Skip to main content

The Role of AAA+ Proteases in Mitochondrial Protein Biogenesis, Homeostasis and Activity Control

  • Chapter
  • First Online:

Part of the book series: Subcellular Biochemistry ((SCBI,volume 66))

Abstract

Mitochondria are specialised organelles that are structurally and functionally integrated into cells in the vast majority of eukaryotes. They are the site of numerous enzymatic reactions, some of which are essential for life. The double lipid membrane of the mitochondrion, that spatially defines the organelle and is necessary for some functions, also creates a physical but semi-permeable barrier to the rest of the cell. Thus to ensure the biogenesis, regulation and maintenance of a functional population of proteins, an autonomous protein handling network within mitochondria is required. This includes resident mitochondrial protein translocation machinery, processing peptidases, molecular chaperones and proteases. This review highlights the contribution of proteases of the AAA+ superfamily to protein quality and activity control within the mitochondrion. Here they are responsible for the degradation of unfolded, unassembled and oxidatively damaged proteins as well as the activity control of some enzymes. Since most knowledge about these proteases has been gained from studies in the eukaryotic microorganism Saccharomyces cerevisiae, much of the discussion here centres on their role in this organism. However, reference is made to mitochondrial AAA+ proteases in other organisms, particularly in cases where they play a unique role such as the mitochondrial unfolded protein response. As these proteases influence mitochondrial function in both health and disease in humans, an understanding of their regulation and diverse activities is necessary.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  1. Todde V, Veenhuis M, van der Klei IJ (2009) Autophagy: principles and significance in health and disease. Biochim Biophys Acta 1792(1):3–13

    PubMed  CAS  Google Scholar 

  2. Wong E, Cuervo AM (2010) Integration of clearance mechanisms: the proteasome and autophagy. Cold Spring Harb Perspect Biol 2(12):a006734

    PubMed  CAS  Google Scholar 

  3. Yang Z, Klionsky DJ (2009) An overview of the molecular mechanism of autophagy. Curr Top Microbiol Immunol 335:1–32

    PubMed  CAS  Google Scholar 

  4. Buchberger A (2013) Roles of Cdc48 in regulated protein degradation in yeast. In: Dougan DA (ed) Regulated proteolysis in microorganisms. Springer, Subcell Biochem 66:195–222

    Google Scholar 

  5. Kwasniak M, Pogorzelec L, Migdal I, Smakowska E et al (2012) Proteolytic system of plant mitochondria. Physiol Plant 145(1):187–195

    PubMed  CAS  Google Scholar 

  6. Ezaki J, Kominami E, Ueno T (2011) Peroxisome degradation in mammals. IUBMB Life 63(11):1001–1008

    PubMed  CAS  Google Scholar 

  7. Druyan R, DeBernard B, Rabinowitz M (1969) Turnover of cytochromes labeled with delta-aminolevulinic acid-3H in rat liver. J Biol Chem 244(21):5874–5878

    PubMed  CAS  Google Scholar 

  8. Swick RW, Rexroth AK, Stange JL (1968) The metabolism of mitochondrial proteins. 3. The dynamic state of rat liver mitochondria. J Biol Chem 243(13):3581–3587

    PubMed  CAS  Google Scholar 

  9. Wheeldon LW, Dianoux AC, Bof M, Vignais PV (1974) Stable and labile products of mitochondrial protein synthesis in vitro. Eur J Biochem 46(1):189–199

    PubMed  CAS  Google Scholar 

  10. Desautels M, Goldberg AL (1982) Demonstration of an ATP-dependent, vanadate-sensitive endoprotease in the matrix of rat liver mitochondria. J Biol Chem 257(19):11673–11679

    PubMed  CAS  Google Scholar 

  11. Desautels M, Goldberg AL (1982) Liver mitochondria contain an ATP-dependent, vanadate-sensitive pathway for the degradation of proteins. Proc Natl Acad Sci U S A 79(6):1869–1873

    PubMed  CAS  Google Scholar 

  12. Kalnov SL, Novikova LA, Zubatov AS, Luzikov VN (1979) Participation of a mitochondrial proteinase in the breakdown of mitochondrial translation products in yeast. FEBS Lett 101(2):355–358

    PubMed  CAS  Google Scholar 

  13. Yasuhara T, Mera Y, Nakai T, Ohashi A (1994) ATP-dependent proteolysis in yeast mitochondria. J Biochem 115(6):1166–1171

    PubMed  CAS  Google Scholar 

  14. Arlt H, Tauer R, Feldmann H, Neupert W et al (1996) The YTA10-12 complex, an AAA protease with chaperone-like activity in the inner membrane of mitochondria. Cell 85(6):875–885

    PubMed  CAS  Google Scholar 

  15. Kang SG, Ortega J, Singh SK, Wang N et al (2002) Functional proteolytic complexes of the human mitochondrial ATP-dependent protease, hClpXP. J Biol Chem 277(23):21095–21102

    PubMed  CAS  Google Scholar 

  16. Kutejova E, Durcova G, Surovkova E, Kuzela S (1993) Yeast mitochondrial ATP-dependent protease: purification and comparison with the homologous rat enzyme and the bacterial ATP-dependent protease La. FEBS Lett 329(1–2):47–50

    PubMed  CAS  Google Scholar 

  17. Kuzela S, Goldberg AL (1994) Mitochondrial ATP-dependent protease from rat liver and yeast. Methods Enzymol 244:376–383

    PubMed  CAS  Google Scholar 

  18. Leonhard K, Herrmann JM, Stuart RA, Mannhaupt G et al (1996) AAA proteases with catalytic sites on opposite membrane surfaces comprise a proteolytic system for the ATP-dependent degradation of inner membrane proteins in mitochondria. EMBO J 15(16):4218–4229

