1
|
Solano YJ, Kiser PD. Double-duty isomerases: a case study of isomerization-coupled enzymatic catalysis. Trends Biochem Sci 2024; 49:703-716. [PMID: 38760195 DOI: 10.1016/j.tibs.2024.04.007] [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: 02/15/2024] [Revised: 04/08/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
Abstract
Enzymes can usually be unambiguously assigned to one of seven classes specifying the basic chemistry of their catalyzed reactions. Less frequently, two or more reaction classes are catalyzed by a single enzyme within one active site. Two examples are an isomerohydrolase and an isomero-oxygenase that catalyze isomerization-coupled reactions crucial for production of vision-supporting 11-cis-retinoids. In these enzymes, isomerization is obligately paired and mechanistically intertwined with a second reaction class. A handful of other enzymes carrying out similarly coupled isomerization reactions have been described, some of which have been subjected to detailed structure-function analyses. Herein we review these rarefied enzymes, focusing on the mechanistic and structural basis of their reaction coupling with the goal of revealing catalytic commonalities.
Collapse
Affiliation(s)
- Yasmeen J Solano
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA 92697, USA
| | - Philip D Kiser
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA 92697, USA; Department of Clinical Pharmacy Practice, University of Irvine School of Pharmacy and Pharmaceutical Sciences, Irvine, CA 92697, USA; Department of Ophthalmology, Gavin Herbert Eye Institute - Center for Translational Vision Research, University of California Irvine School of Medicine, Irvine, CA 92697, USA; Research Service, VA Long Beach Healthcare System, Long Beach, CA 90822, USA.
| |
Collapse
|
2
|
Ito A, Matsuda N, Ukita Y, Okumura M, Chihara T. Akaluc/AkaLumine bioluminescence system enables highly sensitive, non-invasive and temporal monitoring of gene expression in Drosophila. Commun Biol 2023; 6:1270. [PMID: 38097812 PMCID: PMC10721803 DOI: 10.1038/s42003-023-05628-x] [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: 04/25/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Bioluminescence generated by luciferase and luciferin has been extensively used in biological research. However, detecting signals from deep tissues in vivo poses a challenge to traditional methods. To overcome this, the Akaluc and AkaLumine bioluminescent systems were developed, resulting in improved signal detection. We evaluate the potential of Akaluc/AkaLumine in Drosophila melanogaster to establish a highly sensitive, non-invasive, and temporal detection method for gene expression. Our results show that oral administration of AkaLumine to flies expressing Akaluc provided a higher luminescence signal than Luc/D-luciferin, with no observed harmful effects on flies. The Akaluc/AkaLumine system allows for monitoring of dynamic temporal changes in gene expression. Additionally, using the Akaluc fusion gene allows for mRNA splicing monitoring. Our findings indicate that the Akaluc/AkaLumine system is a powerful bioluminescence tool for analyzing gene expression in deep tissues and small numbers of cells in Drosophila.
Collapse
Affiliation(s)
- Akira Ito
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Nagisa Matsuda
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Yumiko Ukita
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Misako Okumura
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Takahiro Chihara
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan.
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan.
| |
Collapse
|
3
|
Rayhan M, Siddiquee MF, Shahriar A, Ahmed H, Mahmud AR, Alam MS, Uddin MR, Acharjee M, Shimu MSS, Shamsir MS, Emran TB. Structural characterization of a novel luciferase-like-monooxygenase from Pseudomonas meliae– an in-silico approach.. [DOI: 10.1101/2023.03.27.534437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractBackgroundLuciferase is a well-known oxidative enzyme that produces bioluminescence. ThePseudomonas meliaeis a plant pathogen that causes wood rot on nectarine and peach and possesses a luciferase-like monooxygenase. After activation, it produces bioluminescence, and the pathogen’s bioluminescence is a visual indicator of diseased plants.MethodsThe present study aims to model and characterize the luciferase-like monooxygenase protein inP. meliaefor its similarity to well-established luciferase. In this study, the luciferase-like monooxygenase fromP. meliaeinfects chinaberry plants has been modeled first and then studied by comparing it with existing known luciferase. Also, the similarities between uncharacterized luciferase fromP. meliaeand template fromGeobacillus thermodenitrificanswere analyzed to find the novelty ofP. meliae.ResultsThe results suggest that the absence of bioluminescence inP. meliaecould be due to the evolutionary mutation in positions 138 and 311. The active site remains identical except for two amino acids;P. meliaeTyr138 instead of His138 and Leu311 instead of His311. Therefore, theP. meliaewill have a potential future application, and mutation of the residues 138 and 311 can be restored luciferase light-emitting ability.ConclusionsThis study will help further improve, activate, and repurpose the luciferase fromP. meliaeas a reporter for gene expression.
Collapse
|
4
|
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
|
5
|
Comparison of Bioluminescent Substrates in Natural Infection Models of Neglected Parasitic Diseases. Int J Mol Sci 2022; 23:ijms232416074. [PMID: 36555716 PMCID: PMC9781651 DOI: 10.3390/ijms232416074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
The application of in vivo bioluminescent imaging in infectious disease research has significantly increased over the past years. The detection of transgenic parasites expressing wildtype firefly luciferase is however hampered by a relatively low and heterogeneous tissue penetrating capacity of emitted light. Solutions are sought by using codon-optimized red-shifted luciferases that yield higher expression levels and produce relatively more red or near-infrared light, or by using modified bioluminescent substrates with enhanced cell permeability and improved luminogenic or pharmacokinetic properties. In this study, the in vitro and in vivo efficacy of two modified bioluminescent substrates, CycLuc1 and AkaLumine-HCl, were compared with that of D-luciferin as a gold standard. Comparisons were made in experimental and insect-transmitted animal models of leishmaniasis (caused by intracellular Leishmania species) and African trypanosomiasis (caused by extracellular Trypanosoma species), using parasite strains expressing the red-shifted firefly luciferase PpyRE9. Although the luminogenic properties of AkaLumine-HCl and D-luciferin for in vitro parasite detection were comparable at equal substrate concentrations, AkaLumine-HCl proved to be unsuitable for in vivo infection follow-up due to high background signals in the liver. CycLuc1 presented a higher in vitro luminescence compared to the other substrates and proved to be highly efficacious in vivo, even at a 20-fold lower dose than D-luciferin. This efficacy was consistent across infections with the herein included intracellular and extracellular parasitic organisms. It can be concluded that CycLuc1 is an excellent and broadly applicable alternative for D-luciferin, requiring significantly lower doses for in vivo bioluminescent imaging in rodent models of leishmaniasis and African trypanosomiasis.
Collapse
|
6
|
Ley-Ngardigal S, Bertolin G. Approaches to monitor ATP levels in living cells: where do we stand? FEBS J 2022; 289:7940-7969. [PMID: 34437768 DOI: 10.1111/febs.16169] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/30/2021] [Accepted: 08/25/2021] [Indexed: 01/14/2023]
Abstract
ATP is the most universal and essential energy molecule in cells. This is due to its ability to store cellular energy in form of high-energy phosphate bonds, which are extremely stable and readily usable by the cell. This energy is key for a variety of biological functions such as cell growth and division, metabolism, and signaling, and for the turnover of biomolecules. Understanding how ATP is produced and hydrolyzed with a spatiotemporal resolution is necessary to understand its functions both in physiological and in pathological contexts. In this review, first we will describe the organization of the electron transport chain and ATP synthase, the main molecular motor for ATP production in mitochondria. Second, we will review the biochemical assays currently available to estimate ATP quantities in cells, and we will compare their readouts, strengths, and weaknesses. Finally, we will explore the palette of genetically encoded biosensors designed for microscopy-based approaches, and show how their spatiotemporal resolution opened up the possibility to follow ATP levels in living cells.
