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Fukuta K, Kato DI, Maeda J, Tsuruta A, Suzuki H, Nagano Y, Tsukamoto H, Niwa K, Terauchi M, Toyoda A, Fujiyama A, Noguchi H. Genome assembly of Genji firefly (Nipponoluciola cruciata) reveals novel luciferase-like luminescent proteins without peroxisome targeting signal. DNA Res 2024; 31:dsae006. [PMID: 38494174 DOI: 10.1093/dnares/dsae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 01/12/2024] [Accepted: 03/01/2024] [Indexed: 03/19/2024] Open
Abstract
The Genji firefly, Nipponoluciola cruciata, is an aquatic firefly endemic to Japan, inhabiting a wide area of the Japanese archipelago. The luminescence of fireflies is a scientifically interesting phenomenon, and many studies have evaluated this species in Japan. In this study, we sequenced the whole genome of male N. cruciata and constructed a high-quality genome assembly of 662 Mb with a BUSCO completeness of 99.1% in the genome mode. Using the detected set of 15,169 protein-coding genes, the genomic structures and genetic background of luminescence-related genes were also investigated. We found four new firefly luciferase-like genes in the genome. The highest bioluminescent activity was observed for LLa2, which originated from ancestral PDGY, a mitochondrial acyl-CoA synthetase. A thioesterase candidate, NcruACOT1, which is involved in d-luciferin biosynthesis, was expressed in the lantern. Two opsins were also detected and the absorption wavelength of the UV-type opsin candidate shifted from UV to blue. These findings provide an important resource for unravelling the adaptive evolution of fireflies in terms of luminescence and vision.
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Affiliation(s)
- Kentaro Fukuta
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
- Data Analysis Division, Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Dai-Ichiro Kato
- Department of Science, Graduate School of Science and Engineering, Kagoshima University, Kagoshima 890-0065, Japan
| | - Juri Maeda
- Department of Science, Graduate School of Science and Engineering, Kagoshima University, Kagoshima 890-0065, Japan
| | - Atsuhiro Tsuruta
- Department of Science, Graduate School of Science and Engineering, Kagoshima University, Kagoshima 890-0065, Japan
| | | | - Yukio Nagano
- Analytical Research Center for Experimental Sciences, Saga University, Saga 840-8502, Japan
| | - Hisao Tsukamoto
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Kazuki Niwa
- Advanced Quantum Measurement Group, Research Institute for Physical Measurement, National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8563, Japan
| | - Makoto Terauchi
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
- Data Analysis Division, Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Sequencing Division, Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Asao Fujiyama
- Data Analysis Division, Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Comparative Genomics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hideki Noguchi
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
- Data Analysis Division, Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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Ikenaga T, Nakamura T, Tajiri T, Tsuji M, Kato DI, Ineno T, Kobayashi Y, Tsutsui N, Kiyohara S. Diversity and evolution of serotonergic cells in taste buds of elasmobranchs and ancestral actinopterygian fish. Cell Tissue Res 2023; 394:431-439. [PMID: 37851111 DOI: 10.1007/s00441-023-03837-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 10/05/2023] [Indexed: 10/19/2023]
Abstract
A subset of gustatory cells are serotonin immunoreactive (ir) in the mammalian taste bud. In the taste bud of lamprey, elongated gustatory-like cells are also serotonin-ir. In contrast, flattened serotonin-ir cells are located only in the basal region of the taste buds in the teleosts and amphibians. These serotonin-ir cells are termed as basal cells. To evaluate the evolution and diversity of serotonergic cells in the taste bud of amniote animals, we explored the distribution and morphology of serotonin-ir cells in the taste buds of ancestral actinopterygian fish (spotted gar, sturgeon, Polypterus senegalus) and elasmobranch (stingray). In all examined animals, the taste buds contained serotonin-ir cells in their basal part. The number of serotonin-ir basal cells in each taste bud was different between these fish species. They were highest in the stingray and decreased in the order of the Polypterus, sturgeon, and gar. While serotonin immunoreactivity was observed only in the basal cells in the taste buds of the ancestral actinopterygian fish, some elongated cells were also serotonin-ir in addition to the basal cells in the stingray taste buds. mRNA of tryptophan hydroxylase 1 (tph1), a rate-limiting enzyme of the serotonin synthesis, is expressed in both the elongated and basal cells of stingray taste buds, indicating that these cells synthesize the serotonin by themselves. These results suggest that the serotonin-ir basal cells arose from the ancestor of the cartilaginous fish, and serotonin-ir cells in the elasmobranch taste bud exhibit an intermediate aspect between the lamprey and actinopterygian fish.
