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Kato K, Hamaguchi T, Kumazawa M, Nakajima Y, Ifuku K, Hirooka S, Hirose Y, Miyagishima SY, Suzuki T, Kawakami K, Dohmae N, Yonekura K, Shen JR, Nagao R. The structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs. Proc Natl Acad Sci U S A 2024; 121:e2319658121. [PMID: 38442179 PMCID: PMC10945839 DOI: 10.1073/pnas.2319658121] [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: 11/08/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the species of organisms. However, the structural and evolutionary correlations of red-lineage LHCs are unknown. Here, we determined a 1.92-Å resolution cryoelectron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga Cyanidium caldarium RK-1 (NIES-2137), which is an important taxon in the Cyanidiophyceae. We subsequently investigated the correlations of PSI-LHCIs from different organisms through structural comparisons and phylogenetic analysis. The PSI-LHCI structure obtained shows five LHCI subunits surrounding a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in the red-lineage algae showed clear orthology of LHCs between C. caldarium and Cyanidioschyzon merolae, whereas no orthologous relationships were found between C. caldarium Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.
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Affiliation(s)
- Koji Kato
- Division of Photosynthesis and Structural Biology, Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama700-8530, Japan
| | - Tasuku Hamaguchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi980-8577, Japan
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo679-5148, Japan
| | - Minoru Kumazawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Yoshiki Nakajima
- Division of Photosynthesis and Structural Biology, Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama700-8530, Japan
| | - Kentaro Ifuku
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka411-8540, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Aichi441-8580, Japan
| | - Shin-ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka411-8540, Japan
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Shizuoka411-8540, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Saitama351-0198, Japan
| | - Keisuke Kawakami
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo679-5148, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Saitama351-0198, Japan
| | - Koji Yonekura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi980-8577, Japan
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo679-5148, Japan
| | - Jian-Ren Shen
- Division of Photosynthesis and Structural Biology, Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama700-8530, Japan
| | - Ryo Nagao
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, Shizuoka422-8529, Japan
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Yamamoto K, Tochikawa S, Miura Y, Matsunobu S, Hirose Y, Eki T. Sensing chemical-induced DNA damage using CRISPR/Cas9-mediated gene-deletion yeast-reporter strains. Appl Microbiol Biotechnol 2024; 108:188. [PMID: 38300351 PMCID: PMC10834598 DOI: 10.1007/s00253-024-13020-w] [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: 07/28/2023] [Revised: 01/09/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
Microorganism-based genotoxicity assessments are vital for evaluating potential chemical-induced DNA damage. In this study, we developed both chromosomally integrated and single-copy plasmid-based reporter assays in budding yeast using a RNR3 promoter-driven luciferase gene. These assays were designed to compare the response to genotoxic chemicals with a pre-established multicopy plasmid-based assay. Despite exhibiting the lowest luciferase activity, the chromosomally integrated reporter assay showed the highest fold induction (i.e., the ratio of luciferase activity in the presence and absence of the chemical) compared with the established plasmid-based assay. Using CRISPR/Cas9 technology, we generated mutants with single- or double-gene deletions, affecting major DNA repair pathways or cell permeability. This enabled us to evaluate reporter gene responses to genotoxicants in a single-copy plasmid-based assay. Elevated background activities were observed in several mutants, such as mag1Δ cells, even without exposure to chemicals. However, substantial luciferase induction was detected in single-deletion mutants following exposure to specific chemicals, including mag1Δ, mms2Δ, and rad59Δ cells treated with methyl methanesulfonate; rad59Δ cells exposed to camptothecin; and mms2Δ and rad10Δ cells treated with mitomycin C (MMC) and cisplatin (CDDP). Notably, mms2Δ/rad10Δ cells treated with MMC or CDDP exhibited significantly enhanced luciferase induction compared with the parent single-deletion mutants, suggesting that postreplication and for nucleotide excision repair processes predominantly contribute to repairing DNA crosslinks. Overall, our findings demonstrate the utility of yeast-based reporter assays employing strains with multiple-deletion mutations in DNA repair genes. These assays serve as valuable tools for investigating DNA repair mechanisms and assessing chemical-induced DNA damage. KEY POINTS: • Responses to genotoxic chemicals were investigated in three types of reporter yeast. • Yeast strains with single- and double-deletions of DNA repair genes were tested. • Two DNA repair pathways predominantly contributed to DNA crosslink repair in yeast.
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Affiliation(s)
- Kosuke Yamamoto
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Shintaro Tochikawa
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Yuuki Miura
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Shogo Matsunobu
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Yuu Hirose
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
- Laboratory of Genomics and Photobiology, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Toshihiko Eki
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan.
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Shichinohe M, Ohkawa S, Hirose Y, Eki T. Sensing chemical-induced genotoxicity and oxidative stress via yeast-based reporter assays using NanoLuc luciferase. PLoS One 2023; 18:e0294571. [PMID: 37992069 PMCID: PMC10664910 DOI: 10.1371/journal.pone.0294571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/03/2023] [Accepted: 11/04/2023] [Indexed: 11/24/2023] Open
Abstract
Mutagens and oxidative agents damage biomolecules, such as DNA; therefore, detecting genotoxic and oxidative chemicals is crucial for maintaining human health. To address this, we have developed several types of yeast-based reporter assays designed to detect DNA damage and oxidative stress. This study aimed to develop a novel yeast-based assay using a codon-optimized stable or unstable NanoLuc luciferase (yNluc and yNluCP) gene linked to a DNA damage- or oxidative stress-responsive promoter, enabling convenient sensing genotoxicity or oxidative stress, respectively. End-point luciferase assays using yeasts with a chromosomally integrated RNR3 promoter (PRNR3)-driven yNluc gene exhibited high levels of chemiluminescence via NanoLuc luciferase and higher fold induction by hydroxyurea than a multi-copy plasmid-based assay. Additionally, the integrated reporter system detected genotoxicity caused by four different types of chemicals. Oxidants (hydrogen peroxide, tert-butyl hydroperoxide, and menadione) were successfully detected through transient expressions of luciferase activity in real-time luciferase assay using yeasts with a chromosomally integrated TRX2 promoter (PTRX2)-linked yNlucCP gene. However, the luciferase activity was gradually induced in yeasts with a multi-copy reporter plasmid, and their expression profiles were notably distinct from those observed in chromosomally integrated yeasts. The responses of yNlucCP gene against three oxidative chemicals, but not diamide and zinc oxide suspension, were observed using chromosomally integrated reporter yeasts. Given that yeast cells with chromosomally integrated PRNR3-linked yNluc and PTRX2-linked yNlucCP genes express strong chemiluminescence signals and are easily maintained and handled without restrictive nutrient medium, these yeast strains with NanoLuc reporters may prove useful for screening potential genotoxic and oxidative chemicals.
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Affiliation(s)
| | - Shun Ohkawa
- Molecular Genetics Laboratory, Toyohashi, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Laboratory of Genomics and Photobiology, Toyohashi University of Technology, Toyohashi, Aichi, Japan
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Kenmotsu H, Masuma T, Murakami J, Hirose Y, Eki T. Distinct prokaryotic and eukaryotic communities and networks in two agricultural fields of central Japan with different histories of maize-cabbage rotation. Sci Rep 2023; 13:15435. [PMID: 37723228 PMCID: PMC10507100 DOI: 10.1038/s41598-023-42291-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/02/2023] [Accepted: 09/07/2023] [Indexed: 09/20/2023] Open
Abstract
Crop rotation is an important agricultural practice for homeostatic crop cultivation. Here, we applied high-throughput sequencing of ribosomal RNA gene amplicons to investigate soil biota in two fields of central Japan with different histories of maize-cabbage rotation. We identified 3086 eukaryotic and 17,069 prokaryotic sequence variants (SVs) from soil samples from two fields rotating two crops at three different growth stages. The eukaryotic and prokaryotic communities in the four sample groups of two crops and two fields were clearly distinguished using β-diversity analysis. Redundancy analysis showed the relationships of the communities in the fields to pH and nutrient, humus, and/or water content. The complexity of eukaryotic and prokaryotic networks was apparently higher in the cabbage-cultivated soils than those in the maize-cultivated soils. The node SVs (nSVs) of the networks were mainly derived from two eukaryotic phyla: Ascomycota and Cercozoa, and four prokaryotic phyla: Pseudomonadota, Acidobacteriota, Actinomycetota, and Gemmatimonadota. The networks were complexed by cropping from maize to cabbage, suggesting the formation of a flexible network under crop rotation. Ten out of the 16 eukaryotic nSVs were specifically found in the cabbage-cultivated soils were derived from protists, indicating the potential contribution of protists to the formation of complex eukaryotic networks.
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Affiliation(s)
- Harutaro Kenmotsu
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan
| | - Tomoro Masuma
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan
| | - Junya Murakami
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan
- Research Center for Agrotechnology and Biotechnology, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan.
- Research Center for Agrotechnology and Biotechnology, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan.
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Valenta J, Tsujii N, Yamaoka H, Honda F, Hirose Y, Sakurai H, Terada N, Naka T, Nakane T, Koizumi T, Ishii H, Hiraoka N, Mori T. Unusually strong electronic correlation and field-induced ordered phase in YbCo 2. J Phys Condens Matter 2023; 35:285601. [PMID: 37015243 DOI: 10.1088/1361-648x/acca5a] [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] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
We report the first study of electrical resistivity, magnetization, and specific heat on YbCo2. The measurements on a single-phased sample of YbCo2bring no evidence of magnetic ordering down to 0.3 K in a zero magnetic field. The manifestations of low Kondo temperature are observed. The specific heat value divided by temperature,C/T, keeps increasing logarithmically beyond 7 J/mol K2with decreasing temperature down to 0.3 K without no sign of magnetic ordering, suggesting a very large electronic specific heat. Analysis of the magnetic specific heat indicates that the large portion of the low-temperature specific heat is not explained simply by the low Kondo temperature but is due to the strong intersite magnetic correlation in both the 3dand 4felectrons. Temperature-dependent measurements under static magnetic fields up to 7 T are carried out, which show the evolution of field-induced transition above 2 T. The transition temperature increases with increasing field, pointing to a ferromagnetic character. The extrapolation of the transition temperature to zero field suggests that YbCo2is in the very proximity of the quantum critical point. These results indicate that in the unique case of YbCo2, the itinerant electron magnetism of Co 3d-electrons and the Kondo effect within the vicinity of quantum criticality of Yb 4f-local moments can both play a role.
