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Salehian M, Emamzadeh R, Nazari M. Exploring the Potential of Arginine to Increase Coelenterazine-Renilla Luciferase Affinity and Enzyme Stability: Kinetic and Molecular Dynamics Studies. Protein J 2024:10.1007/s10930-024-10208-x. [PMID: 38824468 DOI: 10.1007/s10930-024-10208-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2024] [Indexed: 06/03/2024]
Abstract
Renilla luciferase catalyzes the oxidation of coelenterazine to coelenteramide and results in the emission of a photon of light. Although Renilla luciferase has various applications in biotechnology, its low thermal stability limits the development of its applications. Arginine is a well-known stabilizing amino acid that plays a key role in protein stabilization against inactivation. However, its impact on enzyme properties is unpredictable. This study investigates the impact of arginine on the kinetics and thermal stability of Renilla luciferase. The enzyme's performance was significantly enhanced in the presence of arginine, with catalytic efficiency increasing by 3.31-fold and 3.08-fold when exposed to 0.2 M and 0.3 M arginine, respectively. Additionally, arginine improved the thermal stability of Renilla luciferase. Molecular dynamics simulation showed that the addition of 0.2 M arginine reduced the binding of coelenteramide, the reaction product and an enzyme inhibitor, to the active site of the Renilla luciferase. Therefore, the release of the product was accelerated, and the affinity of Renilla luciferase for coelenterazine increased. Furthermore, Molecular dynamics studies indicated an increased network of water molecules surrounding Renilla luciferase in the presence of 0.2 M arginine. This network potentially enhances the hydrophobic effect on the protein structure, ultimately improving enzyme stability. The findings of this study hold promise for the development of commercial kits incorporating Renilla luciferase.
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Affiliation(s)
- Maryam Salehian
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Rahman Emamzadeh
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Mahboobeh Nazari
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
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Torres Chavez AG, McKenna MK, Balasubramanian K, Riffle L, Patel NL, Kalen JD, St. Croix B, Leen AM, Bajgain P. A dual-luciferase bioluminescence system for the assessment of cellular therapies. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200763. [PMID: 38596291 PMCID: PMC10869576 DOI: 10.1016/j.omton.2024.200763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/17/2023] [Accepted: 01/05/2024] [Indexed: 04/11/2024]
Abstract
Bioluminescence imaging is a well-established platform for evaluating engineered cell therapies in preclinical studies. However, despite the discovery of new luciferases and substrates, optimal combinations to simultaneously monitor two cell populations remain limited. This makes the functional assessment of cellular therapies cumbersome and expensive, especially in preclinical in vivo models. In this study, we explored the potential of using a green bioluminescence-emitting click beetle luciferase, CBG99, and a red bioluminescence-emitting firefly luciferase mutant, Akaluc, together to simultaneously monitor two cell populations. Using various chimeric antigen receptor T cells and tumor pairings, we demonstrate that these luciferases are suitable for real-time tracking of two cell types using 2D and 3D cultures in vitro and experimental models in vivo. Our data show the broad compatibility of this dual-luciferase (duo-luc) system with multiple bioluminescence detection equipment ranging from benchtop spectrophotometers to live animal imaging systems. Although this study focused on investigating complex CAR T cells and tumor cell interactions, this duo-luc system has potential utility for the simultaneous monitoring of any two cellular components-for example, to unravel the impact of a specific genetic variant on clonal dominance in a mixed population of tumor cells.
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Affiliation(s)
| | - Mary K. McKenna
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Lisa Riffle
- Small Animal Imaging Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Nimit L. Patel
- Small Animal Imaging Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Joseph D. Kalen
- Small Animal Imaging Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Brad St. Croix
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ann M. Leen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pradip Bajgain
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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Khoshnevisan G, Emamzadeh R, Nazari M, Oliayi M, Sariri R. Uncovering the role of sorbitol in Renilla luciferase kinetics: Insights from spectroscopic and molecular dynamics studies. Biochem Biophys Rep 2024; 37:101617. [PMID: 38371529 PMCID: PMC10873868 DOI: 10.1016/j.bbrep.2023.101617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 02/20/2024] Open
Abstract
Renilla luciferase catalyzes the oxidation of coelenterazine to coelenteramide, resulting in the emission of a photon of light. This study investigated the impact of sorbitol on the structural and kinetic properties of Renilla luciferase using circular dichroism, fluorescence spectroscopy, and molecular dynamics simulations. Our investigation, carried out using circular dichroism and fluorescence analyses, as well as a thermal stability assay, has revealed that sorbitol induces conformational changes in the enzyme but does not improve its thermal stability. Moreover, through kinetic studies, it has been demonstrated that at a concentration of 0.4 M, sorbitol enhances the catalytic efficiency of Renilla luciferase. However, at higher concentrations, sorbitol results in a decrease in catalytic efficiency. Additionally, molecular dynamics simulations have shown that sorbitol increases the presence of hydrophobic pockets on the enzyme's surface. These simulations have also provided evidence that at a concentration of 0.4 M, sorbitol facilitates substrate access to the active site of the enzyme. Nevertheless, at higher concentrations, sorbitol obstructs substrate trafficking, most likely due to its impact on the gateway to the active site. This study may provide insights into the kinetic changes observed in enzymes with buried active sites, such as those with α/β hydrolase fold.
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Affiliation(s)
| | - Rahman Emamzadeh
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mahboobeh Nazari
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Mina Oliayi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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Dunuweera AN, Dunuweera SP, Ranganathan K. A Comprehensive Exploration of Bioluminescence Systems, Mechanisms, and Advanced Assays for Versatile Applications. Biochem Res Int 2024; 2024:8273237. [PMID: 38347947 PMCID: PMC10861286 DOI: 10.1155/2024/8273237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/10/2023] [Accepted: 01/21/2024] [Indexed: 02/15/2024] Open
Abstract
Bioluminescence has been a fascinating natural phenomenon of light emission from living creatures. It happens when the enzyme luciferase facilitates the oxidation of luciferin, resulting in the creation of an excited-state species that emits light. Although there are many bioluminescent systems, few have been identified. D-luciferin-dependent systems, coelenterazine-dependent systems, Cypridina luciferin-based systems, tetrapyrrole-based luciferins, bacterial bioluminescent systems, and fungal bioluminescent systems are natural bioluminescent systems. Since different bioluminescence systems, such as various combinations of luciferin-luciferase pair reactions, have different light emission wavelengths, they benefit industrial applications such as drug discovery, protein-protein interactions, in vivo imaging in small animals, and controlling neurons. Due to the expression of luciferase and easy permeation of luciferin into most cells and tissues, bioluminescence assays are applied nowadays with modern technologies in most cell and tissue types. It is a versatile technique in a variety of biomedical research. Furthermore, there are some investigated blue-sky research projects, such as bioluminescent plants and lamps. This review article is mainly based on the theory of diverse bioluminescence systems and their past, present, and future applications.
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Affiliation(s)
| | | | - K. Ranganathan
- Department of Botany, University of Jaffna, Jaffna 40000, Sri Lanka
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Calabretta MM, Michelini E. Current advances in the use of bioluminescence assays for drug discovery: an update of the last ten years. Expert Opin Drug Discov 2024; 19:85-95. [PMID: 37814480 DOI: 10.1080/17460441.2023.2266989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/02/2023] [Indexed: 10/11/2023]
Abstract
INTRODUCTION Bioluminescence is a well-established optical detection technique widely used in several bioanalytical applications, including high-throughput and high-content screenings. Thanks to advances in synthetic biology techniques and deep learning, a wide portfolio of luciferases is now available with tuned emission wavelengths, kinetics, and high stability. These luciferases can be implemented in the drug discovery and development pipeline, allowing high sensitivity and multiplexing capability. AREAS COVERED This review summarizes the latest advancements of bioluminescent systems as toolsets in drug discovery programs for in vitro applications. Particular attention is paid to the most advanced bioluminescence-based technologies for drug screening over the past 10 years (from 2013 to 2023) such as cell-free assays, cell-based assays based on genetically modified cells, bioluminescence resonance energy transfer, and protein complementation assays in 2D and 3D cell models. EXPERT OPINION The availability of tuned bioluminescent proteins with improved emission and stability properties is vital for the development of bioluminescence assays for drug discovery, spanning from reporter gene technology to protein-protein techniques. Further studies, combining machine learning with synthetic biology, will be necessary to obtain new tools for sustainable and highly predictive bioluminescent drug discovery platforms.
