1
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De Silva ARI, Page RC. Ubiquitination detection techniques. Exp Biol Med (Maywood) 2023; 248:1333-1346. [PMID: 37787047 PMCID: PMC10625345 DOI: 10.1177/15353702231191186] [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] [Indexed: 10/04/2023] Open
Abstract
Ubiquitination is an intricately regulated post-translational modification that involves the covalent attachment of ubiquitin to a substrate protein. The complex dynamic nature of the ubiquitination process regulates diverse cellular functions including targeting proteins for degradation, cell cycle, deoxyribonucleic acid (DNA) damage repair, and numerous cell signaling pathways. Ubiquitination also serves as a crucial mechanism in protein quality control. Dysregulation in ubiquitination could result in lethal disease conditions such as cancers and neurodegenerative diseases. Therefore, the ubiquitination cascade has become an attractive target for therapeutic interventions. Enormous efforts have been made to detect ubiquitination involving different detection techniques to better grasp the underlying molecular mechanisms of ubiquitination. This review discusses a wide range of techniques stretching from the simplest assays to real-time assays. This includes western blotting/immunoblotting, fluorescence assays, chemiluminescence assays, spectrophotometric assays, and nanopore sensing assays. This review compares these applications, and the inherent advantages and limitations.
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Affiliation(s)
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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2
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Wu Y, Jiang T. Developments in FRET- and BRET-Based Biosensors. MICROMACHINES 2022; 13:mi13101789. [PMID: 36296141 PMCID: PMC9610962 DOI: 10.3390/mi13101789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 05/25/2023]
Abstract
Resonance energy transfer technologies have achieved great success in the field of analysis. Particularly, fluorescence resonance energy transfer (FRET) and bioluminescence resonance energy transfer (BRET) provide strategies to design tools for sensing molecules and monitoring biological processes, which promote the development of biosensors. Here, we provide an overview of recent progress on FRET- and BRET-based biosensors and their roles in biomedicine, environmental applications, and synthetic biology. This review highlights FRET- and BRET-based biosensors and gives examples of their applications with their design strategies. The limitations of their applications and the future directions of their development are also discussed.
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Affiliation(s)
- Yuexin Wu
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Tianyu Jiang
- Shenzhen Research Institute of Shandong University, Shenzhen 518000, China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao 266237, China
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3
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Geethakumari AM, Ahmed WS, Rasool S, Fatima A, Nasir Uddin SM, Aouida M, Biswas KH. A genetically encoded BRET-based SARS-CoV-2 M pro protease activity sensor. Commun Chem 2022; 5:117. [PMID: 36187754 PMCID: PMC9516532 DOI: 10.1038/s42004-022-00731-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/07/2022] [Indexed: 01/27/2023] Open
Abstract
The main protease, Mpro, is critical for SARS-CoV-2 replication and an appealing target for designing anti-SARS-CoV-2 agents. Therefore, there is a demand for the development of improved sensors to monitor its activity. Here, we report a pair of genetically encoded, bioluminescence resonance energy transfer (BRET)-based sensors for detecting Mpro proteolytic activity in live cells as well as in vitro. The sensors were generated by sandwiching peptides containing the Mpro N-terminal autocleavage sites, either AVLQSGFR (short) or KTSAVLQSGFRKME (long), in between the mNeonGreen and NanoLuc proteins. Co-expression of the sensors with Mpro in live cells resulted in their cleavage while mutation of the critical C145 residue (C145A) in Mpro completely abrogated their cleavage. Additionally, the sensors recapitulated the inhibition of Mpro by the well-characterized pharmacological agent GC376. Further, in vitro assays with the BRET-based Mpro sensors revealed a molecular crowding-mediated increase in the rate of Mpro activity and a decrease in the inhibitory potential of GC376. The sensors developed here will find direct utility in studies related to drug discovery targeting the SARS-CoV-2 Mpro and functional genomics application to determine the effect of sequence variation in Mpro.
