1
|
Filali-Mouncef Y, Leytens A, Vargas Duarte P, Zampieri M, Dengjel J, Reggiori F. An APEX2-based proximity-dependent biotinylation assay with temporal specificity to study protein interactions during autophagy in the yeast Saccharomyces cerevisiae. Autophagy 2024; 20:2323-2337. [PMID: 38958087 PMCID: PMC11423678 DOI: 10.1080/15548627.2024.2366749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 05/30/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
Autophagosome biogenesis is a complex process orchestrated by dynamic interactions between Atg (autophagy-related) proteins and characterized by the turnover of specific cargoes, which can differ over time and depending on how autophagy is stimulated. Proteomic analyses are central to uncover protein-protein interaction networks and when combined with proximity-dependent biotinylation or proximity labeling (PL) approaches, they also permit to detect transient and weak interactions. However, current PL procedures for yeast Saccharomyces cerevisiae, one of the leading models for the study of autophagy, do not allow to keep temporal specificity and thus identify interactions and cargoes at a precise time point upon autophagy induction. Here, we present a new ascorbate peroxidase 2 (APEX2)-based PL protocol adapted to yeast that preserves temporal specificity and allows uncovering neighbor proteins by either western blot or proteomics. As a proof of concept, we applied this new method to identify Atg8 and Atg9 interactors and detected known binding partners as well as potential uncharacterized ones in rich and nitrogen starvation conditions. Also, as a proof of concept, we confirmed the spatial proximity interaction between Atg8 and Faa1. We believe that this protocol will be a new important experimental tool for all those researchers studying the mechanism and roles of autophagy in yeast, but also other cellular pathways in this model organism.Abbreviations: APEX2, ascorbate peroxidase 2, Atg, autophagy-related; BP, biotin phenol; Cvt, cytoplasm-to-vacuole targeting; ER, endoplasmic reticulum; LN2, liquid nitrogen; MS, mass spectrometry; PAS, phagophore assembly site; PL, proximity labeling; PE, phosphatidylethanolamine; PPINs, protein-protein interaction networks; PPIs, protein-protein interactions; RT, room temperature; SARs, selective autophagy receptors; WT, wild-type.
Collapse
Affiliation(s)
- Yasmina Filali-Mouncef
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, AV, The Netherlands
| | - Alexandre Leytens
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Mattia Zampieri
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, AV, The Netherlands
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus C, Denmark
| |
Collapse
|
2
|
Noguchi K, Suzuki H, Abe R, Horiuchi K, Onoguchi-Mizutani R, Akimitsu N, Ogawa S, Akiyama T, Ike Y, Ino Y, Kimura Y, Ryo A, Doi H, Tanaka F, Suzuki Y, Toyoda A, Yamaguchi Y, Takahashi H. Multi-omics analysis using antibody-based in situ biotinylation technique suggests the mechanism of Cajal body formation. Cell Rep 2024; 43:114734. [PMID: 39283744 DOI: 10.1016/j.celrep.2024.114734] [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: 08/20/2023] [Revised: 04/30/2024] [Accepted: 08/23/2024] [Indexed: 09/28/2024] Open
Abstract
Membrane-less subcellular compartments play important roles in various cellular functions. Although techniques exist to identify components of cellular bodies, a comprehensive method for analyzing both static and dynamic states has not been established. Here, we apply an antibody-based in situ biotinylation proximity-labeling technique to identify components of static and dynamic nuclear bodies. Using this approach, we comprehensively identify DNA, RNA, and protein components of Cajal bodies (CBs) and then clarify their interactome. By inhibiting transcription, we capture dynamic changes in CBs. Our analysis reveals that nascent small nuclear RNAs (snRNAs) transcribed in CBs contribute to CB formation by assembling RNA-binding proteins, including frontotemporal dementia-related proteins, RNA-binding motif proteins, and heterogeneous nuclear ribonucleoproteins.
Collapse
Affiliation(s)
- Keisuke Noguchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Keiko Horiuchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Rena Onoguchi-Mizutani
- R&D Department, Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Nobuyoshi Akimitsu
- R&D Department, Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Shintaro Ogawa
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Tomohiko Akiyama
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Yoko Ike
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Yoko Ino
- Advance Medical Research Center, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 216-0004, Japan
| | - Yayoi Kimura
- Advance Medical Research Center, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 216-0004, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 216-0004, Japan; Department of Virology III, National Institute of Infectious Diseases, 4-7-1, Gakuen Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, Kanagawa 226-8501, Japan.
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan.
| |
Collapse
|
3
|
Sha Z, Benkovic SJ. Purinosomes spatially co-localize with mitochondrial transporters. J Biol Chem 2024; 300:107620. [PMID: 39098527 PMCID: PMC11402301 DOI: 10.1016/j.jbc.2024.107620] [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: 02/22/2024] [Revised: 06/26/2024] [Accepted: 07/20/2024] [Indexed: 08/06/2024] Open
Abstract
In this study, we advance our understanding of the spatial relationship between the purinosome, a liquid condensate consisting of six enzymes involved in de novo purine biosynthesis, and mitochondria. Previous research has shown that purinosomes move along tubulin toward mitochondria, suggesting a direct uptake of glycine from mitochondria. Here, we propose that the purinosome is located proximally to the mitochondrial transporters SLC25A13 and SLC25A38, facilitating the uptake of glycine, aspartate, and glutamate, essential factors for purine synthesis. We utilized the proximity ligation assay and APEX proximity labeling to investigate the association between purinosome proteins and mitochondrial transporters. Our results indicate that purinosome assembly occurs close to the mitochondrial membrane under purine-deficient conditions, with the transporters migrating to be adjacent to the purinosome. Furthermore, both targeted and non-targeted analyses suggest that the SLC25A13-APEX2-V5 probe accurately reflects endogenous cellular status. These findings provide insights into the spatial organization of purine biosynthesis and lay the groundwork for further investigations into additional proteins involved in this pathway.
Collapse
Affiliation(s)
- Zhou Sha
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA.
| |
Collapse
|
4
|
Zhang H, Zhang D, Li L, Willard B, Runge KW. In Vivo Proximity Labeling Identifies a New Function for the Lifespan and Autophagy-regulating Kinase Pef1, an Ortholog of Human Cdk5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598664. [PMID: 38915521 PMCID: PMC11195251 DOI: 10.1101/2024.06.12.598664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Cdk5 is a highly-conserved, noncanonical cell division kinase important to the terminal differentiation of mammalian cells in multiple organ systems. We previously identified Pef1, the Schizosaccharomyces pombe ortholog of cdk5, as regulator of chronological lifespan. To reveal the processes impacted by Pef1, we developed APEX2-biotin phenol-mediated proximity labeling in S. pombe. Efficient labeling required a short period of cell wall digestion and eliminating glucose and nitrogen sources from the medium. We identified 255 high-confidence Pef1 neighbors in growing cells and a novel Pef1-interacting partner, the DNA damage response protein Rad24. The Pef1-Rad24 interaction was validated by reciprocal proximity labeling and co-immunoprecipitation. Eliminating Pef1 partially rescued the DNA damage sensitivity of cells lacking Rad24. To monitor how Pef1 neighbors change under different conditions, cells induced for autophagy were labeled and 177 high-confidence Pef1 neighbors were identified. Gene ontology (GO) analysis of the Pef1 neighbors identified proteins participating in processes required for autophagosome expansion including regulation of actin dynamics and vesicle-mediated transport. Some of these proteins were identified in both exponentially growing and autophagic cells. Pef1-APEX2 proximity labeling therefore identified a new Pef1 function in modulating the DNA damage response and candidate processes that Pef1 and other cdk5 orthologs may regulate.
