Identification of highly-disrupted tRNA genes in nuclear genome of the red alga, Cyanidioschyzon merolae 10D

Akiko Soma; Junichi Sugahara; Akinori Onodera; Nozomu Yachie; Akio Kanai; Satoru Watanabe; Hirofumi Yoshikawa; Mio Ohnuma; Haruko Kuroiwa; Tsuneyoshi Kuroiwa; Yasuhiko Sekine

doi:10.1038/srep02321

Identification of highly-disrupted tRNA genes in nuclear genome of the red alga, Cyanidioschyzon merolae 10D

Akiko Soma, Junichi Sugahara, Akinori Onodera, Nozomu Yachie, Akio Kanai, Satoru Watanabe, Hirofumi Yoshikawa, Mio Ohnuma, Haruko Kuroiwa, Tsuneyoshi Kuroiwa, Yasuhiko Sekine

Graduate School of Media and Governance

Research output: Contribution to journal › Article › peer-review

12 Citations (Scopus)

Abstract

The limited locations of tRNA introns are crucial for eukaryal tRNA-splicing endonuclease recognition. However, our analysis of the nuclear genome of an early-diverged red alga, Cyanidioschyzon merolae, demonstrated the first evidence of nuclear-encoded tRNA genes that contain ectopic and/or multiple introns. Some genes exhibited both intronic and permuted structures in which the 39-half of the tRNA coding sequence lies upstream of the 59-half, and an intron is inserted into either half. These highly disrupted tRNA genes, which account for 63% of all nuclear tRNA genes, are expressed via the orderly and sequential processing of bulge-helix-bulge (BHB) motifs at intron-exon junctions and termini of permuted tRNA precursors, probably by a C. merolae tRNA-splicing endonuclease with an unidentified subunit architecture. The results revealed a considerable diversity in eukaryal tRNA intron properties and endonuclease architectures, which will help to elucidate the acquisition mechanism of the BHB-mediated disrupted tRNA genes.

Original language	English
Article number	2321
Journal	Scientific reports
Volume	3
DOIs	https://doi.org/10.1038/srep02321
Publication status	Published - 2013

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@article{0516c4309cde401ca7ad9844a8f9085b,

title = "Identification of highly-disrupted tRNA genes in nuclear genome of the red alga, Cyanidioschyzon merolae 10D",

abstract = "The limited locations of tRNA introns are crucial for eukaryal tRNA-splicing endonuclease recognition. However, our analysis of the nuclear genome of an early-diverged red alga, Cyanidioschyzon merolae, demonstrated the first evidence of nuclear-encoded tRNA genes that contain ectopic and/or multiple introns. Some genes exhibited both intronic and permuted structures in which the 39-half of the tRNA coding sequence lies upstream of the 59-half, and an intron is inserted into either half. These highly disrupted tRNA genes, which account for 63% of all nuclear tRNA genes, are expressed via the orderly and sequential processing of bulge-helix-bulge (BHB) motifs at intron-exon junctions and termini of permuted tRNA precursors, probably by a C. merolae tRNA-splicing endonuclease with an unidentified subunit architecture. The results revealed a considerable diversity in eukaryal tRNA intron properties and endonuclease architectures, which will help to elucidate the acquisition mechanism of the BHB-mediated disrupted tRNA genes.",

author = "Akiko Soma and Junichi Sugahara and Akinori Onodera and Nozomu Yachie and Akio Kanai and Satoru Watanabe and Hirofumi Yoshikawa and Mio Ohnuma and Haruko Kuroiwa and Tsuneyoshi Kuroiwa and Yasuhiko Sekine",

