The N-end rule pathway and regulation by proteolysis

Protein Science

Volumn 20, Issue 8, 2011, Pages 1298-1345

  Varshavsky, Alexander ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Arginylation; Leucylation; N degron; N end rule; Proteolysis; Ubiquitin

Indexed keywords

6 O METHYLGUANINE; ACYLTRANSFERASE; ALKYLATING AGENT; AMIDASE; ARGININE; ARGINYLTRANSFERASE; CALPAIN; CASPASE; CELL PROTEIN; COHESIN; DNA; GUANINE NUCLEOTIDE BINDING PROTEIN; HEME; HEMIN; INTEGRASE; LEUCYLTRANSFERASE; LISTERIOLYSIN O; METHIONYL AMINOPEPTIDASE; METHYLATED DNA PROTEIN CYSTEINE METHYLTRANSFERASE; METHYLNITRONITROSOGUANIDINE; N DEGRON; NITRIC OXIDE; OXYGEN; PROOPIOMELANOCORTIN; PROTEASOME; PROTEIN; TRANSFERASE; UBIQUITIN; UBIQUITIN PROTEIN LIGASE E3; UNCLASSIFIED DRUG; VASCULOTROPIN;

ACETYLATION; AMINO TERMINAL SEQUENCE; ANEUPLOIDY; APOPTOSIS; ARGINYLATION; BACTERIAL INFECTION; BACTERIAL VIRULENCE; BINDING AFFINITY; BINDING SITE; BIRTH DEFECT; BRAIN FUNCTION; CANCER CELL; CARBOXY TERMINAL SEQUENCE; CHEMICAL MODIFICATION; DEAMINATION; DNA REPAIR; EUKARYOTE; GENE SEGREGATION; GENETIC REGULATION; HALF LIFE TIME; HEART DEVELOPMENT; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; IN VIVO STUDY; JOHANSON BLIZZARD SYNDROME; LAST COMMON ANCESTOR; LIPID METABOLISM; MEIOSIS; MISSENSE MUTATION; MITOCHONDRION; N END RULE PATHWAY; NERVOUS SYSTEM DEVELOPMENT; NONHUMAN; PANCREAS FUNCTION; PRIORITY JOURNAL; PROKARYOTE; PROTEIN BINDING; PROTEIN CLEAVAGE; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN PROCESSING; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; PROTEIN TARGETING; PROTEIN TRANSPORT; REVIEW; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; SPERMATOGENESIS; UBIQUITINATION; VIRUS INFECTION; AMINO ACID SEQUENCE; ANIMAL; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE;

BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

ACETYLATION; AMINO ACID SEQUENCE; ANIMALS; EVOLUTION, MOLECULAR; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR SEQUENCE DATA; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTEOLYSIS; UBIQUITINATION;

EID: 79960683356     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.666     Document Type: Review

References (341)

1. Varshavsky A (2004) Spalog and sequelog: neutral terms for spatial and sequence similarity. Curr Biol 14:R181-R183.
2. Varshavsky A (1991) Naming a targeting signal. Cell 64:13-15.
3. Hwang C-S, Shemorry A, Varshavsky A (2010) N-terminal acetylation of cellular proteins creates specific degradation signals. Science 327:973-977.
4. Bachmair A, Finley D, Varshavsky A (1986) In vivo half-life of a protein is a function of its amino-terminal residue. Science 234:179-186.
5. Varshavsky A (1996) The N-end rule: functions, mysteries, uses. Proc Natl Acad Sci USA 93:12142-12149.
6. Varshavsky A (2008) Discovery of cellular regulation by protein degradation. J Biol Chem 283:34469-34489.
7. Hershko A, Ciechanover A, Varshavsky A (2000) The ubiquitin system. Nat Med 10:1073-1081.
8. Varshavsky A (2006) The early history of the ubiquitin field. Protein Sci 15:647-654.
9. Bachmair A, Varshavsky A (1989) The degradation signal in a short-lived protein. Cell 56:1019-1032. (Pubitemid 19091014)
10. Gonda DK, Bachmair A, Wünning I, Tobias JW, Lane WS, Varshavsky A (1989) Universality and structure of the N-end rule. J Biol Chem 264:16700-16712.
11. Chau V, Tobias JW, Bachmair A, Marriott D, Ecker DJ, Gonda DK, Varshavsky A (1989) A multiubiquitin chain is confined to specific lysine in a targeted short-lived protein. Science 243:1576-1583. (Pubitemid 19090506)
12. Bartel B, Wünning I, Varshavsky A (1990) The recognition component of the N-end rule pathway. EMBO J 9:3179-3189.
13. Johnson ES, Gonda DK, Varshavsky A (1990) Cistrans recognition and subunit-specific degradation of short-lived proteins. Nature 346:287-291.
14. Tobias JW, Shrader TE, Rocap G, Varshavsky A (1991) The N-end rule in bacteria. Science 254:1374-1377. (Pubitemid 21917472)
15. Tasaki T, Kwon YT (2007) The mammalian N-end rule pathway: new insights into its components and physiological roles. Trends Biochem Sci 32:520-528. (Pubitemid 350008070)
16. Mogk A, Schmidt R, Bukau B (2007) The N-end rule pathway of regulated proteolysis: prokaryotic and eukaryotic strategies. Trends Cell Biol 17:165-172. (Pubitemid 46507804)
17. Ravid T, Hochstrasser M (2008) Diversity of degradation signals in the ubiquitin-proteasome system. Nat Rev Mol Cell Biol 9:679-689.
18. Graciet E, Wellmer F (2010) The plant N-end rule pathway: structure and functions. Trends Plant Sci 15:447-453.
19. Schrader EK, Harstad KG, Matouschek A (2009) Targeting proteins for degradation. Nat Chem Biol 5:815-822.
20. Dantuma NP, Lindsten K, Glas R, Jellne M, Masucci MG (2000) Short-lived green fluorescent proteins for quantifying ubiquitin/proteasome-dependent proteolysis in living cells. Nature Biotechnol 18:494-496.
21. Baker RT, Varshavsky A (1991) Inhibition of the Nend rule pathway in living cells. Proc Natl Acad Sci USA 87:2374-2378.
22. Xie Y, Varshavsky A (1999) The E2-E3 interaction in the N-end rule pathway: the RING-H2 finger of E3 is required for the synthesis of multiubiquitin chain. EMBO J 18:6832-6844.
23. Baker RT, Varshavsky A (1995) Yeast N-terminal amidase: a new enzyme and component of the N-end rule pathway. J Biol Chem 270:12065-12074.
24. Suzuki T, Varshavsky A (1999) Degradation signals in the lysine-asparagine sequence space. EMBO J 18:6017-6026. (Pubitemid 29515678)
25. Kwon YT, Balogh SA, Davydov IV, Kashina AS, Yoon JK, Xie Y, Gaur A, Hyde L, Denenberg VH, Varshavsky A (2000) Altered activity, social behavior, and spatial memory in mice lacking the NTAN1 amidase and the asparagine branch of the N-end rule pathway. Mol Cell Biol 20:4135-4148. (Pubitemid 30314511)
26. Kwon YT, Kashina AS, Davydov IV, Hu R-G, An JY, Seo JW, Du F, Varshavsky A (2002) An essential role of N-terminal arginylation in cardiovascular development. Science 297:96-99. (Pubitemid 34743100)
27. Turner GC, Du F, Varshavsky A (2000) Peptides accelerate their uptake by activating a ubiquitin-dependent proteolytic pathway. Nature 405:579-583. (Pubitemid 30367731)
28. Rao H, Uhlmann F, Nasmyth K, Varshavsky A (2001) Degradation of a cohesin subunit by the N-end rule pathway is essential for chromosome stability. Nature 410:955-960.
29. Du F, Navarro-Garcia F, Xia Z, Tasaki T, Varshavsky A (2002) Pairs of dipeptides synergistically activate the binding of substrate by ubiquitin ligase through dissociation of its autoinhibitory domain. Proc Natl Acad Sci USA 99:14110-14115. (Pubitemid 35257633)
30. Kwon YT, Xia ZX, An JY, Tasaki T, Davydov IV, Seo JW, Xie Y, Varshavsky A (2003) Female lethality and apoptosis of spermatocytes in mice lacking the UBR2 ubiquitin ligase of the N-end rule pathway. Mol Cell Biol 23:8255-8271. (Pubitemid 37377515)
31. Tasaki T, Mulder LCF, Iwamatsu A, Lee MJ, Davydov IV, Varshavsky A, Muesing M, Kwon YT (2005) A family of mammalian E3 ubiquitin ligases that contain the UBR box motif and recognize N-degrons. Mol Cell Biol 25:7120-7136. (Pubitemid 41105909)
32. Hu R-G, Sheng J, Xin Q, Xu Z, Takahashi TT, Varshavsky A (2005) The N-end rule pathway as a nitric oxide sensor controlling the levels of multiple regulators. Nature 437:981-986. (Pubitemid 41486974)
33. Lee MJ, Tasaki T, Moroi K, An JY, Kimura S, Davydov IV, Kwon YT (2005) RGS4 and RGS5 are in vivo substrates of the N-end rule pathway. Proc Natl Acad Sci USA 102:15030-15035. (Pubitemid 41513329)
34. Zenker M, Mayerle J, Lerch MM, Tagariello A, Zerres K, Durie PR, Beier M, Hülskamp G, Guzman C, Rehder H, Beemer FA, Hamel B, Vanlieferinghen P, Gershoni-Baruch R, Vieira MW, Dumic M, Auslender R, Gil-da-Silva-Lopes VL, Steinlicht S, Rauh R, Shalev SA, Thiel C, Winterpacht A, Kwon YT, Varshavsky A, Reis A (2005) Deficiency of UBR1, a ubiquitin ligase of the N-end rule pathway, causes pancreatic dysfunction, malformations and mental retardation (Johanson-Blizzard syndrome). Nat Genet 37:1345-1350. (Pubitemid 41722190)
35. Hu R-G, Brower CS, Wang H, Davydov IV, Sheng J, Zhou J, Kwon YT, Varshavsky A (2006) Arginyl-transferase, its specificity, putative substrates, bidirectional promoter, and splicing-derived isoforms. J Biol Chem 281:32559-32573. (Pubitemid 46036811)
36. Hu R-G, Wang H, Xia Z, Varshavsky A (2008) The Nend rule pathway is a sensor of heme. Proc Natl Acad Sci USA 105:76-81.
