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Metabolomics-centered mining of plant metabolic diversity and function:Past decade and future perspectives

Molecular Plant 2023年第1期16卷 43-63页

作者： Shuangqian Shen Chuansong Zhan chenkun yang Alisdair R.Fernie Jie Luo Sanya Nanfan Research Institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China College of Tropical Crops Hainan UniversityHaikou 570228China Max Planck Institute of Molecular Plant Physiology Potsdam-Golm 14476Germany

Plants are natural experts in organic synthesis,being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival *** is a research discipline that integrates the capabilities of several types of research including analytical chemistry,statistics,and *** ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of *** is usually performed by targeting either a specific cell,a specific tissue,or the entire *** advances in science and technology over the last three decades have propelled us into the era of multi-omics,in which metabolomics,despite at an earlier developmental stage than genomics,transcriptomics,and proteomics,offers the distinct advantage of studying the cellular entities that have the greatest influence on end ***,we summarize the state of the art of metabolite detection and identification,and illustrate these techniques with four case study applications:(i)comparing metabolite composition within and between species,(ii)assessing spatio-temporal metabolic changes during plant development,(iii)mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses,and(iv)assessing the performance of metabolomics as a means of functional gene identification,metabolic pathway elucidation,and metabolomics-assisted breeding through analyzing plant populations with diverse genetic *** addition,we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets,including those from genomics,transcriptomics,proteomics,epigenomics,phenomics,microbiomes,and ion-omics ***,we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.

关键词： metabolomics multi-omics high-throughput metabolic profiling bioactive markers

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Benefiting others and self: Production of vitamins in plants

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Journal of Integrative Plant Biology 2021年第1期63卷 210-227页

作者： Yufei Li chenkun yang Hasan Ahmad Mohamed Maher Chuanying Fang Jie Luo National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China College of Tropical Crops Hainan UniversityHaikou 570228China

Vitamins maintain growth and development in humans, animals, and plants. Because plants serve as essential producers of vitamins, increasing the vitamin contents in plants has become a goal of crop breeding worldwide. Here, we begin with a summary of the functions of vitamins. We then review the achievements to date in elucidating the molecular mechanisms underlying how vitamins are synthesized, transported, and regulated in plants. We also stress the exploration of variation in vitamins by the use of forward genetic approaches, such as quantitative trait locus mapping and genome-wide association studies. Overall, we conclude that exploring the diversity of vitamins could provide new insights into plant metabolism and crop breeding.

关键词： crop breeding forward genetic plants vitamins

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The shikimate pathway regulates programmed cell death

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Journal of Genetics and Genomics 2022年第10期49卷 943-951页

作者： Xuerui Lu Shixi Shi Chong Wu Xueao Zheng chenkun yang Jie Luo Shunping Yan Hubei Hongshan Laboratory WuhanHubei 430070China College of Life Science and Technology Huazhong Agricultural UniversityWuhanHubei 430070China National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhanHubei 430070China

Programmed cell death(PCD)is essential for both plant development and stress responses including ***,how plants control PCD is not *** shikimate pathway is one of the most important metabolic pathways in plants,but its relationship to PCD is ***,we show that the shikimate pathway promotes PCD in *** identify a photoperiod-dependent lesion-mimic mutant named Lesion in short-day(lis),which forms spontaneous lesions in short-day *** cloning and whole-genome resequencing reveal that LIS encodes MEE32,a bifunctional enzyme in the shikimate *** analysis shows that the level of shikimate is dramatically increased in *** genetic screenings,three suppressors of lis(slis)are identified and the causal genes are *** encode proteins upstream of MEE32 in the shikimate ***,exogenous shikimate treatment causes *** study uncovers a link between the shikimate pathway and PCD,and suggests that the accumulation of shikimate is an alternative explanation for the action of glyphosate,the most successful herbicide.