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Affiliation(s)
- J Valenta
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki, 305-0047, Japan
| | - N Tsujii
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki, 305-0047, Japan
| | - H Yamaoka
- RIKEN Spring-8 Center, Sayo, Hyogo 679-5148, Japan
| | - F Honda
- Institute for Materials Research, Tohoku University, Ōarai, Ibaraki 311-1313, Japan
- Central Institute of Radioisotope Science and Safety, Kyushu University, Fukuoka 819-0395, Japan
| | - Y Hirose
- Department of Physics, Niigata University, Niigata 950-2181, Japan
| | - H Sakurai
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki, 305-0047, Japan
| | - N Terada
- Research Center for Magnetic and Spintronic Materials, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
| | - T Naka
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki, 305-0047, Japan
| | - T Nakane
- Research Center for Electronic and Optical Materials, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047, Japan
| | - T Koizumi
- Institute for Materials Research, Tohoku University, Ōarai, Ibaraki 311-1313, Japan
- Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - H Ishii
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - N Hiraoka
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - T Mori
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki, 305-0047, Japan
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Maruyama J, Inoue H, Hirose Y, Nakabachi A. 16S rRNA Gene Sequencing of Six Psyllid Species of the Family Carsidaridae Identified Various Bacteria Including Symbiopectobacterium. Microbes Environ 2023; 38:ME23045. [PMID: 37612118 PMCID: PMC10522848 DOI: 10.1264/jsme2.me23045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Received: 05/15/2023] [Accepted: 06/23/2023] [Indexed: 08/25/2023] Open
Abstract
Psyllids (Hemiptera: Sternorrhyncha: Psylloidea) are plant sap-sucking insects that are closely associated with various microbes. To obtain a more detailed understanding of the ecological and evolutionary behaviors of microbes in Psylloidea, the bacterial populations of six psyllid species, belonging to the family Carsidaridae, were analyzed using high-throughput amplicon sequencing of the 16S rRNA gene. The majority of the secondary symbionts identified in the present study were gammaproteobacteria, particularly those of the order Enterobacterales, including Arsenophonus and Sodalis, which are lineages found in a wide variety of insect hosts. Additionally, Symbiopectobacterium, another Enterobacterales lineage, which has recently been recognized and increasingly shown to be vertically transmitted and mutualistic in various invertebrates, was identified for the first time in Psylloidea. This lineage is closely related to Pectobacterium spp., which are plant pathogens, but forms a distinct clade exhibiting no pathogenicity to plants. Non-Enterobacterales gammaproteobacteria found in the present study were Acinetobacter, Pseudomonas (both Pseudomonadales), Delftia, Comamonas (both Burkholderiales), and Xanthomonas (Xanthomonadales), a putative plant pathogen. Regarding alphaproteobacteria, three Wolbachia (Rickettsiales) lineages belonging to supergroup B, the major group in insect lineages, were detected in four psyllid species. In addition, a Wolbachia lineage of supergroup O, a minor group recently found for the first time in Psylloidea, was detected in one psyllid species. These results suggest the pervasive transfer of bacterial symbionts among animals and plants, providing deeper insights into the evolution of the interactions among these organisms.
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Affiliation(s)
- Junnosuke Maruyama
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441–8580, Japan
| | - Hiromitsu Inoue
- Institute for Plant Protection, National Agriculture and Food Research Organization, Higashihiroshima, Hiroshima 739–2494, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441–8580, Japan
| | - Atsushi Nakabachi
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441–8580, Japan
- Research Institute for Technological Science and Innovation, Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441–8580, Japan
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Meng L, Xie L, Hirose Y, Nishiuchi T, Yoshida N. Reduced graphene oxide increases cells with enlarged outer membrane of Citrifermentans bremense and exopolysaccharides secretion. Biosens Bioelectron 2022; 218:114754. [DOI: 10.1016/j.bios.2022.114754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022]
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Otsu T, Eki T, Hirose Y. A hybrid type of chromatic acclimation regulated by the dual green/red photosensory systems in cyanobacteria. Plant Physiol 2022; 190:779-793. [PMID: 35751608 PMCID: PMC9434153 DOI: 10.1093/plphys/kiac284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacteria are phototrophic bacteria that perform oxygenic photosynthesis. They use a supermolecular light-harvesting antenna complex, the phycobilisome (PBS), to capture and transfer light energy to photosynthetic reaction centers. Certain cyanobacteria alter the absorption maxima and/or overall structure of their PBSs in response to the ambient light wavelength-a process called chromatic acclimation (CA). One of the most well-known CA types is the response to green and red light, which is controlled by either the RcaEFC or CcaSR photosensory system. Here, we characterized a hybrid type of CA in the cyanobacterium Pleurocapsa sp. Pasteur Culture Collection (PCC) 7319 that uses both RcaEFC and CcaSR systems. In vivo spectroscopy suggested that strain PCC 7319 alters the relative composition of green-absorbing phycoerythrin and red-absorbing phycocyanin in the PBS. RNA sequencing and promoter motif analyses suggested that the RcaEFC system induces a gene operon for phycocyanin under red light, whereas the CcaSR system induces a rod-membrane linker gene under green light. Induction of the phycoerythrin genes under green light may be regulated through a yet unidentified photosensory system called the Cgi system. Spectroscopy analyses of the isolated PBSs suggested that hemidiscoidal and rod-shaped PBSs enriched with phycoerythrin were produced under green light, whereas only hemidiscoidal PBSs enriched with phycocyanin were produced under red light. PCC 7319 uses the RcaEFC and CcaSR systems to regulate absorption of green or red light (CA3) and the amount of rod-shaped PBSs (CA1), respectively. Cyanobacteria can thus flexibly combine diverse CA types to acclimate to different light environments.
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Affiliation(s)
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Tempaku, Toyohashi, Aichi 441-8580, Japan
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Ohtsubo Y, Hirose Y, Nagata Y. Algorisms used for in silico finishing of bacterial genomes based on short-read assemblage implemented in GenoFinisher, AceFileViewer, and ShortReadManager. Biosci Biotechnol Biochem 2022; 86:693-703. [PMID: 35425950 DOI: 10.1093/bbb/zbac032] [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: 01/12/2022] [Accepted: 02/26/2022] [Indexed: 11/13/2022]
Abstract
In these days, for bacterial genome sequence determination, ultralong reads with homopolymeric troubles are used in combinations with short reads, resulting in genomic sequences with possible incorrect uniformity of repeat sequences. We have been determining complete bacterial genomic sequences based on NGS short reads and Newbler assemblage by utilizing functions implemented in 3 software GenoFinisher, AceFileViewer, and ShortReadManager without conducting additional experiments for gap closing, proving the concept that NGS short reads enclose enough information to determine complete genome sequences. Although some manual in silico tasks are to be conducted, they will ultimately be solved in a single pipeline. In this review, we describe the tools and implemented ideas that have enabled complete sequence determination solely based on short reads, which would be useful for establishing the basis for the future development of a short-read-based assembler that enables complete and accurate genome sequence determination at a lower cost.
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Affiliation(s)
- Yoshiyuki Ohtsubo
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarogaoka, Tenpaku, Toyohashi, Japan
| | - Yuji Nagata
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, Japan
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Nakane D, Enomoto G, Bähre H, Hirose Y, Wilde A, Nishizaka T. Thermosynechococcus switches the direction of phototaxis by a c-di-GMP-dependent process with high spatial resolution. eLife 2022; 11:73405. [PMID: 35535498 PMCID: PMC9090330 DOI: 10.7554/elife.73405] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 08/27/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Many cyanobacteria, which use light as an energy source via photosynthesis, show directional movement towards or away from a light source. However, the molecular and cell biological mechanisms for switching the direction of movement remain unclear. Here, we visualized type IV pilus-dependent cell movement in the rod-shaped thermophilic cyanobacterium Thermosynechococcus vulcanus using optical microscopy at physiological temperature and light conditions. Positive and negative phototaxis were controlled on a short time scale of 1 min. The cells smoothly moved over solid surfaces towards green light, but the direction was switched to backward movement when we applied additional blue light illumination. The switching was mediated by three photoreceptors, SesA, SesB, and SesC, which have cyanobacteriochrome photosensory domains and synthesis/degradation activity of the bacterial second messenger cyclic dimeric GMP (c-di-GMP). Our results suggest that the decision-making process for directional switching in phototaxis involves light-dependent changes in the cellular concentration of c-di-GMP. Direct visualization of type IV pilus filaments revealed that rod-shaped cells can move perpendicular to the light vector, indicating that the polarity can be controlled not only by pole-to-pole regulation but also within-a-pole regulation. This study provides insights into previously undescribed rapid bacterial polarity regulation via second messenger signalling with high spatial resolution.
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Affiliation(s)
- Daisuke Nakane
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Tokyo, Japan
| | - Gen Enomoto
- Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Heike Bähre
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Japan
| | - Annegret Wilde
- Institute of Biology III, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
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Murakami T, Takeuchi N, Mori H, Hirose Y, Edwards A, Irvine-Fynn T, Li Z, Ishii S, Segawa T. Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light-harvesting mechanisms in glacier cryoconite. Microbiome 2022; 10:50. [PMID: 35317857 PMCID: PMC8941735 DOI: 10.1186/s40168-022-01238-7] [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] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Cryoconite granules are mineral-microbial aggregates found on glacier surfaces worldwide and are hotspots of biogeochemical reactions in glacier ecosystems. However, despite their importance within glacier ecosystems, the geographical diversity of taxonomic assemblages and metabolic potential of cryoconite communities around the globe remain unclear. In particular, the genomic content of cryoconite communities on Asia's high mountain glaciers, which represent a substantial portion of Earth's ice masses, has rarely been reported. Therefore, in this study, to elucidate the taxonomic and ecological diversities of cryoconite bacterial consortia on a global scale, we conducted shotgun metagenomic sequencing of cryoconite acquired from a range of geographical areas comprising Polar (Arctic and Antarctic) and Asian alpine regions. RESULTS Our metagenomic data indicate that compositions of both bacterial taxa and functional genes are particularly distinctive for Asian cryoconite. Read abundance of the genes responsible for denitrification was significantly more abundant in Asian cryoconite than the Polar cryoconite, implying that denitrification is more enhanced in Asian glaciers. The taxonomic composition of Cyanobacteria, the key primary producers in cryoconite communities, also differs between the Polar and Asian samples. Analyses on the metagenome-assembled genomes and fluorescence emission spectra reveal that Asian cryoconite is dominated by multiple cyanobacterial lineages possessing phycoerythrin, a green light-harvesting component for photosynthesis. In contrast, Polar cryoconite is dominated by a single cyanobacterial species Phormidesmis priestleyi that does not possess phycoerythrin. These findings suggest that the assemblage of cryoconite bacterial communities respond to regional- or glacier-specific physicochemical conditions, such as the availability of nutrients (e.g., nitrate and dissolved organic carbon) and light (i.e., incident shortwave radiation). CONCLUSIONS Our genome-resolved metagenomics provides the first characterization of the taxonomic and metabolic diversities of cryoconite from contrasting geographical areas, highlighted by the distinct light-harvesting approaches of Cyanobacteria and nitrogen utilization between Polar and Asian cryoconite, and implies the existence of environmental controls on the assemblage of cryoconite communities. These findings deepen our understanding of the biodiversity and biogeochemical cycles of glacier ecosystems, which are susceptible to ongoing climate change and glacier decline, on a global scale. Video abstract.
