Roles of Cdc48 in regulated protein degradation in yeast

Subcellular Biochemistry

Volumn 66, Issue , 2013, Pages 195-222

  Buchberger, Alexander ^a  

^a UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; CDC48 PROTEIN; CELL CYCLE PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

METABOLISM; PROTEIN DEGRADATION; REVIEW; SACCHAROMYCES CEREVISIAE;

ADENOSINE TRIPHOSPHATASES; CELL CYCLE PROTEINS; PROTEOLYSIS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84887405374     PISSN: 03060225     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-94-007-5940-4_8     Document Type: Article

References (168)

1. Baumeister W, Walz J, Zuhl F, Seemuller E (1998) The proteasome: paradigm of a selfcompartmentalizing protease. Cell 92(3):367-380
2. Lasker K, Förster F, Bohn S, Walzthoeni T (2012) Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci USA 109(5):1380-1387
3. Kornfeld S, Mellman I (1989) The biogenesis of lysosomes. Annu Rev Cell Biol 5:483-525
4. Clague MJ, Urbe S (2010) Ubiquitin: same molecule, different degradation pathways. Cell 143(5):682-685
5. Katzmann DJ, Odorizzi G, Emr SD (2002) Receptor downregulation and multivesicular-body sorting. Nat Rev Mol Cell Biol 3(12):893-905
6. Nakatogawa H, Suzuki K, Kamada Y, Ohsumi Y (2009) Dynamics and diversity in autophagy mechanisms: lessons from yeast. Nat Rev Mol Cell Biol 10(7):458-467
7. Kirkin V, McEwan DG, Novak I, Dikic I (2009) A role for ubiquitin in selective autophagy. Mol Cell 34(3):259-269
8. Kraft C, Peter M, Hofmann K (2010) Selective autophagy: ubiquitin-mediated recognition and beyond. Nat Cell Biol 12(9):836-841
9. Hershko A, Ciechanover A (1998) The ubiquitin system. Annu Rev Biochem 67:425-479
10. Ikeda F, Dikic I (2008) Atypical ubiquitin chains: new molecular signals. 'Protein modi fications: beyond the usual suspects' review series. EMBO Rep 9(6):536-542
11. Komander D (2009) The emerging complexity of protein ubiquitination. Biochem Soc Trans 37(Pt 5):937-953
12. Behrends C, Harper JW (2011) Constructing and decoding unconventional ubiquitin chains. Nat Struct Mol Biol 18(5):520-528
13. Komander D, Clague MJ, Urbe S (2009) Breaking the chains: structure and function of the deubiquitinases. Nat Rev Mol Cell Biol 10(8):550-563
14. Pickart CM, Fushman D (2004) Polyubiquitin chains: polymeric protein signals. Curr Opin Chem Biol 8(6):610-616
15. Hochstrasser M (1996) Ubiquitin-dependent protein degradation. Annu Rev Genet 30:405-439
16. Xu P, Duong DM, Seyfried NT, Cheng D et al (2009) Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell 137(1):133-145
17. Hicke L, Dunn R (2003) Regulation of membrane protein transport by ubiquitin and ubiquitin-binding proteins. Annu Rev Cell Dev Biol 19:141-172
18. Chen ZJ (2005) Ubiquitin signalling in the NF-[kappa]B pathway. Nat Cell Biol 7(8):758-765
19. Piper RC, Katzmann DJ (2007) Biogenesis and function of multivesicular bodies. Annu Rev Cell Dev Biol 23:519-547
20. Hanson PI, Whiteheart SW (2005) AAA+ proteins: have engine, will work. Nat Rev Mol Cell Biol 6(7):519-529
21. Bays NW, Hampton RY (2002) Cdc48-Ufd1-Npl4: stuck in the middle with Ub. Curr Biol 12(10):R366-R371
22. Elsasser S, Finley D (2005) Delivery of ubiquitinated substrates to protein-unfolding machines. Nat Cell Biol 7(8):742-749
23. Buchberger A (2010) Control of ubiquitin conjugation by Cdc48 and its cofactors. Subcell Biochem 54:17-30
24. Ju JS, Weihl CC (2010) Inclusion body myopathy, Paget's disease of the bone and frontotemporal dementia: a disorder of autophagy. Hum Mol Genet 19(R1):R38-R45
