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RNA Technologies for Mitochondrial Genetics

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From Nucleic Acids Sequences to Molecular Medicine

Part of the book series: RNA Technologies ((RNATECHN))

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Abstract

Mitochondria ensure fundamental functions in eukaryotic cells. They possess their own genetic system that provides a number of essential polypeptides of the oxidative phosphorylation chain. As a consequence, the respiratory complexes are built from both nuclear-encoded and organellar-encoded subunits. Mitochondrial biogenesis and response to the energetic or metabolic demands of the cell thus relies on elaborate regulation networks and continuous cross talk with the nucleus, as well as with plastids in plants. Main questions remain open regarding these control mechanisms and their relation with the complex transcriptional and posttranscriptional processes that take place in mitochondria. In particular, the field of organelle noncoding RNAs is growing and points to an involvement of mitochondria in cellular RNA interference. To gain further knowledge, manipulating the organelle genetic system is the obvious way to go, but mitochondrial transformation remains restricted to a couple of unicellular organisms. The scientific challenge is of wide relevance, as mutations or rearrangements in the mitochondrial genome cause incurable neurodegenerative diseases in human or lead to cytoplasmic male sterility in plants. RNA technologies may provide another path, as mitochondria naturally import several types of RNA, depending on the organism. Exploiting the natural mechanisms to target customized RNAs to or into mitochondria has begun. Considering their high specificity versus interfering RNAs, catalytic RNAs are of particular interest for such strategies. Major breakthrough has already been obtained in silencing mitochondrial RNAs through the import of trans-cleaving hammerhead ribozymes.

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References

  • Adhya S (2008) Leishmania mitochondrial tRNA importers. Int J Biochem Cell Biol 40:2681–2685

    Article  PubMed  CAS  Google Scholar 

  • Adhya S, Mahato B, Jash S et al (2011) Mitochondrial gene therapy: the tortuous path from bench to bedside. Mitochondrion 11:839–844

    Article  PubMed  CAS  Google Scholar 

  • Ahmed AU, Fisher PR (2009) Import of nuclear-encoded mitochondrial proteins: a cotranslational perspective. Int Rev Cell Mol Biol 273:49–68

    Article  PubMed  CAS  Google Scholar 

  • Allen JO, Fauron CM, Minx P et al (2007) Comparisons among two fertile and three male-sterile mitochondrial genomes of maize. Genetics 177:1173–1192

    Article  PubMed  CAS  Google Scholar 

  • Alverson AJ, Rice DW, Dickinson S et al (2011) Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber. Plant Cell 23:2499–2513

    Article  PubMed  CAS  Google Scholar 

  • Amiott EA, Jaehning JA (2006) Mitochondrial transcription is regulated via an ATP “sensing” mechanism that couples RNA abundance to respiration. Mol Cell 22:329–338

    Article  PubMed  CAS  Google Scholar 

  • Ammerman ML, Fisk JC, Read LK (2008) gRNA/pre-mRNA annealing and RNA chaperone activities of RBP16. RNA 14:1069–1080

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Asin-Cayuela J, Gustafsson CM (2007) Mitochondrial transcription and its regulation in mammalian cells. Trends Biochem Sci 32:111–117

    Article  PubMed  CAS  Google Scholar 

  • Bandiera S, Hanein S, Lyonnet S (2011a) Mitochondria as novel players of the cellular RNA interference. J Biol Chem 286:le19

    Article  PubMed  CAS  Google Scholar 

  • Bandiera S, Ruberg S, Girard M et al (2011b) Nuclear outsourcing of RNA interference components to human mitochondria. PLoS One 6:e20746

    Article  PubMed  CAS  Google Scholar 

  • Barbrook AC, Howe CJ, Kurniawan DP et al (2010) Organization and expression of organellar genomes. Philos Trans R Soc Lond B Biol Sci 365:785–797

    Article  PubMed  CAS  Google Scholar 

  • Barrey E, Saint-Auret G, Bonnamy B et al (2011) Pre-microRNA and mature microRNA in human mitochondria. PLoS One 6:e20220

    Article  PubMed  CAS  Google Scholar 

  • Been MD, Wickham GS (1997) Self-cleaving ribozymes of hepatitis delta virus RNA. Eur J Biochem 247:741–753

    Article  PubMed  CAS  Google Scholar 

  • Beitzinger M, Peters L, Zhu JY et al (2007) Identification of human microRNA targets from isolated argonaute protein complexes. RNA Biol 4:76–84

    Article  PubMed  CAS  Google Scholar 

  • Bender A, Krishnan KJ, Morris CM et al (2006) High levels of mitochondrial DNA deletions in substantia nigra neurons in aging and Parkinson disease. Nat Genet 38:515–517

    Article  PubMed  CAS  Google Scholar 

  • Bian Z, Li LM, Tang R et al (2010) Identification of mouse liver mitochondria-associated miRNAs and their potential biological functions. Cell Res 20:1076–1078

    Article  PubMed  Google Scholar 

  • Binder S, Brennicke A (2003) Gene expression in plant mitochondria: transcriptional and post-transcriptional control. Philos Trans R Soc Lond B Biol Sci 358:181–189

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Bokori-Brown M, Holt IJ (2006) Expression of algal nuclear ATP synthase subunit 6 in human cells results in protein targeting to mitochondria but no assembly into ATP synthase. Rejuvenation Res 9:455–469

    Article  PubMed  CAS  Google Scholar 

  • Bonen L (2008) Cis- and trans-splicing of group II introns in plant mitochondria. Mitochondrion 8:26–34

    Article  PubMed  CAS  Google Scholar 

  • Bonnefoy N, Remacle C, Fox TD (2007) Genetic transformation of Saccharomyces cerevisiae and Chlamydomonas reinhardtii mitochondria. Methods Cell Biol 80:525–548

    Article  PubMed  CAS  Google Scholar 

  • Bonnet C, Kaltimbacher V, Ellouze S et al (2007) Allotopic mRNA localization to the mitochondrial surface rescues respiratory chain defects in fibroblasts harboring mitochondrial DNA mutations affecting complex I or V subunits. Rejuvenation Res 10:127–144

    Article  PubMed  CAS  Google Scholar 

  • Bonnet C, Augustin S, Ellouze S et al (2008) The optimized allotopic expression of ND1 or ND4 genes restores respiratory chain complex I activity in fibroblasts harboring mutations in these genes. Biochim Biophys Acta 1783:1707–1717

    Article  PubMed  CAS  Google Scholar 

  • Börner GV, Mörl M, Janke A et al (1996) RNA editing changes the identity of a mitochondrial tRNA in marsupials. EMBO J 15:5949–5957

    PubMed  Google Scholar 

  • Bouzaidi-Tiali N, Aeby E, Charriere F et al (2007) Elongation factor 1a mediates the specificity of mitochondrial tRNA import in T. brucei. EMBO J 26:4302–4312

    Article  PubMed  CAS  Google Scholar 

  • Brandina I, Smirnov A, Kolesnikova O et al (2007) tRNA import into yeast mitochondria is regulated by the ubiquitin-proteasome system. FEBS Lett 581:4248–4254

    Article  PubMed  CAS  Google Scholar 

  • Brandon M, Baldi P, Wallace DC (2006) Mitochondrial mutations in cancer. Oncogene 25:4647–4662

    Article  PubMed  CAS  Google Scholar 

  • Brown GG, Zhang M (1995) Mitochondrial plasmids: DNA and RNA. In: Levings III CS, Vasil IK (ed) The molecular biology of plant mitochondria. Kluwer Academic Publishers, Dordrecht, the Netherlands, pp. 61-91

    Google Scholar 

  • Bruske EI, Sendfeld F, Schneider A (2009) Thiolated tRNAs of Trypanosoma brucei are imported into mitochondria and dethiolated after import. J Biol Chem 284:36491–36499

    Article  PubMed  CAS  Google Scholar 

  • Burzio VA, Villota C, Villegas J et al (2009) Expression of a family of noncoding mitochondrial RNAs distinguishes normal from cancer cells. Proc Natl Acad Sci USA 106:9430–9434