Collapse
Affiliation(s)
- Seyta Ley-Ngardigal
- CNRS, Univ Rennes, IGDR (Genetics and Development Institute of Rennes), Rennes, France.,LVMH Research Perfumes and Cosmetics, Saint-Jean-de-Braye, France
| | - Giulia Bertolin
- CNRS, Univ Rennes, IGDR (Genetics and Development Institute of Rennes), Rennes, France
| |
Collapse
|
7
|
Li W, Zhang J, Yu X, Meng F, Huang J, Zhang L, Wang S. Aristolochic acid I exposure decreases oocyte quality. Front Cell Dev Biol 2022; 10:838992. [PMID: 36036003 PMCID: PMC9402977 DOI: 10.3389/fcell.2022.838992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Oocyte quality is a determinant of a successful pregnancy. The final step of oocyte development is oocyte maturation, which is susceptible to environmental exposures. Aristolochic acids (AAs), widely existing in Aristolochia and Asarum plants that have been used in traditional medicine, can result in a smaller ovary and fewer superovulated oocytes after in vivo exposure to mice. However, whether AAs affect oocyte maturation and the underlying mechanism(s) are unclear. In this study, we focused on the effect of Aristolochic acid I (AAI), a major compound of AAs, on the maturation of in vitro cultured mouse oocytes. We showed that AAI exposure significantly decreased oocyte quality, including elevated aneuploidy, accompanied by aberrant chiasma patterns and spindle organization, and decreased first polar body extrusion and fertilization capability. Moreover, embryo development potential was also dramatically decreased. Further analyses revealed that AAI exposure significantly decreased mitochondrial membrane potential and ATP synthesis and increased the level of reactive oxygen species (ROS), implying impaired mitochondrial function. Insufficient ATP supply can cause aberrant spindle assembly and excessive ROS can cause premature loss of sister chromatid cohesion and thus alterations in chiasma patterns. Both aberrant spindles and changed chiasma patterns can contribute to chromosome misalignment and thus aneuploidy. Therefore, AAI exposure decreases oocyte quality probably via impairing mitochondrial function.
Collapse
Affiliation(s)
- Weidong Li
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong, China
| | - Jiaming Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaoxia Yu
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fei Meng
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ju Huang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Liangran Zhang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Shunxin Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China
- *Correspondence: Shunxin Wang,
| |
Collapse
|
8
|
White D, Yang Q. Genetically Encoded ATP Biosensors for Direct Monitoring of Cellular ATP Dynamics. Cells 2022; 11:1920. [PMID: 35741049 PMCID: PMC9221525 DOI: 10.3390/cells11121920] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 12/06/2022] Open
Abstract
Adenosine 5'-triphosphate, or ATP, is the primary molecule for storing and transferring energy in cells. ATP is mainly produced via oxidative phosphorylation in mitochondria, and to a lesser extent, via glycolysis in the cytosol. In general, cytosolic glycolysis is the primary ATP producer in proliferative cells or cells subjected to hypoxia. On the other hand, mitochondria produce over 90% of cellular ATP in differentiated cells under normoxic conditions. Under pathological conditions, ATP demand rises to meet the needs of biosynthesis for cellular repair, signaling transduction for stress responses, and biochemical processes. These changes affect how mitochondria and cytosolic glycolysis function and communicate. Mitochondria undergo remodeling to adapt to the imbalanced demand and supply of ATP. Otherwise, a severe ATP deficit will impair cellular function and eventually cause cell death. It is suggested that ATP from different cellular compartments can dynamically communicate and coordinate to adapt to the needs in each cellular compartment. Thus, a better understanding of ATP dynamics is crucial to revealing the differences in cellular metabolic processes across various cell types and conditions. This requires innovative methodologies to record real-time spatiotemporal ATP changes in subcellular regions of living cells. Over the recent decades, numerous methods have been developed and utilized to accomplish this task. However, this is not an easy feat. This review evaluates innovative genetically encoded biosensors available for visualizing ATP in living cells, their potential use in the setting of human disease, and identifies where we could improve and expand our abilities.
Collapse
Affiliation(s)
- Donnell White
- Cardiovascular Center of Excellence, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA;
- Department of Pharmacology and Experimental Therapeutics, School of Graduate Studies, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Qinglin Yang
- Cardiovascular Center of Excellence, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA;
- Department of Pharmacology and Experimental Therapeutics, School of Graduate Studies, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| |
Collapse
|
9
|
Kanie S, Miura D, Jimi N, Hayashi T, Nakamura K, Sakata M, Ogoh K, Ohmiya Y, Mitani Y. Violet bioluminescent Polycirrus sp. (Annelida: Terebelliformia) discovered in the shallow coastal waters of the Noto Peninsula in Japan. Sci Rep 2021; 11:19097. [PMID: 34580316 PMCID: PMC8476577 DOI: 10.1038/s41598-021-98105-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/03/2021] [Indexed: 11/09/2022] Open
Abstract
Terebellidae worms have large numbers of tentacles responsible for various biological functions. Some Terebellidae worms whose tentacles emit light are found around the world, including exceptional violet-light-emitting Polycirrus spp. found in Europe and North America. However, there is no video-recorded observation of the luminous behavior of such unique species in nature, and the genetic information related to their ecology are lacking. Here, for the first time, we video-recorded the violet-light-emitting behavior of an undescribed Japanese worm in its natural habitat. The worm was designated as Polycirrus sp. ISK based on morphological observations, and the luminescence spectrum showed a peak at 444 nm, which is an exceptionally short wavelength for bioluminescence in a shallow coastal water environment. An analysis of differentially expressing genes based on separate RNA-Seq analysis for the tentacles and the rest of body revealed the specific expression of genes that are probably involved in innate immunity in the tentacles exposed to predators. We also found a Renilla luciferase homologous gene, but coelenterazine was not detected in the worm extract by analyses using a liquid chromatography and a recombinant Renilla luciferase. These results will promote an understanding of the ecology and luminescence mechanisms of luminous Polycirrus spp.
Collapse
Affiliation(s)
- Shusei Kanie
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan
| | - Daisuke Miura
- Biomedical Research Institute, AIST, Tsukuba, 305-8566, Japan
| | - Naoto Jimi
- National Institute of Polar Research, Tachikawa, Tokyo, 190-8518, Japan
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, Mie, 517-0004, Japan
| | - Taro Hayashi
- Olympus Corporation, Hachioji, Tokyo, 192-8512, Japan
| | - Koji Nakamura
- Japan Underwater Films Co., Ltd., 2-11-15, Nakaochiai, Shinjyuku, Tokyo, 161-0032, Japan
| | - Masahiko Sakata
- Japan Underwater Films Co., Ltd., 2-11-15, Nakaochiai, Shinjyuku, Tokyo, 161-0032, Japan
| | - Katsunori Ogoh
- Olympus Corporation, Hachioji, Tokyo, 192-8512, Japan
- HATENOURUMA, Hachioji, Tokyo, 192‑0023, Japan
| | - Yoshihiro Ohmiya
- Biomedical Research Institute, AIST, Ikeda, 563-8577, Japan
- Osaka Institute of Technology (OIT), Osaka, 535-8585, Japan
| | - Yasuo Mitani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan.
