1
|
Monterroza L, Parrilla MM, Samaranayake SG, Rivera-Rodriguez DE, Yoon SB, Bommireddy R, Hosten J, Barragan LC, Marcus A, Dobosh BS, Selvaraj P, Tirouvanziam R. Tumor-Intrinsic Enhancer of Zeste Homolog 2 Controls Immune Cell Infiltration, Tumor Growth, and Lung Metastasis in a Triple-Negative Breast Cancer Model. Int J Mol Sci 2024; 25:5392. [PMID: 38791429 PMCID: PMC11121204 DOI: 10.3390/ijms25105392] [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: 04/02/2024] [Revised: 05/06/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive and highly metastatic type of tumor. TNBC is often enriched in tumor-infiltrating neutrophils (TINs), which support cancer growth in part by counteracting tumor-infiltrating lymphocytes (TILs). Prior studies identified the enhancer of zeste homolog 2 (EZH2) as a pro-tumor methyltransferase in primary and metastatic TNBCs. We hypothesized that EZH2 inhibition in TNBC cells per se would exert antitumor activity by altering the tumor immune microenvironment. To test this hypothesis, we used CRISPR to generate EZH2 gene knockout (KO) and overexpressing (OE) lines from parent (wild-type-WT) 4T1 cells, an established murine TNBC model, resulting in EZH2 protein KO and OE, respectively. In vitro, EZH2 KO and OE cells showed early, transient changes in replicative capacity and invasiveness, and marked changes in surface marker profile and cytokine/chemokine secretion compared to WT cells. In vivo, EZH2 KO cells showed significantly reduced primary tumor growth and a 10-fold decrease in lung metastasis compared to WT cells, while EZH2 OE cells were unchanged. Compared to WT tumors, TIN:TIL ratios were greatly reduced in EZH2 KO tumors but unchanged in EZH2 OE tumors. Thus, EZH2 is key to 4T1 aggressiveness as its tumor-intrinsic knockout alters their in vitro secretome and in vivo primary tumor growth, TIN/TIL poise, and metastasis.
Collapse
Affiliation(s)
- Lenore Monterroza
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (L.M.); (M.M.P.); (J.H.); (B.S.D.)
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Maria M. Parrilla
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (L.M.); (M.M.P.); (J.H.); (B.S.D.)
| | | | - Dormarie E. Rivera-Rodriguez
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA; (D.E.R.-R.); (L.C.B.)
| | - Sung Bo Yoon
- Department of Hematology & Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; (S.B.Y.); (A.M.)
| | - Ramireddy Bommireddy
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Justin Hosten
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (L.M.); (M.M.P.); (J.H.); (B.S.D.)
| | - Luisa Cervantes Barragan
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA; (D.E.R.-R.); (L.C.B.)
| | - Adam Marcus
- Department of Hematology & Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; (S.B.Y.); (A.M.)
| | - Brian S. Dobosh
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (L.M.); (M.M.P.); (J.H.); (B.S.D.)
| | - Periasamy Selvaraj
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Rabindra Tirouvanziam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (L.M.); (M.M.P.); (J.H.); (B.S.D.)
| |
Collapse
|
2
|
Zeke A, Alexa A, Reményi A. Discovery and Characterization of Linear Motif Mediated Protein-Protein Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:59-71. [PMID: 38507200 DOI: 10.1007/978-3-031-52193-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
There are myriads of protein-protein complexes that form within the cell. In addition to classical binding events between globular domains, many protein-protein interactions involve short disordered protein regions. The latter contain so-called linear motifs binding specifically to ordered protein domain surfaces. Linear binding motifs are classified based on their consensus sequence, where only a few amino acids are conserved. In this chapter we will review experimental and in silico techniques that can be used for the discovery and characterization of linear motif mediated protein-protein complexes involved in cellular signaling, protein level and gene expression regulation.