Collapse
Affiliation(s)
- Haitao Zhang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at CWRU
| | - Dongmei Zhang
- Lerner Research Institute Proteomics Core and Case Comprehensive Cancer Center Cleveland Clinic Lerner College of Medicine at CWRU
| | - Ling Li
- Lerner Research Institute Proteomics Core and Case Comprehensive Cancer Center Cleveland Clinic Lerner College of Medicine at CWRU
| | - Belinda Willard
- Lerner Research Institute Proteomics Core and Case Comprehensive Cancer Center Cleveland Clinic Lerner College of Medicine at CWRU
| | - Kurt W. Runge
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at CWRU
- Department of Genomics and Genome Sciences, Case Western Reserve University School of Medicine
| |
Collapse
|
5
|
Blank HM, Griffith WP, Polymenis M. Targeting APEX2 to the mRNA encoding fatty acid synthase β in yeast identifies interacting proteins that control its abundance in the cell cycle. Mol Biol Cell 2023; 34:br20. [PMID: 37792491 PMCID: PMC10848943 DOI: 10.1091/mbc.e23-05-0166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/06/2023] Open
Abstract
Profiling the repertoire of proteins associated with a given mRNA during the cell cycle is unstudied. Furthermore, it is easier to ask and answer what mRNAs a specific protein might bind to than the other way around. Here, we implemented an RNA-centric proximity labeling technology at different points in the cell cycle in highly synchronous yeast cultures. To understand how the abundance of FAS1, encoding fatty acid synthase, peaks late in the cell cycle, we identified proteins that interact with the FAS1 transcript in a cell cycle-dependent manner. We used dCas13d-APEX2 fusions to target FAS1 and label nearby proteins, which were then identified by mass spectrometry. The glycolytic enzyme Tdh3p, a known RNA-binding protein, interacted with the FAS1 mRNA, and it was necessary for the periodic abundance of Fas1p in the cell cycle. These results point to unexpected connections between major metabolic pathways. They also underscore the role of mRNA-protein interactions for gene expression during cell division.
Collapse
Affiliation(s)
- Heidi M. Blank
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Wendell P. Griffith
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| |
Collapse
|
6
|
Kreis E, König K, Misir M, Niemeyer J, Sommer F, Schroda M. TurboID reveals the proxiomes of Chlamydomonas proteins involved in thylakoid biogenesis and stress response. PLANT PHYSIOLOGY 2023; 193:1772-1796. [PMID: 37310689 PMCID: PMC10602608 DOI: 10.1093/plphys/kiad335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 06/14/2023]
Abstract
In Chlamydomonas (Chlamydomonas reinhardtii), the VESICLE-INDUCING PROTEIN IN PLASTIDS 1 and 2 (VIPP1 and VIPP2) play roles in the sensing and coping with membrane stress and in thylakoid membrane biogenesis. To gain more insight into these processes, we aimed to identify proteins interacting with VIPP1/2 in the chloroplast and chose proximity labeling (PL) for this purpose. We used the transient interaction between the nucleotide exchange factor CHLOROPLAST GRPE HOMOLOG 1 (CGE1) and the stromal HEAT SHOCK PROTEIN 70B (HSP70B) as test system. While PL with APEX2 and BioID proved to be inefficient, TurboID resulted in substantial biotinylation in vivo. TurboID-mediated PL with VIPP1/2 as baits under ambient and H2O2 stress conditions confirmed known interactions of VIPP1 with VIPP2, HSP70B, and the CHLOROPLAST DNAJ HOMOLOG 2 (CDJ2). Proteins identified in the VIPP1/2 proxiomes can be grouped into proteins involved in the biogenesis of thylakoid membrane complexes and the regulation of photosynthetic electron transport, including PROTON GRADIENT REGULATION 5-LIKE 1 (PGRL1). A third group comprises 11 proteins of unknown function whose genes are upregulated under chloroplast stress conditions. We named them VIPP PROXIMITY LABELING (VPL). In reciprocal experiments, we confirmed VIPP1 in the proxiomes of VPL2 and PGRL1. Our results demonstrate the robustness of TurboID-mediated PL for studying protein interaction networks in the chloroplast of Chlamydomonas and pave the way for analyzing functions of VIPPs in thylakoid biogenesis and stress responses.
Collapse
Affiliation(s)
- Elena Kreis
- Molekulare Biotechnologie & Systembiologie, RPTU Kaiserslautern-Landau, Paul-Ehrlich Straße 23, D-67663 Kaiserslautern, Germany
| | - Katharina König
- Molekulare Biotechnologie & Systembiologie, RPTU Kaiserslautern-Landau, Paul-Ehrlich Straße 23, D-67663 Kaiserslautern, Germany
| | - Melissa Misir
- Molekulare Biotechnologie & Systembiologie, RPTU Kaiserslautern-Landau, Paul-Ehrlich Straße 23, D-67663 Kaiserslautern, Germany
| | - Justus Niemeyer
- Molekulare Biotechnologie & Systembiologie, RPTU Kaiserslautern-Landau, Paul-Ehrlich Straße 23, D-67663 Kaiserslautern, Germany
| | - Frederik Sommer
- Molekulare Biotechnologie & Systembiologie, RPTU Kaiserslautern-Landau, Paul-Ehrlich Straße 23, D-67663 Kaiserslautern, Germany
| | - Michael Schroda
- Molekulare Biotechnologie & Systembiologie, RPTU Kaiserslautern-Landau, Paul-Ehrlich Straße 23, D-67663 Kaiserslautern, Germany
| |
Collapse
|
7
|
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: 10] [Impact Index Per Article: 10.0] [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.
Collapse
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.
| |
Collapse
|
8
|
Lau CS, Dowle A, Thomas GH, Girr P, Mackinder LCM. A phase-separated CO2-fixing pyrenoid proteome determined by TurboID in Chlamydomonas reinhardtii. THE PLANT CELL 2023; 35:3260-3279. [PMID: 37195994 PMCID: PMC10473203 DOI: 10.1093/plcell/koad131] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 05/19/2023]
Abstract
Phase separation underpins many biologically important cellular events such as RNA metabolism, signaling, and CO2 fixation. However, determining the composition of a phase-separated organelle is often challenging due to its sensitivity to environmental conditions, which limits the application of traditional proteomic techniques like organellar purification or affinity purification mass spectrometry to understand their composition. In Chlamydomonas reinhardtii, Rubisco is condensed into a crucial phase-separated organelle called the pyrenoid that improves photosynthetic performance by supplying Rubisco with elevated concentrations of CO2. Here, we developed a TurboID-based proximity labeling technique in which proximal proteins in Chlamydomonas chloroplasts are labeled by biotin radicals generated from the TurboID-tagged protein. By fusing 2 core pyrenoid components with the TurboID tag, we generated a high-confidence pyrenoid proxiome that contains most known pyrenoid proteins, in addition to new pyrenoid candidates. Fluorescence protein tagging of 7 previously uncharacterized TurboID-identified proteins showed that 6 localized to a range of subpyrenoid regions. The resulting proxiome also suggests new secondary functions for the pyrenoid in RNA-associated processes and redox-sensitive iron-sulfur cluster metabolism. This developed pipeline can be used to investigate a broad range of biological processes in Chlamydomonas, especially at a temporally resolved suborganellar resolution.
Collapse
Affiliation(s)
- Chun Sing Lau
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Adam Dowle
- Department of Biology, University of York, York YO10 5DD, UK
| | - Gavin H Thomas
- Department of Biology, University of York, York YO10 5DD, UK
| | - Philipp Girr
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Luke C M Mackinder
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| |
Collapse
|
9
|
Hadjicharalambous A, Whale AJ, Can G, Skehel JM, Houseley JM, Zegerman P. Checkpoint kinase interaction with DNA polymerase alpha regulates replication progression during stress. Wellcome Open Res 2023; 8:327. [PMID: 37766847 PMCID: PMC10521137 DOI: 10.12688/wellcomeopenres.19617.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2023] [Indexed: 09/29/2023] Open
Abstract
Background: In eukaryotes, replication stress activates a checkpoint response, which facilitates genome duplication by stabilising the replisome. How the checkpoint kinases regulate the replisome remains poorly understood. The aim of this study is to identify new targets of checkpoint kinases within the replisome during replication stress. Methods: Here we use an unbiased biotin proximity-ligation approach in Saccharomyces cerevisiae to identify new interactors and substrates of the checkpoint kinase Rad53 in vivo. Results: From this screen, we identified the replication initiation factor Sld7 as a Rad53 substrate, and Pol1, the catalytic subunit of polymerase a, as a Rad53-interactor. We showed that CDK phosphorylation of Pol1 mediates its interaction with Rad53. Combined with other interactions between Rad53 and the replisome, this Rad53-Pol1 interaction is important for viability and replisome progression during replication stress. Conclusions: Together, we explain how the interactions of Rad53 with the replisome are controlled by both replication stress and the cell cycle, and why these interactions might be important for coordinating the stabilisation of both the leading and lagging strand machineries.
