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Diverse nucleotide substitutions in rice base editing mediated by novel TadA variants

Plant Communications 2024年第8期5卷 104-112页

作者： Man Yu Yongjie Kuang Chenyang Wang Xuemei Wu Shaofang Li Dawei Zhang Wenxian Sun Xueping Zhou Bin Ren Huanbin Zhou State key laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China Department of Plant Pathology China Agricultural UniversityBeijing 100193China Scientific Observing and Experimental Station of Crop Pests in Guilin Ministry of Agriculture and Rural AffairsGuilin 541399China Ministry of Education key laboratory for Bio-resource and Eco-Environment College of Life ScienceState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengdu 610064China State key laboratory of Vegetable Biobreeding National Engineering Research Center for VegetablesBeijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry ScienceBeijing 100097China State key laboratory of Rice Biology Institute of BiotechnologyZhejiang UniversityHangzhou 310058China key laboratory of gene Editing Technologies(Hainan) Ministry of Agricultural and Rural AffairsSanya 572024China

CRISPR-mediated base editors have been widely used to correct defective alleles and create novel alleles by artificial evolution for the rapid genetic improvement of *** editing capabilities of base editors strictly rely on the performance of various nucleotide modification *** with the welldeveloped adenine base editors(ABEs),cytosine base editors(CBEs)and dual base editors suffer from unstable editing efficiency and patterns at different genomic loci in rice,significantly limiting their ***,we comprehensively examined the base editing activities of multiple evolved TadA8e variants in *** found that both TadA-CDd and TadA-E27R/N46L achieved more robust C-to-T editing than previously reported hyperactive hAID*D,and TadA-CDd outperformed TadA-E27R/N46L.A C-to-G base editor(CGBE)engineered with TadA-CDd and OsUNG performed highly efficient C-to-G editing in rice compared with that of *** addition,a dual base editor constructed with a single protein,TadDE,enabled simultaneous,highly efficient C-to-T and A-to-G editing in ***,our results demonstrate that TadA8e derivatives improve both CBEs and dual base editors in rice,providing a powerful way to induce diverse nucleotide substitutions for plant genome editing.

关键词： CRISPR TadA variants cytosine base editing dual base editor rice

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Morroniside from Corni Fructus ameliorates type 2 diabetes in mice by regulating intestinal microbiota dysbiosis

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Food Science and Human Wellness 2024年

作者： Xueqi Tang Yilin Bai Yinxia Wu Yue Yang Xiaobo Yu Jing Chen Xiaochang Xue Jiefang Kang National Engineering laboratory for resource development of Endangered Crude Drugs in Northwest China The key laboratory of Medicinal resources and Natural Pharmaceutical Chemistry， The Ministry of Education college of life sciences， Shaanxi Normal University

As one of the most common metabolic diseases， type 2 diabetes (T2D) has become a public health concern with rising global prevalence. Corni fructus (CF)， a traditional Chinese herb utilized for centuries as homologous medicinal and food resources， has been widely used to treat glucose and lipid metabolism disorders. However， as a core active ingredient of CF， whether and how morroniside (MOR) improves T2D is still unclear. This study aimed to explore the pathways by which MOR ameliorates T2D in mice induced by high-fat diet (HFD) and low-dose streptozotocin (STZ) through 16S rRNA gene sequencing. We found that MOR treatment significantly ameliorated body weight loss， hyperglycemia， hyperlipidemia and insulin resistance in T2D mice. In addition， MOR remarkably improved inflammation- and oxidative stress-driven hepatic and pancreatic injuries in the model mice. Mechanistically， MOR rehabilitated the dysregulated diversity and constitution of the gut microbiota in T2D mice， with significant changes in relative abundance in genus such as Lactobacillus， Lachnospiraceae＿NK4A136＿Group， and Lachnospiraceae＿UCG-006 which are believed to be highly correlated with serum parameters and insulin resistance in mice with T2D. Therefore， we infer that MOR improves T2D at least partially by maintaining the host microbiota homeostasis， and MOR may be a promising candidate for T2D treatment.

