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Di Meo F, Kale B, Koomen JM, Perna F. Mapping the cancer surface proteome in search of target antigens for immunotherapy. Mol Ther 2024:S1525-0016(24)00474-X. [PMID: 39068512 DOI: 10.1016/j.ymthe.2024.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/26/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024] Open
Abstract
Immune-based therapeutic interventions recognizing proteins localized on the cell surface of cancer cells are emerging as a promising cancer treatment. Antibody-based therapies and engineered T cells are now approved by the Food and Drug Administration to treat some malignancies. These therapies utilize a few cell surface proteins highly expressed on cancer cells to release the negative regulation of immune activation that limits antitumor responses (e.g., PD-1, PD-L1, CTLA4) or to redirect the T cell specificity toward blood cancer cells (e.g., CD19 and B cell maturation antigen). One limitation preventing broader application of these novel therapeutic strategies to all cancer types is the lack of suitable target antigens for all indications owing in part to the challenges in identifying such targets. Ideal target antigens are cell surface proteins highly expressed on malignant cells and absent in healthy tissues. Technological advances in mass spectrometry, enrichment protocols, and computational tools for cell surface protein isolation and annotation have recently enabled comprehensive analyses of the cancer cell surface proteome, from which novel immunotherapeutic target antigens may emerge. Here, we review the most recent progress in this field.
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Affiliation(s)
- Francesco Di Meo
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Tampa, FL, USA
| | - Brandon Kale
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Tampa, FL, USA
| | - John M Koomen
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Fabiana Perna
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Tampa, FL, USA.
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2
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Bae J, Kim J, Choi J, Lee H, Koh M. Split Proteins and Reassembly Modules for Biological Applications. Chembiochem 2024; 25:e202400123. [PMID: 38530024 DOI: 10.1002/cbic.202400123] [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: 02/08/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Split systems, modular entities enabling controlled biological processes, have become instrumental in biological research. This review highlights their utility across applications like gene regulation, protein interaction identification, and biosensor development. Covering significant progress over the last decade, it revisits traditional split proteins such as GFP, luciferase, and inteins, and explores advancements in technologies like Cas proteins and base editors. We also examine reassembly modules and their applications in diverse fields, from gene regulation to therapeutic innovation. This review offers a comprehensive perspective on the recent evolution of split systems in biological research.
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Affiliation(s)
- Jieun Bae
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic Science, Soongsil University, Seoul, 06978, Republic of Korea
| | - Jongdoo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Hwiyeong Lee
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Minseob Koh
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
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3
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Kang M, Wang Z, Ge X. One-step production of fully biotinylated and glycosylated human Fc gamma receptors. Biotechnol Prog 2024; 40:e3392. [PMID: 37734055 PMCID: PMC10922510 DOI: 10.1002/btpr.3392] [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: 07/07/2023] [Revised: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
Initiating and regulating humoral immunity, Fc gamma receptors (FcγRs) have been identified both as therapeutics and as drug targets, and thus production of biologically active FcγRs is highly demanded for biopharmaceutical development. Focusing on low-affinity FcγRs IIA (131H/R allotypes), IIB, and IIIA (176F/V), this study used human 293-F cells to achieve correct post-translational modifications (PTMs) including biotinylation, N-glycosylation, and disulfides. Approaches involving co-expression of FcγR-AviTag and Escherichia coli biotin ligase BirA, endoplasmic reticulum retention, stable and transient transfections, and optimization of transgene ratio were investigated. Protein electrophoresis under reducing and non-reducing conditions, enzymatic deglycosylation, streptavidin pull-down assays, and binding kinetic analysis collectively indicated that the produced FcγR ectodomains were fully biotinylated, N-glycosylated, had formed disulfide bond, and exhibited expected binding affinities toward IgG1 trastuzumab and its Fc mutants. A clear trade-off between production yield and PTM quality was also observed. Achieving multiple types of PTMs completely by one-step cell culture should have applications for the production of a variety of complex proteins of biomedical importance.
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Affiliation(s)
- Minhyo Kang
- Department of Chemical and Environmental Engineering, University of California Riverside, CA, USA
- Present address: Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC Canada
| | - Zening Wang
- Department of Chemical and Environmental Engineering, University of California Riverside, CA, USA
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, TX, USA
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California Riverside, CA, USA
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, TX, USA
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4
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Ahmadian Elmi M, Motamed N, Picard D. Proteomic Analyses of the G Protein-Coupled Estrogen Receptor GPER1 Reveal Constitutive Links to Endoplasmic Reticulum, Glycosylation, Trafficking, and Calcium Signaling. Cells 2023; 12:2571. [PMID: 37947649 PMCID: PMC10650109 DOI: 10.3390/cells12212571] [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: 08/25/2023] [Revised: 10/14/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
The G protein-coupled estrogen receptor 1 (GPER1) has been proposed to mediate rapid responses to the steroid hormone estrogen. However, despite a strong interest in its potential role in cancer, whether it is indeed activated by estrogen and how this works remain controversial. To provide new tools to address these questions, we set out to determine the interactome of exogenously expressed GPER1. The combination of two orthogonal methods, namely APEX2-mediated proximity labeling and immunoprecipitation followed by mass spectrometry, gave us high-confidence results for 73 novel potential GPER1 interactors. We found that this GPER1 interactome is not affected by estrogen, a result that mirrors the constitutive activity of GPER1 in a functional assay with a Rac1 sensor. We specifically validated several hits highlighted by a gene ontology analysis. We demonstrate that CLPTM1 interacts with GPER1 and that PRKCSH and GANAB, the regulatory and catalytic subunits of α-glucosidase II, respectively, associate with CLPTM1 and potentially indirectly with GPER1. An imbalance in CLPTM1 levels induces nuclear association of GPER1, as does the overexpression of PRKCSH. Moreover, we show that the Ca2+ sensor STIM1 interacts with GPER1 and that upon STIM1 overexpression and depletion of Ca2+ stores, GPER1 becomes more nuclear. Thus, these new GPER1 interactors establish interesting connections with membrane protein maturation, trafficking, and calcium signaling.
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Affiliation(s)
- Maryam Ahmadian Elmi
- Department of Cellular and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran 14155-6455, Iran
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Sciences III, Quai Ernest-Ansermet 30, CH-1211 Genève, Switzerland
| | - Nasrin Motamed
- Department of Cellular and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran 14155-6455, Iran
| | - Didier Picard
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Sciences III, Quai Ernest-Ansermet 30, CH-1211 Genève, Switzerland
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5
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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] [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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6
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Xu Y, Yang J, Li W, Song S, Shi Y, Wu L, Sun J, Hou M, Wang J, Jia X, Zhang H, Huang M, Lu T, Gan J, Feng Y. Three enigmatic BioH isoenzymes are programmed in the early stage of mycobacterial biotin synthesis, an attractive anti-TB drug target. PLoS Pathog 2022; 18:e1010615. [PMID: 35816546 PMCID: PMC9302846 DOI: 10.1371/journal.ppat.1010615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/21/2022] [Accepted: 05/24/2022] [Indexed: 11/19/2022] Open
Abstract
Tuberculosis (TB) is one of the leading infectious diseases of global concern, and one quarter of the world’s population are TB carriers. Biotin metabolism appears to be an attractive anti-TB drug target. However, the first-stage of mycobacterial biotin synthesis is fragmentarily understood. Here we report that three evolutionarily-distinct BioH isoenzymes (BioH1 to BioH3) are programmed in biotin synthesis of Mycobacterium smegmatis. Expression of an individual bioH isoform is sufficient to allow the growth of an Escherichia coli ΔbioH mutant on the non-permissive condition lacking biotin. The enzymatic activity in vitro combined with biotin bioassay in vivo reveals that BioH2 and BioH3 are capable of removing methyl moiety from pimeloyl-ACP methyl ester to give pimeloyl-ACP, a cognate precursor for biotin synthesis. In particular, we determine the crystal structure of dimeric BioH3 at 2.27Å, featuring a unique lid domain. Apart from its catalytic triad, we also dissect the substrate recognition of BioH3 by pimeloyl-ACP methyl ester. The removal of triple bioH isoforms (ΔbioH1/2/3) renders M. smegmatis biotin auxotrophic. Along with the newly-identified Tam/BioC, the discovery of three unusual BioH isoforms defines an atypical ‘BioC-BioH(3)’ paradigm for the first-stage of mycobacterial biotin synthesis. This study solves a long-standing puzzle in mycobacterial nutritional immunity, providing an alternative anti-TB drug target.
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Affiliation(s)
- Yongchang Xu
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Jie Yang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Science, Fudan University, Shanghai, The People’s Republic of China
| | - Weihui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, The People’s Republic of China
| | - Shuaijie Song
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Yu Shi
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Lihan Wu
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Jingdu Sun
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, The People’s Republic of China
| | - Mengyun Hou
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Jinzi Wang
- Guangxi Key Laboratory of Utilization of Microbial and Botanical Resources & Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, Guangxi, The People’s Republic of China
| | - Xu Jia
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, The People’s Republic of China
| | - Huimin Zhang
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Man Huang
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Science, Fudan University, Shanghai, The People’s Republic of China
- * E-mail: (JG); (YF)
| | - Youjun Feng
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, The People’s Republic of China
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, The People’s Republic of China
- * E-mail: (JG); (YF)
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7
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Smythe P, Efthimiou G. In Silico Genomic and Metabolic Atlas of Limosilactobacillus reuteri DSM 20016: An Insight into Human Health. Microorganisms 2022; 10:microorganisms10071341. [PMID: 35889060 PMCID: PMC9320016 DOI: 10.3390/microorganisms10071341] [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: 05/19/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/23/2022] Open
Abstract
Probiotics are bacterial strains that are known to provide host health benefits. Limosilactobacillus reuteri is a well-documented lactic acid bacterium that has been cultured from numerous human sites. The strain investigated was L. reuteri DSM 20016, which has been found to produce useful metabolites. The strain was explored using genomic and proteomic tools, manual searches, and databases, including KEGG, STRING, BLAST Sequence Similarity Search, and UniProt. This study located over 200 key genes that were involved in human health benefit pathways. L. reuteri DSM 20016 has metabolic pathways to produce acetate, propionate, and lactate, and there is evidence of a pathway for butanoate production through a FASII mechanism. The bacterium produces histamine through the hdc operon, which may be able to suppress proinflammatory TNF, and the bacterium also has the ability to synthesize folate and riboflavin, although whether they are secreted is yet to be explored. The strain can bind to human Caco2 cells through srtA, mapA/cnb, msrB, and fbpA and can compete against enteric bacteria using reuterin, which is an antimicrobial that induces oxidative stress. The atlas could be used for designing metabolic engineering approaches to improve beneficial metabolite biosynthesis and better probiotic-based cures.