Collapse
Affiliation(s)
| | - Alex J. Whale
- Epigenetics Programme, Babraham Institute, University of Cambridge, Cambridge, England, CB22 3AT, UK
| | - Geylani Can
- Department of Biochemistry, University of Cambridge, Cambridge, England, CB2 1GA, UK
| | - J. Mark Skehel
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, London, England, CB2 0QH, UK
| | - Jonathan M. Houseley
- Epigenetics Programme, Babraham Institute, University of Cambridge, Cambridge, England, CB22 3AT, UK
| | - Philip Zegerman
- Department of Biochemistry, University of Cambridge, Cambridge, England, CB2 1GA, UK
| |
Collapse
|
10
|
Obeng EM, Fianu I, Danquah MK. Multivalent ACE2 engineering-A promising pathway for advanced coronavirus nanomedicine development. NANO TODAY 2022; 46:101580. [PMID: 35942040 PMCID: PMC9350675 DOI: 10.1016/j.nantod.2022.101580] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/26/2022] [Accepted: 07/30/2022] [Indexed: 05/06/2023]
Abstract
The spread of coronavirus diseases has resulted in a clarion call to develop potent drugs and vaccines even as different strains appear beyond human prediction. An initial step that is integral to the viral entry into host cells results from an active-targeted interaction of the viral spike (S) proteins and the cell surface receptor, called angiotensin-converting enzyme 2 (ACE2). Thus, engineered ACE2 has been an interesting decoy inhibitor against emerging coronavirus infestation. This article discusses promising innovative ACE2 engineering pathways for current and emerging coronavirus therapeutic development. First, we provide a brief discussion of some ACE2-associated human coronaviruses and their cell invasion mechanism. Then, we describe and contrast the individual spike proteins and ACE2 receptor interactions, highlighting crucial hotspots across the ACE2-associated coronaviruses. Lastly, we address the importance of multivalency in ACE2 nanomedicine engineering and discuss novel approaches to develop and achieve multivalent therapeutic outcomes. Beyond coronaviruses, these approaches will serve as a paradigm to develop new and improved treatment technologies against pathogens that use ACE2 receptor for invasion.
Collapse
Affiliation(s)
- Eugene M Obeng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Isaac Fianu
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, 615 McCallie Ave, Chattanooga, TN 37403, United States
| |
Collapse
|
11
|
A Validated Set of Ascorbate Peroxidase-Based Organelle Markers for Electron Microscopy of Saccharomyces cerevisiae. mSphere 2022; 7:e0010722. [PMID: 35727034 PMCID: PMC9429943 DOI: 10.1128/msphere.00107-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Genetically encoded tags, such as engineered ascorbate peroxidase APEX2, offer unique advantages for the specific labeling of subcellular structures in electron microscopy (EM). However, the use of APEX2 in EM investigation of yeast has been limited. Here we describe the development of APEX2-based organelle markers for Saccharomyces cerevisiae. We found that with regard to APEX2 -catalyzed formation of diaminobenzidine precipitation, cell wall removal was not essential during sample preparation, yet the presence of fluorescent proteins in APEX2 chimeras had a negative impact. We showed that major organelles including endoplasmic reticulum, early Golgi, late Golgi/early endosomes, late endosomes, mitochondria, peroxisomes, and lipid droplets could be labeled by appropriate APEX2 chimeras. The subcellular localization of our APEX2 chimeras was verified by EM visualization and supplemented with immunofluorescence colocalization analysis when necessary, validating their feasibility as organelle markers. IMPORTANCE Yeast is an excellent single cellular model system for studying basic cellular processes. However, yeast cells are much smaller than most animal and plant cells, making the observation and recognition of yeast subcellular structures challenging. Here we developed a set of yeast organelle markers for use in electron microscopy and documented our technical approach for using this method.
Collapse
|
12
|
Abstract
![]()
Proximity
labeling can be defined as an enzymatic “in-cell”
chemical reaction that catalyzes the proximity-dependent modification
of biomolecules in live cells. Since the modified proteins can be
isolated and identified via mass spectrometry, this method has been
successfully utilized for the characterization of local proteomes
such as the sub-mitochondrial proteome and the proteome at membrane
contact sites, or spatiotemporal interactome information in live cells,
which are not “accessible” via conventional methods.
Currently, proximity labeling techniques can be applied not only for
local proteome mapping but also for profiling local RNA and DNA, in
addition to showing great potential for elucidating spatial cell–cell
interaction networks in live animal models. We believe that proximity
labeling has emerged as an essential tool in “spatiomics,”
that is, for the extraction of spatially distributed biological information
in a cell or organism. Proximity labeling is a multidisciplinary
chemical technique. For
a decade, we and other groups have engineered it for multiple applications
based on the modulation of enzyme chemistry, chemical probe design,
and mass analysis techniques that enable superior mapping results.
The technique has been adopted in biology and chemistry. This “in-cell”
reaction has been widely adopted by biologists who modified it into
an in vivo reaction in animal models. In our laboratory, we conducted
in vivo proximity labeling reactions in mouse models and could successfully
obtain the liver-specific secretome and muscle-specific mitochondrial
matrix proteome. We expect that proximity reaction can further contribute
to revealing tissue-specific localized molecular information in live
animal models. Simultaneously, chemists have also adopted the
concept and employed
chemical “photocatalysts” as artificial enzymes to develop
new proximity labeling reactions. Under light activation, photocatalysts
can convert the precursor molecules to the reactive species via electron
transfer or energy transfer and the reactive molecules can react with
proximal biomolecules within a definite lifetime in an aqueous solution.
To identify the modified biomolecules by proximity labeling, the modified
biomolecules should be enriched after lysis and sequenced using sequencing
tools. In this analysis step, the direct detection of modified residue(s)
on the modified proteins or nucleic acids can be the proof of their
labeling event by proximal enzymes or catalysts in the cell. In this
Account, we introduce the basic concept of proximity labeling and
the multidirectional advances in the development of this method. We
believe that this Account may facilitate further utilization and modification
of the method in both biological and chemical research communities,
thereby revealing unknown spatially distributed molecular or cellular
information or spatiome.
Collapse
Affiliation(s)
- Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| |
Collapse
|
13
|
Vilen Z, Reeves AE, O’Leary TR, Joeh E, Kamasawa N, Huang ML. Cell Surface Engineering Enables Surfaceome Profiling. ACS Chem Biol 2022; 18:701-710. [PMID: 35443134 PMCID: PMC9901301 DOI: 10.1021/acschembio.1c00865] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cell surface proteins (CSPs) are vital molecular mediators for cells and their extracellular environment. Thus, understanding which CSPs are displayed on cells, especially in different cell states, remains an important endeavor in cell biology. Here, we describe the integration of cell surface engineering with radical-mediated protein biotinylation to profile CSPs. This method relies on the prefunctionalization of cells with cholesterol lipid groups, followed by sortase-catalyzed conjugation with an APEX2 ascorbate peroxidase enzyme. In the presence of biotin-phenol and H2O2, APEX2 catalyzes the formation of highly reactive biotinyl radicals that covalently tag electron-rich residues within CSPs for subsequent streptavidin-based enrichment and analysis by quantitative mass spectrometry. While APEX2 is traditionally used to capture proximity-based interactomes, we envisioned using it in a "baitless" manner on cell surfaces to capture CSPs. We evaluate this strategy in light of another CSP labeling method that relies on the presence of cell surface sialic acid. Using the APEX2 strategy, we describe the CSPs found in three mammalian cell lines and compare CSPs in adherent versus three-dimensional pancreatic adenocarcinoma cells.
Collapse
Affiliation(s)
- Zak Vilen
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284,Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037
| | - Abigail E. Reeves
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284,Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037
| | - Timothy R. O’Leary
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284
| | - Eugene Joeh
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284,Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037
| | - Naomi Kamasawa
- The Imaging Center and Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL, 33458
| | - Mia L. Huang
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284,Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Corresponding author:
| |
Collapse
|
14
|
Weiner E, Pinskey JM, Nicastro D, Otegui MS. Electron microscopy for imaging organelles in plants and algae. PLANT PHYSIOLOGY 2022; 188:713-725. [PMID: 35235662 PMCID: PMC8825266 DOI: 10.1093/plphys/kiab449] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/23/2021] [Indexed: 05/31/2023]
Abstract
Recent developments in both instrumentation and image analysis algorithms have allowed three-dimensional electron microscopy (3D-EM) to increase automated image collections through large tissue volumes using serial block-face scanning EM (SEM) and to achieve near-atomic resolution of macromolecular complexes using cryo-electron tomography (cryo-ET) and sub-tomogram averaging. In this review, we discuss applications of cryo-ET to cell biology research on plant and algal systems and the special opportunities they offer for understanding the organization of eukaryotic organelles with unprecedently resolution. However, one of the most challenging aspects for cryo-ET is sample preparation, especially for multicellular organisms. We also discuss correlative light and electron microscopy (CLEM) approaches that have been developed for ET at both room and cryogenic temperatures.
