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Deng K, Li Z, Huang T, Huang J. Noncoding RNAs in regulation of plant secondary metabolism. Plant Physiol Biochem 2024; 211:108718. [PMID: 38733939 DOI: 10.1016/j.plaphy.2024.108718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Plant secondary metabolites (PSMs) are a large class of structurally diverse molecules, mainly consisting of terpenoids, phenolic compounds, and nitrogen-containing compounds, which play active roles in plant development and stress responses. The biosynthetic processes of PSMs are governed by a sophisticated regulatory network at multiple levels. Noncoding RNAs (ncRNAs) such as microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs) may serve as post-transcriptional regulators for plant secondary metabolism through acting on genes encoding either transcription factors or participating enzymes in relevant metabolic pathways. High-throughput sequencing technologies have facilitated the large-scale identifications of ncRNAs potentially involved in plant secondary metabolism in model plant species as well as certain species with enriched production of specific types of PSMs. Moreover, a series of miRNA-target modules have been functionally characterized to be responsible for regulating PSM biosynthesis and accumulation in plants under abiotic or biotic stresses. In this review, we will provide an overview of current findings on the ncRNA-mediated regulation of plant secondary metabolism with special attention to its participation in plant stress responses, and discuss possible issues to be addressed in future fundamental research and breeding practice.
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Affiliation(s)
- Keyin Deng
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China
| | - Ziwei Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China
| | - Jianzi Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China.
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Wang WQ, Liu XF, Zhu YJ, Zhu JZ, Liu C, Wang ZY, Shen XX, Allan AC, Yin XR. Identification of miRNA858 long-loop precursors in seed plants. Plant Cell 2024; 36:1637-1654. [PMID: 38114096 PMCID: PMC11062470 DOI: 10.1093/plcell/koad315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/20/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
MicroRNAs (miRNAs) are a class of nonprotein-coding short transcripts that provide a layer of post-transcriptional regulation essential to many plant biological processes. MiR858, which targets the transcripts of MYB transcription factors, can affect a range of secondary metabolic processes. Although miR858 and its 187-nt precursor have been well studied in Arabidopsis (Arabidopsis thaliana), a systematic investigation of miR858 precursors and their functions across plant species is lacking due to a problem in identifying the transcripts that generate this subclass. By re-evaluating the transcript of miR858 and relaxing the length cut-off for identifying hairpins, we found in kiwifruit (Actinidia chinensis) that miR858 has long-loop hairpins (1,100 to 2,100 nt), whose intervening sequences between miRNA generating complementary sites were longer than all previously reported miRNA hairpins. Importantly, these precursors of miR858 containing long-loop hairpins (termed MIR858L) are widespread in seed plants including Arabidopsis, varying between 350 and 5,500 nt. Moreover, we showed that MIR858L has a greater impact on proanthocyanidin and flavonol levels in both Arabidopsis and kiwifruit. We suggest that an active MIR858L-MYB regulatory module appeared in the transition of early land plants to large upright flowering plants, making a key contribution to plant secondary metabolism.
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Affiliation(s)
- Wen-qiu Wang
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Xiao-fen Liu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yong-jing Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Jia-zhen Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Chao Liu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Zhi-ye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Xing-Xing Shen
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Xue-ren Yin
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
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Liu BK, Xv BJ, Si CC, Shi WQ, Ding GZ, Tang LX, Xv M, Shi CY, Liu HJ. Effect of potassium fertilization on storage root number, yield, and appearance quality of sweet potato ( Ipomoea batatas L.). Front Plant Sci 2024; 14:1298739. [PMID: 38455375 PMCID: PMC10917953 DOI: 10.3389/fpls.2023.1298739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024]
Abstract
Increasing storage root number is a pivotal approach to enhance both storage root (SR) yield and appearance quality of sweet potato. Here, 2-year field experiments were conducted to investigate the effect of 0 (K0), 120 (K1), 240 (K2), and 360 (K3) kg ha-1 potassium fertilizer (K2O) on lignin metabolism, root growth, storage root yield, and uniformity. The results demonstrated that potassium (K) application led to a decrease in the activities of key enzymes involved in lignin biosynthesis, including phenylalanine deaminase (PAL), 4-coumarate coenzyme A ligase (4-CL), cinnamic acid dehydrogenase (CAD), polyphenol oxidase (PPO), and peroxidase (POD). This resulted in a significant reduction in lignin and G-type lignin contents in potential SRs compared to K0 treatment within 10-30 days after planting (DAP). BJ553 exhibited a significant decrease in PAL activity, as well as lignin and G-type contents at 10 DAP, whereas YS25 showed delayed effects until 20 DAP. However, the number and distribution of secondary xylem conduits as well as the mid-column diameter area in roots were increased in K2 treatment. Interestingly, K2 treatment exhibited significantly larger potential SR diameter than other treatments at 15, 20, and 25 DAP. At harvest, K2 treatment increased the SR number, the single SR weight, and overall yield greatly compared with K0 treatment, with an average increase of 19.12%, 16.54%, and 16.92% respectively. The increase of SR number in BJ553 was higher than that of YS25. Furthermore, K2 treatment exhibited the lowest coefficient of variation for both SR length and diameter, indicating a higher yield of middle-sized SRs. In general, appropriate potassium application could effectively suppress lignin biosynthesis, leading to a reduction in the degree of pericycle lignification in potential SRs. This promotes an increase in the number of storage roots and ultimately enhances both yield and appearance quality of sweet potato. The effect of potassium fertilizer on lignin metabolism in BJ553 roots was earlier and resulted in a greater increase in the SR number compared to YS25.
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Affiliation(s)
- Ben-kui Liu
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Bing-jie Xv
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Cheng-cheng Si
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
| | - Wen-qing Shi
- Shandong Agricultural Technology Extension Center, Jinan, Shandong, China
| | - Guo-zheng Ding
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Li-xue Tang
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Ming Xv
- Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Chun-yv Shi
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Hong-jvan Liu
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
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Liu Y, Ge L, Tang H, Zheng J, Hu J, Wang J, Yang X, Zhang R, Wang X, Li X, Zhang Y, Shi Q. cGMP functions as an important messenger involved in SlSAMS1-regulated salt stress tolerance in tomato. Plant Physiol Biochem 2023; 204:108097. [PMID: 37864930 DOI: 10.1016/j.plaphy.2023.108097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/04/2023] [Accepted: 10/12/2023] [Indexed: 10/23/2023]
Abstract
Salt stress adversely affects the growth, development, and yield of tomato (Solanum lycopersicum). SAM Synthetase (SAMS), which is responsible for the biosynthesis of S-adenosylmethionine (SAM, a precursor of polyamine biosynthesis), participates in plant response to abiotic stress. However, the regulatory mechanism of SAMS-mediated salt stress tolerance remains elusive. In this study, we characterized a SAMS homologue SlSAMS1 in tomato. We found that SlSAMS1 is highly expressed in tomato roots, and its expression can be induced by salt stress. Crucially, overexpression of SlSAMS1 in tomato enhances salt stress tolerance. Through metabolomic profiling, we identified some differentially accumulated metabolites, especially, a secondary messenger guanosine 3',5'-cyclic monophosphate (cGMP) which may play a key role in SlSAMS1-regulated salt tolerance. A series of physiological and biochemical data suggest that cGMP alleviates salt stress-induced growth inhibition, and potentially acts downstream of the polyamine-nitric oxide (PA-NO) signaling pathway to trigger H2O2 signaling in response to salt stress. Taken together, the study reveals that SlSAMS1 regulates tomato salt tolerance via the PA-NO-cGMP-H2O2 signal module. Our findings elucidate the regulatory pathway of SlSAMS1-induced plant response to salt stress and indicate a pivotal role of cGMP in salt tolerance.
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Affiliation(s)
- Yue Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, PR China
| | - Lianjing Ge
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, PR China
| | - Huimeng Tang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, PR China
| | - Jinhui Zheng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, PR China
| | - Jinxiang Hu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, PR China
| | - Jingru Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, PR China
| | - Xiaoyu Yang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, PR China
| | - Ruimin Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, PR China
| | - Xiaoyun Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, PR China
| | - Xiuming Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, PR China
| | - Yan Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, PR China.
| | - Qinghua Shi
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, PR China.
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Chen SP, Kuo YW, Lin JS. Review: Defense responses in sweetpotato (Ipomoea batatas L.) against biotic stress. Plant Sci 2023; 337:111893. [PMID: 37813194 DOI: 10.1016/j.plantsci.2023.111893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023]
Abstract
Sweetpotato (Ipomoea batatas L.) is regarded as amongst the world's most important crops for food, vegetable, forage, and raw material for starch and alcohol production. Since pest attack and disease infection are the main limiting aspects frequently causing the yield loss and quality degradation of sweetpotato, it is a great demand to develop the effective defense strategies for maintaining productivity. In the past decade, many studies have focused on dynamic analysis at the physiological, biochemical, and molecular responses of sweetpotatoes to environmental challenges. This review offers an overview of the defense mechanisms against biotic stresses in sweetpotato observed so far, particularly insect herbivory and pathogen infections. The defenses of sweetpotato include the regulation of the toxic and anti-digestive proteins, plant-derived compounds, physical barrier formation, and sugar distribution. Ipomoelin and sporamin have been extensively researched for the defense against herbivore wounding. Herbivory-induced plant volatiles, chlorogenic acid, and latex phytochemicals play important roles in defenses for insect herbivory. Induction of IbSWEET10 reduces sugar content to mediate F. oxysporum resistance. Therefore, these researches provide the genetic strategies for improving resistance bioengineering and breeding of sweetpotato crops and future prospects for research in this field.
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Affiliation(s)
- Shi-Peng Chen
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei 11114, Taiwan.
| | - Yun-Wei Kuo
- Department of Agronomy, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan; Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan.
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Hu Y, Ji J, Cheng H, Luo R, Zhang J, Li W, Wang X, Zhang J, Yao Y. The miR408a-BBP-LAC3/CSD1 module regulates anthocyanin biosynthesis mediated by crosstalk between copper homeostasis and ROS homeostasis during light induction in Malus plants. J Adv Res 2023; 51:27-44. [PMID: 36371057 PMCID: PMC10491975 DOI: 10.1016/j.jare.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/19/2022] [Accepted: 11/06/2022] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION The expression of miR408 is affected by copper (Cu) conditions and positively regulates anthocyanin biosynthesis in Arabidopsis. However, the underlying mechanisms by which miR408 regulates anthocyanin biosynthesis mediated by Cu homeostasis and reactive oxygen species (ROS) homeostasis remain unclear in Malus plants. OBJECTIVES Our study aims to elucidate how miR408a and its target, basic blue protein (BBP) regulate Cu homeostasis and ROS homeostasis, and anthocyanin biosynthesis in Malus plants. METHODS The roles of miR408a and its target BBP in regulating anthocyanin biosynthesis, Cu homeostasis, and ROS homeostasis were mainly identified in Malus plants. RESULTS We found that the BBP protein interacted with the copper-binding proteins LAC3 (laccase) and CSD1 (Cu/Zn SOD superoxide dismutase), indicating a potential crosstalk between Cu homeostasis and ROS homeostasis might be mediated by miR408 to regulate the anthocyanin accumulation. Further studies showed that overexpressing miR408a or suppressing BBP transiently significantly increased the expression of genes related to Cu binding and Cu transport, leading to anthocyanin accumulation under light induction in apple fruit and Malus plantlets. Consistently, opposite results were obtained when repressing miR408a or overexpressing BBP. Moreover, light induction significantly increased the expression of miR408a, CSD1, and LAC3, but significantly reduced the BBP expression, resulting in increased Cu content and anthocyanin accumulation. Furthermore, excessive Cu significantly increased the anthocyanin accumulation, accompanied by reduced expression of miR408a and Cu transport genes, and upregulated expression of Cu binding proteins including BBP, LAC3, and CSD1 to maintain the Cu homeostasis and ROS homeostasis in Malus plantlets. CONCLUSION Our findings provide new insights into the mechanism by which the miR408a-BBP-LAC3/CSD1 module perceives light and Cu signals regulating Cu and ROS homeostasis, ultimately affecting anthocyanin biosynthesis in Malus plants.
