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Delhaye L, Moschonas GD, Fijalkowska D, Verhee A, De Sutter D, Van de Steene T, De Meyer M, Grzesik H, Van Moortel L, De Bosscher K, Jacobs T, Eyckerman S. Leveraging a self-cleaving peptide for tailored control in proximity labeling proteomics. CELL REPORTS METHODS 2024:100818. [PMID: 38986614 DOI: 10.1016/j.crmeth.2024.100818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 05/15/2024] [Accepted: 06/17/2024] [Indexed: 07/12/2024]
Abstract
Protein-protein interactions play an important biological role in every aspect of cellular homeostasis and functioning. Proximity labeling mass spectrometry-based proteomics overcomes challenges typically associated with other methods and has quickly become the current state of the art in the field. Nevertheless, tight control of proximity-labeling enzymatic activity and expression levels is crucial to accurately identify protein interactors. Here, we leverage a T2A self-cleaving peptide and a non-cleaving mutant to accommodate the protein of interest in the experimental and control TurboID setup. To allow easy and streamlined plasmid assembly, we built a Golden Gate modular cloning system to generate plasmids for transient expression and stable integration. To highlight our T2A Split/link design, we applied it to identify protein interactions of the glucocorticoid receptor and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid and non-structural protein 7 (NSP7) proteins by TurboID proximity labeling. Our results demonstrate that our T2A split/link provides an opportune control that builds upon previously established control requirements in the field.
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Affiliation(s)
- Louis Delhaye
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium; OncoRNALab, Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium
| | - George D Moschonas
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Daria Fijalkowska
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Annick Verhee
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Delphine De Sutter
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Tessa Van de Steene
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Margaux De Meyer
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Hanna Grzesik
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Laura Van Moortel
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Karolien De Bosscher
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Thomas Jacobs
- VIB-UGent Center for Plant Systems Biology, VIB, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.
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2
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Bareja A, Lee DE, Ho T, Waitt G, McKay LH, Hannou SA, Orenduff MC, McGreevy KM, Binder A, Ryan CP, Soderblom EJ, Belsky DW, Ferrucci L, Das JK, Banskota N, Kraus VB, Huebner JL, Kraus WE, Huffman KM, Baht GS, Horvath S, Parmer RJ, Miles LA, White JP. Liver-derived plasminogen mediates muscle stem cell expansion during caloric restriction through the plasminogen receptor Plg-R KT. Cell Rep 2024; 43:113881. [PMID: 38442019 PMCID: PMC11075744 DOI: 10.1016/j.celrep.2024.113881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 08/08/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
An intriguing effect of short-term caloric restriction (CR) is the expansion of certain stem cell populations, including muscle stem cells (satellite cells), which facilitate an accelerated regenerative program after injury. Here, we utilized the MetRSL274G (MetRS) transgenic mouse to identify liver-secreted plasminogen as a candidate for regulating satellite cell expansion during short-term CR. Knockdown of circulating plasminogen prevents satellite cell expansion during short-term CR. Furthermore, loss of the plasminogen receptor KT (Plg-RKT) is also sufficient to prevent CR-related satellite cell expansion, consistent with direct signaling of plasminogen through the plasminogen receptor Plg-RKT/ERK kinase to promote proliferation of satellite cells. Importantly, we are able to replicate many of these findings in human participants from the CALERIE trial. Our results demonstrate that CR enhances liver protein secretion of plasminogen, which signals directly to the muscle satellite cell through Plg-RKT to promote proliferation and subsequent muscle resilience during CR.
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Affiliation(s)
- Akshay Bareja
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - David E Lee
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - Tricia Ho
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC, USA
| | - Greg Waitt
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC, USA
| | - Lauren H McKay
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of Chapel Hill, Chapel Hill, NC, USA
| | - Sarah A Hannou
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - Melissa C Orenduff
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - Kristen M McGreevy
- Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA
| | - Alexandra Binder
- Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA; Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA
| | - Calen P Ryan
- Columbia University Mailman School of Public Health, New York, NY, USA
| | - Erik J Soderblom
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC, USA
| | - Daniel W Belsky
- Columbia University Mailman School of Public Health, New York, NY, USA
| | - Luigi Ferrucci
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jayanta Kumar Das
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nirad Banskota
- Longitudinal Studies Section, Translation Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Virginia B Kraus
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA
| | - Janet L Huebner
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - William E Kraus
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA
| | - Kim M Huffman
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA
| | - Gurpreet S Baht
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA; Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC 27701, USA
| | - Steve Horvath
- Computational Biology and Genomics Core, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA; Altos Labs, San Diego, CA, USA
| | - Robert J Parmer
- Department of Medicine, Veterans Administration San Diego Healthcare System, San Diego, CA, USA; Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lindsey A Miles
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - James P White
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA.
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3
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Sobo JM, Alagna NS, Sun SX, Wilson KL, Reddy KL. Lamins: The backbone of the nucleocytoskeleton interface. Curr Opin Cell Biol 2024; 86:102313. [PMID: 38262116 DOI: 10.1016/j.ceb.2023.102313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024]
Abstract
The nuclear lamina (NL) is a crucial component of the inner nuclear membrane (INM) and consists of lamin filaments and associated proteins. Lamins are type V intermediate filament proteins essential for maintaining the integrity and mechanical properties of the nucleus. In human cells, 'B-type' lamins (lamin B1 and lamin B2) are ubiquitously expressed, while 'A-type' lamins (lamin A, lamin C, and minor isoforms) are expressed in a tissue- and development-specific manner. Lamins homopolymerize to form filaments that localize primarily near the INM, but A-type lamins also localize to and function in the nucleoplasm. Lamins play central roles in the assembly, structure, positioning, and mechanics of the nucleus, modulating cell signaling and influencing development, differentiation, and other activities. This review highlights recent findings on the structure and regulation of lamin filaments, providing insights into their multifaceted functions, including their role as "mechanosensors", delving into the emerging significance of lamin filaments as vital links between cytoskeletal and nuclear structures, chromatin organization, and the genome.
