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Role of Intra- and Inter-mitochondrial Membrane Contact Sites in Yeast Phospholipid Biogenesis

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Organelle Contact Sites

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 997))

Abstract

Eukaryotic cells exhibit intracellular compartments called organelles wherein various specialized enzymatic reactions occur. Despite the specificity of the characteristic functions of organelles, recent studies have shown that distinct organelles physically connect and communicate with each other to maintain the integrity of their functions. In yeast, multiple inter- and intramitochondrial membrane contact sites (MCSs) were identified to date and were proposed to be involved in phospholipid biogenesis. In the present article, we focus on inter- and intra-organellar MCSs involving mitochondria and their tethering factors, such as the ERMES (endoplasmic reticulum (ER)–mitochondria encounter structure) complex and EMC (conserved ER membrane protein complex) between mitochondria and the ER, vCLAMP (vacuole and mitochondria patch) between mitochondria and vacuoles, and the MICOS (mitochondrial contact site) complex between the mitochondrial outer and inner membranes (MOM and MIM). All of these membrane-tethering factors were proposed to be involved in phospholipid biogenesis. Furthermore, the existence of functional interconnections among multiple organelle contact sites is suggested. In the present article, we summarize the latest discoveries in regard to MCSs and MCS-forming factors involving mitochondria and discuss their molecular functions, with particular focus on phospholipid metabolism in yeast.

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References

  • Aaltonen MJ, Friedman JR, Osman C, Salin B, di Rago JP, Nunnari J, Langer T, Tatsuta T (2016) MICOS and phospholipid transfer by Ups2–Mdm35 organize membrane lipid synthesis in mitochondria. J Cell Biol 213:525–534

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Achleitner G, Gaigg B, Krasser A, Kainersdorfer E, Kohlwein SD, Perktold A, Zellnig G, Daum G (1999) Association between the endoplasmic reticulum and mitochondria of yeast facilitates interorganelle transport of phospholipids through membrane contact. Eur J Biochem 264:545–553

    Article  CAS  PubMed  Google Scholar 

  • AhYoung AP, Jiang J, Zhang J, Khoi Dang X, Loo JA, Zhou ZH, Egea PF (2015) Conserved SMP domains of the ERMES complex bind phospholipids and mediate tether assembly. Proc Natl Acad Sci USA 112:E3179–E3188

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Balderhaar HJK, Ungermann C (2013) CORVET and HOPS tethering complexes- coordinators of endosome and lysosome fusion. J Cell Sci 126:1307–1316

    Article  CAS  PubMed  Google Scholar 

  • Berger KH, Sogo LF, Yaffe MP (1997) Mdm12p, a component required for mitochondrial inheritance that is conserved between budding and fission yeast. J Cell Biol 136:545–553

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boldogh IR, Nowakowski DW, Yang HC, Chung H, Karmon S, Royes P, Pon LA (2003) A protein complex containing Mdm10p, Mdm12p, and Mmm1p links mitochondrial membranes and DNA to the cytoskeleton-based segregation machinery. Mol Biol Cell 14:4618–4627

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Burgess SM, Delannoy M, Jensen RE (1994) MMM1 encodes a mitochondrial outer membrane protein essential for establishing and maintaining the structure of yeast mitochondria. J Cell Biol 126:1375–1391

    Article  CAS  PubMed  Google Scholar 

  • Choi JY, Wu WI, Voelker DR (2005) Phosphatidylserine decarboxylases as genetic and biochemical tools for studying phospholipid traffic. Anal Biochem 347:165–175

    Article  CAS  PubMed  Google Scholar 

  • Clancey CJ, Chang SC, Dowhan W (1993) Cloning of a gene (PSD1) encoding phosphatidylserine decarboxylase from Saccharomyces cerevisiae by complementation of an Escherichia coli mutant. J Biol Chem 268:24580–24590

