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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.
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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
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2
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Kundrata R, Hoffmannova J, Hinson KR, Keller O, Packova G. Rhagophthalmidae Olivier, 1907 (Coleoptera, Elateroidea): described genera and species, current problems, and prospects for the bioluminescent and paedomorphic beetle lineage. Zookeys 2022; 1126:55-130. [PMID: 36760860 PMCID: PMC9881481 DOI: 10.3897/zookeys.1126.90233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/12/2022] [Indexed: 02/11/2023] Open
Abstract
Rhagophthalmidae are a small beetle family known from the eastern Palaearctic and Oriental realms. Rhagophthalmidae are closely related to railroad worms (Phengodidae) and fireflies (Lampyridae) with which they share highly modified paedomorphic females and the ability to emit light. Currently, Rhagophthalmidae include 66 species classified in the following 12 genera: Bicladodrilus Pic, 1921 (two spp.), Bicladum Pic, 1921 (two spp.), Dioptoma Pascoe, 1860 (two spp.), Diplocladon Gorham, 1883 (two spp.), Dodecatoma Westwood, 1849 (eight spp.), Falsophrixothrix Pic, 1937 (six spp.), Haplocladon Gorham, 1883 (two spp.), Menghuoius Kawashima, 2000 (three spp.), Mimoochotyra Pic, 1937 (one sp.), Monodrilus Pic, 1921 (two spp. in two subgenera), Pseudothilmanus Pic, 1918 (two spp.), and Rhagophthalmus Motschulsky, 1854 (34 spp.). The replacement name Haplocladongorhami Kundrata, nom. nov. is proposed for Diplocladonhasseltii Gorham, 1883b (described in subgenus Haplocladon) which is preoccupied by Diplocladonhasseltii Gorham, 1883a. The genus Reductodrilus Pic, 1943 is tentatively placed in Lampyridae: Ototretinae. Lectotypes are designated for Pseudothilmanusalatus Pic, 1918 and P.marginalis Pic, 1918. Interestingly, in the eastern part of their distribution, Rhagophthalmidae have remained within the boundaries of the Sunda Shelf and the Philippines demarcated by the Wallace Line, which separates the Oriental and Australasian realms. This study is intended to be a first step towards a comprehensive revision of the group on both genus and species levels. Additionally, critical problems and prospects for rhagophthalmid research are briefly discussed.
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Affiliation(s)
- Robin Kundrata
- Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 77900, Olomouc, Czech RepublicPalacky UniversityOlomoucCzech Republic
| | - Johana Hoffmannova
- Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 77900, Olomouc, Czech RepublicPalacky UniversityOlomoucCzech Republic
| | - Kevin R. Hinson
- EpiLogic GmbH Agrarbiologische Forschung und Beratung, Hohenbachernstr. 19–21, 85354, Freising, GermanyEpiLogic GmbH Agrarbiologische Forschung und BeratungFreisingGermany
| | - Oliver Keller
- Florida State Collection of Arthropods, Florida Department of Agriculture and Consumer Services, P.O. Box 147100, Gainesville, FL, 32614-7100, USAFlorida Department of Agriculture and Consumer ServicesGainesvilleUnited States of America
| | - Gabriela Packova
- Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 77900, Olomouc, Czech RepublicPalacky UniversityOlomoucCzech Republic
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Abu Seri N, Abd Rahman A. Fireflies in South East Asia: Species Diversity, Distribution, and Habitat (2015-2021). PERTANIKA JOURNAL OF TROPICAL AGRICULTURAL SCIENCE 2021; 44. [DOI: 10.47836/pjtas.44.4.02] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Fireflies are one of the most famous luminous insects that emit bioluminescence. The most famous fireflies in Southeast Asia are Pteroptyx , of the order Coleoptera and the Lampyridae family. This review paper combined the data on the species diversity and firefly distribution in Southeast Asian countries such as Malaysia, the Philippines, Indonesia, Cambodia, Myanmar, Singapore, Sri Lanka, Papua New Guinea, Laos, Thailand, and Vietnam published in 2015-2021. Some countries have limited data and no studies to identify firefly species and their habitat from 2015 to 2021; the data before 2015 was used. Furthermore, the lack of studies by Southeast Asian researchers regarding the richness of firefly species has been reviewed. Malaysian and Thailand researchers are among the forerunners in the study related to fireflies in the Southeast Asian region compared to other Southeast Asian countries. Lastly, not much is known about the display trees or habitat of fireflies in many areas such as the Philippines, Indonesia, Cambodia, Myanmar, Singapore, Sri Lanka, Papua New Guinea, Laos, Thailand, and Vietnam. More studies are warranted to be conducted in the future on firefly species and their habitat.
