1
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Ni L, Shen R, Luo H, Li X, Zhang X, Huang L, Deng Y, Liao X, Wu Y, Duan C, Xie X. GlmS plays a key role in the virulence factor expression and biofilm formation ability of Staphylococcus aureus promoted by advanced glycation end products. Virulence 2024; 15:2352476. [PMID: 38741276 PMCID: PMC11095574 DOI: 10.1080/21505594.2024.2352476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
Staphylococcus aureus (S. aureus) is well known for its biofilm formation ability and is responsible for serious, chronic refractory infections worldwide. We previously demonstrated that advanced glycation end products (AGEs), a hallmark of chronic hyperglycaemia in diabetic tissues, enhanced biofilm formation by promoting eDNA release via sigB upregulation in S. aureus, contributing to the high morbidity and mortality of patients presenting a diabetic foot ulcer infection. However, the exact regulatory network has not been completely described. Here, we used pull-down assay and LC-MS/MS to identify the GlmS as a candidate regulator of sigB in S. aureus stimulated by AGEs. Dual-luciferase assays and electrophoretic mobility shift assays (EMSAs) revealed that GlmS directly upregulated the transcriptional activity of sigB. We constructed NCTC 8325 ∆glmS for further validation. qRT-PCR analysis revealed that AGEs promoted both glmS and sigB expression in the NCTC 8325 strain but had no effect on NCTC 8325 ∆glmS. NCTC 8325 ∆glmS showed a significant attenuation in biofilm formation and virulence factor expression, accompanied by a decrease in sigB expression, even under AGE stimulation. All of the changes, including pigment deficiency, decreased haemolysis ability, downregulation of hla and hld expression, and less and sparser biofilms, indicated that sigB and biofilm formation ability no longer responded to AGEs in NCTC 8325 ∆glmS. Our data extend the understanding of GlmS in the global regulatory network of S. aureus and demonstrate a new mechanism by which AGEs can upregulate GlmS, which directly regulates sigB and plays a significant role in mediating biofilm formation and virulence factor expression.
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Affiliation(s)
- Lijia Ni
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Institution of Antibiotic, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rui Shen
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Institution of Antibiotic, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hua Luo
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Institution of Antibiotic, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xuexue Li
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaofan Zhang
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lisi Huang
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Institution of Antibiotic, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yawen Deng
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Institution of Antibiotic, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyan Liao
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Institution of Antibiotic, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yonglin Wu
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chaohui Duan
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoying Xie
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Institution of Antibiotic, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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2
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Breckels LM, Hutchings C, Ingole KD, Kim S, Lilley KS, Makwana MV, McCaskie KJA, Villanueva E. Advances in spatial proteomics: Mapping proteome architecture from protein complexes to subcellular localizations. Cell Chem Biol 2024; 31:1665-1687. [PMID: 39303701 DOI: 10.1016/j.chembiol.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]
Abstract
Proteins are responsible for most intracellular functions, which they perform as part of higher-order molecular complexes, located within defined subcellular niches. Localization is both dynamic and context specific and mislocalization underlies a multitude of diseases. It is thus vital to be able to measure the components of higher-order protein complexes and their subcellular location dynamically in order to fully understand cell biological processes. Here, we review the current range of highly complementary approaches that determine the subcellular organization of the proteome. We discuss the scale and resolution at which these approaches are best employed and the caveats that should be taken into consideration when applying them. We also look to the future and emerging technologies that are paving the way for a more comprehensive understanding of the functional roles of protein isoforms, which is essential for unraveling the complexities of cell biology and the development of disease treatments.
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Affiliation(s)
- Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Charlotte Hutchings
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kishor D Ingole
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Suyeon Kim
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Mehul V Makwana
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kieran J A McCaskie
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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3
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Baek K, Metivier RJ, Roy Burman SS, Bushman JW, Lumpkin RJ, Abeja DM, Lakshminarayan M, Yue H, Ojeda S, Verano AL, Gray NS, Donovan KA, Fischer ES. Unveiling the hidden interactome of CRBN molecular glues with chemoproteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612438. [PMID: 39314457 PMCID: PMC11419069 DOI: 10.1101/2024.09.11.612438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Targeted protein degradation and induced proximity refer to strategies that leverage the recruitment of proteins to facilitate their modification, regulation or degradation. As prospective design of glues remains challenging, unbiased discovery methods are needed to unveil hidden chemical targets. Here we establish a high throughput affinity purification mass spectrometry workflow in cell lysates for the unbiased identification of molecular glue targets. By mapping the targets of 20 CRBN-binding molecular glues, we identify 298 protein targets and demonstrate the utility of enrichment methods for identifying novel targets overlooked using established methods. We use a computational workflow to estimate target confidence and perform a biochemical screen to identify a lead compound for the new non-ZF target PPIL4. Our study provides a comprehensive inventory of targets chemically recruited to CRBN and delivers a robust and scalable workflow for identifying new drug-induced protein interactions in cell lysates.
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4
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Stockhammer A, Spalt C, Klemt A, Benz LS, Harel S, Natalia V, Wiench L, Freund C, Kuropka B, Bottanelli F. When less is more - a fast TurboID knock-in approach for high-sensitivity endogenous interactome mapping. J Cell Sci 2024; 137:jcs261952. [PMID: 39056144 PMCID: PMC11385326 DOI: 10.1242/jcs.261952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
In recent years, proximity labeling has established itself as an unbiased and powerful approach to map the interactome of specific proteins. Although physiological expression of labeling enzymes is beneficial for the mapping of interactors, generation of the desired cell lines remains time-consuming and challenging. Using our established pipeline for rapid generation of C- and N-terminal CRISPR-Cas9 knock-ins (KIs) based on antibiotic selection, we were able to compare the performance of commonly used labeling enzymes when endogenously expressed. Endogenous tagging of the µ subunit of the adaptor protein (AP)-1 complex with TurboID allowed identification of known interactors and cargo proteins that simple overexpression of a labeling enzyme fusion protein could not reveal. We used the KI strategy to compare the interactome of the different AP complexes and clathrin and were able to assemble lists of potential interactors and cargo proteins that are specific for each sorting pathway. Our approach greatly simplifies the execution of proximity labeling experiments for proteins in their native cellular environment and allows going from CRISPR transfection to mass spectrometry analysis and interactome data in just over a month.
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Affiliation(s)
- Alexander Stockhammer
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Carissa Spalt
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Antonia Klemt
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Laila S Benz
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Shelly Harel
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Vini Natalia
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Lukas Wiench
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Benno Kuropka
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Francesca Bottanelli
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
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5
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Lin Z, Liu D, Xu Y, Wang M, Yu Y, Diener AC, Liu KH. Pupylation-based proximity-tagging of FERONIA-interacting proteins in Arabidopsis. Mol Cell Proteomics 2024:100828. [PMID: 39147029 DOI: 10.1016/j.mcpro.2024.100828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 06/11/2024] [Accepted: 08/07/2024] [Indexed: 08/17/2024] Open
Abstract
The plasma membrane-localized receptor kinase FERONIA (FER) plays critical roles in a remarkable variety of biological processes throughout the life cycle of Arabidopsis thaliana. Revealing the molecular connections of FER that underlie these processes starts with identifying the proteins that interact with FER. We applied pupylation-based interaction tagging (PUP-IT) to survey cellular proteins in proximity to FER, encompassing weak and transient interactions that can be difficult to capture for membrane proteins. We reproducibly identified 581, 115, and 736 specific FER-interacting protein candidates in protoplasts, seedlings, and flowers, respectively. We also confirmed fourteen previously characterized FER-interacting proteins. Protoplast transient gene expression expedited the testing of new gene constructs for PUP-IT analyses and the validation of candidate proteins. We verified the proximity labeling of five selected candidates that were not previously characterized as FER-interacting proteins. The PUP-IT method could be a valuable tool to survey and validate protein-protein interactions for targets of interest in diverse subcellular compartments in plants.
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Affiliation(s)
- Zhuoran Lin
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Di Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Yifan Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Mengyang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - YongQi Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Andrew C Diener
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Kun-Hsiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China; Institute of Future Agriculture, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China; Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
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6
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Mukhopadhyay U, Levantovsky S, Carusone TM, Gharbi S, Stein F, Behrends C, Bhogaraju S. A ubiquitin-specific, proximity-based labeling approach for the identification of ubiquitin ligase substrates. SCIENCE ADVANCES 2024; 10:eadp3000. [PMID: 39121224 PMCID: PMC11313854 DOI: 10.1126/sciadv.adp3000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 07/03/2024] [Indexed: 08/11/2024]
Abstract
Over 600 E3 ligases in humans execute ubiquitination of specific target proteins in a spatiotemporal manner to elicit desired signaling effects. Here, we developed a ubiquitin-specific proximity-based labeling method to selectively biotinylate substrates of a given ubiquitin ligase. By fusing the biotin ligase BirA and an Avi-tag variant to the candidate E3 ligase and ubiquitin, respectively, we were able to specifically enrich bona fide substrates of a ligase using a one-step streptavidin pulldown under denaturing conditions. We applied our method, which we named Ub-POD, to the really interesting new gene (RING) E3 ligase RAD18 and identified proliferating cell nuclear antigen and several other critical players in the DNA damage repair pathway. Furthermore, we successfully applied Ub-POD to the RING ubiquitin ligase tumor necrosis factor receptor-associated factor 6 and a U-box-type E3 ubiquitin ligase carboxyl terminus of Hsc70-interacting protein. We anticipate that our method could be widely adapted to all classes of ubiquitin ligases to identify substrates.
