The last two groups of viruses of the Baltimore classification system are reverse transcribing (RT) viruses (Groups VI and VII). These viruses are unique in that they use a reverse transcriptase in their life cycle. Reverse transcriptases are RNA-dependent DNA polymerases (RdDP), meaning they make DNA copies from RNA templates. In comparison with other polymerases (DdDPs, DdRPs, and RdRPs) discussed in the previous blog, RdDPs are low fidelity enzymes because they have no 3’ to 5’ exonuclease activity, and they need specific primers to initiate DNA synthesis. All RT viruses code their RdDPs in the genomes and package the enzymes in the virions.
Group VI contains single-stranded RNA viruses with a DNA intermediate in their life cycle. Viruses in this group are also called retroviruses, and the most famous example is the human immunodeficiency virus (HIV), the etiologic agent of acquired immunodeficiency syndrome (AIDS). Retroviruses are spherical enveloped particles with a diameter of ~ 100 nm. Though the virus has a linear (+) ss RNA genome, two identical copies of the (+) RNA strands are packaged into the viral particle. The two strands run in a parallel direction and are held together by base-pairing at several regions. In addition, a specific cellular transfer RNA (tRNA) is bound near the 5’ end of each RNA strand. This tRNA serves as the primer for the initiation of reverse transcription. Different retroviruses use different cellular tRNAs.
The life cycle of retroviruses can be divided into early and late stages. The virus finds its target cell during the early stage through specific binding between the viral surface protein and the cellular receptor. It then enters the cell by fusing the viral envelope with the cytoplasmic membrane. Once inside the cell, the viral RNA genome is converted into linear ds DNA (called proviral DNA) by reverse transcriptase. The proviral DNA is then transported into the nucleus and integrated into the host chromosome at a random site. The integration is catalyzed by a viral encoded integrase, packaged in the virion and delivered to the infected cell with the viral genome. In the late stage, the proviral DNA is transcribed by the host DdRP to generate more full-length RNA genomes or mRNAs for translation. The RNAs are released into the cytoplasm, where viral proteins are synthesized, and new viral particles are assembled and then extruded from the infected cell.
Group VII viruses are double-stranded DNA viruses with an RNA intermediate in their life cycle. However, the genome is not a complete double-strand. It is partial double-stranded with a single-stranded region. Upon infection, the viral genome is released in the cytoplasm and then transported into the nucleus, where it is converted into covalently closed circular (ccc) DNA, just like a plasmid DNA. The ccc DNA then serves as the template for transcription by host DdRP to generate viral mRNAs and one pregenome RNA. These RNAs are sent back to the cytoplasm. mRNAs are used as templates for viral protein synthesis. Next, the pregenome RNA with a reverse transcriptase bound at its 5’ end is packaged into nucleocapsids, where the reverse transcriptase serves as its own primer to initiate viral DNA synthesis. After the viral genome is reproduced, the new viral particle is formed by budding into the lumen of the endoplasmic reticulum and Golgi membrane and then released upon fusion with the plasma membrane. It is worth mentioning that the ccc DNA is not replicated in the nucleus by the host DdDP. Genomes of all new virions are made from the pregenome RNA by the viral reverse transcriptase. This distinctive life cycle broadened our understanding of reverse transcription. A well-studied example of this group is the hepatitis B virus (HBV) that can cause chronic or acute hepatitis, cirrhosis, and liver cancer.
In summary, Group VI and VII viruses all use a distinctive viral-encoded enzyme, reverse transcriptase (RdDP), in their lifecycle. There is no doubt that reverse transcriptase is a critical antiviral target. But on the other hand, the mechanisms of genome replication of the two groups are quite dissimilar (see the comparison in the table below).