    Article  PubMed  CAS  Google Scholar 

  • Butcher SE, Heckman JE, Burke JM (1995) Reconstitution of hairpin ribozyme activity following separation of functional domains. J Biol Chem 270:29648–29651

    Article  PubMed  CAS  Google Scholar 

  • Buzayan JM, Gerlach WL, Bruening G (1986) Satellite tobacco ringspot virus RNA: A subset of the RNA sequence is sufficient for autolytic processing. Proc Natl Acad Sci USA 83:8859–8862

    Article  PubMed  CAS  Google Scholar 

  • Campbell GR, Ziabreva I, Reeve AK et al (2011) Mitochondrial DNA deletions and neurodegeneration in multiple sclerosis. Ann Neurol 69:481–492

    Article  PubMed  CAS  Google Scholar 

  • Chang DD, Clayton DA (1989) Mouse RNAase MRP RNA is encoded by a nuclear gene and contains a decamer sequence complementary to a conserved region of mitochondrial RNA substrate. Cell 56:131–139

    Article  PubMed  CAS  Google Scholar 

  • Chase CD (2007) Cytoplasmic male sterility: a window to the world of plant mitochondrial-nuclear interactions. Trends Genet 23:81–90

    Article  PubMed  CAS  Google Scholar 

  • Chateigner-Boutin AL, Small I (2010) Plant RNA editing. RNA Biol 7:213–219

    Article  PubMed  CAS  Google Scholar 

  • Chateigner-Boutin AL, Small I (2011) Organellar RNA editing. WIREs RNA 2:493–506

    Article  PubMed  CAS  Google Scholar 

  • Chatterjee S, Home P, Mukherjee S et al (2006) An RNA-binding respiratory component mediates import of type II tRNAs into Leishmania mitochondria. J Biol Chem 281:25270–25277

    Article  PubMed  CAS  Google Scholar 

  • Choisne N, Carneiro VT, Pelletier G et al (1998) Implication of 5′-flanking sequence elements in expression of a plant tRNA(Leu) gene. Plant Mol Biol 36:113–123

    Article  PubMed  CAS  Google Scholar 

  • Clement SL, Mingler MK, Koslowsky DJ (2004) An intragenic guide RNA location suggests a complex mechanism for mitochondrial gene expression in Trypanosoma brucei. Eukaryot Cell 3:862–869

    Article  PubMed  CAS  Google Scholar 

  • Clifton SW, Minx P, Fauron CM et al (2004) Sequence and comparative analysis of the maize NB mitochondrial genome. Plant Physiol 136:3486–3503

    Article  PubMed  CAS  Google Scholar 

  • Corell RA, Feagin JE, Riley GR et al (1993) Trypanosoma brucei minicircles encode multiple guide RNAs which can direct editing of extensively overlapping sequences. Nucleic Acids Res 21:4313–4320

    Article  PubMed  CAS  Google Scholar 

  • Corral-Debrinski M (2007) mRNA specific subcellular localization represents a crucial step for fine-tuning of gene expression in mammalian cells. Biochim Biophys Acta 1773:473–475

    Article  PubMed  CAS  Google Scholar 

  • Costa FF (2010) Non-coding RNAs: meet thy masters. Bioessays 32:599–608

    Article  PubMed  CAS  Google Scholar 

  • Crausaz Esseiva A, Marechal-Drouard L, Cosset A et al (2004) The T-stem determines the cytosolic or mitochondrial localization of trypanosomal tRNAsMet. Mol Biol Cell 15:2750–2757

    Article  PubMed  Google Scholar 

  • Crisell P, Thompson S, James W (1993) Inhibition of HIV-1 replication by ribozymes that show poor activity in vitro. Nucleic Acids Res 21:5251–5255

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Curtis EA, Bartel DP (2001) The hammerhead cleavage reaction in monovalent cations. RNA 7:546–552

    Article  PubMed  CAS  Google Scholar 

  • de la Pena M, Garcia-Robles I (2010) Ubiquitous presence of the hammerhead ribozyme motif along the tree of life. RNA 16:1943–1950

    Article  PubMed  CAS  Google Scholar 

  • Delage L, Duchêne AM, Zaepfel M et al (2003) The anticodon and the D-domain sequences are essential determinants for plant cytosolic tRNA(Val) import into mitochondria. Plant J 34:623–633

    Article  PubMed  CAS  Google Scholar 

  • Devaux F, Lelandais G, Garcia M et al (2010) Posttranscriptional control of mitochondrial biogenesis: spatio-temporal regulation of the protein import process. FEBS Lett 584:4273–4279

    Article  PubMed  CAS  Google Scholar 

  • Dietrich A, Maréchal-Drouard L, Carneiro V et al (1996) A single base change prevents import of cytosolic tRNA(Ala) into mitochondria in transgenic plants. Plant J 10:913–918

    Article  PubMed  CAS  Google Scholar 

  • Doersen CJ, Guerrier-Takada C, Altman S et al (1985) Characterization of an RNase P activity from HeLa cell mitochondria. Comparison with the cytosol RNase P activity. J Biol Chem 260:5942–5949

    PubMed  CAS  Google Scholar 

  • Dörner M, Altmann M, Pääbo S et al (2001) Evidence for import of a lysyl-tRNA into marsupial mitochondria. Mol Biol Cell 12:2688–2698

    PubMed  Google Scholar 

  • Dreher TW (2009) Role of tRNA-like structures in controlling plant virus replication. Virus Res 139:217–229

    Article  PubMed  CAS  Google Scholar 

  • Duroc Y, Gaillard C, Hiard S et al (2005) Biochemical and functional characterization of ORF138, a mitochondrial protein responsible for Ogura cytoplasmic male sterility in Brassicaceae. Biochimie 87:1089–1100

    Article  PubMed  CAS  Google Scholar 

  • Eliyahu E, Pnueli L, Melamed D et al (2010) Tom20 mediates localization of mRNAs to mitochondria in a translation-dependent manner. Mol Cell Biol 30:284–294

    Article  PubMed  CAS  Google Scholar 

  • Eliyahu E, Lesnik C, Arava Y (2012) The protein chaperone Ssa1 affects mRNA localization to the mitochondria. FEBS Lett 586:64–69

    Article  PubMed  CAS  Google Scholar 

  • Ellouze S, Augustin S, Bouaita A et al (2008) Optimized allotopic expression of the human mitochondrial ND4 prevents blindness in a rat model of mitochondrial dysfunction. Am J Hum Genet 83:373–387

    Article  PubMed  CAS  Google Scholar 

  • Entelis NS, Kolesnikova OA, Dogan S et al (2001) 5 S rRNA and tRNA import into human mitochondria. Comparison of in vitro requirements. J Biol Chem 276:45642–45653

    Article  PubMed  CAS  Google Scholar 

  • Entelis N, Brandina I, Kamenski P et al (2006) A glycolytic enzyme, enolase, is recruited as a cofactor of tRNA targeting toward mitochondria in Saccharomyces cerevisiae. Genes Dev 20:1609–1620

    Article  PubMed  CAS  Google Scholar 

  • Esteban JA, Walter NG, Kotzorek G et al (1998) Structural basis for heterogeneous kinetics: reengineering the hairpin ribozyme. Proc Natl Acad Sci USA 95:6091–6096

    Article  PubMed  CAS  Google Scholar 

  • Farajollahi S, Maas S (2010) Molecular diversity through RNA editing: a balancing act. Trends Genet 26:221–230

    Article  PubMed  CAS  Google Scholar 

  • Fechter P, Rudinger-Thirion J, Florentz C et al (2001) Novel features in the tRNA-like world of plant viral RNAs. Cell Mol Life Sci 58:1547–1561

    Article  PubMed  CAS  Google Scholar 

  • Fedor MJ (2009) Comparative enzymology and structural biology of RNA self-cleavage. Annu Rev Biophys Biomol Struct 38:271–299

