Lexis and Grammar of Mitochondrial RNA Processing in Trypanosomes

. 2020 Apr ; 36 (4) : 337-355. [epub] 20200228

Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic

Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem, přehledy

Perzistentní odkaz   https://www.medvik.cz/link/pmid32191849

Grantová podpora
R01 GM084065 NIGMS NIH HHS - United States
R01 AI091914 NIAID NIH HHS - United States
R01 GM129041 NIGMS NIH HHS - United States
R01 AI014102 NIAID NIH HHS - United States
R01 AI125487 NIAID NIH HHS - United States
R01 AI064653 NIAID NIH HHS - United States
R15 AI135885 NIAID NIH HHS - United States
MR/L019701/1 Medical Research Council - United Kingdom
R01 AI061580 NIAID NIH HHS - United States
R21 AI139448 NIAID NIH HHS - United States
R01 AI113157 NIAID NIH HHS - United States
R01 AI101057 NIAID NIH HHS - United States

Odkazy

PubMed 32191849
PubMed Central PMC7083771
DOI 10.1016/j.pt.2020.01.006
PII: S1471-4922(20)30016-7
Knihovny.cz E-zdroje

Trypanosoma brucei spp. cause African human and animal trypanosomiasis, a burden on health and economy in Africa. These hemoflagellates are distinguished by a kinetoplast nucleoid containing mitochondrial DNAs of two kinds: maxicircles encoding ribosomal RNAs (rRNAs) and proteins and minicircles bearing guide RNAs (gRNAs) for mRNA editing. All RNAs are produced by a phage-type RNA polymerase as 3' extended precursors, which undergo exonucleolytic trimming. Most pre-mRNAs proceed through 3' adenylation, uridine insertion/deletion editing, and 3' A/U-tailing. The rRNAs and gRNAs are 3' uridylated. Historically, RNA editing has attracted major research effort, and recently essential pre- and postediting processing events have been discovered. Here, we classify the key players that transform primary transcripts into mature molecules and regulate their function and turnover.

Center for Global Infectious Disease Research Seattle Children's Research Institute Seattle WA 98109 USA

Department of Biochemistry and Biophysics Texas A and M University College Station TX 77843 USA

Department of Biochemistry and Molecular Biology University of Georgia Athens GA 30602 USA

Department of Chemistry and Biochemistry University of Bern Bern CH 3012 Switzerland

Department of Microbiology and Immunology University at Buffalo Jacobs School of Medicine and Biomedical Sciences Buffalo NY 14203 USA

Department of Microbiology Immunology and Molecular Genetics University of California Los Angeles CA90095 USA

Department of Microbiology The Ohio State University Columbus OH 43210 USA

Department of Molecular and Cell Biology Boston University Medical Campus Boston MA 02118 USA

Department of Molecular Cell and Systems Biology University of California Riverside Riverside CA 92521 USA

Department of Molecular Genetics Darmstadt University of Technology 64287 Darmstadt Germany

Institute of Cell Biology University of Bern Baltzerstrasse 4 Bern CH 3012 Switzerland

Institute of Immunology and Infection Research University of Edinburgh Edinburgh EH9 3FL UK

Institute of Parasitology Biology Centre Czech Academy of Sciences and Faculty of Sciences University of South Bohemia České Budějovice Czech Republic

Institute of Parasitology McGill University 21 111 Lakeshore Road Ste Anne de Bellevue H9X3V9 Québec Canada

Life Science Research Centre Faculty of Science University of Ostrava Ostrava Czech Republic; Martsinovsky Institute of Medical Parasitology Sechenov University Moscow Russia

Parasitology Laboratory Wadsworth Center New York State Department of Health Albany NY 12201 USA

School of Life Science and Technology ShanghaiTech University Shanghai 201210 China

University of Minnesota Medical School Duluth campus Duluth MN 55812 USA

Zobrazit více v PubMed

Steverding D (2008) The history of African trypanosomiasis. Parasit. Vectors 1, 3. PubMed PMC

Maslov DA et al. (2019) Recent advances in trypanosomatid research: genome organization, expression, metabolism, taxonomy and evolution. Parasitology 146, 1–27 PubMed

Ramrath DJF et al. (2018) Evolutionary shift toward protein based architecture in trypanosomal mitochondrial ribosomes. Science 362, eaau7735. PubMed

Simpson AM et al. (1989) Kinetoplastid mitochondria contain functional tRNAs which are encoded in nuclear DNA and also small minicircle and maxicircle transcripts of unknown function. Nucleic Acids Res. 17, 5427–5445 PubMed PMC