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Affiliation(s)
- Joan M Sobo
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Nicholas S Alagna
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sean X Sun
- Department of Mechanical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Katherine L Wilson
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Karen L Reddy
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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4
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Guo J, Guo S, Lu S, Gong J, Wang L, Ding L, Chen Q, Liu W. The development of proximity labeling technology and its applications in mammals, plants, and microorganisms. Cell Commun Signal 2023; 21:269. [PMID: 37777761 PMCID: PMC10544124 DOI: 10.1186/s12964-023-01310-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/07/2023] [Indexed: 10/02/2023] Open
Abstract
Protein‒protein, protein‒RNA, and protein‒DNA interaction networks form the basis of cellular regulation and signal transduction, making it crucial to explore these interaction networks to understand complex biological processes. Traditional methods such as affinity purification and yeast two-hybrid assays have been shown to have limitations, as they can only isolate high-affinity molecular interactions under nonphysiological conditions or in vitro. Moreover, these methods have shortcomings for organelle isolation and protein subcellular localization. To address these issues, proximity labeling techniques have been developed. This technology not only overcomes the limitations of traditional methods but also offers unique advantages in studying protein spatial characteristics and molecular interactions within living cells. Currently, this technique not only is indispensable in research on mammalian nucleoprotein interactions but also provides a reliable approach for studying nonmammalian cells, such as plants, parasites and viruses. Given these advantages, this article provides a detailed introduction to the principles of proximity labeling techniques and the development of labeling enzymes. The focus is on summarizing the recent applications of TurboID and miniTurbo in mammals, plants, and microorganisms. Video Abstract.
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Affiliation(s)
- Jieyu Guo
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Shuang Guo
- Medicine Research Institute, Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Siao Lu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Jun Gong
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Long Wang
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Liqiong Ding
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Qingjie Chen
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
| | - Wu Liu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
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5
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Borna Disease Virus 1 Phosphoprotein Forms a Tetramer and Interacts with Host Factors Involved in DNA Double-Strand Break Repair and mRNA Processing. Viruses 2022; 14:v14112358. [PMID: 36366462 PMCID: PMC9692295 DOI: 10.3390/v14112358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 01/31/2023] Open
Abstract
Determining the structural organisation of viral replication complexes and unravelling the impact of infection on cellular homeostasis represent important challenges in virology. This may prove particularly useful when confronted with viruses that pose a significant threat to human health, that appear unique within their family, or for which knowledge is scarce. Among Mononegavirales, bornaviruses (family Bornaviridae) stand out due to their compact genomes and their nuclear localisation for replication. The recent recognition of the zoonotic potential of several orthobornaviruses has sparked a surge of interest in improving our knowledge on this viral family. In this work, we provide a complete analysis of the structural organisation of Borna disease virus 1 (BoDV-1) phosphoprotein (P), an important cofactor for polymerase activity. Using X-ray diffusion and diffraction experiments, we revealed that BoDV-1 P adopts a long coiled-coil α-helical structure split into two parts by an original β-strand twist motif, which is highly conserved across the members of whole Orthobornavirus genus and may regulate viral replication. In parallel, we used BioID to determine the proximal interactome of P in living cells. We confirmed previously known interactors and identified novel proteins linked to several biological processes such as DNA repair or mRNA metabolism. Altogether, our study provides important structure/function cues, which may improve our understanding of BoDV-1 pathogenesis.
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Neumann-Staubitz P, Kitsberg D, Buxboim A, Neumann H. A method to map the interaction network of the nuclear lamina with genetically encoded photo-crosslinkers in vivo. Front Chem 2022; 10:905794. [PMID: 36110135 PMCID: PMC9468544 DOI: 10.3389/fchem.2022.905794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/29/2022] [Indexed: 11/23/2022] Open
Abstract
Lamins are intermediate filaments that assemble in a meshwork at the inner nuclear periphery of metazoan cells. The nuclear periphery fulfils important functions by providing stability to the nuclear membrane, connecting the cytoskeleton with chromatin, and participating in signal transduction. Mutations in lamins interfere with these functions and cause severe, phenotypically diverse diseases collectively referred to as laminopathies. The molecular consequences of these mutations are largely unclear but likely include alterations in lamin-protein and lamin-chromatin interactions. These interactions are challenging to study biochemically mainly because the lamina is resistant to high salt and detergent concentrations and co-immunoprecipitation are susceptible to artefacts. Here, we used genetic code expansion to install photo-activated crosslinkers to capture direct lamin-protein interactions in vivo. Mapping the Ig-fold of laminC for interactions, we identified laminC-crosslink products with laminB1, LAP2, and TRIM28. We observed significant changes in the crosslink intensities between laminC mutants mimicking different phosphorylation states. Similarly, we found variations in laminC crosslink product intensities comparing asynchronous cells and cells synchronized in prophase. This method can be extended to other laminC domains or other lamins to reveal changes in their interactome as a result of mutations or cell cycle stages.
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Affiliation(s)
| | - Daniel Kitsberg
- Institute of Life Science, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amnon Buxboim
- Institute of Life Science, Hebrew University of Jerusalem, Jerusalem, Israel
- Rachel and Selim Benin School of Computer Science and Engineering, Hebrew University of Jerusalem, Jerusalem, Israel
- Alexander Grass Center for Bioengineering, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Heinz Neumann
- University of Applied Sciences Darmstadt, Darmstadt, Germany
- *Correspondence: Heinz Neumann,
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Belmont AS. Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture. Cold Spring Harb Perspect Biol 2022; 14:a041268. [PMID: 34400557 PMCID: PMC9248822 DOI: 10.1101/cshperspect.a041268] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This work reviews nuclear compartments, defined broadly to include distinct nuclear structures, bodies, and chromosome domains. It first summarizes original cytological observations before comparing concepts of nuclear compartments emerging from microscopy versus genomic approaches and then introducing new multiplexed imaging approaches that promise in the future to meld both approaches. I discuss how previous models of radial distribution of chromosomes or the binary division of the genome into A and B compartments are now being refined by the recognition of more complex nuclear compartmentalization. The poorly understood question of how these nuclear compartments are established and maintained is then discussed, including through the modern perspective of phase separation, before moving on to address possible functions of nuclear compartments, using the possible role of nuclear speckles in modulating gene expression as an example. Finally, the review concludes with a discussion of future questions for this field.