37. Graciet E, Hu RG, Piatkov K, Rhee JH, Schwarz EM, Varshavsky A (2006) Aminoacyl-transferases and the N-end rule pathway of prokaryotic/eukaryotic specificity in a human pathogen. Proc Natl Acad Sci USA 103:3078-3083. (Pubitemid 43346427)
38. Xia Z, Webster A, Du F, Piatkov K, Ghislain M, Varshavsky A (2008) Substrate-binding sites of UBR1, the ubiquitin ligase of the N-end rule pathway. J Biol Chem 283:24011-24028.
39. Hwang C-S, Varshavsky A (2008) Regulation of peptide import through phosphorylation of Ubr1, the ubiquitin ligase of the N-end rule pathway. Proc Natl Acad Sci USA 105:19188-19193.
40. Hwang C-S, Shemorry A, Varshavsky A (2009) Two proteolytic pathways regulate DNA repair by co-targeting the Mgt1 alkyguanine transferase. Proc Natl Acad Sci USA 106:2142-2147.
41. Brower CS, Varshavsky A (2009) Ablation of arginylation in the mouse N-end rule pathway: loss of fat, higher metabolic rate, damaged spermatogenesis, and neurological perturbations. PLoS ONE 4:e7757.
42. Wang H, Piatkov KI, Brower CS, Varshavsky A (2009) Glutamine-specific N-terminal amidase, a component of the N-end rule pathway. Mol Cell 34:686-695.
43. Tasaki T, Zakrzewska A, Dudgeon D, Jiang Y, Lazo JS, Kwon YT (2009) The substrate recognition domains of the N-end rule pathway. J Biol Chem 284: 1884-1895.
44. Hwang C-S, Shemorry A, Varshavsky A (2010) The Nend rule pathway is mediated by a complex of the RING-type Ubr1 and HECT-type Ufd4 ubiquitin ligases. Nat Cell Biol 12:1177-1185.
45. Xie Y (2011) Structure, assembly and homeostatic regulation of the 26S proteasome. J Mol Cell Biol 2:308-317.
46. Förster F, Lasker K, Nickell S, Sali A, Baumeister W (2010) Toward an integrated structural model of the 26S proteasome. Mol Cell Proteomics 9:1666-1677.
47. Stadtmueller BM, Hill CP (2011) Proteasome activators. Mol Cell 41:8-19.
48. Ikeda F, Crosetto N, Dikic I (2010) What determines the specificity and outcomes of ubiquitin signaling? Cell 143:677-693.
49. Gallastegui N, Groll M (2010) The 26S proteasome: assembly and function of a destructive machine. Trends Biochem Sci 35:634-642.
50. Liu F, Walters KJ (2010) Multitasking with ubiquitin through multivalent interactions. Trends Biochem Sci 35:352-360.
51. Ulrich HD, Walden H (2010) Ubiquitin signalling in DNA replication and repair. Nat Rev Mol Cell Biol 11:479-489.
52. Stolz A, Wolf DH (2010) Endoplasmic reticulum-associated protein degradation: a chaperone-assisted journey to hell. Biochim Biophys Acta 1803:694-705.
53. 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 109:1561-1574.
54. Finley D (2009) Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annu Rev Biochem 78:477-513.
55. Isaacson MK, Ploegh HL (2009) Ubiquitination, ubiquitin-like modifiers, and deubiquitination in viral infection. Cell Host Microbe 5:559-570.
56. Marques AJ, Palanimurugan R, Matias AC, Ramos PC, Dohmen RJ (2009) Catalytic mechanism and assembly of the proteasome. Chem Rev 109:1509-1536.
57. Deshaies RJ, Joazeiro CAP (2009) RING domain E3 ubiquitin ligases. Annu Rev Biochem 78:399-434.
58. Hochstrasser M (2009) Origin and function of ubiquitin-like proteins. Nature 458:422-429.
59. Vembar SS, Brodsky JL (2008) One step at a time: endoplasmic reticulum-associated degradation. Nat Rev Mol Cell Biol 9:944-958.
60. Bergink S, Jentsch S (2009) Principles of ubiquitin and SUMO modifications in DNA repair. Nature 458:461-467.
61. Reyes-Turcu FE, Ventii KH, Wilkinson KD (2009) Regulation and cellular roles of ubiquitin-specific deubiquitinating enzymes. Annu Rev Biochem 78:363-397.
62. Daulni A, Tansey WP (2009) Damage control: DNA repair, transcription, and the ubiquitin-proteasome system. DNA Repair 8:444-448.
63. Hirsch C, Gauss R, Horn SC, Neuber O, Sommer T (2009) The ubiquitylation machinery of the endoplasmic reticulum. Nature 458:453-460.
64. Dye BT, Schulman BA (2007) Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins. Annu Rev Biophys Biomol Struct 36:131-150. (Pubitemid 46998113)
65. Wolf DH, Hilt W (2004) The proteasome: a proteolytic nanomachine of cell regulation and waste disposal. Biochim Biophys Acta 1695:19-31. (Pubitemid 39574965)
66. Darwin KH (2009) Prokaryotic ubiquitin-like protein, proteasomes, and pathogenesis. Nat Rev Microbiol 7:485-491.
67. Burns KE, Liu W-T, Boshoff HIM, Dorrestein PC, Barry CE, III (2009) Proteasomal protein degradation in mycobacteria is dependent upon a prokaryotic ubiquitin-like protein. J Biol Chem 284:3069-3075.
68. Cerda-Maira FA, Pearce MJ, Fuortes M, Bishai WR, Hubbard SR, Darwin KH (2010) Molecular analysis of the prokaryotic ubiquitin-like protein (Pup) conjugation pathway in Mycobacterium tuberculosis. Mol Microbiol 77:1123-1135.
69. Sutter M, Damberger FF, Imkamp F, Allain FHT, Weber-Ban E (2010) Prokaryotic ubiquitin-like protein (Pup) is coupled to substrates via the side chain of its C-terminal glutamate. J Am Chem Soc 132:5610-5612.
70. Humbard MA, Miranda HV, Lim J-M, Krause DJ, Pritz JR, Zhou G, Chen SH, Wells L, Maupin-Furlow JA (2010) Ubiquitin-like small archaeal modifier proteins (SAMPS) in Haloferax volcanii. Nature 463:54-60.
71. Shrader TE, Tobias JW, Varshavsky A (1993) The Nend rule in Escherichia coli: cloning and analysis of the leucyl, phenylalanyl-tRNA-protein transferase gene aat. J Bact 175:4364-4374. (Pubitemid 23206937)
72. Erbse A, Schmidt R, Bornemann T, Schneider-Mergener J, Mogk A, Zahn R, Dougan DA, Bukau B (2006) ClpS is an essential component of the N-end rule pathway in Escherichia coli. Nature 439:753-756. (Pubitemid 43237625)
73. Wang KH, Roman-Hernandez G, Grant RA, Sauer TT, Baker TA (2008) The molecular basis of N-end rule recognition. Mol Cell 32:406-414.
74. Schuenemann VJ, Kralik SM, Albrecht R, Spall SK, Truscott KN, Dougan DA, Zeth K (2009) Structural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS. EMBO Rep 10:508-514.
75. Román-Hernández G, Grant RA, Sauer RT, Baker TA (2009) Molecular basis of substrate selection by the N-end rule adaptor protein ClpS. Proc Natl Acad Sci USA 106:8888-8893.
76. 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 72:506-517.
77. Ninnis RL, Spall SK, Talbo GH, Truscott KN, Dougan DA (2009) Modification of PATase by L/F-transferase generates a ClpS-dependent N-end rule substrate in Escherichia coli. EMBO J 28:1732-1744.
78. De Donatis GM, Singh SK, Viswanathan S, Maurizi MR (2010) A single ClpS monomer is sufficient to direct the activity of the ClpA hexamer. J Biol Chem 285:8771-8781.
79. Hou JY, Sauer RT, Baker TA (2008) Distinct structural elements of the adaptor ClpS are required for regulating degradation by ClpAP. Nat Struct Mol Biol 15:288-294. (Pubitemid 351654046)
80. Varshavsky A (2008) The N-end rule at atomic resolution. Nat Struct Mol Biol 15:1238-1240.
81. Dougan DA, Truscott KN, Zeth K (2010) The bacterial N-end rule pathway: expect the unexpected. Mol Microbiol 76:545-558.
82. Román-Hernández G, Hou JY, Grant RA, Sauer RT, Baker TA (2011) The ClpS adaptor mediates staged delivery of N-end rule substrates to the AAA+ ClpAP protease. Mol Cell., in press.
