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

Abstract

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 tRNASer (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.Electronic supplementary materialThe online version of this article (doi:10.1007/s00294-011-0338-2) contains supplementary material, which is available to authorized users.

Genetic aspects of mitochondrial genome evolution

“…This situation is conserved with minor differences at least among vertebrates (Coucheron et al, 2011). 5'UTRs are absent in general.…”

“…Sequence box II, located in the D-loop, acts as a sequence-dependent termination element for transcription originating from the light strand promoter (Pham et al, 2006). This situation appears to be largely conserved throughout the vertebrates (Coucheron et al, 2011). The box II sequence itself is conserved at least throughout the mammals (Sbisá et al, 1997).…”

Complete mitochondrial genomes of two cockroaches, Blattella germanica and Periplaneta americana, and the phylogenetic position of termites

“…In order to discuss the phylogenetic relationships within Orthopteroidea, we used concatenated nucleotide/amino acid sequences of 13 protein-coding genes and whole mtDNA sequences (Coucheron et al 2011;Jung et al 2010;Kim et al 2006;Minegishi et al 2005) of 29 relevant species whose complete mitogenome sequences were available in GenBank as the markers to reconstruct phylogenetic trees. The sequences of one Plecoptera specie (Pteronarcys princeps) and three Ephemeroptera species (Parafronurus youi, Ephemera orientalis and Siphlonurus immanis) were used as outgroup.…”

Termination of Protein Synthesis in Mammalian Mitochondria

“…canonical termination signals were used (19). It was just such visual inspection of the human mtDNA that, taken together with evolutionary comparisons, led to the assumption that the AGA/AGG triplets that are decoded as arginine in the cytosol had been reassigned as termination triplets (20,21).…”