    PubMed  CAS  Google Scholar 

  19. Nakai T, Yasuhara T, Fujiki Y, Ohashi A (1995) Multiple genes, including a member of the AAA family, are essential for degradation of unassembled subunit 2 of cytochrome c oxidase in yeast mitochondria. Mol Cell Biol 15(8):4441–4452

    PubMed  CAS  Google Scholar 

  20. Pajic A, Tauer R, Feldmann H, Neupert W et al (1994) Yta10p is required for the ATP-dependent degradation of polypeptides in the inner membrane of mitochondria. FEBS Lett 353(2):201–206

    PubMed  CAS  Google Scholar 

  21. Pearce DA, Sherman F (1995) Degradation of cytochrome oxidase subunits in mutants of yeast lacking cytochrome c and suppression of the degradation by mutation of yme1. J Biol Chem 270(36):20879–20882

    PubMed  CAS  Google Scholar 

  22. Watabe S, Kimura T (1985) ATP-dependent protease in bovine adrenal cortex. Tissue specificity, subcellular localization, and partial characterization. J Biol Chem 260(9):5511–5517

    PubMed  CAS  Google Scholar 

  23. Haynes CM, Petrova K, Benedetti C, Yang Y et al (2007) ClpP mediates activation of a mitochondrial unfolded protein response in C. elegans. Dev Cell 13(4):467–480

    PubMed  CAS  Google Scholar 

  24. Haynes CM, Yang Y, Blais SP, Neubert TA et al (2010) The matrix peptide exporter HAF-1 signals a mitochondrial UPR by activating the transcription factor ZC376.7 in C. elegans. Mol Cell 37(4):529–540

    PubMed  CAS  Google Scholar 

  25. Heo JM, Rutter J (2011) Ubiquitin-dependent mitochondrial protein degradation. Int J Biochem Cell Biol 43(10):1422–1426

    PubMed  CAS  Google Scholar 

  26. Karbowski M, Youle RJ (2011) Regulating mitochondrial outer membrane proteins by ubiquitination and proteasomal degradation. Curr Opin Cell Biol 23(4):476–482

    PubMed  CAS  Google Scholar 

  27. Scott I, Youle RJ (2010) Mitochondrial fission and fusion. Essays Biochem 47:85–98

    PubMed  CAS  Google Scholar 

  28. Drago I, Pizzo P, Pozzan T (2011) After half a century mitochondrial calcium in- and efflux machineries reveal themselves. EMBO J 30(20):4119–4125

    PubMed  CAS  Google Scholar 

  29. Smith DJ, Ng H, Kluck RM, Nagley P (2008) The mitochondrial gateway to cell death. IUBMB Life 60(6):383–389

    PubMed  CAS  Google Scholar 

  30. West AP, Shadel GS, Ghosh S (2011) Mitochondria in innate immune responses. Nat Rev Immunol 11(6):389–402

    PubMed  CAS  Google Scholar 

  31. Gray MW, Burger G, Lang BF (2001) The origin and early evolution of mitochondria. Genome Biol 2(6):reviews 1018.1–reviews 1018.5

    Google Scholar 

  32. Friedman JR, Lackner LL, West M, DiBenedetto JR et al (2011) ER tubules mark sites of mitochondrial division. Science 334(6054):358–362

    PubMed  CAS  Google Scholar 

  33. Harner M, Korner C, Walther D, Mokranjac D et al (2011) The mitochondrial contact site complex, a determinant of mitochondrial architecture. EMBO J 30(21):4356–4370

    PubMed  CAS  Google Scholar 

  34. Hoppins S, Collins SR, Cassidy-Stone A, Hummel E et al (2011) A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria. J Cell Biol 195(2):323–340

    PubMed  CAS  Google Scholar 

  35. Kornmann B, Currie E, Collins SR, Schuldiner M et al (2009) An ER-mitochondria tethering complex revealed by a synthetic biology screen. Science 325(5939):477–481

    PubMed  CAS  Google Scholar 

  36. Kornmann B, Osman C, Walter P (2011) The conserved GTPase Gem1 regulates endoplasmic reticulum-mitochondria connections. Proc Natl Acad Sci U S A 108(34):14151–14156

    PubMed  CAS  Google Scholar 

  37. Stroud DA, Oeljeklaus S, Wiese S, Bohnert M et al (2011) Composition and topology of the endoplasmic reticulum-mitochondria encounter structure. J Mol Biol 413(4):743–750

    PubMed  CAS  Google Scholar 

  38. von der Malsburg K, Muller JM, Bohnert M, Oeljeklaus S et al (2011) Dual role of mitofilin in mitochondrial membrane organization and protein biogenesis. Dev Cell 21(4):694–707

    PubMed  Google Scholar 

  39. Sickmann A, Reinders J, Wagner Y, Joppich C et al (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci U S A 100(23):13207–13212

    PubMed  CAS  Google Scholar 

  40. Young JC, Hoogenraad NJ, Hartl FU (2003) Molecular chaperones Hsp90 and Hsp70 deliver preproteins to the mitochondrial import receptor Tom70. Cell 112(1):41–50

    PubMed  CAS  Google Scholar 

  41. Vogtle FN, Wortelkamp S, Zahedi RP, Becker D et al (2009) Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability. Cell 139(2):428–439

    PubMed  Google Scholar 

  42. Gakh O, Cavadini P, Isaya G (2002) Mitochondrial processing peptidases. Biochim Biophys Acta 1592(1):63–77

    PubMed  CAS  Google Scholar 

  43. Chacinska A, Koehler CM, Milenkovic D, Lithgow T et al (2009) Importing mitochondrial proteins: machineries and mechanisms. Cell 138(4):628–644

