1
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Zhang Z, Zhang Y, Liu JL. eCRUIS captures RNA-protein interaction in vitro and in vivo. Exp Cell Res 2024; 438:114051. [PMID: 38631547 DOI: 10.1016/j.yexcr.2024.114051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/19/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
As an information bridge between DNA and protein, RNA regulates cellular processes and gene expression in various ways. From its synthesis to degradation, RNA is associated with a range of RNA-binding proteins. Therefore, it is necessary to develop innovative methods to study the interaction between RNA and proteins. Previously, we developed an RNA-centric method, called CRISPR-based RNA-United Interacting System (CRUIS), to capture RNA-protein interaction in cells. On this basis, here we develop an enhanced CRUIS (eCRUIS) by combining the power of dCas13d and the engineered promiscuous ligase TurboID. The current version allows us to rapidly label RNA-binding proteins on the target RNA within 30 minutes, potentially for in vivo use. By introducing bait-assay with exogenous RNA, we confirm that eCRUIS can effectively label RNA-binding proteins on bait RNA in a short time. eCRUIS provides a broader range of in vitro and in vivo applications for studying RNA-protein interactions.
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Affiliation(s)
- Ziheng Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yuanbing Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom; Shanghai Clinical Research and Trial Center, Shanghai, 201210, China.
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2
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Yu H, Liu D, Zhang Y, Tang R, Fan X, Mao S, Lv L, Chen F, Qin H, Zhang Z, van Aalten DMF, Yang B, Yuan K. Tissue-specific O-GlcNAcylation profiling identifies substrates in translational machinery in Drosophila mushroom body contributing to olfactory learning. eLife 2024; 13:e91269. [PMID: 38619103 PMCID: PMC11018347 DOI: 10.7554/elife.91269] [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: 07/23/2023] [Accepted: 03/14/2024] [Indexed: 04/16/2024] Open
Abstract
O-GlcNAcylation is a dynamic post-translational modification that diversifies the proteome. Its dysregulation is associated with neurological disorders that impair cognitive function, and yet identification of phenotype-relevant candidate substrates in a brain-region specific manner remains unfeasible. By combining an O-GlcNAc binding activity derived from Clostridium perfringens OGA (CpOGA) with TurboID proximity labeling in Drosophila, we developed an O-GlcNAcylation profiling tool that translates O-GlcNAc modification into biotin conjugation for tissue-specific candidate substrates enrichment. We mapped the O-GlcNAc interactome in major brain regions of Drosophila and found that components of the translational machinery, particularly ribosomal subunits, were abundantly O-GlcNAcylated in the mushroom body of Drosophila brain. Hypo-O-GlcNAcylation induced by ectopic expression of active CpOGA in the mushroom body decreased local translational activity, leading to olfactory learning deficits that could be rescued by dMyc overexpression-induced increase of protein synthesis. Our study provides a useful tool for future dissection of tissue-specific functions of O-GlcNAcylation in Drosophila, and suggests a possibility that O-GlcNAcylation impacts cognitive function via regulating regional translational activity in the brain.
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Affiliation(s)
- Haibin Yu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Dandan Liu
- Life Sciences Institute, Zhejiang University, HangzhouZhejiangChina
| | - Yaowen Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Ruijun Tang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Xunan Fan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Song Mao
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Lu Lv
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Fang Chen
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Hongtao Qin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan UniversityChangshaChina
| | - Zhuohua Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaChina
| | - Daan MF van Aalten
- Department of Molecular Biology and Genetics, University of AarhusAarhusDenmark
| | - Bing Yang
- Life Sciences Institute, Zhejiang University, HangzhouZhejiangChina
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaChina
- The Biobank of Xiangya Hospital, Central South UniversityChangshaChina
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3
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Guo J, Guo S, Lu S, Gong J, Wang L, Ding L, Chen Q, Liu W. The development of proximity labeling technology and its applications in mammals, plants, and microorganisms. Cell Commun Signal 2023; 21:269. [PMID: 37777761 PMCID: PMC10544124 DOI: 10.1186/s12964-023-01310-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/07/2023] [Indexed: 10/02/2023] Open
Abstract
Protein‒protein, protein‒RNA, and protein‒DNA interaction networks form the basis of cellular regulation and signal transduction, making it crucial to explore these interaction networks to understand complex biological processes. Traditional methods such as affinity purification and yeast two-hybrid assays have been shown to have limitations, as they can only isolate high-affinity molecular interactions under nonphysiological conditions or in vitro. Moreover, these methods have shortcomings for organelle isolation and protein subcellular localization. To address these issues, proximity labeling techniques have been developed. This technology not only overcomes the limitations of traditional methods but also offers unique advantages in studying protein spatial characteristics and molecular interactions within living cells. Currently, this technique not only is indispensable in research on mammalian nucleoprotein interactions but also provides a reliable approach for studying nonmammalian cells, such as plants, parasites and viruses. Given these advantages, this article provides a detailed introduction to the principles of proximity labeling techniques and the development of labeling enzymes. The focus is on summarizing the recent applications of TurboID and miniTurbo in mammals, plants, and microorganisms. Video Abstract.