25. Ritz D, Vuk M, Kirchner P, Bug M et al (2011) Endolysosomal sorting of ubiquitylated caveolin-1 is regulated by VCP and UBXD1 and impaired by VCP disease mutations. Nat Cell Biol 13(9):1116-1123
26. Dargemont C, Ossareh-Nazari B (2012) Cdc48/p97, a key actor in the interplay between autophagy and ubiquitin/proteasome catabolic pathways. Biochim Biophys Acta 1823(1): 138-144
27. Watts GD, Wymer J, Kovach MJ, Mehta SG et al (2004) Inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia is caused by mutant valosin-containing protein. Nat Genet 36(4):377-381
28. Weihl CC, Pestronk A, Kimonis VE (2009) Valosin-containing protein disease: inclusion body myopathy with Paget's disease of the bone and fronto-temporal dementia. Neuromuscul Disord 19(5):308-315
29. Johnson JO, Mandrioli J, Benatar M, Abramzon Y et al (2010) Exome sequencing reveals VCP mutations as a cause of familial ALS. Neuron 68(5):857-864
30. Rouiller I, Butel VM, Latterich M, Milligan RA et al (2000) A major conformational change in p97 AAA ATPase upon ATP binding. Mol Cell 6(6):1485-1490
31. Zhang X, Shaw A, Bates PA, Newman RH et al (2000) Structure of the AAA ATPase p97. Mol Cell 6(6):1473-1484
32. DeLaBarre B, Brunger AT (2005) Nucleotide dependent motion and mechanism of action of p97/VCP. J Mol Biol 347(2):437-452
33. DeLaBarre B, Brunger AT (2003) Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains. Nat Struct Biol 10(10):856-863
34. Beuron F, Flynn TC, Ma J, Kondo H et al (2003) Motions and negative cooperativity between p97 domains revealed by cryo-electron microscopy and quantised elastic deformational model. J Mol Biol 327(3):619-629
35. Pye VE, Dreveny I, Briggs LC, Sands C et al (2006) Going through the motions: the ATPase cycle of p97. J Struct Biol 156(1):12-28
36. Song C, Wang Q, Li CC (2003) ATPase activity of p97-valosin-containing protein (VCP). D2 mediates the major enzyme activity, and D1 contributes to the heat-induced activity. J Biol Chem 278(6):3648-3655
37. Ye Y, Meyer HH, Rapoport TA (2003) Function of the p97-Ufd1-Npl4 complex in retrotranslocation from the ER to the cytosol: dual recognition of nonubiquitinated polypeptide segments and polyubiquitin chains. J Cell Biol 162(1):71-84
38. DeLaBarre B, Christianson JC, Kopito RR, Brunger AT (2006) Central pore residues mediate the p97/VCP activity required for ERAD. Mol Cell 22(4):451-462
39. Esaki M, Ogura T (2010) ATP-bound form of the D1 AAA domain inhibits an essential function of Cdc48p/p97. Biochem Cell Biol 88(1):109-117
40. Nishikori S, Esaki M, Yamanaka K, Sugimoto S et al (2011) Positive cooperativity of the p97 AAA ATPase is critical for essential functions. J Biol Chem 286(18):15815-15820
41. Wang Q, Song C, Li CC (2003) Hexamerization of p97-VCP is promoted by ATP binding to the D1 domain and required for ATPase and biological activities. Biochem Biophys Res Commun 300(2):253-260
42. Zolkiewski M (2006) A camel passes through the eye of a needle: protein unfolding activity of Clp ATPases. Mol Microbiol 61(5):1094-1100
43. Sauer RT, Baker TA (2011) AAA+ proteases: ATP-fueled machines of protein destruction. Annu Rev Biochem 80:587-612
44. 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
45. Ernst R, Claessen JH, Mueller B, Sanyal S et al (2011) Enzymatic blockade of the ubiquitinproteasome pathway. PLoS Biol 8(3):e1000605
46. Claessen JH, Kundrat L, Ploegh HL (2011) Protein quality control in the ER: balancing the ubiquitin checkbook. Trends Cell Biol 22(1):22-32
