1
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Dash R, Holsinger KA, Chordia MD, Gh. MS, Pires MM. Bioluminescence-Based Determination of Cytosolic Accumulation of Antibiotics in Escherichia coli. ACS Infect Dis 2024; 10:1602-1611. [PMID: 38592927 PMCID: PMC11091882 DOI: 10.1021/acsinfecdis.3c00684] [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: 12/11/2023] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
Antibiotic resistance is an alarming public health concern that affects millions of individuals across the globe each year. A major challenge in the development of effective antibiotics lies in their limited ability to permeate cells, noting that numerous susceptible antibiotic targets reside within the bacterial cytosol. Consequently, improving the cellular permeability is often a key consideration during antibiotic development, underscoring the need for reliable methods to assess the permeability of molecules across cellular membranes. Currently, methods used to measure permeability often fail to discriminate between the arrival within the cytoplasm and the overall association of molecules with the cell. Additionally, these techniques typically possess throughput limitations. In this work, we describe a luciferase-based assay designed for assessing the permeability of molecules in the cytosolic compartment of Gram-negative bacteria. Our findings demonstrate a robust system that can elucidate the kinetics of intracellular antibiotic accumulation in live bacterial cells in real time.
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Affiliation(s)
- Rachita Dash
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Kadie A. Holsinger
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Mahendra D. Chordia
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Mohammad Sharifian Gh.
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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2
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Dash R, Holsinger KA, Chordia MD, Sharifian Gh M, Pires MM. Bioluminescence-Based Determination of Cytosolic Accumulation of Antibiotics in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570448. [PMID: 38106213 PMCID: PMC10723488 DOI: 10.1101/2023.12.06.570448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Antibiotic resistance is an alarming public health concern that affects millions of individuals across the globe each year. A major challenge in the development of effective antibiotics lies in their limited ability to permeate into cells, noting that numerous susceptible antibiotic targets reside within the bacterial cytosol. Consequently, improving cellular permeability is often a key consideration during antibiotic development, underscoring the need for reliable methods to assess the permeability of molecules across cellular membranes. Currently, methods used to measure permeability often fail to discriminate between arrival within the cytoplasm and the overall association of molecules with the cell. Additionally, these techniques typically possess throughput limitations. In this work, we describe a luciferase-based assay designed for assessing the permeability of molecules into the cytosolic compartment of Gram-negative bacteria. Our findings demonstrate a robust system that can elucidate the kinetics of intracellular antibiotics accumulation in live bacterial cells in real time.
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3
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Bolt YV, Dubinnyi MA, Litvinenko VV, Kotlobay AA, Belozerova OA, Zagitova RI, Shmygarev VI, Yatskin ON, Guglya EB, Kublitski VS, Baranov MS, Yampolsky IV, Kaskova ZM, Tsarkova AS. Total Synthesis of Racemic Thieno[3,2- f]thiochromene Tricarboxylate, a Luciferin from Marine Polychaeta Odontosyllis undecimdonta. Org Lett 2023. [PMID: 37366567 DOI: 10.1021/acs.orglett.3c01696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
We report the first total synthesis of racemic Odontosyllis undecimdonta luciferin, a thieno[3,2-f]thiochromene tricarboxylate comprising a 6-6-5-fused tricyclic skeleton with three sulfur atoms in different electronic states. The key transformation is based on tandem condensation of bifunctional thiol-phosphonate, obtained from dimethyl acetylene dicarboxylate, with benzothiophene-6,7-quinone. The presented convergent approach provides the synthesis of the target compound with a previously unreported fused heterocyclic core in 11 steps, thus allowing for unambiguous confirmation of the chemical structure of Odontosyllis luciferin by 2D-NMR spectroscopy.
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Affiliation(s)
- Yaroslav V Bolt
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Maxim A Dubinnyi
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Veronika V Litvinenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexey A Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Olga A Belozerova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Renata I Zagitova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Vladimir I Shmygarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Oleg N Yatskin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Elena B Guglya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Vadim S Kublitski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Ilia V Yampolsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Planta LLC, Moscow 109507, Russia
| | - Zinaida M Kaskova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Aleksandra S Tsarkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
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4
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Liu YJ. Understanding the complete bioluminescence cycle from a multiscale computational perspective: A review. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2022. [DOI: 10.1016/j.jphotochemrev.2022.100537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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5
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Niwa K, Kato DI. Biosynthesis-Inspired Deracemizative Production of D-Luciferin In Vitro by Combining Luciferase and Thioesterase. Methods Mol Biol 2022; 2524:53-58. [PMID: 35821462 DOI: 10.1007/978-1-0716-2453-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Due to the strict enantioselectivity of firefly luciferase (FLuc), only D-luciferin can be used as a substrate for the bioluminescence (BL) reaction. Unfortunately, luciferin racemizes easily and accumulation of nonluminous L-luciferin has negative influences on the light-emitting reaction. By a detailed analysis of luciferin chirality, however, it becomes clarified that L-luciferin is the biosynthetic precursor of D-luciferin in fireflies and undergoes the enzymatic chiral inversion. By the chiral inversion reaction, the enantiopurity of luciferin can be maintained in the reaction mixture for applications using FLuc. Thus, chirality is crucial for the BL reaction and essential for investigating and applying the biosynthesis of D-luciferin. Here, we describe the methods for the analysis of chiral inversion reaction using high-performance liquid chromatography (HPLC) with a chiral column. We also introduce an example of an in vitro deracemizative BL reaction system using a combination of FLuc and fatty acyl-CoA thioesterase, which is inspired by the chiral inversion mechanism in the biosynthetic pathway of D-luciferin.
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Affiliation(s)
- Kazuki Niwa
- Research Institute for Physical Measurement, National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Dai-Ichiro Kato
- Department of Science, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan.
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6
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Kitada N, Saito R, Obata R, Iwano S, Karube K, Miyawaki A, Hirano T, Maki SA. Development of near-infrared firefly luciferin analogue reacted with wild-type and mutant luciferases. Chirality 2020; 32:922-931. [PMID: 32367573 PMCID: PMC7383472 DOI: 10.1002/chir.23236] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 02/06/2023]
Abstract
Interestingly, only the D-form of firefly luciferin produces light by luciferin-luciferase (L-L) reaction. Certain firefly luciferin analogues with modified structures maintain bioluminescence (BL) activity; however, all L-form luciferin analogues show no BL activity. To this date, our group has developed luciferin analogues with moderate BL activity that produce light of various wavelengths. For in vivo bioluminescence imaging, one of the important factors for detection sensitivity is tissue permeability of the number of photons emitted by L-L reaction, and the wavelengths of light in the near-infrared (NIR) range (700-900 nm) are most appropriate for the purpose. Some NIR luciferin analogues by us had performance for in vivo experiments to make it possible to detect photons from deep target tissues in mice with high sensitivity, whereas only a few of them can produce NIR light by the L-L reactions with wild-type luciferase and/or mutant luciferase. Based on the structure-activity relationships, we designed and synthesized here a luciferin analogue with the 5-allyl-6-dimethylamino-2-naphthylethenyl moiety. This analogue exhibited NIR BL emissions with wild-type luciferase (λmax = 705 nm) and mutant luciferase AlaLuc (λmax = 655 nm).