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Affiliation(s)
- Takanori Ikenaga
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan.
| | - Tastufumi Nakamura
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Tatsushi Tajiri
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Minaki Tsuji
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Dai-Ichiro Kato
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Toshinao Ineno
- Aquaculture Research Institute, Shingu Station, Kindai University, Wakayama, Japan
| | - Yasuhisa Kobayashi
- Department of Fisheries, Faculty of Agriculture, Kindai University, Nara, 631-0052, Japan
- Faculty of Science, Ushimado Marine Institute (UMI), Okayama University, Okayama, 701-4303, Japan
| | - Naoaki Tsutsui
- Department of Life Sciences, Graduate School of Bioresources, Mie University, Mie, 514-8507, Japan
- Faculty of Science, Ushimado Marine Institute (UMI), Okayama University, Okayama, 701-4303, Japan
| | - Sadao Kiyohara
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
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Negoro S, Shibata N, Kato DI, Tanaka Y, Yasuhira K, Nagai K, Oshima S, Furuno Y, Yokoyama R, Miyazaki K, Takeo M, Hengphasatporn K, Shigeta Y, Lee YH, Higuchi Y. X-ray crystallographic and mutational analysis of the NylC precursor: catalytic mechanism of autocleavage and substrate hydrolysis of nylon hydrolase. FEBS J 2023. [PMID: 36799721 DOI: 10.1111/febs.16755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/04/2023] [Accepted: 02/16/2023] [Indexed: 02/18/2023]
Abstract
Nylon hydrolase (NylC), a member of the N-terminal nucleophile (Ntn) hydrolase superfamily, is responsible for the degradation of various aliphatic nylons, including nylon-6 and nylon-66. NylC is initially expressed as an inactive precursor (36 kDa), but the precursor is autocatalytically cleaved at Asn266/Thr267 to generate an active enzyme composed of 27 and 9 kDa subunits. We isolated various mutants with amino acid changes at the catalytic centre. X-ray crystallographic analysis revealed that the NylC precursor forms a doughnut-shaped quaternary structure composed of four monomers (molecules A-D) with D2 symmetry. Catalytic residues in the precursor are covered by loop regions at the A/B interface (equivalent to the C/D interface). However, the catalytic residues are exposed to the solvent environment through autocleavage followed by movements of the loop regions. T267A, D306A and D308A mutations resulted in a complete loss of autocleavage. By contrast, in the T267S mutant, autocleavage proceeded slowly at a constant reaction rate (k = 2.8 × 10-5 s-1 ) until complete conversion, but the reaction was inhibited by K189A and N219A mutations. Based on the crystallographic and molecular dynamic simulation analyses, we concluded that the Asp308-Asp306-Thr267 triad, resembling the Glu-Ser-Ser triad conserved in Ntn-hydrolase family enzymes, is responsible for autocleavage and that hydrogen-bonding networks connecting Thr267 with Lys189 and Asn219 are required for increasing the nucleophilicity of Thr267-OH in both the water accessible and water inaccessible systems. Furthermore, we determined that NylC employs the Asp308-Asp306-Thr267 triad as catalytic residues for substrate hydrolysis, but the reaction requires Lys189 and Tyr146 as additional catalytic/substrate-binding residues specific for nylon hydrolysis.
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Affiliation(s)
- Seiji Negoro
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Naoki Shibata
- Department of Life Science, Graduate School of Science, University of Hyogo, Ako-gun, Japan
| | - Dai-Ichiro Kato
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Yusuke Tanaka
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Kengo Yasuhira
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Keisuke Nagai
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Shohei Oshima
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Yoko Furuno
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Risa Yokoyama
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Kaito Miyazaki
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Masahiro Takeo
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | | | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Young-Ho Lee
- Institute for Protein Research, Osaka University, Suita, Japan.,Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju-si, South Korea.,Bio-Analytical Science, University of Science and Technology, Daejeon, South Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, South Korea
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Science, University of Hyogo, Ako-gun, Japan
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Niwa K, Kato DI. Biosynthesis-Inspired Deracemizative Production of D-Luciferin In Vitro by Combining Luciferase and Thioesterase. Methods Mol Biol 2022; 2524:53-58. [PMID: 35821462 DOI: 10.1007/978-1-0716-2453-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Due to the strict enantioselectivity of firefly luciferase (FLuc), only D-luciferin can be used as a substrate for the bioluminescence (BL) reaction. Unfortunately, luciferin racemizes easily and accumulation of nonluminous L-luciferin has negative influences on the light-emitting reaction. By a detailed analysis of luciferin chirality, however, it becomes clarified that L-luciferin is the biosynthetic precursor of D-luciferin in fireflies and undergoes the enzymatic chiral inversion. By the chiral inversion reaction, the enantiopurity of luciferin can be maintained in the reaction mixture for applications using FLuc. Thus, chirality is crucial for the BL reaction and essential for investigating and applying the biosynthesis of D-luciferin. Here, we describe the methods for the analysis of chiral inversion reaction using high-performance liquid chromatography (HPLC) with a chiral column. We also introduce an example of an in vitro deracemizative BL reaction system using a combination of FLuc and fatty acyl-CoA thioesterase, which is inspired by the chiral inversion mechanism in the biosynthetic pathway of D-luciferin.
