Article

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

ABSTRACT

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.

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Available from: Georgette N. Kiethega, Oct 11, 2014
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    • "The expression of the gene coding for DpRNL was assessed by mapping RNA-seq reads from a total-RNA library of D. papillatum onto the contig carrying the gene. Library construction and read processing have been described earlier[19]. Cutadapt version 1.2.1[70]was used to remove adapters at 5′ and 3′ termini of reads with an error rate of 0.1 and to clip low-quality sequences with a threshold of 20. "
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    • "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. "
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