Collapse
Affiliation(s)
- András Zeke
- Institute of Organic Chemistry, HUN-REN Research Center for Natural Sciences, Budapest, Hungary
| | - Anita Alexa
- Institute of Organic Chemistry, HUN-REN Research Center for Natural Sciences, Budapest, Hungary
| | - Attila Reményi
- Institute of Organic Chemistry, HUN-REN Research Center for Natural Sciences, Budapest, Hungary.
| |
Collapse
|
3
|
Pan C, Ye J, Zhang S, Li X, Shi Y, Guo Y, Wang K, Sun P, Wu J, Wang H, Zhu L. Production of a promising modular proteinaceous self-assembled delivery system for vaccination. NANOSCALE 2023. [PMID: 37326289 DOI: 10.1039/d2nr06718h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Recently, there have been enormous advances in nano-delivery materials, especially safer and more biocompatible protein-based nanoparticles. Generally, proteinaceous nanoparticles (such as ferritin and virus-like particles) are self-assembled from some natural protein monomers. However, to ensure their capability of assembly, it is difficult to upgrade the protein structure through major modifications. Here, we have developed an efficient orthogonal modular proteinaceous self-assembly delivery system that could load antigens with an attractive coupling strategy. In brief, we constructed a nanocarrier by fusing two orthogonal domains-a pentameric cholera toxin B subunit and a trimer forming peptide-and an engineered streptavidin monomer for binding biotinylated antigens. After successfully preparing the nanoparticles, the receptor-binding domain of SARS-CoV-2 spike protein and influenza virus haemagglutination antigen are used as model antigens for further evaluation. We found that the biotinylated antigen is able to bind to the nanoparticles with high affinity and achieve efficient lymph node drainage when loaded on the nanoparticles. Then, T cells are greatly activated and the formation of germinal centers is observed. Experiments of two mouse models demonstrate the strong antibody responses and prophylactic effects of these nanovaccines. Thus, we establish a proof-of-concept for the delivery system with the potential to load diverse antigen cargos to generate high-performance nanovaccines, thereby offering an attractive platform technology for nanovaccine preparation.
Collapse
Affiliation(s)
- Chao Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| | - Jingqin Ye
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| | - Sen Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Millitary Medical Sciences, Beijing, 100071, PR China
| | - Xiang Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| | - Yixin Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| | - Yan Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| | - Kangfeng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
- College of Life Science, Hebei University, Baoding, 071002, PR China
| | - Peng Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
- School of Medicine, Tsinghua University, Beijing, 100084, PR China
| | - Jun Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| | - Hengliang Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| | - Li Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, PR China.
| |
Collapse
|
4
|
Sharifi Tabar M, Parsania C, Chen H, Su XD, Bailey CG, Rasko JE. Illuminating the dark protein-protein interactome. CELL REPORTS METHODS 2022; 2:100275. [PMID: 36046620 PMCID: PMC9421580 DOI: 10.1016/j.crmeth.2022.100275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In living systems, a complex network of protein-protein interactions (PPIs) underlies most biochemical events. The human protein-protein interactome has been surveyed using yeast two-hybrid (Y2H)- and mass spectrometry (MS)-based approaches such as affinity purification coupled to MS (AP-MS). Despite decades of systematic investigations and collaborative multi-disciplinary efforts, there is no "gold standard" for documenting PPIs. A surprisingly large fraction of the human interactome remains uncharted, which we refer to as the "dark interactome." In this review, we highlight the complexity of the human interactome and discuss the current status of the human reference interactome maps. We discuss why a large proportion of the human interactome has remained refractory to traditional approaches. We propose an experimental model that can enable the identification of the dark interactome in a cell-type-specific manner. We also propose a framework to implement when embarking on studies designed to rigorously identify and characterize protein interactions.