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Affiliation(s)
- Urbi Mukhopadhyay
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Sophie Levantovsky
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Teresa Maria Carusone
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Sarah Gharbi
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sagar Bhogaraju
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042 Grenoble, France
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7
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Fujimoto Y, Nakazawa N. The roles of FHL2 as a mechanotransducer for cellular functions in the mechanical environment. Front Cell Dev Biol 2024; 12:1431690. [PMID: 39129787 PMCID: PMC11310055 DOI: 10.3389/fcell.2024.1431690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 07/03/2024] [Indexed: 08/13/2024] Open
Abstract
The cell has multiple mechanisms for sensing and responding to dynamic changes in the mechanical environment. In the process, intracellular signaling is activated to modulate gene expression. Recent studies have shown that multifunctional signaling molecules that link intracellular force and gene expression are important for understanding cellular functions in the mechanical environment. This review discusses recent studies on one of the mechanotransducers, Four-and-a-half LIM domains 2 (FHL2), which localizes to focal adhesions (FAs), actin cytoskeleton, and nucleus. FHL2 localizes to FAs and the actin cytoskeleton in the cell on stiff substrate. In this situation, intracellular tension of F-actin by Myosin II is critical for FHL2 localization to FAs and actin stress fibers. In the case, a conserved phenylalanine in each LIM domain is responsible for its localization to F-actin. On the other hand, lower tension of F-actin in the cell on a soft substrate causes FHL2 to be released into the cytoplasm, resulting in its localization in the nucleus. At the molecular level, phosphorylation of specific tyrosine in FHL2 by FAK, non-receptor tyrosine kinase, is critical to nuclear localization. Finally, by binding to transcription factors, FHL2 modulates gene expression for cell proliferation as a transcriptional co-factor. Thus, FHL2 is involved in mechano-sensing and -transduction in the cell in a mechanical environment.
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Affiliation(s)
- Yukari Fujimoto
- Graduate School of Science and Engineering, Kindai University, Higashiosaka, Japan
| | - Naotaka Nakazawa
- Department of Energy and Materials, Faculty of Science and Engineering, Kindai University, Higashiosaka, Japan
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8
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Xiao Y, Yuan Y, Liu Y, Lin Z, Zheng G, Zhou D, Lv D. Targeted Protein Degradation: Current and Emerging Approaches for E3 Ligase Deconvolution. J Med Chem 2024; 67:11580-11596. [PMID: 38981094 DOI: 10.1021/acs.jmedchem.4c00723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Targeted protein degradation (TPD), including the use of proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) to degrade proteins, is an emerging strategy to develop novel therapies for cancer and beyond. PROTACs or MGDs function by inducing the proximity between an E3 ligase and a protein of interest (POI), leading to ubiquitination and consequent proteasomal degradation of the POI. Notably, one major issue in TPD is the lack of ligandable E3 ligases, as current studies predominantly use CUL4CRBN and CUL2VHL. The TPD community is seeking to expand the landscape of ligandable E3 ligases, but most discoveries rely on phenotypic screens or serendipity, necessitating systematic target deconvolution. Here, we examine and discuss both current and emerging E3 ligase deconvolution approaches for degraders discovered from phenotypic screens or monovalent glue chemistry campaigns, highlighting future prospects for identifying more ligandable E3 ligases.
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Affiliation(s)
- Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Yaxia Yuan
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Yi Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
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9
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Zhang S, Tang Q, Zhang X, Chen X. Proximitomics by Reactive Species. ACS CENTRAL SCIENCE 2024; 10:1135-1147. [PMID: 38947200 PMCID: PMC11212136 DOI: 10.1021/acscentsci.4c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 07/02/2024]
Abstract
The proximitome is defined as the entire collection of biomolecules spatially in the proximity of a biomolecule of interest. More broadly, the concept of the proximitome can be extended to the totality of cells proximal to a specific cell type. Since the spatial organization of biomolecules and cells is essential for almost all biological processes, proximitomics has recently emerged as an active area of scientific research. One of the growing strategies for proximitomics leverages reactive species-which are generated in situ and spatially confined, to chemically tag and capture proximal biomolecules and cells for systematic analysis. In this Outlook, we summarize different types of reactive species that have been exploited for proximitomics and discuss their pros and cons for specific applications. In addition, we discuss the current challenges and future directions of this exciting field.
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Affiliation(s)
- Shaoran Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Qi Tang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
| | - Xu Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Xing Chen
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
- Synthetic
and Functional Biomolecules Center, Peking
University, Beijing 100871, People’s
Republic of China
- Key
Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry
of Education, Peking University, Beijing 100871, People’s Republic of China
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10
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Chamrád I, Simerský R, Lenobel R, Novák O. Exploring affinity chromatography in proteomics: A comprehensive review. Anal Chim Acta 2024; 1306:342513. [PMID: 38692783 DOI: 10.1016/j.aca.2024.342513] [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: 12/12/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.
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Affiliation(s)
- Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic.
| | - Radim Simerský
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
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11
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Matsunaga S, Ito N. Nuclear pores beyond macromolecule channels. NATURE PLANTS 2024; 10:842-843. [PMID: 38773270 DOI: 10.1038/s41477-024-01704-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Affiliation(s)
- Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan.
| | - Nanami Ito
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
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12
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Liu X, Abad L, Chatterjee L, Cristea IM, Varjosalo M. Mapping protein-protein interactions by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38742660 DOI: 10.1002/mas.21887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Protein-protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization and function of the proteome, and their perturbation is associated with various diseases, such as cancer, neurodegeneration, and infectious diseases. Recent advances in mass spectrometry (MS)-based protein interactomics have significantly expanded our understanding of the PPIs in cells, with techniques that continue to improve in terms of sensitivity, and specificity providing new opportunities for the study of PPIs in diverse biological systems. These techniques differ depending on the type of interaction being studied, with each approach having its set of advantages, disadvantages, and applicability. This review highlights recent advances in enrichment methodologies for interactomes before MS analysis and compares their unique features and specifications. It emphasizes prospects for further improvement and their potential applications in advancing our knowledge of PPIs in various biological contexts.
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Affiliation(s)
- Xiaonan Liu
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, Katowice, Poland
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lawrence Abad
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Lopamudra Chatterjee
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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13
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Feng R, Liu F, Li R, Zhou Z, Lin Z, Lin S, Deng S, Li Y, Nong B, Xia Y, Li Z, Zhong X, Yang S, Wan G, Ma W, Wu S, Songyang Z. The rapid proximity labeling system PhastID identifies ATP6AP1 as an unconventional GEF for Rheb. Cell Res 2024; 34:355-369. [PMID: 38448650 PMCID: PMC11061317 DOI: 10.1038/s41422-024-00938-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/02/2024] [Indexed: 03/08/2024] Open
Abstract
Rheb is a small G protein that functions as the direct activator of the mechanistic target of rapamycin complex 1 (mTORC1) to coordinate signaling cascades in response to nutrients and growth factors. Despite extensive studies, the guanine nucleotide exchange factor (GEF) that directly activates Rheb remains unclear, at least in part due to the dynamic and transient nature of protein-protein interactions (PPIs) that are the hallmarks of signal transduction. Here, we report the development of a rapid and robust proximity labeling system named Pyrococcus horikoshii biotin protein ligase (PhBPL)-assisted biotin identification (PhastID) and detail the insulin-stimulated changes in Rheb-proximity protein networks that were identified using PhastID. In particular, we found that the lysosomal V-ATPase subunit ATP6AP1 could dynamically interact with Rheb. ATP6AP1 could directly bind to Rheb through its last 12 amino acids and utilizes a tri-aspartate motif in its highly conserved C-tail to enhance Rheb GTP loading. In fact, targeting the ATP6AP1 C-tail could block Rheb activation and inhibit cancer cell proliferation and migration. Our findings highlight the versatility of PhastID in mapping transient PPIs in live cells, reveal ATP6AP1's role as an unconventional GEF for Rheb, and underscore the importance of ATP6AP1 in integrating mTORC1 activation signals through Rheb, filling in the missing link in Rheb/mTORC1 activation.
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Affiliation(s)
- Ran Feng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, Guangdong, China
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Feng Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Ruofei Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhifen Zhou
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhuoheng Lin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Song Lin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shengcheng Deng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yingying Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Baoting Nong
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ying Xia
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhiyi Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaoqin Zhong
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shuhan Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Gang Wan
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenbin Ma
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Su Wu
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
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14
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Ito Y, Nagamoto S, Takano T. Synaptic proteomics decode novel molecular landscape in the brain. Front Mol Neurosci 2024; 17:1361956. [PMID: 38726307 PMCID: PMC11079194 DOI: 10.3389/fnmol.2024.1361956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
Synapses play a pivotal role in forming neural circuits, with critical implications for brain functions such as learning, memory, and emotions. Several advances in synaptic research have demonstrated the diversity of synaptic structure and function, which can form thousands of connections depending on the neuronal cell types. Moreover, synapses not only interconnect neurons but also establish connections with glial cells such as astrocytes, which play a key role in the architecture and function of neuronal circuits in the brain. Emerging evidence suggests that dysfunction of synaptic proteins contributes to a variety of neurological and psychiatric disorders. Therefore, it is crucial to determine the molecular networks within synapses in various neuronal cell types to gain a deeper understanding of how the nervous system regulates brain function. Recent advances in synaptic proteome approaches, such as fluorescence-activated synaptosome sorting (FASS) and proximity labeling, have allowed for a detailed and spatial analysis of many cell-type-specific synaptic molecules in vivo. In this brief review, we highlight these novel spatial proteomic approaches and discuss the regulation of synaptic formation and function in the brain. This knowledge of molecular networks provides new insight into the understanding of many neurological and psychiatric disorders.
