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
2013 Scientific Reports  
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
more » ... ighly 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. C yanidioschyzon merolae 10D is an ultrasmall unicellular red alga that inhabits an extreme environment (pH 1-3, 40-50uC), and represents one of the most ancestral forms of eukaryotes 1-3 . A primary search of the complete 16.5 Mbp nuclear genome sequence predicted only 30 tRNA genes, which are insufficient to decode 61 codons 2 . This paucity of tRNA genes was partly solved by our discovery of a distinctive type of disrupted tRNA gene; we identified 11 circularly permuted tRNA genes, in which the 39-half of the tRNA coding sequence lies upstream of the 59-half in the genome 4 . Biochemical analyses defined a processing pathway in which the termini of the tRNA precursor (pre-tRNAs) are ligated to form a characteristic circular RNA intermediate, which is then processed at the acceptor stem to generate the functional termini 4 . Notably, the sequences adjacent to the termini in these pre-tRNAs potentially form a bulge-helix-bulge (BHB) motif, which was originally found around the intron-exon junctions of nuclear and archaeal tRNAs 5 . To date, permuted tRNAs have only been found in some unicellular algae and archaea 6,7 . These observations suggest that BHB motifs, and the tRNA intron splicing system by which they are processed, must have been a prerequisite for the development of such disrupted tRNA genes in early-rooted eukaryotes and archaea. Here, we report the identification of an alternative type of BHB-mediated disrupted tRNA gene that harbors atypical introns. Introns found in nuclear and archaeal tRNAs are cleaved by the proteinaceous tRNA-splicing endonuclease 8-11 . Nuclear tRNA introns are generally short, comprise a relaxed BHB motif, and are located exclusively between positions 37 and 38 (37/38), which is 39 adjacent to the anticodon (the canonical position) 5,12 . This limited location of the intron is considered crucial for the precise recognition of pre-tRNA by the eukaryal tRNA-splicing endonucleases [8] [9] [10] [11] [13] [14] [15] [16] [17] [18] . However, we found that a number of C. merolae nuclear-encoded tRNA genes contain single or multiple ectopic introns, which has not been reported in eukaryotes. Some genes contained both intronic and permuted gene structures. Further analysis revealed that the BHB motifs in pre-tRNAs are processed in an order that correlates with the theoretical free energy and the position of each motif in the cloverleaf structure. It also indicated that the C. merolae tRNA-splicing endonuclease may show a non-canonical subunit composition. Our findings provide a new insight into the tRNA processing system in eukaryotes and a OPEN SUBJECT AREAS: RNA SPLICING SMALL RNAS GENE EXPRESSION TRNAS
doi:10.1038/srep02321 pmid:23900518 pmcid:PMC3728597 fatcat:kjzbkpozczd27or3qmhbjocove