1
|
Hiers RD, Khajotia SS, Merritt J, Esteban Florez FL. Optimization of an ultra-bright real-time high-throughput renilla luciferase assay for antibacterial assessment of Streptococcus mutans biofilms. Dent Mater 2024; 40:1313-1321. [PMID: 38876827 PMCID: PMC11330348 DOI: 10.1016/j.dental.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
OBJECTIVE The present work demonstrates the optimization of a renilla-based real-time, ultra-bright, non-disruptive, high-throughput bioluminescence assay (HTS) to assess the metabolism of intact Streptococcus mutans biofilms and its utility in screening the antibacterial efficacy of experimental nanofilled dental adhesive resins containing varying concentrations of nitrogen-doped titanium dioxide nanoparticles (N_TiO2). METHODS Optimization of the assay was achieved by screening real-time bioluminescence changes in intact Streptococcus mutans biofilms imposed by the various experimental biofilm growth parameters investigated (bacterial strain, growth media, sucrose concentration, dilution factor, and inoculum volume). The optimized assay was then used to characterize the antibacterial efficacy of experimental nanofilled dental adhesive resins. The assay's ability to discriminate between bacteriostatic and bactericidal approaches was also investigated. RESULTS Relative Light Units (RLU) values from the HTS optimization were analyzed by multivariate ANOVA (α = 0.05) and coefficients of variation. An optimized HTS bioluminescence assay was developed displaying RLUs values (brightness) that are much more intense when comparing to other previously reported bioluminescence assays, thereby decreasing the error associated with bioluminescence assays and displaying better utility while investigating the functionalities of antimicrobial nanofilled experimental dental adhesive resins with proven long-term properties. SIGNIFICANCE The present study is anticipated to positively impact subsequent research on dental materials and oral microbiology because it serves as a valuable screening tool in metabolic-based assays with increased sensitivity and robustness. The assay reported is anticipated to be further optimized to be used as a co-reporter for other Luc based assays.
Collapse
Affiliation(s)
- Rochelle Denise Hiers
- The University of Oklahoma Health Sciences Center, Department of Restorative Sciences, Division of Dental Biomaterials, College of Dentistry, 1201 N. Stonewall Avenue, Oklahoma City, OK 73117, USA.
| | - Sharukh Soli Khajotia
- The University of Oklahoma Health Sciences Center, Department of Restorative Sciences, Division of Dental Biomaterials, College of Dentistry, 1201 N. Stonewall Avenue, Oklahoma City, OK 73117, USA.
| | - Justin Merritt
- Oregon Health & Science University, Department of Restorative Dentistry, School of Dentistry, MRB424, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, USA.
| | - Fernando Luis Esteban Florez
- The University of Oklahoma Health Sciences Center, Department of Restorative Sciences, Division of Dental Biomaterials, College of Dentistry, 1201 N. Stonewall Avenue, Oklahoma City, OK 73117, USA.
| |
Collapse
|
2
|
Kim H, Jung SO, Lee S, Lee Y. Bioluminescent Systems for Theranostic Applications. Int J Mol Sci 2024; 25:7563. [PMID: 39062805 PMCID: PMC11277111 DOI: 10.3390/ijms25147563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Bioluminescence, the light produced by biochemical reactions involving luciferases in living organisms, has been extensively investigated for various applications. It has attracted particular interest as an internal light source for theranostic applications due to its safe and efficient characteristics that overcome the limited penetration of conventional external light sources. Recent advancements in protein engineering technologies and protein delivery platforms have expanded the application of bioluminescence to a wide range of theranostic areas, including bioimaging, biosensing, photodynamic therapy, and optogenetics. This comprehensive review presents the fundamental concepts of bioluminescence and explores its recent applications across diverse fields. Moreover, it discusses future research directions based on the current status of bioluminescent systems for further expansion of their potential.
Collapse
Affiliation(s)
- Hyemin Kim
- Department of Cosmetics Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.O.J.); (S.L.); (Y.L.)
| | | | | | | |
Collapse
|
3
|
Porta-de-la-Riva M, Morales-Curiel LF, Carolina Gonzalez A, Krieg M. Bioluminescence as a functional tool for visualizing and controlling neuronal activity in vivo. NEUROPHOTONICS 2024; 11:024203. [PMID: 38348359 PMCID: PMC10861157 DOI: 10.1117/1.nph.11.2.024203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/15/2024]
Abstract
The use of bioluminescence as a reporter for physiology in neuroscience is as old as the discovery of the calcium-dependent photon emission of aequorin. Over the years, luciferases have been largely replaced by fluorescent reporters, but recently, the field has seen a renaissance of bioluminescent probes, catalyzed by unique developments in imaging technology, bioengineering, and biochemistry to produce luciferases with previously unseen colors and intensity. This is not surprising as the advantages of bioluminescence make luciferases very attractive for noninvasive, longitudinal in vivo observations without the need of an excitation light source. Here, we review how the development of dedicated and specific sensor-luciferases afforded, among others, transcranial imaging of calcium and neurotransmitters, or cellular metabolites and physical quantities such as forces and membrane voltage. Further, the increased versatility and light output of luciferases have paved the way for a new field of functional bioluminescence optogenetics, in which the photon emission of the luciferase is coupled to the gating of a photosensor, e.g., a channelrhodopsin and we review how they have been successfully used to engineer synthetic neuronal connections. Finally, we provide a primer to consider important factors in setting up functional bioluminescence experiments, with a particular focus on the genetic model Caenorhabditis elegans, and discuss the leading challenges that the field needs to overcome to regain a competitive advantage over fluorescence modalities. Together, our paper caters to experienced users of bioluminescence as well as novices who would like to experience the advantages of luciferases in their own hand.
Collapse
Affiliation(s)
- Montserrat Porta-de-la-Riva
- ICFO—Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Luis-Felipe Morales-Curiel
- ICFO—Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Adriana Carolina Gonzalez
- ICFO—Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Michael Krieg
- ICFO—Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| |
Collapse
|
4
|
Dunuweera AN, Dunuweera SP, Ranganathan K. A Comprehensive Exploration of Bioluminescence Systems, Mechanisms, and Advanced Assays for Versatile Applications. Biochem Res Int 2024; 2024:8273237. [PMID: 38347947 PMCID: PMC10861286 DOI: 10.1155/2024/8273237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/10/2023] [Accepted: 01/21/2024] [Indexed: 02/15/2024] Open
Abstract
Bioluminescence has been a fascinating natural phenomenon of light emission from living creatures. It happens when the enzyme luciferase facilitates the oxidation of luciferin, resulting in the creation of an excited-state species that emits light. Although there are many bioluminescent systems, few have been identified. D-luciferin-dependent systems, coelenterazine-dependent systems, Cypridina luciferin-based systems, tetrapyrrole-based luciferins, bacterial bioluminescent systems, and fungal bioluminescent systems are natural bioluminescent systems. Since different bioluminescence systems, such as various combinations of luciferin-luciferase pair reactions, have different light emission wavelengths, they benefit industrial applications such as drug discovery, protein-protein interactions, in vivo imaging in small animals, and controlling neurons. Due to the expression of luciferase and easy permeation of luciferin into most cells and tissues, bioluminescence assays are applied nowadays with modern technologies in most cell and tissue types. It is a versatile technique in a variety of biomedical research. Furthermore, there are some investigated blue-sky research projects, such as bioluminescent plants and lamps. This review article is mainly based on the theory of diverse bioluminescence systems and their past, present, and future applications.
