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Mycorrhizal symbiosis modulates the rhizosphere microbiota to promote rhizobia–legume symbiosis

Molecular Plant 2021年第3期14卷 503-516页

作者： Xiaolin Wang Huan Feng Yayu Wang Mingxing Wang Xingguang Xie Huizhong Chang Like Wang Jicheng Qu Kai Sun Wei He Chunyan Wang Chuanchao Dai Zhaohui Chu Changfu Tian Nan Yu Xuebin Zhang Huan Liu Ertao Wang National Key Laboratory of Plant Molecular Genetics Chinese Academy of Sciences Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200032China Shanghai Key Laboratory of Plant Molecular Sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China College of Forestry Northwest A&F UniversityYangling 712100China State Key Laboratory of Agricultural genomics BGI-ShenzhenShenzhen 518083China Jiangsu Key Laboratory for Microbes and functional genomics Jiangsu Engineering and Technology Research Center for Industrialization of Microbial ResourcesCollege of Life SciencesNanjing Normal UniversityNanjing 210023China State Key Laboratory of Crop Biology College of AgronomyShandong Agricultural UniversityTaianChina Shanghai Hanyubio Co. LtdShanghai 201201China State Key Laboratory of Agrobiotechnology College of Biological SciencesChina Agricultural UniversityBeijing 100193China center for Multi-Omics research Collaborative Innovation Center of Crop Stress BiologyHenan ProvinceKaifeng 475001China institute of Plant Stress Biology State Key Laboratory of Cotton BiologyDepartment of BiologyHenan UniversityKaifeng 475001China

Plants establish symbioses with mutualistic fungi,such as arbuscular mycorrhizal(AM)fungi,and bacteria,such as rhizobia,to exchange key nutrients and *** and symbionts have coevolved and represent vital components of terrestrial *** employ an ancestral AM signaling pathway to establish intracellular symbioses,including the legume–rhizobia symbiosis,in their ***,the relationship between the AM and rhizobial symbioses in native soil is poorly ***,we examined how these distinct symbioses affect root-associated bacterial communities in Medicago truncatula by performing quantitative microbiota profiling(QMP)of 16S rRNA *** found that *** mutants that cannot establish AM or rhizobia symbiosis have an altered microbial load(quantitative abundance)in the rhizosphere and roots,and in particular that AM symbiosis is required to assemble a normal quantitative root-associated microbiota in native ***,quantitative microbial co-abundance network analyses revealed that AM symbiosis affects Rhizobiales hubs among plant microbiota and benefits the plant *** QMP of rhizobial rpoB and AM fungal SSU rRNA genes,we revealed a new layer of interaction whereby AM symbiosis promotes rhizobia accumulation in the rhizosphere of *** further showed that AM symbiosis-conditioned microbial communities within the *** rhizosphere could promote nodulation in different legume plants in native *** that the AM and rhizobial symbioses are critical for crop growth,our findings might inform strategies to improve agricultural ***,our work sheds light on the co-evolution of these intracellular symbioses during plant adaptation to native soil conditions.

关键词： arbuscular mycorrhizae rhizobia symbiosis rhizosphere microbiota quantitative microbiota profiling rpoB

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GeoChip-based analysis of the microbial community functional structures in simultaneous desulfurization and denitrification process

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Journal of Environmental Sciences 2014年第7期26卷 1375-1382页

作者： Hao Yu Chuan Chen Jincai Ma Wenzong Liu Jizhong Zhou Duu-Jong Lee Nanqi Ren Aijie Wang School of Environmental Science and engineering Liaoning Technical University State Key Laboratory of Urban Water Resource and Environment Harbin Institute of Technology Biosciences and Biotechnology Division Lawrence Livermore National LaboratoryLivermore CA 94550 USA research center for Eco-Environmental Sciences Chinese Academy of Sciences Institute for Environmental genomics Department of Botany and Microbiology University of OklahomaNorman OK 73019 USA Department of Chemical engineering National Taiwan University

