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Katayama M, Murakami S, Ishida H, Matsugo H, Sekine W, Ohira K, Takenaka-Uema A, Horimoto T. Antigenic commonality and divergence of hemagglutinin-esterase-fusion protein among influenza D virus lineages revealed using epitope mapping. J Virol 2024; 98:e0190823. [PMID: 38345383 PMCID: PMC10949428 DOI: 10.1128/jvi.01908-23] [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: 12/04/2023] [Accepted: 01/20/2024] [Indexed: 03/20/2024] Open
Abstract
Influenza D virus (IDV) is one of the causative agents of bovine respiratory disease complex, which is the most common and economically burdensome disease affecting the cattle industry, and the need for an IDV vaccine has been proposed to enhance disease control. IDVs are classified into five genetic lineages based on the coding sequences of the hemagglutinin-esterase-fusion (HEF) protein, an envelope glycoprotein, which is the main target of protective antibodies against IDV infection. Herein, we prepared a panel of monoclonal antibodies (mAbs) against the HEF protein of viruses of various lineages to investigate the antigenic characteristics of IDVs and found that the mAbs could be largely separated into three groups. The first, second, and third groups demonstrated lineage-specific reactivity, cross-reactivity to viruses of multiple but not all lineages, and cross-reactivity to viruses of all lineages, respectively. Analyzing the escape mutant viruses from virus-neutralizing mAbs revealed that the receptor-binding region of the HEF molecule harbors virus-neutralizing epitopes that are conserved across multiple lineage viruses. In contrast, the apex region of the molecule possessed epitopes unique to each lineage virus. Furthermore, reverse genetics-generated recombinant viruses with point mutations revealed that amino acids within positions 210-214 of the HEF protein determined the antigenic specificity of each lineage virus. Taken together, this study reveals considerable antigenic variation among IDV lineages, although they are presumed to form a single serotype in terms of HEF antigenicity. Characterization of the antigenic epitope structure of HEF may contribute to selecting and creating effective vaccine viruses against IDV.IMPORTANCEInfluenza D viruses (IDVs) are suggested to create cross-reactive single serotypes in hemagglutinin-esterase-fusion (HEF) antigenicity, as indicated by serological analyses among distinct HEF lineage viruses. This is supported by the high identities of HEF gene sequences among strains, unlike the hemagglutinin (HA) genes of the influenza A virus that exhibit HA subtypes. Herein, we analyzed HEF antigenicity using a monoclonal antibody panel prepared from several virus lineages and found the existence of lineage-conserved and lineage-specific epitopes in HEF molecules. These findings confirm the HEF commonality and divergence among IDVs and provide useful information for constructing a vaccine containing a recombinant IDV virus with an engineered HEF gene, thereby leading to broad immunogenicity.
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Affiliation(s)
- Misa Katayama
- Laboratory of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shin Murakami
- Laboratory of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroho Ishida
- Laboratory of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Laboratory of Infectious Diseases, School of Veterinary Medicine, Azabu University, Kanagawa, Japan
| | - Hiromichi Matsugo
- Laboratory of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Laboratory of RNA Viruses, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Wataru Sekine
- Laboratory of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kosuke Ohira
- Laboratory of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Akiko Takenaka-Uema
- Laboratory of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Taisuke Horimoto
- Laboratory of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Kojima M, Makita N, Miyata K, Yoshino M, Iwase A, Ohashi M, Surjana A, Kudo T, Takeda-Kamiya N, Toyooka K, Miyao A, Hirochika H, Ando T, Shomura A, Yano M, Yamamoto T, Hobo T, Sakakibara H. A cell wall-localized cytokinin/purine riboside nucleosidase is involved in apoplastic cytokinin metabolism in Oryza sativa. Proc Natl Acad Sci U S A 2023; 120:e2217708120. [PMID: 37639600 PMCID: PMC10483608 DOI: 10.1073/pnas.2217708120] [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: 11/01/2022] [Accepted: 07/18/2023] [Indexed: 08/31/2023] Open
Abstract
