1
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Hasegawa H. Temperature-dependent intracellular crystallization of firefly luciferase in mammalian cells is suppressed by D-luciferin and stabilizing inhibitors. Exp Cell Res 2024; 440:114131. [PMID: 38876374 DOI: 10.1016/j.yexcr.2024.114131] [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: 04/30/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024]
Abstract
Firefly luciferase (Fluc) from Photinus pyralis is one of the most widely used reporter proteins in biomedical research. Despite its widespread use, Fluc's protein phase transition behaviors and phase separation characteristics have not received much attention. Current research uncovers Fluc's intrinsic property to phase separate in mammalian cells upon a simple cell culture temperature change. Specifically, Fluc spontaneously produced needle-shaped crystal-like inclusion bodies upon temperature shift to the hypothermic temperatures ranging from 25 °C to 31 °C. The crystal-like inclusion bodies were not associated with or surrounded by membranous organelles and were likely built from the cytosolic pool of Fluc. Furthermore, the crystal-like inclusion formation was suppressed when cells were cultured in the presence of D-luciferin and its synthetic analog, as well as the benzothiazole family of so-called stabilizing inhibitors. These two classes of compounds inhibited intracellular Fluc crystallization by different modes of action as they had contrasting effects on steady-state luciferase protein accumulation levels. This study suggests that, under substrate insufficient conditions, the excess Fluc phase separates into a crystal-like state that can modulate intracellular soluble enzyme availability and protein turnover rate.
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Affiliation(s)
- Haruki Hasegawa
- Discovery Protein Science, Department of Large Molecule Discovery and Research Data Science Amgen Inc., South San Francisco, CA 94080, USA.
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2
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Inouye S, Matsuda K, Nakamura M. Enzymatic sulfation of coelenterazine by human cytosolic aryl sulfotransferase SULT1A1: identification of coelenterazine C2-benzyl monosulfate by LC/ESI-TOF-MS. Biochem Biophys Res Commun 2023; 665:133-140. [PMID: 37163933 DOI: 10.1016/j.bbrc.2023.05.007] [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: 04/16/2023] [Accepted: 05/02/2023] [Indexed: 05/12/2023]
Abstract
Coelenterazine (CTZ) is known as a light-emitting source for the bioluminescence reaction in marine organisms. CTZ has two phenolic hydroxy groups at the C2-benzyl and C6-phenyl positions, and a keto-enol type hydroxy group at the C3-position in the core structure of imidazopyrazinone (= 3,7-dihydroimidazopyrazin-3-one). These hydroxy groups in CTZ could be sulfated by sulfotransferase(s), and the sulfates of Watasenia luciferin (CTZ disulfate at the C2- and C6-positions) and Renilla pre-luciferin (CTZ 3-enol sulfate) have been identified in marine organisms. To characterize the sulfation process of CTZ, human cytosolic aryl sulfotransferase SULT1A1 (SUTase) was used as a model enzyme. The sulfated products catalyzed by SUTase with 3'-phosphoadenosine 5'-phosphosulfate (PAPS) were analyzed by LC/ESI-TOF-MS. The product was the monosulfate of CTZ and identified as the C2-benzyl sulfate of CTZ (CTZ C2-benzyl monosulfate), but CTZ disulfate, CTZ 3-enol sulfate, and CTZ C6-phenyl monosulfate were not detected. The non-enzymatic oxidation products of dehydrocoelenterazine (dCTZ, dehydrogenated derivative of CTZ), coelenteramide (CTMD), and coelenteramine (CTM) from CTZ were also identified as their monosulfates.
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Affiliation(s)
- Satoshi Inouye
- Department of Biochemistry, School of Dentistry, Aichi Gakuin University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya, 464-8650, Japan.
