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Kambara K, Shimura H, Fujino K, Masuta C. Metagenomic Analyses of Viruses in the Orchid Mycorrhizal Interaction Using Improved Assemble Tools. Methods Mol Biol 2024; 2732:67-81. [PMID: 38060118 DOI: 10.1007/978-1-0716-3515-5_5] [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: 12/08/2023]
Abstract
In nature, mycorrhizal association with soil-borne fungi is indispensable for orchid species. Compatible mycorrhizal fungi form endo-mycorrhizal structures in orchid cells, and the fungal structures are digested in orchid cells to be supplied to orchids as nutrition. Because orchid seeds lack the reserves for germination, they keep receiving nutrition through mycorrhizal formation from seed germination until nonphotosynthetic young seedlings develop leaves and become photoautotrophic. Seeds of all orchids germinate with the help of their own fungal partners, and therefore, specific partnership has been acquired in a long evolutionary history between orchids and fungi. Assuming that horizontal transmission of viruses may occur in such a close relationship, we are focusing on viruses that infect orchids and their mycorrhizal fungi. We prepared aseptically germinated orchid plants (i.e., fungi-free plants) together with pure-cultured fungal isolates and conducted transcriptome analyses (RNA-seq) by next-generation sequencing (NGS) approach. To reconstruct virus-related sequences that would have been present in the RNA sample of interest, de novo assembly process is required using short read sequences obtained from RNA-seq. In the previous version of our protocol (see Viral Metagenomics, first edition 2018), virus searches were conducted using contig sets constructed by a single assembler, but this time we devised a method to construct more reliable contigs using multiple assemblers and again reinvestigated that viruses could be detected. Because the virus detection efficiency and number of detected virus species clearly differed depending on the assembly pipeline and the number of the input data, multiple methods should be used to identify viral infection, if possible.
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Affiliation(s)
- Kota Kambara
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Tokyo, Japan
| | - Hanako Shimura
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan.
| | - Kaien Fujino
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Chikara Masuta
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
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Zhang X, Fujino K, Shimura H. Transcriptomic Analyses Reveal the Role of Cytokinin and the Nodal Stem in Microtuber Sprouting in Potato ( Solanum tuberosum L.). Int J Mol Sci 2023; 24:17534. [PMID: 38139361 PMCID: PMC10743403 DOI: 10.3390/ijms242417534] [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: 11/18/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
In potatoes, tuber secondary growth, especially sprouting, deforms the tubers and severely lowers their commercial value. Tuber sprouting is induced by signal substances, such as gibberellin (GA), which are transported to the tuber from the plant body. The molecular mechanism underlying GA-induced sprouting remains ambiguous. Here, we tried to recreate tuber secondary growth using in vitro stemmed microtubers (MTs) (with the nodal stem attached) and MT halves (with the nodal stem entirely removed). Our experiments showed that GA alone could initiate the sprouting of stemmed microtubers; however, GA failed to initiate MT halves unless 6-benzyladenine, a synthetic cytokinin CK, was co-applied. Here, we analyzed the transcriptional profiles of sprouting buds using these in vitro MTs. RNA-seq analysis revealed a downregulation of cytokinin-activated signaling but an upregulation of the "Zeatin biosynthesis" pathway, as shown by increased expression of CYP735A, CISZOG, and UGT85A1 in sprouting buds; additionally, the upregulation of genes, such as IAA15, IAA22, and SAUR50, associated with auxin-activated signaling and one abscisic acid (ABA) negative regulator, PLY4, plays a vital role during sprouting growth. Our findings indicate that the role of the nodal stem is synonymous with CK in sprouting growth, suggesting that CK signaling and homeostasis are critical to supporting GA-induced sprouting. To effectively control tuber sprouting, more effort is required to be devoted to these critical genes.
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Affiliation(s)
| | - Kaien Fujino
- Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan; (X.Z.)
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Kambara K, Fujino K, Shimura H. Construction of a de novo assembly pipeline using multiple transcriptome data sets from Cypripedium macranthos (Orchidaceae). PLoS One 2023; 18:e0286804. [PMID: 37279244 DOI: 10.1371/journal.pone.0286804] [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: 03/18/2023] [Accepted: 05/23/2023] [Indexed: 06/08/2023] Open
Abstract
The family Orchidaceae comprises the most species of any monocotyledonous family and has interesting characteristics such as seed germination induced by mycorrhizal fungi and flower morphology that co-adapted with pollinators. In orchid species, genomes have been decoded for only a few horticultural species, and there is little genetic information available. Generally, for species lacking sequenced genomes, gene sequences are predicted by de novo assembly of transcriptome data. Here, we devised a de novo assembly pipeline for transcriptome data from the wild orchid Cypripedium (lady slipper orchid) in Japan by mixing multiple data sets and integrating assemblies to create a more complete and less redundant contig set. Among the assemblies generated by combining various assemblers, Trinity and IDBA-Tran yielded good assembly with higher mapping rates and percentages of BLAST hit contigs and complete BUSCO. Using this contig set as a reference, we analyzed differential gene expression between protocorms grown aseptically or with mycorrhizal fungi to detect gene expressions required for mycorrhizal interaction. A pipeline proposed in this study can construct a highly reliable contig set with little redundancy even when multiple transcriptome data are mixed, and can provide a reference that is adaptable to DEG analysis and other downstream analysis in RNA-seq.
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Affiliation(s)
- Kota Kambara
- Faculty of Agriculture, Hokkaido University, Kita-ku, Sapporo, Japan
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo, Japan
| | - Kaien Fujino
- Faculty of Agriculture, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Hanako Shimura
- Faculty of Agriculture, Hokkaido University, Kita-ku, Sapporo, Japan
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Oku S, Ueno K, Sawazaki Y, Maeda T, Jitsuyama Y, Suzuki T, Onodera S, Fujino K, Shimura H. Functional characterization and vacuolar localization of fructan exohydrolase derived from onion (Allium cepa). J Exp Bot 2022; 73:4908-4922. [PMID: 35552692 DOI: 10.1093/jxb/erac197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Fructans such as inulin and levan accumulate in certain taxonomic groups of plants and are a reserve carbohydrate alternative to starch. Onion (Allium cepa L.) is a typical plant species that accumulates fructans, and it synthesizes inulin-type and inulin neoseries-type fructans in the bulb. Although genes for fructan biosynthesis in onion have been identified so far, no genes for fructan degradation had been found. In this study, phylogenetic analysis predicted that we isolated a putative vacuolar invertase gene (AcpVI1), but our functional analyses demonstrated that it encoded a fructan 1-exohydrolase (1-FEH) instead. Assessments of recombinant proteins and purified native protein showed that the protein had 1-FEH activity, hydrolyzing the β-(2,1)-fructosyl linkage in inulin-type fructans. Interestingly, AcpVI1 had an amino acid sequence close to those of vacuolar invertases and fructosyltransferases, unlike all other FEHs previously found in plants. We showed that AcpVI1 was localized in the vacuole, as are onion fructosyltransferases Ac1-SST and Ac6G-FFT. These results indicate that fructan-synthesizing and -degrading enzymes are both localized in the vacuole. In contrast to previously reported FEHs, our data suggest that onion 1-FEH evolved from a vacuolar invertase and not from a cell wall invertase. This demonstrates that classic phylogenetic analysis on its own is insufficient to discriminate between invertases and FEHs, highlighting the importance of functional markers in the nearby active site residues.
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Affiliation(s)
- Satoshi Oku
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Keiji Ueno
- Graduate School of Dairy Science, Rakuno Gakuen University, Ebetsu, 069-8501, Japan
| | - Yukiko Sawazaki
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Tomoo Maeda
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, 036-8561, Japan
| | - Yutaka Jitsuyama
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Takashi Suzuki
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Shuichi Onodera
- Graduate School of Dairy Science, Rakuno Gakuen University, Ebetsu, 069-8501, Japan
| | - Kaien Fujino
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Hanako Shimura
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
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Masuda K, Hikida R, Fujino K. The plant nuclear lamina proteins NMCP1 and NMCP2 form a filamentous network with lateral filament associations. J Exp Bot 2021; 72:6190-6204. [PMID: 34086868 PMCID: PMC8483785 DOI: 10.1093/jxb/erab243] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 06/18/2021] [Indexed: 05/25/2023]
Abstract
Plant genomes lack genes encoding intermediate filament proteins, including lamins; however, functional lamin analogues are presumed to exist in plants. Plant-specific coiled-coil proteins, that is, nuclear matrix constituent proteins (NMCPs), are the most likely candidates as the structural elements of the nuclear lamina because they exhibit a lamin-like domain arrangement. They are exclusively localized at the nuclear periphery and have functions that are analogous to those of lamins. However, their assembly into filamentous polymers has not yet been confirmed. In this study, we examined the higher-order structure of NMCP1 and NMCP2 in Apium graveolens cells by using stimulated emission depletion microscopy combined with immunofluorescence cell labelling. Our analyses revealed that NMCP1 and NMCP2 form intricate filamentous networks, which include thick segments consisting of filament bundles, forming a dense filamentous layer extending across the nuclear periphery. Furthermore, the outermost chromatin distribution was found to be in the nucleoplasm-facing region of the nuclear lamina. Recombinant Daucus carota NMCP1 with a His-tag produced in Escherichia coli refolded into dimers and self-assembled into filaments and filament bundles. These results suggest that NMCP1 and NMCP2 organize into the nuclear lamina by forming a filamentous network with filament bundles that localize at the nuclear periphery.
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Affiliation(s)
- Kiyoshi Masuda
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Sapporo 060-8589, Hokkaido, Japan
| | - Riku Hikida
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Sapporo 060-8589, Hokkaido, Japan
| | - Kaien Fujino
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Sapporo 060-8589, Hokkaido, Japan
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Yamamori K, Ogasawara K, Ishiguro S, Koide Y, Takamure I, Fujino K, Sato Y, Kishima Y. Revision of the relationship between anther morphology and pollen sterility by cold stress at the booting stage in rice. Ann Bot 2021; 128:559-575. [PMID: 34232290 PMCID: PMC8422894 DOI: 10.1093/aob/mcab091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/06/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS Cold stress in rice (Oryza sativa) plants at the reproductive stage prevents normal anther development and causes pollen sterility. Tapetum hypertrophy in anthers has been associated with pollen sterility in response to cold at the booting stage. Here, we re-examined whether the relationships between anther abnormality and pollen sterility caused by cold stress at the booting stage in rice can be explained by a monovalent factor such as tapetum hypertrophy. METHODS After exposing plants to a 4-d cold treatment at the booting stage, we collected and processed anthers for transverse sectioning immediately and at the flowering stage. We anatomically evaluated the effect of cold treatment on anther internal morphologies, pollen fertilities and pollen numbers in the 13 cultivars with various cold sensitivities. KEY RESULTS We observed four types of morphological anther abnormalities at each stage. Pollen sterility was positively correlated with the frequency of undeveloped locules, but not with tapetum hypertrophy as commonly believed. In cold-sensitive cultivars grown at low temperatures, pollen sterility was more frequent than anther morphological abnormalities, and some lines showed remarkably high pollen sterility without any anther morphological alterations. Most morphological anomalies occurred only in specific areas within large and small locules. Anther length tended to shorten in response to cold treatment and was positively correlated with pollen number. One cultivar showed a considerably reduced pollen number, but fertile pollen grains under cold stress. We propose three possible relationships to explain anther structure and pollen sterility and reduction due to cold stress. CONCLUSIONS The pollen sterility caused by cold stress at the booting stage was correlated with the frequency of entire locule-related abnormalities, which might represent a phenotypic consequence, but not a direct cause of pollen abortion. Multivalent factors might underlie the complicated relationships between anther abnormality and pollen sterility in rice.