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Affiliation(s)
- Paisleigh Smythe
- Centre for Atherothrombosis and Metabolic Disease, Hull York Medical School, Castle Hill Hospital, Daisy Building, Hull HU16 5JQ, UK;
| | - Georgios Efthimiou
- Department of Biomedical and Forensic Sciences, University of Hull, Cottingham Road, Hardy Building, Hull HU6 7RX, UK
- Correspondence: ; Tel.: +44-(0)1482-465970
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8
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Alwash M, Gariépy J. Labeling Cell Surface Receptors with Ligand.BirA* Bispecifics. ACS Pharmacol Transl Sci 2022; 5:62-69. [PMID: 36742360 PMCID: PMC9890520 DOI: 10.1021/acsptsci.1c00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BirA*, a mutant form of the biotinylating enzyme BirA, can nonspecifically biotinylate ε-amino groups on lysines of proteins. Based on the promiscuous labeling nature of BirA*, plasmids expressing fusion constructs of BirA* to a given ligand have been used to transfect eukaryotic cells, leading to the biotinylation of intracellular proteins interacting or in close proximity to such Ligand.BirA* constructs. Mass spectrometry performed on the recovered biotinylated partners allows one to map intracellular protein interactors, a technique known as BioID. In contrast, the expression and purification of recombinant Ligand.BirA* constructs could serve as a powerful tool for labeling and detecting cell surface receptors. Here, we report the design and expression of recombinant Affibody.BirA* constructs, ZEGFR:1907.BirA* and ZHER2:243.BirA*, as protein bispecifics able to biotinylate their respective receptors EGFR and HER2 on the surface of MDA-MB-231 (EGFR+, EpCaM+, and CD44+) and SK-OV-3 (HER2++, EGFR+, EpCaM+, and CD44+) cancer cells. These Affibody.BirA* constructs retain both their BirA* enzymatic activity as well as their receptor-binding function. Importantly, MDA-MB-231 and SK-OV-3 cells biotinylated with Affibody.BirA* constructs did label their receptors EGFR and HER2 but did not biotinylate irrelevant antigens such as EpCaM or CD44 present on the surface of both cell lines. Ligand.BirA* bispecifics may represent a promising class of agents to identify unknown receptors on cell surfaces.
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Affiliation(s)
- Mays Alwash
- Sunnybrook
Research Institute, 2075
Bayview Avenue, Toronto, Ontario M4N 3M5, Canada,Department
of Pharmaceutical Sciences, University of
Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Jean Gariépy
- Sunnybrook
Research Institute, 2075
Bayview Avenue, Toronto, Ontario M4N 3M5, Canada,Department
of Pharmaceutical Sciences, University of
Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada,Department
of Medical Biophysics, University of Toronto, 101 College St Suite 15-701, Toronto, Ontario M5G 1L7, Canada,
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9
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Ito N, Takahashi T, Shiiba I, Nagashima S, Inatome R, Yanagi S. MITOL regulates phosphatidic acid-binding activity of RMDN3/PTPIP51. J Biochem 2021; 171:529-541. [PMID: 34964862 DOI: 10.1093/jb/mvab153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/19/2021] [Indexed: 11/12/2022] Open
Abstract
The transfer of phospholipids from the endoplasmic reticulum to mitochondria via the mitochondria-endoplasmic reticulum (ER) contact site (MERCS) is essential for maintaining mitochondrial function and integrity. Here, we identified RMDN3/PTPIP51, possessing phosphatidic acid (PA)-transfer activity, as a neighboring protein of the mitochondrial E3 ubiquitin ligase MITOL/MARCH5 by proximity-dependent biotin labeling using APEX2. We found that MITOL interacts with and ubiquitinates RMDN3. Mutational analysis identified lysine residue 89 in RMDN3 as a site of ubiquitination by MITOL. Loss of MITOL or the substitution of lysine 89 to arginine in RMDN3 significantly reduced the PA-binding activity of RMDN3, suggesting that MITOL regulates the transport of PA to mitochondria by activating RMDN3. Our findings imply that ubiquitin signaling regulates phospholipid transport at the MERCS.
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Affiliation(s)
- Naoki Ito
- Laboratory of Regenerative Medicine, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.,Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
| | - Takara Takahashi
- Laboratory of Regenerative Medicine, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.,Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
| | - Isshin Shiiba
- Laboratory of Regenerative Medicine, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.,Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
| | - Shun Nagashima
- Laboratory of Regenerative Medicine, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Ryoko Inatome
- Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
| | - Shigeru Yanagi
- Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
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10
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Smith M, Abdesselem HB, Mullins M, Tan TM, Nel AJM, Al-Nesf MAY, Bensmail I, Majbour NK, Vaikath NN, Naik A, Ouararhni K, Mohamed-Ali V, Al-Maadheed M, Schell DT, Baros-Steyl SS, Anuar ND, Ismail NH, Morris PE, Mamat RNR, Rosli NSM, Anwar A, Ellan K, Zain RM, Burgers WA, Mayne ES, El-Agnaf OMA, Blackburn JM. Age, Disease Severity and Ethnicity Influence Humoral Responses in a Multi-Ethnic COVID-19 Cohort. Viruses 2021; 13:v13050786. [PMID: 33925055 PMCID: PMC8146997 DOI: 10.3390/v13050786] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 12/16/2022] Open
Abstract
The COVID-19 pandemic has affected all individuals across the globe in some way. Despite large numbers of reported seroprevalence studies, there remains a limited understanding of how the magnitude and epitope utilization of the humoral immune response to SARS-CoV-2 viral anti-gens varies within populations following natural infection. Here, we designed a quantitative, multi-epitope protein microarray comprising various nucleocapsid protein structural motifs, including two structural domains and three intrinsically disordered regions. Quantitative data from the microarray provided complete differentiation between cases and pre-pandemic controls (100% sensitivity and specificity) in a case-control cohort (n = 100). We then assessed the influence of disease severity, age, and ethnicity on the strength and breadth of the humoral response in a multi-ethnic cohort (n = 138). As expected, patients with severe disease showed significantly higher antibody titers and interestingly also had significantly broader epitope coverage. A significant increase in antibody titer and epitope coverage was observed with increasing age, in both mild and severe disease, which is promising for vaccine efficacy in older individuals. Additionally, we observed significant differences in the breadth and strength of the humoral immune response in relation to ethnicity, which may reflect differences in genetic and lifestyle factors. Furthermore, our data enabled localization of the immuno-dominant epitope to the C-terminal structural domain of the viral nucleocapsid protein in two independent cohorts. Overall, we have designed, validated, and tested an advanced serological assay that enables accurate quantitation of the humoral response post natural infection and that has revealed unexpected differences in the magnitude and epitope utilization within a population.
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Affiliation(s)
- Muneerah Smith
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (M.S.); (M.M.); (A.J.M.N.); (D.T.S.); (S.S.B.-S.)
| | - Houari B. Abdesselem
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar. Foundation, Doha P.O. Box 34110, Qatar; (H.B.A.); (I.B.); (N.K.M.); (N.N.V.); (A.N.); (K.O.)
- Proteomics Core Facility, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Michelle Mullins
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (M.S.); (M.M.); (A.J.M.N.); (D.T.S.); (S.S.B.-S.)
| | - Ti-Myen Tan
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
| | - Andrew J. M. Nel
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (M.S.); (M.M.); (A.J.M.N.); (D.T.S.); (S.S.B.-S.)
| | | | - Ilham Bensmail
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar. Foundation, Doha P.O. Box 34110, Qatar; (H.B.A.); (I.B.); (N.K.M.); (N.N.V.); (A.N.); (K.O.)
| | - Nour K. Majbour
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar. Foundation, Doha P.O. Box 34110, Qatar; (H.B.A.); (I.B.); (N.K.M.); (N.N.V.); (A.N.); (K.O.)
| | - Nishant N. Vaikath
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar. Foundation, Doha P.O. Box 34110, Qatar; (H.B.A.); (I.B.); (N.K.M.); (N.N.V.); (A.N.); (K.O.)
| | - Adviti Naik
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar. Foundation, Doha P.O. Box 34110, Qatar; (H.B.A.); (I.B.); (N.K.M.); (N.N.V.); (A.N.); (K.O.)
| | - Khalid Ouararhni
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar. Foundation, Doha P.O. Box 34110, Qatar; (H.B.A.); (I.B.); (N.K.M.); (N.N.V.); (A.N.); (K.O.)
| | - Vidya Mohamed-Ali
- Anti-Doping Laboratory Qatar, Sports City Road, Aspire Zone, Doha P.O. Box 27775, Qatar; (V.M.-A.); (M.A.-M.)
| | - Mohammed Al-Maadheed
- Anti-Doping Laboratory Qatar, Sports City Road, Aspire Zone, Doha P.O. Box 27775, Qatar; (V.M.-A.); (M.A.-M.)
| | - Darien T. Schell
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (M.S.); (M.M.); (A.J.M.N.); (D.T.S.); (S.S.B.-S.)
| | - Seanantha S. Baros-Steyl
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (M.S.); (M.M.); (A.J.M.N.); (D.T.S.); (S.S.B.-S.)
| | - Nur D. Anuar
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
| | - Nur H. Ismail
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
| | - Priscilla E. Morris
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
| | - Raja N. R. Mamat
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
| | - Nurul S. M. Rosli
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
| | - Arif Anwar
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
| | - Kavithambigai Ellan
- Virology Lab, Level 2, Block C7, Infectious Disease Research Centre, Institute for Medical Research, Setia Alam, Selangor 40170, Malaysia; (K.E.); (R.M.Z.)
| | - Rozainanee M. Zain
- Virology Lab, Level 2, Block C7, Infectious Disease Research Centre, Institute for Medical Research, Setia Alam, Selangor 40170, Malaysia; (K.E.); (R.M.Z.)
| | - Wendy A. Burgers
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa;
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Elizabeth S. Mayne
- Department of Immunology, National Health Laboratory Service (NHLS) and University of the Witwatersrand, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg 2196, South Africa;
| | - Omar M. A. El-Agnaf
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar. Foundation, Doha P.O. Box 34110, Qatar; (H.B.A.); (I.B.); (N.K.M.); (N.N.V.); (A.N.); (K.O.)