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Affiliation(s)
- Anupriya M. Geethakumari
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Wesam S. Ahmed
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Saad Rasool
- Division of Genomics and Precision Medicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Asma Fatima
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - S. M. Nasir Uddin
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Mustapha Aouida
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Kabir H. Biswas
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
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4
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Lin Y, Jiang J. Rapid Validation of Transcriptional Enhancers Using a Transient Reporter Assay. Methods Mol Biol 2021; 2328:253-259. [PMID: 34251631 DOI: 10.1007/978-1-0716-1534-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Enhancers are one of the main classes of cis-regulatory elements (CREs) in the regulation of plant gene expression. Plant enhancers can be predicted based on genomic signatures associated with open chromatin. However, predicted enhancers need to be validated experimentally. We developed an experimental system for rapid enhancer validation. Predicted enhancer candidates are cloned into a vector containing a minimal 35S promoter and a luciferase reporter gene. The construct is then agroinfiltrated into Nicotiana benthamiana leaves followed by bioluminescence signal detection and analysis. Positive bioluminescence signals indicate the enhancer function of each candidate, and the relative signal strength from different enhancers can be quantitatively measured and compared. In summary, we have developed an efficient and rapid plant enhancer validation assay based on a bioluminescent luciferase reporter and agroinfiltration-based N. benthamiana leaf transient expression. This assay can be used for the initial screening of candidate enhancers that are active in leaf tissue. The system can potentially be used to examine the activity of candidate enhancers under different environmental conditions.
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Affiliation(s)
- Yuan Lin
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
- Department of Horticulture, Michigan State University, East Lansing, MI, USA.
- Michigan State University AgBioResearch, East Lansing, MI, USA.
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5
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Nelson AC, Turbyville TJ, Dharmaiah S, Rigby M, Yang R, Wang TY, Columbus J, Stephens R, Taylor T, Sciacca D, Onsongo G, Sarver A, Subramanian S, Nissley DV, Simanshu DK, Lou E. RAS internal tandem duplication disrupts GTPase-activating protein (GAP) binding to activate oncogenic signaling. J Biol Chem 2020; 295:9335-9348. [PMID: 32393580 PMCID: PMC7363148 DOI: 10.1074/jbc.ra119.011080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 05/06/2020] [Indexed: 12/31/2022] Open
Abstract
The oncogene RAS is one of the most widely studied proteins in cancer biology, and mutant active RAS is a driver in many types of solid tumors and hematological malignancies. Yet the biological effects of different RAS mutations and the tissue-specific clinical implications are complex and nuanced. Here, we identified an internal tandem duplication (ITD) in the switch II domain of NRAS from a patient with extremely aggressive colorectal carcinoma. Results of whole-exome DNA sequencing of primary and metastatic tumors indicated that this mutation was present in all analyzed metastases and excluded the presence of any other clear oncogenic driver mutations. Biochemical analysis revealed increased interaction of the RAS ITD with Raf proto-oncogene Ser/Thr kinase (RAF), leading to increased phosphorylation of downstream MAPK/ERK kinase (MEK)/extracellular signal-regulated kinase (ERK). The ITD prevented interaction with neurofibromin 1 (NF1)-GTPase-activating protein (GAP), providing a mechanism for sustained activity of the RAS ITD protein. We present the first crystal structures of NRAS and KRAS ITD at 1.65-1.75 Å resolution, respectively, providing insight into the physical interactions of this class of RAS variants with its regulatory and effector proteins. Our in-depth bedside-to-bench analysis uncovers the molecular mechanism underlying a case of highly aggressive colorectal cancer and illustrates the importance of robust biochemical and biophysical approaches in the implementation of individualized medicine.