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Affiliation(s)
- Yujing Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Jiayi Ji
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China; Beijing Forestry University, China
| | - Hao Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Rongli Luo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Wenjing Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Xingsui Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China.
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China.
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Tsai WA, Sung PH, Kuo YW, Chen MC, Jeng ST, Lin JS. Involvement of microRNA164 in responses to heat stress in Arabidopsis. Plant Sci 2023; 329:111598. [PMID: 36657663 DOI: 10.1016/j.plantsci.2023.111598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/28/2022] [Accepted: 01/14/2023] [Indexed: 06/17/2023]
Abstract
MicroRNAs (miRNAs) are considered to be integral parts of plant stress regulatory networks. Under long-term heat stress, miR164 is induced. Conversely, its targets are repressed. Transgenic overexpressors (164OE) and mutants of MIR164 (mir164) were used to study miR164's functions during heat responses. Target gene expression decreased in 164OE transgenic plants and increased in mir164a-4 and mir164b mutants. Under heat stress, the mir164 mutants presented heat-sensitive phenotypes, while 164OE transgenic plants showed better thermotolerance than wild-type (WT) plants. Overexpression of miR164 decreased heat-inhibition of hypocotyl lengths. Under heat stress, miR164 target genes modulated the expression of chlorophyll b reductase and chlorophyll catabolic genes, reducing the chlorophyll a/b ratio. More H2O2 accumulated in the mir164 mutants under heat stress, which may have caused oxidative damage. In addition, expression of HSPs was altered in the experimental plants compared to that of the WT. Overall, miR164 influenced target gene expression, altering development, chlorophyll a/b ratio, H2O2-caused damage, and HSPs expression under long-term heat stress. These phenomena, in turn, likely influence the thermotolerance of plants.
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Affiliation(s)
- Wei-An Tsai
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia.
| | - Po-Han Sung
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Yun-Wei Kuo
- Department of Agronomy, National Chung Hsing University, Taichung 40227, Taiwan; Institute of Flowers, Sanming Academy of Agricultural Sciences, Sanming 365000, Fujian, China.
| | - Ming-Cheng Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan.
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Sreekumar S, Divya K, Joy N, Soniya EV. De novo transcriptome profiling unveils the regulation of phenylpropanoid biosynthesis in unripe Piper nigrum berries. BMC Plant Biol 2022; 22:501. [PMID: 36284267 PMCID: PMC9597958 DOI: 10.1186/s12870-022-03878-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Black pepper (Piper nigrum L.) is rich in bioactive compounds that make it an imperative constituent in traditional medicines. Although the unripe fruits have long been used in different Ayurvedic formulations, the mechanism of gene regulation resulting in the production of the bioactive compounds in black pepper is not much investigated. Exploring the regulatory factors favouring the production of bioactive compounds ultimately help to accumulate the medicinally important content of black pepper. The factors that enhance the biosynthesis of these compounds could be potential candidates for metabolic engineering strategies to obtain a high level production of significant biomolecules. RESULTS Being a non-model plant, de novo sequencing technology was used to unravel comprehensive information about the genes and transcription factors that are expressed in mature unripe green berries of P. nigrum from which commercially available black pepper is prepared. In this study, the key gene regulations involved in the synthesis of bioactive principles in black pepper was brought out with a focus on the highly expressed phenylpropanoid pathway genes. Quantitative real-time PCR analysis of critical genes and transcription factors in the different developmental stages from bud to the mature green berries provides important information useful for choosing the developmental stage that would be best for the production of a particular bioactive compound. Comparison with a previous study has also been included to understand the relative position of the results obtained from this study. CONCLUSIONS The current study uncovered significant information regarding the gene expression and regulation responsible for the bioactivity of black pepper. The key transcription factors and enzymes analyzed in this study are promising targets for achieving a high level production of significant biomolecules through metabolic engineering.
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Affiliation(s)
- Sweda Sreekumar
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India
- Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Kattupalli Divya
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India
- Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Nisha Joy
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, Scotland
| | - E V Soniya
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India.
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Chen TC, Chou SY, Chen MC, Lin JS. IbTLD modulates reactive oxygen species scavenging and DNA protection to confer salinity stress tolerance in tobacco. Plant Sci 2022; 323:111415. [PMID: 35963494 DOI: 10.1016/j.plantsci.2022.111415] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Plants accumulate reactive oxygen species (ROS) that may damage the cells under prolonged stress conditions. Reduction of the excessive ROS production can alleviate oxidative damage and enhance the survival rates under stress. TLDc-containing protein (TLD) was reported to confer tolerance to oxidative stress, but the regulatory mechanism of TLD remains unclear. In this study, we ectopically overexpressed the Ipomoea batatas TLDc gene (IbTLD) in tobacco and characterized its functions. RNA-sequencing analysis and Gene Ontology term enrichment analysis revealed that IbTLD up-regulates auxin-responsive genes in response to oxidative stress. Under salinity stress, the IbTLD transgenic lines showed higher germination rates, chlorophyll contents, and root lengths than wild type (W38). In addition, the IbTLD transgenic lines showed higher expression of ROS scavenging genes, nudix hydrolases, ROS scavenging enzyme activity, and lesser DNA damage compared to W38 under salinity stress. Therefore, our results suggest that IbTLD activates the expression of ROS scavenging genes and confers tolerance to salinity stress in planta.
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Affiliation(s)
- Tsung-Chi Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan.
| | - Si-Yun Chou
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Ming-Cheng Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan.
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Villalobos-Escobedo JM, Martínez-Hernández JP, Pelagio-Flores R, González-De la Rosa PM, Carreras-Villaseñor N, Abreu-Goodger C, Herrera-Estrella AH. Trichoderma atroviride hyphal regeneration and conidiation depend on cell-signaling processes regulated by a microRNA-like RNA. Microb Genom 2022; 8. [PMID: 36239595 DOI: 10.1099/mgen.0.000869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability to respond to injury is essential for the survival of an organism and involves analogous mechanisms in animals and plants. Such mechanisms integrate coordinated genetic and metabolic reprogramming events requiring regulation by small RNAs for adequate healing of the wounded area. We have previously reported that the response to injury of the filamentous fungus Trichoderma atroviride involves molecular mechanisms closely resembling those of plants and animals that lead to the formation of new hyphae (regeneration) and the development of asexual reproduction structures (conidiophores). However, the involvement of microRNAs in this process has not been investigated in fungi. In this work, we explore the participation of microRNA-like RNAs (milRNAs) molecules by sequencing messenger and small RNAs during the injury response of the WT strain and RNAi mutants. We found that Dcr2 appears to play an important role in hyphal regeneration and is required to produce the majority of sRNAs in T. atroviride. We also determined that the three main milRNAs produced via Dcr2 are induced during the damage-triggered developmental process. Importantly, elimination of a single milRNA phenocopied the main defects observed in the dcr2 mutant. Our results demonstrate the essential role of milRNAs in hyphal regeneration and asexual development by post-transcriptionally regulating cellular signalling processes involving phosphorylation events. These observations allow us to conclude that fungi, like plants and animals, in response to damage activate fine-tuning regulatory mechanisms.
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Affiliation(s)
- José M Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico
| | - J Pedro Martínez-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico
| | - Ramón Pelagio-Flores
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico.,Present address: Facultad de Químico Farmacobiología, Universidad Michoacana de San Nicolás de Hidalgo, C.P. 58030 Morelia, Michoacán, Mexico
| | - Pablo M González-De la Rosa
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico.,Present address: Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Nohemí Carreras-Villaseñor
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico.,Present address: Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C. C.P. 91070 Xalapa, Veracruz, Mexico
| | - Cei Abreu-Goodger
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico.,Present address: Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Alfredo H Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico
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11
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Ren Y, Jiang H, Ma L, Yang J, Si H, Bai J, Prusky D, Bi Y. Interference Expression of StMSD Inhibited the Deposition of Suberin and Lignin at Wounds of Potato Tubers by Reducing the Production of H2O2. Antioxidants (Basel) 2022; 11:1901. [PMID: 36290624 PMCID: PMC9598499 DOI: 10.3390/antiox11101901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Superoxide dismutase (SOD) actively participates in the wound stress of plants. However, whether StMSD mediates the generation of H2O2 and the deposition of suberin polyphenolic and lignin at potato tuber wounds is elusive. In this study, we developed the StMSD interference expression of potato plants and tubers by Agrobacterium tumefaciens-mediated transformation. The StSOD expression showed a marked downregulation in StMSD-interference tubers, especially StCSD2 and StCSD3. The content of O2•− exhibited a noticeable increase together with the inhibition in H2O2 accumulation. Moreover, the gene expression levels of StPAL (phenylalanine ammonia-lyase) and StC4H (cinnamate-4-hydroxylase) were downregulated in StMSD-interference tubers, and less suberin polyphenolic and lignin depositions at the wounds were observed. Taken together, the interference expression of StMSD can result in less suberin polyphenolic and lignin deposition by inhibiting the disproportionation of O2•− to H2O2 and restraining phenylpropanoid metabolism in tubers.
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12
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Wang X, Yao S, Htet WPPM, Yue Y, Zhang Z, Sun K, Chen S, Luo K, Fan D. MicroRNA828 negatively regulates lignin biosynthesis in stem of Populus tomentosa through MYB targets. Tree Physiol 2022; 42:1646-1661. [PMID: 35220431 DOI: 10.1093/treephys/tpac023] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Lignin biosynthesis in the sclerenchyma cells is strictly controlled by a complex network of genetic and environmental signals. In the last decades, the transcriptional regulation of lignin synthesis in woody species has been established. However, the role of microRNA-mediated post-transcriptional modulation in secondary cell wall biosynthesis remains poorly understood. Here, we identified a microRNA, miR828, involved in the regulation specific to lignin biosynthesis during stem development in Populus tomentosa Carr. miR828 is preferentially expressed in the secondary vascular tissues during stem development. Two MYB genes (MYB171 and MYB011) were validated as direct targets of miR828 by degradome analysis and green fluorescent protein signal detection. Overexpression of miR828 in poplar downregulated genes for lignin biosynthesis, resulting in reduced lignin content in cell walls. Conversely, suppression of miR828 in plants by the short tandem target mimics elevated the expression of lignin biosynthetic genes and increased lignin deposition. We further revealed that poplar MYB171, as the most abundant miR828 target in the stem, is a positive regulator for lignin biosynthesis. Transient expression assays showed that both MYB171 and MYB011 activated PAL1 and CCR2 transcription, whereas the introduction of miR828 significantly suppressed their expression that was induced by MYB171 or MYB011. Collectively, our results demonstrate that the miR828-MYBs module precisely regulates lignin biosynthesis during the stem development in P. tomentosa through transcriptional and post-transcriptional manners.
