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Ishii K, Kazama Y, Hirano T, Fawcett JA, Sato M, Hirai MY, Sakai F, Shirakawa Y, Ohbu S, Abe T. Genomic view of heavy-ion-induced deletions associated with distribution of essential genes in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2024; 15:1352564. [PMID: 38693931 PMCID: PMC11061394 DOI: 10.3389/fpls.2024.1352564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/11/2024] [Indexed: 05/03/2024]
Abstract
Heavy-ion beam, a type of ionizing radiation, has been applied to plant breeding as a powerful mutagen and is a promising tool to induce large deletions and chromosomal rearrangements. The effectiveness of heavy-ion irradiation can be explained by linear energy transfer (LET; keV µm-1). Heavy-ion beams with different LET values induce different types and sizes of mutations. It has been suggested that deletion size increases with increasing LET value, and complex chromosomal rearrangements are induced in higher LET radiations. In this study, we mapped heavy-ion beam-induced deletions detected in Arabidopsis mutants to its genome. We revealed that deletion sizes were similar between different LETs (100 to 290 keV μm-1), that their upper limit was affected by the distribution of essential genes, and that the detected chromosomal rearrangements avoid disrupting the essential genes. We also focused on tandemly arrayed genes (TAGs), where two or more homologous genes are adjacent to one another in the genome. Our results suggested that 100 keV µm-1 of LET is enough to disrupt TAGs and that the distribution of essential genes strongly affects the heritability of mutations overlapping them. Our results provide a genomic view of large deletion inductions in the Arabidopsis genome.
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Affiliation(s)
- Kotaro Ishii
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
- Department of Radiation Measurement and Dose Assessment, Institute for Radiological Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yusuke Kazama
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Japan
| | - Tomonari Hirano
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Jeffrey A. Fawcett
- RIKEN Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), Wako, Japan
| | - Muneo Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Science, Nagoya University, Nagoya, Japan
| | | | - Yuki Shirakawa
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
| | - Sumie Ohbu
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
| | - Tomoko Abe
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
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2
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Ezaki K, Koga H, Takeda-Kamiya N, Toyooka K, Higaki T, Sakamoto S, Tsukaya H. Precocious cell differentiation occurs in proliferating cells in leaf primordia in Arabidopsis angustifolia3 mutant. FRONTIERS IN PLANT SCIENCE 2024; 15:1322223. [PMID: 38689848 PMCID: PMC11058843 DOI: 10.3389/fpls.2024.1322223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/02/2024] [Indexed: 05/02/2024]
Abstract
During leaf development, the timing of transition from cell proliferation to expansion is an important factor in determining the final organ size. However, the regulatory system involved in this transition remains less understood. To get an insight into this system, we investigated the compensation phenomenon, in which the cell number decreases while the cell size increases in organs with determinate growth. Compensation is observed in several plant species suggesting coordination between cell proliferation and expansion. In this study, we examined an Arabidopsis mutant of ANGUSTIFOLIA 3 (AN3)/GRF-INTERACTING FACTOR 1, a positive regulator of cell proliferation, which exhibits the compensation. Though the AN3 role has been extensively investigated, the mechanism underlying excess cell expansion in the an3 mutant remains unknown. Focusing on the early stage of leaf development, we performed kinematic, cytological, biochemical, and transcriptome analyses, and found that the cell size had already increased during the proliferation phase, with active cell proliferation in the an3 mutant. Moreover, at this stage, chloroplasts, vacuoles, and xylem cells developed earlier than in the wild-type cells. Transcriptome data showed that photosynthetic activity and secondary cell wall biosynthesis were activated in an3 proliferating cells. These results indicated that precocious cell differentiation occurs in an3 cells. Therefore, we suggest a novel AN3 role in the suppression of cell expansion/differentiation during the cell proliferation phase.
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Affiliation(s)
- Kazune Ezaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroyuki Koga
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Noriko Takeda-Kamiya
- Technology Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Kiminori Toyooka
- Technology Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Takumi Higaki
- Faculty of Advanced Science and Technology, Kumamoto University, Chuo-ku, Kumamoto, Japan
- International Research Organization for Advanced Science and Technology, Kumamoto University, Chuo-ku, Kumamoto, Japan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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3
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Kawade K, Tabeta H, Ferjani A, Hirai MY. The Roles of Functional Amino Acids in Plant Growth and Development. PLANT & CELL PHYSIOLOGY 2023; 64:1482-1493. [PMID: 37489637 DOI: 10.1093/pcp/pcad071] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/04/2023] [Accepted: 07/03/2023] [Indexed: 07/26/2023]
Abstract
Plants incorporate acquired carbon and nitrogen into amino acid metabolism, whereby the building blocks of proteins and the precursors of various metabolites are produced. This fundamental demand requires tight amino acid metabolism to sustain physiological homeostasis. There is increasing evidence that amino acid metabolism undergoes plastic alteration to orchestrate specific growth and developmental events. Consequently, there has been a gradual exploration of the interface at which amino acid metabolism and plant morphogenesis are mutually affected. This research progress offers an opportunity to explore amino acid metabolism, with the goal to understand how it can be modulated to serve special cellular needs and regulate specific growth and developmental pathways. Continuous improvements in the sensitivity and coverage of metabolomics technology, along with the development of chemoinformatics, have allowed the investigation of these research questions. In this review, we summarize the roles of threonine, serine, arginine and γ-aminobutyric acid as representative examples of amino acids relevant to specific developmental processes in plants ('functional amino acids'). Our objective is to expand perspectives regarding amino acid metabolism beyond the conventional view that it is merely life-supporting machinery.
