Trans-splicing and RNA editing of LSU rRNA in <i>Diplonema</i> mitochondria

Valach, Matus; Moreira, Sandrine; Kiethega, Georgette N.; Burger, Gertraud

doi:10.1093/nar/gkt1152

Cited by 29 publications

(40 citation statements)

References 46 publications

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“…Essentially all genes are broken up into up to 11 modules that are on average 170 bp long (43–534 bp; Table ) and whose breakpoints are apparently located at random positions. The only contiguous gene in D. papillatum mtDNA specifies the mitochondrial small subunit ribosomal RNA (mt‐SSU rRNA), which happens to be exceptionally short (366 bp)—to our knowledge, the smallest of its kind .…”

Section: Unusual Features Of the D Papillatum Mitochondrial Genomementioning

confidence: 99%

Perfection of eccentricity: Mitochondrial genomes of diplonemids

Burger

Valach

2018

IUBMB Life

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Mitochondria are the sandbox of evolution as exemplified most particularly by the diplonemids, a group of marine microeukaryotes. These protists are uniquely characterized by their highly multipartite mitochondrial genome and systematically fragmented genes whose pieces are spread out over several dozens of chromosomes. The type species Diplonema papillatum was the first member of this group in which the expression of fragmented mitochondrial genes was investigated experimentally. We now know that gene expression involves separate transcription of gene pieces (modules), RNA editing of module transcripts, and module joining to mature mRNAs and rRNAs. The mechanism of cognate module recognition and ligation is distinct from known intron splicing and remains to be uncovered. Here, we review the current status of research on mitochondrial genome architecture, as well as gene complement, structure, and expression modes in diplonemids. Further, we discuss the potential molecular mechanisms of posttranscriptional processing, and finally reflect on the evolutionary trajectories and trends of mtDNA evolution as seen in this protist group. © 2018 IUBMB Life, 70(12):1197Life, 70(12): -1206Life, 70(12): , 2018

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Section: Unusual Features Of the D Papillatum Mitochondrial Genomementioning

confidence: 99%

Perfection of eccentricity: Mitochondrial genomes of diplonemids

Burger

Valach

2018

IUBMB Life

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“…2). 17 We demonstrated that Us are appended to the module upstream of the junction, before this terminus engages in trans-splicing. 14 Table 1.…”

Section: Trans-splicing Of Fragmented Genesmentioning

confidence: 86%

“…3 Therefore, we enriched mitochondrial transcripts by oligo(dT) purification, which facilitated their characterization via targeted RT-PCR 10,13,14 and transcriptomics. 11,17 In silico approaches A standard procedure in eukaryotic genomics is to generate reads by whole-genome/random-fragment approach and assemble these reads (ideally yielding chromosome-size contigs). Mapping of transcriptome (RNA-Seq) reads against the genome locates genes and introns and allows one to spot potential polymorphisms and RNA editing sites.…”

Section: Experimental/biochemistry Approachesmentioning

confidence: 99%

Post-transcriptional mending of gene sequences: Looking under the hood of mitochondrial gene expression in diplonemids

et al. 2016

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The instructions to make proteins and structural RNAs are laid down in gene sequences. Yet, in certain instances, these primary instructions need to be modified considerably during gene expression, most often at the transcript level. Here we review a case of massive post-transcriptional revisions via trans-splicing and RNA editing, a phenomenon occurring in mitochondria of a recently recognized protist group, the diplonemids. As of now, the various post-transcriptional steps have been cataloged in detail, but how these processes function is still unknown. Since genetic manipulation techniques such as gene replacement and RNA interference have not yet been established for these organisms, alternative strategies have to be deployed. Here, we discuss the experimental and bioinformatics approaches that promise to unravel the molecular machineries of trans-splicing and RNA editing in Diplonema mitochondria.

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“…Like E. gracilis, two LSU fragments (534 and 352 nt) are present, encoded on two Class B chromosomes (Valach et al 2014). These RNAs are trans-spliced to produce a single LSU rRNA of approximately 900 nt and appear to go through other additional processing steps.…”

Section: Mitochondrial Ribosomal Rnamentioning

confidence: 99%

Euglena Transcript Processing

McWatters

Russell

2017

Advances in Experimental Medicine and Biology

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RNA transcript processing is an important stage in the gene expression pathway of all organisms and is subject to various mechanisms of control that influence the final levels of gene products. RNA processing involves events such as nuclease-mediated cleavage, removal of intervening sequences referred to as introns and modifications to RNA structure (nucleoside modification and editing). In Euglena, RNA transcript processing was initially examined in chloroplasts because of historical interest in the secondary endosymbiotic origin of this organelle in this organism. More recent efforts to examine mitochondrial genome structure and RNA maturation have been stimulated by the discovery of unusual processing pathways in other Euglenozoans such as kinetoplastids and diplonemids. Eukaryotes containing large genomes are now known to typically contain large collections of introns and regulatory RNAs involved in RNA processing events, and Euglena gracilis in particular has a relatively large genome for a protist. Studies examining the structure of nuclear genes and the mechanisms involved in nuclear RNA processing have revealed that indeed Euglena contains large numbers of introns in the limited set of genes so far examined and also possesses large numbers of specific classes of regulatory and processing RNAs, such as small nucleolar RNAs (snoRNAs). Most interestingly, these studies have also revealed that Euglena possesses novel processing pathways generating highly fragmented cytosolic ribosomal RNAs and subunits and non-conventional intron classes removed by unknown splicing mechanisms. This unexpected diversity in RNA processing pathways emphasizes the importance of identifying the components involved in these processing mechanisms and their evolutionary emergence in Euglena species.

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Trans-splicing and RNA editing of LSU rRNA in Diplonema mitochondria

Cited by 29 publications

References 46 publications

Perfection of eccentricity: Mitochondrial genomes of diplonemids

Perfection of eccentricity: Mitochondrial genomes of diplonemids

Post-transcriptional mending of gene sequences: Looking under the hood of mitochondrial gene expression in diplonemids

Euglena Transcript Processing

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