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Ofori PA, Mizuno A, Suzuki M, Martinoia E, Reuscher S, Aoki K, Shibata D, Otagaki S, Matsumoto S, Shiratake K. Genome-wide analysis of ATP binding cassette (ABC) transporters in tomato. PLoS One 2018; 13:e0200854. [PMID: 30048467 PMCID: PMC6062036 DOI: 10.1371/journal.pone.0200854] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/03/2018] [Indexed: 11/18/2022] Open
Abstract
ATP binding cassette (ABC) transporters are proteins that actively mediate the transport of a wide range of molecules, such as organic acids, metal ions, phytohormones and secondary metabolites. Therefore, ABC transporters must play indispensable roles in growth and development of tomato, including fruit development. Most ABC transporters have transmembrane domains (TMDs) and belong to the ABC protein family, which includes not only ABC transporters but also soluble ABC proteins lacking TMDs. In this study, we performed a genome-wide identification and expression analysis of genes encoding ABC proteins in tomato (Solanum lycopersicum), which is a valuable horticultural crop and a model plant for studying fleshy fruits. In the tomato genome, a total of 154 genes putatively encoding ABC transporters, including 9 ABCAs, 29 ABCBs, 26 ABCCs, 2 ABCDs, 2 ABCEs, 6 ABCFs, 70 ABCGs and 10 ABCIs, were identified. Gene expression data from the eFP Browser and reverse transcription-semi-quantitative PCR analysis revealed their tissue-specific and development-specific expression profiles. This work suggests physiological roles of ABC transporters in tomato and provides fundamental information for future studies of ABC transporters not only in tomato but also in other Solanaceae species.
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Affiliation(s)
- Peter Amoako Ofori
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Ayaka Mizuno
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mami Suzuki
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Enrico Martinoia
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Stefan Reuscher
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Koh Aoki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | | | - Shungo Otagaki
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Shogo Matsumoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- * E-mail:
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Minami A, Yano K, Gamuyao R, Nagai K, Kuroha T, Ayano M, Nakamori M, Koike M, Kondo Y, Niimi Y, Kuwata K, Suzuki T, Higashiyama T, Takebayashi Y, Kojima M, Sakakibara H, Toyoda A, Fujiyama A, Kurata N, Ashikari M, Reuscher S. Time-Course Transcriptomics Analysis Reveals Key Responses of Submerged Deepwater Rice to Flooding. Plant Physiol 2018; 176:3081-3102. [PMID: 29475897 PMCID: PMC5884608 DOI: 10.1104/pp.17.00858] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 02/15/2018] [Indexed: 05/29/2023]
Abstract
Water submergence is an environmental factor that limits plant growth and survival. Deepwater rice (Oryza sativa) adapts to submergence by rapidly elongating its internodes and thereby maintaining its leaves above the water surface. We performed a comparative RNA sequencing transcriptome analysis of the shoot base region, including basal nodes, internodes, and shoot apices of seedlings at two developmental stages from two varieties with contrasting deepwater growth responses. A transcriptomic comparison between deepwater rice cv C9285 and nondeepwater rice cv Taichung 65 revealed both similar and differential expression patterns between the two genotypes during submergence. The expression of genes related to gibberellin biosynthesis, trehalose biosynthesis, anaerobic fermentation, cell wall modification, and transcription factors that include ethylene-responsive factors was significantly different between the varieties. Interestingly, in both varieties, the jasmonic acid content at the shoot base decreased during submergence, while exogenous jasmonic acid inhibited submergence-induced internode elongation in cv C9285, suggesting that jasmonic acid plays a role in the submergence response of rice. Furthermore, a targeted de novo transcript assembly revealed transcripts that were specific to cv C9285, including submergence-induced biotic stress-related genes. Our multifaceted transcriptome approach using the rice shoot base region illustrates a differential response to submergence between deepwater and nondeepwater rice. Jasmonic acid metabolism appears to participate in the submergence-mediated internode elongation response of deepwater rice.
