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| 1 | The Structure and Function of Major Plant Metabolite Modifications显示文摘Plants produce a myriad of structurally and functionally diverse metabolites that play many different roles in plant growth and development and in plant response to continually changing environmental conditions as well as abiotic and biotic stresses. This metabolic diversity is, to a large extent, due to chemical modification of the basic skeletons of metabolites. Here, we review the major known plant metabolite modifications and summarize the progress that has been achieved and the challenges we are facing in the field. We focus on discussing both technical and functional aspects in studying the influences that various modifications have on biosynthesis, degradation, transport, and storage of metabolites, as well as their bioactivity and toxicity. Finally, we discuss some emerging insights into the evolution of metabolic pathways and metabolite functionality. | Shouchuang Wang Saleh Alseekh Alisdair R.Fernie Jie Luo | 2019 | Molecular Plant2019，12，7： | 13 |
| 2 | MicroTom Metabolic Network: Rewiring Tomato Metabolic Regulatory Network throughout the Growth Cycle显示文摘Tomato(Solanum lycopersicum)is a major horticultural crop worldwide and has emerged as a preeminent model for metabolic research.Although many research efforts have focused on the analysis of metabolite differences between varieties and species,the dynamics of metabolic changes during the tomato growth cycle and the regulatory networks that underlie these changes are poorly understood.In this study,we integrated high-resolution spatio-temporal metabolome and transcriptome data to systematically explore the metabolic landscape across 20 major tomato tissues and growth stages.In the resulting MicroTom Metabolic Network,the 540 detected metabolites and their co-expressed genes could be divided into 10 distinct clusters based on their biological functions.Using this dataset,we constructed a global map of the major metabolic changes that occur throughout the tomato growth cycle and dissected the underlying regulatory network.In addition to verifying previously well-established regulatory networks for important metabolites,we identified novel transcription factors that regulate the biosynthesis of important secondary metabolites such as steroidal glycoalkaloids and flavonoids.Our findings provide insights into spatiotemporal changes in tomato metabolism and generate a valuable resource for the study of metabolic regulatory processes in model plants. | Yan Li Yang Chen Lu Zhou Shengjie You Heng Deng Ya Chen Saleh Alseekh Yong Yuan Rao Fu Zixin Zhang Dan Su Alisdair R.Fernie Mondher Bouzayen Tao Ma Mingchun Liu Yang Zhang | 2020 | Molecular Plant2020，13，8： | 10 |
| 3 | 低糖野生种与高糖栽培种西瓜果实代谢产物组分差异分析显示文摘采用高效液相色谱—串联质谱(UHPLC–MS/MS)技术对西瓜5份具有代表性的材料果实进行代谢产物分析,在此基础上选取栽培西瓜高糖材料‘97103’和野生西瓜低糖材料‘PI296341’,利用气相色谱—质谱联用(GC–MS)方法对主代谢产物进行定量分析。从成熟果实中定量鉴定出58种代谢物,其中22种在‘97103’和‘PI296341’间存在显著差异。韧皮部运输的棉籽糖在野生低糖材料果实中大量滞留,而在栽培高糖材料中极少积累。综合差异代谢物及其代谢途径分析发现,高糖材料‘97103’果实在水苏糖、棉籽糖等光合产物卸载途径及蔗糖积累代谢途径上的代谢产物积累较高;而低糖材料‘PI296341’,则在氨基酸代谢、有机酸代谢途径及6–磷酸葡萄糖等糖代谢途径上产物积累较高。这些发现为野生西瓜进化到栽培种果实品质的代谢产物积累和调控提供了重要依据,也可为提高西瓜品质提供指导。 | 崔霞霞 王亚钦 任毅 Alisdair R Fernie Saleh Alseekh 何洪巨 宫国义 张海英 郭绍贵 张洁 许勇 | 2018 | 园艺学报2018，45，4： | 4 |