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Affiliation(s)
- Andrew C Nelson
- Department of Laboratory Medicine & Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Thomas J Turbyville
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Srisathiyanarayanan Dharmaiah
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Megan Rigby
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Rendong Yang
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Ting-You Wang
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - John Columbus
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Robert Stephens
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Troy Taylor
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Drew Sciacca
- Department of Laboratory Medicine & Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Getiria Onsongo
- Department of Laboratory Medicine & Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Anne Sarver
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Dwight V Nissley
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Emil Lou
- Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota, USA
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6
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Pavlinov I, Salkovski M, Aldrich LN. Beclin 1-ATG14L Protein-Protein Interaction Inhibitor Selectively Inhibits Autophagy through Disruption of VPS34 Complex I. J Am Chem Soc 2020; 142:8174-8182. [PMID: 32320221 DOI: 10.1021/jacs.9b12705] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Autophagy, a catabolic recycling process, has been implicated as a critical pathway in cancer. Its role in maintaining cellular homeostasis helps to nourish hypoxic, nutrient-starved tumors and protects them from chemotherapy-induced death. Recent efforts to target autophagy in cancer have focused on kinase inhibition, which has led to molecules that lack specificity due to the multiple roles of key kinases in this pathway. For example, the lipid kinase VPS34 is present in two multiprotein complexes responsible for the generation of phosphatidylinositol-3-phosphate. Complex I generates the autophagosome, and Complex II is crucial for endosomal trafficking. Molecules targeting VPS34 inhibit both complexes, which inhibits autophagy but causes undesirable defects in vesicle trafficking. The lack of specific autophagy modulators has limited the utility of autophagy inhibition as a therapeutic strategy. We hypothesize that disruption of the Beclin 1-ATG14L protein-protein interaction, which is required for the formation, proper localization, and function of VPS34 Complex I but not Complex II, will disrupt Complex I formation and selectively inhibit autophagy. To this end, a high-throughput, cellular NanoBRET assay was developed targeting this interaction. An initial screen of 2560 molecules yielded 19 hits that effectively disrupted the interaction, and it was confirmed that one hit disrupted VPS34 Complex I formation and inhibited autophagy. In addition, the molecule did not disrupt the Beclin 1-UVRAG interaction, critical for VPS34 Complex II, and thus had little impact on vesicle trafficking. This molecule is a promising new tool that is critical for understanding how modulation of the Beclin 1-ATG14L interaction affects autophagy. More broadly, its discovery demonstrates that targeting protein-protein interactions found within the autophagy pathway is a viable strategy for the discovery of autophagy-specific probes and therapeutics.
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Affiliation(s)
- Ivan Pavlinov
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago Illinois 60607, United States
| | - Maryna Salkovski
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago Illinois 60607, United States
| | - Leslie N Aldrich
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago Illinois 60607, United States
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7
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Song J, Zhang J. Self-illumination of Carbon Dots by Bioluminescence Resonance Energy Transfer. Sci Rep 2019; 9:13796. [PMID: 31551471 PMCID: PMC6760201 DOI: 10.1038/s41598-019-50242-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/09/2019] [Indexed: 01/06/2023] Open
Abstract
Carbon-dots (CDs), the emerging fluorescent nanoparticles, show special multicolor properties, chemical stability, and biocompatibility, and are considered as the new and advanced imaging probe in replacement of molecular fluorophores and semiconductor quantum dots. However, the requirement of external high power light source limits the application of fluorescent nanomaterials in bio-imaging. The present study aims to take advantage of bioluminescence resonance energy transfer mechanism (BRET) in creating self-illuminating C-dots. Renilla luciferase (Rluc) is chosen as the BRET donor molecule. Conjugation of Renilla luciferase and C-dots is necessary to keep their distance close for energy transfer. The optimal condition for achieving BRET is investigated by studying the effects of different factors on the performance of BRET, including the type of conjugation, concentration of carbon dots, and conjugation time. The linear relationship of BRET efficiency as a function of the amount of C-dots in the range of 0.20–0.80 mg/mL is observed. The self-illuminating carbon dots could be applied in bioimaging avoiding the tissue damage from the external high power light source.
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Affiliation(s)
- Jisu Song
- School of Biomedical Engineering, University of Western Ontario, London, Ontario, N6A 5B9, Canada
| | - Jin Zhang
- School of Biomedical Engineering, University of Western Ontario, London, Ontario, N6A 5B9, Canada. .,Department of Chemical and Biochemical Engineering, University of Western Ontario, London, Ontario, N6A 5B9, Canada.
