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Rayhan M, Siddiquee MF, Shahriar A, Ahmed H, Mahmud AR, Alam MS, Uddin MR, Acharjee M, Shimu MSS, Shamsir MS, Emran TB. Structural characterization of a novel luciferase-like-monooxygenase from Pseudomonas meliae– an in-silico approach.. [DOI: 10.1101/2023.03.27.534437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractBackgroundLuciferase is a well-known oxidative enzyme that produces bioluminescence. ThePseudomonas meliaeis a plant pathogen that causes wood rot on nectarine and peach and possesses a luciferase-like monooxygenase. After activation, it produces bioluminescence, and the pathogen’s bioluminescence is a visual indicator of diseased plants.MethodsThe present study aims to model and characterize the luciferase-like monooxygenase protein inP. meliaefor its similarity to well-established luciferase. In this study, the luciferase-like monooxygenase fromP. meliaeinfects chinaberry plants has been modeled first and then studied by comparing it with existing known luciferase. Also, the similarities between uncharacterized luciferase fromP. meliaeand template fromGeobacillus thermodenitrificanswere analyzed to find the novelty ofP. meliae.ResultsThe results suggest that the absence of bioluminescence inP. meliaecould be due to the evolutionary mutation in positions 138 and 311. The active site remains identical except for two amino acids;P. meliaeTyr138 instead of His138 and Leu311 instead of His311. Therefore, theP. meliaewill have a potential future application, and mutation of the residues 138 and 311 can be restored luciferase light-emitting ability.ConclusionsThis study will help further improve, activate, and repurpose the luciferase fromP. meliaeas a reporter for gene expression.
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Kasembeli MM, Kaparos E, Bharadwaj U, Allaw A, Khouri A, Acot B, Tweardy DJ. Aberrant function of pathogenic STAT3 mutant proteins is linked to altered stability of monomers and homodimers. Blood 2023; 141:1411-1424. [PMID: 36240433 PMCID: PMC10651785 DOI: 10.1182/blood.2021015330] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 09/22/2022] [Accepted: 10/04/2022] [Indexed: 11/20/2022] Open
Abstract
STAT3 mutations, predominantly in the DNA-binding domain (DBD) and Src-homology 2 domain (SH2D), cause rare cases of immunodeficiency, malignancy, and autoimmunity. The exact mechanisms by which these mutations abrogate or enhance STAT3 function are not completely understood. Here, we examined how loss-of-function (LOF) and gain-of-function (GOF) STAT3 mutations within the DBD and SH2D affect monomer and homodimer protein stability as well as their effect on key STAT3 activation events, including recruitment to phosphotyrosine (pY) sites within peptide hormone receptors, tyrosine phosphorylation at Y705, dimerization, nuclear translocation, and DNA binding. The DBD LOF mutants showed reduced DNA binding when homodimerized, whereas the DBD GOF mutants showed increased DNA binding. DBD LOF and GOF mutants showed minimal changes in other STAT3 functions or in monomer or homodimer protein stability. However, SH2D LOF mutants demonstrated reduced conformational stability as either monomers or homodimers, leading to decreased pY-peptide recruitment, tyrosine phosphorylation, dimerization, nuclear localization, and DNA binding. In contrast, cancer-causing SH2D GOF mutants showed increased STAT3 homodimer stability, which increased their DNA binding. Of note, a small-molecule inhibitor of STAT3 that targets the tyrosine phosphopeptide-binding pocket within the STAT3 SH2D potently inhibited cell proliferation driven by STAT3 SH2D GOF mutants. These findings indicate that the stability of STAT3 protein monomer and homodimer is critical for the pathogenesis of diseases caused by SH2D LOF and GOF mutations and suggest that agents that modulate STAT3 monomer and/or homodimer protein stability may have therapeutic value in diseases caused by these mutations.
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Affiliation(s)
- Moses M. Kasembeli
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Efiyenia Kaparos
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Uddalak Bharadwaj
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ahmad Allaw
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alain Khouri
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bianca Acot
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David J. Tweardy
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
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103
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Meng L, Cao X, Li C, Li J, Xie H, Shi J, Han M, Shen H, Liu C. Housekeeping gene stability in Pesudomonas aeruginosa PAO1 under the pressure of commonly used antibiotics in molecular microbiology assays. Front Microbiol 2023; 14:1140515. [PMID: 36992935 PMCID: PMC10040570 DOI: 10.3389/fmicb.2023.1140515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/14/2023] [Indexed: 03/16/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen notorious for its remarkable capacity of multi-drug resistance, and has become one of the most important model bacteria in clinical bacteriology research. Quantitative real-time PCR is a reliable method widely used in gene expression analysis, for which the selection of a set of appropriate housekeeping genes is a key prerequisite for the accuracy of the results. However, it is easy to overlook that the expression level of housekeeping gene may vary in different conditions, especially in the condition of molecular microbiology assays, where tested strains are generally cultured under the pre-set antibiotic selection pressures, and how this affects the stability of commonly used housekeeping genes remains unclear. In this study, the expression stability of ten classic housekeeping genes (algD, gyrA, anr, nadB, recA, fabD, proC, ampC, rpoS, and rpsL) under the pressure of eight laboratory commonly used antibiotics (kanamycin, gentamycin, tetracycline, chloramphenicol, hygromycin B, apramycin, tellurite, and zeocin) were tested. Results showed that the stability of housekeeping gene expression was indeed affected by the types of antibiotics added, and of course the best reference gene set varied for different antibiotics. This study provides a comprehensive summary of the effects of laboratory antibiotics on the stability of housekeeping genes in P. aeruginosa, highlighting the necessity to select housekeeping genes according to the type of antibiotics used in the initial stage of experiment.
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Affiliation(s)
- Lingning Meng
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Xiaoli Cao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Chuchu Li
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jia Li
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Hui Xie
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Jiping Shi
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Mei Han
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
- Han Shen,
| | - Chang Liu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
- *Correspondence: Chang Liu,
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Mano H, Kushioka T, Kise S, Nagao C, Iijima A, Nishikawa M, Ikushiro S, Yasuda K, Matsuoka S, Sakaki T. Development of nanoluciferase-based sensing system that can specifically detect 1α,25-dihydroxyvitamin D in living cells. J Steroid Biochem Mol Biol 2023; 227:106233. [PMID: 36503079 DOI: 10.1016/j.jsbmb.2022.106233] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/01/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Previously, we reported a FLucN-LXXLL+LBD-FLucC system that detects VDR ligands using split firefly luciferase techniques, ligand binding domain (LBD) of VDR, and LXXLL sequences that interact with LBD after VDR ligand binding. In vivo, 25-hydroxyvitamin D3 (25(OH)D3) and 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3) act as VDR ligands that bind to VDR, and regulate bone-related gene expression. Therefore, the amount of 25(OH)D3 and 1α,25(OH)2D3 are indicators of bone-related diseases such as rickets and osteoporosis. In this study, we have developed a novel LgBiT-LXXLL+LBD-SmBiT system using NanoLuc Binary Technology (NanoBiT), which has an emission intensity several times higher than that of the split-type firefly luciferase. Furthermore, by using genetic engineering techniques, we attempted to construct a novel system that can specifically detect 1α,25(OH)2D3. Because histidine residues at positions 305 and 397 play important roles in forming a hydrogen bond with a hydroxyl group at position C25 of 25(OH)D3 and 1α,25(OH)2D3, His305 and His397 were each substituted by other amino acids. Consequently, the three mutant VDRs, H305D, H397N, and H397E were equally useful to detect 1α,25(OH)2D3 specifically. In addition, among the 58 variants of the LXXLL sequences, LPYEGSLLLKLLRAPVEE showed the greatest increase in luminescence upon the addition of 25(OH)D3 or 1α,25(OH)2D3. Thus, our novel system using NanoBiT appear to be useful for detecting native vitamin D or its derivatives.
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Affiliation(s)
- Hiroki Mano
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Takuya Kushioka
- FANCL Research Institute, FANCL Corporation, 12-13 Kamishinano, Totsuka, Yokohama, Kanagawa 244-0806, Japan
| | - Satoko Kise
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Chika Nagao
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Ayano Iijima
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Miyu Nishikawa
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Shinichi Ikushiro
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Kaori Yasuda
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Sayuri Matsuoka
- FANCL Research Institute, FANCL Corporation, 12-13 Kamishinano, Totsuka, Yokohama, Kanagawa 244-0806, Japan
| | - Toshiyuki Sakaki
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
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Khambhati K, Bhattacharjee G, Gohil N, Dhanoa GK, Sagona AP, Mani I, Bui NL, Chu D, Karapurkar JK, Jang SH, Chung HY, Maurya R, Alzahrani KJ, Ramakrishna S, Singh V. Phage engineering and phage-assisted CRISPR-Cas delivery to combat multidrug-resistant pathogens. Bioeng Transl Med 2023; 8:e10381. [PMID: 36925687 PMCID: PMC10013820 DOI: 10.1002/btm2.10381] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/30/2022] [Accepted: 07/16/2022] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance ranks among the top threats to humanity. Due to the frequent use of antibiotics, society is facing a high prevalence of multidrug resistant pathogens, which have managed to evolve mechanisms that help them evade the last line of therapeutics. An alternative to antibiotics could involve the use of bacteriophages (phages), which are the natural predators of bacterial cells. In earlier times, phages were implemented as therapeutic agents for a century but were mainly replaced with antibiotics, and considering the menace of antimicrobial resistance, it might again become of interest due to the increasing threat of antibiotic resistance among pathogens. The current understanding of phage biology and clustered regularly interspaced short palindromic repeats (CRISPR) assisted phage genome engineering techniques have facilitated to generate phage variants with unique therapeutic values. In this review, we briefly explain strategies to engineer bacteriophages. Next, we highlight the literature supporting CRISPR-Cas9-assisted phage engineering for effective and more specific targeting of bacterial pathogens. Lastly, we discuss techniques that either help to increase the fitness, specificity, or lytic ability of bacteriophages to control an infection.