    CAS  Google Scholar 

  • Fedor MJ, Uhlenbeck OC (1990) Substrate sequence effects on “hammerhead” RNA catalytic efficiency. Proc Natl Acad Sci USA 87:1668–1672

    Article  PubMed  CAS  Google Scholar 

  • Fedor MJ, Williamson JR (2005) The catalytic diversity of RNAs. Nat Rev Mol Cell Biol 6:399–412

    Article  PubMed  CAS  Google Scholar 

  • Fedoruk-Wyszomirska A, Wyszko E, Giel-Pietraszuk M et al (2007) High hydrostatic pressure approach proves RNA catalytic activity without magnesium. Int J Biol Macromol 41:30–35

    Article  PubMed  CAS  Google Scholar 

  • Feldstein PA, Bruening G (1993) Catalytically active geometry in the reversible circularization of ‘mini-monomer’ RNAs derived from the complementary strand of tobacco ringspot virus satellite RNA. Nucleic Acids Res 21:1991–1998

    Article  PubMed  CAS  Google Scholar 

  • Fernandez-Silva P, Enriquez JA, Montoya J (2003) Replication and transcription of mammalian mitochondrial DNA. Exp Physiol 88:41–56

    Article  PubMed  CAS  Google Scholar 

  • Ferré-D’Amaré AR, Scott WG (2010) Small self-cleaving ribozymes. Cold Spring Harb Perspect Biol 2:a003574

    Article  PubMed  CAS  Google Scholar 

  • Fey J, Maréchal-Drouard L (1999) Compilation and analysis of plant mitochondrial promoter sequences: an illustration of a divergent evolution between monocot and dicot mitochondria. Biochem Biophys Res Commun 256:409–414

    Article  PubMed  CAS  Google Scholar 

  • Frei U, Peiretti EG, Wenzel G (2004) Significance of cytoplasmic DNA in plant breeding. In: Janick J (ed) Plant Breeding Reviews. Wiley, Hoboken, pp 175–210

    Google Scholar 

  • Fujii S, Toda T, Kikuchi S et al (2011) Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions. BMC Genomics 12:279

    Article  PubMed  Google Scholar 

  • Gabay-Laughnan S, Kuzmin EV, Monroe J et al (2009) Characterization of a novel thermosensitive restorer of fertility for cytoplasmic male sterility in maize. Genetics 182:91–103

    Article  PubMed  CAS  Google Scholar 

  • Gadir N, Haim-Vilmovsky L, Kraut-Cohen J et al (2011) Localization of mRNAs coding for mitochondrial proteins in the yeast Saccharomyces cerevisiae. RNA 17:1551–1565

    Article  PubMed  CAS  Google Scholar 

  • Gallagher LJ, Betz SK, Chase CD (2002) Mitochondrial RNA editing truncates a chimeric open reading frame associated with S male-sterility in maize. Curr Genet 42:179–184

    Article  PubMed  CAS  Google Scholar 

  • Ganguly A, Bevilacqua PC, Hammes-Schiffer S (2011) Quantum mechanical/molecular mechanical study of the HDV ribozyme: impact of the catalytic metal ion on the mechanism. J Phys Chem Lett 2:2906–2911

    Article  PubMed  CAS  Google Scholar 

  • Garcia M, Delaveau T, Goussard S et al (2010) Mitochondrial presequence and open reading frame mediate asymmetric localization of messenger RNA. EMBO Rep 11:285–291

    Article  PubMed  CAS  Google Scholar 

  • Gaspari M, Larsson NG, Gustafsson CM (2004) The transcription machinery in mammalian mitochondria. Biochim Biophys Acta 1659:148–152

    Article  PubMed  CAS  Google Scholar 

  • Geiduschek EP, Tocchini-Valentini GP (1988) Transcription by RNA polymerase III. Annu Rev Biochem 57:873–914

    Article  PubMed  CAS  Google Scholar 

  • Giegé P, Sweetlove LJ, Cognat V et al (2005) Coordination of nuclear and mitochondrial genome expression during mitochondrial biogenesis in Arabidopsis. Plant Cell 17:1497–1512

    Article  PubMed  CAS  Google Scholar 

  • Giraud E, Van Aken O, Ho LH et al (2009) The transcription factor ABI4 is a regulator of mitochondrial retrograde expression of ALTERNATIVE OXIDASE1a. Plant Physiol 150:1286–1296

    Article  PubMed  CAS  Google Scholar 

  • Golden DE, 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

    Article  PubMed  CAS  Google Scholar 

  • Golden DE, Hajduk SL (2006) The importance of RNA structure in RNA editing and a potential proofreading mechanism for correct guide RNA:pre-mRNA binary complex formation. J Mol Biol 359:585–596

    Article  PubMed  CAS  Google Scholar 

  • Göringer HU, Katari VS, Böhm C (2011) The structural landscape of native editosomes in African trypanosomes. WIREs RNA 2:395–407

    Article  PubMed  CAS  Google Scholar 

  • Grams J, McManus MT, Hajduk SL (2000) Processing of polycistronic guide RNAs is associated with RNA editing complexes in Trypanosoma brucei. EMBO J 19:5525–5532

    Article  PubMed  CAS  Google Scholar 

  • Greaves LC, Reeve AK, Taylor RW et al (2012) Mitochondrial DNA and disease. J Pathol 226:274–286

    Article  PubMed  CAS  Google Scholar 

  • Griffiths AJ (1995) Natural plasmids of filamentous fungi. Microbiol Rev 59:673–685

    PubMed  CAS  Google Scholar 

  • Guja KE, Garcia-Diaz M (2011) Hitting the brakes: termination of mitochondrial transcription. Biochim Biophys Acta. doi:10.1016/j.bbagrm.2011.1011.1004

  • Guy J, Qi X, Pallotti F et al (2002) Rescue of a mitochondrial deficiency causing Leber hereditary optic neuropathy. Ann Neurol 52:534–542

    Article  PubMed  CAS  Google Scholar 

  • Hajduk S, Ochsenreiter T (2010) RNA editing in kinetoplastids. RNA Biol 7:229–236

    Article  PubMed  CAS  Google Scholar 

  • Hammond JA, Rambo RP, Filbin ME et al (2009) Comparison and functional implications of the 3D architectures of viral tRNA-like structures. RNA 15:294–307

    Article  PubMed  CAS  Google Scholar 

  • Hampel A, Tritz R (1989) RNA catalytic properties of the minimum (-)sTRSV sequence. Biochemistry 28:4929–4933

    Article  PubMed  CAS  Google Scholar 

  • Handa H (2003) The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana. Nucleic Acids Res 31:5907–5916

    Article  PubMed  CAS  Google Scholar 

  • Handa H (2008) Linear plasmids in plant mitochondria: peaceful coexistences or malicious invasions? Mitochondrion 8:15–25

    Article  PubMed  CAS  Google Scholar 

  • Hashimi H, Cicova Z, Novotna L 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

    Article  PubMed  CAS  Google Scholar 

  • Hernandez A, Panigrahi A, Cifuentes-Rojas C et al (2008) Determinants for association and guide RNA-directed endonuclease cleavage by purified RNA editing complexes from Trypanosoma brucei. J Mol Biol 381:35–48

    Article  PubMed  CAS  Google Scholar 

  • Hernandez A, Madina BR, Ro K 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

    Article  PubMed  CAS  Google Scholar 

  • Heyne K, Mannebach S, Wuertz E et al (2004) Identification of a putative p53 binding sequence within the human mitochondrial genome. FEBS Lett 578:198–202

    Article  PubMed  CAS  Google Scholar 

  • Hock MB, Kralli A (2009) Transcriptional control of mitochondrial biogenesis and function. Annu Rev Physiol 71:177–203

    Article  PubMed  CAS  Google Scholar 

  • Holec S, Lange H, Kuhn K et al (2006) Relaxed transcription in Arabidopsis mitochondria is counterbalanced by RNA stability control mediated by polyadenylation and polynucleotide phosphorylase. Mol Cell Biol 26:2869–2876

