Benne, R. et al. Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 46, 819–826 (1986).
Blum, B., Bakalara, N. & Simpson, L. A model for RNA editing in kinetoplastid mitochondria: RNA molecules transcribed from maxicircle DNA provide the edited information. Cell 60, 189–198 (1990).
Seiwert, S. D., Heidmann, S. & Stuart, K. Direct visualization of uridylate deletion in vitro suggests a mechanism for kinetoplastid RNA editing. Cell 84, 831–841 (1996).
Kable, M. L., Seiwert, S. D., Heidmann, S. & Stuart, K. RNA editing: a mechanism for gRNA-specified uridylate insertion into precursor mRNA. Science 273, 1189–1195 (1996).
Aphasizheva, I. & Aphasizhev, R. U-insertion/deletion mRNA-editing holoenzyme: definition in sight. Trends Parasitol. 13, 1078–1083 (2015).
Aphasizheva, I. et al. Lexis and grammar of mitochondrial RNA processing in trypanosomes. Trends Parasitol. 36, 337–355 (2020).
Blum, B. & Simpson, L. Guide RNAs in kinetoplastid mitochondria have a nonencoded 3’ oligo-(U) tail involved in recognition of the pre-edited region. Cell 62, 391–397 (1990).
Blum, B. & Simpson, L. Formation of gRNA/mRNA chimeric molecules in vitro, the initial step of RNA editing, is dependent on an anchor sequence. Proc. Natl Acad. Sci. USA 89, 11944–11948 (1992).
Liu, S. et al. Structural basis of gRNA stabilization and mRNA recognition in trypanosomal RNA editing. Science 381, eadg4725 (2023).
Trotter, J. R., Ernst, N. L., Carnes, J., Panicucci, B. & Stuart, K. A deletion site editing endonuclease in Trypanosoma brucei. Mol. Cell 20, 403–412 (2005).
Carnes, J., Trotter, J. R., Ernst, N. L., Steinberg, A. & Stuart, K. An essential RNase III insertion editing endonuclease in Trypanosoma brucei. Proc. Natl Acad. Sci. USA 102, 16614–16619 (2005).
Panigrahi, A. K. et al. Compositionally and functionally distinct editosomes in Trypanosoma brucei. RNA 12, 1038–1049 (2006).
Carnes, J., Trotter, J. R., Peltan, A., Fleck, M. & Stuart, K. RNA editing in Trypanosoma brucei requires three different editosomes. Mol. Cell. Biol. 28, 122–130 (2008).
Carnes, J., Soares, C. Z., Wickham, C. & Stuart, K. Endonuclease associations with three distinct editosomes in Trypanosoma brucei. J. Biol. Chem. 286, 19320–19330 (2011).
Carnes, J. et al. In vivo cleavage specificity of Trypanosoma brucei editosome endonucleases. Nucleic Acids Res. 45, 4667–4686 (2017).
Carnes, J., McDermott, S. M., Lewis, I., Tracy, M. & Stuart, K. Domain function and predicted structure of three heterodimeric endonuclease subunits of RNA editing catalytic complexes in Trypanosoma brucei. Nucleic Acids Res. 50, 10123–10139 (2022).
Carnes, J., McDermott, S. M. & Stuart, K. RNA editing catalytic complexes edit multiple mRNA sites non-processively in Trypanosoma brucei. Mol. Biochem. Parasitol. 256, 111596 (2023).
Golas, M. M. et al. Snapshots of the RNA editing machine in trypanosomes captured at different assembly stages in vivo. EMBO J. 28, 766–778 (2009).
Li, F. et al. Structure of the core editing complex (L-complex) involved in uridine insertion/deletion RNA editing in trypanosomatid mitochondria. Proc. Natl Acad. Sci. USA 106, 12306–12310 (2009).
Cruz-Reyes, J., Mooers, B. H. M., Doharey, P. K., Meehan, J. & Gulati, S. Dynamic RNA holo-editosomes with subcomplex variants: insights into the control of trypanosome editing. Wiley Interdiscip. Rev. RNA 9, e1502 (2018).
Aphasizhev, R., Aphasizheva, I. & Simpson, L. A tale of two TUTases. Proc. Natl Acad. Sci. USA 100, 10617–10622 (2003).
Ernst, N. L. et al. TbMP57 is a 3’ terminal uridylyl transferase (TUTase) of the Trypanosoma brucei editosome. Mol. Cell 11, 1525–1536 (2003).