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Affiliation(s)
- Khushal Khambhati
- Department of Biosciences, School of ScienceIndrashil UniversityRajpurMehsanaGujaratIndia
| | - Gargi Bhattacharjee
- Department of Biosciences, School of ScienceIndrashil UniversityRajpurMehsanaGujaratIndia
| | - Nisarg Gohil
- Department of Biosciences, School of ScienceIndrashil UniversityRajpurMehsanaGujaratIndia
| | - Gurneet K. Dhanoa
- School of Life SciencesUniversity of Warwick, Gibbet Hill CampusCoventryUnited Kindgom
| | - Antonia P. Sagona
- School of Life SciencesUniversity of Warwick, Gibbet Hill CampusCoventryUnited Kindgom
| | - Indra Mani
- Department of MicrobiologyGargi College, University of DelhiNew DelhiIndia
| | - Nhat Le Bui
- Center for Biomedicine and Community HealthInternational School, Vietnam National UniversityHanoiVietnam
| | - Dinh‐Toi Chu
- Center for Biomedicine and Community HealthInternational School, Vietnam National UniversityHanoiVietnam
- Faculty of Applied SciencesInternational School, Vietnam National UniversityHanoiVietnam
| | | | - Su Hwa Jang
- Graduate School of Biomedical Science and EngineeringHanyang UniversitySeoulSouth Korea
- Hanyang Biomedical Research InstituteHanyang UniversitySeoulSouth Korea
| | - Hee Yong Chung
- Graduate School of Biomedical Science and EngineeringHanyang UniversitySeoulSouth Korea
- Hanyang Biomedical Research InstituteHanyang UniversitySeoulSouth Korea
- College of MedicineHanyang UniversitySeoulSouth Korea
| | - Rupesh Maurya
- Department of Biosciences, School of ScienceIndrashil UniversityRajpurMehsanaGujaratIndia
| | - Khalid J. Alzahrani
- Department of Clinical Laboratories SciencesCollege of Applied Medical Sciences, Taif UniversityTaifSaudi Arabia
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and EngineeringHanyang UniversitySeoulSouth Korea
- College of MedicineHanyang UniversitySeoulSouth Korea
| | - Vijai Singh
- Department of Biosciences, School of ScienceIndrashil UniversityRajpurMehsanaGujaratIndia
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106
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van Solinge TS, Mahjoum S, Ughetto S, Sammarco A, Broekman ML, Breakefield XO, O’Brien KP. Illuminating cellular and extracellular vesicle-mediated communication via a split-Nanoluc reporter in vitro and in vivo. CELL REPORTS METHODS 2023; 3:100412. [PMID: 36936071 PMCID: PMC10014296 DOI: 10.1016/j.crmeth.2023.100412] [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: 03/30/2022] [Revised: 09/01/2022] [Accepted: 01/30/2023] [Indexed: 02/25/2023]
Abstract
Tools to effectively demonstrate and quantify functional delivery in cellular communication have been lacking. This study reports the use of a fluorescently labeled split Nanoluc reporter system to demonstrate and quantify functional transfer between cells in vitro and in a subcutaneous tumor mouse model. Our construct allows monitoring of direct, indirect, and specifically extracellular vesicle-mediated functional communication.
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Affiliation(s)
- Thomas S. van Solinge
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Neurosurgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Shadi Mahjoum
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stefano Ughetto
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Oncology, University of Turin, Candiolo, Italy
| | - Alessandro Sammarco
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Italy
| | - Marike L.D. Broekman
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Neurosurgery, Leiden University Medical Center, Leiden, the Netherlands
- Department of Neurosurgery, Haaglanden Medical Center, The Hague, the Netherlands
| | - Xandra O. Breakefield
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Killian P. O’Brien
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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107
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Braun P, Raab R, Bugert JJ, Braun S. Recombinant Reporter Phage rTUN1:: nLuc Enables Rapid Detection and Real-Time Antibiotic Susceptibility Testing of Klebsiella pneumoniae K64 Strains. ACS Sens 2023; 8:630-639. [PMID: 36719711 PMCID: PMC9972469 DOI: 10.1021/acssensors.2c01822] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/09/2023] [Indexed: 02/01/2023]
Abstract
The emergence of multi-drug-resistant Klebsiella pneumoniae (Kp) strains constitutes an enormous threat to global health as multi-drug resistance-associated treatment failure causes high mortality rates in nosocomial infections. Rapid pathogen detection and antibiotic resistance screening are therefore crucial for successful therapy and thus patient survival. Reporter phage-based diagnostics offer a way to speed up pathogen identification and resistance testing as integration of reporter genes into highly specific phages allows real-time detection of phage replication and thus living host cells. Kp-specific phages use the host's capsule, a major virulence factor of Kp, as a receptor for adsorption. To date, 80 different Kp capsule types (K-serotypes) have been described with predominant capsule types varying between different countries and continents. Therefore, reporter phages need to be customized according to the locally prevailing variants. Recently, we described the autographivirus vB_KpP_TUN1 (TUN1), which specifically infects Kp K64 strains, the most predominant capsule type at the military hospital in Tunis (MHT) that is also associated with high mortality rates. In this work, we developed the highly specific recombinant reporter phage rTUN1::nLuc, which produces nanoluciferase (nLuc) upon host infection and thus enables rapid detection of Kp K64 cells in clinical matrices such as blood and urine. At the same time, rTUN1::nLuc allows for rapid antibiotic susceptibility testing and therefore identification of suitable antibiotic treatment in less than 3 h.
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Affiliation(s)
- Peter Braun
- Bundeswehr Institute of
Microbiology, 80937Munich, Germany
| | - Rene Raab
- Bundeswehr Institute of
Microbiology, 80937Munich, Germany
| | | | - Simone Braun
- Bundeswehr Institute of
Microbiology, 80937Munich, Germany
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108
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Kang YS, Kirby JE. A Versatile Nanoluciferase Reporter Reveals Structural Properties Associated with a Highly Efficient, N-Terminal Legionella pneumophila Type IV Secretion Translocation Signal. Microbiol Spectr 2023; 11:e0233822. [PMID: 36815834 PMCID: PMC10100965 DOI: 10.1128/spectrum.02338-22] [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] [Received: 12/06/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
Many Gram-negative pathogens rely on type IV secretion systems (T4SS) for infection. One limitation has been the lack of ideal reporters to identify T4SS translocated effectors and study T4SS function. Most reporter systems make use of fusions to reporter proteins, in particular, β-lactamase (TEM) and calmodulin-dependent adenylate cyclase (CYA), that allow detection of translocated enzymatic activity inside host cells. However, both systems require costly reagents and use complex, multistep procedures for loading host cells with substrate (TEM) or for analysis (CYA). Therefore, we have developed and characterized a novel reporter system using nanoluciferase (NLuc) fusions to address these limitations. Serendipitously, we discovered that Nluc itself is efficiently translocated by Legionella pneumophila T4SS in an IcmSW chaperone-dependent manner via an N-terminal translocation signal. Extensive mutagenesis in the NLuc N terminus suggested the importance of an α-helical domain spanning D5 to V9, as mutations predicted to disrupt this structure, with one exception, were translocation defective. Notably, NLuc was capable of translocating several proteins examined when fused to the N or C terminus, while maintaining robust luciferase activity. In particular, it delivered the split GFP11 fragment into J774 macrophages transfected with GFPopt, thereby resulting in in vivo assembly of superfolder green fluorescent protein (GFP). This provided a bifunctional assay in which translocation could be assayed by fluorescence microplate, confocal microscopy, and/or luciferase assays. We further identified an optimal NLuc substrate which allowed a robust, inexpensive, one-step, high-throughput screening assay to identify T4SS translocation substrates and inhibitors. Taken together, these results indicate that NLuc provides both new insight into and also tools for studying T4SS biology. IMPORTANCE Type IV secretion systems (T4SS) are used by Gram-negative pathogens to coopt host cell function. However, the translocation signals recognized by T4SS are not fully explained by primary amino acid sequence, suggesting yet-to-be-defined contributions of secondary and tertiary structure. Here, we unexpectedly identified nanoluciferase (NLuc) as an efficient IcmSW-dependent translocated T4SS substrate, and we provide extensive mutagenesis data suggesting that the first N-terminal, alpha-helix domain is a critical translocation recognition motif. Notably, most existing reporter systems for studying translocated proteins make use of fusions to reporters to permit detection of translocated enzymatic activity inside the host cell. However, existing systems require extremely costly substrates, complex technical procedures to isolate eukaryotic cytoplasm for analysis, and/or are insensitive. Importantly, we found that NLuc provides a powerful, cost-effective new tool to address these limitations and facilitate high-throughput exploration of secretion system biology.
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Affiliation(s)
- Yoon-Suk Kang
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - James E. Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
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Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
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110
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Rasor BJ, Chirania P, Rybnicky GA, Giannone RJ, Engle NL, Tschaplinski TJ, Karim AS, Hettich RL, Jewett MC. Mechanistic Insights into Cell-Free Gene Expression through an Integrated -Omics Analysis of Extract Processing Methods. ACS Synth Biol 2023; 12:405-418. [PMID: 36700560 DOI: 10.1021/acssynbio.2c00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cell-free systems derived from crude cell extracts have developed into tools for gene expression, with applications in prototyping, biosensing, and protein production. Key to the development of these systems is optimization of cell extract preparation methods. However, the applied nature of these optimizations often limits investigation into the complex nature of the extracts themselves, which contain thousands of proteins and reaction networks with hundreds of metabolites. Here, we sought to uncover the black box of proteins and metabolites in Escherichia coli cell-free reactions based on different extract preparation methods. We assess changes in transcription and translation activity from σ70 promoters in extracts prepared with acetate or glutamate buffer and the common post-lysis processing steps of a runoff incubation and dialysis. We then utilize proteomic and metabolomic analyses to uncover potential mechanisms behind these changes in gene expression, highlighting the impact of cold shock-like proteins and the role of buffer composition.
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Affiliation(s)
- Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Payal Chirania
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Grant A Rybnicky
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard J Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, United States.,Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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111
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Practical Guidance for Developing Small-Molecule Optical Probes for In Vivo Imaging. Mol Imaging Biol 2023; 25:240-264. [PMID: 36745354 DOI: 10.1007/s11307-023-01800-1] [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: 08/23/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 02/07/2023]
Abstract
The WMIS Education Committee (2019-2022) reached a consensus that white papers on molecular imaging could be beneficial for practitioners of molecular imaging at their early career stages and other scientists who are interested in molecular imaging. With this consensus, the committee plans to publish a series of white papers on topics related to the daily practice of molecular imaging. In this white paper, we aim to provide practical guidance that could be helpful for optical molecular imaging, particularly for small molecule probe development and validation in vitro and in vivo. The focus of this paper is preclinical animal studies with small-molecule optical probes. Near-infrared fluorescence imaging, bioluminescence imaging, chemiluminescence imaging, image-guided surgery, and Cerenkov luminescence imaging are discussed in this white paper.
