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Review
. 2016 Jan-Feb;7(1):33-51.
doi: 10.1002/wrna.1313. Epub 2015 Nov 2.

Trypanosome RNA editing: the complexity of getting U in and taking U out

Laurie K Read  1 , Julius Lukeš  2   3   4 , Hassan Hashimi  2   3
Affiliations
Review

Trypanosome RNA editing: the complexity of getting U in and taking U out

Laurie K Read et al. Wiley Interdiscip Rev RNA. 2016 Jan-Feb.

Abstract

RNA editing, which adds sequence information to RNAs post-transcriptionally, is a widespread phenomenon throughout eukaryotes. The most complex form of this process is the uridine (U) insertion/deletion editing that occurs in the mitochondria of kinetoplastid protists. RNA editing in these flagellates is specified by trans-acting guide RNAs and entails the insertion of hundreds and deletion of dozens of U residues from mitochondrial RNAs to produce mature, translatable mRNAs. An emerging model indicates that the machinery required for trypanosome RNA editing is much more complicated than previously appreciated. A family of RNA editing core complexes (RECCs), which contain the required enzymes and several structural proteins, catalyze cycles of U insertion and deletion. A second, dynamic multiprotein complex, the Mitochondrial RNA Binding 1 (MRB1) complex, has recently come to light as another essential component of the trypanosome RNA editing machinery. MRB1 likely serves as the platform for kinetoplastid RNA editing, and plays critical roles in RNA utilization and editing processivity. MRB1 also appears to act as a hub for coordination of RNA editing with additional mitochondrial RNA processing events. This review highlights the current knowledge regarding the complex molecular machinery involved in trypanosome RNA editing. WIREs RNA 2016, 7:33-51. doi: 10.1002/wrna.1313 For further resources related to this article, please visit the WIREs website.