83. Choi WS, Jeong B-C, Joo YJ, Lee M-R, Kim J, Eck MJ, Song HK (2010) Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases. Nat Struct Mol Biol 17:1175-1181.
84. Matta-Camacho E, Kozlov G, Li FF, Gehring K (2010) Structural basis of substrate recognition and specificity in the N-end rule pathway. Nat Struct Mol Biol 17:1182-1188.
85. Sriram SM, Kwon YT (2010) The structural basis of N-end rule recognition. Nat Struct Mol Biol 17:1164-1165.
86. Jörnvall H (1975) Acetylation of protein N-terminal amino groups: structural observations on alpha-amino acetylated proteins. J Theor Biol 55:1-12.
87. Mullen JR, Kayne PS, Moerschell RP, Tsunasawa S, Gribskov M, Colavito-Shepanski M, Grunstein M, Sherman F, Sternglanz R (1989) Identification and characterization of genes and mutants for an N-terminal acetyltransferase from yeast. EMBO J 8:2067-2075. (Pubitemid 19273535)
88. Park EC, Szostak JW (1992) ARD1 and NAT1 proteins form a complex that has N-terminal acetyltransferase activity. EMBO J 11:2087-2093.
89. Gautschi M, Just S, Mun A, Ross S, Rücknagel P, Dubaquié Y, Ehrenhofer-Murray A, Rospert S (2003) The yeast N-alpha-acetyltransferase NatA is quantitatively anchored to the ribosome and interacts with nascent polypeptides. Mol Cell Biol 23:7403-7414. (Pubitemid 37211018)
90. Song O-K, Wang X, Waterborg JH, Sternglanz R (2003) An N-alpha-acetyltransferase responsible for acetylation of the N-terminal residues of histones H4 and H2A. J Biol Chem 278:38109-38112. (Pubitemid 37221696)
91. Arnesen T, Van Damme P, Polevoda B, Helsens K, Evjenth R, Colaert N, Varhaug JE, Vandekerckhove J, Lillehaug JR, Sherman F, Gevaert K (2009) Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast to humans. Proc Natl Acad Sci USA 106:8157-8162.
92. Polevoda B, Sherman F (2003) N-terminal acetyltransferases and sequence requirements for N-terminal acetylation of eukaryotic proteins. J Mol Biol 325:595-622. (Pubitemid 36268685)
93. Goetze S, Qeli E, Mosimann C, Staes A, Gerrits B, Roschitzki B, Mohanty S, Niederer EM, Laczko E, Timmerman E, Lange V, Hafen E, Aebersold R, Vandekerckhove J, Basler K, Ahrens CH, Gevaert K, Brunner E (2009) Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. PLoS Biol 7:e1000236.
94. Starheim KK, Gromyko D, Evjens E, Ryningen A, Varhaug JE, Lillehaug JR, Arnesen T (2009) Knockdown of human N-alpha-terminal acetyltransferase complex C leads to p53-dependent apoptosis and aberrant human Arl8b localization. Mol Cell Biol 29:3569-3581.
95. Polevoda B, Brown S, Cardillo TS, Rigby S, Sherman F (2008) Yeast N(alpha)-terminal acetyltransferases are associated with ribosomes. J Cell Biochem 103:492-508. (Pubitemid 351171920)
96. Addlagatta A, Hu X, Liu JO, Matthews BW (2005) Structural basis for the functional differences between Type I and Type II human methionine aminopeptidases. Biochemistry 44:14741-14749. (Pubitemid 41612254)
97. Lowther WT, Matthews BW (2002) Metalloaminopeptidases: common functional themes in disparate structural surroundings. Chem Rev 102:4581-4608.
98. Moerschell RP, Hosokawa Y, Tsunasawa S, Sherman F (1990) The specificities of yeast methionine amino-peptidase and acetylation of amino-terminal methionine in vivo. Processing of altered iso-1-cytochromes created by oligonucleotide transformation. J Biol Chem 265:19638-19643. (Pubitemid 120013909)
99. Li X, Chang Y-H (1995) Amino-terminal protein processing in Saccharomyces cerevisiae is an essential function that requires two distinct methionine amino-peptidases. Proc Natl Acad Sci USA 92:12357-12361. (Pubitemid 26014069)
100. Bradshaw RA, Brickey WW, Walker KW (1998) N-terminal processing: the methionine aminopeptidase and N-alpha-acetyl transferase families. Trends Biochem Sci 23:263-267. (Pubitemid 28343371)
101. Frottin F, Martinez A, Peynot P, Mitra S, Holz RC, Giglione C, Meinnel T (2006) The proteomics of N-terminal methionine cleavage.Mol Cell Proteomics 5:2336-2349.
102. Helbig AO, Gauci S, Raijmakers R, van Breukelen B, Slijper M, Mohammed S, Heck AJR (2010) Profiling of N-acetylated protein termini provides in-depth insights into the N-terminal nature of the proteome. Mol Cell Proteom 9:928-939.
103. Grunstein M (1990) Histone function in transcription. Annu Rev Cell Biol 6:643-678.
104. Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325:834-840.
105. Behnia R, Panic B, Whyte JRC, Munro S (2004) Targeting of the Arf-like GTPase Arl3p to the Golgi requires N-terminal acetylation and the membrane protein Sys1p. Nat Cell Biol 6:405-413. (Pubitemid 38607500)
106. Setty SRG, Strochlic TI, Tong AHY, Boone C, Burd CG (2004) Golgi targeting of ARF-like GTPase Arl3p requires its N-alpha-acetylation and the integral membrane protein Sys1p. Nat Cell Biol 6:414-419. (Pubitemid 38607501)
107. Jackson CL (2004) N-terminal acetylation targets GTPases to membranes. Nat Cell Biol 6:379-380.
108. Hofmann I, Munro S (2006) An N-terminally acetylated Arf-like GTPase is localised to lysosomes and effects their motility. J Cell Sci 119:1494-1503. (Pubitemid 43732978)
109. Graham TR (2004) Membrane targeting: getting Arl to the Golgi. Curr Biol 14:R483-R485.
110. Coulton AT, East DA, Galinska-Rakoczy A, Lehman W, Mulvihill DP (2010) The recruitment of acetylated and unacetylated tropomyosin to distinct actin polymers permits the discrete regulation of specific myosins in fission yeast. J Cell Sci 123:3235-3243.
111. Balzi E, Choder M, Chen W, Varshavsky A, Goffeau A (1990) Cloning and functional analysis of the arginyl-tRNA-protein transferase gene ATE1 of Saccharomyces cerevisiae. J Biol Chem 265:7464-7471.
112. Kwon YT, Kashina AS, Varshavsky A (1999) Alternative splicing results in differential expression, activity, and localization of the two forms of arginyl-tRNA-protein transferase, a component of the N-end rule pathway. Mol Cell Biol 19:182-193. (Pubitemid 29018421)
113. Graciet E, Walter E, Maoiléidigh DÓ, Pollmann S, Meyerowitz EM, Varshavsky A, Wellmer F (2009) The N-end rule pathway controls multiple functions during Arabidopsis shoot and leaf development. Proc Natl Acad Sci USA 106:13618-13623.
114. Wang J, Han X, Saha S, Xu T, Rai R, Zhang F, Wolf YI, Wolfson A, Yates JR, III, Kashina A (2011) Arginyltransferase is an ATP-independent self-regulating enzyme that forms distinct functional complexes in vivo. Chem Biol 18:121-130.
115. Stewart AE, Arfin SM, Bradshaw RA (1995) The sequence of porcine protein N-terminal asparagine amidohydrolase. A new component of the N-end rule pathway. J Biol Chem 270:25-28.
116. Grigoryev S, Stewart AE, Kwon YT, Arfin SM, Bradshaw RA, Jenkins NA, Copeland NG, Varshavsky A (1996) A mouse amidase specific for N-terminal asparagine. The gene, the enzyme, and their function in the N-end rule pathway. J Biol Chem 271:28521-28532. (Pubitemid 26374675)
117. Cantor JR, Stone EM, Georgiou G (2011) Expression and biochemical characterization of the human enzyme N-terminal asparagine amidohydrolase. Biochemistry 50:3025-3033.
118. Davydov IV, Varshavsky A (2000) RGS4 is arginylated and degraded by the N-end rule pathway in vitro. J Biol Chem 275:22931-22941. (Pubitemid 30646180)
119. Eisele F, Wolf DH (2008) Degradation of misfolded proteins in the cytoplasm by the ubiquitin ligase Ubr1. FEBS Lett 582:4143-4146.
120. Heck JW, Cheung SK, Hampton RY (2010) Cytoplasmic protein quality control degradation mediated by parallel actions of the E3 ubiquitin ligases Ubr1 and San1. Proc Natl Acad Sci USA 107:1106-1111.
121. Prasad R, Kawaguchi S, Ng DTW (2010) A nucleus-based quality control mechanism for cytosolic proteins. Mol Biol Cell 21:2117-2127.
122. Nillegoda NB, Theodoraki MA, Mandal AK, Mayo KJ, Ren HY, Sultana R, Wu K, Johnson J, Cyr DM, Caplan AJ (2010) Ubr1 and Ubr2 function in a quality control pathway for degradation of unfolded cytosolic proteins. Mol Biol Cell 21:2102-2116.
123. Ouyang Y, Kwon YT, An JY, Eller D, Tsai S-C, Diaz-Perez S, Trke J, Teitell MA, Marahrens Y (2006) Loss of Ubr2, an E3 ubiquitin ligase, leads to chromosome fragility and impaired homologous recombinational repair. Mut Res 596:64-75.
