Accessory replication proteins and the accuracy of reverse transcription: implications for retroviral genetic diversity

LOUIS M. MANSKY mansky@creighton.edu DEPARTMIaN'r OF MEDICAL MICROBIOLOGY AND IMMUNOLOGY, CREIGHTON UNWERSITY SCHOOL OF MEDICINE, 2500 CALIEOI~'aA PLAZA, OMAHA, NE 68178-0213, USA. Retrovirus populations are notorious for their high degree of genetic vari- ability. This variability is exemplified by the rapid appearance of antibody- and drug-resistant human immuno- deficiency virus type 1 (HIV-1) strainsL However, how HW-1 vari- ation relates to disease progression is an ongoing debate x. It has been pro- posed that the high rate of retrovirus variation is the result of the unique mechanism by which these viruses replicate 3. Exciting new results now indicate that retroviml proteins can influence the accuracy of virus repli- cation. It is likely that these influences have an important contribution to variation in retrovirus populations. Variation in retrovirus populations has been observed since their dis- covery, but has become of increasing importance because of the evolu- tionary potential of HIV-1 and its impact on drug therapy and vaccine development. Recent evidence indi- cates that HW-1, like most RNA viruses, forms complex 'quasispecies' populations that can evolve very rapidly due to their high mutation rate. However, not all retroviruses exhibit the high genetic diversity of HW-1, suggesting that the variation and evolution of retrovirus popu- lations can be modeled by applying the theories of punctuated equilibria and the adaptive landscapeL4. Retroviruf~.s contain two copies of viral RNA as their genome in virus particles. Upon virus entry into a per- missible host cell, the viral RNA is converted to a double-stranded DNA by the vitally encoded enzyme pres- ent in virus particles, reverse tran- scriptase. This conversion process, called reverse transcription, involves two strand transfers. The first involves transfer of a minus-strand DNA prod- uct primed from a tRNA present in the virus pamcle to the 3' end of the viral RNA. The second transfer in- volves a plus-strand DNA primed from a nick introduced into the poly- purine tract of the viral RNA to the 3' end of the newly synthesized minus- strand DNA. It is thought that instead of steady processive polymerization, reverse transcriptase frequently pauses and enters a metastable state 3. These pause sites are typically sequences and/or structures where continued polymerization of the primer grow- ing point is difficult. When reverse tmnscriptase leaves this metastable state, polymerization of the growing primer continues either at the next base or transfers to another base at a different location on the same tem- plate or another template. This trans- fer can be the result of reverse tran- scriptase moving or another portion of the template displacing the tem- plate at the site of polymerization. TIG APRIL 1997 VOL. 13 NO. 4 I'll; SO t 68-,)525,)')01062.7 The polymerization of reverse tmn- scriptase at locations other than the next base can give rise to base-pair substitution, fmmeshifi, deletion, and deletion with insertion mutations, as well as homologous and nonhomolo- gons recombination. In vitro