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Affiliation(s)
- Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
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8
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Mattola S, Salokas K, Aho V, Mäntylä E, Salminen S, Hakanen S, Niskanen EA, Svirskaite J, Ihalainen TO, Airenne KJ, Kaikkonen-Määttä M, Parrish CR, Varjosalo M, Vihinen-Ranta M. Parvovirus nonstructural protein 2 interacts with chromatin-regulating cellular proteins. PLoS Pathog 2022; 18:e1010353. [PMID: 35395063 PMCID: PMC9020740 DOI: 10.1371/journal.ppat.1010353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 04/20/2022] [Accepted: 03/15/2022] [Indexed: 11/28/2022] Open
Abstract
Autonomous parvoviruses encode at least two nonstructural proteins, NS1 and NS2. While NS1 is linked to important nuclear processes required for viral replication, much less is known about the role of NS2. Specifically, the function of canine parvovirus (CPV) NS2 has remained undefined. Here we have used proximity-dependent biotin identification (BioID) to screen for nuclear proteins that associate with CPV NS2. Many of these associations were seen both in noninfected and infected cells, however, the major type of interacting proteins shifted from nuclear envelope proteins to chromatin-associated proteins in infected cells. BioID interactions revealed a potential role for NS2 in DNA remodeling and damage response. Studies of mutant viral genomes with truncated forms of the NS2 protein suggested a change in host chromatin accessibility. Moreover, further studies with NS2 mutants indicated that NS2 performs functions that affect the quantity and distribution of proteins linked to DNA damage response. Notably, mutation in the splice donor site of the NS2 led to a preferred formation of small viral replication center foci instead of the large coalescent centers seen in wild-type infection. Collectively, our results provide insights into potential roles of CPV NS2 in controlling chromatin remodeling and DNA damage response during parvoviral replication. Parvoviruses are small, nonenveloped DNA viruses, that besides being noteworthy pathogens in many animal species, including humans, are also being developed as vectors for gene and cancer therapy. Canine parvovirus is an autonomously replicating parvovirus that encodes two nonstructural proteins, NS1 and NS2. NS1 is required for viral DNA replication and packaging, as well as gene expression. However, very little is known about the function of NS2. Our studies indicate that NS2 serves a previously undefined important function in chromatin modification and DNA damage responses. Therefore, it appears that although both NS1 and NS2 are needed for a productive infection they play very different roles in the process.
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Affiliation(s)
- Salla Mattola
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Kari Salokas
- Institute of Biotechnology and Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Vesa Aho
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Elina Mäntylä
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sami Salminen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Satu Hakanen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Einari A. Niskanen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Julija Svirskaite
- Institute of Biotechnology and Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Teemu O. Ihalainen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kari J. Airenne
- Kuopio Center for Gene and Cell Therapy (KCT), Kuopio, Finland
| | | | - Colin R. Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, University of Cornell, Ithaca, New York, United States of America
| | - Markku Varjosalo
- Institute of Biotechnology and Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Maija Vihinen-Ranta
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
- * E-mail:
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9
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Abstract
Lamins interact with a host of nuclear membrane proteins, transcription factors, chromatin regulators, signaling molecules, splicing factors, and even chromatin itself to form a nuclear subcompartment, the nuclear lamina, that is involved in a variety of cellular processes such as the governance of nuclear integrity, nuclear positioning, mitosis, DNA repair, DNA replication, splicing, signaling, mechanotransduction and -sensation, transcriptional regulation, and genome organization. Lamins are the primary scaffold for this nuclear subcompartment, but interactions with lamin-associated peptides in the inner nuclear membrane are self-reinforcing and mutually required. Lamins also interact, directly and indirectly, with peripheral heterochromatin domains called lamina-associated domains (LADs) and help to regulate dynamic 3D genome organization and expression of developmentally regulated genes.
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Affiliation(s)
- Xianrong Wong
- Laboratory of Developmental and Regenerative Biology, Skin Research Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore 138648
| | - Ashley J Melendez-Perez
- Department of Biological Chemistry and Center for Epigenetics, Johns Hopkins University of Medicine, Baltimore, Maryland 21205, USA
| | - Karen L Reddy
- Department of Biological Chemistry and Center for Epigenetics, Johns Hopkins University of Medicine, Baltimore, Maryland 21205, USA
- Sidney Kimmel Cancer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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10
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Gerassimovich YA, Miladinovski-Bangall SJ, Bridges KM, Boateng L, Ball LE, Valafar H, Nag A. Proximity-dependent biotinylation detects associations between SARS coronavirus nonstructural protein 1 and stress granule-associated proteins. J Biol Chem 2021; 297:101399. [PMID: 34774526 PMCID: PMC8580555 DOI: 10.1016/j.jbc.2021.101399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 10/28/2021] [Accepted: 11/08/2021] [Indexed: 11/17/2022] Open
Abstract
The nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus and severe acute respiratory syndrome coronavirus 2 is a critical viral protein that suppresses host gene expression by blocking the assembly of the ribosome on host mRNAs. To understand the mechanism of inhibition of host gene expression, we sought to identify cellular proteins that interact with nsp1. Using proximity-dependent biotinylation followed by proteomic analyses of biotinylated proteins, here we captured multiple dynamic interactions of nsp1 with host cell proteins. In addition to ribosomal proteins, we identified several pre-mRNA processing proteins that interact with nsp1, including splicing factors and transcription termination proteins, as well as exosome, and stress granule (SG)-associated proteins. We found that the interactions with transcription termination factors are primarily governed by the C-terminal region of nsp1 and are disrupted by the mutation of amino acids K164 and H165 that are essential for its host shutoff function. We further show that nsp1 interacts with Ras GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) and colocalizes with G3BP1 in SGs under sodium arsenite-induced stress. Finally, we observe that the presence of nsp1 disrupts the maturation of SGs over a long period. Isolation of SG core at different times shows a gradual loss of G3BP1 in the presence of nsp1.