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Affiliation(s)
- Takumi Murakami
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | - Nozomu Takeuchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba, Japan
| | - Hiroshi Mori
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Aichi, Japan
| | - Arwyn Edwards
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology, Aberystwyth University, Aberystwyth, UK
| | - Tristram Irvine-Fynn
- Interdisciplinary Centre for Environmental Microbiology, Aberystwyth University, Aberystwyth, UK
- Department of Geography and Earth Sciences, Aberystwyth University, Aberystwyth, UK
| | - Zhongqin Li
- State Key Laboratory of Cryospheric Sciences/Tien Shan Glaciological Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Satoshi Ishii
- Department of Soil, Water and Climate, University of Minnesota, St. Paul, MN USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN USA
| | - Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Yamanashi, Japan
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12
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Okuda Y, Miyoshi R, Kamo T, Fujisawa T, Nagae T, Mishima M, Eki T, Hirose Y, Unno M. Raman Spectroscopy of an Atypical C15-E,syn Bilin Chromophore in Cyanobacteriochrome RcaE. J Phys Chem B 2022; 126:813-821. [DOI: 10.1021/acs.jpcb.1c09652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuji Okuda
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Risako Miyoshi
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takanari Kamo
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takayuki Nagae
- Synchrotron Radiation Research Center, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Masaki Mishima
- Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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13
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Nakabachi A, Inoue H, Hirose Y. Microbiome analyses of 12 psyllid species of the family Psyllidae identified various bacteria including Fukatsuia and Serratia symbiotica, known as secondary symbionts of aphids. BMC Microbiol 2022; 22:15. [PMID: 34996376 PMCID: PMC8740488 DOI: 10.1186/s12866-021-02429-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 01/04/2023] Open
Abstract
Background Psyllids (Hemiptera: Psylloidea) comprise a group of plant sap-sucking insects that includes important agricultural pests. They have close associations not only with plant pathogens, but also with various microbes, including obligate mutualists and facultative symbionts. Recent studies are revealing that interactions among such bacterial populations are important for psyllid biology and host plant pathology. In the present study, to obtain further insight into the ecological and evolutionary behaviors of bacteria in Psylloidea, we analyzed the microbiomes of 12 psyllid species belonging to the family Psyllidae (11 from Psyllinae and one from Macrocorsinae), using high-throughput amplicon sequencing of the 16S rRNA gene. Results The analysis showed that all 12 psyllids have the primary symbiont, Candidatus Carsonella ruddii (Gammaproteobacteria: Oceanospirillales), and at least one secondary symbiont. The majority of the secondary symbionts were gammaproteobacteria, especially those of the family Enterobacteriaceae (order: Enterobacteriales). Among them, symbionts belonging to “endosymbionts3”, which is a genus-level monophyletic group assigned by the SILVA rRNA database, were the most prevalent and were found in 9 of 11 Psyllinae species. Ca. Fukatsuia symbiotica and Serratia symbiotica, which were recognized only as secondary symbionts of aphids, were also identified. In addition to other Enterobacteriaceae bacteria, including Arsenophonus, Sodalis, and “endosymbionts2”, which is another genus-level clade, Pseudomonas (Pseudomonadales: Pseudomonadaceae) and Diplorickettsia (Diplorickettsiales: Diplorickettsiaceae) were identified. Regarding Alphaproteobacteria, the potential plant pathogen Ca. Liberibacter europaeus (Rhizobiales: Rhizobiaceae) was detected for the first time in Anomoneura mori (Psyllinae), a mulberry pest. Wolbachia (Rickettsiales: Anaplasmataceae) and Rickettsia (Rickettsiales: Rickettsiaceae), plausible host reproduction manipulators that are potential tools to control pest insects, were also detected. Conclusions The present study identified various bacterial symbionts including previously unexpected lineages in psyllids, suggesting considerable interspecific transfer of arthropod symbionts. The findings provide deeper insights into the evolution of interactions among insects, bacteria, and plants, which may be exploited to facilitate the control of pest psyllids in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02429-2.
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Affiliation(s)
- Atsushi Nakabachi
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan. .,Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan.
| | - Hiromitsu Inoue
- Institute for Plant Protection, National Agriculture and Food Research Organization, Higashihiroshima, Hiroshima, 739-2494, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan
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14
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Nakabachi A, Inoue H, Hirose Y. High-resolution Microbiome Analyses of Nine Psyllid Species of the Family Triozidae Identified Previously Unrecognized but Major Bacterial Populations, including Liberibacter and Wolbachia of Supergroup O. Microbes Environ 2022; 37:ME22078. [PMID: 36476840 PMCID: PMC9763047 DOI: 10.1264/jsme2.me22078] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Psyllids (Hemiptera: Sternorrhyncha: Psylloidea) are plant sap-sucking insects that include important agricultural pests. To obtain insights into the ecological and evolutionary behaviors of microbes, including plant pathogens, in Psylloidea, high-resolution ana-lyses of the microbiomes of nine psyllid species belonging to the family Triozidae were performed using high-throughput amplicon sequencing of the 16S rRNA gene. Analyses identified various bacterial populations, showing that all nine psyllids have at least one secondary symbiont, along with the primary symbiont "Candidatus Carsonella ruddii" (Gammaproteobacteria: Oceanospirillales: Halomonadaceae). The majority of the secondary symbionts were gammaproteobacteria, particularly those of the order Enterobacterales, which included Arsenophonus and Serratia symbiotica, a bacterium formerly recognized only as a secondary symbiont of aphids (Hemiptera: Sternorrhyncha: Aphidoidea). The non-Enterobacterales gammaproteobacteria identified in the present study were Diplorickettsia (Diplorickettsiales: Diplorickettsiaceae), a potential human pathogen, and Carnimonas (Oceanospirillales: Halomonadaceae), a lineage detected for the first time in Psylloidea. Regarding alphaproteobacteria, the potential plant pathogen "Ca. Liberibacter europaeus" (Rhizobiales: Rhizobiaceae) was detected for the first time in Epitrioza yasumatsui, which feeds on the Japanese silverberry Elaeagnus umbellata (Elaeagnaceae), an aggressive invasive plant in the United States and Europe. Besides the detection of Wolbachia (Rickettsiales: Anaplasmataceae) of supergroup B in three psyllid species, a lineage belonging to supergroup O was identified for the first time in Psylloidea. These results suggest the rampant transfer of bacterial symbionts among animals and plants, thereby providing deeper insights into the evolution of interkingdom interactions among multicellular organisms and bacteria, which will facilitate the control of pest psyllids.
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Affiliation(s)
- Atsushi Nakabachi
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441–8580, Japan,Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441–8580, Japan, Corresponding author. E-mail: ; Tel: +81–532–44–6901
| | - Hiromitsu Inoue
- Institute for Plant Protection, National Agriculture and Food Research Organization, Higashihiroshima, Hiroshima 739–2494, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441–8580, Japan
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15
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Kenmotsu H, Takabayashi E, Takase A, Hirose Y, Eki T. Use of universal primers for the 18S ribosomal RNA gene and whole soil DNAs to reveal the taxonomic structures of soil nematodes by high-throughput amplicon sequencing. PLoS One 2021; 16:e0259842. [PMID: 34780544 PMCID: PMC8592498 DOI: 10.1371/journal.pone.0259842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/28/2021] [Indexed: 12/04/2022] Open
Abstract
Nematodes are abundant metazoans that play crucial roles in nutrient recycle in the pedosphere. Although high-throughput amplicon sequencing is a powerful tool for the taxonomic profiling of soil nematodes, polymerase chain reaction (PCR) primers for amplification of the 18S ribosomal RNA (SSU) gene and preparation of template DNAs have not been sufficiently evaluated. We investigated nematode community structure in copse soil using four nematode-specific (regions 1–4) and two universal (regions U1 and U2) primer sets for the SSU gene regions with two DNAs prepared from copse-derived mixed nematodes and whole soil. The major nematode-derived sequence variants (SVs) identified in each region was detected in both template DNAs. Order level taxonomy and feeding type of identified nematode-derived SVs were distantly related between the two DNA preparations, and the region U2 was closely related to region 4 in the non-metric multidimensional scaling (NMDS) based on Bray-Curtis dissimilarity. Thus, the universal primers for region U2 could be used to analyze soil nematode communities. We further applied this method to analyze the nematodes living in two sampling sites of a sweet potato-cultivated field, where the plants were differently growing. The structure of nematode-derived SVs from the two sites was distantly related in the principal coordinate analysis (PCoA) with weighted unifrac distances, suggesting their distinct soil environments. The resultant ecophysiological status of the nematode communities in the copse and field on the basis of feeding behavior and maturity indices was fairly consistent with those of the copse- and the cultivated house garden-derived nematodes in prior studies. These findings will be useful for the DNA metabarcoding of soil eukaryotes, including nematodes, using soil DNAs.
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Affiliation(s)
- Harutaro Kenmotsu
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Emi Takabayashi
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Akinori Takase
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Yuu Hirose
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, Japan
- Research Center for Agrotechnology and Biotechnology, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Toshihiko Eki
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, Japan
- Research Center for Agrotechnology and Biotechnology, Toyohashi University of Technology, Toyohashi, Aichi, Japan
- * E-mail:
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16
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Hirose Y, Ohtsubo Y, Misawa N, Yonekawa C, Nagao N, Shimura Y, Fujisawa T, Kanesaki Y, Katoh H, Katayama M, Yamaguchi H, Yoshikawa H, Ikeuchi M, Eki T, Nakamura Y, Kawachi M. Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade. DNA Res 2021; 28:6408441. [PMID: 34677568 PMCID: PMC8634303 DOI: 10.1093/dnares/dsab024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 09/25/2021] [Accepted: 10/19/2021] [Indexed: 12/03/2022] Open
Abstract
Cyanobacteria are a diverse group of Gram-negative prokaryotes that perform oxygenic photosynthesis. Cyanobacteria have been used for research on photosynthesis and have attracted attention as a platform for biomaterial/biofuel production. Cyanobacteria are also present in almost all habitats on Earth and have extensive impacts on global ecosystems. Given their biological, economical, and ecological importance, the number of high-quality genome sequences for Cyanobacteria strains is limited. Here, we performed genome sequencing of Cyanobacteria strains in the National Institute for Environmental Studies microbial culture collection in Japan. We sequenced 28 strains that can form a heterocyst, a morphologically distinct cell that is specialized for fixing nitrogen, and 3 non-heterocystous strains. Using Illumina sequencing of paired-end and mate-pair libraries with in silico finishing, we constructed highly contiguous assemblies. We determined the phylogenetic relationship of the sequenced genome assemblies and found potential difficulties in the classification of certain heterocystous clades based on morphological observation. We also revealed a bias on the sequenced strains by the phylogenetic analysis of the 16S rRNA gene including unsequenced strains. Genome sequencing of Cyanobacteria strains deposited in worldwide culture collections will contribute to understanding the enormous genetic and phenotypic diversity within the phylum Cyanobacteria.
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Affiliation(s)
- Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tenpaku, Toyohashi, Aichi, 441-8580, Japan
| | - Yoshiyuki Ohtsubo
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi, 980-0812, Japan
| | - Naomi Misawa
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tenpaku, Toyohashi, Aichi, 441-8580, Japan
| | - Chinatsu Yonekawa
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tenpaku, Toyohashi, Aichi, 441-8580, Japan
| | - Nobuyoshi Nagao
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tenpaku, Toyohashi, Aichi, 441-8580, Japan
| | - Yohei Shimura
- Biodiversity Division, National Institute for Environmental Studies, 16-1 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Takatomo Fujisawa
- Department of Informatics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, 836 Oya, Suruga, Shizuoka, Shizuoka, 422-8529, Japan
| | - Hiroshi Katoh
- Advanced Science Research Promotion Center, Mie University, 1577 Kurima, Tsu, Mie, 514-8507, Japan
| | - Mitsunori Katayama
- College of Industrial Technology, Nihon University, 1-2-1 Izumi, Narashino, Chiba, 275-8575, Japan
| | - Haruyo Yamaguchi
- Biodiversity Division, National Institute for Environmental Studies, 16-1 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tenpaku, Toyohashi, Aichi, 441-8580, Japan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, 16-1 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
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Nakabachi A, Piel J, Malenovský I, Hirose Y. Comparative Genomics Underlines Multiple Roles of Profftella, an Obligate Symbiont of Psyllids: Providing Toxins, Vitamins, and Carotenoids. Genome Biol Evol 2021; 12:1975-1987. [PMID: 32797185 PMCID: PMC7643613 DOI: 10.1093/gbe/evaa175] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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] [Accepted: 08/11/2020] [Indexed: 12/27/2022] Open
Abstract
The Asian citrus psyllid Diaphorina citri (Insecta: Hemiptera: Psylloidea), a serious pest of citrus species worldwide, harbors vertically transmitted intracellular mutualists, Candidatus Profftella armatura (Profftella_DC, Gammaproteobacteria: Burkholderiales) and Candidatus Carsonella ruddii (Carsonella_DC, Gammaproteobacteria: Oceanospirillales). Whereas Carsonella_DC is a typical nutritional symbiont, Profftella_DC is a unique defensive symbiont with organelle-like features, including intracellular localization within the host, perfect infection in host populations, vertical transmission over evolutionary time, and drastic genome reduction down to much less than 1 Mb. Large parts of the 460-kb genome of Profftella_DC are devoted to genes for synthesizing a polyketide toxin; diaphorin. To better understand the evolution of this unusual symbiont, the present study analyzed the genome of Profftella_Dco, a sister lineage to Profftella_DC, using Diaphorina cf. continua, a host psyllid congeneric with D. citri. The genome of coresiding Carsonella (Carsonella_Dco) was also analyzed. The analysis revealed nearly perfect synteny conservation in these genomes with their counterparts from D. citri. The substitution rate analysis further demonstrated genomic stability of Profftella which is comparable to that of Carsonella. Profftella_Dco and Profftella_DC shared all genes for the biosynthesis of diaphorin, hemolysin, riboflavin, biotin, and carotenoids, underlining multiple roles of Profftella, which may contribute to stabilizing symbiotic relationships with the host. However, acyl carrier proteins were extensively amplified in polyketide synthases DipP and DipT for diaphorin synthesis in Profftella_Dco. This level of acyl carrier protein augmentation, unprecedented in modular polyketide synthases of any known organism, is not thought to influence the polyketide structure but may improve the synthesis efficiency.