124. Schnupf P, Zhou J, Varshavsky A, Portnoy DA (2007) Listeriolysin O secreted by Listeria monocytogenes into the host cell cytosol is degraded by the N-end rule pathway. Inflammation Immunity 75:5135-5147. (Pubitemid 350033600)
125. Yoshida S, Ito M, Gallis J, Nishida I, Watanabe A (2002) A delayed leaf senescence mutant is defective in arginyl-tRNA-protein arginyl-transferase, a component of the N-end rule pathway in Arabidopsis. Plant J 32:129-137. (Pubitemid 35180930)
126. Holman TJ, Jones PD, Russell L, Medhurst A, Ubeda TS, Talloji P, Marquez J, Schmuths H, Tung SA, Taylor I, Footitt S, Bachmair A, Theodoulou FL, Holdsworth MJ (2009) The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis. Proc Natl Acad Sci USA 106:4549-4554.
127. Rai R, Wong CC, Xu T, Leu NA, Dong DW, Guo C, McLaughlin KJ, Yates JR, III, Kashina A (2008) Arginyltransferase regulates alpha cardiac actin function, myofibril formation and contractility during heart development. Development 135:3881-3889.
128. Saha S, Mundia MM, Zhang F, Demers RW, Korobova F, Svitkina T, Perieteanu AA, Dawson JF, Kashina A (2010) Arginylation regulates intracellular actin polymer level by modulating actin properties and binding of capping and severing proteins. Mol Biol Cell 21:1350-1361.
129. Kurosaka S, Leu NA, Zhang F, Bunte R, Saha S, Wang J, Guo C, He W, Kashina A (2010) Arginylation-dependent neural crest cell migration is essential for mouse development. PLoS Genet 6:e1000878.
130. Zhang F, Saha S, Shabalina SA, Kashina A (2010) Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradation. Science 329:1534-1537.
131. de Groot RJ, Rümenapf T, Kuhn RJ, Strauss JH (1991) Sindbis virus RNA polymerase is degraded by the N-end rule pathway. Proc Natl Acad Sci USA 88:8967-8971. (Pubitemid 21915551)
132. Mulder LCF, Muesing MA (2000) Degradation of HIV-1 integrase by the N-end rule pathway. J Biol Chem 275:29749-29753. (Pubitemid 32043857)
133. Lloyd AG, Ng YS, Muesing MA, Simon V, Mulder LC (2007) Characterization of HIV-1 integrase N-terminal mutant viruses. Virology 360:129-135.
134. Lecker SH, Solomon V, Price SR, Kwon YT, Mitch WE, Goldberg AL (1999) Ubiquitin conjugation by the N-end rule pathway and mRNAs for its components increase in muscles of diabetic rats. J Clin Invest 104:1411-1420.
135. Karakozova M, Kozak M, Wong CC, Bailey AO, Yates JR, III, Mogilner A, Zebroski H, Kashina A (2006) Arginylation of beta-actin regulates actin cytoskeleton and cell motility. Science 313:192-196. (Pubitemid 44066244)
136. Caprio MA, Sambrooks CL, Durand ES, Hallak M (2010) The arginylation-dependent association of calreticulin with stress granules is regulated by calcium. Biochem J 429:63-72.
137. Yang F, Cheng Y, An JY, Kwon YT, Eckardt S, Leu NA, McLaughlin KJ, Wang PJ (2010) The ubiquitin ligase Ubr2, a recognition E3 component of the N-end rule pathway, stabilizes Tex.19.1 during spermatogenesis. PLoS One 5:e14017.
138. Xia Z, Turner GC, Hwang C-S, Byrd C, Varshavsky A (2008) Amino acids induce peptide uptake via accelerated degradation of CUP9, the transcriptional repressor of the PTR2 peptide transporter. J Biol Chem 283:28958-28968.
139. Turner GC, Varshavsky A (2000) Detecting and measuring cotranslational protein degradation in vivo. Science 289:2117-2120.
140. Ditzel M, Wilson R, Tenev T, Zachariou A, Paul A, Deas E, Meier P (2003) Degradation of DIAP1 by the N-end rule pathway is essential for regulating apoptosis. Nat Cell Biol 5:467-473. (Pubitemid 36592271)
141. Varshavsky A (2003) The N-end rule and regulation of apoptosis. Nat Cell Biol 5:373-376.
142. O'Neill GM, Golemis EA (2001) Proteolysis of the docking protein HEF1 and implications for focal adhesion dynamics. Mol Cell Biol 21:5094-5108. (Pubitemid 32656406)
143. Law SF, O'Neill GM, Fashena SJ, Einarson MB, Golemis EA (2000) The docking protein HEF1 is an apoptotic mediator at focal adhesion sites. Mol Cell Biol 20:5194-5195.
144. Foveau B, Leroy C, Ancot F, Deheuninck J, Li Z, Fafeur V, Tulasne D (2007) Amplification of apoptosis through sequential caspase cleavage the Met tyrosine kinase receptor. Cell Death Diff 14:752-764. (Pubitemid 46444513)
145. Tulasne D, Deheuninck J, Lourenco FC, Lamballe F, Ji Z, Leroy C, Puchois E, Moumen A, Maina F, Mehlen P, Fafeur V (2004) Proapoptotic function of the MET tyrosine kinase receptor through caspase cleavage. Mol Cell Biol 24:10328-10339. (Pubitemid 39507870)
146. Goldschneider D, Mehlen P (2010) Dependence receptors: a new paradigm in cell signaling and cancer. Oncogene 29:1865-1882.
147. Ancot F, Foveau B, Lefebvre J, Leroy C, Tulasne D (2009) Proteolytic cleavages give receptor tyrosine kinases the gift of ubiquity. Oncogene 28:2185-2195.
148. Conacci-Sorrell M, Ngouenet C, Eisenman RN (2010) Myc-nick: a cytoplasmic cleavage product of Myc that promotes alpha-tubulin acetylation and cell differentiation. Cell 142:480-493.
149. Wu YM, Huang CL, Kung HJ, Huang CYF (2001) Proteolytic activation of Etk/Bmx tyrosine kinase by caspases. J Biol Chem 276:17672-17678.
150. Furne C, Ricard J, Cabrera JR, Pays L, Bethea JR, Mehlen P, Liebl DJ (2009) EphrinB3 is anti-apoptotic ligand that inhibits the dependence receptor functions of EphA4 receptors during adult neurogenesis. Biochim Biohys Acta 1793:231-238.
151. Tu S, Cerione RA (2001) Cdc42 is a substrate for caspase and influences Fas-induced apoptosis. J Biol Chem 276:19656-19663.
152. Chen L, Marechal V, Moreau J, Levine AJ, Chen J (1997) Proteolytic cleavage of the mdm2 oncoprotein during apoptosis. J Biol Chem 272:22966-22973. (Pubitemid 27386122)
153. Leverrier S, Vallentin A, Joubert D (2002) Positive feedback of protein kinase C proteolytic activation during apoptosis. Biochem J 368:905-913. (Pubitemid 36042693)
154. Emoto Y, Kisaki H, Manome Y, Kharbanda S, Kufe D (1996) Activation of protein kinase C-delta in human myeloid leukemia cells treated with 1-beta-D-arbabinofuranosylcytosine. Blood 87:1990-1996. (Pubitemid 26068915)
155. Datta R, Kojima H, Yoshida K, Kufe D (1997) Caspase-3-mediated cleavage of protein kinase C-theta in induction of apoptosis. J Biol Chem 272:20317-20320. (Pubitemid 27355576)
156. Nicholson DW (1999) Caspase structure, proteolytic substrates, and function during apoptotic cell death. Cell Death Diff 6:1028-1042.
157. Fischer U, Jänicke RU, Schultze-Osthoff K (2003) Many cuts to ruin: a comprehensive update of caspase substrates. Cell Death Diff 10:786-100.
158. Agard NJ, Maltby D, Wells JA (2010) Inflammatory stimuli regulate caspase substrate profiles. Mol Cell Proteom 9.5:880-893.
159. Cathelin S, Rébé C, Haddaoui L, Simioni N, Verdier F, Fontenay M, Launay S, Mayeux P, Solary E (2006) Identification of proteins cleaved downstream of caspase activation in monocytes undergoing macrophage differentiation. J Biol Chem 281:17779-17788. (Pubitemid 44035577)
160. Pop C, Salvesen GS (2009) Human caspases: activation, specificity, and regulation. J Biol Chem 284:21777-21781.
161. Storr SJ, Carragher NO, Frame MC, Parr T, Martin SG (2011) The calpain system and cancer. Nat Rev Cancer 11:364-374.
162. Uhlmann F (2004) The mechanism of sister chromatid cohesion. Exp Cell Res 296:80-85.
163. Hsieh J-D, Cheng EH-Y, Korsmeyer SJ (2003) Taspase1: a threonine aspartase required for cleavage of MLL and proper HOX gene expression. Cell 115:293-303. (Pubitemid 37487703)
164. Hailfinger S, Lenz G, Ngo V, Posvitz-Fejfar A, Rebeaud F, Guzzardi M, Penas E-MM, Dierlamm J, Chan WC, Staudt LM, Thome M (2009) Essential role of MALT1 protease activity in activated B cell-like diffuse large B-cell lymphoma. Proc Natl Acad Sci USA 106:19946-19951.