47. Sowa ME, Bennett EJ, Gygi SP, Harper JW (2009) De fining the human deubiquitinating enzyme interaction landscape. Cell 138(2):389-403
48. Gerega A, Rockel B, Peters J, Tamura T et al (2005) VAT, the thermoplasma homolog of mammalian p97/VCP, is an N domain-regulated protein unfoldase. J Biol Chem 280(52): 42856-42862
49. Rothballer A, Tzvetkov N, Zwickl P (2007) Mutations in p97/VCP induce unfolding activity. FEBS Lett 581(6):1197-1201
50. Prakash S, Tian L, Ratliff KS, Lehotzky RE et al (2004) An unstructured initiation site is required for ef ficient proteasome-mediated degradation. Nat Struct Mol Biol 11(9):830-837
51. Beskow A, Grimberg KB, Bott LC, Salomons FA et al (2009) A conserved unfoldase activity for the p97 AAA-ATPase in proteasomal degradation. J Mol Biol 394(4):732-746
52. Beuron F, Dreveny I, Yuan X, Pye VE et al (2006) Conformational changes in the AAA ATPase p97-p47 adaptor complex. EMBO J 25(9):1967-1976
53. Schuberth C, Buchberger A (2008) UBX domain proteins: major regulators of the AAA ATPase Cdc48/p97. Cell Mol Life Sci 65(15):2360-2371
54. Johnson ES, Ma PC, Ota IM, Varshavsky A (1995) A proteolytic pathway that recognizes ubiquitin as a degradation signal. J Biol Chem 270(29):17442-17456
55. Zhang S, Guha S, Volkert FC (1995) The Saccharomyces SHP1 gene, which encodes a regulator of phosphoprotein phosphatase 1 with differential effects on glycogen metabolism, meiotic differentiation, and mitotic cell cycle progression. Mol Cell Biol 15(4): 2037-2050
56. Schuberth C, Richly H, Rumpf S, Buchberger A (2004) Shp1 and Ubx2 are adaptors of Cdc48 involved in ubiquitin-dependent protein degradation. EMBO Rep 5(8):818-824
57. Cheng YL, Chen RH (2010) The AAA-ATPase Cdc48 and cofactor Shp1 promote chromosome bi-orientation by balancing Aurora B activity. J Cell Sci 123(Pt 12):2025-2034
58. Fernandez-Saiz V, Buchberger A (2010) Imbalances in p97 co-factor interactions in human proteinopathy. EMBO Rep 11(6):479-485
59. Manno A, Noguchi M, Fukushi J, Motohashi Y et al (2010) Enhanced ATPase activities as a primary defect of mutant valosin-containing proteins that cause inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia. Genes Cells 15(8):911-922
60. Rumpf S, Jentsch S (2006) Functional division of substrate processing cofactors of the ubiquitin-selective Cdc48 chaperone. Mol Cell 21(2):261-269
61. Stolz A, Hilt W, Buchberger A, Wolf DH (2011) Cdc48: a power machine in protein degradation. Trends Biochem Sci 36(10):515-523
62. Bohm S, Lamberti G, Fernandez-Saiz V, Stapf C et al (2011) Cellular functions of Ufd2 and Ufd3 in proteasomal protein degradation depend on Cdc48 binding. Mol Cell Biol 31(7):1528-1539
63. Yeung HO, Kloppsteck P, Niwa H, Isaacson RL et al (2008) Insights into adaptor binding to the AAA protein p97. Biochem Soc Trans 36(Pt 1):62-67
64. Meyer HH, Shorter JG, Seemann J, Pappin D et al (2000) A complex of mammalian ufd1 and npl4 links the AAA-ATPase, p97, to ubiquitin and nuclear transport pathways. EMBO J 19(10):2181-2192
65. Schuberth C, Buchberger A (2005) Membrane-bound Ubx2 recruits Cdc48 to ubiquitin ligases and their substrates to ensure ef ficient ER-associated protein degradation. Nat Cell Biol 7(10):999-1006
66. Neuber O, Jarosch E, Volkwein C, Walter J et al (2005) Ubx2 links the Cdc48 complex to ER-associated protein degradation. Nat Cell Biol 7(10):993-998
67. Verma R, Oania R, Fang R, Smith GT et al (2011) Cdc48/p97 mediates UV-dependent turnover of RNA Pol II. Mol Cell 41(1):82-92