The elemental sulfur （S^0） recover）, was evaluated in the presence of hi,ate in two development models of simultaneous desulfurization and denitrification （SDD） process. At the loading rates of 0.9 kg S/（m^***） for sulfide and 0.4 kg N/（m^***） for nitrate, SO conversion rate was 91.1% in denitrifying sulfide removal （DSR） model which was higher than in integrated simultaneous desulfurization and denitrification （ISDD） model （25.6%）. A comprehensive analysis of functional diversity, structure and metabolic potential of microbial communities was examined in two models by using functional gene array （GeoChip 2.0）. GeoChip data indicated that diversity indices, community structure, and abundance of functional genes were distinct between two models. Diversity indices （Simpson＇s diversity index （1/D） and Shannon-Weaver index （H′）） of all detected genes showed that with elevated infiuent loading rate, the functional diversity decreased in ISDD model but increased in DSR model. In contrast to ISDD model, the overall abundance of dsr genes was lower in DSR model, while some functional genes targeting from nitrate-reducing sulfide-oxidizingbacteria {NR-SOB）, such as Thiobacillus denitrficans, Sulfurimonas denitrificans, and Paracoccus pantotrophus were more abundant in DSR model which were highly associated with the change of SO conversion rate obtained in two models. The results obtained in this study provide additional insights into the microbial metabolic mechanisms involved in ISDD and DSR models, which in turn will improve the overall performance of SDD process.

关键词： Expanded granular sludge bedElemental sulfur recoverymicrobial communityfunctional gene array

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The genomes of medicinal skullcaps reveal the polyphyletic origins of clerodane diterpene biosynthesis in the family Lamiaceae

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Molecular Plant 2023年第3期16卷 549-570页

作者： Haixiu Li Song Wu Ruoxi Lin Yiren Xiao Ana Luisa Malaco Morotti Ya Wang Meytal Galilee Haowen Qin Tao Huang Yong Zhao Xun Zhou Jun Yang Qing Zhao Angelos K.Kanellis Cathie Martin Evangelos C.Tatsis National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200032China University of Chinese Academy of Sciences Beijing 100049China Novogene Bioinformatics Institute BeijingChina Shanghai Key Laboratory of Plant functional genomics and Resources Shanghai Chenshan Botanical GardenShanghai Chenshan Plant Science Research CenterChinese Academy of SciencesShanghai 201602 Group of Biotechnology of Pharmaceutical Plants Lab.of PharmacognosyDepartment of Pharmaceutical SciencesAristotle University of Thessaloniki54124 ThessalonikiGreece John Innes Centre Norwich NR47UHUK CEPAMS-CAS-JIC Centre of Excellence for Plant and microbial Sciences Shanghai 200032China

The presence of anticancer clerodane diterpenoids is a chemotaxonomic marker for the traditional Chinese medicinal plant Scutellaria barbata,although the molecular mechanisms behind clerodane biosynthesis are ***,we report a high-quality assembly of the 414.98 Mb genome of *** into 13 *** phylogenomic and biochemical data,we mapped the plastidial metabolism of kaurene(gibberellins),abietane,and clerodane diterpenes in three species of the family Lamiaceae(Scutellaria barbata,Scutellaria baicalensis,and Salvia splendens),facilitating the identification of genes involved in the biosynthesis of the clerodanes,kolavenol,and *** show that clerodane biosynthesis evolved through recruitment and neofunctionalization of genes from gibberellin and abietane *** the assumed monophyletic origin of clerodane biosynthesis,which is widespread in species of the Lamiaceae,our data show distinct evolutionary lineages and suggest polyphyletic origins of clerodane biosynthesis in the family *** study not only provides significant insights into the evolution of clerodane biosynthetic pathways in the mint family,Lamiaceae,but also will facilitate the production of anticancer clerodanes through future metabolic engineering efforts.

关键词： Scutellaria barbata genome clerodane diterpenoids biosynthesis specialized metabolism evolution

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Ratiometric fluorescence immunoassay of SARS-CoV-2 nucleocapsid protein via Si-FITC nanoprobe-based inner filter effect

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Nano research 2023年第4期16卷 5383-5390页

作者： Guobin Mao Yang Yang Shijie Cao Silu Ye Yifang Li Wei Zhao Hongwei An Yingxia Liu Junbiao Dai Yingxin Ma CAS Key Laboratory of Quantitative engineering Biology Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China Guangxi University of Chinese Medicine Nanning 530001China Shenzhen Key Laboratory of Pathogen and Immunity National Clinical Research Center for infectious diseaseState Key Discipline of Infectious DiseaseShenzhen Third People’s HospitalSecond Hospital Affiliated to Southern University of Science and TechnologyShenzhen 518112China

