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Zhang D, Zhou H, Zhou D, Wu J, Liu L, Guo Y, Wang T, Tan C, Chen D, Ge X, Yan M. The introgression of BjMYB113 from Brassica juncea leads to purple leaf trait in Brassica napus. BMC PLANT BIOLOGY 2024; 24:735. [PMID: 39090544 PMCID: PMC11295638 DOI: 10.1186/s12870-024-05418-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 07/15/2024] [Indexed: 08/04/2024]
Abstract
The purple leaves of Brassica napus are abundant in anthocyanins, which are renowned for their role in conferring distinct colors, stress tolerance, and health benefits, however the genetic basis of this trait in B. napus remains largely unelucidated. Herein, the purple leaf B. napus (PL) exhibited purple pigments in the upper epidermis and a substantial increase in anthocyanin accumulation, particularly of cyanidin, compared to green leaf B. napus (GL). The genetic control of the purple leaf trait was attributed to a semi-dominant gene, pl, which was mapped to the end of chromosome A03. However, sequencing of the fragments amplified by the markers linked to pl indicated that they were all mapped to chromosome B05 from B. juncea. Within this B05 chromosomal segment, the BjMYB113 gene-specific marker showed perfect co-segregation with the purple leaf trait in the F2 population, suggesting that the BjMYB113 introgression from B. juncea was the candidate gene for the purple leaf trait in B. napus. To further verify the function of candidate gene, CRISPR/Cas9 was performed to knock out the BjMYB113 gene in PL. The three myb113 mutants exhibited evident green leaf phenotype, absence of purple pigments in the adaxial epidermis, and a significantly reduced accumulation of anthocyanin compared to PL. Additionally, the genes involved in positive regulatory (TT8), late anthocyanin biosynthesis (DFR, ANS, UFGT), as well as transport genes (TT19) were significantly suppressed in the myb113 mutants, further confirming that BjMYB113 was response for the anthocyanin accumulation in purple leaf B. napus. This study contributes to an advanced understanding of the regulation mechanism of anthocyanin accumulation in B. napus.
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Affiliation(s)
- Dawei Zhang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Science, Hunan University of Science and Technology, Xiangtan, 411201, China
- Yuelushan Laboratory, Changsha, 410128, China
- Hunan Research Center of Heterosis Utilization in Rapeseed, Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Hongfeng Zhou
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Dinggang Zhou
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Jinfeng Wu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Science, Hunan University of Science and Technology, Xiangtan, 411201, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Lili Liu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Science, Hunan University of Science and Technology, Xiangtan, 411201, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Yiming Guo
- Yuelushan Laboratory, Changsha, 410128, China
- Hunan Research Center of Heterosis Utilization in Rapeseed, Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Tonghua Wang
- Yuelushan Laboratory, Changsha, 410128, China
- Hunan Research Center of Heterosis Utilization in Rapeseed, Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Chen Tan
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Daozong Chen
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Xianhong Ge
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingli Yan
- Yuelushan Laboratory, Changsha, 410128, China.
- Hunan Research Center of Heterosis Utilization in Rapeseed, Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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Feng Z, Admas T, Cheng B, Meng Y, Pan R, Zhang W. UGT gene family identification and functional analysis of HvUGT1 under drought stress in wild barley. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1225-1238. [PMID: 39184559 PMCID: PMC11341513 DOI: 10.1007/s12298-024-01487-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 08/27/2024]
Abstract
Drought stress poses a significant threat to global agriculture, highlighting the urgent need to elucidate the molecular mechanisms underlying plant drought tolerance. The UDP-glycosyltransferase (UGT) gene family plays crucial roles in diverse biological processes in plants. In this study, we conducted a comprehensive analysis of the UGT gene family in wild barley EC_S1, focusing on gene characteristics, subcellular localization, phylogenetic relationships, and protein structure. A total of 175 UGT gene family members were identified, exhibiting diverse patterns in protein length, molecular weight, isoelectric point, hydrophilicity, and subcellular localization. Most genes are located at chromosome ends. Phylogenetic analysis grouped the UGT genes into seven clusters, with barley-specific group E. Expression analysis across barley tissues showed upregulation in roots and senescent leaves, implying diverse roles. Under drought stress, expression patterns varied, with drought-tolerant varieties showing fewer changes than sensitive ones. Clustering analysis revealed distinct expression patterns, suggesting regulatory functions in barley's drought response. As a case, the HvUGT1 was cloned. Overexpression of HvUGT1 in Arabidopsis enhanced drought tolerance, with increased water retention, reduced cell damage, and elevated flavonoid levels. Conversely, HvUGT1 silencing in wild barley decreased drought tolerance, accompanied by reduced antioxidant enzyme activity and flavonoid content. These results highlight HvUGT1's importance in enhancing plant drought tolerance, possibly through flavonoid-mediated ROS clearance. The research provides gene resources and valuable insights for the development of drought-resistant crops through targeted genetic manipulation strategies. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01487-w.
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Affiliation(s)
- Zhenbao Feng
- Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, 434025 China
| | - Tayachew Admas
- Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, 434025 China
| | - Bingyun Cheng
- Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, 434025 China
| | - Yutong Meng
- Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, 434025 China
| | - Rui Pan
- Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, 434025 China
| | - Wenying Zhang
- Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, 434025 China
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Shang H, Li C, Cai Z, Hao Y, Cao Y, Jia W, Han L, White JC, Ma C, Xing B. Biosynthesized Selenium Nanoparticles as an Effective Tool to Combat Soil Metal Stresses in Rice ( Oryza sativa L.). ACS NANO 2024. [PMID: 38952034 DOI: 10.1021/acsnano.4c04215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Nanotechnology has demonstrated significant potential to improve agricultural production and increase crop tolerance to abiotic stress including exposure to heavy metals. The present study investigated the mechanisms by which aloe vera extract gel-biosynthesized (AVGE) selenium nanoparticles (Se NPs) alleviated cadmium (Cd)-induced toxicity to rice (Oryza sativa L.). AVGE Se NPs, chemically synthesized bare Se NPs, and NaSeO3 as an ionic control were applied to Cd-stressed rice seedlings via root exposure in both hydroponic and soil systems. Upon exposure to AVGE Se NPs at 15 mg Se/L, the fresh root biomass was significantly increased by 100.7% and 19.5% as compared to Cd control and conventional bare Se NPs. Transcriptional analyses highlighted that AVGE Se NPs activated stress signaling and defense related pathways, including glutathione metabolism, phenylpropanoid biosynthesis and plant hormone signal transduction. Specifically, exposure to AVGE Se NPs upregulated the expression of genes associated with the gibberellic acid (GA) biosynthesis by and 4.79- and 3.29-fold as compared to the Cd-alone treatment and the untreated control, respectively. Importantly, AVGE Se NPs restored the composition of the endophyte community and recruit of beneficial species under Cd exposure; the relative abundance of Azospirillum was significantly increased in roots, shoots, and the rhizosphere soil by 0.73-, 4.58- and 0.37-fold, respectively, relative to the Cd-alone treatment. Collectively, these findings highlight the significant potential of AVGE Se NPs to enhance plant growth and to minimize the Cd-induced toxicity in rice and provide a promising nanoenabled strategy to enhance food safety upon crop cultivation in contaminated agricultural soils.
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Affiliation(s)
- Heping Shang
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Chunyang Li
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Zeyu Cai
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Yi Hao
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Yini Cao
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Weili Jia
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Lanfang Han
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Jason C White
- The Connecticut Agricultural Experiment Station, New Haven, Connecticut 06511, United States
| | - Chuanxin Ma
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, Massachusetts 01003, United States
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Guo B, Chen F, Liu G, Li W, Li W, Zhuang J, Zhang X, Wang L, Lei B, Hu C, Liu Y. Effects and mechanisms of proanthocyanidins-derived carbon dots on alleviating salt stress in rice by muti-omics analysis. Food Chem X 2024; 22:101422. [PMID: 38756474 PMCID: PMC11096822 DOI: 10.1016/j.fochx.2024.101422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/17/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Carbon dots (CDs) with different structures were prepared by electrolysis (PE-CDs) and hydrothermal (PH-CDs) methods using proanthocyanidins as precursors. The smaller size and lower zeta potential enabled the PE-CDs treated rice seedlings to exhibit greater resistance to salt stress. The fresh weight of rice seedlings under salt stress was significantly increased by spraying CDs every other day for two weeks. PE-CDs treated group exhibited a faster electron transport rate, and the SOD activity and flavonoid content were 2.5-fold and 0.23-fold higher than those of the salt stress-treated group. Furthermore, the metabolomics and transcriptomics analysis revealed that the PsaC gene of photosystem I was significantly up-regulated under PE-CDs treatment, which accelerated electron transfer in photosystem I. The up-regulation of BX1 and IGL genes encoding indole synthesis allowed rice to enhance stress tolerance through tryptophan and benzoxazine biosynthesis pathways. These findings offer help in purposefully synthesizing CDs and boosting food production.