Hancock K and Hajduk SL (1990) The mitochondrial tRNAs of Trypanosoma brucei are nuclear encoded. J. Biol. Chem 265, 19208–19215 PubMed

Benne R et al. (1986) Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 46, 819–826 PubMed

Gray MW et al. (2010) Cell biology. Irremediable complexity? Science 330, 920–921 PubMed

Ochsenreiter T et al. (2008) Alternative mRNA editing in trypanosomes is extensive and may contribute to mitochondrial protein diversity. PLoS ONE 3, e1566. PubMed PMC

Ochsenreiter T et al. (2007) KISS: the kinetoplastid RNA editing sequence search tool. RNA 13, 1–4 PubMed PMC

Kirby LE et al. (2016) Analysis of the Trypanosoma brucei EATRO 164 bloodstream guide RNA transcriptome. PLoS Negl. Trop. Dis 10, e0004793. PubMed PMC

Koslowsky D et al. (2014) The insect-phase gRNA transcriptome in Trypanosoma brucei. Nucleic Acids Res. 42, 1873–1886 PubMed PMC

Aphasizhev R and Aphasizheva I (2014) Mitochondrial RNA editing in trypanosomes: Small RNAs in control. Biochimie 100, 125–131 PubMed PMC

Aphasizhev R and Aphasizheva I (2011) Uridine insertion/deletion mRNA editing in trypanosomes: a playground for RNA-guided information transfer. Wiley Interdiscip. Rev. RNA 2, 669–685 PubMed PMC

Hashimi H et al. (2013) Dual core processing: MRB1 is an emerging kinetoplast RNA editing complex. Trends Parasitol. 29, 91–99 PubMed PMC

Read LK et al. (2016) Trypanosome RNA editing: the complexity of getting U in and taking U out. Wiley Interdiscip. Rev. RNA 7, 33–51 PubMed PMC

Goringer HU (2012) ‘Gestalt,’ composition and function of the Trypanosoma brucei editosome. Annu. Rev. Microbiol 66, 65–82 PubMed

Cruz-Reyes J et al. (2018) Dynamic RNA holo-editosomes with subcomplex variants: Insights into the control of trypanosome editing. Wiley Interdiscip. Rev. RNA 9, e1502. PubMed PMC

Zimmer SL et al. (2018) High throughput sequencing revolution reveals conserved fundamentals of U-indel editing. Wiley Interdiscip. Rev. RNA 9, e1487 PubMed PMC

Sement FM et al. (2018) Transcription initiation defines kinetoplast RNA boundaries. Proc. Natl. Acad. Sci. U. S. A 115, E10323–E10332 PubMed PMC

Suematsu T et al. (2016) Antisense transcripts delimit exonucleolytic activity of the mitochondrial 3’ processome to generate guide RNAs. Mol. Cell 61, 364–378 PubMed PMC

Aphasizheva I and Aphasizhev R (2010) RET1-catalyzed uridylylation shapes the mitochondrial transcriptome in Trypanosoma brucei. Mol. Cell. Biol 30, 1555–1567 PubMed PMC

Mattiacio JL and Read LK (2008) Roles for TbDSS-1 in RNA surveillance and decay of maturation by-products from the 12S rRNA locus. Nucleic Acids Res. 36, 319–329 PubMed PMC

Ryan CM and Read LK (2005) UTP-dependent turnover of Trypanosoma brucei mitochondrial mRNA requires UTP polymerization and involves the RET1 TUTase. RNA 11, 763–773 PubMed PMC

Kao CY and Read LK (2005) Opposing effects of polyadenylation on the stability of edited and unedited mitochondrial RNAs in Trypanosoma brucei. Mol. Cell. Biol 25, 1634–1644 PubMed PMC

Zhang L et al. (2017) PPR polyadenylation factor defines mitochondrial mRNA identity and stability in trypanosomes. EMBOJ. 36, 2435–2454 PubMed PMC

Aphasizheva I et al. (2011) Pentatricopeptide repeat proteins stimulate mRNA adenylation/uridylation to activate mitochondrial translation in trypanosomes. Mol. Cell 42, 106–117 PubMed PMC

Etheridge RD et al. (2008) 3’ adenylation determines mRNA abundance and monitors completion of RNA editing in T. brucei mitochondria. EMBO J. 27, 1596–1608 PubMed PMC

Mesitov MV et al. (2019) Pentatricopeptide repeat poly(A) binding protein KPAF4 stabilizes mitochondrial mRNAs in Trypanosoma brucei. Nat. Commun 10, 146. PubMed PMC