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Affiliation(s)
- Koichi Yamamori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kei Ogasawara
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Seiya Ishiguro
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Itsuro Takamure
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kaien Fujino
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yutaka Sato
- National Agriculture and Food Research Organization, Hokkaido Agricultural Research Center, Sapporo, Japan
| | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
- For correspondence. E-mail
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Yoon HS, Fujino K, Liu S, Takano T, Tsugama D. NDR/LATS-family protein kinase genes are indispensable for embryogenesis in Arabidopsis. FEBS Open Bio 2021; 11:2600-2606. [PMID: 34320276 PMCID: PMC8409290 DOI: 10.1002/2211-5463.13257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 11/10/2022] Open
Abstract
NDR/LATS‐family protein kinases are conserved among eukaryotes. These protein kinases in yeast and animals phosphorylate specific targets and regulate the cell cycle. Arabidopsis thaliana has eight NDR/LATS‐family protein kinase genes (NDR1‐8), of which NDR2, NDR4, and NDR5 are involved in regulating pollen development. However, the functions of the other NDR/LATS‐family protein kinase genes in plants are unclear. Here, we show that three putative phosphorylation sites of an Arabidopsis basic leucine zipper transcription factor, VIP1, correspond to NDR/LATS‐family protein kinase phosphorylation motifs and that two of these three sites are phosphorylated by NDR2, NDR3, or NDR8 in vitro. Expression of NDR1‐8 was detected in various tissues. An NDR4 NDR6 NDR7 NDR8 quadruple mutation caused embryonic lethality These results suggest that different NDR/LATS‐family protein kinases in plants have distinct physiological roles.
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Affiliation(s)
- Hyuk Sung Yoon
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishitokyo-shi, Japan
| | - Kaien Fujino
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo-shi, Japan
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, China
| | - Tetsuo Takano
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishitokyo-shi, Japan
| | - Daisuke Tsugama
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishitokyo-shi, Japan
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Yoon HS, Fujino K, Liu S, Takano T, Tsugama D. The B″-family subunits of protein phosphatase 2A are necessary for in-vitro dephosphorylation of the Arabidopsis mechanosensory transcription factor VIP1. Biochem Biophys Res Commun 2020; 534:353-358. [PMID: 33342519 DOI: 10.1016/j.bbrc.2020.11.078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 11/28/2022]
Abstract
Protein phosphatase 2A (PP2A) B″-family subunits have Ca2+-binding EF-hand motifs and can bind PP2A substrates. Arabidopsis thaliana PP2A B″-family subunits are encoded by six genes, and bind a transcription factor, VIP1. VIP1 is dephosphorylated and nuclear-localized by hypo-osmotic stress. However, whether PP2A B″-family subunits mediate the VIP1 dephosphorylation is unclear. Here, we show by yeast two-hybrid and in vitro pull down assays that Arabidopsis PP2A B″-family subunits bind Arabidopsis PP2A A (scaffold) subunits. We also show that VIP1 dephosphorylation in vitro can be induced by a PP2A B″-family subunit.
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Affiliation(s)
- Hyuk Sung Yoon
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo, 188-0002, Japan
| | - Kaien Fujino
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, Hangzhou, 311300, PR China
| | - Tetsuo Takano
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo, 188-0002, Japan
| | - Daisuke Tsugama
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo, 188-0002, Japan.
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Fukuie Y, Shimoyama H, Morishita T, Tsugama D, Fujino K. A putative AGAMOUS ortholog is a candidate for the gene determining ease of dehulling in Tartary buckwheat (Fagopyrum tataricum). Planta 2020; 251:85. [PMID: 32198546 DOI: 10.1007/s00425-020-03374-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/10/2020] [Indexed: 05/08/2023]
Abstract
Tartary buckwheat rice-type cultivars, which allow easy dehulling, lacked periclinal cell divisions that proceed underneath the epidermis in the proximity of ovary midribs in non-rice-type cultivars. The easy dehulling in these cultivars was associated with a G→A substitution in an AGAMOUS ortholog. Ease of dehulling in Tartary buckwheat (Fagopyrum tataricum) can affect the quality of its products. Tartary buckwheat cultivars that allow easy dehulling are called rice-type cultivars. The rice and non-rice hull types are determined by a single gene, but this gene is unclear. Here, we show that cells underneath the epidermis in the proximity of ovary midribs undergo periclinal cell divisions in non-rice-type cultivars but do not in a rice-type cultivar. The cells that arose from the periclinal cell divisions later underwent lignification, which should increase mechanical strength of hulls. In RNA sequencing, a partial mRNA of an AGAMOUS ortholog in Tartary buckwheat (FtAG) was found to be absent in the rice-type cultivar. Cloning of this gene revealed that this is a 42-bp deletion due to a G→A substitution at a splice acceptor site in the FtAG genomic region. In F2 progeny derived from a cross between non-rice-type and rice-type cultivars, all the rice-type plants exhibited the homozygous A/A allele at this site, whereas all the Tartary-type plants exhibited either the homozygous G/G allele or the heterozygous A/G allele. These results suggest that FtAG is a candidate for the gene that determines ease of dehulling in Tartary buckwheat. The DNA marker that we developed to distinguish the FtAG alleles can be useful in breeding Tartary buckwheat cultivars.
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Affiliation(s)
- Yuka Fukuie
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan
| | - Hana Shimoyama
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan
- Division of African Area Studies, Graduate School of Asian and African Area Studies, Kyoto University, 46 Yoshida-shimo-adachi-cho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8304, Japan
| | - Toshikazu Morishita
- National Agriculture and Food Research Organization (NARO) Hokkaido Agricultural Research Center, Memuro Upland Farming Research Station, Shinsei, Memuro, Kasai, Hokkaido, 082-0081, Japan
- Radiation Breeding Division, Institute of Crop Science, NARO, 2425 Kamimurata, Hitachiomiya, Ibaraki, 319-2293, Japan
| | - Daisuke Tsugama
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan
- Asian Natural Environmental Science Center, The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, Tokyo, 188-0002, Japan
| | - Kaien Fujino
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan.
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Yoon HS, Fujino K, Liu S, Takano T, Tsugama D. VIP1, a bZIP protein, interacts with the catalytic subunit of protein phosphatase 2A in Arabidopsis thaliana. Plant Signal Behav 2019; 15:1706026. [PMID: 31861962 PMCID: PMC7053879 DOI: 10.1080/15592324.2019.1706026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 11/25/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 06/10/2023]
Abstract
VirE2-INTERACTING PROTEIN1 (VIP1) is a basic leucine zipper protein in Arabidopsis thaliana. VIP1 changes its subcellular localization from the cytoplasm to the nucleus when cells are exposed to mechanical or hypo-osmotic stress. The nuclear localization of VIP1 is inhibited either by inhibitors of calcium signaling or by inhibitors of protein phosphatases 1, 2A and 4 (PP1, PP2A and PP4, respectively). VIP1 binds to the PP2A B"-family subunits, which have calcium-binding EF-hand motifs and which act as the regulatory, substrate-recruiting B subunit of PP2A. The VIP1 de-phosphorylation can therefore be mediated by PP2A. However, details of the PP2A-mediated de-phosphorylation of VIP1 are unclear. Here, with yeast two-hybrid assays and in-vitro pull-down assays, we show that VIP1 does not interact with the scaffolding A subunit of PP2A, but that VIP1 does interact with the catalytic C subunits. Our data raise the possibility that not only the B"-family B subunit of PP2A but also its C subunit contributes to the PP2A-mediated de-phosphorylation of VIP1.
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Affiliation(s)
- Hyuk Sung Yoon
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Japan
| | - Kaien Fujino
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Hokkaido, Japan
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, P.R. China
| | - Tetsuo Takano
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Japan
| | - Daisuke Tsugama
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Japan
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Tsugama D, Fujino K. Data of whole genome sequencing of five garden asparagus ( Asparagus officinalis) individuals with the MinION nanopore sequencer. Data Brief 2019; 28:104838. [PMID: 31832531 PMCID: PMC6889792 DOI: 10.1016/j.dib.2019.104838] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/11/2019] [Accepted: 11/11/2019] [Indexed: 11/18/2022] Open
Abstract
Garden asparagus (Asparagus officinalis) is a perennial, dioecious crop. Genomic DNA samples were prepared from five A. officinalis individuals that differ in sex and phenotypes, and sequenced with the MinION nanopore sequencer. The obtained data were 1.5–5 Gb/sample, and the average read length was larger than 1.4 kb for all the samples. The resulting reads were mapped to the existing A. officinalis genome sequence. The existing A. officinalis transcript sequences were mapped to the MinION-derived reads. On the basis of these mapping results, flanking sequences of five partial gene fragments that previously had not been mapped to any region of the existing genome were determined by genomic PCR followed by Sanger sequencing. These sequences enabled to estimate the genomic positions of those five partial gene fragments. The MinION-derived data and the flanking sequences of the five gene fragments were deposited in the NCBI (National Center for Biotechnology Information) SRA (Sequence Read Archive) database and the NCBI Nucleotide database, respectively.
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Affiliation(s)
- Daisuke Tsugama
- Asian Natural Environmental Science Center, The University of Tokyo, Japan.,Research Faculty of Agriculture, Hokkaido University, Japan
| | - Kaien Fujino
- Research Faculty of Agriculture, Hokkaido University, Japan
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Tsugama D, Yoon HS, Fujino K, Liu S, Takano T. Protein phosphatase 2A regulates the nuclear accumulation of the Arabidopsis bZIP protein VIP1 under hypo-osmotic stress. J Exp Bot 2019; 70:6101-6112. [PMID: 31504762 PMCID: PMC6859724 DOI: 10.1093/jxb/erz384] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 06/14/2019] [Accepted: 08/16/2019] [Indexed: 05/21/2023]
Abstract
VIP1 is a bZIP transcription factor in Arabidopsis thaliana. When cells are exposed to mechanical stress, VIP1 transiently accumulates in the nucleus, where it regulates the expression of its target genes and suppresses mechanical stress-induced root waving. The nuclear-cytoplasmic shuttling of VIP1 is regulated by phosphorylation and calcium-dependent signaling, but specific regulators of these processes remain to be identified. Here, inhibitors of protein phosphatase 2A (PP2A) are shown to inhibit both the mechanical stress-induced dephosphorylation and nuclear accumulation of VIP1. The PP2A B subunit, which recruits substrates of PP2A holoenzyme, is classified into B, B', B'', and B''' families. Using bimolecular fluorescence complementation, in vitro pull-down, and yeast two-hybrid assays, we show that VIP1 interacts with at least two of the six members of the Arabidopsis PP2A B''-family subunit, which have calcium-binding EF-hand motifs. VIP1AAA, a constitutively nuclear-localized VIP1 variant with substitutions in putative phosphorylation sites of VIP1, suppressed the root waving induced by VIP1-SRDX (a repression domain-fused variant of VIP1). These results support the idea that VIP1 is dephosphorylated by PP2A and that the dephosphorylation suppresses the root waving. The phosphorylation sites of VIP1 and its homologs were narrowed down by in vitro phosphorylation, yeast two-hybrid, and protein subcellular localization assays.