| 4 | Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex显示文摘While the structures of plant primary metabolic pathways are generally well defined and highly conserved across species,those defining specialized metabolism are less well characterized and more highly variable across species.In this study,we investigated polyphenolic metabolism in the lycopersicum complex by characterizing the underlying biosynthetic and decorative reactions that constitute the metabolic network of polyphenols across eight different species of tomato.For this purpose,GC-MS-and LC-MS-based metabolomics of different tissues of Solatium lycopersicum and wild tomato species were carried out,in concert with the evaluation of cross-hybridized microarray data for MapMan-based transcriptomic analysis,and publicly available RNA-sequencing data for annotation of biosynthetic genes.The combined data were used to compile species-specific metabolic networks of polyphenolic metabolism,allowing the establishment of an entire pan-species biosynthetic framework as well as annotation of the functions of decoration enzymes involved in the formation of metabolic diversity of the flavonoid pathway.The combined results are discussed in the context of the current understanding of tomato flavonol biosynthesis as well as a global view of metabolic shifts during fruit ripening.Our results provide an example as to how large-scale biology approaches can be used for the definition and refinement of large specialized metabolism pathways. | Takayuki Tohge Federico Scossa Regina Wendenburg Pierre Frasse llse Balbo Mutsumi Watanabe Saleh Alseekh Sagar Sudam Jadhav Jay C.Delfin Marc Lohse Patrick Giavalisco Bjoern Usadel Youjun Zhang Jie Luo Mondher Bouzayen Alisdair R.Fernie | 2020 | Molecular Plant2020，13，7： | 3 |
| 5 | Quantitative Trait Loci Analysis Identifies a Prominent Gene Involved in the Production of Fatty Acid-Derived Flavor Volatiles in Tomato显示文摘到进在西红柿的类脂化合物新陈代谢的基因规定的获得卓见,我们进行了跟随水果果皮和茄属 pennellii 基因渗入的叶织物介绍的 lipidomic 的分析衬里的新陈代谢的特点 loci (mQTL )(IL ) 。提高为选择水果特定的 mQTL 印射分辨率,我们在独立地导出的 S 的一个子集介绍了类脂化合物。pennellii 回交生来的线,以及在 near-isogenic sub-IL ? 人口。我们识别了控制班 III 脂肪分解酵素家庭, LIP1 和 LIP2 的几类脂化合物,和二个成员的层次的通常认为的 lecithin:cholesterol acyltransferase,那与 diacylglycerols (DAG ) 和 triacylglycerols (标签) 的减少的层次被联系。这个班的脂肪分解酵素从 acylglycerols 的甘油脊梁劈开丰满的酸。释放的丰满的酸用作风味 volatiles 的先锋。我们证明那 LIP1 表情与丰满的导出酸的不稳定的层次相关。我们进一步用转基因的植物在标签和 DAG 故障和不稳定的合成证实 LIP1 的功能。一起拿,我们的学习广泛地在西红柿描绘了脂性的混合物的基因建筑学并且在分子的水平证明从甘油脊梁的免费的丰满的酸的版本能在下游地不稳定的合成上有主要影响。 | Karolina Garbowicz Zhongyuan Liu Saleh Alseekh Denise Tieman Mark Taylor Anastasiya Kuhalskaya Itai Ofner Dani Zamir Harry J. Klee Alisdair R. Fernie Yariv Brotman | 2018 | Molecular Plant2018，11，9： | 2 |
| 6 | Characterization of PetM cytochrome b6f subunit 7 domain-containing protein in tomato显示文摘In recent years,multiple advances have been made in understanding the photosynthetic machinery in model organisms.Knowledge transfer to horticultural important fruit crops is challenging and time-consuming due to restrictions in gene editing tools and prolonged life cycles.Here,we characterize a gene encoding a PetM domain-containing protein in tomato.The CRISPR/Cas9 knockout lines of the PetM showed impairment in the chloroplastic electron transport rate(ETR),reduced CO_(2) assimilation,and reduction of carotenoids and chlorophylls(Chl)under several light conditions.Further,growth-condition-dependent elevation or repression of Chl a/b ratios and de-epoxidation states were identified,underlining possible impairment compensation mechanisms.However,under low light and glasshouse conditions,there were basal levels in CO_(2) assimilation and ETR,indicating a potential role of the PetM domain in stabilizing the cytochrome b6f complex(Cb6f)under higher light irradiance and increasing its quantum efficiency.This suggests a potential evolutionary role in which this domain might stabilize the site of the Cb6f regulating ratios of cyclic and linear electron transport and its potential importance during the conquest of terrestrial ecosystems during which plants were exposed to higher irradiance.Finally,the results are discussed with regard to metabolism and their implication to photosynthesis from an agronomic perspective. | Mustafa Bulut Adriano Nunes-Nesi Alisdair R.Fernie Saleh Alseekh | 2023 | Horticulture Research2023，10，12： | 0 |
