Fidelity of HIV-1 reverse transcriptase copying a hypervariable region of the HIV-1 env gene

Mutagenesis by human immunodeficiency virus reverse transcriptase: incorporation of O6-methyldeoxyguanosine triphosphate

The high frequency of incorporation of non-complementary nucleotides by HIV-1 reverse transcriptase is likely to be a major factor in the exceptionally rapid accumulation of viral mutations during the course of AIDS infections. To investigate whether this high level of infidelity is also associated with the incorporation of nucleotide analogs, we analyzed O6-methyldeoxyguanosine triphosphate and compared the incorporation of this analog by HIV-1 reverse transcriptase to that catalyzed by other DNA synthesizing enzymes. Our results indicate that O6-methyldeoxyguanosine triphosphate serves as a substrate for DNA synthesized in vitro by HIV-1 RT on both DNA and RNA templates. The product DNA contains the modified purine; it is sensitive to the repair enzyme, O6-methylguanine methyltransferase, which specifically reacts with DNA containing methylated guanines at the O6 position. Using a forward mutation assay we demonstrated that the nucleotide analog incorporated by HIV-1 RT is mutagenic. The mutations produced are single-base substitutions opposite template thymidines and result in A:T --> G:C transitions. The incorporation of a mutagenic nucleotide by HIV-1 RT highlights the possibility of increasing the rate of mutagenesis of HIV by the use of nucleotides that form non-complementary base pairs at high frequency.

Misincorporation by HIV-1 reverse transcriptase promotes recombination via strand transfer synthesis

Genome heterogeneity in retroviruses derives from poor fidelity of the reverse transcriptase (RT) and recombination via RT-catalyzed strand transfer synthesis. RTs lack proofreading ability, and they proficiently extend primers with mismatched termini. Recombination reactions carried out in vitro are accompanied by a high frequency of base substitution errors, suggesting a relationship. Here we provide evidence that misincorporation during RNA-directed DNA synthesis promotes strand transfer recombination. Experiments involved measurement of DNA synthesis, RNase H-directed cleavage, and strand transfer synthesis from preformed mismatched primers on RNA templates by human immunodeficiency virus (HIV) RT in vitro. A significant pause in synthesis occurred from a G(primer). rA(template) mismatch compared to the synthesis from a correctly paired (T.A) primer. The misincorporation-induced pause allowed an unusually large area of RT-RNase H-directed cleavage of the template RNA beneath the primer. Strand transfer to an acceptor molecule with sequence identical to the template RNA was about 50% more efficient than if the primer had had a correctly paired terminus. Overall transfer was measured over a large region of homology. Assuming that enhanced transfer occurs primarily at the site of the mismatch, the actual increase in transfer at that site must have been 1-2 orders of magnitude. Inclusion of a different acceptor molecule with complete complementarity to the originally mismatched 3' primer terminus resulted in an additional 2-fold increase in strand transfer efficiency. Overall, these results suggest the mechanism by which misincorporation during minus strand DNA synthesis in retroviral replication would promote high frequency recombination.

Nucleotide substitution patterns can predict the requirements for drug-resistance of HIV-1 proteins

The enzyme reverse transcriptase (RT) plays a fundamental role in the replication of the human immunodeficiency virus type 1 (HIV-1) and several antiviral agents that target this key enzyme have been developed. Unfortunately, treatment of patients with RT inhibitors results in the appearance of drug-resistant variants with specific mutations in the RT protein. We hypothesized that if "difficult' resistance mutations (e.g. transversions/double-hits) are consistently observed at certain positions, it is likely that "easier' nucleotide substitutions (transitions/single-hits) at that codon do not result in a drug-resistant and/or active RT enzyme. In this study, we examined codon changes involved in RT drug resistance against nucleoside and non-nucleoside inhibitors and listed all easier substitutions, which apparently were not selected, either due to reduced enzyme RT activity or lack of drug resistance. These predictions on the requirements for resistance were confirmed by published mutational data on RT variants. We also propose that differences in mutation type can explain the order of appearance of substitutions in case multiple amino acid changes are required for optimal fitness. Differences in mutation pattern have been reported for drug-resistant HIV-1 variants selected in tissue culture compared with variants found in treated patients. In contrast to the in vivo situation, a relatively small population size is handled in in vitro tissue culture systems and this may limit the chances of creating a resistance mutation. Indeed, inspection of the codon changes indicates that the in vitro culture system is more strongly biased towards the relatively easy nucleotide substitutions. These results suggest that the nucleotide substitution pattern can provide important information on RT drug resistance.

Cystatins in health and disease

Proteolytic enzymes have many physiological functions in plants, bacteria, viruses, protozoa and mammals. They play a role in processes such as food digestion, complement activation or blood coagulation. The action of proteolytic enzymes is biologically controlled by proteinase inhibitors and increasing attention is being paid to the physiological significance of these natural inhibitors in pathological processes. The reason for this growing interest is that uncontrolled proteolysis can lead to irreversible damage e.g. in chronic inflammation or tumor metastasis. This review focusses on the possible role of the cystatins, natural and specific inhibitors of the cysteine proteinases, in pathological processes.

Comparison of self-sustained sequence-replication reaction systems

The 3SR (self-sustained sequence-replication) reaction is a very efficient method for isothermal amplification of target DNA or RNA sequences in vitro. This method requires three enzymatic activities: reverse transcriptase, DNA-dependent RNA polymerase and Escherichia coli ribonuclease H. We have modified the original protocol by using human immunodeficiency virus (HIV)-1 reverse transcriptase instead of avian myeloblastosis virus (AMV) reverse transcriptase to allow amplification with T7 RNA polymerase but without E. coli ribonuclease H. Comparison of the incorporation kinetics between the conventional three-enzyme 3SR and our two-enzyme 3SR shows differences in the kinetic behaviour. Furthermore, by the new two-enzyme 3SR, the amplified RNA is obtained in a purer form compared with the experiments with three-enzyme 3SR. The aim of our research is to adapt 3SR as a useful tool for darwinian evolutionary experiments.

Mechanisms of retroviral mutation

Retroviruses, like other RNA viruses, mutate at very high rates (0.05-1 mutations per genome per replication cycle) and exist as complex genetically heterogeneous populations ('quasispecies') that are ever changing. De novo mutations are generated by inherently error-prone steps in the retroviral life cycle that introduce base substitutions, frame shifts, genetic rearrangements and hypermutations.

Isolation and characterization of TK-deficient mutants of African swine fever virus

African swine fever virus induces the synthesis of thymidine kinase (TK) in BHK TK-negative cells as an immediate early protein. The TK gene is not essential for growth of ASFV in cell culture and a stable viral strain deficient in TK has been isolated (E70NTKp). The genetic lesion of this ASFV TK- strain was identified by TK gene nucleotide sequencing, showing a nucleotide deletion leading to a -1 frameshift and a nonsense codon residue downstream of the deletion. The availability of this viable ASFV variant deficient in TK activity allows the insertion of foreign genes in the ASFV genome for genetic and biochemical studies.