- Correspondence: (O.M.A.E.-A.); (J.M.B.); Tel.: +97-455-935-568 (O.M.A.E.-A.); +27-214-066-071 (J.M.B.)
| | - Jonathan M. Blackburn
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (M.S.); (M.M.); (A.J.M.N.); (D.T.S.); (S.S.B.-S.)
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- Correspondence: (O.M.A.E.-A.); (J.M.B.); Tel.: +97-455-935-568 (O.M.A.E.-A.); +27-214-066-071 (J.M.B.)
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11
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Zapatero-Belinchón FJ, Carriquí-Madroñal B, Gerold G. Proximity labeling approaches to study protein complexes during virus infection. Adv Virus Res 2021; 109:63-104. [PMID: 33934830 DOI: 10.1016/bs.aivir.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cellular compartmentalization of proteins and protein complex formation allow cells to tightly control biological processes. Therefore, understanding the subcellular localization and interactions of a specific protein is crucial to uncover its biological function. The advent of proximity labeling (PL) has reshaped cellular proteomics in infection biology. PL utilizes a genetically modified enzyme that generates a "labeling cloud" by covalently labeling proteins in close proximity to the enzyme. Fusion of a PL enzyme to a specific antibody or a "bait" protein of interest in combination with affinity enrichment mass spectrometry (AE-MS) enables the isolation and identification of the cellular proximity proteome, or proxisome. This powerful methodology has been paramount for the mapping of membrane or membraneless organelles as well as for the understanding of hard-to-purify protein complexes, such as those of transmembrane proteins. Unsurprisingly, more and more infection biology research groups have recognized the potential of PL for the identification of host-pathogen interactions. In this chapter, we introduce the enzymes commonly used for PL labeling as well as recent promising advancements and summarize the major achievements in organelle mapping and nucleic acid PL. Moreover, we comprehensively describe the research on host-pathogen interactions using PL, giving special attention to studies in the field of virology.
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Affiliation(s)
- Francisco José Zapatero-Belinchón
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
| | - Belén Carriquí-Madroñal
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Gisa Gerold
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
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12
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Biochemical and structural characterization of the BioZ enzyme engaged in bacterial biotin synthesis pathway. Nat Commun 2021; 12:2056. [PMID: 33824341 PMCID: PMC8024396 DOI: 10.1038/s41467-021-22360-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/12/2021] [Indexed: 01/07/2023] Open
Abstract
Biotin is an essential micro-nutrient across the three domains of life. The paradigm earlier step of biotin synthesis denotes "BioC-BioH" pathway in Escherichia coli. Here we report that BioZ bypasses the canonical route to begin biotin synthesis. In addition to its origin of Rhizobiales, protein phylogeny infers that BioZ is domesticated to gain an atypical role of β-ketoacyl-ACP synthase III. Genetic and biochemical characterization demonstrates that BioZ catalyzes the condensation of glutaryl-CoA (or ACP) with malonyl-ACP to give 5'-keto-pimeloyl ACP. This intermediate proceeds via type II fatty acid synthesis (FAS II) pathway, to initiate the formation of pimeloyl-ACP, a precursor of biotin synthesis. To further explore molecular basis of BioZ activity, we determine the crystal structure of Agrobacterium tumefaciens BioZ at 1.99 Å, of which the catalytic triad and the substrate-loading tunnel are functionally defined. In particular, we localize that three residues (S84, R147, and S287) at the distant bottom of the tunnel might neutralize the charge of free C-carboxyl group of the primer glutaryl-CoA. Taken together, this study provides molecular insights into the BioZ biotin synthesis pathway.
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13
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Smolobochkin AV, Gazizov AS, Burilov AR, Pudovik MA, Sinyashin OG. Advances in the synthesis of heterocycles bearing an endocyclic urea moiety. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4988] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Sprenger M, Brunke S, Hube B, Kasper L. A TRP1-marker-based system for gene complementation, overexpression, reporter gene expression and gene modification in Candida glabrata. FEMS Yeast Res 2020; 20:6027539. [PMID: 33289831 PMCID: PMC7787354 DOI: 10.1093/femsyr/foaa066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/04/2020] [Indexed: 01/14/2023] Open
Abstract
Although less prevalent than its relative Candida albicans, the yeast Candida glabrata is a successful pathogen of humans, which causes life-threatening candidiasis. It is thus vital to understand the pathogenicity mechanisms and contributing genes in C. glabrata. However, gene complementation as a tool for restoring the function of a previously deleted gene is not standardized in C. glabrata, and it is less frequently used than in C. albicans. In this study, we established a gene complementation strategy using genomic integration at the TRP1 locus. We prove that our approach can not only be used for integration of complementation cassettes, but also for overexpression of markers like fluorescent proteins and the antigen ovalbumin, or of potential pathogenicity-related factors like the biotin transporter gene VHT1. With urea amidolyase Dur1,2 as an example, we demonstrate the application of the gene complementation approach for the expression of sequence-modified genes. With this approach, we found that a lysine-to-arginine mutation in the biotinylation motif of Dur1,2 impairs urea-dependent growth of C. glabrata and C. albicans. Taken together, the TRP1-based gene complementation approach is a valuable tool for investigating novel gene functions and for elucidating their role in the pathobiology of C. glabrata.
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Affiliation(s)
- Marcel Sprenger
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Sascha Brunke
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Bernhard Hube
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany.,Institute of Microbiology, Friedrich Schiller University, Neugasse 25, 07743 Jena, Germany
| | - Lydia Kasper
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany
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15
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Zheng J, Chen X, Yang Y, Tan CSH, Tian R. Mass Spectrometry-Based Protein Complex Profiling in Time and Space. Anal Chem 2020; 93:598-619. [DOI: 10.1021/acs.analchem.0c04332] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiong Chen
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yun Yang
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Chris Soon Heng Tan
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
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16
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Proximity labeling in mammalian cells with TurboID and split-TurboID. Nat Protoc 2020; 15:3971-3999. [PMID: 33139955 DOI: 10.1038/s41596-020-0399-0] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 08/18/2020] [Indexed: 12/19/2022]
Abstract
This protocol describes the use of TurboID and split-TurboID in proximity labeling applications for mapping protein-protein interactions and subcellular proteomes in live mammalian cells. TurboID is an engineered biotin ligase that uses ATP to convert biotin into biotin-AMP, a reactive intermediate that covalently labels proximal proteins. Optimized using directed evolution, TurboID has substantially higher activity than previously described biotin ligase-related proximity labeling methods, such as BioID, enabling higher temporal resolution and broader application in vivo. Split-TurboID consists of two inactive fragments of TurboID that can be reconstituted through protein-protein interactions or organelle-organelle interactions, which can facilitate greater targeting specificity than full-length enzymes alone. Proteins biotinylated by TurboID or split-TurboID are then enriched with streptavidin beads and identified by mass spectrometry. Here, we describe fusion construct design and characterization (variable timing), proteomic sample preparation (5-7 d), mass spectrometric data acquisition (2 d), and proteomic data analysis (1 week).
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17
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Bosch JA, Chen CL, Perrimon N. Proximity-dependent labeling methods for proteomic profiling in living cells: An update. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 10:e392. [PMID: 32909689 DOI: 10.1002/wdev.392] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/11/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022]
Abstract
Characterizing the proteome composition of organelles and subcellular regions of living cells can facilitate the understanding of cellular organization as well as protein interactome networks. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially restricted proteomes. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. The tagged endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, spatial expression is achieved by fusing the enzyme to specific proteins or signal peptides that target to particular subcellular regions. Although these technologies have only been introduced recently, they have already provided deep insights into a wide range of biological processes. Here, we provide an updated description and comparison of proximity labeling methods, as well as their applications and improvements. As each method has its own unique features, the goal of this review is to describe how different proximity labeling methods can be used to answer different biological questions. This article is categorized under: Technologies > Analysis of Proteins.
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Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Chiao-Lin Chen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston, Massachusetts, USA
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18
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Samavarchi-Tehrani P, Samson R, Gingras AC. Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches. Mol Cell Proteomics 2020; 19:757-773. [PMID: 32127388 PMCID: PMC7196579 DOI: 10.1074/mcp.r120.001941] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
The study of protein subcellular distribution, their assembly into complexes and the set of proteins with which they interact with is essential to our understanding of fundamental biological processes. Complementary to traditional assays, proximity-dependent biotinylation (PDB) approaches coupled with mass spectrometry (such as BioID or APEX) have emerged as powerful techniques to study proximal protein interactions and the subcellular proteome in the context of living cells and organisms. Since their introduction in 2012, PDB approaches have been used in an increasing number of studies and the enzymes themselves have been subjected to intensive optimization. How these enzymes have been optimized and considerations for their use in proteomics experiments are important questions. Here, we review the structural diversity and mechanisms of the two main classes of PDB enzymes: the biotin protein ligases (BioID) and the peroxidases (APEX). We describe the engineering of these enzymes for PDB and review emerging applications, including the development of PDB for coincidence detection (split-PDB). Lastly, we briefly review enzyme selection and experimental design guidelines and reflect on the labeling chemistries and their implication for data interpretation.
