151
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Ge Y, Chen L, Liu S, Zhao J, Zhang H, Chen PR. Enzyme-Mediated Intercellular Proximity Labeling for Detecting Cell-Cell Interactions. J Am Chem Soc 2019; 141:1833-1837. [PMID: 30676735 DOI: 10.1021/jacs.8b10286] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Cell-cell interactions and communications play fundamental roles in life processes but remain largely uncharacterized. We developed an enzyme-mediated proximity cell labeling (EXCELL) strategy as a general method to detect and record cell-cell interactions under living conditions. EXCELL relies on an evolved Staphylococcus aureus transpeptidase sortase A variant (mgSrtA) capable of promiscuous labeling of various cell surface proteins containing a monoglycine residue at the N-terminus. Displaying mgSrtA on the surface of a cell of interest allows the labeling and detection of interacting cells in a proximity-dependent fashion.
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Affiliation(s)
- Yun Ge
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing , China
| | - Long Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing , China
| | - Shibo Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing , China
| | - Jingyi Zhao
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing , China
| | - Heng Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing , China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing , China.,Peking-Tsinghua Center for Life Sciences , Peking University , Beijing , China
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152
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Abbasi S, Schild-Poulter C. Mapping the Ku Interactome Using Proximity-Dependent Biotin Identification in Human Cells. J Proteome Res 2019; 18:1064-1077. [PMID: 30585729 DOI: 10.1021/acs.jproteome.8b00771] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Ku heterodimer, composed of Ku70 and Ku80, is best characterized for its role in repairing double-stranded DNA breaks but is also known to participate in other regulatory processes. Despite our understanding of Ku protein interplay during DNA repair, the extent of Ku's protein interactions in other processes has never been fully determined. Using proximity-dependent biotin identification (BioID) and affinity purification coupled to mass spectrometry (AP-MS) with wild-type Ku70, we identified candidate proteins that interact with the Ku heterodimer in HEK293 cells, in the absence of exogenously induced DNA damage. BioID analysis identified approximately 250 nuclear proteins, appearing in at least two replicates, including known Ku-interacting factors such as MRE11A, WRN, and NCOA6. Meanwhile, AP-MS analysis identified approximately 50 candidate proteins. Of the novel protein interactors identified, many were involved in functions already suspected to involve Ku such as transcriptional regulation, DNA replication, and DNA repair, while several others suggest that Ku may be involved in additional functions such as RNA metabolism, chromatin-remodeling, and microtubule dynamics. Using a combination of BioID and AP-MS, this is the first report that comprehensively characterizes the Ku protein interaction landscape, revealing new cellular processes and protein complexes involving the Ku complex.
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Affiliation(s)
- Sanna Abbasi
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry , University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Caroline Schild-Poulter
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry , University of Western Ontario , London , Ontario N6A 5B7 , Canada
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153
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Abstract
The centriole is an ancient microtubule-based organelle with a conserved nine-fold symmetry. Centrioles form the core of centrosomes, which organize the interphase microtubule cytoskeleton of most animal cells and form the poles of the mitotic spindle. Centrioles can also be modified to form basal bodies, which template the formation of cilia and play central roles in cellular signaling, fluid movement, and locomotion. In this review, we discuss developments in our understanding of the biogenesis of centrioles and cilia and the regulatory controls that govern their structure and number. We also discuss how defects in these processes contribute to a spectrum of human diseases and how new technologies have expanded our understanding of centriole and cilium biology, revealing exciting avenues for future exploration.
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Affiliation(s)
- David K Breslow
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA;
| | - Andrew J Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
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154
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Kovalski JR, Bhaduri A, Zehnder AM, Neela PH, Che Y, Wozniak GG, Khavari PA. The Functional Proximal Proteome of Oncogenic Ras Includes mTORC2. Mol Cell 2019; 73:830-844.e12. [PMID: 30639242 DOI: 10.1016/j.molcel.2018.12.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 10/29/2018] [Accepted: 11/29/2018] [Indexed: 12/31/2022]
Abstract
Proximity-dependent biotin labeling (BioID) may identify new targets for cancers driven by difficult-to-drug oncogenes such as Ras. Therefore, BioID was used with wild-type (WT) and oncogenic mutant (MT) H-, K-, and N-Ras, identifying known interactors, including Raf and PI3K, as well as a common set of 130 novel proteins proximal to all Ras isoforms. A CRISPR screen of these proteins for Ras dependence identified mTOR, which was also found proximal to MT Ras in human tumors. Oncogenic Ras directly bound two mTOR complex 2 (mTORC2) components, mTOR and MAPKAP1, to promote mTORC2 kinase activity at the plasma membrane. mTORC2 enabled the Ras pro-proliferative cell cycle transcriptional program, and perturbing the Ras-mTORC2 interaction impaired Ras-dependent neoplasia in vivo. Combining proximity-dependent proteomics with CRISPR screening identified a new set of functional Ras-associated proteins, defined mTORC2 as a new direct Ras effector, and offers a strategy for finding new proteins that cooperate with dominant oncogenes.
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Affiliation(s)
- Joanna R Kovalski
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA; Program in Cancer Biology, Stanford University, Stanford, CA 94305, USA
| | - Aparna Bhaduri
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94131, USA
| | - Ashley M Zehnder
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Poornima H Neela
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Yonglu Che
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA; Program in Cancer Biology, Stanford University, Stanford, CA 94305, USA
| | - Glenn G Wozniak
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA; Program in Cancer Biology, Stanford University, Stanford, CA 94305, USA; VA Palo Alto Healthcare System, Palo Alto, CA 94304, USA.
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155
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Abstract
Lipid droplets (LDs) are ubiquitous lipid storage organelles composed of a neutral lipid core surrounded by a phospholipid monolayer that is decorated with integral and peripheral proteins. Accurate identification of LD proteins using biochemical fractionation methods has been challenging due to the presence of contaminant proteins from co-fractionating organelles. Here, we describe a method to identify high-confidence LD proteomes that employs an engineered ascorbate peroxidase (APEX2) to induce spatially and temporally restricted biotinylation of LD proteins. This proximity labeling method can be broadly applied to define the composition of the LD proteome in any cultured cell line and can be utilized to examine LD proteome dynamics.
