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Anisimova AS, Karagöz GE. Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells. RNA 2023; 29:1818-1836. [PMID: 37582618 PMCID: PMC10578486 DOI: 10.1261/rna.079714.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023]
Abstract
The conserved family of RNA-binding proteins (RBPs), IGF2BPs, plays an essential role in posttranscriptional regulation controlling mRNA stability, localization, and translation. Mammalian cells express three isoforms of IGF2BPs: IGF2BP1-3. IGF2BP3 is highly overexpressed in cancer cells, and its expression correlates with a poor prognosis in various tumors. Therefore, revealing its target RNAs with high specificity in healthy tissues and in cancer cells is of crucial importance. Photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) identifies the binding sites of RBPs on their target RNAs at nucleotide resolution in a transcriptome-wide manner. Here, we optimized the PAR-CLIP protocol to study RNA targets of endogenous IGF2BP3 in a human colorectal carcinoma cell line. To this end, we first established an immunoprecipitation protocol to obtain highly pure endogenous IGF2BP3-RNA complexes. Second, we modified the protocol to use highly sensitive infrared (IR) fluorescent dyes instead of radioactive probes to visualize IGF2BP3-crosslinked RNAs. We named the modified method "IR-PAR-CLIP." Third, we compared RNase cleavage conditions and found that sequence preferences of the RNases impact the number of the identified IGF2BP3 targets and introduce a systematic bias in the identified RNA motifs. Fourth, we adapted the single adapter circular ligation approach to increase the efficiency in library preparation. The optimized IR-PAR-CLIP protocol revealed novel RNA targets of IGF2BP3 in a human colorectal carcinoma cell line. We anticipate that our IR-PAR-CLIP approach provides a framework for studies of other RBPs.
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Affiliation(s)
- Aleksandra S Anisimova
- Max Perutz Labs, Vienna BioCenter Campus (VBC), 1030 Vienna, Austria
- Medical University of Vienna, Center for Medical Biochemistry, 1030 Vienna, Austria
- Vienna BioCenter PhD Program, a Doctoral School of the University of Vienna and the Medical University of Vienna, 1030 Vienna, Austria
| | - G Elif Karagöz
- Max Perutz Labs, Vienna BioCenter Campus (VBC), 1030 Vienna, Austria
- Medical University of Vienna, Center for Medical Biochemistry, 1030 Vienna, Austria
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Picchianti L, Sánchez de Medina Hernández V, Zhan N, Irwin NA, Groh R, Stephani M, Hornegger H, Beveridge R, Sawa-Makarska J, Lendl T, Grujic N, Naumann C, Martens S, Richards TA, Clausen T, Ramundo S, Karagöz GE, Dagdas Y. Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and autophagy. EMBO J 2023; 42:e112053. [PMID: 36762703 PMCID: PMC10183829 DOI: 10.15252/embj.2022112053] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
UFMylation involves the covalent modification of substrate proteins with UFM1 (Ubiquitin-fold modifier 1) and is important for maintaining ER homeostasis. Stalled translation triggers the UFMylation of ER-bound ribosomes and activates C53-mediated autophagy to clear toxic polypeptides. C53 contains noncanonical shuffled ATG8-interacting motifs (sAIMs) that are essential for ATG8 interaction and autophagy initiation. However, the mechanistic basis of sAIM-mediated ATG8 interaction remains unknown. Here, we show that C53 and sAIMs are conserved across eukaryotes but secondarily lost in fungi and various algal lineages. Biochemical assays showed that the unicellular alga Chlamydomonas reinhardtii has a functional UFMylation pathway, refuting the assumption that UFMylation is linked to multicellularity. Comparative structural analyses revealed that both UFM1 and ATG8 bind sAIMs in C53, but in a distinct way. Conversion of sAIMs into canonical AIMs impaired binding of C53 to UFM1, while strengthening ATG8 binding. Increased ATG8 binding led to the autoactivation of the C53 pathway and sensitization of Arabidopsis thaliana to ER stress. Altogether, our findings reveal an ancestral role of sAIMs in UFMylation-dependent fine-tuning of C53-mediated autophagy activation.