| |
Collapse
|
10
|
Tsarkova AS. Luciferins Under Construction: A Review of Known Biosynthetic Pathways. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.667829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bioluminescence, or the ability of a living organism to generate visible light, occurs as a result of biochemical reaction where enzyme, known as a luciferase, catalyzes the oxidation of a small-molecule substrate, known as luciferin. This advantageous trait has independently evolved dozens of times, with current estimates ranging from the most conservative 40, based on the biochemical diversity found across bioluminescence systems (Haddock et al., 2010) to 100, taking into account the physiological mechanisms involved in the behavioral control of light production across a wide range of taxa (Davis et al., 2016; Verdes and Gruber, 2017; Bessho-Uehara et al., 2020a; Lau and Oakley, 2021). Chemical structures of ten biochemically unrelated luciferins and several luciferase gene families have been described; however, a full biochemical pathway leading to light emission has been elucidated only for two: bacterial and fungal bioluminescence systems. Although the recent years have been marked by extraordinary discoveries and promising breakthroughs in understanding the molecular basis of multiple bioluminescence systems, the mechanisms of luciferin biosynthesis for many organisms remain almost entirely unknown. This article seeks to provide a succinct overview of currently known luciferins’ biosynthetic pathways.
Collapse
|
11
|
He JW, Liu GC, Dong PX, Dong ZW, Zhao RP, Wang W, Li XY. Molecular cloning, characterization, and evolution analysis of the luciferase genes from three sympatric sibling fireflies (Lampyridae: Lampyrinae, Diaphanes). Photochem Photobiol Sci 2021; 20:1053-1067. [PMID: 34347281 DOI: 10.1007/s43630-021-00080-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/21/2021] [Indexed: 11/24/2022]
Abstract
Firefly adult bioluminescence functions as signal communication between sexes. How sympatric sibling species with similar glow pattern recognize their conspecific mates remains largely unknown. To better understand the role of the luciferases of sympatric fireflies in recognizing mates, we cloned the luciferase genes of three sympatric forest dwelling fireflies (Diaphanes nubilus, Diaphanes pectinealis, and Diaphanes sp2) and evaluated their enzyme characteristics. Our data show that the amino acid (AA) sequences of all three luciferases are highly conserved, including the identities (D. nubilus vs D. pectinealis: 99%; D. nubilus vs Diaphanes sp2: 98.5%; D. pectinealis vs Diaphanes sp2: 99.4%) and the protein structures. Three recombinant luciferases produced in vitro all possess significant luminescence activity at pH 7.8, and similar maximum emission spectrum (D. nubilus: 562 nm; D. pectinealis and Diaphanes sp2: 564 nm). They show the highest activity at 10 °C (D. pectinealis, Diaphanes sp2) and 15 °C (D. nubilus), and completely inactivation at 45 °C. Their KM for D-luciferin and ATP were 2.7 μM and 92 μM (D. nubilus), 3.7 μM and 49 μM (D. pectinealis), 3.5 μM and 46 μM (Diaphanes sp2). Phylogenetic analyses support that D. nubilus is sister to D. pectinealis with Diaphanes sp2 at their base, which further cluster with Pyrocoelia. All combined data indicate that sympatric Diaphanes species have similar luciferase characteristics, suggesting that other strategies (e.g., pheromone, active time, etc.) may be adopted to recognize mates. Our data provide new insights into Diaphanes luciferases and their evolution.
Collapse
Affiliation(s)
- Jin-Wu He
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Gui-Chun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Ping-Xuan Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Dezhou University, Dezhou, 253023, Shandong, China
| | - Zhi-Wei Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Ruo-Ping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
| | - Xue-Yan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
| |
Collapse
|
12
|
Love AC, Prescher JA. Seeing (and Using) the Light: Recent Developments in Bioluminescence Technology. Cell Chem Biol 2020; 27:904-920. [PMID: 32795417 PMCID: PMC7472846 DOI: 10.1016/j.chembiol.2020.07.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/10/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023]
Abstract
Bioluminescence has long been used to image biological processes in vivo. This technology features luciferase enzymes and luciferin small molecules that produce visible light. Bioluminescent photons can be detected in tissues and live organisms, enabling sensitive and noninvasive readouts on physiological function. Traditional applications have focused on tracking cells and gene expression patterns, but new probes are pushing the frontiers of what can be visualized. The past few years have also seen the merger of bioluminescence with optogenetic platforms. Luciferase-luciferin reactions can drive light-activatable proteins, ultimately triggering signal transduction and other downstream events. This review highlights these and other recent advances in bioluminescence technology, with an emphasis on tool development. We showcase how new luciferins and engineered luciferases are expanding the scope of optical imaging. We also highlight how bioluminescent systems are being leveraged not just for sensing-but also controlling-biological processes.
Collapse
Affiliation(s)
- Anna C Love
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.
| |
Collapse
|
13
|
D’Ambrosio HK, Derbyshire ER. Investigating the Role of Class I Adenylate-Forming Enzymes in Natural Product Biosynthesis. ACS Chem Biol 2020; 15:17-27. [PMID: 31815417 DOI: 10.1021/acschembio.9b00865] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Adenylate-forming enzymes represent one of the most important enzyme classes in biology, responsible for the activation of carboxylate substrates for biosynthetic modifications. The byproduct of the adenylate-forming enzyme acetyl-CoA synthetase, acetyl-CoA, is incorporated into virtually every primary and secondary metabolic pathway. Modification of acetyl-CoA by an array of other adenylate-forming enzymes produces complex classes of natural products including nonribosomal peptides, polyketides, phenylpropanoids, lipopeptides, and terpenes. Adenylation domains possess a variety of unique structural and functional features that provide for such diversification in their resulting metabolites. As the number of organisms with sequenced genomes increases, more adenylate-forming enzymes are being identified, each with roles in metabolite production that have yet to be characterized. In this Review, we explore the broad role of class I adenylate-forming enzymes in the context of natural product biosynthesis and how they contribute to primary and secondary metabolism by focusing on important work conducted in the field. We highlight features of subclasses from this family that facilitate the production of structurally diverse metabolites, including those from noncanonical adenylation domains, and additionally discuss when biological roles for these compounds are known.