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8
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Li P, Wang L, Di LJ. Applications of Protein Fragment Complementation Assays for Analyzing Biomolecular Interactions and Biochemical Networks in Living Cells. J Proteome Res 2019; 18:2987-2998. [PMID: 31274323 DOI: 10.1021/acs.jproteome.9b00154] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein-protein interactions (PPIs) are indispensable for the dynamic assembly of multiprotein complexes that are central players of nearly all of the intracellular biological processes, such as signaling pathways, metabolic pathways, formation of intracellular organelles, establishment of cytoplasmic skeletons, etc. Numerous approaches have been invented to study PPIs both in vivo and in vitro, including the protein-fragment complementation assay (PCA), which is a widely applied technology to study PPIs and biomolecular interactions. PCA is a technology based on the expression of the bait and prey proteins in fusion with two complementary reporter protein fragments, respectively, that will reassemble when in close proximity. The reporter protein can be the enzymes or fluorescent proteins. Recovery of the enzymatic activity or fluorescent signal can be the indicator of PPI between the bait and prey proteins. Significant effort has been invested in developing many derivatives of PCA, along with various applications, in order to address specific questions. Therefore, a prompt review of these applications is important. In this review, we will categorize these applications according to the scenarios that the PCAs were applied and expect to provide a reference guideline for the future selection of PCA methods in solving a specific problem.
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Affiliation(s)
- Peipei Li
- Cancer Center, Faculty of Health Sciences , University of Macau , Macau , SAR of China
| | - Li Wang
- Cancer Center, Faculty of Health Sciences , University of Macau , Macau , SAR of China.,Metabolomics Core, Faculty of Health Sciences , University of Macau , Macau , SAR of China
| | - Li-Jun Di
- Cancer Center, Faculty of Health Sciences , University of Macau , Macau , SAR of China
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9
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Red-shifted bioluminescence Resonance Energy Transfer: Improved tools and materials for analytical in vivo approaches. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.04.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Rhee SY, Birnbaum KD, Ehrhardt DW. Towards Building a Plant Cell Atlas. TRENDS IN PLANT SCIENCE 2019; 24:303-310. [PMID: 30777643 PMCID: PMC7449582 DOI: 10.1016/j.tplants.2019.01.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 05/03/2023]
Abstract
Enormous societal challenges, such as feeding and providing energy for a growing population in a dramatically changing climate, necessitate technological advances in plant science. Plant cells are fundamental organizational units that mediate the production, transport, and storage of our primary food sources, and they sequester a significant proportion of the world's carbon. New technologies allow comprehensive descriptions of cells that could accelerate research across fields of plant science. Complementary to the efforts towards understanding the cellular diversity in human brain and immune systems, a Plant Cell Atlas (PCA) that maps molecular machineries to cellular and subcellular domains, follows their dynamic movements, and describes their interactions would accelerate discovery in plant science and help to solve imminent societal problems.
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Affiliation(s)
- Seung Y Rhee
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA.
| | | | - David W Ehrhardt
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA.
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11
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Cui Y, Zhang X, Yu M, Zhu Y, Xing J, Lin J. Techniques for detecting protein-protein interactions in living cells: principles, limitations, and recent progress. SCIENCE CHINA-LIFE SCIENCES 2019; 62:619-632. [DOI: 10.1007/s11427-018-9500-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 02/12/2019] [Indexed: 01/07/2023]
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12
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Lin Y, Meng F, Fang C, Zhu B, Jiang J. Rapid validation of transcriptional enhancers using agrobacterium-mediated transient assay. PLANT METHODS 2019; 15:21. [PMID: 30873216 PMCID: PMC6402126 DOI: 10.1186/s13007-019-0407-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 02/28/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Enhancers are one of the most important classes of cis-regulatory elements (CREs) and play key roles in regulation of transcription in higher eukaryotes. Enhancers are difficult to identify because they lack positional constraints relative to their cognate genes. Excitingly, several recent studies showed that plant enhancers can be predicted based on their distinct features associated with open chromatin. However, experimental validation is necessary to confirm the predicted enhancer function. RESULTS We developed a rapid enhancer validation system based on Nicotiana benthamiana. A set of 12 intergenic and intronic enhancers, identified in Arabidopsis thaliana, were cloned into a vector containing a minimal 35S promoter and a luciferase reporter gene, and were then infiltrated into N. benthamiana leaves mediated by agrobacterium. The enhancer activity of each candidate was quantitatively assayed based on bioluminescence measurement. The data from this luciferase-based validation was correlated with previous data derived from transgenic assays in A. thaliana. In addition, the relative strength of different enhancers for driving the reporter gene can be quantitatively compared. We demonstrate that this system can also be used to map the functional activity of a candidate enhancer under different environmental conditions. CONCLUSIONS In summary, we developed a rapid and efficient plant enhancer validation system based on a luciferase reporter and N. benthamiana-based leaf agroinfiltration. This system can be used for initial screening of leaf-specific enhancers and for validating candidate leaf enhancers from dicot species. It can potentially be used to examine the activity of candidate enhancers under different environmental conditions.