68. Pye VE, Beuron F, Keetch CA, McKeown C et al (2007) Structural insights into the p97- Ufd1-Npl4 complex. Proc Natl Acad Sci USA 104(2):467-472
69. Hanzelmann P, Buchberger A, Schindelin H (2011) Hierarchical binding of cofactors to the AAA ATPase p97. Structure 19(6):833-843
70. Heo JM, Livnat-Levanon N, Taylor EB, Jones KT et al (2010) A stress-responsive system for mitochondrial protein degradation. Mol Cell 40(3):465-480
71. Ballar P, Pabuccuoglu A, Kose FA (2011) Different p97/VCP complexes function in retrotranslocation step of mammalian ER-associated degradation (ERAD). Int J Biochem Cell Biol 43(4):613-621
72. Ballar P, Shen Y, Yang H, Fang S (2006) The role of a novel p97/valosin-containing proteininteracting motif of gp78 in endoplasmic reticulum-associated degradation. J Biol Chem 281(46):35359-35368
73. Uchiyama K, Jokitalo E, Kano F, Murata M et al (2002) VCIP135, a novel essential factor for p97/p47-mediated membrane fusion, is required for Golgi and ER assembly in vivo. J Cell Biol 159(5):855-866
74. Wang Y, Satoh A, Warren G, Meyer HH (2004) VCIP135 acts as a deubiquitinating enzyme during p97-p47-mediated reassembly of mitotic Golgi fragments. J Cell Biol 164(7):973-978
75. Uchiyama K, Totsukawa G, Puhka M, Kaneko Y et al (2006) p37 is a p97 adaptor required for Golgi and ER biogenesis in interphase and at the end of mitosis. Dev Cell 11(6):803-816
76. Totsukawa G, Kaneko Y, Uchiyama K, Toh H et al (2011) VCIP135 deubiquitinase and its binding protein, WAC, in p97ATPase-mediated membrane fusion. EMBO J 30(17): 3581-3593
77. Kern M, Fernandez-Saiz V, Schafer Z, Buchberger A (2009) UBXD1 binds p97 through two independent binding sites. Biochem Biophys Res Commun 380(2):303-307
78. Stapf C, Cartwright E, Bycroft M, Hofmann K et al (2011) The general de finition of the p97/ valosin-containing protein (VCP)-interacting motif (VIM) delineates a new family of p97 cofactors. J Biol Chem 286(44):38670-38678
79. Alexandru G, Graumann J, Smith GT, Kolawa NJ et al (2008) UBXD7 binds multiple ubiquitin ligases and implicates p97 in HIF1alpha turnover. Cell 134(5):804-816
80. Ghislain M, Dohmen RJ, Levy F, Varshavsky A (1996) Cdc48p interacts with Ufd3p, a WD repeat protein required for ubiquitin-mediated proteolysis in Saccharomyces cerevisiae. EMBO J 15(18):4884-4899
81. Lambertson D, Chen L, Madura K (1999) Pleiotropic defects caused by loss of the proteasome-interacting factors Rad23 and Rpn10 of Saccharomyces cerevisiae. Genetics 153(1):69-79
82. Rape M, Hoppe T, Gorr I, Kalocay M et al (2001) Mobilization of processed, membranetethered SPT23 transcription factor by CDC48(UFD1/NPL4), a ubiquitin-selective chaperone. Cell 107(5):667-677
83. Rao H, Sastry A (2002) Recognition of speci fic ubiquitin conjugates is important for the proteolytic functions of the ubiquitin-associated domain proteins Dsk2 and Rad23. J Biol Chem 277(14):11691-11695
84. Koegl M, Hoppe T, Schlenker S, Ulrich HD et al (1999) A novel ubiquitination factor, E4, is involved in multiubiquitin chain assembly. Cell 96(5):635-644
85. Thrower JS, Hoffman L, Rechsteiner M, Pickart CM (2000) Recognition of the polyubiquitin proteolytic signal. EMBO J 19(1):94-102
86. Richly H, Rape M, Braun S, Rumpf S et al (2005) A series of ubiquitin binding factors connects CDC48/p97 to substrate multiubiquitylation and proteasomal targeting. Cell 120(1):73-84