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Affiliation(s)
- Nobuo Kitada
- Department of Engineering Science, Graduate School of Informatics and Engineering,, The University of Electro-Communications, Chofu, Japan.,Center for Neuroscience and Biomedical Engineering, The University of Electro-Communications, Chofu, Japan
| | - Ryohei Saito
- Department of Engineering Science, Graduate School of Informatics and Engineering,, The University of Electro-Communications, Chofu, Japan.,School of Pharmacy, Tokyo University of Pharmacy and Life Science, Tokyo, Japan
| | - Rika Obata
- Department of Engineering Science, Graduate School of Informatics and Engineering,, The University of Electro-Communications, Chofu, Japan
| | - Satoshi Iwano
- Laboratory for Cell Function and Dynamics, Center for Brain Science, Saitama, Japan
| | - Kazuma Karube
- Department of Engineering Science, Graduate School of Informatics and Engineering,, The University of Electro-Communications, Chofu, Japan
| | - Atsushi Miyawaki
- Laboratory for Cell Function and Dynamics, Center for Brain Science, Saitama, Japan
| | - Takashi Hirano
- Department of Engineering Science, Graduate School of Informatics and Engineering,, The University of Electro-Communications, Chofu, Japan
| | - Shojiro A Maki
- Department of Engineering Science, Graduate School of Informatics and Engineering,, The University of Electro-Communications, Chofu, Japan.,Center for Neuroscience and Biomedical Engineering, The University of Electro-Communications, Chofu, Japan
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7
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Adams ST, Miller SC. Enzymatic promiscuity and the evolution of bioluminescence. FEBS J 2020; 287:1369-1380. [PMID: 31828943 PMCID: PMC7217382 DOI: 10.1111/febs.15176] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/26/2019] [Accepted: 12/10/2019] [Indexed: 01/18/2023]
Abstract
Bioluminescence occurs when an enzyme, known as a luciferase, oxidizes a small-molecule substrate, known as a luciferin. Nature has evolved multiple distinct luciferases and luciferins independently, all of which accomplish the impressive feat of light emission. One of the best-known examples of bioluminescence is exhibited by fireflies, a class of beetles that use d-luciferin as their substrate. The evolution of bioluminescence in beetles is thought to have emerged from ancestral fatty acyl-CoA synthetase (ACS) enzymes present in all insects. This theory is supported by multiple lines of evidence: Beetle luciferases share high sequence identity with these enzymes, often retain ACS activity, and some ACS enzymes from nonluminous insects can catalyze bioluminescence from synthetic d-luciferin analogues. Recent sequencing of firefly genomes and transcriptomes further illuminates how the duplication of ACS enzymes and subsequent diversification drove the evolution of bioluminescence. These genetic analyses have also uncovered candidate enzymes that may participate in luciferin metabolism. With the publication of the genomes and transcriptomes of fireflies and related insects, we are now better positioned to dissect and learn from the evolution of bioluminescence in beetles.
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Affiliation(s)
- Spencer T. Adams
- Department of Biochemistry and Molecular Pharmacology, University of
Massachusetts Medical School, Worcester, MA 01605 USA
| | - Stephen C. Miller
- Department of Biochemistry and Molecular Pharmacology, University of
Massachusetts Medical School, Worcester, MA 01605 USA
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8
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Wilkinson IVL, Reynolds JK, Galan SRG, Vuorinen A, Sills AJ, Pires E, Wynne GM, Wilson FX, Russell AJ. Characterisation of utrophin modulator SMT C1100 as a non-competitive inhibitor of firefly luciferase. Bioorg Chem 2019; 94:103395. [PMID: 31733898 DOI: 10.1016/j.bioorg.2019.103395] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022]
Abstract
Firefly luciferase (FLuc) is a powerful tool for molecular and cellular biology, and popular in high-throughput screening and drug discovery. However, FLuc assays have been plagued with positive and negative artefacts due to stabilisation and inhibition by small molecules from a range of chemical classes. Here we disclose Phase II clinical compound SMT C1100 for the treatment of Duchenne muscular dystrophy as an FLuc inhibitor (KD of 0.40 ± 0.15 µM). Enzyme kinetic studies using SMT C1100 and other non-competitive inhibitors including resveratrol and NFκBAI4 identified previously undescribed modes of inhibition with respect to FLuc's luciferyl adenylate intermediate. Employing a photoaffinity strategy to identify SMT C1100's binding site, a photolabelled SMT C1100 probe instead underwent FLuc-dependent photooxidation. Our findings support novel binding sites on FLuc for non-competitive inhibitors.
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Affiliation(s)
- Isabel V L Wilkinson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Jessica K Reynolds
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Sébastien R G Galan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Aini Vuorinen
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Adam J Sills
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Elisabete Pires
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Graham M Wynne
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Francis X Wilson
- Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon, Oxfordshire OX14 4SB, UK
| | - Angela J Russell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK; Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3PQ, UK.
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9
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Cheng YY, Liu YJ. Luciferin Regeneration in Firefly Bioluminescence via Proton-Transfer-Facilitated Hydrolysis, Condensation and Chiral Inversion. Chemphyschem 2019; 20:1719-1727. [PMID: 31090243 DOI: 10.1002/cphc.201900306] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/07/2019] [Indexed: 01/06/2023]
Abstract
Firefly bioluminescence is produced via luciferin enzymatic reactions in luciferase. Luciferin has to be unceasingly replenished to maintain bioluminescence. How is the luciferin reproduced after it has been exhausted? In the early 1970s, Okada proposed the hypothesis that the oxyluciferin produced by the previous bioluminescent reaction could be converted into new luciferin for the next bioluminescent reaction. To some extent, this hypothesis was evidenced by several detected intermediates. However, the detailed process and mechanism of luciferin regeneration remained largely unknown. For the first time, we investigated the entire process of luciferin regeneration in firefly bioluminescence by density functional theory calculations. This theoretical study suggests that luciferin regeneration consists of three sequential steps: the oxyluciferin produced from the last bioluminescent reaction generates 2-cyano-6-hydroxybenzothiazole (CHBT) in the luciferin regenerating enzyme (LRE) via a hydrolysis reaction; CHBT combines with L-cysteine in vivo to form L-luciferin via a condensation reaction; and L-luciferin inverts into D-luciferin in luciferase and thioesterase. The presently proposed mechanism not only supports the sporadic evidence from previous experiments but also clearly describes the complete process of luciferin regeneration. This work is of great significance for understanding the long-term flashing of fireflies without an in vitro energy supply.