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Affiliation(s)
- Daisuke Tsugama
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Midori-cho, Nishitokyo-shi, Tokyo, Japan
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, Japan
- Correspondence:
| | - Hyuk Sung Yoon
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Midori-cho, Nishitokyo-shi, Tokyo, Japan
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, Japan
| | - Kaien Fujino
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, Japan
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Hangzhou, PR China
| | - Tetsuo Takano
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Midori-cho, Nishitokyo-shi, Tokyo, Japan
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Fujino K, Motooka Y, Matsushima R, Ito T, Suzuki M, Yasufuku K. EP1.12-03 The Significance of INSM1 Expression in Small Cell Lung Cancer. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.2248] [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: 10/25/2022]
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14
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Ide M, Masuda K, Tsugama D, Fujino K. Death of female flower microsporocytes progresses independently of meiosis-like process and can be accelerated by specific transcripts in Asparagus officinalis. Sci Rep 2019; 9:2703. [PMID: 30804374 PMCID: PMC6389975 DOI: 10.1038/s41598-019-39125-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 01/16/2019] [Indexed: 11/18/2022] Open
Abstract
Asparagus officinalis (garden asparagus) is a dioecious perennial crop, and the dioecy (i.e., sex) of A. officinalis can affect its productivity. In A. officinalis, flower anthers in female plants fail to accumulate callose around microsporocytes, fail to complete meiosis, and degenerate due to cell death. Although 13 genes have been implicated in the anther development of male and female flowers, it is unclear how these genes regulate the cell death in female flower anthers. The aim of this study was to narrow down factors involved in this process. TUNEL staining and Feulgen staining of female flower microsporocytes suggest that female microsporocytes enter a previously undetected meiosis-like process, and that the cell death occurs independently of this meiosis-like process, excluding the possibility that the cell death is caused by the cessation of meiosis. RNA sequencing with individual floral organs (tepals, pistils and stamens) revealed that several genes possibly regulating the cell death, such as metacaspase genes and a Bax inhibitor-1 gene, are differentially regulated between female and male flower anthers, and that genes involved in callose accumulation are up-regulated only in male flower anthers. These genes are likely involved in regulating the cell death in female flower anthers in A. officinalis.
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Affiliation(s)
- Mayui Ide
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan
| | - Kiyoshi Masuda
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan
| | - Daisuke Tsugama
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan.
| | - Kaien Fujino
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan
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Osmani Z, Jin S, Mikami M, Endo M, Atarashi H, Fujino K, Yamada T, Nakahara KS. CRISPR/Cas9-Mediated Editing of Genes Encoding rgs-CaM-like Proteins in Transgenic Potato Plants. Methods Mol Biol 2019; 2028:153-165. [PMID: 31228114 DOI: 10.1007/978-1-4939-9635-3_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
A tobacco calmodulin-like protein, rgs-CaM, has been shown to interact with viruses in a variety of ways; it contributes to geminivirus infections but is also involved in primed immunity to the cucumber mosaic virus. Sequence similarity searches revealed several calmodulin-like proteins similar to rgs-CaM (rCML) in Arabidopsis and other Solanaceae plants, including potato (Solanum tuberosum). To analyze the functions of each rCML, mutations were introduced into potato rCMLs using the CRISPR/Cas9 system. Here, we describe our protocol of the CRISPR/Cas9-mediated targeted mutagenesis in stably transformed potato plants.
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Affiliation(s)
- Zhila Osmani
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.,Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Shinnosuke Jin
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Masafumi Mikami
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
| | - Masaki Endo
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Hiroki Atarashi
- Research and Development Organization, Kikkoman Corporation, Noda, Japan
| | - Kaien Fujino
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Tetsuya Yamada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kenji S Nakahara
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.
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Tsugama D, Liu S, Fujino K, Takano T. Calcium signalling regulates the functions of the bZIP protein VIP1 in touch responses in Arabidopsis thaliana. Ann Bot 2018; 122:1219-1229. [PMID: 30010769 PMCID: PMC6324745 DOI: 10.1093/aob/mcy125] [Citation(s) in RCA: 10] [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: 04/28/2018] [Accepted: 06/12/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS VIP1 is a bZIP transcription factor in Arabidopsis thaliana. VIP1 and its close homologues transiently accumulate in the nucleus when cells are exposed to hypo-osmotic and/or mechanical stress. Touch-induced root bending is enhanced in transgenic plants overexpressing a repression domain-fused form of VIP1 (VIP1-SRDXox), suggesting that VIP1, possibly with its close homologues, suppresses touch-induced root bending. The aim of this study was to identify regulators of these functions of VIP1 in mechanical stress responses. METHODS Co-immunoprecipitation analysis using VIP1-GFP fusion protein expressed in Arabidopsis plants identified calmodulins as VIP1-GFP interactors. In vitro crosslink analysis was performed using a hexahistidine-tagged calmodulin and glutathione S-transferase-fused forms of VIP1 and its close homologues. Plants expressing GFP-fused forms of VIP1 and its close homologues (bZIP59 and bZIP29) were submerged in hypotonic solutions containing divalent cation chelators, EDTA and EGTA, and a potential calmodulin inhibitor, chlorpromazine, to examine their effects on the nuclear-cytoplasmic shuttling of those proteins. VIP1-SRDXox plants were grown on medium containing 40 mm CaCl2, 40 mm MgCl2 or 80 mm NaCl. MCA1 and MCA2 are mechanosensitive calcium channels, and the hypo-osmotic stress-dependent nuclear-cytoplasmic shuttling of VIP1-GFP in the mca1 mca2 double knockout mutant background was examined. KEY RESULTS In vitro crosslink products were detected in the presence of CaCl2, but not in its absence. EDTA, EGTA and chlorpromazine all inhibited both the nuclear import and the nuclear export of VIP1-GFP, bZIP59-GFP and bZIP29-GFP. Either 40 mm CaCl2or 80 mm NaCl enhanced the VIP-SRDX-dependent root bending. The nuclear-cytoplasmic shuttling of VIP1 was observed even in the mca1 mca2 mutant. CONCLUSIONS VIP1 and its close homologues can interact with calmodulins. Their nuclear-cytoplasmic shuttling requires neither MCA1 nor MCA2, but does require calcium signalling. Salt stress affects the VIP1-dependent regulation of root bending.
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Affiliation(s)
- Daisuke Tsugama
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo-shi, Hokkaido, Japan
- Asian Natural Environmental Science Center, The University of Tokyo, Nishitokyo-shi, Tokyo, Japan
- For correspondence. E-mail:
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Hangzhou, PR China
| | - Kaien Fujino
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo-shi, Hokkaido, Japan
| | - Tetsuo Takano
- Asian Natural Environmental Science Center, The University of Tokyo, Nishitokyo-shi, Tokyo, Japan
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Motooka Y, Fujino K, Yasufuku K, Suzuki M, Ito T. P3.09-14 Pathobiology of Notch2 in Lung Cancer. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1783] [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: 10/28/2022]
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18
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Kato T, Jin C, Ujiie H, Fujino K, Lee D, Wada H, Hu H, Wu L, Weersink R, Chen J, Kanno H, Hatanaka Y, Hatanaka K, Matsuno Y, De Perrot M, Wilson B, Zheng G, Yasufuku K. MA12.09 Preclinical Investigations of Folate Receptor Targeted Nanoparticles for Photodynamic Therapy of Malignant Pleural Mesothelioma. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.418] [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: 11/27/2022]
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19
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Kinoshita T, Ujiie H, Chen J, Ding L, Chan H, Gregor A, Bernards N, Mcveigh P, Fujino K, Lee C, Motooka Y, Inage T, Valic M, Weersink R, Wilson B, Zheng G, Asamura H, Yasufuku K. P3.16-05 A Nanotechnology-Enabled Strategy for Image-Guided Transbronchial and Transpleural Photothermal Therapy of Peripheral Lung Cancer. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1912] [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: 10/28/2022]
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Tsugama D, Liu S, Fujino K, Takano T. B-family subunits of protein phosphatase 2A are necessary for pollen development but not for female gametophyte development in Arabidopsis. Biochem Biophys Res Commun 2018; 505:176-180. [PMID: 30243715 DOI: 10.1016/j.bbrc.2018.09.088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 11/30/2022]
Abstract
Protein phosphatase 2A (PP2A) is a heterotrimeric protein complex conserved among eukaryotes. The B subunit of PP2A determines the substrate specificity of the PP2A holoenzyme, and is classified into the B, B', B″ and B‴ families. Arabidopsis thaliana has two isoforms of the B-family subunit (ATBA and ATBB). A double knockout of their genes is lethal, but which developmental process is primarily impaired by the double knockout is unclear. Identifying such a process helps understand PP2A-mediated signaling more deeply. Here, genetic characterization of new knockout mutants for these genes shows that they are necessary for pollen development but not for female gametophyte development. Compared to wild-type pollen grains, the mutant pollen grains exhibited lower enzyme activities, germinated less frequently on stigmas, and exhibited the aberrant numbers of sperm cell nuclei, suggesting that ATBA and ATBB play pleiotropic roles in pollen development. The amino acids stabilizing the interaction between the human PP2A A and B-family subunits are conserved in an Arabidopsis A subunit (AtPP2AA2), ATBA and ATBB. His-tagged AtPP2AA2 co-immunoprecipitated with either Myc-tagged ATBA or Myc-tagged ATBB in vitro, confirming their interactions. Proteins that regulate pollen development and that undergo dephosphorylation are likely primary targets of ATBA and ATBB.
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Affiliation(s)
- Daisuke Tsugama
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan; Asian Natural Environmental Science Center, The University of Tokyo 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo, 188-0002, Japan.