Collapse
Affiliation(s)
- Mehdi Sharifi Tabar
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chirag Parsania
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Hong Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Charles G. Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, NSW 2006, Australia
- Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - John E.J. Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, NSW 2006, Australia
- Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| |
Collapse
|
5
|
Construction of Orthogonal Modular Proteinaceous Nanovaccine Delivery Vectors Based on mSA-Biotin Binding. NANOMATERIALS 2022; 12:nano12050734. [PMID: 35269221 PMCID: PMC8911943 DOI: 10.3390/nano12050734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/16/2022] [Accepted: 02/19/2022] [Indexed: 12/16/2022]
Abstract
Proteinaceous nanovaccine delivery systems have significantly promoted the development of various high-efficiency vaccines. However, the widely used method of coupling the expression of scaffolds and antigens may result in their structural interference with each other. Monovalent streptavidin (mSA) is a short monomer sequence, which has a strong affinity for biotin. Here, we discuss an orthogonal, modular, and highly versatile self-assembled proteinaceous nanoparticle chassis that facilitates combinations with various antigen cargos by using mSA and biotin to produce nanovaccines. We first improved the yield of these nanoparticles by appending a short sugar chain on their surfaces in a constructed host strain. After confirming the strong ability to induce both Th1- and Th2-mediated immune responses based on the plasma cytokine spectrum from immunized mice, we further verified the binding ability of biotinylated nanoparticles to mSA-antigens. These results demonstrate that our biotinylated nanoparticle chassis could load both protein and polysaccharide antigens containing mSA at a high affinity. Our approach thus offers an attractive technology for combining nanoparticles and antigen cargos to generate various high-performance nanovaccines. In particular, the designed mSA connector (mSA containing glycosylation modification sequences) could couple with polysaccharide antigens, providing a new attractive strategy to prepare nanoscale conjugate vaccines.
Collapse
|
6
|
Pfeiffer CT, Paulo JA, Gygi SP, Rockman HA. Proximity labeling for investigating protein-protein interactions. Methods Cell Biol 2022; 169:237-266. [PMID: 35623704 PMCID: PMC10782847 DOI: 10.1016/bs.mcb.2021.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The study of protein complexes and protein-protein interactions is of great importance due to their fundamental roles in cellular function. Proximity labeling, often coupled with mass spectrometry, has become a powerful and versatile tool for studying protein-protein interactions by enriching and identifying proteins in the vicinity of a specified protein-of-interest. Here, we describe and compare traditional approaches to investigate protein-protein interactions to current day state-of-the-art proximity labeling methods. We focus on the wide array of proximity labeling strategies and underscore studies using diverse model systems to address numerous biological questions. In addition, we highlight current advances in mass spectrometry-based technology that exhibit promise in improving the depth and breadth of the data acquired in proximity labeling experiments. In all, we show the diversity of proximity labeling strategies and emphasize the broad range of applications and biological inquiries that can be addressed using this technology.
Collapse
Affiliation(s)
- Conrad T Pfeiffer
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Howard A Rockman
- Department of Medicine, Duke University Medical Center, Durham, NC, United States; Department of Cell Biology, Duke University Medical Center, Durham, NC, United States.
| |
Collapse
|
7
|
Proximity labeling identifies a repertoire of site-specific R-loop modulators. Nat Commun 2022; 13:53. [PMID: 35013239 PMCID: PMC8748879 DOI: 10.1038/s41467-021-27722-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/06/2021] [Indexed: 11/11/2022] Open
Abstract
R-loops are three-stranded nucleic acid structures that accumulate on chromatin in neurological diseases and cancers and contribute to genome instability. Using a proximity-dependent labeling system, we identified distinct classes of proteins that regulate R-loops in vivo through different mechanisms. We show that ATRX suppresses R-loops by interacting with RNAs and preventing R-loop formation. Our proteomics screen also discovered an unexpected enrichment for proteins containing zinc fingers and homeodomains. One of the most consistently enriched proteins was activity-dependent neuroprotective protein (ADNP), which is frequently mutated in ASD and causal in ADNP syndrome. We find that ADNP resolves R-loops in vitro and that it is necessary to suppress R-loops in vivo at its genomic targets. Furthermore, deletion of the ADNP homeodomain severely diminishes R-loop resolution activity in vitro, results in R-loop accumulation at ADNP targets, and compromises neuronal differentiation. Notably, patient-derived human induced pluripotent stem cells that contain an ADNP syndrome-causing mutation exhibit R-loop and CTCF accumulation at ADNP targets. Our findings point to a specific role for ADNP-mediated R-loop resolution in physiological and pathological neuronal function and, more broadly, to a role for zinc finger and homeodomain proteins in R-loop regulation, with important implications for developmental disorders and cancers. R-loops are three-stranded nucleic acid structures that contribute to genome instability and accumulate in neurological diseases. Here the authors identify R-loop proximal factors, which are enriched for zinc finger and homeodomain proteins, including activity-dependent neuroprotective protein (ADNP). ADNP plays a role in R-loop resolution and loss-of-function leads to R-loop accumulation.