    PubMed  CAS  Google Scholar 

  44. Mokranjac D, Neupert W (2010) The many faces of the mitochondrial TIM23 complex. Biochim Biophys Acta 1797(6–7):1045–1054

    PubMed  CAS  Google Scholar 

  45. Ott M, Herrmann JM (2010) Co-translational membrane insertion of mitochondrially encoded proteins. Biochim Biophys Acta 1803(6):767–775

    PubMed  CAS  Google Scholar 

  46. Mossmann D, Meisinger C, Vogtle FN (2012) Processing of mitochondrial presequences. Biochim Biophys Acta 1819(9–10):1098–1106

    PubMed  CAS  Google Scholar 

  47. Taylor AB, Smith BS, Kitada S, Kojima K et al (2001) Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences. Structure 9(7):615–625

    PubMed  CAS  Google Scholar 

  48. Rawlings ND, Morton FR, Kok CY, Kong J et al (2008) MEROPS: the peptidase database. Nucleic Acids Res 36(Database issue):320–325

    Google Scholar 

  49. Vogtle FN, Prinz C, Kellermann J, Lottspeich F et al (2011) Mitochondrial protein turnover: role of the precursor intermediate peptidase Oct1 in protein stabilization. Mol Biol Cell 22(13):2135–2143

    PubMed  Google Scholar 

  50. Naamati A, Regev-Rudzki N, Galperin S, Lill R et al (2009) Dual targeting of Nfs1 and discovery of its novel processing enzyme, Icp55. J Biol Chem 284(44):30200–30208

    PubMed  CAS  Google Scholar 

  51. Dougan DA, Truscott KN, Zeth K (2010) The bacterial N-end rule pathway: expect the unexpected. Mol Microbiol 76(3):545–558

    PubMed  CAS  Google Scholar 

  52. Varshavsky A (2011) The N-end rule pathway and regulation by proteolysis. Protein Sci 20(8):1298–1345

    CAS  Google Scholar 

  53. Gur E, Ottofuelling R, Dougan DA (2013) Machines of destruction – AAA+ proteases and the adaptors that control them. In: Dougan DA (ed) Regulated proteolysis in microorganisms. Springer, Subcell Biochem 66:3–33

    Google Scholar 

  54. Bonn F, Tatsuta T, Petrungaro C, Riemer J et al (2011) Presequence-dependent folding ensures MrpL32 processing by the m-AAA protease in mitochondria. EMBO J 30(13):2545–2556

    PubMed  CAS  Google Scholar 

  55. Koppen M, Bonn F, Ehses S, Langer T (2009) Autocatalytic processing of m-AAA protease subunits in mitochondria. Mol Biol Cell 20(19):4216–4224

    PubMed  CAS  Google Scholar 

  56. Nolden M, Ehses S, Koppen M, Bernacchia A et al (2005) The m-AAA protease defective in hereditary spastic paraplegia controls ribosome assembly in mitochondria. Cell 123(2):277–289

    PubMed  CAS  Google Scholar 

  57. Osman C, Wilmes C, Tatsuta T, Langer T (2007) Prohibitins interact genetically with Atp23, a novel processing peptidase and chaperone for the F1Fo-ATP synthase. Mol Biol Cell 18(2):627–635

    PubMed  CAS  Google Scholar 

  58. Zeng X, Neupert W, Tzagoloff A (2007) The metalloprotease encoded by ATP23 has a dual function in processing and assembly of subunit 6 of mitochondrial ATPase. Mol Biol Cell 18(2):617–626

    PubMed  CAS  Google Scholar 

  59. Esser K, Tursun B, Ingenhoven M, Michaelis G et al (2002) A novel two-step mechanism for removal of a mitochondrial signal sequence involves the mAAA complex and the putative rhomboid protease Pcp1. J Mol Biol 323(5):835–843

    PubMed  CAS  Google Scholar 

  60. Herlan M, Vogel F, Bornhovd C, Neupert W et al (2003) Processing of Mgm1 by the rhomboid-type protease Pcp1 is required for maintenance of mitochondrial morphology and of mitochondrial DNA. J Biol Chem 278(30):27781–27788

    PubMed  CAS  Google Scholar 

  61. McQuibban GA, Saurya S, Freeman M (2003) Mitochondrial membrane remodelling regulated by a conserved rhomboid protease. Nature 423(6939):537–541

    PubMed  CAS  Google Scholar 

  62. 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(6):2342–2356

    PubMed  CAS  Google Scholar 

  63. Tatsuta T, Augustin S, Nolden M, Friedrichs B et al (2007) m-AAA protease-driven membrane dislocation allows intramembrane cleavage by rhomboid in mitochondria. EMBO J 26(2):325–335

    PubMed  CAS  Google Scholar 

  64. Hartl FU, Bracher A, Hayer-Hartl M (2011) Molecular chaperones in protein folding and proteostasis. Nature 475(7356):324–332

    PubMed  CAS  Google Scholar 

  65. Voos W, Rottgers K (2002) Molecular chaperones as essential mediators of mitochondrial biogenesis. Biochim Biophys Acta 1592(1):51–62

    PubMed  CAS  Google Scholar 

  66. Marom M, Azem A, Mokranjac D (2011) Understanding the molecular mechanism of protein translocation across the mitochondrial inner membrane: still a long way to go. Biochim Biophys Acta 1808(3):990–1001

    PubMed  CAS  Google Scholar 

  67. Voos W (2009) Mitochondrial protein homeostasis: the cooperative roles of chaperones and proteases. Res Microbiol 160(9):718–725

    PubMed  CAS  Google Scholar 

  68. Truscott KN, Lowth BR, Strack PR, Dougan DA (2010) Diverse functions of mitochondrial AAA+ proteins: protein activation, disaggregation, and degradation. Biochem Cell Biol 88(1):97–108