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Affiliation(s)
- Kazuki Niwa
- Research Institute for Physical Measurement, National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Dai-Ichiro Kato
- Department of Science, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan.
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5
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Ikenaga T, Shimomai R, Hagio H, Kimura S, Matsumoto K, Kato DI, Uesugi K, Takeuchi A, Yamamoto N, Hibi M. Morphological analysis of the cerebellum and its efferent system in a basal actinopterygian fish, Polypterus senegalus. J Comp Neurol 2021; 530:1231-1246. [PMID: 34729771 DOI: 10.1002/cne.25271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/07/2022]
Abstract
Although all vertebrate cerebella contain granule cells, Purkinje cells, and efferent neurons, the cellular arrangement and neural circuitry are highly diverse. In amniotes, cerebellar efferent neurons form clusters, deep cerebellar nuclei, lie deep in the cerebellum, and receive synaptic inputs from Purkinje cells but not granule cells. However, in the cerebellum of teleosts, the efferent neurons, called eurydendroid cells, lie near the cell bodies of Purkinje cells and receive inputs both from axons of Purkinje cells and granule cell parallel fibers. It is largely unknown how the cerebellar structure evolved in ray-finned fish (actinopterygians). To address this issue, we analyzed the cerebellum of a bichir Polypterus senegalus, one of the most basal actinopterygians. We found that the cell bodies of Purkinje cells are not aligned in a layer; incoming climbing fibers terminate mainly on the basal portion of Purkinje cells, revealing that the Polypterus cerebellum has unique features among vertebrate cerebella. Retrograde labeling and marker analyses of the efferent neurons revealed that their cell bodies lie in restricted granular areas but not as deep cerebellar nuclei in the cerebellar white matter. The efferent neurons have long dendrites like eurydendroid cells, although they do not reach the molecular layer. Our findings suggest that the efferent system of the bichir cerebellum has intermediate features between teleosts and amniote vertebrates, and provides a model to understand the basis generating diversity in actinopterygian cerebella.
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Affiliation(s)
- Takanori Ikenaga
- Department of Science, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Rinko Shimomai
- Department of Science, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Hanako Hagio
- Institute for Advanced Research, Nagoya University, Nagoya, Japan.,Laboratory of Fish Biology, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.,Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Satoru Kimura
- Department of Science, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Kazumasa Matsumoto
- Department of Science, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Dai-Ichiro Kato
- Department of Science, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Kentaro Uesugi
- Research and Utilization Division, Japan Synchrotron Radiation Research Institute/SPring-8, Hyogo, Japan
| | - Akihisa Takeuchi
- Research and Utilization Division, Japan Synchrotron Radiation Research Institute/SPring-8, Hyogo, Japan
| | - Naoyuki Yamamoto
- Laboratory of Fish Biology, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Masahiko Hibi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
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Negoro S, Kato DI, Ohki T, Yasuhira K, Kawashima Y, Nagai K, Takeo M, Shibata N, Kamiya K, Shigeta Y. Structural and functional characterization of nylon hydrolases. Methods Enzymol 2020; 648:357-389. [PMID: 33579412 DOI: 10.1016/bs.mie.2020.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Biodegradation of synthetic polymers is recognized as a useful way to reduce their environmental load and pollution, loss of natural resources, extensive energy consumption, and generation of greenhouse gases. The potential use of enzymes responsible for the degradation of the targeted polymers is an effective approach which enables the conversion of the used polymers to original monomers and/or other useful compounds. In addition, the enzymes are expected to be applicable in industrial processes such as improving the surface structures of the polymers. Especially, conversion of the solid polymers to soluble oligomers/monomers is a key step for the biodegradation of the polymers. Regarding the hydrolysis of polyamides, three enzymes, 6-aminohexanoate-cyclic-dimer hydrolase (NylA), 6-aminohexanoate-dimer hydrolase (NylB), and 6-aminohexanoate-oligomer endo-hydrolase (nylon hydrolase, NylC), are found in several bacterial strains. In this chapter, we describe our approach for the screening of microorganisms which degrade nylons and related compounds; preparation of substrates; assay of hydrolytic activity for soluble and insoluble substrates; and X-ray crystallographic and computational approaches for analysis of structure and catalytic mechanisms of the nylon-degrading enzymes.