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112
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Burström V, Ågren R, Betari N, Valle-León M, Garro-Martínez E, Ciruela F, Sahlholm K. Dopamine-induced arrestin recruitment and desensitization of the dopamine D4 receptor is regulated by G protein-coupled receptor kinase-2. Front Pharmacol 2023; 14:1087171. [PMID: 36778010 PMCID: PMC9911804 DOI: 10.3389/fphar.2023.1087171] [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: 11/02/2022] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
The dopamine D4 receptor (D4R) is expressed in the retina, prefrontal cortex, and autonomic nervous system and has been implicated in attention deficit hyperactivity disorder (ADHD), substance use disorders, and erectile dysfunction. D4R has also been investigated as a target for antipsychotics due to its high affinity for clozapine. As opposed to the closely related dopamine D2 receptor (D2R), dopamine-induced arrestin recruitment and desensitization at the D4R have not been studied in detail. Indeed, some earlier investigations could not detect arrestin recruitment and desensitization of this receptor upon its activation by agonist. Here, we used a novel nanoluciferase complementation assay to study dopamine-induced recruitment of β-arrestin2 (βarr2; also known as arrestin3) and G protein-coupled receptor kinase-2 (GRK2) to the D4R in HEK293T cells. We also studied desensitization of D4R-evoked G protein-coupled inward rectifier potassium (GIRK; also known as Kir3) current responses in Xenopus oocytes. Furthermore, the effect of coexpression of GRK2 on βarr2 recruitment and GIRK response desensitization was examined. The results suggest that coexpression of GRK2 enhanced the potency of dopamine to induce βarr2 recruitment to the D4R and accelerated the rate of desensitization of D4R-evoked GIRK responses. The present study reveals new details about the regulation of arrestin recruitment to the D4R and thus increases our understanding of the signaling and desensitization of this receptor.
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Affiliation(s)
- Viktor Burström
- Department of Integrative Medical Biology, Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Richard Ågren
- Department of Neuroscience, Karolinska Institutet, Solna, Sweden
| | - Nibal Betari
- Department of Integrative Medical Biology, Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Marta Valle-León
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain,Neuropharmacology and Pain Group, Neuroscience Program, Institut d'Investigació Biomèdica de Bellvitge, IDIBELL, Barcelona, Spain
| | - Emilio Garro-Martínez
- Department of Integrative Medical Biology, Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Francisco Ciruela
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain,Neuropharmacology and Pain Group, Neuroscience Program, Institut d'Investigació Biomèdica de Bellvitge, IDIBELL, Barcelona, Spain
| | - Kristoffer Sahlholm
- Department of Integrative Medical Biology, Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden,Department of Neuroscience, Karolinska Institutet, Solna, Sweden,Pharmacology Unit, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain,Neuropharmacology and Pain Group, Neuroscience Program, Institut d'Investigació Biomèdica de Bellvitge, IDIBELL, Barcelona, Spain,*Correspondence: Kristoffer Sahlholm,
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113
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Mi L, Yu Q, Mudiyanselage APK, Wu R, Sun Z, Zheng R, Ren K, You M. Genetically Encoded RNA-Based Bioluminescence Resonance Energy Transfer (BRET) Sensors. ACS Sens 2023; 8:308-316. [PMID: 36608281 PMCID: PMC10630924 DOI: 10.1021/acssensors.2c02213] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
RNA-based nanostructures and molecular devices have become popular for developing biosensors and genetic regulators. These programmable RNA nanodevices can be genetically encoded and modularly engineered to detect various cellular targets and then induce output signals, most often a fluorescence readout. Although powerful, the high reliance of fluorescence on the external excitation light raises concerns about its high background, photobleaching, and phototoxicity. Bioluminescence signals can be an ideal complementary readout for these genetically encoded RNA nanodevices. However, RNA-based real-time bioluminescent reporters have been rarely developed. In this study, we reported the first type of genetically encoded RNA-based bioluminescence resonance energy transfer (BRET) sensors that can be used for real-time target detection in living cells. By coupling a luciferase bioluminescence donor with a fluorogenic RNA-based acceptor, our BRET system can be modularly designed to image and detect various cellular analytes. We expect that this novel RNA-based bioluminescent system can be potentially used broadly in bioanalysis and nanomedicine for engineering biosensors, characterizing cellular RNA-protein interactions, and high-throughput screening or in vivo imaging.
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Affiliation(s)
- Lan Mi
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | | | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Zhining Sun
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Ru Zheng
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA 01003, USA
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114
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Wu S, Hernandez Villegas NC, Sirkis DW, Thomas-Wright I, Wade-Martins R, Schekman R. Unconventional secretion of α-synuclein mediated by palmitoylated DNAJC5 oligomers. eLife 2023; 12:e85837. [PMID: 36626307 PMCID: PMC9876576 DOI: 10.7554/elife.85837] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Alpha-synuclein (α-syn), a major component of Lewy bodies found in Parkinson's disease (PD) patients, has been found exported outside of cells and may mediate its toxicity via cell-to-cell transmission. Here, we reconstituted soluble, monomeric α-syn secretion by the expression of DnaJ homolog subfamily C member 5 (DNAJC5) in HEK293T cells. DNAJC5 undergoes palmitoylation and anchors on the membrane. Palmitoylation is essential for DNAJC5-induced α-syn secretion, and the secretion is not limited by substrate size or unfolding. Cytosolic α-syn is actively translocated and sequestered in an endosomal membrane compartment in a DNAJC5-dependent manner. Reduction of α-syn secretion caused by a palmitoylation-deficient mutation in DNAJC5 can be reversed by a membrane-targeting peptide fusion-induced oligomerization of DNAJC5. The secretion of endogenous α-syn mediated by DNAJC5 is also found in a human neuroblastoma cell line, SH-SY5Y, differentiated into neurons in the presence of retinoic acid, and in human-induced pluripotent stem cell-derived midbrain dopamine neurons. We propose that DNAJC5 forms a palmitoylated oligomer to accommodate and export α-syn.
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Affiliation(s)
- Shenjie Wu
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | | | - Daniel W Sirkis
- Memory and Aging Center, Department of Neurology, University of California, San FranciscoSan FranciscoUnited States
| | - Iona Thomas-Wright
- Oxford Parkinson’s Disease Centre, Department of Physiology, Anatomy and Genetics and Kavli Institute for Nanoscience Discovery, University of OxfordOxfordUnited Kingdom
| | - Richard Wade-Martins
- Oxford Parkinson’s Disease Centre, Department of Physiology, Anatomy and Genetics and Kavli Institute for Nanoscience Discovery, University of OxfordOxfordUnited Kingdom
| | - Randy Schekman
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
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115
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Baljinnyam B, Ronzetti M, Simeonov A. Advances in luminescence-based technologies for drug discovery. Expert Opin Drug Discov 2023; 18:25-35. [PMID: 36562206 PMCID: PMC9892298 DOI: 10.1080/17460441.2023.2160441] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Luminescence-based technologies, specifically bioluminescence and chemiluminescence, are powerful tools with extensive use in drug discovery. Production of light during chemiluminescence and bioluminescence, unlike fluorescence, doesn't require an excitation light source, resulting in high signal-to-noise ratio, less background interference, and no issues from phototoxicity and photobleaching. These characteristics of luminescence technologies offer unique advantages for experimental designs, allowing for greater flexibility to target a wide range of proteins and biological processes for drug discovery at different stages. AREAS COVERED This review provides a basic overview of luciferase-based technologies and details recent advances and use cases of luciferase and luciferin variations and their applicability in the drug discovery toolset. The authors expand upon specific applications of luciferase technologies, including chemiluminescent and bioluminescent-based microscopy. Finally, the authors lay out forward-looking statements on the field of luminescence and how it may shape the translational scientists' work moving forward. EXPERT OPINION The demand for improved luciferase and luciferin pairs correlates strongly with efforts to improve the sensitivity and robustness of high-throughput assays. As luminescent reporter systems improve, so will the expansion of use cases for luminescence-based technologies in early-stage drug discovery. With the synthesis of novel, non-enzymatic chemiluminescence-based probes, which previously were restrained to only basic research applications, they may now be readily implemented in drug discovery campaigns.
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Affiliation(s)
- Bolormaa Baljinnyam
- Staff Scientist, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Michael Ronzetti
- Predoctoral IRTA Fellow, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Anton Simeonov
- Group Leader, Scientific Director, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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116
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Patterson AT, Styczynski MP. Rapid and Finely-Tuned Expression for Deployable Sensing Applications. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:141-161. [PMID: 37316621 DOI: 10.1007/10_2023_223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Organisms from across the tree of life have evolved highly efficient mechanisms for sensing molecules of interest using biomolecular machinery that can in turn be quite valuable for the development of biosensors. However, purification of such machinery for use in in vitro biosensors is costly, while the use of whole cells as in vivo biosensors often leads to long sensor response times and unacceptable sensitivity to the chemical makeup of the sample. Cell-free expression systems overcome these weaknesses by removing the requirements associated with maintaining living sensor cells, allowing for increased function in toxic environments and rapid sensor readout at a production cost that is often more reasonable than purification. Here, we focus on the challenge of implementing cell-free protein expression systems that meet the stringent criteria required for them to serve as the basis for field-deployable biosensors. Fine-tuning expression to meet these requirements can be achieved through careful selection of the sensing and output elements, as well as through optimization of reaction conditions via tuning of DNA/RNA concentrations, lysate preparation methods, and buffer conditions. Through careful sensor engineering, cell-free systems can continue to be successfully used for the production of tightly regulated, rapidly expressing genetic circuits for biosensors.
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Affiliation(s)
- Alexandra T Patterson
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mark P Styczynski
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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117
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Silva BSC, Schrader TA, Schrader M, Carmichael RE. Generation of Reporter Cell Lines for Endogenous Expression Analysis of Peroxisomal Proteins. Methods Mol Biol 2023; 2643:247-270. [PMID: 36952191 DOI: 10.1007/978-1-0716-3048-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Peroxisomes are multifunctional, ubiquitous, and dynamic organelles. They are responsible for diverse metabolic and physiological functions and communicate with other organelles, including the ER, mitochondria, lipid droplets, and lysosomes, through membrane contact sites. However, despite their importance for healthy cell function, remarkably, little is known about how peroxisomes and peroxisomal proteins are regulated under physiological conditions in human cells. Here, we present a method to generate reporter cell lines to measure endogenous expression of peroxisomal proteins of interest. By CRISPR-mediated knock-in of an easily detectable protein-coding tag in-frame into the relevant genomic loci, endogenous levels of the protein of interest in a cell population can be quantified in a high-throughput manner under different conditions. This has important implications for the fundamental understanding of how peroxisomal proteins are regulated and may reveal the therapeutic potential of modulating peroxisomal protein expression to improve cell performance.
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Affiliation(s)
- Beatriz S C Silva
- Faculty of Health and Life Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Tina A Schrader
- Faculty of Health and Life Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Michael Schrader
- Faculty of Health and Life Sciences, Biosciences, University of Exeter, Exeter, UK.
| | - Ruth E Carmichael
- Faculty of Health and Life Sciences, Biosciences, University of Exeter, Exeter, UK.