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Affiliation(s)
- Kensuke Kawade
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570 Japan
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan
| | | | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, 4-1-1 Nukuikita-machi, Koganei, Tokyo, 184-8501 Japan
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902 Japan
| | - Masami Yokota Hirai
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
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4
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Tojo H, Tabeta H, Gunji S, Hirai MY, David P, Javot H, Ferjani A. Roles of type II H +-PPases and PPsPase1/PECP2 in early developmental stages and PPi homeostasis of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1031426. [PMID: 36778688 PMCID: PMC9911876 DOI: 10.3389/fpls.2023.1031426] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
The regulation of intracellular pyrophosphate (PPi) level is crucial for proper morphogenesis across all taxonomic kingdoms. PPi is released as a byproduct from ~200 metabolic reactions, then hydrolyzed by either membrane-bound (H+-PPase) or soluble pyrophosphatases (PPases). In Arabidopsis, the loss of the vacuolar H+-PPase/FUGU5, a key enzyme in PPi homeostasis, results in delayed growth and a number of developmental defects, pointing to the importance of PPi homeostasis in plant morphogenesis. The Arabidopsis genome encodes several PPases in addition to FUGU5, such as PPsPase1/PECP2, VHP2;1 and VHP2;2, although their significance regarding PPi homeostasis remains elusive. Here, to assess their contribution, phenotypic analyses of cotyledon aspect ratio, palisade tissue cellular phenotypes, adaxial side pavement cell complexity, stomatal distribution, and etiolated seedling length were performed, provided that they were altered due to excess PPi in a fugu5 mutant background. Overall, our analyses revealed that the above five traits were unaffected in ppspase1/pecp2, vhp2;1 and vhp2;2 loss-of-function mutants, as well as in fugu5 mutant lines constitutively overexpressing PPsPase1/PECP2. Furthermore, metabolomics revealed that ppspase1/pecp2, vhp2;1 and vhp2;2 etiolated seedlings exhibited metabolic profiles comparable to the wild type. Together, these results indicate that the contribution of PPsPase1/PECP2, VHP2;1 and VHP2;2 to PPi levels is negligible in comparison to FUGU5 in the early stages of seedling development.
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Affiliation(s)
- Hiroshi Tojo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Hiromitsu Tabeta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Shizuka Gunji
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Masami Y. Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Pascale David
- Aix Marseille Univ, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
| | - Hélène Javot
- Aix Marseille Univ, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
- Aix Marseille Univ, CEA, CNRS, BIAM, Marseille, France
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
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Tabeta H, Gunji S, Kawade K, Ferjani A. Leaf-size control beyond transcription factors: Compensatory mechanisms. FRONTIERS IN PLANT SCIENCE 2023; 13:1024945. [PMID: 36756231 PMCID: PMC9901582 DOI: 10.3389/fpls.2022.1024945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Plant leaves display abundant morphological richness yet grow to characteristic sizes and shapes. Beginning with a small number of undifferentiated founder cells, leaves evolve via a complex interplay of regulatory factors that ultimately influence cell proliferation and subsequent post-mitotic cell enlargement. During their development, a sequence of key events that shape leaves is both robustly executed spatiotemporally following a genomic molecular network and flexibly tuned by a variety of environmental stimuli. Decades of work on Arabidopsis thaliana have revisited the compensatory phenomena that might reflect a general and primary size-regulatory mechanism in leaves. This review focuses on key molecular and cellular events behind the organ-wide scale regulation of compensatory mechanisms. Lastly, emerging novel mechanisms of metabolic and hormonal regulation are discussed, based on recent advances in the field that have provided insights into, among other phenomena, leaf-size regulation.
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Affiliation(s)
- Hiromitsu Tabeta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Shizuka Gunji
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
| | - Kensuke Kawade
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
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6
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Gunji S, Kawade K, Tabeta H, Horiguchi G, Oikawa A, Asaoka M, Hirai MY, Tsukaya H, Ferjani A. Tissue-targeted inorganic pyrophosphate hydrolysis in a fugu5 mutant reveals that excess inorganic pyrophosphate triggers developmental defects in a cell-autonomous manner. FRONTIERS IN PLANT SCIENCE 2022; 13:945225. [PMID: 35991393 PMCID: PMC9386291 DOI: 10.3389/fpls.2022.945225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Excess PPi triggers developmental defects in a cell-autonomous manner. The level of inorganic pyrophosphate (PPi) must be tightly regulated in all kingdoms for the proper execution of cellular functions. In plants, the vacuolar proton pyrophosphatase (H+-PPase) has a pivotal role in PPi homeostasis. We previously demonstrated that the excess cytosolic PPi in the H+-PPase loss-of-function fugu5 mutant inhibits gluconeogenesis from seed storage lipids, arrests cell division in cotyledonary palisade tissue, and triggers a compensated cell enlargement (CCE). Moreover, PPi alters pavement cell (PC) shape, stomatal patterning, and functioning, supporting specific yet broad inhibitory effects of PPi on leaf morphogenesis. Whereas these developmental defects were totally rescued by the expression of the yeast soluble pyrophosphatase IPP1, sucrose supply alone canceled CCE in the palisade tissue but not the epidermal developmental defects. Hence, we postulated that the latter are likely triggered by excess PPi rather than a sucrose deficit. To formally test this hypothesis, we adopted a spatiotemporal approach by constructing and analyzing fugu5-1 PDF1 pro ::IPP1, fugu5-1 CLV1 pro ::IPP1, and fugu5-1 ICL pro ::IPP1, whereby PPi was removed specifically from the epidermis, palisade tissue cells, or during the 4 days following seed imbibition, respectively. It is important to note that whereas PC defects in fugu5-1 PDF1 pro ::IPP1 were completely recovered, those in fugu5-1 CLV1 pro ::IPP1 were not. In addition, phenotypic analyses of fugu5-1 ICL pro ::IPP1 lines demonstrated that the immediate removal of PPi after seed imbibition markedly improved overall plant growth, abolished CCE, but only partially restored the epidermal developmental defects. Next, the impact of spatial and temporal removal of PPi was investigated by capillary electrophoresis time-of-flight mass spectrometry (CE-TOF MS). Our analysis revealed that the metabolic profiles are differentially affected among all the above transgenic lines, and consistent with an axial role of central metabolism of gluconeogenesis in CCE. Taken together, this study provides a conceptual framework to unveil metabolic fluctuations within leaf tissues with high spatio-temporal resolution. Finally, our findings suggest that excess PPi exerts its inhibitory effect in planta in the early stages of seedling establishment in a tissue- and cell-autonomous manner.