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Affiliation(s)
- Yuan Lin
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Fanli Meng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, 150030 China
| | - Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Bo Zhu
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan 610101 China
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
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13
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Nag JK, Kancharla A, Maoz M, Turm H, Agranovich D, Gupta CL, Uziely B, Bar-Shavit R. Low-density lipoprotein receptor-related protein 6 is a novel coreceptor of protease-activated receptor-2 in the dynamics of cancer-associated β-catenin stabilization. Oncotarget 2018; 8:38650-38667. [PMID: 28418856 PMCID: PMC5503561 DOI: 10.18632/oncotarget.16246] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 02/17/2017] [Indexed: 01/28/2023] Open
Abstract
Protease-activated receptor-2 (PAR2) plays a central role in cancer; however, the molecular machinery of PAR2-instigated tumors remains to be elucidated. We show that PAR2 is a potent inducer of β-catenin stabilization, a core process in cancer biology, leading to its transcriptional activity. Novel association of low-density lipoprotein-related protein 6 (LRP6), a known coreceptor of Frizzleds (Fz), with PAR2 takes place following PAR2 activation. The association between PAR2 and LRP6 was demonstrated employing co-immunoprecipitation, bioluminescence resonance energy transfer (BRET), and confocal microscopy analysis. The association was further supported by ZDOCK protein-protein server. PAR2-LRP6 interaction promotes rapid phosphorylation of LRP6, which results in the recruitment of Axin. Confocal microscopy of PAR2-driven mammary gland tumors in vivo, as well as in vitro confirms the association between PAR2 and LRP6. Indeed, shRNA silencing of LRP6 potently inhibits PAR2-induced β-catenin stabilization, demonstrating its critical role in the induced path. We have previously shown a novel link between protease-activated receptor-1 (PAR1) and β-catenin stabilization, both in a transgenic (tg) mouse model with overexpression of human PAR1 (hPar1) in the mammary glands, and in cancer epithelial cell lines. Unlike in PAR1-Gα13 axis, both Gα12 and Gα13 are equally involved in PAR2-induced β-catenin stabilization. Disheveled (DVL) is translocated to the cell nucleus through the DVL-PDZ domain. Collectively, our data demonstrate a novel PAR2-LRP6-Axin interaction as a key axis of PAR2-induced β-catenin stabilization in cancer. This newly described axis enhances our understanding of cancer biology, and opens new avenues for future development of anti-cancer therapies.
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Affiliation(s)
- Jeetendra Kumar Nag
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Arun Kancharla
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Myriam Maoz
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Hagit Turm
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Daniel Agranovich
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Chhedi Lal Gupta
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh 226026, India
| | - Beatrice Uziely
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Rachel Bar-Shavit
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
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14
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Zhang Y, Robertson JB, Xie Q, Johnson CH. Monitoring Intracellular pH Change with a Genetically Encoded and Ratiometric Luminescence Sensor in Yeast and Mammalian Cells. Methods Mol Biol 2018; 1461:117-30. [PMID: 27424899 DOI: 10.1007/978-1-4939-3813-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
"pHlash" is a novel bioluminescence-based pH sensor for measuring intracellular pH, which is developed based on Bioluminescence Resonance Energy Transfer (BRET). pHlash is a fusion protein between a mutant of Renilla luciferase (RLuc) and a Venus fluorophore. The spectral emission of purified pHlash protein exhibits pH dependence in vitro. When expressed in either yeast or mammalian cells, pHlash reports basal pH and cytosolic acidification. In this chapter, we describe an in vitro characterization of pHlash, and also in vivo assays including in yeast cells and in HeLa cells using pHlash as a cytoplasmic pH indicator.