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Affiliation(s)
- Xianqiang Wang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Shu Yao
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Win Pa Pa Myo Htet
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Yuchen Yue
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Zhuanzhuan Zhang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Kuan Sun
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Sijie Chen
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Di Fan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
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13
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Zhu X, Su M, Wang B, Wei X. Transcriptome analysis reveals the main metabolic pathway of c-GMP induced by salt stress in tomato ( Solanum lycopersicum) seedlings. Funct Plant Biol 2022; 49:784-798. [PMID: 35930479 DOI: 10.1071/fp21337] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
Tomato (Solanum lycopersicum L.) is a model crop as well as an important food worldwide. In arid areas, increasing soil salinity has limited higher yields in tomato production. As a second messenger molecule, cyclic guanosine monophosphate (c-GMP) plays an indispensable role in plant response to salt stress by regulating cell processes to promote plant growth and development. However, this mechanism has not been fully explored in tomato seedlings. In this experiment, tomato seeds were cultured in four treatments: (1) distilled water (CK); (2) 20μM c-GMP (T1); (3) 50mM NaCl (T2); and (4) 20μM c-GMP+50mM NaCl (T3). The results show that 20μM c-GMP effectively alleviated the inhibitory effect of 50mM NaCl on growth and development, and induced the expression of 1580 differentially expressed genes (DEGs). Seedlings in the CK vs T1 shared 95 upregulated and 442 downregulated DEGs, whereas T2 vs T3 shared 271 upregulated and 772 downregulated DEGs. Based on KEGG (Kyoto Encyclopaedia of Genes and Genomes) analysis, the majority of DEGs were involved in metabolism; exogenous c-GMP induced significant enrichment of pathways associated with carbohydrates, phenylpropanoids and fatty acid metabolism. Most PMEs , acCoA , PAL , PODs , FADs , and AD were upregulated, and GAPDHs , PL , PG , BXL4 , and β-G were downregulated, which reduced susceptibility of tomato seedlings to salt and promoted their salt tolerance. The application of c-GMP increased soluble sugar, flavonoid and lignin contents, reduced accumulation of malondialdehyde (MDA), and enhanced the activity of peroxidase (POD). Thus, our results provide insights into the molecular mechanisms associated with salt tolerance of tomato seedlings.
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Affiliation(s)
- Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; and Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; and College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Meifei Su
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; and College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Baoqiang Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; and College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaohong Wei
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; and Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; and College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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14
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Zeng C, Wu H, Cao M, Zhou C, Wang X, Fu S. Integrated Analysis of the miRNAome and Transcriptome Reveals miRNA-mRNA Regulatory Networks in Catharanthus roseus Through Cuscuta campestris-Mediated Infection With " Candidatus Liberibacter asiaticus". Front Microbiol 2022; 13:799819. [PMID: 35308338 PMCID: PMC8928264 DOI: 10.3389/fmicb.2022.799819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/27/2022] [Indexed: 12/30/2022] Open
Abstract
Citrus Huanglongbing (HLB) is the most devastating disease of citrus caused by the Gram-negative phloem-limited bacterium "Candidatus Liberibacter asiaticus" (CLas). It can be transmitted by the Asian citrus psyllid "Diaphorina citri," by grafting, and by the holoparasitic dodder. In this study, the non-natural host periwinkle (Catharanthus roseus) was infected via dodder (Cuscuta campestris) from CLas-infected citrus plants, and the asymptomatic leaves (AS) were subjected to transcriptomic and small-RNA profiling. The results were analyzed together with a transcriptome dataset from the NCBI repository that included leaves for which symptoms had just occurred (S) and yellowing leaves (Y). There were 3,675 differentially expressed genes (DEGs) identified in AS, and 6,390 more DEGs in S and further 2109 DEGs in Y. These DEGs were commonly enriched in photosystem, chloroplast, membrane, oxidation-reduction process, metal/zinc ion binding on GO. A total of 14,974 DEGs and 336 DE miRNAs (30 conserved and 301 novel) were identified. Through weighted gene co-expression network and nested network analyses, two critical nested miRNA-mRNA regulatory networks were identified with four conserved miRNAs. The primary miR164-NAC1 network is potentially involved in plant defense responses against CLas from the early infection stage to symptom development. The secondary network revealed the regulation of secondary metabolism and nutrient homeostasis through miR828-MYB94/miR1134-HSF4 and miR827-ATG8 regulatory networks, respectively. The findings discovered new potential mechanisms in periwinkle-CLas interactions, and its confirmation can be done in citrus-CLas system later on. The advantages of periwinkle plants in facilitating the quick establishment and greater multiplication of CLas, and shortening latency for disease symptom development make it a great surrogate for further studies, which could expedite our understanding of CLas pathogenesis.
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Affiliation(s)
| | | | | | | | - Xuefeng Wang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
| | - Shimin Fu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
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Ren L, Zhang T, Wu H, Ge X, Wan H, Chen S, Li Z, Ma D, Wang A. Blocking IbmiR319a Impacts Plant Architecture and Reduces Drought Tolerance in Sweet Potato. Genes (Basel) 2022; 13:genes13030404. [PMID: 35327958 PMCID: PMC8953241 DOI: 10.3390/genes13030404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 01/15/2023] Open
Abstract
MicroRNA319 (miR319) plays a key role in plant growth, development, and multiple resistance by repressing the expression of targeted TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) genes. Two members, IbmiR319a and IbmiR319c, were discovered in the miR319 gene family in sweet potato (Ipomoea batatas [L.] Lam). Here, we focused on the biological function and potential molecular mechanism of the response of IbmiR319a to drought stress in sweet potato. Blocking IbmiR319a in transgenic sweet potato (MIM319) resulted in a slim and tender phenotype and greater sensitivity to drought stress. Microscopic observations revealed that blocking IbmiR319a decreased the cell width and increased the stomatal distribution in the adaxial leaf epidermis, and also increased the intercellular space in the leaf and petiole. We also found that the lignin content was reduced, which led to increased brittleness in MIM319. Quantitative real-time PCR showed that the expression levels of key genes in the lignin biosynthesis pathway were much lower in the MIM319 lines than in the wild type. Ectopic expression of IbmiR319a-targeted genes IbTCP11 and IbTCP17 in Arabidopsis resulted in similar phenotypes to MIM319. We also showed that the expression of IbTCP11 and IbTCP17 was largely induced by drought stress. Transcriptome analysis indicated that cell growth-related pathways, such as plant hormonal signaling, were significantly downregulated with the blocking of IbmiR319a. Taken together, our findings suggest that IbmiR319a affects plant architecture by targeting IbTCP11/17 to control the response to drought stress in sweet potato.
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Affiliation(s)
- Lei Ren
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Tingting Zhang
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Haixia Wu
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Xinyu Ge
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Huihui Wan
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Shengyong Chen
- Zhanjiang Academy of Agricultural Sciences, Zhanjiang 524094, China;
| | - Zongyun Li
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Daifu Ma
- Key Laboratory for Biology and Genetic Breeding of Sweetpotato (Xuzhou), Ministry of Agriculture/Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou Institute of Agricultural Sciences, Xuzhou 221131, China
- Correspondence: (D.M.); (A.W.); Tel.: +86-516-82189200 (D.M.); +86-516-83400033 (A.W.)
| | - Aimin Wang
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (L.R.); (T.Z.); (H.W.); (X.G.); (H.W.); (Z.L.)
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
- Correspondence: (D.M.); (A.W.); Tel.: +86-516-82189200 (D.M.); +86-516-83400033 (A.W.)
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16
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Zhao JH, Guo HS. RNA silencing: From discovery and elucidation to application and perspectives. J Integr Plant Biol 2022; 64:476-498. [PMID: 34964265 DOI: 10.1111/jipb.13213] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
RNA silencing (or RNA interference, RNAi) is a conserved mechanism for regulating gene expression in eukaryotes. The discovery of natural trans-kingdom RNAi indicated that small RNAs act as signaling molecules and enable communication between organisms in different kingdoms. The phenomenon and potential mechanisms of trans-kingdom RNAi are among the most exciting research topics. To better understand trans-kingdom RNAi, we review the history of the discovery and elucidation of RNAi mechanisms. Based on canonical RNAi mechanisms, we summarize the major points of divergence around RNAi pathways in the main eukaryotes' kingdoms, including plants, animals, and fungi. We review the representative incidents associated with the mechanisms and applications of trans-kingdom RNAi in crop protection, and discuss the critical factors that should be considered to develop successful trans-kingdom RNAi-based crop protection strategies.
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Affiliation(s)
- Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049, China
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17
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Hu Y, Cheng H, Zhang Y, Zhang J, Niu S, Wang X, Li W, Zhang J, Yao Y. The MdMYB16/MdMYB1-miR7125-MdCCR module regulates the homeostasis between anthocyanin and lignin biosynthesis during light induction in apple. New Phytol 2021; 231:1105-1122. [PMID: 33908060 DOI: 10.1111/nph.17431] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/19/2021] [Indexed: 05/22/2023]
Abstract
Light induces anthocyanin accumulation and hence decides the coloration of apple fruit. It also plays a key role in regulating the biosynthesis of other secondary metabolites. However, the crosstalk between anthocyanin and lignin metabolism during light induction, which affects the edible quality and visual quality of apple fruit, respectively, have rarely been characterized. In this study, we identified and functionally elucidated the roles of miR7125 and its target, cinnamoyl-coenzyme A reductase gene (CCR), in regulating the homeostasis between anthocyanin and lignin biosynthesis during light induction. Overexpressing miR7125 or inhibiting CCR transiently in apple fruit promoted anthocyanin biosynthesis but reduced lignin production under light-induced conditions. Consistently, opposite results were observed under the background of repressed miR7125 or overexpressed CCR. We found that the repressor MdMYB16 and the activator MdMYB1 bound to the miR7125 promoter. Transient repression of MdMYB16 upregulated miR7125 expression significantly, accompanied by decreased levels of MdCCR transcript, resulting in a reduction in the lignin biosynthesis and an increase in anthocyanin accumulation. However, transient overexpression of MdMYB16 produced the opposite effects to MdMYB16-RNAi. The results reveal a novel mechanism by which the MdMYB16/MdMYB1-miR7125-MdCCR module collaboratively regulates homeostasis between anthocyanin and lignin biosynthesis under light induction in apple.
