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Late-stage cascade of oxidation reactions during the biosynthesis of oxalicine B in Penicillium oxalicum

Acta Pharmaceutica Sinica B 2023年第1期13卷 256-270页

作者： Tao Zhang Guowei Gu Guodong Liu Jinhua Su Zhilai Zhan Jianyuan Zhao Jinxiu Qian Guowei Cai Shan Cen Dewu Zhang Liyan Yu Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100050China state Key Laboratory of Microbial Technology National Glycoengineering Research CenterShandong UniversityQingdao 266237China The Third Medical center The General Hospital of People's Liberation ArmyBeijing 100039China national resource center for Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China

Oxalicine B(1)is an a-pyrone meroterpenoid with a unique bispirocyclic ring system derived from Penicillium *** biosynthetic pathway of 15-deoxyoxalicine B(4)was preliminarily reported in Penicillium canescens,however,the genetic base and biochemical characterization of tailoring reactions for oxalicine B(1)has remained *** this study,we characterized three oxygenases from the metabolic pathway of oxalicine B(1),including a cytochrome P450 hydroxylase OxaL,a hydroxylating Fe(II)/a-KG-dependent dioxygenase OxaK,and a multifunctional cytochrome P450 ***,OxaK can catalyze various multicyclic intermediates or shunt products of oxalicines with impressive substrate *** was further proven via biochemical assays to have the ability to convert 15-hydroxdecaturin A(3)to 1 with a spiro-lactone core skeleton through oxidative *** also solved the mystery of OxaL that controls C-15 *** investigation of the wild-type strain and deletants enabled us to identify 10 metabolites including three new compounds,and the isolated compounds displayed potent anti-influenza A virus bioactivities exhibiting IC50values in the range of 4.0-19.9μmol/*** studies have allowed us to propose a late-stage biosynthetic pathway for oxalicine B(1)and create downstream derivatizations of oxalicines by employing enzymatic strategies.

关键词： Oxalicine B Meroterpenoid Biosynthesis Cytochrome P450 Anti-IAV activity

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Identification of New Allele of FLOURY ENDOSPERM2 in White-Core Endosperm Mutant of Rice

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Rice science 2022年第5期29卷 407-411,I0017,I0018页

作者： BAO Jinsong ZHANG Yu ZHAO Jiajia CHEN Yaling WU Weixun CAO Liyong XU Feifei Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs and Zhejiang Province/Institute of Nuclear Agricultural Sciences College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058China Hainan Institute of Zhejiang University Yazhou DistrictSanya 572025China Laboratory of plant genetic Improvement and Biotechnology Jiangxi Normal UniversityNanchang 330000China State Key Laboratory of Rice Biology/Chinese national center for Rice Improvement China National Rice Research InstituteHangzhou 310006China

Identification of regulatory genes from chalky/floury endosperm mutants is an important approach to understand the mechanism of starch biosynthesis to accelerate rice grain quality improvement.A mutant GM645,identified from 60Coγ-irradiation of an indica rice Guanglu’ai 4(GLA4),exhibited white-core endosperm and altered starch physicochemical ***,the causal gene responsible for the white-core endosperm in GM645 has not been ***,we developed a recombined inbred line(RIL,F7)population derived from a cross between GM645 and a japonica rice Tainong 67(TN67)with translucent *** analysis combined with next generation sequencing revealed five single nucleotide polymorphisms(SNPs)in four candidate genes that were highly associated with the white-core *** them,one base pair deletion in Os04g0645100 resulted in a frame shift mutation after the 983th amino acid(aa),and a premature stop codon occurred after the other 11 ***,functional annotation revealed that Os04g0645100 was previously characterized as the FLOURY ENDOSPERM2(FLO2)***-length coding sequence from Os04g0645100 driven by the maize ubiquitin promoter was transformed into GM645,and seeds from these transgenic plants expressing Os04g0645100 were largely rescued to translucent,indicating that Os04g0645100 was responsible for the whitecore endosperm in GM645.

