1
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Liao QQ, Shu X, Sun W, Mandapaka H, Xie F, Zhang Z, Dai T, Wang S, Zhao J, Jiang H, Zhang L, Lin J, Li SW, Coin I, Yang F, Peng J, Li K, Wu H, Zhou F, Yang B. Capturing Protein-Protein Interactions with Acidic Amino Acids Reactive Cross-Linkers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308383. [PMID: 38073323 DOI: 10.1002/smll.202308383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/14/2023] [Indexed: 05/18/2024]
Abstract
Acidic residues (Asp and Glu) have a high prevalence on protein surfaces, but cross-linking reactions targeting these residues are limited. Existing methods either require high-concentration coupling reagents or have low structural compatibility. Here a previously reported "plant-and-cast" strategy is extended to develop heterobifunctional cross-linkers. These cross-linkers first react rapidly with Lys sidechains and then react with Asp and Glu sidechains, in a proximity-enhanced fashion. The cross-linking reaction proceeds at neutral pH and room temperature without coupling reagents. The efficiency and robustness of cross-linking using model proteins, ranging from small monomeric proteins to large protein complexes are demonstrated. Importantly, it is shown that this type of cross-linkers are efficient at identifying protein-protein interactions involving acidic domains. The Cross-linking mass spectrometry (XL-MS) study with p53 identified 87 putative binders of the C-terminal domain of p53. Among them, SARNP, ZRAB2, and WBP11 are shown to regulate the expression and alternative splicing of p53 target genes. Thus, these carboxylate-reactive cross-linkers will further expand the power of XL-MS in the analysis of protein structures and protein-protein interactions.
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Affiliation(s)
- Qing-Qing Liao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Xin Shu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wei Sun
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Hyma Mandapaka
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Feng Xie
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zhengkui Zhang
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Tong Dai
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Shuai Wang
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Jinghua Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital Fudan University, Shanghai, 200438, China
| | - Hong Jiang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Long Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital Fudan University, Shanghai, 200438, China
| | - Shu-Wei Li
- Nanjing Apollomics Biotech, Inc, Nanjing, Jiangsu, 210033, China
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, 04103, Leipzig, Germany
| | - Fan Yang
- Department of Biophysics, Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jinrong Peng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Kui Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Haifan Wu
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Fangfang Zhou
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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2
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Selcuk K, Leitner A, Braun L, Le Blanc F, Pacak P, Pot S, Vogel V. Transglutaminase 2 has higher affinity for relaxed than for stretched fibronectin fibers. Matrix Biol 2024; 125:113-132. [PMID: 38135164 DOI: 10.1016/j.matbio.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
Transglutaminase 2 (TG2) plays a vital role in stabilizing extracellular matrix (ECM) proteins through enzymatic crosslinking during tissue growth, repair, and inflammation. TG2 also binds non-covalently to fibronectin (FN), an essential component of the ECM, facilitating cell adhesion, migration, proliferation, and survival. However, the interaction between TG2 and fibrillar FN remains poorly understood, as most studies have focused on soluble or surface-adsorbed FN or FN fragments, which differ in their conformations from insoluble FN fibers. Using a well-established in vitro FN fiber stretch assay, we discovered that the binding of a crosslinking enzyme to ECM fibers is mechano-regulated. TG2 binding to FN is tuned by the mechanical tension of FN fibers, whereby TG2 predominantly co-localizes to low-tension FN fibers, while fiber stretching reduces their affinity for TG2. This mechano-regulated binding relies on the proximity between the N-terminal β-sandwich and C-terminal β-barrels of TG2. Crosslinking mass spectrometry (XL-MS) revealed a novel TG2-FN synergy site within TG2's C-terminal β-barrels that interacts with FN regions located outside of the canonical gelatin binding domain, specifically FNI2 and FNIII14-15. Combining XL-MS distance restraints with molecular docking revealed the mechano-regulated binding mechanism between TG2 and modules FNI7-9 by which mechanical forces regulate TG2-FN interactions. This highlights a previously unrecognized role of TG2 as a tension sensor for FN fibers. This novel interaction mechanism has significant implications in physiology and mechanobiology, including how forces regulate cell adhesion, spreading, migration, phenotype modulation, depending on the tensional state of ECM fibers. Data are available via ProteomeXchange with identifier PXD043976.