Collapse
Affiliation(s)
| | | | - K. Ranganathan
- Department of Botany, University of Jaffna, Jaffna 40000, Sri Lanka
| |
Collapse
|
5
|
Zhang X, Meng Z, Beusch CM, Gharibi H, Cheng Q, Lyu H, Di Stefano L, Wang J, Saei AA, Végvári Á, Gaetani M, Zubarev RA. Ultralight Ultrafast Enzymes. Angew Chem Int Ed Engl 2024; 63:e202316488. [PMID: 38009610 DOI: 10.1002/anie.202316488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Inorganic materials depleted of heavy stable isotopes are known to deviate strongly in some physicochemical properties from their isotopically natural counterparts. Here we explored for the first time the effect of simultaneous depletion of the heavy carbon, hydrogen, oxygen and nitrogen isotopes on the bacterium E. coli and the enzymes expressed in it. Bacteria showed faster growth, with most proteins exhibiting higher thermal stability, while for recombinant enzymes expressed in depleted media, faster kinetics was discovered. At room temperature, luciferase, thioredoxin and dihydrofolate reductase and Pfu DNA polymerase showed up to a 250 % increase in activity compared to the native counterparts, with an additional ∼50 % increase at 10 °C. Diminished conformational and vibrational entropy is hypothesized to be the cause of the accelerated kinetics. Ultralight enzymes may find an application where extreme reaction rates are required.
Collapse
Affiliation(s)
- Xuepei Zhang
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Zhaowei Meng
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Christian M Beusch
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Hassan Gharibi
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Qing Cheng
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Hezheng Lyu
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Luciano Di Stefano
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
- European Research Institute for the Biology of Aging, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Jijing Wang
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Amir A Saei
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Massimiliano Gaetani
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
- Chemical Proteomics Core Facility, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177, Stockholm, Sweden
- Chemical Proteomics, Science for Life Laboratory (SciLifeLab), 17177, Stockholm, Sweden
| | - Roman A Zubarev
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
- >Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, 119146, Moscow, Russia
- The National Medical Research Center for Endocrinology, Moskva, 115478 Moscow, Russia
| |
Collapse
|
6
|
Calabretta MM, Michelini E. Current advances in the use of bioluminescence assays for drug discovery: an update of the last ten years. Expert Opin Drug Discov 2024; 19:85-95. [PMID: 37814480 DOI: 10.1080/17460441.2023.2266989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/02/2023] [Indexed: 10/11/2023]
Abstract
INTRODUCTION Bioluminescence is a well-established optical detection technique widely used in several bioanalytical applications, including high-throughput and high-content screenings. Thanks to advances in synthetic biology techniques and deep learning, a wide portfolio of luciferases is now available with tuned emission wavelengths, kinetics, and high stability. These luciferases can be implemented in the drug discovery and development pipeline, allowing high sensitivity and multiplexing capability. AREAS COVERED This review summarizes the latest advancements of bioluminescent systems as toolsets in drug discovery programs for in vitro applications. Particular attention is paid to the most advanced bioluminescence-based technologies for drug screening over the past 10 years (from 2013 to 2023) such as cell-free assays, cell-based assays based on genetically modified cells, bioluminescence resonance energy transfer, and protein complementation assays in 2D and 3D cell models. EXPERT OPINION The availability of tuned bioluminescent proteins with improved emission and stability properties is vital for the development of bioluminescence assays for drug discovery, spanning from reporter gene technology to protein-protein techniques. Further studies, combining machine learning with synthetic biology, will be necessary to obtain new tools for sustainable and highly predictive bioluminescent drug discovery platforms.
Collapse
Affiliation(s)
- Maria Maddalena Calabretta
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Center for Applied Biomedical Research (CRBA), IRCCS St. Orsola Hospital, Bologna, Italy
| | - Elisa Michelini
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Center for Applied Biomedical Research (CRBA), IRCCS St. Orsola Hospital, Bologna, Italy
- Health Sciences and Technologies Interdepartmental Center for Industrial Research (HSTICIR), University of Bologna, Bologna, Italy
| |
Collapse
|
7
|
Klein MA, Lazarev S, Gervasi C, Cowan C, Machleidt T, Friedman Ohana R. Luciferase Calibrants Enable Absolute Quantitation of Bioluminescence Power. ACS MEASUREMENT SCIENCE AU 2023; 3:496-503. [PMID: 38145021 PMCID: PMC10740115 DOI: 10.1021/acsmeasuresciau.3c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 12/26/2023]
Abstract
Bioluminescence emitted from a luciferase-catalyzed oxidation of luciferin has been broadly utilized to report on biological events, predominantly through relative changes in the light output. Recent advances in protein engineering and synthetic chemistry have yielded bioluminescent systems with markedly improved brightness and bioavailability. These developments have enabled not only the detection of biological events at far lower expression levels but also new opportunities utilizing bioluminescence to power photochemistry in cells. Regardless of the application, bioluminescence analyses have leaned heavily on the use of luminometers to measure the light output of a system. Current luminometers report the light output of a sample in relative units, limiting the ability to compare data between instruments and preventing the absolute power of a bioluminescent system from being quantified. Luminescent solution calibrants comprising luciferases and their cognate luciferins that have been characterized for absolute light output would enable calibration of any given luminometer for absolute photon counting. To this end, we have built a custom light detection apparatus and used it alongside wavelength-matched LED light sources emitting at 450 and 561 nm to characterize the absolute power of a series of NanoLuc and firefly luciferase solutions, respectively. This approach revealed that these two common luciferases produce 3.72 × 10-18 and 7.25 × 10-20 watts/molecule, respectively. Components of these luminescent solution calibrants are commercially available and produce stable bioluminescent signals over 2-5 min, enabling any luminometer to be calibrated for power measurements of bioluminescence emitted by these two luciferases in units of watts or photons per second.