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Affiliation(s)
- Anzu Minami
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Kenji Yano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Rico Gamuyao
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Takeshi Kuroha
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Madoka Ayano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Masanari Nakamori
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Masaya Koike
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yuma Kondo
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yoko Niimi
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Takamasa Suzuki
- Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
- ERATO Higashiyama Live-Holonics Project, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Tetsuya Higashiyama
- Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
- ERATO Higashiyama Live-Holonics Project, Nagoya University, Nagoya, Aichi 464-8602, Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya Aichi 464-8601, Japan
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Mishima 411-8540, Japan
| | - Asao Fujiyama
- Center for Information Biology, National Institute of Genetics, Mishima 411-8540, Japan
| | - Nori Kurata
- Genetic Strains Research Center, National Institute of Genetics, Mishima 411-8540, Japan
| | - Motoyuki Ashikari
- Genetic Strains Research Center, National Institute of Genetics, Mishima 411-8540, Japan
| | - Stefan Reuscher
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
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3
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Gamuyao R, Nagai K, Ashikari M, Reuscher S. A new outlook on sporadic flowering of bamboo. Plant Signal Behav 2017; 12:e1343780. [PMID: 28650217 PMCID: PMC5586395 DOI: 10.1080/15592324.2017.1343780] [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] [Indexed: 05/04/2023]
Abstract
Moso bamboo (Phyllostachys edulis) is a temperate grass species with a tree-like habitus and an unusual reproduction strategy. While flowering is irregular and infrequent, new clonal bamboo shoots are established from an underground rhizome network during the spring season. In our previous study, we performed transcriptome analyses using bamboo shoot buds to understand the initiation of bamboo stem elongation. Interestingly, the expression profile in the shoot apical meristem (SAM) region of young bamboo shoots is similar to that of other plants. Specifically, some of the genes that control the timing of flowering and floral development are active in the SAM region. This data raises the question of how bamboo shoots start to elongate, and why they do not proceed to a seasonal cycle of flowering. Our analyses of the activation of shoot buds and subsequent rapid stem elongation provide new hints to unravel the unpredictable flowering pattern of bamboo. In this short communication, we discuss how bamboo might coordinate and integrate the vegetative and reproductive phases in relation to shoot emergence and stem elongation.
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Affiliation(s)
- Rico Gamuyao
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Stefan Reuscher
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- CONTACT Stefan Reuscher Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Nagoya, Aichi 464–8601, Japan
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Gamuyao R, Nagai K, Ayano M, Mori Y, Minami A, Kojima M, Suzuki T, Sakakibara H, Higashiyama T, Ashikari M, Reuscher S. Hormone Distribution and Transcriptome Profiles in Bamboo Shoots Provide Insights on Bamboo Stem Emergence and Growth. Plant Cell Physiol 2017; 58:702-716. [PMID: 28204696 DOI: 10.1093/pcp/pcx023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 11/04/2016] [Accepted: 02/01/2017] [Indexed: 05/20/2023]
Abstract
Growth and development are tightly co-ordinated events in the lifetime of living organisms. In temperate bamboo plants, spring is the season when environmental conditions are suitable for the emergence of new shoots. Previous studies demonstrated that bamboo plants undergo an energy-consuming 'fast stem growth' phase. However, the events during the initiation of stem elongation in bamboo are poorly understood. To understand the onset of bamboo stem growth, we performed hormone and transcriptome profiling of tissue regions in newly elongating shoots of the Moso bamboo Phyllostachys edulis. The growth hormones auxins, cytokinins and gibberellins accumulated in the shoot apex, while the stress hormones ABA, salicylic acid (SA) and jasmonic acid (JA) are predominantly found in the lower part of the stem. The mature basal part of the stem showed enrichment of transcripts associated with cell wall metabolism and biosynthesis of phenylpropanoid metabolites, such as lignin. In the young upper stem region, expression of cell formation- and DNA synthesis-related genes was enriched. Moreover, the apical region showed enhanced expression of genes involved in meristem maintenance, leaf differentiation and development, abaxial/adaxial polarity and flowering. Our findings integrate the spatial regulation of hormones and transcriptome programs during the initiation of bamboo stem growth.
