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Identification of a sequence element immediately upstream of the polypurine tract that is essential for replication of simian immunodeficiency virus
Abstract
A short stretch of T-rich sequences immediately upstream of the polypurine tract (PPT) is highly conserved in the proviral genomes of human and simian immunodeficiency viruses (HIV and SIV). To investigate whether this 'U-box' influences SIVmac239 replication, we analyzed the properties of mutants with changes in this region of the viral genome. All mutants were either retarded in their growth (up to one month delay) or did not replicate detectably in CEMx174 cells. When U-box mutants did replicate detectably, compensatory changes were consistently observed in the viral genome. The most common compensatory change was the acquisition of thymidines immediately upstream of the PPT, but marked expansion in the length of the PPT was also observed. U-box mutants produced transiently by transfection were severely impaired in their ability to produce reverse transcripts in infectivity assays. Analysis of transiently produced mutant virus revealed no defect in RNA packaging or virus assembly. These results identify a new structural element important for an early step in the viral life cycle that includes reverse transcription.
... The site of initiation of the plus-strand DNA, the polypurine tract (PPT), lies near the 3Ј end of the genomic RNA. The PPT elements of different retroviruses and retroelements exhibit considerable sequence variation but always include a stretch of 10 to 20 purines, often flanked on the 5Ј side by a T-rich block (20,32,33). As minus-strand DNA synthesis proceeds, the RNA genome enters into an RNA:DNA hybrid, and so the RNA becomes susceptible to the RNase H activity of RT. ...
... The structure of these molecules suggests that the mutant generates plus-strand DNAs with aberrant 5Ј termini. These results extend recent findings that mutations in the region immediately upstream of the PPT in simian immunodeficiency virus (20), Mo-MuLV (33), and the pararetrovirus cauliflower mosaic virus (26) cause a reduction in viral replication and defects late in reverse transcription. ...
... Although experiments carried out in vitro show that the PPT sequence is the key element required for plus-strand priming, this work and two other recently published papers (20,33) demonstrate the importance of additional upstream sequences for reverse transcription and plus-strand synthesis. Examination of simian immunodeficiency virus revealed that the sequence upstream of the PPT is rich in thymidines; this region, conserved in most retroviruses, was accordingly named the U box (20). ...
Experiments were performed to determine the function of a 28-nucleotide untranslated sequence lying between the envelope gene
and the polypurine tract (PPT) sequence in the Moloney murine leukemia virus (Mo-MuLV) genome. A mutant virus carrying a deletion
of this sequence (Mo-MuLVΔ28) replicated more slowly than wild-type (wt) virus and reverted by recombination with endogenous
sequences during growth in NIH 3T3 cells. We show that this deletion did not affect the level of viral protein expression
or genomic RNA packaging. Mo-MuLVΔ28 served as a helper virus as efficiently as the wt virus; in contrast, a retroviral vector
harboring this mutation exhibited reduced transduction efficiency, indicating that the mutation acts not in trans but in cis. Analysis of acutely infected cells revealed that reduced levels of viral DNA were generated by reverse transcription of
the Mo-MuLVΔ28 RNA as compared to the wt RNA. Analysis of DNA circle junctions revealed that plus-strand DNA of Mo-MuLVΔ28
but not wt virus often retained the PPT and additional upstream sequences. These structures suggest that aberrant 5′ ends
of plus-strand DNA were generated by a failure to remove the PPT RNA primer and/or by mispriming at sites upstream of the
PPT. These data demonstrate that the major role of the sequences immediately upstream of the PPT is specifying efficient and
accurate plus-strand DNA synthesis.
... Interestingly, the upstream portion of the HIV PPT does not appear to be required for efficient primer extension, while preserving of the G-tract is essential (Powell & Levin, 1996). Such data suggests All sequence data are from DDBJ/EMBL/GenBank, and most have been presented previously (Ilyinskii & Desrosiers, 1998). Sequences are aligned via the UG base tandem of att (italics). ...
... Also common to most retroviruses and LTR-retrotransposons is a U-rich region immediately 5 to the PPT shown to be required for efficient viral repli-cation. In SIVmac239 and Mo-MLV, mutation or deletion of this motif delayed or prevented viral replication by interfering with reverse transcription (Bacharach, Gonsky, Lim, & Goff, 2000;Ilyinskii & Desrosiers, 1998;Robson & Telesnitsky, 1999). Additionally, DNA circle junctions resulting from infection by Mo-MLV strains lacking the U-rich motif frequently contained insertions of the PPT and upstream flanking sequences (Bacharach et al., 2000), suggesting this motif may play a role in selection and/or removal of the plus-strand primer. ...
... Additionally, DNA circle junctions resulting from infection by Mo-MLV strains lacking the U-rich motif frequently contained insertions of the PPT and upstream flanking sequences (Bacharach et al., 2000), suggesting this motif may play a role in selection and/or removal of the plus-strand primer. An alternative, or perhaps additional function of the U-rich region may be to prevent misalignment or slippage that might occur during minus-strand synthesis over homopolymeric tracts within the PPT (Ilyinskii & Desrosiers, 1998;Robson & Telesnitsky, 1999). The latter hypothesis is consistent with the observation that SIVmac239 and Mo-MLV revertants frequently contained a poly-A insertion at the PPT 5 terminus, and that in HIV, the U-rich motif does not appear to be required for plus-strand cleavage or initiation in vitro (Powell & Levin, 1996). ...
During the course of reverse transcription, human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) initiates plus-strand DNA synthesis from two highly conserved, purine-rich RNA segments of the viral genome referred to as the 3' and central polypurine tracts (3' and cPPTs). Processing of these elements occurs in several sequential steps including (1) minus-strand DNA synthesis over the PPT(s), (2) ribonuclease H (RNase H) mediated cleavage at the PPT 3' terminus, (3) plus-strand DNA synthesis from the nascent RNA primer(s), and (4) primer removal. Completing each of these steps precisely and specifically is essential, as failure to do so can result in reduced virus replication and/or impaired integration of viral DNA into the host cell genome. In this review, plus-strand primer processing in HIV-1 is discussed from biochemical, structural, and historical perspectives. A comparative analysis of PPT-processing in different LTR-containing retroelements is also presented.
... It is possible that the T(-16)A mutation, which appears not to affect siRNA resistance, was present in the 3 0 PPT of the original v120-A escape variant because it effectively extends the mutant plus-strand primer to the wild type length; i.e. from 5 0 -UUU^UUAAAAGAAAAG GGGGG^A (17-nt) for the wild type to 5 0 -UU^UUAAAAAGAAAAGGGGG^AA (17 nt) for the mutant. Alternatively, the T(-16)A mutation may have been produced by slippage during reverse transcription [42] and was retained only because the selection pressure against it was negligible. Regardless, of the two mutations identified in the v120-A escape variant, T(-16)A has the lesser effect on both RNase H processing of the HIV-1 PPT and on viral fitness. ...
... However, complete removal of one or both A-tracts greatly reduces the efficiency of plusstrand primer generation and utilization [25]. Some evidence also suggests that the U-A junction at the PPT 5 0 terminus is important for preventing slippage during reverse transcription of HIV-1 RNA, as demonstrated in SIV mutants in which the U-tract immediately upstream from the 3 0 PPT had been deleted [42]. ...
... It is possible that the T(-16)A mutation, which appears not to affect siRNA resistance, was present in the 3 0 PPT of the original v120-A escape variant because it effectively extends the mutant plus-strand primer to the wild type length; i.e. from 5 0 -UUU^UUAAAAGAAAAG GGGGG^A (17-nt) for the wild type to 5 0 -UU^UUAAAAAGAAAAGGGGG^AA (17 nt) for the mutant. Alternatively, the T(-16)A mutation may have been produced by slippage during reverse transcription [42] and was retained only because the selection pressure against it was negligible. Regardless, of the two mutations identified in the v120-A escape variant, T(-16)A has the lesser effect on both RNase H processing of the HIV-1 PPT and on viral fitness. ...
... However, complete removal of one or both A-tracts greatly reduces the efficiency of plusstrand primer generation and utilization [25]. Some evidence also suggests that the U-A junction at the PPT 5 0 terminus is important for preventing slippage during reverse transcription of HIV-1 RNA, as demonstrated in SIV mutants in which the U-tract immediately upstream from the 3 0 PPT had been deleted [42]. ...
Converting single-stranded viral RNA into double stranded DNA for integration is an essential step in HIV-1 replication. Initial polymerization of minus-strand DNA is primed from a host derived tRNA, whereas subsequent plus-strand synthesis requires viral primers derived from the 3' and central polypurine tracts (3' and cPPTs). The 5' and 3' termini of these conserved RNA sequence elements are precisely cleaved by RT-associated RNase H to generate specific primers that are used to initiate plus-strand DNA synthesis. In this study, siRNA wad used to produce a replicative HIV-1 variant contained G(-1)A and T(-16)A substitutions within/adjacent to the 3'PPT sequence. Introducing either or both mutations into the 3'PPT region or only the G(-1)A substitution in the cPPT region of NL4-3 produced infectious virus with decreased fitness relative to the wild-type virus. In contrast, introducing the T(-16)A or both mutations into the cPPT rendered the virus(es) incapable of replication, most likely due to the F185L integrase mutation produced by this nucleotide substitution. Finally, the effects of G(-1)A and T(-16)A mutations on cleavage of the 3'PPT were examined using an in vitro RNase H cleavage assay. Substrate containing both mutations was mis-cleaved to a greater extent than either wild-type substrate or substrate containing the T(-16)A mutation alone, which is consistent with the observed effects of the equivalent nucleotide substitutions on the replication fitness of NL4-3 virus. In conclusion, siRNA targeting of the HIV-1 3'PPT region can substantially suppress virus replication, and this selective pressure can be used to generate infectious virus containing mutations within or near the HIV-1 PPT. Moreover, in-depth analysis of the resistance mutations demonstrates that although virus containing a G(-1)A mutation within the 3'PPT is capable of replication, this nucleotide substitution shifts the 3'-terminal cleavage site in the 3'PPT by one nucleotide (nt) and significantly reduces viral fitness.
... In monkeys infected with SIV containing a 182-bp deletion in the region that is uniquely nef, the virus progressively loses much of the remaining nef sequences that are overlapped by U3 (22). However, this nef mutant virus consistently retains regions of nef sequence that contribute to virus replication in a cis-acting fashion; these include the polypurine tract, the U3 terminal sequences and, importantly, the transcriptional enhancer element contained within the 80 bp immediately upstream of NF-B (18,33,36,(42)(43)(44). It is thus curious that, in the current study, SIV seFIG. ...
... In addition, terminal sequences at the 5 end of U3 are absolutely required for proviral DNA integration by the virus-encoded integrase (10,19). U-box sequences, just upstream of the polypurine tract, are also required for replication at the RT step (18). The sequences of these HIV-1 cis-acting elements all differ slightly from their SIV counterparts. ...
A nef gene is present in all primate lentiviruses, including human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus of macaque monkeys (SIVmac). However, the nef genes of HIV-1 and SIVmac exhibit minimal sequence identity, and not all properties are shared by the two. Nef sequences of SIVmac239 were replaced by four independent nef alleles of HIV-1 in a context that was optimal for expression. The sources of the HIV-1 nef sequences included NL 4-3, a variant NL 4-3 gene derived from a recombinant-infected rhesus monkey, a patient nef allele, and a nef consensus sequence. Of 16 rhesus monkeys infected with these SHIVnef chimeras, 9 maintained high viral loads for prolonged periods, as observed with the parental SIVmac239, and 6 have died with AIDS 52 to 110 weeks postinfection. Persistent high loads were observed at similar frequencies with the four different SIV recombinants that expressed these independent HIV-1 nef alleles. Infection with other recombinant SHIVnef constructions resulted in sequence changes in infected monkeys that either created an open nef reading frame or optimized the HIV-1 nef translational context. The HIV-1 nef gene was uniformly retained in all SHIVnef-infected monkeys. These results demonstrate that HIV-1 nef can substitute for SIVmac nef in vivo to produce a pathogenic infection. However, the model suffers from an inability to consistently obtain persisting high viral loads in 100% of the infected animals, as is observed with the parental SIVmac239.
... Because the bulk of the replication intermediate is nonspecifically hydrolyzed, structural features of the PPT (a) render it RNase H-insensitive and (b) control precise cleavage at the junction with adjacent U3 DNA or RNA sequences (1). Although several reports have studied PPT processing relative to alterations in its sequence (2)(3)(4)(5)(6) or that of the cognate retroviral polymerase (7)(8)(9), the structural basis for this remains elusive. The recent structure of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) bound to a PPTcontaining RNA/DNA duplex has provided important mechanistic insights regarding the PPT resistance to hydrolysis (10). ...
... Therefore, it is impossible to conclude whether the specific cleavage at the PPT/U3 junction is a result of RT positioning at the 5Ј primer end or whether other structural features of the PPT contribute to the selectivity. To address this question, we tested substrates that lacked the (U) 5 sequence or contained a 10-ribonucleotide extension at the PPT 5Ј terminus. The data in Fig 7 conclusively 19-nt length was critical, then RT positioned at the 5Ј end of the shortened PPT RNA (15 nt) should yield enhanced hydrolysis rates at positions ϩ3 or ϩ4, which represent conventional RNase H cleavage sites (see Fig. 7). ...
Precise cleavage at the polypurine tract (PPT)/U3 junction by human immunodeficiency virus type 1 (HIV-1) reverse transcriptase
RNase H is critical for generating a correct viral DNA end for subsequent integration. Using potassium permanganate (KMnO4) modification, we have identified a significant distortion in the nucleic acid structure at the HIV-1 PPT/U3 junction in
the absence of trans-acting factors. Unusually high reactivity of template thymine +1 is detected when the PPT primer is extended
by DNA or RNA at its 3′ terminus. Chemical footprinting suggests that the extent of base unstacking in the wild-type species
is comparable when the +1 A:T base pair is replaced by a C:T mismatch. However, reactivity of this template base is diminished
after alterations to upstream (rA)4:(dT)4 or (rG)6:(dC)6 tracts. Importantly, there is a correlation between the structural deformation at base pair +1 and precise cleavage at the
PPT/U3 junction by HIV-1 reverse transcriptase/RNase H. KMnO4 modification also revealed unusually high reactivity for one of two (dT)4:(rA)4 duplexes upstream of the PPT/U3 junction, suggesting a significant structural distortion within the PPT itself in the absence
of the retroviral polymerase. Structural abnormalities in this region are not only essential for resistance of the PPT to
hydrolysis but also significantly impact the conformation of the PPT/U3 junction. Our data collectively suggest that the entire
PPT sequence contributes to the structural distortion at the PPT/U3 junction, potentially providing a mechanism for its selective
processing.