Aphasizheva I et al. (2016) Ribosome-associated pentatricopeptide repeat proteins function as translational activators in mitochondria of trypanosomes. Mol. Microbiol 99, 1043–1058 PubMed PMC

Ridlon L et al. (2013) The importance of the 45S ribosomal small subunit-related complex for mitochondrial translation in Trypanosoma brucei. J. Biol. Chem 288, 32963–32978 PubMed PMC

Saurer M et al. (2019) Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machinery. Science 365, 1144–1149 PubMed

Stuart KD et al. (2005) Complex management: RNA editing in trypanosomes. Trends Biochem. Sci 30, 97–105 PubMed

Simpson L et al. (2010) Guide to the nomenclature of kinetoplastid RNA editing: a proposal. Protist 161, 2–6 PubMed PMC

Read LK et al. (1992) Extensive editing of both processed and preprocessed maxicircle CR6 transcripts in Trypanosoma brucei. J. Biol. Chem 267, 1123–1128 PubMed

Koslowsky DJ and Yahampath G (1997) Mitochondrial mRNA 3’ cleavage polyadenylation and RNA editing in Trypanosoma brucei are independent events. Mol. Biochem. Parasitol 90, 81–94 PubMed

Michelotti EF et al. (1992) Trypanosoma brucei mitochondrial ribosomal RNA synthesis, processing and developmentally regulated expression. Mol. Biochem. Parasitol 54, 31–42 PubMed

Carnes J et al. (2015) Bloodstream form Trypanosoma brucei do not require mRPN1 for gRNA processing. RNA 21, 28–35 PubMed PMC

Adler BK et al. (1991) Modification of Trypanosoma brucei mitochondrial rRNA by posttranscriptional 3’ polyuridine tail formation. Mol. Cell. Biol 11, 5878–5884 PubMed PMC

Bhat GJ et al. (1991) The two ATPase 6 mRNAs of Leishmania tarentolae differ at their 3’ ends. Mol. Biochem. Parasitol 48, 139–150 PubMed

Blum B et al. (1990) A model for RNA editing in kinetoplastid mitochondria: ‘Guide’ RNA molecules transcribed from maxicircle DNA provide the edited information. Cell 60, 189–198 PubMed

Madina BR et al. (2011) Guide RNA biogenesis involves a novel RNase III family endoribonuclease in Trypanosoma brucei. RNA 17, 1821–1830 PubMed PMC

Schnaufer A et al. (2001) An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei. Science 291, 2159–2161 PubMed

Aphasizhev R et al. (2003) A tale of two TUTases. Proc. Natl. Acad. Sci. U. S. A 100, 10617–10622 PubMed PMC

Aphasizhev R et al. (2002) Trypanosome mitochondrial 3’ terminal uridylyl transferase (TUTase): the key enzyme in U-insertion/deletion RNA editing. Cell 108, 637–648 PubMed

Aphasizheva I et al. (2004) RNA-editing terminal uridylyl transferase 1: identification of functional domains by mutational analysis. J. Biol. Chem 279, 24123–24130 PubMed

Aphasizheva I et al. (2014) RNA binding and core complexes constitute the U-insertion/deletion editosome. Mol. Cell. Biol 34, 4329–4342 PubMed PMC

Aphasizhev R et al. (2016) Constructive edge of uridylation-induced RNA degradation. RNA Biol. 13, 1078–1083 PubMed PMC

Menezes MR et al. (2018) 3’ RNA uridylation in epitranscriptomics, gene regulation, and disease. Front. Mol. Biosci 5, 61. PubMed PMC

Jasmer D and Stuart K (1986) Sequence organization in African trypanosome minicircles is defined by 18 base pair inverted repeats. Mol. Biochem. Parasitol 18, 321–332 PubMed

Pollard VW et al. (1990) Organization of minicircle genes for guide RNAs in Trypanosoma brucei. Cell 63, 783–790 PubMed

Cooper S et al. (2019) Assembly and annotation of the mitochondrial minicircle genome of a differentiation-competent strain of Trypanosoma brucei. Nucleic Acids Res. 47, 11304–11325 PubMed PMC

Simpson L et al. (2015) Comparison of the mitochondrial genomes and steady state transcriptomes of two strains of the trypanosomatid parasite, Leishmania tarentolae. PLoS Negl. Trop. Dis 9, e0003841. PubMed PMC

Simpson RM et al. (2016) High-throughput sequencing of partially edited trypanosome mRNAs reveals barriers to editing progression and evidence for alternative editing. RNA 22, 677–695 PubMed PMC