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Affiliation(s)
| | - Reuben Samson
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada.
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19
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Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9. Genome Biol 2020; 21:59. [PMID: 32138752 PMCID: PMC7059722 DOI: 10.1186/s13059-020-01973-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/23/2020] [Indexed: 12/11/2022] Open
Abstract
The spatiotemporal control of 3D genome is fundamental for gene regulation, yet it remains challenging to profile high-resolution chromatin structure at cis-regulatory elements (CREs). Using C-terminally biotinylated dCas9, endogenous biotin ligases, and pooled sgRNAs, we describe the dCas9-based CAPTURE method for multiplexed analysis of locus-specific chromatin interactions. The redesigned system allows for quantitative analysis of the spatial configuration of a few to hundreds of enhancers or promoters in a single experiment, enabling comparisons across CREs within and between gene clusters. Multiplexed analyses of the spatiotemporal configuration of erythroid super-enhancers and promoter-centric interactions reveal organizational principles of genome structure and function.
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20
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Krishnan A, Kloehn J, Lunghi M, Soldati-Favre D. Vitamin and cofactor acquisition in apicomplexans: Synthesis versus salvage. J Biol Chem 2020; 295:701-714. [PMID: 31767680 PMCID: PMC6970920 DOI: 10.1074/jbc.aw119.008150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Apicomplexa phylum comprises diverse parasitic organisms that have evolved from a free-living ancestor. These obligate intracellular parasites exhibit versatile metabolic capabilities reflecting their capacity to survive and grow in different hosts and varying niches. Determined by nutrient availability, they either use their biosynthesis machineries or largely depend on their host for metabolite acquisition. Because vitamins cannot be synthesized by the mammalian host, the enzymes required for their synthesis in apicomplexan parasites represent a large repertoire of potential therapeutic targets. Here, we review recent advances in metabolic reconstruction and functional studies coupled to metabolomics that unravel the interplay between biosynthesis and salvage of vitamins and cofactors in apicomplexans. A particular emphasis is placed on Toxoplasma gondii, during both its acute and latent stages of infection.
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Affiliation(s)
- Aarti Krishnan
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva CMU, 1 Rue Michel-Servet, 1211 Geneva 4 Switzerland
| | - Joachim Kloehn
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva CMU, 1 Rue Michel-Servet, 1211 Geneva 4 Switzerland
| | - Matteo Lunghi
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva CMU, 1 Rue Michel-Servet, 1211 Geneva 4 Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva CMU, 1 Rue Michel-Servet, 1211 Geneva 4 Switzerland
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21
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Krishnan A, Kloehn J, Lunghi M, Soldati-Favre D. Vitamin and cofactor acquisition in apicomplexans: Synthesis versus salvage. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49928-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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22
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He J, Ma S, Wu S, Xu J, Tian J, Li J, Gee SJ, Hammock BD, Li QX, Xu T. Construction of Immunomagnetic Particles with High Stability in Stringent Conditions by Site-Directed Immobilization of Multivalent Nanobodies onto Bacterial Magnetic Particles for the Environmental Detection of Tetrabromobisphenol-A. Anal Chem 2019; 92:1114-1121. [PMID: 31763820 DOI: 10.1021/acs.analchem.9b04177] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Bacterial magnetic particles (BMPs) are an attractive carrier material for immunoassays because of their nanoscale size, dispersal ability, and membrane-bound structure. Antitetrabromobisphenol-A (TBBPA) nanobodies (Nbs) in the form of monovalence (Nb1), bivalence (Nb2), and trivalence (Nb3) were biotinylated and immobilized onto streptavidin (SA)-derivatized BMPs to construct the complexes of BMP-SA-Biotin-Nb1, -Nb2, and -Nb3, respectively. An increasing order of binding capability of BMP-SA-Biotin-Nb1, -Nb2, and -Nb3 to TBBPA was observed. These complexes showed high resilience to temperature (90 °C), methanol (100%), high pH (12), and strong ionic strength (1.37 M NaCl). A BMP-SA-Biotin-Nb3-based enzyme linked immunosorbent assay (ELISA) for TBBPA dissolved in methanol was developed, showing a half-maximum inhibition concentration (IC50) of 0.42 ng mL-1. TBBPA residues in landfill leachate, sewage, and sludge samples determined by this assay were in a range of <LOD-1.17 ng mL-1, <LOD-0.75 ng mL-1, and <LOD-3.65 ng g-1 (dw), respectively, correlating well with the results by liquid chromatography tandem mass spectrometry. The BMP-SA-Biotin-Nb3 was reusable at least three times without significant loss of the binding capability. The BMP-SA-Biotin-Nb3-based ELISA, with a total assay time of less than 30 min, is promising for the rapid monitoring of TBBPA in the environment.
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Affiliation(s)
- Jinxin He
- Suzhou Vicheck Biotechnology Co. Ltd. , Suzhou 215128 , China
| | | | - Sha Wu
- Suzhou Vicheck Biotechnology Co. Ltd. , Suzhou 215128 , China
| | | | | | - Ji Li
- Suzhou Vicheck Biotechnology Co. Ltd. , Suzhou 215128 , China
| | - Shirley J Gee
- Department of Entomology and UCD Comprehensive Cancer Center , University of California , Davis , California 95616 , United States
| | - Bruce D Hammock
- Department of Entomology and UCD Comprehensive Cancer Center , University of California , Davis , California 95616 , United States
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering , University of Hawaii at Manoa , 1955 East-West Road , Honolulu , Hawaii 96822 , United States
| | - Ting Xu
- Suzhou Vicheck Biotechnology Co. Ltd. , Suzhou 215128 , China
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23
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Song H, Luo Q, Deng X, Ji C, Li D, Munankarmy A, Jian W, Zhao J, Fang L. VGLL4 interacts with STAT3 to function as a tumor suppressor in triple-negative breast cancer. Exp Mol Med 2019; 51:1-13. [PMID: 31748508 PMCID: PMC6868227 DOI: 10.1038/s12276-019-0338-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/08/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive malignancy with a poor prognosis, and there are no effective molecular-targeted drugs for TNBC patients in clinical practice. The JAK-STAT pathway is implicated in tumorigenesis and the progression of various cancers. In this study, the results demonstrated that VGLL4 is expressed at low levels in both TNBC specimens and cell lines and that VGLL4 expression is negatively correlated with Ki67 expression and tumor size in TNBC patients. VGLL4 knockdown can promote the growth of TNBC cells, while VGLL4 overexpression significantly suppresses the growth of TNBC cells in vitro. More importantly, VGLL4 significantly inhibits tumor progression in a nude mouse model. In addition, VGLL4 is a direct target of miR-454, and the upregulation of miR-454 decreases VGLL4 expression and promotes the cell growth of TNBC cells. Furthermore, we also demonstrated that VGLL4 interacts with STAT3, the core component of the JAK-STAT pathway, leading to the inactivation of STAT3 and the inhibition of STAT3 downstream transcription. Collectively, these findings indicate that VGLL4 expression is negatively associated with poor prognosis in TNBC patients. High expression of miR-454 may be one of the causes of the downregulation of VGLL4 in TNBC, and VGLL4 acts as a tumor suppressor in TNBC by interacting with STAT3 and subsequently suppresses the STAT3 signaling axis, providing potential biomarkers and therapeutic approaches for this fatal disease. Targeting the regulation or activity of a tumor suppressor protein that is deactivated in triple-negative breast cancer (TNBC) holds promise for the treatment of this highly aggressive form of cancer. Lin Fang and colleagues at Tongji University in Shanghai, China, showed that low levels of the protein vestigial-like family member 4 (VGLL4) promoted TNBC cell proliferation and migration, whereas overexpression of VGLL4 prevented the growth of these cells in mice. VGLL4 acts as a tumor suppressor by interfering with a signaling pathway that drives tumor growth. Furthermore, they found that VGLL4 expression is regulated by a small RNA molecule that is highly expressed in TNBC patients with poor prospects of survival. These findings provide new insights into the mechanisms underlying TNBC and highlight potential strategies for the development of targeted therapies.
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Affiliation(s)
- Hongming Song
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China.,Breast Disease Center, The Affiliated Hospital of Qingdao University, 59 Haier Road, Qingdao, 266000, Shandong, China
| | - Qifeng Luo
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China
| | - Xiaochong Deng
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China
| | - Changle Ji
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China
| | - Dengfeng Li
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China
| | - Amik Munankarmy
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China
| | - Wei Jian
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China
| | - Junyong Zhao
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China
| | - Lin Fang
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China.
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24
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Stevens LM, Zhang Y, Volnov Y, Chen G, Stein DS. Isolation of secreted proteins from Drosophila ovaries and embryos through in vivo BirA-mediated biotinylation. PLoS One 2019; 14:e0219878. [PMID: 31658274 PMCID: PMC6816556 DOI: 10.1371/journal.pone.0219878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023] Open
Abstract
The extraordinarily strong non-covalent interaction between biotin and avidin (kD = 10-14-10-16) has permitted this interaction to be used in a wide variety of experimental contexts. The Biotin Acceptor Peptide (BAP), a 15 amino acid motif that can be biotinylated by the E. coli BirA protein, has been fused to proteins-of-interest, making them substrates for in vivo biotinylation. Here we report on the construction and characterization of a modified BirA bearing signals for secretion and endoplasmic reticulum (ER) retention, for use in experimental contexts requiring biotinylation of secreted proteins. When expressed in the Drosophila female germline or ovarian follicle cells under Gal4-mediated transcriptional control, the modified BirA protein could be detected and shown to be enzymatically active in ovaries and progeny embryos. Surprisingly, however, it was not efficiently retained in the ER, and instead appeared to be secreted. To determine whether this secreted protein, now designated secBirA, could biotinylate secreted proteins, we generated BAP-tagged versions of two secreted Drosophila proteins, Torsolike (Tsl) and Gastrulation Defective (GD), which are normally expressed maternally and participate in embryonic pattern formation. Both Tsl-BAP and GD-BAP were shown to exhibit normal patterning activity. Co-expression of Tsl-BAP together with secBirA in ovarian follicle cells resulted in its biotinylation, which permitted its isolation from both ovaries and progeny embryos using Avidin-coupled affinity matrix. In contrast, co-expression with secBirA in the female germline did not result in detectable biotinylation of GD-BAP, possibly because the C-terminal location of the BAP tag made it inaccessible to BirA in vivo. Our results indicate that secBirA directs biotinylation of proteins bound for secretion in vivo, providing access to powerful experimental approaches for secreted proteins-of-interest. However, efficient biotinylation of target proteins may vary depending upon the location of the BAP tag or other structural features of the protein.