The global pandemic caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)virus has necessitated rapid,easy-to-use,and accurate diagnostic methods to monitor the virus ***,a ratiometric fluorescence enzyme-linked immunosorbent assay(ELISA)was developed using Si-fluorescein isothiocyanate nanoparticles(FITC NPs)for detecting SARSCoV-2 nucleocapsid(N)***-FITC NPs were prepared by a one-pot hydrothermal method using 3-aminopropyl triethoxysilane(APTES)-FITC as the Si *** method did not need post-modification and avoided the reduction in quantum yield and *** p-nitrophenyl(pNP)produced by the alkaline phosphatase(ALP)-mediated hydrolysis of pnitrophenyl phosphate(pNPP)could quench Si fluorescence in Si-FITC NPs via the inner filter *** ELISA,an immunocomplex was formed by the recognition of capture antibody/N protein/reporter ***-linked secondary antibody bound to the reporter antibody and induced pNPP hydrolysis to specifically quench Si fluorescence in Si-FITC *** change in fluorescence intensity ratio could be used for detecting N protein,with a wide linearity range(0.01-10.0 and 50-300 ng/mL)and low detection limit(0.002 ng/mL).The concentration of spiked SARS-CoV-2 N protein could be determined accurately in human ***,this proposed method can accurately distinguish coronavirus disease 2019(COVID-19)and non-COVID-19 patient ***,this simple,sensitive,and accurate method can be applied for the early diagnosis of SARS-CoV-2 virus infection.

关键词： Si-fluorescein isothiocyanate(FITC)nanoparticles ratiometric fluorescent probe severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) inner filter effect enzyme-linked immunosorbent assay(ELISA)

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Gene editing:from technologies to applications in research and beyond

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Science China(Life Sciences) 2022年第4期65卷 657-659页

作者： Wensheng Wei Caixia Gao Biomedical Pioneering Innovation center Beijing Advanced Innovation Center for GenomicsPeking-Tsinghua Center for Life SciencesPeking University Genome Editing Research CenterState Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking UniversityBeijing100871China State Key Laboratory of Plant Cell and Chromosome engineering Center for Genome EditingInstitute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing100101China College of Advanced Agricultural Sciences University of Chinese Academy of SciencesBeijing100049China

Cutting-edge gene editing technologies enable broadened genomic alternations and accelerate opportunities to use these tools in biomedicine, agriculture, and animal model development. In this issue, Li et al.(2022) reviews the tools of gene editing and highlights key technological developments and its broad applications in biomedicine, hoping to accelerate new discoveries and therapies in biomedicine.

关键词： development editing

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Therapeutic targeting miR130b counteracts diffuse large B-cell lymphoma progression via OX40/OX40L-mediated interaction with Th17 cells

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Signal Transduction and Targeted Therapy 2022年第4期7卷 1297-1310页

作者： Rui Sun Pei-Pei Zhang Xiang-Qin Weng Xiao-Dong Gao Chuan-Xin Huang Li Wang Xiao-Xia Hu Peng-Peng Xu Lin Cheng Lu Jiang Di Fu Bin Qu Yan Zhao Yan Feng Hong-Jing Dou Zhong Zheng Wei-Li Zhao Shanghai Institute of Hematology State Key Laboratory of Medical GenomicsNational Research Center for Translational Medicine at ShanghaiRuijin HospitalShanghai Jiao Tong University of MedicineShanghaiChina State Key Laboratory of Metal Matrix Composites School of Materials Science and EngineeringNational Research Center for Translational Medicine at ShanghaiShanghai Jiao Tong UniversityShanghaiChina Department of Immunobiology and Microbiology Shanghai Institute of ImmunologyShanghai Jiao Tong University School of MedicineShanghaiChina Department of Laboratory Medicine Shanghai RuiJin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina State Key Laboratory of microbial Metabolism School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina

MicroRNAs(miRNAs)are involved in lymphoma progression by regulating the tumor *** miR130b is overexpressed in diffuse large B-cell lymphoma(DLBCL),inducing Th17 cell *** further illustrate its biological significance and therapeutic rationale,miR130b was detected by quantitative real-time PCR in the serum samples of 532 newly diagnosed DLBCL *** mechanism of miR130b on lymphoma progression and the tumor microenvironment was investigated both in vitro and in *** targeting miR130b was also evaluated,including OX40 agonistic antibody and lipid nanoparticles(LNPs)-miR130b *** results showed that serum miR130b significantly correlated with tumor miR130b and serum interleukin-17,indicating lymphoma relapse and inferior survival of DLBCL ***130b overexpression altered tumor microenvironment signaling pathways and increased Th17 cell *** mechanism of action,miR130b downregulated tumor OX40L expression by directly targeting IFNAR1/p-STAT1 axis,recruiting Th17 cells via OX40/OX40L interaction,thereby promoting immunosuppressive function of Th17 *** co-culture systems of B-lymphoma cells with immune cells,miR130b inhibited lymphoma cell autophagy,which could be counteracted by OX40 agonistic antibody and LNPs-miR130b *** murine xenograft model established with subcutaneous injection of A20 cells,both OX40 agonistic antibody and LNPs-miR130b antagomir remarkably inhibited Th17 cells and retarded miR130b-overexpressing tumor *** conclusion,as an oncogenic biomarker of DLBCL,miR130b was related to lymphoma progression through modulating OX40/OX40L-mediated lymphoma cell interaction with Th17 cells,attributing to B-cell lymphoma sensitivity towards OX40 agonistic *** miR130b using LNPs-miR130b antagomir could also be a potential immunotherapeutic strategy in treating OX40-altered lymphoid malignancies.