Collapse
Affiliation(s)
- Hannah K. D’Ambrosio
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Emily R. Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, North Carolina 27710, United States
| |
Collapse
|
14
|
Liu G, Zhang R, Hou Q, He J, Dong Z, Zhao R, Wang W, Li X. Cloning and Characterization of Luciferase from the Chinese Firefly
Lamprigera yunnana. Photochem Photobiol 2019; 95:1186-1194. [DOI: 10.1111/php.13109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/31/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Gui‐Chun Liu
- Center for Ecological and Environmental Sciences Key Laboratory for Space Bioscience & Biotechnology Northwestern Polytechnical University Xi'an China
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Ru Zhang
- Center for Ecological and Environmental Sciences Key Laboratory for Space Bioscience & Biotechnology Northwestern Polytechnical University Xi'an China
| | - Qing‐Bai Hou
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Jin‐Wu He
- Center for Ecological and Environmental Sciences Key Laboratory for Space Bioscience & Biotechnology Northwestern Polytechnical University Xi'an China
| | - Zhi‐Wei Dong
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Ruo‐Ping Zhao
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Wen Wang
- Center for Ecological and Environmental Sciences Key Laboratory for Space Bioscience & Biotechnology Northwestern Polytechnical University Xi'an China
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Xue‐Yan Li
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| |
Collapse
|
15
|
Nowroozi-Nejad Z, Bahramian B, Hosseinkhani S. Efficient immobilization of firefly luciferase in a metal organic framework: Fe-MIL-88(NH2) as a mighty support for this purpose. Enzyme Microb Technol 2019; 121:59-67. [DOI: 10.1016/j.enzmictec.2018.10.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/13/2018] [Accepted: 10/26/2018] [Indexed: 01/07/2023]
|
16
|
Genomic and protein structure analysis of the luciferase from the Iranian bioluminescent beetle, Luciola sp. Int J Biol Macromol 2018; 124:689-698. [PMID: 30502432 DOI: 10.1016/j.ijbiomac.2018.11.264] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 11/21/2022]
Abstract
To date, two Iranian luciferase genes from the Lampyris turkestanicus and Lampyroidea maculata have been carefully studied. Here, we report the cloning and characterization of the gene and protein of luciferase enzyme from the beetle of an Iranian lampyrid species, Luciola sp. (Coleoptera-Lampyridae). In this study, a Luciola sp. firefly was collected from the Yasouj area of Iran and its luciferase gene sequence was cloned and characterized. The genomic DNA length for this luciferase was the 1950 bp that combined of seven exons and separated by six introns. The results of multiple sequence alignment show that this gene has the most similarity with DNA gene luciferase from the Hotaria unmunsana species. Further analysis determined accurately the location of these introns in the luciferase gene. However, the deduced amino acid sequences of the luciferase gene (548 residues) showed that this luciferase had 97.8% resemblance to luciferase from Lampyroidea maculata species. By in silico modeling of firefly luciferase in an I-TASSER server, the 3D structure of this enzyme was evaluated. The results of phylogenetic tree analysis display the close evolutionary relationship of this luciferase gene and luciferase gene from the Lampyroidea maculata and Hotaria unmunsana.
Collapse
|
17
|
Kanie S, Nakai R, Ojika M, Oba Y. 2-S-cysteinylhydroquinone is an intermediate for the firefly luciferin biosynthesis that occurs in the pupal stage of the Japanese firefly, Luciola lateralis. Bioorg Chem 2018; 80:223-229. [DOI: 10.1016/j.bioorg.2018.06.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 11/27/2022]
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Liu PH, Urban PL. Spontaneous luminescence color change in the firefly luciferase assay system. Anal Biochem 2017; 539:54-59. [PMID: 29029977 DOI: 10.1016/j.ab.2017.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 01/18/2023]
Abstract
The temporal effects of luciferase reaction luminescence have only been discussed in the context of light intensity (flash vs. glow). However, alterations in the color of the light emitted over the course of the luciferase reaction have not been reported. Here, we show a temporal change in the light color emitted during the reaction catalyzed by unmodified firefly luciferase when concentrations of one of the substrates, adenosine triphosphate (ATP), are gradually increased. The temporal color change from green to red occurs within the first few minutes of the luciferase reaction when an ATP-containing solution is either added or synthesized in situ with the aid of an autocatalytic reaction occurring simultaneously. This color change is not accompanied by pH changes. An analysis of the red and green channels demonstrates dissimilar kinetics, suggesting the co-existence of two or more temporally shifted luminescence pathways. The implications of these findings might improve dual-color biosensing/imaging protocols and influence the engineering of biophotonic systems.
Collapse
Affiliation(s)
- Pei-Han Liu
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Rd, Hsinchu, 300, Taiwan
| | - Pawel L Urban
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Rd, Hsinchu, 300, Taiwan; Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan.
| |
Collapse
|
20
|
Chen F, Sun H, Liu H, Li D, Li Y, Hou T. Prediction of luciferase inhibitors by the high-performance MIEC-GBDT approach based on interaction energetic patterns. Phys Chem Chem Phys 2017; 19:10163-10176. [DOI: 10.1039/c6cp08232g] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The MIEC-GBDT model can be used as a powerful tool to identify potential interference compounds in luciferase-based high-throughput screening.
Collapse
Affiliation(s)
- Fu Chen
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Huiyong Sun
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Hui Liu
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Dan Li
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
- State Key Lab of CAD&CG
| |
Collapse
|
21
|
Ioka S, Saitoh T, Maki SA, Imoto M, Nishiyama S. Development of a luminescence-controllable firefly luciferin analogue using selective enzymatic cyclization. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.09.069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
22
|
Feeney KA, Putker M, Brancaccio M, O'Neill JS. In-depth Characterization of Firefly Luciferase as a Reporter of Circadian Gene Expression in Mammalian Cells. J Biol Rhythms 2016; 31:540-550. [PMID: 28112045 PMCID: PMC5117186 DOI: 10.1177/0748730416668898] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Firefly luciferase (Fluc) is frequently used to report circadian gene expression rhythms in mammalian cells and tissues. During longitudinal assays it is generally assumed that enzymatic substrates are in saturating excess, such that total bioluminescence is directly proportional to Fluc protein level. To test this assumption, we compared the enzyme kinetics of purified luciferase with its activity in mammalian cells. We found that Fluc activity in solution has a lower Michaelis constant (Km) for luciferin, lower temperature dependence, and lower catalytic half-life than Fluc in cells. In consequence, extracellular luciferin concentration significantly affects the apparent circadian amplitude and phase of the widely used PER2::LUC reporter in cultured fibroblasts, but not in SCN, and we suggest that this arises from differences in plasma membrane luciferin transporter activity. We found that at very high concentrations (>1 mM), luciferin lengthens circadian period, in both fibroblasts and organotypic SCN slices. We conclude that the amplitude and phase of circadian gene expression inferred from bioluminescence recordings should be treated with some caution, and we suggest that optimal luciferin concentration should be determined empirically for each luciferase reporter and cell type.
Collapse
Affiliation(s)
- Kevin A Feeney
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Marrit Putker
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Marco Brancaccio
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - John S O'Neill
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Solgi Z, Khalifeh K, Hosseinkhani S, Ranjbar B. Surface Arginine Saturation Effect on Unfolding Reaction of Firefly Luciferase: A Thermodynamic and Kinetic Perspective. Photochem Photobiol 2016; 92:688-93. [DOI: 10.1111/php.12614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/08/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Zahra Solgi
- Department of Biophysics; Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Khosrow Khalifeh
- Department of Biology; Faculty of Sciences; University of Zanjan; Zanjan Iran
| | - Saman Hosseinkhani
- Department of Biochemistry; Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Bijan Ranjbar
- Department of Biophysics; Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| |
Collapse
|
25
|
A luciferin analogue generating near-infrared bioluminescence achieves highly sensitive deep-tissue imaging. Nat Commun 2016; 7:11856. [PMID: 27297211 PMCID: PMC4911627 DOI: 10.1038/ncomms11856] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 05/06/2016] [Indexed: 12/12/2022] Open
Abstract
In preclinical cancer research, bioluminescence imaging with firefly luciferase and D-luciferin has become a standard to monitor biological processes both in vitro and in vivo. However, the emission maximum (λmax) of bioluminescence produced by D-luciferin is 562 nm where light is not highly penetrable in biological tissues. This emphasizes a need for developing a red-shifted bioluminescence imaging system to improve detection sensitivity of targets in deep tissue. Here we characterize the bioluminescent properties of the newly synthesized luciferin analogue, AkaLumine-HCl. The bioluminescence produced by AkaLumine-HCl in reactions with native firefly luciferase is in the near-infrared wavelength ranges (λmax=677 nm), and yields significantly increased target-detection sensitivity from deep tissues with maximal signals attained at very low concentrations, as compared with D-luciferin and emerging synthetic luciferin CycLuc1. These characteristics offer a more sensitive and accurate method for non-invasive bioluminescence imaging with native firefly luciferase in various animal models. D-luciferin is the standard bioluminescent substrate for in vitro and in vivo imaging. Here the authors introduce AkaLumine-HCl, a soluble luciferin analogue with a near-infrared emission maximum, which allows deep tissue imaging at lower concentrations than D-luciferin.