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Affiliation(s)
- Leslie M. Stevens
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Yuan Zhang
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Yuri Volnov
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Geng Chen
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - David S. Stein
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
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25
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Wang J, Hua M, Li Y, Ma F, Zheng P, Hu B. Achieving high nitrogen removal efficiency by optimizing nitrite-dependent anaerobic methane oxidation process with growth factors. WATER RESEARCH 2019; 161:35-42. [PMID: 31176104 DOI: 10.1016/j.watres.2019.05.101] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/05/2019] [Accepted: 05/29/2019] [Indexed: 06/09/2023]
Abstract
Nitrite-dependent anaerobic methane oxidation (N-DAMO) is a newly discovered bioprocess which uses methane as electron donor to reduce nitrite into dinitrogen. It is a promising clean bioprocess for denitrification in wastewater treatment. However, the low reaction rate and slow growth rate of N-DAMO bacteria within NC10 phylum limit the application of the process. In this study, we chose vitamin, heme, nucleobase and betaine to investigate their short- and long-term effects on N-DAMO bacteria. The concentrations of the growth factors of medium were improved according to the short-term experiments. The results were subsequently verified via long-term inoculations and were applied in a magnetically stirred gas lift reactor (MSGLR). The results indicated that nucleobase and betaine (5.0 and 200 μg L-1, respectively) significantly stimulated the N-DAMO activity, whereas vitamin and heme had no significant effects in the tested concentration ranges. During the long-term incubation, N-DAMO bacteria continuously increased and finally achieved a relative abundance of 14.4% on day 300. Notably, larger aggregates of N-DAMO bacteria were observed at the end of the long-term incubation. And the nitrogen removal rate of the MSGLR increased to 70 mg N L-1 day-1, with the total nitrogen removal efficiency over 99.0%. However, the addition of betaine introduced methyl into the reactors and this made methylotrophs account a considerable part of the bacterial community, which limited the enrichment degree of N-DAMO bacteria. This work will contribute to the engineering application and enrichment of N-DAMO bacteria.
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Affiliation(s)
- Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Miaolian Hua
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Yufen Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, 310058, China.
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26
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Nayak A, Bhushan B. An overview of the recent trends on the waste valorization techniques for food wastes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 233:352-370. [PMID: 30590265 DOI: 10.1016/j.jenvman.2018.12.041] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 12/09/2018] [Accepted: 12/14/2018] [Indexed: 05/05/2023]
Abstract
A critical and up-to-date review has been conducted on the latest individual valorization technologies aimed at the generation of value-added by-products from food wastes in the form of bio-fuels, bio-materials, value added components and bio-based adsorbents. The aim is to examine the associated advantages and drawbacks of each technique separately along with the assessment of process parameters affecting the efficiency of the generation of the bio-based products. Challenges faced during the processing of the wastes to each of the bio-products have been explained and future scopes stated. Among the many hurdles encountered in the successful and high yield generation of the bio-products is the complexity and variability in the composition of the food wastes along with the high inherent moisture content. Also, individual technologies have their own process configurations and operating parameters which may affect the yield and composition of the desired end product. All these require extensive study of the composition of the food wastes followed by their effective pre-treatments, judicial selection of the technological parameters and finally optimization of not only the process configurations but also in relation to the input food waste material. Attempt has also been made to address the hurdles faced during the implementation of such technologies on an industrial scale.
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Affiliation(s)
- A Nayak
- Innovació i Recerca Industrial I Sostenible, S.L., 08860, Spain; Graphic Era University, Dehradun, 248002, India.
| | - Brij Bhushan
- Graphic Era University, Dehradun, 248002, India; Chemical Engineering Department, Universitat Politechnica Catalunya, UPC-BarcelonaTECH, Barcelona, 08860, Spain
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27
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Vandemoortele G, De Sutter D, Moliere A, Pauwels J, Gevaert K, Eyckerman S. A Well-Controlled BioID Design for Endogenous Bait Proteins. J Proteome Res 2018; 18:95-106. [PMID: 30525648 DOI: 10.1021/acs.jproteome.8b00367] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The CRISPR/Cas9 revolution is profoundly changing the way life sciences technologies are used. Many assays now rely on engineered clonal cell lines to eliminate the overexpression of bait proteins. Control cell lines are typically nonengineered cells or engineered clones, implying a considerable risk for artifacts because of clonal variation. Genome engineering can also transform BioID, a proximity labeling method that relies on fusing a bait protein to a promiscuous biotin ligase, BirA*, resulting in the tagging of vicinal proteins. We here propose an innovative design to enable BioID for endogenous proteins wherein we introduce a T2A-BirA* module at the C-terminus of endogenous p53 by genome engineering, leading to bicistronic expression of both p53 and BirA* under control of the endogenous promoter. By targeting a Cas9-cytidine deaminase base editor to the T2A autocleavage site, we can efficiently derive an isogenic population expressing a functional p53-BirA* fusion protein. Using quantitative proteomics we show significant benefits over the classical ectopic expression of p53-BirA*, and we provide a first well-controlled view of the proximal proteins of endogenous p53 in colon carcinoma cells. This novel application for base editors expands the CRISPR/Cas9 toolbox and can be a valuable addition for synthetic biology.
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Affiliation(s)
- Giel Vandemoortele
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Delphine De Sutter
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Aline Moliere
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Jarne Pauwels
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
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28
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Ohmuro-Matsuyama Y, Yamashita T, Gomi K, Yamaji H, Ueda H. Evaluation of protein-ligand interactions using the luminescent interaction assay FlimPIA with streptavidin-biotin linkage. Anal Biochem 2018; 563:61-66. [PMID: 30316750 DOI: 10.1016/j.ab.2018.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/05/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
Abstract
Post-translational modifications, such as phosphorylation, are crucial in the regulation of protein-protein interactions and protein function in cell signaling. Here, we studied the interaction between the transactivation domain peptide of cancer suppressor protein p53 and its negative regulator Mdm2 using a novel protein-protein interaction assay, based on the modified FlimPIA using the streptavidin-biotin interaction to link the p53 peptide and the probe enzyme. We succeeded in detecting an attenuation in the affinity of p53 towards Mdm2 caused by the phosphorylation at Thr18. It showed that the targets, which are not easy to fuse with the FlimPIA probes, such as phosphorylated peptides can be used in this system. Also, the use of streptavidin nanobeads was found effective to get clearer signal, probably due to concentration of the detection system onto the bead surface. The system was further applied to the detection of FKBP-FRB interaction using biotinylated FKBP domain, which suggested another potential merit of this system that allows to avoid misfolding and steric hindrance often observed for the fusion protein approach.
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Affiliation(s)
- Yuki Ohmuro-Matsuyama
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259-R1-18 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan; The Japan Society for the Promotion of Science, 8 Ichiban-Cho, Chiyoda-ku, Tokyo, 102-8472, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Takahiro Yamashita
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Keiko Gomi
- Kikkoman Corporation, 250 Noda, Noda, Chiba, 278-8601, Japan
| | - Hideki Yamaji
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Hiroshi Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259-R1-18 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
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29
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Jamilloux Y, Lagrange B, Di Micco A, Bourdonnay E, Provost A, Tallant R, Henry T, Martinon F. A proximity-dependent biotinylation (BioID) approach flags the p62/sequestosome-1 protein as a caspase-1 substrate. J Biol Chem 2018; 293:12563-12575. [PMID: 29929983 DOI: 10.1074/jbc.ra117.000435] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 06/08/2018] [Indexed: 01/24/2023] Open
Abstract
The inflammasome is a major component of the innate immune system, and its main function is to activate caspase-1, a cysteine protease that promotes inflammation by inducing interleukin-1β (IL-1β) maturation and release into the extracellular milieu. To prevent uncontrolled inflammation, this complex is highly regulated. When it is assembled, the inflammasome is insoluble, which has long precluded the analysis of its interactions with other proteins. Here we used the proximity-dependent biotinylation assay (BioID) to identify proteins associated with caspase-1 during inflammasome activation. Using the BioID in a cell-free system in which the inflammasome had been activated, we found that a caspase-1-biotin ligase fusion protein selectively labeled 111 candidates, including the p62/sequestosome-1 protein (p62). Using co-immunoprecipitation experiments, we demonstrated that p62 interacts with caspase-1. This interaction promoted caspase-1-mediated cleavage of p62 at Asp-329. Mechanistic and functional analyses revealed that caspase-1-mediated cleavage of p62 leads to loss of its interaction with the autophagosomal protein microtubule-associated protein 1 light chain 3 β (LC3B). Strikingly, overexpression of a p62 N-terminal fragment generated upon caspase-1 cleavage decreased IL-1β release, whereas overexpression of p62's C-terminal portion enhanced IL-1β release, by regulating pro-IL1β levels. Overall, the overexpression of both fragments together decreased IL-1β release. Taken together, our results indicate that caspase-1-mediated p62 cleavage plays a complex role in balancing caspase-1-induced inflammation.