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Affiliation(s)
- Yevgeniy A Gerassimovich
- Natural Sciences and Engineering, University of South Carolina Upstate, Spartanburg, South Carolina, USA
| | | | - Kaitlin M Bridges
- Natural Sciences and Engineering, University of South Carolina Upstate, Spartanburg, South Carolina, USA
| | - Linkel Boateng
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina, USA
| | - Lauren E Ball
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Homayoun Valafar
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina, USA
| | - Anita Nag
- Natural Sciences and Engineering, University of South Carolina Upstate, Spartanburg, South Carolina, USA.
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11
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Garcia YA, Velasquez EF, Gao LW, Gholkar AA, Clutario KM, Cheung K, Williams-Hamilton T, Whitelegge JP, Torres JZ. Mapping Proximity Associations of Core Spindle Assembly Checkpoint Proteins. J Proteome Res 2021; 20:3414-3427. [PMID: 34087075 PMCID: PMC8256817 DOI: 10.1021/acs.jproteome.0c00941] [Citation(s) in RCA: 10] [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: 11/24/2020] [Indexed: 12/25/2022]
Abstract
The spindle assembly checkpoint (SAC) is critical for sensing defective microtubule-kinetochore attachments and tension across the kinetochore and functions to arrest cells in prometaphase to allow time to repair any errors before proceeding into anaphase. Dysregulation of the SAC leads to chromosome segregation errors that have been linked to human diseases like cancer. Although much has been learned about the composition of the SAC and the factors that regulate its activity, the proximity associations of core SAC components have not been explored in a systematic manner. Here, we have taken a BioID2-proximity-labeling proteomic approach to define the proximity protein environment for each of the five core SAC proteins BUB1, BUB3, BUBR1, MAD1L1, and MAD2L1 in mitotic-enriched populations of cells where the SAC is active. These five protein association maps were integrated to generate a SAC proximity protein network that contains multiple layers of information related to core SAC protein complexes, protein-protein interactions, and proximity associations. Our analysis validated many known SAC complexes and protein-protein interactions. Additionally, it uncovered new protein associations, including the ELYS-MAD1L1 interaction that we have validated, which lend insight into the functioning of core SAC proteins and highlight future areas of investigation to better understand the SAC.
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Affiliation(s)
- Yenni A. Garcia
- Department of Chemistry and Biochemistry,
University of California, Los Angeles, California 90095,
United States
| | - Erick F. Velasquez
- Department of Chemistry and Biochemistry,
University of California, Los Angeles, California 90095,
United States
| | - Lucy W. Gao
- Pasarow Mass Spectrometry Laboratory, The Jane and
Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of
Medicine, University of California, Los Angeles, California
90095, United States
| | - Ankur A. Gholkar
- Department of Chemistry and Biochemistry,
University of California, Los Angeles, California 90095,
United States
| | - Kevin M. Clutario
- Department of Chemistry and Biochemistry,
University of California, Los Angeles, California 90095,
United States
| | - Keith Cheung
- Department of Chemistry and Biochemistry,
University of California, Los Angeles, California 90095,
United States
| | - Taylor Williams-Hamilton
- Department of Chemistry and Biochemistry,
University of California, Los Angeles, California 90095,
United States
| | - Julian P. Whitelegge
- Pasarow Mass Spectrometry Laboratory, The Jane and
Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of
Medicine, University of California, Los Angeles, California
90095, United States
- Molecular Biology Institute, University of
California, Los Angeles, California 90095, United
States
- Jonsson Comprehensive Cancer Center,
University of California, Los Angeles, California 90095,
United States
| | - Jorge Z. Torres
- Department of Chemistry and Biochemistry,
University of California, Los Angeles, California 90095,
United States
- Molecular Biology Institute, University of
California, Los Angeles, California 90095, United
States
- Jonsson Comprehensive Cancer Center,
University of California, Los Angeles, California 90095,
United States
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12
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Wong X, Cutler JA, Hoskins VE, Gordon M, Madugundu AK, Pandey A, Reddy KL. Mapping the micro-proteome of the nuclear lamina and lamina-associated domains. Life Sci Alliance 2021; 4:e202000774. [PMID: 33758005 PMCID: PMC8008952 DOI: 10.26508/lsa.202000774] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 01/13/2023] Open
Abstract
The nuclear lamina is a proteinaceous network of filaments that provide both structural and gene regulatory functions by tethering proteins and large domains of DNA, the so-called lamina-associated domains (LADs), to the periphery of the nucleus. LADs are a large fraction of the mammalian genome that are repressed, in part, by their association to the nuclear periphery. The genesis and maintenance of LADs is poorly understood as are the proteins that participate in these functions. In an effort to identify proteins that reside at the nuclear periphery and potentially interact with LADs, we have taken a two-pronged approach. First, we have undertaken an interactome analysis of the inner nuclear membrane bound LAP2β to further characterize the nuclear lamina proteome. To accomplish this, we have leveraged the BioID system, which previously has been successfully used to characterize the nuclear lamina proteome. Second, we have established a system to identify proteins that bind to LADs by developing a chromatin-directed BioID system. We combined the BioID system with the m6A-tracer system which binds to LADs in live cells to identify both LAD proximal and nuclear lamina proteins. In combining these datasets, we have further characterized the protein network at the nuclear lamina, identified putative LAD proximal proteins and found several proteins that appear to interface with both micro-proteomes. Importantly, several proteins essential for LAD function, including heterochromatin regulating proteins related to H3K9 methylation, were identified in this study.