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Affiliation(s)
- Yuan-Yuan Cheng
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
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10
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Bazhin AA, Chambon M, Vesin J, Bortoli J, Collins JW, Turcatti G, Chou CJ, Goun EA. A Universal Assay for Aminopeptidase Activity and Its Application for Dipeptidyl Peptidase-4 Drug Discovery. Anal Chem 2018; 91:1098-1104. [PMID: 30511572 DOI: 10.1021/acs.analchem.8b04672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Aminopeptidases, such as dipeptidyl peptidase-4 (DPP-4, CD26), are potent therapeutic targets for pharmacological interventions because they play key roles in many important pathological pathways. To analyze aminopeptidase activity in vitro (including high-throughput screening [HTS]), in vivo, and ex vivo, we developed a highly sensitive and quantitative bioluminescence-based readout method. We successfully applied this method to screening drugs with potential DPP-4 inhibitory activity. Using this method, we found that cancer drug mitoxantrone possesses significant DPP-4 inhibitory activity both in vitro and in vivo. The pharmacophore of mitoxantrone was further investigated by testing a variety of its structural analogues.
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Affiliation(s)
| | | | | | | | | | | | - Chieh Jason Chou
- Microbiome and Metabolism , Nestlé Institute of Health Sciences SA , Lausanne 1015 , Switzerland
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11
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Clark L, Leatherby D, Krilich E, Ropelewski AJ, Perozich J. In silico analysis of class I adenylate-forming enzymes reveals family and group-specific conservations. PLoS One 2018; 13:e0203218. [PMID: 30180199 PMCID: PMC6122825 DOI: 10.1371/journal.pone.0203218] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/16/2018] [Indexed: 12/24/2022] Open
Abstract
Luciferases, aryl- and fatty-acyl CoA synthetases, and non-ribosomal peptide synthetase proteins belong to the class I adenylate-forming enzyme superfamily. The reaction catalyzed by the adenylate-forming enzymes is categorized by a two-step process of adenylation and thioesterification. Although all of these proteins perform a similar two-step process, each family may perform the process to yield completely different results. For example, luciferase proteins perform adenylation and oxidation to produce the green fluorescent light found in fireflies, while fatty-acyl CoA synthetases perform adenylation and thioesterification with coenzyme A to assist in metabolic processes involving fatty acids. This study aligned a total of 374 sequences belonging to the adenylate-forming superfamily. Analysis of the sequences revealed five fully conserved residues throughout all sequences, as well as 78 more residues conserved in at least 60% of sequences aligned. Conserved positions are involved in magnesium and AMP binding and maintaining enzyme structure. Also, ten conserved sequence motifs that included most of the conserved residues were identified. A phylogenetic tree was used to assign sequences into nine different groups. Finally, group entropy analysis identified novel conservations unique to each enzyme group. Common group-specific positions identified in multiple groups include positions critical to coordinating AMP and the CoA-bound product, a position that governs active site shape, and positions that help to maintain enzyme structure through hydrogen bonds and hydrophobic interactions. These positions could serve as excellent targets for future research.
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Affiliation(s)
- Louis Clark
- Department of Biology, Franciscan University of Steubenville, Steubenville, OH, United States of America
| | - Danielle Leatherby
- Department of Biology, Franciscan University of Steubenville, Steubenville, OH, United States of America
| | - Elizabeth Krilich
- Department of Biology, Franciscan University of Steubenville, Steubenville, OH, United States of America
| | - Alexander J Ropelewski
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - John Perozich
- Department of Biology, Franciscan University of Steubenville, Steubenville, OH, United States of America
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12
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Alata I, Pérez-Mellor A, Ben Nasr F, Scuderi D, Steinmetz V, Gobert F, Jaïdane NE, Zehnacker-Rentien A. Does the Residues Chirality Modify the Conformation of a Cyclo-Dipeptide? Vibrational Spectroscopy of Protonated Cyclo-diphenylalanine in the Gas Phase. J Phys Chem A 2017; 121:7130-7138. [DOI: 10.1021/acs.jpca.7b06159] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ivan Alata
- Institut
des Sciences Moléculaires d’Orsay, CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Ariel Pérez-Mellor
- Institut
des Sciences Moléculaires d’Orsay, CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Feriel Ben Nasr
- Institut
des Sciences Moléculaires d’Orsay, CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
- Laboratoire
de Spectroscopie Atomique Moléculaire et Applications, Université de Tunis El Manar, Tunis 1060, Tunisia
| | - Debora Scuderi
- Laboratoire
de Chimie Physique, CNRS, UMR8000, Univ. Paris-Sud, Orsay F-91405, France
| | - Vincent Steinmetz
- Laboratoire
de Chimie Physique, CNRS, UMR8000, Univ. Paris-Sud, Orsay F-91405, France
| | - Fabrice Gobert
- Laboratoire
de Chimie Physique, CNRS, UMR8000, Univ. Paris-Sud, Orsay F-91405, France
| | - Nejm-Eddine Jaïdane
- Laboratoire
de Spectroscopie Atomique Moléculaire et Applications, Université de Tunis El Manar, Tunis 1060, Tunisia
| | - Anne Zehnacker-Rentien
- Institut
des Sciences Moléculaires d’Orsay, CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
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13
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Maeda J, Kato DI, Okuda M, Takeo M, Negoro S, Arima K, Ito Y, Niwa K. Biosynthesis-inspired deracemizative production of d-luciferin by combining luciferase and thioesterase. Biochim Biophys Acta Gen Subj 2017; 1861:2112-2118. [DOI: 10.1016/j.bbagen.2017.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/17/2017] [Accepted: 04/24/2017] [Indexed: 10/19/2022]
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14
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Vongsangnak W, Chumnanpuen P, Sriboonlert A. Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae). PeerJ 2016; 4:e2534. [PMID: 27761329 PMCID: PMC5068357 DOI: 10.7717/peerj.2534] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 09/06/2016] [Indexed: 12/31/2022] Open
Abstract
Bioluminescence, which living organisms such as fireflies emit light, has been studied extensively for over half a century. This intriguing reaction, having its origins in nature where glowing insects can signal things such as attraction or defense, is now widely used in biotechnology with applications of bioluminescence and chemiluminescence. Luciferase, a key enzyme in this reaction, has been well characterized; however, the enzymes involved in the biosynthetic pathway of its substrate, luciferin, remains unsolved at present. To elucidate the luciferin metabolism, we performed a de novo transcriptome analysis using larvae of the firefly species, Luciola aquatilis. Here, a comparative analysis is performed with the model coleopteran insect Tribolium casteneum to elucidate the metabolic pathways in L. aquatilis. Based on a template luciferin biosynthetic pathway, combined with a range of protein and pathway databases, and various prediction tools for functional annotation, the candidate genes, enzymes, and biochemical reactions involved in luciferin metabolism are proposed for L. aquatilis. The candidate gene expression is validated in the adult L. aquatilis using reverse transcription PCR (RT-PCR). This study provides useful information on the bio-production of luciferin in the firefly and will benefit to future applications of the valuable firefly bioluminescence system.