    Article  PubMed  CAS  Google Scholar 

  • Holec S, Lange H, Canaday J et al (2008) Coping with cryptic and defective transcripts in plant mitochondria. Biochim Biophys Acta 1779:566–573

    Article  PubMed  CAS  Google Scholar 

  • Holzmann J, Frank P, Loffler E et al (2008) RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme. Cell 135:462–474

    Article  PubMed  CAS  Google Scholar 

  • Hong M, Simpson L (2003) Genomic organization of Trypanosoma brucei kinetoplast DNA minicircles. Protist 154:265–279

    Article  PubMed  CAS  Google Scholar 

  • Horton TL, Landweber LF (2002) Rewriting the information in DNA: RNA editing in kinetoplastids and myxomycetes. Curr Opin Microbiol 5:620–626

    Article  PubMed  CAS  Google Scholar 

  • Hotchkiss G, Maijgren-Steffensson C, Ahrlund-Richter L (2004) Efficacy and mode of action of hammerhead and hairpin ribozymes against various HIV-1 target sites. Mol Ther 10:172–180

    Article  PubMed  CAS  Google Scholar 

  • Huang L, Mollet S, Souquere S et al (2011) Mitochondria associate with P-bodies and modulate microRNA-mediated RNA interference. J Biol Chem 286:24219–24230

    Article  PubMed  CAS  Google Scholar 

  • Imanishi H, Hattori K, Wada R et al (2011) Mitochondrial DNA mutations regulate metastasis of human breast cancer cells. PLoS One 6:e23401

    Article  PubMed  CAS  Google Scholar 

  • Janke A, Pääbo S (1993) Editing of a tRNA anticodon in marsupial mitochondria changes its codon recognition. Nucleic Acids Res 21:1523–1525

    Article  PubMed  CAS  Google Scholar 

  • Jimenez RM, Delwart E, Luptak A (2011) Structure-based search reveals hammerhead ribozymes in the human microbiome. J Biol Chem 286:7737–7743

    Article  PubMed  CAS  Google Scholar 

  • Jones AW, Yao Z, Vicencio JM et al (2011) PGC-1 family coactivators and cell fate: roles in cancer, neurodegeneration, cardiovascular disease and retrograde mitochondria-nucleus signalling. Mitochondrion. doi:10.1016/j.mito.2011.1009.1009

  • Kala S, Salavati R (2010) OB-fold domain of KREPA4 mediates high-affinity interaction with guide RNA and possesses annealing activity. RNA 16:1951–1967

    Article  PubMed  CAS  Google Scholar 

  • Kaltimbacher V, Bonnet C, Lecoeuvre G et al (2006) mRNA localization to the mitochondrial surface allows the efficient translocation inside the organelle of a nuclear recoded ATP6 protein. RNA 12:1408–1417

    Article  PubMed  CAS  Google Scholar 

  • Kaneko T, Suzuki T, Kapushoc ST et al (2003) Wobble modification differences and subcellular localization of tRNAs in Leishmania tarentolae: implication for tRNA sorting mechanism. EMBO J 22:657–667

    Article  PubMed  CAS  Google Scholar 

  • Karicheva OZ, Kolesnikova OA, Schirtz T et al (2011) Correction of the consequences of mitochondrial 3243A > G mutation in the MT-TL1 gene causing the MELAS syndrome by tRNA import into mitochondria. Nucleic Acids Res 39:8173–8186

    Article  PubMed  CAS  Google Scholar 

  • Khvorova A, Lescoute A, Westhof E et al (2003) Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Biol 10:708–712

    Article  PubMed  CAS  Google Scholar 

  • Kiss T, Filipowicz W (1992) Evidence against a mitochondrial location of the 7-2/MRP RNA in mammalian cells. Cell 70:11–16

    Article  PubMed  CAS  Google Scholar 

  • Kloc M, Zearfoss NR, Etkin LD (2002) Mechanisms of subcellular mRNA localization. Cell 108:533–544

    Article  PubMed  CAS  Google Scholar 

  • Kolesnikova OA, Entelis NS, Mireau H et al (2000) Suppression of mutations in mitochondrial DNA by tRNAs imported from the cytoplasm. Science 289:1931–1933

    Article  PubMed  CAS  Google Scholar 

  • Kolesnikova OA, Entelis NS, Jacquin-Becker C et al (2004) Nuclear DNA-encoded tRNAs targeted into mitochondria can rescue a mitochondrial DNA mutation associated with the MERRF syndrome in cultured human cells. Hum Mol Genet 13:2519–2534

    Article  PubMed  CAS  Google Scholar 

  • Kolesnikova O, Kazakova H, Comte C et al (2010) Selection of RNA aptamers imported into yeast and human mitochondria. RNA 16:926–941

    Article  PubMed  CAS  Google Scholar 

  • Kore AR, Vaish NK, Kutzke U et al (1998) Sequence specificity of the hammerhead ribozyme revisited; the NHH rule. Nucleic Acids Res 26:4116–4120

    Article  PubMed  CAS  Google Scholar 

  • Koslowsky DJ, Riley GR, Feagin JE et al (1992) Guide RNAs for transcripts with developmentally regulated RNA editing are present in both life cycle stages of Trypanosoma brucei. Mol Cell Biol 12:2043–2049

    PubMed  CAS  Google Scholar 

  • Koslowsky DJ, Reifur L, Yu LE et al (2004) Evidence for U-tail stabilization of gRNA/mRNA interactions in kinetoplastid RNA editing. RNA Biol 1:28–34

    Article  PubMed  CAS  Google Scholar 

  • Kren BT, Wong PY, Sarver A et al (2009) MicroRNAs identified in highly purified liver-derived mitochondria may play a role in apoptosis. RNA Biol 6:65–72

    Article  PubMed  CAS  Google Scholar 

  • Kubo T, Newton KJ (2008) Angiosperm mitochondrial genomes and mutations. Mitochondrion 8:5–14

    Article  PubMed  CAS  Google Scholar 

  • Kuhn K, Weihe A, Borner T (2005) Multiple promoters are a common feature of mitochondrial genes in Arabidopsis. Nucleic Acids Res 33:337–346

    Article  PubMed  CAS  Google Scholar 

  • Kuhn K, Richter U, Meyer EH et al (2009) Phage-type RNA polymerase RPOTmp performs gene-specific transcription in mitochondria of Arabidopsis thaliana. Plant Cell 21:2762–2779

    Article  PubMed  CAS  Google Scholar 

  • Kumar R, Maréchal-Drouard L, Akama K et al (1996) Striking differences in mitochondrial tRNA import between different plant species. Mol Gen Genet 252:404–411

    Article  PubMed  CAS  Google Scholar 

  • Landerer E, Villegas J, Burzio VA et al (2011) Nuclear localization of the mitochondrial ncRNAs in normal and cancer cells. Cell Oncol 34:297–305

    Article  CAS  Google Scholar 

  • Lee TS, Giambasu G, Harris ME et al (2011) Characterization of the structure and dynamics of the HDV ribozyme at different stages along the reaction path. J Phys Chem Lett 2:2538–2543

    Article  PubMed  CAS  Google Scholar 

  • Leister D, Wang X, Haberer G et al (2011) Intracompartmental and intercompartmental transcriptional networks coordinate the expression of genes for organellar functions. Plant Physiol 157:386–404

    Article  PubMed  CAS  Google Scholar 

  • Leung SS, Koslowsky DJ (1999) Mapping contacts between gRNA and mRNA in trypanosome RNA editing. Nucleic Acids Res 27:778–787

    Article  PubMed  CAS  Google Scholar 

  • Leung SS, Koslowsky DJ (2001a) Interactions of mRNAs and gRNAs involved in trypanosome mitochondrial RNA editing: structure probing of an mRNA bound to its cognate gRNA. RNA 7:1803–1816

    PubMed  CAS  Google Scholar 

  • Leung SS, Koslowsky DJ (2001b) RNA editing in Trypanosoma brucei: characterization of gRNA U-tail interactions with partially edited mRNA substrates. Nucleic Acids Res 29:703–709

