Center, National Cancer Institute, Frederick, Maryland 21702,3 Center for Advanced Biotechnology and Medicine (CABM) and Rutgers University Chemistry Department, Piscataway, New Jersey 08854-56382
Received 30 August 2002/ Accepted 3 May 2003
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The crystal structure of HIV-1 RT in a complex with an RNA-DNA primer template whose sequence was derived from the PPT has provided information on the interactions of RT and its template-primer (18). The complex of HIV-1 RT and an RNA-DNA duplex differs from the complex of HIV-1 RT and a DNA-DNA duplex; however, there are considerable similarities (8, 18). In a complex with RT, both DNA-DNA and RNA-DNA duplexes have a bend of about 40° 5 to 9 bp from the polymerase active site. In the DNA-DNA-containing complex, the bend in the nucleic acid is associated with a transition from A-form to B-form geometry; a similar transition has been observed in DNA-DNA substrates bound to other polymerases.The majority of the contacts between the enzyme and the nucleic acid are near the polymerase active site, where the nucleic acid geometry is closer to A-form. Farther from the polymerase active site, the geometry of the DNA-DNA duplex is closer to B-form. The RNA-DNA duplex adopts a geometry between A-form and B-form (H-form). During viral replication, the PPT must remain resistant to RNase H degradation long enough to serve as the primer for plus-strand DNA synthesis. In the RT-RNA-DNA complex, the 4 bp adjacent to the RNase H active site are properly base paired; however, there are two unpaired bases in the RNA-DNA duplex, one in the primer strand and the other in the template strand. These two unpaired bases shift the base pairing out of and then back to the normal register; this unusual structure may contribute to the PPT primer's resistance to RNase H degradation. In the RT-RNA-DNA complex, there are additional contacts between the nucleic acid and the protein relative to the RT-DNA-DNA complex. HIV-1 RT interacts with several of the 2' hydroxyl groups of the RNA template. Near the RNase H active site, a network of amino acids interacts with the DNA primer strand. These amino acids form the RNase H primer grip, which plays a role in positioning the primer strand relative to the RNase H active site and helps determine cleavage specificity.
The connection domain of HIV-1 RT has not been well characterized. It plays a structural role in the protein, linking the polymerase and RNase H domains of the protein and aligning the two domains so that both active sites can simultaneously contact an RNA-DNA substrate. It is likely that retroviral RTs were derived by the fusion of a polymerase and an RNase H, which were originally physically separate enzymes; a structural role for the connection domain fits this evolutionary hypothesis (7). However, the crystal structure of HIV-1 RT in complex with an RNA-DNA template-primer derived from the PPT shows that there are amino acids in the connection domain that make specific contacts with the nucleic acid (18). This finding suggests that amino acids in the connection domain may also play a role in helping to bind and properly position the nucleic acid substrate in the vicinity of the RNase H active site. To test this hypothesis, we generated a series of mutations in the amino acid residues in the connection domain of HIV-1 RT that contact the DNA primer or the RNA template. There are nucleic acid contacts involving both the p66 and p51 subunits. Amino acids K395 and E396 in the p51 subunit and amino acids A360, H361, and T362 in the p66 subunit contact the DNA primer strand; K390 in the p51 subunit contacts the RNA template strand. We wanted to determine if mutations in any of these amino acids would affect the replication of the virus. In particular, we wanted to know if the mutations would alter the binding and proper positioning of the RNA strand, which might affect the efficiency and specificity of RNase H cleavage. The ends of the linear viral DNA are determined by specific RNase H cleavages; the cleavage specificity of RNase H was monitored in vivo using the two-long-terminal-repeat (2-LTR) circle junction sequence as a surrogate for the ends of the viral DNA. The 2-LTR circles arise from the joining of the ends of unintegrated viral DNA, presumably by host cell ligases (12). We used the sequence of the 2-LTR circle junctions to characterize the effects of mutations in the RNase H domain of HIV-1 RT that contact the RNA primer and DNA template in the vicinity of the RNase H active site. There are mutations in the RNase H domain that increase the frequency of aberrant viral DNA ends (10). We analyzed the 2-LTR circle junction sequences derived from infecting cells with wild-type virus and viruses containing mutations in amino acids in the connection domain that contact the RNA-DNA template-primer. The results indicate that most of the mutations in the connection domain have relatively small effects on the virus titer; however, one of the mutations (H361A) decreased the virus titer to about 25% of that of the wild-type virus. The sequence of the 2-LTR circle junctions indicates that most of the mutations that contact the primer strand have relatively subtle effects on RNase H activity and specificity. However, the mutation that had the largest effect on the titer (H361A) also had a significant effect on RNase H cleavage; this amino acid contacts the nucleic acid through the p66 subunit. A mutation in one of the amino acids that contacts the nucleic acid through the p51 subunit (E396A) also had a significant effect on RNase H cleavage, but this mutation had a smaller effect on the titer than did H361A.