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Affiliation(s)
- Yuki Ito
- Division of Molecular Systems for Brain Function, Institute for Advanced Study, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Division of Integrated Omics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Sayaka Nagamoto
- Division of Molecular Systems for Brain Function, Institute for Advanced Study, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Tetsuya Takano
- Division of Molecular Systems for Brain Function, Institute for Advanced Study, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Neurophysiology, Keio University School of Medicine, Tokyo, Japan
- PRESTO, Japan Science and Technology Agency, Saitama, Japan
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15
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Merino-Cacho L, Barroso-Gomila O, Hernández-Sánchez S, Ramirez J, Mayor U, Sutherland JD, Barrio R. Biotin-Based Strategies to Explore the World of Ubiquitin and Ubiquitin-Like Modifiers. Chembiochem 2024; 25:e202300746. [PMID: 38081789 DOI: 10.1002/cbic.202300746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/07/2023] [Indexed: 01/06/2024]
Abstract
A complex code of cellular signals is mediated by ubiquitin and ubiquitin-like (Ub/UbL) modifications on substrate proteins. The so-called Ubiquitin Code specifies protein fates, such as stability, subcellular localization, functional activation or suppression, and interactions. Hundreds of enzymes are involved in placing and removing Ub/UbL on thousands of substrates, while the consequences of modifications and the mechanisms of specificity are still poorly defined. Challenges include rapid and transient engagement of enzymes and Ub/UbL interactors, low stoichiometry of modified versus non-modified cellular substrates, and protease-mediated loss of Ub/UbL in lysates. To decipher this complexity and confront the challenges, many tools have been created to trap and identify substrates and interactors linked to Ub/UbL modification. This review focuses on an assortment of biotin-based tools developed for this purpose (for example BioUbLs, UbL-ID, BioE3, BioID), taking advantage of the strong affinity of biotin-streptavidin and the stringent lysis/washing approach allowed by it, paired with sensitive mass-spectrometry-based proteomic methods. Knowing how substrates change during development and disease, the consequences of substrate modification, and matching substrates to particular UbL-ligating enzymes will contribute new insights into how Ub/UbL signaling works and how it can be exploited for therapies.
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Affiliation(s)
- Laura Merino-Cacho
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Sandra Hernández-Sánchez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
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16
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Holdgate GA, Bardelle C, Berry SK, Lanne A, Cuomo ME. Screening for molecular glues - Challenges and opportunities. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100136. [PMID: 38104659 DOI: 10.1016/j.slasd.2023.12.008] [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: 09/01/2023] [Revised: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 12/19/2023]
Abstract
Molecular glues are small molecules, typically smaller than PROTACs, and usually with improved physicochemical properties that aim to stabilise the interaction between two proteins. Most often this approach is used to improve or induce an interaction between the target and an E3 ligase, but other interactions which stabilise interactions to increase activity or to inhibit binding to a natural effector have also been demonstrated. This review will describe the effects of induced proximity, discuss current methods used to identify molecular glues and introduce approaches that could be adapted for molecular glue screening.
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Affiliation(s)
| | - Catherine Bardelle
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Sophia K Berry
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Alice Lanne
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
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17
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Wang Y, Qin W. Revealing protein trafficking by proximity labeling-based proteomics. Bioorg Chem 2024; 143:107041. [PMID: 38134520 DOI: 10.1016/j.bioorg.2023.107041] [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: 10/26/2023] [Revised: 11/22/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
Protein trafficking is a fundamental process with profound implications for both intracellular and intercellular functions. Proximity labeling (PL) technology has emerged as a powerful tool for capturing precise snapshots of subcellular proteomes by directing promiscuous enzymes to specific cellular locations. These enzymes generate reactive species that tag endogenous proteins, enabling their identification through mass spectrometry-based proteomics. In this comprehensive review, we delve into recent advancements in PL-based methodologies, placing particular emphasis on the label-and-fractionation approach and TransitID, for mapping proteome trafficking. These methodologies not only facilitate the exploration of dynamic intracellular protein trafficking between organelles but also illuminate the intricate web of intercellular and inter-organ protein communications.
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Affiliation(s)
- Yankun Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Wei Qin
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China; MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China; The State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, China.
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18
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Tan H, Zhou Y, Dinius E, Lozano-Durán R. The Ti-TAN plasmid toolbox for TurboID-based proximity labeling assays in Nicotiana benthamiana. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:166-168. [PMID: 38294100 DOI: 10.1111/jipb.13610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
The Ti-TAN TurboID plasmid toolbox enables proximity labeling applications in transient assays in Nicotiana benthamiana in a fast and cost-efficient manner, making TurboID-based proximity labeling broadly accessible to plant scientists.
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Affiliation(s)
- Huang Tan
- Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, D-72076, Germany
| | - Yu Zhou
- Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, D-72076, Germany
| | - Erik Dinius
- Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, D-72076, Germany
| | - Rosa Lozano-Durán
- Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, D-72076, Germany
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19
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Yamada K, Shioya R, Nishino K, Furihata H, Hijikata A, Kaneko MK, Kato Y, Shirai T, Kosako H, Sawasaki T. Proximity extracellular protein-protein interaction analysis of EGFR using AirID-conjugated fragment of antigen binding. Nat Commun 2023; 14:8301. [PMID: 38097606 PMCID: PMC10721602 DOI: 10.1038/s41467-023-43931-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023] Open
Abstract
Receptor proteins, such as epidermal growth factor receptor (EGFR), interact with other proteins in the extracellular region of the cell membrane to drive intracellular signalling. Therefore, analysis of extracellular protein-protein interactions (exPPIs) is important for understanding the biological function of receptor proteins. Here, we present an approach using a proximity biotinylation enzyme (AirID) fusion fragment of antigen binding (FabID) to analyse the proximity exPPIs of EGFR. AirID was C-terminally fused to the Fab fragment against EGFR (EGFR-FabID), which could then biotinylate the extracellular region of EGFR in several cell lines. Liquid Chromatography-Mass Spectrometry (LC-MS/MS) analysis indicated that many known EGFR interactors were identified as proximity exPPIs, along with many unknown candidate interactors, using EGFR-FabID. Interestingly, these proximity exPPIs were influenced by treatment with EGF ligand and its specific kinase inhibitor, gefitinib. These results indicate that FabID provides accurate proximity exPPI analysis of target receptor proteins on cell membranes with ligand and drug responses.
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Affiliation(s)
- Kohdai Yamada
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Ryouhei Shioya
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hirotake Furihata
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Atsushi Hijikata
- Laboratory of Computational Genomics, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, 192-0392, Japan
| | - Mika K Kaneko
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Tsuyoshi Shirai
- Department of Bioscience, Nagahama Institute of BioScience and Technology, 1266 Tamura, Nagahama, 526-0829, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan.
| | - Tatsuya Sawasaki
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan.
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20
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Terasawa K, Seike T, Sakamoto K, Ohtake K, Terada T, Iwata T, Watabe T, Yokoyama S, Hara‐Yokoyama M. Site-specific photo-crosslinking/cleavage for protein-protein interface identification reveals oligomeric assembly of lysosomal-associated membrane protein type 2A in mammalian cells. Protein Sci 2023; 32:e4823. [PMID: 37906694 PMCID: PMC10659947 DOI: 10.1002/pro.4823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/16/2023] [Accepted: 10/21/2023] [Indexed: 11/02/2023]
Abstract
Genetic code expansion enables site-specific photo-crosslinking by introducing photo-reactive non-canonical amino acids into proteins at defined positions during translation. This technology is widely used for analyzing protein-protein interactions and is applicable in mammalian cells. However, the identification of the crosslinked region still remains challenging. Here, we developed a new method to identify the crosslinked region by pre-installing a site-specific cleavage site, an α-hydroxy acid (Nε -allyloxycarbonyl-α-hydroxyl-l-lysine acid, AllocLys-OH), into the target protein. Alkaline treatment cleaves the crosslinked complex at the position of the α-hydroxy acid residue and thus helps to identify which side of the cleavage site, either closer to the N-terminus or C-terminus, the crosslinked site is located within the target protein. A series of AllocLys-OH introductions narrows down the crosslinked region. By applying this method, we identified the crosslinked regions in lysosomal-associated membrane protein type 2A (LAMP2A), a receptor of chaperone-mediated autophagy, in mammalian cells. The results suggested that at least two interfaces are involved in the homophilic interaction, which requires a trimeric or higher oligomeric assembly of adjacent LAMP2A molecules. Thus, the combination of site-specific crosslinking and site-specific cleavage promises to be useful for revealing binding interfaces and protein complex geometries.
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Affiliation(s)
- Kazue Terasawa
- Department of Biochemistry, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
- LiberoThera Co., Ltd.Chuo‐kuJapan
| | - Tatsuro Seike
- Department of Periodontology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Kensaku Sakamoto
- Laboratory for Nonnatural Amino Acid TechnologyRIKEN Center for Biosystems Dynamics ResearchYokohamaJapan
- Department of Drug Target Protein ResearchShinshu University School of MedicineNaganoJapan
| | - Kazumasa Ohtake
- Laboratory for Nonnatural Amino Acid TechnologyRIKEN Center for Biosystems Dynamics ResearchYokohamaJapan
- Department of Electrical Engineering and BioscienceWaseda UniversityTokyoJapan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Tetsuro Watabe
- Department of Biochemistry, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Shigeyuki Yokoyama
- Department of Drug Target Protein ResearchShinshu University School of MedicineNaganoJapan
- Laboratory for Protein Function and Structural BiologyRIKEN Cluster for Science, Technology and Innovation HubYokohamaJapan
- Department of Structural Biology and Biochemistry, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Miki Hara‐Yokoyama
- Department of Biochemistry, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
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21
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Liu L, Gray JL, Tate EW, Yang A. Bacterial enzymes: powerful tools for protein labeling, cell signaling, and therapeutic discovery. Trends Biotechnol 2023; 41:1385-1399. [PMID: 37328400 DOI: 10.1016/j.tibtech.2023.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/01/2023] [Accepted: 05/16/2023] [Indexed: 06/18/2023]
Abstract
Bacteria have evolved a diverse set of enzymes that enable them to subvert host defense mechanisms as well as to form part of the prokaryotic immune system. Due to their unique and varied biochemical activities, these bacterial enzymes have emerged as key tools for understanding and investigating biological systems. In this review, we summarize and discuss some of the most prominent bacterial enzymes used for the site-specific modification of proteins, in vivo protein labeling, proximity labeling, interactome mapping, signaling pathway manipulation, and therapeutic discovery. Finally, we provide a perspective on the complementary advantages and limitations of using bacterial enzymes compared with chemical probes for exploring biological systems.