    CAS  PubMed  Google Scholar 

  • Cohen Y, Klug YA, Dimitrov L, Erez Z, Chuartzman SG, Elinger D, Yofe I, Soliman K, Gärtner J, Thoms S et al (2014) Peroxisomes are juxtaposed to strategic sites on mitochondria. Mol BioSyst 10:1742–1748

    Article  CAS  PubMed  Google Scholar 

  • Connerth M, Tatsuta T, Haag M, Klecker T, Westermann B, Langer T (2012) Intramitochondrial transport of phosphatidic acid in yeast by a lipid transfer protein. Science 338:815–818

    Article  CAS  PubMed  Google Scholar 

  • Dimmer KS, Fritz S, Fuchs F, Messerschmitt M, Weinbach N, Neupert W, Westermann B (2002) Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae. Mol Biol Cell 13:847–853

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Elbaz-Alon Y, Rosenfeld-Gur E, Shinder V, Futerman AH, Geiger T, Schuldiner M (2014) A dynamic interface between vacuoles and mitochondria in yeast. Dev Cell 30:95–102

    Article  CAS  PubMed  Google Scholar 

  • Elbaz-Alon Y, Eisenberg-Bord M, Shinder V, Stiller SB, Shimoni E, Wiedemann N, Geiger T, Schuldiner M (2015) Lam6 Regulates the Extent of Contacts between Organelles. Cell Rep 12:7–14

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fransson Å, Ruusala A, Aspenström P (2003) Atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. J Biol Chem 278:6495–6502

    Article  CAS  PubMed  Google Scholar 

  • Frederick RL, McCaffery JM, Cunningham KW, Okamoto K, Shaw JM (2004) Yeast Miro GTPase, Gem1p, regulates mitochondrial morphology via a novel pathway. J Cell Biol 167:87–98

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Friedman JR, Mourier A, Yamada J, McCaffery JM, Nunnari J (2015) MICOS coordinates with respiratory complexes and lipids to establish mitochondrial inner membrane architecture. eLife 4

    Google Scholar 

  • Gibellini F, Smith TK (2010) The Kennedy pathway-De novo synthesis of phosphatidylethanolamine and phosphatidylcholine. IUBMB Life 62:414–428

    Article  CAS  PubMed  Google Scholar 

  • Harner M, Körner C, Walther D, Mokranjac D, Kaesmacher J, Welsch U, Griffith J, Mann M, Reggiori F, Neupert W (2011) The mitochondrial contact site complex, a determinant of mitochondrial architecture. EMBO J 30:4356–4370

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Henry SA, Kohlwein SD, Carman GM (2012) Metabolism and regulation of glycerolipids in the yeast Saccharomyces cerevisiae. Genetics 190:317–349

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hobbs AEA, Srinivasan M, Mccaffery JM, Jensen RE (2001) Mmm1p, a mitochondrial outer membrane protein, is connected to mtDNA nucleoids and required for mtDNA stability. J Cell Biol 152:401–410

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hönscher C, Mari M, Auffarth K, Bohnert M, Griffith J, Geerts W, van der Laan M, Cabrera M, Reggiori F, Ungermann C (2014) Cellular metabolism regulates contact sites between vacuoles and mitochondria. Dev Cell 30:86–94

    Article  PubMed  Google Scholar 

  • Hoppins S, Collins SR, Cassidy-Stone A, Hummel E, DeVay RM, Lackner LL, Westermann B, Schuldiner M, Weissman JS, Nunnari J (2011) A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria. J Cell Biol 195:323–340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Horvath SE, Daum G (2013) Lipids of mitochondria. Prog Lipid Res 52:590–614

    Article  CAS  PubMed  Google Scholar 

  • Jonikas MC, Collins SR, Denic V, Oh E, Quan EM, Schmid V, Weibezahn J, Schwappach B, Walter P, Weissman JS et al (2009) Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum. Science 323:1693–1697

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khafif M, Cottret L, Balagué C, Raffaele S (2014) Identification and phylogenetic analyses of VASt, an uncharacterized protein domain associated with lipid-binding domains in Eukaryotes. BMC Bioinformatics 15:222