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Affiliation(s)
- Wanwipa Vongsangnak
- Department of Zoology, Kasetsart University, Bangkok, Thailand; Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pramote Chumnanpuen
- Department of Zoology, Kasetsart University, Bangkok, Thailand; Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Ajaraporn Sriboonlert
- Department of Genetics, Kasetsart University, Bangkok, Thailand; Centre for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok, Thailand
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15
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Hemmati R, Hosseinkhani S, Sajedi RH, Azad T, Tashakor A, Bakhtiari N, Ataei F. Luciferin-Regenerating Enzyme Mediates Firefly Luciferase Activation Through Direct Effects of D-Cysteine on Luciferase Structure and Activity. Photochem Photobiol 2015; 91:828-36. [PMID: 25665080 DOI: 10.1111/php.12430] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 02/03/2015] [Indexed: 12/01/2022]
Abstract
Luciferin-regenerating enzyme (LRE) contributes to in vitro recycling of D-luciferin. In this study, reinvestigation of the luciferase-based LRE assay is reported. Here, using quick change site-directed mutagenesis seven T-LRE (Lampyris turkestanicusLRE) mutants were constructed and the most functional mutant of T-LRE (T(69)R) was selected for this research and the effects of D- and L-cysteine on T(69)R T-LRE-luciferase-coupled assay are examined. Our results demonstrate that bioluminescent signal of T(69)R T-LRE-luciferase-coupled assay increases and then reach equilibrium state in the presence of 5 mm D-cysteine. In addition, results reveal that 5 mm D- and L-cysteine in the absence of T(69)R T-LRE cause a significant increase in bioluminescence intensity of luciferase over a long time as well as decrease in decay rate. Based on activity measurements, far-UV CD analysis, ANS fluorescence and DLS (Dynamic light scattering) results, D-cysteine increases the activity of luciferase due to weak redox potential, antiaggregatory effects, induction of changes in conformational structure and kinetics properties. In conclusion, in spite of previous reports on the effect of LRE on luciferase bioluminescent intensity, the majority of increase in luciferase light output and time-course originate from the direct effects of D-cysteine on structure and activity of firefly luciferase.
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Affiliation(s)
- Roohullah Hemmati
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Taha Azad
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amin Tashakor
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Nuredin Bakhtiari
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Farangis Ataei
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Latent luciferase activity in the fruit fly revealed by a synthetic luciferin. Proc Natl Acad Sci U S A 2014; 111:4443-8. [PMID: 24616520 DOI: 10.1073/pnas.1319300111] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Beetle luciferases are thought to have evolved from fatty acyl-CoA synthetases present in all insects. Both classes of enzymes activate fatty acids with ATP to form acyl-adenylate intermediates, but only luciferases can activate and oxidize d-luciferin to emit light. Here we show that the Drosophila fatty acyl-CoA synthetase CG6178, which cannot use d-luciferin as a substrate, is able to catalyze light emission from the synthetic luciferin analog CycLuc2. Bioluminescence can be detected from the purified protein, live Drosophila Schneider 2 cells, and from mammalian cells transfected with CG6178. Thus, the nonluminescent fruit fly possesses an inherent capacity for bioluminescence that is only revealed upon treatment with a xenobiotic molecule. This result expands the scope of bioluminescence and demonstrates that the introduction of a new substrate can unmask latent enzymatic activity that differs significantly from an enzyme's normal function without requiring mutation.
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17
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Kato DI, Hiraishi Y, Maenaka M, Yokoyama K, Niwa K, Ohmiya Y, Takeo M, Negoro S. Interconversion of ketoprofen recognition in firefly luciferase-catalyzed enantioselective thioesterification reaction using from Pylocoeria miyako (PmL) and Hotaria parvura (HpL) just by mutating two amino acid residues. J Biotechnol 2013; 168:277-83. [DOI: 10.1016/j.jbiotec.2013.04.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 04/15/2013] [Accepted: 04/18/2013] [Indexed: 10/26/2022]
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18
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Poutiainen PK, Palvimo JJ, Hinkkanen AE, Valkonen A, Väisänen TK, Laatikainen R, Pulkkinen JT. Discovery of 5-Benzyl-3-phenyl-4,5-dihydroisoxazoles and 5-Benzyl-3-phenyl-1,4,2-dioxazoles as Potent Firefly Luciferase Inhibitors. J Med Chem 2013; 56:1064-73. [DOI: 10.1021/jm301516q] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | | | - Ari E. Hinkkanen
- A. I. Virtanen Institute for Molecular
Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211Kuopio, Finland
| | - Arto Valkonen
- Department of Chemistry, University of Jyväskylä, P.O. Box 35,
FI-40014 Jyväskylä, Finland
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Sundlov JA, Fontaine DM, Southworth TL, Branchini BR, Gulick AM. Crystal structure of firefly luciferase in a second catalytic conformation supports a domain alternation mechanism. Biochemistry 2012; 51:6493-5. [PMID: 22852753 DOI: 10.1021/bi300934s] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Beetle luciferases catalyze a two-step reaction that includes the initial adenylation of the luciferin substrate, followed by an oxidative decarboxylation that ultimately produces light. Evidence for homologous acyl-CoA synthetases supports a domain alternation catalytic mechanism in which these enzymes' C-terminal domain rotates by ~140° to adopt two conformations that are used to catalyze the two partial reactions. While many structures exist of acyl-CoA synthetases in both conformations, to date only biochemical evidence supports domain alternation with luciferase. We have determined the structure of a cross-linked luciferase enzyme that is trapped in the second conformation. This new structure supports the role of the second catalytic conformation and provides insights into the biochemical mechanism of the luciferase oxidative step.