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Affiliation(s)
- Shizuka Gunji
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
- United Graduate School of Education, Tokyo Gakugei University, Tokyo, Japan
| | - Kensuke Kawade
- National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Sciences, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hiromitsu Tabeta
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
- Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
| | - Mariko Asaoka
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Department of Applied Biosciences, Graduate School of Bioagricultural Science, Nagoya University, Nagoya, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
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7
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Nakayama H, Koga H, Long Y, Hamant O, Ferjani A. Looking beyond the gene network - metabolic and mechanical cell drivers of leaf morphogenesis. J Cell Sci 2022; 135:275072. [PMID: 35438169 DOI: 10.1242/jcs.259611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The above-ground organs in plants display a rich diversity, yet they grow to characteristic sizes and shapes. Organ morphogenesis progresses through a sequence of key events, which are robustly executed spatiotemporally as an emerging property of intrinsic molecular networks while adapting to various environmental cues. This Review focuses on the multiscale control of leaf morphogenesis. Beyond the list of known genetic determinants underlying leaf growth and shape, we focus instead on the emerging novel mechanisms of metabolic and biomechanical regulations that coordinate plant cell growth non-cell-autonomously. This reveals how metabolism and mechanics are not solely passive outcomes of genetic regulation but play instructive roles in leaf morphogenesis. Such an integrative view also extends to fluctuating environmental cues and evolutionary adaptation. This synthesis calls for a more balanced view on morphogenesis, where shapes are considered from the standpoints of geometry, genetics, energy and mechanics, and as emerging properties of the cellular expression of these different properties.
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Affiliation(s)
- Hokuto Nakayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 113-0033 Tokyo, Japan
| | - Hiroyuki Koga
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 113-0033 Tokyo, Japan
| | - Yuchen Long
- Department of Biological Sciences, The National University of Singapore, Singapore 117543, Singapore
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69007 Lyon, France
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, 184-8501 Tokyo, Japan
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8
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Tabeta H, Higashi Y, Okazaki Y, Toyooka K, Wakazaki M, Sato M, Saito K, Hirai MY, Ferjani A. Skotomorphogenesis exploits threonine to promote hypocotyl elongation. QUANTITATIVE PLANT BIOLOGY 2022; 3:e26. [PMID: 37077988 PMCID: PMC10095960 DOI: 10.1017/qpb.2022.19] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 05/02/2023]
Abstract
Mobilisation of seed storage reserves is important for seedling establishment in Arabidopsis. In this process, sucrose is synthesised from triacylglycerol via core metabolic processes. Mutants with defects in triacylglycerol-to-sucrose conversion display short etiolated seedlings. We found that whereas sucrose content in the indole-3-butyric acid response 10 (ibr10) mutant was significantly reduced, hypocotyl elongation in the dark was unaffected, questioning the role of IBR10 in this process. To dissect the metabolic complexity behind cell elongation, a quantitative-based phenotypic analysis combined with a multi-platform metabolomics approach was applied. We revealed that triacylglycerol and diacylglycerol breakdown were disrupted in ibr10, resulting in low sugar content and poor photosynthetic ability. Importantly, batch-learning self-organised map clustering revealed that threonine level was correlated with hypocotyl length. Consistently, exogenous threonine supply stimulated hypocotyl elongation, indicating that sucrose levels are not always correlated with etiolated seedling length, suggesting the contribution of amino acids in this process.
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Affiliation(s)
- Hiromitsu Tabeta
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | | | - Mayumi Wakazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Masami Y Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
- Author for correspondence: A. Ferjani, E-mail:
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9
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Double Mutant Analysis with the Large Flower Mutant, ohbana1, to Explore the Regulatory Network Controlling the Flower and Seed Sizes in Arabidopsis thaliana. PLANTS 2021; 10:plants10091881. [PMID: 34579413 PMCID: PMC8473154 DOI: 10.3390/plants10091881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 12/19/2022]
Abstract
Two growth processes, cell proliferation and expansion, determine plant species-specific organ sizes. A large flower mutant in Arabidopsis thaliana, ohbana1 (ohb1), was isolated from a mutant library. In the ohb1 flowers, post-mitotic cell expansion and endoreduplication of nuclear DNA were promoted. The whole-genome resequencing and genetic analysis results showed that the loss of function in MEDIATOR16 (MED16), a mediator complex subunit, was responsible for the large flower phenotypes exhibited by ohb1. A phenotypic analysis of the mutant alleles in MED16 and the double mutants created by crossing ohb1 with representative large flower mutants revealed that MED16 and MED25 share part of the negative petal size regulatory pathways. Furthermore, the double mutant analyses suggested that there were genetically independent pathways leading to cell size restrictions in the floral organs which were not related to the MED complex. Several double mutants also formed larger and heavier seeds than the wild type and single mutant plants, which indicated that MED16 was involved in seed size regulation. This study has revealed part of the size-regulatory network in flowers and seeds through analysis of the ohb1 mutant, and that the size-regulation pathways are partially different between floral organs and seeds.