In the final step of cytokinin biosynthesis, the main pathway is the elimination of a ribose-phosphate moiety from the cytokinin nucleotide precursor by phosphoribohydrolase, an enzyme encoded by a gene named LONELY GUY (LOG). This reaction accounts for most of the cytokinin supply needed for regulating plant growth and development. In contrast, the LOG-independent pathway, in which dephosphorylation and deribosylation sequentially occur, is also thought to play a role in cytokinin biosynthesis, but the gene entity and physiological contribution have been elusive. In this study, we profiled the phytohormone content of chromosome segment substitution lines of Oryza sativa and searched for genes affecting the endogenous levels of cytokinin ribosides by quantitative trait loci analysis. Our approach identified a gene encoding an enzyme that catalyzes the deribosylation of cytokinin nucleoside precursors and other purine nucleosides. The cytokinin/purine riboside nucleosidase 1 (CPN1) we identified is a cell wall-localized protein. Loss-of-function mutations (cpn1) were created by inserting a Tos17-retrotransposon that altered the cytokinin composition in seedling shoots and leaf apoplastic fluid. The cpn1 mutation also abolished cytokinin riboside nucleosidase activity in leaf extracts and attenuated the trans-zeatin riboside-responsive expression of cytokinin marker genes. Grain yield of the mutants declined due to altered panicle morphology under field-grown conditions. These results suggest that the cell wall-localized LOG-independent cytokinin activating pathway catalyzed by CPN1 plays a role in cytokinin control of rice growth. Our finding broadens our spatial perspective of the cytokinin metabolic system.
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Affiliation(s)
- Mikiko Kojima
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya464-8601, Japan
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama230-0045, Japan
| | - Nobue Makita
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama230-0045, Japan
| | - Kazuki Miyata
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya464-8601, Japan
| | - Mika Yoshino
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya464-8601, Japan
| | - Akira Iwase
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama230-0045, Japan
| | - Miwa Ohashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya464-8601, Japan
| | - Alicia Surjana
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya464-8601, Japan
| | - Toru Kudo
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama230-0045, Japan
| | | | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama230-0045, Japan
| | - Akio Miyao
- National Institute of Agrobiological Sciences, Tsukuba305-8602, Japan
- Institute of Crop Science, National Agricultural and Food Research Organization, Tsukuba305-8518, Japan
| | | | - Tsuyu Ando
- National Institute of Agrobiological Sciences, Tsukuba305-8602, Japan
- Institute of Crop Science, National Agricultural and Food Research Organization, Tsukuba305-8518, Japan
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki305-0854, Japan
| | - Ayahiko Shomura
- National Institute of Agrobiological Sciences, Tsukuba305-8602, Japan
- Institute of Crop Science, National Agricultural and Food Research Organization, Tsukuba305-8518, Japan
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki305-0854, Japan
| | - Masahiro Yano
- National Institute of Agrobiological Sciences, Tsukuba305-8602, Japan
- Institute of Crop Science, National Agricultural and Food Research Organization, Tsukuba305-8518, Japan
| | - Toshio Yamamoto
- National Institute of Agrobiological Sciences, Tsukuba305-8602, Japan
- Institute of Crop Science, National Agricultural and Food Research Organization, Tsukuba305-8518, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki710-0046, Japan
| | - Tokunori Hobo
- Bioscience and Biotechnology Center, Nagoya University, Chikusa, Nagoya464-8601, Japan
| | - Hitoshi Sakakibara
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya464-8601, Japan
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama230-0045, Japan
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Yasuda T, Harada N, Hatoko T, Ichimura A, Ikeguchi-Ogura E, Murata Y, Wada N, Kiyobayashi S, Yamane S, Hirasawa A, Inagaki N. Inhibition of GPR120 signaling in intestine ameliorates insulin resistance and fatty liver under high-fat diet feeding. Am J Physiol Endocrinol Metab 2023; 324:E449-E460. [PMID: 37074989 DOI: 10.1152/ajpendo.00329.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
G-protein-coupled receptor (GPR) 120 is expressed in enteroendocrine cells secreting glucagon-like peptide-1 (GLP-1), glucose-dependent insulinotropic polypeptide/gastric inhibitory polypeptide (GIP), and cholecystokinin (CCK). Although GPR120 signaling in adipose tissue and macrophages has been reported to ameliorate obesity and insulin resistance on high long-chain triglyceride (LCT) diet, intestine-specific roles of GPR120 are unclear. To clarify the metabolic effect of GPR120 in intestine, we generated intestine-specific GPR120-knockout (GPR120int-/-) mice. In comparison with floxed GPR120 (WT) mice, GPR120int-/- mice exhibited reduced GIP secretion and CCK action without change of insulin, GLP-1, or peptide YY (PYY) secretion after single administration of LCT. Under a high-LCT diet, GPR120int-/- mice showed mild reduction of body weight and substantial amelioration of insulin resistance and fatty liver. Moreover, liver and white adipose tissue (WAT) of GPR120int-/- mice exhibited increased Akt phosphorylation and reduced gene expression of suppressor of cytokine signaling (SOCS) 3, which inhibits insulin signaling. In addition, gene expression of inflammatory cytokines in WAT and lipogenic molecules in liver were reduced in GPR120int-/- mice. These findings suggest that inhibition of GPR120 signaling in intestine ameliorates insulin resistance and fatty liver under high-LCT diet feeding.