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Affiliation(s)
- Seiji Negoro
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan.
| | - Dai-Ichiro Kato
- Department of Science, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Taku Ohki
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Kengo Yasuhira
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Yasuyuki Kawashima
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Keisuke Nagai
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Masahiro Takeo
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Naoki Shibata
- Department of Picobiology, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo, Japan
| | - Katsumasa Kamiya
- Education Development Center, Kanagawa Institute of Technology, Atsugi, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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Kato DI, Suzuki H, Tsuruta A, Maeda J, Hayashi Y, Arima K, Ito Y, Nagano Y. Evaluation of the population structure and phylogeography of the Japanese Genji firefly, Luciola cruciata, at the nuclear DNA level using RAD-Seq analysis. Sci Rep 2020; 10:1533. [PMID: 32001772 PMCID: PMC6992745 DOI: 10.1038/s41598-020-58324-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 01/13/2020] [Indexed: 11/09/2022] Open
Abstract
The Genji firefly, Luciola cruciata, is widely distributed throughout the major Japanese islands (Honshu, Shikoku, and Kyushu) and distinguished into two ecological types on the basis of the flash interval of the mate-seeking males (4-sec slow-flash or 2-sec fast-flash intervals). The boundary of the ecological types corresponds to the Fossa Magna, a great rupture zone that separates eastern and western Japan. Although the degree of genetic differentiation of the two types has been evaluated using allozyme and mitochondrial DNA sequence data, it has not been evaluated using genome-wide data. Based on the genome-wide data obtained using single-end restriction-site-associated DNA (RAD-Seq), principal component, gene-level phylogenetic tree, admixture, and Wright's fixation index analyses, we identified three phylogenetic groups in L. cruciata: East-Honshu, West-Honshu, and Kyushu. This grouping corresponds to the ecological types: East-Honshu to the slow-flash type and West-Honshu and Kyushu to the fast-flash type. Although introgression was exceptionally observed around adjacent or artificially transplanted areas, gene flow among the groups was almost absent in the natural populations. The phylogenetic tree under the coalescent model also evaluated differentiation among the East-Honshu, West-Honshu and Kyushu groups. Furthermore, because the distribution patterns of the three groups are consistent with the geological history of Japanese islands, a vicariant speciation scenario of L. cruciata is concluded. In addition, we identified genetic markers that can be used to distinguish the three genetic groups for genetic management of firefly transplantation in nature conservation and regeneration.
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Affiliation(s)
- Dai-Ichiro Kato
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, 890-0065, Japan.
| | - Hirobumi Suzuki
- Japan Fireflies Society, 2-1-24 Shinmei, Hino, Tokyo, 191-0016, Japan
| | - Atsuhiro Tsuruta
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, 890-0065, Japan
| | - Juri Maeda
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, 890-0065, Japan
| | - Yoshinobu Hayashi
- Department of Biology, Keio University, 4-1-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8521, Japan
| | - Kazunari Arima
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, 890-0065, Japan
| | - Yuji Ito
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, 890-0065, Japan
| | - Yukio Nagano
- Analytical Research Center for Experimental Sciences, Saga University, 1 Honjo-machi, Saga, 840-8502, Japan
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Takeo M, Yamamoto K, Sonoyama M, Miyanaga K, Kanbara N, Honda K, Kato DI, Negoro S. Characterization of the 3-methyl-4-nitrophenol degradation pathway and genes of Pseudomonas sp. strain TSN1. J Biosci Bioeng 2018; 126:355-362. [PMID: 29699943 DOI: 10.1016/j.jbiosc.2018.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/14/2018] [Accepted: 04/02/2018] [Indexed: 11/18/2022]
Abstract
3-Methyl-4-nitrophenol (3M4NP) is formed in soil as a hydrolysis product of fenitrothion, one of the major organophosphorus pesticides. A Pseudomonas strain was isolated as a 3M4NP degrader from a crop soil and designated TSN1. This strain utilized 3M4NP as a sole carbon and energy source. To elucidate the biodegradation pathway, we performed transposon mutagenesis with pCro2a (mini-Tn5495) and obtained three mutants accumulating a dark pink compound(s) from 3M4NP. Rescue cloning and sequence analysis revealed that in all mutants, the transposon disrupted an identical aromatic compound meta-cleaving dioxygenase gene, and a monooxygenase gene was located just downstream of the dioxygenase gene. These two genes were designated mnpC and mnpB, respectively. The gene products showed high identity with the methylhydroquinone (MHQ) monooxygenase (58%) and the 3-methylcatechol 2,3-dioxygenase (54%) of a different 3M4NP degrader Burkholderia sp. NF100. The transposon mutants converted 3M4NP or MHQ into two identical metabolites, one of which was identified as 2-hydroxy-5-methyl-1,4-benzoquinone (2H5MBQ) by GC/MS analysis. Furthermore, two additional genes (named mnpA1 and mnpA2), almost identical to the p-nitrophenol monooxygenase and the p-benzoquinone reductase genes of Pseudomonas sp. WBC-3, were isolated from the total DNA of strain TSN1. Disruption of mnpA1 resulted in the complete loss of the 3M4NP degradation activity, demonstrating that mnpA1 encodes the initial monooxygenase for 3M4NP degradation. The purified mnpA2 gene product could efficiently reduce methyl p-benzoquinone (MBQ) into MHQ. These results suggest that strain TSN1 degrades 3M4NP via MBQ, MHQ, and 2H5MBQ in combination with mnpA1A2 and mnpCB, existing at different loci on the genome.