Collapse
|
26
|
Mass spectrometry analysis and transcriptome sequencing reveal glowing squid crystal proteins are in the same superfamily as firefly luciferase. Sci Rep 2016; 6:27638. [PMID: 27279452 PMCID: PMC4899746 DOI: 10.1038/srep27638] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/18/2016] [Indexed: 01/14/2023] Open
Abstract
The Japanese firefly squid Hotaru-ika (Watasenia scintillans) produces intense blue light from photophores at the tips of two arms. These photophores are densely packed with protein microcrystals that catalyse the bioluminescent reaction using ATP and the substrate coelenterazine disulfate. The squid is the only organism known to produce light using protein crystals. We extracted microcrystals from arm tip photophores and identified the constituent proteins using mass spectrometry and transcriptome libraries prepared from arm tip tissue. The crystals contain three proteins, wsluc1–3, all members of the ANL superfamily of adenylating enzymes. They share 19 to 21% sequence identity with firefly luciferases, which produce light using ATP and the unrelated firefly luciferin substrate. We propose that wsluc1–3 form a complex that crystallises inside the squid photophores, and that in the crystal one or more of the proteins catalyses the production of light using coelenterazine disulfate and ATP. These results suggest that ANL superfamily enzymes have independently evolved in distant species to produce light using unrelated substrates.
Collapse
|
27
|
Omori K, Kobayashi E, Komatsu H, Rawson J, Agrawal G, Parimi M, Oancea AR, Valiente L, Ferreri K, Al-Abdullah IH, Kandeel F, Takahashi M, Mullen Y. Involvement of a proapoptotic gene (BBC3) in islet injury mediated by cold preservation and rewarming. Am J Physiol Endocrinol Metab 2016; 310:E1016-26. [PMID: 27117005 PMCID: PMC4935146 DOI: 10.1152/ajpendo.00441.2015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 03/31/2016] [Indexed: 12/23/2022]
Abstract
Long-term pancreatic cold ischemia contributes to decreased islet number and viability after isolation and culture, leading to poor islet transplantation outcome in patients with type 1 diabetes. In this study, we examined mechanisms of pancreatic cold preservation and rewarming-induced injury by interrogating the proapoptotic gene BBC3/Bbc3, also known as Puma (p53 upregulated modulator of apoptosis), using three experimental models: 1) bioluminescence imaging of isolated luciferase-transgenic ("Firefly") Lewis rat islets, 2) cold preservation of en bloc-harvested pancreata from Bbc3-knockout (KO) mice, and 3) cold preservation and rewarming of human pancreata and isolated islets. Cold preservation-mediated islet injury occurred during rewarming in "Firefly" islets. Silencing Bbc3 by transfecting Bbc3 siRNA into islets in vitro prior to cold preservation improved postpreservation mitochondrial viability. Cold preservation resulted in decreased postisolation islet yield in both wild-type and Bbc3 KO pancreata. However, after culture, the islet viability was significantly higher in Bbc3-KO islets, suggesting that different mechanisms are involved in islet damage/loss during isolation and culture. Furthermore, Bbc3-KO islets from cold-preserved pancreata showed reduced HMGB1 (high-mobility group box 1 protein) expression and decreased levels of 4-hydroxynonenal (4-HNE) protein adducts, which was indicative of reduced oxidative stress. During human islet isolation, BBC3 protein was upregulated in digested tissue from cold-preserved pancreata. Hypoxia in cold preservation increased BBC3 mRNA and protein in isolated human islets after rewarming in culture and reduced islet viability. These results demonstrated the involvement of BBC3/Bbc3 in cold preservation/rewarming-mediated islet injury, possibly through modulating HMGB1- and oxidative stress-mediated injury to islets.
Collapse
Affiliation(s)
- Keiko Omori
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute of the City of Hope, Duarte, California;
| | - Eiji Kobayashi
- Center for Development of Advanced Medical Technology and Department of Organ Fabrication, Keio University School of Medicine, Tokyo, Japan
| | - Hirotake Komatsu
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute of the City of Hope, Duarte, California
| | - Jeffrey Rawson
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute of the City of Hope, Duarte, California
| | - Garima Agrawal
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute of the City of Hope, Duarte, California
| | - Mounika Parimi
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute of the City of Hope, Duarte, California
| | - Alina R Oancea
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute of the City of Hope, Duarte, California
| | - Luis Valiente
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute of the City of Hope, Duarte, California
| | - Kevin Ferreri
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute of the City of Hope, Duarte, California
| | - Ismail H Al-Abdullah
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute of the City of Hope, Duarte, California
| | - Fouad Kandeel
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute of the City of Hope, Duarte, California
| | - Masafumi Takahashi
- Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan; and
| | - Yoko Mullen
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute of the City of Hope, Duarte, California
| |
Collapse
|
28
|
Magalhães CM, Esteves da Silva JCG, Pinto da Silva L. Chemiluminescence and Bioluminescence as an Excitation Source in the Photodynamic Therapy of Cancer: A Critical Review. Chemphyschem 2016; 17:2286-94. [DOI: 10.1002/cphc.201600270] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/22/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Carla M. Magalhães
- Centro de Investigação em Química; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; R. Campo Alegre 687 4169-007 Porto Portugal
| | - Joaquim C. G. Esteves da Silva
- Centro de Investigação em Química; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; R. Campo Alegre 687 4169-007 Porto Portugal
- Centro de Investigação em Química; Departamento de Geociências, Ambiente e Ordenamento do Território; Faculdade de Ciências; Universidade do Porto; R. Campo Alegre 687 4169-007 Porto Portugal
| | - Luís Pinto da Silva
- Centro de Investigação em Química; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; R. Campo Alegre 687 4169-007 Porto Portugal
| |
Collapse
|
29
|
Ioka S, Saitoh T, Iwano S, Suzuki K, Maki SA, Miyawaki A, Imoto M, Nishiyama S. Synthesis of Firefly Luciferin Analogues and Evaluation of the Luminescent Properties. Chemistry 2016; 22:9330-7. [PMID: 27220106 DOI: 10.1002/chem.201600278] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Indexed: 11/11/2022]
Abstract
Five new firefly luciferin (1) analogues were synthesized and their light emission properties were examined. Modifications of the thiazoline moiety in 1 were employed to produce analogues containing acyclic amino acid side chains (2-4) and heterocyclic rings derived from amino acids (5 and 6) linked to the benzothiazole moiety. Although methyl esters of all of the synthetic derivatives exhibited chemiluminescence activity, only carboluciferin (6), possessing a pyrroline-substituted benzothiazole structure, had bioluminescence (BL) activity (λmax =547 nm). Results of bioluminescence studies with AMP-carboluciferin (AMP=adenosine monophosphate) and AMP-firefly luciferin showed that the nature of the thiazoline mimicking moiety affected the adenylation step of the luciferin-luciferase reaction required for production of potent BL. In addition, BL of 6 in living mice differed from that of 1 in that its luminescence decay rate was slower.
