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Wu S, Gao Y, Zhang Q, Liu F, Hu W. Application of Multi-Omics Technologies to the Study of Phytochromes in Plants. Antioxidants (Basel) 2024; 13:99. [PMID: 38247523 PMCID: PMC10812741 DOI: 10.3390/antiox13010099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Phytochromes (phy) are distributed in various plant organs, and their physiological effects influence plant germination, flowering, fruiting, and senescence, as well as regulate morphogenesis throughout the plant life cycle. Reactive oxygen species (ROS) are a key regulatory factor in plant systemic responses to environmental stimuli, with an attractive regulatory relationship with phytochromes. With the development of high-throughput sequencing technology, omics techniques have become powerful tools, and researchers have used omics techniques to facilitate the big data revolution. For an in-depth analysis of phytochrome-mediated signaling pathways, integrated multi-omics (transcriptomics, proteomics, and metabolomics) approaches may provide the answer from a global perspective. This article comprehensively elaborates on applying multi-omics techniques in studying phytochromes. We describe the current research status and future directions on transcriptome-, proteome-, and metabolome-related network components mediated by phytochromes when cells are subjected to various stimulation. We emphasize the importance of multi-omics technologies in exploring the effects of phytochromes on cells and their molecular mechanisms. Additionally, we provide methods and ideas for future crop improvement.
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Affiliation(s)
- Shumei Wu
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
| | - Yue Gao
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
| | - Qi Zhang
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
| | - Fen Liu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
| | - Weiming Hu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
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Mu XR, Wang YB, Bao QX, Wei YT, Zhao ST, Tao WZ, Liu YX, Wang WN, Yu FH, Tong C, Wang JW, Gu CY, Wang QM, Liu XR, Sai N, Zhu JL, Zhang J, Loake GJ, Meng LS. Glucose status within dark-grown etiolated cotyledons determines seedling de-etiolation upon light irradiation. PLANT PHYSIOLOGY 2023; 194:391-407. [PMID: 37738410 DOI: 10.1093/plphys/kiad508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/24/2023]
Abstract
Exposure of dark-grown etiolated seedlings to light triggers the transition from skotomorphogenesis/etiolation to photomorphogenesis/de-etiolation. In the life cycle of plants, de-etiolation is essential for seedling development and plant survival. The mobilization of soluble sugars (glucose [Glc], sucrose, and fructose) derived from stored carbohydrates and lipids to target organs, including cotyledons, hypocotyls, and radicles, underpins de-etiolation. Therefore, dynamic carbohydrate biochemistry is a key feature of this phase transition. However, the molecular mechanisms coordinating carbohydrate status with the cellular machinery orchestrating de-etiolation remain largely opaque. Here, we show that the Glc sensor HEXOKINASE 1 (HXK1) interacts with GROWTH REGULATOR FACTOR5 (GRF5), a transcriptional activator and key plant growth regulator, in Arabidopsis (Arabidopsis thaliana). Subsequently, GRF5 directly binds to the promoter of phytochrome A (phyA), encoding a far-red light (FR) sensor/cotyledon greening inhibitor. We demonstrate that the status of Glc within dark-grown etiolated cotyledons determines the de-etiolation of seedlings when exposed to light irradiation by the HXK1-GRF5-phyA molecular module. Thus, following seed germination, accumulating Glc within dark-grown etiolated cotyledons stimulates a HXK1-dependent increase of GRF5 and an associated decrease of phyA, triggering the perception, amplification, and relay of HXK1-dependent Glc signaling, thereby facilitating the de-etiolation of seedlings following light irradiation. Our findings, therefore, establish how cotyledon carbohydrate signaling under subterranean darkness is sensed, amplified, and relayed, determining the phase transition from skotomorphogenesis to photomorphogenesis on exposure to light irradiation.