    PubMed  CAS  Google Scholar 

  69. van Dyck L, Dembowski M, Neupert W, Langer T (1998) Mcx1p, a ClpX homologue in mitochondria of Saccharomyces cerevisiae. FEBS Lett 438(3):250–254

    PubMed  Google Scholar 

  70. Craig EA, Marszalek J (2002) A specialized mitochondrial molecular chaperone system: a role in formation of Fe/S centers. Cell Mol Life Sci 59(10):1658–1665

    PubMed  CAS  Google Scholar 

  71. Reinders J, Sickmann A (2007) Proteomics of yeast mitochondria. Methods Mol Biol 372:543–557

    PubMed  CAS  Google Scholar 

  72. Sliwa D, Dairou J, Camadro JM, Santos R (2012) Inactivation of mitochondrial aspartate aminotransferase contributes to the respiratory deficit of yeast frataxin-deficient cells. Biochem J 441(3):945–953

    PubMed  CAS  Google Scholar 

  73. Erzberger JP, Berger JM (2006) Evolutionary relationships and structural mechanisms of AAA+ proteins. Annu Rev Biophys Biomol Struct 35:93–114

    PubMed  CAS  Google Scholar 

  74. Ogura T, Wilkinson AJ (2001) AAA+ superfamily ATPases: common structure–diverse function. Genes Cells 6(7):575–597

    PubMed  CAS  Google Scholar 

  75. Van Melderen L, Aertsen A (2009) Regulation and quality control by Lon-dependent proteolysis. Res Microbiol 160(9):645–651

    PubMed  Google Scholar 

  76. Goldberg AL (1992) The mechanism and functions of ATP-dependent proteases in bacterial and animal cells. Eur J Biochem 203(1–2):9–23

    PubMed  CAS  Google Scholar 

  77. Suzuki CK, Suda K, Wang N, Schatz G (1994) Requirement for the yeast gene LON in intramitochondrial proteolysis and maintenance of respiration. Science 264(5161):891

    PubMed  CAS  Google Scholar 

  78. Van Dyck L, Pearce DA, Sherman F (1994) PIM1 encodes a mitochondrial ATP-dependent protease that is required for mitochondrial function in the yeast Saccharomyces cerevisiae. J Biol Chem 269(1):238–242

    PubMed  Google Scholar 

  79. Wagner I, Arlt H, van Dyck L, Langer T et al (1994) Molecular chaperones cooperate with PIM1 protease in the degradation of misfolded proteins in mitochondria. EMBO J 13(21):5135–5145

    PubMed  CAS  Google Scholar 

  80. Savel’ev AS, Novikova LA, Kovaleva IE, Luzikov VN et al (1998) ATP-dependent proteolysis in mitochondria. m-AAA protease and PIM1 protease exert overlapping substrate specificities and cooperate with the mtHsp70 system. J Biol Chem 273(32):20596–20602

    PubMed  Google Scholar 

  81. Hanson PI, Whiteheart SW (2005) AAA+ proteins: have engine, will work. Nat Rev Mol Cell Biol 6(7):519–529

    PubMed  CAS  Google Scholar 

  82. Striebel F, Kress W, Weber-Ban E (2009) Controlled destruction: AAA+ ATPases in protein degradation from bacteria to eukaryotes. Curr Opin Struct Biol 19(2):209–217

    PubMed  CAS  Google Scholar 

  83. Sauer RT, Baker TA (2011) AAA+ proteases: ATP-fueled machines of protein destruction. Annu Rev Biochem 80:587–612

    PubMed  CAS  Google Scholar 

  84. Botos I, Melnikov EE, Cherry S, Tropea JE et al (2004) The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site. J Biol Chem 279(9):8140–8148

    PubMed  CAS  Google Scholar 

  85. Wagner I, van Dyck L, Savel’ev AS, Neupert W et al (1997) Autocatalytic processing of the ATP-dependent PIM1 protease: crucial function of a pro-region for sorting to mitochondria. EMBO J 16(24):7317–7325

    PubMed  CAS  Google Scholar 

  86. Stahlberg H, Kutejova E, Suda K, Wolpensinger B et al (1999) Mitochondrial Lon of Saccharomyces cerevisiae is a ring-shaped protease with seven flexible subunits. Proc Natl Acad Sci U S A 96(12):6787–6790

    PubMed  CAS  Google Scholar 

  87. Cha SS, An YJ, Lee CR, Lee HS et al (2010) Crystal structure of Lon protease: molecular architecture of gated entry to a sequestered degradation chamber. EMBO J 29(20):3520–3530

    PubMed  CAS  Google Scholar 

  88. Ondrovicova G, Liu T, Singh K, Tian B et al (2005) Cleavage site selection within a folded substrate by the ATP-dependent lon protease. J Biol Chem 280(26):25103–25110

    PubMed  CAS  Google Scholar 

  89. Rep M, van Dijl JM, Suda K, Schatz G et al (1996) Promotion of mitochondrial membrane complex assembly by a proteolytically inactive yeast Lon. Science 274(5284):103–106

    PubMed  CAS  Google Scholar 

  90. van Dijl JM, Kutejova E, Suda K, Perecko D et al (1998) The ATPase and protease domains of yeast mitochondrial Lon: roles in proteolysis and respiration-dependent growth. Proc Natl Acad Sci U S A 95(18):10584–10589

    PubMed  Google Scholar 

  91. Major T, von Janowsky B, Ruppert T, Mogk A et al (2006) Proteomic analysis of mitochondrial protein turnover: identification of novel substrate proteins of the matrix protease pim1. Mol Cell Biol 26(3):762–776