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Affiliation(s)
- Masahiro Takeo
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Kenta Yamamoto
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Masashi Sonoyama
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Kana Miyanaga
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Nana Kanbara
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Koichi Honda
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Dai-Ichiro Kato
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
| | - Seiji Negoro
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
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Takehara I, Fujii T, Tanimoto Y, Kato DI, Takeo M, Negoro S. Correction to: Metabolic pathway of 6-aminohexanoate in the nylon oligomer-degrading bacterium Arthrobacter sp. KI72: identification of the enzymes responsible for the conversion of 6-aminohexanoate to adipate. Appl Microbiol Biotechnol 2017; 102:815. [PMID: 29234852 DOI: 10.1007/s00253-017-8682-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The original publication of this paper contains mistakes for Tables 1 and 2 legends as well as the sublabels in Figs. 2, 4, 5, 6, and 7.
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Affiliation(s)
- Ikki Takehara
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Tsubasa Fujii
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Yuuki Tanimoto
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Dai-Ichiro Kato
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, 1-21-35 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Masahiro Takeo
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Seiji Negoro
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan.
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10
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Maeda J, Kato DI, Arima K, Ito Y, Toyoda A, Noguchi H. The complete mitochondrial genome sequence and phylogenetic analysis of Luciola lateralis, one of the most famous firefly in Japan (Coleoptera: Lampyridae). Mitochondrial DNA B Resour 2017; 2:546-547. [PMID: 33473894 PMCID: PMC7799510 DOI: 10.1080/23802359.2017.1365640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We will report the complete mitochondrial genome sequence of Japanese firefly ‘Heike Botaru’, Luciola lateralis (Coleoptera: Lampyridae). Total length of this mitogenome was 16,719 bp and the composition of each base was A (42.50%), C (9.01%), G (14.16%), T (34.33%), respectively. The obtained sequence fulfils general mitogenome composition of metazoan (13 protein coding sequences (CDSs), 22 tRNA genes, two rRNA subunits, and an AT-rich region). From the phylogenetic tree analysis using 25 kinds of insect mitogenome including firefly family was found that L. lateralis is the closest to the genus Aquatica.
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Affiliation(s)
- Juri Maeda
- Department of Chemistry and Biosciences, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Dai-Ichiro Kato
- Department of Chemistry and Biosciences, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Kazunari Arima
- Department of Chemistry and Biosciences, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Yuji Ito
- Department of Chemistry and Biosciences, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Hideki Noguchi
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Japan
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11
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Maeda J, Kato DI, Arima K, Ito Y, Toyoda A, Noguchi H. The complete mitogenome and phylogenetic analysis of Japanese firefly 'Genji Botaru' Luciola cruciata (Coleoptera: Lampyridae). Mitochondrial DNA B Resour 2017; 2:522-523. [PMID: 33490463 PMCID: PMC7800388 DOI: 10.1080/23802359.2017.1365641] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We performed mitogenome analysis of Japanese firefly Luciola cruciata (Coleoptera: Lampyridae), which is unique species in Japan. It is classified into six haplotypes based on the difference of COII sequence on mitochondrial DNA. The complete mitogenome sequence of Tohoku group has been registered so far, we newly analysed West Japan groups which belong to different haplotype. The total length of analysed mitogenome was 15,990 bp, being one base longer than the case of Tohoku’s firefly. The base substitution was found at 273 positions over the whole mitochondrial sequence, while amino acid substitution accompanying it was observed at only 11 positions.
