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Two gene clusters and their positive regulator SlMYB13 that have undergone domestication-associated negative selection control phenolamide accumulation and drought tolerance in tomato

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Molecular Plant 2024年第4期17卷 579-597页

作者： Peng Cao Jun Yang Linghao Xia Zhonghui Zhang Zeyong Wu Yingchen Hao Penghui Liu Chao Wang Chun Li Jie Yang Jun Lai Xianggui Li Meng Deng Shouchuang Wang School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication) Hainan UniversitySanya 572025China College of Tropical Agriculture and Forestry Hainan UniversityHaikou 572208China Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture Hainan UniversityHaikou 572208China

Among plant metabolites,phenolamides,which are conjugates of hydroxycinnamic acid derivatives and polyamines,play important roles in plant adaptation to abiotic and biotic stresses.However,the molecular mechanisms underlying phenolamide metabolism and regulation as well as the effects of domestication and breeding on phenolamide diversity in tomato remain largely unclear.In this study,we performed a metabolite-based genome-wide association study and identified two biosynthetic gene clusters(BGC7 and BGC11)containing 12 genes involved in phenolamide metabolism,including four biosynthesis genes(two 4CL genes,one C3H gene,and one CPA gene),seven decoration genes(five AT genes and two UGT genes),and one transport protein gene(DTX29).Using gene co-expression network analysis we further discovered that SlMYB13 positively regulates the expression of two gene clusters,thereby promoting phenolamide accumulation.genetic and physiological analyses showed that BGC7,BGC11 and SlMYB13 enhance drought tolerance by enhancing scavenging of reactive oxygen species and increasing abscisic acid content in tomato.Natural variation analysis suggested that BGC7,BGC11 and SlMYB13 were negatively selected during tomato domestication and improvement,leading to reduced phenolamide content and drought tolerance of cultivated tomato.Collectively,our study discovers a key mechanism of phenolamide biosynthesis and regulation in tomato and reveals that crop domestication and improvement shapes metabolic diversity to affect plant environmental adaptation.

关键词： tomato phenolamides gene cluster drought tolerance natural variation evolution

Multiomics analyses of two Leonurus species illuminate leonurine biosynthesis and its evolution

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Molecular Plant 2024年第1期17卷 158-177页

作者： Peng Li Meng-Xiao Yan Pan Liu Dan-Jie Yang Ze-Kun He Yun Gao Yan Jiang Yu Kong Xin Zhong Sheng Wu Jun Yang Hong-Xia Wang Yan-Bo Huang Le Wang Xiao-Ya Chen Yong-Hong Hu Qing Zhao Ping Xu shanghai Key Laboratory of Plant Functional Genomics and Resources Shanghai Chenshan Botanical GardenShanghai Chenshan Plant Science Research CenterChineseAcademy of SciencesShanghaiChina College of Life Sciences Shanghai Normal UniversityShanghai 200234China State Key Laboratory of Plant Molecular genetics CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina University of the Chinese Academy of Sciences Beijing 100049China The Research Center of Chiral Drugs Innovation Research Institute of Traditional Chinese MedicineShanghai University of Traditional Chinese Medicine1200 Cailun RoadShanghai 201203China College of Chemistry and Chemical Engineering Shanghai University of Engineering ScienceShanghai 201620China

The Lamiaceae family is renowned for its terpenoid-based medicinal components,but Leonurus,which has traditional medicinal uses,stands out for its alkaloid-rich composition.Leonurine,the principal active compound found in Leonurus,has demonstrated promising effects in reducing blood lipids and treating strokes.However,the biosynthetic pathway of leonurine remains largely unexplored.Here,we present the chromosome-level genome sequence assemblies of Leonurus japonicus,known for its high leonurine production,and Leonurus sibiricus,characterized by very limited leonurine production.By integrating genomics,RNA sequencing,metabolomics,and enzyme activity assay data,we constructed the leonurine biosynthesis pathway and identified the arginine decarboxylase(ADC),uridine diphosphate glucosyltransferase(UGT),and serine carboxypeptidase-like(SCPL)acyltransferase enzymes that catalyze key reactions in this pathway.Further analyses revealed that the UGT–SCPL gene cluster evolved by gene duplication in the ancestor of Leonurus and neofunctionalization of SCPL in L.japonicus,which contributed to the accumulation of leonurine specifically in L.japonicus.Collectively,our comprehensive study illuminates leonurine biosynthesis and its evolution in Leonurus.

