Characterization of mitochondrial mRNAs in codfish reveals unique features compared to mammals

• Published in: Current genetics 2011-06, Vol.57 (3), p.213-222
• Main Authors: Coucheron, Dag H., Nymark, Marianne, Breines, Ragna, Karlsen, Bård Ove, Andreassen, Morten, Jørgensen, Tor Erik, Moum, Truls, Johansen, Steinar D.
• Format: Article
• Language: English
• Subjects: 3' Untranslated Regions - genetics; 5' Untranslated Regions - genetics; Animals; Antisense Elements (Genetics) - chemistry; Antisense Elements (Genetics) - metabolism; Basale biofag: 470; Base Sequence; Basic biosciences: 470; Biochemistry; Biomedical and Life Sciences; Cell Biology; Codon, Terminator - chemistry; Gadidae; Gadiformes - genetics; Gadiformes - metabolism; Gadus; Gadus morhua; Gene Expression Regulation; High-Throughput Nucleotide Sequencing; Humans; Life Sciences; Mammals - genetics; Mammals - metabolism; Marine; Matematikk og Naturvitenskap: 400; Mathematics and natural science: 400; Microbial Genetics and Genomics; Microbiology; Mitochondria - genetics; Mitochondria - metabolism; Molecular biology: 473; Molecular Sequence Data; Molekylærbiologi: 473; Open Reading Frames; Plant Sciences; Poly A - genetics; Poly A - metabolism; Polyadenylation; Proteomics; Research Article; RNA, Messenger - analysis; RNA, Messenger - chemistry; RNA, Transfer - analysis; RNA, Transfer - chemistry; Teleostei; VDP; Vertebrates
• ISSN: 0172-8083; 1432-0983
• DOI: 10.1007/s00294-011-0338-2

Expression and processing of mitochondrial gene transcripts are fundamental to mitochondrial function, but information from early vertebrates like teleost fishes is essentially lacking. We have analyzed mitogenome sequences of ten codfishes (family Gadidae), and provide complete sequences from three new species (Saithe, Pollack and Blue whiting). Characterization of the mitochondrial mRNAs in Saithe and Atlantic cod identified a set of ten poly(A) transcripts, and six UAA stop codons are generated by posttranscriptional polyadenylation. Structural assessment of poly(A) sites is consistent with an RNaseP cleavage activity 5′ of tRNA acceptor-like stems. COI, ND5 and ND6 mRNAs were found to harbor 3′ UTRs with antisense potential extending into neighboring gene regions. While the 3′ UTR of COI mRNA is complementary to the tRNA Ser (UCN) and highly similar to that detected in human mitochondria, the ND5 and ND6 3′ UTRs appear more heterogenic. Deep sequencing confirms expression of all mitochondrial mRNAs and rRNAs, and provides information about the precise 5′ ends in mature transcripts. Our study supports an overall evolutionary conservation in mitochondrial RNA processing events among vertebrates, but reveals some unique 5′ and 3′ end characteristics in codfish mRNAs with implications to antisense regulation of gene expression.