Collapse
Affiliation(s)
- Shuji Ioka
- Department of Chemistry, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Kohoku-ku, 223-8522, Yokohama, Japan.,Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Kohoku-ku, 223-8522, Yokohama, Japan
| | - Tsuyoshi Saitoh
- Department of Chemistry, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Kohoku-ku, 223-8522, Yokohama, Japan.,International Institute for Integrative Sleep Medicine (WPI-IIS), University of Tsukuba, Tennodai 1-1-1, Tsukuba-si, 305-8577, Ibaraki, Japan
| | - Satoshi Iwano
- Department of Engineering Science, The University of Electro-Communications, Chofugadake 1-5-1, Chofu, 182-8585, Tokyo, Japan.,Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Hirosawa 2-1, Wako, 351-0198, Saitama, Japan
| | - Koji Suzuki
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Kohoku-ku, 223-8522, Yokohama, Japan
| | - Shojiro A Maki
- Department of Engineering Science, The University of Electro-Communications, Chofugadake 1-5-1, Chofu, 182-8585, Tokyo, Japan
| | - Atsushi Miyawaki
- Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Hirosawa 2-1, Wako, 351-0198, Saitama, Japan
| | - Masaya Imoto
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Kohoku-ku, 223-8522, Yokohama, Japan
| | - Shigeru Nishiyama
- Department of Chemistry, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Kohoku-ku, 223-8522, Yokohama, Japan.
| |
Collapse
|
30
|
Tseng KL, Lee YZ, Chen YR, Lyu PC. 1H, 15N and 13C resonance assignments of light organ-associated fatty acid-binding protein of Taiwanese fireflies. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:71-74. [PMID: 26373428 DOI: 10.1007/s12104-015-9640-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/09/2015] [Indexed: 06/05/2023]
Abstract
Fatty acid-binding proteins (FABPs) are a family of proteins that modulate the transfer of various fatty acids in the cytosol and constitute a significant portion in many energy-consuming cells. The ligand binding properties and specific functions of a particular type of FABP seem to be diverse and depend on the respective binding cavity as well as the cell type from which this protein is derived. Previously, a novel FABP (lcFABP; lc: Luciola cerata) was identified in the light organ of Taiwanese fireflies. The lcFABP was proved to possess fatty acids binding capabilities, especially for fatty acids of length C14-C18. However, the structural details are unknown, and the structure-function relationship has remained to be further investigated. In this study, we finished the (1)H, (15)N and (13)C chemical shift assignments of (15)N/(13)C-enriched lcFABP by solution NMR spectroscopy. In addition, the secondary structure distribution was revealed based on the backbone N, H, Cα, Hα, C and side chain Cβ assignments. These results can provide the basis for further structural exploration of lcFABP.
Collapse
Affiliation(s)
- Kai-Li Tseng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, 30013, Taiwan, ROC
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, 30013, Taiwan, ROC
| | - Yun-Ru Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, 30013, Taiwan, ROC
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, 30013, Taiwan, ROC.
- Department of Medical Sciences, National Tsing Hua University, Hsinchu, Taiwan, ROC.
| |
Collapse
|
31
|
Sharpe ML, Dearden PK, Gimenez G, Krause KL. Comparative RNA seq analysis of the New Zealand glowworm Arachnocampa luminosa reveals bioluminescence-related genes. BMC Genomics 2015; 16:825. [PMID: 26486607 PMCID: PMC4617951 DOI: 10.1186/s12864-015-2006-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 10/03/2015] [Indexed: 01/12/2023] Open
Abstract
Background The New Zealand glowworm is the larva of a carnivorous fungus gnat that produces bioluminescence to attract prey. The bioluminescent system of the glowworm is evolutionarily distinct from other well-characterised systems, especially that of the fireflies, and the molecules involved have not yet been identified. We have used high throughput sequencing technology to produce a transcriptome for the glowworm and identify transcripts encoding proteins that are likely to be involved in glowworm bioluminescence. Results Here we report the sequencing and annotation of the first transcriptome of the glowworm, and a differential analysis of expression from the glowworm light organ compared with non-light organ tissue. The analysis identified six transcripts encoding proteins that are potentially involved in glowworm bioluminescence. Three of these proteins are members of the ANL superfamily of adenylating enzymes, with similar amino acid sequences to that of the luciferase enzyme found in fireflies (31 to 37 % identical), and are candidate luciferases for the glowworm bioluminescent system. The remaining three transcripts encode putative aminoacylase, phosphatidylethanolamine-binding and glutathione S-transferase proteins. Conclusions This research provides a basis for further biochemical studies into how the glowworm produces light, and a source of genetic information to aid future ecological and evolutionary studies of the glowworm. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2006-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Miriam L Sharpe
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
| | - Peter K Dearden
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
| | - Gregory Gimenez
- Otago Genomics & Bioinformatics Facility, University of Otago, Dunedin, New Zealand.
| | - Kurt L Krause
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
| |
Collapse
|
32
|
Wang W, Zhao Q, Luo M, Li M, Wang D, Wang Y, Liu Q. Immobilization of Firefly Luciferase on PVA-co-PE Nanofibers Membrane as Biosensor for Bioluminescent Detection of ATP. ACS APPLIED MATERIALS & INTERFACES 2015; 7:20046-52. [PMID: 26275118 DOI: 10.1021/acsami.5b07339] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The bioluminescent reaction catalyzed by firefly luciferase has become widely established as an outstanding analytical system for assay of adenosine triphosphate (ATP). When in solution, the luciferase is unstable and cannot be reused. The problem can be partially solved by immobilizing the luciferase on solid substrates. The poly(vinyl alcohol-co-ethylene) (PVA-co-PE) nanofibers membrane has abundant active hydroxyl groups on the surface. The PVA-co-PE nanofibers membrane was first activated by cyanuric chloride with triazinyl group. Then the activated PVA-co-PE nanofibers membrane was subsequently reacted with 1,3-propanediamine and biotin. The firefly luciferase was immobilized onto the surface of 1,3-propanediamine- and biotin-functionalized membranes. The surface chemical structure and morphologies of nanofibers membranes were characterized by FTIR-ATR spectra and SEM. The hydrophilicity of membranes was tested by water contact angle measurements. The detection of fluorescence intensity displayed that the firefly-luciferase-immobilized PVA-co-PE nanofibers membranes indicated high catalytic activity and efficiency. Especially, the firefly-luciferase-immobilized nanofiber membrane which was functionalized by biotin can be a promising candidate as biosensor for bioluminescent detection of ATP because of its high detection sensitivity.