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Affiliation(s)
- Baoyan Guo
- Key Laboratory for Biobased Materials and Energy of Ministry of Education/Guangdong Provincial Engineering Technology Research Center for Optical Agriculture, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Fengqiong Chen
- Key Laboratory for Biobased Materials and Energy of Ministry of Education/Guangdong Provincial Engineering Technology Research Center for Optical Agriculture, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Guo Liu
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wentao Li
- Key Laboratory for Biobased Materials and Energy of Ministry of Education/Guangdong Provincial Engineering Technology Research Center for Optical Agriculture, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Wei Li
- Key Laboratory for Biobased Materials and Energy of Ministry of Education/Guangdong Provincial Engineering Technology Research Center for Optical Agriculture, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Jianle Zhuang
- Key Laboratory for Biobased Materials and Energy of Ministry of Education/Guangdong Provincial Engineering Technology Research Center for Optical Agriculture, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Xuejie Zhang
- Key Laboratory for Biobased Materials and Energy of Ministry of Education/Guangdong Provincial Engineering Technology Research Center for Optical Agriculture, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Lashuang Wang
- Guangdong Tianzi Natural Inc, Guangzhou 510642, China
| | - Bingfu Lei
- Key Laboratory for Biobased Materials and Energy of Ministry of Education/Guangdong Provincial Engineering Technology Research Center for Optical Agriculture, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Chaofan Hu
- Key Laboratory for Biobased Materials and Energy of Ministry of Education/Guangdong Provincial Engineering Technology Research Center for Optical Agriculture, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Yingliang Liu
- Key Laboratory for Biobased Materials and Energy of Ministry of Education/Guangdong Provincial Engineering Technology Research Center for Optical Agriculture, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
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Zhang X, Han C, Wang Y, Liu T, Liang Y, Cao Y. Integrated analysis of transcriptomics and metabolomics of garden asparagus (Asparagus officinalis L.) under drought stress. BMC PLANT BIOLOGY 2024; 24:563. [PMID: 38879466 PMCID: PMC11179350 DOI: 10.1186/s12870-024-05286-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 06/10/2024] [Indexed: 06/19/2024]
Abstract
BACKGROUND Drought is a leading environmental factor affecting plant growth. To explore the drought tolerance mechanism of asparagus, this study analyzed the responses of two asparagus varieties, namely, 'Jilv3' (drought tolerant) and 'Pacific Early' (drought sensitive), to drought stress using metabolomics and transcriptomics. RESULTS In total, 2,567 and 7,187 differentially expressed genes (DEGs) were identified in 'Pacific Early' and 'Jilv3', respectively, by comparing the transcriptome expression patterns between the normal watering treatment and the drought stress treatment. These DEGs were significantly enriched in the amino acid biosynthesis, carbon metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction pathways. In 'Jilv3', DEGs were also enriched in the following energy metabolism-related pathways: citrate cycle (TCA cycle), glycolysis/gluconeogenesis, and pyruvate metabolism. This study also identified 112 and 254 differentially accumulated metabolites (DAMs) in 'Pacific Early' and 'Jilv3' under drought stress compared with normal watering, respectively. The amino acid, flavonoid, organic acid, and soluble sugar contents were more significantly enhanced in 'Jilv3' than in 'Pacific Early'. According to the metabolome and transcriptome analysis, in 'Jilv3', the energy supply of the TCA cycle was improved, and flavonoid biosynthesis increased. As a result, its adaptability to drought stress improved. CONCLUSIONS These findings help to better reveal the molecular mechanism underlying how asparagus responds to drought stress and improve researchers' ability to screen drought-tolerant asparagus varieties as well as breed new varieties.
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Affiliation(s)
- Xuhong Zhang
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
- Shijiazhuang Landscape Management and Protection Center, Shijiazhuang, China
| | - Changzhi Han
- College of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Yubo Wang
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Tao Liu
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Yuqin Liang
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yanpo Cao
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
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An Q, Zheng N, Ji Y, Sun S, Wang S, Li X, Chen C, Li N, Pan J. Exploration the interaction of cadmium and copper toxic effects in pakchoi (Brassica chinensis L) roots through combinatorial transcriptomic and weighted gene co-expression network analysis. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 359:120956. [PMID: 38669883 DOI: 10.1016/j.jenvman.2024.120956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 02/27/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
The interaction between cadmium(Cd) and copper(Cu) during combined pollution can lead to more complex toxic effects on humans and plants.However, there is still a lack of sufficient understanding regarding the types of interactions at the plant molecular level and the response strategies of plants to combined pollution. To assess this, we investigated the phenotypic and transcriptomic patterns of pakchoi (Brassica chinensis L) roots in response to individual and combined pollution of Cd and Cu. The results showed that compared to single addition, the translocation factor of heavy metals in roots significantly decreased (p < 0.05) under the combined addition, resulting in higher accumulation of Cd and Cu in the roots. Transcriptomic analysis of pakchoi roots revealed that compared to single pollution, there were 312 and 1926 differentially expressed genes (DEGs) specifically regulated in the Cd2Cu20 and Cd2Cu100 combined treatments, respectively. By comparing the expression of these DEGs among different treatments, we found that the combined pollution of Cd and Cu mainly affected the transcriptome of the roots in an antagonistic manner. Enrichment analysis indicated that pakchoi roots upregulated the expression of genes involved in glucosetransferase activity, phospholipid homeostasis, proton transport, and the biosynthesis of phenylpropanoids and flavonoids to resist Cd and Cu combined pollution. Using weighted gene co-expression network analysis (WGCNA), we identified hub genes related to the accumulation of Cd and Cu in the roots, which mainly belonged to the LBD, thaumatin-like protein, ERF, MYB, WRKY, and TCP transcription factor families. This may reflect a transcription factor-driven trade-off strategy between heavy metal accumulation and growth in pakchoi roots. Additionally, compared to single metal pollution, the expression of genes related to Nramp, cation/H+ antiporters, and some belonging to the ABC transporter family in the pakchoi roots was significantly upregulated under combined pollution. This could lead to increased accumulation of Cd and Cu in the roots. These findings provide new insights into the interactions and toxic mechanisms of multiple metal combined pollution at the molecular level in plants.
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Affiliation(s)
- Qirui An
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China
| | - Na Zheng
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China; Northeast Institute of Geography and Agricultural Ecology, Chinese Academy of Sciences, Changchun, Jilin, China.
| | - Yining Ji
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China
| | - Siyu Sun
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China
| | - Sujing Wang
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China
| | - Xiaoqian Li
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China
| | - Changcheng Chen
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China
| | - Ning Li
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of New Energy and Environment, Jilin University, China
| | - Jiamin Pan
- Northeast Institute of Geography and Agricultural Ecology, Chinese Academy of Sciences, Changchun, Jilin, China
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Terletskaya NV, Mamirova A, Ashimuly K, Vibe YP, Krekova YA. Anatomical and Metabolome Features of Haloxylon aphyllum and Haloxylon persicum Elucidate the Resilience against Gall-Forming Insects. Int J Mol Sci 2024; 25:4738. [PMID: 38731957 PMCID: PMC11084765 DOI: 10.3390/ijms25094738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Globally, gall-forming insects significantly contribute to the degradation of desert ecosystems. Recent studies have demonstrated that Haloxylon persicum suffers less damage from gall-formers compared to Haloxylon aphyllum. However, the mechanisms driving the long-term metabolic responses of these species to gall-forming biotic stress in their natural environment remain unclear. The current study comparatively analyzes the anatomical features and metabolomic changes in H. aphyllum and H. persicum damaged by gall-forming insects. This research aimed to uncover potential metabolic tolerance mechanisms through GC-MS analysis. The study findings indicate that gall-forming insects cause a reduction in nearly all the anatomical structures of Haloxylon shoots, with the effects being less severe in H. persicum than in H. aphyllum. Thus, the metabolic pathways responsible for the biosynthesis of biologically active substances that enhance resistance to gall inducers were different, specifically in H. aphyllum-the biosynthesis of fatty acids (+their derivatives) and γ-tocopherol (vitamin E) and H. persicum-the biosynthesis of fatty acids (+their derivatives), dialkyl ethers, carbohydrates (+their derivatives), aromatic acid derivatives, phytosterols, γ-tocopherol (vitamin E), phenols, and terpenoids. The results suggest that the modulation of metabolic pathways under biotic stress plays a crucial role in the enhanced survival and growth of H. persicum.
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Affiliation(s)
- Nina V. Terletskaya
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan;
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan
| | - Aigerim Mamirova
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan
| | - Kazhybek Ashimuly
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan;
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan
| | - Yekaterina P. Vibe
- A.N. Bukeikhan Kazakh Research Institute of Forestry and Agroforestry, Kirov 58, Shchuchinsk 021704, Kazakhstan; (Y.P.V.); (Y.A.K.)
| | - Yana A. Krekova
- A.N. Bukeikhan Kazakh Research Institute of Forestry and Agroforestry, Kirov 58, Shchuchinsk 021704, Kazakhstan; (Y.P.V.); (Y.A.K.)