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Affiliation(s)
- Jesse A Sundlov
- Hauptman-Woodward Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
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20
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Pinto da Silva L, Vieira J, Esteves da Silva JC. Comparative theoretical study of the binding of luciferyl-adenylate and dehydroluciferyl-adenylate to firefly luciferase. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.06.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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21
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Abstract
Bioluminescence imaging of live cells has recently been recognized as an important alternative to fluorescence imaging. Fluorescent probes are much brighter than bioluminescent probes (luciferase enzymes) and, therefore, provide much better spatial and temporal resolution and much better contrast for delineating cell structure. However, with bioluminescence imaging there is virtually no background or toxicity. As a result, bioluminescence can be superior to fluorescence for detecting and quantifying molecules and their interactions in living cells, particularly in long-term studies. Structurally diverse luciferases from beetle and marine species have been used for a wide variety of applications, including tracking cells in vivo, detecting protein-protein interactions, measuring levels of calcium and other signaling molecules, detecting protease activity, and reporting circadian clock gene expression. Such applications can be optimized by the use of brighter and variously colored luciferases, brighter microscope optics, and ultrasensitive, low-noise cameras. This article presents a review of how bioluminescence differs from fluorescence, its applications to cellular imaging, and available probes, optics, and detectors. It also gives practical suggestions for optimal bioluminescence imaging of single cells.
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22
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Kato DI, Tatsumi T, Bansho A, Teruya K, Yoshida H, Takeo M, Negoro S. Enantiodifferentiation of ketoprofen by Japanese firefly luciferase from Luciola lateralis. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2011.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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da Silva LP, da Silva JCGE. Kinetics of inhibition of firefly luciferase by dehydroluciferyl-coenzyme A, dehydroluciferin and L-luciferin. Photochem Photobiol Sci 2011; 10:1039-45. [PMID: 21409209 DOI: 10.1039/c0pp00379d] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The inhibition mechanisms of the firefly luciferase (Luc) by three of the most important inhibitors of the reactions catalysed by Luc, dehydroluciferyl-coenzyme A (L-CoA), dehydroluciferin (L) and L-luciferin (L-LH(2)) were investigated. Light production in the presence and absence of these inhibitors (0.5 to 2 μM) has been measured in 50 mM Hepes buffer (pH = 7.5), 10 nM Luc, 250 μM ATP and D-luciferin (D-LH(2), from 3.75 up to 120 μM). Nonlinear regression analysis with the appropriate kinetic models (Henri-Michaelis-Menten and William-Morrison equations) reveals that L-CoA is a non-competitive inhibitor of Luc (K(i) = 0.88 ± 0.03 μM), L is a tight-binding uncompetitive inhibitor (K(i) = 0.00490 ± 0.00009 μM) and L-LH(2) acts as a mixed-type non-competitive-uncompetitive inhibitor (K(i) = 0.68 ± 0.14 μM and αK(i) = 0.34 ± 0.16 μM). The K(m) values obtained for L-CoA, L and L-LH(2) were 16.1 ± 1.0, 16.6 ± 2.3 and 14.4 ± 0.96 μM, respectively. L and L-LH(2) are strong inhibitors of Luc, which may indicate an important role for these compounds in Luc characteristic flash profile. L-CoA K(i) supports the conclusion that CoA can stimulate the light emission reaction by provoking the formation of a weaker inhibitor.
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Affiliation(s)
- Luís Pinto da Silva
- Centro de Investigação em Química (UP), Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.
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24
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Prado RA, Barbosa JA, Ohmiya Y, Viviani VR. Structural evolution of luciferase activity in Zophobas mealworm AMP/CoA-ligase (protoluciferase) through site-directed mutagenesis of the luciferin binding site. Photochem Photobiol Sci 2011; 10:1226-32. [DOI: 10.1039/c0pp00392a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Leitão JM, Esteves da Silva JC. Firefly luciferase inhibition. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2010; 101:1-8. [DOI: 10.1016/j.jphotobiol.2010.06.015] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 06/09/2010] [Accepted: 06/29/2010] [Indexed: 01/25/2023]
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26
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Viviani VR, Scorsato V, Prado RA, Pereira JGC, Niwa K, Ohmiya Y, Barbosa JARG. The origin of luciferase activity in Zophobas mealworm AMP/CoA-ligase (protoluciferase): luciferin stereoselectivity as a switch for the oxygenase activity. Photochem Photobiol Sci 2010; 9:1111-9. [PMID: 20526507 DOI: 10.1039/c0pp00080a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Beetle luciferases evolved from AMP/CoA-ligases. However, it is unclear how the new luciferase activity evolved. In order to clarify this question, we compared the luminescence and catalytic properties of a recently cloned luciferase-like enzyme from Zophobas mealworm, an AMP/CoA-ligase displaying weak luminescence activity, with those of cloned luciferases from the three main families of luminescent beetles: Phrixthrix hirtus railroad worm; Pyrearinus termitilluminans click beetle and Photinus pyralis firefly. The catalytic constant of the mealworm enzyme was 2-4 orders of magnitude lower than that of beetle luciferases, but 3 orders of magnitude above the non-catalyzed chemiluminescence of luciferyl-adenylate in buffer. Studies with D- and L-luciferin and their adenylates show that the luminescence reaction of the luciferase-like enzyme and beetle luciferases are stereoselective for D-luciferin and its adenylate, and that the selectivity is determined mainly at the adenylation step. Modelling studies showed that the luciferin binding site cavity of this enzyme is smaller and more hydrophobic than that of beetle luciferases. Therefore Zophobas mealworm enzyme displays true luciferase activity, keeping the attributes of an ancient protoluciferase. These results suggest that stereoselectivity for D-luciferin may have been a key event for the origin of oxygenase/luciferase activity in AMP/CoA-ligases, and that efficient luciferase activity may have further evolved mainly by increasing the catalytic constant of the oxidative reaction and the quantum yield of bioluminescence.
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Affiliation(s)
- Vadim R Viviani
- Laboratório de Bioquímica e Biotecnologia de Sistemas Bioluminescentes, Universidade Federal de São Carlos (UFSCAR), Campus de Sorocaba, Sorocaba, SP, Brazil.