87. Saeki Y, Tayama Y, Toh-e A, Yokosawa H (2004) De finitive evidence for Ufd2-catalyzed elongation of the ubiquitin chain through Lys48 linkage. Biochem Biophys Res Commun 320(3):840-845
88. Buchberger A (2002) From UBA to UBX: new words in the ubiquitin vocabulary. Trends Cell Biol 12(5):216-221
89. Kim I, Mi K, Rao H (2004) Multiple interactions of rad23 suggest a mechanism for ubiquitylated substrate delivery important in proteolysis. Mol Biol Cell 15(7):3357-3365
90. Zhao S, Ulrich HD (2010) Distinct consequences of posttranslational modi fication by linear versus K63-linked polyubiquitin chains. Proc Natl Acad Sci U S A 107(17): 7704-7709
91. Hanzelmann P, Stingele J, Hofmann K, Schindelin H et al (2010) The yeast E4 ubiquitin ligase Ufd2 interacts with the ubiquitin-like domains of Rad23 and Dsk2 via a novel and distinct ubiquitin-like binding domain. J Biol Chem 285(26):20390-20398
92. Baek GH, Kim I, Rao H (2011) The Cdc48 ATPase modulates the interaction between two proteolytic factors Ufd2 and Rad23. Proc Natl Acad Sci USA 108(33):13558-13563
93. 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
94. Ismail N, Ng DT (2006) Have you HRD? Understanding ERAD is DOAble! Cell 126(2):237-239
95. Vashist S, Ng DT (2004) Misfolded proteins are sorted by a sequential checkpoint mechanism of ER quality control. J Cell Biol 165(1):41-52
96. Ravid T, Kreft SG, Hochstrasser M (2006) Membrane and soluble substrates of the Doa10 ubiquitin ligase are degraded by distinct pathways. EMBO J 25(3):533-543
97. Swanson R, Locher M, Hochstrasser M (2001) A conserved ubiquitin ligase of the nuclear envelope/endoplasmic reticulum that functions in both ER-associated and Matalpha2 repressor degradation. Genes Dev 15(20):2660-2674
98. Hwang CS, Shemorry A, Varshavsky A (2010) N-terminal acetylation of cellular proteins creates speci fic degradation signals. Science 327(5968):973-977
99. Bagola K, Mehnert M, Jarosch E, Sommer T (2011) Protein dislocation from the ER. Biochim Biophys Acta 1808(3):925-936
100. Claessen JH, Kundrat L, Ploegh HL (2012) Protein quality control in the ER: balancing the ubiquitin checkbook. Trends Cell Biol 22(1):22-32
101. Bays NW, Gardner RG, Seelig LP, Joazeiro CA et al (2001) Hrd1p/Der3p is a membraneanchored ubiquitin ligase required for ER-associated degradation. Nat Cell Biol 3(1):24-29
102. Ye Y, Meyer HH, Rapoport TA (2001) The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol. Nature 414(6864):652-656
103. Braun S, Matuschewski K, Rape M, Thoms S et al (2002) Role of the ubiquitin-selective CDC48(UFD1/NPL4) chaperone (segregase) in ERAD of OLE1 and other substrates. EMBO J 21(4):615-621
104. Jarosch E, Taxis C, Volkwein C, Bordallo J et al (2002) Protein dislocation from the ER requires polyubiquitination and the AAA-ATPase Cdc48. Nat Cell Biol 4(2):134-139
105. Rabinovich E, Kerem A, Frohlich KU, Diamant N et al (2002) AAA-ATPase p97/Cdc48p, a cytosolic chaperone required for endoplasmic reticulum-associated protein degradation. Mol Cell Biol 22(2):626-634
106. Nakatsukasa K, Huyer G, Michaelis S, Brodsky JL (2008) Dissecting the ER-associated degradation of a misfolded polytopic membrane protein. Cell 132(1):101-112
107. Medicherla B, Kostova Z, Schaefer A, Wolf DH (2004) A genomic screen identi fies Dsk2p and Rad23p as essential components of ER-associated degradation. EMBO Rep 5(7):692-697
108. Alberts SM, Sonntag C, Schafer A, Wolf DH (2009) Ubx4 modulates cdc48 activity and in fluences degradation of misfolded proteins of the endoplasmic reticulum. J Biol Chem 284(24):16082-16089