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8
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Zhou T, Li Q, Huang X, Chen C. Analysis Transcriptome and Phytohormone Changes Associated with the Allelopathic Effects of Ginseng Hairy Roots Induced by Different-Polarity Ginsenoside Components. Molecules 2024; 29:1877. [PMID: 38675697 PMCID: PMC11053915 DOI: 10.3390/molecules29081877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/08/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The allelopathic autotoxicity of ginsenosides is an important cause of continuous cropping obstacles in ginseng planting. There is no report on the potential molecular mechanism of the correlation between polarity of ginsenoside components and their allelopathic autotoxicity. This study applied a combination of metabolomics and transcriptomics analysis techniques, combined with apparent morphology, physiological indexes, and cell vitality detection of the ginseng hairy roots, through which the molecular mechanism of correlation between polarity and allelopathic autotoxicity of ginsenosides were comprehensively studied. The hairy roots of ginseng presented more severe cell apoptosis under the stress of low-polarity ginsenoside components (ZG70). ZG70 exerted allelopathic autotoxicity by regulating the key enzyme genes of cis-zeatin (cZ) synthesis pathway, indole-3-acetic acid (IAA) synthesis pathway, and jasmonates (JAs) signaling transduction pathway. The common pathway for high-polarity ginsenoside components (ZG50) and ZG70 to induce the development of allelopathic autotoxicity was through the expression of key enzymes in the gibberellin (GA) signal transduction pathway, thereby inhibiting the growth of ginseng hairy roots. cZ, indole-3-acetamid (IAM), gibberellin A1 (GA1), and jasmonoyl-L-isoleucine (JA-ILE) were the key response factors in this process. It could be concluded that the polarity of ginsenoside components were negatively correlated with their allelopathic autotoxicity.
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Affiliation(s)
- Tingting Zhou
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
- School of Medical Technology, Beihua University, Jilin 132013, China
| | - Qiong Li
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Xin Huang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Changbao Chen
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
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Wang W, Wu L, Shi Y, Yin Q, Wang X, Wang M, Li X, Qiu S, Wan H, Zhang Y, Wang B, Xiang L, Gao R, Matinur Y. Integrated Full-Length Transcriptomics and Metabolomics Reveal Glycosyltransferase Involved in the Biosynthesis of Flavonol Glycosides in Laportea bulbifera. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8269-8283. [PMID: 38557049 DOI: 10.1021/acs.jafc.4c00488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Many species of the Urticaceae family are important cultivated fiber plants that are known for their economic and industrial values. However, their secondary metabolite profiles and associated biosynthetic mechanisms have not been well-studied. Using Laportea bulbifera as a model, we conducted widely targeted metabolomics, which revealed 523 secondary metabolites, including a unique accumulation of flavonol glycosides in bulblet. Through full-length transcriptomic and RNA-seq analyses, the related genes in the flavonoid biosynthesis pathway were identified. Finally, weighted gene correlation network analysis and functional characterization revealed four LbUGTs, including LbUGT78AE1, LbUGT72CT1, LbUGT71BX1, and LbUGT71BX2, can catalyze the glycosylation of flavonol aglycones (kaempferol, myricetin, gossypetin, and quercetagetin) using UDP-Gal and UDP-Glu as the sugar donors. LbUGT78AE1 and LbUGT72CT1 showed substrate promiscuity, whereas LbUGT71BX1 and LbUGT71BX2 exhibited different substrate and sugar donor selectivity. These results provide a genetic resource for studying Laportea in the Urticaceae family, as well as key enzymes responsible for the metabolism of valuable flavonoid glycosides.
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Affiliation(s)
- Wenting Wang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Lan Wu
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yuhua Shi
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qinggang Yin
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiaotong Wang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Mengyue Wang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiwen Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shi Qiu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Huihua Wan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yongping Zhang
- National Engineering Technology Research Center for Miao Medicine, College of Pharmaceutical Sciences, Guizhou University of Traditional Chinese Medicine, Huaxi University Town, Dongqing South Road, Guiyang, Guizhou 550025, People's Republic of China
| | - Bo Wang
- National Engineering Technology Research Center for Miao Medicine, College of Pharmaceutical Sciences, Guizhou University of Traditional Chinese Medicine, Huaxi University Town, Dongqing South Road, Guiyang, Guizhou 550025, People's Republic of China
| | - Li Xiang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Prescription Laboratory of Xinjiang Traditional Uyghur Medicine, Xinjiang Institute of Traditional Uyghur Medicine, Urmuqi 830000, China
| | - Ranran Gao
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yusup Matinur
- Prescription Laboratory of Xinjiang Traditional Uyghur Medicine, Xinjiang Institute of Traditional Uyghur Medicine, Urmuqi 830000, China
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10
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Zhang X, Li Z, Zhao C, Chen T, Wang X, Sun X, Zhao X, Lu X, Xu G. Leveraging Unidentified Metabolic Features for Key Pathway Discovery: Chemical Classification-driven Network Analysis in Untargeted Metabolomics. Anal Chem 2024; 96:3409-3418. [PMID: 38354311 DOI: 10.1021/acs.analchem.3c04591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Untargeted metabolomics using liquid chromatography-electrospray ionization-high-resolution tandem mass spectrometry (UPLC-ESI-MS/MS) provides comprehensive insights into the dynamic changes of metabolites in biological systems. However, numerous unidentified metabolic features limit its utilization. In this study, a novel approach, the Chemical Classification-driven Molecular Network (CCMN), was proposed to unveil key metabolic pathways by leveraging hidden information within unidentified metabolic features. The method was demonstrated by using the herbivore-induced metabolic response in corn silk as a case study. Untargeted metabolomics analysis using UPLC-MS/MS was performed on wild corn silk and two genetically modified lines (pre- and postinsect treatment). Global annotation initially identified 256 (ESI-) and 327 (ESI+) metabolites. MS/MS-based classifications predicted 1939 (ESI-) and 1985 (ESI+) metabolic features into the chemical classes. CCMNs were then constructed using metabolic features shared classes, which facilitated the structure- or class annotation for completely unknown metabolic features. Next, 844/713 significantly decreased and 1593/1378 increased metabolites in ESI-/ESI+ modes were defined in response to insect herbivory, respectively. Method validation on a spiked maize sample demonstrated an overall class prediction accuracy rate of 95.7%. Potential key pathways were prescreened by a hypergeometric test using both structure- and class-annotated differential metabolites. Subsequently, CCMN was used to deeply amend and uncover the pathway metabolites deeply. Finally, 8 key pathways were defined, including phenylpropanoid (C6-C3), flavonoid, octadecanoid, diterpenoid, lignan, steroid, amino acid/small peptide, and monoterpenoid. This study highlights the effectiveness of leveraging unidentified metabolic features. CCMN-based key pathway analysis reduced the bias in conventional pathway enrichment analysis. It provides valuable insights into complex biological processes.
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Affiliation(s)
- Xiuqiong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Zaifang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Chunxia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Tiantian Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Xinxin Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Xiaoshan Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
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11
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Yin Y, Qiao S, Kang Z, Luo F, Bian Q, Cao G, Zhao G, Wu Z, Yang G, Wang Y, Yang Y. Transcriptome and Metabolome Analyses Reflect the Molecular Mechanism of Drought Tolerance in Sweet Potato. PLANTS (BASEL, SWITZERLAND) 2024; 13:351. [PMID: 38337884 PMCID: PMC10857618 DOI: 10.3390/plants13030351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024]
Abstract
Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most widely cultivated crops in the world, with outstanding stress tolerance, but drought stress can lead to a significant decrease in its yield. To reveal the response mechanism of sweet potato to drought stress, an integrated physiological, transcriptome and metabolome investigations were conducted in the leaves of two sweet potato varieties, drought-tolerant zhenghong23 (Z23) and a more sensitive variety, jinong432 (J432). The results for the physiological indexes of drought showed that the peroxidase (POD) and superoxide dismutase (SOD) activities of Z23 were 3.68 and 1.21 times higher than those of J432 under severe drought, while Z23 had a higher antioxidant capacity. Transcriptome and metabolome analysis showed the importance of the amino acid metabolism, respiratory metabolism, and antioxidant systems in drought tolerance. In Z23, amino acids such as asparagine participated in energy production during drought by providing substrates for the citrate cycle (TCA cycle) and glycolysis (EMP). A stronger respiratory metabolism ability could better maintain the energy supply level under drought stress. Drought stress also activated the expression of the genes encoding to antioxidant enzymes and the biosynthesis of flavonoids such as rutin, resulting in improved tolerance to drought. This study provides new insights into the molecular mechanisms of drought tolerance in sweet potato.