Chung CZ et al. (2017) Tipping the balance of RNA stability by 3’ editing of the transcriptome. Biochim. Biophys. Acta Gen. Subj 1861, 2971–2979 PubMed

Ryan CM et al. (2003) Polyadenylation regulates the stability of Trypanosoma brucei mitochondrial RNAs. J. Biol. Chem 278, 32753–32762 PubMed

Small ID and Peeters N (2000) The PPR motif–ma TPR related motif prevalent in plant organellar proteins. Trends Biochem. Sci 25, 46–47 PubMed

Shen C et al. (2016) Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins. Nat. Commun 7, 11285. PubMed PMC

Barkan A and Small I (2014) Pentatricopeptide repeat proteins in plants. Annu. Rev. Plant Biol 65, 415–442 PubMed

Pfalz J et al. (2009) Site-specific binding of a PPR protein defines and stabilizes 5’ and 3’ mRNA termini in chloroplasts. EMBO J. 28, 2042–2052 PubMed PMC

Cheng S et al. (2016) Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants. Plant J. 85, 532–547 PubMed

Feagin JE et al. (1988) Creation of AUG initiation codons by addition of uridines within cytochrome b transcripts of kinetoplastids. PNAS 85, 539–543 PubMed PMC

Koslowsky DJ et al. (1990) The MURF3 gene of T. brucei contains multiple domains of extensive editing and is homologous to a subunit of NADH dehydrogenase. Cell 62, 901–911 PubMed

Seiwert SD et al. (1996) Direct visualization of uridylate deletion in vitro suggests a mechanism for kinetoplastid RNA editing. Cell 84, 831–841 PubMed

Kable ML et al. (1996) RNA editing: a mechanism for gRNAspecified uridylate insertion into precursor mRNA [see comments]. Science 273, 1189–1195 PubMed

Seiwert SD and Stuart K (1994) RNA editing: transfer of genetic information from gRNA to precursor mRNA in vitro. Science 266, 114–117 PubMed

Sturm NR and Simpson L (1990) Kinetoplast DNA minicircles encode guide RNAs for editing of cytochrome oxidase subunit III mRNA. Cell 61, 879–884 PubMed

Golden DE and Hajduk SL (2005) The 3’-untranslated region of cytochrome oxidase II mRNA functions in RNA editing of African trypanosomes exclusively as a cis guide RNA. RNA 11, 29–37 PubMed PMC

Koslowsky DJ et al. (1991) Cycles of progressive realignment of gRNA with mRNA in RNA editing. Cell 67, 537–546 PubMed

Simpson RM et al. (2017) Trypanosome RNA Editing Mediator Complex proteins have distinct functions in gRNA utilization. Nucleic Acids Res. 45, 7965–7983 PubMed PMC

Gerasimov ES et al. (2018) Trypanosomatid mitochondrial RNA editing: dramatically complex transcript repertoires revealed with a dedicated mapping tool. Nucleic Acids Res. 46,765–781 PubMed PMC

Maslov DA and Simpson L (1992) The polarity of editing within a multiple gRNA-mediated domain is due to formation of anchors for upstream gRNAs by downstream editing. Cell 70, 459–467 PubMed

Igo RP Jr. et al. (2002) RNA sequence and base pairing effects on insertion editing in Trypanosoma brucei. Mol. Cell. Biol 22, 1567–1576 PubMed PMC

Blanc V et al. (1999) The mitochondrial RNA ligase from Leishmania tarentolae can join RNA molecules bridged by a complementary RNA. J. Biol. Chem 274, 24289–24296 PubMed

Cruz-Reyes J et al. (2001) Trypanosome RNA editing: simple guide RNA features enhance U deletion 100-fold. Mol. Cell. Biol 21, 884–892 PubMed PMC

Aphasizhev R et al. (2003) Isolation of a U-insertion/deletion editing complex from Leishmania tarentolae mitochondria. EMBO J. 22, 913–924 PubMed PMC

Panigrahi AK et al. (2003) Identification of novel components of Trypanosoma brucei editosomes. RNA 9, 484–492 PubMed PMC

Golas MM et al. (2009) Snapshots of the RNA editing machine in trypanosomes captured at different assembly stages in vivo. EMBO J. 28, 766–778 PubMed PMC

Li F et al. (2009) Structure of the core editing complex (L-complex) involved in uridine insertion/deletion RNA editing in trypanosomatid mitochondria. Proc. Natl. Acad. Sci. U. S. A 106, 12306–12310 PubMed PMC