Collapse
|
8
|
Wang J, Ma Y, Li J, Zhang Q, Pan X, Lu W, Zhang J. Effective and transient mapping of protein-protein interactions: Application of novel releasable photoaffinity linkers. Drug Dev Res 2021; 83:368-378. [PMID: 34424555 DOI: 10.1002/ddr.21866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 11/09/2022]
Abstract
Herein, two novel multifunctional releasable photoaffinity linkers were developed for effective and transient tracking interacting proteins with the overall objective of understanding their in vivo biological functions in real-time. These linkers could be used for the chemical modification of protein under moderate experimental conditions to form protein photoaffinity probes. These probes incorporated with both photoaffinity labels and tag-transfer, enable photo-crosslinking of bait proteins along with the release of unrelated groups. These photoaffinity linkers can be utilized to construct probes for disease markers, which could enable rapid diagnosis in a clinical setting at minimal interference with normal physiology.
Collapse
Affiliation(s)
- Jin Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yuexiang Ma
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jing Li
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Qingqing Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xiaoyan Pan
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Wen Lu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jie Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
9
|
Wang Z, Li Z, Su T, Han X, Hou Z, Zheng Y, Liu J, Xu J, Yang J, Liu H. BirA*-protein A fusion protein based BioEnhancer amplifies western blot immunosignal. Electrophoresis 2021; 42:793-799. [PMID: 33354816 DOI: 10.1002/elps.202000167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 11/08/2022]
Abstract
Western blot (protein immunoblot) is a widely used analytical technique in molecular biology. Utilizing the specific recognizing primary antibody, proteins immobilized on various matrix are investigated by subsequent visualization steps, for example, by the horse radish peroxidase conjugated secondary antibody incubation. Methods to improve the sensitivity in protein identification or quantification are appreciated by biochemists. Herein, we report a new strategy to amplify Western blot signals by constructing a probe with proximal labeling and IgG targeting abilities. The R118G mutation attenuated the biotin-AMP binding affinity of the bacterial biotin ligase BirA*, offering a proximity-dependent labeling ability, which could be used as a signal amplifier. We built a BirA*-protein A fusion protein (BioEnhancer) that specifically binds to IgG and adds biotin tags to its proximal amine groups, enhancing the immunosignal of target proteins. In our experiments, the BioEnhancer system amplified the immunosignal by tenfold compared to the standard western blot. Additionally, our strategy could couple with other signal enhancement methods to further increase the western blot sensitivity.
Collapse
Affiliation(s)
- Zhen Wang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Ziyang Li
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Tian Su
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Xiao Han
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Zhanwu Hou
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Yupeng Zheng
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Jiachen Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Jun Xu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Jeffy Yang
- Sulich Medicine and Dentistry, Western University, London, Canada
| | - Huadong Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an, P. R. China
| |
Collapse
|
10
|
Li J, Fan YY, Wang M, Duan HL, Zhang J, Dang FQ, Zhang L, Zhang ZQ. A Light-Up Strategy with Aggregation-Induced Emission for Identification of HIV-I RNA-Binding Small Molecules. Anal Chem 2020; 92:13532-13538. [PMID: 32900180 DOI: 10.1021/acs.analchem.0c03010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence methods are important tools to identify RNA-binding small molecules and further employed to study RNA-protein interactions. Most reported fluorescence strategies are based on covalent labeling of ligand or RNA, which can impede the binding between them to some extent, or light-off fluorescent indicator displacement methods, which ask for particular indicators. Herein, a label-free fluorescence strategy based on the light-on aggregation-induced emission (AIE) feature of tetraphenylethene (TPE) derivative to screen RNA-binding small molecules is presented. As a result of electrostatic interaction, the selected peptides can induce self-assembly of the TPE derivative to produce strong fluorescent emission; when the peptides are bound to RNA molecules, the TPE derivative is in the deaggregated form and shows no or minimum fluorescence. Based on the phenomenon, a competitive displacement assay combined with the TPE reporter was employed to characterize selected small molecules for their binding abilities to HIV-I RNAs. This AIE feature enables the fluorescence-off state of the TPE derivative in the presence of RNA-peptide complex to be "lightened up" quickly as the RNA-binding molecule is introduced and the peptide is competitively released. This strategy was carried out to test several small molecule binders, and the results are consistent with previous reports. This report gives an inspiring example of AIE-based fluorescent assay for HIV-I RNA-binding molecule screening, which may further be explored to build a drug screening platform for RNA-protein interference.
