DIRS-1 and the other tyrosine recombinase retrotransposons

Abstract

DIRS-1 is a retroelement from the slime mold Dictyostelium discoideum. Until recently only two related retrotransposons had been described: PAT from the nematode Panagrellus redivivus and Prt1 from the zygomycete fungus Phycomyces blakesleeanus. Analyses of the reverse transcriptase sequences encoded by these three elements suggested that they were closely related to each other and more distantly related to the Ty3/gypsy Long Terminal Repeat (LTR) retroelements. They have several unusual structural features that distinguish them from typical LTR elements. For instance, they each encode a tyrosine recombinase (YR), but not a DDE-type integrase or an aspartic protease. Although the DIRS-1-related elements are bordered by terminal repeats these differ from typical LTRs in a number of ways. In DIRS-1, for example, the terminal repeats are inverted (complementary), non-identical in sequence, and the outer edges of the terminal sequences are repeated (adjacent to each other) in the internal region. PAT has so-called “split” direct repeats in which the unrelated terminal sequences appear as direct repeats adjacent to each other in the internal region. The only repetition displayed by Prt1 is the presence of short inverted terminal repeats, but the sequenced copy of this element is believed to be a truncated version of an element with a structure resembling DIRS-1. The unusual structure of the terminal repeats of the DIRS1-like elements appears to be related to their replication via free circular intermediates. Site-specific recombination is believed to integrate the circle without creating duplications of the target sites. In recognition of these important distinctions it is proposed that the retrotransposons that encode tyrosine recombinases be called the tyrosine recombinase (or YR) retrotransposons. Recently a large number of additional YR retrotransposons have been described, including elements from fungi (zygomycetes and basidiomycetes), plants (green algae) and a wide range of animals including nematodes, insects, sea urchins, fish and amphibia, while remnants of elements related to DIRS-1 occur in the human genome. The complete set of YR retrotransposons can be divided into two major groups, the DIRS elements and the Ngaro elements, the two groups forming distinct clades on phylogenetic trees based on alignments of RT/RH and recombinase sequences, and also having some structural distinctions. A third group of transposable elements, which we call Cryptons, also carry tyrosine recombinases. These elements do not encode a reverse transcriptase and so are believed to be DNA transposons not retrotransposons. They have been detected in several pathogenic fungi, including the basidiomycete Cryptococcus neoformans, and the ascomycetes Coccidioides posadasii and Histoplasma capsulatum. Sequence comparisons suggest that the Crypton YRs are related to those of the YR retrotransposons. We suggest that the YR retrotransposons arose from the combination of a Crypton-like YR DNA transposon and the RT/RH encoding sequence of a ...

Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification

“…Also in this clade are MTase domains that are embedded in the polyprotein of DIRS1‐type retrotransposons (Figs. 1C and 3) 82, and which were probably derived from the cellular PCIF1. These elements are highly mobile across species, and are seen in diverse eukaryotes (Fig.…”

Tyrosine Recombinase Retrotransposons and Transposons

“…The recombination of a circular DNA into the genome using a sitespecific recombinase would not generate a target site duplication. This model of replication, based on the work of Cappello et al (5), has already been described in detail (11). DIRS1 related elements in fish: DrDirs1, TnDirs1…”

“…The phylogenetic relationships among a large number of retroelements were examined using an alignment of their RT and RH encoding ORFs (8,11). The analysis indicates that the major groups of elements Ty1/copia, Ty3/gypsy, BEL, VIPER, Ngaro, PAT-like and DIRS-like elements were all resolved into monophyletic groups with high levels of bootstrap support (8,11). With respect to the tyrosine recombinase retrotransposons, the most important aspect of these RT/RH phylogenetic trees was that they clearly distinguished the Ngaro, DIRS and PAT groups.…”

Transposable elements as drivers of genomic and biological diversity in vertebrates

“…Another open reading frame called gag is present upstream of pol. Gag frequently overlaps partially with pol and encodes a structural (Poulter & Goodwin 2005). These elements have more complex repeats and encode, beside an RT/RnaseH protein, a tyrosine transposase instead of the integrase found in other LTR retrotransposons.…”