关键词： Lamiaceae Leonurus japonicus Leonurus sibiricus genome sequence alkaloids leonurine gene cluster biosynthetic pathway evolution

GST family genes in jujube actively respond to phytoplasma infection

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Horticultural Plant Journal 2024年第1期10卷 77-90页

作者： Qipeng Wang Liman Zhang Chaoling Xue Yao Zhang Xiangrui Meng Zhiguo Liu Mengjun Liu Jin Zhao College of Life Science Hebei Agricultural UniversityBaodingHebei 071000China Hebei Key Laboratory of Plant Physiology and Molecular Pathology Hebei Agricultural UniversityBaodingHebei 071000China Research Center of Chinese Jujube Hebei Agricultural UniversityBaodingHebei 071000China

Jujube witches’broom(JWB)caused by phytoplasma has a severely negative effect on multiple metabolisms in jujube.The GST gene family in plants participates in the regulation of a variety of biotic and abiotic stresses.This study aims to identify and reveal the changes in the jujube GST gene family in response to phytoplasma infection.Here,70 ZjGSTs were identified in the jujube genome and divided into 8 classes.Among them,the Tau-class,including 44 genes,was the largest.Phylogenetic analysis indicated that Tau-class genes were highly conserved among species,such as Arabidopsis,cotton,chickpea,and rice.Through chromosome location analysis,37.1%of genes were clustered,and 8 of 9 gene clusters were composed of Tau class members.Through RT-PCR,qRT-PCR and enzyme activity detection,the results showed that the expression of half(20/40)of the tested ZjGSTs was inhibited by phytoplasma infection in field and tissue culture conditions,and GST activity was also significantly reduced.In the resistant and susceptible varieties under phytoplasma infection,ZjGSTU49-ZjGSTU54 in the cluster IV showed opposite expression patterns,which may be due to functional divergence during evolution.Some upregulated genes(ZjGSTU45,ZjGSTU49,ZjGSTU59,and ZjGSTU70)might be involved in the process of jujube against JWB.The yeast two-hybrid results showed that all 6 Tauclass proteins tested could form homodimers or heterodimers.Overall,the comprehensive analysis of the jujube GST gene family revealed that ZjGSTs responded actively to phytoplasma infection.Furthermore,some screened genes(ZjGSTU24,ZjGSTU49-52,ZjGSTU70,and ZjDHAR10)will contribute to further functional studies of jujube-phytoplasma interactions.

关键词： Chinese jujube GST gene Family Phytoplasma gene cluster Expression Protein interaction

Characterization of inthomycin biosynthetic gene cluster revealing new insights into carboxamide formation

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Chinese Journal of Natural Medicines 2020年第9期18卷 677-683页

作者： WANG Yong-Jiang WANG Li HE Xin XU Dong-Dong TANG Jun MA Ya-Tuan YAN Yi-Jun GU Yu-Cheng YANG Jing HUANG Sheng-Xiong State Key Laboratory of Phytochemistry and P/ant Resources in West China and CAS Center for Excellence in Molecular Plant SciencesKunming Institute of BotanyChinese Academy of SciencesKunming 650201.China College of Chemistry and Pharmacy Norhwest Agriculture and Forestry UniversityYangling 712100.China Savaid Medical School University of Chinese Academy of ScienrcesBejing 100049.China Syngenta Jelott's Hill International Research Centre BracknellBerkshire RG426EYU.K.

Inthomycins are polyketide antibiotics which contain a terminal carboxamide group and a triene chain. Inthomycin B(1) and its two new analogues 2 and 3 were isolated from the crude extract of Streptomyces pactum L8. Identification of the gene cluster for inthomycin biosynthesis as well as the ^(15)N-labeled glycine incorporation into inthomycins are described. Combined with the gene deletion of the rare P450 domain in the NRPS module, a formation mechanism of carboxamide moiety in inthomycins was proposed via an oxidative release of the assembly chain assisted by the P450 domain.