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Affiliation(s)
- Atsushi Nakabachi
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, Japan.,Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, Japan
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | - Igor Malenovský
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Yuu Hirose
- Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, Japan
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18
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Hirose Y, Shiozaki T, Hamano I, Yoshihara S, Tokumoto H, Eki T, Harada N. A specific combination of dual index adaptors decreases the sensitivity of amplicon sequencing with the Illumina platform. DNA Res 2021; 27:5893952. [PMID: 32810209 PMCID: PMC7547650 DOI: 10.1093/dnares/dsaa017] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/11/2020] [Indexed: 11/14/2022] Open
Abstract
Amplicon sequencing is a powerful approach in microbiome studies as it detects live organisms with high sensitivity. This approach determines the composition of sequence variants of marker genes using high-throughput DNA sequencers. The use of dual index adaptors is the fundamental technique for pooling DNA libraries for Illumina sequencers and is believed not to affect the results. However, here, we observed a decrease of sequence quality in samples containing a specific combination of indexes, namely N704 and S507 in Nextera kits, in multiple runs on the Illumina MiSeq sequencer operated in different facilities. This decrease was also observed when sequencing randomly fragmented DNA of Escherichia coli and was not observed when either individual adaptor was used. Each end of the DNA library with this index combination contains a complementary sequence motif, which potentially inhibits proper cluster generation and/or subsequent sequencing. Community analysis of the 16S and 18S rRNA amplicons using QIIME2 revealed significant decreases in α-diversity in the samples containing the N704/S507 index combination, resulting from loss of low-abundance sequence variants during denoising. Our data underscore the importance of quality validation of sequence reads in developing dual index techniques and suggest cautious interpretation of microbiome data containing low-quality sequence reads.
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Affiliation(s)
- Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Takuhei Shiozaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan
| | - Itsuki Hamano
- Department of Biological Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Shizue Yoshihara
- Department of Biological Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Hayato Tokumoto
- Department of Biological Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Naomi Harada
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan
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Unno M, Hirose Y, Mishima M, Kikukawa T, Fujisawa T, Iwata T, Tamogami J. Spectroscopic approach for exploring structure and function of photoreceptor proteins. Biophys Physicobiol 2021; 18:127-130. [PMID: 34178563 PMCID: PMC8214923 DOI: 10.2142/biophysico.bppb-v18.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/11/2021] [Indexed: 12/01/2022] Open
Affiliation(s)
- Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Yuu Hirose
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Masaki Mishima
- Department of Molecular Biophysics, Tokyo University of Pharmacy and Life Sciences, School of Pharmacy, Hachioji, Tokyo 192-0392, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science and Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Tatsuya Iwata
- Department of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
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Kamo T, Eki T, Hirose Y. Pressurized Liquid Extraction of a Phycocyanobilin Chromophore and Its Reconstitution with a Cyanobacteriochrome Photosensor for Efficient Isotopic Labeling. Plant Cell Physiol 2021; 62:334-347. [PMID: 33386854 PMCID: PMC8112840 DOI: 10.1093/pcp/pcaa164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Linear tetrapyrrole compounds (bilins) are chromophores of the phytochrome and cyanobacteriochrome classes of photosensors and light-harvesting phycobiliproteins. Various spectroscopic techniques, such as resonance Raman, Fourier transform-infrared and nuclear magnetic resonance, have been used to elucidate the structures underlying their remarkable spectral diversity, in which the signals are experimentally assigned to specific structures using isotopically labeled bilin. However, current methods for isotopic labeling of bilins require specialized expertise, time-consuming procedures and/or expensive reagents. To address these shortcomings, we established a method for pressurized liquid extraction of phycocyanobilin (PCB) from the phycobiliprotein powder Lina Blue and also the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis). PCB was efficiently cleaved in ethanol with three extractions (5 min each) under nitrogen at 125�C and 100 bars. A prewash at 75�C was effective for removing cellular pigments of Synechocystis without PCB cleavage. Liquid chromatography and mass spectrometry suggested that PCB was cleaved in the C3-E (majority) and C3-Z (partial) configurations. 15N- and 13C/15N-labeled PCBs were prepared from Synechocystis cells grown with NaH13CO3 and/or Na15NO3, the concentrations of which were optimized based on cell growth and pigmentation. Extracted PCB was reconstituted with a recombinant apoprotein of the cyanobacteriochrome-class photosensor RcaE. Yield of the photoactive holoprotein was improved by optimization of the expression conditions and cell disruption in the presence of Tween 20. Our method can be applied for the isotopic labeling of other PCB-binding proteins and for the commercial production of non-labeled PCB for food, cosmetic and medical applications.
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Affiliation(s)
- Takanari Kamo
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580 Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580 Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580 Japan
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Shiozaki T, Itoh F, Hirose Y, Onodera J, Kuwata A, Harada N. A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin. PLoS One 2021; 16:e0245936. [PMID: 33596231 PMCID: PMC7888612 DOI: 10.1371/journal.pone.0245936] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/08/2021] [Indexed: 01/04/2023] Open
Abstract
Plankton samples have been routinely collected and preserved in formalin in many laboratories and museums for more than 100 years. Recently, attention has turned to use DNA information from formalin-fixed samples to examine changes in plankton diversity over time. However, no molecular ecological studies have evaluated the impact of formalin fixation on the genetic composition of the plankton community structure. Here, we developed a method for extracting DNA from archived formalin-preserved plankton samples to determine their community structure by a DNA metabarcoding approach. We found that a lysis solution consisting of borate-NaOH buffer (pH 11) with SDS and proteinase K effectively cleaved the cross-link formed by formalin fixation. DNA was extracted from samples preserved for decades in formalin, and the diatom community of the extracted DNA was in good agreement with the microscopy analysis. Furthermore, we stored a plankton sample for 1.5 years and demonstrated that 18S rRNA gene community structures did not change significantly from non-formalin-fixed, time-zero samples. These results indicate that our method can be used to describe the original community structure of plankton archived in formalin for years. Our approach will be useful for examining the long-term variation of plankton diversity by metabarcoding analysis of 18S rRNA gene community structure.
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Affiliation(s)
- Takuhei Shiozaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
- * E-mail:
| | - Fumihiro Itoh
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Japan
| | - Jonaotaro Onodera
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Akira Kuwata
- Shiogama field station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Naomi Harada
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
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Shimura Y, Fujisawa T, Hirose Y, Misawa N, Kanesaki Y, Nakamura Y, Kawachi M. Complete sequence and structure of the genome of the harmful algal bloom-forming cyanobacterium Planktothrix agardhii NIES-204 T and detailed analysis of secondary metabolite gene clusters. Harmful Algae 2021; 101:101942. [PMID: 33526179 DOI: 10.1016/j.hal.2020.101942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Planktothrix species are distributed worldwide, and these prevalent cyanobacteria occasionally form potentially devastating toxic blooms. Given the ecological and taxonomic importance of Planktothrix agardhii as a bloom species, we set out to determine the complete genome sequence of the type strain Planktothrix agardhii NIES-204. Remarkably, we found that the 5S ribosomal RNA genes are not adjacent to the 16S and 23S ribosomal RNA genes. The genomic structure of P. agardhii NIES-204 is highly similar to that of another P. agardhii strain isolated from a geographically distant site, although they differ distinctly by a large inversion. We identified numerous gene clusters that encode the components of the metabolic pathways that generate secondary metabolites. We found that the aeruginosin biosynthetic gene cluster was more similar to that of another toxic bloom-forming cyanobacterium Microcystis aeruginosa than to that of other strains of Planktothrix, suggesting horizontal gene transfer. Prenyltransferases encoded in the prenylagaramide gene cluster of Planktothrix strains were classified into two phylogenetically distinct types, suggesting a functional difference. In addition to the secondary metabolite gene clusters, we identified genes for inorganic nitrogen and phosphate uptake components and gas vesicles. Our findings contribute to further understanding of the ecologically important genus Planktothrix.
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Affiliation(s)
- Yohei Shimura
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan.
| | - Takatomo Fujisawa
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Hibarigaoka 1-1, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Naomi Misawa
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Hibarigaoka 1-1, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
| | - Yasukazu Nakamura
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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Nakabachi A, Malenovský I, Gjonov I, Hirose Y. 16S rRNA Sequencing Detected Profftella, Liberibacter, Wolbachia, and Diplorickettsia from Relatives of the Asian Citrus Psyllid. Microb Ecol 2020; 80:410-422. [PMID: 32052099 DOI: 10.1007/s00248-020-01491-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
The Asian citrus psyllid Diaphorina citri (Hemiptera: Psylloidea) is a serious pest of citrus species worldwide because it transmits Candidatus Liberibacter spp. (Alphaproteobacteria: Rhizobiales), the causative agents of the incurable citrus disease, huanglongbing or greening disease. Diaphorina citri possesses a specialized organ called a bacteriome, which harbors vertically transmitted intracellular mutualists, Ca. Carsonella ruddii (Gammaproteobacteria: Oceanospirillales) and Ca. Profftella armatura (Gammaproteobacteria: Betaproteobacteriales). Whereas Carsonella is a typical nutritional symbiont, Profftella is an unprecedented type of toxin-producing defensive symbiont, unusually sharing organelle-like features with nutritional symbionts. Additionally, many D. citri strains are infected with Wolbachia, which manipulate reproduction in various arthropod hosts. In the present study, in an effort to obtain insights into the evolution of symbioses between Diaphorina and bacteria, microbiomes of psyllids closely related to D. citri were investigated. Bacterial populations of Diaphorina cf. continua and Diaphorina lycii were analyzed using Illumina sequencing of 16S rRNA gene amplicons and compared with data obtained from D. citri. The analysis revealed that all three Diaphorina spp. harbor Profftella as well as Carsonella lineages, implying that Profftella is widespread within the genus Diaphorina. Moreover, the analysis identified Ca. Liberibacter europaeus and Diplorickettsia sp. (Gammaproteobacteria: Diplorickettsiales) in D. cf. continua, and a total of four Wolbachia (Alphaproteobacteria: Rickettsiales) lineages in the three psyllid species. These results provide deeper insights into the interactions among insects, bacteria, and plants, which would eventually help to better manage horticulture.
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Affiliation(s)
- Atsushi Nakabachi
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan.
- Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan.
| | - Igor Malenovský
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37, Brno, Czech Republic
| | - Ilia Gjonov
- Department of Zoology and Anthropology, Faculty of Biology, Sofia University, Dragan Tzankov 8, 1164, Sofia, Bulgaria
| | - Yuu Hirose
- Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan
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Kumsab J, Tobe R, Kurihara T, Hirose Y, Omori T, Mihara H. Characterization of a novel class of glyoxylate reductase belonging to the β-hydroxyacid dehydrogenase family in Acetobacter aceti. Biosci Biotechnol Biochem 2020; 84:2303-2310. [PMID: 32729375 DOI: 10.1080/09168451.2020.1797470] [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] [Indexed: 10/23/2022]
Abstract
Enzymes related to β-hydroxyacid dehydrogenases/3-hydroxyisobutyrate dehydrogenases are ubiquitous, but most of them have not been characterized. An uncharacterized protein with moderate sequence similarities to Gluconobacter oxydans succinic semialdehyde reductase and plant glyoxylate reductases/succinic semialdehyde reductases was found in the genome of Acetobacter aceti JCM20276. The corresponding gene was cloned and expressed in Escherichia coli. The gene product was purified and identified as a glyoxylate reductase that exclusively catalyzed the NAD(P)H-dependent reduction of glyoxylate to glycolate. The strict substrate specificity of this enzyme to glyoxylate, the diverged sequence motifs for its binding sites with cofactors and substrates, and its phylogenetic relationship to homologous enzymes suggested that this enzyme represents a novel class of enzymes in the β-hydroxyacid dehydrogenase family. This study may provide an important clue to clarify the metabolism of glyoxylate in bacteria. Abbreviations: GR: glyoxylate reductase; GRHPR: glyoxylate reductase/hydroxypyruvate reductase; HIBADH: 3-hydroxyisobutyrate dehydrogenase; SSA: succinic semialdehyde; SSAR: succinic semialdehyde reductase.
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Affiliation(s)
- Jakkaphan Kumsab
- College of Life Sciences, Ritsumeikan University , Kusatsu, Japan
| | - Ryuta Tobe
- College of Life Sciences, Ritsumeikan University , Kusatsu, Japan
| | - Tatsuo Kurihara
- Institute for Chemical Research, Kyoto University , Kyoto, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology , Toyohashi, Japan
| | - Taketo Omori
- Department of Biomedical Engineering, Osaka Institute of Technology , Osaka, Japan
| | - Hisaaki Mihara
- College of Life Sciences, Ritsumeikan University , Kusatsu, Japan
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25
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Ohbayashi R, Hirooka S, Onuma R, Kanesaki Y, Hirose Y, Kobayashi Y, Fujiwara T, Furusawa C, Miyagishima SY. Evolutionary Changes in DnaA-Dependent Chromosomal Replication in Cyanobacteria. Front Microbiol 2020; 11:786. [PMID: 32411117 PMCID: PMC7198777 DOI: 10.3389/fmicb.2020.00786] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 01/17/2020] [Accepted: 04/02/2020] [Indexed: 12/02/2022] Open
Abstract
Replication of the circular bacterial chromosome is initiated at a unique origin (oriC) in a DnaA-dependent manner in which replication proceeds bidirectionally from oriC to ter. The nucleotide compositions of most bacteria differ between the leading and lagging DNA strands. Thus, the chromosomal DNA sequence typically exhibits an asymmetric GC skew profile. Further, free-living bacteria without genomes encoding dnaA were unknown. Thus, a DnaA-oriC-dependent replication initiation mechanism may be essential for most bacteria. However, most cyanobacterial genomes exhibit irregular GC skew profiles. We previously found that the Synechococcus elongatus chromosome, which exhibits a regular GC skew profile, is replicated in a DnaA-oriC-dependent manner, whereas chromosomes of Synechocystis sp. PCC 6803 and Nostoc sp. PCC 7120, which exhibit an irregular GC skew profile, are replicated from multiple origins in a DnaA-independent manner. Here we investigate the variation in the mechanisms of cyanobacterial chromosome replication. We found that the genomes of certain free-living species do not encode dnaA and such species, including Cyanobacterium aponinum PCC 10605 and Geminocystis sp. NIES-3708, replicate their chromosomes from multiple origins. Synechococcus sp. PCC 7002, which is phylogenetically closely related to dnaA-lacking free-living species as well as to dnaA-encoding but DnaA-oriC-independent Synechocystis sp. PCC 6803, possesses dnaA. In Synechococcus sp. PCC 7002, dnaA was not essential and its chromosomes were replicated from a unique origin in a DnaA-oriC independent manner. Our results also suggest that loss of DnaA-oriC-dependency independently occurred multiple times during cyanobacterial evolution and raises a possibility that the loss of dnaA or loss of DnaA-oriC dependency correlated with an increase in ploidy level.
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Affiliation(s)
- Ryudo Ohbayashi
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan
| | - Ryo Onuma
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Japan
| | - Yusuke Kobayashi
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan
| | - Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan.,Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan.,Universal Biology Institute, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan.,Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
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Sato T, Kikukawa T, Miyoshi R, Kajimoto K, Yonekawa C, Fujisawa T, Unno M, Eki T, Hirose Y. Correction: Protochromic absorption changes in the two-cysteine photocycle of a blue/orange cyanobacteriochrome. J Biol Chem 2020; 295:1767. [PMID: 32034012 DOI: 10.1074/jbc.aac120.012567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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27
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Sakai S, Matsuda R, Adachi R, Akiyama H, Maitani T, Ohno Y, Oka M, Abe A, Seiki K, Oda H, Shiomi K, Urisu A, Arakawa F, Futo S, Haraguchi H, Hirose Y, Hirota M, Iidzuka T, Kan K, Kanayama S, Koike T, Kojima K, Minegishi Y, Mori Y, Nishihara R, Sato H, Yamaguchi A, Yamakawa H, Yasuda K. Interlaboratory Evaluation of Two Enzyme-Linked Immunosorbent Assay Kits for the Determination of Crustacean Protein in Processed Foods. J AOAC Int 2019. [DOI: 10.1093/jaoac/91.1.123] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The labeling of foods containing material derived from crustaceans such as shrimp and crab is to become mandatory in Japan because of increases in the number of allergy patients. To ensure proper labeling, 2 novel sandwich enzyme-linked immunosorbent assay (ELISA) kits for the determination of crustacean protein in processed foods, the N kit (Nissui Pharmaceutical Co., Ltd, Ibaraki, Japan) and the M kit (Maruha Nichiro Holdings, Inc., Ibaraki, Japan), have been developed. Five types of model processed foods containing 10 and/or 11.9 g/g crustacean soluble protein were prepared for interlaboratory evaluation of the performance of these kits. The N kit displayed a relatively high level of reproducibility relative standard deviation (interlaboratory precision; 4.08.4 RSDR) and sufficient recovery (6586) for all the model processed foods. The M kit displayed sufficient reproducibility (17.620.5 RSDR) and a reasonably high level of recovery (82103). The repeatability relative standard deviation (RSDr) values regarding the detection of crustacean proteins in the 5 model foods were mostly <5.1 RSDr for the N kit and 9.9 RSDr for the M kit. In conclusion, the results of this interlaboratory evaluation suggest that both these ELISA kits would be very useful for detecting crustacean protein in processed foods.
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Affiliation(s)
- Shinobu Sakai
- National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Rieko Matsuda
- National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Reiko Adachi
- National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Hiroshi Akiyama
- National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Tamio Maitani
- National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Yasuo Ohno
- National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Michihiro Oka
- Nissui Pharmaceutical Co, Ltd, 1075-2, Hokunanmoro, Yuki, Ibaraki 307-0036, Japan
| | - Akihisa Abe
- Nippon Suisan Kaisha, Ltd, 559-6, Kitano-machi, Hachioji, Tokyo 192-0906, Japan
| | - Kohsuke Seiki
- Maruha Nichiro Holdings, Inc., 16-2, Wadai, Tsukuba, Ibaraki 300-4295, Japan
| | - Hiroshi Oda
- Maruha Nichiro Holdings, Inc., 16-2, Wadai, Tsukuba, Ibaraki 300-4295, Japan
| | - Kazuo Shiomi
- Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Atsuo Urisu
- Fujita Health University, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
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Sakai S, Adachi R, Akiyama H, Teshima R, Doi H, Shibata H, Urisu A, Arakawa F, Haraguchi H, Hirose Y, Hirota M, Iidzuka T, Ikeno K, Kojima K, Maeda S, Minegishi Y, Mishima T, Oguchi K, Seki T, Yamakawa H, Yano T, Yasuda K. Determination of Walnut Protein in Processed Foods by Enzyme-Linked Immunosorbent Assay: Interlaboratory Study. J AOAC Int 2019. [DOI: 10.1093/jaoac/93.4.1255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Because food allergens from tree nuts, including walnuts, are a frequent cause of adverse food reactions for allergic patients, the labeling of foods containing ingredients derived from tree nuts is required in numerous countries. According to Japanese regulations, the labeling of food products containing walnuts is recommended. To ensure proper labeling, a novel sandwich ELISA kit for the determination of walnut protein in processed foods (Walnut Protein [2S-Albumin] Kit; Morinaga Institute of Biological Science, Inc.; walnut kit) has been developed. We prepared seven types of incurred samples (model processed foods: biscuits, bread, sponge cake, orange juice, jelly, chicken meatballs, and rice gruel) containing 10 g walnut soluble protein/g of food for use in interlaboratory evaluations of the walnut kit. The walnut kit displayed sufficient reproducibility relative standard deviations (interlaboratory precision: 5.89.9 RSDR) and a high level of recovery (81119) for all the incurred samples. All the repeatability relative standard deviation (RSDr) values for the incurred samples that were examined were less than 6.0. The results of this interlaboratory evaluation suggested that the walnut kit could be used as a precise and reliable tool for determination of walnut protein in processed foods.
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Affiliation(s)
- Shinobu Sakai
- National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Reiko Adachi
- National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Hiroshi Akiyama
- National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Reiko Teshima
- National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Hirotoshi Doi
- Morinaga Institute of Biological Science, Inc., 2-1-16, Sachiura, Kanazawa-ku, Yokohama 236-0003, Japan
| | - Haruki Shibata
- Morinaga Institute of Biological Science, Inc., 2-1-16, Sachiura, Kanazawa-ku, Yokohama 236-0003, Japan
| | - Atsuo Urisu
- Fujita Health University, The Second Teaching Hospital, 3-6-10, Otobashi, Nakagawa-ku, Nagoya 454-8509, Japan
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Sakai S, Adachi R, Akiyama H, Teshima R, Morishita N, Matsumoto T, Urisu A, Arakawa F, Endo Y, Haraguchi H, Hirose Y, Hirota M, Iidzuka T, Kojima K, Minegishi Y, Mishima T, Nishihara R, Seki T, Yamakawa H, Yano T, Yasuda K. Enzyme-Linked Immunosorbent Assay Kit for the Determination of Soybean Protein in Processed Foods: Interlaboratory Evaluation. J AOAC Int 2019. [DOI: 10.1093/jaoac/93.1.243] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The labeling of foods containing ingredients derived from soybean is recommended in Japan because of an increasing number of patients who are allergic to soybeans. To ensure proper labeling, a novel sandwich ELISA kit for the determination of soybean protein in processed foods (FASTKIT Ver. II, Soybean, Nippon Meat Packers, Inc.; soy kit) has been developed. Five types of incurred samples (model processed foods: rice gruel, sausage, sweet adzuki bean soup, sweet potato cake, and tomato sauce) containing 10 g soybean soluble protein/g food were prepared for use in interlaboratory evaluations of the soy kit. The soy kit displayed a sufficient RSDR value (interlaboratory precision: 9.313.4 RSDR) and a high level of recovery (97114) for all the incurred samples. The RSDr value for the incurred samples was mostly <4.8. The results of this interlaboratory evaluation suggest that the soy kit can be used as a precise and reliable tool for the determination of soybean proteins in processed foods.