Collapse
Affiliation(s)
- Wenwen Wang
- School of Materials Science and Engineering, Wuhan Textile University , Wuhan 430073, China
| | - Qinghua Zhao
- School of Materials Science and Engineering, Wuhan Textile University , Wuhan 430073, China
| | - Mengying Luo
- School of Materials Science and Engineering, Wuhan Textile University , Wuhan 430073, China
| | - Mufang Li
- School of Materials Science and Engineering, Wuhan Textile University , Wuhan 430073, China
| | - Dong Wang
- School of Materials Science and Engineering, Wuhan Textile University , Wuhan 430073, China
| | - Yuedan Wang
- School of Materials Science and Engineering, Wuhan Textile University , Wuhan 430073, China
| | - Qiongzhen Liu
- School of Materials Science and Engineering, Wuhan Textile University , Wuhan 430073, China
| |
Collapse
|
33
|
Marques SM, Gonçalves LM, Esteves da Silva JCG. An Optimized Firefly Luciferase Bioluminescent Assay for the Analysis of Free Fatty Acids. Photochem Photobiol 2015; 91:980-4. [DOI: 10.1111/php.12458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 04/03/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Simone M. Marques
- Centro de Investigação em Química da Universidade do Porto (CIQ-UP); Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Porto Portugal
| | - Luís M. Gonçalves
- Requimte/LAQV; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Porto Portugal
| | - Joaquim C. G. Esteves da Silva
- Centro de Investigação em Química da Universidade do Porto (CIQ-UP); Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Porto Portugal
| |
Collapse
|
34
|
Butterworth KT, Redmond KM, McMahon SJ, Cole AJ, Jain S, McCarthy HO, O'Sullivan JM, Hounsell AR, Prise KM. Conventional in vivo irradiation procedures are insufficient to accurately determine tumor responses to non-uniform radiation fields. Int J Radiat Biol 2014; 91:257-61. [PMID: 25347147 DOI: 10.3109/09553002.2014.980468] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE To determine differences in overall tumor responses measured by volumetric assessment and bioluminescence imaging (BLI) following exposure to uniform and non-uniform radiation fields in an ectopic prostate tumor model. MATERIALS AND METHODS Bioluminescent human prostate tumor xenografts were established by subcutaneous implantation into male mice. Tumors were irradiated with uniform or non-uniform field configurations using conventional in vivo irradiation procedures performed using a 225 kVp generator with custom lead shielding. Tumor responses were measured using Vernier calipers and by BLI using an in vivo imaging system. Survival was defined as the time to quadroupling of pre-treatment tumor volume. RESULTS The correlation between BLI and tumor volume measurements was found to be different for un-irradiated (R = 0.61), uniformly irradiated (R = 0.34) and partially irradiated (R = 0.30) tumors. Uniformly irradiated tumors resulted in an average tumor growth delay of 60 days with median survival of 75 days, compared to partially irradiated tumors which showed an average growth delay of 24 days and median survival of 38 days. CONCLUSIONS Correlation between BLI and tumor volume measurements is lower for partially irradiated tumors than those exposed to uniform dose distributions. The response of partially irradiated tumors suggests non-uniformity in response beyond physical dose distribution within the target volume. Dosimetric uncertainty associated with conventional in vivo irradiation procedures prohibits their ability to accurately determine tumor response to non-uniform radiation fields and stresses the need for image guided small animal radiation research platforms.
Collapse
Affiliation(s)
- Karl T Butterworth
- Centre for Cancer Research and Cell Biology, Queen's University Belfast , Belfast
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Yu H, Zhao Y, Guo C, Gan Y, Huang H. The role of proline substitutions within flexible regions on thermostability of luciferase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:65-72. [PMID: 25448017 DOI: 10.1016/j.bbapap.2014.10.017] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/19/2014] [Accepted: 10/21/2014] [Indexed: 11/18/2022]
Abstract
Improving the stability of firefly luciferase has been a critical issue for its wider industrial applications. Studies about hyperthermophile proteins show that flexibility could be an effective indicator to find out weak spots to engineering thermostability of proteins. However, the relationship among flexibility, activity and stability in most of proteins is unclear. Proline is the most rigid residue and can be introduced to rigidify flexible regions to enhance thermostability of proteins. We firstly apply three different methods, molecular dynamics (MD) simulation, B-FITTER and framework rigidity optimized dynamics algorithm (FRODA) to determine the flexible regions of Photinus pyralis luciferase: Fragment 197-207; Fragment 471-481 and Fragment 487-495. Then, introduction of proline is used to rigidify these flexible regions. Two mutants D476P and H489P within most flexible regions are finally designed. In the results, H489P mutant shows improved thermostability while maintaining its catalytic efficiency compared to that of wild type luciferase. Flexibility analysis confirms that the overall rigidity and local rigidity of H489P mutant are greatly strengthened. D476P mutant shows decreased thermosatbility and the reason for this is elucidated at the molecular level. S307P mutation is randomly chosen outside the flexible regions as a control. Thermostability analysis shows that S307P mutation has decreased kinetic stability and enhanced thermodynamic stability.
Collapse
Affiliation(s)
- Haoran Yu
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin PR China
| | - Yang Zhao
- National Institutes for Food and Drug Control (NIFDC), Beijing 100050, PR China
| | - Chao Guo
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin PR China
| | - Yiru Gan
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin PR China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin PR China.
| |
Collapse
|
36
|
Quantum/molecular mechanics study of firefly bioluminescence on luciferase oxidative conformation. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.05.061] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
37
|
Pinto da Silva L, Esteves da Silva JC. Study of firefly luciferin oxidation and isomerism as possible inhibition pathways for firefly bioluminescence. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2013.12.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
38
|
Biosynthesis of firefly luciferin in adult lantern: decarboxylation of L-cysteine is a key step for benzothiazole ring formation in firefly luciferin synthesis. PLoS One 2013; 8:e84023. [PMID: 24391868 PMCID: PMC3877152 DOI: 10.1371/journal.pone.0084023] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 11/07/2013] [Indexed: 12/05/2022] Open
Abstract
Background Bioluminescence in fireflies and click beetles is produced by a luciferase-luciferin reaction. The luminescence property and protein structure of firefly luciferase have been investigated, and its cDNA has been used for various assay systems. The chemical structure of firefly luciferin was identified as the ᴅ-form in 1963 and studies on the biosynthesis of firefly luciferin began early in the 1970’s. Incorporation experiments using 14C-labeled compounds were performed, and cysteine and benzoquinone/hydroquinone were proposed to be biosynthetic component for firefly luciferin. However, there have been no clear conclusions regarding the biosynthetic components of firefly luciferin over 30 years. Methodology/Principal Findings Incorporation studies were performed by injecting stable isotope-labeled compounds, including ʟ-[U-13C3]-cysteine, ʟ-[1-13C]-cysteine, ʟ-[3-13C]-cysteine, 1,4-[D6]-hydroquinone, and p-[2,3,5,6-D]-benzoquinone, into the adult lantern of the living Japanese firefly Luciola lateralis. After extracting firefly luciferin from the lantern, the incorporation of stable isotope-labeled compounds into firefly luciferin was identified by LC/ESI-TOF-MS. The positions of the stable isotope atoms in firefly luciferin were determined by the mass fragmentation of firefly luciferin. Conclusions We demonstrated for the first time that ᴅ- and ʟ-firefly luciferins are biosynthesized in the lantern of the adult firefly from two ʟ-cysteine molecules with p-benzoquinone/1,4-hydroquinone, accompanied by the decarboxylation of ʟ-cysteine.