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Affiliation(s)
- Lorenzo Picchianti
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Víctor Sánchez de Medina Hernández
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Ni Zhan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Nicholas At Irwin
- Department of Zoology, University of Oxford, Oxford, UK.,Merton College, University of Oxford, Oxford, UK
| | - Roan Groh
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Madlen Stephani
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Harald Hornegger
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Justyna Sawa-Makarska
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Thomas Lendl
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Nenad Grujic
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Christin Naumann
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Sascha Martens
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | | | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Silvia Ramundo
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - G Elif Karagöz
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
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Abstract
Since its discovery more than 25 years ago, great progress has been made in our understanding of the unfolded protein response (UPR), a homeostatic mechanism that adjusts endoplasmic reticulum (ER) function to satisfy the physiological demands of the cell. However, if ER homeostasis is unattainable, the UPR switches to drive cell death to remove defective cells in an effort to protect the health of the organism. This functional dichotomy places the UPR at the crossroads of the adaptation versus apoptosis decision. Here, we focus on new developments in UPR signaling mechanisms, in the interconnectivity among the signaling pathways that make up the UPR in higher eukaryotes, and in the coordination between the UPR and other fundamental cellular processes.
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Affiliation(s)
- G Elif Karagöz
- Max Perutz Labs Vienna, Medical University of Vienna, Vienna, Austria
| | - Tomás Aragón
- Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, Pamplona, Spain
| | - Diego Acosta-Alvear
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, Santa Barbara, CA, USA
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Karagöz GE, Acosta-Alvear D, Walter P. The Unfolded Protein Response: Detecting and Responding to Fluctuations in the Protein-Folding Capacity of the Endoplasmic Reticulum. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a033886. [PMID: 30670466 DOI: 10.1101/cshperspect.a033886] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most of the secreted and plasma membrane proteins are synthesized on membrane-bound ribosomes on the endoplasmic reticulum (ER). They require engagement of ER-resident chaperones and foldases that assist in their folding and maturation. Since protein homeostasis in the ER is crucial for cellular function, the protein-folding status in the organelle's lumen is continually surveyed by a network of signaling pathways, collectively called the unfolded protein response (UPR). Protein-folding imbalances, or "ER stress," are detected by highly conserved sensors that adjust the ER's protein-folding capacity according to the physiological needs of the cell. We review recent developments in the field that have provided new insights into the ER stress-sensing mechanisms used by UPR sensors and the mechanisms by which they integrate various cellular inputs to adjust the folding capacity of the organelle to accommodate to fluctuations in ER protein-folding demands.
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Affiliation(s)
- G Elif Karagöz
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143
| | - Diego Acosta-Alvear
- Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Peter Walter
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143
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5
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Karagöz GE, Peschek J, Walter P, Acosta-Alvear D. In vitro RNA Cleavage Assays to Characterize IRE1-dependent RNA Decay. Bio Protoc 2019; 9:e3307. [PMID: 33654817 PMCID: PMC7854161 DOI: 10.21769/bioprotoc.3307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/24/2019] [Accepted: 07/21/2019] [Indexed: 11/24/2022] Open
Abstract
The kinase/RNase IRE1 is a key effector of the cellular response to endoplasmic reticulum stress. The RNase activity of IRE1 can be measured in cells or in the test tube. Here we describe a protocol for the in vitro cleavage and analysis of RNA substrates of IRE1. The method consists of the in vitro transcription, purification and re-folding of IRE1 substrate RNAs followed by their cleavage using recombinant cytosolic kinase/RNase domains of IRE1 and the separation of the resulting fragments by denaturing polyacrylamide gel electrophoresis. This protocol allows the study of the cleavage kinetics of IRE1's RNA substrates in vitro.
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Affiliation(s)
- G. Elif Karagöz
- Max Perutz Labs Vienna, Medical University of Vienna, Vienna, Austria
| | - Jirka Peschek
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, USA
| | - Peter Walter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, USA
| | - Diego Acosta-Alvear
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
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6
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Acosta-Alvear D, Karagöz GE, Fröhlich F, Li H, Walther TC, Walter P. The unfolded protein response and endoplasmic reticulum protein targeting machineries converge on the stress sensor IRE1. eLife 2018; 7:43036. [PMID: 30582518 PMCID: PMC6336407 DOI: 10.7554/elife.43036] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 12/23/2018] [Indexed: 12/16/2022] Open
Abstract
The protein folding capacity of the endoplasmic reticulum (ER) is tightly regulated by a network of signaling pathways, known as the unfolded protein response (UPR). UPR sensors monitor the ER folding status to adjust ER folding capacity according to need. To understand how the UPR sensor IRE1 maintains ER homeostasis, we identified zero-length crosslinks of RNA to IRE1 with single nucleotide precision in vivo. We found that IRE1 specifically crosslinks to a subset of ER-targeted mRNAs, SRP RNA, ribosomal and transfer RNAs. Crosslink sites cluster in a discrete region of the ribosome surface spanning from the A-site to the polypeptide exit tunnel. Moreover, IRE1 binds to purified 80S ribosomes with high affinity, indicating association with ER-bound ribosomes. Our results suggest that the ER protein translocation and targeting machineries work together with the UPR to tune the ER’s protein folding load.