关键词： Programmed cell death Shikimate pathway Lesion-mimic mutant Immunity Photoperiod Arabidopsis

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A UV-B-responsive glycosyltransferase,OsUGT706C2,modulates flavonoid metabolism in rice

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Science China(Life Sciences) 2020年第7期63卷 1037-1052页

作者： Feng Zhang Hao Guo Jiacheng Huang chenkun yang Yufei Li Xuyang Wang Lianghuan Qu Xianqing Liu Jie Luo National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Hu az hong Agricultural UniversityWuhan 430070China Institute of Tropical Agriculture and Forestry of Hainan University Haikou 570288China

Although natural variations in rice flavonoids exist, and biochemical characterization of a few flavonoid glycosyltransferases has been reported, few studies focused on natural variations in tricin-lignan-glycosides and their underlying genetic basis. In this study, we carried out metabolic profiling of tricin-lignan-glycosides and identified a major quantitative gene annotated as a UDPdependent glycosyltransferase OsUGT706C2 by metabolite-based genome-wide association analysis. The putative flavonoid glycosyltransferase OsUGT706C2 was characterized as a flavonoid 7-O-glycosyltransferas in vitro and in vivo. Although the in vitro enzyme activity of OsUGT706C2 was similar to that of OsUGT706D1, the expression pattern and induced expression profile of OsUGT706C2 were very different from those of OsUGT706D1. Besides, OsUGT706C2 was specifically induced by UV-B. Constitutive expression of OsUGT706C2 in rice may modulate phenylpropanoid metabolism at both the transcript and metabolite levels. Furthermore, overexpressing OsUGT706C2 can enhance UV-B tolerance by promoting ROS scavenging in rice. Our findings might make it possible to use the glycosyltransferase OsUGT706C2 for crop improvement with respect to UVB adaptation and/or flavonoid accumulation, which may contribute to stable yield.

关键词： flavone glycosyltransferase natural variation Oryza sativa tricin-lignan-glycosides metabolomics UV-B tolerance

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OsRLCK160 contributes to flavonoid accumulation and UV-B tolerance by regulating OsbZIP48 in rice

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Science China(Life Sciences) 2022年第7期65卷 1380-1394页

作者： Feng Zhang Jiacheng Huang Hao Guo chenkun yang Yufei Li Shuangqian Shen Chuansong Zhan Lianghuan Qu Xianqing Liu Shouchuang Wang Wei Chen Jie Luo National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 430070China College of Tropical Crops Hainan UniversityHaikouHainan 570288China

Plants produce specialized metabolites to adapt to the ever-changing *** are antioxidants essential for growth,development,and breeding with increased stress resistance in ***,the mechanism of the involvement of flavonoids in ultraviolet-B(UV-B)stress in rice(Oryza sativa)is largely *** this study,we cloned and functionally identified a receptor-like kinase(OsRLCK160)and a bZIP transcription factor(OsbZIP48)positively regulating flavonoid accumulation through metabolite-based genome-wide association study of the flavonoid content in ***,OsRLCK160 interacted with and phosphorylated OsbZIP48 to regulate the flavonoid accumulation and participate in UV-B tolerance in *** study indicates the importance of applying OsRLCK160 and OsbZIP48 to advance the fundamental understanding of stable rice production and breed UV-B-tolerant rice varieties,which may contribute to breeding high-yield rice varieties.

关键词： flavonoids natural variation Oryza sativa receptor-like kinase transcription factor UV-B tolerance

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Rice metabolic regulatory network spanning the entire life cycle

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Molecular Plant 2022年第2期15卷 258-275页

作者： chenkun yang Shuangqian Shen Shen Zhou Yufei Li Yuyuan Mao Junjie Zhou Yuheng Shi Longxu An Qianqian Zhou Wenju Peng Yuanyuan Lyu Xuemei Liu Wei Chen Shouchuang Wang Lianghuan Qu Xianqing Liu Alisdair R.Fernie Jie Luo National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China College of Tropical Crops Hainan UniversityHaikou 570228China Sanya Nanfan Research Institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 430070China Max Planck Institute of Molecular Plant Physiology Potsdam-Golm 14476Germany Centre of Plant Systems Biology and Biotechnology Plovdiv 4000Bulgaria