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, Hangzhou, 311300, PR China
| | - Kaien Fujino
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan
| | - Tetsuo Takano
- Asian Natural Environmental Science Center, The University of Tokyo 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo, 188-0002, Japan
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Tsugama D, Liu S, Fujino K, Takano T. Possible inhibition of Arabidopsis VIP1-mediated mechanosensory signaling by streptomycin. Plant Signal Behav 2018; 13:e1521236. [PMID: 30235047 PMCID: PMC6204804 DOI: 10.1080/15592324.2018.1521236] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/24/2018] [Accepted: 08/29/2018] [Indexed: 05/21/2023]
Abstract
VIP1 (VIRE2-INTERACTING PROTEIN 1) and its close homologues are Arabidopsis thaliana bZIP proteins regulating stress responses and root tropisms. They are present in the cytoplasm under steady conditions, but transiently accumulate in the nucleus when cells are exposed to mechanical stress such as hypo-osmotic stress and touch. This pattern of changes in subcellular localization is unique to VIP1 and its close homologues, and can be useful to further characterize mechanical stress signaling in plants. A recent study showed that calcium signaling regulates this pattern of subcellular localization. Here, we show that a possible calcium channel inhibitor, streptomycin, also inhibits the nuclear accumulation of VIP1. Candidates for the specific regulators of the mechanosensitive calcium signaling are further discussed.
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Affiliation(s)
- Daisuke Tsugama
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Hokkaido, Japan
- Asian Natural Environmental Science Center, The University of Tokyo, Tokyo, Japan
- CONTACT Daisuke Tsugama
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, P.R. China
| | - Kaien Fujino
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Hokkaido, Japan
| | - Tetsuo Takano
- Asian Natural Environmental Science Center, The University of Tokyo, Tokyo, Japan
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Tahara M, Brose M, Wirth L, Suzuki T, Fujino K, Batty N, Dutcus C, Gianoukakis A. Impact of duration of dose interruption on the efficacy of lenvatinib (LEN) in a phase 3 sudy in patients (pts) with radioiodine refractory differentiated thyroid cancer (RR-DTC). Ann Oncol 2017. [DOI: 10.1093/annonc/mdx368.007] [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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Ogihara T, Amano N, Mitsui Y, Fujino K, Ohta H, Takahashi K, Matsuura H. Determination of the Absolute Configuration of a Monoglyceride Antibolting Compound and Isolation of Related Compounds from Radish Leaves (Raphanus sativus). J Nat Prod 2017; 80:872-878. [PMID: 28333463 DOI: 10.1021/acs.jnatprod.6b00746] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A monoglyceride (1) has been reported to possess an antibolting effect in radish (Raphanus sativus), but its absolute configuration at the C-2 position was not determined earlier. In this work, the absolute configuration of 1 was determined to be (2S), and it was also accompanied by one new (2) and two known monoglycerides (3 and 4). The chemical structure of 2 was determined as β-(7'Z,10'Z,13'Z)-hexadecatrienoic acid monoglyceride (β-16:3 monoglyceride). Qualitative and quantitative analytical methods for compounds 1-4 were developed, using two deuterium-labeled compounds (8 and 9) as internal standards. The results revealed a broader range of distribution of 1-4 in several annual winter crops. It was also found that these isolated compounds have an inhibitory effect on the root elongation of Arabidopsis thaliana seedlings at concentrations of 25 and 50 μM in the medium. However, the inhibitory effect of 1 was not dependent on coronatin-insensitive 1 (COI1) protein, which may suggest the involvement of an unidentified signaling system other than jasmonic acid signaling.
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Affiliation(s)
- Tsuyoshi Ogihara
- Research Faculty of Agriculture, Hokkaido University , Sapporo 060-8589, Japan
| | - Naruki Amano
- Research Faculty of Agriculture, Hokkaido University , Sapporo 060-8589, Japan
| | - Yuki Mitsui
- Tokyo University of Agriculture , 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Kaien Fujino
- Research Faculty of Agriculture, Hokkaido University , Sapporo 060-8589, Japan
| | - Hiroyuki Ohta
- School of Life Science and Technology, Tokyo Institute of Technology , 4259-B65 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Kosaku Takahashi
- Research Faculty of Agriculture, Hokkaido University , Sapporo 060-8589, Japan
| | - Hideyuki Matsuura
- Research Faculty of Agriculture, Hokkaido University , Sapporo 060-8589, Japan
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Mochizuki R, Tsugama D, Yamazaki M, Fujino K, Masuda K. Identification of candidates for interacting partners of the tail domain of DcNMCP1, a major component of the Daucus carota nuclear lamina-like structure. Nucleus 2017; 8:312-322. [PMID: 28146370 PMCID: PMC5499906 DOI: 10.1080/19491034.2017.1280210] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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] [Indexed: 10/26/2022] Open
Abstract
NMCP/CRWN (NUCLEAR MATRIX CONSTITUENT PROTEIN/CROWDED NUCLEI) is a major component of a protein fibrous meshwork (lamina-like structure) on the plant inner nuclear membrane. NMCP/CRWN contributes to regulating nuclear shape and nuclear functions. An NMCP/CRWN protein in Daucus carota (DcNMCP1) is localized to the nuclear periphery in interphase cells, and surrounds chromosomes in cells in metaphase and anaphase. The N-terminal region and the C-terminal region of DcNMCP1 are both necessary for localizing DcNMCP1 to the nuclear periphery. Here candidate interacting partners of the amino acid position 975-1053 of DcNMCP1 (T975-1053), which is present in the C-terminal region and contains a conserved sequence that plays a role in localizing DcNMCP1 to the nuclear periphery, are screened for. Arabidopsis thaliana nuclear proteins were subjected to far-Western blotting with GST-fused T975-1053 as a probe, and signals were detected at the positions corresponding to ∼70, ∼40, and ∼18 kDa. These ∼70, ∼40, and ∼18 kDa nuclear proteins were identified by mass spectrometry, and subjected to a yeast 2-hybrid (Y2H) analysis with T975-1053 as bait. In this analysis, the ∼40 kDa protein ARP7, which is a nuclear actin-related protein possibly involved in regulating chromatin structures, was confirmed to interact with T975-1053. Independently of the far-Western blotting, a Y2H screen was performed using T975-1053 as bait. Targeted Y2H assays confirmed that 3 proteins identified in the screen, MYB3, SINAT1, and BIM1, interact with T975-1053. These proteins might have roles in NMCP/CRWN protein-mediated biologic processes.
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Affiliation(s)
- Ryota Mochizuki
- a Laboratory of Crop Physiology, Research Faculty of Agriculture , Hokkaido University , Sapporo-shi , Hokkaido , Japan
| | - Daisuke Tsugama
- a Laboratory of Crop Physiology, Research Faculty of Agriculture , Hokkaido University , Sapporo-shi , Hokkaido , Japan
| | - Michihiro Yamazaki
- a Laboratory of Crop Physiology, Research Faculty of Agriculture , Hokkaido University , Sapporo-shi , Hokkaido , Japan
| | - Kaien Fujino
- a Laboratory of Crop Physiology, Research Faculty of Agriculture , Hokkaido University , Sapporo-shi , Hokkaido , Japan
| | - Kiyoshi Masuda
- a Laboratory of Crop Physiology, Research Faculty of Agriculture , Hokkaido University , Sapporo-shi , Hokkaido , Japan
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Zhou H, Hirata M, Osawa R, Fujino K, Kishima Y. Detainment of Tam3 Transposase at Plasma Membrane by Its BED-Zinc Finger Domain. Plant Physiol 2017; 173:1492-1501. [PMID: 28008001 PMCID: PMC5291012 DOI: 10.1104/pp.16.00996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 12/15/2016] [Indexed: 05/29/2023]
Abstract
Transposable elements (TEs) are considered to be parasites of host genomes because they act as powerful mutagens. If not kept in check, they can cause gene disruption, genome rearrangement, and genomic takeover. Hence, activities of TEs are under the rigid control of hosts. To date, all identified TE regulations have been epigenetic dependent, with the exception of the DNA transposon Tam3. Blocking nuclear translocation of Tam3 transposase (TPase) is consistent with the suppression of Tam3 in Antirrhinum majus In this article, we discovered that epigenetic-independent regulation of Tam3 is mediated by the BED-zinc finger (Znf-BED) domain of Tam3 TPase. The host targets the N terminus of the Znf-BED domain, which contains two highly conserved aromatic amino acids, to detain Tam3 TPase at the plasma membrane and to silence Tam3. Zinc finger proteins perform broader functions in transcriptional regulation through their DNA binding ability. Our data revealed that the posttranslational epigenetic-independent silencing against TEs was a result of the protein binding ability of the Znf-BED domain.