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de Paiva FCR, Chan K, Samborskyy M, Silber AM, Leadlay PF, Dias MVB. The crystal structure of AjiA1 reveals a novel structural motion mechanism in the adenylate-forming enzyme family. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:1201-1210. [DOI: 10.1107/s2059798320013431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/07/2020] [Indexed: 11/10/2022]
Abstract
Adenylate-forming enzymes (AFEs) are a mechanistic superfamily of proteins that are involved in many cellular roles. In the biosynthesis of benzoxazole antibiotics, an AFE has been reported to play a key role in the condensation of cyclic molecules. In the biosynthetic gene cluster for the benzoxazole AJI9561, AjiA1 catalyzes the condensation of two 3-hydroxyanthranilic acid (3-HAA) molecules using ATP as a co-substrate. Here, the enzymatic activity of AjiA1 is reported together with a structural analysis of its apo form. The structure of AjiA1 was solved at 2.0 Å resolution and shows a conserved fold with other AFE family members. AjiA1 exhibits activity in the presence of 3-HAA (K
m = 77.86 ± 28.36, k
cat = 0.04 ± 0.004) and also with the alternative substrate 3-hydroxybenzoic acid (3-HBA; K
m = 22.12 ± 31.35, k
cat = 0.08 ± 0.005). The structure of AjiA1 in the apo form also reveals crucial conformational changes that occur during the catalytic cycle of this enzyme which have not been described for any other AFE member. Consequently, the results shown here provide insights into this protein family and a new subgroup is proposed for enzymes that are involved in benzoxazole-ring formation.
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Zhang R, He J, Dong Z, Liu G, Yin Y, Zhang X, Li Q, Ren Y, Yang Y, Liu W, Chen X, Xia W, Duan K, Hao F, Lin Z, Yang J, Chang Z, Zhao R, Wan W, Lu S, Peng Y, Ge S, Wang W, Li X. Genomic and experimental data provide new insights into luciferin biosynthesis and bioluminescence evolution in fireflies. Sci Rep 2020; 10:15882. [PMID: 32985577 PMCID: PMC7522259 DOI: 10.1038/s41598-020-72900-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/09/2020] [Indexed: 02/08/2023] Open
Abstract
Fireflies are among the most charismatic insects for their spectacular bioluminescence, but the origin and evolution of bioluminescence remain elusive. Especially, the genic basis of luciferin (D-luciferin) biosynthesis and light patterns is largely unknown. Here, we present the high-quality reference genomes of two fireflies Lamprigera yunnana (1053 Mb) and Abscondita terminalis (501 Mb) with great differences in both morphology and luminous behavior. We sequenced the transcriptomes and proteomes of luminous organs of two species. We created the CRISPR/Cas9-induced mutants of Abdominal B gene without luminous organs in the larvae of A. terminalis and sequenced the transcriptomes of mutants and wild-types. Combining gene expression analyses with comparative genomics, we propose a more complete luciferin synthesis pathway, and confirm the convergent evolution of bioluminescence in insects. Using experiments, the function of the firefly acyl-CoA thioesterase (ACOT1) to convert L-luciferin to D-luciferin was validated for the first time. Comparisons of three-dimension reconstruction of luminous organs and their differentially expressed genes among two species suggest that two positive genes in the calcium signaling pathway and structural difference of luminous organs may play an important role in the evolution of flash pattern. Altogether, our results provide important resources for further exploring bioluminescence in insects.
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Affiliation(s)
- Ru Zhang
- 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
| | - Jinwu 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
| | - Zhiwei Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Guichun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Yuan Yin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Xinying Zhang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Yandong Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Yongzhi Yang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Wei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Xianqing Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Wenhao Xia
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Kang Duan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Fei Hao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Zeshan Lin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Jie Yang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Zhou Chang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Ruoping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Wenting Wan
- 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
| | - Sihan Lu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Yanqiong Peng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Siqin Ge
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 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.