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Affiliation(s)
- Lu Liu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Janine L Gray
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK.
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China.
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22
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Sarhadi TR, Panse JS, Nagotu S. Mind the gap: Methods to study membrane contact sites. Exp Cell Res 2023; 431:113756. [PMID: 37633408 DOI: 10.1016/j.yexcr.2023.113756] [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: 03/28/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/28/2023]
Abstract
Organelles are dynamic entities whose functions are essential for the optimum functioning of cells. It is now known that the juxtaposition of organellar membranes is essential for the exchange of metabolites and their communication. These functional apposition sites are termed membrane contact sites. Dynamic membrane contact sites between various sub-cellular structures such as mitochondria, endoplasmic reticulum, peroxisomes, Golgi apparatus, lysosomes, lipid droplets, plasma membrane, endosomes, etc. have been reported in various model systems. The burgeoning area of research on membrane contact sites has witnessed several manuscripts in recent years that identified the contact sites and components involved. Several methods have been developed to identify, measure and analyze the membrane contact sites. In this manuscript, we aim to discuss important methods developed to date that are used to study membrane contact sites.
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Affiliation(s)
- Tanveera Rounaque Sarhadi
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Janhavee Shirish Panse
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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23
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Guo J, Guo S, Lu S, Gong J, Wang L, Ding L, Chen Q, Liu W. The development of proximity labeling technology and its applications in mammals, plants, and microorganisms. Cell Commun Signal 2023; 21:269. [PMID: 37777761 PMCID: PMC10544124 DOI: 10.1186/s12964-023-01310-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/07/2023] [Indexed: 10/02/2023] Open
Abstract
Protein‒protein, protein‒RNA, and protein‒DNA interaction networks form the basis of cellular regulation and signal transduction, making it crucial to explore these interaction networks to understand complex biological processes. Traditional methods such as affinity purification and yeast two-hybrid assays have been shown to have limitations, as they can only isolate high-affinity molecular interactions under nonphysiological conditions or in vitro. Moreover, these methods have shortcomings for organelle isolation and protein subcellular localization. To address these issues, proximity labeling techniques have been developed. This technology not only overcomes the limitations of traditional methods but also offers unique advantages in studying protein spatial characteristics and molecular interactions within living cells. Currently, this technique not only is indispensable in research on mammalian nucleoprotein interactions but also provides a reliable approach for studying nonmammalian cells, such as plants, parasites and viruses. Given these advantages, this article provides a detailed introduction to the principles of proximity labeling techniques and the development of labeling enzymes. The focus is on summarizing the recent applications of TurboID and miniTurbo in mammals, plants, and microorganisms. Video Abstract.
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Affiliation(s)
- Jieyu Guo
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Shuang Guo
- Medicine Research Institute, Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Siao Lu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Jun Gong
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Long Wang
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Liqiong Ding
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Qingjie Chen
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
| | - Wu Liu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
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24
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Yamanaka S, Furihata H, Yanagihara Y, Taya A, Nagasaka T, Usui M, Nagaoka K, Shoya Y, Nishino K, Yoshida S, Kosako H, Tanokura M, Miyakawa T, Imai Y, Shibata N, Sawasaki T. Lenalidomide derivatives and proteolysis-targeting chimeras for controlling neosubstrate degradation. Nat Commun 2023; 14:4683. [PMID: 37596276 PMCID: PMC10439208 DOI: 10.1038/s41467-023-40385-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 07/21/2023] [Indexed: 08/20/2023] Open
Abstract
Lenalidomide, an immunomodulatory drug (IMiD), is commonly used as a first-line therapy in many haematological cancers, such as multiple myeloma (MM) and 5q myelodysplastic syndromes (5q MDS), and it functions as a molecular glue for the protein degradation of neosubstrates by CRL4CRBN. Proteolysis-targeting chimeras (PROTACs) using IMiDs with a target protein binder also induce the degradation of target proteins. The targeted protein degradation (TPD) of neosubstrates is crucial for IMiD therapy. However, current IMiDs and IMiD-based PROTACs also break down neosubstrates involved in embryonic development and disease progression. Here, we show that 6-position modifications of lenalidomide are essential for controlling neosubstrate selectivity; 6-fluoro lenalidomide induced the selective degradation of IKZF1, IKZF3, and CK1α, which are involved in anti-haematological cancer activity, and showed stronger anti-proliferative effects on MM and 5q MDS cell lines than lenalidomide. PROTACs using these lenalidomide derivatives for BET proteins induce the selective degradation of BET proteins with the same neosubstrate selectivity. PROTACs also exert anti-proliferative effects in all examined cell lines. Thus, 6-position-modified lenalidomide is a key molecule for selective TPD using thalidomide derivatives and PROTACs.
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Affiliation(s)
- Satoshi Yamanaka
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
- Division of Proteo-Interactome, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Hirotake Furihata
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Yuta Yanagihara
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, 791-0295, Japan
| | - Akihito Taya
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Takato Nagasaka
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Mai Usui
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Koya Nagaoka
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Yuki Shoya
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Shuhei Yoshida
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, 791-0295, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Yuuki Imai
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, 791-0295, Japan
| | - Norio Shibata
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan.
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25
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Wang Y, Li W, Ye B, Bi X. Chemical and Biological Strategies for Profiling Protein-Protein Interactions in Living Cells. Chem Asian J 2023; 18:e202300226. [PMID: 37089007 PMCID: PMC10946512 DOI: 10.1002/asia.202300226] [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: 03/16/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/25/2023]
Abstract
Protein-protein interactions (PPIs) play critical roles in almost all cellular signal transduction events. Characterization of PPIs without interfering with the functions of intact cells is very important for basic biology study and drug developments. However, the ability to profile PPIs especially those weak/transient interactions in their native states remains quite challenging. To this end, many endeavors are being made in developing new methods with high efficiency and strong operability. By coupling with advanced fluorescent microscopy and mass spectroscopy techniques, these strategies not only allow us to visualize the subcellular locations and monitor the functions of protein of interest (POI) in real time, but also enable the profiling and identification of potential unknown interacting partners in high-throughput manner, which greatly facilitates the elucidation of molecular mechanisms underlying numerous pathophysiological processes. In this review, we will summarize the typical methods for PPIs identification in living cells and their principles, advantages and limitations will also be discussed in detail.
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Affiliation(s)
- You‐Yu Wang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
| | - Wenyi Li
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityVictoria3086Australia
| | - Bang‐Ce Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
| | - Xiao‐Bao Bi
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
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26
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Yamada K, Soga F, Tokunaga S, Nagaoka H, Ozawa T, Kishi H, Takashima E, Sawasaki T. GATS tag system is compatible with biotin labelling methods for protein analysis. Sci Rep 2023; 13:10243. [PMID: 37353572 PMCID: PMC10290147 DOI: 10.1038/s41598-023-36858-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/11/2023] [Indexed: 06/25/2023] Open
Abstract
Polypeptide tags and biotin labelling technologies are widely used for protein analyses in biochemistry and cell biology. However, many peptide tag epitopes contain lysine residues (or amino acids) that are masked after biotinylation. Here, we propose the GATS tag system without a lysine residue and with high sensitivity and low non-specific binding using a rabbit monoclonal antibody against Plasmodium falciparum glycosylphosphatidylinositol (GPI)-anchored micronemal antigen (PfGAMA). From 14 monoclonal clones, an Ra3 clone was selected as it recognized an epitope-TLSVGVQNTF-without a lysine residue; this antibody and epitope tag set was called the GATS tag system. Surface plasmon resonance analysis showed that the tag system had a high affinity of 8.71 × 10-9 M. GATS tag indicated a very low background with remarkably high sensitivity and specificity in immunoblotting using the lysates of mammalian cells. It also showed a high sensitivity for immunoprecipitation and immunostaining of cultured human cells. The tag system was highly sensitive in both biotin labelling methods for proteins using NHS-Sulfo-biotin and BioID (proximity-dependent biotin identification) in the human cells, as opposed to a commercially available tag system having lysine residues, which showed reduced sensitivity. These results showed that the GATS tag system is suitable for methods such as BioID involving labelling lysine residues.
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Affiliation(s)
- Kohdai Yamada
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Fumiya Soga
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Soh Tokunaga
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Hikaru Nagaoka
- Division of Malaria Research, Proteo-Science Center, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Tatsuhiko Ozawa
- Department of Immunology, Faculty of Medicine, Academic Assembly, Advanced Antibody Drug Development Center, University of Toyama, Toyama, 930-0194, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Faculty of Medicine, Academic Assembly, Advanced Antibody Drug Development Center, University of Toyama, Toyama, 930-0194, Japan
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan.