... This possibility was tested by introducing two alterations immediately 5Ј of the Ty3 PPT, changing the sequence from 5Ј-rC-rC-rC-rU-3Ј to either 5Ј-rC-rU-rC-rU-3Ј (mutant C 3 U) or 5Ј-rU-rU-rU-rU-3Ј (mutant 3C 3 3U). The latter sequence closely resembles the U-rich region 5Ј of the HIV-1 PPT, which has been shown to play a role in its utilization (31,32). To control for potential destabilization of the duplex resulting from C 3 U substitutions, each RNA primer was extended by an additional 7 nucleotides at its 5Ј terminus (Fig. 6A). ...
... Data of Fig. 6 implicate a cis-acting element (i.e. the short dG:rC block immediately upstream of the (ϩ) strand primer) in Ty3 PPT recognition. Regions 5Ј of the PPTs of murine leukemia (31) and simian immunodeficiency virus (32) have also been shown to control the efficiency and accuracy with which they are processed. Likewise, in vivo studies with another long terminal repeat-containing retrotransposon, Ty1, have shown that an A:T-rich region immediately upstream of the PPT participates in its selection (33). ...
Despite diverging in sequence and size, the polypurine tract (PPT) primers of retroviruses and long terminal repeat-containing retrotransposons are accurately processed from (+) U3 RNA and DNA by their cognate reverse transcriptases (RTs). In this paper, we demonstrate that misalignment of the Ty3 retrotransposon RT on the human immunodeficiency virus-1 PPT induces imprecise removal of adjacent (+)-RNA and failure to release (+)-DNA from the primer. Based on these observations, we explored the structural basis of Ty3 PPT recognition by chemically synthesizing RNA/DNA hybrids whose (-)-DNA template was substituted with the non-hydrogen-bonding thymine isostere 2,4-difluoro-5-methylbenzene (F). We observed a consistent spatial correlation between the site of T --> F substitution and enhanced ribonuclease H (RNase H) activity approximately 12-13 bp downstream. In the most pronounced case, dual T --> F substitution at PPT positions -1/-2 redirects RNase H cleavage almost exclusively to the novel site. The structural features of this unusual base suggest that its insertion into the Ty3 PPT (-)-DNA template weakens the duplex, inducing a destabilization that is recognized by a structural element of Ty3 RT approximately 12-13 bp from its RNase H catalytic center. A likely candidate for this interaction is the thumb subdomain, whose minor groove binding tract most likely contacts the duplex. The spatial relationship derived from T --> F substitution also infers that Ty3 PPT processing requires recognition of sequences in its immediate 5' vicinity, thereby locating the RNase H catalytic center over the PPT-U3 junction, a notion strengthened by additional mutagenesis studies of this paper.
... LNA substitutions also increase the local organization of the phosphate backbone and significantly enhance the stability of nucleic acid duplexes, the latter most likely reflecting a greater degree of stacking with neighboring bases (49). Using a scanning strategy of overlapping LNA doublets and triplets in the PPT (Ϫ) DNA template, A-like duplex geometry was introduced locally throughout the PPT-containing RNA/ DNA hybrid and immediately adjacent dA⅐rU tract, alteration of which also affects PPT function (50,51). Our current studies indicate that modifying either extremity of the PPT impairs hydrolysis at the PPT/U3 junction, whereas the intervening sequence can be substituted with minimal consequences for hydrolysis. ...
... Experimental Strategy-The structures of the individual LNA-inducing nucleobases and strategy for their pairwise insertion into the PPT (Ϫ) DNA template are illustrated in Figs. 1, A and B, respectively. Because all four nucleobases were commercially available, this allowed us to evaluate the homopolymeric dA⅐rU tract immediately adjacent to the PPT, a region whose alteration affects PPT usage in HIV-1 (53), Moloney murine leukemia virus (51), and simian immunodeficiency virus (50). Although dC was commercially available as the 5-methyl derivative, x-ray crystallography (4) suggests that relatively few contacts are made to nucleobases of the RNA/ DNA hybrid, suggesting steric interference would be minimal. ...
Unusual base-pairing in a co-crystal of reverse transcriptase (RT) and a human immunodeficiency virus type 1 (HIV-1) polypurine tract (PPT)-containing RNA/DNA hybrid suggests local nucleic acid flexibility mediates selection of the plus-strand primer. Structural elements of HIV-1 RT potentially participating in recognition of this duplex include the thumb subdomain and the ribonuclease H (RNase H) primer grip, the latter comprising elements of the connection subdomain and RNase H domain. To investigate how stabilizing HIV-1 PPT structure influences its recognition, we modified the (-) DNA template by inserting overlapping locked nucleic acid (LNA) doublets and triplets. Modified RNA/DNA hybrids were evaluated for cleavage at the PPT/U3 junction. Altered specificity was observed when the homopolymeric dA.rU tract immediately 5' of the PPT was modified, whereas PPT/U3 cleavage was lost after substitutions in the adjacent dT.rA tract. In contrast, the "unzipped" portion of the PPT was moderately insensitive to LNA insertions. Although a portion of the dC.rG and neighboring dT.rA tract were minimally affected by LNA insertion, RNase H activity was highly sensitive to altering the junction between these structural elements. Using 3'-end-labeled PPT RNA primers, we also identified novel cleavage sites ahead (+5/+6) of the PPT/U3 junction. Differential cleavage at the PPT/U3 junction and U3 + 5/+6 site in response to LNA-induced template modification suggests two binding modes for HIV-1 RT, both of which may be controlled by the interaction of its thumb subdomain (potentially via the minor groove binding track) at either site of the unzipped region.
... A short stretch of T-rich motif (TTTT) immediately upstream of the cPPT is correlated with the ultraconservation found in positions 900-901. These codon positions were experimentally shown to be important for reverse transcription (Ilyinskii and Desrosiers, 1998). Among the 48 conserved codons, a second region (positions 934-947) exhibits exceptionally high level of Ks conservation ( Figure 4B). ...
... Our analysis revealed a 50-codon-long sequence in the pol open reading frame with exceptionally low synonymous and non-synonymous rates. This sequence roughly starts and ends with sequences known to be functionally important, namely the TTTT-rich box, the cPPT and the CTS signals, all act in cis during the process of HIV-1 reverse transcription ( Charneau and Clavel, 1991;Charneau et al., 1994;Ilyinskii and Desrosiers, 1998). This further indicates that our model has the ability to identify important regulatory sequences embedded in open reading frames. ...
Codon evolutionary models are widely used to infer the selection forces acting on a protein. The non-synonymous to synonymous rate ratio (denoted by Ka/Ks) is used to infer specific positions that are under purifying or positive selection. Current evolutionary models usually assume that only the non-synonymous rates vary among sites while the synonymous substitution rates are constant. This assumption ignores the possibility of selection forces acting at the DNA or mRNA levels. Towards a more realistic description of sequence evolution, we present a model that accounts for among-site-variation of both synonymous and non-synonymous substitution rates. Furthermore, we alleviate the widespread assumption that positions evolve independently of each other. Thus, possible sources of bias caused by random fluctuations in either the synonymous or non-synonymous rate estimations at a single site is removed. Our model is based on two hidden Markov models that operate on the spatial dimension: one describes the dependency between adjacent non-synonymous rates while the other describes the dependency between adjacent synonymous rates. The presented model is applied to study the selection pressure across the HIV-1 genome. The new model better describes the evolution of all HIV-1 genes, as compared to current codon models. Using both simulations and real data analyses, we illustrate that accounting for synonymous rate variability and dependency greatly increases the accuracy of Ka/Ks estimation and in particular of positively selected sites. Finally, we discuss the applicability of the developed model to infer the selection forces in regulatory and overlapping regions of the HIV-1 genome.
Contact: talp@post.tau.ac.il
... Substitution of the HIV-1 pA signal with the SV40 pA signal (i.e. the same signal as inserted into the 3' LTR) resulted in a greatly decreased virus titre. The SV40 pA signal is very strong(Ilyinskii, P. O. and Desrosiers, R. C. 1998) and may have cause premature polyadenylation of the transcripts.However, analysis of a previous version of this vector, pHIV1SDm253SV40, demonstrated that insertion of the SV40 pA signal into the 5' LTR does not result in a significant amount of premature polyadenylation, with full length genomic RNA only decreasing 2-fold(Koldej, R. ...
... We observed the same features in unchallenged macaques infected with SIVmac251⌬nef (data not shown). These data are consistent with previous in vitro and in vivo observations for SIVmac239⌬nef-infected monkeys (12,29,34,50). Thus, in the absence of a functional nef, certain regions overlapping nef and U3 are lost, suggesting that these regions are dedicated solely to the encoding of Nef. ...
Live attenuated simian immunodeficiency virus (SIV) is the most efficient vaccine yet developed in monkey models of human
immunodeficiency virus infection. In all successful vaccine trials, attenuation was achieved by inactivating at least the
nefgene. We investigated some virological and immunological characteristics of five rhesus macaques immunized with anef-inactivated SIVmac251 molecular clone (SIVmac251Δnef) and challenged 15 months later with the pathogenic SIVmac251 isolate. Three animals were killed 2 weeks postchallenge (p.c.)
to search for the challenge virus and to assess immunological changes in various organs. The other two animals have been monitored
up for 7 years p.c., with clinical and nefgene changes being noted. The animals killed showed no increase in viral load and no sign of a secondary immune response,
although the challenged virus was occasionally detected by PCR. In one of the monkeys being monitored, the vaccine virus persisted
and an additional deletion occured in nef. In the other monkey that was monitored, the challenge and the vaccine (Δnef) viruses were both detected by PCR until a virus with a hybrid nefallele was isolated 48 months p.c. This nef hybrid encodes a 245-amino-acid protein. Thus, our results show (i) that monkeys were not totally protected against homologous
virus challenge but controlled the challenge very efficiently in the absence of a secondary immune response, and (ii) that
the challenge and vaccine viruses may persist in a replication-competent form for long periods after the challenge, possibly
resulting in recombination between the two viruses.
... In the present study, we describe the crystal structure of an RNA/DNA dodecamer duplex containing the 11 5 0 bases of the PPT motif of HIV-1 preceded by a u residue from the 'U-box' (Ilyinskii & Desrosiers, 1998 ...
The crystal structure of an RNA/DNA hybrid dodecamer, r(5'-uaaaagaaaagg):d(5'-CCTTTTCTTTTA), which contains three-quarters of the polypurine tract (PPT) sequence of the HIV RNA genome is reported. The hybrid structure was determined at 1.6 Å resolution and was found to have the A-form conformation. However, the presence of alternate conformations along the RNA template strand indicated increased flexibility of the PPT sequence. Two segments (at nucleotides 1-2 and 6-8) of the RNA chain have two conformations exhibiting differences in torsion and pseudorotation angles. For conformation I((1-2), (6-8)), 25% of the RNA sugars have the C2'-exo pucker and the rest have the expected C3'-endo pucker. The II(1-2) and II(6-8) conformations of the RNA strand have one sugar with the C2'-exo pucker. None of the ribose rings exist in the C2'-endo form, in contrast to a previous report which postulated a C2'-endo ribose as a key structural element of the PPT. The widths of the minor groove for conformations I((1-2), (6-8)) and II((1-2), (6-8)) of the RNA strand are 9.2-10.5 and 9.4-10.7 Å, respectively. Both ranges are very close to the intervals accepted for A-form RNA duplexes. On the opposing DNA primer strand most of the sugars are C3'-endo, except for the 3'-terminal sugars, which are C2'-endo (T22) or O4'-endo (T23 and A24). The duplex includes a noncanonical u1(anti)·A24(syn) base interaction with only one hydrogen bond between the bases. This noncanonical base interaction at the 5'-end of the template distorts the values of the helical parameters of the adjacent base pair.
... We cloned a 118-bp sequence from pol of HIV-1, encompassing the central polypurine tract and termination sequences [7][8][9] , into a self-inactivating lentiviral vector upstream of an expression cassette for enhanced green fluorescent protein (GFP) in the sense (cPPT(s)) or antisense (cPPT(as)) orientation (Fig. 1a). We produced VSV-pseudotyped vectors with the non-modified and cPPT transfer constructs, matched the content of viral par- Fig. 2 The cPPT sequence does not affect encapsidation or reverse transcription of vector RNA, but enhances nuclear translocation of the transcripts within target cells. ...
Gene-transfer vectors based on lentiviruses are distinguished by their ability to transduce non-dividing cells. The HIV-1 proteins Matrix, Vpr and Integrase have been implicated in the nuclear import of the viral genome in non-dividing cells. Here we show that a sequence within pol is also required in cis. It contains structural elements previously associated with the progress of reverse transcription in target cells. We restored these elements in cis within late-generation lentiviral vectors. The new vector transduced to a much higher efficiency several types of human primary cells, when both growing and growth-arrested, including haematopoietic stem cells assayed by long-term repopulation of NOD/SCID mice. On in vivo administration into SCID mice, the vector induced higher plasma levels of human clotting factor IX (F.IX) than non-modified vector. Our results indicate that nuclear translocation of the genome is a rate-limiting step in lentiviral infection of both dividing and non-dividing cells, and that it depends on protein and nucleic acid sequence determinants. Full rescue of this step in lentivirus-based vectors improves performance for gene-therapy applications.
... Noad et al. have similarly established that T-rich sequences upstream of the PPT are required for plus-strand priming for the pararetrovirus cauliflower mosaic virus (16). Additionally, Ilyinskii et al. have demonstrated that the T stretch upstream of the simian immunodeficiency virus (SIV) PPT is required for SIV replication (11), and a T stretch upstream of the Ty1 PPT is important for plus-strand priming and transposition of that yeast retroelement (33). ...
Retrovirus plus-strand synthesis is primed by a cleavage remnant of the polypurine tract (PPT) region of viral RNA. In this
study, we tested replication properties for Moloney murine leukemia viruses with targeted mutations in the PPT and in conserved
sequences upstream, as well as for pools of mutants with randomized sequences in these regions. The importance of maintaining
some purine residues within the PPT was indicated both by examining the evolution of random PPT pools and from the replication
properties of targeted mutants. Although many different PPT sequences could support efficient replication and one mutant that
contained two differences in the core PPT was found to replicate as well as the wild type, some sequences in the core PPT
clearly conferred advantages over others. Contributions of sequences upstream of the core PPT were examined with deletion
mutants. A conserved T-stretch within the upstream sequence was examined in detail and found to be unimportant to helper functions.
