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Intracellularly synthesized ssDNA for continuous genome engineering

Trends in Biotechnology 2025年第6期43卷 1356-1370页

作者： Liu, Wenqian Pan, Yingjia Zhang, Yu Dong, Chang Huang, Lei Lian, Jiazhang Key Laboratory of Biomass Chemical Engineering of Ministry of Education and State Key Laboratory of Biobased Transportation Fuel Technology College of Chemical and Biological Engineering Zhejiang University Hangzhou310027 China BGI Research Hangzhou310030 China ZJU-Hangzhou Global Scientific and Technological Innovation Center Zhejiang University Hangzhou310000 China

Despite the prevalence of genome editing tools, there are still some limitations in dynamic and continuous genome editing. In vivo single-stranded DNA (ssDNA)-mediated genome mutation has emerged as a valuable and promising approach for continuous genome editing. In this review, we summarize the various types of intracellular ssDNA production systems and notable achievements in genome engineering in both prokaryotic and eukaryotic cells. We also review progress in the development of applications based on retron-based systems, which have demonstrated significant potential in molecular recording, multiplex genome editing, high-throughput functional variant screening, and gene-specific continuous in vivo evolution. Furthermore, we discuss the major challenges of ssDNA-mediated continuous genome editing and its prospects for future applications. © 2024 Elsevier Ltd

关键词： Genome

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Ancestral origins and post-admixture adaptive evolution of highland Tajiks

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National Science Review 2024年第9期11卷 145-157页

作者： Jia Wen Jiaojiao Liu Qidi Feng Yan Lu Kai Yuan Xiaoxi Zhang Chao Zhang Yang Gao Xiaoji Wang Dolikun Mamatyusupu Shuhua Xu State Key Laboratory of Genetic Engineering Human Phenome InstituteZhangjiang Fudan International Innovation CenterCenter for Evolutionary BiologySchool of Life Sciences Department of Liver Surgery and Transplantation Liver Cancer InstituteZhongshan HospitalFudan University School of Life Science and Technology Shanghai Tech University Key Laboratory of Computational Biology Shanghai Institute of Nutrition and Health University of Chinese Academy of Sciences Chinese Academy of Sciences Ministry of Education Key Laboratory of Contemporary Anthropology Fudan University College of the Life Sciences and Technology Xinjiang University

It remains debatable how many genes and how various the mechanisms are behind human adaptation to extreme environments, such as high altitudes. Despite extensive studies on Tibetans, Andeans and Ethiopians, new insights are expected to be provided with careful analysis of underrepresented highlanders living in a different geographical region, such as the Tajiks, who reside on the Pamir Plateau at an average altitude exceeding 4000 meters. Moreover, genetic admixture, as we observed in the current whole-genome deep-sequencing study of Xinjiang Tajiks(XJT), offers a unique opportunity to explore how admixture may facilitate adaptation to high-altitude environments. Compared with other extensively studied highlanders,XJT showed pronounced admixture patterns: most of their ancestry are derived from West Eurasians(34.5%–48.3%) and South Asians(21.4%–40.0%), and some minor ancestry from East Asians and Siberians(3.62%–17.5%). The greater genetic diversity in XJT than in their ancestral source populations provides a genetic basis for their adaptation to high-altitude environments. The admixture gain of functional adaptive components from ancestral populations could facilitate adaptation to high-altitude ***, admixture-facilitated adaptation was strongly associated with skin-related candidate genes that respond to UV radiation(e.g. HERC2 and BNC2) and cardiovascular-system-related genes(e.g. MPI and BEST1). Notably, no adaptive variants of genes showing outstanding natural selection signatures in the Tibetan or Andean highlanders were identified in XJT, including EPAS1 and EGLN1, indicating that a different set of genes contributed to XJT's survival on the Pamir Plateau, although some genes underlying natural selection in XJT have been previously reported in other highlanders. Our results highlight the unique genetic adaptations in XJT and propose that admixture may play a vital role in facilitating high-altitude adaptation. By introducing and elevatin

关键词： Tajiks population structure genetic admixture highland local adaptation epidermis protection cardiovascular system

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Accurate genomic prediction for grain yield and grain moisture content of maize hybrids using multi-environment data

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Journal of Integrative Plant Biology 2025年第5期67卷 1379-1394页