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Affiliation(s)
- Jieyu Guo
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Shuang Guo
- Medicine Research Institute, Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Siao Lu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Jun Gong
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Long Wang
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Liqiong Ding
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Qingjie Chen
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
| | - Wu Liu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
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4
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Sunna S, Bowen C, Zeng H, Rayaprolu S, Kumar P, Bagchi P, Dammer EB, Guo Q, Duong DM, Bitarafan S, Natu A, Wood L, Seyfried NT, Rangaraju S. Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines. Mol Cell Proteomics 2023; 22:100546. [PMID: 37061046 PMCID: PMC10205547 DOI: 10.1016/j.mcpro.2023.100546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/17/2023] Open
Abstract
Different brain cell types play distinct roles in brain development and disease. Molecular characterization of cell-specific mechanisms using cell type-specific approaches at the protein (proteomic) level can provide biological and therapeutic insights. To overcome the barriers of conventional isolation-based methods for cell type-specific proteomics, in vivo proteomic labeling with proximity-dependent biotinylation of cytosolic proteins using biotin ligase TurboID, coupled with mass spectrometry (MS) of labeled proteins, emerged as a powerful strategy for cell type-specific proteomics in the native state of cells without the need for cellular isolation. To complement in vivo proximity labeling approaches, in vitro studies are needed to ensure that cellular proteomes using the TurboID approach are representative of the whole-cell proteome and capture cellular responses to stimuli without disruption of cellular processes. To address this, we generated murine neuroblastoma (N2A) and microglial (BV2) lines stably expressing cytosolic TurboID to biotinylate the cellular proteome for downstream purification and analysis using MS. TurboID-mediated biotinylation captured 59% of BV2 and 65% of N2A proteomes under homeostatic conditions. TurboID labeled endolysosome, translation, vesicle, and signaling proteins in BV2 microglia and synaptic, neuron projection, and microtubule proteins in N2A neurons. TurboID expression and biotinylation minimally impacted homeostatic cellular proteomes of BV2 and N2A cells and did not affect lipopolysaccharide-mediated cytokine production or resting cellular respiration in BV2 cells. MS analysis of the microglial biotin-labeled proteins captured the impact of lipopolysaccharide treatment (>500 differentially abundant proteins) including increased canonical proinflammatory proteins (Il1a, Irg1, and Oasl1) and decreased anti-inflammatory proteins (Arg1 and Mgl2).
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Affiliation(s)
- Sydney Sunna
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Christine Bowen
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Hollis Zeng
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Sruti Rayaprolu
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Prateek Kumar
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Pritha Bagchi
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Eric B Dammer
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Qi Guo
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Duc M Duong
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Sara Bitarafan
- George W. Woodruff School of Mechanical Engineering, Wallace H. Coulter Department of Biomedical Engineering, and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Aditya Natu
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Levi Wood
- George W. Woodruff School of Mechanical Engineering, Wallace H. Coulter Department of Biomedical Engineering, and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA.
| | - Srikant Rangaraju
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA.