109. Tran JR, Tomsic LR, Brodsky JL (2011) A Cdc48p-associated factor modulates endoplasmic reticulum-associated degradation, cell stress, and ubiquitinated protein homeostasis. J Biol Chem 286(7):5744-5755
110. Zhang Y, Nijbroek G, Sullivan ML, McCracken AA et al (2001) Hsp70 molecular chaperone facilitates endoplasmic reticulum-associated protein degradation of cystic fibrosis transmembrane conductance regulator in yeast. Mol Biol Cell 12(5):1303-1314
111. Han S, Liu Y, Chang A (2007) Cytoplasmic Hsp70 promotes ubiquitination for endoplasmic reticulum-associated degradation of a misfolded mutant of the yeast plasma membrane ATPase, PMA1. J Biol Chem 282(36):26140-26149
112. Taxis C, Hitt R, Park SH, Deak PM et al (2003) Use of modular substrates demonstrates mechanistic diversity and reveals differences in chaperone requirement of ERAD. J Biol Chem 278(38):35903-35913
113. Hampton RY (2002) Proteolysis and sterol regulation. Annu Rev Cell Dev Biol 18:345-378
114. Hampton RY, Garza RM (2009) Protein quality control as a strategy for cellular regulation: lessons from ubiquitin-mediated regulation of the sterol pathway. Chem Rev 109(4):1561-1574
115. Hampton RY, Gardner RG, Rine J (1996) Role of 26S proteasome and HRD genes in the degradation of 3-hydroxy-3-methylglutaryl-CoA reductase, an integral endoplasmic reticulum membrane protein. Mol Biol Cell 7(12):2029-2044
116. Bays NW, Wilhovsky SK, Goradia A, Hodgkiss-Harlow K et al (2001) HRD4/NPL4 is required for the proteasomal processing of ubiquitinated ER proteins. Mol Biol Cell 12(12):4114-4128
117. Carroll SM, Hampton RY (2010) Usa1p is required for optimal function and regulation of the Hrd1p endoplasmic reticulum-associated degradation ubiquitin ligase. J Biol Chem 285(8):5146-5156
118. Gardner RG, Shearer AG, Hampton RY (2001) In vivo action of the HRD ubiquitin ligase complex: mechanisms of endoplasmic reticulum quality control and sterol regulation. Mol Cell Biol 21(13):4276-4291
119. Sato BK, Schulz D, Do PH, Hampton RY (2009) Misfolded membrane proteins are speci fically recognized by the transmembrane domain of the Hrd1p ubiquitin ligase. Mol Cell 34(2):212-222
120. Hoppe T, Matuschewski K, Rape M, Schlenker S et al (2000) Activation of a membranebound transcription factor by regulated ubiquitin/proteasome-dependent processing. Cell 102(5):577-586
121. Verma R, Chen S, Feldman R, Schieltz D et al (2000) Proteasomal proteomics: identi fication of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of af finity-puri fied proteasomes. Mol Biol Cell 11(10):3425-3439
122. Isakov E, Stanhill A (2011) Stalled proteasomes are directly relieved by P97 recruitment. J Biol Chem 286(35):30274-30283
123. Shcherbik N, Zoladek T, Nickels JT, Haines DS (2003) Rsp5p is required for ER bound Mga2p120 polyubiquitination and release of the processed/tethered transactivator Mga2p90. Curr Biol 13(14):1227-1233
124. Shcherbik N, Haines DS (2007) Cdc48p(Npl4p/Ufd1p) binds and segregates membraneanchored/ tethered complexes via a polyubiquitin signal present on the anchors. Mol Cell 25(3):385-397
125. Siepe D, Jentsch S (2009) Prolyl isomerase Pin1 acts as a switch to control the degree of substrate ubiquitylation. Nat Cell Biol 11(8):967-972
126. Russell SJ, Steger KA, Johnston SA (1999) Subcellular localization, stoichiometry, and protein levels of 26 S proteasome subunits in yeast. J Biol Chem 274(31):21943-21952
127. Laporte D, Salin B, Daignan-Fornier B, Sagot I (2008) Reversible cytoplasmic localization of the proteasome in quiescent yeast cells. J Cell Biol 181(5):737-745
