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Amaral DT, Kaplan RA, Takishita TKE, de Souza DR, Oliveira AG, Rosa SP. Glowing wonders: exploring the diversity and ecological significance of bioluminescent organisms in Brazil. Photochem Photobiol Sci 2024; 23:1373-1392. [PMID: 38733516 DOI: 10.1007/s43630-024-00590-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: 12/11/2023] [Accepted: 04/27/2024] [Indexed: 05/13/2024]
Abstract
Bioluminescence, the emission of light by living organisms, is a captivating and widespread phenomenon with diverse ecological functions. This comprehensive review explores the biodiversity, mechanisms, ecological roles, and conservation challenges of bioluminescent organisms in Brazil, a country known for its vast and diverse ecosystems. From the enchanting glow of fireflies and glow-in-the-dark mushrooms to the mesmerizing displays of marine dinoflagellates and cnidarians, Brazil showcases a remarkable array of bioluminescent species. Understanding the biochemical mechanisms and enzymes involved in bioluminescence enhances our knowledge of their evolutionary adaptations and ecological functions. However, habitat loss, climate change, and photopollution pose significant threats to these bioluminescent organisms. Conservation measures, interdisciplinary collaborations, and responsible lighting practices are crucial for their survival. Future research should focus on identifying endemic species, studying environmental factors influencing bioluminescence, and developing effective conservation strategies. Through interdisciplinary collaborations, advanced technologies, and increased funding, Brazil can unravel the mysteries of its bioluminescent biodiversity, drive scientific advancements, and ensure the long-term preservation of these captivating organisms.
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Affiliation(s)
- Danilo T Amaral
- Centro de Ciências Naturais E Humanas, Universidade Federal Do ABC (UFABC), Santo André, São Paulo, Brazil.
- Programa de Pós Graduação Em Biotecnociência, Universidade Federal Do ABC (UFABC), Avenida Dos Estados, Bloco A, Room 504-3. ZIP 09210-580, Santo André, São Paulo, 5001, Brazil.
| | - Rachel A Kaplan
- Department of Chemistry and Biochemistry, Yeshiva University, 245 Lexington Avenue, New York, NY, 10016, USA
| | | | - Daniel R de Souza
- Laboratório de Estudos Avançados Em Jornalismo, Universidade Estadual de Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Anderson G Oliveira
- Department of Chemistry and Biochemistry, Yeshiva University, 245 Lexington Avenue, New York, NY, 10016, USA
| | - Simone Policena Rosa
- Instituto de Recursos Naturais (IRN), Universidade Federal de Itajubá (UNIFEI), Itajubá, MG, Brazil
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Viviani VR, Benites GR, Souza DR, Pelentir GF, Reis RM, Bechara EJH, Tomazini A. The orange light emitting luciferase from the rare Euryopa clarindae adult railroadworm (Coleoptera:Phengodidae): structural/functional and evolutionary relationship with green and red emitting luciferases. Photochem Photobiol Sci 2024; 23:257-269. [PMID: 38141147 DOI: 10.1007/s43630-023-00515-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Railroadworms luciferases emit the widest range of bioluminescence colors among beetles, ranging from green to red, being model enzymes to investigate the structure and bioluminescence colors relationships. Only three active railroadworms luciferases from the larval stage have been cloned and investigated: the Phrixothrix hirtus head lanterns red-emitting luciferase (PhRE); the Phrixothrix vivianii lateral lanterns green emitting luciferases (PvGR) and the Phengodes sp. dorsal lanterns yellow-green emitting luciferase (Ph). No active luciferase emitting in the yellow-orange region, however, has been cloned yet. Here we report the cloning and characterization of the orange emitting luciferase from the adult males of a rare Brazilian Cerrado railroadworm, Euryopa clarindae, and the transcriptional identification of two isozymes from the Amazon forest Mastinomorphus sp. railroadworm. The luciferase of E. clarindae has 548 residues, emits orange bioluminescence (600 nm), and displays intermediate kinetic values [KM(luciferin) = 50 µM, KM(ATP) ~ 170 µM] between those reported for green-emitting lateral lanterns and red emitting head lanterns luciferases. It displays 74-78% identity with the lateral lanterns luciferases of other railroadworms and 70% with the head lantern PhRE luciferase, and 96% with the larval Mastinomorphus sp. Mast-1, suggesting that this larva could be from the Euryopa genus. The phylogenetic analysis and kinetic/functional properties, place this orange-emitting enzyme as an intermediate form between the green-emitting lateral lanterns and red-emitting head lanterns luciferases. Major structural differences that could be associated with bioluminescence color determination are a relatively larger cavity size, and substitutions in the loops 223-235 and 311-316, especially N/C/T311, and their interactions which may help to close the bottom of LBS.