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Affiliation(s)
- Takuma Yasuda
- Department of Diabetes, Endocrinology and Nutrition, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Norio Harada
- Department of Diabetes, Endocrinology and Nutrition, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomonobu Hatoko
- Department of Diabetes, Endocrinology and Nutrition, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsuhiko Ichimura
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Eri Ikeguchi-Ogura
- Department of Diabetes, Endocrinology and Nutrition, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuki Murata
- Department of Diabetes, Endocrinology and Nutrition, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Naoki Wada
- Department of Diabetes, Endocrinology and Nutrition, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sakura Kiyobayashi
- Department of Diabetes, Endocrinology and Nutrition, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shunsuke Yamane
- Department of Diabetes, Endocrinology and Nutrition, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akira Hirasawa
- Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Japan
| | - Nobuya Inagaki
- Department of Diabetes, Endocrinology and Nutrition, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan
- P.I.I.F. Tazuke-Kofukai Medical Research Institute, Kitano Hospital, Osaka, Japan
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Mishina K, Suzuki T, Oono Y, Yamashita Y, Zhu H, Ogawa T, Ohta M, Doman K, Xu W, Takahashi D, Miyazaki T, Tagiri A, Soma C, Horita H, Nasuda S, De Oliveira R, Paux E, Chen G, Pourkheirandish M, Wu J, Liu C, Komatsuda T. Wheat Ym2 originated from Aegilops sharonensis and confers resistance to soil-borne Wheat yellow mosaic virus infection to the roots. Proc Natl Acad Sci U S A 2023; 120:e2214968120. [PMID: 36897977 PMCID: PMC10089197 DOI: 10.1073/pnas.2214968120] [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: 09/05/2022] [Accepted: 01/30/2023] [Indexed: 03/12/2023] Open
Abstract
Wheat yellow mosaic virus (WYMV) is a pathogen transmitted into its host's roots by the soil-borne vector Polymyxa graminis. Ym1 and Ym2 genes protect the host from the significant yield losses caused by the virus, but the mechanistic basis of these resistance genes remains poorly understood. Here, it has been shown that Ym1 and Ym2 act within the root either by hindering the initial movement of WYMV from the vector into the root and/or by suppressing viral multiplication. A mechanical inoculation experiment on the leaf revealed that the presence of Ym1 reduced viral infection incidence, rather than viral titer, while that of Ym2 was ineffective in the leaf. To understand the basis of the root specificity of the Ym2 product, the gene was isolated from bread wheat using a positional cloning approach. The candidate gene encodes a CC-NBS-LRR protein and it correlated allelic variation with respect to its sequence with the host's disease response. Ym2 (B37500) and its paralog (B35800) are found in the near-relatives, respectively, Aegilops sharonensis and Aegilops speltoides (a close relative of the donor of bread wheat's B genome), while both sequences, in a concatenated state, are present in several accessions of the latter species. Structural diversity in Ym2 has been generated via translocation and recombination between the two genes and enhanced by the formation of a chimeric gene resulting from an intralocus recombination event. The analysis has revealed how the Ym2 region has evolved during the polyploidization events leading to the creation of cultivated wheat.