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Affiliation(s)
- Rico Gamuyao
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Madoka Ayano
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Yoshinao Mori
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Anzu Minami
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Suehiro, Tsurumi, Yokohama, Japan
| | - Takamasa Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Suehiro, Tsurumi, Yokohama, Japan
| | - Tetsuya Higashiyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Stefan Reuscher
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
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Furuta T, Ashikari M, Jena KK, Doi K, Reuscher S. Adapting Genotyping-by-Sequencing for Rice F2 Populations. G3 (Bethesda) 2017; 7:881-893. [PMID: 28082325 PMCID: PMC5345719 DOI: 10.1534/g3.116.038190] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 01/09/2017] [Indexed: 12/30/2022]
Abstract
Rapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population, and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross of Oryza sativa ssp. japonica cv. Nipponbare and the African wild rice species O. longistaminata While most GBS pipelines aim to analyze mainly homozygous populations, we attempted to genotype a highly heterozygous F2 population. We show how species- and population-specific improvements of established protocols can drastically increase sample throughput and genotype quality. Using as few as 50,000 reads for some individuals (134,000 reads on average), we were able to generate up to 8154 informative SNP markers in 1081 F2 individuals. Additionally, the effects of enzyme choice, read coverage, and data postprocessing are evaluated. Using GBS-derived markers, we were able to assemble a genetic map of 1536 cM. To demonstrate the usefulness of our GBS pipeline, we determined quantitative trait loci (QTL) for the number of tillers. We were able to map four QTL to chromosomes 1, 3, 4, and 8, and partially confirm their effects using introgression lines. We provide an example of how to successfully use GBS with heterozygous F2 populations. By using the comparatively low-cost MiSeq platform, we show that the GBS method is flexible and cost-effective, even for smaller laboratories.
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Affiliation(s)
- Tomoyuki Furuta
- Bioscience and Biotechnology Center, Nagoya University, 464-8601, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, 464-8601, Japan
| | - Kshirod K Jena
- Plant Breeding Division, International Rice Research Institute, 1301 Manila, Philippines
| | - Kazuyuki Doi
- Associated Field Science and Research Center, Nagoya University, 470-0151, Japan
| | - Stefan Reuscher
- Bioscience and Biotechnology Center, Nagoya University, 464-8601, Japan
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Detterbeck A, Pongrac P, Rensch S, Reuscher S, Pečovnik M, Vavpetič P, Pelicon P, Holzheu S, Krämer U, Clemens S. Spatially resolved analysis of variation in barley (Hordeum vulgare) grain micronutrient accumulation. New Phytol 2016; 211:1241-54. [PMID: 27125321 DOI: 10.1111/nph.13987] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 03/23/2016] [Indexed: 05/21/2023]
Abstract
Genetic biofortification requires knowledge on natural variation and the underlying mechanisms of micronutrient accumulation. We therefore studied diversity in grain micronutrient concentrations and spatial distribution in barley (Hordeum vulgare), a genetically tractable model cereal and an important crop with widespread cultivation. We assembled a diverse collection of barley cultivars and landraces and analysed grain micronutrient profiles in genebank material and after three independent cultivations. Lines with contrasting grain zinc (Zn) accumulation were selected for in-depth analysis of micronutrient distribution within the grain by micro-proton-induced X-ray emission (μ-PIXE). Also, we addressed association with grain cadmium (Cd) accumulation. The analysis of > 120 lines revealed substantial variation, especially in grain Zn concentrations. A large fraction of this variation is due to genetic differences. Grain dissection and μ-PIXE analysis of contrasting lines showed that differences in grain Zn accumulation apply to all parts of the grain including the endosperm. Cd concentrations exceeded the Codex Alimentarius threshold in most of the representative barley lines after cultivation in a Cd-contaminated agricultural soil. Two important conclusions for biofortification are: first, high-Zn grains contain more Zn also in the consumed parts of the grain; and second, higher micronutrient concentrations are strongly associated with higher Cd accumulation.