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Affiliation(s)
- Diego Acosta-Alvear
- Howard Hughes Medical Institute, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - G Elif Karagöz
- Howard Hughes Medical Institute, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Florian Fröhlich
- Harvard School of Public Health, Harvard Medical School, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Han Li
- Howard Hughes Medical Institute, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Tobias C Walther
- Howard Hughes Medical Institute, United States.,Harvard School of Public Health, Harvard Medical School, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Peter Walter
- Howard Hughes Medical Institute, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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7
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Karagöz GE, Acosta-Alvear D, Nguyen HT, Lee CP, Chu F, Walter P. An unfolded protein-induced conformational switch activates mammalian IRE1. eLife 2017; 6:30700. [PMID: 28971800 PMCID: PMC5699868 DOI: 10.7554/elife.30700] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/02/2017] [Indexed: 12/17/2022] Open
Abstract
The unfolded protein response (UPR) adjusts the cell’s protein folding capacity in the endoplasmic reticulum (ER) according to need. IRE1 is the most conserved UPR sensor in eukaryotic cells. It has remained controversial, however, whether mammalian and yeast IRE1 use a common mechanism for ER stress sensing. Here, we show that similar to yeast, human IRE1α’s ER-lumenal domain (hIRE1α LD) binds peptides with a characteristic amino acid bias. Peptides and unfolded proteins bind to hIRE1α LD’s MHC-like groove and induce allosteric changes that lead to its oligomerization. Mutation of a hydrophobic patch at the oligomerization interface decoupled peptide binding to hIRE1α LD from its oligomerization, yet retained peptide-induced allosteric coupling within the domain. Importantly, impairing oligomerization of hIRE1α LD abolished IRE1’s activity in living cells. Our results provide evidence for a unifying mechanism of IRE1 activation that relies on unfolded protein binding-induced oligomerization. Proteins are long string-like molecules that fold into specific three-dimensional shapes. Most proteins that a cell uses to communicate with its environment are folded within a part of the cell called the endoplasmic reticulum. Dedicated sensor proteins in this cellular compartment track this process to make sure that it continues to meet the cell’s demand for protein folding. If it cannot meet the demand, unfolded or poorly folded proteins build up, which stresses the cell. IRE1 is a sensor protein that detects stress in the endoplasmic reticulum. It is found in a range of organisms from yeast to humans, where it spans the membrane that encloses the endoplasmic reticulum. When unfolded proteins accumulate, IRE1 proteins come together and form so-called oligomers. The IRE1 oligomers then become active and send signals outside of the endoplasmic reticulum. These signals adjust the cell’s protein-folding capacity according to its needs at that time. The yeast version of IRE1 directly recognizes unfolded proteins in the endoplasmic reticulum. Yet, its human counterpart was found to have a different three-dimensional structure, which suggested that it might use a different mechanism to detect the stress. Now, Karagöz et al. show that, as in yeast, the sensor part of human IRE1 does indeed bind to unfolded proteins directly. This binding causes this part of the protein to engage other copies of IRE1 and form the oligomers. To understand this interaction in more detail, Karagöz et al. used a technique called nuclear magnetic resonance spectroscopy to monitor changes in the shape of proteins. These observations revealed that binding to an unfolded protein causes other parts of IRE1 protein to change shape. In turn, these shape changes act as a switch that causes the oligomers to form. Stopping the sensor domains from forming oligomers inactivated the IRE1 protein in mammalian cells; this rendered IRE1 unresponsive to stress within the endoplasmic reticulum. The regulation of IRE1 affects many health disorders, including diabetes, cancer and neurodegenerative diseases. By showing that unfolded proteins switch IRE1 into its active, oligomeric state, these findings might lead to new approaches to manipulate IRE1’s activity with small molecules to help to treat these diseases.