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Affiliation(s)
- Yunfei Zhang
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
- Modern Experiment Technology Center, Anhui University, Hefei, Anhui, 230601, China
| | - J Brian Robertson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Qiguang Xie
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
- Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei, China
| | - Carl Hirschie Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.
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15
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Gagarinova A, Phanse S, Cygler M, Babu M. Insights from protein-protein interaction studies on bacterial pathogenesis. Expert Rev Proteomics 2017; 14:779-797. [DOI: 10.1080/14789450.2017.1365603] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alla Gagarinova
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada
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16
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In Vivo Analysis of Protein-Protein Interactions with Bioluminescence Resonance Energy Transfer (BRET): Progress and Prospects. Int J Mol Sci 2016; 17:ijms17101704. [PMID: 27727181 PMCID: PMC5085736 DOI: 10.3390/ijms17101704] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 11/17/2022] Open
Abstract
Proteins are the elementary machinery of life, and their functions are carried out mostly by molecular interactions. Among those interactions, protein-protein interactions (PPIs) are the most important as they participate in or mediate all essential biological processes. However, many common methods for PPI investigations are slightly unreliable and suffer from various limitations, especially in the studies of dynamic PPIs. To solve this problem, a method called Bioluminescence Resonance Energy Transfer (BRET) was developed about seventeen years ago. Since then, BRET has evolved into a whole class of methods that can be used to survey virtually any kinds of PPIs. Compared to many traditional methods, BRET is highly sensitive, reliable, easy to perform, and relatively inexpensive. However, most importantly, it can be done in vivo and allows the real-time monitoring of dynamic PPIs with the easily detectable light signal, which is extremely valuable for the PPI functional research. This review will take a comprehensive look at this powerful technique, including its principles, comparisons with other methods, experimental approaches, classifications, applications, early developments, recent progress, and prospects.
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Abstract
Application of bioluminescence resonance energy transfer (BRET) assay has been of special value in measuring dynamic events such as protein-protein interactions (PPIs) in vitro or in vivo. It was only in the late 1990s the BRET assay using RLuc-YFP was introduced for biological research showing its use in determining interaction of two proteins involved in circadian rhythm. Several inherent attributes such as rapid and fairly sensitive ratiometric measurements, assessment of PPI irrespective of protein location in cellular compartment, and cost-effectiveness consenting to high-throughput assay development make BRET a popular genetic reporter-based assay for PPI studies. In BRET-based screening, within a defined proximity range of 10-100 Å, excited state energy of the luminescence molecule can excite the acceptor fluorophore in the form of resonance energy transfer, causing it to emit at its characteristic emission wavelength. Based on this principle, several such donor-acceptor pairs, using the Renilla luciferase or its mutants as donor and either GFP2, YFP, mOrange, TagRFP, or TurboFP as acceptor, have been reported for use.In recent years, BRET-related research has become significantly versatile in the assay format and its applicability by adopting the assay on multiple detection devices such as small-animal optical imaging platform or bioluminescence microscope. Beyond the scope of quantitative measurement of PPIs and protein dimerization, molecular optical imaging applications based on BRET assays have broadened its scope for screening of pharmacological compounds by unifying in vitro, live cell, and in vivo animal/plant measurement all on one platform. Taking examples from the literature, this chapter contributes to in-depth methodological details on how to perform in vitro and in vivo BRET experiments, and illustrates its advantages as a single-format assay.
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Affiliation(s)
- Shalini Dimri
- Molecular Functional Imaging Lab, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
| | - Soumya Basu
- Molecular Functional Imaging Lab, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
| | - Abhijit De
- Molecular Functional Imaging Lab, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India.
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Snider J, Kotlyar M, Saraon P, Yao Z, Jurisica I, Stagljar I. Fundamentals of protein interaction network mapping. Mol Syst Biol 2015; 11:848. [PMID: 26681426 PMCID: PMC4704491 DOI: 10.15252/msb.20156351] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Studying protein interaction networks of all proteins in an organism (“interactomes”) remains one of the major challenges in modern biomedicine. Such information is crucial to understanding cellular pathways and developing effective therapies for the treatment of human diseases. Over the past two decades, diverse biochemical, genetic, and cell biological methods have been developed to map interactomes. In this review, we highlight basic principles of interactome mapping. Specifically, we discuss the strengths and weaknesses of individual assays, how to select a method appropriate for the problem being studied, and provide general guidelines for carrying out the necessary follow‐up analyses. In addition, we discuss computational methods to predict, map, and visualize interactomes, and provide a summary of some of the most important interactome resources. We hope that this review serves as both a useful overview of the field and a guide to help more scientists actively employ these powerful approaches in their research.