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Yheskel M, Sidoli S, Secombe J. Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5. Epigenetics Chromatin 2023; 16:8. [PMID: 36803422 PMCID: PMC9938590 DOI: 10.1186/s13072-023-00481-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/03/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND KDM5 family proteins are multi-domain regulators of transcription that when dysregulated contribute to cancer and intellectual disability. KDM5 proteins can regulate transcription through their histone demethylase activity in addition to demethylase-independent gene regulatory functions that remain less characterized. To expand our understanding of the mechanisms that contribute to KDM5-mediated transcription regulation, we used TurboID proximity labeling to identify KDM5-interacting proteins. RESULTS Using Drosophila melanogaster, we enriched for biotinylated proteins from KDM5-TurboID-expressing adult heads using a newly generated control for DNA-adjacent background in the form of dCas9:TurboID. Mass spectrometry analyses of biotinylated proteins identified both known and novel candidate KDM5 interactors, including members of the SWI/SNF and NURF chromatin remodeling complexes, the NSL complex, Mediator, and several insulator proteins. CONCLUSIONS Combined, our data shed new light on potential demethylase-independent activities of KDM5. In the context of KDM5 dysregulation, these interactions may play key roles in the alteration of evolutionarily conserved transcriptional programs implicated in human disorders.
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Affiliation(s)
- Matanel Yheskel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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6
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Nguyen TTM, Munkhzul C, Kim J, Kyoung Y, Vianney M, Shin S, Ju S, Pham-Bui HA, Kim J, Kim JS, Lee M. In vivo profiling of the Zucchini proximal proteome in the Drosophila ovary. Development 2023; 150:286990. [PMID: 36762624 DOI: 10.1242/dev.201220] [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: 08/23/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are small RNAs that play a conserved role in genome defense. The piRNA processing pathway is dependent on the sequestration of RNA precursors and protein factors in specific subcellular compartments. Therefore, a highly resolved spatial proteomics approach can help identify the local interactions and elucidate the unknown aspects of piRNA biogenesis. Herein, we performed TurboID proximity labeling to investigate the interactome of Zucchini (Zuc), a key factor of piRNA biogenesis in germline cells and somatic follicle cells of the Drosophila ovary. Quantitative mass spectrometry analysis of biotinylated proteins defined the Zuc-proximal proteome, including the well-known partners of Zuc. Many of these were enriched in the outer mitochondrial membrane (OMM), where Zuc was specifically localized. The proximal proteome of Zuc showed a distinct set of proteins compared with that of Tom20, a representative OMM protein, indicating that chaperone function-related and endomembrane system/vesicle transport proteins are previously unreported interacting partners of Zuc. The functional relevance of several candidates in piRNA biogenesis was validated by derepression of transposable elements after knockdown. Our results present potential Zuc-interacting proteins, suggesting unrecognized biological processes.
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Affiliation(s)
- Thi Thanh My Nguyen
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Choijamts Munkhzul
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Jeesoo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yeonju Kyoung
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Michele Vianney
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Sanghee Shin
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Seonmin Ju
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hoang-Anh Pham-Bui
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Junhyung Kim
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Mihye Lee
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
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7
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Abstract
In this chapter, we highlight examples of the diverse array of developmental, cellular, and biochemical insights that can be gained by using Drosophila melanogaster oogenesis as a model tissue. We begin with an overview of ovary development and adult oogenesis. Then we summarize how the adult Drosophila ovary continues to advance our understanding of stem cells, cell cycle, cell migration, cytoplasmic streaming, nurse cell dumping, and cell death. We also review emerging areas of study, including the roles of lipid droplets, ribosomes, and nuclear actin in egg development. Finally, we conclude by discussing the growing conservation of processes and signaling pathways that regulate oogenesis and female reproduction from flies to humans.
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8
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Zhang Y, Zhang B, Liu JL. STAMP: Spatio-Temporal Association Mapping of Proteins. Methods Mol Biol 2023; 2626:365-379. [PMID: 36715916 DOI: 10.1007/978-1-0716-2970-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We describe a tool, Spatio-Temporal Association Mapping of Proteins (STAMP), for identifying protein interactomes via proximity labeling. For a proof-of-principle study, we use cytidine 5'-triphosphate synthase (CTPS) as an example. CTPS, a metabolic enzyme, forms filamentous structures termed cytoophidia in various tissues. We apply STAMP to a variety of developmental stages and tissues in Drosophila including adult ovaries. Using a cell-specific GAL4 driver, we verify that TurboID can biotinylate the bait protein CTPS, making possible the identification of protein-protein interactions (PPIs) in individual cells. Using the wild-type and mutant CTPS as bait proteins, STAMP results in two distinct sets of proximate proteomes. Our results suggest that STAMP is a feasible tool to catch in vivo PPIs in situ at a defined spatiotemporal resolution.