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Affiliation(s)
- Kohei Mishina
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
| | - Takako Suzuki
- Hokkaido Research Organization, Agricultural Research Department, Chuo Agricultural Experiment Station, Naganuma, Hokkaido069-1395, Japan
| | - Youko Oono
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba271-8510Japan
| | - Yoko Yamashita
- Hokkaido Research Organization, Agricultural Research Department, Chuo Agricultural Experiment Station, Naganuma, Hokkaido069-1395, Japan
| | - Hongjing Zhu
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba271-8510Japan
| | - Taiichi Ogawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8634, Japan
| | - Masaru Ohta
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
| | - Kohei Doman
- Hokkaido Research Organization, Agricultural Research Department, Chuo Agricultural Experiment Station, Naganuma, Hokkaido069-1395, Japan
| | - Wenjing Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong250100, China
- Shandong Wheat Technology Innovation Center, Jinan, Shandong250100, China
| | - Daichi Takahashi
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata940-2188, Japan
| | - Taiga Miyazaki
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata940-2188, Japan
| | - Akemi Tagiri
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
| | - Chihiro Soma
- Hokkaido Research Organization, Agricultural Research Department, Chuo Agricultural Experiment Station, Naganuma, Hokkaido069-1395, Japan
| | - Harukuni Horita
- Hokkaido Research Organization, Agricultural Research Department, Chuo Agricultural Experiment Station, Naganuma, Hokkaido069-1395, Japan
| | - Shuhei Nasuda
- Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Romain De Oliveira
- Université Clermont Auvergne, National Research Institute for Agriculture, Food & Environment (INRAE), Genetics, Diversity & Ecophysiology of Cereals, 63000Clermont-Ferrand, France
- Gencovery69009Lyon, France
| | - Etienne Paux
- Université Clermont Auvergne, National Research Institute for Agriculture, Food & Environment (INRAE), Genetics, Diversity & Ecophysiology of Cereals, 63000Clermont-Ferrand, France
- VetAgro Sup,63370Lempdes, France
| | - Guoxiong Chen
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou730000, China
| | | | - Jianzhong Wu
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
| | - Cheng Liu
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong250100, China
- Shandong Wheat Technology Innovation Center, Jinan, Shandong250100, China
| | - Takao Komatsuda
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong250100, China
- Shandong Wheat Technology Innovation Center, Jinan, Shandong250100, China
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Nishikawa S, Ogawa Y, Shiraiwa K, Nozawa R, Nakayama M, Eguchi M, Shimoji Y. Rational Design of Live-Attenuated Vaccines against Genome-Reduced Pathogens. Microbiol Spectr 2022; 10:e0377622. [PMID: 36453908 PMCID: PMC9769512 DOI: 10.1128/spectrum.03776-22] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/04/2022] [Indexed: 12/03/2022] Open
Abstract
To develop safe and highly effective live vaccines, rational vaccine design is necessary. Here, we sought a simple approach to rationally develop a safe attenuated vaccine against the genome-reduced pathogen Erysipelothrix rhusiopathiae. We examined the mRNA expression of all conserved amino acid biosynthetic genes remaining in the genome after the reductive evolution of E. rhusiopathiae. Reverse transcription-quantitative PCR (qRT-PCR) analysis revealed that half of the 14 genes examined were upregulated during the infection of murine J774A.1 macrophages. Gene deletion was possible only for three proline biosynthesis genes, proB, proA, and proC, the last of which was upregulated 29-fold during infection. Five mutants bearing an in-frame deletion of one (ΔproB, ΔproA, or ΔproC mutant), two (ΔproBA mutant), or three (ΔproBAC mutant) genes exhibited attenuated growth during J774A.1 infection, and the attenuation and vaccine efficacy of these mutants were confirmed in mice and pigs. Thus, for the rational design of live vaccines against genome-reduced bacteria, the selective targeting of genes that escaped chromosomal deletions during evolution may be a simple approach for identifying genes which are specifically upregulated during infection. IMPORTANCE Identification of bacterial genes that are specifically upregulated during infection can lead to the rational construction of live vaccines. For this purpose, genome-based approaches, including DNA microarray analysis and IVET (in vivo expression technology), have been used so far; however, these methods can become laborious and time-consuming. In this study, we used a simple in silico approach and showed that in genome-reduced bacteria, the genes which evolutionarily remained conserved for metabolic adaptations during infection may be the best targets for the deletion and construction of live vaccines.
