Interplay between reverse transcription and host restriction

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Infectious agents have infected prokaryotes and eukaryotes throughout evolution. Indeed, there is co-evolution of organisms and their infectious agents, with development of protective responses in the hosts and adaptive countermeasures by the infectious agents. Infectious endemic retroviruses like murine leukemia virus (MLV) have existed in mice for millions of years and provide us with an outstanding model system to understand how mammalian hosts suppress virus replication and conversely, how viruses counteract this restriction. One system of viral restriction is conferred by the apolipoprotein B mRNA editing enzyme, catalytic peptide 3 (A3) family of proteins, which are packaged into retroviruses in virion-producing cells and after infection of target cells, either block reverse transcription or deaminate deoxycytidine residues in single-stranded DNA, resulting in uracils and G-to-A mutations in the viral genome. The products of retrovirus reverse transcription (ssRNA, ssDNA and dsDNA) are also sensed by host nucleic acid sensors. Sensor binding to viral nucleic acid leads to the production of anti-viral cytokines and chemokines, such as type I interferons, which “warns” surrounding cells to arm themselves against infection by producing proteins such as A3. These host anti-viral events are believed to occur largely in the cytoplasm, where A3 proteins and many host sensors are believed to function. Retroviruses enter cells when the viral and host membranes fuse and capsids are deposited in the cytoplasm. Reverse transcription initiates from within the capsid and capsid dissociation and reverse transcription are mutually dependent; because DNA is more rigid than RNA, without capsid dissociation, reverse transcription cannot proceed and conversely, the generation of DNA facilitates capsid dissociation. The reverse transcription complex not only consists of viral RNA, DNA and the viral proteins reverse transcriptase and integrase, but viral capsid and other proteins such as the MLV protein p12, which is needed for tethering of the proviral DNA to host chromatin to achieve integration. Recently, there has been much debate as to whether reverse transcription occurs solely in the cytoplasm or in the nucleus or both. Our lab pioneered the use of in vivo mouse models to study how A3 proteins restrict retrovirus infection and has used A3 and nucleic acid sensor knockout (KO) mice and genetically engineered animals that express human A3 proteins in these studies. Our data, based on our analysis of A3 KO mice and cells, suggest that the initial step occurs in the cytoplasm but that reverse transcription may also occur in the cytoplasm. With these mouse models, we have the tools to carry out in vitro, ex vivo and in vivo studies to determine how A3-mediated restriction and sensing of reverse transcripts are integrated with reverse transcription and nuclear entry for MLV and its natural host, the mouse. To accomplish this, we propose 3 aims, that will determine: I. Where in the cells APOBEC3 proteins block reverse transcription or deaminate viral DNA; II. What stage in reverse transcription and where in the cell the host base excision repair enzyme, UNG, removes uracil from APOBEC3G-deaminated viral DNA and the consequences of this for viral escape; III. Whether host sensing of viral nucleic acid takes place in the cytoplasm, nucleus or both compartments. Determination of when and where these events occur is critical to understanding how retroviruses, including HIV, evade host immunity and the identification of which steps are likely to be the best targets for interventional therapies at the early stages of infection.