Rusche LN et al. (1997) Purification of a functional enzymatic editing complex from Trypanosoma brucei mitochondria. EMBO J. 16, 4069–4081 PubMed PMC

Guo X et al. (2012) KREPB6, KREPB7, and KREPB8 are important for editing endonuclease function in Trypanosoma brucei. RNA 18, 308–320 PubMed PMC

Carnes J et al. (2012) KREX2 is not essential for either procyclic or bloodstream form Trypanosoma brucei. PLoS ONE 7, e33405. PubMed PMC

Ernst NL et al. (2009) Differential functions of two editosome exoUases in Trypanosoma brucei. RNA 15, 947–957 PubMed PMC

Carnes J et al. (2008) RNA Editing in Trypanosoma brucei requires three different editosomes. Mol. Cell. Biol 28, 122–130 PubMed PMC

Carnes J et al. (2017) In vivo cleavage specificity of Trypanosoma brucei editosome endonucleases. Nucleic Acids Res. 45, 4667–4686 PubMed PMC

Macrae IJ and Doudna JA (2007) Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Curr. Opin. Struct. Biol 17, 138–145 PubMed

Carnes J et al. (2012) Mutational analysis of Trypanosoma brucei editosome proteins KREPB4 and KREPB5 reveals domains critical for function. RNA 18, 1897–1909 PubMed PMC

McDermott SM et al. (2019) Editosome RNase III domain interactions are essential for editing and differ between life cycle stages in Trypanosoma brucei. RNA 25, 1150–1163 PubMed PMC

McDermott SM and Stuart K (2017) The essential functions of KREPB4 are developmentally distinct and required for endonuclease association with editosomes. RNA 23, 1672–1684 PubMed PMC

McDermott SM et al. (2016) The Architecture of Trypanosoma brucei editosomes. Proc. Natl. Acad. Sci. U. S. A 113, E6476–E6485 PubMed PMC

Schnaufer A et al. (2003) Separate Insertion and deletion subcomplexes of the Trypanosoma brucei RNA editing complex. Mol. Cell 12, 307–319 PubMed

Schnaufer A et al. (2010) A protein–protein interaction map of trypanosome ~20S editosomes. J. Biol. Chem 285, 5282–5295 PubMed PMC

Kang X et al. (2006) Reconstitution of full-round uridinedeletion RNA editing with three recombinant proteins. Proc. Natl. Acad. Sci. U. S. A 103, 13944–13949 PubMed PMC

Gao G et al. (2005) Functional complementation of Trypanosoma brucei RNA in vitro editing with recombinant RNA ligase. Proc. Natl. Acad. Sci. U. S. A 102, 4712–4717 PubMed PMC

Rogers K et al. (2007) Uridylate-specific 3’ 5’-exoribonucleases involved in uridylate-deletion RNA editing in trypanosomatid mitochondria. J. Biol. Chem 282, 29073–29080 PubMed

Ringpis GE et al. (2010) Mechanism of U insertion RNA editing in trypanosome mitochondria: the bimodal TUTase activity of the core complex. J. Mol. Biol 399, 680–695 PubMed PMC

Ringpis GE et al. (2010) Mechanism of U-insertion RNA editing in trypanosome mitochondria: characterization of RET2 functional domains by mutational analysis. J. Mol. Biol 399, 696–706 PubMed PMC

Ernst NL et al. (2003) TbMP57 is a 3’ terminal uridylyl transferase (TUTase) of the Trypanosoma brucei editosome. Mol. Cell 11, 1525–1536 PubMed

Deng J et al. (2005) Structural basis for UTP specificity of RNA editing TUTases from Trypanosoma brucei. EMBO J. 24,4007–4017 PubMed PMC

Gao G and Simpson L (2003) 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 PubMed

Huang CE et al. (2001) Roles for ligases in the RNA editing complex of Trypanosoma brucei: band IV is needed for U-deletion and RNA repair. EMBO J. 20, 4694–4703 PubMed PMC

Pollard VW et al. (1992) Native mRNA editing complexes from Trypanosoma brucei mitochondria. EMBO J. 11, 4429–4438 PubMed PMC

Osato D et al. (2009) Uridine insertion/deletion RNA editing in trypanosomatid mitochondria: In search of the editosome. RNA 15, 1338–1344 PubMed PMC

Aphasizheva I and Aphasizhev R (2015) U-insertion/deletion mRNA-editing holoenzyme: definition in sight. Trends Parasitol. 13, 1078–1083 PubMed PMC