note = "Funding Information: We thank A. Muto and S. Maruyama for valuable discussions; K. Tanaka, O. Misumi, M. Matsuzaki, Y. Yoshida, N. Sato, T. Fujiwara and M. Monma for technical advice; and R. Saito, Y. Ohashi and K. Kurokawa for advice on the computational analysis. This work was supported by a grant from the Nakajima Foundation (to A.S.), a Grant-in-Aid for Young Scientists B (23770211 to A.S.), the Frontier project {\textquoteleft}Adaptation and Evolution of Extremophiles{\textquoteright} (to Y.S.) and the Strategic Research Foundation Grant-aided Project for Private Universities (S1201003 to Y.S.) from the Ministry of Education, Culture, Sports, Science, and Technology, Japan.",

year = "2013",

doi = "10.1038/srep02321",

language = "English",

volume = "3",

journal = "Scientific Reports",

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T1 - Identification of highly-disrupted tRNA genes in nuclear genome of the red alga, Cyanidioschyzon merolae 10D

AU - Soma, Akiko

AU - Sugahara, Junichi

AU - Onodera, Akinori

AU - Yachie, Nozomu

AU - Kanai, Akio

AU - Watanabe, Satoru

AU - Yoshikawa, Hirofumi

AU - Ohnuma, Mio

AU - Kuroiwa, Haruko

AU - Kuroiwa, Tsuneyoshi

AU - Sekine, Yasuhiko

N1 - Funding Information: We thank A. Muto and S. Maruyama for valuable discussions; K. Tanaka, O. Misumi, M. Matsuzaki, Y. Yoshida, N. Sato, T. Fujiwara and M. Monma for technical advice; and R. Saito, Y. Ohashi and K. Kurokawa for advice on the computational analysis. This work was supported by a grant from the Nakajima Foundation (to A.S.), a Grant-in-Aid for Young Scientists B (23770211 to A.S.), the Frontier project ‘Adaptation and Evolution of Extremophiles’ (to Y.S.) and the Strategic Research Foundation Grant-aided Project for Private Universities (S1201003 to Y.S.) from the Ministry of Education, Culture, Sports, Science, and Technology, Japan.

PY - 2013

Y1 - 2013

N2 - The limited locations of tRNA introns are crucial for eukaryal tRNA-splicing endonuclease recognition. However, our analysis of the nuclear genome of an early-diverged red alga, Cyanidioschyzon merolae, demonstrated the first evidence of nuclear-encoded tRNA genes that contain ectopic and/or multiple introns. Some genes exhibited both intronic and permuted structures in which the 39-half of the tRNA coding sequence lies upstream of the 59-half, and an intron is inserted into either half. These highly disrupted tRNA genes, which account for 63% of all nuclear tRNA genes, are expressed via the orderly and sequential processing of bulge-helix-bulge (BHB) motifs at intron-exon junctions and termini of permuted tRNA precursors, probably by a C. merolae tRNA-splicing endonuclease with an unidentified subunit architecture. The results revealed a considerable diversity in eukaryal tRNA intron properties and endonuclease architectures, which will help to elucidate the acquisition mechanism of the BHB-mediated disrupted tRNA genes.

AB - The limited locations of tRNA introns are crucial for eukaryal tRNA-splicing endonuclease recognition. However, our analysis of the nuclear genome of an early-diverged red alga, Cyanidioschyzon merolae, demonstrated the first evidence of nuclear-encoded tRNA genes that contain ectopic and/or multiple introns. Some genes exhibited both intronic and permuted structures in which the 39-half of the tRNA coding sequence lies upstream of the 59-half, and an intron is inserted into either half. These highly disrupted tRNA genes, which account for 63% of all nuclear tRNA genes, are expressed via the orderly and sequential processing of bulge-helix-bulge (BHB) motifs at intron-exon junctions and termini of permuted tRNA precursors, probably by a C. merolae tRNA-splicing endonuclease with an unidentified subunit architecture. The results revealed a considerable diversity in eukaryal tRNA intron properties and endonuclease architectures, which will help to elucidate the acquisition mechanism of the BHB-mediated disrupted tRNA genes.

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JF - Scientific Reports

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Identification of highly-disrupted tRNA genes in nuclear genome of the red alga, Cyanidioschyzon merolae 10D

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