- Center for Excellence in Animal Evolution and Genetics, Kunming, 650223, Yunnan, China.
| | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
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6
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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
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7
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Lower SE, Stanger-Hall KF, Hall DW. Molecular variation across populations of a widespread North American firefly, Photinus pyralis, reveals that coding changes do not underlie flash color variation or associated visual sensitivity. BMC Evol Biol 2018; 18:129. [PMID: 30170542 PMCID: PMC6119266 DOI: 10.1186/s12862-018-1251-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/20/2018] [Indexed: 01/22/2023] Open
Abstract
Background Genes underlying signal production and reception are expected to evolve to maximize signal detection in specific environments. Fireflies vary in their light signal color both within and between species, and thus provide an excellent system in which to study signal production and reception in the context of signaling environments. Differences in signal color have been hypothesized to be due to variation in the sequence of luciferase, the enzyme that catalyzes the light reaction. Similarly, differences in visual sensitivity, which are expected to match signal color, have been hypothesized to be due to variation in the sequence of opsins, the protein component of visual pigments. Here we investigated (1) whether sequence variation in luciferase correlates with variation in signal color and (2) whether sequence variation in opsins correlates with inferred matching visual sensitivity across populations of a widespread North American firefly species, Photinus pyralis. We further tested (3) whether selection has acted on these loci by examining their population-level differentiation relative to the distribution of differentiation derived from a genome-wide sample of loci generated by double-digest RADseq. Results We found virtually no coding variation in luciferase or opsins. However, there was extreme divergence in non-coding variation in luciferase across populations relative to a panel of random genomic loci. Conclusions The absence of protein variation at both loci challenges the paradigm that variation in signal color and visual sensitivity in fireflies is exclusively due to coding variation in luciferase and opsin genes. Instead, flash color variation within species must involve other mechanisms, such as abdominal pigmentation or regulation of light organ physiology. Evidence for selection at non-coding variation in luciferase suggests that selection is targeting luciferase regulation and may favor differ expression levels across populations. Electronic supplementary material The online version of this article (10.1186/s12862-018-1251-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah E Lower
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA. .,Present address: Department of Biology, Bucknell University, Lewisburg, PA, 17837, USA.
| | | | - David W Hall
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
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8
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Watkins OC, Sharpe ML, Perry NB, Krause KL. New Zealand glowworm (Arachnocampa luminosa) bioluminescence is produced by a firefly-like luciferase but an entirely new luciferin. Sci Rep 2018; 8:3278. [PMID: 29459729 PMCID: PMC5818473 DOI: 10.1038/s41598-018-21298-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 02/01/2018] [Indexed: 01/07/2023] Open
Abstract
The New Zealand glowworm, Arachnocampa luminosa, is well-known for displays of blue-green bioluminescence, but details of its bioluminescent chemistry have been elusive. The glowworm is evolutionarily distant from other bioluminescent creatures studied in detail, including the firefly. We have isolated and characterised the molecular components of the glowworm luciferase-luciferin system using chromatography, mass spectrometry and 1H NMR spectroscopy. The purified luciferase enzyme is in the same protein family as firefly luciferase (31% sequence identity). However, the luciferin substrate of this enzyme is produced from xanthurenic acid and tyrosine, and is entirely different to that of the firefly and known luciferins of other glowing creatures. A candidate luciferin structure is proposed, which needs to be confirmed by chemical synthesis and bioluminescence assays. These findings show that luciferases can evolve independently from the same family of enzymes to produce light using structurally different luciferins.
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Affiliation(s)
- Oliver C Watkins
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- New Zealand Institute for Plant and Food Research Ltd., Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Miriam L Sharpe
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Nigel B Perry
- New Zealand Institute for Plant and Food Research Ltd., Department of Chemistry, University of Otago, Dunedin, New Zealand.