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27
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Abstract
Proteins are workhorses in the cell; they form stable and more often dynamic, transient protein-protein interactions, assemblies, and networks and have an intimate interplay with DNA and RNA. These network interactions underlie fundamental biological processes and play essential roles in cellular function. The proximity-dependent biotinylation labeling approach combined with mass spectrometry (PL-MS) has recently emerged as a powerful technique to dissect the complex cellular network at the molecular level. In PL-MS, by fusing a genetically encoded proximity-labeling (PL) enzyme to a protein or a localization signal peptide, the enzyme is targeted to a protein complex of interest or to an organelle, allowing labeling of proximity proteins within a zoom radius. These biotinylated proteins can then be captured by streptavidin beads and identified and quantified by mass spectrometry. Recently engineered PL enzymes such as TurboID have a much-improved enzymatic activity, enabling spatiotemporal mapping with a dramatically increased signal-to-noise ratio. PL-MS has revolutionized the way we perform proteomics by overcoming several hurdles imposed by traditional technology, such as biochemical fractionation and affinity purification mass spectrometry. In this review, we focus on biotin ligase-based PL-MS applications that have been, or are likely to be, adopted by the plant field. We discuss the experimental designs and review the different choices for engineered biotin ligases, enrichment, and quantification strategies. Lastly, we review the validation and discuss future perspectives.
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Affiliation(s)
- Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Ruben Shrestha
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
| | - Sumudu S Karunadasa
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
| | - Pei-Qiao Xie
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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28
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Sim J, Lee A, Kim D, Kim KL, Park BJ, Park KM, Kim K. A Combination of Bio-Orthogonal Supramolecular Clicking and Proximity Chemical Tagging as a Supramolecular Tool for Discovery of Putative Proteins Associated with Laminopathic Disease. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2208088. [PMID: 36843266 DOI: 10.1002/smll.202208088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/08/2023] [Indexed: 05/25/2023]
Abstract
Protein mutations alter protein-protein interactions that can lead to a number of illnesses. Mutations in lamin A (LMNA) have been reported to cause laminopathies. However, the proteins associated with the LMNA mutation have mostly remained unexplored. Herein, a new chemical tool for proximal proteomics is reported, developed by a combination of proximity chemical tagging and a bio-orthogonal supramolecular latching based on cucurbit[7]uril (CB[7])-based host-guest interactions. As this host-guest interaction acts as a noncovalent clickable motif that can be unclicked on-demand, this new chemical tool is exploited for reliable detection of the proximal proteins of LMNA and its mutant that causes laminopathic dilated cardiomyopathy (DCM). Most importantly, a comparison study reveals, for the first time, mutant-dependent alteration in LMNA proteomic environments, which allows to identify putative laminopathic DCM-linked proteins including FOXJ3 and CELF2. This study demonstrates the feasibility of this chemical tool for reliable proximal proteomics, and its immense potential as a new research platform for discovering biomarkers associated with protein mutation-linked diseases.
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Affiliation(s)
- Jaehwan Sim
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Ara Lee
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 37673, Republic of Korea
- Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Dasom Kim
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Kyung Lock Kim
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 37673, Republic of Korea
| | - Bum-Joon Park
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Kyeng Min Park
- Department of Biochemistry, Daegu Catholic University School of Medicine, Daegu, 42471, Republic of Korea
| | - Kimoon Kim
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
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29
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Inoue R, Fukutani Y, Niwa T, Matsunami H, Yohda M. Identification and Characterization of Proteins That Are Involved in RTP1S-Dependent Transport of Olfactory Receptors. Int J Mol Sci 2023; 24:ijms24097829. [PMID: 37175532 PMCID: PMC10177996 DOI: 10.3390/ijms24097829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Olfaction is mediated via olfactory receptors (ORs) that are expressed on the cilia membrane of olfactory sensory neurons in the olfactory epithelium. The functional expression of most ORs requires the assistance of receptor-transporting proteins (RTPs). We examined the interactome of RTP1S and OR via proximity biotinylation. Deubiquitinating protein VCIP135, the F-actin-capping protein sub-unit alpha-2, and insulin-like growth factor 2 mRNA-binding protein 2 were biotinylated via AirID fused with OR, RTP1S-AirID biotinylated heat shock protein A6 (HSPA6), and double-stranded RNA-binding protein Staufen homolog 2 (STAU2). Co-expression of HSPA6 partially enhanced the surface expression of Olfr544. The surface expression of Olfr544 increased by 50-80%. This effect was also observed when RTP1S was co-expressed. Almost identical results were obtained from the co-expression of STAU2. The interactions of HSPA6 and STAU2 with RTP1S were examined using a NanoBit assay. The results show that the RTP1S N-terminus interacted with the C-terminal domain of HSP6A and the N-terminal domain of STAU2. In contrast, OR did not significantly interact with STAU2 and HSPA6. Thus, HSP6A and STAU2 appear to be involved in the process of OR traffic through interaction with RTP1S.
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Affiliation(s)
- Ryosuke Inoue
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Yosuke Fukutani
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Tatsuya Niwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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30
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Nakamura KN, Yamauchi H, Mima H, Yerun C, Ohtsuka S, Magari M, Morishita R, Tokumitsu H. Rapid detection of calmodulin/target interaction via the proximity biotinylation method. Biochem Biophys Res Commun 2023; 659:29-33. [PMID: 37031591 DOI: 10.1016/j.bbrc.2023.03.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 03/29/2023] [Indexed: 04/04/2023]
Abstract
Calmodulin (CaM) is known to function as a central signal transducer in calcium-mediated intracellular pathways. In this study, a fusion molecule of a recently developed proximity biotinylation enzyme (AirID) with rat CaM (AirID-CaM) was expressed and purified to near homogeneity using an E. coli expression system to examine the physical interactions between CaM and its target proteins by converting the interaction to biotinylation of CaM targets under nondenatured conditions. AirID-CaM catalyzed a Ca2+-dependent biotinylation of a target protein kinase (Ca2+/CaM-dependent protein kinase kinase α/1, CaMKKα/1) in vitro, which was suppressed by the addition of excess amounts of CaM, and AirID alone did not catalyze the biotinylation of CaMKKα/1, indicating that the biotinylation of CaMKKα/1 by AirID-CaM likely occurs in an interaction-dependent manner. Furthermore, we also observed the Ca2+-dependent biotinylation of GST-CaMKIα and GST-CaMKIV by AirID-CaM, suggesting that AirID-CaM can be useful for the rapid detection of CaM/target interactions with relatively high sensitivity.
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31
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Schaack GA, Sullivan OM, Mehle A. Identifying Protein-Protein Interactions by Proximity Biotinylation with AirID and splitAirID. Curr Protoc 2023; 3:e702. [PMID: 36939277 PMCID: PMC10031415 DOI: 10.1002/cpz1.702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Proteins frequently function in high-order complexes. Defining protein-protein interactions is essential to acquiring a full understanding of their activity and regulation. Proximity biotinylation has emerged as a highly specific approach to capture transient and stable interactions in living cells or organisms. Proximity biotinylation exploits promiscuous biotinylating enzymes fused to a bait protein, resulting in the biotinylation of adjacent endogenous proteins. Biotinylated interactors are purified under very strict conditions and identified by mass spectrometry to obtain a high-confidence list of candidate binding partners. AirID is a recently described biotin ligase specifically engineered for proximity labeling. This protocol details proximity biotinylation by AirID, using protein complexes that form during a type I interferon response as an example. It covers the construction and validation of AirID fusion proteins and the enrichment and identification of biotinylated interactors. We describe a variation on the protocol using splitAirID. In this case, AirID is split into two inactive fragments and ligase activity is only restored upon dimerization of the bait proteins. This permits selective detection of proteins that interact with homo- or heterodimeric forms of the bait. The protocol considers design strategies, optimization, and the properties of different biotin ligases to identify optimal conditions for each experimental question. We also discuss common pitfalls and how to troubleshoot them. These approaches allow proximity biotinylation to be a powerful tool for defining protein interactomes. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Construction and functional validation of AirID fusion proteins Alternate Protocol: Construction and functional validation of splitAirID fusion proteins Support Protocol: Western blot for biotinylated proteins Basic Protocol 2: Biotinylation, enrichment, and identification of protein interactors.
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Affiliation(s)
| | | | - Andrew Mehle
- Department of Medical Microbiology & Immunology, University of Wisconsin – Madison, Madison, WI 53706, USA
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32
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Pei J, Xiao Y, Liu X, Hu W, Sobh A, Yuan Y, Zhou S, Hua N, Mackintosh SG, Zhang X, Basso KB, Kamat M, Yang Q, Licht JD, Zheng G, Zhou D, Lv D. Piperlongumine conjugates induce targeted protein degradation. Cell Chem Biol 2023; 30:203-213.e17. [PMID: 36750097 PMCID: PMC10074544 DOI: 10.1016/j.chembiol.2023.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/31/2022] [Accepted: 01/17/2023] [Indexed: 02/09/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that degrade target proteins through recruiting E3 ligases. However, their application is limited in part because few E3 ligases can be recruited by known E3 ligase ligands. In this study, we identified piperlongumine (PL), a natural product, as a covalent E3 ligase recruiter, which induces CDK9 degradation when it is conjugated with SNS-032, a CDK9 inhibitor. The lead conjugate 955 can potently degrade CDK9 in a ubiquitin-proteasome-dependent manner and is much more potent than SNS-032 against various tumor cells in vitro. Mechanistically, we identified KEAP1 as the E3 ligase recruited by 955 to degrade CDK9 through a TurboID-based proteomics study, which was further confirmed by KEAP1 knockout and the nanoBRET ternary complex formation assay. In addition, PL-ceritinib conjugate can degrade EML4-ALK fusion oncoprotein, suggesting that PL may have a broader application as a covalent E3 ligase ligand in targeted protein degradation.