Evolution of virus pools containing randomized T-stretch sequences demonstrated marked preference for the wild-type sequence
in six of its eight positions. These findings demonstrate that maintenance of the T-rich element is more important to viral
replication than is maintenance of the core PPT.
... Four thymidine nucleotides are located upstream of the cPPT (Table 1). A similar "U box" is present in many of the U3PPT and cPPT regions of the primate lentiviruses (16,19,27). However, unlike HIV-1, the U box is absent upstream of any FIV U3PPT, where TCCT or, less commonly, AAAT or CTGC is found (Table 1). ...
A duplication of the polypurine tract (PPT) at the center of the human immunodeficiency virus type 1 (HIV-1) genome (the cPPT) has been shown to prime a separate plus-strand initiation and to result in a plus-strand displacement (DNA flap) that plays a role in nuclear import of the viral preintegration complex. Feline immunodeficiency virus (FIV) is a lentivirus that infects nondividing cells, causes progressive CD4(+) T-cell depletion, and has been used as a substrate for lentiviral vectors. However, the PPT sequence is not duplicated elsewhere in the FIV genome and a central plus-strand initiation or strand displacement has not been identified. Using Southern blotting of S1 nuclease-digested FIV preintegration complexes isolated from infected cells, we detected a single-strand discontinuity at the approximate center of the reverse-transcribed genome. Primer extension analyses assigned the gap to the plus strand, and mapped the 5' terminus of the downstream (D+) segment to a guanine residue in a purine-rich tract in pol (AAAAGAAGAGGTAGGA). RACE experiments then mapped the 3' terminus of the upstream plus (U+)-strand segment to a T nucleotide located 88 nucleotides downstream of the D+ strand 5' terminus, thereby identifying the extent of D+ strand displacement and the central termination sequence of this virus. Unlike HIV, the FIV cPPT is significantly divergent in sequence from its 3' counterpart (AAAAAAGAAAAAAGGGTGG) and contains one and in some cases two pyrimidines. An invariant thymidine located -2 to the D+ strand origin is neither required nor optimal for codon usage at this position. Although the mapped cPPTs of FIV and HIV-1 act in cis, they encode homologous amino acids in integrase.
... The polypurine tract located in the central position (cPPT) in all LV genomes has been shown to facilitate nuclear translocation of pre-integration complexes and to enhance vector efficiency in both dividing and nondividing cells. Associated with the central termination site (CTS) which dictates the reverse transcriptase (RT) ejection in the specific context of strand displacement synthesis, the cPPT cis-acting benefit for proviral nuclear facilitation has been clearly demonstrated in the HIV-1 [51,52], SIV [53], EIAV [54] and FIV [55] contexts. A putative cPPT/CTS element has also been maintained in BIV-derived vectors [27]. ...
Gene transfer vectors based on retroviruses including oncogenic retroviruses and lentiviruses provide effective means for the delivery, integration and expression of exogenous genes in mammalian cells. Lentiviral (LV) vectors provide attractive gene delivery vehicles in the context of non-dividing cells. This review summarizes the different optimized LV genetic systems that have been developed to date. In all cases, the production of LV-derived vectors consists of a genetically split gene expression design. The viral elements that are specifically required are (i). the LV packaging helper proteins consisting of at least the gag-pol genes, (ii). the LV transfer vector RNA containing the transgene expression cassette, and (iii). an heterologous glycoprotein. While the genetic requirements and performances of the two former viral elements will be treated herein, the latter element relative to the envelope pseudotyping of LV vectors will not be further described (cf. review by Cosset in this issue).
... We have previously shown, however, that an SIVmac239 TPI variant containing a U3 region that is shortened by 384-bp and does not overlap nef is pathogenic in infected rhesus macaques (Mü nch et al., 2001). The homology between the HIV-1 and SIV U3 LTR sequences is low and it has been demonstrated that the SIVmac U3 region shows a higher degree of functional redundancy compared to the corresponding HIV-1 region (Ilyinskii and Desrosiers, 1998;Pö hlmann et al., 1998). To further evaluate the possible relevance of the modulatory U3 region for HIV-1 replication and pathogenicity in infected humans, we infected ex vivo tonsillary human lymphoid tissue (HLT) with the HIV-1 nef/LTR variants. ...
The LTRs of all primate lentiviruses contain long U3 regions overlapping the nef gene. To assess the relevance of the modulatory U3 region for HIV-1 replication, we inactivated the T-rich region, the Polypurine tract and attachment (att) sequences in nef by silent mutations and inserted intact cis-regulatory elements just upstream of the core enhancer. These modifications severely truncated the U3 region and eliminated the nef overlap. The resulting HIV-1 mutants expressed functional Nef, replicated efficiently and caused CD4+ T cell depletion in ex vivo-infected lymphoid tissue suggesting that the modulatory U3 region might not be essential for efficient HIV-1 gene expression and AIDS pathogenesis.
... To better understand these observations, and determine whether the RNase H cleavages involved in generating or removing the PPT primer are responsible for creating aberrant ends in the linear viral DNA, we used an in vitro RNase H PPT cleavage assay. In brief, RNA/ DNA substrates were prepared that contained the entire HIV-1 PPT sequence, portions of the U3 sequences that are adjacent to the PPT, and the 5′ U-tract sequence, previously shown to be important for viral replication (Bacharach et al., 2000; Ilyinskii and Desrosiers, 1998; Robson and Telesnitsky, 1999) (Fig. 2). 5′-End labeled RNA primers were annealed to their complementary DNA templates, incubated in the presence of HIV-1 RT, and the cleavage products were fractioned by denaturing polyacrylamide gel electrophoresis. ...
The recognition and precise cleavage of the polypurine tract (PPT) of the human immunodeficiency virus type 1 (HIV-1) is an essential step in HIV-1 reverse transcription. The accurate cleavage, and the subsequent removal, of the PPT by the RNase H activity of HIV-1 RT defines the left end of the double-stranded viral DNA genome, the substrate for integration into the host genome. Previous analyses have shown that mutations in the 3'-end (G-tract) of the PPT cause alterations in RNase H cleavage specificity. In particular, mutations at positions 2 and 5 in the G-tract increased the frequency of retention of PPT sequences in the 2-LTR circle junction. To better understand why these mutations affected PPT cleavage in vivo, we analyzed the cleavage of PPT substrates in vitro that contained altered sequences and unusual base substitutions. Our results, herein, confirm that mutations at positions 2 and 5 of the G-tract do significantly alter the cleavage specificity at the PPT/U3 junction, and further suggest that the miscleavages observed in vivo were due to an improper generation of the PPT primer, as opposed to its improper removal. Finally, our results point to the structure of the PPT, rather than the base-specific contacts between the PPT and HIV-1 RT, as the primary determinants of RNase H cleavage specificity at the PPT/U3 junction.
... lanes W and 7). In vivo studies of simian immunodeficiency virus and Moloney murine leukemia virus have demonstrated this conserved sub-motif is critical for virus replication (7,14,35,36). However, although removing the rU:dA tract drastically reduced the levels of reverse transcription in these studies, it is not clear that this effect was directly related to PPT-processing or initiation of (+)-strand DNA synthesis. ...
Despite extensive study, the mechanism by which retroviral reverse transciptases (RTs) specifically utilize polypurine tract
(PPT) RNA for initiation of plus-strand DNA synthesis remains unclear. Three sequence motifs within or adjacent to the purine-rich
elements are highly conserved, namely, a rU:dA tract region immediately 5′ to the PPT, an rA:dT-rich sequence constituting
the upstream portion of the PPT and a downstream rG:dC tract. Using an in vitro HIV-1 model system, we determined that the former two elements define the 5′ terminus of the (+)-strand primer, whereas the
rG:dC tract serves as the primary determinant of initiation specificity. Subsequent analysis demonstrated that G→A or A→G
substitution at PPT positions −2, −4 and +1 (relative to the scissile phosphate) substantially reduces (+)-strand priming.
We explored this observation further using PPT substrates substituted with a variety of nucleoside analogs [inosine (I), purine
riboside (PR), 2-aminopurine (2-AP), 2,6-diaminopurine (2,6-DAP), isoguanine (iG)], or one of the naturally occurring bases
at these positions. Our results demonstrate that for PPT positions −2 or +1, substituting position 2 of the purine was an
important determinant of cleavage specificity. In addition, cleavage specificity was greatly affected by substituting −4G
with an analog containing a 6-NH2 moiety.
Fission yeasts are an ancient group of fungal species that diverged from each other from tens to hundreds of million years ago. Among them is the preeminent model organism Schizosaccharomyces pombe, which has significantly contributed to our understandings of molecular mechanisms underlying fundamental cellular processes. The availability of the genomes of S. pombe and three other fission yeast species S. japonicus, S. octosporus, and S. cryophilus has enabled cross-species comparisons that provide insights into the evolution of genes, pathways, and genomes. Here, we performed genome sequencing on the type strain of the recently identified fission yeast species S. osmophilus and obtained a complete mitochondrial genome and a nuclear genome assembly with gaps only at rRNA gene arrays. A total of 5098 protein-coding nuclear genes were annotated and orthologs for more than 95% of them were identified. Genome-based phylogenetic analysis showed that S. osmophilus is most closely related to S. octosporus and these two species diverged around 16 million years ago. To demonstrate the utility of this S. osmophilus reference genome, we conducted cross-species comparative analyses of centromeres, telomeres, transposons, the mating-type region, Cbp1 family proteins, and mitochondrial genomes. These analyses revealed conservation of repeat arrangements and sequence motifs in centromere cores, identified telomeric sequences composed of two types of repeats, delineated relationships among Tf1/sushi group retrotransposons, characterized the evolutionary origins and trajectories of Cbp1 family domesticated transposases, and discovered signs of interspecific transfer of two types of mitochondrial selfish elements.
This chapter reviews the fundamentals of retrovirus structure and replication, and provides the basic context to understand the biology of this agent. The focus is particularly on the most broadly conserved aspects of the life cycle. Human immunodeficiency virus type 1 (HIV-1) is a lentivirus, a member of a subfamily of retroviruses with complex regulation of viral gene expression and replication. The retrovirus family is a large and diverse group of viruses found in all vertebrates. These viruses replicate through an extraordinary and unique life cycle, differentiating them sharply from other viruses. The virion particles generally contain a genomic RNA that is reverse transcribed into a DNA form of the genome that is integrated into the host chromosomal DNA. The integrated form of the viral DNA, the provirus, then serves as the template for the formation of viral RNAs and proteins that assemble progeny virions. These features of life cycle—especially the reverse flow of genetic information from RNA to DNA and the establishment of the DNA in an integrated form in the host genome—are the defining hallmarks of the retroviruses.
The development of gene transfer vectors from lentiviruses, such as the human immunodeficiency virus 1 (HIV-1), has opened
exciting perspectives for the genetic treatment of a wide array of inherited and acquired diseases, because of their ability
to achieve the efficient delivery, integration, and long-term expression of transgenes into dividing and nondividing cells
both in vitro and in vivo.
The central DNA flap is an important component of lentiviral vectors, but its significance in the context of wild-type human
immunodeficiency virus (HIV) is currently unclear. To address this issue, we have compared the in vitro infection kinetics
of NL4-3 with those of a flap-deficient mutant and evaluated the in vivo growth characteristics of these viruses by using
the SCID-hu mouse model of HIV infection. Flap-deficient virus was only modestly attenuated in vitro, as assessed by single-round
and spreading infection assays, and exhibited levels of replication and pathogenesis close to those of the wild-type in vivo.
Hence, an intact central flap is not essential for HIV replication.
The nef genes of human immunodeficiency virus and simian immunodeficiency virus (SIV) overlap about 80% of the U3 region of the 3′
long terminal repeat (LTR) and contain several essentialcis-acting elements (here referred to as the TPI region): a T-rich region, the polypurine tract, and attachment (att) sequences required for integration. We inactivated the TPI region in the nef reading frame of the pathogenic SIVmac239 clone (239wt) by 13 silent point mutations. To restore viral infectivity, intact
cis-regulatory elements were inserted just downstream of the mutatednef gene. The resulting SIV genome contains U3 regions that are 384 bp shorter than the 517-bp 239wt U3 region. Overall, elimination
of the duplicated Nef coding sequences truncates the proviral genome by 350 bp. Nonetheless, it contains all known coding
sequences and cis-acting elements. The TPI mutant virus expressed functional Nef and replicated like 239wt in all cell culture assays and in
vivo in rhesus macaques. Notably, these SIVmac constructs allow us to study Nef function in the context of replication-competent
viruses without the restrictions of overlapping LTR sequences and important cis-acting elements. The genomes of all known primate lentiviruses contain a large overlap between nefand the U3 region. We demonstrate that this conserved genomic organization is not obligatory for efficient viral replication
and pathogenicity.
A conserved purine-rich motif located near the 3' end of retroviral genomes is involved in the initiation of plus-strand DNA synthesis. We mutated sequences both within and flanking the Moloney murine leukemia virus polypurine tract (PPT) and determined the effects of these alterations on viral DNA synthesis and replication. Our results demonstrated that both changes in highly conserved PPT positions and a mutation that left only the cleavage-proximal half of the PPT intact led to delayed replication and reduced the colony-forming titer of replication defective retroviral vectors. A mutation that altered the cleavage proximal half of the PPT and certain 3' untranslated region mutations upstream of the PPT were incompatible with or severely impaired viral replication. To distinguish defects in plus-strand priming from other replication defects and to assess the relative use of mutant and wild-type PPTs, we examined plus-strand priming from an ectopic, secondary PPT inserted in U3. The results demonstrated that the analyzed mutations within the PPT primarily affected plus-strand priming whereas mutations upstream of the PPT appeared to affect both plus-strand priming and other stages of viral replication.