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Affiliation(s)
- Maria Maddalena Calabretta
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Center for Applied Biomedical Research (CRBA), IRCCS St. Orsola Hospital, Bologna, Italy
| | - Elisa Michelini
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Center for Applied Biomedical Research (CRBA), IRCCS St. Orsola Hospital, Bologna, Italy
- Health Sciences and Technologies Interdepartmental Center for Industrial Research (HSTICIR), University of Bologna, Bologna, Italy
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Zhao X, Hu H, Sun K, Liang W, Wang Z, Jin X, Wang S. Actoeside mitigated the renal proximal tubule cells damage triggered by high glucose through miR-766/VCAM1/NF-κB signalling pathway. Arch Physiol Biochem 2023; 129:1177-1186. [PMID: 34338087 DOI: 10.1080/13813455.2021.1920983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 04/19/2021] [Indexed: 10/20/2022]
Abstract
CONTEXT Diabetic nephropathy (DN) triggered by diabetes mellitus is one of the primary causes of end-stage renal failure worldwide. OBJECTIVE This study intends to explore the function and potential mechanism of actoeside on renal proximal tubule (HK-2) cells damage induced by high-glucose (HG). METHODS The DN model was established in HK-2 cells with 30 mM HG treatment. The viability, apoptosis and inflammation of HK-2 cells were analysed severally via CCK-8, flow cytomery and ELISA. The key factors related to NF-κB were detected by western blotting. RESULTS Actoeside attenuated the HG-induced HK-2 cells damage. The differentially expression of miR-766 and VCAM1 in DN patients was reversed by actoeside. Moreover, the increased phosphorylation levels of p65 NF-κB/IκBα induced by HG were attenuated by actoeside. CONCLUSIONS Actoeside promoted the growth and repressed the apoptosis and inflammation of HK-2 cells via miR-766/VCAM1/NF-κB signalling pathway, affording a promising idea for the treatment of DN.
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Affiliation(s)
- Xiaodong Zhao
- Department of Endocrinology, Zibo Central Hospital, Zibo City, PR China
| | - Honglei Hu
- Department of Endocrinology, Zibo Central Hospital, Zibo City, PR China
| | - Kun Sun
- Department of Nephropathy, Zibo Central Hospital, Zibo City, PR China
| | - Wenlong Liang
- Department of Endocrinology, Zibo Central Hospital, Zibo City, PR China
| | - Zhenzhen Wang
- Department of Endocrinology, Zibo Central Hospital, Zibo City, PR China
| | - Xingqian Jin
- Department of Endocrinology, Zibo Central Hospital, Zibo City, PR China
| | - Shujuan Wang
- Department of Endocrinology, Zibo Central Hospital, Zibo City, PR China
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Mujawar A, Phadte P, Palkina KA, Markina NM, Mohammad A, Thakur BL, Sarkisyan KS, Balakireva AV, Ray P, Yamplosky I, De A. Triple Reporter Assay: A Non-Overlapping Luciferase Assay for the Measurement of Complex Macromolecular Regulation in Cancer Cells Using a New Mushroom Luciferase-Luciferin Pair. SENSORS (BASEL, SWITZERLAND) 2023; 23:7313. [PMID: 37687774 PMCID: PMC10490530 DOI: 10.3390/s23177313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023]
Abstract
This study demonstrates the development of a humanized luciferase imaging reporter based on a recently discovered mushroom luciferase (Luz) from Neonothopanus nambi. In vitro and in vivo assessments showed that human-codon-optimized Luz (hLuz) has significantly higher activity than native Luz in various cancer cell types. The potential of hLuz in non-invasive bioluminescence imaging was demonstrated by human tumor xenografts subcutaneously and by the orthotopic lungs xenograft in immunocompromised mice. Luz enzyme or its unique 3OH-hispidin substrate was found to be non-cross-reacting with commonly used luciferase reporters such as Firefly (FLuc2), Renilla (RLuc), or nano-luciferase (NLuc). Based on this feature, a non-overlapping, multiplex luciferase assay using hLuz was envisioned to surpass the limitation of dual reporter assay. Multiplex reporter functionality was demonstrated by designing a new sensor construct to measure the NF-κB transcriptional activity using hLuz and utilized in conjunction with two available constructs, p53-NLuc and PIK3CA promoter-FLuc2. By expressing these constructs in the A2780 cell line, we unveiled a complex macromolecular regulation of high relevance in ovarian cancer. The assays performed elucidated the direct regulatory action of p53 or NF-κB on the PIK3CA promoter. However, only the multiplexed assessment revealed further complexities as stabilized p53 expression attenuates NF-κB transcriptional activity and thereby indirectly influences its regulation on the PIK3CA gene. Thus, this study suggests the importance of live cell multiplexed measurement of gene regulatory function using more than two luciferases to address more realistic situations in disease biology.
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Affiliation(s)
- Aaiyas Mujawar
- Molecular Functional Imaging Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai 410210, India; (A.M.); (A.M.)
- Faculty of Life Science, Homi Bhabha National Institute, Mumbai 400094, India; (P.P.); (B.L.T.); (P.R.)
| | - Pratham Phadte
- Faculty of Life Science, Homi Bhabha National Institute, Mumbai 400094, India; (P.P.); (B.L.T.); (P.R.)
- Imaging Cell Signalling and Therapeutics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai 410210, India
| | - Ksenia A. Palkina
- Institute of Bioorganic Chemistry (IBCh), Russian Academy of Sciences, Moscow 119991, Russia; (K.A.P.); (N.M.M.); (K.S.S.); (A.V.B.)
- Planta LLC, Bolshoi Boulevard, 42 Street 1, Moscow 121205, Russia
| | - Nadezhda M. Markina
- Institute of Bioorganic Chemistry (IBCh), Russian Academy of Sciences, Moscow 119991, Russia; (K.A.P.); (N.M.M.); (K.S.S.); (A.V.B.)
- Planta LLC, Bolshoi Boulevard, 42 Street 1, Moscow 121205, Russia
| | - Ameena Mohammad
- Molecular Functional Imaging Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai 410210, India; (A.M.); (A.M.)
| | - Bhushan L. Thakur
- Faculty of Life Science, Homi Bhabha National Institute, Mumbai 400094, India; (P.P.); (B.L.T.); (P.R.)
- Imaging Cell Signalling and Therapeutics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai 410210, India
| | - Karen S. Sarkisyan
- Institute of Bioorganic Chemistry (IBCh), Russian Academy of Sciences, Moscow 119991, Russia; (K.A.P.); (N.M.M.); (K.S.S.); (A.V.B.)
- Synthetic Biology Group, MRC London Institute of Medical Sciences, London W12 0NN, UK
| | - Anastasia V. Balakireva
- Institute of Bioorganic Chemistry (IBCh), Russian Academy of Sciences, Moscow 119991, Russia; (K.A.P.); (N.M.M.); (K.S.S.); (A.V.B.)
- Planta LLC, Bolshoi Boulevard, 42 Street 1, Moscow 121205, Russia
| | - Pritha Ray
- Faculty of Life Science, Homi Bhabha National Institute, Mumbai 400094, India; (P.P.); (B.L.T.); (P.R.)
- Imaging Cell Signalling and Therapeutics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai 410210, India
| | - Ilia Yamplosky
- Institute of Bioorganic Chemistry (IBCh), Russian Academy of Sciences, Moscow 119991, Russia; (K.A.P.); (N.M.M.); (K.S.S.); (A.V.B.)
| | - Abhijit De
- Molecular Functional Imaging Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai 410210, India; (A.M.); (A.M.)
- Faculty of Life Science, Homi Bhabha National Institute, Mumbai 400094, India; (P.P.); (B.L.T.); (P.R.)