Aphasizheva, I. et al. RNA binding and core complexes constitute the U-insertion/deletion editosome. Mol. Cell. Biol. 34, 4329–4342 (2014).
Ho, C. M. et al. Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu. Nat. Methods 17, 79–85 (2020).
Aphasizhev, R., Karmarkar, U. & Simpson, L. Are tRNAs imported into the mitochondria of kinetoplastid protozoa as 5’-extended precursors? Mol. Biochem. Parasitol. 93, 73–80 (1998).
Brogli, R., Cristodero, M., Schneider, A. & Polacek, N. A ribosome-bound tRNA half stimulates mitochondrial translation during stress recovery in Trypanosoma brucei. Cell Rep. 42, 113112 (2023).
Ho, C. K., Wang, L. K., Lima, C. D. & Shuman, S. Structure and mechanism of RNA ligase. Structure 12, 327–339 (2004).
Schnaufer, A. et al. An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei. Science 291, 2159–2161 (2001).
Gao, G. & Simpson, L. Is the Trypanosoma brucei REL1 RNA ligase specific for U-deletion RNA editing, and is the REL2 RNA ligase specific for U-insertion editing?. J. Biol. Chem. 278, 27570–27574 (2003).
McDermott, S. M., Luo, J., Carnes, J., Ranish, J. A. & Stuart, K. The architecture of Trypanosoma brucei editosomes. Proc. Natl Acad. Sci. USA 113, E6476–E6485 (2016).
Schnaufer, A. et al. A protein–protein interaction map of trypanosome ~20S editosomes. J. Biol. Chem. 285, 5282–5295 (2010).
Davidge, B. et al. Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA editing catalytic complexes in Trypanosoma brucei. RNA 29, 1591–1609 (2023).
Bohm, C., Katari, V. S., Brecht, M. & Goringer, H. U. Trypanosoma brucei 20 S editosomes have one RNA substrate-binding site and execute RNA unwinding activity. J. Biol. Chem. 287, 26268–26277 (2012).
Finerty, P. J. Jr. & Bass, B. L. Subsets of the zinc finger motifs in dsRBP-ZFa can bind double-stranded RNA. Biochemistry 38, 4001–4007 (1999).
Kang, X. et al. Reconstitution of full-round uridine-deletion RNA editing with three recombinant proteins. Proc. Natl Acad. Sci. USA 103, 13944–13949 (2006).
Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).
Rogers, K., Gao, G. & Simpson, L. Uridylate-specific 3’ 5’-exoribonucleases involved in uridylate-deletion RNA editing in trypanosomatid mitochondria. J. Biol. Chem. 282, 29073–29080 (2007).
Kao, A. et al. Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes. Mol. Cell. Proteomics 10, M110.002212 (2011).
Branon, T. C. et al. Efficient proximity labeling in living cells and organisms with TurboID. Nat. Biotechnol. 36, 880–887 (2018).
Lukes, J. et al. Kinetoplast DNA network: evolution of an improbable structure. Eukaryot. Cell 1, 495–502 (2002).
Gray, M. W., Lukes, J., Archibald, J. M., Keeling, P. J. & Doolittle, W. F. Irremediable complexity? Science 330, 920–921 (2010).
Hochberg, G. K. A. et al. A hydrophobic ratchet entrenches molecular complexes. Nature 588, 503–508 (2020).
Stoltzfus, A. On the possibility of constructive neutral evolution. J. Mol. Evol. 49, 169–181 (1999).
Deng, J., Ernst, N. L., Turley, S., Stuart, K. D. & Hol, W. G. Structural basis for UTP specificity of RNA editing TUTases from Trypanosoma brucei. EMBO J. 24, 4007–4017 (2005).
Ringpis, G. E. et al. Mechanism of U insertion RNA editing in trypanosome mitochondria: the bimodal TUTase activity of the core complex. J. Mol. Biol. 399, 680–695 (2010).
Ringpis, G. E., Stagno, J. & Aphasizhev, R. Mechanism of U-insertion RNA editing in trypanosome mitochondria: characterization of RET2 functional domains by mutational analysis. J. Mol. Biol. 399, 696–706 (2010).
Nandakumar, J., Shuman, S. & Lima, C. D. RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward. Cell 127, 71–84 (2006).