There are two retroviral integration loci. One encodes the transacting IN protein, which is cleaved from the carboxyl terminus of the Gag-Pol polyprotein precursor during virus assembly. The second locus is the cis-acting attachment (att) site, comprising the terminal sequences at the U3 and U5 ends of linear viral cDNA. Integrase and att site mutant viruses can be blocked at different steps of the viral replication cycle. Class I IN mutants are blocked specifically at the integration step. Class II IN mutants, on the other hand, display pleiotropic defects, most notably in virion morphogenesis and/or reverse transcription. Mutations in the U5 end att site can also disrupt reverse transcription in addition to integration. It is prudent to use caution when interpreting results of in vivo mutagenesis experiments that target retroviral IN and the att site.
Priming of plus-strand DNA is a critical step in reverse transcription of retroviruses and retrotrans-posons. All retroelements
use an RNase H-resistant oligoribonucleotide spanning a purine-rich sequence (the polypurine tract or PPT) to prime plus-strand
DNA synthesis. Plus-strand DNA synthesis of the yeast Saccharomyces cerevisiae Ty1-H3 retrotransposon is initiated at two sites, PPT1 and PPT2, located at the upstream boundary of the 3′-long terminal
repeat and near the middle of the pol gene in the integrase coding region. The two plus-strand primers have the same purine-rich sequence GGGTGGTA. This sequence
is not sufficient by itself to generate a plus-strand origin since two identical sequences located upstream of PPT2 in the
integrase coding region are not used efficiently as primers for plus-strand DNA synthesis. Thus, other factors must be involved
in the formation of a specific plus-strand DNA primer. We show here that mutations upstream of the PPT in a highly conserved
T-rich region severely alters plus-strand DNA priming of Ty1. Our results demonstrate the importance of sequences or structural
elements upstream of the PPT for initiation of plus-strand DNA synthesis.
Lentiviral vectors are tools for gene transfer derived from lentiviruses. From their first application to now they have been strongly developed in design, in biosafety and in their ability of transgene expression into target cells. Primate and non-primate derived lentiviral vectors are now available and with both types of systems a lot of studies tuned to improve their performances in a large number of tissues are ongoing. Here we review the state of the art of lentiviral vector systems discussing their potential for gene therapy.
Live-attenuated human immunodeficiency virus type 1 (HIV-1) variants have shown great promise as AIDS vaccines, but continued
replication can lead to the selection of faster-replicating variants that are pathogenic. We therefore designed HIV-1 genomes
that replicate exclusively upon addition of the nontoxic effector doxycycline (dox). This was achieved by replacement of the
viral TAR-Tat system for transcriptional activation by the Escherichia coli-derived Tet system for inducible gene expression. These designer “HIV-rtTA” viruses replicate in a strictly dox-dependent
manner both in a T-cell line and in primary blood cells, and the rate of replication can be fine-tuned by simple variation
of the dox concentration. These HIV-rtTA viruses provide a tool to perform genetics, e.g., selection and optimization experiments,
with the E. coli-derived Tet reagents in a eukaryotic background. Furthermore, such viruses may represent improved vaccine candidates because
their replication can be turned on and off at will.
Retroelements are mobile genetic entities that replicate via reverse transcription of a template RNA. A key component to the life cycle of these elements is the enzyme reverse transcriptase (RT), which copies the single-stranded genomic RNA of the element into a linear double-stranded DNA that is ultimately integrated into the host genome by the element-encoded integrase. RT is a multifunctionnal enzyme which possesses RNA-dependent and DNA-dependent DNA polymerase activities as well as RNase H activity that specifically degrades the RNA strand of RNA-DNA duplexes. At some stages of the replication a strand-displacement activity of RT is also necessary. All activities are essential for the conversion of single-stranded genomic RNA into the double-stranded preintegrative DNA. This review focuses on the role of RT in the different steps of the replication process of retroelements. The features of retrotransposon replication which differ from the retroviral ones will be emphasized. In a second part of the review, the biochemical and enzymatic properties of two newly characterized retrotransposon RTs will be described. The role of the integrase domain in reverse transcriptase activity of some retroviral and retrotransposon RTs will be discussed.
To better understand the mechanism by which Ty1 RNase H creates the polypurine tract (PPT) primer, we have demonstrated the polymerase-dependent hydrolytic activity of Ty1 reverse transcriptase (RT) during minus-strand synthesis. Using RNase H and polymerase mutants of the recombinant Ty1 RT protein, we show that the two domains of Ty1 RT can act independently of one another. Our results indicate that RNA/DNA substrates containing a short RNA PPT, which serve as primers for plus-strand DNA synthesis, are relatively resistant to RNase H cleavage. RNA substrates with a correct 5' end but with 3' end extending beyond the plus-strand initiation site were cleaved specifically to generate the correct 3' end of the PPT. Using long RNA/DNA duplexes containing the PPT, we show that Ty1 RT is able to make specific internal cleavages that could generate the plus-strand primer with correct 5' and 3' ends. Long RNA/DNA duplexes with mutations in the PPT or in a U-rich region upstream of the PPT, which abolish plus-strand initiation in vivo, were not cleaved specifically at the 5' end of the PPT. Our work demonstrates that the in vitro enzyme can recapitulate key processes that control proper replication in vivo.
The ultimate success of gene therapy to cure inherited or acquired genetic diseases relies on the development and on the availability of gene transfer vectors that can efficiently deliver a transgene following their administration in vivo. Several challenging hurdles need to be overcome to reach such a goal. A first prerequisite is that methods that allow the preparation of vectors at high titers and in culture systems with potential for large scale-up need to be optimized (ANDREADIS et al. 1999; KOTANI et al. 1994; SMITH et al. 1996). Second, the gene transfer vectors should not be recognized by the host immune system in order to avoid their inactivation (COSSET et al. 1995b; DEPOLO et al. 1999). Upon their delivery into gene therapy recipients, vectors should also be able to circumvent the numerous biological barriers that are likely to limit their diffusion and bio-distribution in the target organism. They should therefore be able to specifically recognize, penetrate and express the transgene in cells of the gene therapy target tissue (DIAZ et al. 1998; JAGER et al. 1999; RUSSELL and COSSET 1999). Third, they should be able to replicate and to express a transgene in cells that are not proliferating or are slowly proliferating, a predominant situation in vivo. Last, but not least, they should be accepted by both ethical and regulatory authorities. In this respect the development of vectors derived from viruses that are not pathogenic to humans may be preferred.
Recent crystallographic data suggest that conserved residues in the connection subdomain and C-terminal ribonuclease H (RNase H) domain of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) contact the nascent DNA primer and modulate the trajectory of the template relative to the RNase H catalytic center. Within the RNase H domain, these residues include Thr473, Glu475, Lys476, Tyr501, and Ile505, while His539 and Asn474 interact with the scissile phosphate of the RNA template. Amino acid substitutions at several of these positions were evaluated in the context of hydrolysis of nonspecific RNA-DNA hybrids and substrates mimicking specific RNase H-mediated events. With the exception of mutant I505G, which exhibited a dimerization defect, substituting alanine at positions 473-476 and 501 had minimal consequences for DNA synthesis on duplex and hybrid DNA and RNA substrates. In contrast, the efficiency with which most mutants catalyzed polymerization-independent RNase H cleavage was sharply reduced. This deficiency was more pronounced when mutant enzymes were challenged to process the (+) strand polypurine tract (PPT) primer from either (+) RNA or a PPT/(+) DNA RNA/DNA chimera. Reduced polymerization-independent RNase H activity also significantly influenced the rate of DNA strand transfer, suggesting the donor template must be reduced in size below 13 nt before this event proceeds.
A recombinant simian immunodeficiency virus (SIV) derived from strain 239 (SIVmac239) with reverse transcriptase (RT) sequences
from human immunodeficiency virus type 1 (HIV-1) strain HXB2 was severely impaired for replication. Detectable p27Gag levels were not observed until day 65 and peak p27Gag levels were not reached until day 75 after transfection of CEMx174 cells with the recombinant DNA. Sequences from the latter
time point did not contain amino acid substitutions in HIV-1 RT; however, a single nucleotide substitution (thymine to cytosine)
was found at position eight of the SIV primer binding site. We engineered an RT/SHIV genome with the thymine-to-cytosine substitution,
called RT/SHIV/TC, and observed dramatically faster replication kinetics than were observed with the parental RT/SHIV from
which this variant was derived. RT/SHIV/TC provides an improved system for study of the impact of drug resistance mutations
in HIV-1 RT in a relevant animal model.
The nef genes of human and simian immunodeficiency viruses code for a membrane associated protein critical for AIDS development. SIVmac Nef presents C-terminal a 27 amino acid extension absent of HIV-1 Nef. To estimate the influence of this C-terminal domain on virus properties, we constructed viruses derived from SIVmac239 by replacing SIV nef with HIV-1 Lai nef gene (SHIV NefLai4) or with a sequence encoding a Nef fusion protein: HIV-1 Lai Nef/SIV Nef-Cterm (SHIV-Cterm). The recombinant viruses replicated efficiently in vitro in CEMx174 cells and in activated macaque PBMCs. The addition of SIV Nef C-terminal domain to HIV-1 Nef in SHIVNefLai4 did not change the in vitro properties of the chimeric virus, both viruses being more infectious than a nef deleted virus. Although the half-life of Nef fusion protein was augmented, SHIV-Cterm remained slightly less infectious than SIVmac239.
In contrast to other retroviruses, lentiviruses have the unique property of infecting non-proliferating cells. Thus vectors derived from lentiviruses are promising tools for in vivo gene delivery applications. Vectors derived from human primate and non-primate lentiviruses have recently been described and, unlike retroviral vectors derived from murine leukemia viruses, lead to stable integration of the transgene into quiescent cells in various organs. Despite all the safety safeguards that have been progressively introduced in lentiviral vectors, the clinical acceptance of vectors derived from pathogenic lentiviruses is subject to debate. It is therefore essential to design vectors derived from a wide range of lentivirus types and to comparatively examine their properties in terms of transduction efficiency and bio-safety. Here, we review the properties of lentiviral vectors derived from simian immunodeficiency virus (SIV).
The recovery of vectors that are suitable for an in vivo gene delivery has been a recurrent theme in gene therapy research over the last decade. Several challenging hurdles need to be overcome to reach such a goal. First, is a need for methods that allow the preparation of vectors at high titers and in culture systems with potential for large scale-up need to be optimized. Second, the gene transfer vectors should not be recognized by the host immune system in order to avoid inactivation. Upon delivery into gene therapy recipients, vectors should also be able to circumvent the numerous biological barriers that are likely to limit their diffusion and biodistribution in the target organism. They should, therefore, be able to recognize specifically and to penetrate cells of the gene therapy target tissue. Third, they should be able to replicate and to express a transgene in cells that are either not or only slowly proliferating, a predominant situation in vivo. Last, but not least, they should be accepted by both ethical and regulatory authorities. In this respect, the development of vectors derived from viruses that are not pathogenic to human may be preferred.
Both x-ray crystallography and chemical footprinting indicate that bases of the HIV type 1 (HIV-1) polypurine tract (PPT)-containing RNA/DNA hybrid deviate from standard Watson-Crick base pairing. However, the contribution of these structural anomalies to the accuracy of plus-strand primer selection by HIV-1 reverse transcriptase is not immediately clear. To address this issue, DNA templates harboring single and pairwise non-hydrogen-bonding isosteres of cytosine (2-fluoro-4-methylbenzene deoxyribonucleoside) and thymine (2,4-difluoro-5-methylbenzene deoxyribonucleoside) were synthesized and hybridized to PPT-containing RNA primers as a means of locally removing hydrogen bonding and destabilizing paired structure. Cleavage of these hybrids was examined with p66/p51 HIV-1 reverse transcriptase and a mutant carrying an alteration in the p66 RNase H primer shown to specifically impair PPT processing. Analog insertion within the PPT (rG):(dC) and central (rA):(dT) tracts repositioned the RNase H domain such that the RNA/DNA hybrid was cleaved 3-4 bp from the site of insertion, a distance corresponding closely to the spatial separation between the catalytic center and RNase H primer grip. However, PPT processing was significantly impaired when the junction between these tracts was substituted. Substitutions within the upstream (rA):(dT) tract, where maximum distortion had previously been observed, destroyed PPT processing. Collectively, our scanning mutagenesis approach implicates multiple regions of the PPT in the accuracy with which it is excised from (+) U3 RNA and DNA, and also provides evidence for close cooperation between the RNase H primer grip and catalytic center in achieving this cleavage.
The RNase H activity of retroviral reverse transcriptases (RTs) degrades viral genomic RNA after it has been copied into DNA, removes the tRNA used to initiate negative-strand DNA synthesis, and generates and removes the polypurine tract (PPT) primer used to initiate positive-strand DNA synthesis. The cleavages that remove the tRNA and that generate and remove the PPT primer must be specific to generate linear viral DNAs with ends that are appropriate for integration into the host cell genome. The crystal structure of human immunodeficiency virus type 1 (HIV-1) RT in a complex with an RNA/DNA duplex derived from the PPT revealed that the 5' end of the PPT deviates from traditional Watson-Crick base pairing. This unusual structure may play a role in the proper recognition of the PPT by HIV-1 RT. We made substitution mutations in the 5' end of the PPT and determined their effects on virus titer. The results indicated that single and double mutations in the 5' end of the PPT had modest effects on virus replication in a single-cycle assay. More complex mutations had stronger effects on virus titer. Analysis of the two-long-terminal-repeat circle junctions derived from infecting cells with the mutant viruses indicated that the mutations affected RNase H activity, resulting in the retention of PPT sequences on viral DNA. The mutants tested preferentially retained specific segments of the PPT, suggesting an effect on cleavage specificity. These results suggest that structural features of the PPT are important for its recognition and cleavage in vivo.
HIV-1 provides an attractive option as the basis for gene transfer vectors due to its ability to stably transduce non-cycling cell populations. In order to fully utilise the promise of HIV-1 as a vector it is important that the effects of viral cis sequence elements on vector function are carefully delineated.
In this study we have systematically evaluated the effect of various cis elements from the HIV-1 YU-2 genome that have been implicated as either affecting vector performance, or HIV-1 replication, on the efficiency of vector production (titre and infectivity). As a measure of the relative safety of vectors their propensity to inadvertently transfer the gagpol gene to transduced cells was assessed.
Sequences that were found to increase vector titre were from the 5' end of the gag gene, from the 5' and 3' ends of the env gene, from immediately upstream of the polypurine tract, and the central polypurine tract. The substitution of the HIV-1 RRE with heterologous RNA transport elements, or the deletion of the RRE, resulted in greatly reduced vector titres. RNA analysis suggested that the role of the Rev/RRE system extends beyond simply acting as an RNA nuclear export signal. The relative safety of different vector designs was compared and an optimal construct selected.