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Affiliation(s)
- V R Viviani
- Departamento de Física, Química e Matemática, CCTS, Federal University of Sao Carlos: Universidade Federal de Sao Carlos, Sorocaba, SP, Brazil.
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil.
- Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos, Sorocaba, Brazil.
- Graduate Program of Biotechnology, Federal University of São Carlos (UFSCar), São Carlos, Brazil.
| | - G R Benites
- Departamento de Física, Química e Matemática, CCTS, Federal University of Sao Carlos: Universidade Federal de Sao Carlos, Sorocaba, SP, Brazil
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - D R Souza
- Departamento de Física, Química e Matemática, CCTS, Federal University of Sao Carlos: Universidade Federal de Sao Carlos, Sorocaba, SP, Brazil
- Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos, Sorocaba, Brazil
| | - G F Pelentir
- Departamento de Física, Química e Matemática, CCTS, Federal University of Sao Carlos: Universidade Federal de Sao Carlos, Sorocaba, SP, Brazil
- Graduate Program of Biotechnology, Federal University of São Carlos (UFSCar), São Carlos, Brazil
| | - Raone M Reis
- Departamento de Física, Química e Matemática, CCTS, Federal University of Sao Carlos: Universidade Federal de Sao Carlos, Sorocaba, SP, Brazil
- Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos, Sorocaba, Brazil
| | | | - Atilio Tomazini
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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Goh KS, Wang LJ, Ni JH, Wang TY. Luminescent characteristics and mitochondrial COI barcodes of nine cohabitated Taiwanese fireflies. PeerJ 2022; 10:e14195. [PMID: 36325176 PMCID: PMC9620971 DOI: 10.7717/peerj.14195] [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: 07/27/2020] [Accepted: 09/15/2022] [Indexed: 01/24/2023] Open
Abstract
Background Over 50 Taiwanese firefly species have been discovered, but scientists lack information regarding most of their genetics, bioluminescent features, and cohabitating phenomena. In this study, we focus on morphological species identification and phylogeny reconstructed by COI barcoding, as well as luminescent characteristics of cohabited Taiwanese firefly species to determine the key factors that influenced how distinct bioluminescent species evolved to coexist and proliferate within the same habitat. Methods In this study, 366 specimens from nine species were collected in northern Taiwan from April to August, 2016-2019. First, the species and sex of the specimens were morphologically and genetically identified. Then, their luminescent spectra and intensities were recorded using a spectrometer and a power meter, respectively. The habitat temperature, relative humidity, and environmental light intensity were also measured. The cytochrome oxidase I (COI) gene sequence was used as a DNA barcode to reveal the phylogenetic relationships of cohabitated species. Results Nine species-eight adult species (Abscondita chinensis, Abscondita cerata, Aquatica ficta, Luciola curtithorax, Luciola kagiana, Luciola filiformis, Curtos sauteri, and Curtos costipennis) and one larval Pyrocoelia praetexta-were morphologically identified. The nine species could be found in April-August. Six of the eight adult species shared an overlap occurrence period in May. Luminescent spectra analysis revealed that the λ max of studied species ranged from 552-572 nm (yellow-green to orange-yellow). The average luminescent intensity range of these species was about 1.2-14 lux (182.1-2,048 nW/cm2) for males and 0.8-5.8 lux (122.8-850 nW/cm2) for females, and the maximum luminescent intensity of males was 1.01-7.26-fold higher than that of females. Compared with previous studies, this study demonstrates that different λ max, species-specific flash patterns, microhabitat choices, nocturnal activity time, and/or an isolated mating season are key factors that may lead to the species-specific courtship of cohabitated fireflies. Moreover, we estimated that the fireflies start flashing or flying when the environmental light intensity decreased to 6.49-28.1 lux. Thus, based on a rough theoretical calculation, the sensing distance between male and female fireflies might be 1.8-2.7 m apart in the dark. In addition, the mitochondrial COI barcode identified species with high resolution and suggested that most of the studied species have been placed correctly with congeners in previous phylogenies. Several cryptic species were revealed by the COI barcode with 3.27%-12.3% variation. This study renews the idea that fireflies' luminescence color originated from the green color of a Lampyridae ancestor, then red-shifted to yellow-green in Luciolinae, and further changed to orange-yellow color in some derived species.