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Affiliation(s)
- Yumeng Yin
- Cereal Crop Research Institute, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou 450002, China;
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shouchen Qiao
- Cereal Crop Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (S.Q.); (Z.K.); (Q.B.); (G.C.); (G.Z.); (Z.W.); (G.Y.)
| | - Zhihe Kang
- Cereal Crop Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (S.Q.); (Z.K.); (Q.B.); (G.C.); (G.Z.); (Z.W.); (G.Y.)
| | - Feng Luo
- Henan Provincial Center of Seed Industry Development, Zhengzhou 450007, China;
| | - Qianqian Bian
- Cereal Crop Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (S.Q.); (Z.K.); (Q.B.); (G.C.); (G.Z.); (Z.W.); (G.Y.)
| | - Guozheng Cao
- Cereal Crop Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (S.Q.); (Z.K.); (Q.B.); (G.C.); (G.Z.); (Z.W.); (G.Y.)
| | - Guorui Zhao
- Cereal Crop Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (S.Q.); (Z.K.); (Q.B.); (G.C.); (G.Z.); (Z.W.); (G.Y.)
| | - Zhihao Wu
- Cereal Crop Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (S.Q.); (Z.K.); (Q.B.); (G.C.); (G.Z.); (Z.W.); (G.Y.)
| | - Guohong Yang
- Cereal Crop Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (S.Q.); (Z.K.); (Q.B.); (G.C.); (G.Z.); (Z.W.); (G.Y.)
| | - Yannan Wang
- Cereal Crop Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (S.Q.); (Z.K.); (Q.B.); (G.C.); (G.Z.); (Z.W.); (G.Y.)
| | - Yufeng Yang
- Cereal Crop Research Institute, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou 450002, China;
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- Cereal Crop Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (S.Q.); (Z.K.); (Q.B.); (G.C.); (G.Z.); (Z.W.); (G.Y.)
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12
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Xu C, Gui Z, Huang Y, Yang H, Luo J, Zeng X. Integrated Transcriptomics and Metabolomics Analyses Provide Insights into Qingke in Response to Cold Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18345-18358. [PMID: 37966343 DOI: 10.1021/acs.jafc.3c07005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
The survival and productivity of qingke in high altitude (>4300 m, average yearly temperature <0 °C) of the Tibetan Plateau are significantly impacted by low-temperature stress. Uncovering the mechanisms underlying low-temperature stress response in cold-tolerant qingke varieties is crucial for qingke breeding. Herein, we conducted a comprehensive transcriptomic and metabolomic analysis on cold-sensitive (ZQ) and cold-tolerant (XL) qingke varieties under chilling and freezing treatments and identified lipid metabolism pathways as enriched in response to freezing treatment. Additionally, a significant positive correlation was observed between the expression of C-repeat (CRT) binding factor 10A (HvCBF10A) and Gly-Asp-Ser-Leu-motif lipase (HvGDSL) and the accumulation of multiple lipids. Functional analysis confirmed that HvCBF10A directly binds to HvGDSL, and silencing HvCBF10A resulted in a significant decrease in both HvGDSL and lipid levels, consequently impairing the cold tolerance. Overall, HvCBF10A and HvGDSL are functional units in actively regulating lipid metabolism to enhance freezing stress tolerance in qingke.
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Affiliation(s)
- Congping Xu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
- Key Laboratory of Barley Biology and Genetic Improvement on QingHai-Tibet Plateau, Ministry of Agriculture, Lhasa 850002, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850002, China
| | - Zihao Gui
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yuxiao Huang
- Hainan Yazhou Bay grain Laboratory, Sanya 572025, China
| | - Haizhen Yang
- Key Laboratory of Barley Biology and Genetic Improvement on QingHai-Tibet Plateau, Ministry of Agriculture, Lhasa 850002, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850002, China
| | - Jie Luo
- Hainan Yazhou Bay grain Laboratory, Sanya 572025, China
| | - Xingquan Zeng
- Key Laboratory of Barley Biology and Genetic Improvement on QingHai-Tibet Plateau, Ministry of Agriculture, Lhasa 850002, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850002, China
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13
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Rodriguez Gallo MC, Li Q, Talasila M, Uhrig RG. Quantitative Time-Course Analysis of Osmotic and Salt Stress in Arabidopsis thaliana Using Short Gradient Multi-CV FAIMSpro BoxCar DIA. Mol Cell Proteomics 2023; 22:100638. [PMID: 37704098 PMCID: PMC10663867 DOI: 10.1016/j.mcpro.2023.100638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/22/2023] [Accepted: 08/27/2023] [Indexed: 09/15/2023] Open
Abstract
A major limitation when undertaking quantitative proteomic time-course experimentation is the tradeoff between depth-of-analysis and speed-of-analysis. In high complexity and high dynamic range sample types, such as plant extracts, balance between resolution and time is especially apparent. To address this, we evaluate multiple compensation voltage (CV) high field asymmetric waveform ion mobility spectrometry (FAIMSpro) settings using the latest label-free single-shot Orbitrap-based DIA acquisition workflows for their ability to deeply quantify the Arabidopsis thaliana seedling proteome. Using a BoxCarDIA acquisition workflow with a -30 -50 -70 CV FAIMSpro setting, we were able to consistently quantify >5000 Arabidopsis seedling proteins over a 21-min gradient, facilitating the analysis of ∼42 samples per day. Utilizing this acquisition approach, we then quantified proteome-level changes occurring in Arabidopsis seedling shoots and roots over 24 h of salt and osmotic stress, to identify early and late stress response proteins and reveal stress response overlaps. Here, we successfully quantify >6400 shoot and >8500 root protein groups, respectively, quantifying nearly ∼9700 unique protein groups in total across the study. Collectively, we pioneer a short gradient, multi-CV FAIMSpro BoxCarDIA acquisition workflow that represents an exciting new analysis approach for undertaking quantitative proteomic time-course experimentation in plants.
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Affiliation(s)
- M C Rodriguez Gallo
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Q Li
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - M Talasila
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - R G Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada; Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
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14
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Li F, Gong Y, Mason AS, Liu Q, Huang J, Ma M, Xiao M, Wang H, Fu D. Research progress and applications of colorful Brassica crops. PLANTA 2023; 258:45. [PMID: 37462779 DOI: 10.1007/s00425-023-04205-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023]
Abstract
MAIN CONCLUSION We review the application and the molecular regulation of anthocyanins in colorful Brassica crops, the creation of new germplasm resources, and the development and utilization of colorful Brassica crops. Brassica crops are widely cultivated: these include oilseed crops, such as rapeseed, mustards, and root, leaf, and stem vegetable types, such as turnips, cabbages, broccoli, and cauliflowers. Colorful variants exist of these crop species, and asides from increased aesthetic appeal, these may also offer advantages in terms of nutritional content and improved stress resistances. This review provides a comprehensive overview of pigmentation in Brassica as a reference for the selection and breeding of new colorful Brassica varieties for multiple end uses. We summarize the function and molecular regulation of anthocyanins in Brassica crops, the creation of new colorful germplasm resources via different breeding methods, and the development and multifunctional utilization of colorful Brassica crop types.
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Affiliation(s)
- Fuyan Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yingying Gong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Qian Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Juan Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Miao Ma
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Meili Xiao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huadong Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
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15
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Yang F, Lv G. Metabolomic Analysis of the Response of Haloxylon ammodendron and Haloxylon persicum to Drought. Int J Mol Sci 2023; 24:ijms24109099. [PMID: 37240446 DOI: 10.3390/ijms24109099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/14/2023] [Accepted: 05/21/2023] [Indexed: 05/28/2023] Open
Abstract
Haloxylon ammodendron and Haloxylon persicum, as typical desert plants in arid areas, show strong drought tolerance and environmental adaptability and are therefore ideal model plants for studying the molecular mechanisms of drought tolerance. A metabolomic analysis of H. ammodendron and H. persicum in their natural environment is lacking, and their metabolic response to drought therefore remains unclear. To elucidate the response of H. ammodendron and H. persicum to drought at the metabolic level, a non-targeted metabolomics analysis was carried out herein. Under a dry environment, H. ammodendron exhibited 296 and 252 differentially expressed metabolites (DEMs) in the positive and negative ion modes, respectively, whereas 452 and 354 DEMs were identified in the positive and negative ion modes in H. persicum, respectively. The results indicated that H. ammodendron responds to drought by increasing the content of organic nitrogen compounds and lignans, neolignans, and related compounds, and reducing the content of alkaloids and derivatives. By contrast, H. persicum adapts to the dry environment by increasing the content of organic acids and their derivatives and reducing the content of lignans, neolignans, and related compounds. In addition, H. ammodendron and H. persicum improved their osmoregulation ability, reactive oxygen species detoxification ability, and cell membrane stability by regulating the key metabolic pathways and anabolism of associated metabolites. This is the first metabolomics report on the response of H. ammodendron and H. persicum to drought in their natural environment, providing a foundation for the further study of their regulatory mechanisms under drought stress.