Collapse
Affiliation(s)
- Ethan Weiner
- Department of Botany, University of Wisconsin, Madison 53706, Wisconsin
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison 53706, Wisconsin
| | - Justine M Pinskey
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas 75390, Texas
| | - Daniela Nicastro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas 75390, Texas
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin, Madison 53706, Wisconsin
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison 53706, Wisconsin
| |
Collapse
|
15
|
Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS. Subcellular Transcriptomics and Proteomics: A Comparative Methods Review. Mol Cell Proteomics 2022; 21:100186. [PMID: 34922010 PMCID: PMC8864473 DOI: 10.1016/j.mcpro.2021.100186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
The internal environment of cells is molecularly crowded, which requires spatial organization via subcellular compartmentalization. These compartments harbor specific conditions for molecules to perform their biological functions, such as coordination of the cell cycle, cell survival, and growth. This compartmentalization is also not static, with molecules trafficking between these subcellular neighborhoods to carry out their functions. For example, some biomolecules are multifunctional, requiring an environment with differing conditions or interacting partners, and others traffic to export such molecules. Aberrant localization of proteins or RNA species has been linked to many pathological conditions, such as neurological, cancer, and pulmonary diseases. Differential expression studies in transcriptomics and proteomics are relatively common, but the majority have overlooked the importance of subcellular information. In addition, subcellular transcriptomics and proteomics data do not always colocate because of the biochemical processes that occur during and after translation, highlighting the complementary nature of these fields. In this review, we discuss and directly compare the current methods in spatial proteomics and transcriptomics, which include sequencing- and imaging-based strategies, to give the reader an overview of the current tools available. We also discuss current limitations of these strategies as well as future developments in the field of spatial -omics.
Collapse
Affiliation(s)
- Josie A Christopher
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Aikaterini Geladaki
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Department of Genetics, University of Cambridge, Cambridge, UK
| | - Charlotte S Dawson
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Owen L Vennard
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
| |
Collapse
|
16
|
Singer-Krüger B, Jansen RP. Proteomic Mapping by APEX2-Catalyzed Proximity Labeling in Saccharomyces cerevisiae Semipermeabilized Cells. Methods Mol Biol 2022; 2477:261-274. [PMID: 35524122 DOI: 10.1007/978-1-0716-2257-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Enzyme-catalyzed proximity labeling (PL) has proven to be a valuable resource for proteomic mapping of subcellular compartments and protein networks in living cells. We have used engineered ascorbate peroxidase (APEX2) to develop a PL approach for budding yeast. It is based on semipermeabilized cells to overcome poor cellular permeability of the APEX2 substrate biotin-phenol and difficulties in its delivery into the cell. The use of semipermeabilized cells has several advantages, in particular the avoidance of generating fragile spheroplasts and the opportunity of employing cells from a glucose-containing medium for APEX2 tagging. In this protocol we describe how to perform a ratiometric three-state stable isotope labeling by amino acids in cell culture (SILAC) approach that allows to map an open cellular compartment like the yeast nucleus. In particular, we focus on the proteomic sample preparation and provide instructions to achieve high-resolution mapping of a subcellular yeast proteome.
Collapse
Affiliation(s)
- Birgit Singer-Krüger
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
| | - Ralf-Peter Jansen
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Kimmel J, Kehrer J, Frischknecht F, Spielmann T. Proximity-dependent biotinylation approaches to study apicomplexan biology. Mol Microbiol 2021; 117:553-568. [PMID: 34587292 DOI: 10.1111/mmi.14815] [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: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 11/28/2022]
Abstract
In the last 10 years, proximity-dependent biotinylation (PDB) techniques greatly expanded the ability to study protein environments in the living cell that range from specific protein complexes to entire compartments. This is achieved by using enzymes such as BirA* and APEX that are fused to proteins of interest and biotinylate proteins in their proximity. PDB techniques are now also increasingly used in apicomplexan parasites. In this review, we first give an overview of the main PDB approaches and how they compare with other techniques that address similar questions. PDB is particularly valuable to detect weak or transient protein associations under physiological conditions and to study cellular structures that are difficult to purify or have a poorly understood protein composition. We also highlight new developments such as novel smaller or faster-acting enzyme variants and conditional PDB approaches, providing improvements in both temporal and spatial resolution which may offer broader application possibilities useful in apicomplexan research. In the second part, we review work using PDB techniques in apicomplexan parasites and how this expanded our knowledge about these medically important parasites.
Collapse
Affiliation(s)
- Jessica Kimmel
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jessica Kehrer
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,German Center for Infectious Disease Research, DZIF, Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,German Center for Infectious Disease Research, DZIF, Heidelberg, Germany
| | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| |
Collapse
|
19
|
Li T, Xu C, Xu J, Luo J, Yu B, Meng X, Li C, Pan G, Zhou Z. Proteomic Identification of Bombyx mori Organelles Using the Engineered Ascorbate Peroxidase APEX and Development of Silkworm Organelle Proteome Database (SilkOrganPDB). Int J Mol Sci 2021; 22:ijms22095051. [PMID: 34068790 PMCID: PMC8126250 DOI: 10.3390/ijms22095051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022] Open
Abstract
Silkworm Bombyx mori is an economically important insect and a lepidopteran model. Organelle proteome is vital to understanding gene functions; however, it remains to be identified in silkworm. Here, using the engineered ascorbate peroxidase APEX, we constructed transgenic B. mori embryo cells (BmE) expressing APEX-NLS, COX4-APEX, APEX-Rev, and APEX-KDEL in nucleus, mitochondrial matrix (MM), cytosol, and endoplasmic reticulum (ER), and isolated the biotin-labeled proteins using streptavidin-affinity purification, respectively. The isolated proteins were determined using LC-MS/MS and annotated by searching B. mori genomes downloaded from GenBank, SilkBase, SilkDB 2.0, and SilkDB 3.0, resulting in 842, 495, 311, and 445 organelle proteins identified, respectively. We mapped the 296 MM proteins annotated in the GenBank data to mitochondrial protein databases of the fly, human, and mouse, and found that 140 (47%) proteins are homologous to 80 fly proteins, and 65 (22%) proteins match to 31 and 29 human and mouse proteins, respectively. Protein orthology was predicted in multiple insects using OrthoMCL, producing 460 families containing 839 proteins we identified. Out of 460 families, 363 were highly conserved and found in all insects, leaving only three proteins without orthology in other insects, indicating that the identified proteins are highly conserved and probably play important roles in insects. A gene ontology enrichment analysis by clusterProfiler revealed that the nucleus proteins significantly enriched in cellular component terms of nucleus and nucleolus, the MM proteins markedly enriched in molecular function terms of nucleotide binding, and the cytosol proteins mainly enriched in biological process terms of small molecule metabolism. To facilitate the usage and analysis of our data, we developed an open-access database, Silkworm Organelle Proteome Database (SilkOrganPDB), which provides multiple modules for searching, browsing, downloading, and analyzing these proteins, including BLAST, HMMER, Organelle Proteins, Protein Locations, Sequences, Gene Ontology, Homologs, and Phylogeny. In summary, our work revealed the protein composition of silkworm BmE organelles and provided a database resource helpful for understanding the functions and evolution of these proteins.
Collapse
Affiliation(s)
- Tian Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
- Correspondence: (T.L.); (Z.Z.)
| | - Chen Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Jinzhi Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Jian Luo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Bin Yu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Xianzhi Meng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Chunfeng Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Guoqing Pan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Zeyang Zhou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
- College of Life Science, Chongqing Normal University, Chongqing 400047, China
- Correspondence: (T.L.); (Z.Z.)
| |
Collapse
|
20
|
Turnšek J, Brunson JK, Viedma MDPM, Deerinck TJ, Horák A, Oborník M, Bielinski VA, Allen AE. Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. eLife 2021; 10:e52770. [PMID: 33591270 PMCID: PMC7972479 DOI: 10.7554/elife.52770] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Iron is a biochemically critical metal cofactor in enzymes involved in photosynthesis, cellular respiration, nitrate assimilation, nitrogen fixation, and reactive oxygen species defense. Marine microeukaryotes have evolved a phytotransferrin-based iron uptake system to cope with iron scarcity, a major factor limiting primary productivity in the global ocean. Diatom phytotransferrin is endocytosed; however, proteins downstream of this environmentally ubiquitous iron receptor are unknown. We applied engineered ascorbate peroxidase APEX2-based subcellular proteomics to catalog proximal proteins of phytotransferrin in the model marine diatom Phaeodactylum tricornutum. Proteins encoded by poorly characterized iron-sensitive genes were identified including three that are expressed from a chromosomal gene cluster. Two of them showed unambiguous colocalization with phytotransferrin adjacent to the chloroplast. Further phylogenetic, domain, and biochemical analyses suggest their involvement in intracellular iron processing. Proximity proteomics holds enormous potential to glean new insights into iron acquisition pathways and beyond in these evolutionarily, ecologically, and biotechnologically important microalgae.