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118
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Becerra-García RE, Cruz-Valderrama JE, Cerbantez-Bueno VE, Marsch-Martínez N, de Folter S. A NanoLuc-Based Transactivation Assay in Plants. Methods Mol Biol 2023; 2686:553-565. [PMID: 37540377 DOI: 10.1007/978-1-0716-3299-4_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Protein-DNA interactions are determinant of the regulation of gene expression in living organisms. Luminescence studies have been used in a wide range of techniques to identify how gene transcription can be regulated by proteins such as transcription factors (TFs). Despite the great advances in the use of luciferases as reporters in the performance of this mechanism, some of them still have disadvantages that have been tried to be solved by the generation of new luciferases that induce a more stable and perfectly visualizable reaction. NanoLuc is a recently described luciferase that has been characterized by its efficient, stable, and powerful luminescence. These qualities have been considered to create a new and efficient reporter system to detect protein-DNA interactions. In this chapter, we take advantage of NanoLuc and describe its use in a reliable procedure to detect protein-DNA interactions in Nicotiana benthamiana extracts and entire leaves.
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Affiliation(s)
- Rosa Esmeralda Becerra-García
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - José Erik Cruz-Valderrama
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Vincent E Cerbantez-Bueno
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico.
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119
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Singh VA, Kumar CS, Khare B, Kuhn RJ, Banerjee M, Tomar S. Surface decorated reporter-tagged chikungunya virus-like particles for clinical diagnostics and identification of virus entry inhibitors. Virology 2023; 578:92-102. [PMID: 36473281 DOI: 10.1016/j.virol.2022.11.012] [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: 10/29/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
The ever-evolving and versatile VLP technology is becoming an increasingly popular area of science. This study presents surface decorated reporter-tagged VLPs of CHIKV, an enveloped RNA virus of the genus alphavirus and its applications. Western blot, IFA and live-cell imaging confirm the expression of reporter-tagged CHIK-VLPs from transfected HEK293Ts. CryoEM micrographs reveal particle diameter as ∼67nm and 56-70 nm, respectively, for NLuc CHIK-VLPs and mCherry CHIK-VLPs. Our study demonstrates that by exploiting NLuc CHIK-VLPs as a detector probe, robust ratiometric luminescence signal in CHIKV-positive sera compared to healthy controls can be achieved swiftly. Moreover, the potential activity of the Suramin drug as a CHIKV entry inhibitor has been validated through the reporter-tagged CHIK-VLPs. The results reported in this study open new avenues in the eVLPs domain and offer potential for large-scale screening of clinical samples and antiviral agents targeting entry of CHIKV and other alphaviruses.
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Affiliation(s)
- Vedita Anand Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India; Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Chandra Shekhar Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology - Delhi, Hauz Khas, New Delhi, 110016, India
| | - Baldeep Khare
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology - Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
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120
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Wandishin CM, Robbins CJ, Tyson DR, Harris LA, Quaranta V. Real-time luminescence enables continuous drug-response analysis in adherent and suspension cell lines. Cancer Biol Ther 2022; 23:358-368. [PMID: 35443861 PMCID: PMC9037430 DOI: 10.1080/15384047.2022.2065182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/30/2022] [Accepted: 04/04/2022] [Indexed: 11/11/2022] Open
Abstract
The drug-induced proliferation (DIP) rate is a metric of in vitro drug response that avoids inherent biases in commonly used metrics such as 72 h viability. However, DIP rate measurements rely on direct cell counting over time, a laborious task that is subject to numerous challenges, including the need to fluorescently label cells and automatically segment nuclei. Moreover, it is incredibly difficult to directly count cells and accurately measure DIP rates for cell populations in suspension. As an alternative, we use real-time luminescence measurements derived from the cellular activity of NAD(P)H oxidoreductase to efficiently estimate drug response in both adherent and suspension cell populations to a panel of known anticancer agents. For the adherent cell lines, we collect both luminescence reads and direct cell counts over time simultaneously to assess their congruency. Our results demonstrate that the proposed approach significantly speeds up data collection, avoids the need for cellular labels and image segmentation, and opens the door to significant advances in high-throughput screening of anticancer drugs.
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Affiliation(s)
| | - Charles John Robbins
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TNUSA
| | - Darren R. Tyson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TNUSA
| | - Leonard A. Harris
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, ARUSA
| | - Vito Quaranta
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TNUSA
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121
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Nakanishi A, Yamamoto N, Sakihama Y, Okino T, Matoba N. Development of Targeted Protein-Displaying Technology with a Novel Carbon Material. BIOTECH (BASEL (SWITZERLAND)) 2022; 12:biotech12010002. [PMID: 36648828 PMCID: PMC9844296 DOI: 10.3390/biotech12010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
This study reports a new carbon material and its specific display of targeted protein. The properties of the carbon materials fabricated with carbon black MOGUL® were analyzed. The carbon materials were spherical structures with 55.421 µm as a median value. The specific surface area, pore volume, average pore diameter, and total of the acidic functional group were 130 m2·g-1, 0.55 cm3·g-1, 17.2 nm, and 0.29 mEq·g-1, respectively. The adsorption-desorption isoform of the carbon materials showed type IV of the hysteresis loop as defined by IUPAC, indicating non-uniform mesoporous structures (2-50 nm). The distribution of the log differential pore volume also indicated non-uniform porous structures because (i) the difference between the average pore size and the most frequent pore size was significant and (ii) the σ value was larger than the average value regarding the pore sizes. However, 10-90% of the integrated values of the log differential pore volume were 57.4% of the total integrated values, and the distribution was similar to the Gauss distribution model. Although the value of the total of the acidic functional group was 2.5-5.4 times lower than the values of the HPLC columns, the carbon materials require good scaffold quality rather than good HPLC quality. Therefore, the amounts could be enough for the scaffold of biotin hydrazide. To demonstrate the property of displaying the targeted proteins, carbon materials displaying biotin hydrazide by covalent bonding were prepared and avidin-labeled horse radish peroxidase (HRP) was bound to the biotin region. The carbon materials were porous structures, so the unspecific adsorption of HRP was estimated. Then, the maintenance ratios of HRP activities were analyzed in the repeated-use-with-wash processes after each evaluation, resulting in the activities of HRP on the carbon materials being treated with biotin hydrazide being significantly maintained compared to that of the ones without biotin hydrazide. The study revealed the properties of the carbon materials and indicated the display of HRP, suggesting that the carbon materials could be a new material for displaying targeted proteins.
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Affiliation(s)
- Akihito Nakanishi
- Graduate School of Bionics, Tokyo University of Technology, Tokyo 192-0982, Japan
- School of Bioscience and Biotechnology, Tokyo University of Technology, Tokyo 192-0982, Japan
- Correspondence:
| | - Naotaka Yamamoto
- Graduate School of Bionics, Tokyo University of Technology, Tokyo 192-0982, Japan
| | - Yuri Sakihama
- College of Science and Engineering, Aoyama Gakuin University, Sagamihara 252-5258, Japan
| | - Tomoya Okino
- Kansai Coke & Chemicals Co., Ltd., Amagasaki 661-0976, Japan
| | - Naoki Matoba
- Kansai Coke & Chemicals Co., Ltd., Amagasaki 661-0976, Japan
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122
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Apostolidou D, Zhang P, Yang W, Marszalek PE. Mechanical Unfolding and Refolding of NanoLuc via Single-Molecule Force Spectroscopy and Computer Simulations. Biomacromolecules 2022; 23:5164-5178. [PMID: 36350253 DOI: 10.1021/acs.biomac.2c00997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A highly bioluminescent protein, NanoLuc (Nluc), has seen numerous applications in biological assays since its creation. We recently engineered a NanoLuc polyprotein that showed high bioluminescence but displayed a strong misfolding propensity after mechanical unfolding. Here, we present our single-molecule force spectroscopy (SMFS) studies by atomic force microscopy (AFM) and steered molecular dynamics (SMD) simulations on two new hybrid protein constructs comprised of Nluc and I91 titin domains, I91-I91-Nluc-I91-I91-I91-I91 (I912-Nluc-I914) and I91-Nluc-I91-Nluc-I91-Nluc-I91, to characterize the unfolding behavior of Nluc in detail and to further investigate its misfolding properties that we observed earlier for the I912-Nluc3-I912 construct. Our SMFS results confirm that Nluc's unfolding proceeds similarly in all constructs; however, Nluc's refolding differs in these constructs, and its misfolding is minimized when Nluc is monomeric or separated by I91 domains. Our simulations on monomeric Nluc, Nluc dyads, and Nluc triads pinpointed the origin of its mechanical stability and captured interesting unfolding intermediates, which we also observed experimentally.
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Affiliation(s)
- Dimitra Apostolidou
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina27708, United States
| | - Pan Zhang
- Department of Chemistry, Duke University, Durham, North Carolina27708, United States
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina27708, United States
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina27708, United States
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Chow HY, Karchugina S, Groendyke BJ, Toenjes S, Hatcher J, Donovan KA, Fischer ES, Abalakov G, Faezov B, Dunbrack R, Gray NS, Chernoff J. Development and Utility of a PAK1-Selective Degrader. J Med Chem 2022; 65:15627-15641. [PMID: 36416208 PMCID: PMC10029980 DOI: 10.1021/acs.jmedchem.2c00756] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Overexpression of PAK1, a druggable kinase, is common in several malignancies, and inhibition of PAK1 by small molecules has been shown to impede the growth and survival of such cells. Potent inhibitors of PAKs 1-3 have been described, but clinical development has been hindered by recent findings that PAK2 function is required for normal cardiovascular function in adult mice. A unique allosteric PAK1-selective inhibitor, NVS-PAK1-1, provides a potential path forward, but has modest potency. Here, we report the development of BJG-05-039, a PAK1-selective degrader consisting of NVS-PAK1-1 conjugated to lenalidomide, a recruiter of the E3 ubiquitin ligase substrate adaptor Cereblon. BJG-05-039 induced selective degradation of PAK1 and displayed enhanced anti-proliferative effects relative to its parent compound in PAK1-dependent, but not PAK2-dependent, cell lines. Our findings suggest that selective PAK1 degradation may confer more potent pharmacological effects compared with catalytic inhibition and highlight the potential advantages of PAK1-targeted degradation.