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Affiliation(s)
- Yujing Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Hao Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Yan Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Shuqing Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Xingsui Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Wenjing Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
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18
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Li C, Wang M, Qiu X, Zhou H, Lu S. Noncoding RNAs in Medicinal Plants and their Regulatory Roles in Bioactive Compound Production. Curr Pharm Biotechnol 2021; 22:341-359. [PMID: 32469697 DOI: 10.2174/1389201021666200529101942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs), play significant regulatory roles in plant development and secondary metabolism and are involved in plant response to biotic and abiotic stresses. They have been intensively studied in model systems and crops for approximately two decades and massive amount of information have been obtained. However, for medicinal plants, ncRNAs, particularly their regulatory roles in bioactive compound biosynthesis, are just emerging as a hot research field. OBJECTIVE This review aims to summarize current knowledge on herbal ncRNAs and their regulatory roles in bioactive compound production. RESULTS So far, scientists have identified thousands of miRNA candidates from over 50 medicinal plant species and 11794 lncRNAs from Salvia miltiorrhiza, Panax ginseng, and Digitalis purpurea. Among them, more than 30 miRNAs and five lncRNAs have been predicted to regulate bioactive compound production. CONCLUSION The regulation may achieve through various regulatory modules and pathways, such as the miR397-LAC module, the miR12112-PPO module, the miR156-SPL module, the miR828-MYB module, the miR858-MYB module, and other siRNA and lncRNA regulatory pathways. Further functional analysis of herbal ncRNAs will provide useful information for quality and quantity improvement of medicinal plants.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hong Zhou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
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Chaudhary S, Grover A, Sharma PC. MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops. Life (Basel) 2021; 11:life11040289. [PMID: 33800690 PMCID: PMC8066829 DOI: 10.3390/life11040289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.
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Affiliation(s)
- Saurabh Chaudhary
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
- Correspondence: (S.C.); (P.C.S.)
| | - Atul Grover
- Defence Institute of Bio-Energy Research, Defence Research and Development Organisation (DRDO), Haldwani 263139, India;
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi 110078, India
- Correspondence: (S.C.); (P.C.S.)
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20
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Liu Y, Su W, Wang L, Lei J, Chai S, Zhang W, Yang X. Integrated transcriptome, small RNA and degradome sequencing approaches proffer insights into chlorogenic acid biosynthesis in leafy sweet potato. PLoS One 2021; 16:e0245266. [PMID: 33481815 PMCID: PMC7822329 DOI: 10.1371/journal.pone.0245266] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/26/2020] [Indexed: 12/22/2022] Open
Abstract
Leafy sweet potato is rich in total phenolics (TP) which play key roles in health protection, the chlorogenic acid (CGA) constitutes the major components of phenolic compounds in leafy sweet potato. Unfortunately, the mechanism of CGA biosynthesis in leafy sweet potato is unclear. To dissect the mechanisms of CGA biosynthesis, we performed transcriptome, small RNA (sRNA) and degradome sequencing of one low-CGA content and one high-CGA content genotype at two stages. A total of 2,333 common differentially expressed genes (DEGs) were identified, and the enriched DEGs were related to photosynthesis, starch and sucrose metabolism and phenylpropanoid biosynthesis. The functional genes, such as CCR, CCoAOMT and HCT in the CGA biosynthetic pathway were down-regulated, indicating that the way to lignin was altered, and two possible CGA biosynthetic routes were hypothesized. A total of 38 DE miRNAs were identified, and 1,799 targets were predicated for 38 DE miRNAs by using in silico approaches. The target genes were enriched in lignin and phenylpropanoid catabolic processes. Transcription factors (TFs) such as apetala2/ethylene response factor (AP2/ERF) and Squamosa promoter binding protein-like (SPL) predicated in silico were validated by degradome sequencing. Association analysis of the DE miRNAs and transcriptome datasets identified that miR156 family negatively targeted AP2/ERF and SPL. Six mRNAs and six miRNAs were validated by qRT-PCR, and the results showed that the expression levels of the mRNAs and miRNAs were consistent with the sequencing data. This study established comprehensive functional genomic resources for the CGA biosynthesis, and provided insights into the molecular mechanisms involving in this process. The results also enabled the first perceptions of the regulatory roles of mRNAs and miRNAs, and offered candidate genes for leafy sweet potato improvements.
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Affiliation(s)
- Yi Liu
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Wenjin Su
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Lianjun Wang
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Jian Lei
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Shasha Chai
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Wenying Zhang
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Xinsun Yang
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
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21
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Torti P, Raineri J, Mencia R, Campi M, Gonzalez DH, Welchen E. The sunflower TLDc-containing protein HaOXR2 confers tolerance to oxidative stress and waterlogging when expressed in maize plants. Plant Sci 2020; 300:110626. [PMID: 33180706 DOI: 10.1016/j.plantsci.2020.110626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
The sunflower (Helianthus annuus L.) genome encodes six proteins containing a TLDc domain, typical of the eukaryotic OXidation Resistance (OXR) protein family. Expression of sunflower HaOXR2 in Arabidopsis generated plants with increased rosette diameter, higher number of leaves and increased seed production. Maize inbred lines expressing HaOXR2 also showed increased total leaf area per plant. In addition, heterologous expression of HaOXR2 induced an increase in the oxidative stress tolerance in Arabidopsis and maize. Maize transgenic plants expressing HaOXR2 experienced less oxidative damage and exhibited increased photosynthetic performance and efficiency than non-transgenic segregant plants after treatment of leaves with the reactive oxygen species generating compound Paraquat. Expression of HaOXR2 in maize also improved tolerance to waterlogging. The number of expanded leaves, aerial biomass, and stem height and cross-section area were less affected by waterlogging in HaOXR2 expressing plants, which also displayed less aerial tissue damage under these conditions. Transgenic plants also showed an increased production of roots, a typical adaptive stress response. The results show the existence of functional conservation of OXR proteins in dicot and monocot plants and indicate that HaOXR2 could be useful to improve plant performance under conditions that increase oxidative stress.
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Affiliation(s)
- Pablo Torti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina.
| | - Jesica Raineri
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina.
| | - Regina Mencia
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina.
| | - Mabel Campi
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina.
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina.
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina.
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22
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Liu Y, Teng C, Xia R, Meyers BC. PhasiRNAs in Plants: Their Biogenesis, Genic Sources, and Roles in Stress Responses, Development, and Reproduction. Plant Cell 2020; 32:3059-3080. [PMID: 32817252 PMCID: PMC7534485 DOI: 10.1105/tpc.20.00335] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 05/08/2023]
Abstract
Phased secondary small interfering RNAs (phasiRNAs) constitute a major category of small RNAs in plants, but most of their functions are still poorly defined. Some phasiRNAs, known as trans-acting siRNAs, are known to target complementary mRNAs for degradation and to function in development. However, the targets or biological roles of other phasiRNAs remain speculative. New insights into phasiRNA biogenesis, their conservation, and their variation across the flowering plants continue to emerge due to the increased availability of plant genomic sequences, deeper and more sophisticated sequencing approaches, and improvements in computational biology and biochemical/molecular/genetic analyses. In this review, we survey recent progress in phasiRNA biology, with a particular focus on two classes associated with male reproduction: 21-nucleotide (accumulate early in anther ontogeny) and 24-nucloetide (produced in somatic cells during meiosis) phasiRNAs. We describe phasiRNA biogenesis, function, and evolution and define the unanswered questions that represent topics for future research.
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Affiliation(s)
- Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China
- College of Horticulture, South China Agricultural University, Guangzhou 510640, Guangdong, China
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China
- College of Horticulture, South China Agricultural University, Guangzhou 510640, Guangdong, China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, Missouri 65211
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23
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Tang C, Han R, Zhou Z, Yang Y, Zhu M, Xu T, Wang A, Li Z, Dong T. Identification of candidate miRNAs related in storage root development of sweet potato by high throughput sequencing. J Plant Physiol 2020; 251:153224. [PMID: 32634748 DOI: 10.1016/j.jplph.2020.153224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 05/16/2023]
Abstract
Sweet potato (Ipomoea batatas L.) is a food consumed worldwide, an industrial raw material and new energy crop. The storage root is the most economical part of the crop. However, the mechanism of storage root initiation and development is still unclear. In this study, conserved and novel miRNAs during storage root development were identified by high-throughput sequencing technology by constructing small RNA libraries from sweet potato fibrous roots (F) and storage roots at four different developmental stages (storage roots with different diameters: 1 cm, D1; 3 cm, D3; 5 cm, D5 and 10 cm, D10). A total of 61 known miRNAs and 471 novel miRNAs were identified. In addition, 145 differentially expressed miRNAs were identified in the F library compared with the four storage root libraries, with 30 known miRNAs and 115 novel miRNAs. Moreover, the targets of the differentially expressed miRNAs were predicted and their network was further investigated by GO analysis using our previous transcriptome data. The GO analysis revealed that antioxidant activity and binding process were the most enriched terms of the target genes. The secondary structure and expression of six candidate miRNAs including three conserved miRNAs and three novel miRNAs were investigated and their predicted targets were validated by qRT-PCR. The results showed that the expression levels of the miRNAs were all consistent with the sequencing data. Most of the miRNAs and their corresponding targets had obvious negative correlations. This study contributed to elucidating the potential miRNA mediated regulatory mechanism of storage root development in sweet potato. The specific differentially expressed miRNAs in sweet potato storage roots can be used to breed high-yield sweet potatoes and other tuberous root crops.
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Affiliation(s)
- Cheng Tang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Rongpeng Han
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Zhengkun Zhou
- College of Health Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Yiyu Yang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Mingku Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Aimin Wang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
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24
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Zhao T, Tao X, Li M, Gao M, Chen J, Zhou N, Mei G, Fang L, Ding L, Zhou B, Zhang T, Guan X. Role of phasiRNAs from two distinct phasing frames of GhMYB2 loci in cis- gene regulation in the cotton genome. BMC Plant Biol 2020; 20:219. [PMID: 32414380 PMCID: PMC7227086 DOI: 10.1186/s12870-020-02430-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/05/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Phased small interfering RNA (phasiRNA) is primarily derived from the 22-nt miRNA targeting loci. GhMYB2, a gene with potential roles in cotton fiber cell fate determination, is a target gene of miR828 and miR858 in the generation of phasiRNAs. RESULTS In the presented work, through the evaluation of phasing scores and phasiRNA distribution pattern, we found that phasiRNAs from GhMYB2 were derived from the 3' cleavage fragments of 22-nt miR828 and 21-nt miR858 respectively. These two miRNA targeting sites initiated two phasing frames on transcripts of one locus. By means of RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE), we further demonstrated that phasiRNAs derived from the two phasing frames played a role in cis-regulation of GhMYB2. The phasiRNAs derived from GhMYB2 were expressed in the somatic tissues, especially in anther and hypocotyl. We further employed our previous small RNA sequencing data as well as the degradome data of cotton fiber bearing ovules, anthers, hypocotyls and embryogenic calli tissues published in public databases, to validate the expression, phasing pattern and functions of phasiRNAs. CONCLUSIONS The presenting research provide insights of the molecular mechanism of phasiRNAs in regulation of GhMYB2 loci.