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Affiliation(s)
- Fang Yang
- School of Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830017, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Jinghe 833300, China
| | - Guanghui Lv
- School of Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830017, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Jinghe 833300, China
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16
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Wu J, Lv S, Zhao L, Gao T, Yu C, Hu J, Ma F. Advances in the study of the function and mechanism of the action of flavonoids in plants under environmental stresses. PLANTA 2023; 257:108. [PMID: 37133783 DOI: 10.1007/s00425-023-04136-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/11/2023] [Indexed: 05/04/2023]
Abstract
MAIN CONCLUSION This review summarizes the anti-stress effects of flavonoids in plants and highlights its role in the regulation of polar auxin transport and free radical scavenging mechanism. As secondary metabolites widely present in plants, flavonoids play a vital function in plant growth, but also in resistance to stresses. This review introduces the classification, structure and synthetic pathways of flavonoids. The effects of flavonoids in plant stress resistance were enumerated, and the mechanism of flavonoids in plant stress resistance was discussed in detail. It is clarified that plants under stress accumulate flavonoids by regulating the expression of flavonoid synthase genes. It was also determined that the synthesized flavonoids are transported in plants through three pathways: membrane transport proteins, vesicles, and bound to glutathione S-transferase (GST). At the same time, the paper explores that flavonoids regulate polar auxin transport (PAT) by acting on the auxin export carrier PIN-FORMED (PIN) in the form of ATP-binding cassette subfamily B/P-glycoprotein (ABCB/PGP) transporter, which can help plants to respond in a more dominant form to stress. We have demonstrated that the number and location of hydroxyl groups in the structure of flavonoids can determine their free radical scavenging ability and also elucidated the mechanism by which flavonoids exert free radical removal in cells. We also identified flavonoids as signaling molecules to promote rhizobial nodulation and colonization of arbuscular mycorrhizal fungi (AMF) to enhance plant-microbial symbiosis in defense to stresses. Given all this knowledge, we can foresee that the in-depth study of flavonoids will be an essential way to reveal plant tolerance and enhance plant stress resistance.
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Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang, 110036, China.
| | - Sidi Lv
- School of Environmental Science, Liaoning University, Shenyang, 110036, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Tian Gao
- School of Environmental Science, Liaoning University, Shenyang, 110036, China
| | - Chang Yu
- Kerchin District Branch Office, Tongliao City Ecological Environment Bureau, Tongliao, 028006, China
| | - Jianing Hu
- Dalian Neusoft University of Information, Dalian, 116032, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
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17
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Li Y, Jiang D, Liu XY, Li M, Tang YF, Mi J, Ren GX, Liu CS. Multi-Omics Analysis Provides Crucial Insights into the Drought Adaptation of Glycyrrhiza uralensis Fisch. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5391-5402. [PMID: 36971245 DOI: 10.1021/acs.jafc.2c07163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Drought adaptation of plants is closely related to resistance and tolerance to drought stress as well as the ability to recover after the elimination of the stress. Glycyrrhiza uralensis Fisch is a commonly applied herb whose growth and development are greatly affected by drought. Here, we provide the first comprehensive analysis of the transcriptomic, epigenetic, and metabolic responses of G. uralensis to drought stress and rewatering. The hyper-/hypomethylation of genes may lead to up-/downregulated gene expression, and epigenetic changes can be regarded as an important regulatory mechanism of G. uralensis under drought stress and rewatering. Moreover, integrated transcriptome and metabolome analysis revealed that genes and metabolites involved in pathways of antioxidation, osmoregulation, phenylpropanoid biosynthesis, and flavonoid biosynthesis may regulate the drought adaptation of G. uralensis. This work provides crucial insights into the drought adaptation of G. uralensis and offers epigenetic resources for cultivating G. uralensis with high drought adaptation.
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Affiliation(s)
- Yuan Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Dan Jiang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Xin-Yu Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Meng Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yi-Fei Tang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Jiu Mi
- University of Tibetan Medicine, Tibet 850000, China
| | - Guang-Xi Ren
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Chun-Sheng Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
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18
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Fang T, Qian C, Daoura BG, Yan X, Fan X, Zhao P, Liao Y, Shi L, Chang Y, Ma XF. A novel TF molecular switch-mechanism found in two contrasting ecotypes of a psammophyte, Agriophyllum squarrosum, in regulating transcriptional drought memory. BMC PLANT BIOLOGY 2023; 23:167. [PMID: 36997861 PMCID: PMC10061855 DOI: 10.1186/s12870-023-04154-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Prior drought stress may change plants response patterns and subsequently increase their tolerance to the same condition, which can be referred to as "drought memory" and proved essential for plants well-being. However, the mechanism of transcriptional drought memory in psammophytes remains unclear. Agriophyllum squarrosum, a pioneer species on mobile dunes, is widely spread in Northern China's vast desert areas with outstanding ability of water use efficiency. Here we conducted dehydration-rehydration treatment on A. squarrosum semi-arid land ecotype AEX and arid land ecotype WW to dissect the drought memory mechanism of A. squarrosum, and to determine the discrepancy in drought memory of two contrasting ecotypes that had long adapted to water heterogeneity. RESULT Physiological traits monitoring unveiled the stronger ability and longer duration in drought memory of WW than that of AEX. A total of 1,642 and 1,339 drought memory genes (DMGs) were identified in ecotype AEX and WW, respectively. Furthermore, shared DMGs among A. squarrosum and the previously studied species depicted that drought memory commonalities in higher plants embraced pathways like primary and secondary metabolisms; while drought memory characteristics in A. squarrosum were mainly related to response to heat, high light intensity, hydrogen peroxide, and dehydration, which might be due to local adaptation to desert circumstances. Heat shock proteins (HSPs) occupied the center of the protein-protein interaction (PPI) network in drought memory transcription factors (TF), thus playing a key regulatory role in A. squarrosum drought memory. Co-expression analysis of drought memory TFs and DMGs uncovered a novel regulating module, whereby pairs of TFs might function as molecular switches in regulating DMG transforming between high and low expression levels, thus promoting drought memory reset. CONCLUSION Based on the co-expression analysis, protein-protein interaction prediction, and drought memory metabolic network construction, a novel regulatory module of transcriptional drought memory in A. squarrosum was hypothesized here, whereby recurrent drought signal is activated by primary TF switches, then amplified by secondary amplifiers, and thus regulates downstream complicated metabolic networks. The present research provided valuable molecular resources on plants' stress-resistance basis and shed light on drought memory in A. squarrosum.
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Affiliation(s)
- Tingzhou Fang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000 China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chaoju Qian
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000 China
| | - Bachir Goudia Daoura
- Department of Biology, Faculty of Sciences and Technology, Dan Dicko Dankoulodo University, POBox 465, Maradi, Niger
| | - Xia Yan
- Key Laboratory of Eco-hydrology of Inland River Basin, Northwest Institute of Eco- Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, 730000 China
| | - Xingke Fan
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000 China
| | - Pengshu Zhao
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000 China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yuqiu Liao
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000 China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Liang Shi
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000 China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yuxiao Chang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Science, Shenzhen, 518000 China
| | - Xiao-Fei Ma
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000 China
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Sun J, Du L, Qu Z, Wang H, Dong S, Li X, Zhao H. Integrated metabolomics and proteomics analysis to study the changes in Scutellaria baicalensis at different growth stages. Food Chem 2023; 419:136043. [PMID: 37027979 DOI: 10.1016/j.foodchem.2023.136043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 02/28/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023]
Abstract
Scutellaria baicalensis is a functional food that has the potential to treat various diseases. Scutellaria baicalensis can be divided into two types: Ziqin (strip types) and (rotten xylem). Ziqin is used to clear lower energizer large intestine heat syndrome, while Kuqin is used for the treatment of upper energizer lung heat syndrome. At present, the substance basis of the differences between Ziqin and Kuqin is not clear. The changes in metabolite accumulation and protein expression between them were analyzed by the non-targeted metabolomic technique in combination with the label-free proteomics approach. The results showed that the differentially accumulated metabolites and abundant proteins were mainly enriched in the pathways of phenylalanine, tyrosine and tryptophan biosynthesis, phenylpropanoid biosynthesis, flavonoid biosynthesis, flavone and flavonol biosynthesis, isoflavonoid biosynthesis, and anthocyanin biosynthesis. Collectively, these results reveal the changes of Scutellaria baicalensis in different growth years and provide a reference for selecting the appropriate harvest period.
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Cajanus platycarpus Flavonoid 3'5' Hydroxylase_2 ( CpF3'5'H_2) Confers Resistance to Helicoverpa armigera by Modulating Total Polyphenols and Flavonoids in Transgenic Tobacco. Int J Mol Sci 2023; 24:ijms24021755. [PMID: 36675270 PMCID: PMC9862005 DOI: 10.3390/ijms24021755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Pod borer Helicoverpa armigera, a polyphagus herbivorous pest, tremendously incurs crop damage in economically important crops. This necessitates the identification and utility of novel genes for the control of the herbivore. The present study deals with the characterization of a flavonoid 3'5' hydroxylase_2 (F3'5'H_2) from a pigeonpea wild relative Cajanus platycarpus, possessing a robust chemical resistance response to H. armigera. Though F3'5'H_2 displayed a dynamic expression pattern in both C. platycarpus (Cp) and the cultivated pigeonpea, Cajanus cajan (Cc) during continued herbivory, CpF3'5'H_2 showed a 4.6-fold increase vis a vis 3-fold in CcF3'5'H_2. Despite similar gene copy numbers in the two Cajanus spp., interesting genic and promoter sequence changes highlighted the stress responsiveness of CpF3'5'H_2. The relevance of CpF3'5'H_2 in H. armigera resistance was further validated in CpF3'5'H_2-overexpressed transgenic tobacco based on reduced leaf damage and increased larval mortality through an in vitro bioassay. As exciting maiden clues, CpF3'5'H_2 deterred herbivory in transgenic tobacco by increasing total flavonoids, polyphenols and reactive oxygen species (ROS) scavenging capacity. To the best of our knowledge, this is a maiden attempt ascertaining the role of F3'5'H_2 gene in the management of H. armigera. These interesting leads suggest the potential of this pivotal branch-point gene in biotic stress management programs.