Based on our results we have constructed a vector that is both more efficient, and has better safety characteristics, than the widely used pHR' HIV-1 vector construct.
Retroviral conversion of single-stranded RNA into double-stranded DNA requires priming for each strand. While host cellular t-RNA serves as primer for the first strand, the viral polypurine tract (PPT) is primer for the second. Therefore, polypurine tracts of retroviruses are essential for viral replication by reverse transcriptase (RT). These purine tracts are resistant to cleavage during first strand synthesis. In obtaining the primer for second strand synthesis, the RNase H function of RT must cleave the PPT exactly for in vivo transcription to proceed efficiently and proper integration to occur. At the RNase H active site the protein makes contacts primarily along the backbone, with hydrogen bonds to the sugar-phosphate oxygen atoms. A high-resolution structure (1.10A) of the first ten base-pairs of the RNA/DNA hybrid PPT, r-(c-a-a-a-g-a-a-a-a-g)/d-(C-T-T-T-T-C-T-T-T-G), contains the highly deformable r-(a-g-a) steps found in retroviral polypurine tracts. This r-(a-g-a) motif is utilized in the "unzipping" or unpairing of bases that occurs when RT binds a malleable PPT. Another unusual feature found in our high-resolution PPT structure is the sugar switch at RNA adenine 2. All the RNA sugars are the expected C3'-endo, except sugar 2, which is C2'-endo, characteristic of B-form sugars. This local A-to-B conversion adversely affects the pattern of hydrogen bonds from protein to sugar-phosphate backbone, disrupting the catalytic site. Disruption could cause the enzyme to pause at the 5'-end of the PPT, leaving it intact. Pyrimidine-purine (YR) steps are most deformable and the T-A step especially can undergo A-to-B transitions readily.
The ability of the nonlentiviral retrovirus spleen necrosis virus (SNV) to cross-package the genomic RNA of the distantly related human immunodeficiency virus type 1 (HIV-1) and vice versa was analyzed. Such a model may allow us to further study HIV-1 replication and pathogenesis, as well as to develop safe gene therapy vectors. Our results suggest that SNV can cross-package HIV-1 genomic RNA but with lower efficiency than HIV-1 proteins. However, HIV-1-specific proteins were unable to cross-package SNV RNA. We also constructed SNV-based gag-pol chimeric variants by replacing the SNV integrase with the HIV-1 integrase, based on multiple sequence alignments and domain analyses. These analyses revealed that there are conserved domains in all retroviral integrase open reading frames (orf), despite the divergence in the primary sequences. The transcomplementation assays suggested that SNV proteins recognized one of the chimeric variants. This demonstrated that HIV-1 integrase is functional in the SNV gag-pol orf with a lower transduction efficiency, utilizing homologous (SNV) RNA, as well as the heterologous vector RNA of HIV-1. These findings suggest that homology in the conserved sequences of the integrase protein may not be fully competent in the replacement of protein(s) from one retrovirus to another, and there are likely several other factors involved in each of the steps related to replication, integration, and infection. However, further studies to dissect the gag-pol region will be critical for understanding the mechanisms involved in the cleavage of reverse transcriptase, RNase H, and integrase. These studies should provide further insight into the design and development of novel molecular approaches to block HIV-1 replication and to construct a new generation of SNV-based vectors.
This chapter examines a conditionally replicating virus as a novel approach toward an HIV vaccine. Live-attenuated virus vaccines have proven to be highly successful at inducing protective immunity against pathogenic viruses, such as smallpox, polio, and measles. The development of an HIV-1 variant by replacing the natural gene expression mechanism of the virus with an inducible regulatory system is presented. The Tet–rtTA system seems to be the ideal regulatory system to control replication of a conditional live HIV-1 virus vaccine. It is found that controlling virus replication through rtTA instead of tTA will avoid the long-lasting administration of Tc or dox that would be required with tTA. It is observed that to transform the constitutively replicating HIV-1 virus into a conditional live variant, the viral genome was mutated to inactivate the Tat–TAR transcription regulation mechanism and to integrate the Tet system. The 5´TAR RNA hairpin is formed by base pairing of nucleotides from positions +1to +57 relative to the start site of transcription. The substitution of the nef gene with the rtTA gene is also elabroated.
Integrase (IN) and reverse transcriptase (RT) play a central role in transposition of retroelements. The mechanism of integration by IN and the steps of the replication process mediated by RT are briefly described here. Recently, active recombinant forms of Ty1 IN and RT have been obtained. This has allowed a more detailed understanding of their biochemical and structural properties and has made possible combined in vitro and in vivo analyses of their functions. A focus of this review is to discuss some of the results obtained thus far with these two recombinant proteins and to propose future directions.
Point mutations in SIVmac239 Nef disrupting CD4 downmodulation and enhancement of virion infectivity attenuate viral replication in acutely infected rhesus macaques, but changes selected later in infection fully restore Nef function (A. J. Iafrate et al., J. Virol. 74:9836-9844, 2000). To further evaluate the relevance of these Nef functions for viral persistence and disease progression, we analyzed an SIVmac239 Nef mutant containing a deletion of amino acids Q64 to N67 (delta64-67Nef). This mutation inactivates the N-distal AP-2 clathrin adaptor binding element and disrupts the abilities of Nef to downregulate CD4, CD28 and CXCR4 and to stimulate viral replication in vitro. However, it does not impair the downmodulation of CD3 and class I major histocompatibility complex (MHC-I) or MHC-II and the upregulation of the MHC-II-associated invariant chain, and it has only a moderate effect on the enhancement of virion infectivity. Replication of the delta64-67Nef variant in acutely infected macaques was intermediate between grossly nef-deleted and wild-type SIVmac239. Subsequently, three of six macaques developed moderate to high viral loads and developed disease, whereas the remaining animals efficiently controlled SIV replication and showed a more attenuated clinical course of infection. Sequence analysis revealed that the deletion in nef was not repaired in any of these animals. However, some changes that slightly enhanced the ability of Nef to downmodulate CD4 and moderately increased Nef-mediated enhancement of viral replication and infectivity in vitro were observed in macaques developing high viral loads. Our results imply that both the Nef functions that were disrupted by the delta64-67 mutation and the activities that remained intact contribute to viral pathogenicity.
Crystal structures of HIV-1 reverse transcriptase (RT) in complex with either duplex DNA or an RNA/DNA hybrid have provided significant insights into the manner in which this highly versatile enzyme accommodates the conformationally-distinct nucleic acid substrates encountered during the reverse transcription cycle. Biochemical data likewise suggest that unique structural features of the nucleic acid substrates contribute towards recognition by their cognate RT. While site-directed mutagenesis of catalytically- and structurally-critical protein motifs is relatively facile, understanding how nucleic acid structure contributes to its recognition presents a greater challenge. The relative ease with which large DNA and RNA fragments can now be chemically synthesized, in conjunction with the increased availability of ribo- and deoxyribonucleoside analogs, allows nucleic acid structure to be examined with respect to the role of hydrogen bonding, nucleobase stacking, sugar ring geometry and charge of the phosphodiester backbone. This review summarizes our use of nucleoside analogs to understand how the structure of cis-acting regulatory signals mediates their recognition by structurally diverse retroviral and retrotransposon enzymes.
For hepadnaviruses, the RNA primer for plus-strand DNA synthesis is generated by the final RNase H cleavage of the pregenomic RNA at an 11 nt sequence called DR1 during the synthesis of minus-strand DNA. This RNA primer initiates synthesis at one of two distinct sites on the minus-strand DNA template, resulting in two different end products; duplex linear DNA or relaxed circular DNA. Duplex linear DNA is made when initiation of synthesis occurs at DR1. Relaxed circular DNA, the major product, is made when the RNA primer translocates to the sequence complementary to DR1, called DR2 before initiation of DNA synthesis. We studied the mechanism that determines the site of the final RNase H cleavage in hepatitis B virus (HBV). We showed that the sites of the final RNase H cleavage are always a fixed number of nucleotides from the 5' end of the pregenomic RNA. This finding is similar to what was found previously for duck hepatitis B virus (DHBV), and suggests that all hepadnaviruses use a similar mechanism. Also, we studied the role of complementarity between the RNA primer and the acceptor site at DR2 in HBV. By increasing the complementarity, we were able to increase the level of priming at DR2 over that seen in the wild-type virus. This finding suggests that the level of initiation of plus-strand DNA synthesis at DR2 is sub-maximal for wild-type HBV. Finally, we studied the role of the sequence at the 5' end of the RNA primer that is outside of the DR sequence. We found that substitutions or insertions in this region affected the level of priming at DR1 and DR2.
In the quest for an effective vaccine against human immunodeficiency virus (HIV), live attenuated virus vaccines have proven to be very effective in the experimental model system of simian immunodeficiency virus (SIV) in macaques. However, live attenuated HIV vaccines are considered unsafe for use in humans because the attenuated virus may accumulate genetic changes during persistence and evolve to a pathogenic variant. As an alternative approach, we earlier presented a conditionally live HIV-1 variant that replicates exclusively in the presence of doxycycline (DOX). Replication of this vaccine strain can be limited to the time that is needed to provide full protection through transient DOX administration. Since the effectiveness and safety of such a conditionally live AIDS vaccine should be tested in macaques, we constructed a similar DOX-dependent SIVmac239 variant in which the Tat-TAR (trans-acting responsive) transcription control mechanism was functionally replaced by the DOX-inducible Tet-On regulatory mechanism. Moreover, this virus can be used as a tool in SIV biology studies and vaccine research because both the level and duration of replication can be controlled by DOX administration. Unexpectedly, the new SIV variant required a wild-type Tat protein for replication, although gene expression was fully controlled by the incorporated Tet-On system. This result suggests that Tat has a second function in SIV replication in addition to its role in the activation of transcription.
The spatial and temporal relationship between the polymerase and RNase H activities of human immunodeficiency virus type 1 reverse transcriptase has been examined by using a 40-mer RNA template and a series of DNA primers of lengths ranging from 15 to 40 nucleotides, hybridized to the RNA, as substrates. The experiments were executed in the absence and presence of heparin, an efficient trap to sequester any free or dissociated reverse transcriptase, thus facilitating the study of events associated with a single turnover of the enzyme. The results indicate a spatial separation of 18 or 19 nucleotides between the two sites. To examine the effect of concomitant polymerization on the RNase H activity, the substrate was doubly 5' end labeled on the RNA and DNA. This enabled the study of RNase H activity as a function of polymerization in a single experiment, and the results in the absence and presence of heparin indicate a tight temporal coupling between the two activities.
We recently reported that human immunodeficiency virus type 1 (HIV-1) unintegrated linear DNA displays a discontinuity in its plus strand, precisely defined by a second copy of the polypurine tract (PPT) located near the middle of the genome (P. Charneau and F. Clavel, J. Virol. 65:2415-2421, 1991). This central PPT appears to determine a second initiation site for retrovirus DNA plus-strand synthesis. We show here that mutations replacing purines by pyrimidines in the HIV-1 central PPT, which do not modify the overlapping amino acid sequence, are able to significantly slow down viral growth as they reduce plus-strand origin at the center of the genome. One of these mutations, introducing four pyrimidines, results in a 2-week delay in viral growth in CEM cells and abolishes plus-strand origin at the central PPT. The introduction in this mutant of a wild-type copy of the PPT at a different site creates a new plus-strand origin at that site. This new origin also determines the end of the upstream plus-strand segment, probably as a consequence of limited strand displacement-synthesis. Our findings further demonstrate the role of PPTs as initiation sites for the synthesis of the retroviral DNA plus strand and demonstrate the importance of a second such origin for efficient HIV replication in vitro.
Reverse transcription of the retroviral RNA genome begins with tRNA-primed synthesis of a minus-strand DNA, which subsequently acts as the template for the synthesis of plus-strand DNA. This plus-strand DNA is initiated at a unique location and makes use of a purine-rich RNA oligonucleotide derived by RNase H action on the viral RNA. To determine the variables that are relevant to successful specific initiation of plus-strand DNA synthesis, we have used nucleic acid sequences from the genome of Rous sarcoma virus along with three different sources of RNase H: avian myeloblastosis virus DNA polymerase, murine leukemia virus DNA polymerase, and the RNase H of Escherichia coli. Our findings include evidence that specificity is controlled not only by the nucleic acid sequences but also by the RNase H. For example, while the avian reverse transcriptase efficiently and specifically initiates on the sequences of the avian retrovirus, the murine reverse transcriptase initiates specifically but at a location 4 bases upstream of the correct site.
We have analyzed the processing of the RNA primer for (+) strand DNA synthesis by reverse transcriptase of the human immunodeficiency virus 1. To test for specific RNA cleavage and primer usage, we constructed a 99-base pair RNA-DNA hybrid containing the viral polypurine tract and flanking viral sequences. Although the RNase H activity of reverse transcriptase cleaves the RNA strand into multiple fragments, only two primers are extended in the presence of nucleoside triphosphates. The major RNA primer includes the entire polypurine tract except for the last adenosine and has the sequence 5'-UUUUAAAAGAAAAGGGGGG-3'. The minor primer has the same 3' end but is two nucleotides shorter. In a subsequent processing step reverse transcriptase releases the primer intact via a cleavage at the RNA-DNA junction. RNA cleavage, primer extension, and primer removal can take place in a single reaction. However, specificity does not require coupling of the three steps and is preserved in the individual reactions. The polypurine primer is generated and removed after its elongation in the absence of DNA synthesis. Furthermore, the polypurine primer is selected among the several RNA fragments available and extended by reverse transcriptase as well as by p51, a short form of reverse transcriptase lacking RNase H activity.
Better understanding of the pathogenesis of acquired immunodeficiency syndrome (AIDS) would be greatly facilitated by a relevant animal model that uses molecularly cloned virus of defined sequence to induce the disease. Such a system would also be of great value for AIDS vaccine research. An infectious molecular clone of simian immunodeficiency virus (SIV) was identified that induces AIDS in common rhesus monkeys in a time frame suitable for laboratory investigation. These results provide another strong link in the chain of evidence for the viral etiology of AIDS. More importantly, they define a system for molecular dissection of the determinants of AIDS pathogenesis.