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ACBP4-WRKY70-RAP2.12 module positively regulates submergence-induced hypoxia response in Arabidopsis thaliana

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Journal of Integrative Plant Biology 2024年第6期66卷 1052-1067页

作者： Mengyun Guo Yingjun Yao Kangqun Yin† Luna Tan Meng Liu Jing Hou Han Zhang Ruyun Liang Xinran Zhang Heng Yang Xiaoxiao Chen Jinrui Tan Yan Song Shangling Lou Liyang Chen Xuejing Liu Si Tang Yongqi Hu Jin Yan Wensen Fu Kai Yang Ruijia Zhang Xuerui Li Yao Liu Zhen Yan Wei Liu Yu Han Jianquan Liu Kangshan Mao Huanhuan Liu key laboratory for Bio‐resources and Eco‐environment&State key Lab of Hydraulics&Mountain River Engineering Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research StationKey Laboratory for Bio‐resource and Eco‐environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengdu 610065China

ACYL-CoA-BINDING PROTEINs(ACBPs)play crucial regulatory roles during plant response to hypoxia,but their molecular mechanisms remain poorly *** study reveals that ACBP4 serves as a positive regulator of the plant hypoxia response by interacting with WRKY70,influencing its nucleocytoplasmic shuttling in Arabidopsis ***,we demonstrate the direct binding of WRKY70 to the ACBP4 promoter,resulting in its upregulation and suggesting a positive feedback ***,we pinpointed a phosphorylation site at Ser638 of ACBP4,which enhances submergence tolerance,potentially by facilitating WRKY70's nuclear ***,a natural variation in this phosphorylation site of ACBP4 allowed *** to adapt to humid conditions during its historical demographic *** further observed that both phosphorylated ACBP4 and oleoyl-Co A can impede the interaction between ACBP4 and WRKY70,thus promoting WRKY70's nuclear ***,we found that the overexpression of orthologous Bna ***4and Bna ***70 in Brassica napus increases submergence tolerance,indicating their functional similarity across *** summary,our research not only sheds light on the functional significance of the ACBP4 gene in hypoxia response,but also underscores its potential utility in breeding flooding-tolerant oilseed rape varieties.

关键词： ACBP4 Arabidopsis thaliana humid adaptation natural variation RAP2.12 WRKY70

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Chromosomal-level genome and metabolome analyses of highly heterozygous allohexaploid Dendrocalamus brandisii elucidate shoot quality and developmental characteristics

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Journal of Integrative Plant Biology 2024年第6期66卷 1087-1105页

作者： Jutang Jiang Zeyu Zhang Yucong Bai Xiaojing Wang Yuping Dou Ruiman Geng Chongyang Wu Hangxiao Zhang Cunfu Lu Lianfeng Gu Jian Gao key laboratory of National Forestry and Grassland Administration Beijing for Bamboo&Rattan Science and TechnologyInstitute of Gene Science and Industrialization for Bamboo and Rattan ResourcesInternational Center for Bamboo and RattanBeijing 100102China college of Forestry Basic Forestry and Proteomics Research CenterFujian Agriculture and Forestry UniversityFuzhou 350002China School of life Science Peking UniversityBeijing 100871China college of Biological sciences and Biotechnology Beijing Forestry UniversityBeijing 100083China

Dendrocalamus brandisii(Munro)Kurz is a sympodial bamboo species with inimitable taste and flavorful *** rapid growth and use as high-quality material make this bamboo species highly valued for both food processing and wood ***,genome information for *** is lacking,primarily due to its polyploidy and large genome ***,we assembled a high-quality genome for hexaploid ***,which comprises 70chromosomes with a total size of 2,756 Mb,using long-read Hi Fi ***,we accurately separated the genome into its three constituent *** used Oxford Nanopore Technologies long reads to construct a transcriptomic dataset covering 15 tissues for gene annotation to complement our genome assembly,revealing differential gene expression and post-transcriptional *** integrating metabolome analysis,we unveiled that well-balanced lignin formation,as well as abundant flavonoid and fructose contents,contribute to the superior quality of *** *** genomic,transcriptomic,and metabolomic datasets provided a solid foundation for enhancing bamboo shoot quality and developing efficient gene-editing *** study should facilitate research on *** and enhance its use as a food source and wood material by providing crucial genomic resources.