    Article  PubMed  CAS  Google Scholar 

  • Levesque MV, Rouleau SG, Perreault JP (2011) Selection of the most potent specific on/off adaptor-hepatitis delta virus ribozymes for use in gene targeting. Nucleic Acid Ther 21:241–252

    PubMed  CAS  Google Scholar 

  • Li K, Smagula CS, Parsons WJ et al (1994) Subcellular partitioning of MRP RNA assessed by ultrastructural and biochemical analysis. J Cell Biol 124:871–882

    Article  PubMed  CAS  Google Scholar 

  • Li F, Herrera J, Zhou S et al (2011a) 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 USA 108:3542–3547

    Article  PubMed  CAS  Google Scholar 

  • Li P, Jiao J, Gao G et al (2011b) Control of mitochondrial activity by miRNAs. J Cell Biochem. doi:10.1002/jcb.24004

  • Liere K, Weihe A, Börner T (2011) The transcription machineries of plant mitochondria and chloroplasts: composition, function, and regulation. J Plant Physiol 168:1345–1360

    Article  PubMed  CAS  Google Scholar 

  • Lightowlers RN (2011) Mitochondrial transformation: time for concerted action. EMBO Rep 12:480–481

    Article  PubMed  CAS  Google Scholar 

  • Lipinski KA, Kaniak-Golik A, Golik P (2010) Maintenance and expression of the S. cerevisiae mitochondrial genome - from genetics to evolution and systems biology. Biochim Biophys Acta 1797:1086–1098

    Article  PubMed  CAS  Google Scholar 

  • Litonin D, Sologub M, Shi Y et al (2010) Human mitochondrial transcription revisited: only TFAM and TFB2M are required for transcription of the mitochondrial genes in vitro. J Biol Chem 285:18129–18133

    Article  PubMed  CAS  Google Scholar 

  • Liu Z, Butow RA (2006) Mitochondrial retrograde signaling. Annu Rev Genet 40:159–185

    Article  PubMed  CAS  Google Scholar 

  • Ljubicic V, Joseph AM, Saleem A et al (2010) Transcriptional and post-transcriptional regulation of mitochondrial biogenesis in skeletal muscle: effects of exercise and aging. Biochim Biophys Acta 1800:223–234

    Article  PubMed  CAS  Google Scholar 

  • Lorence A, Verpoorte R (2004) Gene transfer and expression in plants. Methods Mol Biol 267:329–350

    PubMed  CAS  Google Scholar 

  • Lu Q, Wierzbicki S, Krasilnikov AS et al (2010) Comparison of mitochondrial and nucleolar RNase MRP reveals identical RNA components with distinct enzymatic activities and protein components. RNA 16:529–537

    Article  PubMed  CAS  Google Scholar 

  • Lukes J, Guilbride DL, Votypka J et al (2002) Kinetoplast DNA network: evolution of an improbable structure. Eukaryot Cell 1:495–502

    Article  PubMed  CAS  Google Scholar 

  • Lukes J, Hashimi H, Zikova A (2005) Unexplained complexity of the mitochondrial genome and transcriptome in kinetoplastid flagellates. Curr Genet 48:277–299

    Article  PubMed  CAS  Google Scholar 

  • Lung B, Zemann A, Madej MJ et al (2006) Identification of small non-coding RNAs from mitochondria and chloroplasts. Nucleic Acids Res 34:3842–3852

    Article  PubMed  CAS  Google Scholar 

  • Madej MJ, Alfonzo JD, Huttenhofer A (2007) Small ncRNA transcriptome analysis from kinetoplast mitochondria of Leishmania tarentolae. Nucleic Acids Res 35:1544–1554

    Article  PubMed  CAS  Google Scholar 

  • Madej MJ, Niemann M, Huttenhofer A et al (2008) Identification of novel guide RNAs from the mitochondria of Trypanosoma brucei. RNA Biol 5:84–91

    Article  PubMed  CAS  Google Scholar 

  • Madina BR, Kuppan G, Vashisht AA et al (2011) Guide RNA biogenesis involves a novel RNase III family endoribonuclease in Trypanosoma brucei. RNA:10.1261/rna.2815911

  • Madison-Antenucci S, Grams J, Hajduk SL (2002) Editing machines: the complexities of trypanosome RNA editing. Cell 108:435–438

    Article  PubMed  CAS  Google Scholar 

  • Magalhaes PJ, Andreu AL, Schon EA (1998) Evidence for the presence of 5 S rRNA in mammalian mitochondria. Mol Biol Cell 9:2375–2382

    PubMed  CAS  Google Scholar 

  • Mahapatra S, Ghosh S, Bera SK et al (1998) The D arm of tRNATyr is necessary and sufficient for import into Leishmania mitochondria in vitro. Nucleic Acids Res 26:2037–2041

    Article  PubMed  CAS  Google Scholar 

  • Man PY, Turnbull DM, Chinnery PF (2002) Leber hereditary optic neuropathy. J Med Genet 39:162–169

    Article  PubMed  CAS  Google Scholar 

  • Manfredi G, Fu J, Ojaimi J et al (2002) Rescue of a deficiency in ATP synthesis by transfer of MTATP6, a mitochondrial DNA-encoded gene, to the nucleus. Nat Genet 30:394–399

    Article  PubMed  CAS  Google Scholar 

  • Mangus DA, Jang SH, Jaehning JA (1994) Release of the yeast mitochondrial RNA polymerase specificity factor from transcription complexes. J Biol Chem 269:26568–26574

    PubMed  CAS  Google Scholar 

  • Maniataki E, Mourelatos Z (2005) Human mitochondrial tRNAMet is exported to the cytoplasm and associates with the Argonaute 2 protein. RNA 11:849–852

    Article  PubMed  CAS  Google Scholar 

  • Mans RM, Guerrier-Takada C, Altman S et al (1990) Interaction of RNase P from Escherichia coli with pseudoknotted structures in viral RNAs. Nucleic Acids Res 18:3479–3487

    Article  PubMed  CAS  Google Scholar 

  • Marc P, Margeot A, Devaux F et al (2002) Genome-wide analysis of mRNAs targeted to yeast mitochondria. EMBO Rep 3:159–164

    Article  PubMed  CAS  Google Scholar 

  • Maréchal-Drouard L, Guillemaut P, Cosset A et al (1990) Transfer RNAs of potato (Solanum tuberosum) mitochondria have different genetic origins. Nucleic Acids Res 18:3689–3696

    Article  PubMed  Google Scholar 

  • Marker C, Zemann A, Terhorst T et al (2002) Experimental RNomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana. Curr Biol 12:2002–2013

    Article  PubMed  CAS  Google Scholar 

  • Martick M, Scott WG (2006) Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126:309–320

    Article  PubMed  CAS  Google Scholar 

  • Martick M, Horan LH, Noller HF et al (2008) A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA. Nature 454:899–902

    Article  PubMed  CAS  Google Scholar 

  • Maslov DA, 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

    Article  PubMed  CAS  Google Scholar 

  • Matsuda D, Dreher TW (2004) The tRNA-like structure of Turnip yellow mosaic virus RNA is a 3′-translational enhancer. Virology 321:36–46

    Article  PubMed  CAS  Google Scholar 

  • McCauley DE, Olson MS (2008) Do recent findings in plant mitochondrial molecular and population genetics have implications for the study of gynodioecy and cytonuclear conflict? Evolution 62:1013–1025

    Article  PubMed  Google Scholar 

  • McDowell SE, Jun JM, Walter NG (2010) Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations. RNA 16:2414–2426

    Article  PubMed  CAS  Google Scholar 

  • Mercer TR, Neph S, Dinger ME et al (2011) The human mitochondrial transcriptome. Cell 146:645–658

    Article  PubMed  CAS  Google Scholar 

  • Michaud M, Maréchal-Drouard L, Duchêne AM (2010) RNA trafficking in plant cells: targeting of cytosolic mRNAs to the mitochondrial surface. Plant Mol Biol 73:697–704