As one of the most important crops in the world,rice(Oryza sativa)is a model plant for metabolome *** many studies have focused on the analysis of specific tissues,the changes in metab-olite abundance across the entire life cycle have not yet been *** this study,combining both tar-geted and nontargeted metabolite profiling methods,a total of 825 annotated metabolites were quantified in rice samples from different tissues covering the entire life *** contents of metabolites in different tissues of rice were significantly different,with various metabolites accumulating in the plumule and radicle during seed *** these data with transcriptome data obtained from the same time period,we constructed the Rice Metabolic Regulation *** metabolites and co-expressed genes were further divided into 12 clusters according to their accumulation patterns,with members within each cluster displaying a uniform and clear pattern of abundance across *** this dataset,we established a comprehensive metabolic profile of the rice life cycle and used two independent strategies to identify novel transcription factors-namely the use of known regulatory genes as bait to screen for new networks underlying lignin metabolism and the unbiased identification of new glycerophospholipid metabolism regulators on the basis of tissue *** study thus demonstrates how guilt-by-association analysis of metabolome and transcriptome data spanning the entire life cycle in cereal crops provides novel resources and tools to aid in understanding the mechanisms underlying important agro-nomic traits.

关键词： rice metabolome transcriptome transcription factor co-expression glycerophospholipid

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Integration of rhythmic metabolome and transcriptome provides insights into the transmission of rhythmic fluctuations and temporal diversity of metabolism in rice

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Science China(Life Sciences) 2022年第9期65卷 1794-1810页

作者： Junjie Zhou Chengyuan Liu Qiyu Chen Ling Liu Shuying Niu Ridong Chen Kang Li yangyang Sun Yuheng Shi chenkun yang Shuangqian Shen Yufei Li Junwei Xing Honglun Yuan Xianqing Liu Chuanying Fang Alisdair R.Fernie Jie Luo College of Tropical Crops Hainan UniversityHaikou 570288China National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China Sanya Nanfan Research Institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China Max-Planck-Institute of Molecular Plant Physiology Potsdam-Golm 144776Germany Center of Plant System Biology and Biotechnology Plovdiv 4000Bulgaria

Various aspects of the organisms adapt to cyclically changing environmental conditions via transcriptional ***,the role of rhythmicity in altering the global aspects of metabolism is poorly ***,we subjected four rice(Oryza sativa)varieties to a range of metabolic profiles and RNA-seq to investigate the temporal relationships of rhythm between transcription and *** than 40%of the rhythmic genes and a quarter of metabolites conservatively oscillated across four rice *** with the metabolome,the transcriptome was more strongly regulated by rhythm;however,the rhythm of metabolites had an obvious opposite trend between day and *** association analysis,the time delay of rhythmic transmission from the transcript to the metabolite level was~4 h under long-day conditions,although the transmission was nearly synchronous for carbohydrate and nucleotide *** rhythmic accumulation of metabolites maintained highly coordinated temporal relationships in the metabolic network,whereas the correlation of some rhythmic metabolites,such as branched-chain amino acids(BCAAs),was significantly different *** further demonstrated that the cumulative diversity of BCAAs was due to the differential expression of branched-chain aminotransferase 2 at *** research reveals the flexible pattern of rice metabolic rhythm existing with conservation and diversity.

关键词： Oryza sativa diurnal cycle metabolome time delay rhythmic diversity

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Elucidation of the melitidin biosynthesis pathway in pummelo

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Journal of Integrative Plant Biology 2023年第11期65卷 2505-2518页

作者： Shuangqian Shen Shouchuang Wang chenkun yang Chao Wang Qianqian Zhou Shen Zhou Ran Zhang Yufei Li Zixuan Wang Liupan Dai Wenjv Peng Yingchen Hao Hao Guo Guangping Cao Xianqing Liu Fan Yao Qiang Xu Alisdair RFernie Jie Luo Sanya Nanfan Research Institute of Hainan University Hainan UniversitySanya 572025China National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research(Wuhan)Huazhong Agricultural UniversityWuhan 430070China Hubei Hongshan Laboratory College of Life Science and TechnologyCollege of Biomedicine and HealthHuazhong Agricultural UniversityWuhan 430070China Key Laboratory of Horticultural Plant Biology of Ministry of Education Huazhong Agricultural UniversityWuhan 430070China Max Planck Institute of Molecular Plant Physiology Potsdam-Golm 14476Germany Centre of Plant Systems Biology and Biotechnology Plovdiv 4000Bulgaria Yazhouwan National Laboratory Sanya 572025China