Effects of mutations in the connection domain on virus titers. Amino acids in the connection domain of HIV-1 RT that contact either the RNA template or the DNA primer strand in the vicinity of the RNase H active site were identified in the crystal structure of HIV-1 RT in a complex with an RNA-DNA duplex whose sequence was derived from the PPT (18) (Fig. 1). K390, K395, and E396 contact the nucleic acid through the p51 subunit; K395 and E396 contact the DNA primer strand, while K390 contacts the RNA template strand. G359, A360, H361, and T362 contact the DNA primer strand through the p66 subunit. As has been previously described, site-directed mutagenesis has been used to introduce amino acid substitutions in amino acids at positions in the RNase H domain that contact the DNA primer strand and RNA template strand in an HIV-1-based vector, pNLNgoMIVR-E-.HSA (Fig. 2A) (10). The vector was derived from the NL4-3 isolate of HIV-1; it does not express the viral env or vpr gene (9). The vector expresses the gene for a murine cell surface marker, the heat-stable antigen (HSA) gene (hsa) from the nef reading frame (26). 293 cells were cotransfected with the vectors and with pHCMV-g, a plasmid that expresses the vesicular stomatitis virus glycoprotein (1, 29). This cotransfection produced virus-containing supernatants that were harvested and used to infect HOS cells. Forty-eight hours after infection, the cells were labeled with antibody directed against HSA and the virus titer was determined by using a fluorescence-activated cell sorter (FACS). The effects of the mutations in the connection domain of RT on virus titers are shown in Fig. 2B. The T362A, K390A, and K395A mutations decreased the virus titers less than twofold. The G359S, A360D, and E396A mutations decreased the virus titers to about 50% of that of the wild-type virus. The mutation H361A decreased the virus titer to about 25% of that of the wild-type virus, suggesting that the contacts involving the amino acid at position 361 are more important for virus infectivity than the contacts involving other amino acids that we analyzed in the connection domain. H361 contacts the phosphate backbone of the DNA primer strand at position -5 relative to the RNase H cleavage site. Y501 in the RNase H domain of RT contacts the same phosphate as H361; it has previously been shown that the Y501A mutation affects the viral titer and RNase H cleavage specificity (10). The other contacts between amino acids in the connection domain and the DNA primer strand are located farther away from the RNase H active site than the contact made by H361.
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FIG. 1. Diagram of the structure of HIV-1 RT in complex with an RNA-DNA template-primer whose sequence is derived from the PPT. The figure shows the portion of the structure near the RNase H active site; the contacts between the nucleic acid and the RNase H domain and the connection domain are indicated. The RNA template strand is shown in turquoise; the DNA primer strand is shown in purple. The scissile phosphate is designated with a green arrow pointing to the phosphate. The RNase H domain is shown in orange; the connection subdomain is shown in yellow. The thumb is in green. The p51 subunit is in gray. Amino acids in the p51 subunit that contact the nucleic acids are marked with an asterisk next to the position number. Amino acids contacting the nucleic acid are labeled. Contacts between individual amino acids and the nucleic acid are shown in red. The RNA strand is numbered relative to the site of cleavage.