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Affiliation(s)
- Hoi-Yee Chow
- Fox Chase Cancer Center, Philadelphia, PA 19111
- National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, China 610041
| | | | - Brian J. Groendyke
- Department of Cancer Biology; Dana Farber Cancer Institute, Boston, MA 02215
- Current address: Blueprint Medicines, Cambridge, MA 02139
| | - Sean Toenjes
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA 94305
| | - John Hatcher
- Department of Cancer Biology; Dana Farber Cancer Institute, Boston, MA 02215
| | - Katherine A. Donovan
- Department of Cancer Biology; Dana Farber Cancer Institute, Boston, MA 02215
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215
| | - Eric S. Fischer
- Department of Cancer Biology; Dana Farber Cancer Institute, Boston, MA 02215
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215
| | | | - Bulat Faezov
- Fox Chase Cancer Center, Philadelphia, PA 19111
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation, 420008
| | | | - Nathanael S. Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA 94305
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124
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Czerniak AS, Kretschmer K, Weiß T, Beck-Sickinger AG. The Chemerin Receptor CMKLR1 Requires Full-Length Chemerin for High Affinity in Contrast to GPR1 as Demonstrated by a New Nanoluciferase-Based Binding Assay. ChemMedChem 2022; 17:e202200413. [PMID: 36178206 PMCID: PMC10092101 DOI: 10.1002/cmdc.202200413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/23/2022] [Indexed: 01/14/2023]
Abstract
To study the binding mode of the adipokine chemerin as well as the short peptide agonist chemerin-9 (C9) to its two receptors chemokine-like receptor 1 (CMKLR1) and G protein-coupled receptor 1 (GPR1), we generated 5-carboxytetramethylrhodamine (TAMRA) modified variants of both ligands. In addition, we labeled GPR1 and CMKLR1 with a nanoluciferase at the N-terminus to perform NanoBRET binding assays. For GPR1, both ligands show high affinity and comparable binding. Significant differences were found for CMKLR1, whereby only full-length chemerin binds with high affinity in saturation and displacement assays. For TAMRA-C9 a biphasic binding consisting of two binding states has been found and no displacement studies could be performed. Thus, we conclude that CMKLR1 requires full-length chemerin for stable binding in contrast to GPR1. This work demonstrates the NanoBRET binding assay as a new tool for binding studies at chemerin receptors and it enables deeper insights into the ligand binding parameters.
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Affiliation(s)
- Anne Sophie Czerniak
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103, Leipzig, Germany
| | - Kevin Kretschmer
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103, Leipzig, Germany
| | - Tina Weiß
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103, Leipzig, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103, Leipzig, Germany
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125
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Cartwright TN, Meyer SK, Higgins JMG. Robustness of NanoBiT luciferase complementation technology in the presence of widely used kinase inhibitors. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:471-475. [PMID: 36162794 DOI: 10.1016/j.slasd.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/08/2022] [Accepted: 09/21/2022] [Indexed: 12/15/2022]
Abstract
Bioluminescence assays using luciferase enzymes are widely used in research to monitor gene expression and an array of other cell properties, and split luciferase enzymes can be used to measure protein interactions in biochemical assays and in living cells. When these methods are employed in chemical library screening efforts, it is vital that the activity of the luciferase enzyme itself is not strongly influenced by library components. Here, we developed a NanoBiT split luciferase assay to measure phosphorylation of Histone H3 peptides and used it to test the robustness of split luciferase to interference from two libraries of commonly used kinase inhibitors, including the Kinase Chemogenomic Set (KCGS). We found that NanoBiT luciferase is not significantly affected by the great majority of kinase inhibitors tested. However, the weak inhibition observed for a small minority of kinase inhibitors encourages the inclusion of suitable controls in NanoBiT (or NanoLuc) assays.
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Affiliation(s)
- Tyrell N Cartwright
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Stephanie K Meyer
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Jonathan M G Higgins
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom.
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126
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Ullrich J, Göhmann PJ, Zemella A, Kubick S. Oligomerization of the heteromeric γ-aminobutyric acid receptor GABA B in a eukaryotic cell-free system. Sci Rep 2022; 12:20742. [PMID: 36456667 PMCID: PMC9715706 DOI: 10.1038/s41598-022-24885-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
Understanding the assembly mechanism and function of membrane proteins is a fundamental problem in biochemical research. Among the membrane proteins, G protein-coupled receptors (GPCRs) represent the largest class in the human body and have long been considered to function as monomers. Nowadays, the oligomeric assembly of GPCRs is widely accepted, although the functional importance and therapeutic intervention remain largely unexplored. This is partly due to difficulties in the heterologous production of membrane proteins. Cell-free protein synthesis (CFPS) with its endogenous endoplasmic reticulum-derived structures has proven as a technique to address this issue. In this study, we investigate for the first time the conceptual CFPS of a heteromeric GPCR, the γ-aminobutyric acid receptor type B (GABAB), from its protomers BR1 and BR2 using a eukaryotic cell-free lysate. Using a fluorescence-based proximity ligation assay, we provide evidence for colocalization and thus suggesting heterodimerization. We prove the heterodimeric assembly by a bioluminescence resonance energy transfer saturation assay providing the manufacturability of a heterodimeric GPCR by CFPS. Additionally, we show the binding of a fluorescent orthosteric antagonist, demonstrating the feasibility of combining the CFPS of GPCRs with pharmacological applications. These results provide a simple and powerful experimental platform for the synthesis of heteromeric GPCRs and open new perspectives for the modelling of protein-protein interactions. Accordingly, the presented technology enables the targeting of protein assemblies as a new interface for pharmacological intervention in disease-relevant dimers.
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Affiliation(s)
- Jessica Ullrich
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
- Institute of Biotechnology, Technische Universität Berlin, Straße Des 17. Juni 135, 10623, Berlin, Germany
| | - Philip Jonas Göhmann
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
- Institute of Biotechnology, Technische Universität Berlin, Straße Des 17. Juni 135, 10623, Berlin, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.
- Institute of Chemistry and Biochemistry-Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany.
- Faculty of Health Science, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany.
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127
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Church G. Picogram-Scale Interstellar Probes via Bioinspired Engineering. ASTROBIOLOGY 2022; 22:1452-1458. [PMID: 36475966 PMCID: PMC9784576 DOI: 10.1089/ast.2022.0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 07/06/2022] [Indexed: 05/04/2023]
Abstract
For exploring nearby stars, let us consider the challenges of a picogram- to nanogram-scale probe to land, replicate, and produce a communications module based on biominerals at the destination. A billion such probes could be launched for similar cost as a single gram-scale probe. One design is a highly reflective light sail, traveling a long straight line toward the gravitational well of a destination star, and then photo-deflected to the closest nonluminous mass-ideally a planet or moon with exposed liquid water.
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Affiliation(s)
- George Church
- Wyss Institute, Harvard University, Boston, Massachusetts, USA
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128
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Hall RN, Weill U, Drees L, Leal-Ortiz S, Li H, Khariton M, Chai C, Xue Y, Rosental B, Quake SR, Sánchez Alvarado A, Melosh NA, Fire AZ, Rink JC, Wang B. Heterologous reporter expression in the planarian Schmidtea mediterranea through somatic mRNA transfection. CELL REPORTS METHODS 2022; 2:100298. [PMID: 36313809 PMCID: PMC9606109 DOI: 10.1016/j.crmeth.2022.100298] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/11/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Planarians have long been studied for their regenerative abilities. Moving forward, tools for ectopic expression of non-native proteins will be of substantial value. Using a luminescent reporter to overcome the strong autofluorescence of planarian tissues, we demonstrate heterologous protein expression in planarian cells and live animals. Our approach is based on the introduction of mRNA through several nanotechnological and chemical transfection methods. We improve reporter expression by altering untranslated region (UTR) sequences and codon bias, facilitating the measurement of expression kinetics in both isolated cells and whole planarians using luminescence imaging. We also examine protein expression as a function of variations in the UTRs of delivered mRNA, demonstrating a framework to investigate gene regulation at the post-transcriptional level. Together, these advances expand the toolbox for the mechanistic analysis of planarian biology and establish a foundation for the development and expansion of transgenic techniques in this unique model system.
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Affiliation(s)
| | - Uri Weill
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Leonard Drees
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Sergio Leal-Ortiz
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Hongquan Li
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Margarita Khariton
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Chew Chai
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yuan Xue
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Center for Regenerative Medicine and Stem Cells, Ben Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Howard Hughes Medical Institute, Kansas City, MO 64110, USA
| | - Nicholas A. Melosh
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Andrew Z. Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jochen C. Rink
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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129
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Macromolecular assembly of bioluminescent protein nanoparticles for enhanced imaging. Mater Today Bio 2022; 17:100455. [PMID: 36304975 PMCID: PMC9593766 DOI: 10.1016/j.mtbio.2022.100455] [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: 08/15/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022] Open
Abstract
Bioluminescence imaging has advantages over fluorescence imaging, such as minimal photobleaching and autofluorescence, and greater signal-to-noise ratios in many complex environments. Although significant achievements have been made in luciferase engineering for generating bright and stable reporters, the full capability of luciferases for nanoparticle tracking has not been comprehensively examined. In biocatalysis, enhanced enzyme performance after immobilization on nanoparticles has been reported. Thus, we hypothesized that by assembling luciferases onto a nanoparticle, the resulting complex could lead to substantially improved imaging properties. Using a modular bioconjugation strategy, we attached NanoLuc (NLuc) or Akaluc bioluminescent proteins to a protein nanoparticle platform (E2), yielding nanoparticles NLuc-E2 and Akaluc-E2, both with diameters of ∼45 nm. Although no significant differences were observed between different conditions involving Akaluc and Akaluc-E2, free NLuc at pH 5.0 showed significantly lower emission values than free NLuc at pH 7.4. Interestingly, NLuc immobilization on E2 nanoparticles (NLuc-E2) emitted increased luminescence at pH 7.4, and at pH 5.0 showed over two orders of magnitude (>200-fold) higher luminescence (than free NLuc), expanding the potential for imaging detection using the nanoparticle even upon endocytic uptake. After uptake by macrophages, the resulting luminescence with NLuc-E2 nanoparticles was up to 7-fold higher than with free NLuc at 48 h. Cells incubated with NLuc-E2 could also be imaged using live bioluminescence microscopy. Finally, biodistribution of nanoparticles into lymph nodes was detected through imaging using NLuc-E2, but not with conventionally-labeled fluorescent E2. Our data demonstrate that NLuc-bound nanoparticles have advantageous properties that can be utilized in applications ranging from single-cell imaging to in vivo biodistribution.
