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Plant gene co-expression defines the biosynthetic pathway of neuroactive alkaloids

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Molecular Plant 2024年第3期17卷 372-374页

作者： Fang Liu' alisdair r.fernie Youjun Zhang Key Laboratory of Seed Innovation Institute of Genetics and Developmental BiologyChinese Academy of Sciences100101 BeijingChina Max Planck Institute of Molecular Plant Physiology Am Muhlenberg 114476 Potsdam-GolmGermany Center for Plant Systems Biology and Biotechnology 4000 PlovdivBulgaria University of Chinese Academy of Sciences 100049 BeijingChina

Transcriptomes comprise gene co-expression clustersor modules,showcasing distinct patterns of coordinated expression among groups of genes across independent biological samples(Serin et al.,2016).The"guilt-by-association"hypothesis suggests the functional importance of these clusters;for example,co-expressed genes associated with metabolism typically contain genes encoding several enzymes associated with the same pathways.

关键词： metabolism alkaloids

WTV2.0:A high-coverage plant volatilomics method with a comprehensive selective ion monitoring acquisition mode

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Molecular Plant 2024年第6期17卷 972-985页

作者： Honglun Yuan Yiding Jiangfang Zhenhuan Liu rongxiu Su Qiao Li Chuanying Fang Sishu Huang Xianqing Liu alisdair r.fernie Jie Luo School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication)and College of Tropical Agriculture and Forestry Hainan UniversitySanya Hainan 572025China Yazhouwan National Laboratory(YNL) Sanya Hainan 572025China Department of Molecular Physiology Max-Planck-Institute of Molecular Plant PhysiologyAm Mühlenberg 1Potsdam-Golm 14476Germany

Volatilomics is essential for understanding the biological functions and fragrance contributions of plant ***,the annotation coverage achieved using current untargeted and widely targeted volatomics(WTV)methods has been limited by low sensitivity and/or low acquisition ***,we introduce WTV 2.0,which enabled the construction of a high-coverage library containing 2111 plant volatiles,and report the development of a comprehensive selective ion monitoring(cSIM)acquisition method,including the selection of characteristic qualitative ions with the minimal ion number for each compound and an optimized segmentation method,that can acquire the smallest but sufficient number of ions for most plant volatiles,as well as the automatic qualitative and semi-quantitative analysis of cSIM ***,the library and acquisition method we developed can be self-expanded by incorporating compounds not present in the library,utilizing the obtained cSIM *** showed that WTV 2.0 increases the median signal-to-noise ratio by 7.6-fold compared with the untargeted method,doubled the annotation coverage compared with the untargeted and WTV 1.0 methods in tomato fruit,and led to the discovery of menthofuran as a novel flavor compound in passion *** 2.0 is a Python library with a user-friendly interface and is applicable to profiling of volatiles and primary metabolites in any species.

关键词： volatilomics widely targeted methods GC-MS selective ion monitoring plant volatiles

The light and hypoxia induced gene ZmPOrB1 determines tocopherol content in the maize kernel

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Science China(Life Sciences) 2024年第3期67卷 435-448页

作者： Nannan Liu Yuanhao Du Shijuan Yan Wei Chen Min Deng Shutu Xu Hong Wang Wei Zhan Wenjie Huang Yan Yin Xiaohong Yang Qiao Zhao alisdair r.fernie Jianbing Yan National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China Hubei Hongshan Laboratory Wuhan 430070China Agro-biological Gene research Center Guangdong Academy of Agricultural SciencesGuangzhou 510640China College of Agronomy Hunan Agricultural UniversityChangsha 410128China College of Agronomy Northwest A&F UniversityXi'an 710000China State Key Laboratory of North China Crop Improvement and regulation Hebei Sub-center of National Maize Improvement Center of ChinaCollege of AgronomyHebei Agricultural UniversityBaoding 071001China College of Life Sciences South-Central Minzu UniversityWuhan 430070China Plant Science Facility of the Institute of Botany Chinese Academy of SciencesBeijing 100093China National Maize Improvement Center of China Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100093China Shenzhen Key Laboratory of Synthetic Genomics Guangdong Provincial Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China Max Planck Institute of Molecular Plant Physiology Potsdam-Golm 14476Germany