Collapse
Affiliation(s)
- Mark A. Klein
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Sergey Lazarev
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Charles Gervasi
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | | | | |
Collapse
|
8
|
Calabretta MM, Gregucci D, Michelini E. New synthetic red- and orange-emitting luciferases to upgrade in vitro and 3D cell biosensing. Analyst 2023; 148:5642-5649. [PMID: 37791570 DOI: 10.1039/d3an01251d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Bioluminescence (BL), i.e., the emission of light in living organisms, has become an indispensable tool for a plethora of applications including bioassays, biosensors, and in vivo imaging. Current efforts are focused on the obtainment of new luciferases having optimized properties, such as improved thermostability at 37 °C, pH-insensitive emission, high quantum yield, extended kinetics and red-shifted emission. To address these issues we have obtained two new synthetic luciferases, an orange and a red-emitting luciferase, which were designed to achieve high sensitivity (BoLuc) and multiplexing capability (BrLuc) for in vitro and in vivo biosensing using as a starting template a recently developed thermostable synthetic luciferase (BgLuc). Both luciferases were characterized in terms of emission behaviour and thermal and pH stability showing promising features as reporter proteins and BL probes. As proof-of-principle application, an inflammation assay based on Human Embryonic Kidney (HEK293T) 3D cell cultures was developed using either the orange or the red-emitting mutant. The assay provided good analytical performance, with limits of detection for Tumor Necrosis Factor (TNFα) of 0.06 and 0.12 ng mL-1 for BoLuc and BrLuc, respectively. Moreover, since these luciferases require the same substrate, D-luciferin, they can be easily implemented in dual-color assays with a significant reduction of total cost per assay.
Collapse
Affiliation(s)
- Maria Maddalena Calabretta
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via Selmi 2, 40126, Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), Azienda Ospedaliero-Universitaria Policlinico S. Orso-la-Malpighi, 40138 Bologna, Italy
| | - Denise Gregucci
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via Selmi 2, 40126, Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), Azienda Ospedaliero-Universitaria Policlinico S. Orso-la-Malpighi, 40138 Bologna, Italy
| | - Elisa Michelini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via Selmi 2, 40126, Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), Azienda Ospedaliero-Universitaria Policlinico S. Orso-la-Malpighi, 40138 Bologna, Italy
- Health Sciences and Technologies Interdepartmental Center for Industrial Research (HSTICIR), University of Bologna, 40126, Bologna, Italy
| |
Collapse
|
9
|
Beyond luciferase-luciferin system: Modification, improved imaging and biomedical application. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
10
|
Williams SJ, Gewing-Mullins JA, Lieberman WK, Kolbaba-Kartchner B, Iqbal R, Burgess HM, Colee CM, Ornelas MY, Reid-McLaughlin ES, Mills JH, Prescher JA, Leconte AM. Biochemical Analysis Leads to Improved Orthogonal Bioluminescent Tools. Chembiochem 2023; 24:e202200726. [PMID: 36592373 PMCID: PMC10265744 DOI: 10.1002/cbic.202200726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/23/2022] [Accepted: 01/02/2023] [Indexed: 01/03/2023]
Abstract
Engineered luciferase-luciferin pairs have expanded the number of cellular targets that can be visualized in tandem. While light production relies on selective processing of synthetic luciferins by mutant luciferases, little is known about the origin of selectivity. The development of new and improved pairs requires a better understanding of the structure-function relationship of bioluminescent probes. In this work, we report a biochemical approach to assessing and optimizing two popular bioluminescent pairs: Cashew/d-luc and Pecan/4'-BrLuc. Single mutants derived from Cashew and Pecan revealed key residues for selectivity and thermal stability. Stability was further improved through a rational addition of beneficial residues. In addition to providing increased stability, the known stabilizing mutations surprisingly also improved selectivity. The resultant improved pair of luciferases are >100-fold selective for their respective substrates and highly thermally stable. Collectively, this work highlights the importance of mechanistic insight for improving bioluminescent pairs and provides significantly improved Cashew and Pecan enzymes which should be immediately suitable for multicomponent imaging applications.
Collapse
Affiliation(s)
- Sierra J Williams
- Department of Chemistry, University of California, Irvine, 1120 Natural Science II, Irvine, CA 92697, USA
| | - Jordan A Gewing-Mullins
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| | - Whitney K Lieberman
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| | - Bethany Kolbaba-Kartchner
- School of Molecular Sciences, Arizona State University, Physical Sciences Center PSd-D102, Tempe, AZ 85287, USA
- The Biodesign Center for Molecular Design and Biomimetics, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA
| | - Reema Iqbal
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| | - Hana M Burgess
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| | - Clair M Colee
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| | - Marya Y Ornelas
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| | - Edison S Reid-McLaughlin
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| | - Jeremy H Mills
- School of Molecular Sciences, Arizona State University, Physical Sciences Center PSd-D102, Tempe, AZ 85287, USA
- The Biodesign Center for Molecular Design and Biomimetics, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, 1120 Natural Science II, Irvine, CA 92697, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, 3205 McGaugh Hall, Irvine, CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, 101 Theory, Suite 100, Irvine, CA 92697, USA
| | - Aaron M Leconte
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| |
Collapse
|
11
|
Mortazavi M, Torkzadeh-Mahani M, Rahimi M, Maleki M, Lotfi S, Riahi-Madvar A. Effects of synonymous mutations on kinetic properties and structure of firefly luciferase: Molecular dynamics simulation, molecular docking, RNA folding, and experimental study. Int J Biol Macromol 2023; 235:123835. [PMID: 36870640 DOI: 10.1016/j.ijbiomac.2023.123835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023]
Abstract
Although synonymous mutations have long been thought to lack striking results, a growing body of research shows these mutations have highly variable effects. In this study, the impact of synonymous mutations in the development of thermostable luciferase was investigated using a combination of experimental and theoretical approaches. Using bioinformatics analysis, the codon usage features in the Lampyridae family's luciferases were studied and four synonymous mutations of Arg in luciferase were created. An exciting result was that the analysis of kinetic parameters showed a slight increase in the thermal stability of the mutant luciferase. AutoDock Vina, %MinMax algorithm, and UNAFold Server were used to perform molecular docking, folding rate, and RNA folding, respectively. Here, it was assumed that in the region (Arg337) with a moderate propensity for coil, synonymous mutation altered the rate of translation, which in turn may lead to a slight change in the structure of the enzyme. According to the molecular dynamics simulation data, local minor global flexibility is observed in the context of the protein conformation. A plausible explanation is that this flexibility may strengthen hydrophobic interactions due to its sensitivity to a molecular collision. Accordingly, thermostability originated mainly from hydrophobic interaction.