关键词： bamboo shoots Dendrocalamus brandisii(Munro)Kurz flavonoid genome lignin

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Isolation,identification,and virulence gene analysis of pathogenic Aeromonas dhakensis in Macrobrachium rosenbergii and histopathological observation

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Journal of Oceanology and Limnology 2024年第2期42卷 664-675页

作者： Xin PENG Haihui TU Xinyi YAO Xuan LAN Zhenxiao ZHONG Jinping LUO Qiongying TANG Shaokui YI Zhenglong XIA Guoliang YANG Zhejiang Provincial key laboratory of Aquatic resources Conservation and development College of Life SciencesHuzhou UniversityHuzhou 313000China Jiangsu Shufeng Prawn Breeding Co. Ltd.Gaoyou 225654China

To identify the cause of mass mortality of adult Macrobrachium rosenbergii in a farm in Gaoyou City,Jiangsu Province,China,a dominant strain named DKQ-1 was isolated from the hepatopancreas of dying *** and identified as Aeromonas dhakensis by purification culture,biochemical characterization,and 16S rRNA and gyrB gene sequence *** results of the challenge test revealed that the strain was highly pathogenic and the 50%lethal dose(LD_(50))in 72 h to *** was 1.54×10^(5)CFU/*** amplification results of virulence genes show that strain DKQ-1 carried 9 virulence genes,including ascV,aexT,aer,act,lip,ompAI,gcaT,acg,and exu,supporting the strong virulence of strain DKQ-1 to *** observation of the hepatopancreas,gills,and intestines indicated that DKQ-1 injection into *** could cause serious tissue damage,which further supported the strong virulence of this *** addition,a drug susceptibility test revealed that strain DKQ-1 was sensitive to 16 kinds of antibiotics,resistant to 9 kinds of antibiotics,and had intermediate resistance to spectinomycin and *** study is the first report of *** isolated from *** and provided a reference for the pathogen identification of bacterial diseases in ***,and for the prevention and treatment caused by ***.

关键词： Aeromonas dhakensis histopathology virulence gene gyrB drug susceptibility test Macrobrachium rosenbergii

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Plant regeneration in the new era:from molecular mechanisms to biotechnology applications

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Science China(life sciences) 2024年第7期67卷 1338-1367页

作者： Chunli Chen Yuxin Hu Momoko Ikeuchi Yuling Jiao Kalika Prasad Ying Hua Su Jun Xiao Lin Xu Weibing Yang Zhong Zhao Wenkun Zhou Yun Zhou Jian Gao Jia-Wei Wang National key laboratory for Germplasm Innovation&Utilization of Horticultural Crops Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China college of life Science and Technology Huazhong Agricultural UniversityWuhan 430070China key laboratory of Plant molecular Physiology Institute of BotanyChinese Academy of Sciences(CAS)China National Botanical GardenBeijing 100093China Division of Biological sciences Graduate School of Science and TechnologyNara Institute of Science and TechnologyNara 630-0192Japan State key laboratory of Protein and Plant gene Research School of Life SciencesPeking UniversityBeijing 100871China Peking-Tsinghua Center for life sciences Center for Quantitative BiologyAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871China Indian Institute of Science Education and Research Pune 411008IndiaThiruvananthapuram 695551India State key laboratory of Wheat Improvement College of Life SciencesShandong Agricultural UniversityTai’an 271018China Sino-German Joint Research Center on Agricultural Biology Shandong Agricultural UniversityTai’an 271018China key laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biology(IGDB)CASBeijing 100101China CAS-JIC Centre of Excellence for Plant and Microbial Science(CEPAMS) IGDBCASBeijing 100101China National key laboratory of Plant molecular genetics CEMPSInstitute of Plant Physiology and Ecology(SIPPE)CASShanghai 200032China CEPAMS SIPPECASShanghai 200032China Hefei National laboratory for Physical sciences at the Microscale CEMPSSchool of Life SciencesDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230027China State key laboratory of Plant Environmental Resilience College of Biological SciencesChina Agricultural UniversityBeijing 100193China Department of Botany and Plant Pathology and Center for Plant Biology Purdue UniversityWest Lafayette 47907USA School of life Science and Technology Shang

Plants or tissues can be regenerated through various *** animal regeneration,cell totipotency and pluripotency are the molecular basis of plant *** systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant ***,plant hormones,cell division,epigenetic remodeling,and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic *** research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species,with various plant species using distinct mechanisms and displaying significant differences in regenerative *** multi-omics studies at the single-cell level,tracking plant regeneration processes in real-time,and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration,improve crop regeneration efficiency,and contribute to future crop design.