Collapse
Affiliation(s)
- Jernej Turnšek
- Biological and Biomedical Sciences, The Graduate School of Arts and Sciences, Harvard UniversityCambridgeUnited States
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
- Wyss Institute for Biologically Inspired Engineering, Harvard UniversityBostonUnited States
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Center for Research in Biological Systems, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
| | - John K Brunson
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
| | | | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, University of California San DiegoLa JollaUnited States
| | - Aleš Horák
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Miroslav Oborník
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy, J. Craig Venter InstituteLa JollaUnited States
| | - Andrew Ellis Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
| |
Collapse
|
21
|
APEX2 Proximity Proteomics Resolves Flagellum Subdomains and Identifies Flagellum Tip-Specific Proteins in Trypanosoma brucei. mSphere 2021; 6:6/1/e01090-20. [PMID: 33568455 PMCID: PMC8141408 DOI: 10.1128/msphere.01090-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Sleeping sickness is a neglected tropical disease caused by the protozoan parasite Trypanosoma brucei. The disease disrupts the sleep-wake cycle, leading to coma and death if left untreated. T. brucei motility, transmission, and virulence depend on its flagellum (cilium), which consists of several different specialized subdomains. Trypanosoma brucei is the protozoan parasite responsible for sleeping sickness, a lethal vector-borne disease. T. brucei has a single flagellum (cilium) that plays critical roles in transmission and pathogenesis. An emerging concept is that the flagellum is organized into subdomains, each having specialized composition and function. The overall flagellum proteome has been well studied, but a critical knowledge gap is the protein composition of individual subdomains. We have tested whether APEX-based proximity proteomics could be used to examine the protein composition of T. brucei flagellum subdomains. As APEX-based labeling has not previously been described in T. brucei, we first fused APEX2 to the DRC1 subunit of the nexin-dynein regulatory complex, a well-characterized axonemal complex. We found that DRC1-APEX2 directs flagellum-specific biotinylation, and purification of biotinylated proteins yields a DRC1 “proximity proteome” having good overlap with published proteomes obtained from purified axonemes. Having validated the use of APEX2 in T. brucei, we next attempted to distinguish flagellar subdomains by fusing APEX2 to a flagellar membrane protein that is restricted to the flagellum tip, AC1, and another one that is excluded from the tip, FS179. Fluorescence microscopy demonstrated subdomain-specific biotinylation, and principal-component analysis showed distinct profiles between AC1-APEX2 and FS179-APEX2. Comparing these two profiles allowed us to identify an AC1 proximity proteome that is enriched for tip proteins, including proteins involved in signaling. Our results demonstrate that APEX2-based proximity proteomics is effective in T. brucei and can be used to resolve the proteome composition of flagellum subdomains that cannot themselves be readily purified. IMPORTANCE Sleeping sickness is a neglected tropical disease caused by the protozoan parasite Trypanosoma brucei. The disease disrupts the sleep-wake cycle, leading to coma and death if left untreated. T. brucei motility, transmission, and virulence depend on its flagellum (cilium), which consists of several different specialized subdomains. Given the essential and multifunctional role of the T. brucei flagellum, there is need for approaches that enable proteomic analysis of individual subdomains. Our work establishes that APEX2 proximity labeling can, indeed, be implemented in the biochemical environment of T. brucei and has allowed identification of proximity proteomes for different flagellar subdomains that cannot be purified. This capacity opens the possibility to study the composition and function of other compartments. We expect this approach may be extended to other eukaryotic pathogens and will enhance the utility of T. brucei as a model organism to study ciliopathies, heritable human diseases in which cilium function is impaired.
Collapse
|
22
|
Dahlgren KK, Gates C, Lee T, Cameron JC. Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002. PHOTOSYNTHESIS RESEARCH 2021; 147:177-195. [PMID: 33280076 PMCID: PMC7880944 DOI: 10.1007/s11120-020-00806-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Cyanobacteria possess unique intracellular organization. Many proteomic studies have examined different features of cyanobacteria to learn about the intracellular structures and their respective functions. While these studies have made great progress in understanding cyanobacterial physiology, the conventional fractionation methods used to purify cellular structures have limitations; specifically, certain regions of cells cannot be purified with existing fractionation methods. Proximity-based proteomics techniques were developed to overcome the limitations of biochemical fractionation for proteomics. Proximity-based proteomics relies on spatiotemporal protein labeling followed by mass spectrometry of the labeled proteins to determine the proteome of the region of interest. We performed proximity-based proteomics in the cyanobacterium Synechococcus sp. PCC 7002 with the APEX2 enzyme, an engineered ascorbate peroxidase. We determined the proteome of the thylakoid lumen, a region of the cell that has remained challenging to study with existing methods, using a translational fusion between APEX2 and PsbU, a lumenal subunit of photosystem II. Our results demonstrate the power of APEX2 as a tool to study the cell biology of intracellular features and processes, including photosystem II assembly in cyanobacteria, with enhanced spatiotemporal resolution.
Collapse
Affiliation(s)
- Kelsey K Dahlgren
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
- Interdisciplinary Quantitative Biology Program (IQ Biology), BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Colin Gates
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Thomas Lee
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Jeffrey C Cameron
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA.
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA.
- National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| |
Collapse
|
23
|
Li Y, Liu K, Zhou Y, Yang J, Zou P. Protocol for Proximity-Dependent Proteomic Profiling in Yeast Cells by APEX and Alk-Ph Probe. STAR Protoc 2020; 1:100137. [PMID: 33377031 PMCID: PMC7757286 DOI: 10.1016/j.xpro.2020.100137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Alk-Ph is a clickable APEX2 substrate developed for spatially restricted protein/RNA labeling in intact yeast cells. Alk-Ph is more water soluble and cell wall permeable than biotin-phenol substrate, allowing more efficient profiling of the subcellular proteome in microorganisms. We describe the protocol for Alk-Ph probe synthesis, APEX2 expression, and protein/RNA labeling in yeast and the workflow for quantitative proteomic experiments and data analysis. Using the yeast mitochondria as an example, we provide guidelines to achieve high-resolution mapping of subcellular yeast proteome and transcriptome. For complete details on the use and execution of this protocol, please refer to Li et al. (2020). Synthesis of clickable APEX probe Alk-Ph Proximity-dependent proteomic profiling in yeast Spatially restricted RNA labeling in yeast
Collapse
Affiliation(s)
- Yi Li
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Keke Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ying Zhou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Jing Yang
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China.,Chinese Institute for Brain Research (CIBR), Beijing 102206, China
| |
Collapse
|
24
|
Tan B, Peng S, Yatim SMJM, Gunaratne J, Hunziker W, Ludwig A. An Optimized Protocol for Proximity Biotinylation in Confluent Epithelial Cell Cultures Using the Peroxidase APEX2. STAR Protoc 2020; 1:100074. [PMID: 33111110 PMCID: PMC7580243 DOI: 10.1016/j.xpro.2020.100074] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The peroxidase APEX2 has been used widely for proximity biotinylation and subsequent proteomics analyses. However, the poor membrane permeability of the biotin phenol substrate and the inhibitory effect of peroxide on the enzyme’s activity has hampered proximity labeling in certain cell culture systems and tissues. Here, we describe an APEX2 protocol that uses alternative peroxide and biotin phenol concentrations. The protocol permits robust proximity biotinylation in confluent epithelial cell cultures and may be applicable to other cell cultures and tissues. For complete details on the use and execution of this protocol, please refer to Tan et al. (2020). APEX2 permits proximity biotinylation in confluent cell cultures Biotin phenol and peroxide concentrations are critical Spatial controls are required to generate specific proximity proteomes
Collapse
Affiliation(s)
- Benedict Tan
- Epithelial Cell Biology Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Singapore 138673, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore 117593, Singapore
| | - Suat Peng
- Quantitative Proteomics Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Singapore 138673, Singapore
| | - Siti Maryam J M Yatim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Jayantha Gunaratne
- Quantitative Proteomics Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Singapore 138673, Singapore.,Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore 117594, Singapore
| | - Walter Hunziker
- Epithelial Cell Biology Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Singapore 138673, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore 117593, Singapore
| | - Alexander Ludwig
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Li Y, Tian C, Liu K, Zhou Y, Yang J, Zou P. A Clickable APEX Probe for Proximity-Dependent Proteomic Profiling in Yeast. Cell Chem Biol 2020; 27:858-865.e8. [DOI: 10.1016/j.chembiol.2020.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/24/2019] [Accepted: 05/08/2020] [Indexed: 10/24/2022]
|
27
|
Ummethum H, Hamperl S. Proximity Labeling Techniques to Study Chromatin. Front Genet 2020; 11:450. [PMID: 32477404 PMCID: PMC7235407 DOI: 10.3389/fgene.2020.00450] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022] Open
Abstract
Mammals contain over 200 different cell types, yet nearly all have the same genomic DNA sequence. It is a key question in biology how the genetic instructions in DNA are selectively interpreted by cells to specify various transcriptional programs and therefore cellular identity. The structural and functional organization of chromatin governs the transcriptional state of individual genes. To understand how genomic loci adopt different levels of gene expression, it is critical to characterize all local chromatin factors as well as long-range interactions in the 3D nuclear compartment. Much of our current knowledge regarding protein interactions in a chromatin context is based on affinity purification of chromatin components coupled to mass spectrometry (AP-MS). AP-MS has been invaluable to map strong protein-protein interactions in the nucleus. However, the interaction is detected after cell lysis and biochemical enrichment, allowing for loss or gain of false positive or negative interaction partners. Recently, proximity-dependent labeling methods have emerged as powerful tools for studying chromatin in its native context. These methods take advantage of engineered enzymes that are fused to a chromatin factor of interest and can directly label all factors in proximity. Subsequent pull-down assays followed by mass spectrometry or sequencing approaches provide a comprehensive snapshot of the proximal chromatin interactome. By combining this method with dCas9, this approach can also be extended to study chromatin at specific genomic loci. Here, we review and compare current proximity-labeling approaches available for studying chromatin, with a particular focus on new emerging technologies that can provide important insights into the transcriptional and chromatin interaction networks essential for cellular identity.