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Affiliation(s)
- Hua Zhou
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Megumi Hirata
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Ryo Osawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Kaien Fujino
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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Yasuo S, Kenichi Y, Ueno N, Arimoto A, Hosono M, Yoshikawa T, Toyokawa A, Kakeji Y, Tsai Y, Tsai C, Sul J, Lim M, Park J, Jang CE, Santilli O, Tripoloni D, Santilli H, Nardelli N, Greco A, Estevez M, Sakurai S, Ryu S, Cesana G, Ciccarese F, Uccelli M, Grava G, Castello G, Carrieri D, Legnani G, Olmi S, Naito M, Yamamoto H, Sawada Y, Mandai Y, Asano H, Ino H, Tsukuda K, Nagahama T, Ando M, Ami K, Arai K, Miladinovic M, Kitanovic A, Lechner M, Mayer F, Meissnitzer M, Fortsner R, Öfner D, Köhler G, Jäger T, Kumata Y, Fukushima R, Inaba T, Yaguchi Y, Horikawa M, Ogawa E, Katayama T, Kumar PS, Unal D, Caparlar C, Akkaya T, Mercan U, Kulacoglu H, Barreiro JJ, Baer IG, García LS, Cumplido PL, Florez LJG, Muñiz PF, Fujino K, Mita K, Ohta E, Takahashi K, Hashimoto M, Nagayasu K, Murabayashi R, Asakawa H, Koizumi K, Hayashi G, Ito H, Felberbauer F, Strobl S, Kristo I, Riss S, Prager G, El Komy H, El Gendi A, Nabil W, Karam M, El Kayal S, Chihara N, Suzuki H, Watanabe M, Uchida E, Chen T, Wang J, Wang H, Bouchiba N, Elbakary T, Ramadan A, Elakkad M, Berney C, Vlasov V, Babii I, Pidmurnyak O, Prystupa M, Asakage N, Molinari P, Contino E, Guzzetti L, Oggioni M, Sambuco M, Berselli M, Farassino L, Cocozza E, Crespi A, Ambrosoli A, Zhao Y. Topic: Inguinal Hernia - Unsolved problem in the daily practice. Hernia 2015; 19 Suppl 1:S293-304. [PMID: 26518826 DOI: 10.1007/bf03355374] [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: 11/24/2022]
Affiliation(s)
- S Yasuo
- Department of Surgery. Social Welfare Organization Saiseikai Imperial Gift Foundation, Inc. Saiseikai Wakakusa Hospital, Yokohama, Japan
| | - Y Kenichi
- Department of Surgery. Social Welfare Organization Saiseikai Imperial Gift Foundation, Inc. Saiseikai Wakakusa Hospital, Yokohama, Japan
| | - N Ueno
- Department of General Surgery, Yodogawa Christian Hospital, Osaka, Japan
| | - A Arimoto
- Department of General Surgery, Takatsuki General Hospital, Takatsuki, Japan
| | - M Hosono
- Division of Gastrointestinal Surgery, Kobe University Hospital, Kobe, Japan
| | - T Yoshikawa
- Department of General Surgery, Takatsuki General Hospital, Takatsuki, Japan
| | - A Toyokawa
- Department of General Surgery, Yodogawa Christian Hospital, Osaka, Japan
| | - Y Kakeji
- Division of Gastrointestinal Surgery, Kobe University Hospital, Kobe, Japan
| | - Y Tsai
- Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taipei, Taiwan
| | - C Tsai
- Taichung Hospital, Ministry of Health and Welfare, Taichung, Taiwan
| | - J Sul
- Chungnam National University Hospital, Daejeon, South Korea
| | - M Lim
- Chungnam National University Hospital, Daejeon, South Korea
| | - J Park
- Chungnam National University Hospital, Daejeon, South Korea
| | | | - O Santilli
- Centro De Patologia Herniaria, Buenos Aires, Argentina
| | - D Tripoloni
- Centro De Patologia Herniaria, Buenos Aires, Argentina
| | - H Santilli
- Centro De Patologia Herniaria, Buenos Aires, Argentina
| | - N Nardelli
- Centro De Patologia Herniaria, Buenos Aires, Argentina
| | - A Greco
- Centro De Patologia Herniaria, Buenos Aires, Argentina
| | - M Estevez
- Centro De Patologia Herniaria, Buenos Aires, Argentina
| | - S Sakurai
- St. Luke's International Hospital, Tokyo, Japan
| | - S Ryu
- Samsung Changwon Hospital, Changwon-si, Gyeongsangnam-do, South Korea
| | - G Cesana
- School of General Surgery, University of Milan, Milan, Italy.,General and Oncologic Surgery Department, S. Marco Hospital, Zingonia, BG, Italy
| | - F Ciccarese
- School of General Surgery, University of Milan, Milan, Italy.,General and Oncologic Surgery Department, S. Marco Hospital, Zingonia, BG, Italy
| | - M Uccelli
- School of General Surgery, University of Milan, Milan, Italy.,General and Oncologic Surgery Department, S. Marco Hospital, Zingonia, BG, Italy
| | - G Grava
- School of General Surgery, University of Milan, Milan, Italy.,General and Oncologic Surgery Department, S. Marco Hospital, Zingonia, BG, Italy
| | - G Castello
- General and Oncologic Surgery Department, S. Marco Hospital, Zingonia, BG, Italy
| | - D Carrieri
- General and Oncologic Surgery Department, S. Marco Hospital, Zingonia, BG, Italy
| | - G Legnani
- General and Oncologic Surgery Department, S. Marco Hospital, Zingonia, BG, Italy
| | - S Olmi
- School of General Surgery, University of Milan, Milan, Italy.,General and Oncologic Surgery Department, S. Marco Hospital, Zingonia, BG, Italy
| | - M Naito
- Department of Surgery, Okayama Medical Center, Okayama, Japan
| | - H Yamamoto
- Department of Surgery, Okayama Medical Center, Okayama, Japan
| | - Y Sawada
- Himeji Daiichi Hospital, Himeji, Japan
| | - Y Mandai
- Okayama University Hospital, Okayama, Japan
| | - H Asano
- Okayama University Hospital, Okayama, Japan
| | - H Ino
- Okayama University Hospital, Okayama, Japan
| | - K Tsukuda
- Okayama University Hospital, Okayama, Japan
| | - T Nagahama
- Department of Surgery, Toshima Hospital, Tokyo, Japan
| | - M Ando
- Department of Surgery, Toshima Hospital, Tokyo, Japan
| | - K Ami
- Department of Surgery, Toshima Hospital, Tokyo, Japan
| | - K Arai
- Department of Surgery, Toshima Hospital, Tokyo, Japan
| | | | - A Kitanovic
- Surgery ward, General hospital, Krusevac, Serbia
| | - M Lechner
- Department of General Surgery, Paracelsus Medical University, Salzburg, Austria
| | - F Mayer
- Department of General Surgery, Paracelsus Medical University, Salzburg, Austria
| | - M Meissnitzer
- Department of Radiology, Paracelsus Medical University, Salzburg, Austria
| | - R Fortsner
- Department of Radiology, Paracelsus Medical University, Salzburg, Austria
| | - D Öfner
- Department of General Surgery, Paracelsus Medical University, Salzburg, Austria
| | - G Köhler
- Department of General Surgery, Sisters of Charity Hospital, Linz, Austria
| | - T Jäger
- Department of General Surgery, Paracelsus Medical University, Salzburg, Austria
| | - Y Kumata
- Department of Surgery, Teikyo University Hospital, Tokyo, Japan
| | - R Fukushima
- Department of Surgery, Teikyo University Hospital, Tokyo, Japan
| | - T Inaba
- Department of Surgery, Teikyo University Hospital, Tokyo, Japan
| | - Y Yaguchi
- Department of Surgery, Teikyo University Hospital, Tokyo, Japan
| | - M Horikawa
- Department of Surgery, Teikyo University Hospital, Tokyo, Japan
| | - E Ogawa
- Department of Surgery, Teikyo University Hospital, Tokyo, Japan
| | - T Katayama
- Department of Surgery, Teikyo University Hospital, Tokyo, Japan
| | - P S Kumar
- ESI-PGIMSR and Medical College, Bangalore, India
| | - D Unal
- Diskapi Teaching and Research Hospital, Ankara, Turkey
| | - C Caparlar
- Diskapi Teaching and Research Hospital, Ankara, Turkey
| | - T Akkaya
- Diskapi Teaching and Research Hospital, Ankara, Turkey
| | - U Mercan
- Diskapi Teaching and Research Hospital, Ankara, Turkey
| | - H Kulacoglu
- Diskapi Teaching and Research Hospital, Ankara, Turkey
| | | | | | | | | | | | | | - K Fujino
- Department of Surgery, New Tokyo Hospital, Matsudo, Japan
| | - K Mita
- Department of Surgery, New Tokyo Hospital, Matsudo, Japan
| | - E Ohta
- Department of Surgery, New Tokyo Hospital, Matsudo, Japan
| | - K Takahashi
- Department of Surgery, New Tokyo Hospital, Matsudo, Japan
| | - M Hashimoto
- Department of Surgery, New Tokyo Hospital, Matsudo, Japan
| | - K Nagayasu
- Department of Surgery, New Tokyo Hospital, Matsudo, Japan
| | - R Murabayashi
- Department of Surgery, New Tokyo Hospital, Matsudo, Japan
| | - H Asakawa
- Department of Surgery, New Tokyo Hospital, Matsudo, Japan
| | - K Koizumi
- Department of Surgery, New Tokyo Hospital, Matsudo, Japan
| | - G Hayashi
- Department of Surgery, New Tokyo Hospital, Matsudo, Japan
| | - H Ito
- Department of Surgery, New Tokyo Hospital, Matsudo, Japan
| | - F Felberbauer
- Div. of General Surgery, Dpt. of Surgery, Medical University of Vienna, Vienna, Austria
| | | | | | | | | | - H El Komy
- Faculty of medicine, Alexandria, Egypt
| | | | - W Nabil
- Faculty of medicine, Alexandria, Egypt
| | - M Karam
- Faculty of medicine, Alexandria, Egypt
| | | | - N Chihara
- Nippon Medical School, Musashikosugi Hospital, Institute of Gastroenterology, Kawasaki, Japan
| | - H Suzuki
- Nippon Medical School, Musashikosugi Hospital, Institute of Gastroenterology, Kawasaki, Japan
| | - M Watanabe
- Nippon Medical School, Musashikosugi Hospital, Institute of Gastroenterology, Kawasaki, Japan
| | - E Uchida
- Department of Surgery, Nippon Medical School, Tokyo, Japan
| | - T Chen
- Department of Biliary-pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - J Wang
- Department of Biliary-pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - H Wang
- Department of Biliary-pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - N Bouchiba
- Al Wakra Hospital, Hamad Medical Corporation, Al Wakra, Qatar
| | - T Elbakary
- Al Wakra Hospital, Hamad Medical Corporation, Al Wakra, Qatar
| | - A Ramadan
- Al Wakra Hospital, Hamad Medical Corporation, Al Wakra, Qatar
| | - M Elakkad
- Al Wakra Hospital, Hamad Medical Corporation, Al Wakra, Qatar
| | - C Berney
- Bankstown-Lidcombe Hospital, University of NSW, Sydney, Australia
| | - V Vlasov
- Khmelnitskiy regional hospital, Khmelnitskiy, Ukraine
| | | | | | | | - N Asakage
- Department of Surgery, Tsudanuma Central General Hospital, Chiba, Japan
| | - P Molinari
- University Of Insubria Anesthesia and Intensive Care, Varese, Italy
| | - E Contino
- University Of Insubria Anesthesia and Intensive Care, Varese, Italy
| | - L Guzzetti
- Department Of Anesthesia and Palliative Care, University Hospital Of Varese, Varese, Italy
| | - M Oggioni
- Department Of Anesthesia and Palliative Care, University Hospital Of Varese, Varese, Italy
| | - M Sambuco
- Department Of Anesthesia and Palliative Care, University Hospital Of Varese, Varese, Italy
| | - M Berselli
- University Hospital Of Varese Department Of Surgery, Varese, Italy
| | - L Farassino
- University Hospital Of Varese Department Of Surgery, Varese, Italy
| | - E Cocozza
- University Hospital Of Varese Department Of Surgery, Varese, Italy
| | - A Crespi
- University Of Insubria Anesthesia and Intensive Care, Varese, Italy
| | - A Ambrosoli
- Department Of Anesthesia and Palliative Care, University Hospital Of Varese, Varese, Italy
| | - Y Zhao
- Department of vascular Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Kuroiwa Y, Nishioka K, Yokota S, Hirai T, Nishioka K, Fujino K, Iguchi Y. Subacute autonomic, endocrine, and cognitive disorders in Japanese girls at puberty after human papillomavirus vaccination. Auton Neurosci 2015. [DOI: 10.1016/j.autneu.2015.07.430] [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: 10/23/2022]
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28
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Gong C, Fujino K, Monteiro LJ, Gomes AR, Drost R, Davidson-Smith H, Takeda S, Khoo US, Jonkers J, Sproul D, Lam EWF. FOXA1 repression is associated with loss of BRCA1 and increased promoter methylation and chromatin silencing in breast cancer. Oncogene 2015; 34:5012-24. [PMID: 25531315 PMCID: PMC4430311 DOI: 10.1038/onc.2014.421] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 01/31/2014] [Revised: 10/01/2014] [Accepted: 11/15/2014] [Indexed: 12/11/2022]
Abstract
FOXA1 expression correlates with the breast cancer luminal subtype and patient survival. RNA and protein analysis of a panel of breast cancer cell lines revealed that BRCA1 deficiency is associated with the downregulation of FOXA1 expression. Knockdown of BRCA1 resulted in the downregulation of FOXA1 expression and enhancement of FOXA1 promoter methylation in MCF-7 breast cancer cells, whereas the reconstitution of BRCA1 in Brca1-deficent mouse mammary epithelial cells (MMECs) promoted Foxa1 expression and methylation. These data suggest that BRCA1 suppresses FOXA1 hypermethylation and silencing. Consistently, the treatment of MMECs with the DNA methylation inhibitor 5-aza-2'-deoxycitydine induced Foxa1 mRNA expression. Furthermore, treatment with GSK126, an inhibitor of EZH2 methyltransferase activity, induced FOXA1 expression in BRCA1-deficient but not in BRCA1-reconstituted MMECs. Likewise, the depletion of EZH2 by small interfering RNA enhanced FOXA1 mRNA expression. Chromatin immunoprecipitation (ChIP) analysis demonstrated that BRCA1, EZH2, DNA methyltransferases (DNMT)1/3a/3b and H3K27me3 are recruited to the endogenous FOXA1 promoter, further supporting the hypothesis that these proteins interact to modulate FOXA1 methylation and repression. Further co-immunoprecipitation and ChIP analysis showed that both BRCA1 and DNMT3b form complexes with EZH2 but not with each other, consistent with the notion that BRCA1 binds to EZH2 and negatively regulates its methyltransferase activity. We also found that EZH2 promotes and BRCA1 impairs the deposit of the gene silencing histone mark H3K27me3 on the FOXA1 promoter. These associations were validated in a familial breast cancer patient cohort. Integrated analysis of the global gene methylation and expression profiles of a set of 33 familial breast tumours revealed that FOXA1 promoter methylation is inversely correlated with the transcriptional expression of FOXA1 and that BRCA1 mutation breast cancer is significantly associated with FOXA1 methylation and downregulation of FOXA1 expression, providing physiological evidence to our findings that FOXA1 expression is regulated by methylation and chromatin silencing and that BRCA1 maintains FOXA1 expression through suppressing FOXA1 gene methylation in breast cancer.