Specialized plant metabolism is a rich resource of compounds for drug *** acylated flavonoid glycoside melitidin is being developed as an anti-cholesterol statin drug candidate,but its biosynthetic route in plants has not yet been fully ***,we describe the gene discovery and functional characterization of a new flavonoid gene cluster(UDP-glucuronosyltransferases(Cg UGTs),1,2rhamnosyltransferase(Cg1,2Rha T),acyltransferases(Cg ATs))that is responsible for melitidin biosynthesis in pummelo(Citrus grandis(L.)Osbeck).Population variation analysis indicated that the tailoring of acyltransferases,specific for bitter substrates,mainly determine the natural abundance of ***,3-hydroxy-3-methylglutaryl-Co A reductase enzyme inhibition assays showed that the product from this metabolic gene cluster,melitidin,may be an effective anti-cholesterol statin drug ***-expression of these clustered genes in Nicotiana benthamiana resulted in the formation of melitidin,demonstrating the potential for metabolic engineering of melitidin in a heterologous plant *** study establishes a biosynthetic pathway for melitidin,which provides genetic resources for the breeding and genetic improvement of pummelo aimed at fortifying the content of biologically active metabolites.

关键词： bioactive metabolites biosynthetic pathway flavonoids melitidin natural variation

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Disease resistance conferred by components of essential chrysanthemum oil and the epigenetic regulation of OsTPS1

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Science China(Life Sciences) 2023年第5期66卷 1108-1118页

作者： Chuansong Zhan Long Lei Hao Guo Shen Zhou Congping Xu Zixin Liu Zichen Wu Yuan Deng Yuanyuan Miao Yu Han Meng Zhang Hua Li Sishu Huang chenkun yang Feng Zhang Yufei Li Ling Liu Xianqing Liu Hafiz Muhammad Khalid Abbas Alisdair R.Fernie Meng Yuan Jie Luo College of Tropical Crops Hainan UniversityHaikou 570228China Sanya Nanfan Research Institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China Max Planck Institute of Molecular Plant Physiology Am Mühlenberg 114476 Potsdam-GolmGermany

The sesquiterpene alpha-bisabolol is the predominant active ingredient in essential oils that are highly valued in the cosmetics industry due to its wound healing,anti-inflammatory,and skin-soothing ***-bisabolol was thought to be restricted to Compositae *** we reveal that alpha-bisabolol is also synthesized in rice,a non-Compositae plant,where it acts as a novel sesquiterpene *** the gene responsible for the biosynthesis of alpha-bisabolol,Os TPS1,conferred bacterial blight resistance in *** analyses revealed that alpha-bisabolol-synthesizing enzymes in rice and Compositae evolved *** experiments demonstrated that the natural variation in the disease resistance level was associated with differential transcription of Os TPS1 due to polymorphisms in its *** demonstrated that Os TPS1 was regulated at the epigenetic level by JMJ705 through the methyl jasmonate *** data reveal the cross-family accumulation and regulatory mechanisms of alpha-bisabolol production.

关键词： alpha-bisabolol epigenetic regulation natural variation

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The NET locus determines the food taste,cooking and nutrition quality of rice

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Science Bulletin 2022年第20期67卷 2045-2049,M0003页

作者： Yufei Li Zhuang yang chenkun yang Zhenhuan Liu Shuangqian Shen Chuansong Zhan Yuanyuan Lyu Feng Zhang Kang Li Yuheng Shi Junjie Zhou Xianqing Liu Chuanying Fang Alisdair R.Fernie Jie Li Jie Luo National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China Sanya Nanfan Research Institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China College of Tropical Crops Hainan UniversityHaikou 570228China Max Planck Institute of Molecular Plant Physiology Potsdam-Golm 14476Germany John Innes Centre Norwich Research ParkNorwichNR47UHUK

Rice(Oryza sativa L)is one of the most important crops world-wide,providing much of the calorific needs for half of the global population[1].Due to the development of the global economy and the improvement of living standards,people's demand for rice has gradually changed from"being fll"to"eating well",with tasty and nutritious varieties being essential for the *** the past few decades,lots of studies have focused on improving the eating and cooking quality(ECQ)of rice to meet the demand for taste[2].Although metabolic engineering has been applied in rice biofortif-cation in recent years[3.4],efforts on improving comprehensive nutrition in rice remain fragmented[5-7].Thus,characterizing QTLs and genes underlying nutrient abundance will provide new guidance for breeding varieties with health benefits.

关键词：数量性状位点育种方案育种过程理想的高营养品质水稻育种蒸煮品质食味

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