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Rotermund A, Staege MS, Brandt S, Luetzkendorf J, Lucas H, Mueller LP, Mueller T. Luciferase Expressing Preclinical Model Systems Representing the Different Molecular Subtypes of Colorectal Cancer. Cancers (Basel) 2023; 15:4122. [PMID: 37627150 PMCID: PMC10452405 DOI: 10.3390/cancers15164122] [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: 06/19/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease. More insight into the biological diversity of CRC is needed to improve therapeutic outcomes. Established CRC cell lines are frequently used and were shown to be representative models of the main subtypes of CRC at the genomic and transcriptomic level. In the present work, we established stable, luciferase expressing derivatives from 10 well-established CRC cell lines, generated spheroids and subcutaneous xenograft tumors in nude mice, and performed comparative characterization of these model systems. Transcriptomic analyses revealed the close relation of cell lines with their derived spheroids and xenograft tumors. The preclinical model systems clustered with patient tumor samples when compared to normal tissue thereby confirming that cell-line-based tumor models retain specific characteristics of primary tumors. Xenografts showed different differentiation patterns and bioluminescence imaging revealed metastatic spread to the lungs. In addition, the models were classified according to the CMS classification system, with further sub-classification according to the recently identified two intrinsic epithelial tumor cell states of CRC, iCMS2 and iCMS3. The combined data showed that regarding primary tumor characteristics, 3D-spheroid cultures resemble xenografts more closely than 2D-cultured cells do. Furthermore, we set up a bioluminescence-based spheroid cytotoxicity assay in order to be able to perform dose-response relationship studies in analogy to typical monolayer assays. Applying the established assay, we studied the efficacy of oxaliplatin. Seven of the ten used cell lines showed a significant reduction in the response to oxaliplatin in the 3D-spheroid model compared to the 2D-monolayer model. Therapy studies in selected xenograft models confirmed the response or lack of response to oxaliplatin treatment. Analyses of differentially expressed genes in these models identified CAV1 as a possible marker of oxaliplatin resistance. In conclusion, we established a combined 2D/3D, in vitro/in vivo model system representing the heterogeneity of CRC, which can be used in preclinical research applications.
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Affiliation(s)
- Arne Rotermund
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
| | - Martin S. Staege
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany;
| | - Sarah Brandt
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
| | - Jana Luetzkendorf
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
| | - Henrike Lucas
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany;
| | - Lutz P. Mueller
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
| | - Thomas Mueller
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
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Quan J, Zhao G, Liu Z, Li L, Lu J, Song G, Kang Y. Competing endogenous RNA (ceRNA) in a non-model animal: Non-coding RNAs respond to heat stress in rainbow trout (Oncorhynchus mykiss) through ceRNA-regulated mechanisms. Int J Biol Macromol 2023; 239:124246. [PMID: 37003385 DOI: 10.1016/j.ijbiomac.2023.124246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 02/21/2023] [Accepted: 03/18/2023] [Indexed: 04/03/2023]
Abstract
BACKGROUND Rainbow trout (Oncorhynchus mykiss) is a typical cold-water fish. With global warming and extreme heat, high summer temperatures are the biggest threat to rainbow trout farming. Rainbow trout initiate stress defense mechanisms in response to thermal stimuli, and competing endogenous RNA (ceRNA) regulation of target genes (mRNAs) mediated by non-coding RNAs (microRNAs [miRNAs], long non-coding RNAs) may be the main strategy for responding to thermal stimuli and enhancing adaptation. RESULTS We screened the LOC110485411-novel-m0007-5p-hsp90ab1 ceRNA relationship pairs for affect heat stress in rainbow trout and validated their targeting relationships and functions based on preliminary high-throughput sequencing analysis results. The transfection of exogenous novel-m0007-5p mimics and inhibitors into primary rainbow trout hepatocytes effectively bound and inhibited the target genes hsp90ab1 and LOC110485411 without significant effects on hepatocyte viability, proliferation, and apoptosis. The inhibitory effect of novel-m0007-5p overexpression on hsp90ab1 and LOC110485411 under heat stress was time-efficient. Similarly, small interfering RNAs (siRNAs) affected hsp90ab1 mRNA expression by silencing LOC110485411 expression time-efficiently. CONCLUSIONS In conclusion, we found that in rainbow trout, LOC110485411 and hsp90ab1 can bind competitively to novel-m0007-5p via 'sponge adsorption' and that interference with LOC110485411 affects hsp90ab1 expression. These results provide potential for anti-stress drug screening in rainbow trout.
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Affiliation(s)
- Jinqiang Quan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Guiyan Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Zhe Liu
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Lanlan Li
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Junhao Lu
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Guolin Song
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Yujun Kang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
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10
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Kim SB, Furuta T, Kamiya G, Kitada N, Paulmurugan R, Maki SA. Bright Molecular Strain Probe Templates for Reporting Protein-Protein Interactions. SENSORS (BASEL, SWITZERLAND) 2023; 23:3498. [PMID: 37050557 PMCID: PMC10098686 DOI: 10.3390/s23073498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Imaging protein-protein interactions (PPIs) is a hot topic in molecular medicine in the postgenomic sequencing era. In the present study, we report bright and highly sensitive single-chain molecular strain probe templates which embed full-length Renilla luciferase 8.6-535SG (RLuc86SG) or Artificial luciferase 49 (ALuc49) as reporters. These reporters were deployed between FKBP-rapamycin binding domain (FRB) and FK506-binding protein (FKBP) as a PPI model. This unique molecular design was conceptualized to exploit molecular strains of the sandwiched reporters appended by rapamycin-triggered intramolecular PPIs. The ligand-sensing properties of the templates were maximized by interface truncations and substrate modulation. The highest fold intensities, 9.4 and 16.6, of the templates were accomplished with RLuc86SG and ALuc49, respectively. The spectra of the templates, according to substrates, revealed that the colors are tunable to blue, green, and yellow. The putative substrate-binding chemistry and the working mechanisms of the probes were computationally modeled in the presence or absence of rapamycin. Considering that the molecular strain probe templates are applicable to other PPI models, the present approach would broaden the scope of the bioassay toolbox, which harnesses the privilege of luciferase reporters and the unique concept of the molecular strain probes into bioassays and molecular imaging.
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Affiliation(s)
- Sung-Bae Kim
- Environmental Management Research Institute (EMRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8569, Japan
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Genta Kamiya
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu 182-8585, Japan
| | - Nobuo Kitada
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu 182-8585, Japan
| | - Ramasamy Paulmurugan
- Molecular Imaging Program at Stanford, Bio-X Program, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Shojiro A. Maki
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu 182-8585, Japan
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S-Series Coelenterazine-Driven Combinatorial Bioluminescence Imaging Systems for Mammalian Cells. Int J Mol Sci 2023; 24:ijms24021420. [PMID: 36674934 PMCID: PMC9865520 DOI: 10.3390/ijms24021420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023] Open
Abstract
A unique combinatorial bioluminescence (BL) imaging system was developed for determining molecular events in mammalian cells with various colors and BL intensity patterns. This imaging system consists of one or multiple reporter luciferases and a series of novel coelenterazine (CTZ) analogues named "S-series". For this study, ten kinds of novel S-series CTZ analogues were synthesized and characterized concerning the BL intensities, spectra, colors, and specificity of various marine luciferases. The characterization revealed that the S-series CTZ analogues luminesce with blue-to-orange-colored BL spectra with marine luciferases, where the most red-shifted BL spectrum peaked at 583 nm. The colors completed a visible light color palette with those of our precedent C-series CTZ analogues. The synthesized substrates S1, S5, S6, and S7 were found to have a unique specificity with marine luciferases, such as R86SG, NanoLuc (shortly, NLuc), and ALuc16. They collectively showed unique BL intensity patterns to identify the marine luciferases together with colors. The marine luciferases, R86SG, NLuc, and ALuc16, were multiplexed into multi-reporter systems, the signals of which were quantitatively unmixed with the specific substrates. When the utility was applied to a single-chain molecular strain probe, the imaging system simultaneously reported three different optical indexes for a ligand, i.e., unique BL intensity and color patterns for identifying the reporters, together with the ligand-specific fold intensities in mammalian cells. This study directs a new combinatorial BL imaging system to specific image molecular events in mammalian cells with multiple optical indexes.