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156
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Abstract
BioID has become an increasingly utilized tool for identifying candidate protein-protein interactions (PPIs) in living cells. This method utilizes a promiscuous biotin ligase, called BioID, fused to a protein of interest that when expressed in cells can be induced to biotinylate interacting and proximate proteins over a period of hours, thus generating a history of protein associations. These biotinylated proteins are subsequently purified and identified via mass spectrometry. Compared to other conventional methods typically used to screen strong PPIs, BioID allows for the detection of weak and transient interactions within a relevant biological setting over a defined period of time. Here we briefly review the scientific progress enabled by the BioID technology, detail an updated protocol for applying the method to proteins in living cells, and offer insights for troubleshooting commonly encountered setbacks.
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Affiliation(s)
- Rhiannon M. Sears
- Enabling Technology Group, Sanford Research, Sioux Falls, SD 57104,Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD 57069
| | - Danielle G. May
- Enabling Technology Group, Sanford Research, Sioux Falls, SD 57104
| | - Kyle J. Roux
- Enabling Technology Group, Sanford Research, Sioux Falls, SD 57104,Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105
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157
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Alberti S. Guilty by Association: Mapping Out the Molecular Sociology of Droplet Compartments. Mol Cell 2018; 69:349-351. [PMID: 29395058 DOI: 10.1016/j.molcel.2018.01.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The molecular interactions driving the formation of stress-inducible granules have largely remained unknown. In two recent papers, Youn et al. (2018) and Markmiller et al. (2018) use proximity labeling proteomics to map out the protein interactome of stress-inducible ribonucleoprotein granules.
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Affiliation(s)
- Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
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158
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Kyriacou E, Heun P. High-resolution mapping of centromeric protein association using APEX-chromatin fibers. Epigenetics Chromatin 2018; 11:68. [PMID: 30445992 PMCID: PMC6238281 DOI: 10.1186/s13072-018-0237-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/26/2018] [Indexed: 08/30/2023] Open
Abstract
BACKGROUND The centromere is a specialized chromosomal locus that forms the basis for the assembly of a multi-protein complex, the kinetochore and ensures faithful chromosome segregation during every cell division. The repetitive nature of the underlying centromeric sequence represents a major obstacle for high-resolution mapping of protein binding using methods that rely on annotated genomes. Here, we present a novel microscopy-based approach called "APEX-chromatin fibers" for localizing protein binding over the repetitive centromeric sequences at kilobase resolution. RESULTS By fusing centromere factors of interest to ascorbate peroxidase, we were able to label their binding profiles on extended chromatin fibers with biotin marks. We applied APEX-chromatin fibers to at least one member of each CCAN complex, most of which show a localization pattern different from CENP-A but within the CENP-A delineated centromeric domain. Interestingly, we describe here a novel characteristic of CENP-I and CENP-B that display extended localization beyond the CENP-A boundaries. CONCLUSIONS Our approach was successfully applied for mapping protein association over centromeric chromatin, revealing previously undescribed localization patterns. In this study, we focused on centromeric factors, but we believe that this approach could be useful for mapping protein binding patterns in other repetitive regions.
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Affiliation(s)
- Eftychia Kyriacou
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.,Faculty of Biology, Albert-Ludwigs Universität Freiburg, Freiburg im Breisgau, Germany.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Patrick Heun
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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159
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2C-BioID: An Advanced Two Component BioID System for Precision Mapping of Protein Interactomes. iScience 2018; 10:40-52. [PMID: 30500481 PMCID: PMC6263017 DOI: 10.1016/j.isci.2018.11.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/26/2018] [Accepted: 11/12/2018] [Indexed: 12/31/2022] Open
Abstract
The modulation of protein-protein interactions (PPIs) is an essential regulatory activity defining diverse cell functions in development and disease. BioID is an unbiased proximity-dependent biotinylation method making use of a biotin-protein ligase fused to a protein of interest and has become an important tool for mapping of PPIs within cellular contexts. We devised an advanced method, 2C-BioID, in which the biotin-protein ligase is kept separate from the protein of interest, until the two are induced to associate by the addition of a dimerizing agent. As proof of principle, we compared the interactomes of lamina-associated polypeptide 2β (LAP2β) with those of lamins A and C, using 2C- and conventional BioID. 2C-BioID greatly enhanced data robustness by facilitating the in silico elimination of non-specific interactors as well as overcoming the problems associated with aberrant protein localization. 2C-BioID therefore significantly strengthens the specificity and reliability of BioID-based interactome analysis, by the more stringent exclusion of false-positives and more efficient intracellular targeting.
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160
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PAQR3 Regulates Endoplasmic Reticulum-to-Golgi Trafficking of COPII Vesicle via Interaction with Sec13/Sec31 Coat Proteins. iScience 2018; 9:382-398. [PMID: 30466064 PMCID: PMC6249397 DOI: 10.1016/j.isci.2018.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/06/2018] [Accepted: 10/29/2018] [Indexed: 11/20/2022] Open
Abstract
Endoplasmic reticulum (ER)-to-Golgi anterograde transport is driven by COPII vesicles mainly composed of a Sec23/Sec24 inner shell and a Sec13/Sec31 outer cage. How COPII vesicles are tethered to the Golgi is not completely understood. We demonstrated here that PAQR3 can facilitate tethering of COPII vesicles to the Golgi. Proximity labeling using PAQR3 fused with APEX2 identified that many proteins involved in intracellular transport are in close proximity to PAQR3. ER-to-Golgi trafficking of N-acetylgalactosaminyltransferase-2 on removal of brefeldin A is delayed by PAQR3 deletion. RUSH assay also revealed that ER-to-Golgi trafficking is affected by PAQR3. The N-terminal end of PAQR3 can interact with the WD domains of Sec13 and Sec31A. PAQR3 enhances Golgi localization of Sec13 and Sec31A. Furthermore, PAQR3 is localized in the ERGIC and cis-Golgi structures, the acceptor sites for COPII vesicles. Taken together, our study uncovers a role for PAQR3 as a player in regulating ER-to-Golgi transport of COPII vesicles.
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161
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Swearingen KE, Lindner SE. Plasmodium Parasites Viewed through Proteomics. Trends Parasitol 2018; 34:945-960. [PMID: 30146456 PMCID: PMC6204299 DOI: 10.1016/j.pt.2018.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/02/2018] [Accepted: 08/05/2018] [Indexed: 12/14/2022]
Abstract
Early sequencing efforts that produced the genomes of several species of malaria parasites (Plasmodium genus) propelled transcriptomic and proteomic efforts. In this review, we focus upon some of the exciting proteomic advances from studies of Plasmodium parasites over approximately the past decade. With improvements to both instrumentation and data-processing capabilities, long-standing questions about the forms and functions of these important pathogens are rapidly being answered. In particular, global and subcellular proteomics, quantitative proteomics, and the detection of post-translational modifications have all revealed important features of the parasite's regulatory mechanisms. Finally, we provide our perspectives on future applications of proteomics to Plasmodium research, as well as suggestions for further improvement through standardization of data deposition, analysis, and accessibility.