    PubMed  CAS  Google Scholar 

  92. Moradas-Ferreira P, Costa V, Piper P, Mager W (1996) The molecular defences against reactive oxygen species in yeast. Mol Microbiol 19(4):651–658

    PubMed  CAS  Google Scholar 

  93. Raha S, Robinson BH (2000) Mitochondria, oxygen free radicals, disease and ageing. Trends Biochem Sci 25(10):502–508

    PubMed  CAS  Google Scholar 

  94. Halliwell B (2006) Oxidative stress and neurodegeneration: where are we now? J Neurochem 97(6):1634–1658

    PubMed  CAS  Google Scholar 

  95. Bender T, Leidhold C, Ruppert T, Franken S et al (2010) The role of protein quality control in mitochondrial protein homeostasis under oxidative stress. Proteomics 10(7):1426–1443

    PubMed  CAS  Google Scholar 

  96. Bota DA, Davies KJ (2002) Lon protease preferentially degrades oxidized mitochondrial aconitase by an ATP-stimulated mechanism. Nat Cell Biol 4(9):674–680

    PubMed  CAS  Google Scholar 

  97. Bota DA, Davies KJ (2001) Protein degradation in mitochondria: implications for oxidative stress, aging and disease: a novel etiological classification of mitochondrial proteolytic disorders. Mitochondrion 1(1):33–49

    PubMed  CAS  Google Scholar 

  98. Nystrom T (2005) Role of oxidative carbonylation in protein quality control and senescence. EMBO J 24(7):1311–1317

    PubMed  Google Scholar 

  99. Bukau B, Weissman J, Horwich A (2006) Molecular chaperones and protein quality control. Cell 125(3):443–451

    PubMed  CAS  Google Scholar 

  100. Leonhardt SA, Fearson K, Danese PN, Mason TL (1993) HSP78 encodes a yeast mitochondrial heat shock protein in the Clp family of ATP-dependent proteases. Mol Cell Biol 13(10):6304–6313

    PubMed  CAS  Google Scholar 

  101. Liberek K, Lewandowska A, Zietkiewicz S (2008) Chaperones in control of protein disaggregation. EMBO J 27(2):328–335

    PubMed  CAS  Google Scholar 

  102. Weibezahn J, Tessarz P, Schlieker C, Zahn R et al (2004) Thermotolerance requires refolding of aggregated proteins by substrate translocation through the central pore of ClpB. Cell 119(5):653–665

    PubMed  CAS  Google Scholar 

  103. von Janowsky B, Major T, Knapp K, Voos W (2006) The disaggregation activity of the mitochondrial ClpB homolog Hsp78 maintains Hsp70 function during heat stress. J Mol Biol 357(3):793–807

    Google Scholar 

  104. Germaniuk A, Liberek K, Marszalek J (2002) A bichaperone (Hsp70-Hsp78) system restores mitochondrial DNA synthesis following thermal inactivation of Mip1p polymerase. J Biol Chem 277(31):27801–27808

    PubMed  CAS  Google Scholar 

  105. Rottgers K, Zufall N, Guiard B, Voos W (2002) The ClpB homolog Hsp78 is required for the efficient degradation of proteins in the mitochondrial matrix. J Biol Chem 277(48):45829–45837

    PubMed  CAS  Google Scholar 

  106. Bateman JM, Iacovino M, Perlman PS, Butow RA (2002) Mitochondrial DNA instability mutants of the bifunctional protein Ilv5p have altered organization in mitochondria and are targeted for degradation by Hsp78 and the Pim1p protease. J Biol Chem 277(49):47946–47953

    PubMed  CAS  Google Scholar 

  107. Morimoto RI (2008) Proteotoxic stress and inducible chaperone networks in neurodegenerative disease and aging. Genes Dev 22(11):1427–1438

    PubMed  CAS  Google Scholar 

  108. Bender T, Lewrenz I, Franken S, Baitzel C et al (2011) Mitochondrial enzymes are protected from stress-induced aggregation by mitochondrial chaperones and the Pim1/LON protease. Mol Biol Cell 22(5):541–554

    PubMed  CAS  Google Scholar 

  109. Elsasser S, Finley D (2005) Delivery of ubiquitinated substrates to protein-unfolding machines. Nat Cell Biol 7(8):742–749

    PubMed  CAS  Google Scholar 

  110. Samanovic M, Li H, Darwin KH (2013) The Pup-Proteasome system of Mycobacterium tuberculosis. In: Dougan DA (ed) Regulated proteolysis in microorganisms. Springer, Subcell Biochem 66:267–295

    Google Scholar 

  111. Gottesman S, Roche E, Zhou Y, Sauer RT (1998) The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev 12(9):1338–1347

    PubMed  CAS  Google Scholar 

  112. Moore SD, Sauer RT (2007) The tmRNA system for translational surveillance and ribosome rescue. Annu Rev Biochem 76:101–124

    PubMed  CAS  Google Scholar 

  113. von Janowsky B, Knapp K, Major T, Krayl M et al (2005) Structural properties of substrate proteins determine their proteolysis by the mitochondrial AAA+ protease Pim1. Biol Chem 386(12):1307–1317

    Google Scholar 

  114. Herman C, Prakash S, Lu CZ, Matouschek A et al (2003) Lack of a robust unfoldase activity confers a unique level of substrate specificity to the universal AAA protease FtsH. Mol Cell 11(3):659–669

    PubMed  CAS  Google Scholar 

  115. Prakash S, Matouschek A (2004) Protein unfolding in the cell. Trends Biochem Sci 29(11):593–600

    PubMed  CAS  Google Scholar 

  116. van Dyck L, Neupert W, Langer T (1998) The ATP-dependent PIM1 protease is required for the expression of intron-containing genes in mitochondria. Genes Dev 12(10):1515–1524