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27
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Niwa K, Nakajima Y, Ohmiya Y. Applications of luciferin biosynthesis: Bioluminescence assays for l-cysteine and luciferase. Anal Biochem 2010; 396:316-8. [DOI: 10.1016/j.ab.2009.09.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2009] [Revised: 09/07/2009] [Accepted: 09/09/2009] [Indexed: 11/16/2022]
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28
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Naumov P, Ozawa Y, Ohkubo K, Fukuzumi S. Structure and Spectroscopy of Oxyluciferin, the Light Emitter of the Firefly Bioluminescence. J Am Chem Soc 2009; 131:11590-605. [PMID: 19722653 DOI: 10.1021/ja904309q] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Panče Naumov
- Department of Material and Life Science, and Frontier Research Base for Global Young Researchers, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka, Japan
| | - Yutaka Ozawa
- Department of Material and Life Science, and Frontier Research Base for Global Young Researchers, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka, Japan
| | - Kei Ohkubo
- Department of Material and Life Science, and Frontier Research Base for Global Young Researchers, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka, Japan
| | - Shunichi Fukuzumi
- Department of Material and Life Science, and Frontier Research Base for Global Young Researchers, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka, Japan
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29
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Marques SM, Esteves da Silva JCG. Firefly bioluminescence: a mechanistic approach of luciferase catalyzed reactions. IUBMB Life 2009; 61:6-17. [PMID: 18949818 DOI: 10.1002/iub.134] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Luciferase is a general term for enzymes catalyzing visible light emission by living organisms (bioluminescence). The studies carried out with Photinus pyralis (firefly) luciferase allowed the discovery of the reaction leading to light production. It can be regarded as a two-step process: the first corresponds to the reaction of luciferase's substrate, luciferin (LH(2)), with ATP-Mg(2+) generating inorganic pyrophosphate and an intermediate luciferyl-adenylate (LH(2)-AMP); the second is the oxidation and decarboxylation of LH(2)-AMP to oxyluciferin, the light emitter, producing CO(2), AMP, and photons of yellow-green light (550- 570 nm). In a dark reaction LH(2)-AMP is oxidized to dehydroluciferyl-adenylate (L-AMP). Luciferase also shows acyl-coenzyme A synthetase activity, which leads to the formation of dehydroluciferyl-coenzyme A (L-CoA), luciferyl-coenzyme A (LH(2)-CoA), and fatty acyl-CoAs. Moreover luciferase catalyzes the synthesis of dinucleoside polyphosphates from nucleosides with at least a 3'-phosphate chain plus an intact terminal pyrophosphate moiety. The LH(2) stereospecificity is a particular feature of the bioluminescent reaction where each isomer, D-LH(2) or L-LH(2), has a specific function. Practical applications of the luciferase system, either in its native form or with engineered proteins, encloses the analytical assay of metabolites like ATP and molecular biology studies with luc as a reporter gene, including the most recent and increasing field of bioimaging.
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Affiliation(s)
- Simone M Marques
- Centro de Investigação em Química (CIQ-UP), Department of Chemistry, Faculty of Sciences, University of Porto, Porto, Portugal
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30
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Auld DS, Zhang YQ, Southall NT, Rai G, Landsman M, MacLure J, Langevin D, Thomas CJ, Austin CP, Inglese J. A basis for reduced chemical library inhibition of firefly luciferase obtained from directed evolution. J Med Chem 2009; 52:1450-8. [PMID: 19215089 PMCID: PMC3430137 DOI: 10.1021/jm8014525] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We measured the "druggability" of the ATP-dependent luciferase derived from the firefly Photuris pennsylvanica that was optimized using directed evolution (Ultra-Glo, Promega). Quantitative high-throughput screening (qHTS) was used to determine IC(50)s of 198899 samples against a formulation of Ultra-Glo luciferase (Kinase-Glo). We found that only 0.1% of the Kinase-Glo inhibitors showed an IC(50) < 10 microM compared to 0.9% found from a previous qHTS against the firefly luciferase from Photinus pyralis (lucPpy). Further, the maximum affinity identified in the lucPpy qHTS was 50 nM, while for Kinase-Glo this value increased to 600 nM. Compounds with interactions stretching outside the luciferin binding pocket were largely lost with Ultra-Glo luciferase. Therefore, Ultra-Glo luciferase will show less compound interference when used as an ATP sensor compared to lucPpy. This study demonstrates the power of large-scale quantitative analysis of structure-activity relationships (>100K compounds) in addressing important questions such as a target's druggability.
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Affiliation(s)
- Douglas S Auld
- NIH Chemical Genomics Center, National Institutes of Health, Bethesda, Maryland 20892-3370, USA.
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31
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Silva Neto AJ, Scorsato V, Arnoldi FGC, Viviani VR. Pyrearinus termitilluminans larval click beetle luciferase: active site properties, structure and function relationships and comparison with other beetle luciferases. Photochem Photobiol Sci 2009; 8:1748-54. [DOI: 10.1039/b9pp00053d] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Abe T, Hashimoto Y, Hosaka H, Tomita-Yokotani K, Kobayashi M. Discovery of amide (peptide) bond synthetic activity in Acyl-CoA synthetase. J Biol Chem 2008; 283:11312-21. [PMID: 18305111 DOI: 10.1074/jbc.m709654200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acyl-CoA synthetase, which is one of the acid-thiol ligases (EC 6.2.1), plays key roles in metabolic and regulatory processes. This enzyme forms a carbon-sulfur bond in the presence of ATP and Mg(2+), yielding acyl-CoA thioesters from the corresponding free acids and CoA. This enzyme belongs to the superfamily of adenylate-forming enzymes, whose three-dimensional structures are analogous to one another. We here discovered a new reaction while studying the short-chain acyl-CoA synthetase that we recently reported (Hashimoto, Y., Hosaka, H., Oinuma, K., Goda, M., Higashibata, H., and Kobayashi, M. (2005) J. Biol. Chem. 280, 8660-8667). When l-cysteine was used as a substrate instead of CoA, N-acyl-l-cysteine was surprisingly detected as a reaction product. This finding demonstrated that the enzyme formed a carbon-nitrogen bond (EC 6.3.1 acid-ammonia (or amide) ligase (amide synthase); EC 6.3.2 acid-amino acid ligase (peptide synthase)) comprising the amino group of the cysteine and the carboxyl group of the acid. N-Acyl-d-cysteine, N-acyl-dl-homocysteine, and N-acyl-l-cysteine methyl ester were also synthesized from the corresponding cysteine analog substrates by the enzyme. Furthermore, this unexpected enzyme activity was also observed for acetyl-CoA synthetase and firefly luciferase, indicating the generality of the new reaction in the superfamily of adenylate-forming enzymes.