| | - Kazuo Matsuda
- Graduate School of Integrated Arts and Sciences, Tokushima University, Tokushima, 770-8502, Japan
| | - Mitsuhiro Nakamura
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, 770-8506, Japan
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3
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Ishimoto T, Okada T, Fujisaka S, Yagi K, Tobe K, Toyooka N, Mori H. A New Method for Albuminuria Measurement Using a Specific Reaction between Albumin and the Luciferin of the Firefly Squid Watasenia scintillans. Int J Mol Sci 2022; 23:ijms23158342. [PMID: 35955470 PMCID: PMC9368953 DOI: 10.3390/ijms23158342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 02/01/2023] Open
Abstract
This study demonstrates that the luciferin of the firefly squid Watasenia scintillans, which generally reacts with Watasenia luciferase, reacted with human albumin to emit light in proportion to the albumin concentration. The luminescence showed a peak wavelength at 540 nm and was eliminated by heat or protease treatment. We used urine samples collected from patients with diabetes to quantify urinary albumin concentration, which is essential for the early diagnosis of diabetic nephropathy. Consequently, we were able to measure urinary albumin concentrations by precipitating urinary proteins with acetone before the reaction with luciferin. A correlation was found with the result of the immunoturbidimetric method; however, the Watasenia luciferin method tended to produce lower albumin concentrations. This may be because the Watasenia luciferin reacts with only intact albumin. Therefore, the quantification method using Watasenia luciferin is a new principle of urinary albumin measurement that differs from already established methods such as immunoturbidimetry and high-performance liquid chromatography.
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Affiliation(s)
- Tetsuya Ishimoto
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan;
- Research Center for Idling Brain Science, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan
- Correspondence:
| | - Takuya Okada
- Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama City, Toyama 930-8555, Japan; (T.O.); (N.T.)
| | - Shiho Fujisaka
- First Department of Internal Medicine, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan; (S.F.); (K.Y.); (K.T.)
| | - Kunimasa Yagi
- First Department of Internal Medicine, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan; (S.F.); (K.Y.); (K.T.)
- Department of Internal Medicine, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa 920-0293, Japan
| | - Kazuyuki Tobe
- First Department of Internal Medicine, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan; (S.F.); (K.Y.); (K.T.)
| | - Naoki Toyooka
- Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama City, Toyama 930-8555, Japan; (T.O.); (N.T.)
- Research Center for Pre-Disease Science, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan
| | - Hisashi Mori
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan;
- Research Center for Idling Brain Science, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan
- Research Center for Pre-Disease Science, University of Toyama, 2630 Sugitani, Toyama City, Toyama 930-0194, Japan
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4
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Kanie S, Miura D, Jimi N, Hayashi T, Nakamura K, Sakata M, Ogoh K, Ohmiya Y, Mitani Y. Violet bioluminescent Polycirrus sp. (Annelida: Terebelliformia) discovered in the shallow coastal waters of the Noto Peninsula in Japan. Sci Rep 2021; 11:19097. [PMID: 34580316 PMCID: PMC8476577 DOI: 10.1038/s41598-021-98105-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/03/2021] [Indexed: 11/09/2022] Open
Abstract
Terebellidae worms have large numbers of tentacles responsible for various biological functions. Some Terebellidae worms whose tentacles emit light are found around the world, including exceptional violet-light-emitting Polycirrus spp. found in Europe and North America. However, there is no video-recorded observation of the luminous behavior of such unique species in nature, and the genetic information related to their ecology are lacking. Here, for the first time, we video-recorded the violet-light-emitting behavior of an undescribed Japanese worm in its natural habitat. The worm was designated as Polycirrus sp. ISK based on morphological observations, and the luminescence spectrum showed a peak at 444 nm, which is an exceptionally short wavelength for bioluminescence in a shallow coastal water environment. An analysis of differentially expressing genes based on separate RNA-Seq analysis for the tentacles and the rest of body revealed the specific expression of genes that are probably involved in innate immunity in the tentacles exposed to predators. We also found a Renilla luciferase homologous gene, but coelenterazine was not detected in the worm extract by analyses using a liquid chromatography and a recombinant Renilla luciferase. These results will promote an understanding of the ecology and luminescence mechanisms of luminous Polycirrus spp.