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12
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Boitet M, Eun H, Achek A, Carla de Almeida Falcão V, Delorme V, Grailhe R. Biolum' RGB: A Low-Cost, Versatile, and Sensitive Bioluminescence Imaging Instrument for a Broad Range of Users. ACS Sens 2022; 7:2556-2566. [PMID: 36001874 DOI: 10.1021/acssensors.2c00457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Luminometer and imaging systems are used to detect and quantify low light produced by a broad range of bioluminescent proteins. Despite their everyday use in research, such instruments are costly and lack the flexibility to accommodate the variety of bioluminescence experiment formats that may require top or bottom signal acquisition, high or medium sensitivity, or multiple wavelength detection. To address the growing need for versatile technologies, we developed a highly customizable bioluminescence imager called Biolum' RGB that uses a consumer color digital camera with a high-aperture lens mounted at the bottom or top of a 3D-printed dark chamber and can quantify bioluminescence emission from cells grown in 384-well microplates and Petri dishes. Taking advantage of RGB detectors, Biolum' RGB can distinguish spectral signatures from various bioluminescence probes and quantify bioluminescence resonant energy transfer occurring during protein-protein interaction events. Although Biolum' RGB can be used with any smartphone, in particular for low bioluminescence signals, we recommend the use of recent digital cameras which offer better sensitivity and high signal/noise ratio. Altogether, Biolum' RGB combines the benefits of a plate reader and imager while providing better image resolution and faster acquisition speed, and as such, it offers an exciting alternative for any laboratory looking for a versatile, low-cost bioluminescence imaging instrument.
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Affiliation(s)
- Maylis Boitet
- Technology Development Platform, Institut Pasteur Korea, Seongnam13488, Republic of Korea.,Division of Bio-Medical Science & Technology, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon34113, Republic of Korea
| | - Hyeju Eun
- Technology Development Platform, Institut Pasteur Korea, Seongnam13488, Republic of Korea
| | - Asma Achek
- Technology Development Platform, Institut Pasteur Korea, Seongnam13488, Republic of Korea
| | | | - Vincent Delorme
- Tuberculosis Research Laboratory, Institut Pasteur Korea, Seongnam13488, Republic of Korea
| | - Regis Grailhe
- Technology Development Platform, Institut Pasteur Korea, Seongnam13488, Republic of Korea.,Division of Bio-Medical Science & Technology, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon34113, Republic of Korea.,Smart-MD, Institut Pasteur Korea, Seongnam13488, Republic of Korea
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13
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Systematic Comparison of Beetle Luciferase-Luciferin Pairs as Sources of Near-Infrared Light for In Vitro and In Vivo Applications. Int J Mol Sci 2022; 23:ijms23052451. [PMID: 35269601 PMCID: PMC8910387 DOI: 10.3390/ijms23052451] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 11/17/2022] Open
Abstract
Luciferases catalyze light-emitting reactions that produce a rainbow of colors from their substrates (luciferins), molecular oxygen, and often additional cofactors. These bioluminescence (BL) systems have afforded an incredible variety of basic research and medical applications. Driven by the importance of BL-based non-invasive animal imaging (BLI) applications, especially in support of cancer research, new BL systems have been developed by engineering beetle luciferase (Luc) variants and synthetic substrate combinations to produce red to near-infrared (nIR) light to improve imaging sensitivity and resolution. To stimulate the application of BLI research and advance the development of improved reagents for BLI, we undertook a systematic comparison of the spectroscopic and BL properties of seven beetle Lucs with LH2 and nine substrates, which included two new quinoline ring-containing analogs. The results of these experiments with purified Luc enzymes in vitro and in live HEK293T cells transfected with luc genes have enabled us to identify Luc/analog combinations with improved properties compared to those previously reported and to provide live cell BL data that may be relevant to in vivo imaging applications. Additionally, we found strong candidate enzyme/substrate pairs for in vitro biomarker applications requiring nIR sources with minimal visible light components. Notably, one of our new substrates paired with a previously developed Luc variant was demonstrated to be an excellent in vitro source of nIR and a potentially useful BL system for improved resolution in BLI.
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14
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Bader CD, Panter F, Garcia R, Tchesnokov EP, Haid S, Walt C, Spröer C, Kiefer AF, Götte M, Overmann J, Pietschmann T, Müller R. Sandacrabins - Structurally Unique Antiviral RNA Polymerase Inhibitors from a Rare Myxobacterium. Chemistry 2022; 28:e202104484. [PMID: 34990513 PMCID: PMC9306752 DOI: 10.1002/chem.202104484] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Indexed: 12/13/2022]
Abstract
Structure elucidation and total synthesis of five unprecedented terpenoid‐alkaloids, the sandacrabins, are reported, alongside with the first description of their producing organism Sandaracinus defensii MSr10575, which expands the Sandaracineae family by only its second member. The genome sequence of S. defensii as presented in this study was utilized to identify enzymes responsible for sandacrabin formation, whereby dimethylbenzimidazol, deriving from cobalamin biosynthesis, was identified as key intermediate. Biological activity profiling revealed that all sandacrabins except congener A exhibit potent antiviral activity against the human pathogenic coronavirus HCoV229E in the three digit nanomolar range. Investigation of the underlying mode of action discloses that the sandacrabins inhibit the SARS‐CoV‐2 RNA‐dependent RNA polymerase complex, highlighting them as structurally distinct non‐nucleoside RNA synthesis inhibitors. The observed segregation between cell toxicity at higher concentrations and viral inhibition opens the possibility for their medicinal chemistry optimization towards selective inhibitors.
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Affiliation(s)
- Chantal D Bader
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Fabian Panter
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124, Braunschweig, Germany.,Helmholtz International Lab for anti-infectives, Campus E8 1, 66123, Saarbrücken, Germany
| | - Ronald Garcia
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Sibylle Haid
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research a joint venture between the Medical School Hannover (MHH) and, The Helmholtz Centre for Infection Research (HZI), Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Christine Walt
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7 and German Centre of Infection Research (DZIF) Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany.,Microbiology, Technical University of Braunschweig, 38106, Braunschweig, Germany
| | - Alexander F Kiefer
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Jörg Overmann
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7 and German Centre of Infection Research (DZIF) Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany.,Microbiology, Technical University of Braunschweig, 38106, Braunschweig, Germany
| | - Thomas Pietschmann
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research a joint venture between the Medical School Hannover (MHH) and, The Helmholtz Centre for Infection Research (HZI), Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124, Braunschweig, Germany.,Helmholtz International Lab for anti-infectives, Campus E8 1, 66123, Saarbrücken, Germany
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15
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Philipp M, Hussnaetter KP, Reindl M, Müntjes K, Feldbrügge M, Schipper K. A Novel Potent Carrier for Unconventional Protein Export in Ustilago maydis. Front Cell Dev Biol 2022; 9:816335. [PMID: 35083222 PMCID: PMC8784666 DOI: 10.3389/fcell.2021.816335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/17/2021] [Indexed: 11/14/2022] Open
Abstract
Recombinant proteins are ubiquitously applied in fields like research, pharma, diagnostics or the chemical industry. To provide the full range of useful proteins, novel expression hosts need to be established for proteins that are not sufficiently produced by the standard platform organisms. Unconventional secretion in the fungal model Ustilago maydis is an attractive novel option for export of heterologous proteins without N-glycosylation using chitinase Cts1 as a carrier. Recently, a novel factor essential for unconventional Cts1 secretion termed Jps1 was identified. Here, we show that Jps1 is unconventionally secreted using a fusion to bacterial β-glucuronidase as an established reporter. Interestingly, the experiment also demonstrates that the protein functions as an alternative carrier for heterologous proteins, showing about 2-fold higher reporter activity than the Cts1 fusion in the supernatant. In addition, Jps1-mediated secretion even allowed for efficient export of functional firefly luciferase as a novel secretion target which could not be achieved with Cts1. As an application for a relevant pharmaceutical target, export of functional bi-specific synthetic nanobodies directed against the SARS-CoV2 spike protein was demonstrated. The establishment of an alternative efficient carrier thus constitutes an excellent expansion of the existing secretion platform.