Collapse
|
39
|
Dioxetanones’ peroxide bond as a charge-shifted bond: implications in the chemiluminescence process. Struct Chem 2013. [DOI: 10.1007/s11224-013-0383-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
40
|
Inouye S, Sahara-Miura Y. A Novel Catalytic Function of Synthetic IgG-Binding Domain (Z Domain) from Staphylococcal Protein A: Light Emission with Coelenterazine. Photochem Photobiol 2013; 90:137-44. [DOI: 10.1111/php.12192] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 10/15/2013] [Indexed: 11/29/2022]
|
41
|
Synthesis and luminescence properties of biphenyl-type firefly luciferin analogs with a new, near-infrared light-emitting bioluminophore. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.09.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
42
|
Nakagomi M, Fujimaki N, Ito A, Toda T, Fukasawa H, Shudo K, Tomita R. A novel aromatic carboxylic acid inactivates luciferase by acylation of an enzymatically active regulatory lysine residue. PLoS One 2013; 8:e75445. [PMID: 24066181 PMCID: PMC3774628 DOI: 10.1371/journal.pone.0075445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/15/2013] [Indexed: 11/21/2022] Open
Abstract
Firefly luciferase (Luc) is widely used as a reporter enzyme in cell-based assays for gene expression. A novel aromatic carboxylic acid, F-53, reported here for the first time, substantially inhibited the enzymatic activity of Luc in a Luc reporter screening. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and tandem mass spectrometry (MS/MS) analyses showed that F-53 modifies Luc at lysine-529 via amidation of the F-53 carboxyl group. The lysine-529 residue of Luc, which plays a regulatory catalytic role, can be acetylated. Luc also has a long-chain fatty acyl-CoA synthase activity. An in vitro assay that involved both recombinant Luc and mouse liver microsomes identified F-53-CoA as the reactive form produced from F-53. However, whereas the inhibitory effect of F-53 is observed in Hela cells that transiently expressed Luc, it is not observed in an in vitro assay that involves recombinant Luc alone. Therefore, insights into the activities of certain mammalian transferases can be translated to better understand the acylation by F-53. The insights from this study about the novel inhibitory modification mechanism might help not only to avoid misinterpretation of the results of Luc-based reporter screening assays but also to explain the pharmacological and toxicological effects of carboxylic acid-containing drugs.
Collapse
Affiliation(s)
- Madoka Nakagomi
- Department of Biology, Research Foundation Itsuu Laboratory, Tokyo, Japan
- * E-mail:
| | - Nobuko Fujimaki
- Department of Chemistry, Research Foundation Itsuu Laboratory, Tokyo, Japan
| | - Ai Ito
- Department of Chemistry, Research Foundation Itsuu Laboratory, Tokyo, Japan
| | - Takahiro Toda
- Department of Biology, Research Foundation Itsuu Laboratory, Tokyo, Japan
| | - Hiroshi Fukasawa
- Department of Biology, Research Foundation Itsuu Laboratory, Tokyo, Japan
| | - Koichi Shudo
- Department of Biology, Research Foundation Itsuu Laboratory, Tokyo, Japan
- Department of Chemistry, Research Foundation Itsuu Laboratory, Tokyo, Japan
| | - Ryoichi Tomita
- Molecular Function Department, Institute of Medicinal Molecular Design, Inc., Tokyo, Japan
| |
Collapse
|
43
|
da Silva LP, Simkovitch R, Huppert D, da Silva JCGE. Oxyluciferin photoacidity: the missing element for solving the keto-enol mystery? Chemphyschem 2013; 14:3441-6. [PMID: 23843204 DOI: 10.1002/cphc.201300402] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/21/2013] [Indexed: 01/07/2023]
Abstract
The oxyluciferin family of fluorophores has been receiving much attention from the research community and several systematic studies have been performed in order to gain more insight regarding their photophysical properties and photoprotolytic cycles. In this minireview, we summarize the knowledge obtained so far and define several possible lines for future research. More importantly, we analyze the impact of the discoveries on the firefly bioluminescence phenomenon made so far and explain how they re-open again the discussion regarding the identity (keto or enol species) of the bioluminophore.
Collapse
Affiliation(s)
- Luís Pinto da Silva
- Centro de Investigação em Química, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre 687, 4169-007 Porto (Portugal), Fax: (+351) 220 402 659
| | | | | | | |
Collapse
|
44
|
Iwano S, Obata R, Miura C, Kiyama M, Hama K, Nakamura M, Amano Y, Kojima S, Hirano T, Maki S, Niwa H. Development of simple firefly luciferin analogs emitting blue, green, red, and near-infrared biological window light. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.03.050] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
45
|
Pinto da Silva L, Esteves da Silva JCG. Interstate Crossing-Induced Chemiexcitation as the Reason for the Chemiluminescence of Dioxetanones. Chemphyschem 2013; 14:1071-9. [DOI: 10.1002/cphc.201200872] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 12/13/2012] [Indexed: 12/22/2022]
|
46
|
Li J, Chen L, Du L, Li M. Cage the firefly luciferin! – a strategy for developing bioluminescent probes. Chem Soc Rev 2013; 42:662-76. [DOI: 10.1039/c2cs35249d] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
47
|
Oba Y, Furuhashi M, Bessho M, Sagawa S, Ikeya H, Inouye S. Bioluminescence of a firefly pupa: involvement of a luciferase isotype in the dim glow of pupae and eggs in the Japanese firefly, Luciola lateralis. Photochem Photobiol Sci 2013; 12:854-63. [DOI: 10.1039/c3pp25363e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
48
|
Liu Y, Fang J, Cai H, Xiao F, Ding K, Hu Y. Identification and synthesis of substituted pyrrolo[2,3-d]pyrimidines as novel firefly luciferase inhibitors. Bioorg Med Chem 2012; 20:5473-82. [PMID: 22898255 DOI: 10.1016/j.bmc.2012.07.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 07/21/2012] [Accepted: 07/21/2012] [Indexed: 01/17/2023]
Abstract
A novel firefly luciferase inhibitor (3a) with a pyrrolo[2,3-d]pyrimidine core was identified in a cell-based NF-κB luciferase reporter gene assay. It potently inhibited the firefly luciferase derived from Photinus pyralis with an IC(50) value of 0.36 ± 0.05 μM. Kinetic analysis of 3a inhibition showed that it is predominantly competitive with respect to D-luciferin and uncompetitive with respect to ATP. Therefore, several pyrrolo[2,3-d]pyrimidine analogues were prepared to further investigate the structure-activity relationship (SAR) for luciferase inhibition. The most potent inhibitor of this series was 4c, which showed an IC(50) value of 0.06 ± 0.01 μM. In addition, molecular docking studies suggested that both 3a and 4c could be accommodated in the D-luciferin binding pocket, which is expected for a predominantly competitive inhibitor with respect to D-luciferin.
Collapse
Affiliation(s)
- Yang Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | | | | | | | | | | |
Collapse
|
49
|
Ebrahimi M, Hosseinkhani S, Heydari A, Khavari-Nejad RA, Akbari J. Improvement of Thermostability and Activity of Firefly Luciferase Through [TMG][Ac] Ionic Liquid Mediator. Appl Biochem Biotechnol 2012; 168:604-15. [DOI: 10.1007/s12010-012-9803-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 06/06/2012] [Indexed: 10/28/2022]
|
50
|
Pinto da Silva L, Esteves da Silva JCG. Firefly chemiluminescence and bioluminescence: efficient generation of excited states. Chemphyschem 2012; 13:2257-62. [PMID: 22532490 DOI: 10.1002/cphc.201200195] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Indexed: 01/13/2023]
Abstract
Firefly luciferase catalyzes a light-emitting reaction in which an excited-state product is formed. Both experimental and theoretical methodologies are used to study this system, and the reactions catalyzed by luciferase are relatively well characterized. However, the mechanism by which an excited-state product is formed is still unknown. This Minireview deals with the current understanding of firefly bioluminescence and chemiluminescence. Thermal decomposition of simple 1,2-dioxetanes is also discussed, due to their role in formation of the excited-state bioluminophore.
Collapse
Affiliation(s)
- Luís Pinto da Silva
- Centro de Investigação em Química, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
| | | |
Collapse
|