    Article  PubMed  CAS  Google Scholar 

  • Mileshina D, Ibrahim N, Boesch P et al (2011) Mitochondrial transfection for studying organellar DNA repair, genome maintenance and aging. Mech Ageing Dev 132:412–423

    Article  PubMed  CAS  Google Scholar 

  • Millar AH, Whelan J, Soole KL et al (2011) Organization and regulation of mitochondrial respiration in plants. Annu Rev Plant Biol 62:79–104

    Article  PubMed  CAS  Google Scholar 

  • Montoya J, Gaines GL, Attardi G (1983) The pattern of transcription of the human mitochondrial rRNA genes reveals two overlapping transcription units. Cell 34:151–159

    Article  PubMed  CAS  Google Scholar 

  • Mukherjee S, Basu S, Home P et al (2007) Necessary and sufficient factors for the import of transfer RNA into the kinetoplast mitochondrion. EMBO Rep 8:589–595

    Article  PubMed  CAS  Google Scholar 

  • Mulhbacher J, St-Pierre P, Lafontaine DA (2010) Therapeutic applications of ribozymes and riboswitches. Curr Opin Pharmacol 10:551–556

    Article  PubMed  CAS  Google Scholar 

  • Muller S, Appel B, Krellenberg T et al (2011) The many faces of the hairpin ribozyme: structural and functional variants of a small catalytic RNA. IUBMB Life. doi:10.1002/iub.1575

  • Nishikura K (2010) Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem 79:321–349

    Article  PubMed  CAS  Google Scholar 

  • Oca-Cossio J, Kenyon L, Hao H et al (2003) Limitations of allotopic expression of mitochondrial genes in mammalian cells. Genetics 165:707–720

    PubMed  CAS  Google Scholar 

  • Ochsenreiter T, Cipriano M, Hajduk SL (2007) KISS: the kinetoplastid RNA editing sequence search tool. RNA 13:1–4

    Article  PubMed  CAS  Google Scholar 

  • Ochsenreiter T, Cipriano M, Hajduk SL (2008) Alternative mRNA editing in trypanosomes is extensive and may contribute to mitochondrial protein diversity. PLoS One 3:e1566

    Article  PubMed  CAS  Google Scholar 

  • Ogihara Y, Yamazaki Y, Murai K et al (2005) Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome. Nucleic Acids Res 33:6235–6250

    Article  PubMed  CAS  Google Scholar 

  • Ojaimi J, Pan J, Santra S et al (2002) An algal nucleus-encoded subunit of mitochondrial ATP synthase rescues a defect in the analogous human mitochondrial-encoded subunit. Mol Biol Cell 13:3836–3844

    Article  PubMed  CAS  Google Scholar 

  • Olmedo-Monfil V, Cortes-Penagos C, Herrera-Estrella A (2004) Three decades of fungal transformation: key concepts and applications. Methods Mol Biol 267:297–313

    PubMed  CAS  Google Scholar 

  • O’Rear JL, Wang S, Feig AL et al (2001) Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations. RNA 7:537–545

    Article  PubMed  Google Scholar 

  • Paquette J, Nicoghosian K, Qi GR et al (1990) The conformation of single-stranded nucleic acids tDNA versus tRNA. Eur J Biochem 189:259–265

    Article  PubMed  CAS  Google Scholar 

  • Paris Z, Rubio MA, Lukes J et al (2009) Mitochondrial tRNA import in Trypanosoma brucei is independent of thiolation and the Rieske protein. RNA 15:1398–1406

    Article  PubMed  CAS  Google Scholar 

  • Pelletier G, Budar F (2007) The molecular biology of cytoplasmically inherited male sterility and prospects for its engineering. Curr Opin Biotechnol 18:1–5

    Article  CAS  Google Scholar 

  • Penschow JL, Sleve DA, Ryan CM et al (2004) TbDSS-1, an essential Trypanosoma brucei exoribonuclease homolog that has pleiotropic effects on mitochondrial RNA metabolism. Eukaryot Cell 3:1206–1216

    Article  PubMed  CAS  Google Scholar 

  • Perales-Clemente E, Fernandez-Silva P, Acin-Perez R et al (2010) Allotopic expression of mitochondrial-encoded genes in mammals: achieved goal, undemonstrated mechanism or impossible task? Nucleic Acids Res 39:225–234

    Article  PubMed  CAS  Google Scholar 

  • Peralta S, Wang X, Moraes CT (2011) Mitochondrial transcription: lessons from mouse models. Biochim Biophys Acta. doi:10.1016/j.bbagrm.2011.1011.1001

  • Perreault J, Weinberg Z, Roth A et al (2011) Identification of hammerhead ribozymes in all domains of life reveals novel structural variations. PLoS Comput Biol 7:e1002031

    Article  PubMed  CAS  Google Scholar 

  • Pfannschmidt T (2010) Plastidial retrograde signalling–a true “plastid factor” or just metabolite signatures? Trends Plant Sci 15:427–435

    Article  PubMed  CAS  Google Scholar 

  • Pley HW, Flaherty KM, McKay DB (1994) Three-dimensional structure of a hammerhead ribozyme. Nature 372:68–74

    Article  PubMed  CAS  Google Scholar 

  • Puranam RS, Attardi G (2001) The RNase P associated with HeLa cell mitochondria contains an essential RNA component identical in sequence to that of the nuclear RNase P. Mol Cell Biol 21:548–561

    Article  PubMed  CAS  Google Scholar 

  • Quenault T, Lithgow T, Traven A (2011) PUF proteins: repression, activation and mRNA localization. Trends Cell Biol 21:104–112

    Article  PubMed  CAS  Google Scholar 

  • Rackham O, Shearwood AM, Mercer TR et al (2011) Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins. RNA 17:2085–2093

    Article  PubMed  CAS  Google Scholar 

  • Reichert A, Rothbauer U, Morl M (1998) Processing and editing of overlapping tRNAs in human mitochondria. J Biol Chem 273:31977–31984

    Article  PubMed  CAS  Google Scholar 

  • Reifur L, Koslowsky DJ (2008) Trypanosoma brucei ATPase subunit 6 mRNA bound to gA6-14 forms a conserved three-helical structure. RNA 14:2195–2211

    Article  PubMed  CAS  Google Scholar 

  • Reifur L, Yu LE, Cruz-Reyes J et al (2010) The impact of mRNA structure on guide RNA targeting in kinetoplastid RNA editing. PLoS One 5:e12235

    Article  PubMed  CAS  Google Scholar 

  • Riley GR, Corell RA, Stuart K (1994) Multiple guide RNAs for identical editing of Trypanosoma brucei apocytochrome b mRNA have an unusual minicircle location and are developmentally regulated. J Biol Chem 269:6101–6108

    PubMed  CAS  Google Scholar 

  • Rinehart J, Krett B, Rubio MA et al (2005) Saccharomyces cerevisiae imports the cytosolic pathway for Gln-tRNA synthesis into the mitochondrion. Genes Dev 19:583–592

    Article  PubMed  CAS  Google Scholar 

  • Robertson M (2010) The evolution of gene regulation, the RNA universe, and the vexed questions of artefact and noise. BMC Biol 8:97

    Article  PubMed  Google Scholar 

  • Rossmanith W, Tullo A, Potuschak T et al (1995) Human mitochondrial tRNA processing. J Biol Chem 270:12885–12891

    Article  PubMed  CAS  Google Scholar 

  • Rubio MA, Rinehart JJ, Krett B et al (2008) Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import. Proc Natl Acad Sci USA 105:9186–9191

    Article  PubMed  CAS  Google Scholar 

  • Ryan CM, Kao CY, Sleve DA et al (2006) Biphasic decay of guide RNAs in Trypanosoma brucei. Mol Biochem Parasitol 146:68–77

    Article  PubMed  CAS  Google Scholar 

  • Salinas T, Duchene AM, Delage L et al (2006) The voltage-dependent anion channel, a major component of the tRNA import machinery in plant mitochondria. Proc Natl Acad Sci USA 103:18362–18367