    Article  PubMed  PubMed Central  Google Scholar 

  • Kodaki T, Yamashita S (1989) Characterization of the methyltransferases in the yeast phosphatidylethanolamine methylation pathway by selective gene disruption. Eur J Biochem 185:243–251

    Article  CAS  PubMed  Google Scholar 

  • Kojima R, Endo T, Tamura Y (2016) A phospholipid transfer function of ER-mitochondria encounter structure revealed in vitro. Sci Rep 6:30777

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kopec KO, Alva V, Lupas AN (2011) Bioinformatics of the TULIP domain superfamily. Biochem Soc Trans 39:1033–1038

    Article  CAS  PubMed  Google Scholar 

  • Kornmann B, Currie E, Collins SR, Schuldiner M, Nunnari J, Weissman JS, Walter P (2009) An ER-mitochondria tethering complex revealed by a synthetic biology screen. Science 325:477–481

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kornmann B, Osman C, Walter P (2011) The conserved GTPase Gem1 regulates endoplasmic reticulum-mitochondria connections. Proc Natl Acad Sci USA 108:14151–14156

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kudo N, Kumagai K, Tomishige N, Yamaji T, Wakatsuki S, Nishijima M, Hanada K, Kato R (2008) Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide. Proc Natl Acad Sci USA 105:488–493

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lahiri S, Chao JT, Tavassoli S, Wong AKO, Choudhary V, Young BP, Loewen CJR, Prinz WA (2014) A conserved endoplasmic reticulum membrane protein complex (EMC) facilitates phospholipid transfer from the ER to mitochondria. PLoS Biol 12:e1001969

    Article  PubMed  PubMed Central  Google Scholar 

  • Lang AB, Peter ATJ, Walter P, Kornmann B (2015) ER–mitochondrial junctions can be bypassed by dominant mutations in the endosomal protein Vps13. J Cell Biol 210:883–890

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mattiazzi Ušaj M, Brložnik M, Kaferle P, Žitnik M, Wolinski H, Leitner F, Kohlwein SD, Zupan B, Petrovič U (2015) Genome-Wide localization study of yeast Pex11 identifies peroxisome–mitochondria interactions through the ERMES complex. J Mol Biol 427:2072–2087

    Article  PubMed  PubMed Central  Google Scholar 

  • Meisinger C, Rissler M, Chacinska A, Sanjuán Szklarz LK, Milenkovic D, Kozjak V, Schönfisch B, Lohaus C, Meyer HE, Yaffe MP et al (2004) The mitochondrial morphology protein Mdm10 functions in assembly of the preprotein translocase of the outer membrane. Dev Cell 7:61–71

    Article  CAS  PubMed  Google Scholar 

  • Meisinger C, Wiedemann N, Rissler M, Strub A, Milenkovic D, Schönfisch B, Müller H, Kozjak V, Pfanner N (2006) Mitochondrial protein sorting: Differentiation of β-barrel assembly by Tom7-mediated segregation of Mdm10. J Biol Chem 281:22819–22826

    Article  CAS  PubMed  Google Scholar 

  • Meisinger C, Pfannschmidt S, Rissler M, Milenkovic D, Becker T, Stojanovski D, Youngman MJ, Jensen RE, Chacinska A, Guiard B et al (2007) The morphology proteins Mdm12/Mmm1 function in the major β-barrel assembly pathway of mitochondria. EMBO J 26:2229–2239

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miliara X, Garnett JA, Tatsuta T, Abid Ali F, Baldie H, Pérez-Dorado I, Simpson P, Yague E, Langer T, Matthews S (2015) Structural insight into the TRIAP1/PRELI-like domain family of mitochondrial phospholipid transfer complexes. EMBO Rep 16:824–835

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miyata N, Watanabe Y, Tamura Y, Endo T, Kuge O (2016) Phosphatidylserine transport by Ups2–Mdm35 in respiration-active mitochondria. J Cell Biol 214:77–88