作者： Jingxin Wang Liwei Liu Kunhui He Takele Weldu Gebrewahid Shang Gao Qingzhen Tian Zhanyi Li Yiqun Song Yiliang Guo Yanwei Li Qinxin Cui Luyan Zhang Jiankang Wang Changling Huang Liang Li Tingting Guo Huihui Li State Key Laboratory of Crop Gene Resources and Breeding National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081 China Nanfan Research Institute Chinese Academy of Agricultural SciencesSanya572024 China Key Laboratory of Maize Engineering Breeding Ministry of Agriculture and Rural AffairsZhangye734000 China Jinxiang Seed Co.Ltd Zhangye734000 China College of Agriculture Aksum University-Shire CampusShire314 Ethiopia

Incorporating genotype-by-environment(GE)interaction effects into genomic prediction(GP)models with multi-environment climate data can improve selection accuracy to accelerate crop breeding but has received little research ***,we conducted a cross-region GP study of grain moisture content(GMC)and grain yield(GY)in maize hybrids in two major Chinese growing regions using data for 19 climatic factors across34 environments in 2020 and *** were conducted in 2,126 hybrids generated from 475 maize inbred lines,using 9,355 single nucleotide polymorphism markers for *** based on genomic best linear unbiased prediction(GBLUP)incorporating GE interaction effects of 19 climatic factors associated with day length,transpiration,temperature,and radiation(GBLUP-GE_(19CF))trained on whole data set outperformed the traditional GBLUP or BayesB models in predicting GMC or GY by 10-fold crossvalidation,achieving prediction accuracies of 0.731 and 0.331,*** refine the climate data,we examined 84 statistical features associated with these climatic factors and identified nine factors most correlated with GMC or *** component analysis of climate data yielded nine principal components responsible for97%of the variability in the *** these nine factors or principal components into the GBLUP-GE framework with a similarity matrix of environments(GBLUP-GE_(9CF)and GBLUPGE_(PCA))provided similar prediction accuracies but could reduce the computational *** addition,increasing the number of test set environments in the training set from 8 to 14 increased the prediction accuracy of GBLUP-GE_(19CF)trained with monthly average climate data for *** prediction accuracy based on concordance,the proportion of overlapping hybrids between the top 50%of predicted and observed values for GMC and GY,indicated that concordance exceeded 50%for the GBLUP-GE_(19CF)model,confirming the reliability of our ***

关键词： GBLUP genomic prediction genotype-by-environment interaction grain yield maize hybrids multi-environment

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The HD-Zip transcription factor LcATHB15 is involved in litchi seed development by promoting the expression of the splicing regulator LcSR45

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Horticultural Plant Journal 2024年第6期10卷 1463-1466页

作者： Hanhan Xie Fei Wang Zidi He Zhijian Liang Jianguo Li Minglei Zhao State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(South China)Ministry of Agriculture and Rural AffairsGuangdong Litchi Engineering Research CenterCollege of HorticultureSouth China Agricultural UniversityGuangzhouGuangdong 510642China

Litchi (Litchi chinensis Sonn.) is a well-known tropical and subtropical woody fruit that originated from southern China (Wei et al.,2017;Hu et al.,2022).Based on the development of the embryo,litchi varieties can be divided into three distinct groups:large-seeded cultivars,small (abortive)-seeded cultivars and partial abortive-seeded *** or the reduction in seed size due to embryo abortion is a desirable trait in fruit trees as it directly influences the texture and economic value of fleshy fruits,making small (abortive)-seeded litchi cultivars the most ***,in current production practices,there is no efficient method available to induce or promote high seed abortion in litchi ***,understanding the stenospermy mechanisms of litchi seed development is of great significance for improving agricultural practices and managing genetic resources.

关键词： cultivar originated development

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Self-Assembly of Bacteria in Alternating-Current Electric Fields

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Chinese Physics Letters 2024年第10期41卷 137-143页

作者： Yan-Ran Li Yi-Wu Zong Hong Zhang Jing-Chao Zhang Chun-Ying Feng Jian-Jun Qiao Hao Song Kun Zhao Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300072China Petrochemical Research Institute of Petrochina Co. Ltd.Beijing 102206China Center for Medical Genetics Sichuan Provincial People’s HospitalUniversity of Electronic Science and Technology of ChinaChengdu 611731China Jiangsu Key Laboratory of Sericultural and Animal Biotechnology School of BiotechnologyJiangsu University of Science and TechnologyZhenjiang 212100China Key Laboratory of Silkworm and Mulberry Genetic Improvement Ministry of Agriculture and Rural AffairsSericultural Scientific Research CenterChinese Academy of Agricultural SciencesZhenjiang 212100China Collaborative Innovation Center of Chemical Science and Engineering Tianjin 300072China The Sichuan Provincial Key Laboratory for Human Disease Gene Study and The Institute of Laboratory Medicine Sichuan Provincial People’s HospitalUniversity of Electronic Science and Technology of ChinaChengdu 610054China Institute of Fundamental and Frontier Sciences University of Electronic Science and Technology of ChinaChengdu 610054China