    Article  PubMed  CAS  Google Scholar 

  • Salinas T, Duchene AM, Marechal-Drouard L (2008) Recent advances in tRNA mitochondrial import. Trends Biochem Sci 33:320–329

    Article  PubMed  CAS  Google Scholar 

  • Sanchez MI, Mercer TR, Davies SM et al (2011) RNA processing in human mitochondria. Cell Cycle 10:2904–2916

    Article  PubMed  CAS  Google Scholar 

  • Scarpulla RC (2008) Transcriptional paradigms in mammalian mitochondrial biogenesis and function. Physiol Rev 88:611–638

    Article  PubMed  CAS  Google Scholar 

  • Scarpulla RC (2011) Nucleus-encoded regulators of mitochondrial function: Integration of respiratory chain expression, nutrient sensing and metabolic stress. Biochim Biophys Acta. doi:10.1016/j.bbagrm.2011.1010.1011

  • Schekman R (2010) Editorial expression of concern: a bifunctional tRNA import receptor from Leishmania mitochondria. Proc Natl Acad Sci USA 107:9476

    Article  CAS  Google Scholar 

  • Scherer LJ, Rossi JJ (2003) Approaches for the sequence-specific knockdown of mRNA. Nat Biotechnol 21:1457–1465

    Article  PubMed  CAS  Google Scholar 

  • Schmid B, Riley GR, Stuart K et al (1995) The secondary structure of guide RNA molecules from Trypanosoma brucei. Nucleic Acids Res 23:3093–3102

    Article  PubMed  CAS  Google Scholar 

  • Schmitz-Linneweber C, Small I (2008) Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci 13:663–670

    Article  PubMed  CAS  Google Scholar 

  • Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic male sterility and fertility restoration. Trends Plant Sci 3:175–180

    Article  Google Scholar 

  • Schneider A (2011) Mitochondrial tRNA import and its consequences for mitochondrial translation. Annu Rev Biochem 80:1033–1053

    Article  PubMed  CAS  Google Scholar 

  • Schneider A, Maréchal-Drouard L (2000) Mitochondrial tRNA import: are there distinct mechanisms? Trends Cell Biol 10:509–513

    Article  PubMed  CAS  Google Scholar 

  • Schon A (1995) Ribonuclease P from plant nuclei and photosynthetic organelles. Mol Biol Rep 22:139–145

    Article  PubMed  Google Scholar 

  • Schon EA, DiMauro S (2007) Mitochondrial mutations: genotype to phenotype. Novartis Found Symp 287:214–233

    Article  PubMed  CAS  Google Scholar 

  • Schumacher MA, Karamooz E, Zikova A et al (2006) Crystal structures of T. brucei MRP1/MRP2 guide-RNA binding complex reveal RNA matchmaking mechanism. Cell 126:701–711

    Article  PubMed  CAS  Google Scholar 

  • Schwarzländer M, König AC, Sweetlove LJ et al (2011) The impact of impaired mitochondrial function on retrograde signalling: a meta-analysis of transcriptomic responses. J Exp Bot. doi:10.1093/jxb/err1374

  • Scott WG (2007) Morphing the minimal and full-length hammerhead ribozymes: implications for the cleavage mechanism. Biol Chem 388:727–735

    Article  PubMed  CAS  Google Scholar 

  • Scott WG, Finch JT, Klug A (1995) The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell 81:991–1002

    Article  PubMed  CAS  Google Scholar 

  • Scott WG, Martick M, Chi YI (2009) Structure and function of regulatory RNA elements: ribozymes that regulate gene expression. Biochim Biophys Acta 1789:634–641

    Article  PubMed  CAS  Google Scholar 

  • Seehafer C, Kalweit A, Steger G et al (2011) From alpaca to zebrafish: hammerhead ribozymes wherever you look. RNA 17:21–26

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Seligmann H (2010) Undetected antisense tRNAs in mitochondrial genomes? Biol Direct 5:39

    Article  PubMed  CAS  Google Scholar 

  • Shepotinovskaya I, Uhlenbeck OC (2010) Enhanced product stability in the hammerhead ribozyme. Biochemistry 49:4494–4500

    Article  PubMed  CAS  Google Scholar 

  • Shlomai J (2004) The structure and replication of kinetoplast DNA. Curr Mol Med 4:623–647

    Article  PubMed  CAS  Google Scholar 

  • Sieber F, Placido A, El Farouk-Ameqrane S et al (2011) A protein shuttle system to target RNA into mitochondria. Nucleic Acids Res 39:e96

    Article  PubMed  CAS  Google Scholar 

  • Silvestri G, Ciafaloni E, Santorelli FM et al (1993) Clinical features associated with the A → G transition at nucleotide 8344 of mtDNA (“MERRF mutation”). Neurology 43:1200–1206

    Article  PubMed  CAS  Google Scholar 

  • Singh S, Narang AS, Mahato RI (2011) Subcellular fate and off-target effects of siRNA, shRNA, and miRNA. Pharm Res 28:2996–3015

    Article  PubMed  CAS  Google Scholar 

  • Small I, Maréchal-Drouard L, Masson J et al (1992) In vivo import of a normal or mutagenized heterologous transfer RNA into the mitochondria of transgenic plants: towards novel ways of influencing mitochondrial gene expression? EMBO J 11:1291–1296

    PubMed  CAS  Google Scholar 

  • Smeitink J, van den Heuvel L, DiMauro S (2001) The genetics and pathology of oxidative phosphorylation. Nat Rev Genet 2:342–352

    Article  PubMed  CAS  Google Scholar 

  • Smirnov A, Tarassov I, Mager-Heckel AM et al (2008) Two distinct structural elements of 5 S rRNA are needed for its import into human mitochondria. RNA 14:749–759

    Article  PubMed  CAS  Google Scholar 

  • Smirnov A, Comte C, Mager-Heckel AM et al (2010) Mitochondrial enzyme rhodanese is essential for 5 S ribosomal RNA import into human mitochondria. J Biol Chem 285:30792–30803

    Article  PubMed  CAS  Google Scholar 

  • Smirnov A, Entelis N, Martin RP et al (2011) Biological significance of 5 S rRNA import into human mitochondria: role of ribosomal protein MRP-L18. Genes Dev 25:1289–1305

    Article  PubMed  CAS  Google Scholar 

  • Spitale RC, Volpini R, Mungillo MV et al (2009) Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core. Biochemistry 48:7777–7779

    Article  PubMed  CAS  Google Scholar 

  • St Johnston D (2005) Moving messages: the intracellular localization of mRNAs. Nat Rev Mol Cell Biol 6:363–375

    Article  PubMed  CAS  Google Scholar 

  • Stuart KD, Schnaufer A, Ernst NL et al (2005) Complex management: RNA editing in trypanosomes. Trends Biochem Sci 30:97–105

    Article  PubMed  CAS  Google Scholar 

  • Sugiyama Y, Watase Y, Nagase M et al (2005) The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants. Mol Genet Genomics 272:603–615

    Article  PubMed  CAS  Google Scholar 

  • Suydam IT, Levandoski SD, Strobel SA (2010) Catalytic importance of a protonated adenosine in the hairpin ribozyme active site. Biochemistry 49:3723–3732

    Article  PubMed  CAS  Google Scholar 

  • Sylvestre J, Margeot A, Jacq C et al (2003) The role of the 3′ untranslated region in mRNA sorting to the vicinity of mitochondria is conserved from yeast to human cells. Mol Biol Cell 14:3848–3856

    Article  PubMed  CAS  Google Scholar 

  • Symons RH (1992) Small catalytic RNAs. Annu Rev Biochem 61:641–671

    Article  PubMed  CAS  Google Scholar 

  • Tarassov I, Entelis N (1992) Mitochondrially-imported cytoplasmic tRNALys (CUU) of Saccharomyces cerevisiae: in vivo and in vitro targetting systems. Nucleic Acids Res 20:1277–1281

    Article  PubMed  CAS  Google Scholar 

  • Tuppen HA, Blakely EL, Turnbull DM et al (2010) Mitochondrial DNA mutations and human disease. Biochim Biophys Acta 1797:113–128