    PubMed  CAS  Google Scholar 

  117. Liu T, Lu B, Lee I, Ondrovicova G et al (2004) DNA and RNA binding by the mitochondrial lon protease is regulated by nucleotide and protein substrate. J Biol Chem 279(14):13902–13910

    PubMed  CAS  Google Scholar 

  118. Lu B, Yadav S, Shah PG, Liu T et al (2007) Roles for the human ATP-dependent Lon protease in mitochondrial DNA maintenance. J Biol Chem 282(24):17363–17374

    PubMed  CAS  Google Scholar 

  119. Chen XJ, Wang X, Butow RA (2007) Yeast aconitase binds and provides metabolically coupled protection to mitochondrial DNA. Proc Natl Acad Sci U S A 104(34):13738–13743

    PubMed  CAS  Google Scholar 

  120. Teichmann U, van Dyck L, Guiard B, Fischer H et al (1996) Substitution of PIM1 protease in mitochondria by Escherichia coli Lon protease. J Biol Chem 271(17):10137–10142

    PubMed  CAS  Google Scholar 

  121. Balaban RS, Nemoto S, Finkel T (2005) Mitochondria, oxidants, and aging. Cell 120(4):483–495

    PubMed  CAS  Google Scholar 

  122. Luce K, Weil AC, Osiewacz HD (2010) Mitochondrial protein quality control systems in aging and disease. Adv Exp Med Biol 694:108–125

    PubMed  CAS  Google Scholar 

  123. Luce K, Osiewacz HD (2009) Increasing organismal healthspan by enhancing mitochondrial protein quality control. Nat Cell Biol 11(7):852–858

    PubMed  CAS  Google Scholar 

  124. Guelin E, Rep M, Grivell LA (1996) Afg3p, a mitochondrial ATP-dependent metalloprotease, is involved in degradation of mitochondrially-encoded Cox1, Cox3, Cob, Su6, Su8 and Su9 subunits of the inner membrane complexes III, IV and V. FEBS Lett 381(1–2):42–46

    CAS  Google Scholar 

  125. Weber ER, Hanekamp T, Thorsness PE (1996) Biochemical and functional analysis of the YME1 gene product, an ATP and zinc-dependent mitochondrial protease from S. cerevisiae. Mol Biol Cell 7(2):307–317

    PubMed  CAS  Google Scholar 

  126. Okuno T, Ogura T (2013) FtsH protease-mediated regulation of various cellular functions. In: Dougan DA (ed) Regulated proteolysis in microorganisms. Springer, Subcell Biochem 66:53–69

    Google Scholar 

  127. Koppen M, Metodiev MD, Casari G, Rugarli EI et al (2007) Variable and tissue-specific subunit composition of mitochondrial m-AAA protease complexes linked to hereditary spastic paraplegia. Mol Cell Biol 27(2):758–767

    PubMed  CAS  Google Scholar 

  128. Guelin E, Rep M, Grivell LA (1994) Sequence of the AFG3 gene encoding a new member of the FtsH/Yme1/Tma subfamily of the AAA-protein family. Yeast 10(10):1389–1394

    PubMed  CAS  Google Scholar 

  129. Schnall R, Mannhaupt G, Stucka R, Tauer R et al (1994) Identification of a set of yeast genes coding for a novel family of putative ATPases with high similarity to constituents of the 26S protease complex. Yeast 10(9):1141–1155

    PubMed  CAS  Google Scholar 

  130. Thorsness PE, White KH, Fox TD (1993) Inactivation of YME1, a member of the ftsH-SEC18-PAS1-CDC48 family of putative ATPase-encoding genes, causes increased escape of DNA from mitochondria in Saccharomyces cerevisiae. Mol Cell Biol 13(9):5418–5426

    PubMed  CAS  Google Scholar 

  131. Tzagoloff A, Yue J, Jang J, Paul MF (1994) A new member of a family of ATPases is essential for assembly of mitochondrial respiratory chain and ATP synthetase complexes in Saccharomyces cerevisiae. J Biol Chem 269(42):26144–26151

    PubMed  CAS  Google Scholar 

  132. Thorsness PE, Fox TD (1993) Nuclear mutations in Saccharomyces cerevisiae that affect the escape of DNA from mitochondria to the nucleus. Genetics 134(1):21–28

    PubMed  CAS  Google Scholar 

  133. Lee S, Augustin S, Tatsuta T, Gerdes F et al (2011) Electron cryomicroscopy structure of a membrane-anchored mitochondrial AAA protease. J Biol Chem 286(6):4404–4411

    PubMed  CAS  Google Scholar 

  134. Gerdes F, Tatsuta T, Langer T (2012) Mitochondrial AAA proteases – towards a molecular understanding of membrane-bound proteolytic machines. Biochim Biophys Acta 1823(1):49–55

    PubMed  CAS  Google Scholar 

  135. Pearce DA, Sherman F (1995) Diminished degradation of yeast cytochrome c by interactions with its physiological partners. Proc Natl Acad Sci U S A 92(9):3735–3739

    PubMed  CAS  Google Scholar 

  136. Weil A, Luce K, Drose S, Wittig I et al (2011) Unmasking a temperature-dependent effect of the P. anserina i-AAA protease on aging and development. Cell Cycle 10(24):4280–4290

    PubMed  CAS  Google Scholar 

  137. Graack HR, Bryant ML, O’Brien TW (1999) Identification of mammalian mitochondrial ribosomal proteins (MRPs) by N-terminal sequencing of purified bovine MRPs and comparison to data bank sequences: the large subribosomal particle. Biochemistry 38(50):16569–16577