关键词： lymphoma miR130b inhibited

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The Genome of Medicinal Plant Macleaya cordata Provides New Insights into Benzylisoquinoline Alkaloids Metabolism

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Molecular Plant 2017年第7期10卷 975-989页

作者： Xiubin Liu Yisong Liu Peng Huang Yongshuo Ma Zhixing Qing Qi Tang Huifen Cao Pi Cheng Yajie Zheng Zejun Yuan Yuan Zhou Jinfeng Liu Zhaoshan Tang Yixiu Zhuo Yancong Zhang Linlan Yu Jialu Huang Peng Yang Qiong Peng dinbo Zhang Wenkai Jiang Zhonghua Zhang Kui Lin Dae-Kyun Ro Xiaoya Chen Xingyao Xiong Yi Shang Sanwen Huang Jianguo Zeng National and Local Union engineering research center of Veterinary Herbal Medicine Resource and Initiative Hunan Co-Innovation center for Utilization of Botanical functional Ingredients Horticulture and Landscape College Veterinary Medicine College Hunan Agricultural University Changsha 410128 China Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture Sino-Dutch Joint Laboratory of Horticultural Genomics Beijing 100081 China Agricuitural Genome Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518124 China School of Pharmacy Hunan University of Chinese Medicine Changsha 410208 China MOE Key Laboratory for Biodiversity Science and Ecological engineering and College of Life Sciences Beijing Normal University Beijing 100875 China Micolta Bioresource Inc. Changsha 410016 China Herbal Extract engineering research center Changsha 410331 China Biotechnology research center Hunan Academy of Agricultural Sciences Changsha 410125 China Novogene Bioinformatics Institute Beijing 100083 China Department of Biological Sciences University of Calgary Calgary T2N1N4 Canada National Key Laboratory of Plant Molecular Genetics National Plant Gene Research Center Institute of Plant Physiology and Ecology Shanghai Institutes forBiological Sciences Chinese Academy of Sciences Shanghai 200032 China Plant Science research center Shanghai Chenshan Botanical Garden Shanghai 201602 China

The overuse of antibiotics in animal agriculture and medicine has caused a series of potential threats to public health. Macleaya cordata is a medicinal plant species from the Papaveraceae family, providing a safe resource for the manufacture of antimicrobial feed additive for livestock. The active constituents from M. cordata are known to include benzylisoquinoline alkaloids （BIAs） such as sanguinarine （SAN） and chelerythrine （CHE）, but their metabolic pathways have yet to be studied in this non-model plant. The active biosynthesis of SAN and CHE in M. cordata was first examined and confirmed by feeding ^13C-labeled tyrosine. To gain further insights, we de novo sequenced the whole genome of M. cordata, the first to be sequenced from the Papaveraceae family. The M. cordata genome covering 378 Mb encodes 22,328 predicted protein-coding genes with 43.5% being transposable elements. As a member of basal eudicot, M. cordata genome lacks the paleohexaploidy event that occurred in almost all eudicots. From the genomics data, a complete set of 16 metabolic genes for SAN and CHE biosynthesis was retrieved, and 14 of their biochemical activities were validated. These genomics and metabolic data show the conserved BIA metabolic pathways in M. cordata and provide the knowledge foundation for future productions of SAN and CHE by crop improvement or microbial pathway reconstruction.

关键词： Macleaya cordata genome Benzylisoquinoline alkaloids Secondary metabolism Sanguinarine Chelerythrine Isotopic labeling

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Foci of Future Studies on Abiotic Stress Tolerance of Maize in the Era of Post-genomics

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Journal of Integrative Agriculture 2012年第8期11卷 1236-1244页

作者： LI You-zhi FAN Xian-wei LIAO Jiang-xiong State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Ministry of Science and Technology/Key Laboratory of Microbial and Plant Genetic Engineering Ministry of Education/College of Life Science and Technology Guangxi University Guangxi 530005 P.R. China Sugarcane research center Chinese Academy of Agriculture Sciences Guangxi 530007 P.R.China