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Affiliation(s)
- Xianrong Wong
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Laboratory of Developmental and Regenerative Biology, Institute of Medical Biology, Agency for Science, Technology and Research (A∗STAR), Immunos, Singapore
| | - Jevon A Cutler
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Victoria E Hoskins
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Molly Gordon
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anil K Madugundu
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHNS), Bangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Akhilesh Pandey
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHNS), Bangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen L Reddy
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Cancer Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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13
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Guedouari H, Ould Amer Y, Pichaud N, Hebert-Chatelain E. Characterization of the interactome of c-Src within the mitochondrial matrix by proximity-dependent biotin identification. Mitochondrion 2021; 57:257-269. [PMID: 33412331 DOI: 10.1016/j.mito.2020.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/09/2020] [Accepted: 12/30/2020] [Indexed: 12/27/2022]
Abstract
C-Src kinase is localized in several subcellular compartments, including mitochondria where it is involved in the regulation of organelle functions and overall metabolism. Surprisingly, the characterization of the intramitochondrial Src interactome has never been fully determined. Using in vitro proximity-dependent biotin identification (BioID) coupled to mass spectrometry, we identified 51 candidate proteins that may interact directly or indirectly with c-Src within the mitochondrial matrix. Pathway analysis suggests that these proteins are involved in a large array of mitochondrial functions such as protein folding and import, mitochondrial organization and transport, oxidative phosphorylation, tricarboxylic acid cycle and metabolism of amino and fatty acids. Among these proteins, we identified 24 tyrosine phosphorylation sites in 17 mitochondrial proteins (AKAP1, VDAC1, VDAC2, VDAC3, LonP1, Hsp90, SLP2, PHB2, MIC60, UBA1, EF-Tu, LRPPRC, ACO2, OAT, ACAT1, ETFβ and ATP5β) as potential substrates for intramitochondrial Src using in silico prediction of tyrosine phospho-sites. Interaction of c-Src with SLP2 and ATP5β was confirmed using coimmunoprecipitation. This study suggests that the intramitochondrial Src could target several proteins and regulate different mitochondrial functions.
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Affiliation(s)
- Hala Guedouari
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, Moncton, NB, Canada; University of Moncton, Dept. of Biology, Moncton, NB, Canada
| | - Yasmine Ould Amer
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, Moncton, NB, Canada; University of Moncton, Dept. of Biology, Moncton, NB, Canada
| | - Nicolas Pichaud
- University of Moncton, Dept. of Chemistry and Biochemistry, Moncton, NB, Canada
| | - Etienne Hebert-Chatelain
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, Moncton, NB, Canada; University of Moncton, Dept. of Biology, Moncton, NB, Canada.
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14
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Béganton B, Coyaud E, Laurent EMN, Mangé A, Jacquemetton J, Le Romancer M, Raught B, Solassol J. Proximal Protein Interaction Landscape of RAS Paralogs. Cancers (Basel) 2020; 12:cancers12113326. [PMID: 33187149 PMCID: PMC7696408 DOI: 10.3390/cancers12113326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/01/2020] [Accepted: 11/07/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary RAS paralogs (HRAS, NRAS and KRAS) are of major interest in biology because they are involved in developmental disorders (e.g., Costello and Noonan syndromes) and in a broad variety of human neoplasia. Many research groups have devoted tremendous efforts to deepen our understanding of the RAS proteins functions and regulations, notably through identifying their functional protein partners. However, while most of these studies were focused on pathogenic RAS mutants, much less research has been dedicated to deciphering the normal activities of RAS paralogs. However, such characterization appears as a prerequisite to clearly identify pathogenic features. We delineated and compared the wild type RAS paralogs proximal interactomes. We detected more than 800 RAS high confident proximal interactors, either shared between paralogs or unique, and validated a subset of data through proximity ligation assays-based validation. Our results describe differential interactors enrichment between RAS paralogs and uncover novel ties between RAS signaling and cellular metabolism. We believe that our findings will support further studies aiming at better understanding how RAS paralogs could be differentially involved in discrete cellular processes and could serve as a basis to template oncogenic mechanism investigations. Abstract RAS proteins (KRAS, NRAS and HRAS) are frequently activated in different cancer types (e.g., non-small cell lung cancer, colorectal cancer, melanoma and bladder cancer). For many years, their activities were considered redundant due to their high degree of sequence homology (80% identity) and their shared upstream and downstream protein partners. However, the high conservation of the Hyper-Variable-Region across mammalian species, the preferential activation of different RAS proteins in specific tumor types and the specific post-translational modifications and plasma membrane-localization of each paralog suggest they could ensure discrete functions. To gain insights into RAS proteins specificities, we explored their proximal protein–protein interaction landscapes using the proximity-dependent biotin identification technology (BioID) in Flp-In T-REx 293 cell lines stably transfected and inducibly expressing wild type KRAS4B, NRAS or HRAS. We identified more than 800 high-confidence proximal interactors, allowing us to propose an unprecedented comparative analysis of wild type RAS paralogs protein networks. These data bring novel information on poorly characterized RAS functions, e.g., its putative involvement in metabolic pathways, and on shared as well as paralog-specific protein networks that could partially explain the complexity of RAS functions. These networks of protein interactions open numerous avenues to better understand RAS paralogs biological activities.
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Affiliation(s)
- Benoît Béganton
- CHU Montpellier, Department of Pathology and Onco-Biology, Univ Montpellier, 34295 Montpellier, France;
- IRCM, INSERM, Univ Montpellier, ICM, 34298 Montpellier, France;
- Correspondence: ; Tel.: +33-467-33-58-71
| | - Etienne Coyaud
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada; (E.C.); (E.M.N.L.); (B.R.)
| | - Estelle M. N. Laurent
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada; (E.C.); (E.M.N.L.); (B.R.)
| | - Alain Mangé
- IRCM, INSERM, Univ Montpellier, ICM, 34298 Montpellier, France;
| | - Julien Jacquemetton
- Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052, CNRS UMR5286, Université Lyon 1, 69008 Lyon, France; (J.J.); (M.L.R.)
| | - Muriel Le Romancer
- Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052, CNRS UMR5286, Université Lyon 1, 69008 Lyon, France; (J.J.); (M.L.R.)