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10
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Tabeta H, Watanabe S, Fukuda K, Gunji S, Asaoka M, Hirai MY, Seo M, Tsukaya H, Ferjani A. An auxin signaling network translates low-sugar-state input into compensated cell enlargement in the fugu5 cotyledon. PLoS Genet 2021; 17:e1009674. [PMID: 34351899 PMCID: PMC8341479 DOI: 10.1371/journal.pgen.1009674] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/18/2021] [Indexed: 01/29/2023] Open
Abstract
In plants, the effective mobilization of seed nutrient reserves is crucial during germination and for seedling establishment. The Arabidopsis H+-PPase-loss-of-function fugu5 mutants exhibit a reduced number of cells in the cotyledons. This leads to enhanced post-mitotic cell expansion, also known as compensated cell enlargement (CCE). While decreased cell numbers have been ascribed to reduced gluconeogenesis from triacylglycerol, the molecular mechanisms underlying CCE remain ill-known. Given the role of indole 3-butyric acid (IBA) in cotyledon development, and because CCE in fugu5 is specifically and completely cancelled by ech2, which shows defective IBA-to-indoleacetic acid (IAA) conversion, IBA has emerged as a potential regulator of CCE. Here, to further illuminate the regulatory role of IBA in CCE, we used a series of high-order mutants that harbored a specific defect in IBA-to-IAA conversion, IBA efflux, IAA signaling, or vacuolar type H+-ATPase (V-ATPase) activity and analyzed the genetic interaction with fugu5-1. We found that while CCE in fugu5 was promoted by IBA, defects in IBA-to-IAA conversion, IAA response, or the V-ATPase activity alone cancelled CCE. Consistently, endogenous IAA in fugu5 reached a level 2.2-fold higher than the WT in 1-week-old seedlings. Finally, the above findings were validated in icl-2, mls-2, pck1-2 and ibr10 mutants, in which CCE was triggered by low sugar contents. This provides a scenario in which following seed germination, the low-sugar-state triggers IAA synthesis, leading to CCE through the activation of the V-ATPase. These findings illustrate how fine-tuning cell and organ size regulation depend on interplays between metabolism and IAA levels in plants.
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Affiliation(s)
- Hiromitsu Tabeta
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan
| | | | - Keita Fukuda
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Tokyo, Japan
| | - Shizuka Gunji
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Tokyo, Japan
| | - Mariko Asaoka
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Tokyo, Japan
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, Lyon, France
| | | | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Tokyo, Japan
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11
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Sergeeva A, Mettler‐Altmann T, Liu H, Mai H, Bauer P. Glycerolipid profile differences between perennial and annual stem zones in the perennial model plant Arabis alpina. PLANT DIRECT 2021; 5:e00302. [PMID: 33506166 PMCID: PMC7814627 DOI: 10.1002/pld3.302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 06/12/2023]
Abstract
The perennial life style is a successful ecological strategy, and Arabis alpina is a recently developed model Brassicaceae species for studying it. One aspect, poorly investigated until today, concerns the differing patterns of allocation, storage, and metabolism of nutrients between perennials and annuals and the yet unknown signals that regulate this process. A. alpina has a complex lateral stem architecture with a proximal vegetative perennial (PZ) and a distal annual flowering zone (AZ) inside the same stems. Lipid bodies (LBs) with triacylglycerols (TAGs) accumulate in the PZ. To identify potential processes of lipid metabolism linked with the perennial lifestyle, we analyzed lipid species in the PZ versus AZ. Glycerolipid fractions, including neutral lipids with mainly TAGs, phospholipids, and glycolipids, were present at higher levels in the PZ as compared to AZ or roots. Concomitantly, contents of specific long-chain and very long-chain fatty acids increased during formation of the PZ. Corresponding gene expression data, gene ontology term enrichment, and correlation analysis with lipid species pinpoint glycerolipid-related genes to be active during the development of the PZ. Possibilities that lipid metabolism genes may be targets of regulatory mechanisms specifying PZ differentiation in A. alpina are discussed.
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Affiliation(s)
- Anna Sergeeva
- Institute of BotanyHeinrich Heine UniversityDüsseldorfGermany
- Cluster of Excellence on Plant Science (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
| | - Tabea Mettler‐Altmann
- Cluster of Excellence on Plant Science (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
- Institute of Plant BiochemistryHeinrich Heine UniversityDüsseldorfGermany
| | - Hongjiu Liu
- Institute of BotanyHeinrich Heine UniversityDüsseldorfGermany
| | - Hans‐Jörg Mai
- Institute of BotanyHeinrich Heine UniversityDüsseldorfGermany
| | - Petra Bauer
- Institute of BotanyHeinrich Heine UniversityDüsseldorfGermany
- Cluster of Excellence on Plant Science (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
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Fujikura U, Ezaki K, Horiguchi G, Seo M, Kanno Y, Kamiya Y, Lenhard M, Tsukaya H. Suppression of class I compensated cell enlargement by xs2 mutation is mediated by salicylic acid signaling. PLoS Genet 2020; 16:e1008873. [PMID: 32584819 PMCID: PMC7343186 DOI: 10.1371/journal.pgen.1008873] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/08/2020] [Accepted: 05/20/2020] [Indexed: 11/18/2022] Open
Abstract