| 7 | Phylogenomic discovery of deleterious mutants completes the potato breeding revolution显示文摘After many decades of attempts,recent years have finally witnessed the reinvention of potato from a clonally propagated autotetraploid to a seed-propagated inbred line-based diploid hybrid(Zhang et al.,2021).This can be anticipated to accelerate potato breeding from a cumbersome,non-accumulative mode to a rapid iterative one(Wu et al.,2023).That said,a major hurdle in achieving this is the fact that the clonally propagated potato has amassed a huge number of deleterious mutations(Zhang et al.,2019).These mutations are at least partially masked in the heterozygous state,but their detrimental effects are exposed during the process of developing inbred lines,rendering this a considerable challenge.While Zhang et al.(2021)previously developed two inbred lines,the first generation of highly homozygous inbred lines,these contained mutations that collectively resulted in negative fitness manifesting in frail growth,reduced fertility,and low yield.In a recent study,Wu et al.(2023)utilized genomic evolutionary rate profiling(GERP)analysis to identify and quantify deleterious mutations at the genome-wide scale. | Alisdair R.Fernie Saleh Alseekh | 2023 | Molecular Plant2023，16，7： | 0 |
| 8 | Genomic,transcriptomic,and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti-cancer metabolites显示文摘Plants accumulate a vast array of secondary metabolites,which constitute a natural resource for pharmaceuticals.Oldenlandia corymbosa belongs to the Rubiaceae family,and has been used in traditional medicine to treat different diseases,including cancer.However,the active metabolites of the plant,their biosynthetic pathway and mode of action in cancer are unknown.To fill these gaps,we exposed this plant to eight different stress conditions and combined different omics data capturing gene expression,metabolic profiles,and anti-cancer activity.Our results show that O.corymbosa extracts are active against breast cancer cell lines and that ursolic acid is responsible for this activity.Moreover,we assembled a high-quality genome and uncovered two genes involved in the biosynthesis of ursolic acid.Finally,we also revealed that ursolic acid causes mitotic catastrophe in cancer cells and identified three high-confidence protein binding targets by Cellular Thermal Shift Assay(CETSA)and reverse docking.Altogether,these results constitute a valuable resource to further characterize the biosynthesis of active metabolites in the Oldenlandia group,while the mode of action of ursolic acid will allow us to further develop this valuable compound. | Irene Julca Daniela Mutwil-Anderwald Vaishnervi Manoj Zahra Khan Soak Kuan Lai Lay K.Yang Ing T.Beh Jerzy Dziekan Yoon P.Lim Shen K.Lim Yee W.Low Yuen I.Lam Seth Tjia Yuguang Mu Qiao W.Tan Przemyslaw Nuc Le M.Choo Gillian Khew Loo Shining Antony Kam James P.Tam Zbynek Bozdech Maximilian Schmidt Bjoern Usadel Yoganathan Kanagasundaram Saleh Alseekh Alisdair Fernie Hoi Y.Li Marek Mutwil | 2023 | Journal of Integrative Plant Biology2023，65，6： | 0 |
| 9 | Integrating multiomics data accelerates elucidation of plant primary and secondary metabolic pathways显示文摘Plants are the most important sources of food for humans,as well as supplying many ingredients that are of great importance for human health.Developing an understanding of the functional components of plant metabolism has attracted considerable attention.The rapid development of liquid chromatography and gas chromatography,coupled with mass spectrometry,has allowed the detection and characterization of many thousands of metabolites of plant origin.Nowadays,elucidating the detailed biosynthesis and degradation pathways of these metabolites represents a major bottleneck in our understanding.Recently,the decreased cost of genome and transcriptome sequencing rendered it possible to identify the genes involving in metabolic pathways.Here,we review the recent research which integrates metabolomic with different omics methods,to comprehensively identify structural and regulatory genes of the primary and secondary metabolic pathways.Finally,we discuss other novel methods that can accelerate the process of identification of metabolic pathways and,ultimately,identify metabolite function(s). | Feng Zhu Weiwei Wen Yunjiang Cheng Saleh Alseekh Alisdair R.Fernie | 2023 | aBIOTECH2023，4，1： | 0 |