关键词： properties white ERM

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Identifying QTL and candidate genes for prolificacy in maize

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The Crop Journal 2023年第2期11卷 531-539页

作者： Min Wang Renyu Zhang Yangzi Zhao Jieyuan Yao Weiya Li Zhixing Yang Fei Sun Xiaohong Yang State Key Laboratory of plant Physiology and Biochemistry and national Maize Improvement center of China China Agricultural UniversityBeijing 100193China Institute of Advanced Agricultural Technology Qilu Normal UniversityJinan 250200ShandongChina

In maize,prolificacy,the number of ears per plant,is a trait of interest to maize breeders for breeding high grain-yielding cultivars or specialty corn,as well as being a model trait for decoding the molecular mechanism of maize *** genetic basis remains largely *** identified a stable quantitative trait locus,qEN7,for ear number on chromosome 7 in both F2 and F2:3 populations derived from a single cross between the nonprolific inbred line Mo17 and the prolific inbred line LAN404 derived from the landrace ***7 explained 10.7%-11.9%of phenotypic variation,and the LAN404 allele at this locus was associated with an increase of around one ear per ***7 was confined by fine-mapping to a 0.56-Mb region containing eight annotated *** of selection,gene expression patterns in various maize tissues,and sequence polymorphisms between the two parental lines suggested that Zm00001d020683,which encodes a putative INDETERMINATE DOMAIN(IDD)transcription factor,is the most likely candidate gene underlying ***00001d020683 is expressed mainly in the vegetative meristem,immature ears,and internodes and has undergone selection during maize *** identification of qEN7 and the prediction of its candidate gene sheds some light on the evolution of maize ear number and provides a novel resource for breeding of multi-ear maize cultivars.

关键词： Prolificacy QTL mapping Fine mapping Selection analysis Maize

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Evolutionary history and climate conditions constrain the flower colours of woody plants in China

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Journal of plant Ecology 2022年第1期15卷 196-207页

作者： Qinggang Wang Qiang Guo Xiulian Chi Shaoqi Zhu Zhiyao Tang Department of Ecology and Ecological Engineering College of Resources and Environmental Sciencesand Key Laboratory of Biodiversity and Organic Farming of Beijing CityChina Agricultural UniversityBeijing 100193China Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education College of Urban and Environmental SciencesPeking UniversityBeijing 100871China State Key Laboratory Breeding base of Dao-di Herbs National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical ScienceBeijing 100700China

In this study,we investigated(i)the differences in flower colour composition among growth forms of woody plants in China and(ii)the influences of biogeographic regions,evolutionary age and climatic conditions on geographic variation in the proportions of different flower *** distribution maps and flower colour information(white,red,yellow,yellow-green,green and blue-purple)of 7673 Chinese woody plant species and a dated genus-level phylogenetic tree,we compared flower colour composition among different growth forms(shrubs,trees and lianas).We further estimated the relationships of geographical patterns in the proportions of different flower colours with seven different biogeographic regions,evolutionary age and different contemporary climatic *** with trees or lianas,shrubs showed a higher proportion of species with anthocyanin-based red and blue-purple *** geographic patterns of flower colour composition of woody plants in China were strongly influenced by regional effects and contemporary climate,especially precipitation and ultraviolet B *** proportion of species with presumably bee-pollinated yellow and blue-purple flowers and stress tolerant anthocyanin-based red and blue-purple flower colours tended to be high in the northwestern part of *** flowers tended to evolve earlier than others,but evolutionary age had quite weak influences on the geographic pattern of flower *** results reflect both evolutionary and environmental constraints on the distribution of flower colours of woody plants in China.

关键词： growth form evolutionary age selection processes woody species biogeographical regions

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The chromosome-level reference genome assembly for Panax notoginseng and insights into ginsenoside biosynthesis

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plant Communications 2021年第1期2卷 54-68页

作者： Zhouqian Jiang Lichan Tu Weifei Yang Yifeng Zhang Tianyuan Hu Baowei Ma Yun Lu Xiuming Cui Jie Gao Xiaoyi Wu Yuru Tong Jiawei Zhou Yadi Song Yuan Liu Nan Liu Luqi Huang Wei Gao School of Traditional Chinese Medicine Capital Medical UniversityBeijingChina School of Pharmaceutical Sciences Capital Medical UniversityBeijingChina Annoroad Gene Technology BeijingChina Faculty of Life Science and Technology Kunming University of Science and TechnologyKunmingChina State Key Laboratory Breeding base of Dao-di Herbs National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina Advanced Innovation center for Human Brain Protection Capital Medical UniversityBeijingChina

Panax notoginseng,a perennial herb of the genus Panax in the family Araliaceae,has played an important role in clinical treatment in China for thousands of years because of its extensive pharmacological ***,we report a high-quality reference genome of ***,with a genome size up to 2.66 Gb and a contig N50 of 1.12 Mb,produced with third-generation PacBio sequencing *** is the first chromosome-level genome assembly for the genus *** genome evolution analysis,we explored phylogenetic and whole-genome duplication events and examined their impact on saponin *** performed a detailed transcriptional analysis of *** and explored genelevel mechanisms that regulate the formation of characteristic ***,we studied the biosynthesis and regulation of saponins at temporal and spatial *** combined multi-omics data to identify genes that encode key enzymes in the *** terpenoid biosynthetic ***,we identified five glycosyltransferase genes whose products catalyzed the formation of different ginsenosides in *** genetic information obtained in this study provides a resource for further exploration of the growth characteristics,cultivation,breeding,and saponin biosynthesis of ***.