| | - Kurt L Krause
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
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9
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Bessho-Uehara M, Oba Y. Identification and characterization of the Luc2-type luciferase in the Japanese firefly, Luciola parvula
, involved in a dim luminescence in immobile stages. LUMINESCENCE 2017; 32:924-931. [DOI: 10.1002/bio.3273] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/01/2016] [Accepted: 11/28/2016] [Indexed: 11/10/2022]
Affiliation(s)
| | - Yuichi Oba
- Graduate School of Bioagricultural Sciences; Nagoya University; Nagoya Japan
- Department of Environmental Biology; Chubu University; Kasugai Japan
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10
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Bessho-Uehara M, Konishi K, Oba Y. Biochemical characteristics and gene expression profiles of two paralogous luciferases from the Japanese firefly Pyrocoelia atripennis (Coleoptera, Lampyridae, Lampyrinae): insight into the evolution of firefly luciferase genes. Photochem Photobiol Sci 2017; 16:1301-1310. [DOI: 10.1039/c7pp00110j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The same green luminescence is generated by two luciferase isoforms: PatLuc1 is used in lanterns of various stages, and PatLuc2 is used in the body of immobile/less-mobile stages.
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Affiliation(s)
- Manabu Bessho-Uehara
- Graduate School of Bioagricultural Sciences
- Nagoya University
- Nagoya 464-8601
- Japan
| | - Kaori Konishi
- Graduate School of Bioagricultural Sciences
- Nagoya University
- Nagoya 464-8601
- Japan
| | - Yuichi Oba
- Graduate School of Bioagricultural Sciences
- Nagoya University
- Nagoya 464-8601
- Japan
- Department of Environmental Biology
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11
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Total evidence phylogeny and the evolution of adult bioluminescence in fireflies (Coleoptera: Lampyridae). Mol Phylogenet Evol 2016; 107:564-575. [PMID: 27998815 DOI: 10.1016/j.ympev.2016.12.017] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 12/10/2016] [Accepted: 12/14/2016] [Indexed: 11/21/2022]
Abstract
Fireflies are some of the most captivating organisms on the planet. They have a rich history as subjects of scientific study, especially in relation to their bioluminescent behavior. Yet, the phylogenetic relationships of fireflies are still poorly understood. Here, we present the first total evidence approach to reconstruct lampyrid phylogeny using both a molecular matrix from six loci and an extensive morphological matrix. Using this phylogeny we test the hypothesis that adult bioluminescence evolved after the origin of the firefly clade. The ancestral state of adult bioluminescence is recovered as non-bioluminescent with one to six gains and five to ten subsequent losses. The monophyly of the family, as well as the subfamilies is also tested. Ototretinae, Cyphonocerinae, Luciolinae (incl. Pristolycus), Amydetinae, "cheguevarinae" sensu Jeng 2008, and Photurinae are highly supported as monophyletic. With the exception of four taxa, Lampyrinae is also recovered as monophyletic with high support. Based on phylogenetic and morphological data Lamprohiza, Phausis, and Lamprigera are transferred to Lampyridae incertae sedis.
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12
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Branchini BR, Southworth TL, Salituro LJ, Fontaine DM, Oba Y. Cloning of the Blue Ghost (
Phausis reticulata
) Luciferase Reveals a Glowing Source of Green Light. Photochem Photobiol 2016; 93:473-478. [DOI: 10.1111/php.12649] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/31/2016] [Indexed: 11/27/2022]
Affiliation(s)
| | | | | | | | - Yuichi Oba
- Department of Environmental Biology College of Bioscience and Biotechnology Chubu University Kasugai Japan
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13
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Lipid metabolism in Rhodnius prolixus: Lessons from the genome. Gene 2016; 596:27-44. [PMID: 27697616 DOI: 10.1016/j.gene.2016.09.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 09/22/2016] [Accepted: 09/28/2016] [Indexed: 01/01/2023]
Abstract
The kissing bug Rhodnius prolixus is both an important vector of Chagas' disease and an interesting model for investigation into the field of physiology, including lipid metabolism. The publication of this insect genome will bring a huge amount of new molecular biology data to be used in future experiments. Although this work represents a promising scenario, a preliminary analysis of the sequence data is necessary to identify and annotate the genes involved in lipid metabolism. Here, we used bioinformatics tools and gene expression analysis to explore genes from different genes families and pathways, including genes for fat breakdown, as lipases and phospholipases, and enzymes from β-oxidation, fatty acid metabolism, and acyl-CoA and glycerolipid synthesis. The R. prolixus genome encodes 31 putative lipase genes, including 21 neutral lipases and 5 acid lipases. The expression profiles of some of these genes were analyzed. We were able to identify nine phospholipase A2 genes. A variety of gene families that participate in fatty acid synthesis and modification were studied, including fatty acid synthase, elongase, desaturase and reductase. Concerning the synthesis of glycerolipids, we found a second isoform of glycerol-3-phosphate acyltransferase that was ubiquitously expressed throughout the organs. Finally, all genes involved in fatty acid β-oxidation were identified, but not a long-chain acyl-CoA dehydrogenase. These results provide fundamental data to be used in future research on insect lipid metabolism and its possible relevance to Chagas' disease transmission.