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Affiliation(s)
- Magnus Philipp
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kai P Hussnaetter
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michèle Reindl
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kira Müntjes
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kerstin Schipper
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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16
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Sarrion-Perdigones A, Gonzalez Y, Chang L, Gallego-Flores T, Young DW, Venken KJT. Multiplex Hextuple Luciferase Assaying. Methods Mol Biol 2022; 2524:433-456. [PMID: 35821491 PMCID: PMC10157609 DOI: 10.1007/978-1-0716-2453-1_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We recently expanded the commonly used dual luciferase assaying method toward multiplex hextuple luciferase assaying, allowing monitoring the activity of five experimental pathways against one control at the same time. In doing so, while our expanded assay utilizes a total of six orthogonal luciferases instead of two, this assay, conveniently, still utilizes the well-established reagents and principles of the widely used dual luciferase assay. Three quenchable D-luciferin-consuming luciferases are measured after addition of D-Luciferin substrate, followed by quenching of their bioluminescence (BL) and the measurement of three coelenterazine (CTZ)-consuming luciferases after addition of CTZ substrate, all in the same vessel. Here, we provide detailed protocols on how to perform such multiplex hextuple luciferase assaying to monitor cellular signal processing upstream of five transcription factors and their corresponding transcription factor-binding motifs, using a constitutive promoter as normalization control. The first protocol is provided on how to perform cell culture in preparation toward genetic or pharmaceutical perturbations, as well as transfecting a multiplex hextuple luciferase reporter vector encoding all luciferase reporter units needed for multiplex hextuple luciferase assaying. The second protocol details on how to execute multiplex hextuple luciferase assaying using a microplate reader appropriately equipped to detect the different BLs emitted by all six luciferases. Finally, the third protocol provides details on analyzing, plotting, and interpreting the data obtained by the microplate reader.
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Affiliation(s)
- Alejandro Sarrion-Perdigones
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Lyra Chang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, USA
| | - Tatiana Gallego-Flores
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Damian W Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, TX, USA.
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17
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Moreira Teixeira L, Mezzanotte L. New bioimaging avenues for organs‐on‐chips by integration of bioluminescence. VIEW 2021. [DOI: 10.1002/viw.20200177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Liliana Moreira Teixeira
- Department of Developmental Bioengineering Technical Medical Centre University of Twente Enschede The Netherlands
| | - Laura Mezzanotte
- Department of Radiology and Nuclear Medicine Erasmus Medical Center Rotterdam The Netherlands
- Department of Molecular Genetics Erasmus Medical Center Rotterdam The Netherlands
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18
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González-Grandío E, Demirer GS, Ma W, Brady S, Landry MP. A Ratiometric Dual Color Luciferase Reporter for Fast Characterization of Transcriptional Regulatory Elements in Plants. ACS Synth Biol 2021; 10:2763-2766. [PMID: 34520169 PMCID: PMC10503406 DOI: 10.1021/acssynbio.1c00248] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plant synthetic biology requires precise characterization of genetic elements to construct complex genetic circuits that can improve plant traits or confer them with new characteristics. Transcriptional reporter assays are essential to quantify the effect of gene expression regulator elements. Additionally, transcriptional reporter systems are a key tool in understanding control of gene expression in biology. In this work, we construct and characterize a dual color luciferase ratiometric reporter system that possesses several advantages over currently used reporters. It is ratiometric, thus reducing variability and increasing consistency between experiments; it is fast, as both reporters can be measured at the same time in a single reaction, and it is less expensive to perform than current dual luciferase reporter assays. We have validated our system quantifying the transcriptional capability of a panel of promoters and terminators commonly used in synthetic biology with a broad range of expression magnitudes, and in a biologically relevant system, nitrate response.
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Affiliation(s)
- Eduardo González-Grandío
- University of California Berkeley, Chemical and Biomolecular Engineering, Berkeley, California 94720, United States
| | - Gozde S Demirer
- University of California Davis, Department of Plant Biology and Genome Center, Davis, California 95616, United States
| | - Wenhe Ma
- University of California Berkeley, Chemical and Biomolecular Engineering, Berkeley, California 94720, United States
| | - Siobhan Brady
- University of California Davis, Department of Plant Biology and Genome Center, Davis, California 95616, United States
| | - Markita P Landry
- University of California Berkeley, Chemical and Biomolecular Engineering, Berkeley, California 94720, United States
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19
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Three-Dimensional X-ray Imaging of β-Galactosidase Reporter Activity by Micro-CT: Implication for Quantitative Analysis of Gene Expression. Brain Sci 2021; 11:brainsci11060746. [PMID: 34199780 PMCID: PMC8230009 DOI: 10.3390/brainsci11060746] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023] Open
Abstract
Acquisition of detailed anatomical and molecular knowledge from intact biological samples while preserving their native three-dimensional structure is still a challenging issue for imaging studies aiming to unravel a system's functions. Three-dimensional micro-CT X-ray imaging with a high spatial resolution in minimally perturbed naive non-transparent samples has recently gained increased popularity and broad application in biomedical research. Here, we describe a novel X-ray-based methodology for analysis of β-galactosidase (lacZ) reporter-driven gene expression in an intact murine brain ex vivo by micro-CT. The method relies on detection of bromine molecules in the product of the enzymatic β-galactosidase reaction. Enhancement of the X-ray signal is observed specifically in the regions of the murine brain where expression of the lacZ reporter gene is also detected histologically. We performed quantitative analysis of the expression levels of lacZ reporter activity by relative radiodensity estimation of the β-galactosidase/X-gal precipitate in situ. To demonstrate the feasibility of the method, we performed expression analysis of the Tsen54-lacZ reporter gene in the murine brain in a semi-quantitative manner. Human mutations in the Tsen54 gene cause pontocerebellar hypoplasia (PCH), a group of severe neurodegenerative disorders with both mental and motor deficits. Comparing relative levels of Tsen54 gene expression, we demonstrate that the highest Tsen54 expression is observed in anatomical brain substructures important for the normal motor and memory functions in mice.
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20
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Exploring interactions between extracellular vesicles and cells for innovative drug delivery system design. Adv Drug Deliv Rev 2021; 173:252-278. [PMID: 33798644 DOI: 10.1016/j.addr.2021.03.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/15/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
Extracellular vesicles (EVs) are submicron cell-secreted structures containing proteins, nucleic acids and lipids. EVs can functionally transfer these cargoes from one cell to another to modulate physiological and pathological processes. Due to their presumed biocompatibility and capacity to circumvent canonical delivery barriers encountered by synthetic drug delivery systems, EVs have attracted considerable interest as drug delivery vehicles. However, it is unclear which mechanisms and molecules orchestrate EV-mediated cargo delivery to recipient cells. Here, we review how EV properties have been exploited to improve the efficacy of small molecule drugs. Furthermore, we explore which EV surface molecules could be directly or indirectly involved in EV-mediated cargo transfer to recipient cells and discuss the cellular reporter systems with which such transfer can be studied. Finally, we elaborate on currently identified cellular processes involved in EV cargo delivery. Through these topics, we provide insights in critical effectors in the EV-cell interface which may be exploited in nature-inspired drug delivery strategies.
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21
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Mostafizar M, Cortes-Pérez C, Snow W, Djordjevic J, Adlimoghaddam A, Albensi BC. Challenges with Methods for Detecting and Studying the Transcription Factor Nuclear Factor Kappa B (NF-κB) in the Central Nervous System. Cells 2021; 10:1335. [PMID: 34071243 PMCID: PMC8228352 DOI: 10.3390/cells10061335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 01/01/2023] Open
Abstract
The transcription factor nuclear factor kappa B (NF-κB) is highly expressed in almost all types of cells. NF-κB is involved in many complex biological processes, in particular in immunity. The activation of the NF-κB signaling pathways is also associated with cancer, diabetes, neurological disorders and even memory. Hence, NF-κB is a central factor for understanding not only fundamental biological presence but also pathogenesis, and has been the subject of intense study in these contexts. Under healthy physiological conditions, the NF-κB pathway promotes synapse growth and synaptic plasticity in neurons, while in glia, NF-κB signaling can promote pro-inflammatory responses to injury. In addition, NF-κB promotes the maintenance and maturation of B cells regulating gene expression in a majority of diverse signaling pathways. Given this, the protein plays a predominant role in activating the mammalian immune system, where NF-κB-regulated gene expression targets processes of inflammation and host defense. Thus, an understanding of the methodological issues around its detection for localization, quantification, and mechanistic insights should have a broad interest across the molecular neuroscience community. In this review, we summarize the available methods for the proper detection and analysis of NF-κB among various brain tissues, cell types, and subcellular compartments, using both qualitative and quantitative methods. We also summarize the flexibility and performance of these experimental methods for the detection of the protein, accurate quantification in different samples, and the experimental challenges in this regard, as well as suggestions to overcome common challenges.