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Affiliation(s)
- Jamie Snider
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Max Kotlyar
- Princess Margaret Cancer Center, IBM Life Sciences Discovery Centre, University Health Network, Ontario, Canada
| | - Punit Saraon
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Zhong Yao
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Igor Jurisica
- Princess Margaret Cancer Center, IBM Life Sciences Discovery Centre, University Health Network, Ontario, Canada
| | - Igor Stagljar
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Wu B, Wang J, Zhao Y, Guo W. Biochemical analysis of Rabin8, the guanine nucleotide exchange factor for Rab8. Methods Cell Biol 2015; 130:59-68. [PMID: 26360028 DOI: 10.1016/bs.mcb.2015.06.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Rab GTPases are master regulators of endosomal trafficking in eukaryotic cells. Among them, Rab8 plays an important role in tubulovesicular trafficking from the trans-Golgi network and recycling endosomes to the plasma membrane. Rab8 is activated by its guanine nucleotide exchange factor, Rabin8. In order to understand the molecular mechanisms that control endosomal recycling to the plasma membrane, it is pivotal to understand how Rabin8 is regulated in cells. Recently, biochemical and cell biological studies have identified several mechanisms for Rabin8 activation, which involves the relief of the intramolecular autoinhibition of Rabin8. Here we describe biochemical methods that we have used recently to study the activation of Rabin8.
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Affiliation(s)
- Bin Wu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Juanfei Wang
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuting Zhao
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Wei Guo
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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Differential processing of Arabidopsis ubiquitin-like Atg8 autophagy proteins by Atg4 cysteine proteases. Proc Natl Acad Sci U S A 2013; 111:863-8. [PMID: 24379391 DOI: 10.1073/pnas.1318207111] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Autophagy is a highly conserved biological process during which double membrane bound autophagosomes carry intracellular cargo material to the vacuole or lysosome for degradation and/or recycling. Autophagosome biogenesis requires Autophagy 4 (Atg4) cysteine protease-mediated processing of ubiquitin-like Atg8 proteins. Unlike single Atg4 and Atg8 genes in yeast, the Arabidopsis genome contains two Atg4 (AtAtg4a and AtAtg4b) and nine Atg8 (AtAtg8a-AtAtg8i) genes. However, we know very little about specificity of different AtAtg4s for processing of different AtAtg8s. Here, we describe a unique bioluminescence resonance energy transfer-based AtAtg8 synthetic substrate to assess AtAtg4 activity in vitro and in vivo. In addition, we developed a unique native gel assay of superhRLUC catalytic activity assay to monitor cleavage of AtAtg8s in vitro. Our results indicate that AtAtg4a is the predominant protease and that it processes AtAtg8a, AtAtg8c, AtAtg8d, and AtAtg8i better than AtAtg4b in vitro. In addition, kinetic analyses indicate that although both AtAtg4s have similar substrate affinity, AtAtg4a is more active than AtAtg4b in vitro. Activity of AtAtg4s is reversibly inhibited in vitro by reactive oxygen species such as H2O2. Our in vivo bioluminescence resonance energy transfer analyses in Arabidopsis transgenic plants indicate that the AtAtg8 synthetic substrate is efficiently processed and this is AtAtg4 dependent. These results indicate that the synthetic AtAtg8 substrate is used efficiently in the biogenesis of autophagosomes in vivo. Transgenic Arabidopsis plants expressing the AtAtg8 synthetic substrate will be a valuable tool to dissect autophagy processes and the role of autophagy during different biological processes in plants.