Panigrahi AK et al. (2007) Mitochondrial complexes in Trypanosoma brucei: a novel complex and a unique oxidoreductase complex. Mol. Cell Proteomics 7, 534–545 PubMed

Weng J et al. (2008) Guide RNA-binding complex from mitochondria of trypanosomatids. Mol. Cell 32, 198–209 PubMed PMC

Hashimi H et al. (2009) Kinetoplastid guide RNA biogenesis is dependent on subunits of the mitochondrial RNA binding complex 1 and mitochondrial RNA polymerase. RNA 15, 588–599 PubMed PMC

Madina BR et al. (2014) Native mitochondrial RNA-binding complexes in kinetoplastid RNA editing differ in guide RNA composition. RNA 20, 1142–1152 PubMed PMC

Huang Z et al. (2015) Integrity of the core mitochondrial RNA binding complex 1 is vital for trypanosome RNA editing. RNA 21, 2088–2102 PubMed PMC

McAdams NM et al. (2019) MRB10130 is a RESC assembly factor that promotes kinetoplastid RNA editing initiation and progression. RNA 25, 1177–1191 PubMed PMC

McAdams NM et al. (2018) MRB7260 is essential for productive protein–RNA interactions within the RNA editing substrate binding complex during trypanosome RNA editing. RNA 24, 540–556 PubMed PMC

Ammerman ML et al. (2010) TbRGG2 facilitates kinetoplastid RNA editing initiation and progression past intrinsic pause sites. RNA 16, 2239–2251 PubMed PMC

Dixit S et al. (2017) Differential binding of mitochondrial transcripts by MRB8170 and MRB4160 regulates distinct editing fates of mitochondrial mRNA in trypanosomes. mBio 8, e02288–16 PubMed PMC

Ammerman ML et al. (2012) Architecture of the trypanosome RNA editing accessory complex, MRB1. Nucleic Acids Res. 40, 5637–5650 PubMed PMC

Aphasizhev R et al. (2003) A 100-kD complex of two RNA binding proteins from mitochondria of Leishmania tarentolae catalyzes RNA annealing and interacts with several RNA editing components. RNA 9, 62–76 PubMed PMC

Nikpour N and Salavati R (2019) The RNA binding activity of the first identified trypanosome protein with Z-DNA-binding domains. Sci. Rep 9, 5904. PubMed PMC

Kumar V et al. (2019) Protein features for assembly of the RNA editing helicase 2 subcomplex (REH2C) in trypanosome holo-editosomes. PLoS One 14, e0211525. PubMed PMC

Madina BR et al. (2015) Native variants of the MRB1 complex exhibit specialized functions in kinetoplastid RNA editing. PLoS ONE 10, e0123441. PubMed PMC

Hernandez A et al. (2010) REH2 RNA helicase in kinetoplastid mitochondria: ribonucleoprotein complexes and essential motifs for unwinding and guide RNA (gRNA) binding. J. Biol. Chem 285, 1220–1228 PubMed PMC

Kumar V et al. (2016) REH2C Helicase and GRBC subcomplexes may base pair through mRNA and small guide RNA in kinetoplastid editosomes. J. Biol. Chem 291, 5753–5764 PubMed PMC

Aphasizheva I et al. (2009) Novel TUTase associates with an editosome-like complex in mitochondria of Trypanosoma brucei. RNA 15, 1322–1337 PubMed PMC

Stagno J et al. (2010) Structure of the mitochondrial editosome-like complex associated TUTase 1 reveals divergent mechanisms of UTP selection and domain organization. J. Mol. Biol 399, 464–475 PubMed PMC

Kao CY and Read LK (2007) Targeted depletion of a mitochondrial nucleotidyltransferase suggests the presence of multiple enzymes that polymerize mRNA 3’ tails in Trypanosoma brucei mitochondria. Mol. Biochem. Parasitol 154, 158–169 PubMed PMC

Missel A et al. (1997) Disruption of a gene encoding a novel mitochondrial DEAD-box protein in Trypanosoma brucei affects edited mRNAs. Mol. Cell. Biol 17, 4895–4903 PubMed PMC

Li F et al. (2011) Trypanosome REH1 is an RNA helicase involved with the 3’−5’ polarity of multiple gRNA-guided uridine insertion/deletion RNA editing. Proc. Natl. Acad. Sci. U. S. A 108, 3542–3547 PubMed PMC

Koller J et al. (1997) Trypanosoma brucei gBP21. An arginine rich mitochondrial protein that binds to guide RNA with high affinity. J. Biol. Chem 272, 3749–3757 PubMed