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FIG. 2. Mutations in the connection domain affect the viral titer. (A) The retroviral vector pNLNgoMIVR-E-.HSA has been previously described (9). Briefly, the vector was derived from the NL4-3 isolate of HIV-1, except for the portion of RT from amino acid 42 to amino acid 427, which was derived from the BH10 strain of HIV-1. The env and vpr genes are inactivated in the vector; consequently, the vector undergoes only a single cycle of replication. The murine hsa gene is expressed in the nef reading frame. HSA is a cell surface marker that allows for the determination of virus titers by labeling infected cells with anti-HSA antibody and then subjecting the cells to FACS analysis. (B) Effects of mutations in the connection domain on the virus titers. Virus titers, normalized to the amount of p24 antigen, are shown relative to that of the wild-type virus (WT) on the y axis; the RT mutations are shown along the x axis. Transfection, infections, and the determination of the virus titers were performed as previously described (9). These results are the averages of the results of three independent experiments.
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FIG. 3. Sequences at the 2-LTR circle junctions from wild-type and mutant viruses. The top of the figure shows the linear viral DNA that is the product of reverse transcription. The PBS is indicated by a white box, the leader sequence downstream of the PBS is shown with gray dots, the PPT is a box with black horizontal bars, the U-tract is a gray box, and the sequences immediately upstream of the U-tract are shown by the box with diagonal bars. This linear viral DNA can be ligated by cellular enzymes in the nucleus of an infected cell to form a 2-LTR circle. A consensus circle junction is shown. The underlined "T" is derived from the riboA located at the end of the minus strand; it is derived from the tRNALys3 primer used by HIV-1 RT to initiate minus-strand DNA synthesis. The 2-LTR circle junctions from cells infected with wild-type virus, with virions containing reduced RNase H activity, or with strains with mutations in the connection domain were amplified by using PCR, cloned into a cloning vector, and sequenced as previously described (10). Approximately 100 circle junctions were analyzed for each of the mutants. The boxes show the fraction of 2-LTR circles in the category specified at the left of the figure. Statistically significant increases, compared to levels with the wild-type virus, are designated by an asterisk.
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2-LTR circle junctions containing PPTs with short flanking sequences could arise by the improper generation of the PPT. If the aberrant PPT is then retained as a result of a failure of RNase H to remove the primer, a PPT plus a short flank (the U-tract) is found at the 2-LTR circle junction. This type of insertion can also arise from plus-strand priming by an aberrant primer. PPTs with short flanking sequences were not observed from 2-LTR circle junctions derived from infecting cells with virions containing wild-type RT or virions with reduced RNase H activity. Aberrant 2-LTR circle junctions containing short flanking sequences were observed at a low frequency (0.01 in each case) after cells were infected with the G359S, A360D, K395A, and E396A mutants. The low frequency of 2-LTR circle junctions with PPTs and flanking sequence observed with the connection domain mutants differs from the larger increases that we found for the RNase H primer grip mutants, suggesting that the contacts with amino acids in the connection domain amino acids are less important than the contacts with amino acids in the RNase H domain in determining RNase H cleavage specificity.
A PPT with a long flanking sequence can arise if RT uses (and removes) a primer upstream of the PPT to initiate plus-strand DNA synthesis or if an aberrant primer is used but not removed. The resulting 2-LTR circle junction contains the PPT with a considerable amount of flanking sequence (typically >20 nucleotides upstream of the PPT). This type of aberrant 2-LTR circle junction was observed at a frequency of 0.02 when RNase H activity in the virions was reduced, at 0.02 with the A360D mutant, and at 0.01 for each of the G359S, K390A, and K395A mutants. These differences are not statistically significant.
If RNase H fails to correctly recognize the 3' ends of the PPT and cleaves within U3 to generate the 3' end of the PPT primer and then the PPT primer is removed, there will be a deletion in the 5' end of U3. We analyzed the frequency of small deletions in U3 or U5 to determine if the connection domain mutants incorrectly generate (and remove) the U3 primer (Table 1). It has previously been shown that the RNase H primer grip mutants caused a dramatic increase in the frequency of 5-bp deletions in the U3 region (10); however, no similar increases in 5-bp deletions were observed with the connection domain mutants. Circle junctions derived from infections with the K390A mutant showed an increase in the frequency of smaller deletions (2 to 3 bp) compared to the frequency with circle junctions from infections with either the wild type or mutants with reduced RNase H activity. However, the differences are small, and it appears that the K390A mutation does not cause significant cleavage within U3.