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130
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Aimaletdinov AM, Gomzikova MO. Tracking of Extracellular Vesicles' Biodistribution: New Methods and Approaches. Int J Mol Sci 2022; 23:11312. [PMID: 36232613 PMCID: PMC9569979 DOI: 10.3390/ijms231911312] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/15/2022] [Accepted: 09/21/2022] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) are nanosized lipid bilayer vesicles that are released by almost all cell types. They range in diameter from 30 nm to several micrometres and have the ability to carry biologically active molecules such as proteins, lipids, RNA, and DNA. EVs are natural vectors and play an important role in many physiological and pathological processes. The amount and composition of EVs in human biological fluids serve as biomarkers and are used for diagnosing diseases and monitoring the effectiveness of treatment. EVs are promising for use as therapeutic agents and as natural vectors for drug delivery. However, the successful use of EVs in clinical practice requires an understanding of their biodistribution in an organism. Numerous studies conducted so far on the biodistribution of EVs show that, after intravenous administration, EVs are mostly localized in organs rich in blood vessels and organs associated with the reticuloendothelial system, such as the liver, lungs, spleen, and kidneys. In order to improve resolution, new dyes and labels are being developed and detection methods are being optimized. In this work, we review all available modern methods and approaches used to assess the biodistribution of EVs, as well as discuss their advantages and limitations.
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Affiliation(s)
| | - Marina O. Gomzikova
- Laboratory of Intercellular Communication, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
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131
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Grayeski PJ, Weidmann CA, Kumar J, Lackey L, Mustoe A, Busan S, Laederach A, Weeks KM. Global 5'-UTR RNA structure regulates translation of a SERPINA1 mRNA. Nucleic Acids Res 2022; 50:9689-9704. [PMID: 36107773 PMCID: PMC9508835 DOI: 10.1093/nar/gkac739] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/11/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
SERPINA1 mRNAs encode the protease inhibitor α-1-antitrypsin and are regulated through post-transcriptional mechanisms. α-1-antitrypsin deficiency leads to chronic obstructive pulmonary disease (COPD) and liver cirrhosis, and specific variants in the 5'-untranslated region (5'-UTR) are associated with COPD. The NM_000295.4 transcript is well expressed and translated in lung and blood and features an extended 5'-UTR that does not contain a competing upstream open reading frame (uORF). We show that the 5'-UTR of NM_000295.4 folds into a well-defined multi-helix structural domain. We systematically destabilized mRNA structure across the NM_000295.4 5'-UTR, and measured changes in (SHAPE quantified) RNA structure and cap-dependent translation relative to a native-sequence reporter. Surprisingly, despite destabilizing local RNA structure, most mutations either had no effect on or decreased translation. Most structure-destabilizing mutations retained native, global 5'-UTR structure. However, those mutations that disrupted the helix that anchors the 5'-UTR domain yielded three groups of non-native structures. Two of these non-native structure groups refolded to create a stable helix near the translation initiation site that decreases translation. Thus, in contrast to the conventional model that RNA structure in 5'-UTRs primarily inhibits translation, complex folding of the NM_000295.4 5'-UTR creates a translation-optimized message by promoting accessibility at the translation initiation site.
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Affiliation(s)
- Philip J Grayeski
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Chase A Weidmann
- Department of Biological Chemistry, Center for RNA Biomedicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jayashree Kumar
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lela Lackey
- Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Department of Molecular and Human Genetics, and Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX 77030, USA
| | - Steven Busan
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
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132
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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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133
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Systematic profiling of conditional degron tag technologies for target validation studies. Nat Commun 2022; 13:5495. [PMID: 36127368 PMCID: PMC9489723 DOI: 10.1038/s41467-022-33246-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 09/08/2022] [Indexed: 12/03/2022] Open
Abstract
Conditional degron tags (CDTs) are a powerful tool for target validation that combines the kinetics and reversible action of pharmacological agents with the generalizability of genetic manipulation. However, successful design of a CDT fusion protein often requires a prolonged, ad hoc cycle of construct design, failure, and re-design. To address this limitation, we report here a system to rapidly compare the activity of five unique CDTs: AID/AID2, IKZF3d, dTAG, HaloTag, and SMASh. We demonstrate the utility of this system against 16 unique protein targets. We find that expression and degradation are highly dependent on the specific CDT, the construct design, and the target. None of the CDTs leads to efficient expression and/or degradation across all targets; however, our systematic approach enables the identification of at least one optimal CDT fusion for each target. To enable the adoption of CDT strategies more broadly, we have made these reagents, and a detailed protocol, available as a community resource. Conditional Degron Tags are a valuable tool to validate and study novel therapeutic targets. Here, the authors compared 5 orthogonal tags across 16 unique proteins and provide a panel of vectors for users to systematically screen the tags with their own protein of interest.
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134
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He Q, Yang L, Lin M, Yang H, Cui X, McCoy MR, Hammock BD, Fang Y, Zhao S. Generation of bioluminescent enzyme immunoassay for ferritin by single-chain variable fragment and its NanoLuc luciferase fusion. Anal Bioanal Chem 2022; 414:6939-6946. [PMID: 35945290 PMCID: PMC9531656 DOI: 10.1007/s00216-022-04261-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/26/2022] [Accepted: 08/01/2022] [Indexed: 11/01/2022]
Abstract
Ferritin, widely present in liver and spleen tissue, is considered as a serological biomarker for liver diseases and cancers. The detection of ferritin may be an important tool in health diagnosis. In this study, 14 non-immunized chicken spleens were utilized to construct a single-chain fragment (scFv) phage library. After 4 rounds of panning, 7 unique clones were obtained. The optimal clone was further screened and combined with NanoLuc luciferase (Nluc) as a dual functional immunoprobe to bioluminescent enzyme immunoassay (BLEIA), which was twice as sensitive as its parental scFv-based double-sandwich enzyme-linked immunoassay (ds-ELISA). The cross-reactivity analysis revealed that the proposed methods were highly selective and suitable for clinical detection. To further verify the performance of the immunoassays, serum samples were tested by the proposed methods and a commercial ELISA kit, and there was a good correlation between the results. These results suggested that scFv fused with Nluc might be a powerful dual functional tool for rapid, practically reliable, and highly sensitive ferritin detection.
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Affiliation(s)
- Qiyi He
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, People's Republic of China
- Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, 510006, People's Republic of China
| | - Li Yang
- Biotherapy Center, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Mingxia Lin
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, People's Republic of China
| | - Huiyi Yang
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, People's Republic of China
| | - Xiping Cui
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, People's Republic of China
| | - Mark R McCoy
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California, Davis, Davis, CA, 95616, USA
| | - Bruce D Hammock
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California, Davis, Davis, CA, 95616, USA
| | - Yanxiong Fang
- Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, 510006, People's Republic of China.
| | - Suqing Zhao
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, People's Republic of China.
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135
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Sekhon H, Ha JH, Loh SN. Engineering protein and DNA tools for creating DNA-dependent protein switches. Methods Enzymol 2022; 675:1-32. [PMID: 36220266 PMCID: PMC10314797 DOI: 10.1016/bs.mie.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Switchable proteins are capable of changing conformations from inactive (OFF) to active (ON) forms in response to inputs such as ligand binding, pH or temperature change, or light absorption. A particularly powerful class of protein switches, exemplified by the Cas nucleases of CRISPR systems, are activated by binding of specific DNA or RNA sequences. The mechanism by which oligonucleotide binding regulates biological activity is complex and highly specialized in the case of Cas enzymes, but recent advancements in protein and DNA engineering have made it possible to introduce this mode of control into other enzymes. This chapter highlights recent examples of protein switches that combine these two fields of engineering for the purpose of creating biosensors that detect pathogen and other genomic sequences. One protein engineering method-alternate frame folding-has the potential to convert many proteins into ligand-activated switches by inserting a binding protein (input domain) into an enzyme (output domain). The steps for doing so are illustrated using GCN4 as a DNA recognition domain and nanoluciferase as a luminescent reporter that changes color as a result of DNA binding. DNA engineering protocols are included for creating DNA tools (de novo designed hairpins and modified aptamers), that enable the biosensor to be activated by arbitrary DNA/RNA sequences and small molecules/proteins, respectively. These methodologies can be applied to other proteins to gain control of their functions by DNA binding.
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Affiliation(s)
- Harsimranjit Sekhon
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States.
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136
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Kuznetsov VI, Liu WH, Klein MA, Denu JM. Potent Activation of NAD +-Dependent Deacetylase Sirt7 by Nucleosome Binding. ACS Chem Biol 2022; 17:2248-2261. [PMID: 35939806 PMCID: PMC9499614 DOI: 10.1021/acschembio.2c00348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sirtuin-7 (Sirt7) is a nuclear NAD+-dependent deacetylase with a broad spectrum of biological functions. Sirt7 overexpression is linked to several pathological states and enhances anticancer drug resistance, making the enzyme a promising target for the development of novel therapeutics. Despite a plethora of reported in vivo functions, the biochemical characterization of recombinant Sirt7 remains inadequate for the development of novel drug candidates. Here, we conduct an extensive biochemical analysis of Sirt7 using newly developed binding and kinetic assays to reveal that the enzyme preferentially interacts with and is activated by nucleosomes. Sirt7 activation by nucleic acids alone is effective toward long-chain acylated hydrophobic substrates, while only nucleosome binding leads to 105-fold activation of the deacetylase activity. Using endogenous chromatin and recombinant acetylated nucleosomes, we reveal that Sirt7 is one of the most efficient deacetylases in the sirtuin family and that its catalytic activity is limited by the rate of dissociation from deacetylated nucleosomes.
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Affiliation(s)
- Vyacheslav I. Kuznetsov
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Wallace H. Liu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Mark A. Klein
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - John M. Denu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
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137
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Jeremiah SS, Miyakawa K, Ryo A. Detecting SARS-CoV-2 neutralizing immunity: highlighting the potential of split nanoluciferase technology. J Mol Cell Biol 2022; 14:mjac023. [PMID: 35416249 PMCID: PMC9387144 DOI: 10.1093/jmcb/mjac023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/22/2022] [Accepted: 03/01/2022] [Indexed: 11/24/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has progressed over 2 years since its onset causing significant health concerns all over the world and is currently curtailed by mass vaccination. Immunity acquired against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be following either infection or vaccination. However, one can never be sure whether the acquired immunity is adequate to protect the individual from subsequent infection because of three important factors: individual variations in humoral response dynamics, waning of protective antibodies over time, and the emergence of immune escape mutants. Therefore, a test that can accurately differentiate the protected from the vulnerable is the need of the hour. The plaque reduction neutralization assay is the conventional gold standard test for estimating the titers of neutralizing antibodies that confer protection. However, it has got several drawbacks, which hinder the practical application of this test for wide-scale usage. Hence, various tests have been developed to detect protective immunity against SARS-CoV-2 that directly or indirectly assess the presence of neutralizing antibodies to SARS-CoV-2 in a lower biosafety setting. In this review, the pros and cons of the currently available assays are elaborated in detail and special focus is put on the scope of the novel split nanoluciferase technology for detecting SARS-CoV-2 neutralizing antibodies.
