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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

Development of a widely targeted volatilomics method for profiling volatilomes in plants

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Molecular Plant 2022年第1期15卷 189-202页

作者： honglun yuan Guangping Cao Xiaodong Hou Menglan Huang Pengmeng Du Tingting Tan Youjin Zhang Haihong Zhou Xianqing Liu Ling Liu Yiding Jiangfang Yufei Li Zhenhuan Liu Chuanying Fang Liqing Zhao Alisdair R.Fernie Jie Luo College of Tropical Crops Hainan UniversityHaikou 570288China Sanya Nanfan Research Institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya572025China College of Chemistry and Environmental Engineering Shenzhen UniversityShenzhen 518060China National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China Department of Molecular Physiology Max-Planck-lnstitute of Molecular Plant PhysiologyAm Muhlenberg 114476 Potsdam-GolmGermany

Volatile organic compounds play essential roles in plant environment interactions as well as determining the fragrance of *** gas chromatography-mass spectrometry-based untargeted metabolo-mics is commonly used to assess plant volatiles,it suffers from high spectral convolution,low detection sensitivity,a limited number of annotated metabolites,and relatively poor ***,we report a widely targeted volatilomics(WTV)method that involves using a“targeted spectra extraction”algorithm to address spectral convolution,constructing a high-coverage MS2 spectral tag library to expand volatile annotation,adapting a multiple reaction monitoring mode to improve sensitivity,and using regression models to adjust for signal *** newly developed method was used to profile the volatilome of rice *** with the untargeted method,the newly developed WTV method shows higher sensitivity(for example,the signal-to-noise ratio of guaicol increased from 4.1 to 18.8),high annotation coverage(the number of annotated volatiles increased from 43 to 132),and better reproducibility(the number of volatiles in quality control samples with relative standard deviation value below 30.0%increased from 14 to 92 after normalization).Using the WTV method,we studied the metabolic responses of tomato to environmental stimuli and profiled the volatilomes of different rice *** results identified benzothiazole as a potential airborne signal priming tomato plants for enhanced defense and 2-nonanone and 2-heptanone as novel aromatic compounds contributing to rice *** case studies suggest that the widely targeted volatilomics method is more efficient than those currently used and may considerably promote plant volatilomics studies.

关键词： widely targeted volatilomics GC-MS MS2T library plant volatilome rice tomato

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

番茄甾体生物碱合成酶基因SlERT1b的功能验证及转录调控

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槟榔碱合成前体物质的空间分布及槟榔碱合成通路解析

热带作物学报 2021年第12期42卷 3451-3461页

作者：黎晗史云霞袁弘伦刘贤青罗杰海南大学生命科学与药学院海南海口 570228 海南大学热带作物学院海南海口 570228

绿色番茄中的甾体生物碱主要以α-番茄碱(α-tomatine)形式存在,使得果实带有苦味而不适宜食用.在果实成熟过程中,α-番茄碱会通过一系列酶促反应生成七叶皂苷A(esculeoside A),使果实适宜食用,然而这一代谢途径尚未被完全解析.本课题... 详细信息

绿色番茄中的甾体生物碱主要以α-番茄碱(α-tomatine)形式存在,使得果实带有苦味而不适宜食用.在果实成熟过程中,α-番茄碱会通过一系列酶促反应生成七叶皂苷A(esculeoside A),使果实适宜食用,然而这一代谢途径尚未被完全解析.本课题组在先前研究中鉴定出一个参与这一代谢途径的糖基转移酶SlERT1b,本研究通过番茄的遗传转化实验研究SlERT1b的功能,并利用LC-MS检测其中的甾体生物碱,验证该基因可发挥糖基转移酶的功能.此外,施加外源乙烯和乙烯抑制剂1-MCP后,发现乙烯可调控SlERT1b基因,并影响甾体生物碱的合成途径.同时鉴定出可以调控SlERT1b基因的转录因子SlJERF1和SlAREB2.该研究结果为今后番茄遗传育种提供理论基础.

