RNA mapping onDrosophilamitochondrial DNA: precursors and template strands

Abstract

Drosophila melanogaster mitochondrial DNA (mtDNA) is closely related to the mammalian and amphibian mtDNA except for gene organization. In Drosophila, genes are distributed in clusters alternatively coded on each strand. Besides the eleven major foreseeable transcripts previously described (MERTEN and PARDUE, 1981, J. Mol. Biol., 153, 1-21), we have characterized two poly A+ transcripts, one major and one minor which could correspond respectively to the ND3 and ND6 reading frames, and 27 poly A+ minor transcripts (0.2 to greater than 3.2 kb) which are distributed along the mtDNA except in the rRNAs, ND 1 and A+ T rich regions. The mapping and length of 25 of these transcripts strongly suggest a precursor role. They would be processed at the level of tRNA or tRNA-like sequences. Most of them are transcribed from the template strand of each gene cluster and their distribution is in agreement with the hypothesis of several transcription origins and terminations located near the extremities of each gene cluster. Quantitatively our results show a large variation in each presumptive mature transcript compared to the other, even in a given gene cluster, suggesting a specific degradation of some of the mature transcripts.

PacBio full-length transcriptome profiling of insect mitochondrial gene expression

“…Eight mRNA transcripts (ND2, COI, COII, ATP8/6, COIII, ND3, ND6 and Cytb) were produced to have the same nucleotide sequences (although thymine replaced by uracil) as the reference genome (major coding strand) has, while three mRNA transcripts (ND5, ND4/ND4L and ND1) and two rRNA transcripts were encoded by the minor coding strand (N strand) opposite to the major coding strand (J strand). Most of these results confirmed the results from the previous study, 6 while we obtained fulllength polyadenylated transcripts of two rRNAs (16S and 12S rRNA), which were originally identified as polyadenylated lrRNAs and nonpolyadenylated srRNAs in Drosophila. 6 Later, short polyA tails were indirectly detected in srRNAs using the circularization and RT-PCR method, but the length of polyA tails could only be estimated to 3-4 or 6-7 bp.…”

“…Most of these results confirmed the results from the previous study, 6 while we obtained fulllength polyadenylated transcripts of two rRNAs (16S and 12S rRNA), which were originally identified as polyadenylated lrRNAs and nonpolyadenylated srRNAs in Drosophila. 6 Later, short polyA tails were indirectly detected in srRNAs using the circularization and RT-PCR method, but the length of polyA tails could only be estimated to 3-4 or 6-7 bp. 3 In this study, the full-length transcriptome data proved mature mRNA and rRNA transcripts have the same 3 0 polyadenylation structure (Supplementary file 2).…”

“…This is similar to the order (16S rRNA D 12S rRNA, COIII, COI D COII, ATP8/6, Cytb, ND5 D ND4/4L D ND2 D ND3 D ND1, and ND6) estimated from densitometric data in the Drosophila study. 6 In this study, the full-length transcripts of three scarce mRNAs (ND3, ND1 and ND6) were observed at different levels.…”

“…4 It was not until after the complete Drosophila yakuba mitochondrial genome was published in 1985 5 that Berthier et al identified the genetic identities of 11 mature mRNAs and two mature rRNAs in 1986. 6 In 2009, Stewart et al used the RACE and RT-PCR methods to characterize the 5 0 and 3 0 ends of the mature mRNA and rRNA transcripts and refined the mitochondrial transcription map constructed by Berthier et al in 1986. 3 Although the previous studies partially revealed the mechanisms of mitochondrial gene transcription, RNA processing and mRNA maturation et al, these fundamental topics are still in the hypothesis stage.…”

Genetic aspects of mitochondrial genome evolution

“…The box II sequence itself is conserved at least throughout the mammals (Sbisá et al, 1997). In Drosophila, RNA synthesis starts at two promoters on the heavy (H) strand and three on the light (L) strand, largely matching the alternating blocks of genes located on heavy and light strand, respectively (Berthier et al, 1986;Torres et al, 2009). Large-scale rearrangements of gene order thus should be expected to affect also the structure of the mitochondrial transcriptome.…”