1736 Nucleic Acids Research, 2012, Vol. 40, No. 4 cerevisiae, also has a role in the translation of mitochondrially encoded subunits of cytochrome c oxidase. Genetics, 158, 573–585. 23. Stribinskis,V., Heyman,H.C., Ellis,S.R., Steffen,M.C. and Martin,N.C. (2005) Rpm2p, a component of yeast mitochondrial RNase P, acts as a transcriptional activator in the nucleus. Mol. Cell Biol., 25, 6546–6558. 24. Schonauer,M.S., Kastaniotis,A.J., Hiltunen,J.K. and Dieckmann,C.L. (2008) Intersection of RNA processing and the type II fatty acid synthesis pathway in yeast mitochondria. Mol. Cell Biol., 28, 6646–6657. 25. Chen,J.Y. and Martin,N.C. (1988) Biosynthesis of tRNA in yeast mitochondria. An endonuclease is responsible for the 30-processing of tRNA precursors. J. Biol. Chem., 263, 13677–13682. 26. Papadimitriou,A. and Gross,H.J. (1996) Pre-tRNA 30-processing in Saccharomyces cerevisiae. Puriﬁcation and characterization of exo- and endoribonucleases. Eur. J. Biochem., 242, 747–759. 27. Vogel,A., Schilling,O., Spath,B. and Marchfelder,A. (2005) The tRNase Z family of proteins: physiological functions, substrate speciﬁcity and structural properties. Biol. Chem., 386, 1253–1264. 28. Rogowska,A.T., Puchta,O., Czarnecka,A.M., Kaniak,A., Stepien,P.P. and Golik,P. (2006) Balance between transcription and RNA degradation is vital for Saccharomyces cerevisiae mitochondria: reduced transcription rescues the phenotype of deﬁcient RNA degradation. Mol. Biol. Cell., 17, 1184–1193. 29. Borowski,L.S., Szczesny,R.J., Brzezniak,L.K. and Stepien,P.P. (2010) RNA turnover in human mitochondria: more questions than answers? Biochim. Biophys. Acta, 1797, 1066–1070. 30. Chernyakov,I., Whipple,J.M., Kotelawala,L., Grayhack,E.J. and Phizicky,E.M. (2008) Degradation of several hypomodiﬁed mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 50-30 exonucleases Rat1 and Xrn1. Genes Dev., 22, 1369–1380. 31. Butler,J.S. (2002) The yin and yang of the exosome. Trends Cell. Biol., 12, 90–96. 32. Carpousis,A.J., Vanzo,N.F. and Raynal,L.C. (1999) mRNA degradation. A tale of poly(A) and multiprotein machines. Trends Genet., 15, 24–28. 33. Gagliardi,D., Stepien,P.P., Temperley,R.J., Lightowlers,R.N. and Chrzanowska-Lightowlers,Z.M. (2004) Messenger RNA stability in mitochondria: different means to an end. Trends Genet., 20, 260–267. 34. Dziembowski,A., Piwowarski,J., Hoser,R., Minczuk,M., Dmochowska,A., Siep,M., van der Spek,H., Grivell,L. and Stepien,P.P. (2003) The yeast mitochondrial degradosome. Its composition, interplay between RNA helicase and RNase activities and the role in mitochondrial RNA metabolism. J. Biol. Chem., 278, 1603–1611. 35. Dmochowska,A., Golik,P. and Stepien,P.P. (1995) The novel nuclear gene DSS-1 of Saccharomyces cerevisiae is necessary for mitochondrial biogenesis. Curr. Genet., 28, 108–112. 36. Stepien,P.P., Margossian,S.P., Landsman,D. and Butow,R.A. (1992) The yeast nuclear gene suv3 affecting mitochondrial post-transcriptional processes encodes a putative ATP-dependent RNA helicase. Proc. Natl Acad. Sci. USA, 89, 6813–6817. 