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Yagi H, Nagano AJ, Kim J, Tamura K, Mochizuki N, Nagatani A, Matsushita T, Shimada T. Fluorescent protein-based imaging and tissue-specific RNA-seq analysis of Arabidopsis hydathodes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1260-1270. [PMID: 33165567 DOI: 10.1093/jxb/eraa519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/31/2020] [Indexed: 06/11/2023]
Abstract
Hydathodes are typically found at leaf teeth in vascular plants and are involved in water release to the outside. Although morphological and physiological analysis of hydathodes has been performed in various plants, little is known about the genes involved in hydathode function. In this study, we performed fluorescent protein-based imaging and tissue-specific RNA-seq analysis in Arabidopsis hydathodes. We used the enhancer trap line E325, which has been reported to express green fluorescent protein (GFP) at its hydathodes. We found that E325-GFP was expressed in small cells found inside the hydathodes (named E cells) that were distributed between the water pores and xylem ends. No fluorescence of the phloem markers pSUC2:GFP and pSEOR1:SEOR1-YFP was observed in the hydathodes. These observations indicate that Arabidopsis hydathodes are composed of three major components: water pores, xylem ends, and E cells. In addition, we performed transcriptome analysis of the hydathode using the E325-GFP line. Microsamples were collected from GFP-positive or -negative regions of E325 leaf margins with a needle-based device (~130 µm in diameter). RNA-seq was performed with each single microsample using a high-throughput library preparation method called Lasy-Seq. We identified 72 differentially expressed genes. Among them, 68 genes showed significantly higher and four genes showed significantly lower expression in the hydathode. Our results provide new insights into the molecular basis for hydathode physiology and development.
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Affiliation(s)
- Hiroki Yagi
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | | | - Jaewook Kim
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Kentaro Tamura
- Department of Environmental and Life Sciences, University of Shizuoka, Shizuoka, Japan
| | - Nobuyoshi Mochizuki
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Akira Nagatani
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tomonao Matsushita
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tomoo Shimada
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
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Yoda T, Hosokawa M, Takahashi K, Sakanashi C, Takeyama H, Kambara H. Site-specific gene expression analysis using an automated tissue micro-dissection punching system. Sci Rep 2017; 7:4325. [PMID: 28659603 PMCID: PMC5489509 DOI: 10.1038/s41598-017-04616-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/17/2017] [Indexed: 11/09/2022] Open
Abstract
Site-specific gene expression analyses are important for understanding tissue functions. Despite rapid developments in DNA-related technologies, the site-specific analysis of whole genome expression for a tissue remains challenging. Thus, a new tool is required for capturing multiple tissue micro-dissections or single cells while retaining the positional information. Here, we describe the development of such a system, which can pick up micro-dissections by punching a tissue repeatedly in a very short period, e.g., 5 s/sampling cycle. A photo of the punched tissue provides information on the dissected positions, allowing site-specific gene expression analysis. We demonstrate the site-specific analysis of a frozen tissue slice of mouse brain by analyzing many micro-dissections produced from the tissue at a 300-μm pitch. The site-specific analysis provided new insights into the gene expression profiles in a tissue and on tissue functions. The analysis of site-specific whole genome expression may therefore, open new avenues in life science.
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Affiliation(s)
- Takuya Yoda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Masahito Hosokawa
- Research Organization for Nano &Life Innovation, Waseda University, 513 Waseda-tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.,PRESTO, Japan Science and Technology Agency (JST), 5-3 Yonban-cho, Chiyoda-ku, Tokyo, 102-0075, Japan
| | - Kiyofumi Takahashi
- Research Organization for Nano &Life Innovation, Waseda University, 513 Waseda-tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Chikako Sakanashi
- Research Organization for Nano &Life Innovation, Waseda University, 513 Waseda-tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.,Research Organization for Nano &Life Innovation, Waseda University, 513 Waseda-tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.,Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-0072, Japan
| | - Hideki Kambara
- Research Organization for Nano &Life Innovation, Waseda University, 513 Waseda-tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.
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Nito K, Kajiyama T, Unten-Kobayashi J, Fujii A, Mochizuki N, Kambara H, Nagatani A. Spatial Regulation of the Gene Expression Response to Shade in Arabidopsis Seedlings. PLANT & CELL PHYSIOLOGY 2015; 56:1306-19. [PMID: 25907567 DOI: 10.1093/pcp/pcv057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 04/01/2015] [Indexed: 05/04/2023]
Abstract
The shade avoidance response, which allows plants to escape from nearby competitors, is triggered by a reduction in the PFR form of phytochrome in response to shade. Classic physiological experiments have demonstrated that the shade signal perceived by the leaves is transmitted to the other parts of the plant. Recently, a simple method was developed to analyze the transcriptome in a single microgram tissue sample. In the present study, we adopted this method to conduct organ-specific transcriptomic analysis of the shade avoidance response in Arabidopsis seedlings. The shoot apical samples, which contained the meristem, basal parts of leaf primordia and short fragments of vasculature, were collected from the topmost part of the hypocotyl and subjected to RNA sequencing analysis. Unexpectedly, many more genes were up-regulated in the shoot apical region than in the cotyledons. Spotlight irradiation demonstrated that the apex-responsive genes were mainly controlled by phytochrome in the cotyledons. In accordance with the involvement of many auxin-responsive genes in this category, auxin biosynthesis was genetically shown to be essential for this response. In contrast, organ-autonomous regulation was more important for the genes that were up-regulated preferentially either in the cotyledons or in both the cotyledons and the apical region. Their responses to shade depended variously on auxin and PIFs (phytochrome-interacting factors), indicating the mechanistic diversity of the organ-autonomous response. Finally, we examined the expression of the auxin synthesis genes, the YUC genes, and found that three YUC genes, which were differently spatially regulated, co-ordinately elevated the auxin level within the shoot apical region.