    PubMed  CAS  Google Scholar 

  138. Graack HR, Wittmann-Liebold B (1998) Mitochondrial ribosomal proteins (MRPs) of yeast. Biochem J 329(Pt 3):433–448

    PubMed  CAS  Google Scholar 

  139. Harms J, Schluenzen F, Zarivach R, Bashan A et al (2001) High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107(5):679–688

    PubMed  CAS  Google Scholar 

  140. Arlt H, Steglich G, Perryman R, Guiard B et al (1998) The formation of respiratory chain complexes in mitochondria is under the proteolytic control of the m-AAA protease. EMBO J 17(16):4837–4847

    PubMed  CAS  Google Scholar 

  141. Casari G, De Fusco M, Ciarmatori S, Zeviani M et al (1998) Spastic paraplegia and OXPHOS impairment caused by mutations in paraplegin, a nuclear-encoded mitochondrial metalloprotease. Cell 93(6):973–983

    PubMed  CAS  Google Scholar 

  142. Di Bella D, Lazzaro F, Brusco A, Plumari M et al (2010) Mutations in the mitochondrial protease gene AFG3L2 cause dominant hereditary ataxia SCA28. Nat Genet 42(4):313–321

    PubMed  Google Scholar 

  143. Potting C, Wilmes C, Engmann T, Osman C et al (2010) Regulation of mitochondrial phospholipids by Ups1/PRELI-like proteins depends on proteolysis and Mdm35. EMBO J 29(17):2888–2898

    PubMed  CAS  Google Scholar 

  144. Osman C, Haag M, Potting C, Rodenfels J et al (2009) The genetic interactome of prohibitins: coordinated control of cardiolipin and phosphatidylethanolamine by conserved regulators in mitochondria. J Cell Biol 184(4):583–596

    PubMed  CAS  Google Scholar 

  145. Sesaki H, Dunn CD, Iijima M, Shepard KA et al (2006) Ups1p, a conserved intermembrane space protein, regulates mitochondrial shape and alternative topogenesis of Mgm1p. J Cell Biol 173(5):651–658

    PubMed  CAS  Google Scholar 

  146. Tamura Y, Endo T, Iijima M, Sesaki H (2009) Ups1p and Ups2p antagonistically regulate cardiolipin metabolism in mitochondria. J Cell Biol 185(6):1029–1045

    PubMed  CAS  Google Scholar 

  147. Tamura Y, Iijima M, Sesaki H (2010) Mdm35p imports Ups proteins into the mitochondrial intermembrane space by functional complex formation. EMBO J 29(17):2875–2887

    PubMed  CAS  Google Scholar 

  148. Dunn CD, Lee MS, Spencer FA, Jensen RE (2006) A genomewide screen for petite-negative yeast strains yields a new subunit of the i-AAA protease complex. Mol Biol Cell 17(1):213–226

    PubMed  CAS  Google Scholar 

  149. Dunn CD, Tamura Y, Sesaki H, Jensen RE (2008) Mgr3p and Mgr1p are adaptors for the mitochondrial i-AAA protease complex. Mol Biol Cell 19(12):5387–5397

    PubMed  CAS  Google Scholar 

  150. Dailey TA, Woodruff JH, Dailey HA (2005) Examination of mitochondrial protein targeting of haem synthetic enzymes: in vivo identification of three functional haem-responsive motifs in 5-aminolaevulinate synthase. Biochem J 386(Pt 2):381–386

    PubMed  CAS  Google Scholar 

  151. Handschin C, Lin J, Rhee J, Peyer AK, Chin S, Wu PH, Meyer UA, Spiegelman BM (2005) Nutritional regulation of hepatic heme biosynthesis and porphyria through PGC-1alpha. Cell 122(4):505–515

    PubMed  CAS  Google Scholar 

  152. Tian Q, Li T, Hou W, Zheng J et al (2011) Lon peptidase 1 (LONP1)-dependent breakdown of mitochondrial 5-aminolevulinic acid synthase protein by heme in human liver cells. J Biol Chem 286(30):26424–26430

    PubMed  CAS  Google Scholar 

  153. Yoshino K, Munakata H, Kuge O, Ito A et al (2007) Haeme-regulated degradation of delta-aminolevulinate synthase 1 in rat liver mitochondria. J Biochem 142(4):453–458

    PubMed  CAS  Google Scholar 

  154. Matsushima Y, Goto Y, Kaguni LS (2010) Mitochondrial Lon protease regulates mitochondrial DNA copy number and transcription by selective degradation of mitochondrial transcription factor A (TFAM). Proc Natl Acad Sci U S A 107(43):18410–18415

    PubMed  CAS  Google Scholar 

  155. Hallberg BM, Larsson NG (2011) TFAM forces mtDNA to make a U-turn. Nat Struct Mol Biol 18(11):1179–1181

    PubMed  CAS  Google Scholar 

  156. Granot Z, Kobiler O, Melamed-Book N, Eimerl S et al (2007) Turnover of mitochondrial steroidogenic acute regulatory (StAR) protein by Lon protease: the unexpected effect of proteasome inhibitors. Mol Endocrinol 21(9):2164–2177

    PubMed  CAS  Google Scholar 

  157. Fukuda R, Zhang H, Kim JW, Shimoda L et al (2007) HIF-1 regulates cytochrome oxidase subunits to optimize efficiency of respiration in hypoxic cells. Cell 129(1):111–122

    PubMed  CAS  Google Scholar 

  158. Tobias JW, Shrader TE, Rocap G, Varshavsky A (1991) The N-end rule in bacteria. Science 254(5036):1374–1377

    PubMed  CAS  Google Scholar 

  159. Ninnis RL, Spall SK, Talbo GH, Truscott KN et al (2009) Modification of PATase by L/F-transferase generates a ClpS-dependent N-end rule substrate in Escherichia coli. EMBO J 28(12):1732–1744