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Affiliation(s)
- Juri Maeda
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Dai-Ichiro Kato
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Kazunari Arima
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Yuji Ito
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Hideki Noguchi
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Japan
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12
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Khan KH, Himeno A, Kosugi S, Nakashima Y, Rafique A, Imamura A, Hatanaka T, Kato DI, Ito Y. IgY-binding peptide screened from a random peptide library as a ligand for IgY purification. J Pept Sci 2017; 23:790-797. [PMID: 28758361 PMCID: PMC5637892 DOI: 10.1002/psc.3027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/22/2017] [Accepted: 07/01/2017] [Indexed: 01/29/2023]
Abstract
Chicken egg yolk immunoglobulin (IgY) is a functional substitute for mammalian IgG for antigen detection. Traditional IgY purification methods involve multi-step procedures resulting in low purity and recovery of IgY. In this study, we developed a simple IgY purification system using IgY-specific peptides identified by T7 phage display technology. From disulfide-constrained random peptide libraries constructed on a T7 phage, we identified three specific binding clones (Y4-4, Y5-14, and Y5-55) through repeated biopanning. The synthetic peptides showed high binding specificity to IgY-Fc and moderate affinity for IgY-Fc (Kd : Y4-4 = 7.3 ± 0.2 μM and Y5-55 = 4.4 ± 0.1 μM) by surface plasmon resonance analysis. To evaluate the ability to purify IgY, we performed immunoprecipitation and affinity high-performance liquid chromatography using IgY-binding peptides; the result indicated that these peptides can be used as affinity ligands for IgY purification. We then used a peptide-conjugated column to purify IgY from egg yolks pre-treated using an optimized delipidation technique. Here, we report the construction of a cost-effective, one-step IgY purification system, with high purity and recovery. © 2017 The Authors. Journal of Peptide Science published by European Peptide Society and John Wiley & Sons Ltd.
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Affiliation(s)
- Kamrul Hasan Khan
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Arisa Himeno
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Shouhei Kosugi
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Yosuke Nakashima
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Abdur Rafique
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Ayana Imamura
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Takaaki Hatanaka
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Dai-Ichiro Kato
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Yuji Ito
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
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13
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Sotokawauchi A, Kato-Murayama M, Murayama K, Hosaka T, Maeda I, Onjo M, Ohsawa N, Kato DI, Arima K, Shirouzu M. Structural basis of cucumisin protease activity regulation by its propeptide. J Biochem 2016; 161:45-53. [DOI: 10.1093/jb/mvw053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/27/2016] [Indexed: 01/13/2023] Open
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14
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Prado RA, Santos CR, Kato DI, Murakami MT, Viviani VR. The dark and bright sides of an enzyme: a three dimensional structure of the N-terminal domain of Zophobas morio luciferase-like enzyme, inferences on the biological function and origin of oxygenase/luciferase activity. Photochem Photobiol Sci 2016; 15:654-65. [PMID: 27101527 DOI: 10.1039/c6pp00017g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Beetle luciferases, the enzymes responsible for bioluminescence, are special cases of CoA-ligases which have acquired a novel oxygenase activity, offering elegant models to investigate the structural origin of novel catalytic functions in enzymes. What the original function of their ancestors was, and how the new oxygenase function emerged leading to bioluminescence remains unclear. To address these questions, we solved the crystal structure of a recently cloned Malpighian luciferase-like enzyme of unknown function from Zophobas morio mealworms, which displays weak luminescence with ATP and the xenobiotic firefly d-luciferin. The three dimensional structure of the N-terminal domain showed the expected general fold of CoA-ligases, with a unique carboxylic substrate binding pocket, permitting the binding and CoA-thioesterification activity with a broad range of carboxylic substrates, including short-, medium-chain and aromatic acids, indicating a generalist function consistent with a xenobiotic-ligase. The thioesterification activity with l-luciferin, but not with the d-enantiomer, confirms that the oxygenase activity emerged from a stereoselective impediment of the thioesterification reaction with the latter, favoring the alternative chemiluminescence oxidative reaction. The structure and site-directed mutagenesis support the involvement of the main-chain amide carbonyl of the invariant glycine G323 as the catalytic base for luciferin C4 proton abstraction during the oxygenase activity in this enzyme and in beetle luciferases (G343).
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Affiliation(s)
- R A Prado
- Department of Physics, Chemistry and Mathematics, Graduate Program of Biotechnology and Environmental Monitoring, CCTS, Federal University of São Carlos (UFScar), Sorocaba, São Paulo, Brazil.