Deng, J., Schnaufer, A., Salavati, R., Stuart, K. D. & Hol, W. G. High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1. J. Mol. Biol. 343, 601–613 (2004).
Igo, R. P. Jr., Lawson, S. D. & Stuart, K. RNA sequence and base pairing effects on insertion editing in Trypanosoma brucei. Mol. Cell. Biol. 22, 1567–1576 (2002).
Igo et al. Role of uridylylate-specific exoribonuclease activity in Trypanosoma brucei RNA editing. Eukar. Cell 1, 112–118 (2002).
Cunningham, M. P. & Harley, J. M. Preservation of living metacyclic forms of the Trypanosoma brucei subgroup. Nature 194, 1186 (1962).
Parrot, L. & Foley, H. Sur la frequence de la leishmaniose du gecko dans le Sud oranais. Arch. Inst. Pasteur d’Algerie 17, 231–232 (1939).
Aphasizheva, I. et al. CTS tag-based methods for investigating mitochondrial RNA modification factors in Trypanosoma brucei. Methods Enzymol. 658, 83–109 (2021).
Wirtz, E., Leal, S., Ochatt, C. & Cross, G. A. A tightly regulated inducible expression system for conditional gene knock-outs and dominant-negative genetics in Trypanosoma brucei. Mol. Biochem. Parasitol. 99, 89–101 (1999).
Puig, O. et al. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24, 218–229 (2001).
LeBowitz, J. H., Coburn, C. M., McMahon-Pratt, D. & Beverley, S. M. Development of a stable Leishmania expression vector and application to the study of parasite surface antigen genes. Proc. Natl Acad. Sci. USA 87, 9736–9740 (1990).
Pelletier, M., Read, L. K. & Aphasizhev, R. Isolation of RNA binding proteins involved in insertion/deletion editing. Methods Enzymol. 424, 69–96 (2007).
Cruz-Reyes, J., Rusche, L., Piller, K. J. & Sollner-Webb, B. T. brucei RNA editing: adenosine nucleotides inversely affect U-deletion and U-insertion reactions at mRNA cleavage. Mol. Cell 1, 401–409 (1998).
Guan, S., Price, J. C., Prusiner, S. B., Ghaemmaghami, S. & Burlingame, A. L. A data processing pipeline for mammalian proteome dynamics studies using stable isotope metabolic labeling. Mol. Cell. Proteomics 10, M111.010728 (2011).
Yu, C. et al. Probing H2O2-mediated structural dynamics of the human 26S proteasome using quantitative cross-linking mass spectrometry (QXL-MS). Mol Cell. Proteomics 18, 954–967 (2019).
Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
Meng, E. C. et al. UCSF ChimeraX: tools for structure building and analysis. Protein Sci. 32, e4792 (2023).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D 74, 519–530 (2018).
Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D 74, 531–544 (2018).
Gan, J. et al. A stepwise model for double-stranded RNA processing by ribonuclease III. Mol. Microbiol. 67, 143–154 (2008).
Dharavath, S., Shaw, G. X. & Ji, X. Structural basis for Dicer-like function of an engineered RNase III variant and insights into the reaction trajectory of two-Mg2+-ion catalysis. RNA Biol. 19, 908–915 (2022).
Song, H. et al. The functional cycle of Rnt1p: five consecutive steps of double-stranded RNA processing by a eukaryotic RNase III. Structure 25, 353–363 (2017).
Dodt, M., Roehr, J. T., Ahmed, R. & Dieterich, C. FLEXBAR—flexible barcode and adapter processing for next-generation sequencing platforms. Biology 1, 895–905 (2012).
Smith, T., Heger, A. & Sudbery, I. UMI-tools: modeling sequencing errors in unique molecular identifiers to improve quantification accuracy. Genome Res. 27, 491–499 (2017).
Vasimuddin, M., Misra, S., Li, H. & Aluru, S. Efficient architecture-aware acceleration of BWA-MEM for multicore systems. In Proc. 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS) 314–324 (2019).
Cooper, S., Wadsworth, E. S., Schnaufer, A. & Savill, N. J. Organization of minicircle cassettes and guide RNA genes in Trypanosoma brucei. RNA 28, 972–992 (2022).
Aphasizheva, I. et al. Novel TUTase associates with an editosome-like complex in mitochondria of Trypanosoma brucei. RNA 15, 1322–1337 (2009).