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Affiliation(s)
- Kristian E Swearingen
- Institute for Systems Biology, Seattle, WA 98109, USA; Center for Infectious Disease Research, Seattle, WA 98109, USA
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA.
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162
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Pankow S, Martínez-Bartolomé S, Bamberger C, Yates JR. Understanding molecular mechanisms of disease through spatial proteomics. Curr Opin Chem Biol 2018; 48:19-25. [PMID: 30308467 DOI: 10.1016/j.cbpa.2018.09.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023]
Abstract
Mammalian cells are organized into different compartments that separate and facilitate physiological processes by providing specialized local environments and allowing different, otherwise incompatible biological processes to be carried out simultaneously. Proteins are targeted to these subcellular locations where they fulfill specialized, compartment-specific functions. Spatial proteomics aims to localize and quantify proteins within subcellular structures.
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Affiliation(s)
- Sandra Pankow
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, United States
| | | | - Casimir Bamberger
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, United States
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, United States.
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163
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Branon TC, Bosch JA, Sanchez AD, Udeshi ND, Svinkina T, Carr SA, Feldman JL, Perrimon N, Ting AY. Efficient proximity labeling in living cells and organisms with TurboID. Nat Biotechnol 2018; 36:880-887. [PMID: 30125270 PMCID: PMC6126969 DOI: 10.1038/nbt.4201] [Citation(s) in RCA: 1000] [Impact Index Per Article: 166.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 07/02/2018] [Indexed: 12/11/2022]
Abstract
Protein interaction networks and protein compartmentalization underlie all signaling and regulatory processes in cells. Enzyme-catalyzed proximity labeling (PL) has emerged as a new approach to study the spatial and interaction characteristics of proteins in living cells. However, current PL methods require over 18 h of labeling time or utilize chemicals with limited cell permeability or high toxicity. We used yeast display-based directed evolution to engineer two promiscuous mutants of biotin ligase, TurboID and miniTurbo, which catalyze PL with much greater efficiency than BioID or BioID2, and enable 10-min PL in cells with non-toxic and easily deliverable biotin. Furthermore, TurboID extends biotin-based PL to flies and worms.
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Affiliation(s)
- Tess C. Branon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Departments of Genetics, Stanford University, Stanford, California, USA
- Departments of Chemistry, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
| | - Justin A. Bosch
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ariana D. Sanchez
- Department of Biology, Stanford University, Stanford, California, USA
| | | | - Tanya Svinkina
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steven A. Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
| | - Alice Y. Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Departments of Genetics, Stanford University, Stanford, California, USA
- Departments of Chemistry, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
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164
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MARCKS regulates neuritogenesis and interacts with a CDC42 signaling network. Sci Rep 2018; 8:13278. [PMID: 30185885 PMCID: PMC6125478 DOI: 10.1038/s41598-018-31578-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 08/21/2018] [Indexed: 01/24/2023] Open
Abstract
Through the process of neuronal differentiation, newly born neurons change from simple, spherical cells to complex, sprawling cells with many highly branched processes. One of the first stages in this process is neurite initiation, wherein cytoskeletal modifications facilitate membrane protrusion and extension from the cell body. Hundreds of actin modulators and microtubule-binding proteins are known to be involved in this process, but relatively little is known about how upstream regulators bring these complex networks together at discrete locations to produce neurites. Here, we show that Myristoylated alanine-rich C kinase substrate (MARCKS) participates in this process. Marcks−/− cortical neurons extend fewer neurites and have less complex neurite arborization patterns. We use an in vitro proteomics screen to identify MARCKS interactors in developing neurites and characterize an interaction between MARCKS and a CDC42-centered network. While the presence of MARCKS does not affect whole brain levels of activated or total CDC42, we propose that MARCKS is uniquely positioned to regulate CDC42 localization and interactions within specialized cellular compartments, such as nascent neurites.
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165
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Apta-Smith MJ, Hernandez-Fernaud JR, Bowman AJ. Evidence for the nuclear import of histones H3.1 and H4 as monomers. EMBO J 2018; 37:embj.201798714. [PMID: 30177573 PMCID: PMC6166134 DOI: 10.15252/embj.201798714] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 07/20/2018] [Accepted: 07/25/2018] [Indexed: 11/09/2022] Open
Abstract
Newly synthesised histones are thought to dimerise in the cytosol and undergo nuclear import in complex with histone chaperones. Here, we provide evidence that human H3.1 and H4 are imported into the nucleus as monomers. Using a tether-and-release system to study the import dynamics of newly synthesised histones, we find that cytosolic H3.1 and H4 can be maintained as stable monomeric units. Cytosolically tethered histones are bound to importin-alpha proteins (predominantly IPO4), but not to histone-specific chaperones NASP, ASF1a, RbAp46 (RBBP7) or HAT1, which reside in the nucleus in interphase cells. Release of monomeric histones from their cytosolic tether results in rapid nuclear translocation, IPO4 dissociation and incorporation into chromatin at sites of replication. Quantitative analysis of histones bound to individual chaperones reveals an excess of H3 specifically associated with sNASP, suggesting that NASP maintains a soluble, monomeric pool of H3 within the nucleus and may act as a nuclear receptor for newly imported histone. In summary, we propose that histones H3 and H4 are rapidly imported as monomeric units, forming heterodimers in the nucleus rather than the cytosol.