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Affiliation(s)
- Sayaka Nishikawa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Yohsuke Ogawa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Kazumasa Shiraiwa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Rieko Nozawa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Momoko Nakayama
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Masahiro Eguchi
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Yoshihiro Shimoji
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
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Nguyen HTM, Akanuma G, Hoa TTM, Nakai Y, Kimura K, Yamamoto K, Inaoka T. Ribosome Reconstruction during Recovery from High-Hydrostatic-Pressure-Induced Injury in Bacillus subtilis. Appl Environ Microbiol 2019; 86:e01640-19. [PMID: 31604775 PMCID: PMC6912085 DOI: 10.1128/aem.01640-19] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023] Open
Abstract
Vegetative cells of Bacillus subtilis can recover from injury after high-hydrostatic-pressure (HHP) treatment at 250 MPa. DNA microarray analysis revealed that substantial numbers of ribosomal genes and translation-related genes (e.g., translation initiation factors) were upregulated during the growth arrest phase after HHP treatment. The transcript levels of cold shock-responsive genes, whose products play key roles in efficient translation, and heat shock-responsive genes, whose products mediate correct protein folding or degrade misfolded proteins, were also upregulated. In contrast, the transcript level of hpf, whose product (Hpf) is involved in ribosome inactivation through the dimerization of 70S ribosomes, was downregulated during the growth arrest phase. Sucrose density gradient sedimentation analysis revealed that ribosomes were dissociated in a pressure-dependent manner and then reconstructed. We also found that cell growth after HHP-induced injury was apparently inhibited by the addition of Mn2+ or Zn2+ to the recovery medium. Ribosome reconstruction in the HHP-injured cells was also significantly delayed in the presence of Mn2+ or Zn2+ Moreover, Zn2+, but not Mn2+, promoted dimer formation of 70S ribosomes in the HHP-injured cells. Disruption of the hpf gene suppressed the Zn2+-dependent accumulation of ribosome dimers, partially relieving the inhibitory effect of Zn2+ on the growth recovery of HHP-treated cells. In contrast, it was likely that Mn2+ prevented ribosome reconstruction without stimulating ribosome dimerization. Our results suggested that both Mn2+ and Zn2+ can prevent ribosome reconstruction, thereby delaying the growth recovery of HHP-injured B. subtilis cells.IMPORTANCE HHP treatment is used as a nonthermal processing technology in the food industry to inactivate bacteria while retaining high quality of foods under suppressed chemical reactions. However, some populations of bacterial cells may survive the inactivation. Although the survivors are in a transient nongrowing state due to HHP-induced injury, they can recover from the injury and then start growing, depending on the postprocessing conditions. The recovery process in terms of cellular components after the injury remains unclear. Transcriptome analysis using vegetative cells of Bacillus subtilis revealed that the translational machinery can preferentially be reconstructed after HHP treatment. We found that both Mn2+ and Zn2+ prolonged the growth-arrested stage of HHP-injured cells by delaying ribosome reconstruction. It is likely that ribosome reconstruction is crucial for the recovery of growth ability in HHP-injured cells. This study provides further understanding of the recovery process in HHP-injured B. subtilis cells.
