Purification and partial characterization of equine infectious anemia virus reverse transcriptase

The efficacy of T cell-mediated immune responses is reduced by the envelope protein of the chimeric HIV-1/SIV-KB9 virus in vivo

Gp120 is a critical component of the envelope of HIV-1. Its role in viral entry is well described. In view of its position on the viral envelope, gp120 is a part of the retrovirus that immune cells encounter first and has the potential to influence antiretroviral immune responses. We propose that high levels of gp120 are present in tissues and may contribute to the failure of the immune system to fully control and ultimately clear the virus. Herein, we show for the first time that lymphoid tissues from acutely HIV-1/SIV (SHIV)-KB9-infected macaques contain deposits of gp120 at concentrations that are high enough to induce suppressive effects on T cells, thus negatively regulating the antiviral CTL response and contributing to virus survival and persistence. We also demonstrate that SHIV-KB9 gp120 influences functional T cell responses during SHIV infection in a manner that suppresses degranulation and cytokine secretion by CTLs. Finally, we show that regulatory T cells accumulate in lymphoid tissues during acute infection and that they respond to gp120 by producing TGFbeta, a known suppressant of cytotoxic T cell activity. These findings have significant implications for our understanding of the contribution of non-entry-related functions of HIV-1 gp120 to the pathogenesis of HIV/AIDS.

Retroviral reverse transcriptases (other than those of HIV-1 and murine leukemia virus): a comparison of their molecular and biochemical properties

This chapter reviews most of the biochemical data on reverse transcriptases (RTs) of retroviruses, other than those of HIV-1 and murine leukemia virus (MLV) that are covered in detail in other reviews of this special edition devoted to reverse transcriptases. The various RTs mentioned are grouped according to their retroviral origins and include the RTs of the alpharetroviruses, lentiviruses (both primate, other than HIV-1, and non-primate lentiviruses), betaretroviruses, deltaretroviruses and spumaretroviruses. For each RT group, the processing, molecular organization as well as the enzymatic activities and biochemical properties are described. Several RTs function as dimers, primarily as heterodimers, while the others are active as monomeric proteins. The comparisons between the diverse properties of the various RTs show the common traits that characterize the RTs from all retroviral subfamilies. In addition, the unique features of the specific RTs groups are also discussed.

Enhancement of equine infectious anemia virus virulence by identification and removal of suboptimal nucleotides

Pathogenicity was reportedly restored to an avirulent molecular clone of equine infectious anemia virus (EIAV) by substitution of 3' sequences from the pathogenic variant strain (EIAV(PV)). However, the incidence of disease in horses/ponies was found to be significantly lower (P = 0.016) with the chimeric clone (EIAV(UK)) than with EIAV(PV). This was attributable to 3' rather than 5' regions of the proviral genome, where EIAV(UK) differs from the consensus EIAV(PV) sequence by having a 68-bp duplication in the 3' LTR and arginine (R(103)) rather than tryptophan (W(103)) at position 103 in the second exon of rev. In EIAV(UK) recipients the duplication was rapidly eliminated and R(103) replaced by W(103) in the viral population. Furthermore, removal of the 3' variant sequences from EIAV(UK) (EIAV(UK3)) resulted in an equivalent (P = 0.013) disease potential in Equus caballus to EIAV(PV). The 68-bp duplication and/or R(103) may limit peak viral RNA accumulation during acute infection.

Role of the Reverse Transcriptase, Nucleocapsid Protein, and Template Structure in the Two-step Transfer Mechanism in Retroviral Recombination