Blom D et al. (2001) Cloning and characterization of two guide RNA-binding proteins from mitochondria of Crithidia fasciculata: gBP27, a novel protein, and gBP29, the orthologue of Trypanosoma brucei gBP21. Nucleic Acids Res. 29, 2950–2962 PubMed PMC

Zikova A et al. (2008) Structure and function of the native and recombinant mitochondrial MRP1/MRP2 complex from Trypanosoma brucei. Int. J. Parasitol 38, 901–912 PubMed PMC

Schumacher MA et al. (2006) Crystal structures of T. bruceiMRP1/MRP2 guide-RNA binding complex reveal RNA matchmaking mechanism. Cell 126, 701–711 PubMed

Muller UF and Goringer HU (2002) Mechanism of the gBP21-mediated RNA/RNA annealing reaction: matchmaking and charge reduction. Nucleic Acids Res. 30, 447–455 PubMed PMC

Muller UF et al. (2001) Annealing of RNA editing substrates facilitated by guide RNA-binding protein gBP21. EMBO J. 20, 1394–1404 PubMed PMC

Tylec BL et al. (2019) Intrinsic and regulated properties of minimally edited trypanosome mRNAs. Nucleic Acids Res. 47, 3640–3657 PubMed PMC

Fisk JC et al. (2009) Distinct and overlapping functions of MRP1/2 and RBP16 in mitochondrial RNA metabolism. Mol. Cell. Biol 29, 5214–5225 PubMed PMC

Vondruskova E et al. (2005) RNA interference analyses suggest a transcript-specific regulatory role for mitochondrial RNA-binding proteins MRP1 and MRP2 in RNA editing and other RNA processing in Trypanosoma brucei. J. Biol. Chem 280, 2429–2438 PubMed

Hayman ML and Read LK (1999) Trypanosoma brucei RBP16 is a mitochondrial Y-box family protein with guide RNA binding activity. J. Biol. Chem 274, 12067–12074 PubMed

Ammerman ML et al. (2008) gRNA/pre-mRNA annealing and RNA chaperone activities of RBP16. RNA 14, 1069–1080 PubMed PMC

Miller MM et al. (2006) RBP16 stimulates trypanosome RNA editing in vitro at an early step in the editing reaction. RNA 12, 1292–1303 PubMed PMC

Pelletier M and Read LK (2003) RBP16 is a multifunctional gene regulatory protein involved in editing and stabilization of specific mitochondrial mRNAs in Trypanosoma brucei. RNA 9, 457–468 PubMed PMC

Miller MM and Read LK (2003) Trypanosoma brucei: functions of RBP16 cold shock and RGG domains in macromolecular interactions. Exp. Parasitol 105, 140–148 PubMed

Vanhamme L et al. (1998) Trypanosoma brucei TBRGG1, a mitochondrial oligo(U)-binding protein that co-localizes with an in vitro RNA editing activity. J. Biol. Chem 273, 21825–21833 PubMed

Hashimi H et al. (2008) TbRGG1, an essential protein involved in kinetoplastid RNA metabolism that is associated with a novel multiprotein complex. RNA 14, 970–980 PubMed PMC

McAdams NM et al. (2015) An arginine-glycine-rich RNA binding protein impacts the abundance of specific mRNAs in the mitochondria of Trypanosoma brucei. Eukaryot. Cell 14, 149–157 PubMed PMC

Shaw PL et al. (2015) Structures of the T. brucei kRNA editing factor MRB1590 reveal unique RNA-binding pore motif contained within an ABC-ATPase fold. Nucleic Acids Res. 43, 7096–7109 PubMed PMC

Madison-Antenucci S and Hajduk SL (2001) RNA editing-associated protein 1 is an RNA binding protein with specificity for preedited mRNA. Mol. Cell 7, 879–886 PubMed

Madison-Antenucci S et al. (1998) Kinetoplastid RNA-editing associated protein 1 (REAP-1): a novel editing complex protein with repetitive domains. EMBO J. 17, 6368–6376 PubMed PMC

Hans J et al. (2007) RNA-editing-associated protein 1 null mutant reveals link to mitochondrial RNA stability. RNA 13, 881–889 PubMed PMC

Dixit S and Lukes J (2018) Combinatorial interplay of RNA binding proteins tunes levels of mitochondrial mRNA in trypanosomes. RNA 24, 1594–1606 PubMed PMC

Zimmer SL et al. (2011) A novel member of the RNase D exoribonuclease family functions in mitochondrial guide RNA metabolism in Trypanosoma brucei. J. Biol. Chem 286, 10329–10340 PubMed PMC