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Affiliation(s)
- Yuanbing Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bo Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China. .,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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9
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Efficient TurboID-based proximity labelling method for identifying terminal sialic acid glycosylation in living cells. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1841-1853. [PMID: 36789692 PMCID: PMC10157534 DOI: 10.3724/abbs.2022184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TurboID, a proximity labelling method based on mutant biotin ligase, is an efficient new technique for recognizing protein-protein interactions and has been successfully applied to living cells. Sialic acid is typically the terminal monosaccharide attached to many glycoproteins and plays many important roles in many biological processes. However, the lack of enrichment methods for terminal sialic acid glycosylation in vivo hinders the identification and analysis of this glycosylation. Here, we introduce TurboID to identify terminal sialic acid glycosylation in living cells. SpCBM, the carbohydrate-binding domain of sialidase from Streptococcus pneumoniae, is fused with TurboID and overexpressed in HeLa cells. After streptavidin-based purification and detection by mass spectrometry, 31 terminal sialic acid N-glycosylated sites and 1359 putative terminal sialic acid glycosylated proteins are identified, many of which are located in the cytoplasm and nucleus.
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10
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TurboID functions as an efficient biotin ligase for BioID applications in Xenopus embryos. Dev Biol 2022; 492:133-138. [PMID: 36270327 PMCID: PMC9643680 DOI: 10.1016/j.ydbio.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/22/2022]
Abstract
BioID is a proximity labeling strategy whose goal is to identify in vivo protein-protein interactions. The central components of this strategy are modified biotin ligase enzymes that promiscuously add biotin groups to proteins in close proximity. The transferred biotin group provides a powerful tag for purification and thus identification of interacting proteins. While a variety of modified biotin ligases were created for BioID, the original enzymes were inefficient, required long incubation times, and high intracellular biotin concentrations for protein labeling. These limitations hinder the application of BioID in contexts such as developing embryos where processes such as cell division and cell fate decisions occur rapidly. Recently, a new biotin ligase called TurboID was developed that addressed many of the deficiencies of previous enzymes. In this paper we compare TurboID to the BioID2 biotin ligase in developing Xenopus embryos. We find that the TurboID enzyme has several advantages over the BioID2 enzyme. TurboID labels proteins efficiently without the addition of additional biotin and occurs at a range of temperatures compatible with the culturing of Xenopus embryos. Biotinylation events occurred rapidly and were limited by TurboID expression and not its activity. Thus, TurboID is an efficient tool for BioID applications in Xenopus embryos and its use should facilitate the identification of interacting proteins in specific networks and complexes during Xenopus development.
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11
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Gao N, Zheng Q, Wang Y, Li X, Li Z, Xiao H. Wun2-mediated integrin recycling promotes apoptotic cell clearance in Drosophila melanogaster. Cell Death Differ 2022; 29:2545-2561. [PMID: 35840760 PMCID: PMC9751302 DOI: 10.1038/s41418-022-01039-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 06/25/2022] [Accepted: 07/04/2022] [Indexed: 01/31/2023] Open
Abstract
Apoptotic cell (AC) clearance is a complex process in which phagocytes recognize, engulf, and digest ACs during organismal development and tissue homeostasis. Impaired efferocytosis results in developmental defects and autoimmune diseases. In the current study, we performed RNA-sequencing to systematically identify regulators involved in the phagocytosis of ACs by Drosophila melanogaster macrophage-like S2 cells, followed by targeted RNA interference screening. Wunen2 (Wun2), a homolog of mammalian lipid phosphate phosphatase (LPP), was deemed as required for efferocytosis both in vitro and in vivo. However, efferocytosis was independent of Wun2 phosphatase activity. Proteomic analysis further revealed that Rab11 and its effector Rip11 are interaction partners of Wun2. Therefore, Wun2 collaborates with Rip11 and Rab11 to mediate efficient recycling of the phagocytic receptor βν integrin subunit to the plasma membrane. The loss of Wun2 results in the routing of βv integrin subunit (Itgbn) into lysosomes, leading to its degradation. The deficiency of βv integrin subunit on the cell surface leads to aberrant and disorganized actin cytoskeleton, thereby influencing the formation of macrophage pseudopodia toward ACs and thus failure to engulf them. The findings of this study provide insights that clarify how phagocytes coordinate AC signals and adopt a precise mechanism for the maintenance of engulfment receptors at their cell membrane surface to regulate efferocytosis.
