19 Evolutionary History of Reverse Transcriptase

Abstract

Historically, the term reverse transcriptase (RT) has been used to designate the protein cleavage product of the retroviral gag-pol-encoded polyprotein with two enzymatic activities: One domain provides the RNA-directed and DNA-directed polymerization functions, whereas the other domain confers ribonuclease H (RNase H) activity. Currently, the term RT refers to the domain of the retroviral protein containing polymerase activity, and the term RNase H denotes the domain with RNase H activity. For simplicity, I use the current usage of RT and RNase H as domains of the RNA-directed DNA polymerase of retroviruses throughout this chapter.

Genetic elements with amino acid sequence identity to the conserved motifs of the retroviral RT domain are considered to be members of the retroid family (Fuetterer and Hohn 1987). This family is composed of retroviruses, two different classes of DNA viruses, two distinct types of retrotransposons, retroposons, group II introns and plasmids of cellular organelles, an orphan group, the retrons of bacteria, and the telomere elongation protein (EST1) of yeast (Fig. 1). The retroid family subgroups are described briefly here to provide the necessary context for the discussion of the evolution of the RT and RNase H domains. A more detailed description of many of the family members can be found in other chapters in this volume.

Retroviruses
The retroviral genome generally encodes structural proteins: a matrix protein (MA), a capsid protein (CA) that forms an icosahedron-like shell, a ribonuclear protein (NC) that associates with the viral RNA, and an envelope protein that inserts into the...