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Yu K, Wei L, Yuan H, Zhang W, Zeng X, Wang B, Wang Y. Genetic architecture of inducible and constitutive metabolic profile related to drought resistance in qingke (Tibetan hulless barley). FRONTIERS IN PLANT SCIENCE 2022; 13:1076000. [PMID: 36561451 PMCID: PMC9763626 DOI: 10.3389/fpls.2022.1076000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Qingke (Tibetan hulless barley, Hordeum vulgare L. var. nudum) is the primary food crop on the Tibet Plateau, the long-term drought and other harsh environments makes qingke an important resource for the study of abiotic resistance. Here, we evaluated the drought sensitivity of 246 qingke varieties. Genome-wide association studies (GWAS) found that root-specific expressed gene CYP84 may be involved in the regulation of drought resistance. Based on widely targeted metabolic profiling, we identified 2,769 metabolites in qingke leaves, of which 302 were significantly changed in response to drought stress, including 4-aminobutyric acid (GABA), proline, sucrose and raffinose. Unexpectedly, these drought-induced metabolites changed more violently in drought-sensitive qingkes, while the constitutive metabolites that had little response to drought stress, such as C-glycosylflavonoids and some amino acids, accumulated excessively in drought-resistant qingkes. Combined with metabolite-based genome-wide association study (mGWAS), a total of 1,006 metabolites under optimal condition and 1,031 metabolites under mild drought stress had significant associated loci. As a marker metabolite induced by drought stress, raffinose was significantly associated with two conservatively adjacent α-galactosidase genes, qRT-PCR suggests that these two genes may jointly regulate the raffinose content in qingke. Besides, as constituent metabolites with stable differences between drought-sensitive and drought-resistant qingkes, a class of C-glycosylflavonoids are simultaneously regulated by a UDP-glucosyltransferase gene. Overall, we performed GWAS for sensitivity and widely targeted metabolites during drought stress in qingke for the first time, which provides new insights into the response mechanism of plant drought stress and drought resistance breeding.
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Affiliation(s)
- Kuohai Yu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Lingling Wei
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Hongjun Yuan
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Weiqin Zhang
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, China
| | - Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Bin Wang
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, China
| | - Yulin Wang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
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Xu C, Abbas HMK, Zhan C, Huang Y, Huang S, Yang H, Wang Y, Yuan H, Luo J, Zeng X. Integrative metabolomic and transcriptomic analyses reveal the mechanisms of Tibetan hulless barley grain coloration. FRONTIERS IN PLANT SCIENCE 2022; 13:1038625. [PMID: 36388537 PMCID: PMC9641248 DOI: 10.3389/fpls.2022.1038625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Cereal grains accumulate anthocyanin during developmental process. The anthocyanin content increases at grain filling stages to develop grain coloration in cereals. However, anthocyanin biosynthesis responsible for grain coloring and its regulatory mechanisms controlled by structural and functional genes remain unclear. Therefore, this study aimed to explore the global map of metabolic changes linked to grain coloration of Tibetan hulless barley (qingke) using an integrative metabolome and transcriptome approach. Grains from three colored qingke cultivars at different developmental stages were considered for molecular and metabolic investigations. A total of 120 differentially accumulated metabolites (DAMs) and 8,327 differentially expressed genes (DEGs) were filtered. DEGs were mainly enriched in the phenylpropanoid and flavonoid pathways. The transcript levels of anthocyanin biosynthesis genes (PAL, C4H, 4CL, CHS, FLS, F3H, F3'H, DFR, ANS, GT, OMT, and MAT) significantly upregulate in colored qingke compared to the non-colored variety. During grain development and maturation, the strong correlation of HvMYC2 expression with anthocyanin contents and anthocyanin biosynthesis genes suggested it as a critical gene in anthocyanin accumulation. Further results confirmed that HvMYC2 could be activated by HvMYB and be a positive regulator of UV-B and cold tolerance in qingke. In addition, verification based on enzymatic assays indicated that six key modifier enzymes could catalyze glycosylation, malonylation, and methylation of anthocyanins, thereby dissecting the major anthocyanin modification pathway in colored qingke. Overall, our study provides global insight into anthocyanin accumulation and the mechanism underlying grain coloration in qingke.
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Affiliation(s)
- Congping Xu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | | | - Chuansong Zhan
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yuxiao Huang
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Sishu Huang
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Haizhen Yang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yulin Wang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Hongjun Yuan
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Jie Luo
- Sanya Nanfan Research Institute of Hainan university, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
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Li X, Liu L, Sun S, Li Y, Jia L, Ye S, Yu Y, Dossa K, Luan Y. Leaf-transcriptome profiles of phoebe bournei provide insights into temporal drought stress responses. FRONTIERS IN PLANT SCIENCE 2022; 13:1010314. [PMID: 36352866 PMCID: PMC9637941 DOI: 10.3389/fpls.2022.1010314] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Phoebe bournei (Hemsl.) Yang is used as a commercial wood in China and is enlisted as a near-threatened species. Prolonged droughts pose a serious threat to young seedlings (1-2 years old). A transcriptome sequencing approach, together with the measurement of growth parameters and biochemical analyses were used to understand P. bournei's drought responses on 15d, 30d, and 45d of drought stress treatment. The stem and root dry weights decreased significantly with drought stress duration. Activities of antioxidative enzymes i.e., peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) increased significantly with the increase in drought stress duration. A total of 13,274, 15,648, and 9,949 genes were differentially expressed in CKvs15d, CKvs30d, and CKvs45d, respectively. The differential expression analyses showed that photosystem I and II underwent structural changes, chlorophyll biosynthesis, and photosynthesis were reduced. The genes annotated as POD, SOD, and CAT were upregulated in drought-treated leaves as compared to control. Additionally, plant-hormone signal transduction, MAPK signaling-plant, phenylpropanoid biosynthesis, flavonoid biosynthesis, and starch and sucrose metabolism pathways showed large-scale expression changes in major genes. We also found that members of 25 transcription factor families were differentially expressed. Our study presents and discusses these transcriptome signatures. Overall, our findings represent key data for breeding towards drought stress tolerance in P. bournei.
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Affiliation(s)
- Xiang Li
- The First Affiliated Hospital of Yunnan University of Traditional Chinese Medicine, Kunming, China
| | - Lanlan Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Shixian Sun
- Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services Southwest Forestry University, Kunming, China
| | - Yanmei Li
- Department of Life Technology Teaching and Research, School of Life Science, Southwest Forestry University, Kunming, China
| | - Lu Jia
- Department of Life Technology Teaching and Research, School of Life Science, Southwest Forestry University, Kunming, China
| | - Shili Ye
- Faculty of Mathematics and Physics, Southwest Forestry University, Kunming, China
| | - Yanxuan Yu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | | | - Yunpeng Luan
- The First Affiliated Hospital of Yunnan University of Traditional Chinese Medicine, Kunming, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
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Qin J, Yue X, Fang S, Qian M, Zhou S, Shang X, Yang W. Nitrogen addition modifies the relative gene expression level and accumulation of carbon-based bioactive substances in Cyclocarya paliurus. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 188:70-80. [PMID: 35988389 DOI: 10.1016/j.plaphy.2022.07.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/18/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
In China, lots of Cyclocarya paliurus plantations have been established for tea and functional food production on nitrogen (N)-limited land. The optimum N levels require for biosynthesis and accumulation of carbon-based bioactive substances vary among plant species. This study integrated field trial with hydroponic culture to assess impact of nitrogen addition on accumulation and relative gene expression level of carbon-based secondary metabolites in C. paliurus. N addition significantly influenced not only contents of polyphenols, flavonoids and triterpenoids and relative gene expression levels of their biosynthetic pathway in C. paliurus leaves but also leaf biomass production and the bioactive substance accumulations. An intermediate N addition induced the highest contents of polyphenols, flavonoids and triterpenoids in leaves, but the optimized accumulation of these bioactive substances in the leaves was the trade-off between their contents and leaf biomass production. Correlation analysis showed that related gene expression levels were closely correlated with contents of their leaf corresponding secondary metabolites. Compared with ratios of carbon/N (C/N) and carbon/phosphorus (C/P) in the soil, ratios of C/N and C/P in the leaves were more strongly related to the contents and accumulations of polyphenols, flavonoids and triterpenoids. To obtain higher yields of targeted phytochemicals, the threshold ratios of C/N and C/P in the leaves are recommended for N and P fertilization at similar sites. Overall, our findings would provide the theoretical basis and technical support for manipulating N fertilization in C. paliurus plantations to obtain higher accumulations of targeted bioactive substances.