128. Jentsch S, Rumpf S (2007) Cdc48 (p97): a "molecular gearbox" in the ubiquitin pathway? Trends Biochem Sci 32(1):6-11
129. Kuhlbrodt K, Janiesch PC, Kevei E, Segref A et al (2011) The Machado-Joseph disease deubiquitylase ATX-3 couples longevity and proteostasis. Nat Cell Biol 13(3):273-281
130. Beaudenon SL, Huacani MR, Wang G, McDonnell DP et al (1999) Rsp5 ubiquitin-protein ligase mediates DNA damage-induced degradation of the large subunit of RNA polymerase II in Saccharomyces cerevisiae. Mol Cell Biol 19(10):6972-6979
131. Woudstra EC, Gilbert C, Fellows J, Jansen L et al (2002) A Rad26-Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage. Nature 415(6874):929-933
132. Wilcox AJ, Laney JD (2009) A ubiquitin-selective AAA-ATPase mediates transcriptional switching by remodelling a repressor-promoter DNA complex. Nat Cell Biol 11(12): 1481-1486
133. Moir D, Stewart SE, Osmond BC, Botstein D (1982) Cold-sensitive cell-division-cycle mutants of yeast: isolation, properties, and pseudoreversion studies. Genetics 100(4): 547-563
134. Fu X, Ng C, Feng D, Liang C (2003) Cdc48p is required for the cell cycle commitment point at start via degradation of the G1-CDK inhibitor Far1p. J Cell Biol 163(1):21-26
135. Archambault V, Chang EJ, Drapkin BJ, Cross FR et al (2004) Targeted proteomic study of the cyclin-Cdk module. Mol Cell 14(6):699-711
136. Cao K, Nakajima R, Meyer HH, Zheng Y (2003) The AAA-ATPase Cdc48/p97 regulates spindle disassembly at the end of mitosis. Cell 115(3):355-367
137. Heubes S, Stemmann O (2007) The AAA-ATPase p97-Ufd1-Npl4 is required for ERAD but not for spindle disassembly in Xenopus egg extracts. J Cell Sci 120(Pt 8):1325-1329
138. Hsieh MT, Chen RH (2011) Cdc48 and cofactors Npl4-Ufd1 are important for G1 progression during heat stress by maintaining cell wall integrity in Saccharomyces cerevisiae. PLoS One 6(4):e18988
139. Schork SM, Bee G, Thumm M, Wolf DH (1994) Catabolite inactivation of fructose-1, 6-bisphosphatase in yeast is mediated by the proteasome. FEBS Lett 349(2):270-274
140. Santt O, Pfirrmann T, Braun B, Juretschke J et al (2008) The yeast GID complex, a novel ubiquitin ligase (E3) involved in the regulation of carbohydrate metabolism. Mol Biol Cell 19(8):3323-3333
141. Barbin L, Eisele F, Santt O, Wolf DH (2010) The Cdc48-Ufd1-Npl4 complex is central in ubiquitin-proteasome triggered catabolite degradation of fructose-1,6-bisphosphatase. Biochem Biophys Res Commun 394(2):335-341
142. Tanaka A, Cleland MM, Xu S, Narendra DP et al (2010) Proteasome and p97 mediate mitophagy and degradation of mitofusins induced by Parkin. J Cell Biol 191(7):1367-1380
143. Xu S, Peng G, Wang Y, Fang S et al (2011) The AAA-ATPase p97 is essential for outer mitochondrial membrane protein turnover. Mol Biol Cell 22(3):291-300
144. Karbowski M, Youle RJ (2011) Regulating mitochondrial outer membrane proteins by ubiquitination and proteasomal degradation. Curr Opin Cell Biol 23(4):476-482
145. Braun RJ, Zischka H (2008) Mechanisms of Cdc48/VCP-mediated cell death: from yeast apoptosis to human disease. Biochim Biophys Acta 1783(7):1418-1435
146. Krick R, Bremer S, Welter E, Schlotterhose P et al (2010) Cdc48/p97 and Shp1/p47 regulate autophagosome biogenesis in concert with ubiquitin-like Atg8. J Cell Biol 190(6):965-973
147. Ohsumi Y (2001) Molecular dissection of autophagy: two ubiquitin-like systems. Nat Rev Mol Cell Biol 2(3):211-216
