Abstract
BackgroundGenes encoded in vertebrate mitochondrial DNAs are transcribed as a polycistronic transcript for both strands, which is later processed into individual mRNAs, rRNAs and tRNAs, followed by modifications, such as polyadenylation at the 3′ end of mRNAs. Although mechanisms of the mitochondrial transcription and RNA processing have been extensively studied using some model organisms, structural variability of mitochondrial mRNAs across different groups of vertebrates is poorly understood. We conducted the high-throughput RNA sequencing to identify major polyadenylation sites for mitochondrial mRNAs in the Japanese grass lizard, Takydromus tachydromoides and compared the polyadenylation profiles with those identified similarly for 23 tetrapod species, featuring sauropsid taxa (reptiles and birds).ResultsAs compared to the human, a major polyadenylation site for the NADH dehydrogenase subunit 5 mRNA of the grass lizard was located much closer to its stop codon, resulting in considerable truncation of the 3′ untranslated region for the mRNA. Among the other sauropsid taxa, several distinct polyadenylation profiles from the human counterpart were found for different mRNAs. They included various truncations of the 3′ untranslated region for NADH dehydrogenase subunit 5 mRNA in four taxa, bird-specific polyadenylation of the light-strand-transcribed NADH dehydrogenase subunit 6 mRNA, and the combination of the ATP synthase subunit 8/6 mRNA with a neighboring mRNA into a tricistronic mRNA in the side-necked turtle Pelusios castaneus. In the last case of P. castaneus, as well as another example for NADH dehydrogenase subunit 1 mRNAs of some birds, the association between the polyadenylation site change and the gene overlap was highlighted. The variations in the polyadenylation profile were suggested to have arisen repeatedly in diverse sauropsid lineages. Some of them likely occurred in response to gene rearrangements in the mitochondrial DNA but the others not.ConclusionsThese results demonstrate structural variability of mitochondrial mRNAs in sauropsids. The efficient and comprehensive characterization of the mitochondrial mRNAs will contribute to broaden our understanding of their structural and functional evolution.
Highlights
Genes encoded in vertebrate mitochondrial DNAs are transcribed as a polycistronic transcript for both strands, which is later processed into individual mRNAs, rRNAs and tRNAs, followed by modifications, such as polyadenylation at the 3′ end of mRNAs
The blastn search was conducted with the Mitochondrial DNA (mtDNA) sequence of the RNA-sequenced individual as a query and the RNA sequencing (RNA-Seq) reads as a database
Analysis of mitochondrial mRNAs with RNA-Seq data Studies on gene expression from vertebrate mtDNAs have been carried out using model organisms by molecular biological characterization of transcripts of some target genes, as well as proteins interacting with the mtDNAs and transcripts
Summary
Genes encoded in vertebrate mitochondrial DNAs are transcribed as a polycistronic transcript for both strands, which is later processed into individual mRNAs, rRNAs and tRNAs, followed by modifications, such as polyadenylation at the 3′ end of mRNAs. mechanisms of the mitochondrial transcription and RNA processing have been extensively studied using some model organisms, structural variability of mitochondrial mRNAs across different groups of vertebrates is poorly understood. Mitochondria DNAs (mtDNAs) in vertebrates are doublestranded circular DNAs that are approximately 17kbp in size They contain intronless genes for 2 rRNAs, 22 tRNAs, 13 respiratory proteins (i.e., cytochrome oxidase subunits I-III, CO1–3; NADH dehydrogenase subunits 1–6 and 4 L, ND1–6 and 4 L; ATP synthase subunits 6 and 8, ATP6 and 8; and cytochrome b, CYTB) together with a major noncoding region (MNCR) or a control region which has a regulatory function for replication and transcription [1, 2]. Protein genes encoded in a mtDNA often do not have a complete stop codon at their 3′ ends, and addition of the polyA tail to the 3′ end of processed mRNAs generates a stop codon, such as UAA [1]
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