Collapse
Affiliation(s)
- Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran.
| | - Masoud Torkzadeh-Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Mehdi Rahimi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Mahmood Maleki
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Safa Lotfi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Ali Riahi-Madvar
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, Kosar University of Bojnord, Bojnord, Iran
| |
Collapse
|
12
|
Maffeis V, Hürlimann D, Krywko-Cendrowska A, Schoenenberger CA, Housecroft CE, Palivan CG. A DNA-Micropatterned Surface for Propagating Biomolecular Signals by Positional on-off Assembly of Catalytic Nanocompartments. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202818. [PMID: 35869606 DOI: 10.1002/smll.202202818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Signal transduction is pivotal for the transfer of information between and within living cells. The composition and spatial organization of specified compartments are key to propagating soluble signals. Here, a high-throughput platform mimicking multistep signal transduction which is based on a geometrically defined array of immobilized catalytic nanocompartments (CNCs) that consist of distinct polymeric nanoassemblies encapsulating enzymes and DNA or enzymes alone is presented. The dual role of single entities or tandem CNCs in providing confined but communicating spaces for complex metabolic reactions and in protecting encapsulated compounds from denaturation is explored. To support a controlled spatial organization of CNCs, CNCs are patterned by means of DNA hybridization to a microprinted glass surface. Specifically, CNC-functionalized DNA microarrays are produced where individual reaction compartments are kept in close proximity by a distinct geometrical arrangement to promote effective communication. Besides a remarkable versatility and robustness, the most prominent feature of this platform is the reversibility of DNA-mediated CNC-anchoring which renders it reusable. Micropatterns of polymer-based nanocompartment assemblies offer an ideal scaffold for the development of the next generation responsive and communicative soft-matter analytical devices for applications in catalysis and medicine.
Collapse
Affiliation(s)
- Viviana Maffeis
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4058, Switzerland
- NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
| | - Dimitri Hürlimann
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4058, Switzerland
- NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
| | - Agata Krywko-Cendrowska
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4058, Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4058, Switzerland
- NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
| | - Catherine E Housecroft
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4058, Switzerland
- NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4058, Switzerland
- NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
| |
Collapse
|
13
|
Martínez-Pérez-Cejuela H, Gregucci D, Calabretta MM, Simó-Alfonso EF, Herrero-Martínez JM, Michelini E. Novel Nanozeolitic Imidazolate Framework (ZIF-8)-Luciferase Biocomposite for Nanosensing Applications. Anal Chem 2022; 95:2540-2547. [PMID: 36473148 PMCID: PMC9893222 DOI: 10.1021/acs.analchem.2c05001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The identification of new strategies to improve the stability of proteins is of utmost importance for a number of applications, from biosensing to biocatalysis. Metal-organic frameworks (MOFs) have been shown as a versatile host platform for the immobilization of proteins, with the potential to protect proteins in harsh conditions. In this work, a new thermostable luciferase mutant has been selected as a bioluminescent protein model to investigate the suitability of MOFs to improve its stability and prompt its applications in real-world applications, for example, ATP detection in portable systems. The luciferase has been immobilized onto zeolitic imidazolate framework-8 (ZIF-8) to obtain a bioluminescent biocomposite with enhanced performance. The biocomposite ZIF-8@luc has been characterized in harsh conditions (e.g., high temperature, non-native pH, etc.). Bioluminescence properties confirmed that MOF enhanced the luciferase stability at acidic pH, in the presence of organic solvents, and at -20 °C. To assess the feasibility of this approach, the recyclability, storage stability, precision, and Michaelis-Menten constants (Km) for ATP and d-luciferin have been also evaluated. As a proof of principle, the suitability for ATP detection was investigated and the biocomposite outperformed the free enzyme in the same experimental conditions, achieving a limit of detection for ATP down to 0.2 fmol.
Collapse
Affiliation(s)
- Héctor Martínez-Pérez-Cejuela
- Department
of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy,Department
of Analytical Chemistry, University of Valencia, C/Dr. Moliner, 50, 46100 Burjassot, Valencia, Spain
| | - Denise Gregucci
- Department
of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy,Center
for Applied Biomedical Research (CRBA), Azienda Ospedaliero-Universitaria Policlinico S. Orsola-Malpighi, 40138 Bologna, Italy
| | - Maria Maddalena Calabretta
- Department
of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy,Center
for Applied Biomedical Research (CRBA), Azienda Ospedaliero-Universitaria Policlinico S. Orsola-Malpighi, 40138 Bologna, Italy
| | | | | | - Elisa Michelini
- Department
of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy,Center
for Applied Biomedical Research (CRBA), Azienda Ospedaliero-Universitaria Policlinico S. Orsola-Malpighi, 40138 Bologna, Italy,Health
Sciences and Technologies Interdepartmental Center for Industrial
Research (HSTICIR), University of Bologna, 40126 Bologna, Italy,. Tel: +39 051 20 9 9533
| |
Collapse
|
14
|
Veggiani G, Villaseñor R, Martyn GD, Tang JQ, Krone MW, Gu J, Chen C, Waters ML, Pearce KH, Baubec T, Sidhu SS. High-affinity chromodomains engineered for improved detection of histone methylation and enhanced CRISPR-based gene repression. Nat Commun 2022; 13:6975. [PMID: 36379931 PMCID: PMC9666628 DOI: 10.1038/s41467-022-34269-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Histone methylation is an important post-translational modification that plays a crucial role in regulating cellular functions, and its dysregulation is implicated in cancer and developmental defects. Therefore, systematic characterization of histone methylation is necessary to elucidate complex biological processes, identify biomarkers, and ultimately, enable drug discovery. Studying histone methylation relies on the use of antibodies, but these suffer from lot-to-lot variation, are costly, and cannot be used in live cells. Chromatin-modification reader domains are potential affinity reagents for methylated histones, but their application is limited by their modest affinities. We used phage display to identify key residues that greatly enhance the affinities of Cbx chromodomains for methylated histone marks and develop a general strategy for enhancing the affinity of chromodomains of the human Cbx protein family. Our strategy allows us to develop powerful probes for genome-wide binding analysis and live-cell imaging. Furthermore, we use optimized chromodomains to develop extremely potent CRISPR-based repressors for tailored gene silencing. Our results highlight the power of engineered chromodomains for analyzing protein interaction networks involving chromatin and represent a modular platform for efficient gene silencing.