Collapse
Affiliation(s)
- Jun Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yao-Yao Fan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Man Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Hui-Ling Duan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Jing Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Fu-Quan Dang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Liqin Zhang
- Inspiratio Biosciences, Inc., Fremont, California 94538, United States
| | - Zhi-Qi Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| |
Collapse
|
11
|
Mishra PK, Yoo CM, Hong E, Rhee HW. Photo-crosslinking: An Emerging Chemical Tool for Investigating Molecular Networks in Live Cells. Chembiochem 2020; 21:924-932. [PMID: 31794116 DOI: 10.1002/cbic.201900600] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/03/2019] [Indexed: 12/13/2022]
Abstract
Studying protein-protein interactions (PPIs) is useful for understanding cellular functions and mechanisms. Evaluating these PPIs under conditions as similar as possible to native conditions can be achieved using photo-crosslinking methods because of their on-demand ability to generate reactive species in situ by irradiation with UV light. Various fusion tag, metabolic incorporation, and amber codon suppression approaches using various crosslinkers containing aryl azide, benzophenone, and diazirines have been applied in live cells. Mass spectrometry and immunological techniques are used to identify crosslinked proteins based on their capture transient and context-dependent interactions. Herein we discuss various incorporation methods and crosslinkers that have been used for interactome mapping in live cells.
Collapse
Affiliation(s)
- Pratyush Kumar Mishra
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.,Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Chang-Mo Yoo
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eunmi Hong
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 360-4 Dongnae-dong, Dong-gu, Daegu, 41061, Republic of Korea
| | - Hyun Woo Rhee
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| |
Collapse
|
12
|
Recent advances in the engineering and application of streptavidin-like molecules. Appl Microbiol Biotechnol 2019; 103:7355-7365. [DOI: 10.1007/s00253-019-10036-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 01/24/2023]
|
13
|
Shields EJ, Petracovici AF, Bonasio R. lncRedibly versatile: biochemical and biological functions of long noncoding RNAs. Biochem J 2019; 476:1083-1104. [PMID: 30971458 PMCID: PMC6745715 DOI: 10.1042/bcj20180440] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/28/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are transcripts that do not code for proteins, but nevertheless exert regulatory effects on various biochemical pathways, in part via interactions with proteins, DNA, and other RNAs. LncRNAs are thought to regulate transcription and other biological processes by acting, for example, as guides that target proteins to chromatin, scaffolds that facilitate protein-protein interactions and complex formation, and orchestrators of phase-separated compartments. The study of lncRNAs has reached an exciting time, as recent advances in experimental and computational methods allow for genome-wide interrogation of biochemical and biological mechanisms of these enigmatic transcripts. A better appreciation for the biochemical versatility of lncRNAs has allowed us to begin closing gaps in our knowledge of how they act in diverse cellular and organismal contexts, including development and disease.
Collapse
Affiliation(s)
- Emily J Shields
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
| | - Ana F Petracovici
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
- Graduate Group in Genetics and Epigenetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A.
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
| |
Collapse
|
14
|
Remnant L, Booth DG, Vargiu G, Spanos C, Kerr ARW, Earnshaw WC. In vitro BioID: mapping the CENP-A microenvironment with high temporal and spatial resolution. Mol Biol Cell 2019; 30:1314-1325. [PMID: 30892990 PMCID: PMC6724601 DOI: 10.1091/mbc.e18-12-0799] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The centromere is located at the primary constriction of condensed chromosomes where it acts as a platform regulating chromosome segregation. The histone H3 variant CENP-A is the foundation for kinetochore formation. CENP-A directs the formation of a highly dynamic molecular neighborhood whose temporal characterization during mitosis remains a challenge due to limitations in available techniques. BioID is a method that exploits a “promiscuous” biotin ligase (BirA118R or BirA*) to identify proteins within close proximity to a fusion protein of interest. As originally described, cells expressing BirA* fusions were exposed to high biotin concentrations for 24 h during which the ligase transferred activated biotin (BioAmp) to other proteins within the immediate vicinity. The protein neighborhood could then be characterized by streptavidin-based purification and mass spectrometry. Here we describe a further development to this technique, allowing CENP-A interactors to be characterized within only a few minutes, in an in vitro reaction in lysed cells whose physiological progression is “frozen.” This approach, termed in vitro BioID (ivBioID), has the potential to study the molecular neighborhood of any structural protein whose interactions change either during the cell cycle or in response to other changes in cell physiology.