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Affiliation(s)
- Marina Mostafizar
- Division of Neurodegenerative Disorders, St. Boniface Hospital Research, Winnipeg, MB R2H 2A6, Canada; (M.M.); (C.C.-P.); (W.S.); (J.D.); (A.A.)
| | - Claudia Cortes-Pérez
- Division of Neurodegenerative Disorders, St. Boniface Hospital Research, Winnipeg, MB R2H 2A6, Canada; (M.M.); (C.C.-P.); (W.S.); (J.D.); (A.A.)
| | - Wanda Snow
- Division of Neurodegenerative Disorders, St. Boniface Hospital Research, Winnipeg, MB R2H 2A6, Canada; (M.M.); (C.C.-P.); (W.S.); (J.D.); (A.A.)
| | - Jelena Djordjevic
- Division of Neurodegenerative Disorders, St. Boniface Hospital Research, Winnipeg, MB R2H 2A6, Canada; (M.M.); (C.C.-P.); (W.S.); (J.D.); (A.A.)
| | - Aida Adlimoghaddam
- Division of Neurodegenerative Disorders, St. Boniface Hospital Research, Winnipeg, MB R2H 2A6, Canada; (M.M.); (C.C.-P.); (W.S.); (J.D.); (A.A.)
| | - Benedict C. Albensi
- Division of Neurodegenerative Disorders, St. Boniface Hospital Research, Winnipeg, MB R2H 2A6, Canada; (M.M.); (C.C.-P.); (W.S.); (J.D.); (A.A.)
- Department of Pharmacology and Therapeutics, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R2H 2A6, Canada
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22
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Abstract
Bioluminescence imaging with luciferase-luciferin pairs is routinely used to monitor cellular functions. Multiple targets can be visualized in tandem using luciferases that process unique substrates, but only a handful of such orthogonal probes are known. Multiplexed studies require additional robust, light-emitting molecules. In this work, we report new luciferins for orthogonal imaging that comprise disubstituted cores. These probes were found to be bright emitters with various engineered luciferases. The unique patterns of light output also provided insight into enzyme-substrate interactions necessary for productive emission. Screening studies identified mutant luciferases that could preferentially process the disubstituted analogues, enabling orthogonal imaging with existing bioluminescent reporters. Further mutational analyses revealed the origins of substrate selectivity. Collectively, this work provides insights into luciferase-luciferin features relevant to bioluminescence and expands the number of probes for multicomponent tracking.
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Affiliation(s)
- Sierra J. Williams
- Department of Chemistry, University of California, Irvine; Irvine, California 92697, United States
| | - Clare S. Hwang
- Department of Public Health, University of California, Irvine; Irvine, California 92697, United States
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine; Irvine, California 92697, United States
- Department of Molecular Biology & Biochemistry, University of California, Irvine; Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine; Irvine, California 92697, United States
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23
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Unravelling the diagnostic and therapeutic potentialities of a novel RNA aptamer isolated against human pituitary tumour transforming gene 1 (PTTG1) protein. Anal Chim Acta 2020; 1138:181-190. [PMID: 33161980 DOI: 10.1016/j.aca.2020.09.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/13/2020] [Accepted: 09/15/2020] [Indexed: 12/19/2022]
Abstract
Human Pituitary Tumour Transforming Gene 1 (PTTG1) is an oncoprotein involved in maintaining chromosome stability and acts as a biomarker for a panel of cancers. In this study, we endeavoured to generate an RNA aptamer against PTTG1. The RNA aptamer, SECURA-3 has an estimated equilibrium dissociation constant of 16.41 ± 6.4 nM. The aptamer was successfully harnessed in several diagnostic platforms including ELASA, aptamer-based dot blot and aptamer-based western blot. SECURA-3 was also unveiled as a potential probe that could replace its counterpart antibody in the histostaining-based detection of PTTG1 in HeLa and MCF-7 formalin-fixed paraffin-embedded cell blocks. In the aspect of therapeutics, SECURA-3 RNA aptamer demonstrates an antagonistic effect by antagonizing the interaction between PTTG1 and CXCR2, as revealed in the in vitro competitive nitrocellulose filter binding assay and dual-luciferase reporter assay in HeLa cells. As the first anti-PTTG1 aptamer, SECURA-3 RNA aptamer has immense diagnostic and therapeutic properties.
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Zambito G, Gaspar N, Ridwan Y, Hall MP, Shi C, Kirkland TA, Encell LP, Löwik C, Mezzanotte L. Evaluating Brightness and Spectral Properties of Click Beetle and Firefly Luciferases Using Luciferin Analogues: Identification of Preferred Pairings of Luciferase and Substrate for In Vivo Bioluminescence Imaging. Mol Imaging Biol 2020; 22:1523-1531. [PMID: 32926287 PMCID: PMC7666294 DOI: 10.1007/s11307-020-01523-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 11/27/2022]
Abstract
Purpose Currently, a variety of red and green beetle luciferase variants are available for bioluminescence imaging (BLI). In addition, new luciferin analogues providing longer wavelength luminescence have been developed that show promise for improved deep tissue imaging. However, a detailed assessment of these analogues (e.g., Akalumine-HCl, CycLuc1, and amino naphthyl luciferin (NH2-NpLH2)) combined with state of the art luciferases has not been performed. The aim of this study was to evaluate for the first time the in vivo brightness and spectral characteristics of firefly (Luc2), click beetle green (CBG99), click beetle red 2 (CBR2), and Akaluc luciferases when paired with different d-luciferin (d-LH2) analogues in vivo. Procedures Transduced human embryonic kidney (HEK 293T) cells expressing individual luciferases were analyzed both in vitro and in mice (via subcutaneous injection). Following introduction of the luciferins to cells or animals, the resulting bioluminescence signal and photon emission spectrum were acquired using a sensitive charge-coupled device (CCD) camera equipped with a series of band pass filters and spectral unmixing software. Results Our in vivo analysis resulted in four primary findings: (1) the best substrate for Luc2, CBG99, and CBR2 in terms of signal strength was d-luciferin; (2) the spectra for Luc2 and CBR2 were shifted to a longer wavelength when Akalumine-HCl was the substrate; (3) CBR2 gave the brightest signal with the near-infrared substrate, NH2-NpLH2; and (4) Akaluc was brighter when paired with either CycLuc1 or Akalumine-HCl when paired with d-LH2. Conclusion We believe that the experimental results described here should provide valuable guidance to end users for choosing the correct luciferin/luciferase pairs for a variety of BLI applications. Electronic supplementary material The online version of this article (10.1007/s11307-020-01523-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giorgia Zambito
- Erasmus Medical Center, Radiology and Nuclear Medicine, Rotterdam, The Netherlands
- Erasmus Medical Center, Molecular Genetics, Rotterdam, The Netherlands
- Medres medical research GmBH, Cologne, Germany
| | - Natasa Gaspar
- Erasmus Medical Center, Radiology and Nuclear Medicine, Rotterdam, The Netherlands
- Erasmus Medical Center, Molecular Genetics, Rotterdam, The Netherlands
- Percuros B.V, Leiden, The Netherlands
| | - Yanto Ridwan
- Erasmus Medical Center, Radiology and Nuclear Medicine, Rotterdam, The Netherlands
- Erasmus Medical Center, Molecular Genetics, Rotterdam, The Netherlands
| | | | - Ce Shi
- Promega Biosciences Incorporated, San Luis Obispo, CA, USA
| | | | | | - Clemens Löwik
- Erasmus Medical Center, Radiology and Nuclear Medicine, Rotterdam, The Netherlands
- Erasmus Medical Center, Molecular Genetics, Rotterdam, The Netherlands
- CHUV Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - Laura Mezzanotte
- Erasmus Medical Center, Radiology and Nuclear Medicine, Rotterdam, The Netherlands.
- Erasmus Medical Center, Molecular Genetics, Rotterdam, The Netherlands.
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Patel AM, Henley A, Parkes MA, Assmann M, Worth GA, Anderson JC, Fielding HH. Shining light on the electronic structure and relaxation dynamics of the isolated oxyluciferin anion. Phys Chem Chem Phys 2020; 22:19022-19032. [PMID: 32808948 DOI: 10.1039/d0cp03276j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Firefly bioluminescence is exploited widely in imaging in the biochemical and biomedical sciences; however, our fundamental understanding of the electronic structure and relaxation processes of the oxyluciferin that emits the light is still rudimentary. Here, we employ photoelectron spectroscopy and quantum chemistry calculations to investigate the electronic structure and relaxation of a series of model oxyluciferin anions. We find that changing the deprotonation site has a dramatic influence on the relaxation pathway following photoexcitation of higher lying electronically excited states. The keto form of the oxyluciferin anion is found to undergo internal conversion to the fluorescent S1 state, whereas we find evidence to suggest that the enol and enolate forms undergo internal conversion to a dipole bound state, possibly via the fluorescent S1 state. Partially resolved vibrational structure points towards the involvement of out-of-plane torsional motions in internal conversion to the dipole bound state, emphasising the combined electronic and structural role that the microenvironment plays in controlling the electronic relaxation pathway in the enzyme.