Collapse
Affiliation(s)
- G Veggiani
- The Anvil Institute, Kitchener, ON, N2G 1H6, Canada.
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, 70803, USA.
| | - R Villaseñor
- Division of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians-University, 82152, Planegg-Martinsried, Germany
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057, Zurich, Switzerland
| | - G D Martyn
- The Anvil Institute, Kitchener, ON, N2G 1H6, Canada
- School of Pharmacy, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - J Q Tang
- The Anvil Institute, Kitchener, ON, N2G 1H6, Canada
- School of Pharmacy, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - M W Krone
- Department of Chemistry, University of North Carolina at Chapel Hill, CB 3290, Chapel Hill, NC, 27599, USA
| | - J Gu
- The Anvil Institute, Kitchener, ON, N2G 1H6, Canada
| | - C Chen
- The Anvil Institute, Kitchener, ON, N2G 1H6, Canada
| | - M L Waters
- Department of Chemistry, University of North Carolina at Chapel Hill, CB 3290, Chapel Hill, NC, 27599, USA
| | - K H Pearce
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - T Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057, Zurich, Switzerland
- Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, 3584, Utrecht, The Netherlands
| | - S S Sidhu
- The Anvil Institute, Kitchener, ON, N2G 1H6, Canada.
- School of Pharmacy, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
| |
Collapse
|
15
|
Satalkar V, Benassi E, Mao Y, Pan X, Ran C, Chen X, Shao Y. Computational Investigation of Substituent Effects on the Fluorescence Wavelengths of Oxyluciferin Analogs. J Photochem Photobiol A Chem 2022; 431:114018. [PMID: 36407037 PMCID: PMC9673899 DOI: 10.1016/j.jphotochem.2022.114018] [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] [Indexed: 11/21/2022]
Abstract
Oxyluciferin, which is the light emitter for firefly bioluminescence, has been subjected to extensive chemical modifications to tune its emission wavelength and quantum yield. However, the exact mechanisms for various electron-donating and withdrawing groups to perturb the photophysical properties of oxyluciferin analogs are still not fully understood. To elucidate the substituent effects on the fluorescence wavelength of oxyluciferin analogs, we applied the absolutely localized molecular orbitals (ALMO)-based frontier orbital analysis to assess various types of interactions (i.e. permanent electrostatics/exchange repulsion, polarization, occupied-occupied orbital mixing, virtual-virtual orbital mixing, and charge-transfer) between the oxyluciferin and substituent orbitals. We suggested two distinct mechanisms that can lead to red-shifted oxyluciferin emission wavelength, a design objective that can help increase the tissue penetration of bioluminescence emission. Within the first mechanism, an electron-donating group (such as an amino or dimethylamino group) can contribute its highest occupied molecular orbital (HOMO) to an out-of-phase combination with oxyluciferin's HOMO, thus raising the HOMO energy of the substituted analog and narrowing its HOMO-LUMO gap. Alternatively, an electron-withdrawing group (such as a nitro or cyano group) can participate in an in-phase virtual-virtual orbital mixing of fragment LUMOs, thus lowering the LUMO energy of the substituted analog. Such an ALMO-based frontier orbital analysis is expected to lead to intuitive principles for designing analogs of not only the oxyluciferin molecule, but also many other functional dyes.
Collapse
Affiliation(s)
- Vardhan Satalkar
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Enrico Benassi
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Chongzhao Ran
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, MA 02129, USA
| | - Xiaoyuan Chen
- Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, 117597, Singapore
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| |
Collapse
|
16
|
A Luciferase Mutant with Improved Brightness and Stability for Whole-Cell Bioluminescent Biosensors and In Vitro Biosensing. BIOSENSORS 2022; 12:bios12090742. [PMID: 36140127 PMCID: PMC9496056 DOI: 10.3390/bios12090742] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022]
Abstract
The availability of new bioluminescent proteins with tuned properties, both in terms of emission wavelength, kinetics and protein stability, is highly valuable in the bioanalytical field, with the potential to improve the sensitivity and analytical performance of the currently used methods for ATP detection, whole-cell biosensors, and viability assays among others. We present a new luciferase mutant, called BgLuc, suitable for developing whole-cell biosensors and in vitro biosensors characterized by a bioluminescence maximum of 548 nm, narrow emission bandwidth, favorable kinetic properties, and excellent pH- and thermo-stabilities at 37 and 45 °C and pH from 5.0 to 8.0. We assessed the suitability of this new luciferase for whole-cell biosensing with a cell-based bioreporter assay for Nuclear Factor-kappa B (NF-kB) signal transduction pathway using 2D and 3D human embryonic kidney (HEK293T) cells, and for ATP detection with the purified enzyme. In both cases the luciferase showed suitable for sensitive detection of the target analytes, with better or similar performance than the commercial counterparts.
Collapse
|
17
|
Younis MH, Tang Z, Cai W. Multimodality imaging of nanoparticle-based vaccines: Shedding light on immunology. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1807. [PMID: 35501142 PMCID: PMC9481661 DOI: 10.1002/wnan.1807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
In recent years, there have been significant innovations in the development of nanoparticle-based vaccines and vaccine delivery systems. For the purposes of both design and evaluation, these nanovaccines are imaged using the wealth of understanding established around medical imaging of nanomaterials. An important insight to the advancement of the field of nanovaccines can be given by an analysis of the design rationale of an imaging platform, as well as the significance of the information provided by imaging. Nanovaccine imaging strategies can be categorized by the imaging modality leveraged, but it is also worth understanding the superiority or convenience of a given modality over others in a given context of a particular nanovaccine. The most important imaging modalities in this endeavor are optical imaging including near-infrared fluorescence imaging (NIRF), emission tomography methods such as positron emission tomography (PET) and single photon emission computed tomography (SPECT) with or without computed tomography (CT) or magnetic resonance (MR), the emerging magnetic particle imaging (MPI), and finally, multimodal applications of imaging which include molecular imaging with magnetic resonance imaging (MRI) and photoacoustic (PA) imaging. One finds that each of these modalities has strengths and weaknesses, but optical and PET imaging tend, in this context, to be currently the most accessible, convenient, and informative modalities. Nevertheless, an important principle is that there is not a one-size-fits-all solution, and that the specific nanovaccine in question must be compatible with a particular imaging modality. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease.