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Affiliation(s)
- Yvan Jamilloux
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland.,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| | - Brice Lagrange
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland.,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| | - Antonia Di Micco
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland.,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| | - Emilie Bourdonnay
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland.,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| | - Angélina Provost
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland.,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| | - Rémy Tallant
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland.,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| | - Thomas Henry
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland, .,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| | - Fabio Martinon
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland, .,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
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30
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Askin S, Bond TEH, Sorenson AE, Moreau MJJ, Antony H, Davis RA, Schaeffer PM. Selective protein unfolding: a universal mechanism of action for the development of irreversible inhibitors. Chem Commun (Camb) 2018; 54:1738-1741. [DOI: 10.1039/c8cc00090e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Selective protein unfolding was combined with high-throughput differential scanning fluorimetry of GFP-tagged proteins for the identification of irreversible enzyme inhibitors.
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Affiliation(s)
- Samuel Askin
- Centre for Biodiscovery & Molecular Development of Therapeutics
- James Cook University
- 142
- James Cook Drive
- Townsville
| | - Thomas E. H. Bond
- Centre for Biodiscovery & Molecular Development of Therapeutics
- James Cook University
- 142
- James Cook Drive
- Townsville
| | - Alanna E. Sorenson
- Centre for Biodiscovery & Molecular Development of Therapeutics
- James Cook University
- 142
- James Cook Drive
- Townsville
| | - Morgane J. J. Moreau
- Centre for Biodiscovery & Molecular Development of Therapeutics
- James Cook University
- 142
- James Cook Drive
- Townsville
| | - Helma Antony
- Centre for Biodiscovery & Molecular Development of Therapeutics
- James Cook University
- 142
- James Cook Drive
- Townsville
| | - Rohan A. Davis
- Griffith Institute for Drug Discovery
- Griffith University
- Brisbane
- Australia
| | - Patrick M. Schaeffer
- Centre for Biodiscovery & Molecular Development of Therapeutics
- James Cook University
- 142
- James Cook Drive
- Townsville
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31
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Kaewsapsak P, Shechner DM, Mallard W, Rinn JL, Ting AY. Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking. eLife 2017; 6:e29224. [PMID: 29239719 PMCID: PMC5730372 DOI: 10.7554/elife.29224] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/06/2017] [Indexed: 12/18/2022] Open
Abstract
The spatial organization of RNA within cells is a crucial factor influencing a wide range of biological functions throughout all kingdoms of life. However, a general understanding of RNA localization has been hindered by a lack of simple, high-throughput methods for mapping the transcriptomes of subcellular compartments. Here, we develop such a method, termed APEX-RIP, which combines peroxidase-catalyzed, spatially restricted in situ protein biotinylation with RNA-protein chemical crosslinking. We demonstrate that, using a single protocol, APEX-RIP can isolate RNAs from a variety of subcellular compartments, including the mitochondrial matrix, nucleus, cytosol, and endoplasmic reticulum (ER), with specificity and sensitivity that rival or exceed those of conventional approaches. We further identify candidate RNAs localized to mitochondria-ER junctions and nuclear lamina, two compartments that are recalcitrant to classical biochemical purification. Since APEX-RIP is simple, versatile, and does not require special instrumentation, we envision its broad application in a variety of biological contexts.
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Affiliation(s)
- Pornchai Kaewsapsak
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Department of GeneticsStanford UniversityStanfordUnited States
- Department of BiologyStanford UniversityStanfordUnited States
- Department of ChemistryStanford UniversityStanfordUnited States
| | - David Michael Shechner
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeUnited States
- Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeUnited States
| | - William Mallard
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeUnited States
- Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeUnited States
| | - John L Rinn
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeUnited States
- Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeUnited States
| | - Alice Y Ting
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Department of GeneticsStanford UniversityStanfordUnited States
- Department of BiologyStanford UniversityStanfordUnited States
- Department of ChemistryStanford UniversityStanfordUnited States
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeUnited States
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32
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Optimizing the fragment complementation of APEX2 for detection of specific protein-protein interactions in live cells. Sci Rep 2017; 7:12039. [PMID: 28955036 PMCID: PMC5617831 DOI: 10.1038/s41598-017-12365-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/07/2017] [Indexed: 12/23/2022] Open
Abstract
Dynamic protein-protein interactions (PPIs) play crucial roles in cell physiological processes. The protein-fragment complementation (PFC) assay has been developed as a powerful approach for the detection of PPIs, but its potential for identifying protein interacting regions is not optimized. Recently, an ascorbate peroxidase (APEX2)-based proximity-tagging method combined with mass spectrometry was developed to identify potential protein interactions in live cells. In this study, we tested whether APEX2 could be employed for PFC. By screening split APEX2 pairs attached to FK506-binding protein 12 (FKBP) and the FKBP12-rapamycin binding (FRB) domain, which interact with each other only in the presence of rapamycin, we successfully obtained an optimized pair for visualizing the interaction between FRB and FKBP12 with high specificity and sensitivity in live cells. The robustness of this APEX2 pair was confirmed by its application toward detecting the STIM1 and Orial1 homodimers in HEK-293 cells. With a subsequent mass spectrometry analysis, we obtained five different biotinylated sites that were localized to the known interaction region on STIM1 and were only detected when the homodimer formed. These results suggest that our PFC pair of APEX2 provides a potential tool for detecting PPIs and identifying binding regions with high specificity in live cells.
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33
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León-Del-Río A, Valadez-Graham V, Gravel RA. Holocarboxylase Synthetase: A Moonlighting Transcriptional Coregulator of Gene Expression and a Cytosolic Regulator of Biotin Utilization. Annu Rev Nutr 2017; 37:207-223. [DOI: 10.1146/annurev-nutr-042617-104653] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alfonso León-Del-Río
- Programa de Investigación de Cáncer de Mama y Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de Mexico 04500, México
| | - Viviana Valadez-Graham
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62250, México
| | - Roy A. Gravel
- Department of Biochemistry & Molecular Biology, the University of Calgary and the Alberta Children's Hospital Research Institute for Child and Maternal Health, Calgary, Alberta T2N 4N1, Canada
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34
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Hung V, Lam SS, Udeshi ND, Svinkina T, Guzman G, Mootha VK, Carr SA, Ting AY. Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation. eLife 2017; 6:24463. [PMID: 28441135 PMCID: PMC5404927 DOI: 10.7554/elife.24463] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/14/2017] [Indexed: 12/24/2022] Open
Abstract
The cytosol-facing membranes of cellular organelles contain proteins that enable signal transduction, regulation of morphology and trafficking, protein import and export, and other specialized processes. Discovery of these proteins by traditional biochemical fractionation can be plagued with contaminants and loss of key components. Using peroxidase-mediated proximity biotinylation, we captured and identified endogenous proteins on the outer mitochondrial membrane (OMM) and endoplasmic reticulum membrane (ERM) of living human fibroblasts. The proteomes of 137 and 634 proteins, respectively, are highly specific and highlight 94 potentially novel mitochondrial or ER proteins. Dataset intersection identified protein candidates potentially localized to mitochondria-ER contact sites. We found that one candidate, the tail-anchored, PDZ-domain-containing OMM protein SYNJ2BP, dramatically increases mitochondrial contacts with rough ER when overexpressed. Immunoprecipitation-mass spectrometry identified ribosome-binding protein 1 (RRBP1) as SYNJ2BP's ERM binding partner. Our results highlight the power of proximity biotinylation to yield insights into the molecular composition and function of intracellular membranes.
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Affiliation(s)
- Victoria Hung
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Stephanie S Lam
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | | | - Tanya Svinkina
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Gaelen Guzman
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Vamsi K Mootha
- Broad Institute of MIT and Harvard, Cambridge, United States.,Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Alice Y Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
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35
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Estrada P, Manandhar M, Dong SH, Deveryshetty J, Agarwal V, Cronan JE, Nair SK. The pimeloyl-CoA synthetase BioW defines a new fold for adenylate-forming enzymes. Nat Chem Biol 2017; 13:668-674. [PMID: 28414711 DOI: 10.1038/nchembio.2359] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 03/02/2017] [Indexed: 01/11/2023]
Abstract
Reactions that activate carboxylates through acyl-adenylate intermediates are found throughout biology and include acyl- and aryl-CoA synthetases and tRNA synthetases. Here we describe the characterization of Aquifex aeolicus BioW, which represents a new protein fold within the superfamily of adenylating enzymes. Substrate-bound structures identified the enzyme active site and elucidated the mechanistic strategy for conjugating CoA to the seven-carbon α,ω-dicarboxylate pimelate, a biotin precursor. Proper position of reactive groups for the two half-reactions is achieved solely through movements of active site residues, as confirmed by site-directed mutational analysis. The ability of BioW to hydrolyze adenylates of noncognate substrates is reminiscent of pre-transfer proofreading observed in some tRNA synthetases, and we show that this activity can be abolished by mutation of a single residue. These studies illustrate how BioW can carry out three different biologically prevalent chemical reactions (adenylation, thioesterification, and proofreading) in the context of a new protein fold.