165. Marambaud P, Shioi J, Serban G, Georgakopoulos A, Sarner S, Nagy V, Baki L, Wen P, Efthimiopoulos S, Shao Z, Wisniewski T, Robakis NK (2002) A presenilin-1/gamma-secretase cleavage releases the E-cadherin intracellular domain and regulates disassembly of adherens junctions. EMBO J 21:1948-1956. (Pubitemid 34437192)
166. Witko-Sarsat V, Canteloup S, Durant S, Desdouets C, Chabernaud R, Lemarchand P, Descamps-Latscha B (2002) Cleavage of p21waf1 by proteinase-3, a myeloid-specific serine protease, potentiates cell proliferation. J Biol Chem 277:47338-47347. (Pubitemid 36159248)
167. Hamilton MH, Cook LA, McRackan TR, Schey KL, Hildebrandt JD (2003) Gamma-2 subunit of G protein heterotrimer is an N-end rule ubiquitylation substrate. Proc Natl Acad Sci USA 100:5081-5086. (Pubitemid 36542661)
168. Prakash S, Inobe T, Hatch AJ, Matouschek A (2009) Substrate selection by the proteasome during degradation of protein complexes. Nat Chem Biol 5:29-36.
169. Inobe T, Fishbain S, Prakash S, Matouschek A (2011) Defining the geometry of the two-component proteasome degron. Nat Chem Biol 7:161-167.
170. Fishbain S, Prakash S, Herrig A, Elsasser S, Matouschek A (2011) Rad23 escapes degradation because it lacks a proteasome initiation region. Nat Commun 2:192.
171. Verhoef LGGC, Heinen C, Selivanova A, Halff EF, Salomons FA, Dantuma NP (2009) Minimal length requirement for proteasomal degradation of ubiquitin-dependent substrates. FASEB J 23:123-133.
172. Heinen C, Ács K, Hoogstraten D, Dantuma NP (2011) C-terminal UBA domains protect ubiquitin receptors by preventing initiation of protein
173. Prakash S, Tian L, Ratliff KS, Lehotzky RE, Matouschek A (2004) An unstructured initiation site is required for efficient proteasome-mediated degradation. Nat Struct Mol Biol 11:830-837. (Pubitemid 39128798)
174. Petroski MD, Deshaies RJ (2003) Context of multiubiquitin chain attachment influences the rate of Sic1 degradation. Mol Cell 11:1435-1444. (Pubitemid 36776531)
175. Piwko W, Jentsch S (2006) Proteasome-mediated protein processing by bidirectional degradation initiated from an internal site. Nat Struct Mol Biol 13:691-697. (Pubitemid 44175161)
176. Takeuchi J, Chen H, Coffino P (2007) Proteasome substrate degradation requires association plus extended peptide. EMBO J 26:123-131. (Pubitemid 46094705)
177. 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 15:4884-4899. (Pubitemid 26315799)
178. Jentsch S, Rumpf S (2007) Cdc48 (p97): a molecular gearbox in the ubiquitin pathway? Trends Biochem Sci 32:6-11.
179. Verma R, Oania R, Fang R, Smith GT, Deshaies RJ (2011) Cdc48/p97 mediates UV-dependent turnover of RNA Pol II. Mol Cell 41:82-92.
180. Xie Y, Varshavsky A (2000) Physical association of ubiquitin ligases and the 26S proteasome. Proc Natl Acad Sci USA 97:2497-2502. (Pubitemid 30159199)
181. Xie Y, Varshavsky A (2002) UFD4 lacking the proteasome-binding region catalyses ubiquitination but is impaired in proteolysis. Nat Cell Biol 4:1003-1007. (Pubitemid 35469433)
182. 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:a004390.
183. Vabulas RM, Hartl FU (2005) Protein synthesis upon acute nutrient restriction relies on proteasome function. Science 310:1960-1963. (Pubitemid 43005990)
184. Medicherla B, Goldberg AL (2008) Heat shock and oxygen radicals stimulate ubiquitin-dependent degradation mainly of newly synthesized proteins. J Cell Biol 182:663-673.
185. Yewdell JW, Lascina JR, Rechsteiner MC, Nicchitta CV (2011) Out with the old, in with the new? Comparing methods for measuring protein degradation. Cell Biol Int 35:457-462.
186. Guo F, Esser L, Singh SK, Maurizi MR, Xia D (2002) Crystal structure of the heterodimeric complex of the adaptor, ClpS, with the N-domain of the AAA+ chaperone, ClpA. J Biol Chem 22:46753-46762. (Pubitemid 35417678)
187. Dougan DA, Reid BG, Horwich AL, Bukau B (2002) ClpS, a substrate modulator of the ClpAP machine. Mol Cell 9:673-683. (Pubitemid 34273796)
188. Zeth K, Ravelli RB, Paal K, Cusack S, Bukau B, Dougan DA (2002) Structural analysis of the adaptor protein ClpS with the N-terminal domain of ClpA. Nat Struct Biol 9:906-911. (Pubitemid 35417058)
189. Wang KH, Oakes ESC, Sauer RT, Baker TA (2008) Tuning the strength of a bacterial N-end rule signal. J Biol Chem 283:24600-24607.
190. Guo F, Maurizi MR, Esser L, Xia D (2002) Crystal structure of ClpA, an Hsp100 chaperone and regulator of ClpAP protease. J Biol Chem 277:46743-46752. (Pubitemid 35417677)
191. Hinnerwisch J, Fenton WA, Furtak KJ, Farr GW, Horwich AL (2005) Loops in the central channel of ClpA chaperone mediate protein folding, unfolding, and translocation. Cell 121:1029-1041. (Pubitemid 40894633)
192. Xia D, Esser L, Singh SK, Guo F, Maurizi MR (2004) Crystallographic investigation of peptide binding sites in the N-domain of the ClpA chaperone. J Struct Biol 146:166-179. (Pubitemid 38369029)
193. Aubin-Tam M-E, Olivares AO, Sauer RT, Baker TA, Lang MJ (2011) Single-molecule protein unfolding and translocation by an ATP-fueled proteolytic machine. Cell 145:257-267.
194. Maillard RA, Gheorghe C, Sen M, Righini M, Tan J, Kaiser CM, Hodges C, Martin A, Bustamante C (2011) ClpX(P) generates mechanical force to unfold and translocate its protein substrates. Cell 145:459-469.
195. Wang KH, Sauer RT, Baker TA (2007) ClpS modulates but is not essential for bacterial N-end rule degradation. Genes Dev 15:403-408.
196. Burton RE, Siddiqui SM, Kim YI, Baker TA, Sauer RT (2001) Effects of protein stability and structure on substrate processing by the ClpXP unfolding and degradation machine. EMBO J 20:3092-3100.
197. Bolon DN, Grant RA, Baker TA, Sauer RT (2004) Nucleotide-dependent substrate handoff from the SsB adaptor to the AAA+ ClpXP protease. Mol Cell 16:343-350. (Pubitemid 39504789)
198. Hwang W, Lang MJ (2009) Mechanical design of of translocating motor proteins. Cell Biochem Biophys 54:11-22.
199. Striebel LC, Kress W, Weber-Ban E (2009) Controlled destruction: AAA+ ATPases in protein degradation from bacteria to eukaryotes. Curr Opt Struct Biol 19:209-217.
200. Baker TA, Sauer RT (2006) ATP-dependent proteases of bacteria: recognition logic and operating principles. Trends Biochem Sci 31:647-653.
201. Gottesman S (2003) Proteolysis in bacterial regulatory circuits. Annu Rev Cell Dev Biol 19:565-587.
202. Iyer LM, Burroughs AM, Aravind L (2006) The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Genome Biol 7:R60.
203. Festa RA, McAllister F, Pearce MJ, Mintseris J, Burns KE, Gygi SP, Darwin KH (2010) Prokaryotic ubiquitin-like protein (Pup) proteome of Mycobacterium tuberculosis. PLoS Biol 5:e8589.
204. Lehmann C, Begley TP, Ealick SE (2006) Structure of the Escherichia coli ThiS-ThiF complex, a key component of the sulfur transfer system in thiamin biosynthesis. Biochemistry 45:11-19. (Pubitemid 43054078)
205. Miranda HV, Nembharda N, Sub D, Hepowita N, Krausea DJ, Pritza JR, Phillipsa C, Söll D, Maupin-Furlowa JA (2011) E1- and ubiquitin-like proteins provide a direct linkb between protein conjugation and sulfur transfer in archaea. Proc Natl Acad Sci USA 108:4417-4422.
206. Burroughs AM, Balaji S, Iyer LM, Aravind L (2007) Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold. Biol Direct 2:18.
207. Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J, Kazama H, Chee GJ, Hattori M, Kanai A, Atomi H, Takai K, Takami H (2011) Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res 39:3204-3223.
208. Hochstrasser M, Varshavsky A (1990) In vivo degradation of a transcriptional regulator: the yeast MATalpha2 repressor. Cell 61:697-708.
209. Xie W, Ngo DT (2010) ERAD substrate recognition in budding yeast. Semin Cell Dev Biol 21:533-539.
210. Lynch M. 2007. The Origins of Genome Architecture. : Sinauer Associates, Inc: Sinauer Associates, Inc.
211. Baltimore D (2009) Discovering Nf-kappaB. Cold Spring Harb Perspect Biol 1:a000026.
212. Coudreuse D, Nurse P (2010) Driving the cell cycle with a minimal CDK control network. Nature 468:1074-1079.
213. Varshavsky A (2005) Ubiquitin fusion technique and related methods. Meth Enzymol 399:777-799.
214. Ecker DJ, Stadel JM, Butt TR, Marsh JA, Monia BP, Powers DA, Gorman JA, Clark PE, Warren F, Shatzman A (1989) Increasing gene expression in yeast by fusion to ubiquitin. J Biol Chem 264:7715-7719. (Pubitemid 19119194)
215. Park EC, Finley D, Szostak JW (1992) A strategy for the generation of conditional mutations by protein destabilization. Proc Natl Acad Sci USA 89:1249-1252.
