Mitochondrial RNA processing in trypanosomes

Abstract

The mitochondrial genome of trypanosomes is composed of ~50 maxicircles and thousands of minicircles. Maxi- (~25 kb) and mini-(~1 kb)circles are catenated and packed into a dense structure called a kinetoplast. Both types of circular DNA are transcribed by a phage-like RNA polymerase: maxicircles yield multicistronic rRNA and mRNA precursors, while guide RNA (gRNA) precursors are produced from minicircles. To function in mitochondrial translation, pre-mRNAs must undergo a nucleolytic processing and 3′ modifications, and often uridine insertion/deletion editing. gRNAs, which represent short (50-60 nt) RNAs directing editing reactions, are produced by 3′ nucleolytic processing of a much longer precursor followed by 3′ uridylation. Ribosomal RNAs are excised from precursors and their 3′ ends are also trimmed and uridylated. All tRNAs are imported from the cytoplasm and some are further modified and edited in the mitochondrial matrix. Historically, the fascinating phenomenon of RNA editing has been extensively studied as an isolated pathway in which nuclear-encoded proteins mediate interactions of maxi- and minicircle transcripts to create open reading frames. However, recent studies unraveled a highly integrated network of mitochondrial genome expression including critical pre- and postediting 3′ mRNA processing, and gRNA and rRNA maturation steps. Here we focus on RNA 3′ adenylation and uridylation as processes essential for biogenesis, stability and functioning of mitochondrial RNAs.

Cancer in the parasitic protozoans Trypanosoma brucei and Toxoplasma gondii

“…Hundreds of types of the heterogeneous minicircles are used as guide RNAs (gRNAs) for the transcription of RNA whereas the maxicircles (20-50 copies in a single kinetoplast) carry out functions similar to those found in the mitochondria of metazoan cells (49,61). The majority of kDNA maxicircle mRNAs undergo RNA editing to insert or delete uridine residues, as specified by template gRNAs, in a process catalyzed by multiprotein complexes called editosomes (62)(63)(64). Interestingly, T. evansi, unlike its ancestor T. brucei, completely lacks maxicircle DNA molecules and has only homologs of minicircles in the kDNA.…”

KREPB6, KREPB7, and KREPB8 are important for editing endonuclease function in Trypanosoma brucei

“…The maxicircles contain 18 genes that encode proteins of the oxidative phosphorylation system and the two mitochondrial rRNAs. Twelve of the 18 maxicircle-encoded mRNAs undergo uridine (U) insertion/ deletion RNA editing, a post-transcriptional process that is directed by minicircle-encoded guide RNAs (gRNAs) and that creates the open reading frames (ORFs) of the functional mRNAs (Hajduk and Ochsenreiter 2010;Stuart et al 2005;Aphasizhev and Aphasizheva 2011). In Trypanosoma brucei, nine mRNAs are extensively edited with hundreds of U's inserted and tens of U's deleted throughout their length, while other transcripts are edited to a limited extent.…”

The Importance of the 45 S Ribosomal Small Subunit-related Complex for Mitochondrial Translation in Trypanosoma brucei

“…Moreover, because the short-tailed forms of the COI and edited Cyb mRNAs do not seem to undergo any shortening or degradation, it is likely that the SSU* down-regulation specifically prevents the extension of the existing short poly(A) tail, which would be done by the KPAP1/RET2 complex after its activation by KPAF1 and KPAF2 (28). It was hypothesized previously that a specific recognition of an edited mRNA by a yet unidentified PPR protein on the 5Ј-end is necessary for the recruitment of the poly(A/U)-tailing machinery to the mRNA 3Ј-end (23). An attractive scenario is that this recognition may be, in fact, mediated by the SSU* complex; then down-regulation of this complex by RNAi would lead to accumulation of the short-tailed forms.…”

“…The completion of editing at the very 5Ј-end is a sign that the entire transcript has been edited downstream. It has been hypothesized that the edited 5Ј-end sequence is recognized by a specific (yet unknown) pentatricopeptide repeat (PPR) protein that directs the polyadenylation/polyuridylation complex to extend the short poly(A) tail, already present in the pre-edited and partially edited mRNA, with the creation of a long poly(A/U) tail (22,23). This structure is thought to signify achievement of the maturity and translatability of the mRNA and promotes its recognition by mitochondrial ribosomes.…”