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Inhibition mechanisms of CRISPR-Cas9 by Acr ⅡA25.1 and AcrⅡA32

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science China life sciences 2024年第09期 1781-1791页

In the ongoing arms race between bacteria and bacteriophages, bacteriophages have evolved anti-CRISPR proteins to counteract bacterial CRISPR-Cas systems. Recently, Acr ⅡA25.1 and Acr ⅡA32 have been found to effectively inhibit the activity of Spy Cas9 both in bacterial and human cells. However, their molecular mechanisms remain elusive. Here, we report the cryo-electron microscopy structures of ternary complexes formed by Acr ⅡA25.1 and Acr ⅡA32 bound to Spy Cas9-sg RNA. Using structural analysis and biochemical experiments, we revealed that Acr ⅡA25.1 and Acr ⅡA32 recognize a novel, previously-unidentified anti-CRISPR binding site on Spy Cas9. We found that both Acr ⅡA25.1 and Acr ⅡA32 directly interact with the WED domain, where they spatially obstruct conformational changes of the WED and PI domains, thereby inhibiting Spy Cas9 from recognizing protospacer adjacent motif(PAM) and unwinding double-stranded DNA. In addition,they may inhibit nuclease activity by blocking the dynamic conformational changes of the Spy Cas9 surveillance complex. In summary, our data elucidate the inhibition mechanisms of two new anti-CRISPR proteins, provide new strategies for the modulation of Spy Cas9 activity,and expand our understanding of the diversity of anti-CRISPR protein inhibition mechanisms.

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J-family genes redundantly regulate flowering time and increase yield in soybean

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The Crop Journal 2024年第3期12卷 944-949页

作者： Haiyang Li Zheng Chen Fan Wang Hongli Xiang Shuangrong Liu Chuanjie Gou Chao Fang Liyu Chen Tiantian Bu Fanjiang Kong Xiaohui Zhao Baohui Liu Xiaoya Lin Guangdong Key Laboratory of Plant Adaptation and Molecular Design/Guangzhou Key Laboratory of Crop gene editing/Innovative center of Molecular genetics and Evolution School of Life SciencesGuangzhou UniversityGuangzhou 510006GuangdongChina

Soybean(Glycine max)is a short-day crop whose flowering time is regulated by *** longjuvenile trait extends its vegetative phase and increases yield under short-day *** variation in J,the major locus controlling this trait,modulates flowering *** report that the three J-family genes influence soybean flowering time,with the triple mutant Guangzhou Mammoth-2 flowering late under short days by inhibiting transcription of E1-family genes.J-family genes offer promising allelic combinations for breeding.

关键词： Soybean Flowering time Yield J-family genes

Enlarged DNA unwinding by Nme2Cas9 permits a broadened base editing window beyond the protospacer

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science China(life sciences) 2024年第2期67卷 424-427页

作者： Ziting Chen Xiangyang Li Qian Zhang Wenjun Sun Xiaoxuan Song Xia Zhang Xingxu Huang Bo Sun school of life science and technology and gene editing center ShanghaiTech UniversityShanghai 201210China Zhejiang Lab HangzhouZhejiang 311121China CAS center for Excellence in Molecular Cell science Shanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai 200031China University of Chinese Academy of sciences Beijing 100049China

Dear Editor,Base editing has been developed to be one of the effective CRISPR-based gene editing techniques(Rees and Liu,2018).Base editors(BEs)take advantage of DNAmodifying enzymes fused with a catalytically impaired CRISPR protein to install base *** BE,DNA-modifying enzymes often process nontarget singlestranded DNA(NTS)generated by Cas proteins.

关键词： install base winding

Mechanisms underlying key agronomic traits and implications for molecular breeding in soybean

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Journal of genetics and Genomics 2024年第4期51卷 379-393页

作者： Chao Fang Haiping Du Lingshuang Wang Baohui Liu Fanjiang Kong Guangdong Key Laboratory of Plant Adaptation and Molecular Design Guangzhou Key Laboratory of Crop Gene EditingInnovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouGuangdong 510006China

Soybean(Glycine max[L.]Merr.)is an important crop that provides protein and vegetable oil for human *** soybean is a photoperiod-sensitive crop,its cultivation and yield are limited by the photoperiodic conditions in the *** contrast to other major crops,soybean has a special plant architecture and a special symbiotic nitrogen fixation system,representing two unique breeding ***,flowering time,plant architecture,and symbiotic nitrogen fixation are three critical or unique yielddetermining *** review summarizes the progress made in our understanding of these three critical yield-determining factors in ***,we propose potential research directions to increase soybean production,discuss the application of genomics and genomic-assisted breeding,and explore research directions to address future challenges,particularly those posed by global climate changes.