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Affiliation(s)
- Jian Qin
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xiliang Yue
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Shengzuo Fang
- College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
| | - Mengyu Qian
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Shuntao Zhou
- Anhui Green and Selenium Technology Development Company in Agriculture and Ecology, Shitai, China
| | - Xulan Shang
- College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wanxia Yang
- College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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25
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Zhang Q, Zheng G, Wang Q, Zhu J, Zhou Z, Zhou W, Xu J, Sun H, Zhong J, Gu Y, Yin Z, Du YL, Du JD. Molecular mechanisms of flavonoid accumulation in germinating common bean (Phaseolus vulgaris) under salt stress. Front Nutr 2022; 9:928805. [PMID: 36105573 PMCID: PMC9465018 DOI: 10.3389/fnut.2022.928805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Flavonoids are important secondary metabolites, active biomolecules in germinating beans, and have prominent applications in food and medicine due to their antioxidant effects. Rutin is a plant flavonoid with a wide biological activity range. In this study, flavonoid (rutin) accumulation and its related molecular mechanisms in germinating common bean (Phaseolus vulgaris) were observed at different time points (0–120 h) under salt stress (NaCl). The rutin content increased from germination onset until 96 h, after which a reducing trend was observed. Metabolome analysis showed that salt stress alters flavonoid content by regulating phenylpropanoid (ko00940) and flavonoid (ko00941) biosynthesis pathways, as well as their enzyme activities, including cinnamyl-alcohol dehydrogenase (CAD), peroxidase (POD), chalcone isomerase (CHI), and flavonol synthase (FLS). The RNA-seq and quantitative real-time PCR (qRT-PCR) analyses also showed that these two pathways were linked to changes in flavonoid content following salt treatment. These results reveal that salt stress effectively enhanced rutin content accumulation in germinating beans, hence it could be employed to enhance the functional quality of germinating common beans.
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Affiliation(s)
- Qi Zhang
- Legume Crop Laboratory, Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Guangyue Zheng
- Legume Crop Laboratory, Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Qi Wang
- Legume Crop Laboratory, Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jixing Zhu
- Legume Crop Laboratory, Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhiheng Zhou
- Legume Crop Laboratory, Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wenshuo Zhou
- Legume Crop Laboratory, Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Junjie Xu
- Legume Crop Laboratory, Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Haoyue Sun
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Jingwen Zhong
- Legume Crop Laboratory, Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yanhua Gu
- Legume Crop Laboratory, Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhengong Yin
- Crop Resources Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yan-li Du
- Legume Crop Laboratory, Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Ji-dao Du
- Legume Crop Laboratory, Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, China
- National Cereals Technology Engineering Research Center, Daqing, China
- *Correspondence: Ji-dao Du
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Zhang F, Zhang X, Luo Y, Li H, Qin X. Biosynthetic mechanisms of isoflavone accumulation affected by different growth patterns in Astragalus mongholicus products. BMC PLANT BIOLOGY 2022; 22:410. [PMID: 35996112 PMCID: PMC9396891 DOI: 10.1186/s12870-022-03769-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND At present, Astragalus mongholicus products on the market represent two growth patterns: imitative wild A. mongholicus (WAM) and cultivated A. mongholicus (CAM). The 6-year-old WAM (A6) and 2-year-old CAM (B2) products are often sold as commodities. This study aimed to explore the effects of the abovementioned growth patterns on the biosynthetic mechanisms of isoflavone accumulation in A. mongholicus products. RESULTS In this paper, the content of calycosin-7-O-β-D-glucoside in 6-year-old WAM (A6) was significantly higher than that in 2-year-old CAM (B2) based on high-performance liquid chromatography. Tissue anatomy indicated that A6 has developed phloem fibers, thickened secondary walls, and a more well-developed vascular system than B2. Thirteen differentially accumulated metabolites were found in A6 and B2 by UHPLC-ESI-Q-TOF-MS/MS, of which isoflavones were highly and significantly enriched in A6. By combining transcriptomics and metabolomics analysis, we found that the metabolomics profile was the same as the transcriptomics profile in both A6 and B2. In total, 11 novel isoflavone-related genes were isolated using BLAST and functional annotation through RNA-Seq and Iso-Seq. The results of integrated analysis, Short Time-series Expression Miner analysis, and Pearson correlation analysis showed that the regulation of four key enzymes, cinnamate 4-hydroxylase, 6-deoxychalcone synthase, chalcone reductase, and chalcone isomerase, led to the high accumulation of isoflavones in A6. In addition, AmUFGT (c778119) and AmUCGT (c303354) were predicted to be 7-O-glycosyltransferases by phylogenetic analysis; these genes catalyze formononetin and calycosin, respectively. CONCLUSIONS The findings of this work will clarify the differences in the biosynthetic mechanism of isoflavone accumulation between A6 and B2, which will guide the cultivation of A. mongholicus.
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Affiliation(s)
- Fusheng Zhang
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China.
| | - Xuan Zhang
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Yangyang Luo
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Huijuan Li
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Xuemei Qin
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China.
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Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology. Int J Mol Sci 2022; 23:ijms23136985. [PMID: 35805979 PMCID: PMC9266571 DOI: 10.3390/ijms23136985] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/19/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023] Open
Abstract
In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.
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Zhou XL, Ma JY, Liu ZD, Dai NF, Yang HQ, Yang L, Wang YH, Shen SK. Gene Co-expression Network and Regression Analysis Identify the Transcriptomic, Physiological, and Biochemical Indicators of the Response of Alpine Woody Plant Rhododendron rex to Drought Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:896691. [PMID: 35693180 PMCID: PMC9174646 DOI: 10.3389/fpls.2022.896691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Increasing severity of drought stress due to global change and extreme weather has been affecting the biodiversity, function, and stability of forest ecosystems. However, despite being an important component in the alpine and subalpine vegetation in forest ecosystems, Rhododendron species have been paid rare attention in the study of molecular mechanism of tolerance or response to drought. Herein, we investigated the correlation of transcriptomic changes with the physiological and biochemical indicators of Rhododendron rex under drought stress by using the co-expression network approach and regression analysis. Compared with the control treatment, the number of significantly differentially expressed unigenes (DEGs) increased with the degree of drought stress. The DEGs were mainly enriched in the cell wall metabolic process, signaling pathways, sugar metabolism, and nitrogen metabolism. Coupled analysis of the transcriptome, physiological, and biochemical parameters indicated that the metabolic pathways were highly correlated with the physiological and biochemical indicators under drought stress, especially the chlorophyll fluorescence parameters, such as the actual photosynthetic efficiency of photosystem II, electron transport rate, photochemical quenching coefficient, and the maximum quantum efficiency of photosystem II photochemistry. The majority of the response genes related to the metabolic pathways, including photosynthesis, sugar metabolism, and phytohormone signal pathway, were highly expressed under drought stress. In addition, genes associated with cell wall, pectin, and galacturonan metabolism also played crucial roles in the response of R. rex to drought stress. The results provided novel insight into the molecular response of the alpine woody species under drought stress and may improve the understanding of the response of forest ecosystems to the global climate change.
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Affiliation(s)
- Xiong-Li Zhou
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, China
| | - Jin-Yan Ma
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Zhen-Dian Liu
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Ni-fei Dai
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Hui-Qin Yang
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Liu Yang
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
| | - Yue-Hua Wang
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
| | - Shi-Kang Shen
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, China
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Tu Z, Xia H, Yang L, Zhai X, Shen Y, Li H. The Roles of microRNA-Long Non-coding RNA-mRNA Networks in the Regulation of Leaf and Flower Development in Liriodendron chinense. FRONTIERS IN PLANT SCIENCE 2022; 13:816875. [PMID: 35154228 PMCID: PMC8829146 DOI: 10.3389/fpls.2022.816875] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/04/2022] [Indexed: 05/27/2023]
Abstract
The leaf and the flower are vital plant organs owing to their roles in photosynthesis and reproduction. Long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and transcription factors (TFs) are very important to the development of these organs. Liriodendron chinense is a common ornamental tree species in southern China with an unusual leaf shape and tulip-like flowers. The genetic mechanisms underlying leaf and flower development in L. chinense and the miRNA-lncRNA-TF regulatory networks are poorly studied. Through the integration and analysis of different types of sequencing data, we identified the miRNA-lncRNA-TF regulatory networks that were related to leaf and flower development. These networks contained 105 miRNAs, 258 lncRNAs, 393 TFs, and 22 endogenous target mimics. Notably, lch-lnc7374-miR156h-SPL3 and lch-lnc7374-miR156j-SPL9 were potential regulators of stamen and pistil development in L. chinense, respectively. miRNA-lncRNA-mRNA regulatory networks were shown to impact anther development, male and female fertility, and petal color by regulating the biosynthesis of phenylpropanoid metabolites. Phenylpropanoid metabolite biosynthesis genes and TFs that were targeted by miRNAs and lncRNAs were differentially expressed in the leaf and flower. Moreover, RT-qPCR analysis confirmed 22 differentially expressed miRNAs, among which most of them showed obvious leaf or flower specificity; miR157a-SPL and miR160a-ARF module were verified by using RLM-RACE, and these two modules were related to leaf and flower development. These findings provide insight into the roles of miRNA-lncRNA-mRNA regulatory networks in organ development and function in L. chinense, and will facilitate further investigation into the regulatory mechanisms of leaf and flower development in L. chinense.