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Affiliation(s)
- Shusei Kanie
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan
| | - Daisuke Miura
- Biomedical Research Institute, AIST, Tsukuba, 305-8566, Japan
| | - Naoto Jimi
- National Institute of Polar Research, Tachikawa, Tokyo, 190-8518, Japan
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, Mie, 517-0004, Japan
| | - Taro Hayashi
- Olympus Corporation, Hachioji, Tokyo, 192-8512, Japan
| | - Koji Nakamura
- Japan Underwater Films Co., Ltd., 2-11-15, Nakaochiai, Shinjyuku, Tokyo, 161-0032, Japan
| | - Masahiko Sakata
- Japan Underwater Films Co., Ltd., 2-11-15, Nakaochiai, Shinjyuku, Tokyo, 161-0032, Japan
| | - Katsunori Ogoh
- Olympus Corporation, Hachioji, Tokyo, 192-8512, Japan
- HATENOURUMA, Hachioji, Tokyo, 192‑0023, Japan
| | - Yoshihiro Ohmiya
- Biomedical Research Institute, AIST, Ikeda, 563-8577, Japan
- Osaka Institute of Technology (OIT), Osaka, 535-8585, Japan
| | - Yasuo Mitani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan.
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Yoshida MA, Imoto J, Kawai Y, Funahashi S, Minei R, Akizuki Y, Ogura A, Nakabayashi K, Yura K, Ikeo K. Genomic and Transcriptomic Analyses of Bioluminescence Genes in the Enope Squid Watasenia scintillans. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:760-771. [PMID: 33098466 PMCID: PMC7708342 DOI: 10.1007/s10126-020-10001-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/28/2020] [Indexed: 05/26/2023]
Abstract
Watasenia scintillans, a sparkling enope squid, has bioluminescence organs to illuminate its body with its own luciferase activity. To clarify the molecular mechanism underlying its scintillation, we analysed high-throughput sequencing data acquired previously and obtained draft genome sequences accomplished with comparative genomic data among the cephalopods. The genome mapped by transcriptome data showed that (1) RNA editing contributed to transcriptome variation of lineage specific genes, such as W. scintillans luciferase, and (2) two types of luciferase enzymes were characterized with reasonable 3D models docked to a luciferin molecule. We report two different types of luciferase in one organism and possibly related to variety of colour types in the W. scintillans fluorescent organs.
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Affiliation(s)
- Masa-Aki Yoshida
- Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Sciences, Shimane University, Oki, Japan.
| | - Junichi Imoto
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
- Fisheries Data Sciences Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Fukuura 2-12-4, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan
| | - Yuri Kawai
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Satomi Funahashi
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Ryuhei Minei
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Yuki Akizuki
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Atsushi Ogura
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, Research Institute, National Center for Child Health and Development, Tokyo, Japan
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan.
- School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
| | - Kazuho Ikeo
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
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6
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Chatragadda R. Terrestrial and marine bioluminescent organisms from the Indian subcontinent: a review. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:747. [PMID: 33150454 DOI: 10.1007/s10661-020-08685-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
The inception of bioluminescence by Harvey (1952) has led to a Nobel Prize to Osamu Shimomura (Chemistry, 2008) in biological research. Consequently, in recent years, bioluminescence-based assays to monitor toxic pollutants as a real-time marker, to study various diseases and their propagation in plants and animals, are developed in many countries. The emission ability of bioluminescence is improved by gene modification, and also, search for novel bioluminescent systems is underway. Over 100 species of organisms belonging to different taxa are known to be luminous in India. However, the diversity and distribution of luminous organisms and their applications are studied scarcely in the Indian scenario. In this context, the present review provides an overview of the current understanding of various bioluminescent organisms, functions, and applications. A detailed checklist of known bioluminescent organisms from India's marine, terrestrial, and freshwater ecosystems is detailed. This review infers that Indian scientists are needed to extend their research on various aspects of luminescent organisms such as biodiversity, genomics, and chemical mechanisms for conservation, ecological, and biomedical applications.
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Affiliation(s)
- Ramesh Chatragadda
- Biological Oceanography Division (BOD), CSIR-National Institute of Oceanography (CSIR-NIO), Dona Paula, Goa, 403004, India.