Selected conserved amino acids in the putative RNase H domain of reverse transcriptase (RT) were modified in a molecularly cloned infectious provirus and in a Moloney murine leukemia virus RT expression vector by site-directed mutagenesis. Substitution of either of two conserved aspartic acid residues in proviral DNA prevented production of infectious particles in transfected NIH 3T3 cells, and the same modifications depressed RT-associated RNase H activity by more than 25-fold with little or no effect on polymerase activity.
The intrinsic properties of reverse transcriptase in reverse transcription were studied using a synthetic, partial ovalbumin mRNA with a synthetic DNA oligonucleotide annealed to the 3'-end of the RNA as a model substrate. With or without concomitant cDNA synthesis, the RNase H activity of avian myeloblastosis virus (AMV)-reverse transcriptase cleaved the substrate at a site which would leave a hybrid of between 7 and 14 base pairs between the 3' termini of the RNA and DNA oligonucleotide. Variability in the exact size of the hybrid probably reflects some weak base preference for cleavage by the enzyme. These short hybrids can be recognized as substrates by Escherichia coli RNase H and can be utilized by reverse transcriptase as sites for continuation of cDNA synthesis. Substrates with 5'-triphosphorylated termini, 3'-OH, 3'-phosphate, 3'-end hairpin structures and 20 base pair hybrids on the middle region of long RNA more than 300 bases or on circular RNA were all cleaved by AMV-reverse transcriptase-associated RNase H, indicating that the RNase H activity is essentially regarded as an endonuclease degrading RNA moiety in RNA-DNA hybrid. The modes of action of reverse transcriptase from murine leukemia virus and Rous-associated virus 2 were the same as that of AMV-reverse transcriptase, except that the size of the remaining hybrid and the specificity for cleavage depended on the reverse transcriptase. We propose a possible model to explain the mode of action of RNase H and RNA-dependent DNA polymerase activities in reverse transcription.
Infection of macaque monkeys with simian immunodeficiency virus (SIV) is probably the best animal model currently available for studying acquired immunodeficiency syndrome. In this report, we describe three infectious molecular clones of SIVmac and one of human immunodeficiency virus type 2 (HIV-2) and their use in the study of cell and species specificity, animal infection, and the relationship of gene sequence to function. Replication of the cloned viruses in different cell lines varied dramatically. Some human CD4+ cell lines (HUT 78 and MT-4) supported the replication of SIVmac and HIV-2, while others (CEM and Jurkat-T) supported the replication of HIV-2 but not SIVmac. Growth of cloned virus in macaque lymphocytes in vitro was predictive of macaque infection in vivo. Macaque lymphocytes supported the replication of SIVmac239 and SIVmac251 but not SIVmac142 or HIV-2ROD. Using virus recovery and antibody response as criteria for infection, macaques that received cloned SIVmac251 and SIVmac239 became infected, while macaques receiving cloned SIVmac142 and HIV-2ROD did not become infected. Nucleotide sequences from the envelope region of all four cloned viruses demonstrated that there is considerable flexibility in the location of the translational termination (stop) signal. These infectious molecular clones will be very useful for future studies directed at the molecular basis for persistence, pathogenicity, tropism, and cell and species specificity.
The GenBank Genetic Sequence Data Bank contains nearly 15000 entries for DNA and RNA sequences that have been reported since
1967. This paper briefly describes the contents of the database, the forms in which the data are distributed, and the services
available to scientists using the GenBank database.
We previously reported that in the endogenous reaction of Rous sarcoma virus disrupted by melittin, plus-strand DNA initiates on a small oligonucleotide primer and that this initiation can be reconstructed in vitro in reactions containing purified minus-strand DNA as template, viral RNA as a source of primer, and reverse transcriptase (Smith et al., J. Virol. 49:200-204, 1984). Further studies on the specificity of initiation in the endogenous reaction have shown the following. (i) The primer was 12 nucleotides in length. Its sequence began with a 5' pyrimidine, followed by 11 purines, ending with rGrA-3'. This sequence was in agreement with the known plus-strand RNA sequence immediately upstream from the initiation site. Thus, the primer began one nucleotide 5' to the so-called polypurine tract that has been found on all retrovirus genomes. (ii) The transition point between RNA primer and DNA product was precisely located. It was before the end of the polypurine tract. Thus the polypurine tract, although essential for virus replication and probably a flag for the priming event, did not define the limits of the RNA primer. After primer removal, the DNA had a 5' phosphate, consistent with generation by the viral RNase H activity. The priming specificity in reconstructed reactions was also examined further, with the following observations. (i) When the source of RNA primer was prehybridized to the template viral DNA, the generation, utilization, and subsequent removal of primer were essentially the same as those observed in the endogenous reaction. In the absence of deliberate prehybridization, some specificity was lost. There were than additional locations for the 5' end of the primer as well as the transition point between RNA primer and DNA. (ii) Purine-rich oligoribonucleotides created by RNase A digestion of viral RNA could prime strong-stop plus DNA, but again with the loss of specificity relative to that in the endogenous reaction. (iii) The 5' end of the minus-strand DNA template was not required for initiation of strong-stop plus DNA. Therefore, the specificity of initiation did not depend upon an intramolecular interaction requiring the two inverted repeat sequences that flank the long terminal repeat.
The v-src coding region was deleted from cloned Rous sarcoma virus DNA, and the deleted clones were tested for infectivity by transfection. All of the coding region, as well as most of the sequences lying between v-src and the unique 3' region (U3), could be deleted without affecting viability. However, at least 9 and at most 29 of the nucleotides in the purine-rich tract adjacent to U3 were necessary for growth, even in the presence of a helper virus. It is concluded that these nucleotides (the polypurine tract) provide a cis-acting function necessary for retrovirus replication.
Two in vitro approaches were used to investigate the priming of strong-stop plus DNA by Rous sarcoma virus. This 340-base DNA species is the first major plus-strand DNA product seen in both infected cells and in endogenous reactions of disrupted virions. In the first approach, we set up a reconstructed system in which strong-stop plus DNA was synthesized by reverse transcriptase from a high-molecular-weight minus-strand viral DNA template. This synthesis was shown to be strictly dependent on the addition of primers to the reaction mixture. The addition of high-molecular-weight RNA from both viral and cellular sources, as well as oligodeoxyguanylate, gave specific synthesis of strong-stop plus DNA, whereas the addition of oligodeoxycytidylate-oligodeoxyadenylate and viral 4S RNA did not. In the second approach, strong-stop plus DNA synthesized in melittin-permeabilized virions was examined on a high-resolution polyacrylamide gel. This DNA was shown to have ca. 11 to 13 ribonucleotides at its 5' end. These results indicate that strong-stop plus DNA is initiated on a preformed RNA primer.
The binding of HIV reverse transcriptase (RT) to heteroduplexes was examined using a substrate consisting of a 42 nt chimeric
nucleic acid composed (5′→3′) of 23 nt of RNA and 19 of DNA. This chimera was hybridized to an internal region of a relatively
long complementary DNA or RNA. When the chimera was bound to DNA and conditions limiting cleavage to a single binding event
between the enzyme and sub strata were employed initial RNase H-directed cleavages occurred 19-21 nt from the chimera 5′-terminus.
A 42 nt strand Identical in sequence to the chimera and composed of only RNA was cleaved at the same locations. Reducing the
length of the DNA portion of the chlmera from 19 to 7 nt did not after the cleavage positions, suggesting that cleavage was
not coordi nated by the DNA 3′-terminus. Under the same conditions cleavage was not detected when the chimera was bound to
RNA. In contrast, addition of dNTPs to the DNA 3′-terminus of the chimera occurred only when the chimera was bound to RNA.
The resuits support preferable binding of AT to RNA-DNA versus DNA-DNA hybrid regions and a model in which the orientation
of binding to heteroduplexes is 5′→3′ (relative to the RNA strand), poiymerase to ANase H active site, wfth sites associated
with the DNA and RNA strand respectively.
Reverse transcription in the yeast retrotransposon Ty1 follows the general "rules" of retroviral replication overall. However, some details of the retroviral and Ty1 reverse transcription processes are different. We have identified and determined the structure of plus-strand strong-stop DNA and examined the effect of polypurine tract deletion mutations on its synthesis. Furthermore, we have defined the stop signal for plus-strand strong-stop DNA synthesis as an unusual 2'-O-ribosylated nucleotide in the primer tRNA. Full-length plus-strand strong-stop DNA, following strand transfer, would have a terminal 2-base mismatch with minus-strand DNA. These findings indicate that the mechanism of plus-strand strong-stop DNA transfer in Ty1 differs from that of the retroviral transfer and suggest that full-length plus-strand strong-stop DNA is not a direct intermediate in Ty1 retrotransposition.
By using a DNA substrate with defined gap size, we found that human immunodeficiency virus type 1 reverse transcriptase (HIV-RT) was able to perform strand displacement DNA synthesis. This activity was not affected first by calf thymus proliferating cell nuclear antigen and replication factor C and second by Escherichia coli single-stranded DNA-binding protein, which together allow DNA polymerase delta to perform strand displacement DNA synthesis (Podust, V., and Hübscher, U. (1993) Nucleic Acids Res. 21, 841-846). 3'-Azido-2',3'-dideoxythymidine triphosphate inhibited displacement completely, indicating that DNA synthesis is required for this reaction. The HIV-RT p66 polypeptide alone could perform limited strand displacement DNA synthesis, whereas the HIV-RT p51 polypeptide was completely inactive, likely due to its inability to replicate extensively on a M13 DNA template. On the other hand the HIV-RT p51 polypeptide enhanced the strand displacement activity of the HIV-RT p66 subunit at a molar ratio of 4:1, mainly by chasing short products into longer ones. Furthermore, kinetic experiments after complementation of HIV-RT p66 with HIV-RT p51 indicated that HIV-RT p51 can restore rate and extent of strand displacement activity by HIV-RT p66 compared with the HIV-RT heterodimer p66/p51, suggesting a function of the 51-kDa polypeptide.
We have determined the extent of RNA cleavage carried out during DNA synthesis by either human immunodeficiency virus (HIV)
or avian myeloblastosis virus (AMV) reverse transcriptases (RTs). Conditions were chosen that allowed the analysis of the
cleavage and synthesis performed by the RT during one binding event on a given template-primer. The maximum quantity of ribonuclease
H (RNase H) sensitive template RNA left after synthesis by the RTs was determined by treatment with Escherichia coli RNase H. RNA cleavage products that were expected to be too short to remain hybridized, less than 13 nucleotides in length,
were quantitated. Results showed that HIV-and AMV-RT degraded about 80% and less than 20%, respectively, of the potentially
degradable RNA to these short products. Survival of longer, hybridized RNA was not a result of synthesis by a population of
RTs that had selectively lost RNase H activity. Using an assay that evaluated the proportion of primers extended versus RNA
templates cleaved during primer-extension by the RTs, we determined that essentially each molecule of HIV-and AMV-RT with
polymerase also has RNase H activity. The results indicate that although both HIVand AMV-RTs cleave the RNA template during
synthesis, the number of cleavages per nucleotide addition with HIV-RT is much greater. They also suggest that some hybridized
RNA segments remain right after the passage of the RT making the first DNA strand. In vivo, these segments would have to be cleaved or displaced in later reactions before second strand DNA synthesis could be completed.
A specific cleavage by the reverse transcriptase-associated RNase H activity generates the RNA primer for plus strand DNA synthesis during reverse transcription. Previously, we used site-directed mutagenesis to define the sequence features of the polypurine tract (PPT) required for correct plus strand priming by the Moloney murine leukemia virus (M-MuLV) reverse transcriptase (Rattray, A. J., and Champoux, J. J. (1989) J. Mol. Biol. 208, 445-456). Although the sequences of human immunodeficiency virus type 1 (HIV-1) and M-MuLV diverge completely outside a 20-base region encompassing the PPT, within this region there are only three differences between the two viruses. Here we show that the HIV-1 reverse transcriptase will utilize the M-MuLV PPT as an origin for plus strand initiation in vitro. This finding enabled us to use the set of PPT mutants previously generated in M-MuLV, in conjunction with a small set of newly derived mutations within the HIV-1 PPT, to study plus strand priming by the HIV-1 reverse transcriptase. Despite the similarity between the two PPT regions, the sequence features important for positioning RNase H for the cleavage reaction that generates the plus strand primer are different for the two viruses. For M-MuLV, the -7A residue is a critical specificity determinant in the priming reaction, whereas for HIV-1, the -2G and -4G residues play key roles in determining the specificity of priming.
Virus derived from the infectious, pathogenic, molecular clone of simian immunodeficiency virus (SIV) called SIVmac239 replicates poorly in primary rhesus monkey alveolar macrophage cultures. Variants with three to nine amino acid changes in the envelope replicate 100 to 1,000 times more efficiently in these macrophage cultures than parental SIVmac239. Early events, including virus entry into cells, were analyzed by measuring the amounts of newly synthesized viral DNA 14 to 16 h after infection of macrophages by using a quantitative polymerase chain reaction method. SIVmac239 ws found to enter macrophages with an efficiency similar to that of the macrophage-tropic derivatives. The assay indeed measured newly synthesized viral DNA since detection was inhibited by the reverse transcriptase inhibitors azidothymidine and foscarnet and by heat inactivation of the virus stock prior to infection. Furthermore, entry of SIVmac239 and macrophage-tropic variant into macrophages was inhibited by monoclonal antibody against CD4. Analysis of the time course of viral DNA accumulation showed that although initial entry of SIVmac239 into cells occurred normally, subsequent logarithmic increases in the amounts of viral DNA associated with spread of virus through the macrophage cultures was blocked. Increasing the amount of SIVmac239 incubated with macrophages increased the amount of virus entering the cell, but this could not overcome the block to replication. Thus, restricted replication of SIVmac239 in macrophages is determined by the envelope, but surprisingly it is not due to restricted virus entry.