关键词： Soybean Grain yield Flowering time Plant architecture Nodulation Symbiotic nitrogen fixation Genome study

Simple method for transformation and gene editing in medicinal plants

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Journal of Integrative Plant Biology 2024年第1期66卷 17-19页

作者： Xuesong Cao Hongtao Xie Minglei Song Lianghui Zhao Hailiang Liu Guofu Li Jian‐Kang Zhu Institute of Advanced Biotechnology and school of life sciences Southern University of Science and TechnologyShenzhen 518055China Bellagen Biotechnology Co.Ltd. Jinan 250000China Institute for Regenerative Medicine Shanghai East HospitalTongji University School of MedicineShanghai 200123China Ministry of Agriculture and Rural Affairs Key Laboratory of gene editing Technologies Nanfan Research InstituteChinese Academy of Agricultural SciencesSanya 572024China

gene-editing technologies have ushered in a significant advancement in plant genetics research and molecular ***,a critical challenge hindering the widespread adoption of these technologies is the efficient delivery of gene-editing *** predominant methods for introducing these tools into plants typically involve Agrobacterium tumefaciens-mediated transformation or particle bombardment(Mao et al.,2019).Unfortunately,these traditional gene delivery methods require delicate and timeconsuming tissue culture procedures and show limited success,especially in medicinal and other less studied plants.A recent breakthrough is the development of the Cut-Dip-Budding(CDB)gene delivery *** CDB system is highly effective for plants with root-suckering *** allows the delivery of transgenes and gene-editing tools into plants through hairy root induction followed by shoot regeneration from transformed hairy roots,bypassing the need for tissue culture processes(Cao et al.,2023).

关键词： transformation culture breakthrough

Knockout of miR396 genes increases seed size and yield in soybean

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Journal of Integrative Plant Biology 2024年第6期66卷 1148-1157页

作者： Hongtao Xie Fei Su Qingfeng Niu Leping Geng Xuesong Cao Minglei Song Jinsong Dong Zai Zheng Rui Guo Yang Zhang Yuanwei Deng Zhanbo Ji Kang Pang Jian‐Kang Zhu Jianhua Zhu school of life sciences Anhui Agricultural UniversityHefei 230036China Research center for Biological Breeding technology Research Institute of Frontier ScienceAnhui Agricultural UniversityHefei 230036China Bellagen Biotechnology Co.Ltd Jinan 250000China Institute of Crop sciences/National Nanfan Research Institute Chinese Academy of Agricultural SciencesKey Laboratory of Gene Editing Technologies(Hainan)Ministry of Agriculture and Rural AffairsSanya 572025China Southern University of science and TechnologyShenzhen 518055China Hainan Yazhou Bay Seed Laboratory Sanya 572024China

Yield improvement has long been an important task for soybean breeding in the world in order to meet the increasing demand for food and animal *** R396 genes have been shown to negatively regulate grain size in rice,but whether mi R396 family members may function in a similar manner in soybean is ***,we generated eight soybean mutants harboring different combinations of homozygous mutations in the six soybean mi R396genes through genome editing with clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease(Cas)12SF01 in the elite soybean cultivar Zhonghuang 302(ZH302).Four triple mutants(mir396aci,mir396acd,mir396adf,and mir396cdf),two quadruple mutants(mir396-abcd and mir396acfi),and two quintuple mutants(mir396abcdf and mir396bcdfi)were *** found that plants of all the mir396 mutants produced larger seeds compared to ZH302 *** tests showed that mir396adf and mir396cdf plants have significantly increased yield in growth zones with relatively high latitude which are suited for ZH302 and moderately increased yield in lower *** contrast,mir396abcdf and mir396bcdfiplants have increased plant height and decreased yield in growth zones with relatively high latitude due to lodging issues,but they are suited for low latitude growth zones with increased yield without lodging *** together,our study demonstrated that loss-of-function of mi R396 genes leads to significantly enlarged seed size and increased yield in soybean,providing valuable germplasms for breeding high-yield soybean.