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Affiliation(s)
- Ting Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang China
| | - Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang China
| | - Menglin Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Mengtao Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Jiedan Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang China
| | - Na Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Gaofu Mei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Lei Fang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang China
| | - Linyun Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Tianzhen Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Xueying Guan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu China
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25
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Weng ST, Kuo YW, King YC, Lin HH, Tu PY, Tung KS, Jeng ST. Regulation of micoRNA2111 and its target IbFBK in sweet potato on wounding. Plant Sci 2020; 292:110391. [PMID: 32005396 DOI: 10.1016/j.plantsci.2019.110391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/25/2019] [Accepted: 12/24/2019] [Indexed: 05/14/2023]
Abstract
Plant microRNAs (miRNAs) are non-coding RNAs, which are composed of 20-24 nucleotides. MiRNAs play important roles in plant growth and responses to biotic and abiotic stresses. Wounding is one of the most serious stresses for plants; however, the regulation of miRNAs in plants upon wounding is not well studied. In this study, miR2111, a wound-repressed miRNA, identified previously in sweet potato (Ipomoea batatas cv Tainung 57) by small RNA deep sequencing was chosen for further analysis. Based on sweet potato transcriptome database, F-box/kelch repeat protein (IbFBK), a target gene of miR2111, was identified. IbFBK is a wound-inducible gene, and the miR2111-induced cleavage site in IbFBK mRNA is between the 10th and 11th nucleotides of miR2111. IbFBK is a component of the E3 ligase SCF (SKP1-Cullin-F-box) complex participating in protein ubiquitination and degradation. The results of yeast two-hybrid and bimolecular fluorescence complementation assays demonstrate that IbFBK was conjugated with IbSKP1 through the F-box domain in IbFBK N-terminus to form SCF complex, and interacted with IbCNR8 through the kelch-repeat domain in IbFBK C-terminus. The interaction of IbFBK and IbCNR8 may lead to the ubiquitination and degradation of IbCNR8. In conclusion, the suppression of miR2111 resulted in the increase of IbFBK, and may regulate protein degradation of IbCNR8 in sweet potato responding to wounding.
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Affiliation(s)
- Shiau-Ting Weng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Yun-Wei Kuo
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan; Academy of Agricultural Sciences, Sanming 365000, Fujian, China.
| | - Yu-Chi King
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Hsin-Hung Lin
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei 11114, Taiwan.
| | - Pin-Yang Tu
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Kuei-Shu Tung
- Institute of Molecular and Cellular Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
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26
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Wani SH, Kumar V, Khare T, Tripathi P, Shah T, Ramakrishna C, Aglawe S, Mangrauthia SK. miRNA applications for engineering abiotic stress tolerance in plants. Biologia (Bratisl) 2020; 75:1063-81. [DOI: 10.2478/s11756-019-00397-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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27
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Zhang J, Tuskan GA, Tschaplinski TJ, Muchero W, Chen JG. Transcriptional and Post-transcriptional Regulation of Lignin Biosynthesis Pathway Genes in Populus. Front Plant Sci 2020; 11:652. [PMID: 32528504 PMCID: PMC7262965 DOI: 10.3389/fpls.2020.00652] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/28/2020] [Indexed: 05/04/2023]
Abstract
Lignin is a heterogeneous polymer of aromatic subunits derived from phenylalanine. It is polymerized in intimate proximity to the polysaccharide components in plant cell walls and provides additional rigidity and compressive strength for plants. Understanding the regulatory mechanisms of lignin biosynthesis is important for genetic modification of the plant cell wall for agricultural and industrial applications. Over the past 10 years the transcriptional regulatory model of lignin biosynthesis has been established in plants. However, the role of post-transcriptional regulation is still largely unknown. Increasing evidence suggests that lignin biosynthesis pathway genes are also regulated by alternative splicing, microRNA, and long non-coding RNA. In this review, we briefly summarize recent progress on the transcriptional regulation, then we focus on reviewing progress on the post-transcriptional regulation of lignin biosynthesis pathway genes in the woody model plant Populus.
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Affiliation(s)
- Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- *Correspondence: Jin Zhang,
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Jin-Gui Chen,
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28
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Abstract
To acquire the eggplant transcriptome under high temperature stress, 18 cDNA libraries were constructed and sequenced. A total of 136.31 Gb of clean data was obtained, and 88.86%–92.35% of the clean reads were mapped to the eggplant reference genome. Under high temperature, the number of down-regulated genes was more than that of up-regulated genes and there were more differentially expressed genes on the 10th day after flowering than on the 15th and 20th days after flowering. On the 10th day after flowering, the key genes CHI, 3GT, F3′5′H, DFR2, ANS, and F3H in anthocyanin synthetic pathway and most ERF, WRKY, bHLH, and MYB transcription factors were all down-regulated. High temperature significantly decreased the total anthocyanin content in peels. The results showed that at the early stage of peel coloring, high temperature inhibited the expressions of key genes in anthocyanin biosynthetic pathways through the regulation of transcription factors, leading to a significant decrease in total anthocyanin content, which might reduce the peel color in eggplant.
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Affiliation(s)
- Ling Ling Lv
- South Subtropical Crops Research Institute, CATAS, Zhanjiang, Guangdong 524091, China; Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Zhanjiang, Guangdong 524091, China
| | | | - Wei Li
- South Subtropical Crops Research Institute, CATAS, Zhanjiang, Guangdong 524091, China; Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Zhanjiang, Guangdong 524091, China
| | - Ke Li
- South Subtropical Crops Research Institute, CATAS, Zhanjiang, Guangdong 524091, China; Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Zhanjiang, Guangdong 524091, China
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29
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Colombatti F, Mencia R, Garcia L, Mansilla N, Alemano S, Andrade AM, Gonzalez DH, Welchen E. The mitochondrial oxidation resistance protein AtOXR2 increases plant biomass and tolerance to oxidative stress. J Exp Bot 2019; 70:3177-3195. [PMID: 30945737 DOI: 10.1093/jxb/erz147] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
This study demonstrates the existence of the oxidation resistance (OXR) protein family in plants. There are six OXR members in Arabidopsis that contain the highly conserved TLDc domain that is characteristic of this eukaryotic protein family. AtOXR2 is a mitochondrial protein able to alleviate the stress sensitivity of a yeast oxr1 mutant. It was induced by oxidative stress and its overexpression in Arabidopsis (oeOXR2) increased leaf ascorbate, photosynthesis, biomass, and seed production, as well as conferring tolerance to methyl viologen, antimycin A, and high light intensities. The oeOXR2 plants also showed higher ABA content, changes in ABA sensitivity, and modified expression of ABA- and stress-regulated genes. While the oxr2 mutants had a similar shoot phenotype to the wild-type, they exhibited increased sensitivity to stress. We propose that by influencing the levels of reactive oxygen species (ROS), AtOXR2 improves the efficiency of photosynthesis and elicits basal tolerance to environmental challenges that increase oxidative stress, allowing improved plant growth and biomass production.
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Affiliation(s)
- Francisco Colombatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Regina Mencia
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Lucila Garcia
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
| | - Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Sergio Alemano
- Laboratorio de Fisiología Vegetal, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Andrea M Andrade
- Laboratorio de Fisiología Vegetal, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
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He L, Tang R, Shi X, Wang W, Cao Q, Liu X, Wang T, Sun Y, Zhang H, Li R, Jia X. Uncovering anthocyanin biosynthesis related microRNAs and their target genes by small RNA and degradome sequencing in tuberous roots of sweetpotato. BMC Plant Biol 2019; 19:232. [PMID: 31159725 PMCID: PMC6547535 DOI: 10.1186/s12870-019-1790-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/18/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Compared with white-fleshed sweetpotato (WFSP), purple-fleshed sweetpotato (PFSP) is a desirable resource for functional food development because of the abundant anthocyanin accumulation in its tuberous roots. Some studies have shown that the expression regulation mediated by miRNA plays an important role in anthocyanin biosynthesis in plants. However, few miRNAs and their corresponding functions related to anthocyanin biosynthesis in tuberous roots of sweetpotato have been known. RESULTS In this study, small RNA (sRNA) and degradome libraries from the tuberous roots of WFSP (Xushu-18) and PFSP (Xuzishu-3) were constructed, respectively. Totally, 191 known and 33 novel miRNAs were identified by sRNA sequencing, and 180 target genes cleaved by 115 known ib-miRNAs and 5 novel ib-miRNAs were identified by degradome sequencing. Of these, 121 miRNAs were differently expressed between Xushu-18 and Xuzishu-3. Integrated analysis of sRNA, degradome sequencing, GO, KEGG and qRT-PCR revealed that 26 differentially expressed miRNAs and 36 corresponding targets were potentially involved in the anthocyanin biosynthesis. Of which, an inverse correlation between the expression of ib-miR156 and its target ibSPL in WFSP and PFSP was revealed by both qRT-PCR and sRNA sequencing. Subsequently, ib-miR156 was over-expressed in Arabidopsis. Interestingly, the ib-miR156 over-expressing plants showed suppressed abundance of SPL and a purplish phenotype. Concomitantly, upregulated expression of four anthocyanin pathway genes was detected in transgenic Arabidopsis plants. Finally, a putative ib-miRNA-target model involved in anthocyanin biosynthesis in sweetpotato was proposed. CONCLUSIONS The results represented a comprehensive expression profiling of miRNAs related to anthocyanin accumulation in sweetpotato and provided important clues for understanding the regulatory network of anthocyanin biosynthesis mediated by miRNA in tuberous crops.
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Affiliation(s)
- Liheng He
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Ruimin Tang
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Xiaowen Shi
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Wenbing Wang
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Qinghe Cao
- Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, 221131, Jiangsu, China
| | - Xiayu Liu
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Ting Wang
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Yan Sun
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China
| | - Hongmei Zhang
- Maize Research Institute, Shanxi Academy of Agricultural Sciences, Xinzhou, China
| | - Runzhi Li
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China.
| | - Xiaoyun Jia
- Shanxi Agriculture University, Taigu, 030801, Shanxi, China.
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Cheng H, Liang Q, Chen X, Zhang Y, Qiao F, Guo D. Hydrogen peroxide facilitates Arabidopsis seedling establishment by interacting with light signalling pathway in the dark. Plant Cell Environ 2019; 42:1302-1317. [PMID: 30474863 DOI: 10.1111/pce.13482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 06/09/2023]
Abstract
Light is essential for the plant establishment. Arabidopsis seedlings germinated in the dark cannot grow leaf and only have closed cotyledons. However, exogenous application of H2 O2 can induce leaves (establishment) in the dark. Comparative transcriptomic analysis revealed that light-responsive genes were activated by H2 O2 treatment. These genes are functionally correlated with photosynthesis, photorespiration, and components of photosystem, such as antenna proteins and light-harvesting chlorophyll proteins. We further found that application of H2 O2 facilitates cell cycle by accelerating G2 -M checkpoint transition in shoot apical meristem. Phytochrome-mediated light signalling pathway was also involved in the H2 O2 -facilitated establishment process. The constitutive photomorphogenesis 1 and phytochrome interacting factor 3 proteins were shown to be down-regulated by H2 O2 treatment and accordingly removed their inhibitory effects on photomorphogenesis in the dark. The crosstalk between oxidation and light signal pathways explains the mechanism that H2 O2 regulates plant dark establishment. The endogenous photorespiratory H2 O2 production was mimicked by overexpression of glycolate oxidase genes and supplement of substrate glycolate. As expected, seedling establishment was also induced by the endogenously produced H2 O2 under dark condition. These findings also suggest that photorespiratory H2 O2 production is at least partially involved in postgermination establishment.