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Affiliation(s)
- King-Siang Goh
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Liang-Jong Wang
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Jing-Han Ni
- Department of Ecological Humanities, Providence University, Taichung, Taiwan
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Trabuco Amaral D, Mitani Y, Aparecida Silva Bonatelli I, Cerri R, Ohmiya Y, Viviani V. Genome analysis of Phrixothrix hirtus (Phengodidae) railroad worm shows the expansion of odorant-binding gene families and positive selection on morphogenesis and sex determination genes. Gene X 2022; 850:146917. [PMID: 36174905 DOI: 10.1016/j.gene.2022.146917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 10/14/2022] Open
Abstract
Among bioluminescent beetles of the Elateroidea superfamily, Phengodidae is the third largest family, with 244 bioluminescent species distributed only in the Americas, but is still the least studied from the phylogenetic and evolutionary points of view. The railroad worm Phrixothrix hirtus is an essential biological model and symbolic species due to its bicolor bioluminescence, being the only organism that produces true red light among bioluminescent terrestrial species. Here, we performed partial genome assembly of P. hirtus, combining short and long reads generated with Illumina sequencing, providing the first source of genomic information and a framework for comparative analyses of the bioluminescent system in Elateroidea. This is the largest genome described in the Elateroidea superfamily, with an estimated size of ∼3.4 Gb, displaying 32 % GC content, and 67 % transposable elements. Comparative genomic analyses showed a positive selection of genes and gene family expansion events of growths and morphogenesis gene products, which could be associated with the atypical anatomical development and morphogenesis found in paedomorphic females and underdeveloped males. We also observed gene family expansion among distinct odorant-binding receptors, which could be associated with the pheromone communication system typical of these beetles, and retrotransposable elements. Common genes putatively regulating bioluminescence production and control, including two luciferase genes corresponding to lateral lanterns green-emitting and head lanterns red-emitting luciferases with 7 exons and 6 introns, and genes potentially involved in luciferin biosynthesis were found, indicating that there are no clear differences about the presence or absence of gene families associated with bioluminescence in Elateroidea.
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Affiliation(s)
- Danilo Trabuco Amaral
- Programa de Pós-Graduação em Biotecnociência, Centro de Ciências Naturais e Humanas. Universidade Federal do ABC (UFABC), Santo André, Brazil
| | - Yasuo Mitani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | | | - Ricardo Cerri
- Department of Computational Science, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Yoshihiro Ohmiya
- Biomedical Research Institute, AIST, Ikeda-Osaka, Japan; Osaka Institute of Technology, OIT, Osaka, Japan
| | - Vadim Viviani
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, Brazil; Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos (UFSCar), Sorocaba, Brazil.
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Liu YJ. Understanding the complete bioluminescence cycle from a multiscale computational perspective: A review. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2022. [DOI: 10.1016/j.jphotochemrev.2022.100537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Purtov KV, Petushkov VN, Rodionova NS, Chepurnykh TV, Kozhemyako VB, Zagitova RI, Shcheglov AS, Ziganshin RH, Tsarkova AS. Similarities and differences between the Chaetopterus variopedatus polychaete luciferases depending on the type of habitat. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2021. [DOI: 10.24075/brsmu.2021.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The marine polychaete Chaetopterus variopedatus (Renier) (family Chaetopteridae) is a cosmopolitan species complex, consisting of distinct populations/ subspecies. The worms release glowing (460 nm) clouds of mucus when disturbed, and their parapodia often glow brightly. Currently, it is still unclear how exactly the bioluminescence system of these polychaetes functions. It has been previously assumed that the C. variopedatus luciferase may be used for detection of ferroptosis, the recently explored pathway of programmed cell death, resulting from accumulation of the ferrous ions. This study was aimed to extract and characterize the C. variopedatus luciferases, as well as to compare luciferases obtained from C. variopedatus of different populations. When extracting the enzyme responsible for bioluminescence from the frozen samples of Brazilian C. variopedatus using the improved method, two active luciferases, L1 and L2, were obtained. We assumed that one of the listed above luciferases was responsible for luminescence of the mucus and the other luciferase was responsible for luminescence in parapodia, and used the method for the distinct samples of mucus and parapodia of the living Far Eastern C. variopedatus. However, mucus of the latter turned out to be non-glowing. It is shown that luciferase L2 is responsible for luminescence in the parapodia of the C. variopedatus polychaete, since this luciferase has been found in the total biomass of Brazilian polychaetes and parapodia of Far Eastern polychaetes. Luminescence of the Brazilian C. variopedatus mucus is attributed to the functioning of luciferase L1, which is lacking in the mucus of the Far Eastern subspecies. The range of luciferase isoforms in polychaetes C. variopedatus depends on the place of origin.