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Affiliation(s)
- C Gong
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - K Fujino
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
- Department of Obstetrics & Gynecology, Faculty of Medicine, Juntendo University, Bunkyoku, Tokyo, Japan
| | - L J Monteiro
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - A R Gomes
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - R Drost
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - H Davidson-Smith
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - S Takeda
- Department of Obstetrics & Gynecology, Faculty of Medicine, Juntendo University, Bunkyoku, Tokyo, Japan
| | - U S Khoo
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - J Jonkers
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - D Sproul
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - E W-F Lam
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
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Mori T, Koga T, Fujino K, Motooka Y, Shibata H, Ikeda K, Shiraishi K, Suzuki M. P-173INTERSTITIAL FLUID PRESSURE MAY BE USED AS A PROGNOSTIC FACTOR FOR LUNG CANCER. Interact Cardiovasc Thorac Surg 2015. [DOI: 10.1093/icvts/ivv204.173] [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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30
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Jang SJ, Sato M, Sato K, Jitsuyama Y, Fujino K, Mori H, Takahashi R, Benitez ER, Liu B, Yamada T, Abe J. A Single-Nucleotide Polymorphism in an Endo-1,4-β-Glucanase Gene Controls Seed Coat Permeability in Soybean. PLoS One 2015; 10:e0128527. [PMID: 26039079 PMCID: PMC4454576 DOI: 10.1371/journal.pone.0128527] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/28/2015] [Indexed: 11/23/2022] Open
Abstract
Physical dormancy, a structural feature of the seed coat known as hard seededness, is an important characteristic for adaptation of plants against unstable and unpredictable environments. To dissect the molecular basis of qHS1, a quantitative trait locus for hard seededness in soybean (Glycine max (L) Merr.), we developed a near-isogenic line (NIL) of a permeable (soft-seeded) cultivar, Tachinagaha, containing a hard-seed allele from wild soybean (G. soja) introduced by successive backcrossings. The hard-seed allele made the seed coat of Tachinagaha more rigid by increasing the amount of β-1,4-glucans in the outer layer of palisade cells of the seed coat on the dorsal side of seeds, known to be a point of entrance of water. Fine-mapping and subsequent expression and sequencing analyses revealed that qHS1 encodes an endo-1,4-β-glucanase. A single-nucleotide polymorphism (SNP) introduced an amino acid substitution in a substrate-binding cleft of the enzyme, possibly reducing or eliminating its affinity for substrates in permeable cultivars. Introduction of the genomic region of qHS1 from the impermeable (hard-seeded) NIL into the permeable cultivar Kariyutaka resulted in accumulation of β-1,4-glucan in the outer layer of palisade cells and production of hard seeds. The SNP allele found in the NIL was further associated with the occurrence of hard seeds in soybean cultivars of various origins. The findings of this and previous studies may indicate that qHS1 is involved in the accumulation of β-1,4-glucan derivatives such as xyloglucan and/or β-(1,3)(1,4)-glucan that reinforce the impermeability of seed coats in soybean.
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Affiliation(s)
- Seong-Jin Jang
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Masako Sato
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Kei Sato
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Yutaka Jitsuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Kaien Fujino
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Ryoji Takahashi
- National Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Eduardo R. Benitez
- National Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Baohui Liu
- Northeast Insititute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150040, China
| | - Tetsuya Yamada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
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Funatsuki H, Suzuki M, Hirose A, Inaba H, Yamada T, Hajika M, Komatsu K, Katayama T, Sayama T, Ishimoto M, Fujino K. Molecular basis of a shattering resistance boosting global dissemination of soybean. Proc Natl Acad Sci U S A 2014; 111:17797-802. [PMID: 25468966 PMCID: PMC4273335 DOI: 10.1073/pnas.1417282111] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pod dehiscence (shattering) is essential for the propagation of wild plant species bearing seeds in pods but is a major cause of yield loss in legume and crucifer crops. Although natural genetic variation in pod dehiscence has been, and will be, useful for plant breeding, little is known about the molecular genetic basis of shattering resistance in crops. Therefore, we performed map-based cloning to unveil a major quantitative trait locus (QTL) controlling pod dehiscence in soybean. Fine mapping and complementation testing revealed that the QTL encodes a dirigent-like protein, designated as Pdh1. The gene for the shattering-resistant genotype, pdh1, was defective, having a premature stop codon. The functional gene, Pdh1, was highly expressed in the lignin-rich inner sclerenchyma of pod walls, especially at the stage of initiation in lignin deposition. Comparisons of near-isogenic lines indicated that Pdh1 promotes pod dehiscence by increasing the torsion of dried pod walls, which serves as a driving force for pod dehiscence under low humidity. A survey of soybean germplasm revealed that pdh1 was frequently detected in landraces from semiarid regions and has been extensively used for breeding in North America, the world's leading soybean producer. These findings point to a new mechanism for pod dehiscence involving the dirigent protein family and suggest that pdh1 has played a crucial role in the global expansion of soybean cultivation. Furthermore, the orthologs of pdh1, or genes with the same role, will possibly be useful for crop improvement.
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Affiliation(s)
- Hideyuki Funatsuki
- Crop Cold Tolerance Research Team, NARO (National Agricultural Research Organization) Hokkaido Agricultural Research Center, Hitsujigaoka 1, Toyohira-ku, Sapporo 062-8555, Japan; Department of Planning and General Administration, NARO Western Region Agricultural Research Center, 6-12-1, Nishifukatsu-cho, Fukuyama 721-8514, Japan;
| | - Masaya Suzuki
- Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Aya Hirose
- Crop Cold Tolerance Research Team, NARO (National Agricultural Research Organization) Hokkaido Agricultural Research Center, Hitsujigaoka 1, Toyohira-ku, Sapporo 062-8555, Japan
| | - Hiroki Inaba
- Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Tetsuya Yamada
- Field Crop Research Division, NARO Institute of Crop Science, 2-1-18, Kannondai, Tsukuba 305-8518, Japan
| | - Makita Hajika
- Field Crop Research Division, NARO Institute of Crop Science, 2-1-18, Kannondai, Tsukuba 305-8518, Japan
| | - Kunihiko Komatsu
- Crop Cold Tolerance Research Team, NARO (National Agricultural Research Organization) Hokkaido Agricultural Research Center, Hitsujigaoka 1, Toyohira-ku, Sapporo 062-8555, Japan
| | - Takeshi Katayama
- Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kagawa 761-0795, Japan; and
| | - Takashi Sayama
- Crop Cold Tolerance Research Team, NARO (National Agricultural Research Organization) Hokkaido Agricultural Research Center, Hitsujigaoka 1, Toyohira-ku, Sapporo 062-8555, Japan; Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2, Kannondai, Tsukuba 305-0856, Japan
| | - Masao Ishimoto
- Crop Cold Tolerance Research Team, NARO (National Agricultural Research Organization) Hokkaido Agricultural Research Center, Hitsujigaoka 1, Toyohira-ku, Sapporo 062-8555, Japan; Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2, Kannondai, Tsukuba 305-0856, Japan
| | - Kaien Fujino
- Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan;
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Takahashi S, Tahara M, Kiyota N, Yamazaki T, Chayahara N, Nakano K, Inagaki R, Toda K, Enokida T, Minami H, Imamura Y, Sasaki T, Suzuki T, Fujino K, Dutcus C. Phase Ii Study of Lenvatinib (Len), a Multi-Targeted Tyrosine Kinase Inhibitor, in Patients (Pts) with All Histologic Subtypes of Advanced Thyroid Cancer (Differentiated, Medullary and Anaplastic). Ann Oncol 2014. [DOI: 10.1093/annonc/mdu340.10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [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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33
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Kimura Y, Fujino K, Ogawa K, Masuda K. Localization of Daucus carota NMCP1 to the nuclear periphery: the role of the N-terminal region and an NLS-linked sequence motif, RYNLRR, in the tail domain. Front Plant Sci 2014; 5:62. [PMID: 24616728 PMCID: PMC3935212 DOI: 10.3389/fpls.2014.00062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/07/2014] [Indexed: 05/24/2023]
Abstract
Recent ultrastructural studies revealed that a structure similar to the vertebrate nuclear lamina exists in the nuclei of higher plants. However, plant genomes lack genes for lamins and intermediate-type filament proteins, and this suggests that plant-specific nuclear coiled-coil proteins make up the lamina-like structure in plants. NMCP1 is a protein, first identified in Daucus carota cells, that localizes exclusively to the nuclear periphery in interphase cells. It has a tripartite structure comprised of head, rod, and tail domains, and includes putative nuclear localization signal (NLS) motifs. We identified the functional NLS of DcNMCP1 (carrot NMCP1) and determined the protein regions required for localizing to the nuclear periphery using EGFP-fused constructs transiently expressed in Apium graveolens epidermal cells. Transcription was driven under a CaMV35S promoter, and the genes were introduced into the epidermal cells by a DNA-coated microprojectile delivery system. Of the NLS motifs, KRRRK and RRHK in the tail domain were highly functional for nuclear localization. Addition of the N-terminal 141 amino acids from DcNMCP1 shifted the localization of a region including these NLSs from the entire nucleus to the nuclear periphery. Using this same construct, the replacement of amino acids in RRHK or its preceding sequence, YNL, with alanine residues abolished localization to the nuclear periphery, while replacement of KRRRK did not affect localization. The sequence R/Q/HYNLRR/H, including YNL and the first part of the sequence of RRHK, is evolutionarily conserved in a subclass of NMCP1 sequences from many plant species. These results show that NMCP1 localizes to the nuclear periphery by a combined action of a sequence composed of R/Q/HYNLRR/H, NLS, and the N-terminal region including the head and a portion of the rod domain, suggesting that more than one binding site is implicated in localization of NMCP1.
