Kinetoplastid guide RNA biogenesis is dependent on subunits of the mitochondrial RNA binding complex 1 and mitochondrial RNA polymerase

. 2009 Apr ; 15 (4) : 588-99. [epub] 20090218

Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid19228586

The mitochondrial RNA binding complex 1 (MRB1) is a recently discovered complex of proteins associated with the TbRGG1 and TbRGG2 proteins in Trypanosoma brucei. Based on the phenotype caused by down-regulation of these two proteins, it was proposed to play an unspecified role in RNA editing. RNAi silencing of three newly characterized protein subunits, guide RNA associated proteins (GAPs) 1 and 2 as well as a predicted DExD/H-box RNA helicase, show they are essential for cell growth in the procyclic stage. Furthermore, their down-regulation leads to inhibition of editing in only those mRNAs for which minicircle-encoded guide (g) RNAs are required. However, editing remains unaffected when the maxicircle-encoded cis-acting gRNA is employed. Interestingly, all three proteins are necessary for the expression of the minicircle-encoded gRNAs. Moreover, down-regulation of a fourth assayed putative MRB1 subunit, Nudix hydrolase, does not appear to destabilize gRNAs, and down-regulation of this protein has a general impact on the stability of maxicircle-encoded RNAs. GAP1 and 2 are also essential for the survival of the bloodstream stage, in which the gRNAs become eliminated upon depletion of either protein. Immunolocalization revealed that GAP1 and 2 are concentrated into discrete spots along the mitochondrion, usually localized in the proximity of the kinetoplast. Finally, we demonstrate that the same mtRNA polymerase known to transcribe the maxicircle mRNAs may also have a role in expression of the minicircle-encoded gRNAs.

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Aphasizhev R., Aphasizheva I., Simpson L. A tale of two TUTases. Proc. Natl. Acad. Sci. 2003;100:10617–10622. PubMed PMC

Benne R., van den Burg J., Brakenhoff J.P., Sloof P., Van Boom J.H., Tromp M.C. Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell. 1986;46:819–826. PubMed

Blum B., Simpson L. Guide RNAs in kinetoplastid mitochondria have a nonencoded 3′ oligo(U) tail involved in recognition of the preedited region. Cell. 1990;62:391–397. PubMed

Blum B., Bakalara N., Simpson L. A model for RNA editing in kinetoplastid mitochondria: “Guide” RNA molecules transcribed from maxicircle DNA provide the edited information. Cell. 1990;60:189–198. PubMed

Carnes J., Trotter J.R., Ernst N.L., Steinberg A.G., Stuart K. An essential RNase III insertion editing endonuclease in Trypanosoma brucei. Proc. Natl. Acad. Sci. 2005;102:16614–16619. PubMed PMC

Carnes J., Trotter J.R., Peltan A., Fleck M., Stuart K. RNA editing in Trypanosoma brucei requires three different editosomes. Mol. Cell. Biol. 2008;28:122–130. PubMed PMC

Cohen L.S., Mikhli C., Jiao X., Kiledjian M., Kunkel G., Davis R.E. Dcp2 decaps m2,2,7 GpppN-capped RNAs, and its activity is sequence and context dependent. Mol. Cell. Biol. 2005;25:8779–8791. PubMed PMC

Domingo G.J., Palazzo S.S., Wang B., Panicucci B., Salavati R., Stuart K.D. Dyskinetoplastic Trypanosoma brucei contains functional editing complexes. Eukaryot. Cell. 2003;2:569–577. PubMed PMC

Etheridge R.D., Aphasizheva I., Gershon P.D., Aphasizhev R. 3′ adenylation determines mRNA abundance and monitors completion of RNA editing in T. brucei mitochondria. EMBO J. 2008;27:1596–1608. PubMed PMC

Fisk J.C., Ammerman M.L., Presnyak V., Read L.K. TbRGG2, an essential RNA editing accessory factor in two Trypanosoma brucei life cycle stages. J. Biol. Chem. 2008;283:23016–23025. PubMed PMC

Fuller-Pace F.V. DExD/H box RNA helicases: Multifunctional proteins with important roles in transcriptional regulation. Nucleic Acids Res. 2006;34:4206–4215. PubMed PMC