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Affiliation(s)
- Shinobu Sakai
- National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Reiko Adachi
- National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Hiroshi Akiyama
- National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Reiko Teshima
- National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Naoki Morishita
- R&D Center Nippon Meat Packers, Inc., 3-3, Midorigahara, Tsukuba, Ibaraki 300-2646, Japan
| | - Takashi Matsumoto
- R&D Center Nippon Meat Packers, Inc., 3-3, Midorigahara, Tsukuba, Ibaraki 300-2646, Japan
| | - Atsuo Urisu
- Fujita Health University, The Second Teaching Hospital, 3-6-10, Otobashi, Nakagawa-ku, Nagoya 454-8509, Japan
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Shiozaki T, Hirose Y, Hamasaki K, Kaneko R, Ishikawa K, Harada N. Eukaryotic Phytoplankton Contributing to a Seasonal Bloom and Carbon Export Revealed by Tracking Sequence Variants in the Western North Pacific. Front Microbiol 2019; 10:2722. [PMID: 31849876 PMCID: PMC6902033 DOI: 10.3389/fmicb.2019.02722] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 07/13/2019] [Accepted: 11/08/2019] [Indexed: 02/05/2023] Open
Abstract
Greater diversity of eukaryotic phytoplankton than expected has been revealed recently through molecular techniques, but little is known about their temporal dynamics or fate in the open ocean. Here, we examined size-fractionated eukaryotic phytoplankton communities from the surface to abyssopelagic zone (5,000 m) throughout the year, by tracking sequence variants of the 18S rRNA gene in the western subtropical North Pacific. The oceanographic conditions were divided into two periods, stratification and mixing, between which the surface phytoplankton community differed. During the mixing period, the abundance of large phytoplankton (≥3 μm) increased, with diatoms and putative Pseudoscourfieldia marina dominating this fraction. Picophytoplankton (<3 μm) also increased during the mixing period and were dominated by Mamiellophyceae. Taxa belonging to prasinophytes (including Ps. marina and Mamiellophyceae) were observed in the epipelagic zone throughout the year, and thus likely seeded the seasonal bloom that occurred during the mixing period. In contrast, diatoms observed during the mixing period mostly represented taxa unique to that period, including coastal species. Numerical particle backtracking experiments indicated that water masses in the surface layer could be transported from coastal areas to the study site. Gene sequences of coastal diatoms were present in the abyssopelagic zone. Therefore, allochthonous species drove the seasonal bloom and could be transported to deep waters. In the abyssopelagic zone, the relative abundance of Ps. marina in deep waters was similar to or higher than that of diatoms during the mixing period. Among picophytoplankton, Mamiellophyceae made up a significant fraction in the abyssopelagic zone, suggesting that prasinophytes are also involved in carbon export. Our molecular survey showed that these previously overlooked phytoplankton species could contribute significantly to the seasonal bloom and biological pump in the subtropical open ocean.
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Affiliation(s)
- Takuhei Shiozaki
- Earth Surface System Research Center, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Japan
| | - Koji Hamasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Tokyo, Japan
| | - Ryo Kaneko
- Arctic Environment Research Center, National Institute of Polar Research, Tachikawa, Japan
| | - Kazuo Ishikawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Tokyo, Japan
| | - Naomi Harada
- Earth Surface System Research Center, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
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Sato T, Kikukawa T, Miyoshi R, Kajimoto K, Yonekawa C, Fujisawa T, Unno M, Eki T, Hirose Y. Protochromic absorption changes in the two-cysteine photocycle of a blue/orange cyanobacteriochrome. J Biol Chem 2019; 294:18909-18922. [PMID: 31649035 DOI: 10.1074/jbc.ra119.010384] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 07/26/2019] [Revised: 10/23/2019] [Indexed: 11/06/2022] Open
Abstract
Cyanobacteriochromes (CBCRs) are phytochrome-related photosensors with diverse spectral sensitivities spanning the entire visible spectrum. They covalently bind bilin chromophores via conserved cysteine residues and undergo 15Z/15E bilin photoisomerization upon light illumination. CBCR subfamilies absorbing violet-blue light use an additional cysteine residue to form a second bilin-thiol adduct in a two-Cys photocycle. However, the process of second thiol adduct formation is incompletely understood, especially the involvement of the bilin protonation state. Here, we focused on the Oscil6304_2705 protein from the cyanobacterium Oscillatoria acuminata PCC 6304, which photoconverts between a blue-absorbing 15Z state ( 15Z Pb) and orange-absorbing 15E state ( 15E Po). pH titration analysis revealed that 15Z Pb was stable over a wide pH range, suggesting that bilin protonation is stabilized by a second thiol adduct. As revealed by resonance Raman spectroscopy, 15E Po harbored protonated bilin at both acidic and neutral pH, but readily converted to a deprotonated green-absorbing 15Z state ( 15Z Pg) at alkaline pH. Site-directed mutagenesis revealed that the conserved Asp-71 and His-102 residues are required for second thiol adduct formation in 15Z Pb and bilin protonation in 15E Po, respectively. An Oscil6304_2705 variant lacking the second cysteine residue, Cys-73, photoconverted between deprotonated 15Z Pg and protonated 15E Pr, similarly to the protochromic photocycle of the green/red CBCR subfamily. Time-resolved spectroscopy revealed 15Z Pg formation as an intermediate in the 15E Pr-to- 15Z Pg conversion with a significant solvent-isotope effect, suggesting the sequential occurrence of 15EP-to-15Z photoisomerization, deprotonation, and second thiol adduct formation. Our findings uncover the details of protochromic absorption changes underlying the two-Cys photocycle of violet-blue-absorbing CBCR subfamilies.
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Affiliation(s)
- Teppei Sato
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Takashi Kikukawa
- Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Kita10 Nishi8, Kita-ku, Sapporo 060-0810, Japan; Faculty of Advanced Life Science, Hokkaido University, Kita10 Nishi8, Kita-ku, Sapporo 060-0810, Japan
| | - Risako Miyoshi
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Kousuke Kajimoto
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Chinatsu Yonekawa
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan.
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Hirose Y, Chihong S, Watanabe M, Yonekawa C, Murata K, Ikeuchi M, Eki T. Diverse Chromatic Acclimation Processes Regulating Phycoerythrocyanin and Rod-Shaped Phycobilisome in Cyanobacteria. Mol Plant 2019; 12:1167-1169. [PMID: 31350170 DOI: 10.1016/j.molp.2019.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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Takami H, Fukushima S, Aoki K, Satomi K, Narumi K, Hama N, Matsushita Y, Fukuoka K, Yamasaki K, Nakamura T, Mukasa A, Saito N, Suzuki T, Yanagisawa T, Nakamura H, Sugiyama K, Tamura K, Maehara T, Nakada M, Nonaka M, Asai A, Yokogami K, Takeshima H, Iuchi T, Kanemura Y, Kobayashi K, Nagane M, Kurozumi K, Yoshimoto K, Matsuda M, Matsumura A, Hirose Y, Tokuyama T, Kumabe T, Ueki K, Narita Y, Shibui S, Totoki Y, Shibata T, Nakazato Y, Nishikawa R, Matsutani M, Ichimura K. Intratumoural immune cell landscape in germinoma reveals multipotent lineages and exhibits prognostic significance. Neuropathol Appl Neurobiol 2019; 46:111-124. [PMID: 31179566 DOI: 10.1111/nan.12570] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 12/13/2018] [Accepted: 06/03/2019] [Indexed: 12/13/2022]
Abstract
AIMS Alterations in microenvironments are a hallmark of cancer, and these alterations in germinomas are of particular significance. Germinoma, the most common subtype of central nervous system germ cell tumours, often exhibits massive immune cell infiltration intermingled with tumour cells. The role of these immune cells in germinoma, however, remains unknown. METHODS We investigated the cellular constituents of immune microenvironments and their clinical impacts on prognosis in 100 germinoma cases. RESULTS Patients with germinomas lower in tumour cell content (i.e. higher immune cell infiltration) had a significantly longer progression-free survival time than those with higher tumour cell contents (P = 0.03). Transcriptome analyses and RNA in-situ hybridization indicated that infiltrating immune cells comprised a wide variety of cell types, including lymphocytes and myelocyte-lineage cells. High expression of CD4 was significantly associated with good prognosis, whereas elevated nitric oxide synthase 2 was associated with poor prognosis. PD1 (PDCD1) was expressed by immune cells present in most germinomas (93.8%), and PD-L1 (CD274) expression was found in tumour cells in the majority of germinomas examined (73.5%). CONCLUSIONS The collective data strongly suggest that infiltrating immune cells play an important role in predicting treatment response. Further investigation should lead to additional categorization of germinoma to safely reduce treatment intensity depending on tumour/immune cell balance and to develop possible future immunotherapies.
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Affiliation(s)
- H Takami
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Department of Neurosurgery, Faculty of Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - S Fukushima
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - K Aoki
- Division of Gene and Immune Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - K Satomi
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - K Narumi
- Division of Gene and Immune Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - N Hama
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Y Matsushita
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - K Fukuoka
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Division of Pediatric Neuro-Oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - K Yamasaki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Department of Pediatrics, Osaka City General Hospital, Osaka, Japan
| | - T Nakamura
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Kanagawa, Japan
| | - A Mukasa
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo Hospital, Tokyo, Japan.,Department of Neurosurgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - N Saito
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - T Suzuki
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Saitama, Japan
| | - T Yanagisawa
- Division of Pediatric Neuro-Oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - H Nakamura
- Department of Neurosurgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.,Department of Neurosurgery, Kurume University, Fukuoka, Japan
| | - K Sugiyama
- Department of Neurosurgery, Faculty of Medicine, Hiroshima University, Hiroshima, Japan
| | - K Tamura
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - T Maehara
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - M Nakada
- Department of Neurosurgery, Graduate School of Medical Science, Kanazawa University, Ishikawa, Japan
| | - M Nonaka
- Department of Neurosurgery, Kansai Medical University Hospital, Osaka, Japan
| | - A Asai
- Department of Neurosurgery, Kansai Medical University Hospital, Osaka, Japan
| | - K Yokogami
- Department of Neurosurgery, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - H Takeshima
- Department of Neurosurgery, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - T Iuchi
- Department of Neurosurgery, Chiba Cancer Center, Chiba, Japan
| | - Y Kanemura
- Department of Neurosurgery, Osaka National Hospital, National Hospital Organization, Osaka, Japan.,Department of Biomedical Research and Innovation, Institute for Clinical Research, Osaka National Hospital, National Hospital Organization, Osaka, Japan
| | - K Kobayashi
- Department of Neurosurgery, Faculty of Medicine, Kyorin University, Tokyo, Japan
| | - M Nagane
- Department of Neurosurgery, Faculty of Medicine, Kyorin University, Tokyo, Japan
| | - K Kurozumi
- Department of Neurological Surgery, Dentistry, and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - K Yoshimoto
- Department of Neurosurgery, Kyusyu University Hospital, Fukuoka, Japan
| | - M Matsuda
- Department of Neurosurgery, University of Tsukuba Hospital, Ibaraki, Japan
| | - A Matsumura
- Department of Neurosurgery, University of Tsukuba Hospital, Ibaraki, Japan
| | - Y Hirose
- Department of Neurosurgery, Fujita Health University Hospital, Aichi, Japan
| | - T Tokuyama
- Department of Neurosurgery, Hamamatsu University Hospital, Shizuoka, Japan
| | - T Kumabe
- Department of Neurosurgery, Kitasato University, Kanagawa, Japan
| | - K Ueki
- Department of Neurosurgery, Dokkyo Medical Univeristy, Tochigi, Japan
| | - Y Narita
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - S Shibui
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Y Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - T Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Y Nakazato
- Department of Pathology, Hidaka Hospital, Gunma, Japan
| | - R Nishikawa
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Kanagawa, Japan
| | - M Matsutani
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Kanagawa, Japan
| | - K Ichimura
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
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Tsukatani Y, Hirose Y, Harada J, Yonekawa C, Tamiaki H. Unusual features in the photosynthetic machinery of Halorhodospira halochloris DSM 1059 revealed by complete genome sequencing. Photosynth Res 2019; 140:311-319. [PMID: 30701482 DOI: 10.1007/s11120-019-00613-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
Halorhodospira halochloris is an anaerobic, halophilic, purple photosynthetic bacterium belonging to γ-Proteobacteria. H. halochloris is also characteristic as a thermophilic phototrophic isolate producing bacteriochlorophyll (BChl) b. Here, we report the complete genome sequence of H. halochloris DSM 1059. The genetic arrangement for this bacterium's photosynthetic apparatus is of particular interest; its genome contains two sets of puf operons encoding the reaction center and core light-harvesting 1 (LH1) complexes having almost identical nucleotide sequences (e.g., 98.8-99.9% of nucleotide identities between two sets of pufLM genes, but 100% of deduced amino acid sequence identities). This duplication of photosynthetic genes may provide a glimpse at natural selection in action. The β-polypeptides of the LH1 complex in purple bacteria usually contain two histidine residues to bind BChl a; however, those of H. halochloris were revealed to have four histidine residues, indicating unusual pigment organization in the LH1 complex of this species. Like in other BChl b-producing phototrophs, the genome of H. halochloris lacks the divinyl reductase genes bciA and bciB. The phylogeny of chlorophyllide a oxidoreductase, which catalyzes committed steps in the synthesis of BChl a and BChl b, indicates that evolution toward BChl b production is convergent. Geranylgeranyl reductase (BchP) of H. halochloris has an insertion region in its primary structure, which could be important for its unusual sequential reduction reactions.