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Affiliation(s)
- G Elif Karagöz
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Diego Acosta-Alvear
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Hieu T Nguyen
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Crystal P Lee
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Peter Walter
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
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8
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Karagöz GE, Duarte AMS, Akoury E, Ippel H, Biernat J, Morán Luengo T, Radli M, Didenko T, Nordhues BA, Veprintsev DB, Dickey CA, Mandelkow E, Zweckstetter M, Boelens R, Madl T, Rüdiger SGD. Hsp90-Tau complex reveals molecular basis for specificity in chaperone action. Cell 2014; 156:963-74. [PMID: 24581495 PMCID: PMC4263503 DOI: 10.1016/j.cell.2014.01.037] [Citation(s) in RCA: 214] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 12/11/2013] [Accepted: 01/15/2014] [Indexed: 12/11/2022]
Abstract
Protein folding in the cell relies on the orchestrated action of conserved families of molecular chaperones, the Hsp70 and Hsp90 systems. Hsp70 acts early and Hsp90 late in the folding path, yet the molecular basis of this timing is enigmatic, mainly because the substrate specificity of Hsp90 is poorly understood. Here, we obtained a structural model of Hsp90 in complex with its natural disease-associated substrate, the intrinsically disordered Tau protein. Hsp90 binds to a broad region in Tau that includes the aggregation-prone repeats. Complementarily, a 106-Å-long substrate-binding interface in Hsp90 enables many low-affinity contacts. This allows recognition of scattered hydrophobic residues in late folding intermediates that remain after early burial of the Hsp70 sites. Our model resolves the paradox of how Hsp90 specifically selects for late folding intermediates but also for some intrinsically disordered proteins-through the eyes of Hsp90 they look the same.
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Affiliation(s)
- G Elif Karagöz
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Afonso M S Duarte
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Elias Akoury
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Hans Ippel
- Biomolecular NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; CARIM School for Cardiovascular Diseases, Biochemistry Group, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Jacek Biernat
- DZNE, German Center for Neurodegenerative Diseases, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Tania Morán Luengo
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Martina Radli
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Tatiana Didenko
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Bryce A Nordhues
- Department of Pharmaceutical Sciences and Department of Molecular Medicine, University of South Florida Health Byrd Alzheimer's Institute, University of South Florida, Tampa, FL 33613, USA
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland and Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Chad A Dickey
- Department of Pharmaceutical Sciences and Department of Molecular Medicine, University of South Florida Health Byrd Alzheimer's Institute, University of South Florida, Tampa, FL 33613, USA
| | - Eckhard Mandelkow
- DZNE, German Center for Neurodegenerative Diseases, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany; CAESAR Research Center, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Markus Zweckstetter
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany; Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University Medical Center, 37073 Göttingen, Germany
| | - Rolf Boelens
- Biomolecular NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Tobias Madl
- Biomolecular NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Institute of Structural Biology, Helmholtz Zentrum München Neuherberg and Biomolecular NMR-Spectroscopy, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany; Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria.
| | - Stefan G D Rüdiger
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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Li Y, Karagöz GE, Seo YH, Zhang T, Jiang Y, Yu Y, Duarte AMS, Schwartz SJ, Boelens R, Carroll K, Rüdiger SGD, Sun D. Sulforaphane inhibits pancreatic cancer through disrupting Hsp90-p50(Cdc37) complex and direct interactions with amino acids residues of Hsp90. J Nutr Biochem 2012; 23:1617-26. [PMID: 22444872 DOI: 10.1016/j.jnutbio.2011.11.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 11/09/2011] [Accepted: 11/14/2011] [Indexed: 12/15/2022]
Abstract
Sulforaphane [1-isothiocyanato-4-(methyl-sulfinyl) butane)], an isothiocyanate derived from cruciferous vegetables, has been shown to possess potent chemopreventive activity. We analyzed the effect of sulforaphane on the proliferation of pancreatic cancer cells. Sulforaphane inhibited pancreatic cancer cell growth in vitro with IC(50)s of around 10-15 μM and induced apoptosis. In pancreatic cancer xenograft mouse model, administration of sulforaphane showed remarkable inhibition of tumor growth without apparent toxicity noticed. We found that sulforaphane induced the degradation of heat shock protein 90 (Hsp90) client proteins and blocked the interaction of Hsp90 with its cochaperone p50(Cdc37) in pancreatic cancer cells. Using nuclear magnetic resonance spectroscopy (NMR) with an isoleucine-specific labeling strategy, we overcame the protein size limit of conventional NMR and studied the interaction of sulforaphane with full-length Hsp90 dimer (170 kDa) in solution. NMR revealed multiple chemical shifts in sheet 2 and the adjacent loop in Hsp90 N-terminal domain after incubation of Hsp90 with sulforaphane. Liquid chromatography coupled to mass spectrometry further mapped a short peptide in this region that was tagged with sulforaphane. These data suggest a new mechanism of sulforaphane that disrupts protein-protein interaction in Hsp90 complex for its chemopreventive activity.
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Affiliation(s)
- Yanyan Li
- Department of Pharmaceutical Sciences, University of Michigan, MI, USA
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