37. Zahedi,R.P., Sickmann,A., Boehm,A.M., Winkler,C., Zufall,N., Schonﬁsch,B., Guiard,B., Pfanner,N. and Meisinger,C. (2006) Proteomic analysis of the yeast mitochondrial outer membrane reveals accumulation of a subclass of preproteins. Mol. Biol. Cell., 17, 1436–1450. 38. Meisinger,C., Sommer,T. and Pfanner,N. (2000) Puriﬁcation of Saccharomcyes cerevisiae mitochondria devoid of microsomal and cytosolic contaminations. Anal. Biochem., 287, 339–342. 39. Daum,G., Bohni,P.C. and Schatz,G. (1982) Import of proteins into mitochondria. Cytochrome b2 and cytochrome c peroxidase are located in the intermembrane space of yeast mitochondria. J. Biol. Chem., 257, 13028–13033. 40. Liu,M. and Spremulli,L. (2000) Interaction of mammalian mitochondrial ribosomes with the inner membrane. J. Biol. Chem., 275, 29400–29406. 41. Schagger,H. (1995) Native electrophoresis for isolation of mitochondrial oxidative phosphorylation protein complexes. Methods Enzymol., 260, 190–202. 42. Schagger,H. and von Jagow,G. (1991) Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal. Biochem., 199, 223–231. 43. Wittig,I., Braun,H.P. and Schagger,H. (2006) Blue native PAGE. Nat Protoc, 1, 418–428. 44. Wittig,I. and Schagger,H. (2007) Electrophoretic methods to isolate protein complexes from mitochondria. Methods Cell Biol., 80, 723–741. 45. Jacob,Y., Seif,E., Paquet,P.O. and Lang,B.F. (2004) Loss of the mRNA-like region in mitochondrial tmRNAs of jakobids. RNA, 10, 605–614. 46. Guerrier-Takada,C. and Altman,S. (2000) Inactivation of gene expression using ribonuclease P and external guide sequences. Methods Enzymol., 313, 442–456. 47. Wessels,H.J., Vogel,R.O., van den Heuvel,L., Smeitink,J.A., Rodenburg,R.J., Nijtmans,L.G. and Farhoud,M.H. (2009) LC-MS/MS as an alternative for SDS-PAGE in blue native analysis of protein complexes. Proteomics, 9, 4221–4228. 48. Fandino,A.S., Rais,I., Vollmer,M., Elgass,H., Schagger,H. and Karas,M. (2005) LC-nanospray-MS/MS analysis of hydrophobic proteins from membrane protein complexes isolated by blue-native electrophoresis. J. Mass Spectrom., 40, 1223–1231. 49. Perkins,D.N., Pappin,D.J., Creasy,D.M. and Cottrell,J.S. (1999) Probability-based protein identiﬁcation by searching sequence databases using mass spectrometry data. Electrophoresis, 20, 3551–3567. 50. Wittig,I. and Schagger,H. (2008) Features and applications of blue-native and clear-native electrophoresis. Proteomics, 8, 3974–3990. 51. Ghaemmaghami,S., Huh,W.K., Bower,K., Howson,R.W., Belle,A., Dephoure,N., O’Shea,E.K. and Weissman,J.S. (2003) Global analysis of protein expression in yeast. Nature, 425, 737–741. 52. Gan,X., Kitakawa,M., Yoshino,K., Oshiro,N., Yonezawa,K. and Isono,K. (2002) Tag-mediated isolation of yeast mitochondrial ribosome and mass spectrometric identiﬁcation of its new components. Eur. J. Biochem., 269, 5203–5214. 53. Smits,P., Smeitink,J.A., van den Heuvel,L.P., Huynen,M.A. and Ettema,T.J. (2007) Reconstructing the evolution of the mitochondrial ribosomal proteome. Nucleic Acids Res., 35, 4686–4703. 54. Schonauer,M.S., Kastaniotis,A.J., Kursu,V.A., Hiltunen,J.K. and Dieckmann,C.L. (2009) Lipoic acid synthesis and attachment in yeast mitochondria. J. Biol. Chem., 284, 23234–23242.