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Affiliation(s)
| | - Kei Miyakawa
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
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138
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Agonist concentration-dependent changes in FPR1 conformation lead to biased signaling for selective activation of phagocyte functions. Proc Natl Acad Sci U S A 2022; 119:e2201249119. [PMID: 35878025 PMCID: PMC9351494 DOI: 10.1073/pnas.2201249119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The bacteria-derived formyl peptide fMet-Leu-Phe (fMLF) is a potent chemoattractant of phagocytes that induces chemotaxis at subnanomolar concentrations. At higher concentrations, fMLF inhibits chemotaxis while stimulating degranulation and superoxide production, allowing phagocytes to kill invading bacteria. How an agonist activates distinct cellular functions at different concentrations remains unclear. Using a bioluminescence resonance energy transfer-based FPR1 biosensor, we found that fMLF at subnanomolar and micromolar concentrations induced distinct conformational changes in FPR1, a Gi-coupled chemoattractant receptor that activates various phagocyte functions. Neutrophil-like HL-60 cells exposed to subnanomolar concentrations of fMLF polarized rapidly and migrated along a chemoattractant concentration gradient. These cells also developed an intracellular Ca2+ concentration gradient. In comparison, high nanomolar and micromolar concentrations of fMLF triggered the PLC-β/diacyl glycerol/inositol trisphosphate pathway downstream of the heterotrimeric Gi proteins, leading to Ca2+ mobilization from intracellular stores and Ca2+ influx from extracellular milieu. A robust and uniform rise in cytoplasmic Ca2+ level was required for degranulation and superoxide production but disrupted cytoplasmic Ca2+ concentration gradient and inhibited chemotaxis. In addition, elevated ERK1/2 phosphorylation and β-arrestin2 membrane translocation were associated with diminished chemotaxis in the presence of fMLF above 1 nM. These findings suggest a mechanism for FPR1 agonist concentration-dependent signaling that leads to a switch from migration to bactericidal activities in phagocytes.
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139
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Weissová K, Fafílek B, Radaszkiewicz T, Celiker C, Macháčková P, Čechová T, Šebestíková J, Hampl A, Bryja V, Krejčí P, Bárta T. LuminoCell: a versatile and affordable platform for real-time monitoring of luciferase-based reporters. Life Sci Alliance 2022; 5:e202201421. [PMID: 35440493 PMCID: PMC9018015 DOI: 10.26508/lsa.202201421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 11/24/2022] Open
Abstract
Luciferase reporter assays represent a simple and sensitive experimental system in cell and molecular biology to study multiple biological processes. However, the application of these assays is often limited by the costs of conventional luminometer instruments and the versatility of their use in different experimental conditions. Therefore, we aimed to develop a small, affordable luminometer allowing continuous measurement of luciferase activity, designed for inclusion into various kinds of tissue culture incubators. Here, we introduce LuminoCell-an open-source platform for the construction of an affordable, sensitive, and portable luminometer capable of real-time monitoring in-cell luciferase activity. The LuminoCell costs $40, requires less than 1 h to assemble, and it is capable of performing real-time sensitive detection of both magnitude and duration of the activity of major signalling pathways in cell cultures, including receptor tyrosine kinases (EGF and FGF), WNT/β-catenin, and NF-κB. In addition, we show that the LuminoCell is suitable to be used in cytotoxicity assays as well as for monitoring periodic circadian gene expression.
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Affiliation(s)
- Kamila Weissová
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Bohumil Fafílek
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Tomasz Radaszkiewicz
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Canan Celiker
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Petra Macháčková
- Cellular Imaging Core Facility, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Tamara Čechová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Jana Šebestíková
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Aleš Hampl
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavel Krejčí
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Tomáš Bárta
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
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140
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Rodríguez de la Fuente L, Cancela IG, Estévez-Salguero ÁM, Iglesias P, Costoya JA. Development of a biosensor based on a new marine luciferase fused to an affibody to assess Her2 expression in living cells. Anal Chim Acta 2022; 1221:340084. [DOI: 10.1016/j.aca.2022.340084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/06/2022] [Accepted: 06/11/2022] [Indexed: 12/01/2022]
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141
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Zhu Y, Sánchez-Tacuba L, Hou G, Kawagishi T, Feng N, Greenberg HB, Ding S. A recombinant murine-like rotavirus with Nano-Luciferase expression reveals tissue tropism, replication dynamics, and virus transmission. Front Immunol 2022; 13:911024. [PMID: 35967392 PMCID: PMC9372724 DOI: 10.3389/fimmu.2022.911024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022] Open
Abstract
Rotaviruses (RVs) are one of the main causes of severe gastroenteritis, diarrhea, and death in children and young animals. While suckling mice prove to be highly useful small animal models of RV infection and pathogenesis, direct visualization tools are lacking to track the temporal dynamics of RV replication and transmissibility in vivo. Here, we report the generation of the first recombinant murine-like RV that encodes a Nano-Luciferase reporter (NLuc) using a newly optimized RV reverse genetics system. The NLuc-expressing RV was replication-competent in cell culture and both infectious and virulent in neonatal mice in vivo. Strong luciferase signals were detected in the proximal and distal small intestines, colon, and mesenteric lymph nodes. We showed, via a noninvasive in vivo imaging system, that RV intestinal replication peaked at days 2 to 5 post infection. Moreover, we successfully tracked RV transmission to uninoculated littermates as early as 3 days post infection, 1 day prior to clinically apparent diarrhea and 3 days prior to detectable fecal RV shedding in the uninoculated littermates. We also observed significantly increased viral replication in Stat1 knockout mice that lack the host interferon signaling. Our results suggest that the NLuc murine-like RV represents a non-lethal powerful tool for the studies of tissue tropism and host and viral factors that regulate RV replication and spread, as well as provides a new tool to facilitate the testing of prophylactic and therapeutic interventions in the future.
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Affiliation(s)
- Yinxing Zhu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Liliana Sánchez-Tacuba
- Veterans Affairs (VA) Palo Alto Health Care System, Department of Veterans Affairs, Palo Alto, CA, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford School of Medicine, Stanford, CA, United States
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA, United States
| | - Gaopeng Hou
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Takahiro Kawagishi
- Veterans Affairs (VA) Palo Alto Health Care System, Department of Veterans Affairs, Palo Alto, CA, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford School of Medicine, Stanford, CA, United States
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA, United States
| | - Ningguo Feng
- Veterans Affairs (VA) Palo Alto Health Care System, Department of Veterans Affairs, Palo Alto, CA, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford School of Medicine, Stanford, CA, United States
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA, United States
| | - Harry B. Greenberg
- Veterans Affairs (VA) Palo Alto Health Care System, Department of Veterans Affairs, Palo Alto, CA, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford School of Medicine, Stanford, CA, United States
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA, United States
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
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142
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Kincaid VA, Wang H, Sondgeroth CA, Torio EA, Ressler VT, Fitzgerald C, Hall MP, Hurst R, Wood MG, Gilden JK, Kirkland TA, Lazar D, Chia-Chang H, Encell LP, Machleidt T, Zhou W, Dart ML. Simple, Rapid Chemical Labeling and Screening of Antibodies with Luminescent Peptides. ACS Chem Biol 2022; 17:2179-2187. [PMID: 35862857 PMCID: PMC9396617 DOI: 10.1021/acschembio.2c00306] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
Sensitive and selective detection assays are essential
for the
accurate measurement of analytes in both clinical and research laboratories.
Immunoassays that rely on nonoverlapping antibodies directed against
the same target analyte (e.g., sandwich enzyme-linked immunosorbent
assays (ELISAs)) are commonly used molecular detection technologies.
Use of split enzyme reporters has simplified the workflow for these
traditionally complex assays. However, identifying functional antibody
pairs for a given target analyte can be cumbersome, as it generally
involves generating and screening panels of antibodies conjugated
to reporters. Accordingly, we sought a faster and easier reporter
conjugation strategy to streamline antibody screening. We describe
here the development of such a method that is based on an optimized
ternary NanoLuc luciferase. This bioluminescence complementation system
is comprised of a reagent-based thermally stable polypeptide (LgTrip)
and two small peptide tags (β9 and β10) with lysine-reactive
handles for direct conjugation onto antibodies. These reagents enable
fast, single-step, wash-free antibody labeling and sensitive functional
screening. Simplicity, speed, and utility of the one-pot labeling
technology are demonstrated in screening antibody pairs for the analyte
interleukin-4. The screen resulted in the rapid development of a sensitive
homogeneous immunoassay for this clinically relevant cytokine.
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Affiliation(s)
| | - Hui Wang
- Promega Biosciences LLC, San Luis Obispo, California 93401, United States
| | | | - Emily A Torio
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | - Connor Fitzgerald
- Promega Biosciences LLC, San Luis Obispo, California 93401, United States
| | - Mary P Hall
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Robin Hurst
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Monika G Wood
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Julia K Gilden
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Thomas A Kirkland
- Promega Biosciences LLC, San Luis Obispo, California 93401, United States
| | - Dan Lazar
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Hsu Chia-Chang
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Lance P Encell
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | - Wenhui Zhou
- Promega Biosciences LLC, San Luis Obispo, California 93401, United States
| | - Melanie L Dart
- Promega Corporation, Madison, Wisconsin 53711, United States
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143
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Arifin DR, Witwer KW, Bulte JWM. Non-Invasive imaging of extracellular vesicles: Quo vaditis in vivo? J Extracell Vesicles 2022; 11:e12241. [PMID: 35844061 PMCID: PMC9289215 DOI: 10.1002/jev2.12241] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 01/11/2023] Open
Abstract
Extracellular vesicles (EVs) are lipid-bilayer delimited vesicles released by nearly all cell types that serve as mediators of intercellular signalling. Recent evidence has shown that EVs play a key role in many normal as well as pathological cellular processes. EVs can be exploited as disease biomarkers and also as targeted, cell-free therapeutic delivery and signalling vehicles for use in regenerative medicine and other clinical settings. Despite this potential, much remains unknown about the in vivo biodistribution and pharmacokinetic profiles of EVs after administration into living subjects. The ability to non-invasively image exogeneous EVs, especially in larger animals, will allow a better understanding of their in vivo homing and retention patterns, blood and tissue half-life, and excretion pathways, all of which are needed to advance clinical diagnostic and/or therapeutic applications of EVs. We present the current state-of-the-art methods for labeling EVs with various diagnostic contrast agents and tracers and the respective imaging modalities that can be used for their in vivo visualization: magnetic resonance imaging (MRI), X-ray computed tomography (CT) imaging, magnetic particle imaging (MPI), single-photon emission computed tomography (SPECT), positron emission tomography (PET), and optical imaging (fluorescence and bioluminescence imaging). We review here the strengths and weaknesses of each of these EV imaging approaches, with special emphasis on clinical translation.