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Affiliation(s)
- Kateryna Selcuk
- Department of Health Sciences and Technology, Institute of Translational Medicine, Laboratory of Applied Mechanobiology, ETH Zurich, Gloriastrasse 37-39 GLC G11, CH-8092 Zurich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland
| | - Lukas Braun
- Department of Health Sciences and Technology, Institute of Translational Medicine, Laboratory of Applied Mechanobiology, ETH Zurich, Gloriastrasse 37-39 GLC G11, CH-8092 Zurich, Switzerland
| | - Fanny Le Blanc
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland
| | - Paulina Pacak
- Department of Health Sciences and Technology, Institute of Translational Medicine, Laboratory of Applied Mechanobiology, ETH Zurich, Gloriastrasse 37-39 GLC G11, CH-8092 Zurich, Switzerland
| | - Simon Pot
- Department of Health Sciences and Technology, Institute of Translational Medicine, Laboratory of Applied Mechanobiology, ETH Zurich, Gloriastrasse 37-39 GLC G11, CH-8092 Zurich, Switzerland
| | - Viola Vogel
- Department of Health Sciences and Technology, Institute of Translational Medicine, Laboratory of Applied Mechanobiology, ETH Zurich, Gloriastrasse 37-39 GLC G11, CH-8092 Zurich, Switzerland.
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3
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Kern C, Radon C, Wende W, Leitner A, Sträßer K. Cross-linking mass spectrometric analysis of the endogenous TREX complex from Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2023; 29:1870-1880. [PMID: 37699651 PMCID: PMC10653388 DOI: 10.1261/rna.079758.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/22/2023] [Indexed: 09/14/2023]
Abstract
The conserved TREX complex has multiple functions in gene expression such as transcription elongation, 3' end processing, mRNP assembly and nuclear mRNA export as well as the maintenance of genomic stability. In Saccharomyces cerevisiae, TREX is composed of the pentameric THO complex, the DEAD-box RNA helicase Sub2, the nuclear mRNA export adaptor Yra1, and the SR-like proteins Gbp2 and Hrb1. Here, we present the structural analysis of the endogenous TREX complex of S. cerevisiae purified from its native environment. To this end, we used cross-linking mass spectrometry to gain structural information on regions of the complex that are not accessible to classical structural biology techniques. We also used negative-stain electron microscopy to investigate the organization of the cross-linked complex used for XL-MS by comparing our endogenous TREX complex with recently published structural models of recombinant THO-Sub2 complexes. According to our analysis, the endogenous yeast TREX complex preferentially assembles into a dimer.
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Affiliation(s)
- Carina Kern
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany
| | - Christin Radon
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Wolfgang Wende
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Katja Sträßer
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany
- Cardio-Pulmonary Institute (CPI), EXC 2026, 35392 Giessen, Germany
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4
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Yu C, Huang L. New advances in cross-linking mass spectrometry toward structural systems biology. Curr Opin Chem Biol 2023; 76:102357. [PMID: 37406423 PMCID: PMC11091472 DOI: 10.1016/j.cbpa.2023.102357] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 07/07/2023]
Abstract
Elucidating protein-protein interaction (PPI) networks and their structural features within cells is central to understanding fundamental biology and associations of cell phenotypes with human pathologies. Owing to technological advancements during the last decade, cross-linking mass spectrometry (XL-MS) has become an enabling technology for delineating interaction landscapes of proteomes as they exist in living systems. XL-MS is unique due to its capability to simultaneously capture PPIs from native environments and uncover interaction contacts though identification of cross-linked peptides, thereby permitting the determination of both identity and connectivity of PPIs in cells. In combination with high resolution structural tools such as cryo-electron microscopy and AI-assisted prediction, XL-MS has contributed significantly to elucidating architectures of large protein assemblies. This review highlights the latest developments in XL-MS technologies and their applications in proteome-wide analysis to advance structural systems biology.
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Affiliation(s)
- Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697, USA.
