Fourteen people with HIV-1 on two decades of antiretroviral therapy had longitudinal measurements of intact, defective, and total proviral DNA. Three patterns of intact proviral DNA decay were revealed: 1) biphasic decline with markedly slower second phase decline; 2) initial decline that transitions to a zero-slope plateau; and 3) initial decline followed by later increases in intact proviral DNA. Defective proviral DNA levels were essentially stable. Mechanisms of slowing or reversal of second phase decay of intact proviral DNA may include the inability to clear cells with intact but transcriptionally silent proviruses and clonal expansion of cells with intact proviruses.

The antiretroviral nucleoside analog 2',3'-dideoxy-3'-thiacytidine (3TC) is a potent inhibitor of wild-type human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), A methionine-to-valine or methionine-to-isoleucine substitution at residue 184 in the HIV-1 YMDD motif, which is located at the RT active site, leads to a high level of resistance to 3TC. We sought to determine whether 3TC can inhibit the replication of wild-type murine leukemia virus (MLV), which contains V223 at the YVDD active site motif of the MLV RT, and of the V223M, V223I, V223A, and V223S mutant RTs. Surprisingly, the wild type and all four of the V223 mutants of MLV RT were highly resistant to 3TC. These results indicate that determinants outside the YVDD motif of MLV RT confer a high level of resistance to 3TC. Therefore, structural differences among similar RTs might result in widely divergent sensitivities to antiretroviral nucleoside analogs.

Error-prone DNA synthesis by retroviral reverse transcriptases (RTs) is a major contributor to variation in retroviral populations. Structural features of retroviral RTs that are important for accuracy of DNA synthesis in vivo are not known. To identify structural elements of murine leukemia virus (MLV) RT important for fidelity in vivo, we developed a D17-based encapsidating cell line (ANGIE P) which is designed to express the amphotropic MLV envelope. ANGIE P also contains an MLV-based retroviral vector (GA-1) which encodes a wild-type bacterial beta-galactosidase gene (lacZ) and a neomycin phosphotransferase gene. Transfection of ANGIE P cells with wild-type or mutated MLV gag-pol expression constructs generated GA-1 virus that was able to undergo only one cycle of viral replication upon infection of D17 cells. The infected D17 cell clones were characterized by staining with 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside (X-Gal), and the frequencies of inactivating mutations in lacZ were quantified. Three mutations in the YVDD motif (V223M, V223S, and V223A) and two mutations in the RNase H domain (S526A and R657S) exhibited frequencies of lacZ inactivation 1.2- to 2.3-fold higher than that for the wild-type MLV RT (P < 0.005). Two mutations (V223I and Y598V) did not affect the frequency of lacZ inactivation. These results establish a sensitive in vivo assay for identification of structural determinants important for accuracy of DNA synthesis and indicate that several structural determinants may have an effect on the in vivo fidelity of MLV RT.

Retroviral populations exhibit a high evolutionary potential, giving rise to extensive genetic variation. Error-prone DNA synthesis catalyzed by reverse transcriptase (RT) generates variation in retroviral populations. Structural features within RTs are likely to contribute to the high rate of errors that occur during reverse transcription. We sought to determine whether amino acids within murine leukemia virus (MLV) RT that contact the deoxyribonucleoside triphosphate (dNTP) substrate are important for in vivo fidelity of reverse transcription. We utilized the previously described ANGIE P encapsidating cell line, which expresses the amphotropic MLV envelope and a retroviral vector (pGA-1). pGA-1 expresses the bacterial beta-galactosidase gene (lacZ), which serves as a reporter of mutations. Extensive mutagenesis was performed on residues likely to interact with the dNTP substrate, and the effects of these mutations on the fidelity of reverse transcription were determined. As expected, most substitution mutations of amino acids that directly interact with the dNTP substrate significantly reduced viral titers (>10,000-fold), indicating that these residues played a critical role in catalysis and viral replication. However, the D153A and A154S substitutions, which are predicted to affect the interactions with the triphosphate, resulted in statistically significant increases in the mutation rate. In addition, the conservative substitution F155W, which may affect interactions with the base and the ribose, increased the mutation rate 2.8-fold. Substitutions of residues in the vicinity of the dNTP-binding site also resulted in statistically significant decreases in fidelity (1. 3- to 2.4-fold). These results suggest that mutations of residues that contact the substrate dNTP can affect viral replication as well as alter the fidelity of reverse transcription.

PURPOSE:To characterize diversities in the extracelhtlar matrices (ECMs) of the corneal and the surrounding limbal epithelium and stroma.METHODS:Immunohistochemical analyses were employed for screening monoclonal antibodies (mAbs) developed against ECM components of the human corneal epithelial basement membrane (BM) zone. In the current study, mAb BM8 was used as the monospecific probe to characterize its antigen (AgBM8) immunochemically, and to immunoselect a complementary DNA (cDNA) clone encoding AgBM8. Direct biochemical and cDNA sequence analyses were performed for the further characterization of AgBM8. An indirect colloidal gold-conjugated antibody technique was employed for immunoelectron microscopic analysis to study the distribution of AgBM8 in the corneal ECMs.RESULTS:The protein AgBM8, isolated from rabbit corneal stromal and epithelial tissues, was identified as the long-splice variant form of type XII collagen based on its size (approximately 340 kDa disulfide-linked subunits), the presence of collagenous domain(s) and a noncollagenous domain of approximately 300 kDa in its subunit structure, and its internal amino acid sequences. The identity of AgBM8 was further confirmed from the amino acid sequence (517 amino acids) deduced from the sequence of a cDNA immunoselected with mAb BM8. Immunofluorescence analyses indicated that the long form of type XII collagen is present in the ECMs of corneal stroma and in the sclera, as well as in the corneal epithelial BM zone but is absent in the limbal and conjunctival epithelial BM zones. It was not detectable in the subepithelial loose connective tissues in the limbus and in the bulbar conjunctiva. Immunoelectron microscopic analyses indicated that the long variant form of type XII collagen is present in corneal epithelial BM, Bowman's membrane, and the interfibrillar matrix of the corneal stroma. In the stroma, colloidal gold was distributed along the collagen fibrils with a periodicity of 150 to 200 nm.CONCLUSIONS:The long variant form of human type XII collagen, a member of the fibril-associated collagens with interrupted triple helices, referred to as FACITs, contributes to the differences in the BM zones of the cornea and limbus. Although many of the dense connective tissues in adult animals contain the short variant form of type XII collagen, human corneal stroma, the BM zone, and the sclera contain the long variant form as the predominant form of type XII collagen. In the corneal stroma, type XII collagen may be organized along the collagen fibrils in a uniform head-to-tail pattern.