关键词： Inthomycins Biosynthesis gene cluster Carboxamide P450

Watermelon domestication was shaped by stepwise selection and regulation of the metabolome

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Science China(Life Sciences) 2023年第3期66卷 579-594页

作者： Pingli Yuan Congping Xu Nan He Xuqiang Lu Xingping Zhang Jianli Shang Hongju Zhu Chengsheng Gong Hanhui Kuang Tang Tang Yong Xu Shuangwu Ma Dexi Sun Weiqin Zhang Muhammad J.Umer Jian Shi Alisdair R.Fernie Wenge Liu Jie Luo Henan Joint International Research Laboratory of South Asian Fruits and Cucurbits Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhou 450009China Hainan Yazhou Bay Seed Laboratory Sanya Nanfan Research Institute of Hainan UniversitySanya 572025China Peking University Institute of Advanced Agricultural Sciences Weifang 261325China College of Horticulture and Forestry Sciences Huazhong Agricultural UniversityWuhan 430070China Wuhan Metware Biotechnology Co. Ltd.Wuhan 430070China National Watermelon and Melon Improvement Center Beijing Academy of Agricultural and Forestry SciencesBeijing 100097China Max-Planck-Institute of Molecular Plant Physiology Potsdam-Golm 144776Germany College of Tropical Crops Hainan UniversityHaikou 572208China

Although crop domestication has greatly aided human civilization,the sequential domestication and regulation of most quality traits remain poorly understood.Here,we report the stepwise selection and regulation of major fruit quality traits that occurred during watermelon evolution.The levels of fruit cucurbitacins and flavonoids were negatively selected during speciation,whereas sugar and carotenoid contents were positively selected during domestication.Interestingly,fruit malic acid and citric acid showed the opposite selection trends during the improvement.We identified a novel gene cluster(CGC1,cucurbitacin gene cluster on chromosome 1)containing both regulatory and structural genes involved in cucurbitacin biosynthesis,which revealed a cascade of transcriptional regulation operating mechanisms.In the CGC1,an allele caused a single nucleotide change in Cl ERF1 binding sites(GCC-box)in the promoter of Cl Bh1,which resulted in reduced expression of Cl Bh1 and inhibition of cucurbitacin synthesis in cultivated watermelon.Functional analysis revealed that a rare insertion of 244 amino acids,which arose in C.amarus and became fixed in sweet watermelon,in Cl OSC(oxidosqualene cyclase)was critical for the negative selection of cucurbitacins during watermelon evolution.This research provides an important resource for metabolomics-assisted breeding in watermelon and for exploring metabolic pathway regulation mechanisms.

关键词： metabolome mGWAS gene cluster domestication cucurbitacin biosynthesis

Genomics-driven discovery of pneumocandin biosynthetic gene cluster in the fungus Glarea lozoyensis

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Genomics-driven discovery of pneumocandin biosynthetic gene ...

Comparative Study of Apoptosis-related gene Loci in Human,Mouse and Rat Genomes

2012年中国菌物学会学术年会

作者： Javier Ortiz-López Gerald F.Bills Zhiqaing An Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en AndaluciaGranadaSpain Brown Foundation Institute of Molecular Medicine University of Texas Health Science Center at HoustonHoustonTX 77030USA

The antifungal caspofungin is a semi-synthetic derivative of the lipohexapetide pneumocandin B produced by the fungus Glarea lozoyensis.A whole genome sequencing approach has identified the pneumocandin biosynthetic gene cluster which contains a nonribosomal peptide synthetase(NRPS,GLNRPS4),a polyketide synthase(PKS,GLPKS4),and at least nine other modifying enzymes.Disruption mutants of GLNRPS4 or GLPKS4 no longer produce pneumocandin and lose their antibiotic activity against Candida albicans.In additional to pneumocandins,the G.lozoyensis genome reveals a rich repertoire of natural product-encoding gene clusters which include 24 PKSs,6 NRPSs,5 PKS-NRPS hybrids,2 dimethylallyltryptophan synthases,and 3 terpene synthases.Characterization of the gene cluster provides a blueprint for bioengineering novel pneumocandin derivatives with more desirable pharmacological properties such as oral availability.Whole genome estimation of secondary metabolite-encoding genes from G.lozoyensis illustrates the huge potential for natural products drug discovery from the vast fungal kingdom.

关键词： Caspofungin pneumocandin Glarea lozoyensis genome gene cluster

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Acta Biochimica et Biophysica Sinica 2005年第5期37卷 341-348页

作者： Yan-Bin YIN Yong ZHANG Peng YU Jing-Chu LUO Ying JIANG Song-Gang LI Center of Bioinformatics, National Laboratory. of genetic Engineering and Protein Engineering, College of Life Sciences Peking University,Beijing 100871, China Center of Bioinformatics National Laboratory of Genetic Engineering and Protein Engineering College of Life Sciences Peking UniversityBeijing 100871 China