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5
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Gao H, Zhao Q, Gong Z, Zhong B, Chen J, Sui Z, Li X, Liang Z, Zhang Y, Zhang L. Alkynyl-Enrichable Carboxyl-Selective Crosslinkers to Increase the Crosslinking Coverage for Deciphering Protein Structures. Anal Chem 2022; 94:12398-12406. [PMID: 36031802 DOI: 10.1021/acs.analchem.2c02205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The coverage of chemical crosslinking coupled with mass spectrometry (CXMS) is of great importance to determine its ability for deciphering protein structures. At present, N-hydroxysuccinimidyl (NHS) ester-based crosslinkers targeting lysines have been predominantly used in CXMS. However, they are not always effective for some proteins with few lysines. Other amino acid residues such as carboxyl could be crosslinked to complement lysines and improve the crosslinking coverage of CXMS, but the low intrinsic chemical reactivity of carboxyl compromises the application of carboxyl-selective crosslinkers for complex samples. To enhance the crosslinking efficiency targeting acidic residues and realize in-depth crosslinking analysis of complex samples, we developed three new alkynyl-enrichable carboxyl-selective crosslinkers with different reactive groups such as hydrazide, amino, and aminooxy. The crosslinking efficiencies of the three crosslinkers were systematically evaluated, giving the best reactivity of the amino-functionalized crosslinker BAP. Furthermore, BAP was extended to the crosslinking analysis of Escherichia coli lysate in combination with efficient crosslink enrichment. A total of 1291 D/E-D/E crosslinks involved in 392 proteins were identified under a false discovery rate (FDR) of ≤1%. Obvious structural complementarity of BAP was exhibited to the lysine-targeting crosslinker, facilitating the capability of CXMS for protein structure elucidation. To the best of our knowledge, this was the first time for the carboxyl-selective crosslinker to achieve proteome-wide crosslinking analysis of the whole cell lysate. Collectively, we believe that this work not only expands on a promising toolkit of CXMS targeting acidic residues but also provides a valuable guideline to advance the performance of carboxyl-selective crosslinkers.
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Affiliation(s)
- Hang Gao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China.,University of Chinese Academy of Sciences, Beijing100039, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China
| | - Zhou Gong
- CAS Innovation Academy for Precision Measurement Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Chinese Academy of Sciences, Wuhan430071, Hubei, China
| | - Bowen Zhong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China
| | - Jing Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China.,School of Chemistry and Material Science, University of Science and Technology of China, Hefei230026, Anhui, China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China
| | - Xiao Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, Liaoning, China
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6
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Sarnowski CP, Bikaki M, Leitner A. Cross-linking and mass spectrometry as a tool for studying the structural biology of ribonucleoproteins. Structure 2022; 30:441-461. [PMID: 35366400 DOI: 10.1016/j.str.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/03/2022] [Accepted: 03/01/2022] [Indexed: 11/17/2022]
Abstract
Cross-linking and mass spectrometry (XL-MS) workflows represent an increasingly popular technique for low-resolution structural studies of macromolecular complexes. Cross-linking reactions take place in the solution state, capturing contact sites between components of a complex that represent the native, functionally relevant structure. Protein-protein XL-MS protocols are widely adopted, providing precise localization of cross-linking sites to single amino acid positions within a pair of cross-linked peptides. In contrast, protein-RNA XL-MS workflows are evolving rapidly and differ in their ability to localize interaction regions within the RNA sequence. Here, we review protein-protein and protein-RNA XL-MS workflows, and discuss their applications in studies of protein-RNA complexes. The examples highlight the complementary value of XL-MS in structural studies of protein-RNA complexes, where more established high-resolution techniques might be unable to produce conclusive data.
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Affiliation(s)
- Chris P Sarnowski
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland; Systems Biology PhD Program, University of Zürich and ETH Zürich, Zurich, Switzerland
| | - Maria Bikaki
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland.