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Affiliation(s)
- Xin-Rong Mu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yi-Bo Wang
- College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui 741600, People's Republic of China
| | - Qin-Xin Bao
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Yu-Ting Wei
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Sheng-Ting Zhao
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Wen-Zhe Tao
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Yu-Xin Liu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Wan-Ni Wang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Fu-Huan Yu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Chen Tong
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Jing-Wen Wang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Cheng-Yue Gu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Qi-Meng Wang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Xin-Ran Liu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Na Sai
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Jin-Lei Zhu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Jian Zhang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Gary J Loake
- Centre for Transformative Biotechnology of Medicinal and Food Plants, Jiangsu Normal University-Edinburgh University, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
- Institute of Molecular Plant Sciences, School of Biological Sciences, Edinburgh University, Edinburgh EH9 3JR, UK
| | - Lai-Sheng Meng
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
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A combination of plasma membrane sterol biosynthesis and autophagy is required for shade-induced hypocotyl elongation. Nat Commun 2022; 13:5659. [PMID: 36216814 PMCID: PMC9550796 DOI: 10.1038/s41467-022-33384-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 09/15/2022] [Indexed: 12/04/2022] Open
Abstract
Plant growth ultimately depends on fixed carbon, thus the available light for photosynthesis. Due to canopy light absorption properties, vegetative shade combines low blue (LB) light and a low red to far-red ratio (LRFR). In shade-avoiding plants, these two conditions independently trigger growth adaptations to enhance light access. However, how these conditions, differing in light quality and quantity, similarly promote hypocotyl growth remains unknown. Using RNA sequencing we show that these two features of shade trigger different transcriptional reprogramming. LB induces starvation responses, suggesting a switch to a catabolic state. Accordingly, LB promotes autophagy. In contrast, LRFR induced anabolism including expression of sterol biosynthesis genes in hypocotyls in a manner dependent on PHYTOCHROME-INTERACTING FACTORs (PIFs). Genetic analyses show that the combination of sterol biosynthesis and autophagy is essential for hypocotyl growth promotion in vegetative shade. We propose that vegetative shade enhances hypocotyl growth by combining autophagy-mediated recycling and promotion of specific lipid biosynthetic processes. Plants subject to vegetative shade receive a low quantity of blue light (LB) and a low ratio of red to far-red light (LFLR). Here the authors show that while LB induces autophagy, LFLR leads to changes in lipid metabolism, and propose that these processes may contribute to shade avoidance responses.
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Nie Y, Yu L, Mao L, Zou W, Zhang X, Zhao J. Vitamin B 1 THIAMIN REQUIRING1 synthase mediates the maintenance of chloroplast function by regulating sugar and fatty acid metabolism in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1575-1595. [PMID: 35603832 DOI: 10.1111/jipb.13283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Vitamin B1 (VB1), including thiamin, thiamin monophosphate (TMP), and thiamin pyrophosphate (TPP), is an essential micronutrient for all living organisms. Nevertheless, the precise function of VB1 in rice remains unclear. Here, we described a VB1 auxotrophic mutant, chlorotic lethal seedling (cles) from the mutation of OsTH1, which displayed collapsed chloroplast membrane system and decreased pigment content. OsTH1 encoded a phosphomethylpyrimidine kinase/thiamin-phosphate pyrophosphorylase, and was expressed in various tissues, especially in seedlings, leaves, and young panicles. The VB1 content in cles was markedly reduced, despite an increase in the expression of VB1 synthesis genes. The decreased TPP content affected the tricarboxylic acid cycle, pentose phosphate pathway, and de novo fatty acid synthesis, leading to a reduction in fatty acids (C16:0 and C18:0) and sugars (sucrose and glucose) of cles. Additionally, irregular expression of chloroplast membrane synthesis genes led to membrane collapse. We also found that alternative splicing and translation allowed OsTH1 to be localized to both chloroplast and cytosol. Our study revealed that OsTH1 was an essential enzyme in VB1 biosynthesis and played crucial roles in seedling growth and development by participating in fatty acid and sugar metabolism, providing new perspectives on VB1 function in rice.