216. Dohmen RJ, Varshavsky A (2005) Heat-inducible degron and the making of conditional mutants. Meth Enzymol 399:799-822. (Pubitemid 41772767)
217. Johnsson N, Varshavsky A (1994) Ubiquitin-assisted dissection of protein transport across cell membranes. EMBO J 13:2686-2698. (Pubitemid 24188402)
218. Johnsson N, Varshavsky A (1994) Split ubiquitin as a sensor of protein interactions in vivo. Proc Natl Acad Sci USA 91:10340-10344. (Pubitemid 24328992)
219. Lévy F, Johnsson N, Rümenapf T, Varshavsky A (1996) Using ubiquitin to follow the metabolic fate of a protein. Proc Natl Acad Sci USA 93:4907-4912. (Pubitemid 26162845)
220. Dohmen RJ, Wu P, Varshavsky A (1994) Heat-inducible degron: a method for constructing temperature-sensitive mutants. Science 263:1273-1276. (Pubitemid 24107546)
221. Müller J, Johnsson N (2008) Split-ubiquitin and the split-protein sensors: chessman for the endgame. Chembiochem 9:2029-2038.
222. Tarassov K, Messier V, Landry CR, Radinovic S, Molina MM, Shames I, Malitskaya Y, Vogel J, Bussey H, Michnick SW (2008) An in vivo map of the yeast protein interactome. Science 320:1465-1470. (Pubitemid 351929421)
223. Michnick SW, Ear PH, Manderson EN, Remy I, Stefan E (2007) Universal strategies in research and drug discovery based on protein-fragment complementation assays. Nat Rev Drug Discov 6:569-582. (Pubitemid 47019445)
224. Kerppola TK (2008) Bimolecular fluorescence complementation (BiFC) analysis as a probe of protein interactions in living cells. Annu Rev Biophys 37:465-487.
225. Magliery TJ, Wilson CG, Pan W, Mishler D, Ghosh I, Hamilton AD, Regan L (2005) Detecting protein-protein interactions with a green fluorescent protein fragment reassembly trap: scope and mechanism. J Am Chem Soc 127:146-157. (Pubitemid 40094379)
226. Varshavsky A (1996) The N-end rule. Cold Spring Harb Symp Quant Biol 60:461-478.
227. Falnes PO, Olsnes S (1998) Modulation of the intracellular stability and toxicity of diphtheria toxin through degradation by the N-end rule pathway. EMBO J 17:615-625. (Pubitemid 28045501)
228. Falnes PO, Welker R, Krausslich HG, Olsnes S (1999) Toxins are activated by HIV-type-1 protease through removal of signal for degradation by the N-end rule pathway. Biochemical J 343:199-207. (Pubitemid 29473896)
229. Shapira A, Gal-Tanamy M, Nahary L, Litvak-Greenfeld D, Zemel R, Tur-Kaspa R, Benhar I (2011) Engineered toxins "zymoxins" are activated by the HCV NS3 protease by removal of an inhibitory protein domain. PLoS One 14:e15916.
230. Jucovic M, Walters FS, Warren GW, Palekar NV, Chen JS (2008) From enzyme to zymogen: engineering Vip2, an ADP-ribosyltransferase from Bacillus cereus, for conditional toxicity. Protein Eng Des 21:631-638.
231. Law SK, Wang RR, Mak AN, Wong KB, Zheng YT, Shaw PC (2010) A switch-on mechanism to activate maize ribosome-inactivating protein for targeting HIV-infected cells. Nucleic Acids Res 38:6803-6812.
232. Johnson RJ, Lin SR, Raines RT (2006) A ribonuclease zymogen activated by the NS3 protease of the hepatitis C virus. FEBS J 273:5457-5465. (Pubitemid 44772401)
233. Turcotte RF, Raines RT (2008) Design and characterization of an HIV-specific ribonuclease zymogen. AIDS Res Hum Retroviruses 24:1357-1363.
234. Pratt MR, Schwartz EC, Muir TW (2007) Small-molecule-mediated rescue of protein function by an inducible proteolytic shunt. Proc Natl Acad Sci USA 104:11209-11214. (Pubitemid 47175120)
235. Johnston JA, Johnson ES, Waller PR, Varshavsky A (1995) Methotrexate inhibits proteolysis of dihydrofolate reductase by the N-end rule pathway. J Biol Chem 270:8172-8178.
236. Lévy F, Johnston JA, Varshavsky A (1999) Analysis of a conditional degradation signal in yeast and mammalian cells. Eur J Biochem 259:244-252. (Pubitemid 29030842)
237. Iwamoto M, Bjöklund T, Lundberg C, Kirik D, Wandless TJ (2010) A general chemical method to regulate protein stability in the mammalian central nervous system. Chem Biol 17:981-988.
238. Taxis C, Stier G, Spadaccini R, Knop M (2009) Efficient protein depletion by genetically controlled deprotection of a dormant N-degron. Mol Systems Biol 5:267.
239. Swanson R, Locher M, Hochstrasser M (2001) A conserved ubiquitin ligase of the nuclear envelope/endoplasmic reticulum that functions in both ERassociated and MATalpha2 repressor degradation. Genes Dev 15:2660-2674. (Pubitemid 32988877)
240. Deng M, Hochstrasser M (2006) Spatially regulated ubiquitin ligation by an ER/nuclear membrane ligase. Nature 443:827-831. (Pubitemid 44622689)
241. Kreft SG, Hochstrasser M (2011) An unusual transmembrane helix in the Doa10 ERAD ubiquitin ligase modulates degradation of its cognate E2. J Biol Chem 286:20163-20174.
242. Mogk A, Bukau B (2010) When the beginning marks the end. Science 327:966-967.
243. Hassink G, Kikkert M, van Voorden S, Lee S-J, Spaapen R, van Laar T, Cloleman CS, Bartee E, Früh K, Chau V, Wiertz E (2005) TEB4 is a C4HC3 RINGfinger containing ubiquitin ligase of the endoplasmic reticulum. Biochem J 388:647-655. (Pubitemid 40839943)
244. Lam YW, Lamond AI, Mann M, Andersen JS (2007) Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins. Curr Biol 17:749-760. (Pubitemid 46635118)
245. Singh RK, Kabbaj M-HM, Paik J, Gunjan A (2009) Histone levels are regulated by phosphorylation and ubiquitylation-dependent proteolysis. Nat Cell Biol 11:925-933.
246. Torres EM, Williams BR, Amon A (2008) Aneuploidy: cells losing their balance. Genetics 179:737-746.
247. Zhang Z, Kulkarni K, Hanrahan SJ, Thompson AJ, Barford D (2010) The APC/C subunit Cdc16/Cut9 is a contiguous tetratricopeptide repeat superhelix with a homodimer interface. EMBO J 29:3733-3744.
248. Zeng L, Zhang Q, Li S, Plotnikov AN, Walsh MJ, Zhou M-M (2010) Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature 466:258-262.
249. Dohmen RJ, Madura K, Bartel B, Varshavsky A (1991) The N-end rule is mediated by the UBC2 (RAD6) ubiquitin-conjugating enzyme. Proc Natl Acad Sci USA 88:7351-7355. (Pubitemid 21915149)
250. Johnson ES, Ma PC, Ota IM, Varshavsky A (1995) A proteolytic pathway that recognizes ubiquitin as a degradation signal. J Biol Chem 270:17442-17456.
251. Ju D, Wang X, Xu H, Xie Y (2007) The armadillo repeats of the Ufd4 ubiquitin ligase recognize ubiquitin-fusion proteins. FEBS Lett 581:265-270. (Pubitemid 46096470)
252. Bernassola F, Karin M, Ciechanover A, Melino G (2008) The HECT family of E3 ubiquitin ligases: multiple players in cancer development. Cancer Cell 14:10-21. (Pubitemid 351885498)
253. Rotin D, Kumar S (2009) Physiological functions of the HECT family of ubiquitin ligases. Nat Rev Mol Biol 10:398-409.
254. Kee Y, Huibregtse JM (2007) Regulation of catalytic activities of HECT ubiquitin ligases. Biochem Biophys Res Commun 354:329-333. (Pubitemid 46161353)
255. Scheffner M, Staub O (2007) HECT E3s and human disease. BMC Biochem 8 (Suppl. I):S6.
256. Johnson ES, Bartel B, Seufert W, Varshavsky A (1992) Ubiquitin as a degradation signal. EMBO J 11:497-505.
257. Koegl M, Hoppe T, Schlenker S, Ulrich HD, Mayer TU, Jentsch S (1999) A novel ubiquitination factor, E4, is involved in multiubiquitin chain assembly. Cell 96:635-644. (Pubitemid 29122806)
258. Park Y, Yoon SK, Yoon JB (2009) The HECT domain of TRIP12 ubiquitinates substrates of the ubiquitin fusion degradation pathway. J Biol Chem 284:1540-1549.
259. Hoppe T (2005) Multiubiquitylation by E4 enzymes: 'one size' doesn't fit all. Trends Biochem Sci 30: 183-187.
260. Hochstrasser M (2006) Lingering mysteries of ubiquitin- chain assembly. Cell 124:27-34.
261. Scott DC, Monda JK, Grace CRR, Duda DM, Kriwacki RW, Kurz T, Schulman BA (2010) A dual mechanism for Rub1 ligation to Cdc53. Mol Cell 39:784-796.