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Affiliation(s)
- Jing Pei
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Xingui Liu
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Wanyi Hu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Amin Sobh
- Division of Hematology/Oncology, University of Florida Health Cancer Center, 2033 Mowry Road, Suite 145, Gainesville, FL 32610, USA
| | - Yaxia Yuan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Shuo Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Nan Hua
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 803, Little Rock, AR 72205, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Kari B Basso
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Manasi Kamat
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Qingping Yang
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Jonathan D Licht
- Division of Hematology/Oncology, University of Florida Health Cancer Center, 2033 Mowry Road, Suite 145, Gainesville, FL 32610, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA.
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA; Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Dongwen Lv
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA; Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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33
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Melkonian K, Stolze SC, Harzen A, Nakagami H. Proximity-Dependent In Vivo Biotin Labeling for Interactome Mapping in Marchantia polymorpha. Methods Mol Biol 2023; 2581:295-308. [PMID: 36413326 DOI: 10.1007/978-1-0716-2784-6_21] [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] [Indexed: 06/16/2023]
Abstract
Weak or transient protein-protein interactions (PPIs) are involved in a manifold of cellular processes in all living organisms, including plants. However, many of these interactions may remain undiscovered by co-immunoprecipitation (Co-IP) approaches due to their low binding affinities or transitory nature. Enzyme-mediated proximity-dependent in vivo biotin labeling can be a powerful strategy to efficiently capture weak and transient PPIs and has been successfully applied in different model angiosperm species. Here, we provide an optimized and robust protocol for biotin ligase-mediated proximity labeling for interactome mapping in the model liverwort Marchantia polymorpha.
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Affiliation(s)
- Katharina Melkonian
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Sara Christina Stolze
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Anne Harzen
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hirofumi Nakagami
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Cologne, Germany.
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Cologne, Germany.
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Detection of Recombinant Proteins SOX2 and OCT4 Interacting in HEK293T Cells Using Real-Time Quantitative PCR. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010107. [PMID: 36676054 PMCID: PMC9862934 DOI: 10.3390/life13010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022]
Abstract
In vivo biotinylation using wild-type and mutants of biotin ligases is now widely applied for the study of cellular proteomes. The commercial availability of kits for the highly efficient purification of biotinylated proteins and their excellent compatibility with LC-MS/MS protocols are the main reasons for the choice of biotin ligases. Since they are all enzymes, however, just a very low expression in cells is required for experiments. Therefore, it can be difficult to perform the quantifications of these enzymes in various samples. Traditional methods, such as western blotting, are not always fit for the detection of the expression levels. Therefore, real-time qRT-PCR, a technology that is more sensitive, was used in this study to quantify the expression of BirA fusions. Using this method, we detected high expression levels of BirA fusions in models of interactions of pluripotency transcription factors to carry out their relative quantification. We also found the absence of the competing endogenous proteins SOX2 and OCT4, as well as no cross-reactivity between BAP/BirA and the endogenous biotinylation system in HEK293T cells. Thus, these data indicated that the high level of biotinylation is due to the in vivo interaction of BAP-X and BirA-Y (X,Y = SOX2, OCT4) in the cell rather than their random collision, a big difference in the expression level of BirA fusions across samples or endogenous biotinylation.
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35
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Oliveira RJD. Coordinate-Dependent Drift-Diffusion Reveals the Kinetic Intermediate Traps of Top7-Based Proteins. J Phys Chem B 2022; 126:10854-10869. [PMID: 36519977 DOI: 10.1021/acs.jpcb.2c07031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The computer-designed Top7 served as a scaffold to produce immunoreactive proteins by grafting of the 2F5 HIV-1 antibody epitope (Top7-2F5) followed by biotinylation (Top7-2F5-biotin). The resulting nonimmunoglobulin affinity proteins were effective in inducing and detecting the HIV-1 antibody. However, the grafted Top7-2F5 design led to protein aggregation, as opposed to the soluble biotinylated Top7-2F5-biotin. The structure-based model predicted that the thermodynamic cooperativity of Top7 increases after grafting and biotin-labeling, reducing their intermediate state populations. In this work, the folding kinetic traps that might contribute to the aggregation propensity are investigated by the diffusion theory. Since the engineered proteins have similar sequence and structural homology, they served as protein models to study the kinetic intermediate traps that were uncovered by characterizing the position-dependent drift-velocity (v(Q)) and the diffusion (D(Q)) coefficients. These coordinate-dependent coefficients were taken into account to obtain the folding and transition path times over the free energy transition states containing the intermediate kinetic traps. This analysis may be useful to predict the aggregated kinetic traps of scaffold-epitope proteins that might compose novel diagnostic and therapeutic platforms.
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Affiliation(s)
- Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG38064-200, Brazil
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36
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Alternative splicing liberates a cryptic cytoplasmic isoform of mitochondrial MECR that antagonizes influenza virus. PLoS Biol 2022; 20:e3001934. [PMID: 36542656 PMCID: PMC9815647 DOI: 10.1371/journal.pbio.3001934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Viruses must balance their reliance on host cell machinery for replication while avoiding host defense. Influenza A viruses are zoonotic agents that frequently switch hosts, causing localized outbreaks with the potential for larger pandemics. The host range of influenza virus is limited by the need for successful interactions between the virus and cellular partners. Here we used immunocompetitive capture-mass spectrometry to identify cellular proteins that interact with human- and avian-style viral polymerases. We focused on the proviral activity of heterogenous nuclear ribonuclear protein U-like 1 (hnRNP UL1) and the antiviral activity of mitochondrial enoyl CoA-reductase (MECR). MECR is localized to mitochondria where it functions in mitochondrial fatty acid synthesis (mtFAS). While a small fraction of the polymerase subunit PB2 localizes to the mitochondria, PB2 did not interact with full-length MECR. By contrast, a minor splice variant produces cytoplasmic MECR (cMECR). Ectopic expression of cMECR shows that it binds the viral polymerase and suppresses viral replication by blocking assembly of viral ribonucleoprotein complexes (RNPs). MECR ablation through genome editing or drug treatment is detrimental for cell health, creating a generic block to virus replication. Using the yeast homolog Etr1 to supply the metabolic functions of MECR in MECR-null cells, we showed that specific antiviral activity is independent of mtFAS and is reconstituted by expressing cMECR. Thus, we propose a strategy where alternative splicing produces a cryptic antiviral protein that is embedded within a key metabolic enzyme.
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37
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Kajimoto S, Ohashi M, Hagiwara Y, Takahashi D, Mihara Y, Motoyama T, Ito S, Nakano S. Enzymatic Conjugation of Modified RNA Fragments by Ancestral RNA Ligase AncT4_2. Appl Environ Microbiol 2022; 88:e0167922. [PMID: 36416557 PMCID: PMC9746290 DOI: 10.1128/aem.01679-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Abstract
Oligonucleotide therapeutics have great potential as a next-generation approach to treating intractable diseases. Large quantities of modified DNA/RNA containing xenobiotic nucleic acids (XNAs) must be synthesized before clinical application. In this study, the ancestral RNA ligase AncT4_2 was designed by ancestral sequence reconstruction (ASR) to perform the conjugation reaction of modified RNA fragments. AncT4_2 had superior properties to native RNA ligase 2 from T4 phage (T4Rnl2), including high productivity, a >2.5-fold-higher turnover number, and >10°C higher thermostability. One remarkable point is the broad substrate selectivity of AncT4_2; the activity of AncT4_2 toward 17 of the modified RNA fragments was higher than that of T4Rnl2. The activity was estimated by measuring the conjugation reaction of two RNA strands, 3'-OH (12 bp) and 5'-PO4 (12 bp), in which the terminal and penultimate positions of the 3'-OH fragment and the first and second positions of the 5'-PO4 fragment were substituted by 2'-fluoro, 2'-O-methyl, 2'-O-methoxyethyl, and 2'-H, respectively. The enzymatic properties of AncT4_2 allowed the enzyme to conjugate large quantities of double-stranded RNA coding for patisiran (>400 μM level), which was formed by four RNA fragments containing 2'-OMe-substituted nucleic acids. Structural analysis of modeled AncT4_2 suggested that protein dynamics were changed by mutation to Gly or indel during ASR and that this may positively impact the conjugation of modified RNA fragments with the enzyme. AncT4_2 is expected to be a key biocatalyst in synthesizing RNA therapeutics by an enzymatic reaction. IMPORTANCE RNA therapeutics is one of the next-generation medicines for treating various diseases. Our designed ancestral RNA ligase AncT4_2 exhibited excellent enzymatic properties, such as high thermal stability, productivity, specific activity, and broad substrate selectivity compared to native enzymes. These advantages create the potential for AncT4_2 to be applied in conjugating the modified RNA fragments containing various xenobiotic nucleic acids. In addition, patisiran, a known polyneuropathy therapeutic, could be synthesized from four fragmented oligonucleotides at a preparative scale. Taken together, these findings indicate AncT4_2 could open the door to synthesizing RNA therapeutics by enzymatic reaction at large-scale production.