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14
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Amaral DT, Mitani Y, Ohmiya Y, Viviani VR. Organization and comparative analysis of the mitochondrial genomes of bioluminescent Elateroidea (Coleoptera: Polyphaga). Gene 2016; 586:254-62. [DOI: 10.1016/j.gene.2016.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 03/08/2016] [Accepted: 04/05/2016] [Indexed: 02/01/2023]
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15
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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.
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Song LY, Zhang Y, Li SF, Hu J, Yin WB, Chen YH, Hao ST, Wang BL, Wang RRC, Hu ZM. Identification of the substrate recognition region in the Δ⁶-fatty acid and Δ⁸-sphingolipid desaturase by fusion mutagenesis. PLANTA 2014; 239:753-763. [PMID: 24366682 DOI: 10.1007/s00425-013-2006-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/03/2013] [Indexed: 06/03/2023]
Abstract
Δ⁸-sphingolipid desaturase and Δ⁶-fatty acid desaturase share high protein sequence identity. Thus, it has been hypothesized that Δ⁶-fatty acid desaturase is derived from Δ⁸-sphingolipid desaturase; however, there is no direct proof. The substrate recognition regions of Δ⁶-fatty acid desaturase and Δ⁸-sphingolipid desaturase, which aid in understanding the evolution of these two enzymes, have not been reported. A blackcurrant Δ⁶-fatty acid desaturase and a Δ⁸-sphingolipid desaturase gene, RnD6C and RnD8A, respectively, share more than 80 % identity in their coding protein sequences. In this study, a set of fusion genes of RnD6C and RnD8A were constructed and expressed in yeast. The Δ⁶- and Δ⁸-desaturase activities of the fusion proteins were characterized. Our results indicated that (1) the exchange of the C-terminal 172 amino acid residues can lead to a significant decrease in both desaturase activities; (2) amino acid residues 114-174, 206-257, and 258-276 played important roles in Δ⁶-substrate recognition, and the last two regions were crucial for Δ⁸-substrate recognition; and (3) amino acid residues 114-276 of Δ⁶-fatty acid desaturase contained the substrate recognition site(s) responsible for discrimination between ceramide (a substrate of Δ⁸-sphingolipid desaturase) and acyl-PC (a substrate of Δ⁶-fatty acid desaturase). Substituting the amino acid residues 114-276 of RnD8A with those of RnD6C resulted in a gain of Δ⁶-desaturase activity in the fusion protein but a loss in Δ⁸-sphingolipid desaturase activity. In conclusion, several regions important for the substrate recognition of Δ⁸-sphingolipid desaturase and Δ⁶-fatty acid desaturase were identified, which provide clues in understanding the relationship between the structure and function in desaturases.
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Affiliation(s)
- Li-Ying Song
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China,
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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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Amaral DT, Arnoldi FGC, Rosa SP, Viviani VR. Molecular phylogeny of Neotropical bioluminescent beetles (Coleoptera: Elateroidea) in southern and central Brazil. LUMINESCENCE 2013; 29:412-22. [DOI: 10.1002/bio.2561] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 04/03/2013] [Accepted: 05/29/2013] [Indexed: 11/10/2022]
Affiliation(s)
- DT Amaral
- Graduate School of Biotechnology and Environmental Monitoring; Campus of Sorocaba; Sorocaba SP Brazil
- Graduate School of Evolutive Genetics and Molecular Biology; Federal University of São Carlos (UFSCar); São Carlos SP Brazil
| | - FGC Arnoldi
- Ribeirão Preto School of Medicine; São Paulo University (USP); Ribeirão Preto São Paulo Brazil
| | - SP Rosa
- Zoology Museum; São Paulo University; São Paulo Brazil
| | - VR Viviani
- Graduate School of Biotechnology and Environmental Monitoring; Campus of Sorocaba; Sorocaba SP Brazil
- Graduate School of Evolutive Genetics and Molecular Biology; Federal University of São Carlos (UFSCar); São Carlos SP Brazil
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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]
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Kondrashov FA. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc Biol Sci 2012; 279:5048-57. [PMID: 22977152 PMCID: PMC3497230 DOI: 10.1098/rspb.2012.1108] [Citation(s) in RCA: 391] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 08/21/2012] [Indexed: 01/13/2023] Open
Abstract
A subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. Concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. At this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. Nevertheless, enough examples have accumulated in the literature that such a possibility should be considered. Here, I review the recent examples of adaptive gene duplications and make an attempt to draw generalizations on what types of genes may be particularly prone to be selected for under certain environmental conditions. The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve our understanding of gene duplications as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications.