Collapse
Affiliation(s)
- Lucy Remnant
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology and
| | - Daniel G Booth
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology and.,Centre for Brain Discovery Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Giulia Vargiu
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology and
| | - Christos Spanos
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology and
| | - Alastair R W Kerr
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology and
| | | |
Collapse
|
15
|
Functional expression of monomeric streptavidin and fusion proteins in Escherichia coli: applications in flow cytometry and ELISA. Appl Microbiol Biotechnol 2018; 102:10079-10089. [PMID: 30250978 DOI: 10.1007/s00253-018-9377-7] [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: 07/13/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 02/06/2023]
Abstract
Monomeric streptavidin (mSA) offers a combination of structural and binding properties that are useful in many applications, including a small size and monovalent biotin binding. Because mSA contains a structurally important disulfide bond, the molecule does not fold correctly when expressed inside the cell. We show that mSA can be expressed in a functional form in Escherichia coli by fusing the OmpA signal sequence at the amino terminus. Expressed mSA is exported to the periplasm, from which the molecule leaks to the medium under vigorous shaking. Purified mSA can be conjugated with FITC and used to label microbeads and yeast cells for analysis by flow cytometry, further expanding the scope of mSA-based applications. Some applications require recombinant fusion of mSA with another protein. mSA fused to EGFP cannot be secreted to the medium but was successfully expressed in an engineered cell line that supports oxidative folding in the cytoplasm. Purified mSA-EGFP and mSA-mCherry bound biotin with high affinity and were successfully used in conventional flow cytometry and imaging flow cytometry. Finally, we demonstrate the use of mSA in ELISA, in which horseradish peroxidase-conjugated mSA and biotinylated secondary antibody are used together to detect primary antibody captured on an ELISA plate. Engineering mSA to introduce additional lysine residues can increase the reporter signal above that of wild-type streptavidin. Together, these examples establish mSA as a convenient reagent with a potentially unique role in biotechnology.
Collapse
|
16
|
Jongsma MLM, Guarda G, Spaapen RM. The regulatory network behind MHC class I expression. Mol Immunol 2017; 113:16-21. [PMID: 29224918 DOI: 10.1016/j.molimm.2017.12.005] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/28/2017] [Accepted: 12/05/2017] [Indexed: 12/22/2022]
Abstract
The MHC class I pathway, presenting endogenously derived peptides to T lymphocytes, is hijacked in many pathological conditions. This affects MHC class I levels and peptide presentation at the cell surface leading to immune escape of cancer cells or microbes. It is therefore important to identify the molecular mechanisms behind MHC class I expression, processing and antigen presentation. The identification of NLRC5 as regulator of MHC class I transcription was a huge step forward in understanding the transcriptional mechanism involved. Nevertheless, many questions concerning MHC class I transcription are yet unsolved. Here we illuminate current knowledge on MHC class I and NLRC5 transcription, we highlight some remaining questions and discuss the use of quickly developing high-content screening tools to reveal unknowns in MHC class I transcription in the near future.
Collapse
Affiliation(s)
- Marlieke L M Jongsma
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory AMC/UvA, Plesmanlaan 125, 1066 CX Amsterdam, The Netherlands
| | - Greta Guarda
- Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland
| | - Robbert M Spaapen
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory AMC/UvA, Plesmanlaan 125, 1066 CX Amsterdam, The Netherlands.
| |
Collapse
|
17
|
Discovery of new RNA classes and global RNA-binding proteins. Curr Opin Microbiol 2017; 39:152-160. [PMID: 29179042 DOI: 10.1016/j.mib.2017.11.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/17/2017] [Indexed: 12/15/2022]
Abstract
The identification of new RNA functions and the functional annotation of transcripts in genomes represent exciting yet challenging endeavours of modern biology. Crucial insights into the biological roles of RNA molecules can be gained from the identification of the proteins with which they form specific complexes. Modern interactome techniques permit to profile RNA-protein interactions in a genome-wide manner and identify new RNA classes associated with globally acting RNA-binding proteins. Applied to a variety of organisms, these methods are already revolutionising our understanding of RNA-mediated biological processes. Here, we focus on one such approach-Gradient sequencing or Grad-seq-which has recently guided the discovery of protein ProQ and its associated small RNAs as a new domain of post-transcriptional control in bacteria.