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7
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Structural architecture of the human NALCN channelosome. Nature 2022; 603:180-186. [PMID: 34929720 DOI: 10.1038/s41586-021-04313-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/07/2021] [Indexed: 11/08/2022]
Abstract
Depolarizing sodium (Na+) leak currents carried by the NALCN channel regulate the resting membrane potential of many neurons to modulate respiration, circadian rhythm, locomotion and pain sensitivity1-8. NALCN requires FAM155A, UNC79 and UNC80 to function, but the role of these auxiliary subunits is not understood3,7,9-12. NALCN, UNC79 and UNC80 are essential in rodents2,9,13, and mutations in human NALCN and UNC80 cause severe developmental and neurological disease14,15. Here we determined the structure of the NALCN channelosome, an approximately 1-MDa complex, as fundamental aspects about the composition, assembly and gating of this channelosome remain obscure. UNC79 and UNC80 are massive HEAT-repeat proteins that form an intertwined anti-parallel superhelical assembly, which docks intracellularly onto the NALCN-FAM155A pore-forming subcomplex. Calmodulin copurifies bound to the carboxy-terminal domain of NALCN, identifying this region as a putative modulatory hub. Single-channel analyses uncovered a low open probability for the wild-type complex, highlighting the tightly closed S6 gate in the structure, and providing a basis to interpret the altered gating properties of disease-causing variants. Key constraints between the UNC79-UNC80 subcomplex and the NALCN DI-DII and DII-DIII linkers were identified, leading to a model of channelosome gating. Our results provide a structural blueprint to understand the physiology of the NALCN channelosome and a template for drug discovery to modulate the resting membrane potential.
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8
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Piersimoni L, Kastritis PL, Arlt C, Sinz A. Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein-Protein Interactions─A Method for All Seasons. Chem Rev 2021; 122:7500-7531. [PMID: 34797068 DOI: 10.1021/acs.chemrev.1c00786] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mass spectrometry (MS) has become one of the key technologies of structural biology. In this review, the contributions of chemical cross-linking combined with mass spectrometry (XL-MS) for studying three-dimensional structures of proteins and for investigating protein-protein interactions are outlined. We summarize the most important cross-linking reagents, software tools, and XL-MS workflows and highlight prominent examples for characterizing proteins, their assemblies, and interaction networks in vitro and in vivo. Computational modeling plays a crucial role in deriving 3D-structural information from XL-MS data. Integrating XL-MS with other techniques of structural biology, such as cryo-electron microscopy, has been successful in addressing biological questions that to date could not be answered. XL-MS is therefore expected to play an increasingly important role in structural biology in the future.
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Affiliation(s)
- Lolita Piersimoni
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Biozentrum, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
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9
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Mohamed WI, Park SL, Rabl J, Leitner A, Boehringer D, Peter M. The human GID complex engages two independent modules for substrate recruitment. EMBO Rep 2021; 22:e52981. [PMID: 34647674 PMCID: PMC8567238 DOI: 10.15252/embr.202152981] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 01/06/2023] Open
Abstract
The human GID (hGID) complex is a conserved E3 ubiquitin ligase regulating diverse biological processes, including glucose metabolism and cell cycle progression. However, the biochemical function and substrate recognition of the multi-subunit complex remain poorly understood. Using biochemical assays, cross-linking mass spectrometry, and cryo-electron microscopy, we show that hGID engages two distinct modules for substrate recruitment, dependent on either WDR26 or GID4. WDR26 and RanBP9 cooperate to ubiquitinate HBP1 in vitro, while GID4 is dispensable for this reaction. In contrast, GID4 functions as an adaptor for the substrate ZMYND19, which surprisingly lacks a Pro/N-end degron. GID4 substrate binding and ligase activity is regulated by ARMC8α, while the shorter ARMC8β isoform assembles into a stable hGID complex that is unable to recruit GID4. Cryo-EM reconstructions of these hGID complexes reveal the localization of WDR26 within a ring-like, tetrameric architecture and suggest that GID4 and WDR26/Gid7 utilize different, non-overlapping binding sites. Together, these data advance our mechanistic understanding of how the hGID complex recruits cognate substrates and provides insights into the regulation of its E3 ligase activity.
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Affiliation(s)
- Weaam I Mohamed
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Sophia L Park
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland.,Life Science Zürich, PhD Program for Molecular Life Sciences, Zürich, Switzerland
| | - Julius Rabl
- Cryo-EM Knowledge Hub (CEMK), Zürich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | | | - Matthias Peter
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
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