Template switching during reverse transcription promotes recombination in retroviruses. Efficient switches have been measured in vitro on hairpin-containing RNA templates by a two-step mechanism. Pausing of the reverse transcriptase (RT) at the hairpin base allowed enhanced cleavage of the initial donor RNA template, exposing regions of the cDNA and allowing the acceptor to base pair with the cDNA. This defines the first or docking step. The primer continued synthesis on the donor, transferring or locking in a second step. Here we determine the enzyme-dependent factors that influence template switching by comparing the RTs from human immunodeficiency virus, type 1 (HIV-1), and equine infectious anemia virus (EIAV). HIV-1 RT promoted transfers with higher efficiency than EIAV RT. We found that both RTs paused strongly at the base of the hairpin. While stalled, HIV-1 RT made closely spaced cuts, whereas EIAV RT made only a single cut. Docking occurred efficiently at the multiply cut but not at the singly cut site. HIV-1 nucleocapsid (NC) protein stimulated strand transfers. It improved RNase H activity of both RTs. It allowed the EIAV RT to make a distribution of cuts, greatly stimulating docking at the base of the hairpin. Most likely, it also promoted strand exchange, allowing transfers to be initiated from sites throughout the hairpin. Minor pause sites beyond the base of the hairpin correlated with the locking sites. The strand exchange properties of NC likely promote this step. We present a model that explains the roles of RNase H specificity, template structure, and properties of NC in the two-step transfer reaction.

Homodimeric reverse transcriptases from rous sarcoma virus mutated within the polymerase or RNase H active site of one subunit are active

Heterodimeric reverse transcriptase (RT) alphabeta from Rous sarcoma virus (RSV) possesses an asymmetric subunit organization with the polymerase and RNase H active sites localized in the alpha subunit. To determine whether homodimeric RSV RTs alpha (63 kDa) or beta (95 kDa) assume alpha subunit organization similar to that of the heterodimer, an essential aspartic acid residue was mutated in the active site of either the polymerase (Asp181 > Asn) or the RNase H (Asp505 > Asn). Homodimeric alpha or beta RT consisting of one wild-type and one mutated subunit exhibit polymerase or RNase H activity, respectively, whereas the corresponding doubly mutated enzymes are inactive, indicating that the catalytic sites of the polymerase and RNase H domains are formed by only one subunit of the homodimer.

Soluble Rous sarcoma virus reverse transcriptases alpha, alphabeta, and beta purified from insect cells are processive DNA polymerases that lack an RNase H 3' --> 5' directed processing activity

Reverse transcriptase (RT) isolated from Rous sarcoma virus (RSV) consists of heterodimeric RTalphabeta, RTalpha, and RTbeta. The alpha subunit (63 kDa) contains an N-terminal polymerase and a C-terminal RNase H domain. The N terminus of beta (95 kDa) corresponds to alpha with the integrase domain attached to the C terminus (32 kDa). We have constructed baculoviruses expressing the genes for alpha or beta or the entire pol (99 kDa). Infection of insect cells with recombinant virus yielded highly active and soluble RSV RT enzymes that could be purified to >90% homogeneity. HPLC gel filtration showed that alpha is a dimeric enzyme that can be partially monomerized upon the addition of 45% Me(2)SO. DNA synthesis on DNA-DNA and DNA-RNA primer-templates in the presence of competitor substrates revealed that alphabeta and beta as well as alpha are processive polymerases. However, the affinity of beta and alphabeta for primer-template substrates appears to be higher than that of alpha. All RSV enzymes investigated have the potential to displace RNA-RNA duplexes more efficiently than human immunodeficiency virus type 1 RT. Unlike human immunodeficiency virus type 1 RT, RSV RTs can catalyze an initial RNase H endonucleolytic cleavage of the RNA template but not a 3' --> 5' directed processing activity.

Expression and purification of retroviral HIV-1 reverse transcriptase

Modern molecular biology techniques have provided valuable tools which allow for the expression of large amounts of enzyme in E. coli. For potential therapeutic targets such as HIV-1 reverse transcriptase, it is desirable that the enzyme studied is pure and correlates to the active form of the enzyme found in vivo. This poses a particular challenge for those researchers studying HIV-RT since a significant degree of heterogeneity is introduced by nonspecific proteolytic cleavage of the p66 subunit by E. coli proteases. The advantage of the purification protocol presented here is that the association of monomers is facilitated by mixing an excess of p51 subunit, which is truncated at a site that is N-terminal to known bacterial cleavage sites, with p66 protein. This avoids enzymatic processing of the larger subunit since the formation of heterodimeric RT is rapid and the dimer is stable against proteolytic cleavage. Therefore, it is possible to isolate a pure homogeneous p66/p51 heterodimer. An enzyme prepared in this manner yields crystals that defract to a 3.2-A resolution. It has also been used to study both sensitivity of HIV-1 RT mutants to azidothymidine triphosphate and the kinetics of a potent nonnucleoside RT inhibitor (L-743,726). Finally, it is interesting to note the similarity of HIV-1 RT with reverse transcriptases from other lentiviruses (FIV and EIAV RT). Both of these enzymes consist of heterodimers of p66 and p51 subunits and share other biophysical characteristics. Purification of these reverse transcriptases can, in all likelihood, be optimized by using methods similar to those described in this chapter.