262. Kwon YT, Levy F, Varshavsky A (1999) Bivalent inhibitor of the N-end rule pathway. J Biol Chem 274:18135-18139.
263. Jacobson RH, Zhang XJ, DuBose RF, Matthews BW (1994) Three-dimensional structure of beta-galactosidase from E. coli. Nature 369:761-766.
264. Lee MJ, Pal K, Tasaki T, Roy S, Jiang S, An JY, Banerjee R, Kwon YT (2008) Synthetic heterovalent inhibitors targeting recognition E3 components of the N-end rule pathway. Proc Natl Acad Sci USA 105:100-105.
265. Shim SY, Wang J, Asada N, Neumayer G, Tran HC, Ishiguro K, Sanada K, Nakatani Y, Nguyen MD (2008) Protein 600 is a microtubule/endoplasmic reticulum-associated protein in CNS neurons. J Neurosci 28:3604-3614.
266. Nakatani Y, Konishi H, Vassilev A, Kurooka H, Ishiguro K, Sawada J, Ikura T, Korsmeyer SJ, Qin J, Herlitz AM (2005) p600, a unique protein required for membrane morphogenesis and cell survival. Proc Natl Acad Sci USA 102:15093-15098. (Pubitemid 41513340)
267. Cojocaru M, Bouchard A, Cloutier P, Cooper JJ, Varzavand K, Price DH, Coulombe B (2011) Transcription factor IIS cooperates with the E3 ligase UBR5 to ubiquitinate the CDK9 subunit of the positive transcription elongation factor B. J Biol Chem 286:5012-5022.
268. Hu G, Wang X, Saunders DN, Henderson M, Russell AJ, Herring BPZ, Zhou J. (2010) Modulation of myocardin function by the ubiquitin E3 ligase UBR5. J Biol Chem 285:11800-11809.
269. Tomaić V, Pim D, Thomas M, Massimi P, Myers MP, Banks L (2011) Regulation of the human papillomavirus type 18 E6/E6AP ubiquitin ligase complex by the HECT domain-containing protein EDD. J Virol 85:3120-3127.
270. An JY, Kim E-A, Jiang Y, Zakrzewska A, Kim DE, Lee MJ, Mook-Jung I, Zhang Y, Kwon YT (2010) UBR2 mediates transcriptional silencing during spermatogenesis via histone ubiquitination. Proc Natl Acad Sci USA 107:1912-1917.
271. An JY, Seo JW, Tasaki T, Lee MJ, Varshavsky A, Kwon YT (2006) Impaired neurogenesis and cardiovascular development in mice lacking the E3 ubiquitin ligases UBR1 and UBR2 of the N-end rule pathway. Proc Natl Acad Sci USA 103:6212-6217.
272. Stary S, Yin X-J, Potuschak T, Schlögelhofer P, Potuschak T, Nizhynska V, Bachmair A (2003) PRT1 of Arabidopsis is a ubiquitin protein ligase of the plant N-end rule pathway with specificity for aromatic amino-terminal residues. Plant Physiol 133:1360-1366. (Pubitemid 37458033)
273. Garzón M, Eifler K, Faust A, Scheel H, Hofmann K, Koncz C, Yephremov A, Bachmair A (2007) PRT6/ At5g02310 encodes an Arabidopsis ubiquitin ligase of the N-end rule pathway with arginine specificity and is not the CER3 locus. FEBS Lett 581:3189-3196. (Pubitemid 46977361)
274. Tasaki T, Sohr R, Xia Z, Hellweg R, Hörtnagl H, Varshavsky A, Kwon YT (2007) Biochemical and genetic studies of UBR3, a ubiquitin ligase with a function in olfactory and other sensory systems. J Biol Chem 282:18510-18520. (Pubitemid 47100206)
275. Wang L, Mao X, Ju D, Xie Y (2004) Rpn4 is a physiological substrate of the Ubr2 ubiquitin ligase. J Biol Chem 279:55218-55223. (Pubitemid 40066517)
276. Lee P, Sowa ME, Gygi SP, Harper JW (2011) Alternative ubiquitin activation/conjugation cascades interact with N-recognin ubiquitin ligases of the N-end rule pathway to control degradation of RGS proteins. Mol Cell (in press).
277. Vögtle FN, Wortelkamp S, Zahedi RP, Becker D, Leidhold C, Gevaert K, Kellermann J, Voos W, Sickmann A, Pfanner N, Meisinger C (2009) Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability. Cell 139:428-439.
278. Schmidt O, Pfanner N, Meisinger C (2010) Mitochondrial protein import: from proteomics to functional mechanisms. Nat Rev Mol Cell Biol 11:655-667.
279. Huang TT, Nijman SMB, Mirchandani KD, Galardy PJ, Cohn MA, Haas W, Gygi SP, Ploegh HP, Bernards R, D'Andrea AD (2006) Regulation of monoubiquitinated PCNA by DUB autocleavage. Nat Cell Biol 8:339-347.
280. Dubnau J, Chiang A-S, Grady L, Barditch J, Gossweiler S, McNeil J, Smith P, Buldoc F, Scott R, Certa U, Broger C, Tully T (2003) The staufen/pumilio pathway is involved in Drosophila long-term memory. Curr Biol 13:286-296. (Pubitemid 36230019)
281. Hirai T, Taniura H, Goto Y, Ogura M, Sng JCG, Yoneda Y (2006) Stimulation of the ubiquitin-proteasome pathway through expression of amidohydrolase for N-terminal asparagine (Ntan1) in cultured rat hippocampal neurons exposed to static magnetism. J Neurochem 96:1519-1530. (Pubitemid 43351612)
282. Brower CS, Veiga L, Jones RH, Varshavsky A (2010) Mouse Dfa is a repressor of TATA-Box promoters and interacts with the Abt1 activator of basal transcription. J Biol Chem 285:17218-17234.
283. Gilles-Gonzalez MA, Gonzalez G (2005) Heme-based sensors: defining characteristics, recent developments, and regulatory hypotheses. J Inorg Biochem 99:1-22.
284. Albig AR, Schiemann WP (2005) Identification and characterization of regulator of G protein signaling 4 (RGS4) as a novel inhibitor of tubulogenesis: RGS4 inhibits mitogen-activated protein kinases and vascular endothelial growth factor signaling. Mol Biol Cell 16:609-625. (Pubitemid 40165559)
285. Berger M, Bergers G, Arnold B, Hämmerling GJ, Ganss R (2005) Regulator of G-protein signaling-5 induction in pericytes coincides with active vessel remodeling during neovascularization. Blood 105:1094-1101. (Pubitemid 40170880)
286. Wong CCL, Xu T, Rai R, Bailey AO, Yates JR, III, Wolf YI, Zebroski H, Kashina A (2007) Global analysis of posttranslational protein arginylation. PLoS Biol 5:e258.
287. Eriste E, Norberg Å, Nepomuceno D, Kuei C, Kamme F, Tran D-T, Strupat K, Jörnvall H, Liu C, Lovenberg TW, Sillard R (2005) A novel form of neurotensin post-translationally modified by arginylation. J Biol Chem 280:35089-35097. (Pubitemid 41532695)
288. Hauf S, Waizenegger IC, Peters J-M (2001) Cohesin cleavage by separase required for anaphase and cytokinesis in human cells. Science 293:1320-1323. (Pubitemid 32777422)
289. Tirziu D, Chorianopoulos E, Moodie KL, Palac RT, Zhuang ZW, Tjwa M, Roncal C, Eriksson U, Fu Q, Elfenbein A, Hall AE, Carmeliet P, Moons L, Simons M (2007) Myocardial hypertrophy in the absence of external stimuli is induced by angiogenesis in mice. J Clin Invest 117:3188-3197. (Pubitemid 350096977)
290. Xie Y, Wolff DW, Wei T, Wang B, Deng C, Kirui JK, Jiang H, Qin H, Abel PW, Tu Y (2009) Breast cancer migration and invasion depend on proteasome degradation of regulator of G-protein signaling 4. Cancer Res 69:5743-5751.
291. Sjögren B, Neubig RR (2010) Thinking outside of the "RGS box": new approaches to therapeutic targeting of regulators of G protein signaling. Mol Pharm 78:550-557.
292. Kwon YT, Xia Z, Davydov IV, Lecker SH, Varshavsky A (2001) Construction and analysis of mouse strains lacking the ubiquitin ligase UBR1 (E3-alpha) of the N-end rule pathway. Mol Cell Biol 21:8007-8021. (Pubitemid 33051792)
293. Wang Y, Mijares M, Gall MD, Turan T, Javier A, Bornemann DJ, Manage K, Warrior R (2010) Drosophila variable nurse cells encodes arrest defective 1 (ARD1), the catalytic subunit of the major N-terminal acetyltransferase complex. Dev Dyn 239:2813-2827.
294. Ingram AK, Cross GA, Horn D (2000) Genetic manipulation indicates that ARD1 is an essential N(alpha)- acetyltransferase in Trypanosoma brucei. Mol Biochem Parasitol 111:309-317. (Pubitemid 32121674)
295. Alagramam K, Naider F, Becker JM (1995) A recognition component of the ubiquitin system is required for peptide transport in Saccharomyces cerevisiae. Mol Microbiol 15:225-234.