Collapse
Affiliation(s)
- Muhsin H. Younis
- Department of Medical Physics, University of Wisconsin, Madison, Wisconsin, USA
| | - Zhongmin Tang
- Department of Radiology, University of Wisconsin, Madison, Wisconsin, USA
| | - Weibo Cai
- Department of Medical Physics, University of Wisconsin, Madison, Wisconsin, USA
- Department of Radiology, University of Wisconsin, Madison, Wisconsin, USA
| |
Collapse
|
18
|
Ohmuro-Matsuyama Y, Furuta T, Matsui H, Kanai M, Ueda H. Miniaturization of Bright Light-Emitting Luciferase ALuc: picALuc. ACS Chem Biol 2022; 17:864-872. [PMID: 35293729 DOI: 10.1021/acschembio.1c00897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Luciferases are widely used as sensitive reporters in various fields ranging from basic biology to medical diagnosis, public health, and food inspection. Scientists have isolated novel luciferases from bioluminescent organisms and concentrated on improving their brightness and thermostability. Recently, small bright luciferases such as artificial luciferase (ALuc) (21 kDa), NanoLuc (19 kDa), GLuc (18 kDa), and TurboLuc (16 kDa) have been reported. However, smaller, brighter, and more stable luciferases are desired for further applications. Here, we constructed the smallest and bright mutant of ALuc, named "picALuc" (13 kDa). picALuc retained the luminescence activity of the full-length ALuc; moreover, its brightness and thermostability were at the same levels as NanoLuc. Furthermore, we showed the advantage of picALuc for the bioluminescence resonance energy transfer-based assay due to its smallness. Our development has opened the door for wider and more practical applications of luciferases.
Collapse
Affiliation(s)
- Yuki Ohmuro-Matsuyama
- Technology Research Laboratory, Shimadzu Corporation, Kyoto 619-0237, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hayato Matsui
- Technology Research Laboratory, Shimadzu Corporation, Kyoto 619-0237, Japan
| | - Masaki Kanai
- Technology Research Laboratory, Shimadzu Corporation, Kyoto 619-0237, Japan
| | - Hiroshi Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| |
Collapse
|
19
|
Zubi YS, Seki K, Li Y, Hunt AC, Liu B, Roux B, Jewett MC, Lewis JC. Metal-responsive regulation of enzyme catalysis using genetically encoded chemical switches. Nat Commun 2022; 13:1864. [PMID: 35387988 PMCID: PMC8987029 DOI: 10.1038/s41467-022-29239-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
Dynamic control over protein function is a central challenge in synthetic biology. To address this challenge, we describe the development of an integrated computational and experimental workflow to incorporate a metal-responsive chemical switch into proteins. Pairs of bipyridinylalanine (BpyAla) residues are genetically encoded into two structurally distinct enzymes, a serine protease and firefly luciferase, so that metal coordination biases the conformations of these enzymes, leading to reversible control of activity. Computational analysis and molecular dynamics simulations are used to rationally guide BpyAla placement, significantly reducing experimental workload, and cell-free protein synthesis coupled with high-throughput experimentation enable rapid prototyping of variants. Ultimately, this strategy yields enzymes with a robust 20-fold dynamic range in response to divalent metal salts over 24 on/off switches, demonstrating the potential of this approach. We envision that this strategy of genetically encoding chemical switches into enzymes will complement other protein engineering and synthetic biology efforts, enabling new opportunities for applications where precise regulation of protein function is critical.
Collapse
Affiliation(s)
- Yasmine S Zubi
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Kosuke Seki
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Ying Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Andrew C Hunt
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Bingqing Liu
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
| | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA.
| |
Collapse
|
20
|
Shank-Retzlaff M, Taverner YP, Joshi P, Renu S, Chitikela A, Koneru A, Wang Z, Bronsart L, Mohanty P. Capillary-Mediated Vitrification: A Novel Approach for Improving Thermal Stability of Enzymes and Proteins. J Pharm Sci 2022; 111:2280-2287. [DOI: 10.1016/j.xphs.2022.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/23/2022] [Accepted: 02/23/2022] [Indexed: 11/29/2022]
|
21
|
Ohmuro-Matsuyama Y, Gomi K, Shimoda T, Yamaji H, Ueda H. Improving the Stability of Protein-Protein Interaction Assay FlimPIA Using a Thermostabilized Firefly Luciferase. Front Bioeng Biotechnol 2021; 9:778120. [PMID: 34858964 PMCID: PMC8631863 DOI: 10.3389/fbioe.2021.778120] [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: 09/16/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
The protein–protein interaction assay is a key technology in various fields, being applicable in drug screening as well as in diagnosis and inspection, wherein the stability of assays is important. In a previous study, we developed a unique protein–protein interaction assay “FlimPIA” based on the functional complementation of mutant firefly luciferases (Fluc). The catalytic step of Fluc was divided into two half steps: D-luciferin was adenylated in the first step, while adenylated luciferin was oxidized in the second step. We constructed two mutants of Fluc from Photinus pyralis (Ppy); one mutant named Donor is defective in the second half reaction, while the other mutant named Acceptor exhibited low activity in the first half reaction. To date, Ppy has been used in the system; however, its thermostability is low. In this study, to improve the stability of the system, we applied Fluc from thermostabilized Luciola lateralis to FlimPIA. We screened suitable mutants as probes for FlimPIA and obtained Acceptor and Donor candidates. We detected the interaction of FKBP12-FRB with FlimPIA using these candidates. Furthermore, after the incubation of the probes at 37°C for 1 h, the luminescence signal of the new system was 2.4-fold higher than that of the previous system, showing significant improvement in the stability of the assay.
Collapse
Affiliation(s)
- Yuki Ohmuro-Matsuyama
- Laboratory of Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan.,Technology Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | | | - Takuya Shimoda
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Hideki Yamaji
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Hiroshi Ueda
- Laboratory of Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| |
Collapse
|
22
|
Clifton BE, Fariz MA, Uechi GI, Laurino P. Evolutionary repair reveals an unexpected role of the tRNA modification m1G37 in aminoacylation. Nucleic Acids Res 2021; 49:12467-12485. [PMID: 34761260 PMCID: PMC8643618 DOI: 10.1093/nar/gkab1067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/13/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
The tRNA modification m1G37, introduced by the tRNA methyltransferase TrmD, is thought to be essential for growth in bacteria because it suppresses translational frameshift errors at proline codons. However, because bacteria can tolerate high levels of mistranslation, it is unclear why loss of m1G37 is not tolerated. Here, we addressed this question through experimental evolution of trmD mutant strains of Escherichia coli. Surprisingly, trmD mutant strains were viable even if the m1G37 modification was completely abolished, and showed rapid recovery of growth rate, mainly via duplication or mutation of the proline-tRNA ligase gene proS. Growth assays and in vitro aminoacylation assays showed that G37-unmodified tRNAPro is aminoacylated less efficiently than m1G37-modified tRNAPro, and that growth of trmD mutant strains can be largely restored by single mutations in proS that restore aminoacylation of G37-unmodified tRNAPro. These results show that inefficient aminoacylation of tRNAPro is the main reason for growth defects observed in trmD mutant strains and that proS may act as a gatekeeper of translational accuracy, preventing the use of error-prone unmodified tRNAPro in translation. Our work shows the utility of experimental evolution for uncovering the hidden functions of essential genes and has implications for the development of antibiotics targeting TrmD.