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Affiliation(s)
| | | | - Andrew James Bowman
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
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166
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Pires HR, Boxem M. Mapping the Polarity Interactome. J Mol Biol 2018; 430:3521-3544. [DOI: 10.1016/j.jmb.2017.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/14/2017] [Accepted: 12/18/2017] [Indexed: 12/11/2022]
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167
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Liu S, Yu F, Hu Q, Wang T, Yu L, Du S, Yu W, Li N. Development of in Planta Chemical Cross-Linking-Based Quantitative Interactomics in Arabidopsis. J Proteome Res 2018; 17:3195-3213. [DOI: 10.1021/acs.jproteome.8b00320] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Shichang Liu
- Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Fengchao Yu
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Qin Hu
- Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Tingliang Wang
- Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lujia Yu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Shengwang Du
- Department of Physics, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Weichuan Yu
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ning Li
- Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- The Hong Kong University of Science and Technology, Shenzhen Research Institute, Shenzhen Guangdong 518057, China
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168
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Samavarchi-Tehrani P, Abdouni H, Samson R, Gingras AC. A Versatile Lentiviral Delivery Toolkit for Proximity-dependent Biotinylation in Diverse Cell Types. Mol Cell Proteomics 2018; 17:2256-2269. [PMID: 29991506 DOI: 10.1074/mcp.tir118.000902] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Indexed: 11/06/2022] Open
Abstract
Proximity-dependent biotinylation strategies have emerged as powerful tools to characterize the subcellular context of proteins in living cells. The popular BioID approach employs an abortive E. coli biotin ligase mutant (R118G; denoted as BirA*), which when fused to a bait protein enables the covalent biotinylation of endogenous proximal polypeptides. This approach has been mainly applied to the study of protein proximity in immortalized mammalian cell lines. To expand the application space of BioID, here we describe a set of lentiviral vectors that enable the inducible expression of BirA*-tagged bait fusion proteins for performing proximity-dependent biotinylation in diverse experimental systems. We benchmark this highly adaptable toolkit across immortalized and primary cell systems, demonstrating the ease, versatility and robustness of the system. We also provide guidelines to perform BioID using these reagents.
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Affiliation(s)
| | - Hala Abdouni
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Reuben Samson
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,§Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Anne-Claude Gingras
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; .,§Department of Molecular Genetics, University of Toronto, Toronto, Canada
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169
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Eremina L, Pashintseva N, Kovalev L, Kovaleva M, Shishkin S. Proteomics of mammalian mitochondria in health and malignancy: From protein identification to function. Anal Biochem 2018; 552:4-18. [DOI: 10.1016/j.ab.2017.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 03/07/2017] [Accepted: 03/23/2017] [Indexed: 12/28/2022]
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170
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Lasswitz L, Chandra N, Arnberg N, Gerold G. Glycomics and Proteomics Approaches to Investigate Early Adenovirus-Host Cell Interactions. J Mol Biol 2018; 430:1863-1882. [PMID: 29746851 PMCID: PMC7094377 DOI: 10.1016/j.jmb.2018.04.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/24/2018] [Accepted: 04/30/2018] [Indexed: 12/14/2022]
Abstract
Adenoviruses as most viruses rely on glycan and protein interactions to attach to and enter susceptible host cells. The Adenoviridae family comprises more than 80 human types and they differ in their attachment factor and receptor usage, which likely contributes to the diverse tropism of the different types. In the past years, methods to systematically identify glycan and protein interactions have advanced. In particular sensitivity, speed and coverage of mass spectrometric analyses allow for high-throughput identification of glycans and peptides separated by liquid chromatography. Also, developments in glycan microarray technologies have led to targeted, high-throughput screening and identification of glycan-based receptors. The mapping of cell surface interactions of the diverse adenovirus types has implications for cell, tissue, and species tropism as well as drug development. Here we review known adenovirus interactions with glycan- and protein-based receptors, as well as glycomics and proteomics strategies to identify yet elusive virus receptors and attachment factors. We finally discuss challenges, bottlenecks, and future research directions in the field of non-enveloped virus entry into host cells.
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Affiliation(s)
- Lisa Lasswitz
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany
| | - Naresh Chandra
- Department of Clinical Microbiology, Virology, Umeå University, SE-90185 Umeå, Sweden; Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-90185 Umea, Sweden
| | - Niklas Arnberg
- Department of Clinical Microbiology, Virology, Umeå University, SE-90185 Umeå, Sweden; Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-90185 Umea, Sweden.
| | - Gisa Gerold
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, SE-90185 Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, SE-90185 Umea, Sweden.
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171
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Khan M, Youn JY, Gingras AC, Subramaniam R, Desveaux D. In planta proximity dependent biotin identification (BioID). Sci Rep 2018; 8:9212. [PMID: 29907827 PMCID: PMC6004002 DOI: 10.1038/s41598-018-27500-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/04/2018] [Indexed: 12/30/2022] Open
Abstract
Proximity dependent biotin identification (BioID) has emerged as a powerful tool for studies of proteome architecture, including insoluble or membrane-associated proteins. The technique has been well established in mammalian cells but has yet to be applied to whole plant systems. Here we demonstrate the application of BioID on leaf tissues of the model plant Arabidopsis thaliana, thereby expanding the versatility of this important technique and providing a powerful proteomics tool for plant biologists.
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Affiliation(s)
- Madiha Khan
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada.,Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, K1A 0C6, Canada
| | - Ji-Young Youn
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, M5G 1X5, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, K1A 0C6, Canada.
| | - Darrell Desveaux
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada. .,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada.
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172
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Linker of nucleoskeleton and cytoskeleton complex proteins in cardiomyopathy. Biophys Rev 2018; 10:1033-1051. [PMID: 29869195 PMCID: PMC6082319 DOI: 10.1007/s12551-018-0431-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 05/24/2018] [Indexed: 12/21/2022] Open
Abstract
The linker of nucleoskeleton and cytoskeleton (LINC) complex couples the nuclear lamina to the cytoskeleton. The LINC complex and its associated proteins play diverse roles in cells, ranging from genome organization, nuclear morphology, gene expression, to mechanical stability. The importance of a functional LINC complex is highlighted by the large number of mutations in genes encoding LINC complex proteins that lead to skeletal and cardiac myopathies. In this review, the structure, function, and interactions between components of the LINC complex will be described. Mutations that are known to cause cardiomyopathy in patients will be discussed alongside their respective mouse models. Furthermore, future challenges for the field and emerging technologies to investigate LINC complex function will be discussed.
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173
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Proteomic approaches beyond expression profiling and PTM analysis. Anal Bioanal Chem 2018; 410:4051-4060. [PMID: 29637251 DOI: 10.1007/s00216-018-1021-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 02/22/2018] [Accepted: 03/12/2018] [Indexed: 12/15/2022]
Abstract
Essentially, all cellular functions are executed by proteins. Different physiological and pathological conditions dynamically control various properties of proteins, including expression levels, post-translational modifications (PTMs), protein-protein interactions, enzymatic activity, etc. Thus far, the vast majority of proteomic efforts have been focused on quantitative profiling of protein abundance/expression and their PTMs. In this article, we review some recent exciting progress in the development of proteomic approaches to examine protein functions from perspectives other than expression levels and PTMs. Specifically, we discuss advancements in proximity-based labeling, analysis of protein termini and newly synthesized proteins, and activity-based protein profiling.