The regulation of leaf size has been studied for decades. Enhancement of post-mitotic cell expansion triggered by impaired cell proliferation in Arabidopsis is an important process for leaf size regulation, and is known as compensation. This suggests a key interaction between cell proliferation and cell expansion during leaf development. Several studies have highlighted the impact of this integration mechanism on leaf size determination; however, the molecular basis of compensation remains largely unknown. Previously, we identified extra-small sisters (xs) mutants which can suppress compensated cell enlargement (CCE) via a specific defect in cell expansion within the compensation-exhibiting mutant, angustifolia3 (an3). Here we revealed that one of the xs mutants, namely xs2, can suppress CCE not only in an3 but also in other compensation-exhibiting mutants erecta (er) and fugu2. Molecular cloning of XS2 identified a deleterious mutation in CATION CALCIUM EXCHANGER 4 (CCX4). Phytohormone measurement and expression analysis revealed that xs2 shows hyper activation of the salicylic acid (SA) response pathway, where activation of SA response can suppress CCE in compensation mutants. All together, these results highlight the regulatory connection which coordinates compensation and SA response. Leaves are determinate organ and size of leaves are determined by intrinsic and extrinsic cues. Cell proliferation and post-mitotic cell expansion should be coordinated during leaf morphogenesis to develop appropriate size depending on its developmental programs. Recent studies highlighted the existence of integrated mechanism which coordinates cell proliferation and cell expansion during leaf development. Compensation, which is enhanced post-mitotic cell expansion accompanied by a significant decrease in cell number during leaf organogenesis, is one of the clues for such coordination. However, the molecular mechanisms linking cell proliferation and cell expansion are still poorly understood. Previously, we reported extra-small sisters 2 (xs2) mutation caused specific defect in cell expansion and it suppressed increased post-mitotic cell enlargement in angustifolia3 (an3) mutant, which exhibits typical compensation. Here we identify the affected gene of xs2 mutant encodes a member of cation calcium exchanger which is believed to be involved in cation homeostasis within cells. Loss of function of this protein causes hyper accumulation of salicylic acid (SA) and increased expression of pathogen related genes. Physiological and genetic studies revealed activated SA signal transduction reduced cell size. It suppressed post-mitotic cell expansion in several compensation mutants not only an3 but partially suppressed in another type of compensation mutant which increases size of mitotic cells. This finding suggests post-mitotic cell expansion pathway is regulated in common by SA-dependent signaling and by compensation signaling during leaf development.
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Affiliation(s)
- Ushio Fujikura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
- * E-mail:
| | - Kazune Ezaki
- Graduate School of Science, The University of Tokyo, Japan
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Japan
| | - Yuri Kanno
- RIKEN Center for Sustainable Resource Science, Japan
| | - Yuji Kamiya
- RIKEN Center for Sustainable Resource Science, Japan
| | - Michael Lenhard
- Institut für Biochemie und Biologie, Universität Potsdam, Potsdam-Golm, Germany
| | - Hirokazu Tsukaya
- Graduate School of Science, The University of Tokyo, Japan
- Okazaki Institute for Integrative Bioscience, Japan
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Vercruysse J, Baekelandt A, Gonzalez N, Inzé D. Molecular networks regulating cell division during Arabidopsis leaf growth. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2365-2378. [PMID: 31748815 PMCID: PMC7178401 DOI: 10.1093/jxb/erz522] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/21/2019] [Indexed: 05/02/2023]
Abstract
Leaves are the primary organs for photosynthesis, and as such have a pivotal role for plant growth and development. Leaf development is a multifactorial and dynamic process involving many genes that regulate size, shape, and differentiation. The processes that mainly drive leaf development are cell proliferation and cell expansion, and numerous genes have been identified that, when ectopically expressed or down-regulated, increase cell number and/or cell size during leaf growth. Many of the genes regulating cell proliferation are functionally interconnected and can be grouped into regulatory modules. Here, we review our current understanding of six important gene regulatory modules affecting cell proliferation during Arabidopsis leaf growth: ubiquitin receptor DA1-ENHANCER OF DA1 (EOD1), GROWTH REGULATING FACTOR (GRF)-GRF-INTERACTING FACTOR (GIF), SWITCH/SUCROSE NON-FERMENTING (SWI/SNF), gibberellin (GA)-DELLA, KLU, and PEAPOD (PPD). Furthermore, we discuss how post-mitotic cell expansion and these six modules regulating cell proliferation make up the final leaf size.
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Affiliation(s)
- Jasmien Vercruysse
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Alexandra Baekelandt
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Nathalie Gonzalez
- INRAE, Université de Bordeaux, UMR1332 Biologie du fruit et Pathologie, INRA Bordeaux Aquitaine, Villenave d’Ornon cedex, France
| | - Dirk Inzé
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Correspondence:
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Ma J, Zhao P, Liu S, Yang Q, Guo H. The Control of Developmental Phase Transitions by microRNAs and Their Targets in Seed Plants. Int J Mol Sci 2020; 21:E1971. [PMID: 32183075 PMCID: PMC7139601 DOI: 10.3390/ijms21061971] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 02/29/2020] [Accepted: 03/12/2020] [Indexed: 12/18/2022] Open
Abstract
Seed plants usually undergo various developmental phase transitions throughout their lifespan, mainly including juvenile-to-adult and vegetative-to-reproductive transitions, as well as developmental transitions within organ/tissue formation. MicroRNAs (miRNAs), as a class of small endogenous non-coding RNAs, are involved in the developmental phase transitions in plants by negatively regulating the expression of their target genes at the post-transcriptional level. In recent years, cumulative evidence has revealed that five miRNAs, miR156, miR159, miR166, miR172, and miR396, are key regulators of developmental phase transitions in plants. In this review, the advanced progress of the five miRNAs and their targets in regulating plant developmental transitions, especially in storage organ formation, are summarized and discussed, combining our own findings with the literature. In general, the functions of the five miRNAs and their targets are relatively conserved, but their functional divergences also emerge to some extent. In addition, potential research directions of miRNAs in regulating plant developmental phase transitions are prospected.
