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

Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics
Nucleic Acids Research (Impact Factor: 9.11). 11/2013; 42(4). DOI: 10.1093/nar/gkt1152
Source: PubMed


Mitochondrial ribosomal RNAs (rRNAs) often display reduced size and deviant secondary structure, and sometimes are fragmented, as are their corresponding genes. Here we report a mitochondrial large subunit rRNA (mt-LSU rRNA) with unprecedented features. In the protist Diplonema, the rnl gene is split into two pieces (modules 1 and 2, 534- and 352-nt long) that are encoded by distinct mitochondrial chromosomes, yet the rRNA is continuous. To reconstruct the post-transcriptional maturation pathway of this rRNA, we have catalogued transcript intermediates by deep RNA sequencing and RT-PCR. Gene modules are transcribed separately. Subsequently, transcripts are end-processed, the module-1 transcript is polyuridylated and the module-2 transcript is polyadenylated. The two modules are joined via trans-splicing that retains at the junction ∼26 uridines, resulting in an extent of insertion RNA editing not observed before in any system. The A-tail of trans-spliced molecules is shorter than that of mono-module 2, and completely absent from mitoribosome-associated mt-LSU rRNA. We also characterize putative antisense transcripts. Antisense-mono-modules corroborate bi-directional transcription of chromosomes. Antisense-mt-LSU rRNA, if functional, has the potential of guiding concomitantly trans-splicing and editing of this rRNA. Together, these findings open a window on the investigation of complex regulatory networks that orchestrate multiple and biochemically diverse post-transcriptional events.


Available from: Georgette N. Kiethega, Oct 11, 2014
  • Source
    • "This trans-splicing is further complicated by the insertion of stretches of uridines between the spliced fragments (Kiethega et al. 2013; Marande and Burger 2007; Valach et al. 2014). Detailed mapping of the mitochondrial genome of Diplonema papillatum revealed that all mitochondrial-encoded genes, including ribosomal (r)RNAs, are fragmented and have to undergo trans-splicing (Vlček et al. 2011; Kiethega et al. 2013; Valach et al. 2014). The combination of RNA editing and trans-splicing qualifies the post-transcriptional processing in the D. papillatum mitochondrion as one of the most complex known. "
    [Show abstract] [Hide abstract]
    ABSTRACT: In this study, we describe the mitochondrial genome of the excavate flagellate Euglena gracilis. Its gene complement is reduced as compared to the well-studied sister groups Diplonemea and Kinetoplastea. We have identified seven protein-coding genes: three subunits of respiratory complex I (nad1, nad4 and nad5), one subunit of complex III (cob), and three subunits of complex IV (cox1, cox2 and a highly divergent cox3). Moreover, fragments of ribosomal RNA genes have also been identified. Genes encoding subunits of complex V, ribosomal proteins and tRNAs were missing, and are likely located in the nuclear genome. While mitochondrial genomes of diplonemids and kinetoplastids possess the most complex RNA processing machineries known, including trans-splicing and editing of the uridine insertion/deletion type, respectively, our transcriptomic data suggest their total absence in E. gracilis. This finding supports a scenario in which the complex mitochondrial processing machineries of both sister groups evolved relatively late in evolution from a streamlined genome and transcriptome of their common predecessor.
    Genome Biology and Evolution 11/2015; DOI:10.1093/gbe/evv229 · 4.23 Impact Factor
  • Source
    • "However, no evidence was found for a cox15-2 gene in any of the jakobids, nor was evidence found for a cox15-1 gene in any jakobid other than A. godoyi. RT-PCR did confirm active transcription of A. godoyi cox15-1 (Supplementary figure S4) as recently reported elsewhere (Valach et al. 2014). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The most gene-rich and bacterial-like mitochondrial genomes (mtDNAs) known are those of Jakobida (Excavata). Of these, the most extreme example to date is the Andalucia godoyi mtDNA, including a cox15 gene encoding the respiratory enzyme heme A synthase (HAS), which is nuclear-encoded in nearly all other mitochondriate eukaryotes. Thus cox15 in eukaryotes appears to be a classic example of mitochondrion-to-nucleus (endosymbiotic) gene transfer, with A. godoyi uniquely retaining the ancestral state. However, our analyses reveal two highly distinct HAS types (encoded by cox15-1 and cox15-2 genes) and identify A. godoyi mitochondrial cox15-encoded HAS as type-1 and all other eukaryotic cox15-encoded HAS as type-2. Molecular phylogeny places the two HAS types in widely separated clades with eukaryotic type-2 HAS clustering with the bulk of alpha-proteobacteria (>670 sequences), while A. godoyi type-1 HAS clusters with an eclectic set of bacteria and archaea including two alpha-proteobacteria missing from the type-2 clade. This wide phylogenetic separation of the two HAS types is reinforced by unique features of their predicted protein structures. Meanwhile, RNA-sequencing and genomic analyses fail to detect either cox15 type in the nuclear genome of any jakobid including A. godoyi. This suggests that not only is cox15-1 a relatively recent acquisition unique to the Andalucia lineage, but the jakobid last common ancestor probably lacked both cox15 types. These results indicate that uptake of foreign genes by mtDNA is more taxonomically widespread than previously thought. They also caution against the assumption that all alpha-proteobacterial-like features of eukaryotes are ancient remnants of endosymbiosis.
    Molecular Biology and Evolution 09/2015; DOI:10.1093/molbev/msv201 · 9.11 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Correspondce to: Laboratoire de Génétique Moléculaire, Institut Universitaire de Recherche Clinique, 641 avenue du Doyen Gaston Giraud, 34093 Montpellier cedex 5, France.
    Journal of Theoretical Biology 05/2015; 379. DOI:10.1016/j.jtbi.2015.05.013 · 2.12 Impact Factor
Show more