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174
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Zuzow N, Ghosh A, Leonard M, Liao J, Yang B, Bennett EJ. Mapping the mammalian ribosome quality control complex interactome using proximity labeling approaches. Mol Biol Cell 2018. [PMID: 29540532 PMCID: PMC5935074 DOI: 10.1091/mbc.e17-12-0714] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Previous genetic and biochemical studies from Saccharomyces cerevisiae have identified a critical ribosome-associated quality control complex (RQC) that facilitates resolution of stalled ribosomal complexes. While components of the mammalian RQC have been examined in vitro, a systematic characterization of RQC protein interactions in mammalian cells has yet to be described. Here we utilize both proximity-labeling proteomic approaches, BioID and APEX, and traditional affinity-based strategies to both identify interacting proteins of mammalian RQC members and putative substrates for the RQC resident E3 ligase, Ltn1. Surprisingly, validation studies revealed that a subset of substrates are ubiquitylated by Ltn1 in a regulatory manner that does not result in subsequent substrate degradation. We demonstrate that Ltn1 catalyzes the regulatory ubiquitylation of ribosomal protein S6 kinase 1 and 2 (RPS6KA1, RPS6KA3). Further, loss of Ltn1 function results in hyperactivation of RSK1/2 signaling without impacting RSK1/2 protein turnover. These results suggest that Ltn1-mediated RSK1/2 ubiquitylation is inhibitory and establishes a new role for Ltn1 in regulating mitogen-activated kinase signaling via regulatory RSK1/2 ubiquitylation. Taken together, our results suggest that mammalian RQC interactions are difficult to observe and may be more transient than the homologous complex in S. cerevisiae and that Ltn1 has RQC-independent functions.
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Affiliation(s)
- Nathan Zuzow
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Arit Ghosh
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Marilyn Leonard
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Jeffrey Liao
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Bing Yang
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Eric J Bennett
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
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175
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Bareja A, Hodgkinson CP, Soderblom E, Waitt G, Dzau VJ. The proximity-labeling technique BioID identifies sorting nexin 6 as a member of the insulin-like growth factor 1 (IGF1)-IGF1 receptor pathway. J Biol Chem 2018. [PMID: 29530981 DOI: 10.1074/jbc.ra118.002406] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The insulin-like growth factor 1 receptor (IGF1R) is a receptor tyrosine kinase with critical roles in various biological processes. Recent results from clinical trials targeting IGF1R indicate that IGF1R signaling pathways are more complex than previously thought. Moreover, it has become increasingly clear that the function of many proteins can be understood only in the context of a network of interactions. To that end, we sought to profile IGF1R-protein interactions with the proximity-labeling technique BioID. We applied BioID by generating a HEK293A cell line that stably expressed the BirA* biotin ligase fused to the IGF1R. Following stimulation by IGF1, biotinylated proteins were analyzed by MS. This screen identified both known and previously unknown interactors of IGF1R. One of the novel interactors was sorting nexin 6 (SNX6), a protein that forms part of the retromer complex, which is involved in intracellular protein sorting. Using co-immunoprecipitation, we confirmed that IGF1R and SNX6 physically interact. SNX6 knockdown resulted in a dramatic diminution of IGF1-mediated ERK1/2 phosphorylation, but did not affect IGF1R internalization. Bioluminescence resonance energy transfer experiments indicated that the SNX6 knockdown perturbed the association between IGF1R and the key adaptor proteins insulin receptor substrate 1 (IRS1) and SHC adaptor protein 1 (SHC1). Intriguingly, even in the absence of stimuli, SNX6 overexpression significantly increased Akt phosphorylation. Our study confirms the utility of proximity-labeling methods, such as BioID, to screen for interactors of cell-surface receptors and has uncovered a role of one of these interactors, SNX6, in the IGF1R signaling cascade.
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Affiliation(s)
- Akshay Bareja
- From the Duke Cardiovascular Research Center, the Mandel Center for Hypertension and Atherosclerosis Research, and
| | - Conrad P Hodgkinson
- From the Duke Cardiovascular Research Center, the Mandel Center for Hypertension and Atherosclerosis Research, and
| | - Erik Soderblom
- the Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27710
| | - Greg Waitt
- the Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27710
| | - Victor J Dzau
- From the Duke Cardiovascular Research Center, the Mandel Center for Hypertension and Atherosclerosis Research, and
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176
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Roux KJ, Kim DI, Burke B, May DG. BioID: A Screen for Protein-Protein Interactions. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2018; 91:19.23.1-19.23.15. [PMID: 29516480 PMCID: PMC6028010 DOI: 10.1002/cpps.51] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BioID is a unique method to screen for physiologically relevant protein interactions that occur in living cells. This technique harnesses a promiscuous biotin ligase to biotinylate proteins based on proximity. The ligase is fused to a protein of interest and expressed in cells, where it biotinylates proximal endogenous proteins. Because it is a rare protein modification in nature, biotinylation of these endogenous proteins by BioID fusion proteins enables their selective isolation and identification with standard biotin-affinity capture. Proteins identified by BioID are candidate interactors for the protein of interest. BioID can be applied to insoluble proteins, can identify weak and/or transient interactions, and is amenable to temporal regulation. Initially applied to mammalian cells, BioID has potential application in a variety of cell types from diverse species. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Kyle J Roux
- Children's Health Research Center, Sanford Research, North Sioux Falls, South Dakota
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota
| | - Dae In Kim
- Children's Health Research Center, Sanford Research, North Sioux Falls, South Dakota
| | - Brian Burke
- Institute of Medical Biology, Immunos, Singapore
| | - Danielle G May
- Children's Health Research Center, Sanford Research, North Sioux Falls, South Dakota
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177
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Stephens R, Lim K, Portela M, Kvansakul M, Humbert PO, Richardson HE. The Scribble Cell Polarity Module in the Regulation of Cell Signaling in Tissue Development and Tumorigenesis. J Mol Biol 2018; 430:3585-3612. [PMID: 29409995 DOI: 10.1016/j.jmb.2018.01.011] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 01/22/2023]
Abstract
The Scribble cell polarity module, comprising Scribbled (Scrib), Discs-large (Dlg) and Lethal-2-giant larvae (Lgl), has a tumor suppressive role in mammalian epithelial cancers. The Scribble module proteins play key functions in the establishment and maintenance of different modes of cell polarity, as well as in the control of tissue growth, differentiation and directed cell migration, and therefore are major regulators of tissue development and homeostasis. Whilst molecular details are known regarding the roles of Scribble module proteins in cell polarity regulation, their precise mode of action in the regulation of other key cellular processes remains enigmatic. An accumulating body of evidence indicates that Scribble module proteins play scaffolding roles in the control of various signaling pathways, which are linked to the control of tissue growth, differentiation and cell migration. Multiple Scrib, Dlg and Lgl interacting proteins have been discovered, which are involved in diverse processes, however many function in the regulation of cellular signaling. Herein, we review the components of the Scrib, Dlg and Lgl protein interactomes, and focus on the mechanism by which they regulate cellular signaling pathways in metazoans, and how their disruption leads to cancer.