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Affiliation(s)
- Jingyi Ma
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
| | - Pan Zhao
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
| | - Shibiao Liu
- College of Biology and Environmental Sciences, Jishou University, Jishou 416000, China;
| | - Qi Yang
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
| | - Huihong Guo
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
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15
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Gunji S, Oda Y, Takigawa-Imamura H, Tsukaya H, Ferjani A. Excess Pyrophosphate Restrains Pavement Cell Morphogenesis and Alters Organ Flatness in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:31. [PMID: 32153602 PMCID: PMC7047283 DOI: 10.3389/fpls.2020.00031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/13/2020] [Indexed: 05/31/2023]
Abstract
In Arabidopsis thaliana, the vacuolar proton-pumping pyrophosphatase (H+-PPase) is highly expressed in young tissues, which consume large amounts of energy in the form of nucleoside triphosphates and produce pyrophosphate (PPi) as a byproduct. We reported that excess PPi in the H+-PPase loss-of-function fugu5 mutant severely compromised gluconeogenesis from seed storage lipids, arrested cell division in cotyledonary palisade tissue, and triggered compensated cell enlargement; this phenotype was recovered upon sucrose supply. Thus, we provided evidence that the hydrolysis of inhibitory PPi, rather than vacuolar acidification, is the major contribution of H+-PPase during seedling establishment. Here, examination of the epidermis revealed that fugu5 pavement cells exhibited defective puzzle-cell formation. Importantly, removal of PPi from fugu5 background by the yeast cytosolic PPase IPP1, in fugu5-1 AVP1pro::IPP1 transgenic lines, restored the phenotypic aberrations of fugu5 pavement cells. Surprisingly, pavement cells in mutants with defects in gluconeogenesis (pck1-2) or the glyoxylate cycle (icl-2; mls-2) showed no phenotypic alteration, indicating that reduced sucrose production from seed storage lipids is not the cause of fugu5 epidermal phenotype. fugu5 had oblong cotyledons similar to those of angustifolia-1 (an-1), whose leaf pavement cells display an abnormal arrangement of cortical microtubules (MTs). To gain insight into the genetic interaction between ANGUSTIFOLIA and H+-PPase in pavement cell differentiation, an-1 fugu5-1 was analyzed. Surprisingly, epidermis developmental defects were synergistically enhanced in the double mutant. In fact, an-1 fugu5-1 pavement cells showed a striking three-dimensional growth phenotype on both abaxial and adaxial sides of cotyledons, which was recovered by hydrolysis of PPi in an-1 fugu5-1 AVP1pro::IPP1. Live imaging revealed that cortical MTs exhibited a reduced velocity, were slightly fragmented and sparse in the above lines compared to the WT. Consistently, addition of PPi in vitro led to a dose-dependent delay of tubulin polymerization, thus supporting a link between PPi and MT dynamics. Moreover, mathematical simulation of three-dimensional growth based on cotyledon proximo-distal and medio-lateral phenotypic quantification implicated restricted cotyledon expansion along the medio-lateral axis in the crinkled surface of an-1 fugu5-1. Together, our data suggest that PPi homeostasis is a prerequisite for proper pavement cell morphogenesis, epidermal growth and development, and organ flattening.
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Affiliation(s)
- Shizuka Gunji
- United Graduate School of Education, Tokyo Gakugei University, Tokyo, Japan
| | - Yoshihisa Oda
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
| | - Hisako Takigawa-Imamura
- Department of Anatomy and Cell Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ali Ferjani
- United Graduate School of Education, Tokyo Gakugei University, Tokyo, Japan
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
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Yang Q, Liu S, Han X, Ma J, Deng W, Wang X, Guo H, Xia X. Integrated transcriptome and miRNA analysis uncovers molecular regulators of aerial stem-to-rhizome transition in the medical herb Gynostemma pentaphyllum. BMC Genomics 2019; 20:865. [PMID: 31730459 PMCID: PMC6858658 DOI: 10.1186/s12864-019-6250-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/30/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gynostemma pentaphyllum is an important perennial medicinal herb belonging to the family Cucurbitaceae. Aerial stem-to-rhizome transition before entering the winter is an adaptive regenerative strategy in G. pentaphyllum that enables it to survive during winter. However, the molecular regulation of aerial stem-to-rhizome transition is unknown in plants. Here, integrated transcriptome and miRNA analysis was conducted to investigate the regulatory network of stem-to-rhizome transition. RESULTS Nine transcriptome libraries prepared from stem/rhizome samples collected at three stages of developmental stem-to-rhizome transition were sequenced and a total of 5428 differentially expressed genes (DEGs) were identified. DEGs associated with gravitropism, cell wall biosynthesis, photoperiod, hormone signaling, and carbohydrate metabolism were found to regulate stem-to-rhizome transition. Nine small RNA libraries were parallelly sequenced, and seven significantly differentially expressed miRNAs (DEMs) were identified, including four known and three novel miRNAs. The seven DEMs targeted 123 mRNAs, and six pairs of miRNA-target showed significantly opposite expression trends. The GpmiR166b-GpECH2 module involved in stem-to-rhizome transition probably promotes cell expansion by IBA-to-IAA conversion, and the GpmiR166e-GpSGT-like module probably protects IAA from degradation, thereby promoting rhizome formation. GpmiR156a was found to be involved in stem-to-rhizome transition by inhibiting the expression of GpSPL13A/GpSPL6, which are believed to negatively regulate vegetative phase transition. GpmiR156a and a novel miRNA Co.47071 co-repressed the expression of growth inhibitor GpRAV-like during stem-to-rhizome transition. These miRNAs and their targets were first reported to be involved in the formation of rhizomes. In this study, the expression patterns of DEGs, DEMs and their targets were further validated by quantitative real-time PCR, supporting the reliability of sequencing data. CONCLUSIONS Our study revealed a comprehensive molecular network regulating the transition of aerial stem to rhizome in G. pentaphyllum. These results broaden our understanding of developmental phase transitions in plants.