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Affiliation(s)
- Yanshen Nie
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Li Yu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Lianlian Mao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Wenxuan Zou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiufeng Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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Mu XR, Tong C, Fang XT, Bao QX, Xue LN, Meng WY, Liu CY, Loake GJ, Cao XY, Jiang JH, Meng LS. Feedback loop promotes sucrose accumulation in cotyledons to facilitate sugar-ethylene signaling-mediated, etiolated-seedling greening. Cell Rep 2022; 38:110529. [PMID: 35294871 DOI: 10.1016/j.celrep.2022.110529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 08/01/2021] [Accepted: 02/24/2022] [Indexed: 11/19/2022] Open
Abstract
De-etiolation is indispensable for seedling survival and development. However, how sugars regulate de-etiolation and how sugars induce ethylene (ET) for seedlings to grow out of soil remain elusive. Here, we reveal how a sucrose (Suc) feedback loop promotes de-etiolation by inducing ET biosynthesis. Under darkness, Suc in germinating seeds preferentially induces 1-amino-cyclopropane-1-carboxylate synthase (ACS7; encoding a key ET biosynthesis enzyme) and associated ET biosynthesis, thereby activating ET core component ETHYLENE-INSENSITIVE3 (EIN3). Activated EIN3 directly inhibits the function of Suc transporter 2 (SUC2; a major Suc transporter) to block Suc export from cotyledons and thereby elevate Suc accumulation of cotyledons to induce ET. Under light, ET-activated EIN3 directly inhibits the function of phytochrome A (phyA; a de-etiolation inhibitor) to promote de-etiolation. We therefore propose that under darkness, the Suc feedback loop (Suc-ACS7-EIN3-|SUC2-Suc) promotes Suc accumulation in cotyledons to guarantee ET biosynthesis, facilitate de-etiolation, and enable seedlings to grow out of soil.
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Affiliation(s)
- Xin-Rong Mu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, People's Republic of China
| | - Chen Tong
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, People's Republic of China
| | - Xing-Tang Fang
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, People's Republic of China
| | - Qin-Xin Bao
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, People's Republic of China
| | - Li-Na Xue
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, People's Republic of China
| | - Wei-Ying Meng
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, People's Republic of China
| | - Chang-Yue Liu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, People's Republic of China
| | - Gary J Loake
- Jiangsu Normal University, Edinburgh University, Centre for Transformative Biotechnology of Medicinal and Food Plants, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu 221116, People's Republic of China; Institute of Molecular Plant Sciences, School of Biological Sciences, Edinburgh University, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Xiao-Ying Cao
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, People's Republic of China.
| | - Ji-Hong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, People's Republic of China.
| | - Lai-Sheng Meng
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu 221116, People's Republic of China.
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6
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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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Siatkowska K, Chraniuk M, Bollin P, Banasiuk R. Light emitting diodes optimisation for secondary metabolites production by Droseraceae plants. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2021; 224:112308. [PMID: 34543848 DOI: 10.1016/j.jphotobiol.2021.112308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 08/11/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
The most abundant active compound in Droseraceae is plumbagin, a naphthoquinone widely used for medical purposes due to its antimicrobial, antitussive, antimalarial and anticancer properties. In this work, we created a light-emitting diode (LED) based culture illumination setup as an alternative to fluorescent lamps traditionally used as a light source in plant in vitro cultures. The plants of Drosera binata and Drosera peltata cultured under LED illumination grew equally well and produced similar amounts of biologically active compounds as plants grown under fluorescent lamps. The plants were cultured on two media differing in mineral composition, sucrose content and pH. Secondary metabolites were extracted with ethanol from the plants after harvesting. The extracts were subjected to HPLC and microbiological analyses. We observed differences in morphology and secondary metabolism between plants of the same species grown on different media. However, we did not note significant changes in secondary metabolite yield under assessed lighting conditions. We propose LEDs as a more efficient, eco-friendly and economically reasonable source of light for big scale in vitro production of plumbagin in Drosera species than fluorescent lamps.