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Affiliation(s)
- KV Purtov
- Institute of Biophysics, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences
| | - VN Petushkov
- Institute of Biophysics, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences
| | - NS Rodionova
- Institute of Biophysics, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences
| | - TV Chepurnykh
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - VB Kozhemyako
- Pacific State Medical University, Vladivostok, Russia
| | - RI Zagitova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - AS Shcheglov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - RH Ziganshin
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - AS Tsarkova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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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.
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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.
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Carrasco-López C, Lui NM, Schramm S, Naumov P. The elusive relationship between structure and colour emission in beetle luciferases. Nat Rev Chem 2020; 5:4-20. [PMID: 37118106 DOI: 10.1038/s41570-020-00238-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2020] [Indexed: 12/23/2022]
Abstract
In beetles, luciferase enzymes catalyse the conversion of chemical energy into light through bioluminescence. The principles of this process have become a fundamental biotechnological tool that revolutionized biological research. Different beetle species can emit different colours of light, despite using the same substrate and highly homologous luciferases. The chemical reasons for these different colours are hotly debated yet remain unresolved. This Review summarizes the structural, biochemical and spectrochemical data on beetle bioluminescence reported over the past three decades. We identify the factors that govern what colour is emitted by wild-type and mutant luciferases. This topic is controversial, but, in general, we note that green emission requires cationic residues in a specific position near the benzothiazole fragment of the emitting molecule, oxyluciferin. The commonly emitted green-yellow light can be readily changed to red by introducing a variety of individual and multiple mutations. However, complete switching of the emitted light from red to green has not been accomplished and the synergistic effects of combined mutations remain unexplored. The minor colour shifts produced by most known mutations could be important in establishing a 'mutational catalogue' to fine-tune emission of beetle luciferases, thereby expanding the scope of their applications.
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Yu M, Liu YJ. Same Luciferin in Different Luciferases Emitting Different-Color Light. A Theoretical Study on Beetle Bioluminescence. J Chem Theory Comput 2020; 16:3904-3909. [PMID: 32396347 DOI: 10.1021/acs.jctc.0c00074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bioluminescent beetles, firefly, click beetle, and railroad worm, naturally emit different-color light via the identical luciferin and bioluminescence (BL) mechanisms. Railroad worm especially emits two colors of light in its dorsal-lateral and cephalic lanterns. Four computational models of bioluminophore (oLu) in luciferases of red-emitting, yellow-green-emitting, red-emitting with additional loop, and red-emitting without C-terminal were built in this paper. To unveil the details of this luciferase effect at the molecular and electronic-state levels, second-order multiconfigurational perturbation calculations were performed following molecular dynamic simulations and time-dependent density functional calculations for the above four oLu-luciferase systems. Via a systematic analysis on properties of oLu at the first singlet state (S1-oLu) in different luciferases, one clearly see the details of the microenvironment and secondary structure of luciferase affecting the excited-state property of S1-oLu, which ultimately result in the variant color of light emission. Typically, the increase in charge transfer of S1-oLu leads to the longer wavelength BL.