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Affiliation(s)
- Qi Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing, 100083, China
| | - Shibiao Liu
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China
| | - Xiaoning Han
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing, 100083, China
| | - Jingyi Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing, 100083, China
| | - Wenhong Deng
- Analytical and Testing Center, Beijing Forestry University, Beijing, 100083, China
| | - Xiaodong Wang
- Centre for Imaging & Systems Biology, College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Huihong Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing, 100083, China.
| | - Xinli Xia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing, 100083, China
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Li Y, Liu Y, Zolman BK. Metabolic Alterations in the Enoyl-CoA Hydratase 2 Mutant Disrupt Peroxisomal Pathways in Seedlings. PLANT PHYSIOLOGY 2019; 180:1860-1876. [PMID: 31138624 PMCID: PMC6670076 DOI: 10.1104/pp.19.00300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/25/2019] [Indexed: 05/03/2023]
Abstract
Mobilization of seed storage compounds, such as starch and oil, is required to provide energy and metabolic building blocks during seedling development. Over 50% of fatty acids in Arabidopsis (Arabidopsis thaliana) seed oil have a cis-double bond on an even-numbered carbon. Degradation of these substrates requires peroxisomal fatty acid β-oxidation plus additional enzyme activities. Such auxiliary enzymes, including the enoyl-CoA hydratase ECH2, convert (R)-3-hydroxyacyl-CoA intermediates to the core β-oxidation substrate (S)-3-hydroxyacyl-CoA. ECH2 was suggested to function in the peroxisomal conversion of indole-3-butyric acid (IBA) to indole-3-acetic acid, because ech2 seedlings have altered IBA responses. The underlying mechanism connecting ECH2 activity and IBA metabolism is unclear. Here, we show that ech2 seedlings have reduced root length, smaller cotyledons, and arrested pavement cell expansion. At the cellular level, reduced oil body mobilization and enlarged peroxisomes suggest compromised β-oxidation. ech2 seedlings accumulate 3-hydroxyoctenoate (C8:1-OH) and 3-hydroxyoctanoate (C8:0-OH), putative hydrolysis products of catabolic intermediates for α-linolenic acid and linoleic acid, respectively. Wild-type seedlings treated with 3-hydroxyoctanoate have ech2-like growth defects and altered IBA responses. ech2 phenotypes are not rescued by Suc or auxin application. However, ech2 phenotypes are suppressed in combination with the core β-oxidation mutants mfp2 or ped1, and ech2 mfp2 seedlings accumulate less C8:1-OH and C8:0-OH than ech2 seedlings. These results indicate that ech2 phenotypes require efficient core β-oxidation. Our findings suggest that low ECH2 activity causes metabolic alterations through a toxic effect of the accumulating intermediates. These effects manifest in altered lipid metabolism and IBA responses leading to disrupted seedling development.
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Affiliation(s)
- Ying Li
- University of Missouri-St. Louis, St. Louis, Missouri 63121
| | - Yu Liu
- University of Missouri-St. Louis, St. Louis, Missouri 63121
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18
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Asaoka M, Inoue SI, Gunji S, Kinoshita T, Maeshima M, Tsukaya H, Ferjani A. Excess Pyrophosphate within Guard Cells Delays Stomatal Closure. PLANT & CELL PHYSIOLOGY 2019; 60:875-887. [PMID: 30649470 DOI: 10.1093/pcp/pcz002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/28/2018] [Indexed: 05/08/2023]
Abstract
A variety of cellular metabolic reactions generate inorganic pyrophosphate (PPi) as an ATP hydrolysis byproduct. The vacuolar H+-translocating pyrophosphatase (H+-PPase) loss-of-function fugu5 mutant is susceptible to drought and displays pleotropic postgerminative growth defects due to excess PPi. It was recently reported that stomatal closure after abscisic acid (ABA) treatment is delayed in vhp1-1, a fugu5 allele. In contrast, we found that specific removal of PPi rescued all of the above fugu5 developmental and growth defects. Hence, we speculated that excess PPi itself, rather than vacuolar acidification, might delay stomatal closure. To test this hypothesis, we constructed transgenic plants expressing the yeast IPP1 gene (encoding a cytosolic pyrophosphatase) driven by a guard cell-specific promoter (pGC1::IPP1) in the fugu5 background. Our measurements confirmed stomatal closure defects in fugu5, further supporting a role for H+-PPase in stomatal functioning. Importantly, while pGC1::IPP1 transgenics morphologically mimicked fugu5, stomatal closure was restored in response to ABA and darkness. Quantification of water loss revealed that fugu5 stomata were almost completely insensitive to ABA. In addition, growth of pGC1::IPP1 plants was promoted compared to fugu5 throughout their life; however, it did not reach the wild type level. fugu5 also displayed an increased stomatal index, in violation of the one-cell-spacing rule, and phenotypes recovered upon removal of PPi by pAVP1::IPP1 (FUGU5, VHP1 and AVP1 are the same gene encoding H+-PPase), but not in the pGC1::IPP1 line. Taken together, these results clearly support our hypothesis that dysfunction in stomata is triggered by excess PPi within guard cells, probably via perturbed guard cell metabolism.