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Affiliation(s)
- Han Cheng
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Danzhou, Hainan, China
- School of Life Science and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Qun Liang
- School of Agricultural Science, Hainan University, Haikou, Hainan, China
| | - Xiang Chen
- School of Agricultural Science, Hainan University, Haikou, Hainan, China
| | - Yuanyuan Zhang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Danzhou, Hainan, China
| | - Fei Qiao
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Science, Danzhou, Hainan, China
| | - Dianjing Guo
- School of Life Science and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
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Cesarino I. Structural features and regulation of lignin deposited upon biotic and abiotic stresses. Curr Opin Biotechnol 2019; 56:209-214. [DOI: 10.1016/j.copbio.2018.12.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/13/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022]
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Lin HH, King YC, Li YC, Lin CC, Chen YC, Lin JS, Jeng ST. The p38-like MAP kinase modulated H 2O 2 accumulation in wounding signaling pathways of sweet potato. Plant Sci 2019; 280:305-313. [PMID: 30824008 DOI: 10.1016/j.plantsci.2018.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 06/09/2023]
Abstract
In sweet potato (Ipomoea batatas cv Tainung 57), MAPK cascades are involved in the regulation of Ipomoelin (IPO) expression upon wounding. p38 MAPK plays an important role in plant's responses to various environmental stresses. However, the role of p38-like MAPK in wounding response is still unknown. In this study, the levels of phosphorylated-p38-like MAPK (pp38-like MAPK) in sweet potato were noticeably reduced after wounding. In addition, SB203580 (SB), a specific inhibitor blocking p38 MAPK phosphorylation, considerably decreased the accumulation of pp38-like MAPK. Expression of a wound-inducible gene IPO was elevated by SB. Moreover, it stimulated hydrogen peroxide (H2O2) production rather than cytosolic Ca2+ elevation in sweet potato leaves. However, NADPH oxidase (NOX) inhibitor diphenyleneiodonium could not inhibit IPO induction stimulated by SB. These results indicated a p38-like MAPK mechanism was involved in the regulation of IPO expression through NOX-independent H2O2 generation. In addition, the presence of the protein phosphatase inhibitor okadaic acid or the MEK1/ERK inhibitor PD98059 repressed the H2O2- or SB-induced IPO expression, demonstrating phosphatase(s) and MEK1/ERK functioning in the downstream of H2O2 and pp38-like MAPK in the signal transduction pathway stimulating IPO. Conclusively, wounding decreased the amount of pp38-like MAPK, stimulated H2O2 production, and then induced IPO expression.
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Affiliation(s)
- Hsin-Hung Lin
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan; Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, 11114, Taiwan
| | - Yu-Chi King
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Chi Li
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Chih-Ching Lin
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan; Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Chi Chen
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, 82444, Taiwan
| | - Jeng-Shane Lin
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan; Department of life sciences, National Chung Hsing University, Taichung, 40227, Taiwan.
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
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Wang YX, Teng RM, Wang WL, Wang Y, Shen W, Zhuang J. Identification of genes revealed differential expression profiles and lignin accumulation during leaf and stem development in tea plant (Camellia sinensis (L.) O. Kuntze). Protoplasma 2019; 256:359-370. [PMID: 30121729 DOI: 10.1007/s00709-018-1299-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/13/2018] [Indexed: 05/23/2023]
Abstract
Lignin is a complex aromatic heteropolymer that plays essential roles in mechanical support, water transport, and response to biotic and abiotic stresses. The tea plant is a leaf-type beverage crop, which serves as a resource for non-alcoholic beverage tea. The content and distribution of lignin in tea plant leaves seriously affect the quality of tea. However, the biosynthetic pathways of lignin remain to be characterized in the tea plant. In the present study, lignin accumulation was investigated in tea plant leaves and stems at three developmental stages. The lignin content continuously increased during leaf and stem development in both tea plant cultivars 'Fudingdabai' and 'Suchazao.' The lignin distribution and anatomical characteristics of the tea plant leaves coincided with lignin accumulation and showed that lignin is mainly distributed in the epidermis, xylem, and vascular bundle sheath. 'Suchazao' exhibits a low lignin content and lacks a vascular bundle sheath. Twelve genes encoding the enzymes involved in the lignin biosynthesis of tea plant were identified and included CsPAL, CsC4H, Cs4CL, CsHCT, CsC3H, CsCCoAOMT, CsCCR, CsCAD, CsF5H, CsCOMT, CsPER, and CsLAC. The expression profiling of lignin biosynthesis-related genes and analysis of lignin accumulation may help elaborate the regulatory mechanisms of lignin biosynthesis in tea plant.
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Affiliation(s)
- Yong-Xin Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rui-Min Teng
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wen-Li Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei Shen
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Kuo YW, Lin JS, Li YC, Jhu MY, King YC, Jeng ST. MicroR408 regulates defense response upon wounding in sweet potato. J Exp Bot 2019; 70:469-483. [PMID: 30403812 PMCID: PMC6322576 DOI: 10.1093/jxb/ery381] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/02/2018] [Indexed: 05/08/2023]
Abstract
MiRNAs play diverse roles in plant development and defense responses by binding to their mRNA targets based on sequence complementarity. Here, we investigated a wound-related miR408 and its target genes in sweet potato (Ipomoea batatas) by small RNA deep sequencing and transcriptome analysis. The expression patterns of miR408 and the miR408 precursor were significantly repressed by wounding and jasmonate (JA). In contrast, expression of the putative target genes IbKCS (3-ketoacyl-CoA synthase 4), IbPCL (plantacyanin), and IbGAUT (galacturonosyltransferase 7-like) of miR408 was increased following wounding, whereas only IbKCS was increased after JA treatment. Target cleavage site mapping and Agrobacterium-mediated transient assay demonstrated that IbKCS, IbPCL, and IbGAUT were the targets of miR408. The expression of miR408 target genes was repressed in transgenic sweet potatoes overexpressing miR408. These data indicated a relationship between miR408 and its target genes. Notably, miR408-overexpressing plants showed a semi-dwarf phenotype and attenuated resistance to insect feeding, while transgenic plants overexpressing IbKCS exhibited more insect resistance than plants overexpressing only the empty vector. Collectively, sweet potato reduces the abundance of miR408 upon wounding to elevate the expression of IbKCS, IbPCL, and IbGAUT. The expression of IbKCS enhances the defense system against herbivore wounding.
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Affiliation(s)
- Yun-Wei Kuo
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Chi Li
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Min-Yao Jhu
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Chi King
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
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Cardoso TCDS, Alves TC, Caneschi CM, Santana DDRG, Fernandes-Brum CN, Reis GLD, Daude MM, Ribeiro THC, Gómez MMD, Lima AA, Gomes LAA, Gomes MDS, Gandolfi PE, Amaral LRD, Chalfun-Júnior A, Maluf WR, de Souza Gomes M. New insights into tomato microRNAs. Sci Rep 2018; 8:16069. [PMID: 30375421 PMCID: PMC6207730 DOI: 10.1038/s41598-018-34202-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/12/2018] [Indexed: 12/21/2022] Open
Abstract
Cultivated tomato, Solanum lycopersicum, is one of the most common fruits in the global food industry. Together with the wild tomato Solanum pennellii, it is widely used for developing better cultivars. MicroRNAs affect mRNA regulation, inhibiting its translation and/or promoting its degradation. Important proteins involved in these processes are ARGONAUTE and DICER. This study aimed to identify and characterize the genes involved in the miRNA processing pathway, miRNA molecules and target genes in both species. We validated the presence of pathway genes and miRNA in different NGS libraries and 6 miRNA families using quantitative RT-PCR. We identified 71 putative proteins in S. lycopersicum and 108 in S. pennellii likely involved in small RNAs processing. Of these, 29 and 32 participate in miRNA processing pathways, respectively. We identified 343 mature miRNAs, 226 pre-miRNAs in 87 families, including 192 miRNAs, which were not previously identified, belonging to 38 new families in S. lycopersicum. In S. pennellii, we found 388 mature miRNAs and 234 pre-miRNAs contained in 85 families. All miRNAs found in S. pennellii were unpublished, being identified for the first time in our study. Furthermore, we identified 2471 and 3462 different miRNA target in S. lycopersicum and S. pennellii, respectively.
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Affiliation(s)
- Thaís Cunha de Sousa Cardoso
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Tamires Caixeta Alves
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Carolina Milagres Caneschi
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Douglas Dos Reis Gomes Santana
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | | | - Gabriel Lasmar Dos Reis
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, 37 - 37200-000, Brazil
| | - Matheus Martins Daude
- Laboratory of Molecular Analysis, Federal University of Tocantins (UFT), Gurupi, 77402-970, Brazil
| | | | - Miguel Maurício Díaz Gómez
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - André Almeida Lima
- Laboratory of Plant Molecular Physiology, Federal University of Lavras (UFLA), Lavras, 3037 - 37200-000, Brazil
| | | | - Marcos de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Peterson Elizandro Gandolfi
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Laurence Rodrigues do Amaral
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Antonio Chalfun-Júnior
- Laboratory of Plant Molecular Physiology, Federal University of Lavras (UFLA), Lavras, 3037 - 37200-000, Brazil
| | - Wilson Roberto Maluf
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, 37 - 37200-000, Brazil
| | - Matheus de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil.
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Saminathan T, Alvarado A, Lopez C, Shinde S, Gajanayake B, Abburi VL, Vajja VG, Jagadeeswaran G, Raja Reddy K, Nimmakayala P, Reddy UK. Elevated carbon dioxide and drought modulate physiology and storage-root development in sweet potato by regulating microRNAs. Funct Integr Genomics 2019; 19:171-90. [PMID: 30244303 DOI: 10.1007/s10142-018-0635-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 09/04/2018] [Accepted: 09/07/2018] [Indexed: 02/06/2023]
Abstract
Elevated CO2 along with drought is a serious global threat to crop productivity. Therefore, understanding the molecular mechanisms plants use to protect these stresses is the key for plant growth and development. In this study, we mimicked natural stress conditions under a controlled Soil-Plant-Atmosphere-Research (SPAR) system and provided the evidence for how miRNAs regulate target genes under elevated CO2 and drought conditions. Significant physiological and biomass data supported the effective utilization of source-sink (leaf to root) under elevated CO2. Additionally, elevated CO2 partially rescued the effect of drought on total biomass. We identified both known and novel miRNAs differentially expressed during drought, CO2, and combined stress, along with putative targets. A total of 32 conserved miRNAs belonged to 23 miRNA families, and 25 novel miRNAs were identified by deep sequencing. Using the existing sweet potato genome database and stringent analyses, a total of 42 and 22 potential target genes were predicted for the conserved and novel miRNAs, respectively. These target genes are involved in drought response, hormone signaling, photosynthesis, carbon fixation, sucrose and starch metabolism, etc. Gene ontology and KEGG ontology functional enrichment revealed that these miRNAs might target transcription factors (MYB, TCP, NAC), hormone signaling regulators (ARF, AP2/ERF), cold and drought factors (corA), carbon metabolism (ATP synthase, fructose-1,6-bisphosphate), and photosynthesis (photosystem I and II complex units). Our study is the first report identifying targets of miRNAs under elevated CO2 levels and could support the molecular mechanisms under elevated CO2 in sweet potato and other crops in the future.