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Affiliation(s)
- Mohan Yu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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Liu G, Dong Z, Hou Q, He J, Zhao R, Wang W, Li X. Second Rhagophthalmid Luciferase Cloned from Chinese Glow‐worm
Menghuoius giganteus
(Rhagophthalmidae: Elateroidea). Photochem Photobiol 2019; 96:46-54. [DOI: 10.1111/php.13172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/23/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Gui‐Chun Liu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
- 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
| | - 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
| | - Ruo‐Ping Zhao
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
- Center for Ecological and Environmental Sciences Key Laboratory for Space Bioscience & Biotechnology Northwestern Polytechnical University Xi’an 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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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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12
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RNA-Seq analysis of the bioluminescent and non-bioluminescent species of Elateridae (Coleoptera): Comparison to others photogenic and non-photogenic tissues of Elateroidea species. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 29:154-165. [PMID: 30472608 DOI: 10.1016/j.cbd.2018.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 10/15/2018] [Indexed: 02/06/2023]
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Fallon TR, Lower SE, Chang CH, Bessho-Uehara M, Martin GJ, Bewick AJ, Behringer M, Debat HJ, Wong I, Day JC, Suvorov A, Silva CJ, Stanger-Hall KF, Hall DW, Schmitz RJ, Nelson DR, Lewis SM, Shigenobu S, Bybee SM, Larracuente AM, Oba Y, Weng JK. Firefly genomes illuminate parallel origins of bioluminescence in beetles. eLife 2018; 7:e36495. [PMID: 30324905 PMCID: PMC6191289 DOI: 10.7554/elife.36495] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022] Open
Abstract
Fireflies and their luminous courtships have inspired centuries of scientific study. Today firefly luciferase is widely used in biotechnology, but the evolutionary origin of bioluminescence within beetles remains unclear. To shed light on this long-standing question, we sequenced the genomes of two firefly species that diverged over 100 million-years-ago: the North American Photinus pyralis and Japanese Aquatica lateralis. To compare bioluminescent origins, we also sequenced the genome of a related click beetle, the Caribbean Ignelater luminosus, with bioluminescent biochemistry near-identical to fireflies, but anatomically unique light organs, suggesting the intriguing hypothesis of parallel gains of bioluminescence. Our analyses support independent gains of bioluminescence in fireflies and click beetles, and provide new insights into the genes, chemical defenses, and symbionts that evolved alongside their luminous lifestyle.
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Affiliation(s)
- Timothy R Fallon
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
| | - Sarah E Lower
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
- Department of BiologyBucknell UniversityLewisburgUnited States
| | - Ching-Ho Chang
- Department of BiologyUniversity of RochesterRochesterUnited States
| | - Manabu Bessho-Uehara
- Department of Environmental BiologyChubu UniversityKasugaiJapan
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaJapan
- Monterey Bay Aquarium Research InstituteMoss LandingUnited States
| | - Gavin J Martin
- Department of BiologyBrigham Young UniversityProvoUnited States
| | - Adam J Bewick
- Department of GeneticsUniversity of GeorgiaAthensUnited States
| | - Megan Behringer
- Biodesign Center for Mechanisms of EvolutionArizona State UniversityTempeUnited States
| | - Humberto J Debat
- Center of Agronomic Research, National Institute of Agricultural TechnologyCórdobaArgentina
| | - Isaac Wong
- Department of BiologyUniversity of RochesterRochesterUnited States
| | - John C Day
- Centre for Ecology and Hydrology (CEH)WallingfordUnited Kingdom
| | - Anton Suvorov
- Department of BiologyBrigham Young UniversityProvoUnited States
| | - Christian J Silva
- Department of BiologyUniversity of RochesterRochesterUnited States
- Department of Plant SciencesUniversity of California DavisDavisUnited States
| | | | - David W Hall
- Department of GeneticsUniversity of GeorgiaAthensUnited States
| | | | - David R Nelson
- Department of Microbiology Immunology and BiochemistryUniversity of Tennessee HSCMemphisUnited States
| | - Sara M Lewis
- Department of BiologyTufts UniversityMedfordUnited States
| | - Shuji Shigenobu
- NIBB Core Research FacilitiesNational Institute for Basic BiologyOkazakiJapan
| | - Seth M Bybee
- Department of BiologyBrigham Young UniversityProvoUnited States
| | | | - Yuichi Oba
- Department of Environmental BiologyChubu UniversityKasugaiJapan
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
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14