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Figures

Figure 1
Figure 1. Distribution of multiple types of RNA editing across eukaryotes
Phylogenetic tree based on Adl, et al.. Only branches with clades that have a demonstrated type of RNA editing are labeled. Adjacent red text summarizes the type of editing.
Figure 2
Figure 2. Mechanism of U insertion/deletion editing
A) Pre-edited mRNAs are transcribed from mitochondrial maxicircles, while the majority of gRNAs are transcribed from the minicircle component of mitochondrial DNA. The gRNA 5’ anchor region (olive) basepairs with the mRNA and the gRNA information region (yellow) directs the number of U's inserted or deleted. The gRNA 3’ oligo(U) tail stabilizes the gRNA/mRNA interaction. Enzymes contained within the RNA editing core complex (RECC) catalyze mRNA endonucleolytic cleavage at an editing sites, U insertion by a 3’ TUTase, and U deletion by a U-specific exoribonuclease as directed by the sequences of gRNAs. Cleaved mRNAs are resealed by RNA ligases. B) Multi-round editing entails sequential utilization of multiple gRNAs. Because the anchor region of a given gRNA basepairs with edited mRNA sequence specified by the prior gRNA, editing progresses in a 3’ to 5’ direction along an mRNA. Multiple black arrowheads symbolize multiple editing sites within an editing block, as defined by the hybridized gRNA. Dashed gRNA labels indicate that they are turned over during/after an editing block has been processed. An editing domain is a stretch of mRNA sequence that requires the gRNA cascade for its processing.
Figure 2
Figure 2. Mechanism of U insertion/deletion editing
A) Pre-edited mRNAs are transcribed from mitochondrial maxicircles, while the majority of gRNAs are transcribed from the minicircle component of mitochondrial DNA. The gRNA 5’ anchor region (olive) basepairs with the mRNA and the gRNA information region (yellow) directs the number of U's inserted or deleted. The gRNA 3’ oligo(U) tail stabilizes the gRNA/mRNA interaction. Enzymes contained within the RNA editing core complex (RECC) catalyze mRNA endonucleolytic cleavage at an editing sites, U insertion by a 3’ TUTase, and U deletion by a U-specific exoribonuclease as directed by the sequences of gRNAs. Cleaved mRNAs are resealed by RNA ligases. B) Multi-round editing entails sequential utilization of multiple gRNAs. Because the anchor region of a given gRNA basepairs with edited mRNA sequence specified by the prior gRNA, editing progresses in a 3’ to 5’ direction along an mRNA. Multiple black arrowheads symbolize multiple editing sites within an editing block, as defined by the hybridized gRNA. Dashed gRNA labels indicate that they are turned over during/after an editing block has been processed. An editing domain is a stretch of mRNA sequence that requires the gRNA cascade for its processing.
Figure 3
Figure 3. RNA editing core complex (RECC or editosome)
A) RECC contains 12 common proteins, of which three (KREX2, KREPA2, and KREL1) comprise a deletion subcomplex and three (KRET2, KREPA1, and KREL2) comprise an insertion subcomplex. OB-fold containing proteins KREPA3, KREPA6, KREPA4, and KREPA5 maintain protein-protein interactions. Zinc-finger containing KREPB4 and KREPB5 are thought to interact with endonucleases KREN1, KREN2, and KREN3 and their respective partners KREPB8, KREPB7, and KREPB6. KRENs interact with the insertion subcomplex and their KRPEB partners interact with the deletion subcomplex. B) There are three distinct classes of RECC, which differ in the associated KREN endonuclease and KREP partner proteins. KREN1/KREPB6 also associate with exoribonuclease KREX1. KREN1 containing RECCs catalyze U deletion, KREN2 containing RECCs catalyze U insertion, and KREN3 containing RECCs catalyze insertion specifically into cox2 mRNA.
Figure 4
Figure 4. MRB1 complex organization
MRB1 is comprised of a core that facilitates editing initiation, a TbRGG2 subcomplex that functions in 3’ to 5’ editing progression, and the MRB10130 protein that may bridge and organize the two subcomplexes. MRB1 core contains the GAP1/2 heterotetramer (bright green) that binds and stabilizes gRNAs and which appears to be dissociable and engages in additional interactions. Light green circle (TbRGG2 subcomplex) and light brown circle (MRB1 core) represent largely RNA-independent interactions determined in studies by Ammerman and colleagues and Aphasizheva and colleagues. Black lines indicate direct interactions by yeast two-hybrid screen. Solid lines, strong interactions; dotted lines, weak interactions; thin lines, interaction in one direction; thick lines, interaction in both directions. The MRB1 complex has also been referred to as RESC (RNA editing substrate binding complex), MRB1 core as GRBC (gRNA binding complex), and TbRGG2 subscomplex as REMC (RNA editing mediator complex).
Figure 5
Figure 5. Full gene PCR assay used to analyze the step of editing in which a given MRB1 protein functions
A) End point PCR is performed with primers targeting the 5’ and 3’ never edited regions present at the ends of all pan-edited RNAs to amplify all versions of a given RNA (pre-edited, partially edited, fully edited). Green, never edited; pink, fully edited; yellow, junction region; blue, pre-edited. B) Agarose gel analysis of full gene PCR amplicons of ATPase 6 RNA in cells either expressing (+) or depleted of (-) MRB3010 or TbRGG2. Red dots indicate products that accumulate in the absence of each protein. Note that pre-edited RNA accumulates upon MRB3010 depletion but not upon TbRGG2 depletion, signifying a role in editing initiation for the former, but not the latter.
Figure 6
Figure 6. Current model for the coordination of numerous complexes in mitochondrial U insertion/deletion RNA editing and mRNA processing
The MRB1 complex (comprised of MRB1 core [including GAP1/2], TbRGG2 subcomplex, and MRB10130) serves as a platform for the editing reaction. RECC, containing the catalytic enzymes, associates transiently with MRB1-associated RNAs. TbRGG2 subcomplex facilitates editing 3’ go 5’ progression (dotted arrow). RNA helicases REH1 and REH2 appear to promote RNA association with MRB1. Following the completion of editing, kPAP1, potentially with assistance from PAMC, catalyzes a long A/U tail on the 3’ end of fully edited mRNA, rendering it competent for translation.
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