| | - Brian Raught
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada; (E.C.); (E.M.N.L.); (B.R.)
| | - Jérôme Solassol
- CHU Montpellier, Department of Pathology and Onco-Biology, Univ Montpellier, 34295 Montpellier, France;
- IRCM, INSERM, Univ Montpellier, ICM, 34298 Montpellier, France;
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15
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Bocanegra JL, Fujita BM, Melton NR, Cowan JM, Schinski EL, Tamir TY, Major MB, Quintero OA. The MyMOMA domain of MYO19 encodes for distinct Miro-dependent and Miro-independent mechanisms of interaction with mitochondrial membranes. Cytoskeleton (Hoboken) 2020; 77:149-166. [PMID: 31479585 PMCID: PMC8556674 DOI: 10.1002/cm.21560] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/13/2019] [Accepted: 08/31/2019] [Indexed: 08/19/2023]
Abstract
MYO19 interacts with mitochondria through a C-terminal membrane association domain (MyMOMA). Specific mechanisms for localization of MYO19 to mitochondria are poorly understood. Using promiscuous biotinylation data in combination with existing affinity-capture databases, we have identified a number of putative MYO19-interacting proteins. We chose to explore the interaction between MYO19 and the mitochondrial GTPase Miro2 by expressing mchr-Miro2 in combination with GFP-tagged fragments of the MyMOMA domain and assaying for recruitment of MYO19-GFP to mitochondria. Coexpression of MYO19898-970 -GFP with mchr-Miro2 enhanced MYO19898-970 -GFP localization to mitochondria. Mislocalizing Miro2 to filopodial tips or the cytosolic face of the nuclear envelope did not recruit MYO19898-970 -GFP to either location. To address the kinetics of the Miro2/MYO19 interaction, we used FRAP analysis and permeabilization-activated reduction in fluorescence analysis. MyMOMA constructs containing a putative membrane-insertion motif but lacking the Miro2-interacting region displayed slow exchange kinetics. MYO19898-970 -GFP, which does not include the membrane-insertion motif, displayed rapid exchange kinetics, suggesting that MYO19 interacting with Miro2 has higher mobility than MYO19 inserted into the mitochondrial outer membrane. Mutation of well-conserved, charged residues within MYO19 or within the switch I and II regions of Miro2 abolished the enhancement of MYO19898-970 -GFP localization in cells ectopically expressing mchr-Miro2. Additionally, expressing mutant versions of Miro2 thought to represent particular nucleotide states indicated that the enhancement of MYO19898-970 -GFP localization is dependent on Miro2 nucleotide state. Taken together, these data suggest that membrane-inserted MYO19 is part of a larger complex, and that Miro2 plays a role in integration of actin- and microtubule-based mitochondrial activities.
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Affiliation(s)
| | | | | | - James M. Cowan
- Department of Biology, University of Richmond, Richmond, Virginia
| | | | - Tigist Y. Tamir
- Department of Pharmacology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
| | - Michael B. Major
- Department of Pharmacology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
- Department of Cell Biology and Physiology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
| | - Omar A. Quintero
- Department of Biology, University of Richmond, Richmond, Virginia
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16
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Song H, Luo Q, Deng X, Ji C, Li D, Munankarmy A, Jian W, Zhao J, Fang L. VGLL4 interacts with STAT3 to function as a tumor suppressor in triple-negative breast cancer. Exp Mol Med 2019; 51:1-13. [PMID: 31748508 PMCID: PMC6868227 DOI: 10.1038/s12276-019-0338-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/08/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive malignancy with a poor prognosis, and there are no effective molecular-targeted drugs for TNBC patients in clinical practice. The JAK-STAT pathway is implicated in tumorigenesis and the progression of various cancers. In this study, the results demonstrated that VGLL4 is expressed at low levels in both TNBC specimens and cell lines and that VGLL4 expression is negatively correlated with Ki67 expression and tumor size in TNBC patients. VGLL4 knockdown can promote the growth of TNBC cells, while VGLL4 overexpression significantly suppresses the growth of TNBC cells in vitro. More importantly, VGLL4 significantly inhibits tumor progression in a nude mouse model. In addition, VGLL4 is a direct target of miR-454, and the upregulation of miR-454 decreases VGLL4 expression and promotes the cell growth of TNBC cells. Furthermore, we also demonstrated that VGLL4 interacts with STAT3, the core component of the JAK-STAT pathway, leading to the inactivation of STAT3 and the inhibition of STAT3 downstream transcription. Collectively, these findings indicate that VGLL4 expression is negatively associated with poor prognosis in TNBC patients. High expression of miR-454 may be one of the causes of the downregulation of VGLL4 in TNBC, and VGLL4 acts as a tumor suppressor in TNBC by interacting with STAT3 and subsequently suppresses the STAT3 signaling axis, providing potential biomarkers and therapeutic approaches for this fatal disease. Targeting the regulation or activity of a tumor suppressor protein that is deactivated in triple-negative breast cancer (TNBC) holds promise for the treatment of this highly aggressive form of cancer. Lin Fang and colleagues at Tongji University in Shanghai, China, showed that low levels of the protein vestigial-like family member 4 (VGLL4) promoted TNBC cell proliferation and migration, whereas overexpression of VGLL4 prevented the growth of these cells in mice. VGLL4 acts as a tumor suppressor by interfering with a signaling pathway that drives tumor growth. Furthermore, they found that VGLL4 expression is regulated by a small RNA molecule that is highly expressed in TNBC patients with poor prospects of survival. These findings provide new insights into the mechanisms underlying TNBC and highlight potential strategies for the development of targeted therapies.
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Affiliation(s)
- Hongming Song
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China.,Breast Disease Center, The Affiliated Hospital of Qingdao University, 59 Haier Road, Qingdao, 266000, Shandong, China
| | - Qifeng Luo
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China
| | - Xiaochong Deng
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China
| | - Changle Ji
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China
| | - Dengfeng Li
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China
| | - Amik Munankarmy
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China
| | - Wei Jian
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China
| | - Junyong Zhao
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China
| | - Lin Fang
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 200072, Shanghai, China.