Collapse
Affiliation(s)
- Henning Ummethum
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Stephan Hamperl
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| |
Collapse
|
28
|
Three-Dimensional Visualization of APEX2-Tagged Erg11 in Saccharomyces cerevisiae Using Focused Ion Beam Scanning Electron Microscopy. mSphere 2020; 5:5/1/e00981-19. [PMID: 32024705 PMCID: PMC7002314 DOI: 10.1128/msphere.00981-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The determination of the exact location of a protein in the cell is essential to the understanding of biological processes. Here, we report for the first time the visualization of a protein of interest in Saccharomyces cerevisiae using focused ion beam scanning electron microscopy (FIB-SEM). As a proof of concept, the integral endoplasmic reticulum (ER) membrane protein Erg11 has been C-terminally tagged with APEX2, which is an engineered peroxidase that catalyzes an electron-dense deposition of 3,3'-diaminobenzidine (DAB), as such marking the location of the fused protein of interest in electron microscopic images. As DAB is unable to cross the yeast cell wall to react with APEX2, cell walls have been partly removed by the formation of spheroplasts. This has resulted in a clear electron-dense ER signal for the Erg11 protein using FIB-SEM. With this study, we have validated the use of the APEX2 tag for visualization of yeast proteins in electron microscopy. Furthermore, we have introduced a methodology that enables precise and three-dimensional (3D) localization studies in yeast, with nanometer resolution and without the need for antibody staining. Because of these properties, the described technique can offer valuable information on the molecular functions of studied proteins.IMPORTANCE With this study, we have validated the use of the APEX2 tag to define the localization of proteins in the model yeast S. cerevisiae As such, FIB-SEM can identify the exact 3D location of a protein of interest in the cell with nanometer-scale resolution. Such detailed imaging could provide essential information on the elucidation of various biological processes. APEX2, which adds electron density to a fused protein of interest upon addition of the substrate DAB, originally was used in mammalian studies. With this study, we expand its use to protein localization studies in one of the most important models in molecular biology.
Collapse
|
29
|
Nguyen TMT, Kim J, Doan TT, Lee MW, Lee M. APEX Proximity Labeling as a Versatile Tool for Biological Research. Biochemistry 2019; 59:260-269. [PMID: 31718172 DOI: 10.1021/acs.biochem.9b00791] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Most proteins are specifically localized in membrane-encapsulated organelles or non-membrane-bound compartments. The subcellular localization of proteins facilitates their functions and integration into functional networks; therefore, protein localization is tightly regulated in diverse biological contexts. However, protein localization has been mainly analyzed through immunohistochemistry or the fractionation of subcellular compartments, each of which has major drawbacks. Immunohistochemistry can examine only a handful of proteins at a time, and fractionation inevitably relies on the lysis of cells, which disrupts native cellular conditions. Recently, an engineered ascorbate peroxidase (APEX)-based proximity labeling technique combined with mass spectrometry was developed, which allows for temporally and spatially resolved proteomic mapping. In the presence of H2O2, engineered APEX oxidizes biotin-phenols into biotin-phenoxyl radicals, and these short-lived radicals biotinylate electron-rich amino acids within a radius of several nanometers. Biotinylated proteins are subsequently enriched by streptavidin and identified by mass spectrometry. This permits the sensitive and efficient labeling of proximal proteins around locally expressed APEX. Through the targeted expression of APEX in the subcellular region of interest, proteomic profiling of submitochondrial spaces, the outer mitochondrial membrane, the endoplasmic reticulum (ER)-mitochondrial contact, and the ER membrane has been performed. Furthermore, this method has been modified to define interaction networks in the vicinity of target proteins and has also been applied to analyze the spatial transcriptome. In this Perspective, we provide an outline of this newly developed technique and discuss its potential applications to address diverse biological questions.
Collapse
Affiliation(s)
- Thanh My Thi Nguyen
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| | - Junhyung Kim
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| | - Thi Tram Doan
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| | - Min-Woo Lee
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| | - Mihye Lee
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| |
Collapse
|
30
|
Santin YG. Uncovering the In Vivo Proxisome Using Proximity‐Tagging Methods. Bioessays 2019; 41:e1900131. [DOI: 10.1002/bies.201900131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/04/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Yoann G. Santin
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la MéditerranéeAix‐Marseille Université – CNRS UMR7255 31 Chemin Joseph Aiguier, CS70071, 13402 Marseille Cedex 09 France
| |
Collapse
|
31
|
Singer‐Krüger B, Fröhlich T, Franz‐Wachtel M, Nalpas N, Macek B, Jansen R. APEX2‐mediated proximity labeling resolves protein networks in
Saccharomyces cerevisiae
cells. FEBS J 2019; 287:325-344. [DOI: 10.1111/febs.15007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/18/2019] [Accepted: 07/17/2019] [Indexed: 12/14/2022]
Affiliation(s)
| | - Theresa Fröhlich
- Interfaculty Institute of Biochemistry University of Tübingen Germany
| | | | | | - Boris Macek
- Proteome Center Tübingen University of Tübingen Germany
| | - Ralf‐Peter Jansen
- Interfaculty Institute of Biochemistry University of Tübingen Germany
| |
Collapse
|
32
|
Nightingale DJH, Lilley KS, Oliver SG. A Protocol to Map the Spatial Proteome Using HyperLOPIT in Saccharomyces cerevisiae. Bio Protoc 2019; 9:e3303. [PMID: 33654815 PMCID: PMC7854154 DOI: 10.21769/bioprotoc.3303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/12/2019] [Accepted: 06/25/2019] [Indexed: 11/02/2022] Open
Abstract
The correct subcellular localization of proteins is vital for cellular function and the study of this process at the systems level will therefore enrich our understanding of the roles of proteins within the cell. Multiple methods are available for the study of protein subcellular localization, including fluorescence microscopy, organelle cataloging, proximity labeling methods, and whole-cell protein correlation profiling methods. We provide here a protocol for the systems-level study of the subcellular localization of the yeast proteome, using a version of hyperplexed Localization of Organelle Proteins by Isotope Tagging (hyperLOPIT) that has been optimized for use with Saccharomyces cerevisiae. The entire protocol encompasses cell culture, cell lysis by nitrogen cavitation, subcellular fractionation, monitoring of the fractionation using Western blotting, labeling of samples with TMT isobaric tags and mass spectrometric analysis. Also included is a brief explanation of downstream processing of the mass spectrometry data to produce a map of the spatial proteome. If required, the nitrogen cavitation lysis and Western blotting portions of the protocol may be performed independently of the mass spectrometry analysis. The protocol in its entirety, however, enables the unbiased, systems-level and high-resolution analysis of the localizations of thousands of proteins in parallel within a single experiment.