296. Byrd C, Turner GC, Varshavsky A (1998) The N-end rule pathway controls the import of peptides through degradation of a transcriptional repressor. EMBO J 17:269-277. (Pubitemid 28041067)
297. Cai H, Kauffman S, Naider F, Becker JM (2006) Genomewide screen reveals a wide regulatory network for di/tripeptide utilization in Saccharomyces cerevisiae. Genetics 172:1459-1476.
298. Cai H, Hauser M, Naider F, Becker JM (2007) Differential regulation and substrate preferences in two peptide transporters of Saccharomyces cerevisiae. Eukaryot Cell 6:1805-1813. (Pubitemid 47585570)
299. Wiles AM, Cai H, Naider F, Becker JM (2006) Nutrient regulation of oligopeptide transport in Saccharomyces cerevisiae. Microbiology 152:3133-3145. (Pubitemid 44542391)
300. Godard P, Urrestarazu A, Vissers S, Kontos K, Bontempi G, van Helden J, André B (2007) Effect of 21 different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae. Mol Cell Biol 27:3065-3086. (Pubitemid 46581319)
301. Andréasson C, Heessen S, Ljungdahl PO (2006) Regulation of transcription factor latency by receptor-activated proteolysis. Genes Dev 20:1563-1568. (Pubitemid 43901095)
302. Wu B, Ottow K, Poulsen P, Gaber RF, Albers E, Kielland-Brandt MC (2006) Competitive intra- and extracellular nutrient sensing by the transporter homologue Ssy1p. J Cell Biol 173:327-331.
303. Boles E, André B (2004) Role of transporter-like sensors in glucose and amino acid signalling in yeast. Top Curr Genet 9:121-153.
304. Liu Z, Thornton J, Spirek M, Butow RA (2008) Activation of the SPS amino acid-sensing pathway in Saccharomyces cerevisiae correlates with the phosphorylation state of a sensor component, Ptr3. Mol Cell Biol 28:551-563.
305. Hergeta M, Baldaufa C, Schölza C, Parceja D, Wiesmüllerb K-H, Tampéa R, Abelea R, Bordignonc E (2011) Conformation of peptides bound to the transporter associated with antigen processing (TAP). Proc Natl Acad Sci USA 108:1349-1354.
306. Kume K, Iizumi Y, Shimada M, Ito Y, Kishi T, Yamaguchi Y, Handa H (2010) Role of N-end rule ligases UBR1 and UBR2 in regulating the leucine-mTOR signaling pathway. Genes Cells 15:339-349.
307. Drummond DA, Wilke CO (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352. (Pubitemid 352010328)
308. Drummond DA, Wilke CO (2009) The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet 10:715-724.
309. Kaganovich D, Kopito R, Frydman J (2008) Misfolded proteins partition between two distinct quality control compartments. Nature 454:1088-1095.
310. Bukau B, Weissman J, Horwich A (2006) Molecular chaperones and protein quality control. Cell 125:443-451.
311. Taipale M, Jarosz DF, Lindquist S (2010) HSP90 at the hub of protein homeostasis: emerging mechanistic insights. Nat Rev Mol Cell Biol 11:515-528.
312. Rosenbaum JC, Fredrickson EK, Oeser ML, Garrett-Engele CM, Locke MN, Richardson LA, Nelson ZW, Hetrick ED, Milac T, Gottschling DE, Gardner RG (2011) Disorder targets misorder in nuclear quality control degradation: a disordered ubiquitin ligase directly recognizes its misfolded substrates. Mol Cell 41:93-106.
313. Hampton RY (2011) San1-mediated quality control: substrate recognition "sans" chaperones. Mol Cell 41:2-3.
314. Gardner RG, Nelson ZW, Gottschling DE (2005) Degradation-mediated protein quality control in the nucleus. Cell 120:803-815. (Pubitemid 40568798)
315. Abramochkin G, Shrader TE (1996) Aminoacyl-tRNA recognition by the leucyl/phenylalanyl-tRNA protein transferase. J Biol Chem 271:22901-22907. (Pubitemid 26304741)
316. Suto K, Shimizu Y, Watanabe K, Ueda T, Fukai S, Nureki O, Tomita K (2006) Crystal structures of leucyl/phenylalanyl-tRNA-protein transferase and its complex with an aminoacyl-tRNA analog. EMBO J 25:5942-5950. (Pubitemid 44967775)
317. Watanabe K, Toh Y, Suto K, Shimizu Y, Oka N, Wada T, Tomita K (2007) Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase. Nature 449:867-871. (Pubitemid 47598606)
318. Dong X, Kato-Murayama M, Muramatsu T, Mori H, Shirouzu M, Bessho Y, Yokoyama S (2007) The crystal structure of leucyl/phenylalanyl-tRNA-protein transferase from Escherichia coli. Prot Sci 16:528-534. (Pubitemid 46327563)
319. Cheek J, Broderick JB (2001) Adenosylmethionine-dependent iron-sulfur enzymes: versatile clsters in a radical new role. J Biol Inorg Chem 6:209-226. (Pubitemid 32823954)
320. Johnson DC, Dean DR, Smith AD, Johnson MK (2005) Structure, functon and formation of biological iron-sulfur clusters. Annu Rev Biochem 74:247-281. (Pubitemid 40995508)
321. Bingel-Erlenmeyer R, Kohler R, Kramer G, Sandikci A, Antolic S, Maier T, Schaffitzel C, Wiedmann B, Bukau B, Ban N (2008) A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing. Nature 452:108-111. (Pubitemid 351355096)
322. Falb M, Aivaliotis M, Garcia-Rizo C, Bisle B, Tebbe A, Klein C, Konstantinidis K, Siedler F, Pfeiffer F, Oesterhelt D (2006) Archaeal N-terminal protein maturation commonly involves N-terminal acetylation: a large-scale proteomics survey. J Mol Biol 362:915-924. (Pubitemid 44353516)
323. Humbard MA, Zhou G, Maupin-Furlow JA (2009) The N-terminal penultimate residue of 20S proteasome alpha1 influences its N-alpha acetylation and protein levels as well as growth rate and stress responses of Haloferax volcanii. J Bact 191:3794-3803.
324. Vögtle F-N, Prinz C, Kellermann J, Lottspeich F, Pfanner N, Meisinger C (2011) Mitochondrial protein turnover: role of the precursor intermediate peptidase Oct1 in protein stabilization. Mol Biol Cell (in press).
325. Schrum JP, Zhu TF, Szostak JW (2010) The origins of cellular life. Cold Spring Harb Perspect Biol 2:a002212.
326. Fox GE (2010) Origin and evolution of the ribosome. Cold Spring Harb Perspect Biol 2:a003483.
327. Åkerfelt M, Morimoto RI, Sistonen L (2010) Heat shock factors: integrators of cell stress, development and lifespan. Nat Rev Mol Cell Biol 11:545-555.
328. Ranea JAG, Sillero A, Thornton JM, Orengo CA (2006) Protein superfamily evolution and the Last Universal Common Ancestor (LUCA). J Mol Evol 63:513-525. (Pubitemid 44611738)
329. Koonin EV, Novozhilov AS (2009) Origin and evolution of the genetic code: the universal enigma. IUBMB Life 61:99-111.
330. Spirin A (2009) The ribosome as a conveying thermal ratchet machine. J Biol Chem 284:21103-22119.
331. Lupas AN, Koretke KK (2003) Bioinformatic analysis of ClpS, a protein module involved in prokaryotic and eukaryotic protein degradation. J Struct Biol 141:77-83. (Pubitemid 36269108)
332. Catic A, Sun ZY, Ratner DM, Misaghi S, Spooner E, Samuelson J, Wagner G, Ploegh HL (2007) Sequence and structure evolved separately in a ribosomal ubiquitin variant. EMBO J 26:3474-3483. (Pubitemid 47123537)
333. Ashida H, Kim M, Schmidt-Supprian M, Ma A, Ogawa M, Sasakawa C (2010) A bacterial E3 ubiquitin ligase IpaH9.8 targets NEMO/IKKγ to dampen the host NF-κB-mediated inflammatory response. Nat Cell Biol 12:66-73.
334. Munro P, Flatau G, Lemichez E (2007) Bacteria and the ubiquitin pathway. Curr Opt Microbiol 10:39-46. (Pubitemid 46223640)
335. Ribet D, Cossart P (2010) Pathogen-mediated post-translational modifications: a re-emerging field. Cell 143:694-702.
336. Hicks SW, Galán JE (2010) Hijacking the host ubiquitin pathway: structural strategies of bacterial E3 ubiquitin ligases. Curr Opt Microbiol 13:41-46.
337. Randow F, Lehner PJ (2009) Viral avoidance and exploitation of the ubiquitin system. Nat Cell Biol 11:527-534.
338. Bedford MT, Richard S (2005) Arginine methylation: an emerging regulator of protein function. Mol Cell 18:263-272. (Pubitemid 41350532)
339. Vossenaar ER, Zendman AJW, van Venrooij WJ, Pruijn GJM (2003) PAD, a growing family of citrullinating enzymes: genes, features and involvement in disease. BioEssays 25:1106-1118. (Pubitemid 37411770)
340. Bitto E, Bingman CA, McCoy JG, Wesenberg GE, Phillips GN (2008) Crystal structure of the uncharacterized human protein C8orf32 with bound peptide. Protein Data Bank, PDB 3CQ9.
341. Pedersen LC, Yee VC, Bishop PD, Le Trong I, Teller DC, Stenkamp RE (1994) Transglutaminase factor XIII uses proteinase-like catalytic triad to crosslink macromolecules. Protein Sci 3:1131-1135. (Pubitemid 24209910)