Expression and purification of the mouse mammary tumor virus gag-pro transframe protein p30 and characterization of its dUTPase activity

The mouse mammary tumor virus gag-pro transframe protein (p30) contains the nucleocapsid protein domain derived from the 3' end of gag, fused to 154 residues encoded by the 5' region of the pro open reading frame. The DNA coding for p30 was cloned into the plasmid pALTER-1, and an additional nucleotide was inserted by site-directed mutagenesis to allow the read-through from the gag into the pro open reading frame. The obtained insert was then cloned into pGEX-2T, a plasmid containing the glutathione S-transferase gene of Schistosoma japonicum and a nucleotide sequence encoding for a thrombin cleavage site. The chimeric protein (GST-p30) was isolated by affinity chromatography on a glutathione-Sepharose 4B column, and after thrombin treatment, the excised p30 was further purified on a single-stranded DNA-agarose column. This protein showed dUTPase activity, with only negligible cleavage of dATP, dGTP, dCTP, dTTP, or UTP. Its apparent Km for dUTP was 28 microM. The enzyme was inhibited by EDTA, but its effect could be reversed by Mg2+ and other divalent cations. dUTPase activity was also detected in purified mouse mammary tumor virus, and p30 was the only protein recognized by antibodies directed towards the carboxyl-terminal sequence of the dUTPase coding region.

The catalytic properties of the reverse transcriptase of the lentivirus equine infectious anemia virus

The reverse transcriptase (RT) of equine infectious anemia virus (EIAV) shares sequence similarity with the RTs of other lentiviruses, particularly with the RTs of human immunodeficiency viruses types 1 and 2 (HIV-1 and HIV-2, respectively), the causative agents of acquired immunodeficiency syndrome (AIDS). There is a 41-42% sequence identity between EIAV RT and both HIV RTs (which have 61% sequence identity to each other). We have compared the enzymic properties of EIAV RT with those of HIV-1 RT. Several aspects of the activities of EIAV RT differ from the corresponding activities of HIV-1 RT. There are significant differences in the inhibition of the DNA polymerase activities by the deoxynucleoside triphosphate analogs, 3'-azido-2,3'-dideoxythymidine triphosphate, dideoxyTTP and dideoxyGTP and by the nonnucleoside inhibitor, tetrahydroimidazo[4,5,1-jk-1,4]benzodiazepin-2-(1H)-one and thione; in the dependence of DNA polymerase and RNase H activities on pH; in the inhibition of the DNA polymerase activities by the thiol-specific reagent N-ethylmaleimide; in the specific DNA polymerase activity; in the inhibition of the ribonuclease H activity by the zinc chelator orthophenanthroline. However, there are several cases in which EIAV RT and HIV-1 RT are more similar than was previously found for HIV-1 RT and HIV-2 RT. These include the Km values for the DNA polymerase activities, the heat stability of the DNA polymerase functions and the specific activity of the RNase H function.