关键词： Cas12SF01 CRISPR/Cas miR396 seed size soybean yield

Elucidating and manipulating pressure-induced water intrusion–extrusion in tunable hydrophobic Co/Zn bimetallic ZIFs:Roles of pore size and hydrogen bond

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Nano Research 2024年第1期17卷 344-353页

作者： Diyi Fang Chuanlei Liu Yu Chen Qilong Peng Kongguo Wu Yuxiang Chen Hao Jiang Yuan Wu Benxian Shen Qiumin Wu Di Wu Hui Sun International Joint Research center of Green Energy Chemical Engineering School of Chemical EngineeringEast China University of Science and TechnologyShanghai 200237China Alexandra Navrotsky Institute for Experimental Thermodynamics The Gene and Linda Voiland School of Chemical Engineering and BioengineeringMaterials Science and Engineeringand Department of ChemistryWashington State UniversityWashington 99163USA

Porous heterogeneous lyophobic systems(HLSs)find potential applications in energy restoring,dissipating,and ***,the development of controllable HLSs still lacks rational structure design of nanoporous materials matching the molecular sizes of adopted *** that,thoroughly understanding the underlying transportation mechanism in the confined nano channels is greatly *** this work,a series of Co/Zn bimetallic zeolitic imidazolate frameworks(ZIFs)with tunable structures were synthesized via regulating the Co to Zn ratios and employed to investigate the intrusion–extrusion of liquid water in confined *** characterizations confirm the heterometallic coordination in the Co/Zn-doped *** intrusion–extrusion experiments unlock the relationship between the intrusion pressure and the nanopore size and realize the evolution of the HLSs between molecular spring and *** addition,cycling tests indicate the reversible structure change of Co/Zn ZIFs encountering pressure-induced water *** combination with molecular dynamics simulations,we present that the water multimers intrude into nanopores of ZIFs in chain-like forms along with dissociation of hydrogen bonds(HBs).Water molecules in the pre-intrusion state exhibit reduced HBs in response to the increase of pressure and linear structure with 1.6–3.0 HBs on *** transition to the post-intrusion situation,the associative configuration of water tends to exhibit the tetrahedral ***,we highlight the roles of pore size and HB in synergically dominating the pressure-induced intrusion–extrusion of liquid water in hydrophobic ***,the present work can also guide the development of functional guest–host systems based on porous architectures.

关键词： heterometallic zeolitic imidazolate frameworks nanopore intrusion hydrogen bonds

Unsynchronized butyrophilin molecules dictate cancer cell evasion of Vγ9Vδ2 T-cell killing

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Cellular & Molecular Immunology 2024年第4期21卷 362-373页

作者： Zeguang Wu Qiezhong Lamao Meichao Gu Xuanxuan Jin Ying Liu Feng Tian Ying Yu Pengfei Yuan Shuaixin Gao Thomas S.Fulford Adam P.Uldrich Catherine C.L Wong Wensheng Wei Biomedical Pioneering Innovation center Peking-Tsinghua Center for Life SciencesPeking University Genome Editing Research CenterState Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking University100871BeijingChina Edigene Inc. Life Science ParkChangping District102206BeijingChina center for Precision Medicine Multi-Omics Research Peking University Health Science CenterPeking University100191BeijingChina Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity The University of MelbourneParkvilleVIC3010Australia Cancer Immunology Program Peter MacCallum Cancer CentreMelbourneVICAustralia State Key Laboratory for Complex Severe and Rare DiseasesClinical Research InstitutePeking Union Medical College HospitalChinese Academy of Medical Science&Peking Union Medical CollegePeking-Tsinghua Center for Life Sciences100871BeijingChina

Vγ9Vδ2 T cells are specialized effector cells that have gained prominence as immunotherapy agents due to their ability to target and kill cells with altered pyrophosphate *** our effort to understand how cancer cells evade the cell-killing activity of Vγ9Vδ2 T cells,we performed a comprehensive genome-scale CRISPR screening of cancer *** found that four molecules belonging to the butyrophilin(BTN)family,specifically BTN2A1,BTN3A1,BTN3A2,and BTN3A3,are critically important and play unique,nonoverlapping roles in facilitating the destruction of cancer cells by primary Vγ9Vδ2 T *** coordinated function of these BTN molecules was driven by synchronized gene expression,which was regulated by IFN-γsignaling and the RFX ***,an enzyme called QPCTL was shown to play a key role in modifying the N-terminal glutamine of these BTN proteins and was found to be a crucial factor in Vγ9Vδ2 T cell killing of cancer *** our research,we offer a detailed overview of the functional genomic mechanisms that underlie how cancer cells escape Vγ9Vδ2 T ***,our findings shed light on the importance of the harmonized expression and function of gene family members in modulating T-cell activity.

关键词： Butyrophilin Vγ9Vδ2 T-cell Cancer-specific immune evasion Glutaminyl-peptide cyclotransferase-like Pyrophosphate metabolite Immunotherapy

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