关键词：番茄甾体生物碱乙烯转录因子

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热带生物学报 2021年第3期12卷 271-278页

作者：徐航刘贤青袁弘伦罗杰海南大学热带作物学院/海南省热带生物资源可持续利用重点实验室海口570228

为探究槟榔中的生物活性成分,本研究以不同组织的槟榔为材料,利用高效液相色谱-质谱联用技术进行了非靶向代谢组学检测,经过定性分析,共获得了158个代谢物(包括氨基酸、脂质、核苷酸、生物碱和类黄酮等物质),首次在槟榔中发现槟榔次碱... 详细信息

为探究槟榔中的生物活性成分,本研究以不同组织的槟榔为材料,利用高效液相色谱-质谱联用技术进行了非靶向代谢组学检测,经过定性分析,共获得了158个代谢物(包括氨基酸、脂质、核苷酸、生物碱和类黄酮等物质),首次在槟榔中发现槟榔次碱己糖苷的存在,并对氨基酸和生物碱进行了相对定量,发现芳香族氨基酸和支链氨基酸主要分布在种子中;烟酸衍生物在叶片中含量较高,槟榔次碱己糖苷和去甲基槟榔碱在外果皮中含量较高,其余生物碱均显示出在果实中尤其是种子中有较多的积累。基于烟酸、葫芦巴碱和槟榔碱的结构相似性,推测槟榔碱的合成通路是以天冬氨酸为起点,以烟酸、葫芦巴碱为基本骨架进行合成的。

关键词：槟榔槟榔碱代谢组空间分布代谢通路

Limosilactobacillus reuteri CCFM1132 Modulates Gut Microbiota and Alleviates Hyperuricemia: A Randomized， Double-Blind， Placebo-Controlled Trial

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Food Science and Human Wellness 2024年

作者： Lei Sun Yang Cao Feng Hang Dongbo yuan honglun Wang Jianxin Zhao Gang Wang Guohong Qiao Liyun Wang State Key Laboratory of Food Science and Resources， Jiangnan University School of Food Science and Technology， Jiangnan University Department of Biostatistics， Harvard T.H.Chan School of Public Health National Engineering Research Center for Functional Food， Jiangnan University (Yangzhou) Institute of Food Biotechnology， Jiangnan University Department of Clinical Laboratory， Yixing People's Hospital， Affiliated to Jiangsu University Qinghai Provincial Key Laboratory of Tibetan Medicine Research Department of Endocrine Metabolism， Yixing People's Hospital， Affiliated to Jiangsu University

This randomized， double-blind， placebo-controlled trial evaluated the uric acid （UA）-lowering effect of Limosilactobacillus reuteri CCFM1132 in young males with hyperuricemia. Participants received 1×1010CFU of L. reuteri CCFM1132 （n=34） or placebo （n=31） daily for 8 weeks. After the intervention， serum UA concentration significantly decreased， along with a reduction in xanthine oxidase （XOD） activity compared to the placebo group （P < 0.01）. Indicators of liver （aspartate transaminase and alanine transaminase） and renal （urea and creatinine） functions improved. Short-chain fatty acid （SCFA） concentrations significantly increased， with an upregulated abundance of SCFA producers （Fusicatenibacter， Ruminococcaceae UCG＿014， and Ruminococcus 1） in the gut. Additionally， correlation analysis revealed that concentrations of SCFAs， particularly acetate and butyrate， were strongly negatively correlated with UA concentration and XOD activity. These findings suggest that L. reuteri CCFM1132 relieves hyperuricemia by enhancing the abundance of SCFA producers in the gut to promote SCFA production and by suppressing XOD activity. This study provides a valuable reference for developing new treatments for hyperuricemia.

关键词：

转录组学挖掘黑果枸杞中花青素生物合成代谢关键bHLH调控基因

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分子植物育种 2023年第6期21卷 1864-1873页

作者：包雪梅胡娜宗渊王洪伦中国科学院西北高原生物研究所中国科学院藏药研究重点实验室西宁810001 中国科学院西北高原生物研究所青海省作物分子育种重点实验室西宁810001 青海师范大学教育学院西宁810016 中国科学院大学北京100049

黑果枸杞果实中富含花青素,为探究黑果枸杞和白果枸杞的基因表达差异,挖掘控制黑果枸杞黑果性状的主效基因,本研究利用RNA-Seq技术对黑果枸杞和白果枸杞进行转录组测序与生物信息学分析。结果表明,黑果枸杞和白果枸杞中共检测到25 279... 详细信息