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Negoro S, Shibata N, Tanaka Y, Yasuhira K, Shibata H, Hashimoto H, Lee YH, Oshima S, Santa R, Oshima S, Mochiji K, Goto Y, Ikegami T, Nagai K, Kato DI, Takeo M, Higuchi Y. Three-dimensional structure of nylon hydrolase and mechanism of nylon-6 hydrolysis. J Biol Chem 2011; 287:5079-90. [PMID: 22187439 DOI: 10.1074/jbc.m111.321992] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We performed x-ray crystallographic analyses of the 6-aminohexanoate oligomer hydrolase (NylC) from Agromyces sp. at 2.0 Å-resolution. This enzyme is a member of the N-terminal nucleophile hydrolase superfamily that is responsible for the degradation of the nylon-6 industry byproduct. We observed four identical heterodimers (27 kDa + 9 kDa), which resulted from the autoprocessing of the precursor protein (36 kDa) and which constitute the doughnut-shaped quaternary structure. The catalytic residue of NylC was identified as the N-terminal Thr-267 of the 9-kDa subunit. Furthermore, each heterodimer is folded into a single domain, generating a stacked αββα core structure. Amino acid mutations at subunit interfaces of the tetramer were observed to drastically alter the thermostability of the protein. In particular, four mutations (D122G/H130Y/D36A/E263Q) of wild-type NylC from Arthrobacter sp. (plasmid pOAD2-encoding enzyme), with a heat denaturation temperature of T(m) = 52 °C, enhanced the protein thermostability by 36 °C (T(m) = 88 °C), whereas a single mutation (G111S or L137A) decreased the stability by ∼10 °C. We examined the enzymatic hydrolysis of nylon-6 by the thermostable NylC mutant. Argon cluster secondary ion mass spectrometry analyses of the reaction products revealed that the major peak of nylon-6 (m/z 10,000-25,000) shifted to a smaller range, producing a new peak corresponding to m/z 1500-3000 after the enzyme treatment at 60 °C. In addition, smaller fragments in the soluble fraction were successively hydrolyzed to dimers and monomers. Based on these data, we propose that NylC should be designated as nylon hydrolase (or nylonase). Three potential uses of NylC for industrial and environmental applications are also discussed.
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Affiliation(s)
- Seiji Negoro
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Hyogo 671-2280
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16
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Niwa K, Ichino Y, Kumata S, Nakajima Y, Hiraishi Y, Kato DI, Viviani VR, Ohmiya Y. Quantum yields and kinetics of the firefly bioluminescence reaction of beetle luciferases. Photochem Photobiol 2011; 86:1046-9. [PMID: 20663080 DOI: 10.1111/j.1751-1097.2010.00777.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantum yields of firefly bioluminescence reactions were determined for beetle luciferases from the three main families of luminous beetles emitting different bioluminescence colors. Quantum yield (QY) was significantly correlated with luminescence spectrum. The green light-emitting luciferase of the Brazilian click beetle, Pyrearinus termitilluminans, whose luminescence spectrum had the shortest peak wavelength of all the luciferases investigated, had the highest QY (0.61). Mutant analyses of active site-substituted Pyrocoelia miyako luciferases showed that, although k(cat) was decreased by the mutations, the QY was not significantly affected.
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Affiliation(s)
- Kazuki Niwa
- National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology(AIST), Tsukuba, Japan
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17
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Ohki T, Shibata N, Higuchi Y, Kawashima Y, Takeo M, Kato DI, Negoro S. Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a beta-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolase. Protein Sci 2009; 18:1662-73. [PMID: 19521995 DOI: 10.1002/pro.185] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Promiscuous 6-aminohexanoate-linear dimer (Ald)-hydrolytic activity originally obtained in a carboxylesterase with a beta-lactamase fold was enhanced about 80-fold by directed evolution using error-prone PCR and DNA shuffling. Kinetic studies of the mutant enzyme (Hyb-S4M94) demonstrated that the enzyme had acquired an increased affinity (K(m) = 15 mM) and turnover (k(cat) = 3.1 s(-1)) for Ald, and that a catalytic center suitable for nylon-6 byproduct hydrolysis had been generated. Construction of various mutant enzymes revealed that the enhanced activity in the newly evolved enzyme is due to the substitutions R187S/F264C/D370Y. Crystal structures of Hyb-S4M94 with bound substrate suggested that catalytic function for Ald was improved by hydrogen-bonding/hydrophobic interactions between the Ald--COOH and Tyr370, a hydrogen-bonding network from Ser187 to Ald--NH(3) (+), and interaction between Ald--NH(3) (+) and Gln27-O(epsilon) derived from another subunit in the homo-dimeric structure. In wild-type Ald-hydrolase (NylB), Ald-hydrolytic activity is thought to be optimized by the substitutions G181D/H266N, which improve an electrostatic interaction with Ald--NH(3) (+) (Kawashima et al., FEBS J 2009; 276:2547-2556). We propose here that there exist at least two alternative modes for optimizing the Ald-hydrolytic activity of a carboxylesterase with a beta-lactamase fold.