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Affiliation(s)
- Huyen Thi Minh Nguyen
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam
| | | | - Tu Thi Minh Hoa
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam
| | - Yuji Nakai
- Institute of Regional Innovation, Hirosaki University, Aomori, Japan
| | - Keitarou Kimura
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Kazutaka Yamamoto
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Takashi Inaoka
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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Yoshida T, Shiraishi T, Hagiwara-Komoda Y, Komatsu K, Maejima K, Okano Y, Fujimoto Y, Yusa A, Yamaji Y, Namba S. The Plant Noncanonical Antiviral Resistance Protein JAX1 Inhibits Potexviral Replication by Targeting the Viral RNA-Dependent RNA Polymerase. J Virol 2019; 93:e01506-18. [PMID: 30429349 PMCID: PMC6340027 DOI: 10.1128/jvi.01506-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 08/30/2018] [Accepted: 11/08/2018] [Indexed: 11/20/2022] Open
Abstract
Understanding the innate immune mechanisms of plants is necessary for the breeding of disease-resistant lines. Previously, we identified the antiviral resistance gene JAX1 from Arabidopsis thaliana, which inhibits infection by potexviruses. JAX1 encodes a unique jacalin-type lectin protein. In this study, we analyzed the molecular mechanisms of JAX1-mediated resistance. JAX1 restricted the multiplication of a potexviral replicon lacking movement-associated proteins, suggesting inhibition of viral replication. Therefore, we developed an in vitro potato virus X (PVX) translation/replication system using vacuole- and nucleus-free lysates from tobacco protoplasts, and we revealed that JAX1 inhibits viral RNA synthesis but not the translation of the viral RNA-dependent RNA polymerase (RdRp). JAX1 did not affect the replication of a resistance-breaking mutant of PVX. Blue native polyacrylamide gel electrophoresis of fractions separated by sucrose gradient sedimentation showed that PVX RdRp constituted the high-molecular-weight complex that seems to be crucial for viral replication. JAX1 was detected in this complex of the wild-type PVX replicon but not in that of the resistance-breaking mutant. In addition, JAX1 interacted with the RdRp of the wild-type virus but not with that of a virus with a point mutation at the resistance-breaking residue. These results suggest that JAX1 targets RdRp to inhibit potexviral replication.IMPORTANCE Resistance genes play a crucial role in plant antiviral innate immunity. The roles of conventional nucleotide-binding leucine-rich repeat (NLR) proteins and the associated defense pathways have long been studied. In contrast, recently discovered resistance genes that do not encode NLR proteins (non-NLR resistance genes) have not been investigated extensively. Here we report that the non-NLR resistance factor JAX1, a unique jacalin-type lectin protein, inhibits de novo potexviral RNA synthesis by targeting the huge complex of viral replicase. This is unlike other known antiviral resistance mechanisms. Molecular elucidation of the target in lectin-type protein-mediated antiviral immunity will enhance our understanding of the non-NLR-mediated plant resistance system.
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Affiliation(s)
- Tetsuya Yoshida
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takuya Shiraishi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuka Hagiwara-Komoda
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ken Komatsu
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kensaku Maejima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukari Okano
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuji Fujimoto
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Akira Yusa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Jang J, Sakai Y, Senoo K, Ishii S. Potentially Mobile Denitrification Genes Identified in Azospirillum sp. Strain TSH58. Appl Environ Microbiol 2019; 85:e02474-18. [PMID: 30413471 PMCID: PMC6328785 DOI: 10.1128/aem.02474-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 10/09/2018] [Accepted: 11/05/2018] [Indexed: 11/20/2022] Open
Abstract
Denitrification ability is sporadically distributed among diverse bacteria, archaea, and fungi. In addition, disagreement has been found between denitrification gene phylogenies and the 16S rRNA gene phylogeny. These facts have suggested potential occurrences of horizontal gene transfer (HGT) for the denitrification genes. However, evidence of HGT has not been clearly presented thus far. In this study, we identified the sequences and the localization of the nitrite reductase genes in the genomes of 41 denitrifying Azospirillum sp. strains and searched for mobile genetic elements that contain denitrification genes. All Azospirillum sp. strains examined in this study possessed multiple replicons (4 to 11 replicons), with their sizes ranging from 7 to 1,031 kbp. Among those, the nitrite reductase gene nirK was located on large replicons (549 to 941 kbp). Genome sequencing showed that Azospirillum strains that had similar nirK sequences also shared similar nir-nor gene arrangements, especially between the TSH58, Sp7T, and Sp245 strains. In addition to the high similarity between nir-nor gene clusters among the three Azospirillum strains, a composite transposon structure was identified in the genome of strain TSH58, which contains the nir-nor gene cluster and the novel IS6 family insertion sequences (ISAz581 and ISAz582). The nirK gene within the composite transposon system was actively transcribed under denitrification-inducing conditions. Although not experimentally verified in this study, the composite transposon system containing the nir-nor gene cluster could be transferred to other cells if it is moved to a prophage region and the phage becomes activated and released outside the cells. Taken together, strain TSH58 most likely acquired its denitrification ability by HGT from closely related Azospirillum sp. denitrifiers.IMPORTANCE The evolutionary history of denitrification is complex. While the occurrence of horizontal gene transfer has been suggested for denitrification genes, most studies report circumstantial evidences, such as disagreement between denitrification gene phylogenies and the 16S rRNA gene phylogeny. Based on the comparative genome analyses of Azospirillum sp. denitrifiers, we identified denitrification genes, including nirK and norCBQD, located on a mobile genetic element in the genome of Azospirillum sp. strain TSH58. The nirK was actively transcribed under denitrification-inducing conditions. Since this gene was the sole nitrite reductase gene in strain TSH58, this strain most likely benefitted by acquiring denitrification genes via horizontal gene transfer. This finding will significantly advance our scientific knowledge regarding the ecology and evolution of denitrification.