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TABLE 1. Frequency of small deletions in U5 or U3
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We also observed 2-LTR circle junctions containing insertions of tRNAs with the leader sequences immediately adjacent to the primer binding site (PBS). These insertions were observed at a frequency of 0.01 for the wild type and for the G359S, A360D, H361A, and E396A mutants. The frequency was increased to 0.04 for the K390A mutant; however, this increase is not statistically significant. We also observed aberrant junctions of this type with the RNase H primer grip Q475A mutant and the N474A + Q475A double mutant. A circle junction with tRNA sequences and the leader could be generated by the retention of the tRNA on the end of the minus-strand DNA (Fig. 4). The retained tRNA can be copied a second time, and the resulting plus-strand DNA can undergo strand invasion to the PBS of the viral DNA in an inter- or intramolecular fashion, which allows RT to copy the sequences adjacent to the PBS (Fig. 4).
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FIG. 4. Model for the capture of tRNA insertions with leader sequences. (i) The dotted gray line represents degraded viral RNA. The solid gray line represents the PPT primer. The solid black line represents viral DNA. The arrowhead represents the RNase H cleavage that removes the PPT primer. The white arrows represent the tRNA primer. (ii) Plus-strand DNA transfer occurs by using the complementary sequences at the PBS. If the tRNA primer is not removed by RNase H during the synthesis of strong-stop plus-strand DNA, it can be copied a second time when the plus strand is extended. (iii) The removal of the tRNA by RNase H generates a linear viral DNA with a plus-strand overhang (shown in red). (iv) The plus-strand overhang is complementary to the tRNA sequence. (v) This plus-strand DNA can undergo strand invasion of the PBS sequence shown in blue. As drawn, it is assumed that DNA synthesis occurs from both viral RNAs; intramolecular strand invasion may also occur. RT extends the DNA that has invaded. Resolution of the products generates a linear viral DNA containing the tRNA and a large leader sequence.
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As has previously been mentioned, retroviral RTs likely evolved from the fusion of two different proteins, one containing a polymerase and the other containing an RNase H (7). The fusion of the two enzymes into a single protein allowed RNase H to make the highly specific cleavages necessary for retroviral reverse transcription. Retroviral RNase H domains are structurally and functionally related to those of Escherichia coli RNase H. The E. coli RNase H has a structural element called the basic loop, which is necessary for enzymatic activity. This basic loop helps the enzyme bind its nucleic acid substrate (11, 22). Murine leukemia virus (MLV) RNase H contains a related basic loop that is essential for virus replication (13, 24). In in vitro assays, recombinant MLV RT lacking the basic loop was deficient in both polymerase and RNase H activities, presumably because it binds the nucleic acid weakly (2). Because it retains the basic loop, the separately expressed MLV RNase H domain retains enzymatic activity. Unlike MLV RT, the RNase H domain of HIV-1 RT has lost the basic loop. If the RNase H domain of HIV-1 RT is separately expressed, it is properly folded but it lacks enzymatic activity. This lack of enzymatic activity is the result of poor substrate binding; activity can be restored to the isolated RNase H domain of HIV-1 RT by the insertion of a basic loop (11, 22). In addition, expressing RNase H domains containing increasing amounts of the N-terminal extensions that included the connection and thumb domains increased the activity of the RNase H domain (21). This finding suggests, in the context of HIV-1 RT, that the lack of a basic loop in the RNase H domain is compensated for, at least in part, by contacts in the polymerase domain. Examination of the crystal structure shows that the majority of nucleic acid contacts involve the fingers, thumb, and palm of the p66 subunit (4, 8, 18). However, there are contacts in the connection domains of both p51 and p66; these connection domain contacts are in positions similar to those that involve the basic loop. We suggest that in HIV-1 RT some of the connection domain contacts may substitute for the loss of the basic loop contacts.
Research in S.H.H.'s laboratory was supported by the National Cancer Institute and by the National Institute for General Medical Sciences. Research in E.A.'s laboratory was supported by grants AI 27690 and GM55609, and S.G.S. was supported by an NIH-NIAID NRSA fellowship (grant AI 09578).
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