Self-assembly of bacteria in electric fields is a promising route to fabricate biomaterials with reversible and specific ***,due to relatively less studies,our understanding of the self-assembly of bacteria in electric fields is still ***,how different bacterial species behave differently in their fieldmediated self-assembly behavior remains to be *** this study,we choose four bacterial species,including Shewanella oneidensis,Pseudomonas aeruginosa,Bacillus subtilis and Lactococcus lactis as model systems,and investigate their self-assembly behavior in alternating-current(AC)electric fields for both diluted and concentrated *** phase diagrams in the plane of applied field strength vs frequency are *** results show that in diluted suspensions,a transition sequence of isotropic–paranematic–string–columnar phases is observed in all strains as the field strength *** of the assembled structures are quantitatively differentiated among different *** concentrated suspensions,besides the isotropic and paranematic phases,a higher ordered phase with interdigitating rectangular crystal domains(OIR)and an ordered phase with smectic A liquid crystal domains are observed for *** and ***,*** findings shed new light on fabricating potential biomaterials by assembling cells of appropriately chosen bacterial species that have desired surface properties under AC electric fields.

关键词： suspensions diluted biomaterials

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A bHLH transcription factor,CsSPT,regulates high-temperature resistance in cucumber

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Horticultural Plant Journal 2024年第2期10卷 503-514页

作者： Yonggui Liang Chenyu Yang Fangyan Ming Bingwei Yu Zhihua Cheng Yixi Wang Zhengkun Qiu Xiaolan Zhang Bihao Cao Shuangshuang Yan Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(South China) Ministry of Agriculture and Rural AffairsGuangdong Vegetable Engineering and Technology Research CenterCollege of HorticultureSouth China Agricultural UniversityGuangzhouGuangdong 510642China State Key Laboratories of Agrobiotechnology Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable CropsMOE Joint Laboratory for International Cooperation in Crop Molecular BreedingChina Agricultural UniversityBeijing 100193China

High-temperature stress threatens the growth and yield of crops. Basic helix-loop-helix(bHLH) transcription factors(TFs) have been shown to play important roles in regulating high-temperature resistance in plants. However, the bHLH TFs responsible for high-temperature tolerance in cucumbers have not been identified. We used transcriptome profiling to screen the high temperature-responsive candidate bHLH TFs in cucumber. Here, we found that the expression of 75 CsbHLH genes was altered under high-temperature stress. The expression of the CsSPT gene was induced by high temperatures in TT(Thermotolerant) cucumber plants. However, the Csspt mutant plants obtained by the CRISPR-Cas9 system showed severe thermosensitive symptoms, including wilted leaves with brown margins and reduced root density and cell *** Csspt mutant plants also exhibited elevated H_(2)O_(2) levels and down-regulated photosystem-related genes under normal ***, there were high relative electrolytic leakage(REC), malondialdehyde(MDA), glutathione(GSH), and superoxide radical(O_(2)^(·-)) levels in the Csspt mutant plants, with decreased Proline content after the high-temperature treatment. Transcriptome analysis showed that the photosystem and chloroplast activities in Csspt mutant plants were extremely disrupted by the high-temperature stress compared with wildtype(WT) plants. Moreover, the plant hormone signal transduction, as well as MAPK and calcium signaling pathways were activated in Csspt mutant plants under high-temperature stress. The HSF and HSP family genes shared the same upregulated expression patterns in Csspt and WT plants under high-temperature conditions. However, most bHLH, NAC, and bZIP family genes were significantly down-regulated by heat in Csspt mutant plants. Thus, these results demonstrated that CsSPT regulated the high-temperature response by recruiting photosynthesis components, signaling pathway molecules, and transcription factors. Our results pro

关键词： Cucumber bHLH CsSPT Photosynthesis High temperature

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Transcriptomics and metabolomics analyses provide insights into postharvest ripening and senescence of tomato fruit under low temperature