Collapse
Affiliation(s)
- Daniel J. H. Nightingale
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, United Kingdom
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, United Kingdom
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, United Kingdom
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, United Kingdom
| | - Stephen G. Oliver
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, United Kingdom
| |
Collapse
|
33
|
Fazal FM, Han S, Parker KR, Kaewsapsak P, Xu J, Boettiger AN, Chang HY, Ting AY. Atlas of Subcellular RNA Localization Revealed by APEX-Seq. Cell 2019; 178:473-490.e26. [PMID: 31230715 PMCID: PMC6786773 DOI: 10.1016/j.cell.2019.05.027] [Citation(s) in RCA: 354] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/31/2018] [Accepted: 05/14/2019] [Indexed: 01/25/2023]
Abstract
We introduce APEX-seq, a method for RNA sequencing based on direct proximity labeling of RNA using the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome as a resource, revealing extensive patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two distinct pathways of messenger RNA localization to mitochondria, each associated with specific sets of transcripts for building complementary macromolecular machines within the organelle. APEX-seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome.
Collapse
Affiliation(s)
- Furqan M Fazal
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shuo Han
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Kevin R Parker
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pornchai Kaewsapsak
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jin Xu
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alistair N Boettiger
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Alice Y Ting
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| |
Collapse
|
34
|
Nightingale DJ, Geladaki A, Breckels LM, Oliver SG, Lilley KS. The subcellular organisation of Saccharomyces cerevisiae. Curr Opin Chem Biol 2019; 48:86-95. [PMID: 30503867 PMCID: PMC6391909 DOI: 10.1016/j.cbpa.2018.10.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 01/06/2023]
Abstract
Subcellular protein localisation is essential for the mechanisms that govern cellular homeostasis. The ability to understand processes leading to this phenomenon will therefore enhance our understanding of cellular function. Here we review recent developments in this field with regard to mass spectrometry, fluorescence microscopy and computational prediction methods. We highlight relative strengths and limitations of current methodologies focussing particularly on studies in the yeast Saccharomyces cerevisiae. We further present the first cell-wide spatial proteome map of S. cerevisiae, generated using hyperLOPIT, a mass spectrometry-based protein correlation profiling technique. We compare protein subcellular localisation assignments from this map, with two published fluorescence microscopy studies and show that confidence in localisation assignment is attained using multiple orthogonal methods that provide complementary data.
Collapse
Affiliation(s)
- Daniel Jh Nightingale
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, United Kingdom; Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Aikaterini Geladaki
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, United Kingdom; Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom; Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, United Kingdom
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, United Kingdom; Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Stephen G Oliver
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, United Kingdom; Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.
| |
Collapse
|
35
|
Larochelle M, Bergeron D, Arcand B, Bachand F. Proximity-dependent biotinylation by TurboID to identify protein-protein interaction networks in yeast. J Cell Sci 2019; 132:jcs.232249. [DOI: 10.1242/jcs.232249] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/29/2019] [Indexed: 01/27/2023] Open
Abstract
The use of proximity-dependent biotinylation assays coupled to mass spectrometry (PDB-MS) has changed the field of protein-protein interaction studies. Yet, despite the recurrent and successful use of BioID-based protein-protein interactions screening in mammalian cells, the implementation of PDB-MS in yeast has not been effective. Here we report a simple and rapid approach in yeast to effectively screen for proximal and interacting proteins in their natural cellular environment by using TurboID, a recently described version of the BirA biotin ligase. Using the protein arginine methyltransferase Rmt3 and the RNA exosome subunits, Rrp6 and Dis3, the application of PDB-MS in yeast by using TurboID was able to recover protein-protein interactions previously identified using other biochemical approaches and provided new complementary information for a given protein bait. The development of a rapid and effective PDB assay that can systematically analyze protein-protein interactions in living yeast cells opens the way for large-scale proteomics studies in this powerful model organism.
Collapse
Affiliation(s)
- Marc Larochelle
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Qc, Canada
| | - Danny Bergeron
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Qc, Canada
| | - Bruno Arcand
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Qc, Canada
| | - François Bachand
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Qc, Canada
| |
Collapse
|
36
|
Abstract
Peroxisomes in fungi are involved in a huge number of different metabolic processes. In addition, non-metabolic functions have also been identified. The proteins that are present in a particular peroxisome determine its metabolic function, whether they are the matrix localized enzymes of the different metabolic pathways or the membrane proteins involved in transport of metabolites across the peroxisomal membrane. Other peroxisomal proteins play a role in organelle biogenesis and dynamics, such as fission, transport and inheritance. Hence, obtaining a complete overview of which proteins are present in peroxisomes at a given time or under a given growth condition provides invaluable insights into peroxisome biology. Bottom up approaches are ideal to follow one or a few proteins at a time but they are not able to give a global view of the content of peroxisomes. To gain such information, top down approaches are required and one that has provided valuable insights into peroxisome function is mass spectrometry based organellar proteomics. Here, we discuss the findings of several such studies in yeast and filamentous fungi and outline new insights into peroxisomal function that were gained from these studies.
Collapse
Affiliation(s)
- Xin Chen
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands
| | - Chris Williams
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands.
| |
Collapse
|
37
|
Bournaud C, Gillet FX, Murad AM, Bresso E, Albuquerque EVS, Grossi-de-Sá MF. Meloidogyne incognita PASSE-MURAILLE (MiPM) Gene Encodes a Cell-Penetrating Protein That Interacts With the CSN5 Subunit of the COP9 Signalosome. FRONTIERS IN PLANT SCIENCE 2018; 9:904. [PMID: 29997646 PMCID: PMC6029430 DOI: 10.3389/fpls.2018.00904] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/07/2018] [Indexed: 05/11/2023]
Abstract
The pathogenicity of phytonematodes relies on secreted virulence factors to rewire host cellular pathways for the benefits of the nematode. In the root-knot nematode (RKN) Meloidogyne incognita, thousands of predicted secreted proteins have been identified and are expected to interact with host proteins at different developmental stages of the parasite. Identifying the host targets will provide compelling evidence about the biological significance and molecular function of the predicted proteins. Here, we have focused on the hub protein CSN5, the fifth subunit of the pleiotropic and eukaryotic conserved COP9 signalosome (CSN), which is a regulatory component of the ubiquitin/proteasome system. We used affinity purification-mass spectrometry (AP-MS) to generate the interaction network of CSN5 in M. incognita-infected roots. We identified the complete CSN complex and other known CSN5 interaction partners in addition to unknown plant and M. incognita proteins. Among these, we described M. incognita PASSE-MURAILLE (MiPM), a small pioneer protein predicted to contain a secretory peptide that is up-regulated mostly in the J2 parasitic stage. We confirmed the CSN5-MiPM interaction, which occurs in the nucleus, by bimolecular fluorescence complementation (BiFC). Using MiPM as bait, a GST pull-down assay coupled with MS revealed some common protein partners between CSN5 and MiPM. We further showed by in silico and microscopic analyses that the recombinant purified MiPM protein enters the cells of Arabidopsis root tips in a non-infectious context. In further detail, the supercharged N-terminal tail of MiPM (NTT-MiPM) triggers an unknown host endocytosis pathway to penetrate the cell. The functional meaning of the CSN5-MiPM interaction in the M. incognita parasitism is discussed. Moreover, we propose that the cell-penetrating properties of some M. incognita secreted proteins might be a non-negligible mechanism for cell uptake, especially during the steps preceding the sedentary parasitic phase.