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Lin JS, Kuo CC, Yang IC, Tsai WA, Shen YH, Lin CC, Liang YC, Li YC, Kuo YW, King YC, Lai HM, Jeng ST. MicroRNA160 Modulates Plant Development and Heat Shock Protein Gene Expression to Mediate Heat Tolerance in Arabidopsis. Front Plant Sci 2018; 9:68. [PMID: 29449855 PMCID: PMC5799662 DOI: 10.3389/fpls.2018.00068] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/12/2018] [Indexed: 05/21/2023]
Abstract
Global warming is causing a negative impact on plant growth and adversely impacts on crop yield. MicroRNAs (miRNAs) are critical in regulating the expression of genes involved in plant development as well as defense responses. The effects of miRNAs on heat-stressed Arabidopsis warrants further investigation. Heat stress increased the expression of miR160 and its precursors but considerably reduced that of its targets, ARF10, ARF16, and ARF17. To study the roles of miR160 during heat stress, transgenic Arabidopsis plants overexpressing miR160 precursor a (160OE) and artificial miR160 (MIM160), which mimics an inhibitor of miR160, were created. T-DNA insertion mutants of miR160 targets were also used to examine their tolerances to heat stress. Results presented that overexpressing miR160 improved seed germination and seedling survival under heat stress. The lengths of hypocotyl elongation and rachis were also longer in 160OE than the wild-type (WT) plants under heat stress. Interestingly, MIM160 plants showed worse adaption to heat. In addition, arf10, arf16, and arf17 mutants presented similar phenotypes to 160OE under heat stress to advance abilities of thermotolerance. Moreover, transcriptome and qRT-PCR analyses revealed that HSP17.6A, HSP17.6II, HSP21, and HSP70B expression levels were regulated by heat in 160OE, MIM160, arf10, arf16, and arf17 plants. Hence, miR160 altered the expression of the heat shock proteins and plant development to allow plants to survive heat stress.
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Affiliation(s)
- Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chia-Chia Kuo
- Department of Life Science, Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - I-Chu Yang
- Department of Life Science, Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Wei-An Tsai
- Department of Crop Environment, Hualien District Agricultural Research and Extension Station, Council of Agriculture, Hualien, Taiwan
| | - Yu-Hsing Shen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Ching Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Chen Liang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Chi Li
- Department of Life Science, Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Yun-Wei Kuo
- Department of Life Science, Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Yu-Chi King
- Department of Life Science, Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Hsi-Mei Lai
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Shih-Tong Jeng
- Department of Life Science, Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
- *Correspondence: Shih-Tong Jeng
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Świeżawska B, Jaworski K, Duszyn M, Pawełek A, Szmidt-Jaworska A. The Hippeastrum hybridum PepR1 gene (HpPepR1) encodes a functional guanylyl cyclase and is involved in early response to fungal infection. J Plant Physiol 2017; 216:100-107. [PMID: 28609666 DOI: 10.1016/j.jplph.2017.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/21/2017] [Accepted: 05/15/2017] [Indexed: 06/07/2023]
Abstract
It is generally known that cyclic GMP widespread in prokaryotic and eukaryotic cells, is involved in essential cellular processes and stress signal transduction. However, in contrast to animals the knowledge about plant guanylyl cyclases (GCs) which catalyze the formation of cGMP from GTP is still quite obscure. Recent studies of plant GCs are focused on identification and functional analysis of a new family of membrane proteins called "moonlighting kinases with GC activity" with guanylyl cyclase catalytic center encapsulated within intracellular kinase domain. Here we report identification and characterization of plasma membrane receptor of peptide signaling molecules - HpPepR1 in Hippeastrum hybridum. Both bioinformatic analysis of amimo acid sequence and in vitro studies revealed that the protein can act as guanylyl cyclase. The predicted amino acid sequence contains highly conserved 14 aa-long search motif in the catalytic center of GCs from lower and higher eukaryotes. Here, we provide experimental evidence to show that the intracellular domain of HpPepR1 can generate cGMP in vitro. Moreover, it was shown that the accumulation of HpPepR1 transcript was sharply increased after Peyronellaea curtisii (=Phoma narcissi) fungal infection, whereas mechanical wounding has no influence on expression profile of studied gene. These results may indicate the participation of cGMP-dependent pathway in rapid, alarm plant reactions induced by pathogen infection.
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Affiliation(s)
- Brygida Świeżawska
- Nicolaus Copernicus University, Chair of Plant Physiology and Biotechnology, Lwowska St. 1, PL 87-100, Torun, Poland.
| | - Krzysztof Jaworski
- Nicolaus Copernicus University, Chair of Plant Physiology and Biotechnology, Lwowska St. 1, PL 87-100, Torun, Poland.
| | - Maria Duszyn
- Nicolaus Copernicus University, Chair of Plant Physiology and Biotechnology, Lwowska St. 1, PL 87-100, Torun, Poland.
| | - Agnieszka Pawełek
- Nicolaus Copernicus University, Chair of Plant Physiology and Biotechnology, Lwowska St. 1, PL 87-100, Torun, Poland.
| | - Adriana Szmidt-Jaworska
- Nicolaus Copernicus University, Chair of Plant Physiology and Biotechnology, Lwowska St. 1, PL 87-100, Torun, Poland.
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Houmani H, Rodríguez-Ruiz M, Palma JM, Corpas FJ. Mechanical wounding promotes local and long distance response in the halophyte Cakile maritima through the involvement of the ROS and RNS metabolism. Nitric Oxide 2017; 74:93-101. [PMID: 28655650 DOI: 10.1016/j.niox.2017.06.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 11/27/2022]
Abstract
Mechanical wounding in plants, which are capable of generating defense responses possibly associated with nitro-oxidative stress, can be caused by (a)biotic factors such as rain, wind, herbivores and insects. Sea rocket (Cakile maritima L.), a halophyte plant belonging to the mustard family Brassicaceae, is commonly found on sandy coasts throughout Europe. Using 7-day-old Cakile maritima L. seedlings, mechanical wounding was induced in hypocotyls by pinching with a striped-tip forceps; after 3 h, several biochemical parameters were analyzed in both the damaged and unwounded organs (green cotyledons and roots). We thus determined NO production, H2O2 content, lipid oxidation as well as protein nitration patterns; we also identified several antioxidant enzymes including catalase, superoxide dismutase (SOD) isozymes, peroxidases, ascorbate-glutathione cycle enzymes and NADP-dehydrogenases. All these parameters were differentially modulated in the damaged (hypocotyls) and unwounded organs, which clearly indicated an induction of CuZnSOD V in the three organs, an increase in protein nitration in green cotyledons and an induction of NADP-isocitrate dehydrogenase activity in roots. On the whole, our results indicate that the wounding of hypocotyls, which showed an active ROS metabolism and oxidative stress, causes long-distance signals that also trigger responses in unwounded tissues with a more active RNS metabolism. These data therefore confirm the existence of local and long-distance responses which counteract negative effects and provide appropriate responses, enabling the wounded seedlings to survive.
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Affiliation(s)
- Hayet Houmani
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Marta Rodríguez-Ruiz
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - José M Palma
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Francisco J Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain.
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Djami-Tchatchou AT, Sanan-Mishra N, Ntushelo K, Dubery IA. Functional Roles of microRNAs in Agronomically Important Plants-Potential as Targets for Crop Improvement and Protection. Front Plant Sci 2017; 8:378. [PMID: 28382044 PMCID: PMC5360763 DOI: 10.3389/fpls.2017.00378] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses toward environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic-or abiotic origin.
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Affiliation(s)
- Arnaud T. Djami-Tchatchou
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg (Auckland Park Kingsway Campus)Johannesburg, South Africa
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Villalobos-Escobedo JM, Herrera-Estrella A, Carreras-Villaseñor N. The interaction of fungi with the environment orchestrated by RNAi. Mycologia 2017; 108:556-71. [DOI: 10.3852/15-246] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/07/2016] [Indexed: 11/10/2022]
Affiliation(s)
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad. Cinvestav Campus Guanajuato. Km 9.6 Libramiento Norte, carretera Irapuato-León. 36821 Irapuato, Guanajuato, Mexico
| | - Nohemí Carreras-Villaseñor
- StelaGenomics México, S de RL de CV, Av. Camino Real de Guanajuato S/N, 36821 Irapuato, Guanajuato, Mexico
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Abstract
Trans-acting small interfering RNAs (ta-siRNAs) are a class of endogenous small RNA, associated with posttranscriptional gene silencing. Their biogenesis requires an initial microRNA (miRNA)-mediated cleavage of precursor RNA. Around 20 different ta-siRNA-producing loci (TASs), whose sequences are conserved, are reported in plants. In tomato, two TAS gene families have been identified, which are found to target auxin response factor gene and bacterial spot disease resistance protein Bs4 gene. Using high-throughput computational and experimental approach, we identified a new locus-producing ta-siRNA in tomato. We have also identified the putative miRNA regulating the production of ta-siRNA from this locus. The ta-siRNAs generated from TAS4 were up-regulated upon infection with a DNA virus. The potential targets of ta-siRNAs were predicted to be variety of proteins including MYB transcription factors and cell cycle regulators for some of the ta-siRNAs produced.
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Affiliation(s)
- Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
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Wang GL, Huang Y, Zhang XY, Xu ZS, Wang F, Xiong AS. Transcriptome-based identification of genes revealed differential expression profiles and lignin accumulation during root development in cultivated and wild carrots. Plant Cell Rep 2016; 35:1743-55. [PMID: 27160835 DOI: 10.1007/s00299-016-1992-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/28/2016] [Indexed: 05/09/2023]
Abstract
Carrot root development associates lignin deposition and regulation. Carrot is consumed worldwide and is a good source of nutrients. However, excess lignin deposition may reduce the taste and quality of carrot root. Molecular mechanisms underlying lignin accumulation in carrot are still lacking. To address this problem, we collected taproots of wild and cultivated carrots at five developmental stages and analyzed the lignin content and characterized the lignin distribution using histochemical staining and autofluorescence microscopy. Genes involved in lignin biosynthesis were identified, and their expression profiles were determined. Results showed that lignin was mostly deposited in xylem vessels of carrot root. In addition, lignin content continuously decreased during root development, which was achieved possibly by reducing the expression of the genes involved in lignin biosynthesis. Carrot root may also prevent cell lignification to meet the demands of taproot growth. Our results will serve as reference for lignin biosynthesis in carrot and may also assist biologists to improve carrot quality.
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Affiliation(s)
- Guang-Long Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin-Yue Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Li YC, Wan WL, Lin JS, Kuo YW, King YC, Chen YC, Jeng ST. Signal transduction and regulation of IbpreproHypSys in sweet potato. Plant Cell Environ 2016; 39:1576-87. [PMID: 26924170 DOI: 10.1111/pce.12729] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 02/04/2016] [Accepted: 02/09/2016] [Indexed: 05/28/2023]
Abstract
Hydroxyproline-rich glycopeptides (HypSys) are small signalling peptides containing 18-20 amino acids. The expression of IbpreproHypSys, encoding the precursor of IbHypSys, was induced in sweet potato (Ipomoea batatas cv. Tainung 57) through wounding and IbHypSys treatments by using jasmonate and H2 O2 . Transgenic sweet potatoes overexpressing (OE) and silencing [RNA interference (RNAi)] IbpreproHypSys were created. The expression of the wound-inducible gene for ipomoelin (IPO) in the local and systemic leaves of OE plants was stronger than the expression in wild-type (WT) and RNAi plants after wounding. Furthermore, grafting experiments indicated that IPO expression was considerably higher in WT stocks receiving wounding signals from OE than from RNAi scions. However, wounding WT scions highly induced IPO expression in OE stocks. These results indicated that IbpreproHypSys expression contributed towards sending and receiving the systemic signals that induced IPO expression. Analysing the genes involved in the phenylpropanoid pathway demonstrated that lignin biosynthesis was activated after synthetic IbHypSys treatment. IbpreproHypSys expression in sweet potato suppressed Spodoptera litura growth. In conclusion, wounding induced the expression of IbpreproHypSys, whose protein product was processed into IbHypSys. IbHypSys stimulated IbpreproHypSys and IPO expression and enhanced lignin biosynthesis, thus protecting plants from insects.