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Affiliation(s)
- Yusuke Tsukatani
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, 237-0061, Japan.
| | - Yuu Hirose
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Aichi, 441-8580, Japan.
| | - Jiro Harada
- Department of Medical Biochemistry, Kurume University School of Medicine, Fukuoka, 830-0011, Japan
| | - Chinatsu Yonekawa
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Aichi, 441-8580, Japan
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Shiga, 525-8577, Japan
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Hirose Y, Chihong S, Watanabe M, Yonekawa C, Murata K, Ikeuchi M, Eki T. Diverse Chromatic Acclimation Processes Regulating Phycoerythrocyanin and Rod-Shaped Phycobilisome in Cyanobacteria. Mol Plant 2019; 12:715-725. [PMID: 30818037 DOI: 10.1016/j.molp.2019.02.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/29/2019] [Accepted: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Cyanobacteria have evolved various photoacclimation processes to perform oxygenic photosynthesis under different light environments. Chromatic acclimation (CA) is a widely recognized and ecologically important type of photoacclimation, whereby cyanobacteria alter the absorbing light colors of a supermolecular antenna complex called the phycobilisome. To date, several CA variants that regulate the green-absorbing phycoerythrin (PE) and/or the red-absorbing phycocyanin (PC) within the hemi-discoidal form of phycobilisome have been characterized. In this study, we identified a unique CA regulatory gene cluster encoding yellow-green-absorbing phycoerythrocyanin (PEC) and a rod-membrane linker protein (CpcL) for the rod-shaped form of phycobilisome. Using the cyanobacterium Leptolyngbya sp. PCC 6406, we revealed novel CA variants regulating PEC (CA7) and the rod-shaped phycobilisome (CA0), which maximize yellow-green light-harvesting capacity and balance the excitation of photosystems, respectively. Analysis of the distribution of CA gene clusters in 445 cyanobacteria genomes revealed eight CA variants responding to green and red light, which are classified based on the presence of PEC, PE, cpcL, and CA photosensor genes. Phylogenetic analysis further suggested that the emergence of CA7 was a single event and preceded that of heterocystous strains, whereas the acquisition of CA0 occurred multiple times. Taken together, these results offer novel insights into the diversity and evolution of the complex cyanobacterial photoacclimation mechanisms.
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Affiliation(s)
- Yuu Hirose
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan.
| | - Song Chihong
- National Institute for Physiological Sciences (NIPS), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Mai Watanabe
- Department of Life Sciences (Biology), The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Chinatsu Yonekawa
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences (NIPS), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Toshihiko Eki
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
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Osoegawa S, Miyoshi R, Watanabe K, Hirose Y, Fujisawa T, Ikeuchi M, Unno M. Identification of the Deprotonated Pyrrole Nitrogen of the Bilin-Based Photoreceptor by Raman Spectroscopy with an Advanced Computational Analysis. J Phys Chem B 2019; 123:3242-3247. [PMID: 30913882 DOI: 10.1021/acs.jpcb.9b00965] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phytochrome and cyanobacteriochrome utilize a linear methine-bridged tetrapyrrole (bilin) to control numerous biological processes. They show a reversible photoconversion between two spectrally distinct states. This photocycle is initiated by a C═C double-bond photoisomerization of the bilin followed by its thermal relaxations with transient and/or stationary changes in the protonation state of the pyrrole moiety. However, it has never been identified which of the four pyrrole nitrogen atoms is deprotonated. Here, we report a resonance Raman spectroscopic study on cyanobacteriochrome RcaE, which has been proposed to contain a deprotonated bilin for its green-absorbing 15 Z state. The observed Raman spectra were well reproduced by a simulated structure whose bilin B ring is deprotonated, with the aid of molecular dynamics and quantum mechanics/molecular mechanics calculations. The results revealed that the deprotonation of B and C rings has the distinct effect on the overall bilin structure, which will be relevant to the color tuning and photoconversion mechanisms of the phytochrome superfamily. Furthermore, this study documents the ability of vibrational spectroscopy combined with the advanced spectral analysis to visualize a proton of a cofactor molecule embedded in a protein moiety.
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Affiliation(s)
- Shinsuke Osoegawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Risako Miyoshi
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Kouhei Watanabe
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Yuu Hirose
- Department of Environmental and Life Sciences , Toyohashi University of Technology , Toyohashi , Aichi 441-8580 , Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology) , The University of Tokyo , Meguro, Tokyo 153-8902 , Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
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Kobayashi T, Miura K, Ishikawa H, Soma D, Ando T, Yuza K, Hirose Y, Katada T, Takizawa K, Nagahashi M, Sakata J, Kameyama H, Wakai T. Long-term Follow-up of Laparoscope-Assisted Living Donor Hepatectomy. Transplant Proc 2018; 50:2597-2600. [DOI: 10.1016/j.transproceed.2018.03.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 03/06/2018] [Indexed: 11/16/2022]
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38
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Nonaka L, Yamamoto T, Maruyama F, Hirose Y, Onishi Y, Kobayashi T, Suzuki S, Nomura N, Masuda M, Yano H. Interplay of a non-conjugative integrative element and a conjugative plasmid in the spread of antibiotic resistance via suicidal plasmid transfer from an aquaculture Vibrio isolate. PLoS One 2018; 13:e0198613. [PMID: 29879198 PMCID: PMC5991714 DOI: 10.1371/journal.pone.0198613] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 05/22/2018] [Indexed: 12/01/2022] Open
Abstract
The capture of antimicrobial resistance genes (ARGs) by mobile genetic elements (MGEs) plays a critical role in resistance acquisition for human-associated bacteria. Although aquaculture environments are recognized as important reservoirs of ARGs, intra- and intercellular mobility of MGEs discovered in marine organisms is poorly characterized. Here, we show a new pattern of interspecies ARGs transfer involving a 'non-conjugative' integrative element. To identify active MGEs in a Vibrio ponticus isolate, we conducted whole-genome sequencing of a transconjugant obtained by mating between Escherichia coli and Vibrio ponticus. This revealed integration of a plasmid (designated pSEA1) into the chromosome, consisting of a self-transmissible plasmid backbone of the MOBH group, ARGs, and a 13.8-kb integrative element Tn6283. Molecular genetics analysis suggested a two-step gene transfer model. First, Tn6283 integrates into the recipient chromosome during suicidal plasmid transfer, followed by homologous recombination between the Tn6283 copy in the chromosome and that in the newly transferred pSEA1. Tn6283 is unusual among integrative elements in that it apparently does not encode transfer function and its excision barely generates unoccupied donor sites. Thus, its movement is analogous to the transposition of insertion sequences rather than to that of canonical integrative and conjugative elements. Overall, this study reveals the presence of a previously unrecognized type of MGE in a marine organism, highlighting diversity in the mode of interspecies gene transfer.
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Affiliation(s)
- Lisa Nonaka
- Department of Microbiology, Dokkyo Medical University School of Medicine, Mibu, Tochigi, Japan
| | - Tatsuya Yamamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Japan
| | | | - Yuu Hirose
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku, Toyohashi, Aichi, Japan
| | - Yuki Onishi
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan
| | | | - Satoru Suzuki
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Japan
| | - Michiaki Masuda
- Department of Microbiology, Dokkyo Medical University School of Medicine, Mibu, Tochigi, Japan
| | - Hirokazu Yano
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Japan
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Komatsu H, Yamamoto J, Suzuki H, Nagao N, Hirose Y, Ohyama T, Umekage S, Kikuchi Y. Involvement of the response regulator CtrA in the extracellular DNA production of the marine bacterium Rhodovulum sulfidophilum. J GEN APPL MICROBIOL 2018. [PMID: 29526925 DOI: 10.2323/jgam.2017.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The marine bacterium Rhodovulum sulfidophilum is a nonsulfur phototrophic bacterium, which is known to produce extracellular nucleic acids in soluble form in culture medium. In the present paper, constructing the response regulator ctrA-deficient mutant of R. sulfidophilum, we found that this mutation causes a significant decrease in the extracellular DNA production. However, by the introduction of a plasmid containing the wild type ctrA gene into the mutant, the amount of extracellular DNA produced was recovered. This is the first and clear evidence that the extracellular DNA production is actively controlled by the CtrA in R. sulfidophilum.
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Affiliation(s)
- Hiroyuki Komatsu
- Department of Environmental and Life Sciences, Toyohashi University of Technology
| | - Junya Yamamoto
- Department of Environmental and Life Sciences, Toyohashi University of Technology
| | - Hiromichi Suzuki
- Department of Environmental and Life Sciences, Toyohashi University of Technology
| | - Nobuyoshi Nagao
- Department of Environmental and Life Sciences, Toyohashi University of Technology
| | - Yuu Hirose
- Department of Environmental and Life Sciences, Toyohashi University of Technology
| | - Takashi Ohyama
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University.,Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University
| | - So Umekage
- Department of Environmental and Life Sciences, Toyohashi University of Technology
| | - Yo Kikuchi
- Department of Environmental and Life Sciences, Toyohashi University of Technology.,Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University
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40
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Hirose Y, Misawa N, Yonekawa C, Nagao N, Watanabe M, Ikeuchi M, Eki T. Characterization of the genuine type 2 chromatic acclimation in the two Geminocystis cyanobacteria. DNA Res 2017; 24:387-396. [PMID: 28338901 PMCID: PMC5737509 DOI: 10.1093/dnares/dsx011] [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: 10/24/2016] [Accepted: 02/22/2017] [Indexed: 01/30/2023] Open
Abstract
Certain cyanobacteria can adjust the wavelengths of light they absorb by remodeling their photosynthetic antenna complex phycobilisome via a process called chromatic acclimation (CA). Although several types of CA have been reported, the diversity of the molecular mechanisms of CA among the cyanobacteria phylum is not fully understood. Here, we characterized the molecular process of CA of Geminocystis sp. strains National Institute of Environmental Studies (NIES)-3708 and NIES-3709. Absorption and fluorescence spectroscopy revealed that both strains dramatically alter their phycoerythrin content in response to green and red light. Whole-genome comparison revealed that the two strains share the typical phycobilisome structure consisting of a central core and peripheral rods, but they differ in the number of rod linkers of phycoerythrin and thus have differing capacity for phycoerythrin accumulation. RNA sequencing analysis suggested that the length of phycoerythrin rods in each phycobilisome is strictly regulated by the green light and red light-sensing CcaS/R system, whereas the total number of phycobilisomes is governed by the excitation-balancing system between phycobilisomes and photosystems. We reclassify the conventional CA types based on the genome information and designate CA of the two strains as genuine type 2, where components of phycoerythrin, but not rod-membrane linker of phycocyanin, are regulated by the CcaS/R system.