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Affiliation(s)
- Shohei Kajimoto
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki, Kanagawa, Japan
| | - Miwa Ohashi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki, Kanagawa, Japan
| | - Yusuke Hagiwara
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki, Kanagawa, Japan
| | - Daisuke Takahashi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki, Kanagawa, Japan
| | - Yasuhiro Mihara
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki, Kanagawa, Japan
| | - Tomoharu Motoyama
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Shizuoka, Japan
| | - Sohei Ito
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Shizuoka, Japan
| | - Shogo Nakano
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Shizuoka, Japan
- PREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
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38
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Motoyama T, Yamamoto Y, Ishida C, Hasebe F, Kawamura Y, Shigeta Y, Ito S, Nakano S. Reaction Mechanism of Ancestral l-Lys α-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis. ACS OMEGA 2022; 7:44407-44419. [PMID: 36506213 PMCID: PMC9730747 DOI: 10.1021/acsomega.2c06334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
The flavin-dependent amine oxidase superfamily contains various l-amino acid oxidases (LAAOs) bearing different substrate specificities and enzymatic properties. LAAOs catalyze the oxidation of the α-amino group of l-amino acids (L-AAs) to produce imino acids and H2O2. In this study, an ancestral l-Lys α-oxidase (AncLLysO2) was designed utilizing genome-mined sequences from the Caulobacter species. The AncLLysO2 exhibited high specificity toward l-Lys; the k cat/K m values toward l-Lys were one and two orders larger than those of l-Arg and l-ornithine, respectively. Liquid chromatography-high resolution mass spectrometry analysis indicated that AncLLysO2 released imino acid immediately from the active site after completion of oxidation of the α-amino group. Crystal structures of the ligand-free, l-Lys- and l-Arg-bound forms of AncLLysO2 were determined at 1.4-1.6 Å resolution, indicating that the active site of AncLLysO2 kept an open state during the reaction and more likely to release products. The structures also indicated the substrate recognition mechanism of AncLLysO2; ε-amino, α-amino, and carboxyl groups of l-Lys formed interactions with Q357, A551, and R77, respectively. Biochemical and molecular dynamics simulation analysis of AncLLysO2 indicated that active site residues that indirectly interact with the substrate are also important to exhibit high activity; for example, the aromatic group of Y219 is important to ensure that the l-Lys substrate is placed in the correct position to allow the reaction to proceed efficiently. Taken together, we propose the reaction mechanism of AncLLysO2.
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Affiliation(s)
- Tomoharu Motoyama
- Graduate
Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yuta Yamamoto
- Department
of Physics, Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Chiharu Ishida
- Graduate
Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Fumihito Hasebe
- Department
of Bioscience, Fukui Prefectural University, Fukui 910-1195, Japan
| | - Yui Kawamura
- Graduate
Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yasuteru Shigeta
- Center
for Computational Sciences, University of
Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8577, Japan
| | - Sohei Ito
- Graduate
Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Shogo Nakano
- Graduate
Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
- PREST, Japan Science and Technology
Agency, Saitama 332-0012, Japan
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39
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Studying the ubiquitin code through biotin-based labelling methods. Semin Cell Dev Biol 2022; 132:109-119. [PMID: 35181195 DOI: 10.1016/j.semcdb.2022.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/15/2022]
Abstract
Post-translational modifications of cellular substrates by members of the ubiquitin (Ub) and ubiquitin-like (UbL) family are crucial for regulating protein homeostasis in organisms. The term "ubiquitin code" encapsulates how this diverse family of modifications, via adding single UbLs or different types of UbL chains, leads to specific fates for substrates. Cancer, neurodegeneration and other conditions are sometimes linked to underlying errors in this code. Studying these modifications in cells is particularly challenging since they are usually transient, scarce, and compartment-specific. Advances in the use of biotin-based methods to label modified proteins, as well as their proximally-located interactors, facilitate isolation and identification of substrates, modification sites, and the enzymes responsible for writing and erasing these modifications, as well as factors recruited as a consequence of the substrate being modified. In this review, we discuss site-specific and proximity biotinylation approaches being currently applied for studying modifications by UbLs, highlighting the pros and cons, with mention of complementary methods when possible. Future improvements may come from bioengineering and chemical biology but even now, biotin-based technology is uncovering new substrates and regulators, expanding potential therapeutic targets to manipulate the Ub code.
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40
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Mathew B, Bathla S, Williams KR, Nairn AC. Deciphering Spatial Protein-Protein Interactions in Brain Using Proximity Labeling. Mol Cell Proteomics 2022; 21:100422. [PMID: 36198386 PMCID: PMC9650050 DOI: 10.1016/j.mcpro.2022.100422] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 01/18/2023] Open
Abstract
Cellular biomolecular complexes including protein-protein, protein-RNA, and protein-DNA interactions regulate and execute most biological functions. In particular in brain, protein-protein interactions (PPIs) mediate or regulate virtually all nerve cell functions, such as neurotransmission, cell-cell communication, neurogenesis, synaptogenesis, and synaptic plasticity. Perturbations of PPIs in specific subsets of neurons and glia are thought to underly a majority of neurobiological disorders. Therefore, understanding biological functions at a cellular level requires a reasonably complete catalog of all physical interactions between proteins. An enzyme-catalyzed method to biotinylate proximal interacting proteins within 10 to 300 nm of each other is being increasingly used to characterize the spatiotemporal features of complex PPIs in brain. Thus, proximity labeling has emerged recently as a powerful tool to identify proteomes in distinct cell types in brain as well as proteomes and PPIs in structures difficult to isolate, such as the synaptic cleft, axonal projections, or astrocyte-neuron junctions. In this review, we summarize recent advances in proximity labeling methods and their application to neurobiology.
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Affiliation(s)
- Boby Mathew
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA.
| | - Shveta Bathla
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Department of Psychiatry, Yale University, New Haven, Connecticut, USA
| | - Kenneth R Williams
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Department of Psychiatry, Yale University, New Haven, Connecticut, USA.
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41
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Switching of Photocatalytic Tyrosine/Histidine Labeling and Application to Photocatalytic Proximity Labeling. Int J Mol Sci 2022; 23:ijms231911622. [PMID: 36232972 PMCID: PMC9569449 DOI: 10.3390/ijms231911622] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022] Open
Abstract
Weak and transient protein interactions are involved in dynamic biological responses and are an important research subject; however, methods to elucidate such interactions are lacking. Proximity labeling is a promising technique for labeling transient ligand–binding proteins and protein–protein interaction partners of analytes via an irreversible covalent bond. Expanding chemical tools for proximity labeling is required to analyze the interactome. We developed several photocatalytic proximity-labeling reactions mediated by two different mechanisms. We found that numerous dye molecules can function as catalysts for protein labeling. We also identified catalysts that selectively modify tyrosine and histidine residues and evaluated their mechanisms. Model experiments using HaloTag were performed to demonstrate photocatalytic proximity labeling. We found that both ATTO465, which catalyzes labeling by a single electron transfer, and BODIPY, which catalyzes labeling by singlet oxygen, catalyze proximity labeling in cells.
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42
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Polo-Like Kinase 2 Plays an Essential Role in Cytoprotection against MG132-Induced Proteasome Inhibition via Phosphorylation of Serine 19 in HSPB5. Int J Mol Sci 2022; 23:ijms231911257. [PMID: 36232565 PMCID: PMC9569985 DOI: 10.3390/ijms231911257] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/27/2022] [Accepted: 09/10/2022] [Indexed: 11/17/2022] Open
Abstract
Protein homeostasis, including protein folding, refolding, and degradation, is thought to decline with aging. HSPB5 (also known as αB-crystallin) prevents target protein aggregation as a molecular chaperone and exhibits a cytoprotective function against various cell stresses. To elucidate the effect of HSPB5 on endoplasmic reticulum (ER) stress, we searched for novel binding proteins of HSPB5 using the proximity-dependent biotin labeling method. Proteins presumed to interact with HSPB5 in cells treated with the proteasome inhibitor MG132 were identified by a reversible biotin-binding capacity method combining tamavidin2-REV magnetic beads and mass spectrometry. We discovered a new binding protein for HSPB5, polo-like kinase 2 (PLK2), which is an apoptosis-related enzyme. The expression of PLK2 was upregulated by MG132 treatment, and it was co-localized with HSPB5 near the ER in L6 muscle cells. Inhibition of PLK2 decreased ER stress-induced phosphorylation of serine 19 in HSPB5 and increased apoptosis by activation of caspase 3 under ER stress. Overexpression of HSPB5 (WT) suppressed the ER stress-induced caspase 3 activity, but this was not observed with phospho-deficient HSPB5 (3A) mutants. These results clarify the role of HSPB5 phosphorylation during ER stress and suggest that the PLK2/HSPB5 pathway plays an essential role in cytoprotection against proteasome inhibition-induced ER stress.
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43
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Kotani N, Araki T, Miyagawa-Yamaguchi A, Amimoto T, Nakano M, Honke K. Proximity Labeling and Proteomics: Get to Know Neighbors. Methods Enzymol 2022; 679:131-162. [PMID: 36682860 DOI: 10.1016/bs.mie.2022.07.031] [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] [Indexed: 01/25/2023]
Abstract
Protein-protein interactions are essential in biological reactions and fundamental to cell-cell communication (e.g., the binding of secreted proteins, such as hormones, to cell membrane receptors) and the subsequent intracellular signal transduction cascade. Several studies have been extensively carried out on protein-protein interactions because they have the potential to resolve various problems in molecular biology. Biochemical methods, such as chemical cross-linking and immunoprecipitation, have long been used to analyze which proteins interact with each other. However, there are some problems, such as unphysiological states and non-specific binding, that require the development of more useful experimental methods. This chapter discusses the "proximity labeling (Proteomics)" analysis technique, which has been attracting attention in protein-protein interaction analysis in recent years and is used in many biological studies. "Membrane proximity labeling (proteomics)," which analyzes the interaction of cell membrane proteins, and "intracellular proximity labeling (proteomics)" will be explained in-depth.