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Affiliation(s)
- Kazumasa Nito
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
| | | | - Junko Unten-Kobayashi
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
| | - Akihiko Fujii
- Central Research Laboratory, Hitachi, Ltd., Tokyo, 185-8601 Japan
| | - Nobuyoshi Mochizuki
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
| | - Hideki Kambara
- Central Research Laboratory, Hitachi, Ltd., Tokyo, 185-8601 Japan
| | - Akira Nagatani
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
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Nagatani A, Mimura T. Editorial: Emerging Technologies for the Study of Plant Environmental Sensing. PLANT & CELL PHYSIOLOGY 2015; 56:1249-51. [PMID: 26163572 PMCID: PMC4498007 DOI: 10.1093/pcp/pcv095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Affiliation(s)
- Akira Nagatani
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Tetsuro Mimura
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
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Ohnishi M, Kadohama N, Suzuki Y, Kajiyama T, Shichijo C, Ishizaki K, Fukaki H, Iida H, Kambara H, Mimura T. Involvement of Ca2+ in Vacuole Degradation Caused by a Rapid Temperature Decrease in Saintpaulia Palisade Cells: A Case of Gene Expression Analysis in a Specialized Small Tissue. PLANT & CELL PHYSIOLOGY 2015; 56:1297-1305. [PMID: 25941231 DOI: 10.1093/pcp/pcv048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/09/2015] [Indexed: 06/04/2023]
Abstract
Saintpaulia (African violet) leaves are known to be damaged by a rapid temperature decrease when cold water is applied to the leaf surface; the injury is ascribed to the chloroplast damage caused by the cytosolic pH decrease following the degradation of the vacuolar membrane in the palisade cells. In this report, we present evidence for the involvement of Ca(2+) in facilitating the collapse of the vacuolar membrane and in turn in the temperature sensitivity of Saintpaulia leaves. In the presence of a Ca(2+) chelator (EGTA) or certain Ca(2+) channel inhibitors (Gd(3+) or La(3+)) but not others (verapamil or nifedipine), the pH of the vacuole, monitored through BCECF (2',7'-bis(carboxyethyl)-4 or 5-carboxyfluorescein) fluorescence, did not increase in response to a rapid temperature drop. These pharmacological observations are consistent with the involvement of mechanosensitive Ca(2+) channels in the collapse of the vacuolar membrane. The high level of expression of an MCA- (Arabidopsis mechanosensitive Ca(2+) channel) like gene, a likely candidate for a mechanosensitive Ca(2+) channel(s) in plant cells, was confirmed in the palisade tissue in Saintpaulia leaves by using a newly developed method of gene expression analysis for the specialized small tissues.
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Affiliation(s)
- Miwa Ohnishi
- Department of Biology, Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada-ku, Kobe, 657-8501 Japan
| | - Noriaki Kadohama
- Department of Biology, Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada-ku, Kobe, 657-8501 Japan
| | - Yoshihiro Suzuki
- Department of Biological Science, Graduate School of Science, Kanagawa University, Tsuchiya 2946, Hiratsuka, Kanagawa, 259-1293 Japan
| | - Tomoharu Kajiyama
- Central Research Laboratory, Hitachi, Ltd., 1-280 Higashi-Koigakubo, Kokubunji-shi, Tokyo, 185-8601, Japan
| | - Chizuko Shichijo
- Department of Biology, Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada-ku, Kobe, 657-8501 Japan
| | - Kimitsune Ishizaki
- Department of Biology, Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada-ku, Kobe, 657-8501 Japan
| | - Hidehiro Fukaki
- Department of Biology, Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada-ku, Kobe, 657-8501 Japan
| | - Hidetoshi Iida
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Tokyo, 184-8501 Japan
| | - Hideki Kambara
- Central Research Laboratory, Hitachi, Ltd., 1-280 Higashi-Koigakubo, Kokubunji-shi, Tokyo, 185-8601, Japan
| | - Tetsuro Mimura
- Department of Biology, Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada-ku, Kobe, 657-8501 Japan
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