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Affiliation(s)
- Yuu Hirose
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Naomi Misawa
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Chinatsu Yonekawa
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Nobuyoshi Nagao
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Mai Watanabe
- Department of Life Sciences (Biology), The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Toshihiko Eki
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
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41
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Kanazawa T, Fujiwara H, Takahashi H, Nishiyama Y, Hirose Y, Yoshida K, Sasaki H. P08.25 Imaging scoring system for preoperative diagnoses of molecular status in gliomas. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox036.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Kono M, Arakawa Y, Mineharu Y, Ohka F, Kinoshita M, Nakae S, Miyashita K, Iuchi T, Hirose Y, Natsume A, Nakada M, Sasaki H. P09.50 Phase I trial of temozolomide plus bevacizumab for newly diagnosed high-grade gliomas in the elderly: Interim report. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox036.306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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43
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Hayashi M, Okada A, Yamamoto K, Okugochi T, Kusaka C, Kudou D, Nemoto M, Inagaki J, Hirose Y, Okajima T, Tamura T, Soda K, Inagaki K. Gene cloning, recombinant expression, purification and characterization of l-methionine decarboxylase from Streptomyces sp. 590. J Biochem 2017; 161:389-398. [PMID: 28003434 DOI: 10.1093/jb/mvw083] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 11/09/2016] [Indexed: 11/14/2022] Open
Abstract
l-Methionine decarboxylase (MetDC) from Streptomyces sp. 590 depends on pyridoxal 5'-phosphate and catalyzes the non-oxidative decarboxylation of l-methionine to produce 3-methylthiopropylamine and carbon dioxide. MetDC gene (mdc) was determined to consist of 1,674 bp encoding 557 amino acids, and the amino acid sequence is similar to that of l-histidine decarboxylases and l-valine decarboxylases from Streptomyces sp. strains. The mdc gene was cloned and recombinant MetDC was heterologously expressed by Escherichia coli. The purification of recombinant MetDC was carried out by DEAE-Toyopearl and Ni-NTA agarose column chromatography. The recombinant enzyme was homodimeric with a molecular mass of 61,000 Da and showed optimal activity between 45 to 55 °C and at pH 6.6, and the stability below 30 °C and between pH 4.6 to 7.0. l-Methionine and l-norleucine were good substrates for MetDC. The Michaelis constants for l-methionine and l-norleucine were 30 and 73 mM, respectively. The recombinant MetDC (0.50 U/ml) severely inhibited growth of human tumour cells A431 (epidermoid ovarian carcinoma cell line) and MDA-MB-231 (breast cancer cell line), however showed relatively low cytotoxicity for human normal cell NHDF-Neo (dermal fibroblast cell line from neonatal foreskin). This study revealed the properties of the gene and the protein sequence of MetDC for the first time.
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Affiliation(s)
- Masaya Hayashi
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Akane Okada
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Kumiko Yamamoto
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Tomomi Okugochi
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Chika Kusaka
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Daizou Kudou
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Michiko Nemoto
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Junko Inagaki
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Yuu Hirose
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Toshihide Okajima
- Institute of Scientific and Industrial Research, Osaka University, 8-1 Miho-gaoka, Osaka 567-0047, Japan
| | - Takashi Tamura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Kenji Soda
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kenji Inagaki
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
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44
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Ohba S, Hirose Y. P08.45 Inhibition of homologous recombination resensitizes temozolomide-resistant glioma cells to temozolomide. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox036.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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45
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Sakata J, Kobayashi T, Ohashi T, Hirose Y, Takano K, Takizawa K, Miura K, Ishikawa H, Toge K, Yuza K, Soma D, Ando T, Wakai T. Prognostic heterogeneity of the seventh edition of UICC Stage III gallbladder carcinoma: Which patients benefit from surgical resection? Eur J Surg Oncol 2017; 43:780-787. [DOI: 10.1016/j.ejso.2017.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/30/2016] [Accepted: 01/09/2017] [Indexed: 01/08/2023] Open
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46
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Kawahara K, Chikamatsu A, Katayama T, Onozuka T, Ogawa D, Morikawa K, Ikenaga E, Hirose Y, Harayama I, Sekiba D, Fukumura T, Hasegawa T. Topotactic fluorination of perovskite strontium ruthenate thin films using polyvinylidene fluoride. CrystEngComm 2017. [DOI: 10.1039/c6ce02358d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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48
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Suzuki H, Sakabe T, Hirose Y, Eki T. Development and evaluation of yeast-based GFP and luciferase reporter assays for chemical-induced genotoxicity and oxidative damage. Appl Microbiol Biotechnol 2016; 101:659-671. [PMID: 27766356 DOI: 10.1007/s00253-016-7911-z] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/21/2016] [Accepted: 09/28/2016] [Indexed: 11/30/2022]
Abstract
We aimed to develop the bioassays for genotixicity and/or oxidative damage using the recombinant yeast. A genotoxicity assay was developed using recombinant Saccharomyces cerevisiae strain BY4741 with a green fluorescent protein (GFP) reporter plasmid, driven by the DNA damage-responsive RNR3 promoter. Enhanced fluorescence induction was observed in DNA repair-deficient strains treated with methyl methanesulfonate, but not with hydrogen peroxide. A GFP reporter yeast strain driven by the oxidative stress-responsive TRX2 promoter was newly developed to assess oxidative damage, but fluorescence was poorly induced by oxidants. In place of GFP, yeast strains with luciferase gene reporter plasmids (luc2 and luc2CP, encoding stable and unstable luciferase, respectively) were prepared. Transient induction of luciferase activity was clearly detected only in a TRX2 promoter-driven luc2CP reporter strain within 90 min of oxidant exposure. However, luciferase was strongly induced by hydroxyurea in the RNR3 promoter-driven luc2 and GFP reporter strains over 8 h after the exposure, suggesting that the RNR3 promoter is continuously upregulated by DNA damage, whereas the TRX2 promoter is transiently activated by oxidative agents. Luciferase activity levels were also increased in a TRX2-promoter-driven luc2CP reporter strain treated with tert-butyl hydroperoxide and menadione and weakly induced with diamide and diethyl maleate. Weakly enhanced luciferase activity induction was detected in the sod1Δ, sod2Δ, and rad27Δ strains treated with hydrogen peroxide compared with that in the wild-type strain. In conclusion, tests using GFP and stable luciferase reporters are useful for genotoxicity, and oxidative damage can be clearly detected by assay with an unstable luciferase reporter.
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Affiliation(s)
- Hajime Suzuki
- Molecular Genetics Laboratory, Division of Bioscience and Biotechnology, Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Takahiro Sakabe
- Molecular Genetics Laboratory, Division of Bioscience and Biotechnology, Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Yuu Hirose
- Molecular Genetics Laboratory, Division of Bioscience and Biotechnology, Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan.,The Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Toshihiko Eki
- Molecular Genetics Laboratory, Division of Bioscience and Biotechnology, Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan.
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49
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Miura K, Kobayashi T, Zhang Z, Soma D, Hirose Y, Ishikawa H, Takizawa K, Nagahashi M, Sakata J, Kameyama H, Minagawa M, Kosugi S, Koyama Y, Wakai T. Study of Immune Tolerance Cases in Adult Living Donor Liver Transplantation. Transplant Proc 2016; 48:1119-22. [PMID: 27320570 DOI: 10.1016/j.transproceed.2015.12.093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 12/30/2015] [Indexed: 10/21/2022]
Abstract
BACKGROUND Complete immune tolerance is the chief goal in organ transplantation. This study aimed to evaluate patients who successfully withdrew from immunosuppressive (IS) agents after living donor liver transplantation (LDLT). MATERIALS AND METHODS A retrospective review of all adult LDLT from July 1999 to March 2012 was conducted. In patients who acquired immune tolerance after LDLT, their background and the course of surgical procedures were evaluated. RESULTS Of a total of 101 adult LDLT patients, 8 patients were completely free of IS agents. Six of these patients (75%) were female, and the median age at the time of transplantation was 56 years (range, 31-66 years). The primary disease causing liver failure was type C liver cirrhosis (50%), fulminant hepatitis (25%), type B liver cirrhosis (12%), and alcoholic liver cirrhosis (12%). The median Child-Pugh score and MELD score were 13 points (range, 8-15 points) and 19 points (range, 10-18 points), respectively. The living related donor was the recipient's child (75%), sibling (12%), or parent (12%). ABO compatibility was identical in 62%, compatible in 25%, and incompatible in 12%. CONCLUSIONS In this study, we evaluated the adult patients who successfully withdrew from IS agents after LDLT. In most cases, it took more than 5 years to reduce IS agents. Because monitoring of the serum transaminase level is not adequate to detect chronic liver fibrosis in immune tolerance cases, further study is required to find appropriate protocols for reducing IS agent use after LDLT.
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Affiliation(s)
- K Miura
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - T Kobayashi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
| | - Z Zhang
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - D Soma
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Y Hirose
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - H Ishikawa
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - K Takizawa
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - M Nagahashi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - J Sakata
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - H Kameyama
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - M Minagawa
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - S Kosugi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Y Koyama
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - T Wakai
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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50
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Kobayashi T, Miura K, Ishikawa H, Soma D, Zhang Z, Yuza K, Hirose Y, Takizawa K, Nagahashi M, Sakata J, Kameyama H, Kosugi S, Wakai T. Successful Endoscopic Management of Acute Necrotic Pancreatitis and Walled Off Necrosis After Auxiliary Partial Orthotopic Living-Donor Liver Transplantation: A Case Report. Transplant Proc 2016; 48:1212-4. [PMID: 27320589 DOI: 10.1016/j.transproceed.2015.12.113] [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] [Received: 12/04/2015] [Accepted: 12/30/2015] [Indexed: 01/06/2023]
Abstract
Endoscopic management of acute necrotic pancreatitis and walled off necrosis is less invasive than surgical treatment and has become the 1st choice for treating pancreatic necrosis and abscess. We treated a case of acute necrotic pancreatitis and walled off necrosis after auxiliary partial orthotopic living-donor liver transplantation (APOLT). A 24-year-old woman was admitted to our university hospital for removal of the internal biliary stent, which had already been placed endoscopically for the treatment of biliary stricture after APOLT. She had been treated for acute liver failure by APOLT 10 years before. After we removed the internal stent with the use of an endoscopic retrograde approach, she presented with severe abdominal pain and a high fever. Her diagnosis was severe acute pancreatitis after endoscopic retrograde cholangiography (ERC). Her symptoms worsened, and she had multiple organ failure. She was transferred to the intensive care unit (ICU). Immunosuppression was discontinued because infection treatment was necessary and the native liver had already recovered sufficiently. After she had been treated for 19 days in the ICU, she recovered from her multiple organ failure. However, abdominal computerized tomography demonstrated the formation of pancreatic walled off necrosis and an abscess on the 20th day after ERC. We performed endoscopic ultrasonography-guided abscess drainage and repeated endoscopic necrosectomy. The walled off necrosis diminished gradually in size, and the symptoms disappeared. The patient was discharged on the 87th day after ERC. This is the 1st report of a case of acute necrotic pancreatitis and walled off necrosis that was successfully treated by endoscopic management after APOLT.
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Affiliation(s)
- T Kobayashi
- Division of Digestive and General Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.
| | - K Miura
- Division of Digestive and General Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - H Ishikawa
- Division of Digestive and General Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - D Soma
- Division of Digestive and General Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Z Zhang
- Division of Digestive and General Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - K Yuza
- Division of Digestive and General Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Y Hirose
- Division of Digestive and General Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - K Takizawa
- Division of Digestive and General Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - M Nagahashi
- Division of Digestive and General Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - J Sakata
- Division of Digestive and General Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - H Kameyama
- Division of Digestive and General Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - S Kosugi
- Division of Digestive and General Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - T Wakai
- Division of Digestive and General Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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