148. Kraft C, Deplazes A, Sohrmann M, Peter M (2008) Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease. Nat Cell Biol 10(5):602-610
149. Ossareh-Nazari B, Bonizec M, Cohen M, Dokudovskaya S et al (2010) Cdc48 and Ufd3, new partners of the ubiquitin protease Ubp3, are required for ribophagy. EMBO Rep 11(7):548-554
150. Ju JS, Fuentealba RA, Miller SE, Jackson E et al (2009) Valosin-containing protein (VCP) is required for autophagy and is disrupted in VCP disease. J Cell Biol 187(6):875-888
151. Tresse E, Salomons FA, Vesa J, Bott LC et al (2010) VCP/p97 is essential for maturation of ubiquitin-containing autophagosomes and this function is impaired by mutations that cause IBMPFD. Autophagy 6(2)
152. Vesa J, Su H, Watts GD, Krause S et al (2009) Valosin containing protein associated inclusion body myopathy: abnormal vacuolization, autophagy and cell fusion in myoblasts. Neuromuscul Disord 19(11):766-772
153. Ren J, Pashkova N, Winistorfer S, Piper RC (2008) DOA1/UFD3 plays a role in sorting ubiquitinated membrane proteins into multivesicular bodies. J Biol Chem 283(31):21599-21611
154. Qiu L, Pashkova N, Walker JR, Winistorfer S et al (2010) Structure and function of the PLAA/ Ufd3-p97/Cdc48 complex. J Biol Chem 285(1):365-372
155. Janiesch PC, Kim J, Mouysset J, Barikbin R et al (2007) The ubiquitin-selective chaperone CDC-48/p97 links myosin assembly to human myopathy. Nat Cell Biol 9(4):379-390
156. Raman M, Havens CG, Walter JC, Harper JW (2011) A genome-wide screen identi fies p97 as an essential regulator of DNA damage-dependent CDT1 destruction. Mol Cell 44(1):72-84
157. Franz A, Orth M, Pirson PA, Sonneville R et al (2011) CDC-48/p97 coordinates CDT-1 degradation with GINS chromatin dissociation to ensure faithful DNA replication. Mol Cell 44(1):85-96
158. Meerang M, Ritz D, Paliwal S, Garajova Z et al (2011) The ubiquitin-selective segregase VCP/p97 orchestrates the response to DNA double-strand breaks. Nat Cell Biol 13(11):1376-1382
159. Acs K, Luijsterburg MS, Ackermann L, Salomons FA et al (2011) The AAA-ATPase VCP/ p97 promotes 53BP1 recruitment by removing L3MBTL1 from DNA double-strand breaks. Nat Struct Mol Biol 18(12):1345-1350
160. Yamanaka K, Sasagawa Y, Ogura T (2012) Recent advances in p97/VCP/Cdc48 cellular functions. Biochim Biophys Acta 1823(1):130-137
161. Meyer H, Bug M, Bremer S (2012) Emerging functions of the VCP/p97 AAA-ATPase in the ubiquitin system. Nat Cell Biol 14(2):117-123
162. Uchiyama K, Kondo H (2005) p97/p47-mediated biogenesis of Golgi and ER. J Biochem 137(2):115-119
163. Meyer HH (2005) Golgi reassembly after mitosis: the AAA family meets the ubiquitin family. Biochim Biophys Acta 1744(3):481-492
164. Buchberger A (2006) Cdc48 (p97) and its cofactors. In: Mayer RJ, Ciechanover AJ, Rechsteiner M (eds) Protein degradation, vol 3: cell biology of the ubiquitin-proteasome system. Wiley-VCH, Weinheim, pp 194-211
165. Seeley ES, Kato M, Margolis N, Wickner W et al (2002) Genomic analysis of homotypic vacuole fusion. Mol Biol Cell 13(3):782-794
166. Sambade M, Alba M, Smardon AM, West RW et al (2005) A genomic screen for yeast vacuolar membrane ATPase mutants. Genetics 170(4):1539-1551
167. Ramadan K, Bruderer R, Spiga FM, Popp O et al (2007) Cdc48/p97 promotes reformation of the nucleus by extracting the kinase Aurora B from chromatin. Nature 450(7173):1258-1262
168. Dobrynin G, Popp O, Romer T, Bremer S et al (2011) Cdc48/p97-Ufd1-Npl4 antagonizes Aurora B during chromosome segregation in HeLa cells. J Cell Sci 124(Pt 9):1571-1580