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Affiliation(s)
- Tomoko Abe
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Fontes R, Fernandes D, Peralta F, Fraga H, Maio I, Esteves da Silva JCG. Pyrophosphate and tripolyphosphate affect firefly luciferase luminescence because they act as substrates and not as allosteric effectors. FEBS J 2008; 275:1500-1509. [PMID: 18279384 DOI: 10.1111/j.1742-4658.2008.06309.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The activating and stabilizing effects of inorganic pyrophosphate, tripolyphosphate and nucleoside triphosphates on firefly luciferase bioluminescence were studied. The results obtained show that those effects are a consequence of the luciferase-catalyzed splitting of dehydroluciferyl-adenylate, a powerful inhibitor formed as a side product in the course of the bioluminescence reaction. Inorganic pyrophosphate, tripolyphosphate, CTP and UTP antagonize the inhibitory effect of dehydroluciferyl-adenylate because they react with it giving rise to products that are, at least, less powerful inhibitors. Moreover, we demonstrate that the antagonizing effects depended on the rate of the splitting reactions being higher in the cases of inorganic pyrophosphate and tripolyphosphate and lower in the cases of CTP and UTP. In the case of inorganic pyrophosphate, the correlation between the rate of dehydroluciferyl-adenylate pyrophosphorolysis and the activating effect on bioluminescence only occurs for low concentrations because inorganic pyrophosphate is, simultaneously, an inhibitor of the bioluminescence reaction. Our results demonstrate that previous reports concerning the activating effects of several nucleotides (including some that do not react with dehydroluciferyl-adenylate) on bioluminescence were caused by the presence of inorganic pyrophosphate contamination in the preparations used.
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Affiliation(s)
- Rui Fontes
- Serviço de Bioquímica (U38-FCT), Faculdade de Medicina da Universidade do Porto, Portugal
| | - Diogo Fernandes
- Serviço de Bioquímica (U38-FCT), Faculdade de Medicina da Universidade do Porto, Portugal., Departamento de Química, Faculdade de Ciências da Universidade do Porto, Centro de Investigação em Química (UP), Portugal
| | - Filipe Peralta
- Departamento de Química, Faculdade de Ciências da Universidade do Porto, Centro de Investigação em Química (UP), Portugal
| | - Hugo Fraga
- Departamento de Química, Faculdade de Ciências da Universidade do Porto, Centro de Investigação em Química (UP), Portugal
| | - Inês Maio
- Serviço de Bioquímica (U38-FCT), Faculdade de Medicina da Universidade do Porto, Portugal
| | - Joaquim C G Esteves da Silva
- Departamento de Química, Faculdade de Ciências da Universidade do Porto, Centro de Investigação em Química (UP), Portugal
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Fraga H. Firefly luminescence: a historical perspective and recent developments. Photochem Photobiol Sci 2008; 7:146-58. [PMID: 18264582 DOI: 10.1039/b719181b] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Significant advances have occurred regarding our knowledge of firefly luciferase mechanisms. Although most of this progress was an outcome of molecular biology and structural studies, important achievements have also occurred on its fundamental chemistry. Those developments are here summarized and presented in a historical perspective.
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Affiliation(s)
- Hugo Fraga
- Centro de Investigação em Química (UP), Departamento de Química, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre 687, 4169-007, Porto, Portugal.
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35
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Viviani VR, Arnoldi FGC, Neto AJS, Oehlmeyer TL, Bechara EJH, Ohmiya Y. The structural origin and biological function of pH-sensitivity in firefly luciferases. Photochem Photobiol Sci 2008; 7:159-69. [DOI: 10.1039/b714392c] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Saito R, Machida S, Suzuki S, Katoh A. Synthesis and Spectroscopic Properties of 2,5-Bis(benzoazol-2-yl)pyrazines. HETEROCYCLES 2008. [DOI: 10.3987/com-07-11226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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37
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Kato DI, Teruya K, Yoshida H, Takeo M, Negoro S, Ohta H. New application of firefly luciferase − it can catalyze the enantioselective thioester formation of 2-arylpropanoic acid. FEBS J 2007; 274:3877-85. [PMID: 17617223 DOI: 10.1111/j.1742-4658.2007.05921.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We introduce a new application of firefly luciferase (EC 1.13.12.7). The firefly luciferases belong to a large superfamily that includes rat liver long-chain acyl-CoA synthetase (LACS1). LACS1 is the enzyme that is involved in the deracemization process of 2-arylpropanoic acid and catalyzes the enantioselective thioester formation of R-acids. Based on the similarity of the reaction mechanisms and the sequences between firefly luciferase and LACS1, we predicted that firefly luciferase also has thioesterification activity toward 2-arylpropanoic acid. From an investigation using three kinds of luciferases from North American firefly and Japanese fireflies, we have confirmed that these luciferases exhibit an enantioselective thioester formation activity and the R-form is transformed to a thioester in preference to the S-form in the presence of ATP, Mg(2+), and CoASH. The enantiomeric excesses of unreacted recovered acid and thioester were determined by chiral phase HPLC analysis and the resulting 2-arylpropanoyl-CoAs were identified by high resolution mass spectroscopy. The K(m) and k(cat) values of thermostable luciferase from Luciola lateralis (LUC-H) toward ketoprofen were determined as 0.22 mM and 0.11 s(-1), respectively. The affinity of ketoprofen was almost the same of d-luciferin. In addition, the calculated E-value toward ketoprofen was approximately 20. These results suggest that LUC-H could catalyze the kinetic resolution of 2-arylpropanoic acid efficiently and would be a new option for the preparation of optically active 2-substituted carboxylic acids.
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Affiliation(s)
- Dai-Ichiro Kato
- Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan.
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Fraga H, Fernandes D, Novotny J, Fontes R, Esteves da Silva JCG. Firefly luciferase produces hydrogen peroxide as a coproduct in dehydroluciferyl adenylate formation. Chembiochem 2006; 7:929-35. [PMID: 16642538 DOI: 10.1002/cbic.200500443] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Firefly luciferase catalyzes the synthesis of H2O2 from the same substrates as the bioluminescence reaction: ATP and luciferin (D-LH2). About 80% of the enzyme-bound intermediate D-luciferyl adenylate (D-LH2-AMP) is oxidized into oxyluciferin, and a photon is emitted during this reaction. The enzyme pathway responsible for the generation of H2O2 is a side reaction in which D-LH2-AMP is oxidized into dehydroluciferyl adenylate (L-AMP). Like the bioluminescence reaction, the luciferase-catalyzed synthesis of H2O2 and L-AMP is a stereospecific process, involving only the natural D enantiomer. However, the intramolecular electron transfer postulated as essential to the light emission process is not involved in this side reaction.