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7
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Parry R, Asgari S. Discovery of Novel Crustacean and Cephalopod Flaviviruses: Insights into the Evolution and Circulation of Flaviviruses between Marine Invertebrate and Vertebrate Hosts. J Virol 2019; 93:e00432-19. [PMID: 31068424 PMCID: PMC6600200 DOI: 10.1128/jvi.00432-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
Most described flaviviruses (family Flaviviridae) are disease-causing pathogens of vertebrates maintained in zoonotic cycles between mosquitoes or ticks and vertebrate hosts. Poor sampling of flaviviruses outside vector-borne flaviviruses such as Zika virus and dengue virus has presented a narrow understanding of flavivirus diversity and evolution. In this study, we discovered three crustacean flaviviruses (Gammarus chevreuxi flavivirus, Gammarus pulex flavivirus, and Crangon crangon flavivirus) and two cephalopod flaviviruses (Southern Pygmy squid flavivirus and Firefly squid flavivirus). Bayesian and maximum likelihood phylogenetic methods demonstrate that crustacean flaviviruses form a well-supported clade and share a more closely related ancestor with terrestrial vector-borne flaviviruses than with classical insect-specific flaviviruses. In addition, we identify variants of Wenzhou shark flavivirus in multiple gazami crab (Portunus trituberculatus) populations, with active replication supported by evidence of an active RNA interference response. This suggests that Wenzhou shark flavivirus moves horizontally between sharks and gazami crabs in ocean ecosystems. Analyses of the mono- and dinucleotide composition of marine flaviviruses compared to that of flaviviruses with known host status suggest that some marine flaviviruses share a nucleotide bias similar to that of vector-borne flaviviruses. Furthermore, we identify crustacean flavivirus endogenous viral elements that are closely related to elements of terrestrial vector-borne flaviviruses. Taken together, these data provide evidence of flaviviruses circulating between marine vertebrates and invertebrates, expand our understanding of flavivirus host range, and offer potential insights into the evolution and emergence of terrestrial vector-borne flaviviruses.IMPORTANCE Some flaviviruses are known to cause disease in vertebrates and are typically transmitted by blood-feeding arthropods such as ticks and mosquitoes. While an ever-increasing number of insect-specific flaviviruses have been described, we have a narrow understanding of flavivirus incidence and evolution. To expand this understanding, we discovered a number of novel flaviviruses that infect a range of crustaceans and cephalopod hosts. Phylogenetic analyses of these novel marine flaviviruses suggest that crustacean flaviviruses share a close ancestor to all terrestrial vector-borne flaviviruses, and squid flaviviruses are the most divergent of all known flaviviruses to date. Additionally, our results indicate horizontal transmission of a marine flavivirus between crabs and sharks. Taken together, these data suggest that flaviviruses move horizontally between invertebrates and vertebrates in ocean ecosystems. This study demonstrates that flavivirus invertebrate-vertebrate host associations have arisen in flaviviruses at least twice and may potentially provide insights into the emergence or origin of terrestrial vector-borne flaviviruses.
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Affiliation(s)
- Rhys Parry
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
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Galeazzo GA, Mirza JD, Dorr FA, Pinto E, Stevani CV, Lohrmann KB, Oliveira AG. Characterizing the Bioluminescence of the Humboldt Squid,
Dosidicus gigas
(d'Orbigny, 1835): One of the Largest Luminescent Animals in the World. Photochem Photobiol 2019; 95:1179-1185. [DOI: 10.1111/php.13106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/27/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Gabriela A. Galeazzo
- Departamento de Oceanografia Física, Química e Geológica Instituto Oceanográfico Universidade de São Paulo São Paulo Brazil
| | - Jeremy D. Mirza
- Departamento de Oceanografia Física, Química e Geológica Instituto Oceanográfico Universidade de São Paulo São Paulo Brazil
- Departamento de Química Instituto de Ciências Ambientais, Químicas e Farmacêuticas Universidade Federal de São Paulo Diadema SP Brazil
| | - Felipe A. Dorr
- Departamento de Análises Clínicas e Toxicológicas Faculdade de Ciências Farmacêuticas Universidade de São Paulo São Paulo SP Brazil
| | - Ernani Pinto
- Departamento de Análises Clínicas e Toxicológicas Faculdade de Ciências Farmacêuticas Universidade de São Paulo São Paulo SP Brazil
| | - Cassius V. Stevani
- Departamento de Química Fundamental Instituto de Química Universidade de São Paulo São Paulo SP Brazil
| | - Karin B. Lohrmann
- Departamento de Biología Marina Facultad de Ciencias del Mar Centro Innovación Acuícola Aquapacífico Universidad Católica del Norte Coquimbo Chile
| | - Anderson G. Oliveira
- Departamento de Oceanografia Física, Química e Geológica Instituto Oceanográfico Universidade de São Paulo São Paulo Brazil
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9
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Yao Z, Zhang BS, Prescher JA. Advances in bioluminescence imaging: new probes from old recipes. Curr Opin Chem Biol 2018; 45:148-156. [PMID: 29879594 PMCID: PMC6076869 DOI: 10.1016/j.cbpa.2018.05.009] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/25/2018] [Accepted: 05/04/2018] [Indexed: 11/18/2022]
Abstract
Bioluminescent probes are powerful tools for visualizing biology in live tissues and whole animals. Recent years have seen a surge in the number of new luciferases, luciferins, and related tools available for bioluminescence imaging. Many were crafted using classic methods of optical probe design and engineering. Here we highlight recent advances in bioluminescent tool discovery and development, along with applications of the probes in cells, tissues, and organisms. Collectively, these tools are improving in vivo imaging capabilities and bolstering new research directions.