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17
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Proteomic navigation using proximity-labeling. Methods 2019; 164-165:67-72. [PMID: 30953756 DOI: 10.1016/j.ymeth.2019.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 10/27/2022] Open
Abstract
The identification of bona fide protein-protein interactions and the mapping of proteomes was greatly enhanced by protein tagging for generic affinity purification methods and analysis by mass spectrometry (AP-MS). The high quality of AP-MS data permitted the development of proteomic navigation by sequential tagging of identified interactions. However AP-MS is laborious and limited to relatively high affinity protein-protein interactions. Proximity labeling, first with the biotin ligase BirA, termed BioID, and then with ascorbate peroxidase, termed APEX, permits a greater reach into the proteome than AP-MS enabling both the identification of a wider field and weaker protein-protein interactions. This additional reach comes with the need for stringent controls. Proximity labeling also permits experiments in living cells allowing spatiotemporal investigations of the proteome. Here we discuss proximity labeling with accompanying methodological descriptions for E. coli and mammalian cells.
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18
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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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19
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Oostdyk LT, Shank L, Jividen K, Dworak N, Sherman NE, Paschal BM. Towards improving proximity labeling by the biotin ligase BirA. Methods 2018; 157:66-79. [PMID: 30419333 DOI: 10.1016/j.ymeth.2018.11.003] [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: 07/24/2018] [Revised: 10/26/2018] [Accepted: 11/06/2018] [Indexed: 11/15/2022] Open
Abstract
The discovery and validation of protein-protein interactions provides a knowledge base that is critical for defining protein networks and how they underpin the biology of the cell. Identification of protein interactions that are highly transient, or sensitive to biochemical disruption, can be very difficult. This challenge has been met by proximity labeling methods which generate reactive species that chemically modify neighboring proteins. The most widely used proximity labeling method is BioID, which features a mutant biotin ligase BirA(Arg118Gly), termed BirA*, fused to a protein of interest. Here, we explore how amino acid substitutions at Arg118 affect the biochemical properties of BirA. We found that relative to wild-type BirA, the Arg118Lys substitution both slightly reduced biotin affinity and increased the release of reactive biotinyl-5'-AMP. BioID using a BirA(Arg118Lys)-Lamin A fusion enabled identification of PCNA as a lamina-proximal protein in HEK293T cells, a finding that was validated by immunofluorescence microscopy. Our data expand on the concept that proximity labeling by BirA fused to proteins of interest can be modulated by amino acid substitutions that affect biotin affinity and the release of biotinyl-5'-AMP.
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Affiliation(s)
- Luke T Oostdyk
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, VA 22908, USA
| | - Leonard Shank
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA
| | - Kasey Jividen
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA
| | - Natalia Dworak
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA
| | - Nicholas E Sherman
- W.M. Keck Biomedical Mass Spectrometry Laboratory, University of Virginia, VA 22908, USA
| | - Bryce M Paschal
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, VA 22908, USA.
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20
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A proximity-tagging system to identify membrane protein-protein interactions. Nat Methods 2018; 15:715-722. [PMID: 30104635 DOI: 10.1038/s41592-018-0100-5] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 05/29/2018] [Indexed: 11/08/2022]
Abstract
The communication between cells and between cellular organelles is often controlled by the interaction of membrane proteins. Although many methods for the detection of protein-protein interactions (PPIs) exist, membrane PPIs remain difficult to detect. Here we developed a proximity-based tagging system, PUP-IT (pupylation-based interaction tagging), to identify membrane protein interactions. In this approach, a small protein tag, Pup, is applied to proteins that interact with a PafA-fused bait, enabling transient and weak interactions to be enriched and detected by mass spectrometry. Pup does not diffuse from the enzyme, which allows high-specificity labeling. We applied this approach to CD28, a critical costimulatory receptor for T lymphocyte activation, and identified known CD28 binding partners and multiple potential interacting proteins. In addition, we demonstrated that this method can identify the interaction between a cell surface receptor and its ligand.
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21
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Ritchie C, Mack A, Harper L, Alfadhli A, Stork PJS, Nan X, Barklis E. Analysis of K-Ras Interactions by Biotin Ligase Tagging. Cancer Genomics Proteomics 2018. [PMID: 28647697 DOI: 10.21873/cgp.20034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Mutations of the human K-Ras 4B (K-Ras) G protein are associated with a significant proportion of all human cancers. Despite this fact, a comprehensive analysis of K-Ras interactions is lacking. Our investigations focus on characterization of the K-Ras interaction network. MATERIALS AND METHODS We employed a biotin ligase-tagging approach, in which tagged K-Ras proteins biotinylate neighbor proteins in a proximity-dependent fashion, and proteins are identified via mass spectrometry (MS) sequencing. RESULTS In transfected cells, a total of 748 biotinylated proteins were identified from cells expressing biotin ligase-tagged K-Ras variants. Significant differences were observed between membrane-associated variants and a farnesylation-defective mutant. In pancreatic cancer cells, 56 K-Ras interaction partners were identified. Most of these were cytoskeletal or plasma membrane proteins, and many have been identified previously as potential cancer biomarkers. CONCLUSION Biotin ligase tagging offers a rapid and convenient approach to the characterization of K-Ras interaction networks.
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Affiliation(s)
- Christopher Ritchie
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Andrew Mack
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Logan Harper
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Philip J S Stork
- Department of Vollum Institute, Oregon Health & Science University, Portland, OR, U.S.A
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, U.S.A
| | - Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A.