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Affiliation(s)
- Anand M Patel
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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26
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Ramongolalaina C. Dual-luciferase assay and siRNA silencing for nodD1 to study the competitiveness of Bradyrhizobium diazoefficiens USDA110 in soybean nodulation. Microbiol Res 2020; 237:126488. [PMID: 32408049 DOI: 10.1016/j.micres.2020.126488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/29/2020] [Accepted: 04/15/2020] [Indexed: 11/13/2022]
Abstract
The symbiosis of soybean with Bradyrhizobium diazoefficiens USDA110, which always competes with other rhizobia in the field, is of great agronomic and environmental importance. Herein, a dual-luciferase reporter assay was utilized to monitor the dynamics of two dominant bradyrhizobia infecting roots of soybean. More explicitly, luciferase-tagged B. diazoefficiens USDA110 (USDA110-FLuc) and Bradyrhizobium elkanii USDA 94 (USDA94-RLuc) were designed, co-inoculated into soybean seeds, and observed for their colonization in root nodules by bioluminescence imaging. The results showed that USDA110-FLuc initiated infection earlier than USDA94-RLuc, but its occupancy in the nodules decreased as the plant grew. A nodulation test showed that nodD1 mutant USDA110 strains, including CRISPR engineered mutants, were less competitive than wild type. I constructed siRNAs to knockdown nodD1 at different target sites and transformed them into the bacteria. Surprisingly, although siRNAs - with 3' end target sites - were able to repress up to 65% of nodD1 expression, the profiling of total RNAs with a bioanalyzer revealed that 23S/16S-rRNA ratios of siRNA-transformed and wild type USDA110 strains were similar, but lower than that of nodD1 mutant. In short, the current work - while reporting the competitiveness of B. diazoefficiens USDA110 in early occupancy of soybean nodules and the gene nodD1 as a key determinant of this infection - gives an insight on siRNA silencing in microbes, and demonstrates a highly efficient imaging approach that could entail many new avenues for many biological research fields.
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Affiliation(s)
- Clarissien Ramongolalaina
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Graduate School of Medicine, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan; Department of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Oiwake, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan.
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27
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Spillmann M, Thurner L, Romantini N, Zimmermann M, Meger B, Behe M, Waldhoer M, Schertler GFX, Berger P. New Insights into Arrestin Recruitment to GPCRs. Int J Mol Sci 2020; 21:ijms21144949. [PMID: 32668755 PMCID: PMC7404097 DOI: 10.3390/ijms21144949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 12/14/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are cellular master regulators that translate extracellular stimuli such as light, small molecules or peptides into a cellular response. Upon ligand binding, they bind intracellular proteins such as G proteins or arrestins, modulating intracellular signaling cascades. Here, we use a protein-fragment complementation approach based on nanoluciferase (split luciferase assay) to assess interaction of all four known human arrestins with four different GPCRs (two class A and two class B receptors) in live cells. Besides directly tagging the 11S split-luciferase subunit to the receptor, we also could demonstrate that membrane localization of the 11S subunit with a CAAX-tag allowed us to probe arrestin recruitment by endogenously expressed GPCRs. Varying the expression levels of our reporter constructs changed the dynamic behavior of our assay, which we addressed with an advanced baculovirus-based multigene expression system. Our detection assay allowed us to probe the relevance of each of the two arrestin binding sites in the different GPCRs for arrestin binding. We observed remarkable differences between the roles of each arresting binding site in the tested GPCRs and propose that the distinct advantages of our system for probing receptor interaction with effector proteins will help elucidate the molecular basis of GPCR signaling efficacy and specificity in different cell types.
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Affiliation(s)
- Martin Spillmann
- Paul Scherrer Institute, Laboratory of Nanoscale Biology, PSI, Forschungsstrasse 111, 5232 Villigen, Switzerland; (M.S.); (L.T.); (B.M.)
| | - Larissa Thurner
- Paul Scherrer Institute, Laboratory of Nanoscale Biology, PSI, Forschungsstrasse 111, 5232 Villigen, Switzerland; (M.S.); (L.T.); (B.M.)
| | - Nina Romantini
- Paul Scherrer Institute, Center for Radiopharmaceutical Sciences (CRS), PSI, Forschungsstrasse 111, 5232 Villigen, Switzerland; (N.R.); (M.B.)
| | - Mirjam Zimmermann
- InterAx Biotech AG, PARK innovAARE, 5234 Villigen, Switzerland; (M.Z.); (M.W.)
| | - Benoit Meger
- Paul Scherrer Institute, Laboratory of Nanoscale Biology, PSI, Forschungsstrasse 111, 5232 Villigen, Switzerland; (M.S.); (L.T.); (B.M.)
| | - Martin Behe
- Paul Scherrer Institute, Center for Radiopharmaceutical Sciences (CRS), PSI, Forschungsstrasse 111, 5232 Villigen, Switzerland; (N.R.); (M.B.)
| | - Maria Waldhoer
- InterAx Biotech AG, PARK innovAARE, 5234 Villigen, Switzerland; (M.Z.); (M.W.)
| | - Gebhard F. X. Schertler
- Paul Scherrer Institute, Division of Biology and Chemistry (BIO), PSI, Forschungsstrasse 111, 5232 Villigen, Switzerland;
| | - Philipp Berger
- Paul Scherrer Institute, Laboratory of Nanoscale Biology, PSI, Forschungsstrasse 111, 5232 Villigen, Switzerland; (M.S.); (L.T.); (B.M.)
- Correspondence: ; Tel.: +41-56-310-4728; Fax: +41-56-310-5288
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Sarrion-Perdigones A, Chang L, Gonzalez Y, Gallego-Flores T, Young DW, Venken KJT. Simultaneous Examination of Cellular Pathways using Multiplex Hextuple Luciferase Assaying. ACTA ACUST UNITED AC 2020; 131:e122. [PMID: 32539239 DOI: 10.1002/cpmb.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Multiplex experimentation that can assay multiple cellular signaling pathways in the same cells requires orthogonal genetically encoded reporters that report over large dynamic ranges. Luciferases are cost-effective, versatile candidates whose output signals can be sensitively detected in a multiplex fashion. Commonly used dual luciferase reporter assays detect one luciferase that is coupled to a single cellular pathway and a second that is coupled to a control pathway for normalization purposes. We have expanded this approach to multiplex hextuple luciferase assays that can report on five cellular signaling pathways and one control, each of which is encoded by a unique luciferase. Light emission by the six luciferases can be distinguished by the use of two distinct substrates, each specific for three luciferases, followed by spectral decomposition of the light emitted by each of the three luciferase enzymes with bandpass filters. Here, we present detailed protocols on how to perform multiplex hextuple luciferase assaying to monitor pathway fluxes through transcriptional response elements for five specific signaling pathways (i.e., c-Myc, NF-κβ, TGF-β, p53, and MAPK/JNK) using the constitutive CMV promoter as normalization control. Protocols are provided for preparing reporter vector plasmids for multiplex reporter assaying, performing cell culture and multiplex luciferase reporter vector plasmid transfection, executing multiplex luciferase assays, and analyzing and interpreting data obtained by a plate reader appropriately equipped to detect the different luminescences. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Preparation of vectors for multiplex hextuple luciferase assaying Basic Protocol 2: Cell culture work for multiplex hextuple luciferase assays Basic Protocol 3: Transfection of luciferase reporter plasmids followed by drug and recombinant protein treatments Basic Protocol 4: Performing the multiplex hextuple luciferase assay.