We examined the ribonuclease H (RNase H) specificity of human immunodeficiency virus reverse transcriptase (HIV-RT) using heteropolymeric RNAs hybridized to complementary DNAs. Experiments were performed in the presence of excess challenger polymer (poly(rA)-oligo(dT)) to reveal cleavages resulting from single enzyme binding events. Previous results suggested that initial RNase H directed cleavages were a fixed distance from a DNA primer terminus recessed on an RNA template, i.e. determined by the binding position of the polymerase active site. The influences of recessed RNA termini were not evaluated. In current experiments, RNAs that were 30, 42, or 50 nucleotides long were hybridized to the same 88 nucleotide long complementary DNA, such that the 5' terminal nucleotide of each RNA was hybridized to the 29th nucleotide from the 3' end of the DNA. In all three cases the RNA was initially cleaved between the 19th and 21st nucleotides from its 5' end. Thus, cleavage was not coordinated by the recessed 3' terminus of the RNA. Subsequent cleavages in either direction on the RNA were also observed. An insertion within the RNA that moved the preferred initial cut sequence 10 nucleotides further from the 5' end of the RNA decreased but did not abolish cleavage at the sequence. However, changing the nucleotide sequence in the region of the preferred cleavage either by the insertion experiment or mutagenesis did not significantly alter its capacity for cleavage. These results demonstrated a dominant position preference, plus a sequence priority. In another experiment, a 25 nucleotide long DNA was hybridized such that its 3' terminal nucleotide was 9 nucleotides from the 5' end of a 60 nucleotide complementary RNA. The preferred RNA cleavage sequence discussed above, was 10-14 nucleotides upstream of the 3' end of the DNA. However, initial cleavages occurred 17-20 nucleotides from the DNA 3' end, consistent with cleavage being coordinated by the recessed 3' terminus of the DNA primer.
The nef reading frame overlaps about 70% of the U3 region of the 3' long terminal repeat (LTR) in primate lentiviruses. We investigated the functional role of these overlapping U3 sequences by analyzing the properties of three mutant forms of the pathogenic SIVmac239 clone. In mutant UScon, 90 of 275 bp in the upstream sequences (US) of U3 were changed in a conservative fashion without changing the predicted nef coding sequence. In mutant USnon, 101 of 275 bp in this region were changed in a nonconservative fashion, again without changing the predicted nef coding sequence. In mutant delta US, 275 bp in this region were deleted. Full-size, immunoreactive nef protein was synthesized in cells infected with the UScon and USnon mutants. The USnon and delta US mutants replicated with similar kinetics and to similar extents as wild-type, parental SIVmac239 in primary rhesus monkey peripheral blood mononuclear cell (PBMC) cultures. The UScon mutant replicated with slightly delayed kinetics in rhesus monkey PBMC cultures. In the CEMx174 cell line, the delta US mutant replicated similarly to the wild type, but the UScon and USnon mutants replicated with significantly delayed kinetics. Analysis of LTR-driven chloramphenicol acetyltransferase (CAT) activity and the effects of 5-azacytidine on virus replication suggested that the growth defect of the point mutants in CEMx174 cells was due in whole or in part to the introduction of multiple CG methylation sites in proviral DNA. Rhesus monkeys were experimentally infected with the UScon and USnon mutants, and the characteristics of the infection were compared with those of the parental SIVmac239. Analysis of the levels of plasma antigenemia, virus load, and CD4+ cells in PBMC revealed no decreased virulence of the mutant viruses. Analysis of lymph node biopsies taken from animals that received mutant viruses revealed histologic changes and levels of virus expression indistinguishable from those of the wild type. Furthermore, the wild-type behavior of the mutant viruses in rhesus monkeys occurred without any specific reversional events through at least 20 weeks of infection. These results, and the recent results of Kirchhoff et al. (F. Kirchoff, H. W. Kestler III, and R. C. Desrosiers, J. Virol. 68:2031-2037, 1994), suggest that these upstream sequences in U3 are primarily or exclusively nef coding sequence.
RNA/DNA hybrids in human immunodeficiency virus (HIV) replication are cleaved by HIV-1 reverse transcriptase (RT) H in locations determined by hybrid structure. Minus strand DNA synthesis is accompanied by cleavage of template viral RNA directed by RT positioned at the growing 3' DNA end. Some RNA remains as oligomers annealed to the new DNA strand and is cut by RTs positioned at the 5' RNA ends. We constructed substrates to the test the hypothesis that internal helix structure, rather than strand end structure, drives the RT to position at 3' DNA and 5' RNA ends. On substrates with an RNA primer recessed on a DNA template, the 5' end of the RNA had a dominant role in the determination of RNase H cleavage positions. If the 5' end region of the RNA could not anneal, cleavage would not occur. Nevertheless, we obtained evidence that helix structure promotes the binding of RT to the end of the helical region closest to the 5' RNA/3' DNA end. When a DNA primer recessed on an RNA template had a 3' unannealed region, cleavage occurred, with RT positioned solely by helical structure at the 5' RNA/3' DNA end of the annealed region of the hybrid. Using substrates having RNA primers annealed to circular DNA templates, we showed that cleavage can be independent of the presence of a DNA 3'end and is directed by the 5' RNA end. Overall, the results suggest that the RT initially binds an internal region of the hybrid and then is driven in the direction to encounter a 3' DNA or 5' RNA end, where it is positioned for catalysts by the strand end. The requirement for two modes of RNA cleavage in viral replication and the unexpected requirement for the 5' RNA end structure are discussed.
After integration in the host cell genome, the HIV-1 provirus is packaged into chromatin. A specific chromatin disruption occurs in the HIV-1 promoter during transcriptional activation in response to TNF-alpha, suggesting that chromatin plays a repressive role in HIV-1 transcription and that chromatin modification(s) might result in transcriptional activation. We have treated several cell lines latently infected with HIV-1 with two new specific inhibitors of histone deacetylase, trapoxin (TPX) and trichostatin A (TSA), to cause a global hyperacetylation of cellular histones. Treatment with both drugs results in the transcriptional activation of the HIV-1 promoter and in a marked increase in virus production. Dose-response curves and kinetic analysis show a close correlation between the level of histone acetylation and HIV-1 gene expression. In contrast, both TPX and TSA have little or no effect on HIV-1 promoter activity following transient transfection of an HIV-1 promoter-reporter plasmid. Activation of HIV-1 transcription by TSA and TPX treatment occurs in the absence of NF-kappa B induction. Chromatin analysis of the HIV-1 genome shows that a single nucleosome (nuc-1) located at the transcription start and known to be disrupted following TNF-alpha treatment, is also disrupted following TPX or TSA treatment. This disruption is independent of transcription as it is resistant to alpha-amanitin. These observations further support the crucial role played by nuc-1 in the suppression of HIV-1 transcription during latency and demonstrate that transcriptional activation of HIV-1 can proceed through a chromatin modification.
Considerable controversy now surrounds the interpretation of the known structures of the nucleic acid polymerases and the orientation of the template-primers relative to the poly- merase active sites. The initial polymerase structure (that of the Klenow fragment of Escherichia coli DNA polymerase I) showed a large groove into which DNA might bind but did not provide sufficient information to make clear the orientation of the DNA relative to the protein (20). This question was ap- parently answered by solving the structure of the reverse tran- scriptase (RT) of human immunodeficiency virus type 1 (HIV-1)(16).Aswillbediscussedinmoredetailbelow,HIV-1 RT has, in addition to the polymerase domain, an RNase H domain, which can be used to define the orientation of the enzyme on an RNA/DNA duplex. The issue of the orientation of the protein relative to the nucleic acid appeared to be completelysettledwhenthestructureofHIV-1RTincomplex withdouble-strandedDNAwasobtained(14).Theorientation of the DNA in this structure is in agreement with the predic- tion made on the basis of the physical relationship of the polymerase and the RNase H domains. However, Pelletier et al. (22) obtained a structure for a complex of rat DNA poly-
At the 3' end of all retroviral genomes there is a short, highly conserved sequence known as the polypurine tract (PPT), which serves as the primer for plus-strand DNA synthesis. We have identified the determinants for in vitro priming by the human immunodeficiency virus type 1 (HIV-1) PPT. We show that when the PPT is removed and placed into different nucleotide contexts, new priming sites are produced at the precise 3' end of the PPT. In addition, we find that a hybrid consisting of a 15- or 20-nucleotide RNA primer annealed to a 35-nucleotide DNA template is competent for initiation of plus-strand synthesis with HIV-1 reverse transcriptase. Thus, no cis-acting elements appear to be required for priming activity. Changes at the 5' end of the PPT have no effect on primer function, whereas the identity of bases at the 3' end is crucial. A primer containing only the 6 G residues from the 3' end of the wild-type PPT sequence and 9 bases of random sequence at the 5' end functions like a wild-type PPT. A short hybrid having a similar helical structure but a primary sequence different from that of the PPT is cleaved imprecisely, resulting in initiation of synthesis at multiple sites; however, total primer extension is close to the wild-type level. We conclude that helical structure as well as the presence of particular bases at the 3' end of the PPT is essential for PPT function.
The ability of human immunodeficiency virus-1 (HIV-1) to undergo efficient reverse transcription is dependent on a number of parameters. These include the binding of the tRNA(3)(Lys) to the HIV-1 primer binding site and the subsequent interaction with the heterodimeric reverse transcriptase. Recently, we demonstrated that TAR RNA was also necessary for efficient HIV-1 reverse transcription. Given the fact that the Tat protein is involved in the activation of HIV-1 gene expression in conjunction with TAR, we wished to determine whether Tat might also be involved in the control of HIV-1 reverse transcription. HIV-1 virions deleted in the tat gene were unable to initiate reverse transcription efficiently upon infection of peripheral blood mononuclear cells (PBMCs). This defect was not due to decreased amounts of genomic RNA, reverse transcriptase or other HIV-1 proteins which were incorporated into the virion. Following transfection of wild-type but not mutant tat genes into cell lines producing HIV-1 lacking tat, the virions produced could be complemented for defects in reverse transcription upon subsequent infection of PBMCs. In contrast, the defect in reverse transcription seen with HIV-1 lacking the tat gene could not be complemented when the target cells rather than the producer cells contained tat. Viruses lacking tat were also defective in endogenous assays of reverse transcription, although these viruses contained similar levels of reverse transcriptase. These results indicate that the Tat protein, in addition to regulating the level of gene expression, is also important for efficient HIV-1 reverse transcription.
A specific terminal structure of preintegrative DNA is required for transposition of retroviruses and LTR-retrotransposons.
We have used an anchored PCR technique to map the 3′ ends of DNA intermediates synthesized inside yeast Ty1 and Ty3 retrotransposon
virus-like particles. We find that, unlike retroviruses, Ty1 replicated DNA does not have two extra base pairs at its 3′ ends.
In contrast some Ty3 preintegrative DNA molecules have two extra nucleotides at the 3′ end of upstream and downstream long
terminal repeats. Moreover we find that some molecules of replicated Ty3 DNA have more than two extra nucleotides at the 3′
end of the upstream LTR. This observation could be accounted for by imprecise RNAse H cutting of the PPT sequence. The site
of Ty1 and Ty3 plus-strand strongstop DNA termination was also examined. Our results confirm that the prominent Ty1 and Ty3
plus-strand strong-stop molecules harbor 12 tRNA templated bases but also show that some Ty1 and Ty3 plusstrand strong-stop
DNA molecules harbor less tRNA templated bases. We propose that these less than full length plus-strand molecules could be
active intermediates in Ty retrotransposon replication.
During the first strand transfer in reverse transcription, minus-strand strong-stop DNA [(-) SSDNA] is annealed to the 3' end of the acceptor RNA in a reaction mediated by base-pairing between terminal repeat sequences in the RNA and their complement in the DNA. The large stem-loop structure in the repeat region known as TAR could interfere with this annealing reaction. We have developed an in vitro human immunodeficiency virus type 1 (HIV-1) system to investigate the effect of TAR on strand transfer. Mutational analysis demonstrates that the presence of TAR in the donor and acceptor templates inhibits strand transfer and is correlated with extensive synthesis of heterogeneous DNAs formed by self-priming from (-) SSDNA. These DNAs are not precursors to the transfer product. Interestingly, products of self-priming are not detected in HIV-1 endogenous reactions; this suggests that virions contain a component which prevents self-priming. Our results show that the viral nucleocapsid protein (NC), which can destabilize secondary structures, drastically reduces self-priming and dramatically increases the efficiency of strand transfer. In addition, the data suggest that the ability to eliminate self-priming is a general property of NC which is manifested during reverse transcriptase pausing at sites of secondary structure in the template. We conclude that this activity of NC is critical for achieving highly efficient and specific viral DNA synthesis. Our findings raise the possibility that inactivation of NC could provide a new approach for targeting reverse transcription in anti-HIV therapy.
Nucleotide segment (+169)AAAA(+172) constitutes an A-rich loop within human immunodeficiency virus type 1 (HIV-1) (HXB2D) RNA and is able to interact with the anticodon loop (33)/USUU(36) of primer tRNA3(Lys). We have shown that the deletion of this A-rich loop resulted in diminished levels of infectivity and reduced synthesis of viral DNA in MT-2 cells and cord blood mononuclear cells. Endogenous reverse transcriptase (RT) assays revealed that the mutated viruses, termed HIV/del-A, generated fewer cDNA products than did wild-type virus, designated HIV/WT. We also employed in vitro RT assays with in vitro-synthesized viral RNA templates, recombinant HIV-1 RT(p66/51), and natural tRNA3(Lys) as primers to show that the mutated RNA templates, designated PBS/del-A, generated less minus-strand strong-stop DNA product than did the wild-type RNA template, designated PBS/WT. The initiation efficiency of reverse transcription from the mutated RNA template was significantly impaired compared with that from the wild-type RNA template when a single-base extension assay from the tRNA3(Lys) primer was employed. However, RT reactions performed with DNA oligonucleotides complementary to the primer binding site (PBS) as primers did not yield differences between the mutated PBS/del-A and wild-type RNA templates. Long-term culture of HIV/del-A in MT-2 cells resulted in the replacement of two G's at nucleotide positions 167 and 168 by two A's that possessed the same relationship to the 5' end of the PBS as did the wild-type A's at positions 171 and 172. In vitro RT assays performed with recombinant enzyme with tRNA3(Lys) as the primer showed that the RNA template thus generated, termed PBS/A2, yielded levels of minus-strand strong-stop DNA product similar to those yielded by the wild-type RNA template. Coincidentally, viruses containing A's at positions 167 and 168 were able to replicate with efficiencies similar to those of the wild-type viruses. Thus, the (+169)AAAA(+172) A-rich loop plays a key role in the synthesis of viral DNA.