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Affiliation(s)
- Kinga Siatkowska
- Institute of Biotechnology and Molecular Medicine, Gdańsk, Poland; Herbiopharm sp. z o.o., Gdańsk, Poland
| | - Milena Chraniuk
- Institute of Biotechnology and Molecular Medicine, Gdańsk, Poland; Herbiopharm sp. z o.o., Gdańsk, Poland
| | - Piotr Bollin
- Institute of Biotechnology and Molecular Medicine, Gdańsk, Poland
| | - Rafał Banasiuk
- Institute of Biotechnology and Molecular Medicine, Gdańsk, Poland; Herbiopharm sp. z o.o., Gdańsk, Poland.
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Ma Z, Chen S, Wang Z, Liu J, Zhang B. Proteome analysis of bermudagrass stolons and rhizomes provides new insights into the adaptation of plant stems to aboveground and underground growth. J Proteomics 2021; 241:104245. [PMID: 33901681 DOI: 10.1016/j.jprot.2021.104245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022]
Abstract
As an important perennial warm-season turfgrass species, bermudagrass (Cynodon dactylon L.) forms underground-growing rhizomes and aboveground-growing stolons simultaneously, making it a fast propagating clonal plant with strong regeneration ability. In the current study, we compared the internode proteomes of rhizomes and stolons at the same developmental stage in the bermudagrass cultivar Yangjiang using iTRAQ. The results indicated that 228 protein species were differentially accumulated in the two specialized stems. In agreement with the different contents of starch, chlorophyll, anthocyanin and H2O2 in the two types of stems, photosynthesis and flavonoid biosynthesis were enriched with differentially accumulated protein species (DAPs) in stolons, whereas starch and sucrose metabolism, glycolysis, and H2O2 metabolism were enriched with DAPs in rhizomes. Burying stolons in the soil resulted in the gradual degradation of chlorophyll and anthocyanin, accumulation of starch, and increment of H2O2, which is similar to the physiological characteristics of rhizomes. These results collectively revealed that stolons and rhizomes of bermudagrass have significant differences at the proteome level and light might play important regulatory roles in the discrepancy of the proteome profiles and specialization of the two stems, providing new insights into the adaptation of plant stems to aboveground and underground growth. BIOLOGICAL SIGNIFICANCE: As two types of specialized stems that grow underground and aboveground respectively, rhizomes and stolons play important roles in overwintering and ecological invasion of many perennial and clonal plants. However, because rhizomes and stolons rarely coexist in single plant species, the differences between the two stems remain unclear at the molecular level. In this study, through an iTRAQ comparative proteomic analysis, we reported the identification of 228 differentially accumulated protein species (DAPs) in rhizomes and stolons of bermudagrass for the first time. We found that the 228 DAPs were interconnected to form protein networks in regulating diverse cellular activities and biochemical reactions. We also observed that stolons growing underground showed similar physiological activities and DAP expression as those of underground-growing rhizomes, suggesting that light might play important regulatory roles in the specialization of stolons and rhizomes. These results expanded our understanding of the mysterious adaption of plant stems to different growth conditions.