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Amaral DT, Silva JR, Viviani VR. Transcriptional comparison of the photogenic and non-photogenic tissues of Phrixothrix hirtus (Coleoptera: Phengodidae) and non-luminescent Chauliognathus flavipes (Coleoptera: Cantharidae) give insights on the origin of lanterns in railroad worms. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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15
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Gouveneaux A, Flood PR, Mallefet J. Unexpected diversity of bioluminescence in planktonic worms. LUMINESCENCE 2016; 32:394-400. [PMID: 27545998 DOI: 10.1002/bio.3192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/02/2016] [Accepted: 06/30/2016] [Indexed: 11/09/2022]
Abstract
The vast majority of pelagic bioluminescent organisms emit a blue light with emission maxima (λmax ) ranging from 450 to 490 nm. Among the known outliers, the tomopterids (Annelida: Polychaeta) are usually described as yellow-emitters (λmax = 565-570 nm) for which bioluminescence functions as a specific recognition signal. Here, we report the first data regarding the colours emitted by four different tomopterid species, Tomopteris pacifica, T. carpenteri, T. septentrionalis and T. planktonis. Surprisingly, T. planktonis is a blue-emitter (λmax = 450 nm). Our pharmacological results on T. planktonis support cholinergic control, as recently demonstrated in the yellow-emitter, T. helgolandica. Moreover, as revealed by epifluorescence microscopy, the light seems to be produced in both species from the same yellow-pigmented parapodial glands. Despite these similarities, tomopterids express an unexpected diversity of bioluminescent colour patterns. This leads us to reassess the ecological value of bioluminescence within this group.
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Affiliation(s)
- A Gouveneaux
- Marine Biology Laboratory, Earth and Life Institute, Catholic University of Louvain, Louvain-la-Neuve, Belgium
| | | | - J Mallefet
- Marine Biology Laboratory, Earth and Life Institute, Catholic University of Louvain, Louvain-la-Neuve, Belgium
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16
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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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17
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Viviani VR, Neves DR, Amaral DT, Prado RA, Matsuhashi T, Hirano T. Bioluminescence of Beetle Luciferases with 6′-Amino-d-luciferin Analogues Reveals Excited Keto-oxyluciferin as the Emitter and Phenolate/Luciferin Binding Site Interactions Modulate Bioluminescence Colors. Biochemistry 2014; 53:5208-20. [DOI: 10.1021/bi500160m] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vadim R. Viviani
- Department
of Physics, Chemistry and Mathematics, Graduate Program of Biotechnology
and Environmental Monitoring, Federal University of São Carlos (UFSCAR), RodoviaJoãoLeme dos Santos, km 110, Itinga, Sorocaba, SP, Brazil
- Graduate
Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCAR), São Carlos, SP, Brazil
| | - Deimison Rodrigues Neves
- Department
of Physics, Chemistry and Mathematics, Graduate Program of Biotechnology
and Environmental Monitoring, Federal University of São Carlos (UFSCAR), RodoviaJoãoLeme dos Santos, km 110, Itinga, Sorocaba, SP, Brazil
| | - Danilo Trabuco Amaral
- Department
of Physics, Chemistry and Mathematics, Graduate Program of Biotechnology
and Environmental Monitoring, Federal University of São Carlos (UFSCAR), RodoviaJoãoLeme dos Santos, km 110, Itinga, Sorocaba, SP, Brazil
- Graduate
Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCAR), São Carlos, SP, Brazil
| | - Rogilene A. Prado
- Department
of Physics, Chemistry and Mathematics, Graduate Program of Biotechnology
and Environmental Monitoring, Federal University of São Carlos (UFSCAR), RodoviaJoãoLeme dos Santos, km 110, Itinga, Sorocaba, SP, Brazil
| | - Takuto Matsuhashi
- Department
of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585, Japan
| | - Takashi Hirano
- Department
of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585, Japan
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18
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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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19