Fidelity of DNA synthesis exhibited in vitro by the reverse transcriptase of the lentivirus equine infectious anemia virus

The lentivirus equine infectious anemia virus (EIAV) shows high genetic variations. To gain insight into the relative contribution of the reverse transcription process to the EIAV mutation rate, the accuracy of DNA synthesis catalyzed in vitro by the reverse transcriptase (RT) of EIAV was determined. Since the RT of EIAV shows a relatively high sequence homology with other lentiviral RTs, most notable being the RTs of human immunodeficiency viruses (HIVs), type 1 and type 2, it was of interest to study the fidelity of EIAV RT as part of an investigation of the structure-function relationship in lentiviral RTs. Like other RTs, EIAV RT was found to lack a 3'-->5' exonuclease activity. The fidelity of EIAV RT was analyzed by studying two distinct steps that lead to base substitution mutations: nucleotide misinsertions and elongation from 3'-terminal DNA mispairs. Analysis of misincorporation rates opposite the template adenine residue in native phi x174am3 DNA showed that EIAV RT catalyzes nucleotide mismatches with a specificity of A:C >> A:G > A:A. Interestingly, the same order of specificity was also detected during mispair extension with three templates tested (i.e., phi x174am3 DNA, rRNA, and synthetic oligo DNA). The mispair extension efficiency and mispair formation appear to be affected mainly by the increase in apparent Km values, rather than by the change in Vmax values. Furthermore, EIAV RT exhibits similar mispair extension efficiencies with both RNA and DNA templates with identical surrounding sequences. However, dissimilarities were detected in mispair extension frequencies with two DNAs which have different sequences, thus emphasizing the importance of the sequences copied.(ABSTRACT TRUNCATED AT 250 WORDS)

Studies on the substrate specificity of the proteinase of equine infectious anemia virus using oligopeptide substrates

The proteinase of the equine infectious anemia virus (EIAV), a lentivirus closely related to human immunodeficiency virus (HIV), was purified from concentrated virus. The specificity of the enzyme was characterized using oligopeptides representing naturally occurring cleavage sites in the Gag and Gag-Pol polyproteins. The length of the substrate binding pocket was found to be 1-2 residues longer than that of HIV proteinases. Although the EIAV and HIV proteinases cleaved most of the peptides at the same bond, some were hydrolyzed by only the EIAV enzyme. Oligopeptides representing cleavage sites in the nucleocapsid protein were also found to be substrates of the EIAV proteinase. However, these peptides were not hydrolyzed by the HIV proteinases. While peptides representing the corresponding sequences in the first cysteine arrays of the nucleocapsid proteins of HIV-1 and HIV-2 were substrates of the proteinases, peptides representing the homologous sequences in the second Cys arrays were resistant against the proteolytic attack. A three-dimensional model of the EIAV proteinase built on the basis of homology with HIV-1 proteinase was used to interpret the differences. In addition to the oligopeptides representing cleavage sites in the Gag and Gag-Pol polyproteins, the EIAV proteinase was also able to cleave an oligopeptide mimicking a cleavage site in the transmembrane protein. Our results suggest that the specificity of lentiviral proteinases share common characteristics, although substantial differences may exist in hydrolysis of some peptides.

High prevalence of serum antibodies to equine infectious anemia virus reverse transcriptase

The immunogenicity of the equine infectious anemia virus (EIAV) reverse transcriptase (RT) was examined by immunoblot assay with recombinant EIAV RT. All of the 19 sera from EIAV-infected horses tested contained antibodies that recognized EIAV RT and directly inhibited the polymerase activity of the enzyme. An examination of sera obtained sequentially from two experimentally infected animals revealed that anti-RT antibodies arise early in infection and increase in level. The appearance of the antibodies correlated with progression toward the asymptomatic period of infection.

Expression of the protease gene of equine infectious anemia virus in Escherichia coli: formation of the mature processed enzyme and specific cleavage of the gag precursor

A 620-bp Bg/II restriction fragment containing the putative protease coding sequence from equine infectious anemia virus (EIAV) proviral DNA was cloned and expressed in E. coli as a Pol precursor protein. In contrast to the 25-kDa fusion protein predicted from the expressed pol sequence, a protein of approximately 10 kDa was generated by apparent autocatalytic processing of the Pol precursor. This mature processed protein was detected in transformed cells using an antisera raised against synthetic peptide from the conserved carboxyl-terminal segment of the predicted EIAV protease coding sequence. Coexpression of this protein with a 35-kDa EIAV Gag-precursor fusion protein resulted in the specific proteolytic processing of the precursor as shown by formation of p26, the major capsid protein of EIAV.