关键词： chromosome-level genome ginsenoside P.notoginseng regulation transcriptome

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plant genome editing using xCas9 with expanded PAM compatibility

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Journal of genetics and Genomics 2019年第5期46卷 277-280页

作者： Jingying Li Jinman Luo Meilian Xu Shaoya Li Jiahui Zhang Huiyuan Li Lei Yan Yunde Zhao Lanqin Xia Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing100081China national Key Laboratory of Crop genetic Improvement and national center of plant Gene Research Huazhong Agricultural UniversityWuhan430070Chin Shaoya Li Jiahui ZhangHuiyuan LiLei Yan Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China Section of Cell and Developmental Biology University of CaliforniaSan DiegoLa JollaCA92093-0V6USA

CRISPR/Cas enables robust genome editing and has revolution-ized both functional genomics and crop *** specificity of Cas-directed DNA cleavage is strictly determined by a chimeric single guide RNA(SgRNA)and a short protospacer adjacent motif(PAM)in the genome(Cong et al,2013;Zetsche et al,2015).The widely used Cas9 from Streptococcus pyogenes(SpCas9)generally recognizes the canonical NGG PAM(where N indicates any nucleicacid base)(Miao et al.,2013;Ma et al,2015),making many regionsuntargetable by ***9 VQR and VRER variants,which recog-nize the non-canonical PAM sequences of NGA and NGCG,respectively,have been used to expand targetable sequences in plants(Hu et al.,2016).In addition,the applications of other Cas endonucleases such as SaCas9(Staphylococcus aureus Cas9)(Ran et al..2015).

关键词： plant genome editing PAM compatibility

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Enhancing phosphorus uptake efficiency through QTL-based selection for root system architecture in maize

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Journal of genetics and Genomics 2016年第11期43卷 663-672页

作者： Riliang Gu Fanjun Chen Lizhi Long Hongguang Cai Zhigang Liu Jiabo Yang Lifeng Wang Huiyong Li Junhui Li Wenxin Liu Guohua Mi Fusuo Zhang Lixing Yuan Key Lab of plant-Soil Interaction MOECenter for ResourcesEnvironment and Food SecurityCollege Resources and Environmental SciencesChina Agricultural University College of Agronomy and Biotechnology China Agricultural University Institute of Agricultural resource and Environment Jilin Academy of Agricultural Sciences Cereal Crops Research Institute Henan Academy of Agricultural Sciences

Root system architecture （RSA） plays an important role in phosphorus （P） acquisition, but enhancing P use efficiency （PUE） in maize via genetic manipulation of RSA has not yet been reported. Here, using a maize recombinant inbred line （RIL） population, we investigated the genetic relationships between PUE and RSA, and developed P-efficient lines by selection of quantitative trait loci （QTLs） that coincide for both traits. In low-P （LP） fields, P uptake efficiency （PupE） was more closely correlated with PUE （r = 0.48 -0.54）, and RSA in hydroponics was significantly related to PupE （r=0.25-0.30） but not to P utilization efficiency （PutE）. QTL analysis detected a chromosome region where two QTLs for PUE, three for PupE and three for RSA were assigned into two QTL clusters, Cl-bin3.04a and Cl-bin3.04b. These QTLs had favorable effects from alleles derived from the large-rooted and high-PupE parent. Marker-assisted selection （MAS） identified nine advanced backcross-derived lines carrying Cl-bin3.04a or Cl-bin3.04b that displayed mean increases of 22%-26% in PUE in LP fields. Furthermore, a line L224 pyramiding Cl- binB.04a and Cl-bin3.04b showed enhanced PupE, relying mainly on changes in root morphology, rather than root physiology, under both hydroponic and field conditions. These results highlight the physiological and genetic contributions of RSA to maize PupE, and provide a successful study case of developing P-efficient crops through QTL-based selection.