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Affiliation(s)
- Jeonghwan Jang
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Yoriko Sakai
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Satoshi Ishii
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota, USA
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, USA
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Ofori PA, Mizuno A, Suzuki M, Martinoia E, Reuscher S, Aoki K, Shibata D, Otagaki S, Matsumoto S, Shiratake K. Genome-wide analysis of ATP binding cassette (ABC) transporters in tomato. PLoS One 2018; 13:e0200854. [PMID: 30048467 PMCID: PMC6062036 DOI: 10.1371/journal.pone.0200854] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [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: 05/16/2018] [Accepted: 07/03/2018] [Indexed: 11/18/2022] Open
Abstract
ATP binding cassette (ABC) transporters are proteins that actively mediate the transport of a wide range of molecules, such as organic acids, metal ions, phytohormones and secondary metabolites. Therefore, ABC transporters must play indispensable roles in growth and development of tomato, including fruit development. Most ABC transporters have transmembrane domains (TMDs) and belong to the ABC protein family, which includes not only ABC transporters but also soluble ABC proteins lacking TMDs. In this study, we performed a genome-wide identification and expression analysis of genes encoding ABC proteins in tomato (Solanum lycopersicum), which is a valuable horticultural crop and a model plant for studying fleshy fruits. In the tomato genome, a total of 154 genes putatively encoding ABC transporters, including 9 ABCAs, 29 ABCBs, 26 ABCCs, 2 ABCDs, 2 ABCEs, 6 ABCFs, 70 ABCGs and 10 ABCIs, were identified. Gene expression data from the eFP Browser and reverse transcription-semi-quantitative PCR analysis revealed their tissue-specific and development-specific expression profiles. This work suggests physiological roles of ABC transporters in tomato and provides fundamental information for future studies of ABC transporters not only in tomato but also in other Solanaceae species.
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Affiliation(s)
- Peter Amoako Ofori
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Ayaka Mizuno
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mami Suzuki
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Enrico Martinoia
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Stefan Reuscher
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Koh Aoki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | | | - Shungo Otagaki
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Shogo Matsumoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- * E-mail:
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Nijo T, Okano Y, Kondo M, Okuhara H, Sekimura H, Fujimoto Y, Hosoe N, Maejima K, Yamaji Y, Namba S. Complete Genome Sequence of a Lily virus X Isolate from Japan. Genome Announc 2018; 6:e01462-17. [PMID: 29371349 PMCID: PMC5786675 DOI: 10.1128/genomea.01462-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 12/15/2017] [Indexed: 11/20/2022]
Abstract
The complete genome sequence of Lily virus X (LVX), which infects lilies, was determined for the first time from lilies in Japan. As with previous reports, the genome of the Japanese LVX isolate lacked an AUG start codon for the triple gene block protein 3-like region.
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Affiliation(s)
- Takamichi Nijo
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukari Okano
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masayoshi Kondo
- Biotechnology Division, Niigata Agricultural Research Institute, Niigata, Japan
| | - Hiroaki Okuhara
- Biotechnology Division, Niigata Agricultural Research Institute, Niigata, Japan
| | - Hiroyo Sekimura
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuji Fujimoto
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Naoi Hosoe
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kensaku Maejima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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