A widespread class of reverse transcriptase-related cellular genes

Abstract

Reverse transcriptases (RTs) polymerize DNA on RNA templates. They fall into several structurally related but distinct classes and form an assemblage of RT-like enzymes that, in addition to RTs, also includes certain viral RNA-dependent RNA polymerases (RdRP) synthesizing RNA on RNA templates. It is generally believed that most RT-like enzymes originate from retrotransposons or viruses and have no specific function in the host cell, with telomerases being the only notable exception. Here we report on the discovery and properties of a unique class of RT-related cellular genes collectively named rvt. We present evidence that rvts are not components of retrotransposons or viruses, but single-copy genes with a characteristic domain structure that may contain introns in evolutionarily conserved positions, occur in syntenic regions, and evolve under purifying selection. These genes can be found in all major taxonomic groups including protists, fungi, animals, plants, and even bacteria, although they exhibit patchy phylogenetic distribution in each kingdom. We also show that the RVT protein purified from one of its natural hosts, Neurospora crassa, exists in a multimeric form and has the ability to polymerize NTPs as well as dNTPs in vitro, with a strong preference for NTPs, using Mn 2+ as a cofactor. The existence of a previously unknown class of single-copy RT-related genes calls for reevaluation of the current views on evolution and functional roles of RNA-dependent polymerases in living cells.D NA-dependent polymerases are essential for cellular function, as they mediate the flow of genetic information from DNA to RNA to proteins (1). In contrast, RNA-dependent polymerases have long been associated with replication of selfish and parasitic genetic elements, such as viruses or transposons. Although the discovery of reverse transcriptase (RT) challenged the concept of unidirectionality of the flow of genetic information, this reverse direction has been reserved for retroviruses, pararetroviruses (hepadna-and caulimoviruses), and other RT-containing multicopy entities such as non-LTR and LTR retrotransposons, group II introns, retrons, and retroplasmids, as well as occasional retro (pseudo)genes (2-4). Similarly, viral RNA-dependent RNA polymerases (RdRPs), enzymes structurally related to RTs, serve to replicate the genomes of viruses that use RNA as genetic material (5). These and certain other polymerases are unified by the architecture known as "right hand," composed of the three subdomains called fingers, palm, and thumb (6). Like all polymerases, they use two-metal-ion catalysis for phosphoryl transfer reactions resulting in nucleotide addition.In 1997, this diverse superfamily of enzymes was joined by the telomerase reverse transcriptase (TERT), a specialized RT that maintains the ends of eukaryotic linear chromosomes by addition of short G-rich repeated DNA sequences that are copied multiple times via reverse transcription of a specific region of the associated RNA template constituting part of the holoenzyme (...

Forks in the tracks: Group II introns, spliceosomes, telomeres and beyond

“…13 The RT of the lactococcal LtrA bears close similarity to Prp8, most strikingly in the thumb domain. In addition to the structural parallel, the interactions of these 2 proteins with RNA are stunningly similar (Fig.…”

“…11,12 RTs also occur in some cellular proteins like telomerase, which performs DNA synthesis at chromosome ends. [11][12][13] Additionally, their similarity to a key spliceosomal protein Prp8, which, despite its lack of RT activity, provided the first suggestion of protein relatedness between group II introns and spliceosomes.…”

Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution

“…Although group II intron RTs and the R2Bm RT lack an RNase H domain, RNase H domains are known to be acquired sporadically in different non-LTR-retrotransposon lineages (135,191). RVT RTs, another potential candidate for an ancestor of Prp8 (181), lack En and integrase domains and are further distinguished from group II intron and non-LTR-retrotransposon RTs by a large acidic insertion within RT-2a and by conserved N-and C-terminal domains that are not found in other proteins (212). Conserved sequence blocks in the RT domain are numbered, and the sequence motif containing two of the conserved aspartic acid residues at the RT active site is shown below for each protein.…”

“…However, bacteria contain diverse retroelements and RTs (see above), as well as single-copy rvt genes. RVTs are of unknown function and found sporadically in all eukaryotic kingdoms (195,196,212,213) (Fig. 6).…”

“…6). Consistent with their single-copy nature, they are not associated with known endonucleases or integrases (212). These considerations leave one pondering whether cellular RT genes originated from retrotransposons or vice versa.…”