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Affiliation(s)
- Fyodor A Kondrashov
- Institució Catalana de Recerca i Estudis Avançats, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra, 88 Dr Aiguader, Barcelona 08003, Spain.
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Amaral DT, Prado RA, Viviani VR. Luciferase from Fulgeochlizus bruchi (Coleoptera:Elateridae), a Brazilian click-beetle with a single abdominal lantern: molecular evolution, biological function and comparison with other click-beetle luciferases. Photochem Photobiol Sci 2012; 11:1259-67. [PMID: 22572857 DOI: 10.1039/c2pp25037c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioluminescent click-beetles emit a wide range of bioluminescence colors (λ(Max) = 534-594 nm) from thoracic and abdominal lanterns, which are used for courtship. Only the luciferases from Pyrophorus and Pyrearinus species were cloned and sequenced. The Brazilian Fulgeochlizus bruchi click-beetle, which inhabits the Central-west Cerrado (Savannas), is noteworthy because, differently from other click-beetles, the adult stage displays only a functional abdominal lantern, which produces a bright green bioluminescence for sexual attraction purposes, and lacks functional thoracic lanterns. We cloned the cDNA for the abdominal lantern luciferase of this species. Notably, the primary sequence of this luciferase showed slightly higher identity with the green emitting dorsal lantern luciferases of the Pyrophorus genus instead of the abdominal lanterns luciferases. This luciferase displays a blue-shifted spectrum (λ(Max) = 540 nm), which is pH-insensitive from pH 7.5 to 9.5 and undergoes a slight red shift and broadening above this pH; the lowest K(M) for luciferin among studied click-beetle luciferases, and the highest optimum pH (9.0) ever reported for a beetle luciferase. At pH 9.0, the K(M) for luciferin increases, showing a decrease of affinity for this substrate, despite the higher activity. The slow luminescence decay rate of F. bruchi luciferase in vitro reaction could be an adaptation of this luciferase for the long and sustained in vivo luminescence display of the click-beetle during the courtship, and could be useful for in vivo intracellular imaging.
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Affiliation(s)
- Danilo T Amaral
- Laboratory of Biochemistry and Biotechnology of Bioluminescence, Graduate Program of Biotechnology and Environmental Monitoring, Department of Physics, Chemistry and Mathematics, Federal University of São Carlos (UFSCar), Campus of Sorocaba, Sorocaba, SP, Brazil
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Oba Y, Yoshida M, Shintani T, Furuhashi M, Inouye S. Firefly luciferase genes from the subfamilies Psilocladinae and Ototretinae (Lampyridae, Coleoptera). Comp Biochem Physiol B Biochem Mol Biol 2011; 161:110-6. [PMID: 22008901 DOI: 10.1016/j.cbpb.2011.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Revised: 10/03/2011] [Accepted: 10/05/2011] [Indexed: 11/29/2022]
Abstract
Firefly luciferase genes have been isolated from approximately 20 species of Lampyrinae, Luciolinae, and Photurinae. These are mostly nocturnal luminescent species that use light signals for sexual communication. In this study, we isolated three cDNAs for firefly luciferase from Psilocladinae (Cyphonocerus ruficollis) and Ototretinae (Drilaster axillaris and Stenocladius azumai), which are diurnal non-luminescent or weakly luminescent species that may use pheromones for communication. The amino acid sequences deduced from the three cDNAs showed 81-89% identities to each other and 60-81% identities with known firefly luciferases. The three purified recombinant proteins showed luminescence and fatty acyl-CoA synthetic activities, as observed in other firefly luciferases. The emission maxima by the three firefly luciferases (λmax, 545-546nm) were shorter than those by known luciferases from the nocturnal fireflies (λmax, 550-568nm). These results suggest that the primary structures and enzymatic properties of luciferases are conserved in Lampyridae, but the luminescence colors were red-shifted in nocturnal species compared to diurnal species.