Collapse
Affiliation(s)
- Caroline Bournaud
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
- *Correspondence: Caroline Bournaud
| | | | - André M. Murad
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - Emmanuel Bresso
- Université de Lorraine, Centre National de la Recherche Scientifique, Inria, Laboratoire Lorrain de Recherche en Informatique et ses Applications, Nancy, France
| | | | - Maria F. Grossi-de-Sá
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
- Post-Graduation Program in Genomic Science and Biotechnology, Universidade Católica de Brasília, Brasília, Brazil
- Maria F. Grossi-de-Sá
| |
Collapse
|
38
|
Nishikiori M, Ahlquist P. Organelle luminal dependence of (+)strand RNA virus replication reveals a hidden druggable target. SCIENCE ADVANCES 2018; 4:eaap8258. [PMID: 29387794 PMCID: PMC5787378 DOI: 10.1126/sciadv.aap8258] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/19/2017] [Indexed: 05/08/2023]
Abstract
Positive-strand RNA viruses replicate their genomes in membrane-bounded cytoplasmic complexes. We show that endoplasmic reticulum (ER)-linked genomic RNA replication by brome mosaic virus (BMV), a well-studied member of the alphavirus superfamily, depends on the ER luminal thiol oxidase ERO1. We further show that BMV RNA replication protein 1a, a key protein for the formation and function of vesicular BMV RNA replication compartments on ER membranes, permeabilizes these membranes to release oxidizing potential from the ER lumen. Conserved amphipathic sequences in 1a are sufficient to permeabilize liposomes, and mutations in these sequences simultaneously block membrane permeabilization, formation of a disulfide-linked, oxidized 1a multimer, 1a's RNA capping function, and productive genome replication. These results reveal new transmembrane complexities in positive-strand RNA virus replication, show that-as previously reported for certain picornaviruses and flaviviruses-some alphavirus superfamily members encode viroporins, identify roles for such viroporins in genome replication, and provide a potential new foundation for broad-spectrum antivirals.
Collapse
Affiliation(s)
- Masaki Nishikiori
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Paul Ahlquist
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
- Corresponding author.
| |
Collapse
|
39
|
Cho IT, Adelmant G, Lim Y, Marto JA, Cho G, Golden JA. Ascorbate peroxidase proximity labeling coupled with biochemical fractionation identifies promoters of endoplasmic reticulum-mitochondrial contacts. J Biol Chem 2017; 292:16382-16392. [PMID: 28760823 PMCID: PMC5625067 DOI: 10.1074/jbc.m117.795286] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 07/14/2017] [Indexed: 11/06/2022] Open
Abstract
To maintain cellular homeostasis, subcellular organelles communicate with each other and form physical and functional networks through membrane contact sites coupled by protein tethers. In particular, endoplasmic reticulum (ER)-mitochondrial contacts (EMC) regulate diverse cellular activities such as metabolite exchange (Ca2+ and lipids), intracellular signaling, apoptosis, and autophagy. The significance of EMCs has been highlighted by reports indicating that EMC dysregulation is linked to neurodegenerative diseases. Therefore, obtaining a better understanding of the physical and functional components of EMCs should provide new insights into the pathogenesis of several neurodegenerative diseases. Here, we applied engineered ascorbate peroxidase (APEX) to map the proteome at EMCs in live HEK293 cells. APEX was targeted to the outer mitochondrial membrane, and proximity-labeled proteins were analyzed by stable isotope labeling with amino acids in culture (SILAC)-LC/MS-MS. We further refined the specificity of the proteins identified by combining biochemical subcellular fractionation to the protein isolation method. We identified 405 proteins with a 2.0-fold cutoff ratio (log base 2) in SILAC quantification from replicate experiments. We performed validation screening with a Split-Rluc8 complementation assay that identified reticulon 1A (RTN1A), an ER-shaping protein localized to EMCs as an EMC promoter. Proximity mapping augmented with biochemical fractionation and additional validation methods reported here could be useful to discover other components of EMCs, identify mitochondrial contacts with other organelles, and further unravel their communication.
Collapse
Affiliation(s)
- Il-Taeg Cho
- From the Department of Pathology, Brigham and Women's Hospital, and
| | - Guillaume Adelmant
- the Departments of Cancer Biology and Pathology, Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Youngshin Lim
- From the Department of Pathology, Brigham and Women's Hospital, and
| | - Jarrod A Marto
- From the Department of Pathology, Brigham and Women's Hospital, and
- the Departments of Cancer Biology and Pathology, Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Ginam Cho
- From the Department of Pathology, Brigham and Women's Hospital, and
| | - Jeffrey A Golden
- From the Department of Pathology, Brigham and Women's Hospital, and
| |
Collapse
|
40
|
Kohli P, Höhne M, Jüngst C, Bertsch S, Ebert LK, Schauss AC, Benzing T, Rinschen MM, Schermer B. The ciliary membrane-associated proteome reveals actin-binding proteins as key components of cilia. EMBO Rep 2017; 18:1521-1535. [PMID: 28710093 DOI: 10.15252/embr.201643846] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 06/06/2017] [Accepted: 06/13/2017] [Indexed: 01/01/2023] Open
Abstract
Primary cilia are sensory, antennae-like organelles present on the surface of many cell types. They have been involved in a variety of diseases collectively termed ciliopathies. As cilia are essential regulators of cell signaling, the composition of the ciliary membrane needs to be strictly regulated. To understand regulatory processes at the ciliary membrane, we report the targeting of a genetically engineered enzyme specifically to the ciliary membrane to allow biotinylation and identification of the membrane-associated proteome. Bioinformatic analysis of the comprehensive dataset reveals high-stoichiometric presence of actin-binding proteins inside the cilium. Immunofluorescence stainings and complementary interaction proteomic analyses confirm these findings. Depolymerization of branched F-actin causes further enrichment of the actin-binding and actin-related proteins in cilia, including Myosin 5a (Myo5a). Interestingly, Myo5a knockout decreases ciliation while enhanced levels of Myo5a are observed in cilia upon induction of ciliary disassembly. In summary, we present a novel approach to investigate dynamics of the ciliary membrane proteome in mammalian cells and identify actin-binding proteins as mechanosensitive components of cilia that might have important functions in cilia membrane dynamics.
Collapse
Affiliation(s)
- Priyanka Kohli
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Christian Jüngst
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sabine Bertsch
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Lena K Ebert
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Astrid C Schauss
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Markus M Rinschen
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany .,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| |
Collapse
|
41
|
Li P, Li J, Wang L, Di LJ. Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Peipei Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Jingjing Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li Wang
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
- Metabolomics Core; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li-Jun Di
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| |
Collapse
|
42
|
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: 40] [Impact Index Per Article: 5.7] [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.
Collapse
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
| |
Collapse
|
43
|
Filling the Void: Proximity-Based Labeling of Proteins in Living Cells. Trends Cell Biol 2016; 26:804-817. [PMID: 27667171 DOI: 10.1016/j.tcb.2016.09.004] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 12/17/2022]
Abstract
There are inherent limitations with traditional methods to study protein behavior or to determine the constituency of proteins in discrete subcellular compartments. In response to these limitations, several methods have recently been developed that use proximity-dependent labeling. By fusing proteins to enzymes that generate reactive molecules, most commonly biotin, proximate proteins are covalently labeled to enable their isolation and identification. In this review we describe current methods for proximity-dependent labeling in living cells and discuss their applications and future use in the study of protein behavior.
Collapse
|
44
|
Hwang J, Ribbens D, Raychaudhuri S, Cairns L, Gu H, Frost A, Urban S, Espenshade PJ. A Golgi rhomboid protease Rbd2 recruits Cdc48 to cleave yeast SREBP. EMBO J 2016; 35:2332-2349. [PMID: 27655872 DOI: 10.15252/embj.201693923] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 09/06/2016] [Indexed: 12/26/2022] Open
Abstract
Hypoxic growth of fungi requires sterol regulatory element-binding protein (SREBP) transcription factors, and human opportunistic fungal pathogens require SREBP activation for virulence. Proteolytic release of fission yeast SREBPs from the membrane in response to low oxygen requires the Golgi membrane-anchored Dsc E3 ligase complex. Using genetic interaction arrays, we identified Rbd2 as a rhomboid family protease required for SREBP proteolytic processing. Rbd2 is an active, Golgi-localized protease that cleaves the transmembrane segment of the TatA rhomboid model substrate. Epistasis analysis revealed that the Dsc E3 ligase acts on SREBP prior to cleavage by Rbd2. Using APEX2 proximity biotinylation, we demonstrated that Rbd2 binds the AAA-ATPase Cdc48 through a C-terminal SHP box. Interestingly, SREBP cleavage required Rbd2 binding of Cdc48, consistent with Cdc48 acting to recruit ubiquitinylated substrates. In support of this claim, overexpressing a Cdc48-binding mutant of Rbd2 bypassed the Cdc48 requirement for SREBP cleavage, demonstrating that Cdc48 likely plays a role in SREBP recognition. In the absence of functional Rbd2, SREBP precursor is degraded by the proteasome, indicating that Rbd2 activity controls the balance between SREBP activation and degradation.
Collapse
Affiliation(s)
- Jiwon Hwang
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Diedre Ribbens
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leah Cairns
- Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - He Gu
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Siniša Urban
- Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter J Espenshade
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|