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Affiliation(s)
- Hugo Fraga
- Centro de Investigação em Química, Departamento de Química, Faculdade de Ciências, Universidade do Porto, R. Campo Alegre 687, 4169-007 Porto, Portugal
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39
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Viviani VR, Ohmiya Y. Bovine serum albumin displays luciferase-like activity in presence of luciferyl adenylate: insights on the origin of protoluciferase activity and bioluminescence colours. LUMINESCENCE 2006; 21:262-7. [PMID: 16791835 DOI: 10.1002/bio.916] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Luciferyl adenylate, the key intermediate in beetle bioluminescence, is produced through adenylation of d-luciferin by beetle luciferases and also by mealworm luciferase-like enzymes which produce a weak red chemiluminescence. However, luciferyl adenylate is only weakly chemiluminescent in water at physiological pH and it is unclear how efficient bioluminescence evolved from its weak chemiluminescent properties. We found that bovine serum albumin (BSA) and neutral detergents enhance luciferyl adenylate chemiluminescence by three orders of magnitude, simulating the mealworm luciferase-like enzyme chemiluminescence properties. These results suggest that the beetle protoluciferase activity arose as an enhanced luciferyl adenylate chemiluminescence in the protein environment of the ancestral AMP-ligase. The predominance of luciferyl adenylate chemiluminescence in the red region under most conditions suggests that red luminescence is a more primitive condition that characterized the original stages of protobioluminescence, whereas yellow-green bioluminescence may have evolved later through the development of a more structured and hydrophobic active site.
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Affiliation(s)
- Vadim R Viviani
- Departamento de Biologia Celular e Molecular, Instituto de Biociências, Universidade Estadual de São Paulo (UNESP), Rio Claro, SP, Brazil.
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Niwa K, Nakamura M, Ohmiya Y. Stereoisomeric bio-inversion key to biosynthesis of fireflyd-luciferin. FEBS Lett 2006; 580:5283-7. [PMID: 16979628 DOI: 10.1016/j.febslet.2006.08.073] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 08/07/2006] [Accepted: 08/30/2006] [Indexed: 11/26/2022]
Abstract
The chirality of the luciferin substrate is critical to the luciferin-luciferase reaction producing bioluminescence. In firefly, the biosynthetic pathway of D-luciferin is still unclear, although it can be synthesized in vitro from D-cysteine. Here, we show that the firefly produces both D- and L-luciferin, and that the amount of active D-luciferin increases gradually with maturation stage. Studies of firefly body extracts indicate the possible conversion of L-cysteine via L-luciferin into D-luciferin, suggesting that the biosynthesis is enzymatically regulated by stereoisomeric bio-inversion of L-luciferin. We conclude that the selection of chirality in living organisms is not as rigid as previously thought.
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Affiliation(s)
- Kazuki Niwa
- Research Institute for Cell Engineering, National Institute of Advanced Industrial Science and Technology, AIST, Japan
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41
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Viviani VR, Arnoldi FGC, Venkatesh B, Neto AJS, Ogawa FGT, Oehlmeyer ATL, Ohmiya Y. Active-site properties of Phrixotrix railroad worm green and red bioluminescence-eliciting luciferases. J Biochem 2006; 140:467-74. [PMID: 16963787 DOI: 10.1093/jb/mvj190] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The luciferases of the railroad worm Phrixotrix (Coleoptera: Phengodidae) are the only beetle luciferases that naturally produce true red bioluminescence. Previously, we cloned the green- (PxGR) and red-emitting (PxRE) luciferases of railroad worms Phrixotrix viviani and P. hirtus[OLE1]. These luciferases were expressed and purified, and their active-site properties were determined. The red-emitting PxRE luciferase displays flash-like kinetics, whereas PxGR luciferase displays slow-type kinetics. The substrate affinities and catalytic efficiency of PxRE luciferase are also higher than those of PxGR luciferase. Fluorescence studies with 8-anilino-1-naphthalene sulfonic acid and 6-p-toluidino-2-naphthalene sulfonic acid showed that the PxRE luciferase luciferin-binding site is more polar than that of PxGR luciferase, and it is sensitive to guanidine. Mutagenesis and modelling studies suggest that several invariant residues in the putative luciferin-binding site of PxRE luciferase cannot interact with excited oxyluciferin. These results suggest that one portion of the luciferin-binding site of the red-emitting luciferase is tighter than that of PxGR luciferase, whereas the other portion could be more open and polar.
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Affiliation(s)
- V R Viviani
- Universidade Federal de Sao Carlos, Campus de Sorocaba, Sorocaba, SP, Brazil.
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Oba Y, Sato M, Inouye S. Cloning and characterization of the homologous genes of firefly luciferase in the mealworm beetle, Tenebrio molitor. INSECT MOLECULAR BIOLOGY 2006; 15:293-9. [PMID: 16756548 DOI: 10.1111/j.1365-2583.2006.00646.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Three homologous genes of firefly luciferase were cloned from the non-luminous beetle Tenebrio molitor. Three gene products for homologues, TmLL-1, TmLL-2 and TmLL-3, showed fatty acyl-coenzyme A (acyl-CoA) synthetic activity, but not luciferase activity with firefly luciferin. The transcripts were detected through the developmental stages in T. molitor. These results suggested that firefly luciferase was evolved from a fatty acyl-coenzyme A synthetase by gene duplications in the insect.
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Affiliation(s)
- Y Oba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.
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Fraga H, Fernandes D, Fontes R, Esteves da Silva JCG. Coenzyme A affects firefly luciferase luminescence because it acts as a substrate and not as an allosteric effector. FEBS J 2005; 272:5206-16. [PMID: 16218952 DOI: 10.1111/j.1742-4658.2005.04895.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effect of CoA on the characteristic light decay of the firefly luciferase catalysed bioluminescence reaction was studied. At least part of the light decay is due to the luciferase catalysed formation of dehydroluciferyl-adenylate (L-AMP), a by-product that results from oxidation of luciferyl-adenylate (LH2-AMP), and is a powerful inhibitor of the bioluminescence reaction (IC50 = 6 nm). We have shown that the CoA induced stabilization of light emission does not result from an allosteric effect but is due to the thiolytic reaction between CoA and L-AMP, which gives rise to dehydroluciferyl-CoA (L-CoA), a much less powerful inhibitor (IC50 = 5 microm). Moreover, the V(max) for L-CoA formation was determined as 160 min(-1), which is one order of magnitude higher than the V(max) of the bioluminescence reaction. Results obtained with CoA analogues also support the thiolytic reaction mechanism: CoA analogues without the thiol group (dethio-CoA and acetyl-CoA) do not react with L-AMP and do not antagonize its inhibitor effect; CoA and dephospho-CoA have free thiol groups, both react with L-AMP and both antagonize its effect. In the case of dephospho-CoA, it was shown that it reacts with L-AMP forming dehydroluciferyl-dephospho-CoA. Its slower reactivity towards L-AMP explains its lower potency as antagonist of the inhibitory effect of L-AMP on the light reaction. Moreover, our results support the conjecture that, in the bioluminescence reaction, the fraction of LH2-AMP that is oxidized into L-AMP, relative to other inhibitory products or intermediates, increases when the concentrations of the substrates ATP and luciferin increases.
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Affiliation(s)
- Hugo Fraga
- Departmento de Química, Faculdade de Ciências da Universidade do Porto, Portugal
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