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Affiliation(s)
- Amelie Detterbeck
- Department of Plant Physiology, University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Paula Pongrac
- Department of Plant Physiology, University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Stefan Rensch
- Department of Plant Physiology, University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Stefan Reuscher
- Department of Plant Physiology, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Matic Pečovnik
- Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
| | - Primož Vavpetič
- Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
| | - Primož Pelicon
- Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
| | - Stefan Holzheu
- Bayreuth Center for Ecology and Environmental Research, University of Bayreuth, Dr.-Hans-Frisch-Str. 1-3, 95440, Bayreuth, Germany
| | - Ute Krämer
- Department of Plant Physiology, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Stephan Clemens
- Department of Plant Physiology, University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
- Bayreuth Center for Ecology and Environmental Research, University of Bayreuth, Dr.-Hans-Frisch-Str. 1-3, 95440, Bayreuth, Germany
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Reuscher S, Fukao Y, Morimoto R, Otagaki S, Oikawa A, Isuzugawa K, Shiratake K. Quantitative Proteomics-Based Reconstruction and Identification of Metabolic Pathways and Membrane Transport Proteins Related to Sugar Accumulation in Developing Fruits of Pear (Pyrus communis). Plant Cell Physiol 2016; 57:505-18. [PMID: 26755692 DOI: 10.1093/pcp/pcw004] [Citation(s) in RCA: 8] [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: 10/15/2015] [Accepted: 01/05/2016] [Indexed: 05/09/2023]
Abstract
During their 6 month development, pear (Pyrus communis) fruits undergo drastic changes in their morphology and their chemical composition. To gain a better understanding of the metabolic pathways and transport processes active during fruit development, we performed a time-course analysis using mass spectrometry (MS)-based protein identification and quantification of fruit flesh tissues. After pre-fractionation of the samples, 2,841 proteins were identified. A principal component analysis (PCA) separated the samples from seven developmental stages into three distinct clusters representing the early, mid and late developmental phase. Over-representation analysis of proteins characteristic of each developmental phase revealed both expected and novel biological processes relevant at each phase. A high abundance of aquaporins was detected in samples from fruits in the cell expansion stage. We were able quantitatively to reconstruct basic metabolic pathways such as the tricarboxylic acid (TCA) cycle, which indicates sufficient coverage to reconstruct other metabolic pathways. Most of the enzymes that presumably contribute to sugar accumulation in pear fruits could be identified. Our data indicate that invertases do not play a major role in the sugar conversions in developing pear fruits. Rather, sucrose might be broken down by sucrose synthases. Further focusing on sugar transporters, we identified several putative sugar transporters from diverse families which showed developmental regulation. In conclusion, our data set comprehensively describes the proteome of developing pear fruits and provides novel insights about sugar accumulation as well as candidate genes for key reactions and transport steps.