| 10 | Tecia solanivora infestation increases tuber starch accumulation in Pastusa Suprema potatoes显示文摘In response to infestation with larvae of the Guatemalan tuber moth(Tecia solanivora), some Solanum tuberosum(potato) varieties exhibit an overcompensation response, whereby the total dry mass of uninfested tubers is increased. Here, we describe early responses,within the first few days, of T. solanivora feeding, in the Colombian potato variety Pastusa Suprema. Nontargeted metabolite profiling showed significant secondary metabolism changes in T. solanivora-infested tubers,but not in uninfested systemic tubers. In contrast,changes in primary metabolism were greater in uninfested systemic tubers than in the infested tubers, with a notable 80% decline in systemic tuber sucrose levels within 1 d of T. solanivora infestation. This suggested either decreased sucrose transport from the leaves orincreased sink strength, i.e., more rapid sucrose to starch conversion in the tubers. Increased sucrose synthesis was indicated by higher rubisco activase and lower starch synthase gene expression in the leaves of infested plants.Elevated sink strength was demonstrated by 45% more total starch deposition in systemic tubers of T. solanivorainfested plants compared to uninfested control plants.Thus, rather than investing in increased defense of uninfested tubers, Pastusa Suprema promotes deposition of photoassimilates in the form of starch as a response to T. solanivora infestation. | Pavan Kumar Etzel Garrido Kun Zhao Yi Zheng Saleh Alseekh Erandi Vargas-Ortiz Alisdair R.Fernie Zhangjun Fei Katja Poveda Georg Jander | 2018 | Journal of Integrative Plant Biology2018，60，11： | 0 |
| 11 | Synthetic biology identifies the minimal gene set required for paclitaxel biosynthesis in a plant chassis显示文摘The diterpenoid paclitaxel(Taxol)is a chemotherapy medication widely used as a first-line treatment against several types of solid cancers.The supply of paclitaxel from natural sources is limited.However,missing knowledge about the genes involved in several specific metabolic steps of paclitaxel biosynthesis has rendered it difficult to engineer the full pathway.In this study,we used a combination of transcriptomics,cell biology,metabolomics,and pathway reconstitution to identify the complete gene set required for the heterologous production of paclitaxel.We identified the missing steps from the current model of paclitaxel biosynthesis and confirmed the activity of most of the missing enzymes via heterologous expression in Nicotiana benthamiana.Notably,we identified a new C4β-C20 epoxidase that could overcome the first bottleneck of metabolic engineering.We used both previously characterized and newly identified oxomutases/epoxidases,taxane 1β-hydroxylase,taxane 9aα-hydroxylase,taxane 9α-dioxygenase,and phenylalanine-CoA ligase,to successfully biosynthesize the key intermediate baccatin Ill and to convert baccatin Ill into paclitaxel in N.benthamiana.In combination,these approaches establisha metabolic route to taxoidbiosynthesis and provide insights into the unique chemistry that plants use to generate complex bioactive metabolites. | Youjun Zhang Lorenz Wiese Hao Fang Saleh Alseekh Leonardo Perez de Souza Federico Scossa John Molloy Mathias Christmann Alisdair R.Fernie | 2023 | Molecular Plant2023，16，12： | 0 |
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