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Affiliation(s)
- Mariko Asaoka
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Tokyo, Japan
| | - Shin-Ichiro Inoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Shizuka Gunji
- United Graduated School of Education, Tokyo Gakugei University, Tokyo, Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Masayoshi Maeshima
- Laboratory of Cell Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, Aichi, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Tokyo, Japan
- United Graduated School of Education, Tokyo Gakugei University, Tokyo, Japan
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19
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Yang Y, Benning C. Functions of triacylglycerols during plant development and stress. Curr Opin Biotechnol 2018; 49:191-198. [DOI: 10.1016/j.copbio.2017.09.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/16/2017] [Accepted: 09/15/2017] [Indexed: 10/18/2022]
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20
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Frick EM, Strader LC. Roles for IBA-derived auxin in plant development. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:169-177. [PMID: 28992091 PMCID: PMC5853464 DOI: 10.1093/jxb/erx298] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/01/2017] [Indexed: 05/18/2023]
Abstract
The plant hormone auxin is a central regulator of plant growth and development. Because auxin plays critical roles in cell division and cell expansion, plants use a number of cellular mechanisms to regulate auxin levels and response. Among these mechanisms is regulated input from the auxin precursor indole-3-butyric acid (IBA) toward the pool of active auxin [indole-3-acetic acid (IAA)]. In this review, we cover the mechanisms of IBA transport and conversion, and discuss specific roles for IBA-derived auxin in driving certain developmental events. We further discuss multiple open questions remaining for the IBA field.
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Affiliation(s)
- Elizabeth M Frick
- NSF Science and Technology Center for Engineering Mechanobiology, Department of Biology, Washington University in St. Louis, USA
| | - Lucia C Strader
- NSF Science and Technology Center for Engineering Mechanobiology, Department of Biology, Washington University in St. Louis, USA
- Correspondence:
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21
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Kazama Y, Ishii K, Hirano T, Wakana T, Yamada M, Ohbu S, Abe T. Different mutational function of low- and high-linear energy transfer heavy-ion irradiation demonstrated by whole-genome resequencing of Arabidopsis mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1020-1030. [PMID: 29024116 DOI: 10.1111/tpj.13738] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 05/06/2023]
Abstract
Heavy-ion irradiation is a powerful mutagen that possesses high linear energy transfer (LET). Several studies have indicated that the value of LET affects DNA lesion formation in several ways, including the efficiency and the density of double-stranded break induction along the particle path. We assumed that the mutation type can be altered by selecting an appropriate LET value. Here, we quantitatively demonstrate differences in the mutation type induced by irradiation with two representative ions, Ar ions (LET: 290 keV μm-1 ) and C ions (LET: 30.0 keV μm-1 ), by whole-genome resequencing of the Arabidopsis mutants produced by these irradiations. Ar ions caused chromosomal rearrangements or large deletions (≥100 bp) more frequently than C ions, with 10.2 and 2.3 per mutant genome under Ar- and C-ion irradiation, respectively. Conversely, C ions induced more single-base substitutions and small indels (<100 bp) than Ar ions, with 28.1 and 56.9 per mutant genome under Ar- and C-ion irradiation, respectively. Moreover, the rearrangements induced by Ar-ion irradiation were more complex than those induced by C-ion irradiation, and tended to accompany single base substitutions or small indels located close by. In conjunction with the detection of causative genes through high-throughput sequencing, selective irradiation by beams with different effects will be a powerful tool for forward genetics as well as studies on chromosomal rearrangements.
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Affiliation(s)
- Yusuke Kazama
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Kotaro Ishii
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Tomonari Hirano
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki, Miyazaki, 889-2192, Japan
| | - Taeko Wakana
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Mieko Yamada
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Sumie Ohbu
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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Takahashi K, Morimoto R, Tabeta H, Asaoka M, Ishida M, Maeshima M, Tsukaya H, Ferjani A. Compensated Cell Enlargement in fugu5 is Specifically Triggered by Lowered Sucrose Production from Seed Storage Lipids. PLANT & CELL PHYSIOLOGY 2017; 58:668-678. [PMID: 28201798 DOI: 10.1093/pcp/pcx021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/31/2017] [Indexed: 05/02/2023]
Abstract
To reveal the logic of size regulation in multicellular organisms, we have used Arabidopsis thaliana as a model organism and its leaves as a model organ. We discovered the existence of a compensatory system, whereby a decrease in leaf cell number often triggers unusual cell enlargement. However, despite the large number of compensation-exhibiting mutants analyzed to date, we have only a limited understanding of the detailed molecular mechanisms triggering the decrease in cell number and subsequent compensated cell enlargement (CCE). CCE in fugu5, the vacuolar type H+-pyrophosphatase loss-of-function mutant, is specific to cotyledons and completely suppressed when sucrose (Suc) is supplied or cytosolic pyrophosphate (PPi) is specifically removed. In addition, several lines of evidence suggest that excess cytosolic PPi in fugu5 impairs gluconeogenesis from triacylglycerol (TAG) to Suc. Here, detailed cellular phenotyping revealed that the loss-of-function mutants icl-2, mls-2 and pck1-2 triggered CCE in cotyledons. All double mutant combinations between fugu5-1 and the above three mutants exhibited compensation, but did not display a further increase in cell size. Importantly, similar phenotypes were observed in icl-2 mls-2, icl-2 pck1-2 and mls-2 pck1-2. Quantification of TAG breakdown and Suc contents further supported our findings. Taken together, we demonstrate that de novo Suc synthesis from TAG is fundamentally important for proper resumption of post-germinative cotyledon development. Moreover, provided that icl-2, mls-2 and pck1-2 are only compromised in Suc biosynthesis de novo from TAG, our findings clearly indicate that lowered Suc production in fugu5, rather than excess cytosolic PPi, is the direct trigger of CCE.
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Affiliation(s)
- Kazuki Takahashi
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Japan
| | | | - Hiromitsu Tabeta
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Japan
| | - Mariko Asaoka
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Japan
- Laboratory of Cell Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Masanori Ishida
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Japan
- Hatoyama High School, Saitama, Hiki-gun, Hatoyama-machi, Japan
| | - Masayoshi Maeshima
- Laboratory of Cell Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Japan
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