Complete minicircle genome ofLeptomonas pyrrhocorisreveals sources of its non-canonical mitochondrial RNA editing events

Abstract

Uridine insertion/deletion (U-indel) editing of mitochondrial mRNA, unique to the protistan class Kinetoplastea, generates canonical as well as potentially non-productive editing events. While the molecular machinery and the role of the guide (g) RNAs that provide required information for U-indel editing are well understood, little is known about the forces underlying its apparently error-prone nature. Analysis of a gRNA:mRNA pair allows the dissection of editing events in a given position of a given mitochondrial transcript. A complete gRNA dataset, paired with a fully characterized mRNA population that includes non-canonically edited transcripts, would allow such an analysis to be performed globally across the mitochondrial transcriptome. To achieve this, we have assembled 67 minicircles of the insect parasite Leptomonas pyrrhocoris, with each minicircle typically encoding one gRNA located in one of two similar-sized units of different origin. From this relatively narrow set of annotated gRNAs, we have dissected all identified mitochondrial editing events in L. pyrrhocoris, the strains of which dramatically differ in the abundance of individual minicircle classes. Our results support a model in which a multitude of editing events are driven by a limited set of gRNAs, with individual gRNAs possessing an inherent ability to guide canonical and non-canonical editing.

Epitranscriptome Analysis of Oxidative Stressed Retinal Epithelial Cells Depicted a Possible RNA Editing Landscape of Retinal Degeneration

“…Twelve types of RNA editing were identified, among which A-to-I and C-to-U were identified as being the canonical RNA editing events, accounting for about 36% of all identified sites, whereas the remaining RNA editing types were the non-canonical ones [ 67 ]. A-to-I RNA editing events, one of the most common types of frequent editing events in mammals, are mediated by the ADAR family of enzymes [ 68 ].…”

Mitochondrial RNA editing in Trypanoplasma borreli: New tools, new revelations

“…The RNAseq data is accessible under SRR9331469 in the Sequence Read Archive [26] . For downstream processing with T -Aligner [27] , [28] , RNAseq reads were quality-checked with FastQC v. 0.11.9 [29] and quality-trimmed with trimmomatic v. 0.39 [30] . Trimmed reads were merged with the paired-end read merger PEAR v. 0.9.6 [31] , and 69.3 % of read pairs were successfully merged.…”

“…At each potential editing site, the percentage of editing events that contribute to the identified translatable product for each gene was determined as described in detail elsewhere [27] , [41] .…”

Genomics of Trypanosomatidae: Where We Stand and What Needs to Be Done?

“…Their analyses revealed novel non-canonical mechanisms, as well as species-specific differences in RNA editing [142,143]. Such studies can delineate not only the structure of maxicircles and minicircles [144][145][146][147], but also predict the guide RNA repertoire in a given species [143,148,149]. As judged from pre-genomic studies carried out on single genes, different lineages of trypanosomatids possess distinct kDNA editing patterns [150].…”