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Horticultural Plant Journal 2023年第1期9卷 109-121页

作者： Chunmei Bai Caie Wu Lili Ma Anzhen Fu Yanyan Zheng Jiawei Han Changbao Li Shuzhi Yuan Shufang Zheng Lipu Gao Xinhua Zhang Qing Wang Demei Meng Jinhua Zuo State Key Laboratory of Food Nutrition and Safety College of Food Science and EngineeringTianjin University of Science&TechnologyTianjin 300457China College of Light Industry and Food Engineering Nanjing Forestry UniversityNanjingJiangsu 210037China Key laboratory of vegetable postharvest processing Ministry of AgricultureBeijing Key Laboratory of Fruit and Vegetable Storage and ProcessingKey Laboratory of Biology and Genetic Improvement of Horticultural Crops(North China)of Ministry of AgricultureKey Laboratory of Urban Agriculture(North)of Ministry of Agriculture and Rural AffairsInstitute of Agri-food Processing and NutritionBeijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China National Engineering Research Center for Information Technology in Agriculture Beijing 100097China School of Agricultural Engineering and Food Science Shandong University of TechnologyZiboShandong 255049China

Tomato is one of the most important vegetable crops in the world and is a model plant used to study the ripening of climacteric fleshy *** the ripening process of tomato fruit,flavor and aroma metabolites,color,texture and plant hormones undergo significant ***,low temperatures delayed the ripening process of tomato fruit,inhibiting flavor compounds and ethylene *** and transcriptomics analyses of tomato fruit stored under low temperature(LT,5°C)and room temperature(RT,25°C)were carried out to investigate the effects of storage temperature on the physiological changes in tomato fruit after *** results of transcriptomics changes revealed that the differentially expressed genes(DEGs)involved in tomato fruit ripening,including several kinds of transcription factors(TFs)(TCP,WRKY,MYB and bZIP),enzymes involved in cell wall metabolism[beta-galactosidase(β-GAL),pectinesterase(PE)and pectate lyase(PL),cellulose and cellulose synthase(CESA)],enzymes associated with fruit flavor and aroma[acetyltransferase(AT),malic enzyme(ME),lipoxygenase(LOX),aldehyde dehydrogenase(ALDH),alcohol dehydrogenase(ADH)and hexokinase(HK)],genes associated with heat stress protein 70 and genes involved in the production of plant hormones such as Ethylene responsive factor 1(ERF1),Auxin/indoleacetic acids protein(AUX/IAA),gibberellin regulated *** on the above results,we constructed a regulatory network model of the effects of different temperatures during the fruit ripening *** to the analysis of the metabolomics results,it was found that the contents of many metabolites in tomato fruit were greatly affected by storage temperature,including,organic acids(L-tartaric acid,a-hydroxyisobutyric acid and 4-acetamidobutyric acid),sugars(melezitose,beta-Dlactose,D-sedoheptulose 7-phosphate,2-deoxyribose 1-phosphate and raffinose)and phenols(coniferin,curcumin and feruloylputrescine).This study revealed the effects of storage tempera

关键词： Metabolomics Tomato Transcriptomics Temperature Fruit ripening

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Methylation across the central dogma in health and diseases: new therapeutic strategies

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Signal Transduction and Targeted Therapy 2023年第9期8卷 4142-4187页

作者： Ruochen Liu Erhu Zhao Huijuan Yu Chaoyu Yuan Muhammad Nadeem Abbas Hongjuan Cui State Key Laboratory of Resource Insects Medical Research InstituteSouthwest UniversityChongqing 400715China Jinfeng Laboratory Chongqing 401329China Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine Chongqing 400716China Engineering Research Center for Cancer Biomedical and Translational Medicine Southwest UniversityChongqing 400715China

The proper transfer of genetic information from DNA to RNA to protein is essential for cell-fate control,development,and *** of DNA,RNAs,histones,and non-histone proteins is a reversible post-synthesis modification that finetunes gene expression and function in diverse physiological *** methylation caused by genetic mutations or environmental stimuli promotes various diseases and accelerates aging,necessitating the development of therapies to correct the disease-driver methylation *** this Review,we summarize the operating system of methylation across the central dogma,which includes writers,erasers,readers,and reader-independent *** then discuss how dysregulation of the system contributes to neurological disorders,cancer,and *** small-molecule compounds that target the modifiers show modest success in certain *** methylome-wide action and lack of specificity lead to undesirable biological effects and cytotoxicity,limiting their therapeutic application,especially for diseases with a monogenic cause or different directions of methylation *** tools capable of site-specific methylation manipulation hold great promise to solve this *** the refinement of delivery vehicles,these new tools are well positioned to advance the basic research and clinical translation of the methylation field.

