Journal
NUCLEIC ACIDS RESEARCH
Volume 39, Issue 22, Pages 9695-9704Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkr692
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Funding
- Ministry of Education, Culture, Sports, Science and Technology of Japan [22370066]
- Institute for Fermentation, Osaka, Japan
- Yamagata Prefectural Government and Tsuruoka City in Japan
- US Department of Energy, Office of Biological and Environmental Research [DE-SC0004665]
- U.S. Department of Energy (DOE) [DE-SC0004665] Funding Source: U.S. Department of Energy (DOE)
- Grants-in-Aid for Scientific Research [22370066] Funding Source: KAKEN
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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: alpha(4), homodimeric: alpha(2), and heterotetrameric: (alpha beta)(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 (epsilon(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 epsilon(2) endonuclease cleaves both canonical and non-canonical bulge-helix-bulge motifs, similar to that of (alpha beta)(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 (alpha beta)(2) endonuclease. Thus, the discovery of epsilon(2) endonuclease in an archaeon deeply branched within Euryarchaeota represents a new example of the coevolution of tRNA and their processing enzymes.
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