关键词： Maize Quantitative trait loci Phosphorus Root system architecture Marker-assisted selection

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Gene editing in plants:progress and challenges

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national Science Review 2019年第3期6卷 421-437页

作者： Yanfei Mao Jose Ramon Botella Yaoguang Liu Jian-Kang Zhu Shanghai center for plant Stress Biology CAS Center of Excellence in Molecular Plant Sciences Chinese Academy of Sciences School of Agriculture and Food Sciences University of Queensland State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of Life Sciences South China Agricultural University Department of Horticulture and Landscape Architecture Purdue University

The clustered regularly interspaced short palindromic repeat(CRISPR)-associated protein 9(Cas9)genome editing system is a powerful tool for targeted gene modifications in a wide range of species,including plants. Over the last few years, this system has revolutionized the way scientists perform genetic studies and crop breeding, due to its simplicity, flexibility, consistency and high efficiency. Considerable progress has been made in optimizing CRISPR/Cas9 systems in plants, particularly for targeted gene mutagenesis. However, there are still a number of important challenges ahead, including methods for the efficient delivery of CRISPR and other editing tools to most plants, and more effective strategies for sequence knock-ins and replacements. We provide our viewpoint on the goals, potential concerns and future challenges for the development and application of plant genome editing tools.

关键词： CRISPR Cas9 genome editing base editing gene targeting crop breeding

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CCGD-ESCC： A Comprehensive Database for genetic Variants Associated with Esophageal Squamous Cell Carcinoma in Chinese Population

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Genomics, Proteomics & Bioinformatics 2018年第4期16卷 262-268页

作者： Linna Peng Sijin Cheng Yuan Lin Qionghua Cui Yingying Luo Jiahui Chu Mingming Shao Wenyi Fan Yamei Chen Ai Lin Yiyi Xi Yanxia Sun Lei Zhang Chao Zhang Wen Tan Ge Gao Chen Wu Dongxin Lin Department of Etiology and Carcinogenesis National Cancer Center/Cancer Hospital Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021China State Key Laboratory of Protein and plant Gene Research School of Life Sciences Center for Bioinformatics Peking UniversityBeijing 100871China Beijing Advanced Innovation center for Genomics (ICG) Peking UniversityBeijing 100871China national Engineering Research center for Beijing Biochip Technology Beijing 102206China School of Life Sciences Peking UniversityBeijing 100871China

Esophageal squamous-cell carcinoma （ESCC） is one of the most lethal malignancies in the world and occurs at particularly higher frequency in China. While several genome-wide association studies （GWAS） of germline variants and whole-genome or whole-exome sequencing studies of somatic mutations in ESCC have been published, there is no comprehensive database publically available for this cancer. Here, we developed the Chinese Cancer Genomic Database-Esophageal Squamous Cell Carcinoma （CCGD-ESCC） database, which contains the associations of 69,593 single nucleotide polymorphisms （SNPs） with ESCC risk in 2022 cases and 2039 controls, survival time of 1006 ESCC patients （survival GWAS） and gene expression （expression quantitative trait loci,eQTL） in 94 ESCC patients. Moreover, this database also provides the associations between8833 somatic mutations and survival time in 675 ESCC patients. Our user-friendly database is a resource useful for biologists and oncologists not only in identifying the associations of genetic variants or somatic mutations with the development and progression of ESCC but also in studying the underlying mechanisms for tumorigenesis of the cancer. CCGD-ESCC is freely accessible at http：//***/ccgd/ESCCdb.

关键词： Esophageal cancer Germline variants Somatic mutations Association databaseChinese population

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A CRISPR/Cas9 toolkit for efficient targeted base editing to induce genetic variations in rice

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Science China(Life Sciences) 2017年第5期60卷 516-519页

作者： Bin Ren Fang Yan Yongjie Kuang Na Li Dawei Zhang Honghui Lin Huanbin Zhou State Key Laboratory for Biology of plant Diseases and Insect Pests Institute of Plant Protection Chinese Academy of Agricultural Sciences Beijing 100193 China Ministry of Education Key Laboratory of Bio-resource and Eco-Environment College of Life Sciences Sichuan University Chengdu 610065 China

Gene-targeting technologies using sequence specific nucleases have been widely adopted to induce genetic modifications in both plant molecular biology research and crop improvement,of which generating targeted point m... 详细信息

关键词：基因变异诱导工具包植物分子生物学水稻编辑基础基因打靶技术

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