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Affiliation(s)
- Yu-Chi Li
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Wei-Lin Wan
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
- Department of Plant Biochemistry, Center for Plant Molecular Biology, University of Tuebingen, Tuebingen, 72076, Germany
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Yun-Wei Kuo
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Chi King
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Chi Chen
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, 82444, Taiwan
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
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Gaupels F, Furch ACU, Zimmermann MR, Chen F, Kaever V, Buhtz A, Kehr J, Sarioglu H, Kogel KH, Durner J. Systemic Induction of NO-, Redox-, and cGMP Signaling in the Pumpkin Extrafascicular Phloem upon Local Leaf Wounding. Front Plant Sci 2016; 7:154. [PMID: 26904092 PMCID: PMC4751408 DOI: 10.3389/fpls.2016.00154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 01/29/2016] [Indexed: 05/29/2023]
Abstract
Cucurbits developed the unique extrafascicular phloem (EFP) as a defensive structure against herbivorous animals. Mechanical leaf injury was previously shown to induce a systemic wound response in the EFP of pumpkin (Cucurbita maxima). Here, we demonstrate that the phloem antioxidant system and protein modifications by NO are strongly regulated during this process. Activities of the central antioxidant enzymes dehydroascorbate reductase, glutathione reductase and ascorbate reductase were rapidly down-regulated at 30 min with a second minimum at 24 h after wounding. As a consequence levels of total ascorbate and glutathione also decreased with similar bi-phasic kinetics. These results hint toward a wound-induced shift in the redox status of the EFP. Nitric oxide (NO) is another important player in stress-induced redox signaling in plants. Therefore, we analyzed NO-dependent protein modifications in the EFP. Six to forty eight hours after leaf damage total S-nitrosothiol content and protein S-nitrosylation were clearly reduced, which was contrasted by a pronounced increase in protein tyrosine nitration. Collectively, these findings suggest that NO-dependent S-nitrosylation turned into peroxynitrite-mediated protein nitration upon a stress-induced redox shift probably involving the accumulation of reactive oxygen species within the EFP. Using the biotin switch assay and anti-nitrotyrosine antibodies we identified 9 candidate S-nitrosylated and 6 candidate tyrosine-nitrated phloem proteins. The wound-responsive Phloem Protein 16-1 (PP16-1) and Cyclophilin 18 (CYP18) as well as the 26.5 kD isoform of Phloem Protein 2 (PP2) were amenable to both NO modifications and could represent important redox-sensors within the cucurbit EFP. We also found that leaf injury triggered the systemic accumulation of cyclic guanosine monophosphate (cGMP) in the EFP and discuss the possible function of this second messenger in systemic NO and redox signaling within the EFP.
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Affiliation(s)
- Frank Gaupels
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherberg, Germany
| | - Alexandra C. U. Furch
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-UniversityJena, Germany
| | - Matthias R. Zimmermann
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-UniversityJena, Germany
| | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical SchoolHannover, Germany
| | - Anja Buhtz
- Department Lothar Willmitzer, Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Julia Kehr
- Biocenter Klein Flottbek, University HamburgHamburg, Germany
| | - Hakan Sarioglu
- Department of Protein Science, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherberg, Germany
| | - Karl-Heinz Kogel
- Research Center for BioSystems, Land Use and Nutrition, Institute of Phytopathology, Justus Liebig University GiessenGiessen, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherberg, Germany
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Guan X, Pang M, Nah G, Shi X, Ye W, Stelly DM, Chen ZJ. miR828 and miR858 regulate homoeologous MYB2 gene functions in Arabidopsis trichome and cotton fibre development. Nat Commun 2015; 5:3050. [PMID: 24430011 DOI: 10.1038/ncomms4050] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 12/03/2013] [Indexed: 01/21/2023] Open
Abstract
Although polyploidy is common in plants and some animals, mechanisms for functional divergence between homoeologous genes are poorly understood. MYB2 gene promotes cotton fibre development and is functionally homologous to Arabidopsis GLABROUS1 (GL1) in trichome formation. The most widely cultivated cotton is an allotetraploid (Gossypium hirsutum, AADD) that contains GhMYB2A and GhMYB2D homoeologs. Here we show that GhMYB2D mRNA accumulates more than GhMYB2A during fibre initiation and is targeted by miR828 and miR858, generating trans-acting siRNAs (ta-siRNAs) in the TAS4 family. Overexpressing GhMYB2A but not GhMYB2D complements the gl1 phenotype. Mutating the miR828-binding site or replacing its downstream sequence in GhMYB2D abolishes ta-siRNA production and restores trichome development in gl1 mutants. Moreover, disrupting Dicer-like protein 4 or RDR6, the biogenesis genes for ta-siRNAs, in the gl1 GhMYB2D overexpressors restores trichome development. These data support a unique role for microRNAs in functional divergence between target homoeologous genes that are important for evolution and selection of morphological traits.
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Affiliation(s)
- Xueying Guan
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Mingxiong Pang
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Gyoungju Nah
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Xiaoli Shi
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Z Jeffrey Chen
- 1] Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712, USA [2] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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Zhang B. MicroRNA: a new target for improving plant tolerance to abiotic stress. J Exp Bot 2015; 66:1749-61. [PMID: 25697792 PMCID: PMC4669559 DOI: 10.1093/jxb/erv013] [Citation(s) in RCA: 283] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 12/14/2014] [Accepted: 12/17/2014] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are an extensive class of endogenous, small RNA molecules that sit at the heart of regulating gene expression in multiple developmental and signalling pathways. Recent studies have shown that abiotic stresses induce aberrant expression of many miRNAs, thus suggesting that miRNAs may be a new target for genetically improving plant tolerance to certain stresses. These studies have also shown that miRNAs respond to environmental stresses in a miRNA-, stress-, tissue-, and genotype-dependent manner. During abiotic stress, miRNAs function by regulating target genes within the miRNA-target gene network and by controlling signalling pathways and root development. Generally speaking, stress-induced miRNAs lead to down-regulation of negative regulators of stress tolerance whereas stress-inhibited miRNAs allow the accumulation and function of positive regulators. Currently, the majority of miRNA-based studies have focused on the identification of miRNAs that are responsive to different stress conditions and analysing their expression profile changes during these treatments. This has predominately been accomplished using deep sequencing technologies and other expression analyses, such as quantitative real-time PCR. In the future, more function and expression studies will be necessary in order to elucidate the common miRNA-mediated regulatory mechanisms that underlie tolerance to different abiotic stresses. The use of artificial miRNAs, as well as overexpression and knockout/down of both miRNAs and their targets, will be the best techniques for determining the specific roles of individual miRNAs in response to environmental stresses.
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Affiliation(s)
- Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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Feng J, Wang J, Fan P, Jia W, Nie L, Jiang P, Chen X, Lv S, Wan L, Chang S, Li S, Li Y. High-throughput deep sequencing reveals that microRNAs play important roles in salt tolerance of euhalophyte Salicornia europaea. BMC Plant Biol 2015; 15:63. [PMID: 25848810 PMCID: PMC4349674 DOI: 10.1186/s12870-015-0451-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/06/2015] [Indexed: 05/07/2023]
Abstract
BACKGROUND microRNAs (miRNAs) are implicated in plant development processes and play pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a suitable model plant to study salt adaptation mechanisms. S. europaea is also a vegetable, forage, and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. Despite its importance, no miRNA has been identified from S. europaea thus far. RESULTS Deep sequencing was performed to investigate small RNA transcriptome of S. europaea. Two hundred and ten conserved miRNAs comprising 51 families and 31 novel miRNAs (including seven miRNA star sequences) belonging to 30 families were identified. About half (13 out of 31) of the novel miRNAs were only detected in salt-treated samples. The expression of 43 conserved and 13 novel miRNAs significantly changed in response to salinity. In addition, 53 conserved and 13 novel miRNAs were differentially expressed between the shoots and roots. Furthermore, 306 and 195 S. europaea unigenes were predicted to be targets of 41 conserved and 29 novel miRNA families, respectively. These targets encoded a wide range of proteins, and genes involved in transcription regulation constituted the largest category. Four of these genes encoding laccase, F-box family protein, SAC3/GANP family protein, and NADPH cytochrome P-450 reductase were validated using 5'-RACE. CONCLUSIONS Our results indicate that specific miRNAs are tightly regulated by salinity in the shoots and/or roots of S. europaea, which may play important roles in salt tolerance of this euhalophyte. The S. europaea salt-responsive miRNAs and miRNAs that target transcription factors, nucleotide binding site-leucine-rich repeat proteins and enzymes involved in lignin biosynthesis as well as carbon and nitrogen metabolism may be applied in genetic engineering of crops with high stress tolerance, and genetic modification of biofuel crops with high biomass and regulatable lignin biosynthesis.
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Affiliation(s)
- Juanjuan Feng
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Jinhui Wang
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Pengxiang Fan
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
- />Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson road, East Lansing, MI 48824 USA
| | - Weitao Jia
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Lingling Nie
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Ping Jiang
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Xianyang Chen
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Sulian Lv
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Lichuan Wan
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Sandra Chang
- />Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
- />Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Shizhong Li
- />Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
- />Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Yinxin Li
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
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50
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Wu J, Wang D, Liu Y, Wang L, Qiao X, Zhang S. Identification of miRNAs involved in pear fruit development and quality. BMC Genomics 2014; 15:953. [PMID: 25366381 PMCID: PMC4233070 DOI: 10.1186/1471-2164-15-953] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 10/23/2014] [Indexed: 01/16/2023] Open
Abstract
Background MicroRNAs (miRNAs) are a class of small, endogenous RNAs that take part in regulating genes through mediating gene expressions at the post-transcriptional level in plants. Previous studies have reported miRNA identification in various plants ranging from model plants to perennial fruit trees. However, the role of miRNAs in pear (Pyrus bretschneideri) fruit development is not clear. Here, we investigated the miRNA profiles of pear fruits from different time stages during development with Illumina HiSeq 2000 platform and bioinformatics analysis. Quantitative real-time PCR was used to validate the expression levels of miRNAs. Results Both conserved and species-specific miRNAs in pear have been identified in this study. Total reads, ranging from 19,030,925 to 25,576,773, were obtained from six small RNA libraries constructed for different stages of fruit development after flowering. Comparative profiling showed that an average of 90 miRNAs was expressed with significant differences between various developmental stages. KEGG pathway analysis on 2,216 target genes of 188 known miRNAs and 1,127 target genes of 184 novel miRNAs showed that miRNAs are widely involved in the regulation of fruit development. Among these, a total of eleven miRNAs putatively participate in the pathway of lignin biosynthesis, nine miRNAs were identified to take part in sugar and acid metabolism, and MiR160 was identified to regulate auxin response factor. Conclusion Comparative analysis of miRNAomes during pear fruit development is presented, and miRNAs were proved to be widely involved in the regulation of fruit development and formation of fruit quality, for example through lignin synthesis, sugar and acid metabolism, and hormone signaling. Combined with computational analysis and experimental confirmation, the research contributes valuable information for further functional research of microRNA in fruit development for pear and other species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-953) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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