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Affiliation(s)
- Dian R. Arifin
- Russell H. Morgan Department of Radiology and Radiological ScienceDivision of MR Researchthe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
- Cellular Imaging Section and Vascular Biology ProgramInstitute for Cell Engineeringthe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Kenneth W. Witwer
- Department of Molecular and Comparative Pathobiologythe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Neurologythe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jeff W. M. Bulte
- Russell H. Morgan Department of Radiology and Radiological ScienceDivision of MR Researchthe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
- Cellular Imaging Section and Vascular Biology ProgramInstitute for Cell Engineeringthe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Oncologythe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Chemical & Biomolecular Engineeringthe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Biomedical Engineeringthe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
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144
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Okano S, Kawaguchi Y, Kawano K, Hirose H, Imanishi M, Futaki S. Split luciferase-based estimation of cytosolic cargo concentration delivered intracellularly via attenuated cationic amphiphilic lytic peptides. Bioorg Med Chem Lett 2022; 72:128875. [DOI: 10.1016/j.bmcl.2022.128875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/02/2022]
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145
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Abstract
Molecular imaging is used to improve the disease diagnosis, prognosis, monitoring of treatment in living subjects. Numerous molecular targets have been developed for various cellular and molecular processes in genetic, metabolic, proteomic, and cellular biologic level. Molecular imaging modalities such as Optical Imaging, Magnetic Resonance Imaging (MRI), Positron Emission Tomography (PET), Single Photon Emission Computed Tomography (SPECT), and Computed Tomography (CT) can be used to visualize anatomic, genetic, biochemical, and physiologic changes in vivo. For in vivo cell imaging, certain cells such as cancer cells, immune cells, stem cells could be labeled by direct and indirect labeling methods to monitor cell migration, cell activity, and cell effects in cell-based therapy. In case of cancer, it could be used to investigate biological processes such as cancer metastasis and to analyze the drug treatment process. In addition, transplanted stem cells and immune cells in cell-based therapy could be visualized and tracked to confirm the fate, activity, and function of cells. In conventional molecular imaging, cells can be monitored in vivo in bulk non-invasively with optical imaging, MRI, PET, and SPECT imaging. However, single cell imaging in vivo has been a great challenge due to an extremely high sensitive detection of single cell. Recently, there has been great attention for in vivo single cell imaging due to the development of single cell study. In vivo single imaging could analyze the survival or death, movement direction, and characteristics of a single cell in live subjects. In this article, we reviewed basic principle of in vivo molecular imaging and introduced recent studies for in vivo single cell imaging based on the concept of in vivo molecular imaging.
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Affiliation(s)
- Seongje Hong
- Department of Anatomy, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Siyeon Rhee
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kyung Oh Jung
- Department of Anatomy, College of Medicine, Chung-Ang University, Seoul 06974, Korea
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
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146
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Construction of a Porcine Reproductive and Respiratory Syndrome Virus with Nanoluc Luciferase Reporter: a Stable and Highly Efficient Tool for Viral Quantification Both In Vitro and In Vivo. Microbiol Spectr 2022; 10:e0027622. [PMID: 35758677 PMCID: PMC9430303 DOI: 10.1128/spectrum.00276-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically important pathogens for the global pork industry, characterized for its genetic variation and unsatisfied heterological protection from vaccines. A high-throughput screening platform for developing anti-PRRSV therapies is urgently needed. Here, an 11-amino-acid subunit HiBiT derived from NanoLuc luciferase was inserted into the PRRSV genome at four loci of the Nsp2 coding region or as an additional TRS2 driven open reading frame (ORF) between the ORF7 and 3′-untranscribed region (3′-UTR), respectively, and five recombinant viruses with luciferase activity were successfully rescued. The virological characteristics of the representative virus RvJX-Nsp2325-HiBiT were investigated. In vitro, it displayed similar growth kinetics as the parental virus and keeps the luciferase activity and genetic stability after eight rounds of serial passages. The concept-proof test confirmed that RvJX-Nsp2325-HiBiT can be easily used to evaluate the efficacy of antiviral reagents by detecting the reduction of luciferase activity, showing a consistent trend with infectious titers, as well as to set a novel convenient virus neutralization assay based on the intensity of luciferase activity. Last, the viral proliferation, virulence, validity, and HiBiT stability were further investigated in pig inoculation study, showing that the luciferase activity can be directly detected in the tissue samples or indirectly from the MARC-145 cells inoculated with sera from RvJX-Nsp2325-HiBiT-inoculated pigs. Taken together, the results indicate that the HiBiT-tagged virus is a convenient and stable tool for evaluating viral propagation both in vitro and in vivo, which can provide a high-efficient platform for screening and evaluating anti-PRRSV therapies. IMPORTANCE Luciferase reporter tagged virus is crucial to viral quantification in the study of viral replication, pathogenesis and exploring antiviral reagents. It is urgently needed for PRRSV academia to construct a stable, fast, and high-throughput reporting system, which can be used both in vitro and in vivo. Here, an 11-amino-acid luciferase subunit was successfully inserted into the PRRSV genome; the feasibility, genetic stability, and efficiency for viral quantification both in vitro and in vivo were characterized; and the results demonstrated it has greatly improved the convenience and efficiency for screening the anti-PRRSV reagents. Furthermore, a novel luciferase-based virus neutralization assay was successfully set, which can eliminate the step of sample gradient dilution and greatly improve the convenience and throughput of neutralizing antibody testing. Predictably, it will greatly facilitate the screening and evaluating anti-PRRSV therapies, as well as the mechanistic study of its replication and pathogenesis in the future.
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147
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Multiplexed bioluminescence microscopy via phasor analysis. Nat Methods 2022; 19:893-898. [PMID: 35739310 DOI: 10.1038/s41592-022-01529-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 05/18/2022] [Indexed: 12/19/2022]
Abstract
Bioluminescence imaging with luciferase-luciferin pairs is a well-established technique for visualizing biological processes across tissues and whole organisms. Applications at the microscale, by contrast, have been hindered by a lack of detection platforms and easily resolved probes. We addressed this limitation by combining bioluminescence with phasor analysis, a method commonly used to distinguish spectrally similar fluorophores. We built a camera-based microscope equipped with special optical filters to directly assign phasor locations to unique luciferase-luciferin pairs. Six bioluminescent reporters were easily resolved in live cells, and the readouts were quantitative and instantaneous. Multiplexed imaging was also performed over extended time periods. Bioluminescent phasor further provided direct measures of resonance energy transfer in single cells, setting the stage for dynamic measures of cellular and molecular features. The merger of bioluminescence with phasor analysis fills a long-standing void in imaging capabilities, and will bolster future efforts to visualize biological events in real time and over multiple length scales.
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148
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Broadly Applicable, Virus-Free Dual Reporter Assay to Identify Compounds Interfering with Membrane Fusion: Performance for HSV-1 and SARS-CoV-2. Viruses 2022; 14:v14071354. [PMID: 35891336 PMCID: PMC9322530 DOI: 10.3390/v14071354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/13/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023] Open
Abstract
Membrane fusion constitutes an essential step in the replication cycle of numerous viral pathogens, hence it represents an important druggable target. In the present study, we established a virus-free, stable reporter fusion inhibition assay (SRFIA) specifically designed to identify compounds interfering with virus-induced membrane fusion. The dual reporter assay is based on two stable Vero cell lines harboring the third-generation tetracycline (Tet3G) transactivator and a bicistronic reporter gene cassette under the control of the tetracycline responsive element (TRE3G), respectively. Cell–cell fusion by the transient transfection of viral fusogens in the presence of doxycycline results in the expression of the reporter enzyme secreted alkaline phosphatase (SEAP) and the fluorescent nuclear localization marker EYFPNuc. A constitutively expressed, secreted form of nanoluciferase (secNLuc) functioned as the internal control. The performance of the SRFIA was tested for the quantification of SARS-CoV-2- and HSV-1-induced cell–cell fusion, respectively, showing high sensitivity and specificity, as well as the reliable identification of known fusion inhibitors. Parallel quantification of secNLuc enabled the detection of cytotoxic compounds or insufficient transfection efficacy. In conclusion, the SRFIA reported here is well suited for high-throughput screening for new antiviral agents and essentially will be applicable to all viral fusogens causing cell–cell fusion in Vero cells.
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149
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Rzepka M, Suhm T, Ott M. Incorporation of reporter genes into mitochondrial DNA in budding yeast. STAR Protoc 2022; 3:101359. [PMID: 35634362 PMCID: PMC9136344 DOI: 10.1016/j.xpro.2022.101359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Many aspects of mitochondrial gene expression are still unknown, which can be attributed to limitations in molecular tools. Here, we present a protocol to introduce reporter genes into the mitochondrial genome of budding yeast, Saccharomyces cerevisiae. Mitochondrially encoded reporter constructs can be used to interrogate various aspects of mitochondrial gene expression. The power of this technique is exemplified by a mitochondrially encoded nanoluciferase, which allows to monitor levels of mitochondrial translation under a variety of growth conditions.
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Affiliation(s)
- Magdalena Rzepka
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Tamara Suhm
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
- Corresponding author
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150
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Abstract
Lymph node mapping for tumor micrometastasis is of great significance for the prevention, prognosis, and treatment of cancer. Currently, the traditional clinical detection methods (computed tomography, magnetic resonance imaging, or positron emission tomography/computed tomography) in clinical lymph node mapping still have some inherent disadvantages, which have prompted the development of various fluorescent probes for lymph node mapping. However, the conventional fluorescent probes such as indocyanine green or methylene blue in lymph node mapping are still accompanied by several problems such as impaired surgical field vision due to dye staining or less accumulation and shorter retention time in the lymph node. In a recent achievement, newly designed nanoparticles are prepared with novel properties that could be attractive for lymph node mapping. In this review, we will provide details on the progress of various nanoparticles for lymph node mapping and emphasize other multivariant properties in different nanoparticles, including strong tumor-targeting affinity and specificity, self-luminescence, and even with the function to kill metastatic cancer cells.
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Affiliation(s)
- Meng Han
- Queen Mary School, Nanchang University, Nanchang, Jiangxi Province 330006, P.R. China
| | - Ruirui Kang
- The Department of Ultrasound, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, P.R. China
| | - Chunquan Zhang
- The Department of Ultrasound, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province 330006, P.R. China
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