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Murley A, Sarsam R, Toulmay A, Yamada J, Prinz W, Nunnari J, Murley A, Sarsam R, Toulmay A, Yamada J et al (2015) Ltc1 is an ER-localized sterol transporter and a component of ER–mitochondria and ER–vacuole contacts. J Cell Biol 209:539–548

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nguyen TT, Lewandowska A, Choi JY, Markgraf DF, Junker M, Bilgin M, Ejsing CS, Voelker DR, Rapoport TA, Shaw JM (2012) Gem1 and ERMES do not directly affect phosphatidylserine transport from ER to mitochondria or mitochondrial inheritance. Traffic 13:880–890

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Osman C, Haag M, Potting C, Rodenfels J, Dip PV, Wieland FT, Brügger B, Westermann B, Langer T (2009) The genetic interactome of prohibitins: coordinated control of cardiolipin and phosphatidylethanolamine by conserved regulators in mitochondria. J Cell Biol 184:583–596

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Porter KR, Palade GE (1957) Studies on the endoplasmic reticulum. J Biophys Biochem Cytol 3:269–300

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Potting C, Wilmes C, Engmann T, Osman C, Langer T (2010) Regulation of mitochondrial phospholipids by Ups1/PRELI-like proteins depends on proteolysis and Mdm35. EMBO J 29:2888–2898

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rabl R, Soubannier V, Scholz R, Vogel F, Mendl N, Vasiljev-Neumeyer A, Körner C, Jagasia R, Keil T, Baumeister W et al (2009) Formation of cristae and crista junctions in mitochondria depends on antagonism between Fcj1 and Su e / g. J Cell Biol 185:1047–1063

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sesaki H, Jensen RE (2004) Ugo1p links the Fzo1p and Mgm1p GTPases for mitochondrial fusion. J Biol Chem 279:28298–28303

    Article  CAS  PubMed  Google Scholar 

  • Sesaki H, Southard SM, Yaffe MP, Jensen RE (2003) Mgm1p, a dynamin-related GTPase, is essential for fusion of the mitochondrial outer membrane. Mol Biol Cell 14:2342–2356

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shiota T, Mabuchi H, Tanaka-Yamano S, Yamano K, Endo T (2011) In vivo protein-interaction mapping of a mitochondrial translocator protein Tom22 at work. Proc Natl Acad Sci USA 108:15179–15183

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Simbeni R, Tangemann K, Schmidt M, Ceolotto C, Paltauf F, Daum G (1993) Import of phosphatidylserine into isolated yeast mitochondria. Biochim Biophys Acta 1145:1–7

    Article  CAS  PubMed  Google Scholar 

  • Sogo LF, Yaffe MP (1994) Regulation of mitochondrial morphology and inheritance by Mdm10p, a protein of the mitochondrial outer membrane. J Cell Biol 126:1361–1373

    Article  CAS  PubMed  Google Scholar 

  • Stroud DA, Oeljeklaus S, Wiese S, Bohnert M, Lewandrowski U, Sickmann A, Guiard B, Van Der Laan M, Warscheid B, Wiedemann N (2011) Composition and topology of the endoplasmic reticulum-mitochondria encounter structure. J Mol Biol 413:743–750

    Article  CAS  PubMed  Google Scholar 

  • Tamura Y, Harada Y, Shiota T, Yamano K, Watanabe K, Yokota M, Yamamoto H, Sesaki H, Endo T (2009a) Tim23-Tim50 pair coordinates functions of translocators and motor proteins in mitochondrial protein import. J Cell Biol 184:129–141

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura Y, Endo T, Iijima M, Sesaki H (2009b) Ups1p and Ups2p antagonistically regulate cardiolipin metabolism in mitochondria. J Cell Biol 185:1029–1045

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura Y, Iijima M, Sesaki H (2010) Mdm35p imports Ups proteins into the mitochondrial intermembrane space by functional complex formation. EMBO J 29:2875–2887