    PubMed  CAS  Google Scholar 

  160. Erbse A, Schmidt R, Bornemann T, Schneider-Mergener J et al (2006) ClpS is an essential component of the N-end rule pathway in Escherichia coli. Nature 439(7077):753–756

    PubMed  CAS  Google Scholar 

  161. Schmidt R, Zahn R, Bukau B, Mogk A (2009) ClpS is the recognition component for Escherichia coli substrates of the N-end rule degradation pathway. Mol Microbiol 72(2):506–517

    PubMed  CAS  Google Scholar 

  162. Schuenemann VJ, Kralik SM, Albrecht R, Spall SK et al (2009) Structural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS. EMBO Rep 10(5):508–514

    PubMed  CAS  Google Scholar 

  163. Dougan DA, Micevski D, Truscott KN (2012) The N-end rule pathway: From recognition by N-recognins, to destruction by AAA+ proteases. Biochim Biophys Acta 1823(1):83–91

    PubMed  CAS  Google Scholar 

  164. Sriram SM, Kim BY, Kwon YT (2011) The N-end rule pathway: emerging functions and molecular principles of substrate recognition. Nat Rev Mol Cell Biol 12(11):735–747

    PubMed  CAS  Google Scholar 

  165. Benedetti C, Haynes CM, Yang Y, Harding HP et al (2006) Ubiquitin-like protein 5 positively regulates chaperone gene expression in the mitochondrial unfolded protein response. Genetics 174(1):229–239

    PubMed  CAS  Google Scholar 

  166. Ron D, Walter P (2007) Signal integration in the endoplasmic reticulum unfolded protein response. Nat Rev Mol Cell Biol 8(7):519–529

    PubMed  CAS  Google Scholar 

  167. Vabulas RM, Raychaudhuri S, Hayer-Hartl M, Hartl FU (2010) Protein folding in the cytoplasm and the heat shock response. Cold Spring Harb Perspect Biol 2(12):a004390

    PubMed  CAS  Google Scholar 

  168. Yoneda T, Benedetti C, Urano F, Clark SG et al (2004) Compartment-specific perturbation of protein handling activates genes encoding mitochondrial chaperones. J Cell Sci 117(Pt 18):4055–4066

    PubMed  CAS  Google Scholar 

  169. Zhao Q, Wang J, Levichkin IV, Stasinopoulos S et al (2002) A mitochondrial specific stress response in mammalian cells. EMBO J 21(17):4411–4419

    PubMed  CAS  Google Scholar 

  170. Barchinger SE, Ades SE (2013) Regulated proteolysis: control of the Escherichia coli σE-dependent cell envelope stress response. In: Dougan DA (ed) Regulated proteolysis in microorganisms. Springer, Dordrecht, pp xxx–xxx

    Google Scholar 

  171. Micevski D, Dougan DA (2013) Proteolytic regulation of stress response pathways in Escherichia coli. In: Dougan DA (ed) Regulated proteolysis in microorganisms. Springer, Subcell Biochem 66:105–128

    Google Scholar 

  172. Molière N, Turgay K (2013) General and regulatory proteolysis in Bacillus subtilis. In: Dougan DA (ed) Regulated proteolysis in microorganisms. Springer, Subcell Biochem 66:73–103

    Google Scholar 

  173. Buchberger A, Bukau B, Sommer T (2010) Protein quality control in the cytosol and the endoplasmic reticulum: brothers in arms. Mol Cell 40(2):238–252

    PubMed  CAS  Google Scholar 

  174. Martinus RD, Garth GP, Webster TL, Cartwright P et al (1996) Selective induction of mitochondrial chaperones in response to loss of the mitochondrial genome. Eur J Biochem 240(1):98–103

    PubMed  CAS  Google Scholar 

  175. Kirstein-Miles J, Morimoto RI (2010) Peptides signal mitochondrial stress. Cell Metab 11(3):177–178

    PubMed  CAS  Google Scholar 

  176. Haynes CM, Ron D (2010) The mitochondrial UPR – protecting organelle protein homeostasis. J Cell Sci 123(Pt 22):3849–3855

    PubMed  CAS  Google Scholar 

  177. Young L, Leonhard K, Tatsuta T, Trowsdale J et al (2001) Role of the ABC transporter Mdl1 in peptide export from mitochondria. Science 291(5511):2135–2138

    PubMed  CAS  Google Scholar 

  178. Truscott KN, Bezawork-Geleta A, Dougan DA (2011) Unfolded protein responses in bacteria and mitochondria: a central role for the ClpXP machine. IUBMB Life 63(11):955–963

    PubMed  CAS  Google Scholar 

  179. Shirihai OS, Gregory T, Yu C, Orkin SH et al (2000) ABC-me: a novel mitochondrial transporter induced by GATA-1 during erythroid differentiation. EMBO J 19(11):2492–2502

    PubMed  CAS  Google Scholar 

  180. Horibe T, Hoogenraad NJ (2007) The chop gene contains an element for the positive regulation of the mitochondrial unfolded protein response. PLoS One 2(9):e835

    PubMed  Google Scholar 

  181. Aldridge JE, Horibe T, Hoogenraad NJ (2007) Discovery of genes activated by the mitochondrial unfolded protein response (mtUPR) and cognate promoter elements. PLoS One 2(9):e874

    PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Wolfgang Voos or Kaye N. Truscott .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Voos, W., Ward, L.A., Truscott, K.N. (2013). The Role of AAA+ Proteases in Mitochondrial Protein Biogenesis, Homeostasis and Activity Control. In: Dougan, D. (eds) Regulated Proteolysis in Microorganisms. Subcellular Biochemistry, vol 66. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5940-4_9

Download citation

Publish with us

Policies and ethics