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22
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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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23
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Pecorari I, Borin D, Sbaizero O. A Perspective on the Experimental Techniques for Studying Lamins. Cells 2017; 6:E33. [PMID: 28994747 PMCID: PMC5755493 DOI: 10.3390/cells6040033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/01/2017] [Accepted: 10/05/2017] [Indexed: 01/29/2023] Open
Abstract
Lamins are type V intermediate filaments that collectively form a meshwork underneath the inner nuclear membrane, called nuclear lamina. Furthermore, they are also present in the nucleoplasm. Lamins are experiencing a growing interest, since a wide range of diseases are induced by mutations in the gene coding for A-type lamins, globally known as laminopathies. Moreover, it has been demonstrated that lamins are involved in other pathological conditions, like cancer. The role of lamins has been studied from several perspectives, exploiting different techniques and procedures. This multidisciplinary approach has contributed to resolving the unique features of lamins and has provided a thorough insight in their role in living organisms. Yet, there are still many unanswered questions, which constantly generate research in the field. The present work is aimed to review some interesting experimental techniques performed so far to study lamins. Scientists can take advantage of this collection for their novel investigations, being aware of the already pursued and consolidated methodologies. Hopefully, advances in these research directions will provide insights to achieve better diagnostic procedures and effective therapeutic options.
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Affiliation(s)
- Ilaria Pecorari
- Department of Engineering and Architecture, University of Trieste, Via Valerio 10, 34127 Trieste, Italy.
| | - Daniele Borin
- Department of Engineering and Architecture, University of Trieste, Via Valerio 10, 34127 Trieste, Italy.
| | - Orfeo Sbaizero
- Department of Engineering and Architecture, University of Trieste, Via Valerio 10, 34127 Trieste, Italy.
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24
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Thanisch K, Song C, Engelkamp D, Koch J, Wang A, Hallberg E, Foisner R, Leonhardt H, Stewart CL, Joffe B, Solovei I. Nuclear envelope localization of LEMD2 is developmentally dynamic and lamin A/C dependent yet insufficient for heterochromatin tethering. Differentiation 2017; 94:58-70. [PMID: 28056360 DOI: 10.1016/j.diff.2016.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/05/2016] [Accepted: 12/06/2016] [Indexed: 11/28/2022]
Abstract
Peripheral heterochromatin in mammalian nuclei is tethered to the nuclear envelope by at least two mechanisms here referred to as the A- and B-tethers. The A-tether includes lamins A/C and additional unknown components presumably INM protein(s) interacting with both lamins A/C and chromatin. The B-tether includes the inner nuclear membrane (INM) protein Lamin B-receptor, which binds B-type lamins and chromatin. Generally, at least one of the tethers is always present in the nuclear envelope of mammalian cells. Deletion of both causes the loss of peripheral heterochromatin and consequently inversion of the entire nuclear architecture, with this occurring naturally in rod photoreceptors of nocturnal mammals. The tethers are differentially utilized during development, regulate gene expression in opposite manners, and play an important role during cell differentiation. Here we aimed to identify the unknown chromatin binding component(s) of the A-tether. We analyzed 10 mouse tissues by immunostaining with antibodies against 7 INM proteins and found that every cell type has specific, although differentially and developmentally regulated, sets of these proteins. In particular, we found that INM protein LEMD2 is concomitantly expressed with A-type lamins in various cell types but is lacking in inverted nuclei of rod cells. Truncation or deletion of Lmna resulted in the downregulation and mislocalization of LEMD2, suggesting that the two proteins interact and pointing at LEMD2 as a potential chromatin binding mediator of the A-tether. Using nuclei of mouse rods as an experimental model lacking peripheral heterochromatin, we expressed a LEMD2 transgene alone or in combination with lamin C in these cells and observed no restoration of peripheral heterochromatin in either case. We conclude that in contrary to the B-tether, the A-tether has a more intricate composition and consists of multiple components that presumably vary, at differing degrees of redundancy, between cell types and differentiation stages.
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Affiliation(s)
- Katharina Thanisch
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Congdi Song
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Dieter Engelkamp
- Transgenic Service Facility, BTE, Franz-Penzoldt-Centre, Friedrich-Alexander-University of Erlangen-Nürnberg, Erwin-Rommel-Str.3, D-91058 Erlangen, Germany
| | - Jeannette Koch
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Audrey Wang
- Institute of Medical Biology, 8A Biomedical Grove and Dept of Biological Sciences, NUS, 138648, Singapore
| | - Einar Hallberg
- Department of Neurochemistry, Stockholm University, Se-106 91 Stockholm, Sweden
| | - Roland Foisner
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Colin L Stewart
- Institute of Medical Biology, 8A Biomedical Grove and Dept of Biological Sciences, NUS, 138648, Singapore.
| | - Boris Joffe
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Irina Solovei
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany.
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25
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Kim DI, Jensen SC, Noble KA, Kc B, Roux KH, Motamedchaboki K, Roux KJ. An improved smaller biotin ligase for BioID proximity labeling. Mol Biol Cell 2016; 27:1188-96. [PMID: 26912792 PMCID: PMC4831873 DOI: 10.1091/mbc.e15-12-0844] [Citation(s) in RCA: 504] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/16/2016] [Indexed: 12/20/2022] Open
Abstract
A smaller promiscuous biotin ligase for proximity biotinylation called BioID2 enables more-selective targeting of fusion proteins, requires less biotin supplementation, exhibits enhanced labeling of proximate proteins, and demonstrates the use of a flexible linker to modulate the biotin-labeling radius. The BioID method uses a promiscuous biotin ligase to detect protein–protein associations as well as proximate proteins in living cells. Here we report improvements to the BioID method centered on BioID2, a substantially smaller promiscuous biotin ligase. BioID2 enables more-selective targeting of fusion proteins, requires less biotin supplementation, and exhibits enhanced labeling of proximate proteins. Thus BioID2 improves the efficiency of screening for protein–protein associations. We also demonstrate that the biotinylation range of BioID2 can be considerably modulated using flexible linkers, thus enabling application-specific adjustment of the biotin-labeling radius.
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Affiliation(s)
- Dae In Kim
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Samuel C Jensen
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Kyle A Noble
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Birendra Kc
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Kenneth H Roux
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Khatereh Motamedchaboki
- Sanford-Burnham Proteomics Facility, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Kyle J Roux
- Sanford Children's Health Research Center, 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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