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Affiliation(s)
- Rebecca Stephens
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Krystle Lim
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Marta Portela
- Department of Molecular, Cellular and Developmental Neurobiology, Cajal Institute (CSIC), Avenida Doctor Arce, 37, Madrid 28002, Spain
| | - Marc Kvansakul
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Patrick O Humbert
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Victoria, Australia; Department of Biochemistry & Molecular Biology, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Helena E Richardson
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Victoria, Australia; Department of Biochemistry & Molecular Biology, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Anatomy & Neurobiology, University of Melbourne, Melbourne, Victoria 3010, Australia.
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178
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Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A. BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation. J Proteome Res 2018; 17:759-769. [PMID: 29249144 PMCID: PMC6092923 DOI: 10.1021/acs.jproteome.7b00775] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biotin-based labeling strategies are widely employed to study protein-protein interactions, subcellular proteomes and post-translational modifications, as well as, used in drug discovery. While the high affinity of streptavidin for biotin greatly facilitates the capture of biotinylated proteins, it still presents a challenge, as currently employed, for the recovery of biotinylated peptides. Here we describe a strategy designated Biotinylation Site Identification Technology (BioSITe) for the capture of biotinylated peptides for LC-MS/MS analyses. We demonstrate the utility of BioSITe when applied to proximity-dependent labeling methods, APEX and BioID, as well as biotin-based click chemistry strategies for identifying O-GlcNAc-modified sites. We demonstrate the use of isotopically labeled biotin for quantitative BioSITe experiments that simplify differential interactome analysis and obviate the need for metabolic labeling strategies such as SILAC. Our data also highlight the potential value of site-specific biotinylation in providing spatial and topological information about proteins and protein complexes. Overall, we anticipate that BioSITe will replace the conventional methods in studies where detection of biotinylation sites is important.
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Affiliation(s)
- Dae In Kim
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Jevon A. Cutler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Pre-Doctoral Training Program in Human Genetics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Chan Hyun Na
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Center for Proteomics Discovery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Sina Reckel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Santosh Renuse
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Center for Proteomics Discovery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Anil K. Madugundu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Raiha Tahir
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Hana L. Goldschmidt
- Solomon H. Snyder Department of Neuroscience, Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Karen L. Reddy
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Richard L. Huganir
- Solomon H. Snyder Department of Neuroscience, Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Xinyan Wu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Natasha E. Zachara
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Oliver Hantschel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Center for Proteomics Discovery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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179
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Liu F, Lössl P, Rabbitts BM, Balaban RS, Heck AJR. The interactome of intact mitochondria by cross-linking mass spectrometry provides evidence for coexisting respiratory supercomplexes. Mol Cell Proteomics 2018; 17:216-232. [PMID: 29222160 PMCID: PMC5795388 DOI: 10.1074/mcp.ra117.000470] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Indexed: 12/22/2022] Open
Abstract
Mitochondria exert an immense amount of cytophysiological functions, but the structural basis of most of these processes is still poorly understood. Here we use cross-linking mass spectrometry to probe the organization of proteins in native mouse heart mitochondria. Our approach provides the largest survey of mitochondrial protein interactions reported so far. In total, we identify 3,322 unique residue-to-residue contacts involving half of the mitochondrial proteome detected by bottom-up proteomics. The obtained mitochondrial protein interactome gives insights in the architecture and submitochondrial localization of defined protein assemblies, and reveals the mitochondrial localization of four proteins not yet included in the MitoCarta database. As one of the highlights, we show that the oxidative phosphorylation complexes I-V exist in close spatial proximity, providing direct evidence for supercomplex assembly in intact mitochondria. The specificity of these contacts is demonstrated by comparative analysis of mitochondria after high salt treatment, which disrupts the native supercomplexes and substantially changes the mitochondrial interactome.
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Affiliation(s)
- Fan Liu
- From the ‡Biomolecular Mass Spectrometry and Proteomics. Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- §Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- ¶Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Rössle-Straβe 10, 13125 Berlin, Germany
| | - Philip Lössl
- From the ‡Biomolecular Mass Spectrometry and Proteomics. Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- §Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Beverley M Rabbitts
- ‖Laboratory of Cardiac Energetics, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Robert S Balaban
- ‖Laboratory of Cardiac Energetics, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Albert J R Heck
- From the ‡Biomolecular Mass Spectrometry and Proteomics. Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
- §Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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180
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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.
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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.
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181
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Bersuker K, Peterson CWH, To M, Sahl SJ, Savikhin V, Grossman EA, Nomura DK, Olzmann JA. A Proximity Labeling Strategy Provides Insights into the Composition and Dynamics of Lipid Droplet Proteomes. Dev Cell 2017; 44:97-112.e7. [PMID: 29275994 DOI: 10.1016/j.devcel.2017.11.020] [Citation(s) in RCA: 207] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/18/2017] [Accepted: 11/27/2017] [Indexed: 01/06/2023]
Abstract
Lipid droplet (LD) functions are regulated by a complement of integral and peripheral proteins that associate with the bounding LD phospholipid monolayer. Defining the composition of the LD proteome has remained a challenge due to the presence of contaminating proteins in LD-enriched buoyant fractions. To overcome this limitation, we developed a proximity labeling strategy that exploits LD-targeted APEX2 to biotinylate LD proteins in living cells. Application of this approach to two different cell types identified the vast majority of previously validated LD proteins, excluded common contaminating proteins, and revealed new LD proteins. Moreover, quantitative analysis of LD proteome dynamics uncovered a role for endoplasmic reticulum-associated degradation in controlling the composition of the LD proteome. These data provide an important resource for future LD studies and demonstrate the utility of proximity labeling to study the regulation of LD proteomes.
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Affiliation(s)
- Kirill Bersuker
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Clark W H Peterson
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Milton To
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Steffen J Sahl
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Victoria Savikhin
- SLAC National Accelerator Center, SSRL, Menlo Park, CA 94025, USA; Stanford Electrical Engineering Department, Stanford University, Stanford, CA 94305, USA
| | - Elizabeth A Grossman
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA; Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA.
