Permuted tRNA genes in the nuclear and nucleomorph genomes of photosynthetic eukaryotes

Shinichiro Maruyama, Junichi Sugahara, Akio Kanai, Hisayoshi Nozaki

    Research output: Contribution to journalArticle

    27 Citations (Scopus)

    Abstract

    Transfer RNA (tRNA) is a central genetic element in the decoding of genome information for all of Earth's life forms. Nevertheless, there are a great number of missing tRNAs that have been left without examination, especially in microbial genomes. Two tRNA gene families remarkable in their structure and expression mechanism have been reported: split and permuted tRNAs. Split tRNAs in archaea are encoded on the genome as two or three fragmented genes and then processed into single tRNA molecules. Permuted tRNAs are organized with the 5′ and 3′ halves of the gene positioned in reverse on the genome and hitherto have been found only in one tiny red alga. Here we reveal a wide-ranging distribution of permuted tRNA genes in the genomes of photosynthetic eukaryotes. This includes in the smallest eukaryotic genome known to date, the nucleomorph genome of the chlorarachniophyte alga Bigelowiella natans. Comparison between cDNA and genomic DNA sequences of two nucleomorph-encoded tRNASer genes confirms that precursors are circularized and processed into mature tRNA molecules in vivo. In the tRNA Ser(AGA), adenine at the wobble position of the codon is likely modified to inosine to expand capacity of the codon recognition. We also show the presence of permuted tRNAs in the ultrasmall free-living green algae Ostreococcus and Micromonas, which are closely related to the B. natans nucleomorph. Conserved intron/leader sequence structures in the intron-containing and permuted tRNAs suggest the ancient origin of the splicing machinery in the common ancestor of eukaryotes and archaea. Meanwhile, a wide but patchy distribution of permuted tRNA genes in the photosynthetic eukaryotes implies that extant permuted tRNAs might have emerged multiple times. Taken together, our data demonstrate that permuted tRNA is an evolutionarily conserved and fundamental element in tiny eukaryotic genomes.

    Original languageEnglish
    Pages (from-to)1070-1076
    Number of pages7
    JournalMolecular biology and evolution
    Volume27
    Issue number5
    DOIs
    Publication statusPublished - 2010 May

    Keywords

    • Endosymbiosis
    • Green algae
    • Intron
    • Nucleomorph
    • Permuted tRNA
    • SPLITS

    ASJC Scopus subject areas

    • Ecology, Evolution, Behavior and Systematics
    • Molecular Biology
    • Genetics

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