Fluorescence-Based Sensors to Monitor Localization and Functions of Linear and K63-Linked Ubiquitin Chains in Cells

被引:129
作者
van Wijk, Sjoerd J. L. [1 ,2 ]
Fiskin, Evgenij [1 ]
Putyrski, Mateusz [2 ]
Pampaloni, Francesco [2 ]
Hou, Jian [3 ]
Wild, Philipp [1 ]
Kensche, Tobias [1 ]
Grecco, Hernan E. [3 ]
Bastiaens, Philippe [3 ]
Dikic, Ivan [1 ,2 ]
机构
[1] Goethe Univ Frankfurt, Sch Med, Inst Biochem 2, D-60590 Frankfurt, Germany
[2] Goethe Univ Frankfurt, Buchmann Inst Mol Life Sci BMLS, D-60438 Frankfurt, Germany
[3] Max Planck Inst Mol Physiol, Dept System Cell Biol, D-44227 Dortmund, Germany
基金
欧洲研究理事会;
关键词
63-LINKED POLYUBIQUITIN CHAINS; STRUCTURAL BASIS; K11-LINKED POLYUBIQUITINATION; RECOGNITION; COMPLEX; PHOSPHORYLATION; INFLAMMATION; RECRUITMENT; SPECIFICITY; DIVERSITY;
D O I
10.1016/j.molcel.2012.06.017
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Ubiquitin chains modify a major subset of the proteome, but detection of ubiquitin signaling dynamics and localization is limited due to a lack of appropriate tools. Here, we employ ubiquitin-binding domain (UBD)-based fluorescent sensors to monitor linear and K63-linked chains in vitro and in vivo. We utilize the UBD in NEMO and ABIN (UBAN) for detection of linear chains, and RAP80 ubiquitin-interacting motif (UIM) and TAB2 Npl4 zinc finger (NZF) domains to detect K63 chains. Linear and K63 sensors decorated the ubiquitin coat surrounding cytosolic Salmonella during bacterial autophagy, whereas K63 sensors selectively monitored Parkin-induced mitophagy and DNA damage responses in fixed and living cells. In addition, linear and K63 sensors could be used to monitor endogenous signaling pathways, as demonstrated by their ability to differentially interfere with TNF- and IL-1-induced NF-kappa B pathway. We propose that UBD-based biosensors could serve as prototypes to track and trace other chain types and ubiquitin-like signals in vivo.
引用
收藏
页码:797 / 809
页数:13
相关论文
共 54 条
[1]   Principles of ubiquitin and SUMO modifications in DNA repair [J].
Bergink, Steven ;
Jentsch, Stefan .
NATURE, 2009, 458 (7237) :461-467
[2]   A Tangled Web of Ubiquitin Chains: Breaking News in TNF-R1 Signaling [J].
Bianchi, Katiuscia ;
Meier, Pascal .
MOLECULAR CELL, 2009, 36 (05) :736-742
[3]   Polyubiquitin Linkage Profiles in Three Models of Proteolytic Stress Suggest the Etiology of Alzheimer Disease [J].
Dammer, Eric B. ;
Na, Chan Hyun ;
Xu, Ping ;
Seyfried, Nicholas T. ;
Duong, Duc M. ;
Cheng, Dongmei ;
Gearing, Marla ;
Rees, Howard ;
Lah, James J. ;
Levey, Allan I. ;
Rush, John ;
Peng, Junmin .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2011, 286 (12) :10457-10465
[4]   Ubiquitin-binding domains - from structures to functions [J].
Dikic, Ivan ;
Wakatsuki, Soichi ;
Walters, Kylie J. .
NATURE REVIEWS MOLECULAR CELL BIOLOGY, 2009, 10 (10) :659-671
[5]   RNF168 Binds and Amplifies Ubiquitin Conjugates on Damaged Chromosomes to Allow Accumulation of Repair Proteins [J].
Doil, Carsten ;
Mailand, Niels ;
Bekker-Jensen, Simon ;
Menard, Patrice ;
Larsen, Dorthe Helena ;
Pepperkok, Rainer ;
Ellenberg, Jan ;
Panier, Stephanie ;
Durocher, Daniel ;
Bartek, Jiri ;
Lukas, Jiri ;
Lukas, Claudia .
CELL, 2009, 136 (03) :435-446
[6]   c-IAP1 and UbcH5 promote K11-linked polyubiquitination of RIP1 in TNF signalling [J].
Dynek, Jasmin N. ;
Goncharov, Tatiana ;
Dueber, Erin C. ;
Fedorova, Anna V. ;
Izrael-Tomasevic, Anita ;
Phu, Lilian ;
Helgason, Elizabeth ;
Fairbrother, Wayne J. ;
Deshayes, Kurt ;
Kirkpatrick, Donald S. ;
Vucic, Domagoj .
EMBO JOURNAL, 2010, 29 (24) :4198-4209
[7]   Global Identification of Modular Cullin-RING Ligase Substrates [J].
Emanuele, Michael J. ;
Elia, Andrew E. H. ;
Xu, Qikai ;
Thoma, Claudio R. ;
Izhar, Lior ;
Leng, Yumei ;
Guo, Ailan ;
Chen, Yi-Ning ;
Rush, John ;
Hsu, Paul Wei-Che ;
Yen, Hsueh-Chi Sherry ;
Elledge, Stephen J. .
CELL, 2011, 147 (02) :459-474
[8]   Recognition and Processing of Ubiquitin-Protein Conjugates by the Proteasome [J].
Finley, Daniel .
ANNUAL REVIEW OF BIOCHEMISTRY, 2009, 78 :477-513
[9]   Exploring the Linkage Dependence of Polyubiquitin Conformations Using Molecular Modeling [J].
Fushman, David ;
Walker, Olivier .
JOURNAL OF MOLECULAR BIOLOGY, 2010, 395 (04) :803-814
[10]   PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1 [J].
Geisler, Sven ;
Holmstroem, Kira M. ;
Skujat, Diana ;
Fiesel, Fabienne C. ;
Rothfuss, Oliver C. ;
Kahle, Philipp J. ;
Springer, Wolfdieter .
NATURE CELL BIOLOGY, 2010, 12 (02) :119-U70