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Affiliation(s)
- Ning Gao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
- Medical College of Yan'an University, Yan'an, Shaanxi, 716000, China
| | - Qian Zheng
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Yanzhe Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Xiaowen Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Zhi Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Hui Xiao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China.
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12
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Connecting Ras and CTP synthase in Drosophila. Exp Cell Res 2022; 416:113155. [DOI: 10.1016/j.yexcr.2022.113155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/03/2022] [Accepted: 04/08/2022] [Indexed: 11/04/2022]
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13
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van de Leemput J, Wen P, Han Z. Using Drosophila Nephrocytes to Understand the Formation and Maintenance of the Podocyte Slit Diaphragm. Front Cell Dev Biol 2022; 10:837828. [PMID: 35265622 PMCID: PMC8898902 DOI: 10.3389/fcell.2022.837828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/01/2022] [Indexed: 12/12/2022] Open
Abstract
The podocyte slit diaphragm (SD) is an essential component of the glomerular filtration barrier and its disruption is a common cause of proteinuria and many types of kidney disease. Therefore, better understanding of the pathways and proteins that play key roles in SD formation and maintenance has been of great interest. Podocyte and SD biology have been mainly studied using mouse and other vertebrate models. However, vertebrates are limited by inherent properties and technically challenging in vivo access to the podocytes. Drosophila is a relatively new alternative model system but it has already made great strides. Past the initial obvious differences, mammalian podocytes and fly nephrocytes are remarkably similar at the genetic, molecular and functional levels. This review discusses SD formation and maintenance, and their dependence on cell polarity, the cytoskeleton, and endo- and exocytosis, as learned from studies in fly nephrocytes and mammalian podocytes. In addition, it reflects on the remaining gaps in our knowledge, the physiological implications for glomerular diseases and how we can leverage the advantages Drosophila has to offer to further our understanding.
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Affiliation(s)
- Joyce van de Leemput
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States.,Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Pei Wen
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States.,Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States.,Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
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14
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Hansen JM, Horowitz A, Lynch EM, Farrell DP, Quispe J, DiMaio F, Kollman JM. Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation. eLife 2021; 10:73368. [PMID: 34734801 PMCID: PMC8641951 DOI: 10.7554/elife.73368] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022] Open
Abstract
Many metabolic enzymes self-assemble into micron-scale filaments to organize and regulate metabolism. The appearance of these assemblies often coincides with large metabolic changes as in development, cancer, and stress. Yeast undergo cytoplasmic acidification upon starvation, triggering the assembly of many metabolic enzymes into filaments. However, it is unclear how these filaments assemble at the molecular level and what their role is in the yeast starvation response. CTP Synthase (CTPS) assembles into metabolic filaments across many species. Here, we characterize in vitro polymerization and investigate in vivo consequences of CTPS assembly in yeast. Cryo-EM structures reveal a pH-sensitive assembly mechanism and highly ordered filament bundles that stabilize an inactive state of the enzyme, features unique to yeast CTPS. Disruption of filaments in cells with non-assembly or pH-insensitive mutations decreases growth rate, reflecting the importance of regulated CTPS filament assembly in homeotstasis.