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura Y, Onguka O, Itoh K, Endo T, Iijima M, Claypool SM, Sesaki H (2012a) Phosphatidylethanolamine Biosynthesis in Mitochondria: Phosphatidylserine (PS) trafficking in independent of a PS decarboxylase and intermembrane space protiens Ups1p and Ups2p. J Biol Chem 287:43961–43971

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura Y, Onguka O, Aiken Hobbs AE, Jensen RE, Iijima M, Claypool SM, Sesaki H (2012b) Role for two conserved intermembrane space proteins, Ups1p and Ups2p, in intra-mitochondrial phospholipid trafficking. J Biol Chem 287:15205–15218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura Y, Sesaki H, Endo T (2014) Phospholipid transport via mitochondria. Traffic 15:933–945

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tatsuta T, Scharwey M, Langer T (2014) Mitochondrial lipid trafficking. Trends Cell Biol 24:44–52

    Article  CAS  PubMed  Google Scholar 

  • Tong A, Evangelista M, Parsons A, Xu H, Bader G, Pagé N, Robinson M, Raghibizadeh S, Hogue C, Bussey H et al (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294:2364–2368

    Article  CAS  PubMed  Google Scholar 

  • Vogel F, Bornhövd C, Neupert W, Reichert AS (2006) Dynamic subcompartmentalization of the mitochondrial inner membrane. J Cell Biol 175:237–247

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • von der Malsburg K, Muller JM, Bohnert M, Oeljeklaus S, Kwiatkowska P, Becker T, Loniewska-Lwowska A, Wiese S, Rao S, Milenkovic D et al (2011) Dual role of mitofilin in mitochondrial membrane organization and protein biogenesis. Dev Cell 21:694–707

    Article  PubMed  Google Scholar 

  • Voss C, Lahiri S, Young BP, Loewen CJ, Prinz WA (2012) ER-shaping proteins facilitate lipid exchange between the ER and mitochondria in S. cerevisiae. J Cell Sci 125:4791–4799

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Watanabe Y, Tamura Y, Kawano S, Endo T (2015) Structural and mechanistic insights into phospholipid transfer by Ups1–Mdm35 in mitochondria. Nat Commun 6:7922

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wong ED, Wagner JA, Scott SV, Okreglak V, Holewinske TJ, Cassidy-Stone A, Nunnari J (2003) The intramitochondrial dynamin-related GTPase, Mgm1p, is a component of a protein complex that mediates mitochondrial fusion. J Cell Biol 160:303–311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wurm CA, Jakobs S (2006) Differential protein distributions define two sub-compartments of the mitochondrial inner membrane in yeast. FEBS Lett 580:5628–5634

    Article  CAS  PubMed  Google Scholar 

  • Yamano K, Tanaka-Yamano S, Endo T (2010) Mdm10 as a dynamic constituent of the TOB/SAM complex directs coordinated assembly of Tom40. EMBO Rep 11:187–193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Youngman MJ, Hobbs AEA, Burgess SM, Srinivasan M, Jensen RE (2004) Mmm2p, a mitochondrial outer membrane protein required for yeast mitochondrial shape and maintenance of mtDNA nucleoids. J Cell Biol 164:677–688

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu F, He F, Yao H, Wang C, Wang J, Li J, Qi X, Xue H, Ding J, Zhang P (2015) Structural basis of intramitochondrial phosphatidic acid transport mediated by Ups1-Mdm35 complex. EMBO Rep 16:813–823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Correspondence to Yasushi Tamura .

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Tamura, Y., Endo, T. (2017). Role of Intra- and Inter-mitochondrial Membrane Contact Sites in Yeast Phospholipid Biogenesis. In: Tagaya, M., Simmen, T. (eds) Organelle Contact Sites. Advances in Experimental Medicine and Biology, vol 997. Springer, Singapore. https://doi.org/10.1007/978-981-10-4567-7_9

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