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Affiliation(s)
- Zhonghua Tu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Hui Xia
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Lichun Yang
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xinyu Zhai
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yufang Shen
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Huogen Li
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Dong T, Sha Y, Liu H, Sun L. Altitudinal Variation of Metabolites, Mineral Elements and Antioxidant Activities of Rhodiola crenulata (Hook.f. & Thomson) H.Ohba. Molecules 2021; 26:7383. [PMID: 34885966 PMCID: PMC8658832 DOI: 10.3390/molecules26237383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 11/17/2022] Open
Abstract
Rhodiolacrenulata (Hook.f. & Thomson) H.Ohba is an alpine medicinal plant that can survive in extreme high altitude environments. However, its changes to extreme high altitude are not yet clear. In this study, the response of Rhodiola crenulata to differences in altitude gradients was investigated through chemical, ICP-MS and metabolomic methods. A targeted study of Rhodiola crenulata growing at three vertical altitudes revealed that the contents of seven elements Ca, Sr, B, Mn, Ni, Cu, and Cd, the phenolic components, the ascorbic acid, the ascorbic acid/dehydroascorbate ratio, and the antioxidant capacity were positively correlated with altitude, while the opposite was true for total ascorbic acid content. Furthermore, 1165 metabolites were identified: flavonoids (200), gallic acids (30), phenylpropanoids (237), amino acids (100), free fatty acids and glycerides (56), nucleotides (60), as well as other metabolites (482). The differential metabolite and biomarker analyses suggested that, with an increasing altitude: (1) the shikimic acid-phenylalanine-phenylpropanoids-flavonoids pathway was enhanced, with phenylpropanoids upregulating biomarkers much more than flavonoids; phenylpropanes and phenylmethanes upregulated, and phenylethanes downregulated; the upregulation of quercetin was especially significant in flavonoids; upregulation of condensed tannins and downregulation of hydrolyzed tannins; upregulation of shikimic acids and amino acids including phenylalanine. (2) significant upregulation of free fatty acids and downregulation of glycerides; and (3) upregulation of adenosine phosphates. Our findings provide new insights on the responses of Rhodiola crenulata to extreme high altitude adversity.
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Affiliation(s)
| | | | | | - Liwei Sun
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (T.D.); (Y.S.); (H.L.)
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Jin H, Wang Y, Zhao P, Wang L, Zhang S, Meng D, Yang Q, Cheong LZ, Bi Y, Fu Y. Potential of Producing Flavonoids Using Cyanobacteria As a Sustainable Chassis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12385-12401. [PMID: 34649432 DOI: 10.1021/acs.jafc.1c04632] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Numerous plant secondary metabolites have remarkable impacts on both food supplements and pharmaceuticals for human health improvement. However, higher plants can only generate small amounts of these chemicals with specific temporal and spatial arrangements, which are unable to satisfy the expanding market demands. Cyanobacteria can directly utilize CO2, light energy, and inorganic nutrients to synthesize versatile plant-specific photosynthetic intermediates and organic compounds in large-scale photobioreactors with outstanding economic merit. Thus, they have been rapidly developed as a "green" chassis for the synthesis of bioproducts. Flavonoids, chemical compounds based on aromatic amino acids, are considered to be indispensable components in a variety of nutraceutical, pharmaceutical, and cosmetic applications. In contrast to heterotrophic metabolic engineering pioneers, such as yeast and Escherichia coli, information about the biosynthesis flavonoids and their derivatives is less comprehensive than that of their photosynthetic counterparts. Here, we review both benefits and challenges to promote cyanobacterial cell factories for flavonoid biosynthesis. With increasing concerns about global environmental issues and food security, we are confident that energy self-supporting cyanobacteria will attract increasing attention for the generation of different kinds of bioproducts. We hope that the work presented here will serve as an index and encourage more scientists to join in the relevant research area.
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Affiliation(s)
- Haojie Jin
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Yan Wang
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, P.R. China
| | - Pengquan Zhao
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Litao Wang
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Su Zhang
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Dong Meng
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Qing Yang
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Ling-Zhi Cheong
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food and Pharmaceutical Science, Ningbo University, Ningbo 315211, China
| | - Yonghong Bi
- State Key Laboratory of Fresh Water Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, P.R. China
| | - Yujie Fu
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
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Ren J, Yang X, Ma C, Wang Y, Zhao J. Melatonin enhances drought stress tolerance in maize through coordinated regulation of carbon and nitrogen assimilation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:958-969. [PMID: 34571389 DOI: 10.1016/j.plaphy.2021.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/15/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Melatonin is a pleiotropic regulatory molecule in plants and is involved in regulating plant tolerance to drought stress. Here, we conducted transcriptomic and physiological analyses to identify metabolic processes associated with the enhanced tolerance of the melatonin-treated maize (Zea mays L.) seedlings to water deficit. Maize seedlings were foliar sprayed with either 50 μM melatonin or water and exposed to drought stress for 12 d in growth chambers. Drought stress significantly suppressed seedling growth, and melatonin application partially alleviated this growth inhibition. RNA-Seq analysis revealed that genes whose expression was significantly altered by melatonin were mainly related to carbon (C) and nitrogen (N) metabolism. Analysis of transcriptomics, enzyme activity, and metabolite content data, melatonin-treated plants exhibited a higher level of relatively stable C and N metabolism than untreated plants; this phenotype of melatonin-treated plants was associated with their higher photosynthesis, sucrose biosynthesis, N assimilation, and protein biosynthesis capacities under drought stress. Overall, our results suggest that melatonin enhances drought stress tolerance in maize through coordinated regulation of C and N metabolism.
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Affiliation(s)
- Jianhong Ren
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, 030800, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shaanxi, 712100, China; College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoxiao Yang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, 030800, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shaanxi, 712100, China; College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chunying Ma
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, 030800, China
| | - Yuling Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, 030800, China
| | - Juan Zhao
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, 030800, China.
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Yang X, Kang Y, Liu Y, Shi M, Zhang W, Fan Y, Yao Y, Li H, Qin S. Integrated analysis of miRNA-mRNA regulatory networks of potato (Solanum tuberosum L.) in response to cadmium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112682. [PMID: 34419646 DOI: 10.1016/j.ecoenv.2021.112682] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Cadmium (Cd) stress is a ubiquitous abiotic stress affecting plant growth worldwide and negatively impacting crop yield and food safety. Potato is the most important non-grain crop globally, but there is limited research available on the response of this crop to Cd stress. This study explored the coping mechanism for Cd stress in potato through analyses of miRNA and mRNA. Tissue culture seedlings (20-day-old) of potato variety 'Atlantic' were cultured for up to 48 h in liquid medium containing 5 mmol/L CdCl2, and phenotypic, physiological, and transcriptomic changes were observed at specific times. With the extension of Cd stress time, the potato leaves gradually wilted and curled, and root salicylic acid (SA), glutathione (GSH), and lignin contents and peroxidase (POD) activity increased, while indole-3-acetic acid (IAA) and zeatin (ZT) contents decreased. Using miRNA-seq, 161 existing miRNAs, 383 known miRNAs, and 7361 novel miRNAs were identified, and, 18 miRNAs were differentially expressed in response to Cd stress. Based on mRNA-seq, 7340 differentially expressed mRNAs (DEGs) were found. Through mRNA-miRNA integrated analysis, miRNA-target gene pairs consisting of 23 DEGs and 33 miRNAs were identified. Furthermore, "glutathione metabolism" "plant hormone signal transduction" and "phenylpropanoid biosynthesis" were established as crucial pathways in the Cd stress response of potato. Novel miRNAs novel-m3483-5p and novel-m2893-5p participate in these pathways through targeted regulation of cinnamic alcohol dehydrogenase (CAD; PG0005359) and alanine aminotransferase (POP; PG0024281), respectively. This study provides information that will help elucidate the complex mechanism of the Cd stress response in potato. Moreover, candidate miRNAs and mRNAs could yield new strategies for the development of Cd-tolerant potato breeding.
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Affiliation(s)
- Xinyu Yang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Yichen Kang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China
| | - Yuhui Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China
| | - Mingfu Shi
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Weina Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Yanling Fan
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Yanhong Yao
- Dingxi Academy of Agricultural Sciences, Dingxi 743000, China
| | - Hong Li
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; College of Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Shuhao Qin
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
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