[Frontiers in Bioscience 8, d117-134, January 1, 2003]

RETROVIRAL MUTATION RATES AND REVERSE TRANSCRIPTASE FIDELITY

Evguenia S. Svarovskaia 1, Sara R. Cheslock 1,2, Wen-Hui Zhang 1, Wei-Shau Hu 1, and Vinay K. Pathak 1

1 HIV Drug Resistance Program, CCR, NCI-Frederick, Frederick, Maryland 21702, 2 Department of Microbiology and Immunology, West Virginia University, Morgantown, WV 26506

TABLE OF CONTENTS

1. Abstract
2. Importance of retroviral genetic variation
3. Historic developments in understanding retroviral genetic variation and RT fidelity
4. Factors that influence retroviral mutation rates
4.1. Reverse transcription
4.2. Other viral proteins
4.3. Nucleotide pools, DNA repair, and mammalian DNA polymerases
4.4. RNA transcription
4.5. RNA modification
4.6. Antiviral nucleoside analogs
5. In vivo fidelity assays and mutation rates
5.1. In vivo fidelity assays
5.2. In vivo mutation rates
6. In vitro fidelity assays and mutation rates
6.1. In vitro fidelity assays
6.2. In vitro mutation rates
7. Spectrum of mutations and their relative frequencies
8. Structural determinants of RT that influence fidelity
8.1. Structure of RT
8.2. Structural determinants of in vivo fidelity
8.3. Structural determinants of in vitro fidelity
8.4. The role of MLV RNase H primer grip and template-primer structure in fidelity
9. Future directions
10. Acknowledgements
11. References

1. ABSTRACT

Genetic variation in retroviral populations provides a mechanism for retroviruses to escape host immune responses and develop resistance to all known antiretroviral drugs. Retroviruses, like all RNA viruses, exhibit a high mutation rate. Polymerization errors during DNA synthesis by reverse transcriptase, which lacks a proofreading activity, is a major mechanism for generating genetic variation within retroviral populations. In this review, we summarize our current understanding of the processes that contribute to the generation of mutations in retroviruses. An overview of in vivo and in vitro studies of retroviral mutation rates determined by various fidelity assays is provided. Extensive mutational analyses of RTs are beginning to elucidate the relationship between structural determinants of RTs and fidelity of DNA synthesis. Recently, it was observed that the Y586F mutation in MLV RT results in a dramatic increase in the mutation rate in the vicinity of adenine-thymie tracts (AAAA, TTTT, and AATT), which are associated with bends in DNA. These results indicate that the template-primer duplex is a component of the polymerase active site and its structure can influence nucleotide selectivity and the mutation rate. Additionally, the results also suggest that the Y586 residue and the RNase H primer grip are structural determinants of RT that have evolved to attenuate the effects of unusual conformations of the template-primer duplex, such as bends in DNA, on fidelity of DNA synthesis.