Tocopherol is an important lipid-soluble antioxidant beneficial for both human health and plant growth. Here, we fine mapped a major QTLqVE1 affecting γ-tocopherol content in maize kernel, positionally cloned and confirmed the underlying gene ZmPOrB1(por1), as a protochlorophyllide oxidoreductase. A 13.7 kb insertion reduced the tocopherol and chlorophyll content, and the photosynthetic activity by repressing ZmPOrB1 expression in embryos of NIL-K22, but did not affect the levels of the tocopherol precursors HGA(homogentisic acid)and PMP(phytyl monophosphate). Furthermore, ZmPOrB1 is inducible by low oxygen and light, thereby involved in the hypoxia response in developing embryos. Concurrent with natural hypoxia in embryos, the redox state has been changed with NO increasing and H_(2)O_(2) decreasing, which lowered γ-tocopherol content via scavenging reactive nitrogen species. In conclusion, we proposed that the lower lightharvesting chlorophyll content weakened embryo photosynthesis, leading to fewer oxygen supplies and consequently diverse hypoxic responses including an elevated γ-tocopherol consumption. Our findings shed light on the mechanism for fine-tuning endogenous oxygen concentration in the maize embryo through a novel feedback pathway involving the light and low oxygen regulation of ZmPOrB1 expression and chlorophyll content.

关键词： maize tocopherol hypoxia photosynthesis ZmPOrB1

revealing the specific regulations of nitric oxide on the postharvest ripening and senescence of bitter melon fruit

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aBIOTECH 2024年第1期5卷 29-45页

作者： Hongwei Wang Ling Li Lili Ma alisdair r.fernie Anzhen Fu Chunmei Bai Zhaoze Sang Susu Guo Fan Zhang Qing Wang Yanyan Zheng Jinhua Zuo Key Laboratory of Vegetable Postharvest Processing Ministry of AgricultureBeijing Key Laboratory of Fruits and Vegetable Storage and ProcessingKey Laboratory of Biology and Genetic Improvement of Horticultural Crops(North China)of Ministry of AgricultureKey Laboratory of Urban Agriculture(North)of Ministry of AgricultureBeijing Vegetable Research CenterInstitute of Agro-Products Processing and Food NutritionBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China College of Food Science and Biotechnology Tianjin Agricultural UniversityTianjin 300392China Max Planck Institute of Molecular Plant Physiology 14476 Potsdam GolmGermany Institute of Food Science and Technology Chinese Academy of Agricultural SciencesBeijingChina

Bitter melon fruit is susceptible to yellowing,softening,and rotting under room-temperature storage conditions,resulting in reduced commercial *** oxide(NO)is an important signaling molecule and plays a crucial role in regulating the fruit postharvest *** this study,we investigated the effects of NO treatment on changes in sensory and firmness of bitter melon fruit during postharvest ***,transcriptomic,metabolomic,and proteomic analyses were performed to elucidate the regulatory mechanisms through which No treatment delays the ripening and senescence of bitter melon *** results show that differentially expressed genes(DEGs)were involved in fruit texture(CSLE,β-Gal,and PME),plant hormone signal transduction(ACS,JAr4,and AUX28),and fruit flavor and aroma(SUS2,LOX,and GDH2).In addition,proteins differentially abundant were associated with fruit texture(PLY,PME,and PGA)and plant hormone signal transduction(PBL15,JAr1,and PYL9).Moreover,No significantly increased the abundance of key enzymes involved in the phenylpropanoid biosynthetic pathway,thus enhancing the disease resistance and alleviating softening of bitter melon ***,differential metabolites mainly included phenolic acids,terpenoids,and *** results provide a theoretical basis for further studies on the physiological changes associated with postharvest ripening and senescence of bitter melon fruit.