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Affiliation(s)
- Yuta Kimura
- Laboratory of Plant Functional Biology, Chair of Botany and Agronomy, Graduate School of Agriculture, Hokkaido UniversityHokkaido, Japan
| | - Kaien Fujino
- Laboratory of Crop Physiology, Chair of Botany and Agronomy, Graduate School of Agriculture, Hokkaido UniversityHokkaido, Japan
| | - Kana Ogawa
- Laboratory of Plant Functional Biology, Chair of Botany and Agronomy, Graduate School of Agriculture, Hokkaido UniversityHokkaido, Japan
| | - Kiyoshi Masuda
- Laboratory of Plant Functional Biology, Chair of Botany and Agronomy, Graduate School of Agriculture, Hokkaido UniversityHokkaido, Japan
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Ishiguro S, Ogasawara K, Fujino K, Sato Y, Kishima Y. Low temperature-responsive changes in the anther transcriptome's repeat sequences are indicative of stress sensitivity and pollen sterility in rice strains. Plant Physiol 2014; 164:671-82. [PMID: 24376281 PMCID: PMC3912097 DOI: 10.1104/pp.113.230656] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Genome-wide transcriptome analyses using microarray probes containing genes and repeat sequences have been performed to examine responses to low temperatures in rice (Oryza sativa). We focused particularly on the rice anther at the booting stage, because a low temperature at this stage can result in pollen abortion. The five rice strains examined in this study showed different pollen fertilities due to a low-temperature treatment during the booting stage. The microarray analyses demonstrated that the low-temperature stress caused genome-wide changes in the transcriptional activities not only of genes but also of repeat sequences in the rice anther. The degree of the temperature-responsive changes varied among the five rice strains. Interestingly, the low-temperature-sensitive strains revealed more changes in the transcriptome when compared with the tolerant strains. The expression patterns of the repeat sequences, including miniature inverted-repeat transposable elements, transposons, and retrotransposons, were correlated with the pollen fertilities of the five strains, with the highest correlation coefficient being 0.979. Even in the low-temperature-sensitive strains, the transcriptomes displayed distinct expression patterns. The elements responding to the low temperatures were evenly distributed throughout the genome, and the major cis-motifs involved in temperature-responsive changes were undetectable from the upstream sequences in the corresponding repeats. The genome-wide responses of transcription to the temperature shift may be associated with chromatin dynamics, which facilitates environmental plasticity. A genome-wide analysis using repeat sequences suggested that stress tolerance could be conferred by insensitivity to the stimuli.
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Ohuchi M, Hashimoto K, Ushiba A, Kishimoto T, Yamane T, Hamamoto T, Tabata T, Tsujita Y, Matsushiga M, Takahashi K, Matsumura K, Fujino K, Eguchi Y. Plasma platelet-derived microparticles to platelet count ratio as a marker of mortality in critically ill patients. Crit Care 2014. [PMCID: PMC4068881 DOI: 10.1186/cc13400] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abe E, Fujino K, Masuda K, Yamaguchi Y. Isolation and Expression Profiling of a CONSTANS-Like Gene and Two FLOWERING LOCUS T-Like Genes from Spinacia oleracea L. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ajps.2014.526420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Fujino K, Irifune T. TEM Studies on the Olivine to Modified Spinel Transformation in Mg 2SiO 4. High-Pressure Research: Application to Earth and Planetary Sciences 2013. [DOI: 10.1029/gm067p0237] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Funatsuki H, Hajika M, Yamada T, Suzuki M, Hagihara S, Tanaka Y, Fujita S, Ishimoto M, Fujino K. Mapping and use of QTLs controlling pod dehiscence in soybean. Breed Sci 2012; 61:554-8. [PMID: 23136494 PMCID: PMC3406785 DOI: 10.1270/jsbbs.61.554] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 09/16/2011] [Indexed: 05/19/2023]
Abstract
While the cultivated soybean, Glycine max (L.) Merr., is more recalcitrant to pod dehiscence (shattering-resistant) than wild soybean, Glycine soja Sieb. & Zucc., there is also significant genetic variation in shattering resistance among cultivated soybean cultivars. To reveal the genetic basis and develop DNA markers for pod dehiscence, several research groups have conducted quantitative trait locus (QTL) analysis using segregated populations derived from crosses between G. max accessions or between a G. max and G. soja accession. In the populations of G. max, a major QTL was repeatedly identified near SSR marker Sat_366 on linkage group J (chromosome 16). Minor QTLs were also detected in several studies, although less commonality was found for the magnitudes of effect and location. In G. max × G. soja populations, only QTLs with a relatively small effect were detected. The major QTL found in G. max was further fine-mapped, leading to the development of specific markers for the shattering resistance allele at this locus. The markers were used in a breeding program, resulting in the production of near-isogenic lines with shattering resistance and genetic backgrounds of Japanese elite cultivars. The markers and lines developed will hopefully contribute to the rapid production of a variety of shattering-resistant soybean cultivars.
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Affiliation(s)
- Hideyuki Funatsuki
- NARO Western Region Agricultural Research Center (NARO/WARC), Nishifukatsu, Fukuyama, Hiroshima 721-8514, Japan
| | - Makita Hajika
- National Institute of Crop Science (NICS), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tetsuya Yamada
- National Institute of Crop Science (NICS), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Masaya Suzuki
- Department of Crop Physiology, Graduate School of Agriculture, Hokkaido University, 9 Kita 9 Nishi, Sapporo, Hokkaido 060-8589, Japan
| | - Seiji Hagihara
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, Shinnsei, Memuro, Hokkaido 082-0071, Japan
| | - Yoshinori Tanaka
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, Shinnsei, Memuro, Hokkaido 082-0071, Japan
| | - Shohei Fujita
- Hokkaido Research Organization Central Agricultural Experiment Station, Naganuma, Hokkaido 069-1395, Japan
| | - Masao Ishimoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Kaien Fujino
- Department of Crop Physiology, Graduate School of Agriculture, Hokkaido University, 9 Kita 9 Nishi, Sapporo, Hokkaido 060-8589, Japan
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Fujino K, Hashida SN, Ogawa T, Natsume T, Uchiyama T, Mikami T, Kishima Y. Temperature controls nuclear import of Tam3 transposase in Antirrhinum. Plant J 2011; 65:146-155. [PMID: 21175897 DOI: 10.1111/j.1365-313x.2010.04405.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
It has been proposed that environmental stimuli can activate transposable elements (TEs), whereas few substantial mechanisms have been shown so far. The class-II element Tam3 from Antirrhinum majus exhibits a unique property of low-temperature-dependent transposition (LTDT). LTDT has proved invaluable in developing the gene isolation technologies that have underpinned much of modern plant developmental biology. Here, we reveal that LTDT involves differential subcellular localization of the Tam3 transposase (TPase) in cells grown at low (15°C) and high (25°C) temperatures. The mechanism is associated with the nuclear import of Tam3 TPase in Antirrhinum cells. At high temperature, the nuclear import of Tam3 TPase is severely restricted in Antirrhinum cells, whereas at low temperature, the nuclear localization of Tam3 TPase is observed in about 20% of the cells. However, in tobacco BY-2 and Allium cepa (onion) cells, Tam3 TPase is transported into most nuclei. In addition to three nuclear localization signals (NLSs), the Tam3 TPase is equipped with a nuclear localization inhibitory domain (NLID), which functions to abolish nuclear import of the TPase at high temperature in Antirrhinum. NLID in Tam3 TPase is considered to interact with Antirrhinum-specific factor(s). The host-specific regulation of the nuclear localization of transposase represents a new repertoire controlling class-II TEs.
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Affiliation(s)
- Kaien Fujino
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, JapanLaboratory of Genetic Engineering, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, JapanLaboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Shin-Nosuke Hashida
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, JapanLaboratory of Genetic Engineering, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, JapanLaboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Takashi Ogawa
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, JapanLaboratory of Genetic Engineering, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, JapanLaboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Tomoko Natsume
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, JapanLaboratory of Genetic Engineering, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, JapanLaboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Takako Uchiyama
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, JapanLaboratory of Genetic Engineering, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, JapanLaboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Tetsuo Mikami
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, JapanLaboratory of Genetic Engineering, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, JapanLaboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yuji Kishima
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, JapanLaboratory of Genetic Engineering, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, JapanLaboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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Seto Y, Nishio-Hamane D, Nagai T, Sata N, Fujino K. Synchrotron X-ray diffraction study for crystal structure of solid carbon dioxide CO2-V. ACTA ACUST UNITED AC 2010. [DOI: 10.1088/1742-6596/215/1/012015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Nagai T, Ishido T, Seto Y, Nishio-Hamane D, Sata N, Fujino K. Pressure-induced spin transition in FeCO3-siderite studied by X-ray diffraction measurements. ACTA ACUST UNITED AC 2010. [DOI: 10.1088/1742-6596/215/1/012002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Uchiyama T, Fujino K, Ogawa T, Wakatsuki A, Kishima Y, Mikami T, Sano Y. Stable transcription activities dependent on an orientation of Tam3 transposon insertions into Antirrhinum and yeast promoters occur only within chromatin. Plant Physiol 2009; 151:1557-69. [PMID: 19759347 PMCID: PMC2773084 DOI: 10.1104/pp.109.142356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 09/09/2009] [Indexed: 05/28/2023]
Abstract
Transposon insertions occasionally occur in the promoter regions of plant genes, many of which are still capable of being transcribed. However, it remains unclear how transcription of such promoters is able to occur. Insertion of the Tam3 transposon into various genes of Antirrhinum majus can confer leaky phenotypes without its excision. These genes, named Tam3-permissible alleles, often contain Tam3 in their promoter regions. Two alleles at different anthocyanin biosynthesis loci, nivea(recurrensTam3) (niv(rec)) and pallida(recurrensTam3) (pal(rec)), both contain Tam3 at a similar position immediately upstream of the promoter TATA-box; however, these insertions had different phenotypic consequences. Under conditions where the inserted Tam3 is immobilized, the niv(rec) line produces pale red petals, whereas the pal(rec) line produces no pigment. These pigmentation patterns are correlated with the level of transcripts from the niv(rec) or pal(rec) alleles, and these transcriptional activities are independent of DNA methylation in their promoter regions. In niv(rec), Tam3 is inserted in an orientation that results in the 3' end of Tam3 adjacent to the 5' region of the gene coding sequence. In contrast, the pal(rec) allele contains a Tam3 insertion in the opposite orientation. Four of five different nonrelated genes that are also Tam3-permissible alleles and contain Tam3 within the promoter region share the same Tam3 orientation as niv(rec). The different transcriptional activities dependent on Tam3 orientation in the Antirrhinum promoters were consistent with expression of luciferase reporter constructs introduced into yeast chromosomes but not with transient expression of these constructs in Antirrhinum cells. These results suggest that for Tam3 to sustain stable transcriptional activity in various promoters it must be embedded in chromatin.