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182
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Cheah JS, Yamada S. A simple elution strategy for biotinylated proteins bound to streptavidin conjugated beads using excess biotin and heat. Biochem Biophys Res Commun 2017; 493:1522-1527. [PMID: 28986262 DOI: 10.1016/j.bbrc.2017.09.168] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 09/30/2017] [Indexed: 12/31/2022]
Abstract
Protein-protein interactions are the molecular basis of cell signaling. Recently, proximity based biotin identification (BioID) has emerged as an alternative approach to traditional co-immunoprecipitation. In this protocol, a mutant biotin ligase promiscuously labels proximal binding partners with biotin, and resulting biotinylated proteins are purified using streptavidin conjugated beads. This approach does not require preservation of protein complexes in vitro, making it an ideal approach to identify transient or weak protein complexes. However, due to the high affinity bond between streptavidin and biotin, elution of biotinylated proteins from streptavidin conjugated beads requires harsh denaturing conditions, which are often incompatible with downstream processing. To effectively release biotinylated proteins bound to streptavidin conjugated beads, we designed a series of experiments to determine optimal binding and elution conditions. Interestingly, the concentrations of SDS and IGEPAL-CA630 during the incubation with streptavidin conjugated beads were the key to effective elution of biotinylated proteins using excess biotin and heating. This protocol provides an alternative method to isolate biotinylated proteins from streptavidin conjugated beads that is suitable for further downstream analysis.
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Affiliation(s)
- Joleen S Cheah
- Biomedical Engineering Department, University of California, Davis, United States
| | - Soichiro Yamada
- Biomedical Engineering Department, University of California, Davis, United States.
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183
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Wu G, Nagala M, Crocker PR. Identification of lectin counter-receptors on cell membranes by proximity labeling. Glycobiology 2017; 27:800-805. [PMID: 28810661 PMCID: PMC5881670 DOI: 10.1093/glycob/cwx063] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/26/2017] [Indexed: 12/31/2022] Open
Abstract
Lectin-glycan interactions play important roles in many biological systems, but the nature of glycoprotein counter-receptors expressed on cell membranes is often poorly understood. To help overcome this problem, we developed a method based on proximity labeling technology. Using a peroxidase-coupled lectin, addition of H2O2 and tyramide-biotin substrates leads to generation of short-range biotin radicals that biotinylate proteins in the immediate vicinity of the bound lectin, which can subsequently be identified. As a proof-of-principle, sialoadhesin-horseradish peroxidase-human IgG1 Fc recombinant protein constructs were precomplexed with anti-Fc antibodies, bound to human erythrocytes and reacted with H2O2 and tyramide-SS-biotin. The erythrocyte membrane protein with strongest biotinylation was identified as glycophorin A, in agreement with early studies using lectin overlay and reglycosylation approaches. As a further test of the method, the plant lectin MAL II was conjugated with horseradish peroxidase and used in proximity labeling of human erythrocytes. Glycophorin A was again selectively labeled, which is consistent with previous reports that MAL II has high affinity for glycophorin. This method could be applied to other lectins to identify their membrane counter-receptors.
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Affiliation(s)
- Gang Wu
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, The Wellcome Trust Building, Dow Street, Dundee DD1 5EH, UK
| | - Manjula Nagala
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, The Wellcome Trust Building, Dow Street, Dundee DD1 5EH, UK
| | - Paul R Crocker
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, The Wellcome Trust Building, Dow Street, Dundee DD1 5EH, UK
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184
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Muñoz-Jiménez C, Ayuso C, Dobrzynska A, Torres-Mendéz A, Ruiz PDLC, Askjaer P. An Efficient FLP-Based Toolkit for Spatiotemporal Control of Gene Expression in Caenorhabditis elegans. Genetics 2017; 206:1763-1778. [PMID: 28646043 PMCID: PMC5560786 DOI: 10.1534/genetics.117.201012] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/19/2017] [Indexed: 02/07/2023] Open
Abstract
Site-specific recombinases are potent tools to regulate gene expression. In particular, the Cre (cyclization recombination) and FLP (flipase) enzymes are widely used to either activate or inactivate genes in a precise spatiotemporal manner. Both recombinases work efficiently in the popular model organism Caenorhabditis elegans, but their use in this nematode is still only sporadic. To increase the utility of the FLP system in C. elegans, we have generated a series of single-copy transgenic strains that stably express an optimized version of FLP in specific tissues or by heat induction. We show that recombination efficiencies reach 100% in several cell types, such as muscles, intestine, and serotonin-producing neurons. Moreover, we demonstrate that most promoters drive recombination exclusively in the expected tissues. As examples of the potentials of the FLP lines, we describe novel tools for induced cell ablation by expression of the PEEL-1 toxin and a versatile FLP-out cassette for generation of GFP-tagged conditional knockout alleles. Together with other recombinase-based reagents created by the C. elegans community, this toolkit increases the possibilities for detailed analyses of specific biological processes at developmental stages inside intact animals.
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Affiliation(s)
- Celia Muñoz-Jiménez
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Cristina Ayuso
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Agnieszka Dobrzynska
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Antonio Torres-Mendéz
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Patricia de la Cruz Ruiz
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, 41013 Seville, Spain
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185
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Khosh-Naucke M, Becker J, Mesén-Ramírez P, Kiani P, Birnbaum J, Fröhlke U, Jonscher E, Schlüter H, Spielmann T. Identification of novel parasitophorous vacuole proteins in P. falciparum parasites using BioID. Int J Med Microbiol 2017; 308:13-24. [PMID: 28784333 DOI: 10.1016/j.ijmm.2017.07.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022] Open
Abstract
Malaria blood stage parasites develop within red blood cells where they are contained in a vacuolar compartment known as the parasitophorous vacuole (PV). This compartment holds a key role in the interaction of the parasite with its host cell. However, the proteome of this compartment has so far not been comprehensively analysed. Here we used BioID in asexual blood stages of the most virulent human malaria parasite Plasmodium falciparum to identify new proteins of the PV. The resulting proteome contained many of the already known PV proteins and validation by GFP-knock-in of 10 previously in P. falciparum uncharacterised hits revealed 5 new PV proteins and two with a partial PV localisation. This included proteins peripherally attached to the inner face of the PV membrane as well as proteins anchored in the parasite plasma membrane that protrude into the PV. Using selectable targeted gene disruption we generated mutants for 2 of the 10 candidates. In contrast we could not select parasites with disruptions for another 3 candidates, strongly suggesting that they are important for parasite growth. Interestingly, one of these included the orthologue of UIS2, a protein previously proposed to regulate protein translation in the parasite cytoplasm but here shown to be an essential PV protein. This work extends the number of known PV proteins and provides a starting point for further functional analyses of this compartment.