关键词： Bitter melon NO treatment Postharvest ripening and senescence

Phylogenomic discovery of deleterious mutants completes the potato breeding revolution

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Molecular Plant 2023年第7期16卷 1103-1105页

作者： alisdair r.fernie Saleh Alseekh Max-Planck-lnstitute of Molecular Plant Physiology Am Muhlenberg 114476 Potsdam-GolmGermany Center for Plant Systems Biology and Biotechnology 4000 PlovdivBulgaria

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 *** 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 *** 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.

关键词： breeding fertility collective

Ancestral genome reconstruction for studies of the green lineage

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Molecular Plant 2023年第4期16卷 657-659页

作者： Marek Mutwil alisdair r.fernie School of Biological Sciences Nanyang Technological University60 Nanyang DriveSingapore 637551Singapore Max-Planck-Institute of Molecular Plant Physiology Am Muhlenberg 114476 Potsdam-GolmGermany

Ancestral sequence reconstruction has become a fundamental aspect of molecular evolution studies being used to trace small-scale sequence modifications through the course of the evolution of *** first proposed in the 1960s(Zuckerkandl and Pauling,1965),it is much more recently that this discipline has attained *** studies were carried out in bacterial,followed by mammalian,systems,but more recently,the approach has additionally been used in plant studies,particularly those focused on the evolution of metabolism(Scossa and fernie,2021).

关键词： Pauling species. attain

Characterization of PetM cytochrome b6f subunit 7 domain-containing protein in tomato

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Horticulture research 2023年第12期10卷 14-25页

作者： Mustafa Bulut Adriano Nunes-Nesi alisdair r.fernie Saleh Alseekh root Biology and Symbiosis Max-Planck-Institute of Molecular Plant PhysiologyAm Mühlenberg 114476 PotsdamGermany Departamento de Biologia Vegetal Universidade Federal de ViçosaViçosa 36570-900 MGBrazil Plant Metabolomics The Center for Plant Systems Biology and Biotechnology4000 PlovdivBulgaria

In recent years,multiple advances have been made in understanding the photosynthetic machinery in model *** transfer to horticultural important fruit crops is challenging and time-consuming due to restrictions in gene editing tools and prolonged life ***,we characterize a gene encoding a PetM domain-containing protein in *** 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 ***,growth-condition-dependent elevation or repression of Chl a/b ratios and de-epoxidation states were identified,underlining possible impairment compensation ***,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 *** 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 ***,the results are discussed with regard to metabolism and their implication to photosynthesis from an agronomic perspective.

关键词： assimilation metabolism consuming

Understanding source-sink interactions: Progress in model plants and translational research to crops

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Molecular Plant 2023年第1期16卷 96-121页

作者： Laise rosado-Souza ryo Yokoyama Uwe Sonnewald alisdair r.fernie Max-Planck-Institute of Molecular Plant Physiology Am Mühlenberg 114476 Potsdam-GolmGermany Department of Biochemistry University of Erlangen-NurembergStaudtstrasse 591058 ErlangenGermany

Agriculture is facing a massive increase in demand per hectare as a result of an ever-expanding population and environmental *** we have learned much about how environmental conditions and diseases impact crop yield,until recently considerably less was known concerning endogenous factors,including within-plant nutrient *** this review,we discuss studies of source-sink interactions covering both fundamental research in model systems under controlled growth conditions and how the findings are being translated to crop plants in the *** this respect we detail efforts aimed at improving and/or combining C3,C4,and CAM modes of photosynthesis,altering the chloroplastic electron transport chain,modulating photorespiration,adopting bacterial/algal carbon-concentrating mechanisms,and enhancing nitrogen-and water-use ***,we discuss how modulating TCA cycle activities and primary metabolism can result in increased rates of photosynthesis and outline the opportunities that evaluating natural variation in photosynthesis may *** source,transport,and sink functions are all covered in this review,we focus on discussing source functions because the majority of research has been conducted in this ***,considerable recent evidence,alongside the evidence from classical studies,demonstrates that both transport and sink functions are also incredibly important determinants of *** thus describe recent evidence supporting this notion and suggest that future strategies for yield improvement should focus on combining improvements in each of these steps to approach yield optimization.

关键词： photosynthesis assimilate transport nitrogen-use efficiency water-use efficiency source-sink natural variance transgenic intervention

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

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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