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Affiliation(s)
- Paola Estrada
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Miglena Manandhar
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Shi-Hui Dong
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jaigeeth Deveryshetty
- Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Vinayak Agarwal
- Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - John E Cronan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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36
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Chen CL, Perrimon N. Proximity-dependent labeling methods for proteomic profiling in living cells. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28387482 DOI: 10.1002/wdev.272] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/03/2017] [Accepted: 02/10/2017] [Indexed: 02/05/2023]
Abstract
Characterizing the proteome composition of organelles and subcellular regions of living cells can facilitate the understanding of cellular organization as well as protein interactome networks. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially restricted proteomes. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins with biotin. The biotinylated endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, spatial expression is achieved by fusing the enzyme to specific proteins or signal peptides that target to particular subcellular regions. Although these technologies have only been introduced recently, they have already provided deep insights into a wide range of biological processes. Here, we describe and compare current methods of proximity labeling as well as their applications. As each method has its own unique features, the goal of this review is to describe how different proximity labeling methods can be used to answer different biological questions. WIREs Dev Biol 2017, 6:e272. doi: 10.1002/wdev.272 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Chiao-Lin Chen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA
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37
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Co-expression of BirA with biotin bait achieves in vivo biotinylation of overexpressed stable N-glycosylated sRAGE in transgenic silkworms. Sci Rep 2017; 7:356. [PMID: 28336960 PMCID: PMC5428419 DOI: 10.1038/s41598-017-00420-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 02/27/2017] [Indexed: 12/23/2022] Open
Abstract
Here, we demonstrated the expression of the N-glycosylated extracellular ligand binding domain of receptor for advanced glycation end products (sRAGE) in middle silk glands (MSGs) of transgenic silkworms using the GAL4/UAS system. Over 1 mg of sRAGE was obtained from one transgenic silkworm. sRAGE purified from the silkworm exhibited good stability and maintained specific ligand-binding ability. In addition, N-glycan analysis of sRAGE revealed that N-glucan completely lacked potentially allergenic fucose. Moreover, co-expression of biotin ligase (BirA) with C-terminal BioEase-tagged sRAGE in MSGs resulted in efficient biotinylation of sRAGE after addition of biotin bait. C-terminal biotinylated sRAGE could be immobilized onto a solid surface in one direction through binding to streptavidin without any loss of ability. The dissociation constant of sRAGE with fructose-BSA, a typical RAGE ligand, was 7.25 × 10−7 M, consistent with that on the mammalian cell surface. Thus, we developed a novel, innovative silkworm expression system for efficient expression of recombinant sRAGE, which could serve as a basis for the elucidation of RAGE-ligand interactions and facilitate the search for new ligands and inhibitors.
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38
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Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2. Nat Protoc 2016; 11:456-75. [PMID: 26866790 DOI: 10.1038/nprot.2016.018] [Citation(s) in RCA: 329] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This protocol describes a method to obtain spatially resolved proteomic maps of specific compartments within living mammalian cells. An engineered peroxidase, APEX2, is genetically targeted to a cellular region of interest. Upon the addition of hydrogen peroxide for 1 min to cells preloaded with a biotin-phenol substrate, APEX2 generates biotin-phenoxyl radicals that covalently tag proximal endogenous proteins. Cells are then lysed, and biotinylated proteins are enriched with streptavidin beads and identified by mass spectrometry. We describe the generation of an appropriate APEX2 fusion construct, proteomic sample preparation, and mass spectrometric data acquisition and analysis. A two-state stable isotope labeling by amino acids in cell culture (SILAC) protocol is used for proteomic mapping of membrane-enclosed cellular compartments from which APEX2-generated biotin-phenoxyl radicals cannot escape. For mapping of open cellular regions, we instead use a 'ratiometric' three-state SILAC protocol for high spatial specificity. Isotopic labeling of proteins takes 5-7 cell doublings. Generation of the biotinylated proteomic sample takes 1 d, acquiring the mass spectrometric data takes 2-5 d and analysis of the data to obtain the final proteomic list takes 1 week.
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39
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Davenport KR, Smith CA, Hofstetter H, Horn JR, Hofstetter O. Site-directed immobilization of a genetically engineered anti-methotrexate antibody via an enzymatically introduced biotin label significantly increases the binding capacity of immunoaffinity columns. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:114-121. [PMID: 26809205 DOI: 10.1016/j.jchromb.2016.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
Abstract
In this study, the effect of random vs. site-directed immobilization techniques on the performance of antibody-based HPLC columns was investigated using a single-domain camelid antibody (VHH) directed against methotrexate (MTX) as a model system. First, the high flow-through support material POROS-OH was activated with disuccinimidyl carbonate (DSC), and the VHH was bound in a random manner via amines located on the protein's surface. The resulting column was characterized by Frontal Affinity Chromatography (FAC). Then, two site-directed techniques were explored to increase column efficiency by immobilizing the antibody via its C-terminus, i.e., away from the antigen-binding site. In one approach, a tetra-lysine tail was added, and the antibody was immobilized onto DSC-activated POROS. In the second site-directed approach, the VHH was modified with the AviTag peptide, and a biotin-residue was enzymatically incorporated at the C-terminus using the biotin ligase BirA. The biotinylated antibody was subsequently immobilized onto NeutrAvidin-derivatized POROS. A comparison of the FAC analyses, which for all three columns showed excellent linearity (R(2)>0.999), revealed that both site-directed approaches yield better results than the random immobilization; the by far highest efficiency, however, was determined for the immunoaffinity column based on AviTag-biotinylated antibody. As proof of concept, all three columns were evaluated for quantification of MTX dissolved in phosphate buffered saline (PBS). Validation using UV-detection showed excellent linearity in the range of 0.04-12μM (R(2)>0.993). The lower limit of detection (LOD) and lower limit of quantification (LLOQ) were found to be independent of the immobilization strategy and were 40nM and 132nM, respectively. The intra- and inter-day precision was below 11.6%, and accuracy was between 90.7% and 112%. To the best of our knowledge, this is the first report of the AviTag-system in chromatography, and the first application of immunoaffinity chromatography for the analysis of MTX.
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Affiliation(s)
- Kaitlynn R Davenport
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA
| | - Christopher A Smith
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA
| | - Heike Hofstetter
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA
| | - James R Horn
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA
| | - Oliver Hofstetter
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA.
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Abstract
The nuclear envelope (NE) is a critical cellular structure whose constituents and roles in a myriad of cellular processes seem ever expanding. To determine the underlying mechanisms by which the NE constituents participate in various cellular events, it is necessary to understand the nature of their protein-protein associations. BioID (proximity-dependent biotin identification) is a recently established method to generate a history of protein-protein associations as they occur over time in living cells. BioID is based on fusion of a bait protein to a promiscuous biotin ligase. Expression of the BioID fusion protein in a relevant cellular environment enables biotinylation of vicinal and interacting proteins of the bait protein, permitting isolation and identification by conventional biotin-affinity capture and mass-spec analysis. In this way, BioID provides unique capabilities to identify protein-protein associations at the NE. In this chapter we provide a detailed protocol for the application of BioID to the study of NE proteins.
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Affiliation(s)
- Dae In Kim
- Sanford Research, Sanford Children's Health Research Center, 2301 E. 60th Street N., Sioux Falls, SD, 57104, USA
| | - Samuel C Jensen
- Sanford Research, Sanford Children's Health Research Center, 2301 E. 60th Street N., Sioux Falls, SD, 57104, USA
| | - Kyle J Roux
- Sanford Research, Sanford Children's Health Research Center, 2301 E. 60th Street N., Sioux Falls, SD, 57104, USA.
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, 57105, USA.
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41
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MINAMI T. Exploratory Research of Chemical Sensors Based on Organic Transistors with Self-Assembled Monolayer-Functionalized Electrodes. KOBUNSHI RONBUNSHU 2016. [DOI: 10.1295/koron.2016-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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Abstract
Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise, and the BioH esterase is responsible for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl acyl carrier protein of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyltransferase followed by sulfur insertion at carbons C-6 and C-8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and, thus, there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system, exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate proteins.
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43
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Yang J, Wagner SA, Beli P. Illuminating Spatial and Temporal Organization of Protein Interaction Networks by Mass Spectrometry-Based Proteomics. Front Genet 2015; 6:344. [PMID: 26648978 PMCID: PMC4665136 DOI: 10.3389/fgene.2015.00344] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/20/2015] [Indexed: 11/13/2022] Open
Abstract
Protein–protein interactions are at the core of all cellular functions and dynamic alterations in protein interactions regulate cellular signaling. In the last decade, mass spectrometry (MS)-based proteomics has delivered unprecedented insights into human protein interaction networks. Affinity purification-MS (AP-MS) has been extensively employed for focused and high-throughput studies of steady state protein–protein interactions. Future challenges remain in mapping transient protein interactions after cellular perturbations as well as in resolving the spatial organization of protein interaction networks. AP-MS can be combined with quantitative proteomics approaches to determine the relative abundance of purified proteins in different conditions, thereby enabling the identification of transient protein interactions. In addition to affinity purification, methods based on protein co-fractionation have been combined with quantitative MS to map transient protein interactions during cellular signaling. More recently, approaches based on proximity tagging that preserve the spatial dimension of protein interaction networks have been introduced. Here, we provide an overview of MS-based methods for analyzing protein–protein interactions with a focus on approaches that aim to dissect the temporal and spatial aspects of protein interaction networks.
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Affiliation(s)
- Jiwen Yang
- Institute of Molecular Biology , Mainz, Germany
| | - Sebastian A Wagner
- Department of Medicine, Hematology and Oncology, Goethe University , Frankfurt, Germany
| | - Petra Beli
- Institute of Molecular Biology , Mainz, Germany
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44
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Lu Y, Hatsugai N, Katagiri F, Ishimaru CA, Glazebrook J. Putative Serine Protease Effectors of Clavibacter michiganensis Induce a Hypersensitive Response in the Apoplast of Nicotiana Species. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1216-26. [PMID: 26075829 DOI: 10.1094/mpmi-02-15-0036-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Clavibacter michiganensis subspp. michiganensis and sepedonicus cause diseases on solanaceous crops. The genomes of both subspecies encode members of the pat-1 family of putative serine proteases known to function in virulence on host plants and induction of hypersensitive responses (HR) on nonhosts. One gene of this family in C. michiganensis subsp. sepedonicus, chp-7, is required for triggering HR in Nicotiana tabacum. Here, further investigation revealed that mutation of the putative catalytic serine residue at position 232 to threonine abolished the HR induction activity of Chp-7, suggesting that enzymatic activity is required. Purified Chp-7 triggered an HR in N. tabacum leaves in the absence of the pathogen, indicating Chp-7 itself is the HR elicitor from C. michiganensis subsp. sepedonicus. Ectopic expression of chp-7 constructs in N. tabacum leaves revealed that Chp-7 targeted to the apoplast triggered an HR while cytoplasmic Chp-7 did not, indicating that Chp-7 induces the HR in the apoplast of N. tabacum leaves. Chp-7 also induced HR in N. sylvestris, a progenitor of N. tabacum, but not in other Nicotiana species tested. ChpG, a related protein from C. michiganensis subsp. michiganensis, also triggered HR in N. tabacum and N. sylvestris. Unlike Chp-7, ChpG triggered HR in N. clevelandii and N. glutinosa.