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Affiliation(s)
- Melissa Khosh-Naucke
- Bernhard Nocht Institute for Tropical Medicine, Parasitology Section, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
| | - Johanna Becker
- Bernhard Nocht Institute for Tropical Medicine, Parasitology Section, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
| | - Paolo Mesén-Ramírez
- Bernhard Nocht Institute for Tropical Medicine, Parasitology Section, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
| | - Parnian Kiani
- Core Facility Mass Spectrometric Proteomics, Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jakob Birnbaum
- Bernhard Nocht Institute for Tropical Medicine, Parasitology Section, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
| | - Ulrike Fröhlke
- Bernhard Nocht Institute for Tropical Medicine, Parasitology Section, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
| | - Ernst Jonscher
- Bernhard Nocht Institute for Tropical Medicine, Parasitology Section, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
| | - Hartmut Schlüter
- Core Facility Mass Spectrometric Proteomics, Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Parasitology Section, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany.
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186
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Liu P, Huang J, Zheng Q, Xie L, Lu X, Jin J, Wang G. Mammalian mitochondrial RNAs are degraded in the mitochondrial intermembrane space by RNASET2. Protein Cell 2017; 8:735-749. [PMID: 28730546 PMCID: PMC5636749 DOI: 10.1007/s13238-017-0448-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 10/28/2022] Open
Abstract
Mammalian mitochondrial genome encodes a small set of tRNAs, rRNAs, and mRNAs. The RNA synthesis process has been well characterized. How the RNAs are degraded, however, is poorly understood. It was long assumed that the degradation happens in the matrix where transcription and translation machineries reside. Here we show that contrary to the assumption, mammalian mitochondrial RNA degradation occurs in the mitochondrial intermembrane space (IMS) and the IMS-localized RNASET2 is the enzyme that degrades the RNAs. This provides a new paradigm for understanding mitochondrial RNA metabolism and transport.
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Affiliation(s)
- Peipei Liu
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jinliang Huang
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qian Zheng
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Leiming Xie
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xinping Lu
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jie Jin
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Geng Wang
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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187
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Lobingier BT, Hüttenhain R, Eichel K, Miller KB, Ting AY, von Zastrow M, Krogan NJ. An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. Cell 2017; 169:350-360.e12. [PMID: 28388416 DOI: 10.1016/j.cell.2017.03.022] [Citation(s) in RCA: 278] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 02/02/2017] [Accepted: 03/15/2017] [Indexed: 11/25/2022]
Abstract
Cells operate through protein interaction networks organized in space and time. Here, we describe an approach to resolve both dimensions simultaneously by using proximity labeling mediated by engineered ascorbic acid peroxidase (APEX). APEX has been used to capture entire organelle proteomes with high temporal resolution, but its breadth of labeling is generally thought to preclude the higher spatial resolution necessary to interrogate specific protein networks. We provide a solution to this problem by combining quantitative proteomics with a system of spatial references. As proof of principle, we apply this approach to interrogate proteins engaged by G-protein-coupled receptors as they dynamically signal and traffic in response to ligand-induced activation. The method resolves known binding partners, as well as previously unidentified network components. Validating its utility as a discovery pipeline, we establish that two of these proteins promote ubiquitin-linked receptor downregulation after prolonged activation.
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Affiliation(s)
- Braden T Lobingier
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, QBI, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Kelsie Eichel
- Program in Biochemistry and Molecular Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Alice Y Ting
- Departments of Genetics, Biology, and Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Mark von Zastrow
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, QBI, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA.
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188
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Cann ML, McDonald IM, East MP, Johnson GL, Graves LM. Measuring Kinase Activity-A Global Challenge. J Cell Biochem 2017; 118:3595-3606. [PMID: 28464261 DOI: 10.1002/jcb.26103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 12/22/2022]
Abstract
The kinase enzymes within a cell, known collectively as the kinome, play crucial roles in many signaling pathways, including survival, motility, differentiation, stress response, and many more. Aberrant signaling through kinase pathways is often linked to cancer, among other diseases. A major area of scientific research involves understanding the relationships between kinases, their targets, and how the kinome adapts to perturbations of the cellular system. This review will discuss many of the current and developing methods for studying kinase activity, and evaluate their applications, advantages, and disadvantages. J. Cell. Biochem. 118: 3595-3606, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Marissa L Cann
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Ian M McDonald
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Michael P East
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Gary L Johnson
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Lee M Graves
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
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189
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Close Encounters - Probing Proximal Proteins in Live or Fixed Cells. Trends Biochem Sci 2017; 42:504-515. [PMID: 28566215 DOI: 10.1016/j.tibs.2017.05.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/25/2017] [Accepted: 05/03/2017] [Indexed: 12/30/2022]
Abstract
The well-oiled machinery of the cellular proteome operates via variable expression, modifications, and interactions of proteins, relaying genomic and transcriptomic information to coordinate cellular functions. In recent years, a number of techniques have emerged that serve to identify sets of proteins acting in close proximity in the course of orchestrating cellular activities. These proximity-dependent assays, including BiFC, BioID, APEX, FRET, and isPLA, have opened up new avenues to examine protein interactions in live or fixed cells. We review herein the current status of proximity-dependent in situ techniques. We compare the advantages and limitations of the methods, underlining recent progress and the growing importance of these techniques in basic research, and we discuss their potential as tools for drug development and diagnostics.
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190
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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
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191
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Chen CL, Perrimon N. Proximity-dependent labeling methods for proteomic profiling in living cells. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28387482 DOI: 10.1002/wdev.272] [Citation(s) in RCA: 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.
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Affiliation(s)
- Chiao-Lin Chen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA
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192
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De Munter S, Görnemann J, Derua R, Lesage B, Qian J, Heroes E, Waelkens E, Van Eynde A, Beullens M, Bollen M. Split-BioID: a proximity biotinylation assay for dimerization-dependent protein interactions. FEBS Lett 2017; 591:415-424. [DOI: 10.1002/1873-3468.12548] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/03/2016] [Accepted: 12/26/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Sofie De Munter
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
| | - Janina Görnemann
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
| | - Rita Derua
- Protein Phosphorylation & Proteomics Lab; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
- SyBioMa; KU Leuven; Belgium
| | - Bart Lesage
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
| | - Junbin Qian
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
| | - Ewald Heroes
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
| | - Etienne Waelkens
- Protein Phosphorylation & Proteomics Lab; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
- SyBioMa; KU Leuven; Belgium
| | - Aleyde Van Eynde
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
| | - Monique Beullens
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
| | - Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
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