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Viviani VR, Prado RA, Neves DR, Kato D, Barbosa JA. A route from darkness to light: emergence and evolution of luciferase activity in AMP-CoA-ligases inferred from a mealworm luciferase-like enzyme. Biochemistry 2013; 52:3963-73. [PMID: 23705763 DOI: 10.1021/bi400141u] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The origin of luciferases and of bioluminescence is enigmatic. In beetles, luciferases seem to have evolved from AMP-CoA-ligases. How the new oxygenase luminogenic function originated from AMP-ligases leading to luciferases is one of the most challenging mysteries of bioluminescence. Comparison of the cloned luciferase-like enzyme from the nonluminescent Zophobas morio mealworm and beetle luciferases showed that the oxygenase activity may have emerged as a stereoselective oxidative drift with d-luciferin, a substrate that cannot be easily thioesterified to CoA as in the case of the l-isomer. While the overall kcat displayed by beetle luciferases is orders of magnitude greater than that of the luciferase-like enzyme, the respective oxidation rates and quantum yields of bioluminescence are roughly similar, suggesting that the rate constant of the AMP-ligase activity exerted on the new d-luciferin substrate in beetle protoluciferases was the main enzymatic property that suffered optimization during the evolution of luciferases. The luciferase-like enzyme and luciferases boost the rate of luciferyl-adenylate chemiluminescent oxidation by factors of 10(6) and 10(7), respectively, as compared to the substrate spontaneous oxidation in buffer. A similar enhancement of luciferyl-adenylate chemiluminescence is provided by nucleophilic aprotic solvents, implying that the peptide bonds in the luciferin binding site of beetle luciferase could provide a similar catalytically favorable environment. These data suggest that the luciferase-like enzyme and other similar AMP-ligases are potential alternative oxygenases. Site-directed mutagenesis studies of the luciferase-like enzyme and the red light-producing luciferase of Phrixotrix hirtus railroadworm confirm here a critical role for T/S345 in luciferase function. Mutations such as I327T/S in the luciferase-like enzyme, which simultaneously increases luciferase activity and promotes blue shifts in the emission spectrum, could have been critical for evolving functional bioluminescence from red-emitting protoluciferases. Through the combination of I327T/S mutations and N-terminal fusion, the luminescence activity of this enzyme was increased to visible levels, with the development of a totally new orange-emitting luciferase. These results open the possibility of engineering luciferase activity in a set of AMP-CoA-ligases.
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Affiliation(s)
- V R Viviani
- Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos (UFSCar), Rodovia João Leme dos Santos, km 110, Itinga, Sorocaba, SP, Brazil.
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20
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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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21
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Peck LS. Organisms and responses to environmental change. Mar Genomics 2011; 4:237-43. [DOI: 10.1016/j.margen.2011.07.001] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 07/06/2011] [Accepted: 07/08/2011] [Indexed: 11/24/2022]
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22
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Viviani VR, Scorsato V, Prado RA, Pereira JGC, Niwa K, Ohmiya Y, Barbosa JARG. The origin of luciferase activity in Zophobas mealworm AMP/CoA-ligase (protoluciferase): luciferin stereoselectivity as a switch for the oxygenase activity. Photochem Photobiol Sci 2010; 9:1111-9. [PMID: 20526507 DOI: 10.1039/c0pp00080a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Beetle luciferases evolved from AMP/CoA-ligases. However, it is unclear how the new luciferase activity evolved. In order to clarify this question, we compared the luminescence and catalytic properties of a recently cloned luciferase-like enzyme from Zophobas mealworm, an AMP/CoA-ligase displaying weak luminescence activity, with those of cloned luciferases from the three main families of luminescent beetles: Phrixthrix hirtus railroad worm; Pyrearinus termitilluminans click beetle and Photinus pyralis firefly. The catalytic constant of the mealworm enzyme was 2-4 orders of magnitude lower than that of beetle luciferases, but 3 orders of magnitude above the non-catalyzed chemiluminescence of luciferyl-adenylate in buffer. Studies with D- and L-luciferin and their adenylates show that the luminescence reaction of the luciferase-like enzyme and beetle luciferases are stereoselective for D-luciferin and its adenylate, and that the selectivity is determined mainly at the adenylation step. Modelling studies showed that the luciferin binding site cavity of this enzyme is smaller and more hydrophobic than that of beetle luciferases. Therefore Zophobas mealworm enzyme displays true luciferase activity, keeping the attributes of an ancient protoluciferase. These results suggest that stereoselectivity for D-luciferin may have been a key event for the origin of oxygenase/luciferase activity in AMP/CoA-ligases, and that efficient luciferase activity may have further evolved mainly by increasing the catalytic constant of the oxidative reaction and the quantum yield of bioluminescence.
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Affiliation(s)
- Vadim R Viviani
- Laboratório de Bioquímica e Biotecnologia de Sistemas Bioluminescentes, Universidade Federal de São Carlos (UFSCAR), Campus de Sorocaba, Sorocaba, SP, Brazil.
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