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Affiliation(s)
- Zi Yao
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Brendan S Zhang
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.
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10
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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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11
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Verdes A, Holford M. Beach to Bench to Bedside: Marine Invertebrate Biochemical Adaptations and Their Applications in Biotechnology and Biomedicine. Results Probl Cell Differ 2018; 65:359-376. [PMID: 30083928 DOI: 10.1007/978-3-319-92486-1_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The ocean covers more than 70% of the surface of the planet and harbors very diverse ecosystems ranging from tropical coral reefs to the deepest ocean trenches, with some of the most extreme conditions of pressure, temperature, and light. Organisms living in these environments have been subjected to strong selective pressures through millions of years of evolution, resulting in a plethora of remarkable adaptations that serve a variety of vital functions. Some of these adaptations, including venomous secretions and light-emitting compounds or ink, represent biochemical innovations in which marine invertebrates have developed novel and unique bioactive compounds with enormous potential for basic and applied research. Marine biotechnology, defined as the application of science and technology to marine organisms for the production of knowledge, goods, and services, can harness the enormous possibilities of these unique bioactive compounds acting as a bridge between biological knowledge and applications. This chapter highlights some of the most exceptional biochemical adaptions found specifically in marine invertebrates and describes the biotechnological and biomedical applications derived from them to improve the quality of human life.
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Affiliation(s)
- Aida Verdes
- Facultad de Ciencias, Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Madrid, Spain.
- Department of Chemistry, Hunter College Belfer Research Center, City University of New York, New York, NY, USA.
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY, USA.
| | - Mandë Holford
- Department of Chemistry, Hunter College Belfer Research Center, City University of New York, New York, NY, USA.
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY, USA.
- The Graduate Center, Program in Biology, Chemistry and Biochemistry, City University of New York, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA.
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12
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Francis WR, Christianson LM, Haddock SHD. Symplectin evolved from multiple duplications in bioluminescent squid. PeerJ 2017; 5:e3633. [PMID: 28785521 PMCID: PMC5541922 DOI: 10.7717/peerj.3633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/11/2017] [Indexed: 01/06/2023] Open
Abstract
The squid Sthenoteuthis oualaniensis, formerly Symplectoteuthis oualaniensis, generates light using the luciferin coelenterazine and a unique enzyme, symplectin. Genetic information is limited for bioluminescent cephalopod species, so many proteins, including symplectin, occur in public databases only as sequence isolates with few identifiable homologs. As the distribution of the symplectin/pantetheinase protein family in Metazoa remains mostly unexplored, we have sequenced the transcriptomes of four additional luminous squid, and make use of publicly available but unanalyzed data of other cephalopods, to examine the occurrence and evolution of this protein family. While the majority of spiralians have one or two copies of this protein family, four well-supported groups of proteins are found in cephalopods, one of which corresponds to symplectin. A cysteine that is critical for symplectin functioning is conserved across essentially all members of the protein family, even those unlikely to be used for bioluminescence. Conversely, active site residues involved in pantetheinase catalysis are also conserved across essentially all of these proteins, suggesting that symplectin may have multiple functions including hydrolase activity, and that the evolution of the luminous phenotype required other changes in the protein outside of the main binding pocket.