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Affiliation(s)
- Alejandro Sarrion-Perdigones
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Lyra Chang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas.,Center for Drug Discovery, Baylor College of Medicine, Houston, Texas
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Tatiana Gallego-Flores
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Current address: Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Damian W Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas.,Center for Drug Discovery, Baylor College of Medicine, Houston, Texas.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.,Therapeutic Innovation Center, Baylor College of Medicine, Houston, Texas
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas.,Center for Drug Discovery, Baylor College of Medicine, Houston, Texas.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.,Therapeutic Innovation Center, Baylor College of Medicine, Houston, Texas.,McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, Texas
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29
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Kitada N, Saito R, Obata R, Iwano S, Karube K, Miyawaki A, Hirano T, Maki SA. Development of near-infrared firefly luciferin analogue reacted with wild-type and mutant luciferases. Chirality 2020; 32:922-931. [PMID: 32367573 PMCID: PMC7383472 DOI: 10.1002/chir.23236] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 02/06/2023]
Abstract
Interestingly, only the D-form of firefly luciferin produces light by luciferin-luciferase (L-L) reaction. Certain firefly luciferin analogues with modified structures maintain bioluminescence (BL) activity; however, all L-form luciferin analogues show no BL activity. To this date, our group has developed luciferin analogues with moderate BL activity that produce light of various wavelengths. For in vivo bioluminescence imaging, one of the important factors for detection sensitivity is tissue permeability of the number of photons emitted by L-L reaction, and the wavelengths of light in the near-infrared (NIR) range (700-900 nm) are most appropriate for the purpose. Some NIR luciferin analogues by us had performance for in vivo experiments to make it possible to detect photons from deep target tissues in mice with high sensitivity, whereas only a few of them can produce NIR light by the L-L reactions with wild-type luciferase and/or mutant luciferase. Based on the structure-activity relationships, we designed and synthesized here a luciferin analogue with the 5-allyl-6-dimethylamino-2-naphthylethenyl moiety. This analogue exhibited NIR BL emissions with wild-type luciferase (λmax = 705 nm) and mutant luciferase AlaLuc (λmax = 655 nm).
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Affiliation(s)
- Nobuo Kitada
- Department of Engineering Science, Graduate School of Informatics and Engineering,, The University of Electro-Communications, Chofu, Japan.,Center for Neuroscience and Biomedical Engineering, The University of Electro-Communications, Chofu, Japan
| | - Ryohei Saito
- Department of Engineering Science, Graduate School of Informatics and Engineering,, The University of Electro-Communications, Chofu, Japan.,School of Pharmacy, Tokyo University of Pharmacy and Life Science, Tokyo, Japan
| | - Rika Obata
- Department of Engineering Science, Graduate School of Informatics and Engineering,, The University of Electro-Communications, Chofu, Japan
| | - Satoshi Iwano
- Laboratory for Cell Function and Dynamics, Center for Brain Science, Saitama, Japan
| | - Kazuma Karube
- Department of Engineering Science, Graduate School of Informatics and Engineering,, The University of Electro-Communications, Chofu, Japan
| | - Atsushi Miyawaki
- Laboratory for Cell Function and Dynamics, Center for Brain Science, Saitama, Japan
| | - Takashi Hirano
- Department of Engineering Science, Graduate School of Informatics and Engineering,, The University of Electro-Communications, Chofu, Japan
| | - Shojiro A Maki
- Department of Engineering Science, Graduate School of Informatics and Engineering,, The University of Electro-Communications, Chofu, Japan.,Center for Neuroscience and Biomedical Engineering, The University of Electro-Communications, Chofu, Japan
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30
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Examining multiple cellular pathways at once using multiplex hextuple luciferase assaying. Nat Commun 2019; 10:5710. [PMID: 31836712 PMCID: PMC6911020 DOI: 10.1038/s41467-019-13651-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 11/14/2019] [Indexed: 01/24/2023] Open
Abstract
Sensitive simultaneous assessment of multiple signaling pathways within the same cells requires orthogonal reporters that can assay over large dynamic ranges. Luciferases are such genetically encoded candidates due to their sensitivity, versatility, and cost-effectiveness. We expand luciferase multiplexing in post-lysis endpoint luciferase assays from two to six. Light emissions are distinguished by a combination of distinct substrates and emission spectra deconvolution. All six luciferase reporter units are stitched together into one plasmid facilitating delivery of all reporter units through a process we termed solotransfection, minimizing experimental errors. We engineer a multiplex hextuple luciferase assay to probe pathway fluxes through five transcriptional response elements against a control constitutive promoter. We can monitor effects of siRNA, ligand, and chemical compound treatments on their target pathways along with the four other probed cellular pathways. We demonstrate the effectiveness and adaptiveness of multiplex luciferase assaying, and its broad application across different research fields. Multiplexed detection of luciferase-based sensors in the same sample is challenging and limited by the substrates’ emission spectra. Here the authors establish a system based on three different luciferases and sequential detection to achieve measurements of up to six parameters within the same experiment.
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31
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Branchini BR, Fontaine DM, Southworth TL, Huta BP, Racela A, Patel KD, Gulick AM. Mutagenesis and Structural Studies Reveal the Basis for the Activity and Stability Properties That Distinguish the Photinus Luciferases scintillans and pyralis. Biochemistry 2019; 58:4293-4303. [PMID: 31560532 DOI: 10.1021/acs.biochem.9b00719] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The dazzling yellow-green light emission of the common North American firefly Photinus pyralis and other bioluminescent organisms has provided a wide variety of prominent research applications like reporter gene assays and in vivo imaging methods. While the P. pyralis enzyme has been extensively studied, only recently has a second Photinus luciferase been cloned from the species scintillans. Even though the enzymes share very high sequence identity (89.8%), the color of the light they emit, their specific activity and their stability to heat, pH, and chemical denaturation are quite different with the scintillans luciferase being generally more resistant. Through the construction and evaluation of the properties of chimeric domain swapped, single point, and various combined variants, we have determined that only six amino acid changes are necessary to confer all of the properties of the scintillans enzyme to wild-type P. pyralis luciferase. Altered stability properties were attributed to four of the amino acid changes (T214N/S276T/H332N/E354N), and single mutations each predominantly changed emission color (Y255F) and specific activity (A222C). Results of a crystallographic study of the P. pyralis enzyme containing the six changes (Pps6) provide some insight into the structural basis for some of the documented property differences.
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Affiliation(s)
- Bruce R Branchini
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Danielle M Fontaine
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Tara L Southworth
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Brian P Huta
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Allison Racela
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Ketan D Patel
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences , University at Buffalo , Buffalo , New York 14203 , United States
| | - Andrew M Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences , University at Buffalo , Buffalo , New York 14203 , United States
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32
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Saito R, Kuchimaru T, Higashi S, Lu SW, Kiyama M, Iwano S, Obata R, Hirano T, Kizaka-Kondoh S, Maki SA. Synthesis and Luminescence Properties of Near-Infrared N-Heterocyclic Luciferin Analogues for In Vivo Optical Imaging. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180350] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ryohei Saito
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
- Brain Science Inspired Life Support Research Center, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Takahiro Kuchimaru
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Shoko Higashi
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Shijia W. Lu
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Masahiro Kiyama
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Satoshi Iwano
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Rika Obata
- Research and Education Center for Natural Sciences, Keio University, 4-1-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8521, Japan
| | - Takashi Hirano
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Shinae Kizaka-Kondoh
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Shojiro A. Maki
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
- Brain Science Inspired Life Support Research Center, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
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33
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Osipova ZM, Shcheglov AS, Yampolsky IV. Bioluminescent imaging: new opportunities. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2018. [DOI: 10.24075/brsmu.2018.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Modern biomedical research technologies actively use bioimaging for studying cells, tissues and whole organisms. Multicolor bioimaging is applied when simultaneous observation of different events at the molecular and cellular level is needed. Bioluminescent imaging methods are the most sensitive, however, their use for multicolor labeling is complicated due to the insufficient number of available uciferin-luciferase pairs. Having a number of advantages compared to previously studied bioluminescent systems, the new bioluminescence systems of higher fungi and marine polychaete Odontosyllis could become a useful expansion of the bioimaging toolbox.
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Affiliation(s)
- ZM Osipova
- Biomolecular Chemistry Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow; Laboratory of Natural Compounds Chemistry, Pirogov Russian National Research Medical University, Moscow
| | - AS Shcheglov
- Biomolecular Chemistry Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow; Laboratory of Natural Compounds Chemistry, Pirogov Russian National Research Medical University, Moscow
| | - IV Yampolsky
- Biomolecular Chemistry Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow; Laboratory of Natural Compounds Chemistry, Pirogov Russian National Research Medical University, Moscow
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