Many genes are involved in mammalian cell apoptosis pathway.These apoptosis genes oftencontain characteristic functional domains,and can be classified into at least 15 functional groups,accordingto previous reports.Using an integrated bioinformatics platform for motif or domain search from threepublic mammalian proteomes(International Protein Index database for human,mouse,and rat),we system-atically cataloged all of the proteins involved in mammalian apoptosis pathway.By localizing those proteinsonto the genomes,we obtained a gene locus centric apoptosis gene catalog for human,mouse and rat.Further phylogenetic analysis showed that most of the apoptosis related gene loci are conserved amongthese three mammals.Interestingly,about one-third of apoptosis gene loci form gene clusters on mammalchromosomes,and exist in the three species,which indicated that mammalian apoptosis gene orders arealso conserved.In addition,some tandem duplicated gene loci were revealed by comparing gene loci clustersin the three species.All data produced in this work were stored in a relational database and may be viewedat http://***/database/apd.php.

关键词： apoptosis gene cluster comparative genomics bioinformatics

Distinct evolution process among type I interferon in mammals

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Protein & Cell 2013年第5期4卷 383-392页

作者： Lei Xu Limin Yang Wenjun Liu CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China China-Japan Joint Laboratory of Molecular Immunology and Molecular Microbiology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

Interferon (IFN) is thought to play an important role in the vertebrate immune system, but systemic knowledge of IFN evolution has yet to be elucidated. To evaluate the phylogenic distribution and evolutionary history of type I IFNs, 13genomes were searched using BLASTn program, and a phylogenetic tree of vertebrate type I IFNs was constructed. In the present study, an IFNδ-like gene in the human genome was identified, refuting the concept that humans have no IFNδ genes, and other mammalian IFN genes were also identified. In the phylogenetic tree, the mammalian IFNβ, IFNɛ, and IFNκ formed a clade separate from the other mammalian type I IFNs, while piscine and avian IFNs formed distinct clades. Based on this phylogenetic analysis and the various characteristics of type I IFNs, the evolutionary history of type I IFNs was further evaluated. Our data indicate that an ancestral IFNα-like gene forms a core from which new IFNs divided during vertebrate evolution. In addition, the data suggest how the other type I IFNs evolved from IFNα and shaped the complex type I IFN system. The promoters of type I IFNs were conserved among different mammals, as well as their genic regions. However, the intergenic regions of type I IFN clusters were not conserved among different mammals, demonstrating a high selection pressure upon type I IFNs during their evolution.

关键词： type I IFN evolutionary history vertebrate gene cluster

Population genetic Structure of the Medicinal Plant Vitex rotundifolia in China: Implications for its Use and Conservation

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Journal of Integrative Plant Biology 2008年第9期50卷 1118-1129页

作者： Yuan Hu Yu Zhu Qiao-Yan Zhang Hai-Liang Xin Lu-Ping Qin Bao-Rong Lu Khalid Rahman Han-Chen Zheng Department of Pharmacognosy School of Pharmacy Second Military Medical University Shanghai 200433 China Chinese People's Liberation Army general Hospital Beijing 100853 China Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering Department of Ecology and Evolutionary Biology Fudan University Shanghai 200433 China Faculty of Science School of Biomolecular Sciences Liverpool John Moores University Liverpool L3 3AF England UK

Vitex rotundifolia L. is an important plant species used in traditional Chinese medicine. For its efficient use and conservation, genetic diversity and clonal variation of V. rotundifolia populations in China were investigated using inter-simple sequence repeat markers. Fourteen natural populations were included to estimate genetic diversity, and a large population with 135 individuals was used to analyze clonal variation and fine-scale spatial genetic structure. The overall genetic diversity （GD） of V. rotundifolia populations in China was moderate （GD=0.190）, with about 40% within-population variation. Across all populations surveyed, the average within-population diversity was moderate （P = 22.6%; GD = 0.086）. A relatively high genetic differentiation （Gst = 0.587） among populations was detected based on the analysis of molecular variance data. Such characteristics of V. rotundifofia are likely attributed to its sexual/asexual reproduction and limited gene flow. The genotypic diversity （D = 0.992） was greater than the average values of a clonal plant, indicating its significant reproduction through seedlings. Spatial autocorrelation analysis showed a clear within-population structure with gene clusters of approximately 20 m. genetic diversity patterns of V. rotundifolia in China provide a useful guide for its efficient use and conservation by selecting particular populations displaying greater variation that may contain required medicinal compounds, and by sampling individuals in a population at 〉20 m spatial intervals to avoid collecting individuals with identical or similar genotypes.

关键词： beach vitex medicinal plant conservation Vitex rotundifolia gene cluster genetic diversity sampling strategy spatial structure.