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Affiliation(s)
- Warren R Francis
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America.,Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Lynne M Christianson
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America
| | - Steven H D Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America
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Du J, Wang X, Nie Q, Yang J, Yao X. Computational study of the binding mechanism of medium chain acyl-CoA synthetase with substrate in Methanosarcina acetivorans. J Biotechnol 2017; 259:160-167. [PMID: 28751277 DOI: 10.1016/j.jbiotec.2017.07.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/19/2017] [Accepted: 07/22/2017] [Indexed: 02/03/2023]
Abstract
The acyl-AMP forming family of adenylating enzymes catalyzes the formation of acyl-CoA from an acyl substrate, ATP, and CoA, which is a metabolite of many catabolic and anabolic processes. The medium-chain acyl-CoA synthetase from Methanosarcina acetivorans, designated MacsMa, uses 2-methylbutyrate as its preferred substrate. It is reported that the interaction between the sidechain of Cys298 and Lys256 of this enzyme is important for the catalytic activity. The mutation of these residues resulted in the changes of the structure stability and the reduced or absence catalytic activity. In the present study, the binding mechanism between the substrate 2-methylbutyrate- AMP (2MeBA) and MacsMa were explored by integrating multiple computational methods including molecular docking, molecular dynamics simulations, binding free energy calculation, active site access channel analysis and principal component analysis. The binding free energy between WT, mutated Macs and substrate was calculated by MM-GBSA method, which indicated that the binding affinity between this enzyme and substrate was stronger in the WT than that in the mutated forms (K256L, K256T and C298Y). Per-residue binding free energy decomposition identified some residues, such as Gly327, Phe350, Gly351, Gln352 and Lys461, which are important for the enzyme and substrate binding affinity. The access channels of the mutant system (MacsK256L, MacsK256T and MacsC298Y) were found to be different from those in the wild-type systems. It suggested that K256L and C298Y induced larger flexibility to the overall protein compared with the WT, whereas K256T induced larger flexibility to the partial protein compared with the WT by PCA vector porcupines. This study provides novel insight to understand the substrate binding mechanism of Macs and useful information for the rational enzyme design.
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Affiliation(s)
- Juan Du
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Xiaolu Wang
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Qingjuan Nie
- Foreign Languages School, Qingdao Agricultural University, Qingdao, China
| | - Jianming Yang
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, China.
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
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Delroisse J, Ullrich-Lüter E, Blaue S, Ortega-Martinez O, Eeckhaut I, Flammang P, Mallefet J. A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence. Open Biol 2017; 7:rsob.160300. [PMID: 28381628 PMCID: PMC5413902 DOI: 10.1098/rsob.160300] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 03/06/2017] [Indexed: 01/31/2023] Open
Abstract
Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases. Here, we identify for the first time a candidate luciferase of a luminous echinoderm, the ophiuroid Amphiura filiformis Phylogenomic analyses identified the brittle star predicted luciferase as homologous to the luciferase of the sea pansy Renilla (Cnidaria), contradicting with the traditional viewpoint according to which luciferases would generally be of convergent origins. The similarity between the Renilla and Amphiura luciferases allowed us to detect the latter using anti-Renilla luciferase antibodies. Luciferase expression was specifically localized in the spines which were demonstrated to be the bioluminescent organs in vivo However, enzymes homologous to the Renilla luciferase but unable to trigger light emission were also identified in non-luminous echinoderms and metazoans. Our findings strongly indicate that those enzymes, belonging to the haloalkane dehalogenase family, might then have been convergently co-opted into luciferases in cnidarians and echinoderms. In these two benthic suspension-feeding species, similar ecological pressures would constitute strong selective forces for the functional shift of these enzymes and the emergence of bioluminescence.
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Affiliation(s)
- Jérôme Delroisse
- Research Institute for Biosciences, Biology of Marine Organisms and Biomimetics, University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Esther Ullrich-Lüter
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115 Berlin, Germany
| | - Stefanie Blaue
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115 Berlin, Germany
| | - Olga Ortega-Martinez
- Department of Marine Science, The Sven Lovén Centre for Marine Sciences - Kristineberg, University of Gothenburg, 45178 Fiskebäckskil, Sweden
| | - Igor Eeckhaut
- Research Institute for Biosciences, Biology of Marine Organisms and Biomimetics, University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Patrick Flammang
- Research Institute for Biosciences, Biology of Marine Organisms and Biomimetics, University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Jérôme Mallefet
- Marine Biology Laboratory, Université Catholique de Louvain, ELI, 3 Place Croix du Sud L7.04.06, 1348 Louvain-La-Neuve, Belgium
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