Taschner A et al. (2012) Nuclear RNase P of Trypanosoma brucei: a single protein in place of the multicomponent RNA protein complex. Cell Rep. 2, 19–25 PubMed PMC

Salavati R et al. (2001) Mitochondrial ribonuclease P activity of Trypanosoma brucei. Mol. Biochem. Parasitol 115, 109–117 PubMed

Kapushoc ST et al. (2002) Differential localization of nuclear encoded tRNAs between the cytosol and mitochondrion in Leishmania tarentolae. RNA 8, 57–68 PubMed PMC

Kapushoc ST et al. (2000) End processing precedes mitochondrial importation and editing of tRNAs in Leishmania tarentolae. J. Biol. Chem 275, 37907–37914 PubMed

Rajappa-Titu L et al. (2016) RNA Editing TUTase 1: structural foundation of substrate recognition, complex interactions and drug targeting. Nucleic Acids Res. 44, 10862–10878 PubMed PMC

Mattiacio JL and Read LK (2009) Evidence for a degradosome-like complex in the mitochondria of Trypanosoma brucei. FEBS Lett. 583, 2333–2338 PubMed PMC

Mingler MK et al. (2006) Identification of pentatricopeptide repeat proteins in Trypanosoma brucei. Mol. Biochem. Parasitol 150, 37–45 PubMed

Pusnik M et al. (2007) Pentatricopeptide repeat proteins in Trypanosoma brucei function in mitochondrial ribosomes. Mol. Cell. Biol 27, 6876–6888 PubMed PMC

Trotter JR et al. (2005) A deletion site editing endonuclease in Trypanosoma brucei. Mol. Cell 20, 403–412 PubMed

Carnes J et al. (2005) An essential RNase III insertion editing endonuclease in Trypanosoma brucei. Proc. Natl. Acad. Sci.U. S. A 102, 16614–16619 PubMed PMC

Drozdz M et al. (2002) TbMP81 is required for RNA editing in Trypanosoma brucei. EMBO J. 21, 1791–1799 PubMed PMC

McDermott SM et al. (2015) Differential editosome protein function between life cycle stages of Trypanosoma brucei. J. Biol. Chem 290, 24914–24931 PubMed PMC

Salavati R et al. (2006) KREPA4, an RNA binding protein es- sential for editosome integrity and survival of Trypanosoma brucei. RNA 12, 819–831 PubMed PMC

Law JA et al. (2007) In Trypanosoma brucei RNA editing,TbMP18 (band VII) is critical for editosome integrity and for both insertional and deletional cleavages. Mol. Cell. Biol 27, 777–787 PubMed PMC

Tarun SZ Jr. et al. (2008) KREPA6 is an RNA-binding protein essential for editosome integrity and survival of Trypanosoma brucei. RNA 14, 347–358 PubMed PMC

McDermott SM et al. (2015) Identification by random mutagenesis of functional domains in KREPB5 that differentially af- fect RNA editing between life cycle stages of Trypanosoma brucei. Mol. Cell. Biol 35, 3945–3961 PubMed PMC

Carnes J et al. (2018) RNase III domain of KREPB9 and KREPB10 association with editosomes in Trypanosoma brucei. mSphere 3, e00585–17 PubMed PMC

Acestor N et al. (2009) The MRB1 complex functions in kinetoplastid RNA processing. RNA 15, 277–286 PubMed PMC

Ammerman ML et al. (2013) A core MRB1 complex component is indispensable for RNA editing in insect and human infective stages of Trypanosoma brucei. PLoS ONE 8, e78015. PubMed PMC

Ammerman ML et al. (2011) MRB3010 is a core component of the MRB1 complex that facilitates an early step of the kinetoplastid RNA editing process. RNA 17, 865–877 PubMed PMC

Kafkova L et al. (2012) Functional characterization of two paralogs that are novel RNA binding proteins influencing mitochondrial transcripts of Trypanosoma brucei. RNA 18, 1846–1861 PubMed PMC

Fisk JC et al. (2008) TbRGG2, an essential RNA editing accessory factor in two Trypanosoma brucei life cycle stages. J. Biol. Chem 283, 23016–23025 PubMed PMC

Foda BM et al. (2012) Multifunctional G-rich and RRM containing domains of TbRGG2 perform separate yet essential functions in trypanosome RNA editing. Eukaryot. Cell 11, 1119–1131 PubMed PMC

Travis B et al. (2019) The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA. Nucleic Acids Res. 47, 2130–2142 PubMed PMC

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