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Affiliation(s)
- You Lu
- 1 Department of Plant Biology
- 2 Microbial and Plant Genomics Institute, and
- 3 Plant Biological Sciences Graduate Program, University of Minnesota, 1445 Gortner Ave., St. Paul, MN 55108, U.S.A
| | - Noriyuki Hatsugai
- 1 Department of Plant Biology
- 2 Microbial and Plant Genomics Institute, and
| | - Fumiaki Katagiri
- 1 Department of Plant Biology
- 2 Microbial and Plant Genomics Institute, and
| | - Carol A Ishimaru
- 2 Microbial and Plant Genomics Institute, and
- 4 Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, U.S.A
| | - Jane Glazebrook
- 1 Department of Plant Biology
- 2 Microbial and Plant Genomics Institute, and
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45
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Azevedo C, Saiardi A. Why always lysine? The ongoing tale of one of the most modified amino acids. Adv Biol Regul 2015; 60:144-150. [PMID: 26482291 DOI: 10.1016/j.jbior.2015.09.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 09/30/2015] [Accepted: 09/30/2015] [Indexed: 11/26/2022]
Abstract
The complex physiology of living organisms must be finely-tuned to permit the flexibility required to respond to the changing environment. Evolution has provided an interconnected and intricate array of regulatory mechanisms to facilitate this fine-tuning. The number of genes cannot alone explain the complexity of these mechanisms. Rather, signalling is regulated at multiple levels, from genomic to transcriptional, translational and post-translational. Post-translational modification (PTM) of proteins offers an additional level of regulation after protein synthesis that allows a rapid, controlled and reversible response to environmental cues. Many amino acid side chains are post-translationally modified. These modifications can either be enzymatic, such as the phosphorylation of serine, threonine and tyrosine residues, or non-enzymatic, such as the nitrosylation of cysteine residues. Strikingly, lysine residues are targeted by a particularly high number of PTMs including acetylation, methylation, ubiquitination and sumoylation. Additionally, lysines have recently been identified as the target of the non-enzymatic PTM polyphosphorylation. This novel PTM sees linear chains of inorganic polyphosphates (polyP) covalently attached to lysine residues. Interestingly, polyphosphorylation is indirectly dependent on inositol pyrophosphates, a class of cellular messengers. The attachment of polyP to lysine occurs through the phosphoramidate bond, which, unlike the phosphester bond, is unstable under the conditions used in common mass spectroscopy. This characteristic, together with the diversity of lysine PTMs, suggests that many other lysine modifications may still remain unidentified, raising the intriguing possibility that lysine PTMs may be the major means by which signalling pathways modify protein behaviour.
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Affiliation(s)
- Cristina Azevedo
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK.
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK.
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46
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Abstract
Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid was discovered 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway, in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin, were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise and the BioH esterase for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl-ACP of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyl transferase, followed by sulfur insertion at carbons C6 and C8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and thus there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate protein.
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47
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Batsios P, Meyer I, Gräf R. Proximity-Dependent Biotin Identification (BioID) in Dictyostelium Amoebae. Methods Enzymol 2015; 569:23-42. [PMID: 26778551 DOI: 10.1016/bs.mie.2015.09.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The identification of a bona fide lamin-like protein in Dictyostelium made this lower eukaryote an attractive model organism to study evolutionarily conserved nuclear envelope (NE) proteins important for nuclear organization and human laminopathies. Proximity-dependent biotin identification (BioID), reported by Roux and colleagues, is a powerful discovery tool for lamin-associated proteins. In this method, living cells express a bait protein (e.g., lamin) fused to an R118G-mutated version of BirA, an Escherichia coli biotinylase. In the presence of biotin, BirA-R118G biotinylates target proteins in close proximity in vivo, which are purified using streptavidin and identified by immunoblotting or mass spectrometry. We adapted the BioID method for use in Dictyostelium amoebae. The protocols described here successfully revealed Dictyostelium lamin-like protein NE81 proximity to Sun1, a conserved inner nuclear membrane protein.
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Affiliation(s)
- Petros Batsios
- Institute for Biochemistry and Biology, Department of Cell Biology, University of Potsdam, Potsdam, Germany
| | - Irene Meyer
- Institute for Biochemistry and Biology, Department of Cell Biology, University of Potsdam, Potsdam, Germany
| | - Ralph Gräf
- Institute for Biochemistry and Biology, Department of Cell Biology, University of Potsdam, Potsdam, Germany.
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48
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Abstract
A- and B-type lamins support the nuclear envelope, contribute to heterochromatin organization, and regulate a myriad of nuclear processes. The mechanisms by which lamins function in different cell types and the mechanisms by which lamin mutations cause over a dozen human diseases (laminopathies) remain unclear. The identification of proteins associated with lamins is likely to provide fundamental insight into these mechanisms. BioID (proximity-dependent biotin identification) is a unique and powerful method for identifying protein-protein and proximity-based interactions in living cells. BioID utilizes a mutant biotin ligase from bacteria that is fused to a protein of interest (bait). When expressed in living cells and stimulated with excess biotin, this BioID-fusion protein promiscuously biotinylates directly interacting and vicinal endogenous proteins. Following biotin-affinity capture, the biotinylated proteins can be identified using mass spectrometry. BioID thus enables screening for physiologically relevant protein associations that occur over time in living cells. BioID is applicable to insoluble proteins such as lamins that are often refractory to study by other methods and can identify weak and/or transient interactions. We discuss the use of BioID to elucidate novel lamin-interacting proteins and its applications in a broad range of biological systems, and provide detailed protocols to guide new applications.
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Affiliation(s)
- Aaron A Mehus
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota, USA
| | - Ruthellen H Anderson
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota, USA
| | - Kyle J Roux
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota, USA.
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49
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Etemadzadeh MH, Arashkia A, Roohvand F, Norouzian D, Azadmanesh K. Isolation, cloning, and expression of E. coli BirA gene for biotinylation applications. Adv Biomed Res 2015; 4:149. [PMID: 26380234 PMCID: PMC4551058 DOI: 10.4103/2277-9175.161576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 03/12/2014] [Indexed: 11/16/2022] Open
Abstract
Background: The key enzyme in biotin-(strept) avidin systems, Escherichia coli BirA biotin ligase, is currently obtained by overexpression of the long protein-tagged versions of the gene to prevent its toxic effect in E. coli. Herein we describe a rather simple and efficient system for expression of E. coli BirA without the application of long-tag proteins. Materials and Methods: The coding sequence of BirA gene was isolated by polymerase chain reaction using DNA extract of E. coli-DH5α as template. BirA amplicon harboring a GS-linker at its C-terminal was cloned into NdeI-XhoI sites of pET24a(+) vector under control of T7 promoter and upstream of the vector-derived 6xHis-tag. pET24-BirA transformed BL21-cells were induced for protein expression by IPTG and analyzed by SDS-PAGE and Western blotting. Protein expression yields were assessed by image analysis of the SDS-PAGE scans using ImageJ software. Result: Agarose gel electrophoresis indicated proper size of the BirA gene amplicon (963 bp) and accuracy of the recombinant pET24-BirA construct. Sequence alignment analysis indicated identical sequence (100%) of our isolate with that of the standard E. coli-K12 BirA gene sequence (accession number: NC_000913.3). SDS-PAGE and Western blot results indicated specific expression of the 36.6 kDa protein corresponding to the BirA protein. Image analysis estimated a yield of 12% of total protein for the BirA expression. Conclusions: By application of pET24a(+) we achieved relatively high expression of BirA in E. coli without application of any long protein-tags. Introduction of the present expression system may provide more readily available source of BirA enzyme for (strept) avidin–biotin applications and studies.
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Affiliation(s)
| | - Arash Arashkia
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Farzin Roohvand
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Dariush Norouzian
- Department of Pilot Biotechnology, Pasteur Institute of Iran, Tehran, Iran
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50
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Rees JS, Li XW, Perrett S, Lilley KS, Jackson AP. Protein Neighbors and Proximity Proteomics. Mol Cell Proteomics 2015; 14:2848-56. [PMID: 26355100 PMCID: PMC4638030 DOI: 10.1074/mcp.r115.052902] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Indexed: 12/31/2022] Open
Abstract
Within cells, proteins can co-assemble into functionally integrated and spatially restricted multicomponent complexes. Often, the affinities between individual proteins are relatively weak, and proteins within such clusters may interact only indirectly with many of their other protein neighbors. This makes proteomic characterization difficult using methods such as immunoprecipitation or cross-linking. Recently, several groups have described the use of enzyme-catalyzed proximity labeling reagents that covalently tag the neighbors of a targeted protein with a small molecule such as fluorescein or biotin. The modified proteins can then be isolated by standard pulldown methods and identified by mass spectrometry. Here we will describe the techniques as well as their similarities and differences. We discuss their applications both to study protein assemblies and to provide a new way for characterizing organelle proteomes. We stress the importance of proteomic quantitation and independent target validation in such experiments. Furthermore, we suggest that there are biophysical and cell-biological principles that dictate the appropriateness of enzyme-catalyzed proximity labeling methods to address particular biological questions of interest.
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Affiliation(s)
- Johanna S Rees
- From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW, the §Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QR, and
| | - Xue-Wen Li
- the ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Sarah Perrett
- the ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Kathryn S Lilley
- the §Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QR, and
| | - Antony P Jackson
- From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW,
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