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Affiliation(s)
- Ziyan Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Si Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhizhi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Bing Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
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Krahmer J, Abbas A, Mengin V, Ishihara H, Romanowski A, Furniss JJ, Moraes TA, Krohn N, Annunziata MG, Feil R, Alseekh S, Obata T, Fernie AR, Stitt M, Halliday KJ. Phytochromes control metabolic flux, and their action at the seedling stage determines adult plant biomass. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3263-3278. [PMID: 33544130 DOI: 10.1093/jxb/erab038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Phytochrome photoreceptors are known to regulate plastic growth responses to vegetation shade. However, recent reports also suggest an important role for phytochromes in carbon resource management, metabolism, and growth. Here, we use 13CO2 labelling patterns in multiallele phy mutants to investigate the role of phytochrome in the control of metabolic fluxes. We also combine quantitative data of 13C incorporation into protein and cell wall polymers, gas exchange measurements, and system modelling to investigate why biomass is decreased in adult multiallele phy mutants. Phytochrome influences the synthesis of stress metabolites such as raffinose and proline, and the accumulation of sugars, possibly through regulating vacuolar sugar transport. Remarkably, despite their modified metabolism and vastly altered architecture, growth rates in adult phy mutants resemble those of wild-type plants. Our results point to delayed seedling growth and smaller cotyledon size as the cause of the adult-stage phy mutant biomass defect. Our data signify a role for phytochrome in metabolic stress physiology and carbon partitioning, and illustrate that phytochrome action at the seedling stage sets the trajectory for adult biomass production.
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Affiliation(s)
- Johanna Krahmer
- Institute of Molecular Plant Sciences, School of Biological Sciences, Daniel Rutherford Building, Max Born Crescent, Kings Buildings, University of Edinburgh, Edinburgh, UK
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Ammad Abbas
- Institute of Molecular Plant Sciences, School of Biological Sciences, Daniel Rutherford Building, Max Born Crescent, Kings Buildings, University of Edinburgh, Edinburgh, UK
| | - Virginie Mengin
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam Golm, Germany
| | - Hirofumi Ishihara
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam Golm, Germany
| | - Andrés Romanowski
- Institute of Molecular Plant Sciences, School of Biological Sciences, Daniel Rutherford Building, Max Born Crescent, Kings Buildings, University of Edinburgh, Edinburgh, UK
| | - James J Furniss
- Institute of Molecular Plant Sciences, School of Biological Sciences, Daniel Rutherford Building, Max Born Crescent, Kings Buildings, University of Edinburgh, Edinburgh, UK
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK
| | | | - Nicole Krohn
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam Golm, Germany
| | | | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam Golm, Germany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam Golm, Germany
| | - Toshihiro Obata
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam Golm, Germany
- Institute of Agriculture and Natural Resources, Department of Biochemistry, University of Nebraska, Lincoln, NE, USA
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam Golm, Germany
| | - Karen J Halliday
- Institute of Molecular Plant Sciences, School of Biological Sciences, Daniel Rutherford Building, Max Born Crescent, Kings Buildings, University of Edinburgh, Edinburgh, UK
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10
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Pang Z, Chen J, Wang T, Gao C, Li Z, Guo L, Xu J, Cheng Y. Linking Plant Secondary Metabolites and Plant Microbiomes: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:621276. [PMID: 33737943 PMCID: PMC7961088 DOI: 10.3389/fpls.2021.621276] [Citation(s) in RCA: 180] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/08/2021] [Indexed: 05/09/2023]
Abstract
Plant secondary metabolites (PSMs) play many roles including defense against pathogens, pests, and herbivores; response to environmental stresses, and mediating organismal interactions. Similarly, plant microbiomes participate in many of the above-mentioned processes directly or indirectly by regulating plant metabolism. Studies have shown that plants can influence their microbiome by secreting various metabolites and, in turn, the microbiome may also impact the metabolome of the host plant. However, not much is known about the communications between the interacting partners to impact their phenotypic changes. In this article, we review the patterns and potential underlying mechanisms of interactions between PSMs and plant microbiomes. We describe the recent developments in analytical approaches and methods in this field. The applications of these new methods and approaches have increased our understanding of the relationships between PSMs and plant microbiomes. Though the current studies have primarily focused on model organisms, the methods and results obtained so far should help future studies of agriculturally important plants and facilitate the development of methods to manipulate PSMs-microbiome interactions with predictive outcomes for sustainable crop productions.
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Affiliation(s)
- Zhiqiang Pang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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