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Affiliation(s)
- Stefan Reuscher
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Yoichiro Fukao
- College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577 Japan
| | - Reina Morimoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Shungo Otagaki
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555 Japan RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045 Japan
| | - Kanji Isuzugawa
- Yamagata Integrated Agricultural Research Center, Sagae, 999-7601 Japan
| | - Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
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Reuscher S, Akiyama M, Yasuda T, Makino H, Aoki K, Shibata D, Shiratake K. The sugar transporter inventory of tomato: genome-wide identification and expression analysis. Plant Cell Physiol 2014; 55:1123-41. [PMID: 24833026 DOI: 10.1093/pcp/pcu052] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The mobility of sugars between source and sink tissues in plants depends on sugar transport proteins. Studying the corresponding genes allows the manipulation of the sink strength of developing fruits, thereby improving fruit quality for human consumption. Tomato (Solanum lycopersicum) is both a major horticultural crop and a model for the development of fleshy fruits. In this article we provide a comprehensive inventory of tomato sugar transporters, including the SUCROSE TRANSPORTER family, the SUGAR TRANSPORTER PROTEIN family, the SUGAR FACILITATOR PROTEIN family, the POLYOL/MONOSACCHARIDE TRANSPORTER family, the INOSITOL TRANSPORTER family, the PLASTIDIC GLUCOSE TRANSLOCATOR family, the TONOPLAST MONOSACCHARIDE TRANSPORTER family and the VACUOLAR GLUCOSE TRANSPORTER family. Expressed sequence tag (EST) sequencing and phylogenetic analyses established a nomenclature for all analyzed tomato sugar transporters. In total we identified 52 genes in tomato putatively encoding sugar transporters. The expression of 29 sugar transporter genes in vegetative tissues and during fruit development was analyzed. Several sugar transporter genes were expressed in a tissue- or developmental stage-specific manner. This information will be helpful to better understand source to sink movement of photoassimilates in tomato. Identification of fruit-specific sugar transporters might be a first step to find novel genes contributing to tomato fruit sugar accumulation.
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Affiliation(s)
- Stefan Reuscher
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 JapanThese authors contributed equally to this work
| | - Masahito Akiyama
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 JapanThese authors contributed equally to this work
| | - Tomohide Yasuda
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
| | - Haruko Makino
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
| | - Koh Aoki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Gakuen-cho, Sakai, 599-8531 Japan
| | - Daisuke Shibata
- Kazusa DNA Research Institute, Kazusa-kamatari, Kisarazu, 292-0818 Japan
| | - Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
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Reuscher S, Akiyama M, Mori C, Aoki K, Shibata D, Shiratake K. Genome-wide identification and expression analysis of aquaporins in tomato. PLoS One 2013; 8:e79052. [PMID: 24260152 PMCID: PMC3834038 DOI: 10.1371/journal.pone.0079052] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [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: 08/19/2013] [Accepted: 09/20/2013] [Indexed: 11/30/2022] Open
Abstract
The family of aquaporins, also called water channels or major intrinsic proteins, is characterized by six transmembrane domains that together facilitate the transport of water and a variety of low molecular weight solutes. They are found in all domains of life, but show their highest diversity in plants. Numerous studies identified aquaporins as important targets for improving plant performance under drought stress. The phylogeny of aquaporins is well established based on model species like Arabidopsis thaliana, which can be used as a template to investigate aquaporins in other species. In this study we comprehensively identified aquaporin encoding genes in tomato (Solanum lycopersicum), which is an important vegetable crop and also serves as a model for fleshy fruit development. We found 47 aquaporin genes in the tomato genome and analyzed their structural features. Based on a phylogenetic analysis of the deduced amino acid sequences the aquaporin genes were assigned to five subfamilies (PIPs, TIPs, NIPs, SIPs and XIPs) and their substrate specificity was assessed on the basis of key amino acid residues. As ESTs were available for 32 genes, expression of these genes was analyzed in 13 different tissues and developmental stages of tomato. We detected tissue-specific and development-specific expression of tomato aquaporin genes, which is a first step towards revealing the contribution of aquaporins to water and solute transport in leaves and during fruit development.
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Affiliation(s)
- Stefan Reuscher
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Masahito Akiyama
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Chiharu Mori
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Koh Aoki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Gakuen-cho, Sakai, Japan
| | - Daisuke Shibata
- Kazusa DNA Research Institute, Kazusa-kamatari, Kisarazu, Japan
| | - Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
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