Reverse transcription of retroviruses is initiated from an 18-nucleotide (nt) primer binding site (PBS), located within the 5' region of viral genomic RNA, to which the host cell-derived tRNA primer is annealed and also involves viral genomic sequences outside the PBS. We constructed proviral DNA clones of human immunodeficiency virus (HIV) that had selective deletions of either a 7-nt segment found immediately downstream of the PBS or an extended nontranslated 54-nt stretch located immediately downstream of the PBS and containing the aforementioned 7-nt segment. Synthesis of minus-strand strong-stop DNA was assessed with MT-4 cells infected with viruses derived from COS-7 cells that had been transfected with these various constructs. We found that similar levels of minus-strand strong-stop DNA as well as DNA produced after template switching were expressed in MT-4 cells infected with COS-7-derived wild-type viruses or with viruses that had the 7-nt segment deleted. In contrast, significantly lower levels of viral DNA were detected in MT-4 cells after infection with viruses that had deletions of the 54-nt stretch. Furthermore, the molecular clone containing the 7-nt deletion was able to replicate with wild-type kinetics, while that containing the 54-nt deletion displayed a significantly diminished capacity in this regard. Further deletion analysis showed that a 16-nt segment at the 3' end of this 54-nt segment was largely responsible for these effects. We also conducted studies to determine levels of viral mRNA in COS-7 cells that had been transfected with equivalent amounts of DNA derived from either a wild-type HIV construct or our various deletion mutants. In the case of transfections performed with the 7-nt deletion mutant and wild-type HIV DNA, high levels of viral mRNA transcripts were detected, which was not the case for the 54 nt-deletion mutant. However, these various mRNAs possessed similar stabilities, as shown through studies in which transcript formation was arrested by treatment of cells with actinomycin D. Thus, the 54-nt segment of 5' nontranslated RNA, located downstream of the PBS, is involved in efficient expression of each of viral DNA, mRNA, and infectious virus.
A synthetic RNA oligonucleotide (15-mer) corresponding to the 3' end of the lysine tRNA primer was hybridized to single-stranded DNA containing the human immunodeficiency virus type 1 (HIV-1) primer-binding site and extended with a DNA polymerase. The resulting structures were used to study primer removal by the RNase H activity of HIV-1 reverse transcriptase. The initial cleavage event removes the RNA primer as a 14-mer and leaves a single ribonucleotide A residue bound to the 5' end of the DNA strand. This result explains the observation by several groups that HIV-1 circle junctions contain 4 bp that are not present in the integrated provirus instead of the predicted 3 bp. Subsequent cleavage events occur at other sites internal to the RNA molecule, and the ribonucleotide A residue on the end of the DNA strand is ultimately removed. Therefore, the biologically relevant cleavage that produces the 14-mer reflects the kinetics of the reaction as well as a specificity for nucleic acid sequence. When the RNA oligonucleotide alone was hybridized to the primer-binding site and tested as a substrate for HIV-1 RNase H, the cleavage pattern near the 3' end of the RNA was altered.
The mode of action of the RNase H activity from HIV-1 was analyzed with a purified recombinant p66/p51 reverse transcriptase RT/RNase H protein and RNA-DNA hybrid consisting of RNA harboring the polypurine tract (ppt) and three complementary synthetic DNA oligonucleotides. Upon incubation of this preformed RNA-DNA hybrid with the p66/p51 RT/RNase H, a cleavage pattern is observed that indicates endonucleolytic RNase H activity with some sequence specificity for the next to last nucleotide of the 3'-end of the ppt RNA and one cut within the ppt. The RNase H avoids cleavage of G or A stretches. During RNA-directed DNA synthesis the RNA is hydrolyzed in a concerted action of RT and RNase H whereby the RNase H exhibits endonuclease as well as 3'-5'-exonuclease activity. The distance between the active centers of the RT and RNase H corresponds to 18 base pairs of the RNA-DNA hybrid. Plus-strand DNA-directed DNA synthesis initiates exactly at the next to last nucleotide of the 3'-end of the ppt RNA by means of the RNase H activity.
The complete nucleotide sequence of an infectious clone of simian immunodeficiency virus of macaques, SIVmac239, has been determined. Virus produced from this molecular clone causes AIDS in rhesus monkeys in a time frame suitable for laboratory investigation. The proviral genome including both long terminal repeats is 10,279 base pairs in length and contains open reading frames for gag, pol, vif, vpr, vpx, tat, rev, and env. The nef gene contains an in-frame premature stop after the 92nd codon. At the nucleotide level, SIVmac239 is closely related to SIVmac251 (98%) and SIVmac142 (96%). It will not be possible to test which features of the viral sequence are critical molecular determinants for the pathogenesis of AIDS.
The start site for human immunodeficiency virus type 1 plus strands within the polypurine tract was mapped by an in vitro analysis to the sequence 5'-ACTG....From this result, it can be inferred that integration of human immunodeficiency virus type 1 must be accompanied by the loss of two base pairs from the polypurine tract-primed long terminal repeat end.
Specific, end-labeled DNA fragments can be simply and rapidly prepared using the polymerase chain reaction (PCR). Such fragments
are suitable for use in DNase I protection footprint assays, chemical sequencing reactions, and for the production and analysis
of paused RNA polymerase transcription complexes. Moreover, a general means of introducing a specific mutation at any position
along the length of such PCR-generated fragments is described. These procedures, which can circumvent the need for large-scale
phage or plasmid growths, preparative gel-electrophoresis and the screening of molecular clones, can facilitate the rapid
study of sequence-specffic interactions of proteins and DNA. A rapid means of removing excess oligonucleotide primers from
completed PCRs is also described.
Employing enzymatic reactions in vitro, we have identified the presence of oligoribonucleotides at the 5' end of strong-stop plus [(+)] DNA. Similar results were obtained whether the strong-stop (+) DNA was synthesized by preparations of detergent-disrupted avian sarcoma virus or reconstructed reactions containing purified reverse transcriptase and a template that mimics the purported natural template for strong-stop (+) DNA synthesis. The latter reactions provide a system to delineate more precisely the discrete requirements necessary for the initiation and synthesis of this species of (+) DNA.
A 190-base-pair DNA-RNA hybrid containing the Moloney murine leukemia virus origin of plus-strand DNA synthesis was constructed and used as a source of template-primer for the reverse transcriptase in vitro. Synthesis was shown to initiate precisely at the known plus-strand origin. The observation that some of the origin fragments retained ribonucleotide residues on their 5' ends suggests that the primer for chain initiation is an RNA molecule left behind by RNase H during the degradation of the RNA moiety of the DNA-RNA hybrid. If the RNase H is responsible for creating the correct primer terminus, then it must possess a specific endonucleolytic activity capable of recognizing the sequence in the RNA where plus strands are initiated. The 16-base RNase A-resistant fragment which spans the plus-strand origin can also serve as a source of the specific plus-strand primer RNA. Evidence is presented that some of the plus-strand origin fragments synthesized in the endogenous reaction contain 5' ribonucleotides, suggesting that specific RNA primers for plus-strand initiation may be generated during reverse transcription in vivo as well.
Reconstructed enzymatic reactions containing purified reverse transcriptase and defined analog substrates which mimic those purported to be natural substances for reverse transcription in vivo were employed to delineate the mechanism of strong-stop (+) DNA synthesis. Our analysis of this system has indicated that strong-stop (+) DNA synthesis is initiated after the introduction of a nick in the viral RNA genome between a polypurine sequence and an inverted repeat that represents the end of the long terminal repeat. Since inhibitors of the reverse transcriptase-associated RNase H activity prevent the introduction of the nick and the synthesis of strong-stop (+) DNA synthesis, it appears that this particular reverse transcriptase-associated enzymatic activity is responsible for the initiation of strong-stop (+) DNA. Our data also indicated that the RNase H activity creates a second nick in the viral RNA genome 11 nucleotides upstream from the strong-stop (+) DNA initiation site since the strong-stop (+) DNA synthesized in these reactions is covalently linked to an oligoribonucleotide 11 residues in length. Nucleotide sequence analysis of the oligoribonucleotide primer molecule indicated that a single homogenous oligomer was associated with strong-stop (+) DNA exhibiting the sequence rArGrGrGrArGrGrGrGrGrA. The oligoribonucleotide primer can be removed from strong-stop (+) DNA by the purified reverse transcriptase, which creates a nick at the junction between the primer and strong-stop (+) DNA. These data demonstrate that the initiation of strong-stop (+) DNA synthesis is mediated by RNase H and that the site of initiation is exactly at the end of the long terminal repeat, providing evidence for yet another function of this reverse transcriptase-associated enzymatic activity in the synthesis of retrovirus DNA.
A primary site for initiation of plus strand DNA synthesis in human immunodeficiency virus (HIV) corresponds to a 19-nucleotide-long purine rich sequence located just upstream of the U3 region, designated the polypurine tract (PPT). The HIV reverse transcriptase (RT) uses its RNase H activity to cut the genomic RNA after minus strand DNA synthesis. A plus strand PPT primer is formed, extended, and then removed. In vitro, the HIV-RT recognizes this primer specifically, using it much more efficiently than other RNA primers. However, the PPT still primes significantly less efficiently than DNA primers. The 19-nucleotide PPT primer is partially resistant to degradation when compared with other oligoribonucleotides. Prior to initiation of DNA synthesis, several nucleotides are removed by the RT from the 3' ends of some of the PPT primers. Cleavage is enhanced in the absence of dNTPs. We suggest that DNA synthesis suppresses primer degradation, so that primer extension and cleavage occur in proper sequence. As a result of 3' end degradation, PPT elongation products contain 5'-RNA segments from 16 to 19 nucleotides in length. These shorter segments are also generated from a longer transcript containing the PPT sequence, indicating that they are not created as a result of binding of the RT to the 5' end of the PPT oligoribonucleotide. Full-length and shorter versions of the PPT primers are cleaved from the extended DNA by RT. These experiments show that HIV-RT has a specificity to generate a primer in the region of the PPT but that the ends of the primer are not well defined.
Long terminal repeat elements and retroviruses require primers for initiation of minus and plus-strand DNA synthesis by reverse transcriptase. Here we demonstrate genetically that plus-strand DNA synthesis of the yeast Ty1 element is initiated at two sites located at the 5' boundary of the 3' long terminal repeat (PPT1) and near the middle of the pol gene in the integrase coding sequence (PPT2). A consequence of the presence of two PPTs is that Ty1 plus-strand DNA exists as segments at some time during replication. Three fragments have been identified: the plus-strand strong-stop DNA initiated at PPT1, a downstream fragment initiated at PPT2 and an upstream fragment spanning the 5'-terminal part of Ty1 and a portion of the TyB gene. Characterization of the 3' ends of the plus-strand DNA fragments reveals (1) that the upstream fragment is elongated beyond PPT2 creating a plus-strand overlap and (2) that the majority of plus-strand strong-stop DNA fragments bear a copy of the minus-strand primer binding site in agreement with the accepted model of retroviral genomic RNA reverse transcription. The two polypurine tracts, PPT1 and PPT2, have an identical sequence GGGTGGTA. Mutations replacing purines by pyrimidines in this sequence significantly diminish or abolish initiation of plus-strand synthesis. Ty1 elements bearing a mutated PPT2 sequence are not defective for transposition whereas mutations in PPT1 abolish transposition.
Ten mutants of the simian immunodeficiency virus (SIV) SIVmac239 bearing deletions (delta) or substitutions (subst) in the NF-kappaB and/or Sp1 binding elements were created, and the replicative capacities of the mutants were analyzed. All mutants, including one extensively mutagenized strain entirely missing the NF-kappaB and four Spl binding elements, replicated with wild-type kinetics and to a wild-type level in peripheral blood mononuclear cell cultures in 50 to 100% of the experiments. One group of mutants replicated very similarly to SIVmac239 in kinetics and yield in CEMxl74 cells (2xNFKappaB > or = SlVmac239 approximately deltaNFkappaB approximately deltaSpl234 approximately substNFkappaB approximately substSpl2 approximately substSp23), while a second group replicated with delayed or slightly delayed kinetics in CEMxl74 cells (SIVmac239 > substSp34 > deltaNFkappaBdeltaSpl234 approximately deltaNFkappaBdeltaSp1 > substSpl234). Reversions or additional mutations were not detected in the U3 and R regions of proviral DNA from CEMxl74 cells infected with the SIVmac239 mutants. Similar results were obtained when mutants of SIVmacMER (a macrophage-competent derivative of SIVmac239) were tested in peripheral blood mononuclear cell and CEMx174 cultures. However, the growth of most mutated viruses was suppressed in primary rhesus monkey alveolar macrophages (SIVmacMER approximately 2xNFkappaB approximately substNFkappaB > deltaNFkappaB > deltaNFkappaBdeltaSpl234 approximately deltaNFkappaBdeltaSpl > deltaSpl234 approximately substSpl2 > substSp23 approximately substSp34 approximately substSpl234 > or = SIVmac239). Thus, changes in the Sp1 binding sites had the most dramatic effects on SIVmac replication in primary macrophage cultures. Analysis of long terminal repeat-driven secreted alkaline phosphatase activity in transient assays showed that, unlike human immunodeficiency virus type 1, the SIV long terminal repeat possesses an enhancer region just upstream of the NF-kappaB element which maintains significant levels of basal transcription in the absence of NF-kappaB and Sp1 sites. This region is responsive to transactivation by Tat. In addition, the SIV TATA box was shown to be stronger than that of human immunodeficiency virus type 1. Therefore, the surprisingly high replicative capacity of NF-kappaB and Sp1 binding site mutants of SIVmac is due to unique features or the enhancer/promoter region.
In an earlier study on minus-strand DNA synthesis catalyzed by murine leukemia virus reverse transcriptase, we described a prominent pause site near the polypurine tract (J. Guo, W. Wu, Z. Y. Yuan, K. Post, R. J. Crouch, and J. G . Levin, Biochemistry 34:5018-5029, 1995). We now report that pausing at this site is due to a stem-loop structure in the RNA template, formed by interaction of a number of bases in the polypurine tract, including the six G's, and a 3' sequence which includes four C's. Addition of human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) protein to reverse transcriptase reactions reduces pausing by approximately 8- to 10-fold and stimulates synthesis of full-length DNA. Thus, NC functions as an accessory protein during elongation of minus-strand DNA and increases the efficiency of DNA synthesis, in this case, by apparently destabilizing a region of secondary structure in the template. Since NC is associated with genomic RNA in the viral core and is likely to be part of a viral replication complex, these results suggest that NC may also promote efficient DNA synthesis during virus replication. Mutational analysis indicates that the features of HIV-1 NC which are important for reduction of pausing include the basic amino acids flanking the first zinc finger, the zinc fingers, and the cysteine and aromatic amino acids within the fingers. These findings suggest that reverse transcription might be targeted by drugs which inactivate the zinc fingers of HIV-1 NC.
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