黑果枸杞果实中富含花青素,为探究黑果枸杞和白果枸杞的基因表达差异,挖掘控制黑果枸杞黑果性状的主效基因,本研究利用RNA-Seq技术对黑果枸杞和白果枸杞进行转录组测序与生物信息学分析。结果表明,黑果枸杞和白果枸杞中共检测到25 279个基因差异表达,其中12 381个基因在黑果枸杞表达上调,12 898个基因表达下调。KEGG富集结果显示,共有571个差异表达基因参与植物次生代谢产物合成,尤其是在黄酮类和花青素生物合成代谢通路中差异最为明显。黑果枸杞中共有8个参与花青素合成代谢的结构基因的表达量均高于白果枸杞,说明花青素的生物合成可能与黑果枸杞黑果性状相关。调控花青素生物合成的bHLH转录因子***5_All的表达水平比白果枸杞增强了2 139.57倍,这个基因很有可能是控制黑果枸杞黑果性状的候选基因。本研究筛选到控制黑果枸杞花青素合成代谢的候选基因,为黑果枸杞的分子遗传机理及进一步的基因功能研究提供了依据。

关键词：黑果枸杞白果枸杞差异表达花青素

西伯利亚白刺NsMYB5调控果实花青素生物合成

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西北农业学报 2023年第8期32卷 1215-1222页

作者：包雪梅宗渊胡娜刘宝龙王洪伦中国科学院藏药研究重点实验室西北高原生物研究所西宁810008 青海师范大学西宁810008 中国科学院大学北京100049 青海省作物分子育种重点实验室西宁810008

基于西伯利亚白刺红果、黑果果皮转录组数据,本研究筛选并克隆获得一个与西伯利亚白刺果实花青素和原花青素合成代谢相关的R2R3-MYB转录因子,命名为NsMYB5。该基因ORF为840 bp,编码279个氨基酸,NsMYB5具有完整的SANT、MYB domain及HLH-M... 详细信息

基于西伯利亚白刺红果、黑果果皮转录组数据,本研究筛选并克隆获得一个与西伯利亚白刺果实花青素和原花青素合成代谢相关的R2R3-MYB转录因子,命名为NsMYB5。该基因ORF为840 bp,编码279个氨基酸,NsMYB5具有完整的SANT、MYB domain及HLH-MYB domain结构域,属于R2R3-MYB转录因子,与调控花青素和原花青素合成相关的香雪兰FhMYB5同源性较高。过表达NsMYB5烟草花瓣和雄蕊积累大量花青素,呈现深紫色,而叶片和茎仅有少量花青素积累,局部呈现淡紫色。转基因株系中花的花青素和原花青素含量均显著高于野生型(P<0.05)。结果表明,NsMYB5可以正向调控花青素和原花青素的合成,这为西伯利亚白刺果实果皮呈色的分子遗传机理提供了理论依据。

关键词：西伯利亚白刺 NsMYB5 花青素原花青素

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高空台多任务模拟指定时间抗扰控制

推进技术 2024年第9期45卷 241-251页

作者：李金柏伦岳斌王宏伦钱秋朦张松但志宏北京航空航天大学自动化科学与电气工程学院北京100191 北京航空航天大学沈元学院北京100191 中国航发四川燃气涡轮研究院高空模拟技术重点实验室四川绵阳621000

针对高空台多任务模拟试验对飞行环境模拟控制系统所提出的高品质、高精度、强抗扰的迫切需求,设计了一种基于障碍李雅普诺夫函数的高空台进气环境模拟指定时间抗扰控制方法。建立了包含进气系统管道容腔和调节阀执行机构的高空台受控... 详细信息

针对高空台多任务模拟试验对飞行环境模拟控制系统所提出的高品质、高精度、强抗扰的迫切需求,设计了一种基于障碍李雅普诺夫函数的高空台进气环境模拟指定时间抗扰控制方法。建立了包含进气系统管道容腔和调节阀执行机构的高空台受控对象模型,并在此基础上进行了仿射形式推导和解耦设计。针对高空台强非线性、强扰动的特性,设计了以指定时间收敛的抗扰控制方法;同时为了抑制推力瞬变过程中系统状态剧烈变化,引入了障碍李雅普诺夫函数对压强和温度误差分别进行限制。在高空台多任务模拟试验控制仿真中,该方法可使压强和温度的绝对积分误差比线性自抗扰控制方法小89.5%和88.9%,在剧烈受扰后调节时间短10.4%和9.0%,而且相比于常规的指定时间方法能够满足所设定的状态误差约束。结果表明,基于障碍李雅普诺夫函数的指定时间抗扰控制方法能够进一步提升多任务模拟试验中的控制精度、调节速度以及抗扰能力。

关键词：高空台进气环境模拟多任务模拟试验指定时间抗扰控制障碍李雅普诺夫函数状态误差约束