Prokaryotic Reverse Transcriptases

The reverse transcription of the genetic code of an RNA molecule back into a complementary DNA copy (cDNA) is usually accomplished by a specially dedicated RNA-dependent DNA polymerase called a reverse transcriptase (RT). Reverse transcription is presumed to have been a central event in the transition from the theorized ancient RNA world of life, in which RNA molecules served as both the source of genetic information, as well as, catalytic functions for cellular life, to the present day DNA-RNA-protein world. Even today reverse transcription continues to occur in most organisms from human cells to bacteria. For example, a wide assortment of genetic elements found in plant, animal, and microbial cells use reverse transcription for at least part of their replication or mobility. These include RNA viruses, DNA viruses, transposons, introns, and mitochondrial plasmids (Eickbush, 1994; Eickbush and Malik, 2002). More astonishing than the wide variety of retroelements that encode a RT is the colossal number of repetitive retrosequences, such as the Alu sequences, that have been generated by these elements in many eukaryotic genomes. These retrosequences are DNAs that usually do not code for RT but have clearly been produced by reverse transcription of an RNA molecule (Kazazian, 2004). In addition to the production of these parasitic DNAs, reverse transcription also serves a vital function for most eukaryotic organisms. Here the essential enzyme telomerase, which functions to maintain the telomere ends of chromosomes, is a type of RT (Lue, 2004). Most RTs are placed in two very broad categories based on the phylogenetic analysis of their amino acid sequence and the type of retroelement that codes for these polymerases. The first group is found in eukaryotic cells and is usually called LTR-containing retroelements because their DNA is flanked by long terminal repeat sequences. These elements include retroviruses and the virus-like retrotransposons called Ty in yeast cells. The second group is called non-LTR retroelements because they are not flanked by long terminal repeats and are a very diverse collection of elements found in both eukaryotic and prokaryotic organisms. These include the mobile group II introns, the L1 retrotransposons, and the various retroelements found in bacteria. Telomerase is phylogenetically related to the RTs from this group and is thus also included in this second category (Eickbush and Malik, 2002). Among the best characterized RTs are the polymerases from retroviruses and include the detailed crystal structure of the RT from the HIV-1 virus (Steitz, 1999). The focus of this chapter is the recently discovered RTs found in bacteria and the interesting genetic elements that encode them. These prokaryotic RTs are considered to be the ancestors of all retroelements found in eukaryotic genomes based on phylogenetic comparisons (Toor et al., 2001). In addition, the bacterial RTs are a very diverse group of proteins with a number of novel properties. Thus, these bacterial RTs represent an emerging new resource for many potential nucleic acid based technologies like RT-PCR. Prokaryotic RTs generally fall into one of three different types depending on the type of retroelement DNA that codes for these proteins. These groups or types are also in agreement with phylogenetic groupings for RTs determined by comparing their amino acid sequences. The three types of retroelements are (1) the group II introns found in both eubacterial and archaeal genomes, (2) retrons, which are also found in eubacteria and some archaea, and (3) the diversity generating retroelements that have thus far been found in the eubacteria