关键词： apical meristem model species regeneration phytohormone plant cell reprogramming somatic embryogenesis

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Di-and tri-methylation of histone H3K36 play distinct roles in DNA double-strand break repair

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Science China(life sciences) 2024年第6期67卷 1089-1105页

作者： Runfa Chen Meng-Jie Zhao Yu-Min Li Ao-Hui Liu Ru-Xin Wang Yu-Chao Mei Xuefeng Chen Hai-Ning Du Hubei key laboratory of Cell Homeostasis College of Life SciencesTaiKang Center for Life and Medical SciencesFrontier Science Center for Immunology and MetabolismHubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan HospitalWuhan UniversityWuhan 430072China Hubei key laboratory of Cell Homeostasis College of Life SciencesTaiKang Center for Life and Medical SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhan 430072China

Histone H3 Lys36(H3K36)methylation and its associated modifiers are crucial for DNA double-strand break(DSB)repair,but the mechanism governing whether and how different H3K36 methylation forms impact repair pathways is ***,we unveil the distinct roles of H3K36 dimethylation(H3K36me2)and H3K36 trimethylation(H3K36me3)in DSB repair via non-homologous end joining(NHEJ)or homologous recombination(HR).Yeast cells lacking H3K36me2 or H3K36me3 exhibit reduced NHEJ or HR efficiency.y Ku70 and Rfa1 bind H3K36me2-or H3K36me3-modified peptides and chromatin,*** these interactions impairs y Ku70 and Rfa1 recruitment to damaged H3K36me2-or H3K36me3-rich loci,increasing DNA damage sensitivity and decreasing repair ***,H3K36me2-enriched intergenic regions and H3K36me3-enriched gene bodies independently recruit y Ku70 or Rfa1 under DSB ***,human KU70 and RPA1,the homologs of y Ku70 and Rfa1,exclusively associate with H3K36me2 and H3K36me3 in a conserved *** findings provide valuable insights into how H3K36me2 and H3K36me3 regulate distinct DSB repair pathways,highlighting H3K36 methylation as a critical element in the choice of DSB repair pathway.

关键词： histone H3K36 methylation Ku70 RPA non-homologous end joining homologous recombination

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OsNPF3.1,a nitrate,abscisic acid and gibberellin transporter gene,is essential for rice tillering and nitrogen utilization efficiency

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Journal of Integrative Agriculture 2024年第4期23卷 1087-1104页

作者： Junnan Hang Bowen Wu Diyang Qiu Guo Yang Zhongming Fang Mingyong Zhang Institute of Rice Industry Technology Research/key laboratory of Functional Agriculture Guizhou Provincial Department of Education/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous RegionMinistry of Education/Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province/College of Agricultural SciencesGuizhou UniversityGuiyang 550025China key laboratory of South China Agricultural Plant molecular Analysis and genetic Improvement/Guangdong Provincial key laboratory of Applied Botany/South China Botanical Garden Chinese Academy of SciencesGuangzhou 510650China Institute of Fruit Tree Research Guangdong Academy of Agricultural SciencesGuangzhou 510640China

Low-affinity nitrate transporter genes have been identified in subfamilies 4-8 of the rice nitrate transporter 1(NRT1)/peptide transporter family(NPF),but the OsNPF3 subfamily responsible for nitrate and phytohormone transport and rice growth and development remains *** this study,we described OsNPF3.1 as an essential nitrate and phytohormone transporter gene for rice tillering and nitrogen utilization efficiency(NUtE).OsNPF3.1 possesses four major haplotypes of its promoter sequence in 517 cultivars,and its expression is positively associated with tiller *** expression was higher in the basal part,culm,and leaf blade than in other parts of the plant,and was strongly induced by nitrate,abscisic acid(ABA)and gibberellin 3(GA_3)in the root and shoot of *** experiments demonstrated that OsNPF3.1 is a pH-dependent low-affinity nitrate transporter,with rice protoplast uptake assays showing it to be an ABA and GA_3 ***3.1 overexpression significantly promoted ABA accumulation in the roots and GA accumulation in the basal part of the plant which inhibited axillary bud outgrowth and rice tillering,especially at high nitrate *** NUtE of OsNPF3.1-overexpressing plants was enhanced under low and medium nitrate concentrations,whereas the NUtE of OsNPF3.1 clustered regularly interspaced short palindromic repeats(CRISPR)plants was increased under high nitrate *** results indicate that OsNPF3.1 transports nitrate and phytohormones in different rice tissues under different nitrate *** altered OsNPF3.1 expression improves NUtE in the OsNPF3.1-overexpressing and CRISPR lines at low and high nitrate concentrations,respectively.

