Giant group I intron in a mitochondrial genome is removed by RNA back-splicing

Abstract

Background The mitochondrial genomes of mushroom corals (Corallimorpharia) are remarkable for harboring two complex group I introns; ND5-717 and COI-884. How these autocatalytic RNA elements interfere with mitochondrial RNA processing is currently not known. Here, we report experimental support for unconventional processing events of ND5-717 containing RNA. Results We obtained the complete mitochondrial genome sequences and corresponding mitochondrial transcriptomes of the two distantly related corallimorpharian species Ricordea yuma and Amplexidiscus fenestrafer . All mitochondrial genes were found to be expressed at the RNA-level. Both introns were perfectly removed by autocatalytic splicing, but COI-884 excision appeared more efficient than ND5-717. ND5-717 was organized into giant group I intron elements of 18.1 kb and 19.3 kb in A. fenestrafer and R. yuma , respectively. The intron harbored almost the entire mitochondrial genome embedded within the P8 peripheral segment. Conclusion ND5-717 was removed by group I intron splicing from a small primary transcript that contained a permutated intron–exon arrangement. The splicing pathway involved a circular exon-containing RNA intermediate, which is a hallmark of RNA back-splicing. ND5-717 represents the first reported natural group I intron that becomes excised by back-splicing from a permuted precursor RNA. Back-splicing may explain why Corallimorpharia mitochondrial genomes tolerate giant group I introns. Electronic supplementary material The online version of this article (10.1186/s12867-019-0134-y) contains supplementary material, which is available to authorized users.

Mitochondrial Group I Introns in Hexacorals Are Regulatory Genetic Elements

“…These rearrangements appear complex and involve a drastic size reduction of the ND5-717 intron from approximately 18 kb (primary arrangement) to 12 kb and 10 kb, respectively ( Figure 2B). The most dramatic mitochondrial genome rearrangement is seen in the deepwater sea anemone Protanthea [16]. Here, the 21 kb mtDNA is arranged along two circular mitochondrial chromosomes, MCh-I and MCh-II ( Figure 2C).…”

“…Interestingly, the smaller MCh-II encodes the mitochondrial COII and one allele of the small subunit (SSU) rRNA. Phylogenetic analysis indicates that MCh-II is horizontally transferred into Protanthea from a distantly related sea anemone [16]. Not all deep-water hexacorals have mtDNA rearrangements.…”

“…Mitochondrial RNAs have been investigated in a few hexacoral species representing sea anemones, colonial anemones, and mushroom corals [6,12,[14][15][16]. RNAseq data were obtained from 454 pyrosequencing and Ion Torrent PGM sequencing.…”

“…RNAseq data were obtained from 454 pyrosequencing and Ion Torrent PGM sequencing. Several general features are noted: (1) ribosomal RNA constituted more than 90% of the reads and is found to be at least 10-20 times more abundant than most OxPhos gene transcripts; (2) all the conventional genes were transcribed, and the Complex IV OxPhos genes appeared most expressed; (3) group I introns were perfectly spliced out from ND5 and COI mRNA precursors; (4) COI-884 intron splicing appeared more efficient than that of the ND5-717 intron, suggesting intron retention of ND5 mRNA [16]; and (5) noncanonical mitochondrial genes, such as the intron-encoded HEG and non-annotated open reading frames (ORFs), were clearly expressed. One of these ORFs, corresponding to a 306-amino-acid unknown protein in the mushroom coral Amplexidiscus, was highly expressed and located at the opposite strand compared to canonical OxPhos genes [16].…”

“…The circular and economically organized mtDNA encodes the same set of 2 ribosomal RNAs and 13 hydrophobic proteins involved in the oxidative phosphorylation (OxPhos) system [11]. However, noncanonical and optional mitochondrial genes may occur in some hexacoral species [11][12][13][14][15][16]. More unusual features, however, are the highly reduced tRNA gene repertoire (only 1-2 tRNA genes) and the presence of complex group I introns [11,[17][18][19][20].…”