title: An extraordinary retrotransposon family encoding dual endonucleases.
abstract: Retrotransposons commonly encode a reverse transcriptase (RT), but other functional domains are variable. The acquisition of new domains is the dominant evolutionary force that brings structural variety to retrotransposons. Non-long-terminal-repeat (non-LTR) retrotransposons are classified into two groups by their structure. Early branched non-LTR retrotransposons encode a restriction-like endonuclease (RLE), and recently branched non-LTR retrotransposons encode an apurinic/apyrimidinic endonuclease-like endonuclease (APE). In this study, we report a novel non-LTR retrotransposon family Dualen, identified from the Chlamydomonas reinhardtii genome. Dualen encodes two endonucleases, RLE and APE, with RT, ribonuclease H, and cysteine protease. Phylogenetic analyses of the RT domains revealed that Dualen is positioned at the midpoint between the early-branched and the recently branched groups. In the APE tree, Dualen was branched earlier than the I group and the Jockey group. The ribonuclease H domains among the Dualen family and other non-LTR retrotransposons are monophyletic. Phylogenies of three domains revealed the monophyly of the Dualen family members. The domain structure and the phylogeny of each domain imply that Dualen is a retrotransposon conserving the domain structure just after the acquisition of APE. From these observations, we discuss the evolution of domain structure of non-LTR retrotransposons.
authors.affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan.
authors.forename: Kenji K
authors.initials: KK
authors.lastname: Kojima
authors.forename: Haruhiko
authors.initials: H
authors.lastname: Fujiwara
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D020134:Catalytic Domain; D016825:Chlamydomonas reinhardtii / Q000235:genetics; D017124:Conserved Sequence; D003546:Cysteine Endopeptidases / Q000737:chemistry; D004720:Endonucleases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012326:RNA Splicing; D016372:RNA, Antisense / Q000235:genetics; D018626:Retroelements / Q000235:genetics*; D016914:Ribonuclease H / Q000235:genetics / Q000378:metabolism
chemical_list: D016372:RNA, Antisense; D018626:Retroelements; D004720:Endonucleases; D016914:Ribonuclease H; D003546:Cysteine Endopeptidases