Genetic and metabolic engineering approaches are powerful tools for improving the tolerance of maize to abiotic stresses because they are faster and can afford greater control over agronomically useful traits. However, in-depth understanding of the molecular mechanisms controlling response to abiotic stresses is the prerequisite for successful implementation of these strategies. A great flaw to dissect the biological mechanisms by genome sequencing is that genome sequencing approach could not reflect real-time molecular actions of plants especially under the stresses because the living organisms rarely live in unchanging environments. Post-genomics such as transcriptomics, metabolomics, and proteomics can generate knowledge that is closer to the biological processes. With the development of post-genomics, it can be expected that voluminous data will be generated. This paper proposes that future research on maize stress tolerance in the era of post-genomics should focus on metabolomics and proteomics; stress tolerance of whole plant rather than individual tissues or organs; coordination of expression of genes among tissues; characterization of promoters of stress-responsive genes; interrelation between mechanisms for tolerance to, and growth recovery from the stress; hexose metabolism as well as the glycolysis pathway; and foundation genotypes.

关键词： maize abiotic stresses research foci era of post-genomics

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Citrus black spot detection using hyperspectral imaging

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International Journal of Agricultural and Biological engineering 2014年第6期7卷 20-27页

作者： Daegwan Kim Thomas F.Burks Mark A.Ritenour Jianwei Qin Asan Institute for Life Sciences Asan Medical CenterSongpa-guSeoul 138-736Korea Department of Agricultural&Biological engineering University of FloridaGainesvilleFL 32611USA Indian River research and Education center(IRREC) University of FloridaFt.PierceFL 34945USA Environmental microbial and Food Safety Laboratory(EMFSL) Agricultural Research ServiceU.S.Department of AgricultureBeltsvilleMD 20705USA

This paper describes the development of a hyperspectral imaging approach for identifying fruits infected with citrus black spot(CBS).Hyperspectral images were taken of healthy fruit and those with CBS symptoms or other potentially confounding peel conditions such as greasy spot,wind scar,or *** angle mapper(SAM)and spectral information divergence(SID)hyperspectral analysis approaches were used to classify fruit samples into two classes:CBS or *** classification accuracy for CBS with SAM approach was 97.90%,and 97.14% with *** combination of hyperspectral images and two classification approaches(SID and SAM)have proven to be effective in recognizing CBS in the presence of other potentially confounding fruit peel *** study result can be a reference for the non-destructive detection of fruits infected with citrus black spot.

关键词： citrus black spot hyperspectral imaging spectral angle mapper spectral information divergence imaging processing

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植物内生真菌拟茎点霉对宿主凋落物的分解作用与调节机制研究（英文）

植物内生真菌拟茎点霉对宿主凋落物的分解作用与调节机制研究（英...

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2014年第七届中国模式真菌研讨会

作者： Hong-Wei Wang Wei Zhang Chun-Lun Su 戴传超 Jiangsu Key Laboratory for Microbes and functional genomics Jiangsu Engineering and Technology Research Center for Industrialization of Microbial ResourcesCollege of Life SciencesNanjing Normal University

Phytoestrogens are plant-derived hormonally active compounds known to cause varied reproductive,immunosuppressive and behavioral effects in *** this study,broad-spectrum endophytic fungi Phomopsis liquidambari(strain B3) was used to decompose luteolin,a common phytoestrogen,as the sole carbon and energy *** optimum concentration of luteolin supplied in culture as the carbon source was determined to be 200 mg L,with maximum biomass of fungal growth and,97%and 99%degraded by *** in liquid culture and soil conditions,*** fungal metabolic pathway of luteolin was investigated using high performance liquid chromatography-mass spectrometry(HPLC-MS).The results showed that luteoli was first decomposed to caffeic acid and *** two intermediate products were degraded to protocatechuic acid and hydroxyquinol,respectively,and then rings were opened by ring-cleavage *** dynamic activities of ring-cleavage dioxygenases,protocatechuate 3,4-dioxygenase and hydroxyquinol 1,2-dioxygenase,were corresponded with changes in corresponding substrate *** novel genes encoding the protocatechuate 3,4-dioxygenase and hydroxyquinol 1,2-dioxygenase were successfully ***,the results of reverse transcription quantitative PCR demonstrate that mRNA expression level of protocatechuate 3,4-dioxygenase and hydroxyquinol 1,2-dioxygenase increased significantly after strain B3 was induced by intermediate product caffeic acid and phloroglucinol,*** results revealed that *** can biodegrade luteolin efficiently and could potentially be used to bioremediate phytoestrogen contamination.

关键词： Endophytic fungi Luteolin HPLC-MS Gene cloning qRT-PCR

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