关键词： rice tillering grain yield phytohormone nitrate transporter nitrogen utilization efficiency

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Global multifaceted biodiversity patterns,centers,and conservation needs in angiosperms

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Science China(life sciences) 2024年第4期67卷 817-828页

作者： Ao Luo Yaoqi Li Nawal Shrestha Xiaoting Xu Xiangyan Su Yichao Li Tong Lyu Kilara Waris Zhiyao Tang Xiaojuan Liu Luxiang Lin Yongsheng Chen Kuiling Zu Wenqi Song Shijia Peng Niklaus E.Zimmermann Loïc Pellissier Zhiheng Wang Institute of Ecology and key laboratory for Earth Surface Processes of the Ministry of Education College of Urban and Environmental SciencesPeking UniversityBeijing 100871China Department of Health and Environmental sciences Xi’an Jiaotong-Liverpool UniversitySuzhou 215123China State key laboratory of Grassland Agro-Ecosystems College of EcologyLanzhou UniversityLanzhou 730000China key laboratory of Bio-resource and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengdu 610065China Land Consolidation and Rehabilitation Center Ministry of Natural ResourcesBeijing 100035China State key laboratory of Vegetation and Environmental Change Institute of BotanyChinese Academy of SciencesBeijing 100093China CAS key laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesKunming 650201China Swiss Federal Research Institute WSL Birmensdorf 8903Switzerland Department of Environmental Systems Science ETH ZürichZürich 8092Switzerland

The Convention on Biological Diversity seeks to conserve at least 30%of global land and water areas by 2030,which is a challenge but also an opportunity to better preserve biodiversity,including flowering plants(angiosperms).Herein,we compiled a large database on distributions of over 300,000 angiosperm species and the key functional traits of 67,024 *** this database,we constructed biodiversity-environment models to predict global patterns of taxonomic,phylogenetic,and functional diversity in terrestrial angiosperms and provide a comprehensive mapping of the three diversity *** further evaluated the current protection status of the biodiversity centers of these diversity *** results showed that geographical patterns of the three facets of plant diversity exhibited substantial spatial mismatches and nonoverlapping conservation *** centers of functional diversity,particularly of herbaceous species,were primarily distributed in temperate regions and under weaker protection compared with other biodiversity centers of taxonomic and phylogenetic *** global assessment of multifaceted biodiversity patterns and centers highlights the insufficiency and unbalanced conservation among the three diversity facets and the two growth forms(woody ***),thus providing directions for guiding the future conservation of global plant diversity.

关键词： angiosperms species richness phylogenetic diversity functional diversity plant traits woody species herbaceous species

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Analysis of Intraspecies Diversity of Rice Reveals Variation Patterns of Oryza sativa Basic Leucine Zippers

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Phyton-International Journal of Experimental Botany 2024年第5期93卷 859-873页

作者： Jing Wang Wenqing Xiao Qingnan Wang Xu Wang Bin Jiang Yangchun Han Yang Sun Anhui Provincial key laboratory of molecular Enzymology and Mechanism of Major Diseases Key Laboratory for Conservation and Use of Important Biological Resources of Anhui ProvinceCollege of Life SciencesAnhui Normal UniversityWuhu241000China Institute of Plant Protection Jiangsu Academy of Agricultural SciencesNanjing210000China

The basic leucine zipper(bZIP)is an important class of transcription factors in plants,playing a critical role in plant growth and development and responses to biotic and abiotic *** to gene presence/absence variations,it is limited to identify bZIP genes based on the reference ***,we performed the bZIP gene family analysis in the rice *** employing a rice pan-genome,ninety-four OsbZIPs(72 core genes and 22 variable genes)were identified and divided into 11 groups in a phylogenetic *** upon Ka/Ks values in 33 accessions,OsbZIPs were subjected to different selection pressures during *** analysis of the effects of structural variations(SVs)on gene expression,gene structure,and conserved domains showed that SVs could significantly alter the expression levels of certain OsbZIPs,leading to gene truncation and the emergence of numerous atypical ***-four differentially expressed OsbZIPs were identified by analyzing RNA-seq data of the Xanthomonas oryzae ***(Xoo)infection susceptible(IR24)and resistant(IRBB67)lines under high temperature,and by counting the number of differentially expressed OsbZIPs in different *** Osb-ZIPs were found to respond to Xoo infection at an early stage and may not be involved in the mechanism of Xa4 and Xa7 resistance to *** multiple variation patterns of OsbZIP genes provide new insights into the OsbZIP genes in *** results provide new resources and offer new directions for functional studies of OsbZIPs.

关键词： Rice OsbZIP pan-genome structure variation atypical gene bacterial blight

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