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Affiliation(s)
| | | | | | | | - Yuji Kishima
- Laboratories of Plant Breeding (T.U., T.O., Y.K., Y.S.), Crop Physiology (K.F.), and Genetic Engineering (A.W., T.M.), Research Faculty of Agriculture, Hokkaido University, Sapporo 060–8589, Japan
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Uchiyama T, Saito Y, Kuwabara H, Fujino K, Kishima Y, Martin C, Sano Y. Multiple regulatory mechanisms influence the activity of the transposon, Tam3, of Antirrhinum. New Phytol 2008; 179:343-355. [PMID: 19086175 DOI: 10.1111/j.1469-8137.2008.02477.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In Antirrhinum, several unique regulations of the transposon, Tam3, have been described. Tam3 activity in Antirrhinum is strictly controlled by the growing temperature of plants (low-temperature-dependent transposition: LTDT), by chromosomal position of Tam3 copy and by two specific repressor genes Stabiliser (St) and New Stabiliser (NSt). Here, the effects of the St and NSt loci on Tam3 transposition are compared. In cotyledons and hypocotyls, Tam3 is active even at high growing temperatures, indicating that LTDT does not operate when these organs are developing. This developmental regulation of Tam3 activity is differentially influenced by the St and NSt loci: St permits Tam3 transposition in cotyledons and hypocotyls, whereas NSt suppresses it in these organs. The effects of these host genes on Tam3 activity at the molecular level were examined. It was found that neither of these genes inhibits the transcription of the Tam3 transposase gene nor its translation, and that the Tam3 transposase has the potential to catalyze transposition in the St and NSt lines. The differences between the effects of St and NSt imply that they regulate Tam3 activity independently. Our molecular data indicate that their influence on Tam3 transposition seems to be nonepigenetic; possible mechanisms for their activity are discussed.
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Affiliation(s)
| | | | | | - Kaien Fujino
- Laboratories of Crop Physiology, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | | | - Cathie Martin
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
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Nonoue Y, Fujino K, Hirayama Y, Yamanouchi U, Lin SY, Yano M. Detection of quantitative trait loci controlling extremely early heading in rice. Theor Appl Genet 2008; 116:715-22. [PMID: 18193402 DOI: 10.1007/s00122-007-0704-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 12/13/2007] [Indexed: 05/08/2023]
Abstract
To clarify the genetic basis of extremely early heading in rice, we conducted quantitative trait locus (QTL) analyses using F2 populations from two genetically wide cross combinations, Hayamasari/Kasalath (HaF2) and Hoshinoyume/Kasalath (HoF2). Hayamasari and Hoshinoyume are extremely early-heading japonica cultivars. Photoperiod sensitivity is completely lost in Hayamasari and weak in Hoshinoyume. Three QTLs, QTL(chr6), QTL(chr7), and QTL(chr8), for days-to-heading (DTH) in HaF2 were detected on chromosomes 6, 7, and 8, respectively, and QTL(chr6) and QTL(chr7) were detected in HoF2. On the basis of the chromosomal locations, QTL(chr6), QTL(chr7), and QTL(chr8) may be likely to be Hd1, Hd4, and Hd5, respectively, which had been detected previously as QTLs for DTH in an F2 population of NipponbarexKasalath. Alleles of QTL(chr7) decreased DTH dramatically in both Hayamasari and Hoshinoyume, suggesting that QTL(chr7) has a major role in determining extremely early heading. In addition, allele-specific interactions were detected between QTL(chr6), QTL(chr7) and QTL(chr8). This result suggests that not only allelic differences but also epistatic interactions contribute to extremely early heading. QTL(chr8) was detected in HaF2, but not in HoF2, suggesting that it determines the difference in DTH between Hayamasari and Hoshinoyume. A major QTL was also detected in the region of QTL(chr8) in QTL analysis using an F2 population of HayamasarixHoshinoyume. This result supports the idea that QTL(chr8) is a major factor that determines the difference in DTH between Hayamasari and Hoshinoyume, and is involved in photoperiod sensitivity.
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Affiliation(s)
- Y Nonoue
- Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
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Futakuchi H, Ueda M, Kanda K, Fujino K, Yamaguchi H, Noda S. Transcriptional expression of survivin and its splice variants in cervical carcinomas. Int J Gynecol Cancer 2007; 17:1092-8. [PMID: 17877643 DOI: 10.1111/j.1525-1438.2007.00833.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The objective of this study was to evaluate transcriptional expression of survivin and the two splice variants (survivin-2B and survivin-ΔEx3) in cervical carcinomas. The gene expression levels of survivin and its splice variants in 11 human cervical carcinoma cell lines and 20 malignant and 12 normal cervical tissue samples were analyzed using quantitative reverse transcription–polymerase chain reaction analysis. Gene expression levels of survivin and survivin-ΔEx3 in cell lines were higher than those in normal cervical tissues (P= 0.0193 and 0.0489). Transcript levels of survivin and survivin-ΔEx3 in carcinoma tissues were also higher than those in normal controls (P= 0.0016 and 0.0011). Gene expression levels of survivin and survivin-ΔEx3 in adenocarcinomas were statistically higher than those in squamous cell carcinomas (P= 0.0260 and 0.0487). There was no significant difference in survivin-2B gene expression between malignant and normal cervical samples or different histologic types. The ratios of survivin-2B/survivin and survivin-ΔEx3/survivin in carcinoma tissues were higher than those in normal controls (P= 0.0288 and 0.0081). Interestingly, the ratio of survivin-2B/survivin was increased in the patients with higher stages and with pelvic lymph node metastasis (P= 0.0205 and 0.0437), respectively. We conclude that survivin and its splice variants might be involved in the pathogenesis and development of cervical carcinomas.
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Affiliation(s)
- H Futakuchi
- Department of Obstetrics and Gynecology, Osaka Medical College, Osaka, Japan
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Nifuku M, Tsujita H, Fujino K, Takaichi K, Barre C, Paya E, Hatori M, Fujiwara S, Horiguchi S, Sochet I. Ignitability assessment of shredder dusts of refrigerator and the prevention of the dust explosion. J Loss Prev Process Ind 2006. [DOI: 10.1016/j.jlp.2005.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Abstract
BACKGROUND AND AIMS Activation of the vanilloid receptor subtype 1 (VR-1) results in release of proinflammatory peptides which initiate an inflammatory cascade known as neurogenic inflammation. We investigated its role in an acute model of surgically induced oesophagitis. METHODS Oesophagitis was induced by pyloric ligation in wild-type and VR-1 deficient mice. A subset of animals were administered the VR-1 antagonist capsazepine, famotidine, or omeprazole one hour before surgery. Five hours after surgery, myeloperoxidase activity (MPO), histological damage scores, intragastric pH, and immunocytochemical analysis of substance P (SP) receptor endocytosis were determined. RESULTS Oesophagitis induced knockout mice exhibited significantly lower levels of MPO activity, histological damage scores, and SP receptor endocytosis than wild-type mice. Inflammatory parameters were significantly reduced by acid inhibition and capsazepine in wild-type mice. CONCLUSIONS We conclude that acute acid induced oesophagitis is reduced in animals lacking VR-1. This suggests that acid induced oesophagitis may act through VR-1 and that inhibition of the receptor may reduce inflammation.
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Affiliation(s)
- K Fujino
- Duke University Medical Center, Box 3117, Durham, NC 27710, USA
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Matsumoto R, Fujino K, Nagata Y, Hashiguchi S, Ito Y, Aihara Y, Takahashi Y, Maeda K, Sugimura K. Molecular characterization of a 10-kDa buckwheat molecule reactive to allergic patients' IgE. Allergy 2004; 59:533-8. [PMID: 15080835 DOI: 10.1046/j.1398-9995.2003.00412.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Using the sera from buckwheat (BW)-allergic patients, several putative causative molecules were reported. However, few molecules were determined on the molecular structure. We demonstrated in 2000 that the major allergen with 24 kDa (BW24KD) is a legumin-like storage protein. OBJECTIVE The aim of this study was to isolate and characterize further a major allergen with 10 kDa by molecular cloning. METHODS AND RESULTS Buckwheat allergens were identified by immunoblotting analysis using sera from 14 allergic and two nonallergic individuals. We identified a protein with 10 kDa (BW10KD) that reacted with immunoglobulin E (IgE) more strongly than with IgG and IgA in 57% of the allergic patients but not with IgE in nonallergic individuals. Analyses were performed by N-terminal amino acid sequencing and molecular cloning. Physiological significance was assessed by an immunoblotting experiment showing that the reactivity of an allergic patient's serum IgE to BW10KD was competitively inhibited by natural BW extracts. CONCLUSION Molecular cloning experiments indicated that BW10KD as a BW allergen was a member of the 2S-albumin multigene family.
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Affiliation(s)
- R Matsumoto
- Department of Bioengineering, Faculty of Engineering, Kagoshima University, Kagoshima, Japan
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Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin SY, Yano M. Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet 2004; 108:794-9. [PMID: 14624339 DOI: 10.1007/s00122-003-1509-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2003] [Accepted: 09/10/2003] [Indexed: 05/05/2023]
Abstract
Low-temperature germination is one of the major determinants for stable stand establishment in the direct seeding method in temperate regions, and at high altitudes of tropical regions. Quantitative trait loci (QTLs) controlling low-temperature germinability in rice were identified using 122 backcross inbred lines (BILs) derived from a cross between temperate japonica varieties, Italica Livorno and Hayamasari. The germination rate at 15 degrees C was measured to represent low-temperature germination and used for QTL analysis. The germination rate at 15 degrees C for 7 days of Italica Livorno and Hayamasari was 98.7 and 26.8%, respectively, and that of BILs ranged from 0 to 83.3%. Using restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers, we constructed a linkage map which corresponded to about 90% of the rice genome. Three putative QTLs associated with low-temperature germination were detected. The most effective QTL, qLTG-3-1 on chromosome 3, accounted for 35.0% of the total phenotypic variation for low-temperature germinability. Two additional QTLs, qLTG-3-2 on chromosome 3 and qLTG-4 on chromosome 4, were detected and accounted for 17.4 and 5.5% of the total phenotypic variation, respectively. The Italica Livorno alleles in all detected QTLs increased the low-temperature germination rate.
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Affiliation(s)
- K Fujino
- Hokkaido Green-Bio Institute, Naganuma, 067-1317, Hokkaido, Japan.
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