title: A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity.
abstract: tRNA splicing endonucleases, essential enzymes found in Archaea and Eukaryotes, are involved in the processing of pre-tRNA molecules. In Archaea, three types of splicing endonuclease [homotetrameric: α(4), homodimeric: α(2), and heterotetrameric: (αβ)(2)] have been identified, each representing different substrate specificity during the tRNA intron cleavage. Here, we discovered a fourth type of archaeal tRNA splicing endonuclease (ε(2)) in the genome of the acidophilic archaeon Candidatus Micrarchaeum acidiphilum, referred to as ARMAN-2 and its closely related species, ARMAN-1. The enzyme consists of two duplicated catalytic units and one structural unit encoded on a single gene, representing a novel three-unit architecture. Homodimeric formation was confirmed by cross-linking assay, and site-directed mutagenesis determined that the conserved L10-pocket interaction between catalytic and structural unit is necessary for the assembly. A tRNA splicing assay reveal that ε(2) endonuclease cleaves both canonical and non-canonical bulge-helix-bulge motifs, similar to that of (αβ)(2) endonuclease. Unlike other ARMAN and Euryarchaeota, tRNAs found in ARMAN-2 are highly disrupted by introns at various positions, which again resemble the properties of archaeal species with (αβ)(2) endonuclease. Thus, the discovery of ε(2) endonuclease in an archaeon deeply branched within Euryarchaeota represents a new example of the coevolution of tRNA and their processing enzymes.
authors: Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.
authors: Kosuke
authors: K
authors: Fujishima
authors: Junichi
authors: J
authors: Sugahara
authors: Christopher S
authors: CS
authors: Miller
authors: Brett J
authors: BJ
authors: Baker
authors: Massimo
authors: M
authors: Di Giulio
authors: Kanako
authors: K
authors: Takesue
authors: Asako
authors: A
authors: Sato
authors: Masaru
authors: M
authors: Tomita
authors: Jillian F
authors: JF
authors: Banfield
authors: Akio
authors: A
authors: Kanai
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D019281:Dimerization; D004722:Endoribonucleases / Q000737:chemistry* / Q000145:classification / Q000378:metabolism*; D019605:Euryarchaeota / Q000201:enzymology* / Q000235:genetics; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs; D010802:Phylogeny; D021122:Protein Subunits / Q000378:metabolism; D012326:RNA Splicing; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D021122:Protein Subunits; D012343:RNA, Transfer; D004722:Endoribonucleases; C051012:splicing endonuclease