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Affiliation(s)
- Taku Ohki
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Hyogo 671-2280, Japan
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18
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Kato DI, Miyamoto K, Ohta H. Preparation of optically active 4-chlorophenylalanine from its racemate by deracemization technique using transformantEscherichia colicells. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500296295] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Kato DI, Teruya K, Yoshida H, Takeo M, Negoro S, Ohta H. New application of firefly luciferase − it can catalyze the enantioselective thioester formation of 2-arylpropanoic acid. FEBS J 2007; 274:3877-85. [PMID: 17617223 DOI: 10.1111/j.1742-4658.2007.05921.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We introduce a new application of firefly luciferase (EC 1.13.12.7). The firefly luciferases belong to a large superfamily that includes rat liver long-chain acyl-CoA synthetase (LACS1). LACS1 is the enzyme that is involved in the deracemization process of 2-arylpropanoic acid and catalyzes the enantioselective thioester formation of R-acids. Based on the similarity of the reaction mechanisms and the sequences between firefly luciferase and LACS1, we predicted that firefly luciferase also has thioesterification activity toward 2-arylpropanoic acid. From an investigation using three kinds of luciferases from North American firefly and Japanese fireflies, we have confirmed that these luciferases exhibit an enantioselective thioester formation activity and the R-form is transformed to a thioester in preference to the S-form in the presence of ATP, Mg(2+), and CoASH. The enantiomeric excesses of unreacted recovered acid and thioester were determined by chiral phase HPLC analysis and the resulting 2-arylpropanoyl-CoAs were identified by high resolution mass spectroscopy. The K(m) and k(cat) values of thermostable luciferase from Luciola lateralis (LUC-H) toward ketoprofen were determined as 0.22 mM and 0.11 s(-1), respectively. The affinity of ketoprofen was almost the same of d-luciferin. In addition, the calculated E-value toward ketoprofen was approximately 20. These results suggest that LUC-H could catalyze the kinetic resolution of 2-arylpropanoic acid efficiently and would be a new option for the preparation of optically active 2-substituted carboxylic acids.
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Affiliation(s)
- Dai-Ichiro Kato
- Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan.
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20
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Takeo M, Prabu SK, Kitamura C, Hirai M, Takahashi H, Kato DI, Negoro S. Characterization of alkylphenol degradation gene cluster in Pseudomonas putida MT4 and evidence of oxidation of alkylphenols and alkylcatechols with medium-length alkyl chain. J Biosci Bioeng 2006; 102:352-61. [PMID: 17116584 DOI: 10.1263/jbb.102.352] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Accepted: 07/25/2006] [Indexed: 11/17/2022]
Abstract
Alkylphenols (APs) are ubiquitous contaminants in aquatic environments and have endocrine disrupting and toxic effects on aquatic organisms. To investigate biodegradation mechanisms of APs, an AP degradation gene cluster was cloned from a butylphenol (BP)-degrading bacterium, Pseudomonas putida MT4. The gene cluster consisted of 13 genes named bupBA1A2A3A4A5A6CEHIFG. From the nucleotide sequences, bupA1A2A3A4A5A6 were predicted to encode a multicomponent phenol hydroxylase (PH), whereas bupBCEHIFG were expected to encode meta-cleavage pathway enzymes. A partial sequence of a putative NtrC-type regulatory gene, bupR, was also found upstream of the gene bupB. This result indicates that APs can be initially oxidized into alkylcatechols (ACs), followed by the meta-cleavage of the aromatic rings. To confirm this pathway, AP degradation tests were carried out using the recombinant P. putida KT2440 harboring the PH genes (bupA1A2A3A4A5A6). The recombinant strain oxidized 4-n-APs with an alkyl chain of up to C7 (< or = C7) efficiently and also several BPs including those with an alkyl chain with some degree of branching. Therefore, it was found that PH had a broad substrate specificity for APs with a medium-length alkyl chain (C3-C7). Moreover, the cell extract of a recombinant Escherichia coli harboring bupB (a catechol 2,3-dioxygenase gene) converted 4-n-ACs with an alkyl chain of < or = C9 into yellow meta-cleavage products with a maximum absorbance at 379 nm, indicating that the second step enzyme in this pathway is also responsible for the degradation of ACs with a medium-length alkyl chain. These results suggest that MT4 is a very useful strain in the biodegradation of a wide range of APs with a medium-length alkyl chain, which known nonylphenol-degrading Sphingomonas strains have never degraded.
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Affiliation(s)
- Masahiro Takeo
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2201, Japan.
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