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Affiliation(s)
- Jesse M Hansen
- Department of Biochemistry, University of Washington, Seattle, United States.,Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, United States
| | - Avital Horowitz
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Eric M Lynch
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Daniel P Farrell
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, United States
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15
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Rosenthal SM, Misra T, Abdouni H, Branon TC, Ting AY, Scott IC, Gingras AC. A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos. Mol Cell Proteomics 2021; 20:100128. [PMID: 34332124 PMCID: PMC8383115 DOI: 10.1016/j.mcpro.2021.100128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/07/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Understanding how proteins are organized in compartments is essential to elucidating their function. While proximity-dependent approaches such as BioID have enabled a massive increase in information about organelles, protein complexes, and other structures in cell culture, to date there have been only a few studies on living vertebrates. Here, we adapted proximity labeling for protein discovery in vivo in the vertebrate model organism, zebrafish. Using lamin A (LMNA) as bait and green fluorescent protein (GFP) as a negative control, we developed, optimized, and benchmarked in vivo TurboID and miniTurbo labeling in early zebrafish embryos. We developed both an mRNA injection protocol and a transgenic system in which transgene expression is controlled by a heat shock promoter. In both cases, biotin is provided directly in the egg water, and we demonstrate that 12 h of labeling are sufficient for biotinylation of prey proteins, which should permit time-resolved analysis of development. After statistical scoring, we found that the proximal partners of LMNA detected in each system were enriched for nuclear envelope and nuclear membrane proteins and included many orthologs of human proteins identified as proximity partners of lamin A in mammalian cell culture. The tools and protocols developed here will allow zebrafish researchers to complement genetic tools with powerful proteomics approaches.
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Affiliation(s)
- Shimon M Rosenthal
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Tvisha Misra
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hala Abdouni
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Tess C Branon
- Department of Genetics, Stanford University, Stanford, California, USA; Department of Biology, Stanford University, Stanford, California, USA; Department of Chemistry, Stanford University, Stanford, California, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Alice Y Ting
- Department of Genetics, Stanford University, Stanford, California, USA; Department of Biology, Stanford University, Stanford, California, USA; Department of Chemistry, Stanford University, Stanford, California, USA; Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Ian C Scott
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada.
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16
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Histone transcription regulator Slm9 is required for cytoophidium biogenesis. Exp Cell Res 2021; 403:112582. [PMID: 33812868 DOI: 10.1016/j.yexcr.2021.112582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/25/2021] [Accepted: 03/28/2021] [Indexed: 11/23/2022]
Abstract
The cytoophidium, a subcellular structure composed of CTP synthase, can be observed during the division of Schizosaccharomyces pombe. Cytoophidium formation changes periodically with the cell cycle of yeast cells. Here, we find that histone chaperone Slm9 is required for the integrity of cytoophidia in fission yeast. When the slm9 gene is knocked out, we observe that morphological characteristics, the abundance of cytoophidia and the division of the yeast cells are significantly affected. Fragmented cytoophidia occur in slm9 mutant cells, a phenomenon rarely observed in wild-type cells. Our study reveals a potential link between a chromosomal regulatory factor and cytoophidium biogenesis.
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17
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Wang QQ, Zhao PA, Tastan ÖY, Liu JL. Polarised maintenance of cytoophidia in Drosophila follicle epithelia. Exp Cell Res 2021; 402:112564. [PMID: 33737069 DOI: 10.1016/j.yexcr.2021.112564] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/06/2021] [Accepted: 03/09/2021] [Indexed: 12/20/2022]
Abstract
The metabolic enzyme CTP synthase (CTPS) can form filamentous structures named cytoophidia in numerous types of cells, including follicle cells. However, the regulation of cytoophidium assembly remains elusive. The apicobasal polarity, a defining characteristic of Drosophila follicle epithelium, is established and regulated by a variety of membrane domains. Here we show that CTPS can form cytoophidia in Drosophila epithelial follicle cells. Cytoophidia localise to the basolateral side of follicle cells. If apical polarity regulators are knocked down, cytoophidia become unstable and distribute abnormally. Knockdown of basolateral polarity regulators has no significant effect on cytoophidia, even though the polarity is disturbed. Our results indicate that cytoophidia are maintained via polarised distribution on the basolateral side of Drosophila follicle epithelia, which is primarily achieved through the apical polarity regulators.
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Affiliation(s)
- Qiao-Qi Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Peiyao A Zhao
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Ömür Y Tastan
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China; MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom.
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