Collapse
Affiliation(s)
- Ben E Clifton
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Muhammad A Fariz
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Gen-Ichiro Uechi
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| |
Collapse
|
23
|
Mutant firefly luciferase enzymes resistant to the inhibition by sodium chloride. Biotechnol Lett 2021; 43:1585-1594. [PMID: 33945054 DOI: 10.1007/s10529-021-03109-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/26/2021] [Indexed: 12/26/2022]
Abstract
OBJECTIVES Firefly luciferase, one of the most extensively studied enzymes, has numerous applications. However, luciferase activity is inhibited by sodium chloride. This study was aimed at obtaining mutant luciferase enzymes resistant to the sodium chloride inhibition. RESULTS We first obtained two mutant luciferase enzymes whose inhibition were alleviated and determined the mutations to be Val288Ile and Glu488Val. Under medical dialysis condition (140 mM sodium chloride), the wild type was inhibited to 44% of its original activity level. In contrast, the single mutants, Val288Ile and Glu488Val, retained 67% and 79% of their original activity, respectively. Next, we introduced Val288Ile and Glu488Val mutations into wild-type luciferase to create a double mutant using site-directed mutagenesis. Notably, the double mutant retained its activity more than 95% of that in the absence of sodium chloride. CONCLUSIONS The mutant luciferase, named luciferase CR, was found to retain its activity in various concentrations of sodium chloride. The luciferase CR may be extensively useful in any bioassay which includes firefly luciferase and is employed in the presence of sodium chloride.
Collapse
|
24
|
Huang J, Zhao X, Bürger M, Wang Y, Chory J. Two interacting ethylene response factors regulate heat stress response. THE PLANT CELL 2021; 33:338-357. [PMID: 33793870 PMCID: PMC8136883 DOI: 10.1093/plcell/koaa026] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/06/2020] [Indexed: 05/05/2023]
Abstract
The ethylene response factor (ERF) transcription factors are integral components of environmental stress signaling cascades, regulating a wide variety of downstream genes related to stress responses and plant development. However, the mechanisms by which ERF genes regulate the heat stress response are not well understood. Here, we uncover the positive role of ethylene signaling, ERF95 and ERF97 in basal thermotolerance of Arabidopsis thaliana. We demonstrate that ethylene signaling-defective mutants exhibit compromised basal thermotolerance, whereas plants with constitutively activated ethylene response show enhanced basal thermotolerance. EIN3 physically binds to the promoters of ERF95 and ERF97. Ectopic constitutive expression of ERF95 or ERF97 increases the basal thermotolerance of plants. In contrast, erf95 erf96 erf97 erf98 quadruple mutants exhibit decreased basal thermotolerance. ERF95 and ERF97 genetically function downstream of EIN3. ERF95 can physically interact with ERF97, and this interaction is heat inducible. ERF95 and ERF97 regulate a common set of target genes, including known heat-responsive genes and directly bind to the promoter of HSFA2. Thus, our study reveals that the EIN3-ERF95/ERF97-HSFA2 transcriptional cascade may play an important role in the heat stress response, thereby establishing a connection between ethylene and its downstream regulation in basal thermotolerance of plants.
Collapse
Affiliation(s)
- Jianyan Huang
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Authors for correspondence: ,
| | - Xiaobo Zhao
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Marco Bürger
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Yurong Wang
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Division of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Joanne Chory
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Authors for correspondence: ,
| |
Collapse
|
25
|
Shi C, Killoran MP, Hall MP, Otto P, Wood MG, Strauss E, Encell LP, Machleidt T, Wood KV, Kirkland TA. 5,5-Dialkylluciferins are thermal stable substrates for bioluminescence-based detection systems. PLoS One 2020; 15:e0243747. [PMID: 33315907 PMCID: PMC7735563 DOI: 10.1371/journal.pone.0243747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/26/2020] [Indexed: 11/18/2022] Open
Abstract
Firefly luciferase-based ATP detection assays are frequently used as a sensitive, cost-efficient method for monitoring hygiene in many industrial settings. Solutions of detection reagent, containing a mixture of a substrate and luciferase enzyme that produces photons in the presence of ATP, are relatively unstable and maintain only a limited shelf life even under refrigerated conditions. It is therefore common for the individual performing a hygiene test to manually prepare fresh reagent at the time of monitoring. To simplify sample processing, a liquid detection reagent with improved thermal stability is needed. The engineered firefly luciferase, Ultra-Glo™, fulfills one aspect of this need and has been valuable for hygiene monitoring because of its high resistance to chemical and thermal inactivation. However, solutions containing both Ultra-Glo™ luciferase and its substrate luciferin gradually lose the ability to effectively detect ATP over time. We demonstrate here that dehydroluciferin, a prevalent oxidative breakdown product of luciferin, is a potent inhibitor of Ultra-Glo™ luciferase and that its formation in the detection reagent is responsible for the decreased ability to detect ATP. We subsequently found that dialkylation at the 5-position of luciferin (e.g., 5,5-dimethylluciferin) prevents degradation to dehydroluciferin and improves substrate thermostability in solution. However, since 5,5-dialkylluciferins are poorly utilized by Ultra-Glo™ luciferase as substrates, we used structural optimization of the luciferin dialkyl modification and protein engineering of Ultra-Glo™ to develop a luciferase/luciferin pair that shows improved total reagent stability in solution at ambient temperature. The results of our studies outline a novel luciferase/luciferin system that could serve as foundations for the next generation of bioluminescence ATP detection assays with desirable reagent stability.