    PubMed  CAS  Google Scholar 

  • Unseld M, Marienfeld JR, Brandt P et al (1997) The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nat Genet 15:57–61

    Article  PubMed  CAS  Google Scholar 

  • Val R, Wyszko E, Valentin C et al (2011) Organelle trafficking of chimeric ribozymes and genetic manipulation of mitochondria. Nucleic Acids Res 39:9262–9274

    Article  PubMed  CAS  Google Scholar 

  • Valkov VT, Scotti N, Kahlau S et al (2009) Genome-wide analysis of plastid gene expression in potato leaf chloroplasts and tuber amyloplasts: transcriptional and posttranscriptional control. Plant Physiol 150:2030–2044

    Article  PubMed  CAS  Google Scholar 

  • Van Aken O, Zhang B, Carrie C et al (2009) Defining the mitochondrial stress response in Arabidopsis thaliana. Mol Plant 2:1310–1324

    Article  PubMed  CAS  Google Scholar 

  • van der Spek H, Arts GJ, Zwaal RR et al (1991) Conserved genes encode guide RNAs in mitochondria of Crithidia fasciculata. EMBO J 10:1217–1224

    PubMed  Google Scholar 

  • Vanhamme L, Perez-Morga D, Marchal C 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

    Article  PubMed  CAS  Google Scholar 

  • Veeraraghavan N, Ganguly A, Chen JH et al (2011) Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions. Biochemistry 50:2672–2682

    Article  PubMed  CAS  Google Scholar 

  • Villegas J, Zarraga AM, Muller I et al (2000) A novel chimeric mitochondrial RNA localized in the nucleus of mouse sperm. DNA Cell Biol 19:579–588

    Article  PubMed  CAS  Google Scholar 

  • Villegas J, Muller I, Arredondo J et al (2002) A putative RNA editing from U to C in a mouse mitochondrial transcript. Nucleic Acids Res 30:1895–1901

    Article  PubMed  CAS  Google Scholar 

  • Villegas J, Burzio V, Villota C et al (2007) Expression of a novel non-coding mitochondrial RNA in human proliferating cells. Nucleic Acids Res 35:7336–7347

    Article  PubMed  CAS  Google Scholar 

  • Wallace DC (1992) Diseases of the mitochondrial DNA. Annu Rev Biochem 61:1175–1212

    Article  PubMed  CAS  Google Scholar 

  • Wan Y, Kertesz M, Spitale RC et al (2011) Understanding the transcriptome through RNA structure. Nat Rev Genet 12:641–655

    Article  PubMed  CAS  Google Scholar 

  • Wang G, Chen HW, Oktay Y et al (2010) PNPASE regulates RNA import into mitochondria. Cell 142:456–467

    Article  PubMed  CAS  Google Scholar 

  • Wang G, Shimada E, Koehler CM et al (2011) PNPASE and RNA trafficking into mitochondria. Biochim Biophys Acta. doi:10.1016/j.bbagrm.2011.1010.1001

  • Webb CH, Lupták A (2011) HDV-like self-cleaving ribozymes. RNA Biol 8:719–727

    Article  PubMed  CAS  Google Scholar 

  • Weinberg MS, Ely A, Passman M et al (2007) Effective anti-hepatitis B virus hammerhead ribozymes derived from multimeric precursors. Oligonucleotides 17:104–112

    Article  PubMed  CAS  Google Scholar 

  • Weng J, Aphasizheva I, Etheridge RD et al (2008) Guide RNA-binding complex from mitochondria of trypanosomatids. Mol Cell 32:198–209

    Article  PubMed  CAS  Google Scholar 

  • Westhof E (1999) Chemical diversity in RNA cleavage. Science 286:61–62

    Article  PubMed  CAS  Google Scholar 

  • Witten JT, Ule J (2011) Understanding splicing regulation through RNA splicing maps. Trends Genet 27:89–97

    Article  PubMed  CAS  Google Scholar 

  • Wong LJ (2007) Diagnostic challenges of mitochondrial DNA disorders. Mitochondrion 7:45–52

    Article  PubMed  CAS  Google Scholar 

  • Woo DK, Phang TL, Trawick JD et al (2009) Multiple pathways of mitochondrial-nuclear communication in yeast: intergenomic signaling involves ABF1 and affects a different set of genes than retrograde regulation. Biochim Biophys Acta 1789:135–145

    Article  PubMed  CAS  Google Scholar 

  • Woodson JD, Chory J (2008) Coordination of gene expression between organellar and nuclear genomes. Nat Rev Genet 9:383–395

    Article  PubMed  CAS  Google Scholar 

  • Xu R, Liu J, Xu F et al (2001) Activity identification of chimeric anti-caspase-3 mRNA hammerhead ribozyme in vitro and in vivo. Sci China C Life Sci 44:618–627

    Article  PubMed  CAS  Google Scholar 

  • Yoshionari S, Koike T, Yokogawa T et al (1994) Existence of nuclear-encoded 5 S-rRNA in bovine mitochondria. FEBS Lett 338:137–142

    Article  PubMed  CAS  Google Scholar 

  • Yu LE, Koslowsky DJ (2006) Interactions of mRNAs and gRNAs involved in trypanosome mitochondrial RNA editing: structure probing of a gRNA bound to its cognate mRNA. RNA 12:1050–1060

    Article  PubMed  CAS  Google Scholar 

  • Zabala G, Gabay-Laughnan S, Laughnan JR (1997) The nuclear gene Rf3 affects the expression of the mitochondrial chimeric sequence R implicated in S-type male sterility in maize. Genetics 147:847–860

    PubMed  CAS  Google Scholar 

  • Zhang SQ, Zhang FD, Xiao HL et al (2004) R region of S type of cytoplasmic male sterility in maize mitochondrial DNA is transcribed in both directions and may be associated with male sterility. Acta Botanica Sinica 46:337–341

    CAS  Google Scholar 

  • Zhou H, Hu H, Lai M (2010a) Non-coding RNAs and their epigenetic regulatory mechanisms. Biol Cell 102:645–655

    Article  PubMed  CAS  Google Scholar 

  • Zhou J, Liu L, Chen J (2010b) Mitochondrial DNA heteroplasmy in Candida glabrata after mitochondrial transformation. Eukaryot Cell 9:806–814

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Zimmer SL, McEvoy SM, Li J 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

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

Our projects are funded by the French Centre National de la Recherche Scientifique (CNRS, UPR2357), the Université de Strasbourg (UdS), the Agence Nationale de la Recherche (ANR-06-MRAR-037-02, ANR-09-BLAN-0240-01), and the Région Alsace. Support through grants from the Polish Ministry of Science and Higher Education and the National Science Center is acknowledged.

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Authors and Affiliations

  1. Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg, France

    André Dietrich, Romain Val, Clarisse Valentin & Anne Cosset

  2. Institute of Bioorganic Chemistry, Polish Academy of Science, Noskowskiego 12/14, 61-704, Poznan, Poland

    Katarzyna Rolle, Marta Gabryelska, Eliza Wyszko, Maciej Szymanski & Jan Barciszewski

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  1. André Dietrich
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  2. Katarzyna Rolle
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  3. Marta Gabryelska
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  4. Eliza Wyszko
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  5. Romain Val
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  7. Clarisse Valentin
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  9. Jan Barciszewski
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Correspondence to André Dietrich .

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Editors and Affiliations

  1. Institute of Chemistry/Biochemistry, Free University Berlin, Thielallee 63, Berlin, 14195, Berlin, Germany

    Volker A. Erdmann

  2. Inst. Bioorganic Chemistry, PAN Poznan, ul. Z. Noskowskiego 12/14, Poznan, 61-704, Poland

    Jan Barciszewski

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Dietrich, A. et al. (2012). RNA Technologies for Mitochondrial Genetics. In: Erdmann, V., Barciszewski, J. (eds) From Nucleic Acids Sequences to Molecular Medicine. RNA Technologies. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-27426-8_13

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