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Affiliation(s)
- Norihiro Kotani
- Medical Research Center, Saitama Medical University, Saitama, Japan; Department of Biochemistry, Saitama Medical University, Saitama, Japan.
| | - Tomoyuki Araki
- Department of Biochemistry, Saitama Medical University, Saitama, Japan
| | | | - Tomoko Amimoto
- Natural Science Center for Basic Research and Development, Hiroshima University, Higashi-Hiroshima, Japan
| | - Miyako Nakano
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Koichi Honke
- Department of Biochemistry, Kochi University Medical School, Nankoku, Japan
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44
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CRISPR-Guided Proximity Labeling of RNA–Protein Interactions. Genes (Basel) 2022; 13:genes13091549. [PMID: 36140717 PMCID: PMC9498842 DOI: 10.3390/genes13091549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 12/02/2022] Open
Abstract
Proximity labeling employs modified biotin ligases or peroxidases that produce reactive radicals to covalently label proximate proteins with biotin in living cells. The resulting biotinylated proteins can then be isolated and identified. A combination of programmable DNA targeting and proximity labeling that maps proteomic landscape at DNA elements with dCas9-APEX2 has been established in living cells. However, defining interactome at RNA elements has lagged behind. In combination with RNA-targeting CRISPR-Cas13, proximity labeling can also be used to identify proteins that interact with specific RNA elements in living cells. From this viewpoint, we briefly summarize the latest advances in CRISPR-guided proximity labeling in studying RNA–protein interactions, and we propose applying the most recent engineered proximity-labeling enzymes to study RNA-centric interactions in the future.
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45
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James Sanford E, Bustamante Smolka M. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 2022; 22:e2200064. [PMID: 35695711 PMCID: PMC9950963 DOI: 10.1002/pmic.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/15/2022]
Abstract
All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.
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Key Words
- LC-MS/MS, technology, bottom-up proteomics, technology, signal transduction, cell biology
- phosphoproteomics, technology, post-translational modification analysis, technology, post-translational modifications, cell biology, mass spectrometry
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Affiliation(s)
- Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853,Corresponding author:
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46
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Lin Z, Woo CM. Methods to characterize and discover molecular degraders in cells. Chem Soc Rev 2022; 51:7115-7137. [PMID: 35899832 DOI: 10.1039/d2cs00261b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cells use many post-translational modifications (PTMs) to tailor proteins and transduce cellular signals. Recent years have witnessed the rapid growth of small molecule and enzymatic strategies to purposely manipulate one particular PTM, ubiquitination, on desired target proteins in cells. These approaches typically act by induced proximity between an E3 ligase and a target protein resulting in ubiquitination and degradation of the substrate in cells. In this review, we cover recent approaches to study molecular degraders and discover their induced substrates in vitro and in live cells. Methods that have been adapted and applied to the development of molecular degraders are described, including global proteomics, affinity-purification, chemical proteomics and enzymatic strategies. Extension of these strategies to edit additional PTMs in cells is also discussed. This review is intended to assist researchers who are interested in editing PTMs with new modalities to select suitable method(s) and guide their studies.
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Affiliation(s)
- Zhi Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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47
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Kubitz L, Bitsch S, Zhao X, Schmitt K, Deweid L, Roehrig A, Barazzone EC, Valerius O, Kolmar H, Béthune J. Engineering of ultraID, a compact and hyperactive enzyme for proximity-dependent biotinylation in living cells. Commun Biol 2022; 5:657. [PMID: 35788163 PMCID: PMC9253107 DOI: 10.1038/s42003-022-03604-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/20/2022] [Indexed: 12/11/2022] Open
Abstract
Proximity-dependent biotinylation (PDB) combined with mass spectrometry analysis has established itself as a key technology to study protein-protein interactions in living cells. A widespread approach, BioID, uses an abortive variant of the E. coli BirA biotin protein ligase, a quite bulky enzyme with slow labeling kinetics. To improve PDB versatility and speed, various enzymes have been developed by different approaches. Here we present a small-size engineered enzyme: ultraID. We show its practical use to probe the interactome of Argonaute-2 after a 10 min labeling pulse and expression at physiological levels. Moreover, using ultraID, we provide a membrane-associated interactome of coatomer, the coat protein complex of COPI vesicles. To date, ultraID is the smallest and most efficient biotin ligase available for PDB and offers the possibility of investigating interactomes at a high temporal resolution. A small-size engineered enzyme, ultraID, is presented for proximity-dependent biotinylation, that shows efficient labeling in mammalian cell culture, E. coli and S. cerevisiae.
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Affiliation(s)
- Lea Kubitz
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Sebastian Bitsch
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Xiyan Zhao
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Kerstin Schmitt
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Georg-August-University Göttingen, Göttingen, Germany
| | - Lukas Deweid
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.,Ferring Pharmaceuticals, Copenhagen, Denmark
| | - Amélie Roehrig
- Heidelberg University Biochemistry Center, Heidelberg, Germany.,Inserm UMRS1138 - FunGeST team, Paris, France
| | - Elisa Cappio Barazzone
- Heidelberg University Biochemistry Center, Heidelberg, Germany.,Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Oliver Valerius
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Georg-August-University Göttingen, Göttingen, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Julien Béthune
- Department of Biotechnology, Hamburg University of Applied Sciences, Hamburg, Germany.
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48
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Sanada T, Yamaguchi J, Furuta Y, Kakuta S, Tanida I, Uchiyama Y. In-resin CLEM of Epon-embedded cells using proximity labeling. Sci Rep 2022; 12:11130. [PMID: 35778550 PMCID: PMC9249884 DOI: 10.1038/s41598-022-15438-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/23/2022] [Indexed: 11/09/2022] Open
Abstract
Biotin ligases have been developed as proximity biotinylation enzymes for analyses of the interactome. However, there has been no report on the application of proximity labeling for in-resin correlative light-electron microscopy of Epon-embedded cells. In this study, we established a proximity-labeled in-resin CLEM of Epon-embedded cells using miniTurbo, a biotin ligase. Biotinylation by miniTurbo was observed in cells within 10 min following the addition of biotin to the medium. Using fluorophore-conjugated streptavidin, intracellular biotinylated proteins were labeled after fixation of cells with a mixture of paraformaldehyde and glutaraldehyde. Fluorescence of these proteins was resistant to osmium tetroxide staining and was detected in 100-nm ultrathin sections of Epon-embedded cells. Ultrastructures of organelles were preserved well in the same sections. Fluorescence in sections was about 14-fold brighter than that in the sections of Epon-embedded cells expressing mCherry2 and was detectable for 14 days. When mitochondria-localized miniTurbo was expressed in the cells, mitochondria-like fluorescent signals were detected in the sections, and ultrastructures of mitochondria were observed as fluorescence-positive structures in the same sections by scanning electron microscopy. Proximity labeling using miniTurbo led to more stable and brighter fluorescent signals in the ultrathin sections of Epon-embedded cells, resulting in better performance of in-resin CLEM.
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Affiliation(s)
- Takahito Sanada
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Junji Yamaguchi
- Laboratory of Morphology and Image Analysis, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yoko Furuta
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Soichiro Kakuta
- Laboratory of Morphology and Image Analysis, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Isei Tanida
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | - Yasuo Uchiyama
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, Tokyo, Japan.
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49
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CF-PPiD technology based on cell-free protein array and proximity biotinylation enzyme for in vitro direct interactome analysis. Sci Rep 2022; 12:10592. [PMID: 35732899 PMCID: PMC9217950 DOI: 10.1038/s41598-022-14872-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 06/14/2022] [Indexed: 12/04/2022] Open
Abstract
Protein–protein interaction (PPI) analysis is a key process to understand protein functions. Recently, we constructed a human protein array (20 K human protein beads array) consisting of 19,712 recombinant human proteins produced by a wheat cell-free protein production system. Here, we developed a cell-free protein array technology for proximity biotinylation-based PPI identification (CF-PPiD). The proximity biotinylation enzyme AirID-fused TP53 and -IκBα proteins each biotinylated specific interacting proteins on a 1536-well magnetic plate. In addition, AirID-fused cereblon was shown to have drug-inducible PPIs using CF-PPiD. Using the human protein beads array with AirID-IκBα, 132 proteins were biotinylated, and then selected clones showed these biological interactions in cells. Although ZBTB9 was not immunoprecipitated, it was highly biotinylated by AirID-IκBα, suggesting that this system detected weak interactions. These results indicated that CF-PPiD is useful for the biochemical identification of directly interacting proteins.
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50
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Freitas FC, Maldonado M, Oliveira Junior AB, Onuchic JN, Oliveira RJD. Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes. J Chem Phys 2022; 156:195101. [PMID: 35597640 DOI: 10.1063/5.0083875] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Biotin-labeled proteins are widely used as tools to study protein-protein interactions and proximity in living cells. Proteomic methods broadly employ proximity-labeling technologies based on protein biotinylation in order to investigate the transient encounters of biomolecules in subcellular compartments. Biotinylation is a post-translation modification in which the biotin molecule is attached to lysine or tyrosine residues. So far, biotin-based technologies proved to be effective instruments as affinity and proximity tags. However, the influence of biotinylation on aspects such as folding, binding, mobility, thermodynamic stability, and kinetics needs to be investigated. Here, we selected two proteins [biotin carboxyl carrier protein (BCCP) and FKBP3] to test the influence of biotinylation on thermodynamic and kinetic properties. Apo (without biotin) and holo (biotinylated) protein structures were used separately to generate all-atom structure-based model simulations in a wide range of temperatures. Holo BCCP contains one biotinylation site, and FKBP3 was modeled with up to 23 biotinylated lysines. The two proteins had their estimated thermodynamic stability changed by altering their energy landscape. In all cases, after comparison between the apo and holo simulations, differences were observed on the free-energy profiles and folding routes. Energetic barriers were altered with the density of states clearly showing changes in the transition state. This study suggests that analysis of large-scale datasets of biotinylation-based proximity experiments might consider possible alterations in thermostability and folding mechanisms imposed by the attached biotins.
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Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| | - Michelli Maldonado
- Departamento de Matemática, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| | - Antonio Bento Oliveira Junior
- Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St., Houston, Texas 77030, USA
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St., Houston, Texas 77030, USA
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
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