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Affiliation(s)
- Yuichi Oba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
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Oba Y, Mori N, Yoshida M, Inouye S. Identification and characterization of a luciferase isotype in the Japanese firefly, Luciola cruciata, involving in the dim glow of firefly eggs. Biochemistry 2010; 49:10788-95. [PMID: 21090686 DOI: 10.1021/bi1016342] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We isolated the cDNA of a luciferase isotype (LcLuc2) from the Japanese firefly, Luciola cruciata (Lampyridae, Coleoptera). The gene product of LcLuc2 (LcLuc2) showed 59% amino acid identity with firefly luciferase LcLuc1, which was previously identified in L. cruciata. The recombinant LcLuc2 showed both luminescence activity and fatty acyl-CoA synthetic activity comparable to those of LcLuc1. The spectral maxima of the luminescence by LcLuc1 and LcLuc2 were 554 and 543 nm, respectively. Reverse transcription-PCR analysis showed that the transcripts of LcLuc1 were abundant in the lanterns of larva, adult male, and adult female, whereas both LcLuc1 and LcLuc2 were expressed in eggs. The luminescence spectra of the lantern extracts from larva, adult male, and adult female were in good agreement with that of recombinant LcLuc1. On the other hand, the emission maximum of the extract from eggs was between those of LcLuc1 and LcLuc2. These results suggest that L. cruciata possesses two luciferases: LcLuc1 is responsible for the major luminescence in larva and adult, whereas LcLuc1 and LcLuc2 are responsible for the dim glow in firefly eggs.
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Affiliation(s)
- Yuichi Oba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
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Imani M, Hosseinkhani S, Ahmadian S, Nazari M. Design and introduction of a disulfide bridge in firefly luciferase: increase of thermostability and decrease of pH sensitivity. Photochem Photobiol Sci 2010; 9:1167-77. [DOI: 10.1039/c0pp00105h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Arnoldi FGC, da Silva Neto AJ, Viviani VR. Molecular insights on the evolution of the lateral and head lantern luciferases and bioluminescence colors in Mastinocerini railroad-worms (Coleoptera: Phengodidae). Photochem Photobiol Sci 2010; 9:87-92. [DOI: 10.1039/b9pp00078j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Oba Y, Kumazaki M, Inouye S. Characterization of luciferases and its paralogue in the Panamanian luminous click beetle Pyrophorus angustus: a click beetle luciferase lacks the fatty acyl-CoA synthetic activity. Gene 2009; 452:1-6. [PMID: 20004235 DOI: 10.1016/j.gene.2009.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2009] [Revised: 11/29/2009] [Accepted: 12/01/2009] [Indexed: 11/29/2022]
Abstract
Two luciferase genes (dPaLuc and vPaLuc) and one paralogue of luciferase (PaLL) were isolated from the Panamanian luminous click beetle, Pyrophorus angustus (Elateridae, Pyrophorinae). The transcripts of dPaLuc and vPaLuc were predominantly detected in the body parts with dorsal photophore and ventral photophore, respectively, and the transcript of PaLL was detected in both parts. The gene products of dPaLuc and vPaLuc possessed luminescence activity with firefly luciferin (lambda(max)=536 and 566 nm, respectively) but did not show significant activity of fatty acyl-CoA synthesis. On the other hand, the gene product of PaLL had fatty acyl-CoA synthetic activity with very weak luminescence activity. The catalytic properties of click beetle luciferase are different from our previous results that firefly luciferase has both luminescence activity and fatty acyl-CoA synthetic activity. These results suggested that the ancestral fatty acyl-CoA synthetase in the Pyrophorinae lineage has undergone gene duplication event, followed by specialization of one copy in luciferase. Subsequently, the luciferase was duplicated again and the two copies diverged in their luminescent color and expression pattern.
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Affiliation(s)
- Yuichi Oba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
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