Golden D.E., Hajduk S.L. The 3′-untranslated region of cytochrome oxidase II mRNA functions in RNA editing of African trypanosomes exclusively as a cis guide RNA. RNA. 2005;11:29–37. PubMed PMC

Grams J., McManus M.T., Hajduk S.L. Processing of polycistronic guide RNAs is associated with RNA editing complexes in Trypanosoma brucei. EMBO J. 2000;19:5525–5532. PubMed PMC

Grams J., Morris J.C., Drew M.E., Wang Z.F., Englund P.T., Hajduk S.L. A trypanosome mitochondrial RNA polymerase is required for transcription and replication. J. Biol. Chem. 2002;277:16952–16959. PubMed

Haile S., Papadopoulou B. Developmental regulation of gene expression in trypanosomatid parasitic protozoa. Curr. Opin. Microbiol. 2007;10:569–577. PubMed

Hashimi H., Zíková A., Panigrahi A.K., Stuart K.D., Lukeš J. TbRGG1, a component of a novel multi-protein complex involved in kinetoplastid RNA editing. RNA. 2008;14:970–980. PubMed PMC

Hermann T., Schmid B., Heumann H., Göringer H.U. A three-dimensional working model for a guide RNA from Trypanosoma brucei. Nucleic Acids Res. 1997;25:2311–2318. PubMed PMC

Klingbeil M.M., Motyka S.A., Englund P.T. Multiple mitochondrial DNA polymerases in Trypanosoma brucei. Mol. Cell. 2002;10:175–186. PubMed

Lai D.-H., Hashimi H., Lun Z.-R., Ayala F.J., Lukeš J. Adaptations of Trypanosoma brucei to gradual loss of kinetoplast DNA: Trypanosoma equiperdum and Trypanosoma evansi are petite mutants of T. brucei. Proc. Natl. Acad. Sci. 2008;105:1999–2004. PubMed PMC

Liu B.Y., Liu Y.N., Motyka S.A., Agbo E.E.C., Englund P.T. Fellowship of the rings: The replication of kinetoplast DNA. Trends Parasitol. 2005;21:363–369. PubMed

Long S., Jirků M., Mach J., Ginger M.L., Sutak R., Richardson D., Tachezy J., Lukeš J. Ancestral roles of eukaryotic frataxin: mitochondrial frataxin function and heterologous expression of hydrogenosomal Trichomonas homologues in trypanosomes. Mol. Microbiol. 2008;69:94–109. PubMed

Lukeš J., Hashimi H., Zíková A. Unexplained complexity of the mitochondrial genome and transcriptome in kinetoplastid flagellates. Curr. Genet. 2005;48:277–299. PubMed

Madison-Antenucci S., Sabatini R.S., Pollard V.W., Hajduk S.L. Kinetoplastid RNA-editing-associated protein 1 (REAP-1): A novel editing complex protein with repetitive domains. EMBO J. 1998;21:6368–6376. PubMed PMC

McClennan A.G. The Nudix hydrolase superfamily. Cell. Mol. Life Sci. 2006;63:123–143. PubMed PMC

Miller M.M., Halbig K., Cruz-Reyes J., Read L.K. RBP16 stimulates trypanosome RNA editing in vitro at an early step in the editing reaction. RNA. 2006;12:1292–1303. PubMed PMC

Müller U.F., Lambert L., Göringer H.U. Annealing of RNA editing substrates facilitated by guide RNA-binding protein gBP21. EMBO J. 2001;20:1394–1404. PubMed PMC

Panigrahi A.K., Schnaufer A., Carmean N., Igo R.P., Jr, Gygi S.P., Ernst N.L., Palazzo S.S., Weston D.S., Aebersold R., Salavati R., et al. Four related proteins of the Trypanosoma brucei RNA editing complex. Mol. Cell. Biol. 2001;21:6833–6840. PubMed PMC

Panigrahi A.K., Ernst N.L., Domingo G.J., Fleck M., Salavati R., Start K.D. Compositionally and functionally distinct editosomes in Trypanosoma brucei. RNA. 2006;12:1038–1049. PubMed PMC