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Zhang C, Wei ZH, Ye BC. Imaging and tracing of intracellular metabolites utilizing genetically encoded fluorescent biosensors. Biotechnol J 2013; 8:1280-91. [DOI: 10.1002/biot.201300001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 08/02/2013] [Accepted: 08/26/2013] [Indexed: 12/11/2022]
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Shaw SL, Ehrhardt DW. Smaller, faster, brighter: advances in optical imaging of living plant cells. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:351-75. [PMID: 23506334 DOI: 10.1146/annurev-arplant-042110-103843] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The advent of fluorescent proteins and access to modern imaging technologies have dramatically accelerated the pace of discovery in plant cell biology. Remarkable new insights into such diverse areas as plant pathogenesis, cytoskeletal dynamics, sugar transport, cell wall synthesis, secretory control, and hormone signaling have come from careful examination of living cells using advanced optical probes. New technologies, both commercially available and on the horizon, promise a continued march toward more quantitative methods for imaging and for extending the optical exploration of biological structure and activity to molecular scales. In this review, we lay out fundamental issues in imaging plant specimens and look ahead to several technological innovations in molecular tools, instrumentation, imaging methods, and specimen handling that show promise for shaping the coming era of plant cell biology.
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Affiliation(s)
- Sidney L Shaw
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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Zhang Y, Xie Q, Robertson JB, Johnson CH. pHlash: a new genetically encoded and ratiometric luminescence sensor of intracellular pH. PLoS One 2012; 7:e43072. [PMID: 22905204 PMCID: PMC3419163 DOI: 10.1371/journal.pone.0043072] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 07/16/2012] [Indexed: 11/19/2022] Open
Abstract
We report the development of a genetically encodable and ratiometic pH probe named “pHlash” that utilizes Bioluminescence Resonance Energy Transfer (BRET) rather than fluorescence excitation. The pHlash sensor–composed of a donor luciferase that is genetically fused to a Venus fluorophore–exhibits pH dependence of its spectral emission in vitro. When expressed in either yeast or mammalian cells, pHlash reports basal pH and cytosolic acidification in vivo. Its spectral ratio response is H+ specific; neither Ca++, Mg++, Na+, nor K+ changes the spectral form of its luminescence emission. Moreover, it can be used to image pH in single cells. This is the first BRET-based sensor of H+ ions, and it should allow the approximation of pH in cytosolic and organellar compartments in applications where current pH probes are inadequate.
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Affiliation(s)
- Yunfei Zhang
- Departments of Biological Science and Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Qiguang Xie
- Departments of Biological Science and Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - J. Brian Robertson
- Departments of Biological Science and Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Carl Hirschie Johnson
- Departments of Biological Science and Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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Adams JP, Adeli A, Hsu CY, Harkess RL, Page GP, Depamphilis CW, Schultz EB, Yuceer C. Plant-based FRET biosensor discriminates environmental zinc levels. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:207-216. [PMID: 21910820 DOI: 10.1111/j.1467-7652.2011.00656.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Heavy metal accumulation in the environment poses great risks to flora and fauna. However, monitoring sites prone to accumulation poses scale and economic challenges. In this study, we present and test a method for monitoring these sites using fluorescent resonance energy transfer (FRET) change in response to zinc (Zn) accumulation in plants as a proxy for environmental health. We modified a plant Zn transport protein by adding flanking fluorescent proteins (FPs) and deploying the construct into two different species. In Arabidopsis thaliana, FRET was monitored by a confocal microscope and had a 1.4-fold increase in intensity as the metal concentration increased. This led to a 16.7% overall error-rate when discriminating between a control (1μm Zn) and high (10mm Zn) treatment after 96h. The second host plant (Populus tremula×Populu salba) also had greater FRET values (1.3-fold increase) when exposed to the higher concentration of Zn, while overall error-rates were greater at 22.4%. These results indicate that as plants accumulate Zn, protein conformational changes occur in response to Zn causing differing interaction between FPs. This results in greater FRET values when exposed to greater amounts of Zn and monitored with appropriate light sources and filters. We also demonstrate how this construct can be moved into different host plants effectively including one tree species. This chimeric protein potentially offers a method for monitoring large areas of land for Zn accumulation, is transferable among species, and could be modified to monitor other specific heavy metals that pose environmental risks.
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Affiliation(s)
- Joshua P Adams
- School of Forest Resources, University of Arkansas at Monticello, Monticello, AR, USA.
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