Collapse
|
18
|
Abstract
Identification of molecular interactions is paramount to understanding how cells function. Most available technologies rely on co-purification of a protein of interest and its binding partners. Therefore, they are limited in their ability to detect low-affinity interactions and cannot be applied to proteins that localize to difficult-to-solubilize cellular compartments. In vivo proximity labeling (IPL) overcomes these obstacles by covalently tagging proteins and RNAs based on their proximity in vivo to a protein of interest. In IPL, a heterobifunctional probe comprising a photoactivatable moiety and biotin is recruited by a monomeric streptavidin tag fused to a protein of interest. Following UV irradiation, candidate interacting proteins and RNAs are covalently biotinylated with tight spatial and temporal control and subsequently recovered using biotin as an affinity handle. Here, we describe experimental protocols to discover novel protein-protein and protein-RNA interactions using IPL. © 2017 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- David B Beck
- Department of Medicine, Columbia University Medical Center, New York, New York
| | - Roberto Bonasio
- Epigenetics Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| |
Collapse
|
19
|
Li P, Li J, Wang L, Di LJ. Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Peipei Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Jingjing Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li Wang
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
- Metabolomics Core; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li-Jun Di
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| |
Collapse
|
20
|
Nainar S, Feng C, Spitale RC. Chemical Tools for Dissecting the Role of lncRNAs in Epigenetic Regulation. ACS Chem Biol 2016; 11:2091-100. [PMID: 27267401 PMCID: PMC5068361 DOI: 10.1021/acschembio.6b00366] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proper control and maintenance of gene expression is critical for cellular identity and maintenance. Transcription of RNA from the genome is intimately controlled by post-translational chemical modification of histone tails and DNA. Recent studies have demonstrated that chromatin-remodeling complexes seek out their target genomic loci through the help of noncoding RNA molecules. Within this Review, we will outline how the use of biochemical techniques has shed light on the mechanisms employed by RNA to guide these complexes and therefore control gene expression.
Collapse
Affiliation(s)
- Sarah Nainar
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, California 92697, United States
| | - Chao Feng
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, California 92697, United States
| | - Robert C. Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, California 92697, United States
| |
Collapse
|
21
|
Rees JS, Li XW, Perrett S, Lilley KS, Jackson AP. Protein Neighbors and Proximity Proteomics. Mol Cell Proteomics 2015; 14:2848-56. [PMID: 26355100 PMCID: PMC4638030 DOI: 10.1074/mcp.r115.052902] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Indexed: 12/31/2022] Open
Abstract
Within cells, proteins can co-assemble into functionally integrated and spatially restricted multicomponent complexes. Often, the affinities between individual proteins are relatively weak, and proteins within such clusters may interact only indirectly with many of their other protein neighbors. This makes proteomic characterization difficult using methods such as immunoprecipitation or cross-linking. Recently, several groups have described the use of enzyme-catalyzed proximity labeling reagents that covalently tag the neighbors of a targeted protein with a small molecule such as fluorescein or biotin. The modified proteins can then be isolated by standard pulldown methods and identified by mass spectrometry. Here we will describe the techniques as well as their similarities and differences. We discuss their applications both to study protein assemblies and to provide a new way for characterizing organelle proteomes. We stress the importance of proteomic quantitation and independent target validation in such experiments. Furthermore, we suggest that there are biophysical and cell-biological principles that dictate the appropriateness of enzyme-catalyzed proximity labeling methods to address particular biological questions of interest.
Collapse
Affiliation(s)
- Johanna S Rees
- From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW, the §Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QR, and
| | - Xue-Wen Li
- the ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Sarah Perrett
- the ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Kathryn S Lilley
- the §Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QR, and
| | - Antony P Jackson
- From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW,
| |
Collapse
|