Collapse
Affiliation(s)
- Ce Shi
- Promega Biosciences, Inc., San Luis Obispo, California, United States of America
| | | | - Mary P. Hall
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Paul Otto
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Monika G. Wood
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Ethan Strauss
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Lance P. Encell
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Thomas Machleidt
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Keith V. Wood
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Thomas A. Kirkland
- Promega Biosciences, Inc., San Luis Obispo, California, United States of America
| |
Collapse
|
26
|
Endo M, Ozawa T. Advanced Bioluminescence System for In Vivo Imaging with Brighter and Red-Shifted Light Emission. Int J Mol Sci 2020; 21:E6538. [PMID: 32906768 PMCID: PMC7555964 DOI: 10.3390/ijms21186538] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 01/04/2023] Open
Abstract
In vivo bioluminescence imaging (BLI), which is based on luminescence emitted by the luciferase-luciferin reaction, has enabled continuous monitoring of various biochemical processes in living animals. Bright luminescence with a high signal-to-background ratio, ideally red or near-infrared light as the emission maximum, is necessary for in vivo animal experiments. Various attempts have been undertaken to achieve this goal, including genetic engineering of luciferase, chemical modulation of luciferin, and utilization of bioluminescence resonance energy transfer (BRET). In this review, we overview a recent advance in the development of a bioluminescence system for in vivo BLI. We also specifically examine the improvement in bioluminescence intensity by mutagenic or chemical modulation on several beetle and marine luciferase bioluminescence systems. We further describe that intramolecular BRET enhances luminescence emission, with recent attempts for the development of red-shifted bioluminescence system, showing great potency in in vivo BLI. Perspectives for future improvement of bioluminescence systems are discussed.
Collapse
Affiliation(s)
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan;
| |
Collapse
|
27
|
Dale R, Ohmuro-Matsuyama Y, Ueda H, Kato N. Non-Steady State Analysis of Enzyme Kinetics in Real Time Elucidates Substrate Association and Dissociation Rates: Demonstration with Analysis of Firefly Luciferase Mutants. Biochemistry 2019; 58:2695-2702. [PMID: 31125202 DOI: 10.1021/acs.biochem.9b00272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Firefly luciferase has been widely used in biotechnology and biophotonics due to photon emission during enzymatic activity. In the past, the effect of amino acid substitutions (mutants) on the enzymatic activity of firefly luciferase has been characterized by the Michaelis constant, KM. The KM is obtained by plotting the maximum relative luminescence units (RLU) detected for several concentrations of the substrate (luciferin or luciferyl-adenylate). The maximum RLU is used because the assay begins to violate the quasi-steady state approximation when RLU decays as a function of time. However, mutations also affect the time to reach and decay from the maximum RLU. These effects are not captured when calculating the KM. To understand changes in the RLU kinetics of firefly luciferase mutants, we used a Michaelis-Menten model with the non-steady state approximation. In this model, we do not assume that the amount of enzyme-substrate complex is at equilibrium throughout the course of the experiment. We found that one of the two mutants analyzed in this study decreases not only the dissociation rate ( koff) but also the association rate ( kon) of luciferyl-adenylate, suggesting the narrowing of the structural pocket containing the catalytic amino acids. Furthermore, comparative analysis of the nearly complete oxidation of luciferyl-adenylate with wild-type and mutant firefly luciferase reveals that the total amount of photons emitted with the mutant is 50-fold larger than that with the wild type, on average. These two results together indicate that the slow supply of luciferyl-adenylate to the enzyme increases the total number of photons emitted from the substrate, luciferyl-adenylate. Analysis with the non-steady state approximation model is generally applicable when enzymatic production kinetics are monitored in real time.
Collapse
Affiliation(s)
- Renee Dale
- Department of Biological Sciences , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
- Department of Experimental Statistics , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Yuki Ohmuro-Matsuyama
- Laboratory for Chemistry and Life Science, Institute of Innovative Research , Tokyo Institute of Technology , Nagatsuta-cho, Yokohama , Kanagawa 226-8503 , Japan
| | - Hiroshi Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research , Tokyo Institute of Technology , Nagatsuta-cho, Yokohama , Kanagawa 226-8503 , Japan
| | - Naohiro Kato
- Department of Biological Sciences , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| |
Collapse
|
28
|
Pozzo T, Higdon SM, Pattathil S, Hahn MG, Bennett AB. Characterization of novel glycosyl hydrolases discovered by cell wall glycan directed monoclonal antibody screening and metagenome analysis of maize aerial root mucilage. PLoS One 2018; 13:e0204525. [PMID: 30256843 PMCID: PMC6157868 DOI: 10.1371/journal.pone.0204525] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/10/2018] [Indexed: 11/19/2022] Open
Abstract
An indigenous maize landrace from the Sierra Mixe region of Oaxaca, Mexico exhibits extensive formation of aerial roots which exude large volumes of a polysaccharide-rich gel matrix or "mucilage" that harbors diazotrophic microbiota. We hypothesize that the mucilage associated microbial community carries out multiple functions, including disassembly of the mucilage polysaccharide. In situ, hydrolytic assay of the mucilage revealed endogenous arabinofuranosidase, galactosidase, fucosidase, mannosidase and xylanase activities. Screening the mucilage against plant cell wall glycan-specific monoclonal antibodies recognized the presence of carbohydrate epitopes of hemicellulosic polysaccharides like xyloglucan (both non-fucosylated and fucosylated), xylan (both substituted and unsubstituted xylan domains) and pectic-arabinogalactans, all of which are potential carbon sources for mucilage microbial residents. Mucilage metagenome annotation using MG-RAST identified the members forming the microbial community, and gene fragments with predicted functions associated with carbohydrate disassembly. Data from the in situ hydrolytic activity and monoclonal antibody screening assays were used to guide the selection of five full length genes with predicted glycosyl hydrolase function from the GenBank database that were similar to gene fragments of high relative abundance in the mucilage metagenomes. These five genes were then synthesized for recombinant production in Escherichia coli. Here we report the characterization of an α-N-arabinofuranosidase (GH51) and an oligosaccharide reducing-end xylanase (GH8) from Flavobacterium johnsoniae; an α-L-fucosidase (GH29) and a xylan β-1,4 xylosidase (GH39) from Spirosoma linguale, and a β-mannosidase (GH2) from Agrobacterium fabrum. Biochemical characterization of these enzymes revealed a β-Mannosidase that also exhibits a secondary activity towards the cleavage of galactosyl residues. We also describe two xylanases (GH8 and GH39) from underexplored glycosyl hydrolase families, one thermostable α-L-Fucosidase (GH29) and a thermostable α-N-Arabinofuranosidase (GH51).
Collapse
Affiliation(s)
- Tania Pozzo
- Department of Plant Sciences, University of California, Davis, CA, United States of America
| | - Shawn M. Higdon
- Department of Plant Sciences, University of California, Davis, CA, United States of America
| | - Sivakumar Pattathil
- Mascoma LLC (Lallemand Inc.), Lebanon, NH, United States of America
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Michael G. Hahn
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States of America
| | - Alan B. Bennett
- Department of Plant Sciences, University of California, Davis, CA, United States of America
| |
Collapse
|