Panigrahi A.K., Zíková A., Halley R.A., Acestor N., Ogata Y., Myler P.J., Stuart K. Mitochondrial complexes in Trypanosoma brucei: A novel complex and a unique oxidoreductase complex. Mol. Cell. Proteomics. 2008;7:534–545. PubMed

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

Pfaffl M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001;29:e45. doi: 10.1093/nar/29.9.e45. PubMed DOI PMC

Schmid B., Riley G.R., Stuart K., Göringer H.U. The secondary structure of guide RNA molecules from Trypanosoma brucei. Nucleic Acids Res. 1995;23:3093–3102. PubMed PMC

Schnaufer A., Panigrahi A.K., Panicucci B., Igo R.P., Jr, Wirtz E., Salavati R., Stuart K. An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei. Science. 2001;291:2159–2162. PubMed

Schnaufer A., Clark-Walker G.D., Steinberg A.G., Stuart K. The F1-ATP synthase complex in bloodstream stage trypanosomes has an unusual and essential function. EMBO J. 2005;24:4029–4040. PubMed PMC

Schumacher M.A., Karamooz E., Zíková A., Trantírek L., Lukeš J. Crystal structures of T. brucei MRP1/MRP2 guide-RNA-binding complex reveals RNA matchmaking mechanism. Cell. 2006;126:701–711. PubMed

Seiwert S.D., Heidmann S., Stuart K. Direct visualization of uridylate deletion in vitro suggests a mechanism for kinetoplastid RNA editing. Cell. 1996;84:831–841. PubMed

Simpson L., Aphasizhev R., Gao G., Kang X. Mitochondrial proteins and complexes in Leishmania and Trypanosoma involved in U insertion/deletion RNA editing. RNA. 2004;10:159–170. PubMed PMC

Sinha K.M., Hines J.C., Downey N., Ray D.S. Mitochondrial DNA ligase in Crithidia fasciculata. Proc. Natl. Acad. Sci. 2004;101:4361–4366. PubMed PMC

Smíd O., Horáková E., Vilímová V., Hrdý I., Cammack R., Horváth A., Lukeš J., Tachezy J. Knockdowns of mitochondrial iron-sulfur cluster assembly proteins IscS and IscU down-regulate the active mitochondrion of procyclic Trypanosoma brucei. J. Biol. Chem. 2006;281:28679–28686. PubMed

Stuart K.D., Schnaufer A., Ernst N.L., Panigrahi A.K. Complex management: RNA editing in trypanosomes. Trends Biochem. Sci. 2005;30:97–105. PubMed

Sturm N., Simpson L. Kinetoplast DNA minicircles encode guide RNAs for editing of cytochrome oxidase subunit III mRNA. Cell. 1990;61:879–884. PubMed

Vanhamme L., Peréz-Morga D., Marechal C., Speijer D., Lambert L., Geuskens M., Alexandre S., Ismaili N., Göringer U., Benne R., et al. Trypanosoma brucei TBRGG1, a mitochondrial oligo(U)-binding protein that co-localizes with an in vitro RNA editing activity. J. Biol. Chem. 1998;273:21825–21833. PubMed

Vassella E., Kramer R., Turner C.M.R., Wankell M., Modes C., Van den Bogaard M., Boshart M. Deletion of a novel protein kinase with PX and FYVE-related domains increases the rate of differentiation of Trypanosoma brucei. Mol. Microbiol. 2001;41:33–46. PubMed

Vondrušková E., van den Burg J., Zíková A., Ernst N.L., Stuart K., Benne R., Lukeš J. RNA interference analyses suggest a transcript-specific regulatory role for MRP1 and MRP2 in RNA editing and other RNA processing in Trypanosoma brucei. J. Biol. Chem. 2005;280:2429–2438. PubMed

Weng J., Aphasizheva I., Etheridge R.D., Huang L., Wang X., Falick A.M., Aphasizhev R. Guide RNA-binding complex from mitochondria of trypanosomatids. Mol. Cell. 2008;32:1–12. PubMed PMC

Zíková A., Kopečná J., Schumacher M.A., Stuart K.D., Trantírek L., Lukeš J. Structure and function of the native and recombinant mitochondrial MRP1/MRP2 complex from Trypanosoma brucei. Int. J. Parasitol. 2008;38:901–912. PubMed PMC

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