关键词： diseases therapeutic limiting

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NIGT1 represses plant growth and mitigates phosphate starvation signaling to balance the growth response tradeoff in rice

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Journal of Integrative Plant Biology 2023年第8期65卷 1874-1889页

作者： Yuxin Zhang Qianqian Zhang Meina Guo Xueqing Wang Tianjie Li Qingyu Wu Lihui Li Keke Yi Wenyuan Ruan National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Beijing 100081China State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Key Laboratory of Plant Nutrition and Fertilizer Ministry of AgricultureInstitute of Agricultural Resources and Regional PlanningBeijing 100081China National Engineering Research Center of Tree Breeding and Ecological Restoration College of Biological Sciences and TechnologyBeijing 100083China

Inorganic phosphate(Pi)availability is an important factor which affects the growth and yield of crops,thus an appropriate and effective response to Pi fluctuation is ***,how crops orchestrate Pi signaling and growth under Pi starvation conditions to optimize the growth defense tradeoff remains *** we show that a Pi starvationinduced transcription factor NIGT1(NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1)controls plant growth and prevents a hyper-response to Pi starvation by directly repressing the expression of growth-related and Pisignaling genes to achieve a balance between growth and response under a varying Pi ***1 directly binds to the promoters of Pi starvation signaling marker genes,like IPS1,mi R827,and SPX2,under Pi-deficient conditions to mitigate the Pi-starvation responsive(PSR).It also directly represses the expression of vacuolar Pi efflux transporter genes VPE1/2 to regulate plant Pi *** further demonstrate that NIGT1 constrains shoot growth by repressing the expression of growth-related regulatory genes,including brassinolide signal transduction master regulator BZR1,cell division regulator CYCB1;1,and DNA replication regulator *** findings reveal the function of NIGT1 in orchestrating plant growth and Pi starvation signaling,and also provide evidence that NIGT1 acts as a safeguard to avoid hyper-response during Pi starvation stress in rice.

关键词： NIGT1 phosphate(Pi) PHRs Pi-starvation responsive(PSR) Pi starvation Pi signaling

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Machine-Learning-Assisted Compositional Design of Refractory High-Entropy Alloys with Optimal Strength and Ductility

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engineering 2025年第3期46卷 214-223页

作者： Cheng Wen Yan Zhang Changxin Wang Haiyou Huang Yuan Wu Turab Lookman Yanjing Su School of Mechanical and Power Engineering Guangdong Ocean UniversityZhanjiang 529500China Beijing Advanced Innovation Center for Materials Genome Engineering University of Science and Technology BeijingBeijing 100083China Corrosion and Protection Center University of Science and Technology BeijingBeijing 100083China State Key Laboratory for Advanced Metals and Materials University of Science and Technology BeijingBeijing 100083China AiMaterials Research LLC Santa FeNM 87501USA

Designing refractory high-entropy alloys(RHEAs)for high-temperature(HT)applications is an outstanding challenge given the vast possible composition space,which contains billions of candidates,and the need to optimize across multiple ***,we present an approach that accelerates the discovery of RHEA compositions with superior strength and ductility by integrating machine learning(ML),genetic search,cluster analysis,and experimental *** iteratively synthesize and characterize 24 predicted compositions after six feedback *** compositions show outstanding combinations of HT yield strength and room-temperature(RT)ductility spanning the ranges of 714–1061 MPa and 17.2%–50.0%fracture strain,*** identify an attractive alloy system,ZrNbMoHfTa,particularly the composition Zr_(0.13)Nb_(0.27)Mo_(0.26)Hf_(0.13)Ta_(0.21),which demonstrates a yield approaching 940 MPa at 1200℃ and favorable RT ductility with 17.2%fracture *** high yield strength at 1200℃ exceeds that reported for RHEAs,with 1200℃ exceeding the service temperature limit for nickel(Ni)-based *** ML-based approach makes it possible to rapidly optimize multiple properties for materials design,thus overcoming the common problems of limited data and a vast composition space in complex materials systems while satisfying multiple objectives.

关键词： Machine learning Refractory high-entropy alloys Multi-objective optimization Strength-ductility design

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