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Functional predictability of universal gene circuits in diverse microbial hosts

Quantitative biology 2024年第2期12卷 129-140页

作者： Chenrui Qin Tong Xu Xuejin Zhao Yeqing Zong Haoqian M.Zhang Chunbo Lou Qi Ouyang Long Qian Peking-Tsinghua Joint Center for Life Sciences Peking UniversityBeijingChina CAS key laboratory of Microbial Physiological and Metabolic Engineering Institute of MicrobiologyChinese Academy of SciencesBeijingChina Bluepha Co. LtdBeijingChina Center for Cell and Gene Circuit Design CAS Key Laboratory of Quantitative Engineering BiologyGuangdong Provincial Key Laboratory of Synthetic GenomicsShenzhen Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina Center for Quantitative biology Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina

Although the principles of synthetic biology were initially established in model bacteria,microbial producers,extremophiles and gut microbes have now emerged as valuable prokaryotic chassis for biological *** the host range in which designed circuits can function reliably and predictably presents a major challenge for the concept of synthetic biology to *** this work,we systematically characterized the cross-species universality of two transcriptional regulatory modules—the T7 RNA polymerase activator module and the repressors module—in three non-model *** found striking linear relationships in circuit activities among different organisms for both *** model fitting revealed host non-specific parameters defining the universality of both ***,a genetic NOT gate and a band-pass filter circuit were constructed from these modules and tested in non-model *** models employing host non-specific parameters were successful in quantitatively predicting circuit behaviors,underscoring the potential of universal biological parts and predictive modeling in synthetic bioengineering.

关键词： circuit predictability host-independent genetic circuits host-nonspecific parameters parts characterization transcriptional regulatory modules

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A flexible,modular and versatile functional part assembly toolkit for gene cluster engineering in Streptomyces

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synthetic and Systems Biotechnology 2024年第1期9卷 69-77页

作者： Xuejin Zhao Yeqing Zong Qiuli Lou Chenrui Qin Chunbo Lou CAS key laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing100101China CAS key laboratory of Microbial Physiological and Metabolic Engineering Institute of MicrobiologyChinese Academy of SciencesBeijing100101China Center for Cell and Gene Circuit Design Key Laboratory of Quantitative Synthetic BiologyShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of Sciences1068 Xueyuan AvenueUniversity TownNanshanShenzhen518055China Peking-Tsinghua Joint Center for Life Sciences Peking UniversityBeijing100871China Center for Quantitative biology Academy for Advanced Interdisciplinary StudiesSchool of PhysicsPeking UniversityBeijing100871China College of Life Sciences University of Chinese Academy of SciencesBeijing100149China

Streptomyces has enormous potential to produce novel natural products(NPs)as it harbors a huge reservoir of uncharacterized and silent natural product biosynthetic gene clusters(BGCs).However,the lack of efficient gene cluster engineering strategies has hampered the pace of new drug ***,we developed an easy-to-use,highly flexible DNA assembly toolkit for gene cluster *** DNA assembly toolkit is compatible with various DNA assembling approaches including Biobrick,Golden Gate,CATCH,yeast homologous recombination-based DNA assembly and homing endonuclease-mediated *** compatibility offers great flexibility in handling multiple genetic parts or refactoring large gene *** demonstrate the utility of this toolkit,we quantified a library of modular regulatory parts,and engineered a gene cluster(act)using characterized promoters that led to increased ***,this work provides a powerful part assembly toolkit that can be used for natural product discovery and optimization in Streptomyces.

关键词： Streptomyces Standard toolkit DNA assembly Gene cluster synthetic biology

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Targeting a disintegrin and metalloprotease(ADAM)17-CD122 axis enhances CD8^(+)T cell effector differentiation and anti-tumor immunity

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Signal Transduction and Targeted Therapy 2024年第7期9卷 3097-3111页

作者： Lina Sun Anjun Jiao Haiyan Liu Renyi Ding Ning Yuan Biao Yang Cangang Zhang Xiaoxuan Jia Gang Wang Yanhong Su Dan Zhang Lin Shi Chenming Sun Aijun Zhang Lianjun Zhang Baojun Zhang Department of Pathogenic Microbiology and Immunology School of Basic Medical SciencesXi’an Jiaotong UniversityXi’anShaanxi 710061China Institute of Infection and Immunity Translational Medicine InstituteXi’an Jiaotong University Health Science CenterXi’anShaanxi 710061China key laboratory of Environment and Genes Related to Diseases Ministry of EducationXi’anShaanxi 710061China Xi’an key laboratory of Immune Related Diseases Xi’anShannxi 710061China Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy Cancer InstituteXuzhou Medical UniversityXuzhouJiangsuChina Department of Pediatrics Qilu Hospital of Shandong UniversityJinanChina National key laboratory of Immunity and Inflammation Suzhou Institute of Systems MedicineChinese Academy of Medical Sciences&Peking Union Medical CollegeSuzhou 215123 JiangsuChina key laboratory of synthetic biology regulatory elements Suzhou Institute of Systems MedicineChinese Academy of Medical Sciences&Peking Union Medical CollegeSuzhou 215123 JiangsuChina

CD8^(+)T cell immune responses are regulated by multi-layer networks,while the post-translational regulation remains largely *** ectodomain shedding is an important post-translational process orchestrating receptor expression and signal transduction through proteolytic cleavage of membrane ***,by targeting the sheddase A Disintegrin and Metalloprotease(ADAM)17,we defined a post-translational regulatory mechanism mediated by the ectodomain shedding in CD8^(+)T *** and proteomic analysis revealed the involvement of post-translational regulation in CD8^(+)T cells.T cellspecific deletion of ADAM17 led to a dramatic increase in effector CD8^(+)T cell differentiation and enhanced cytolytic effects to eliminate pathogens and ***,ADAM17 regulated CD8^(+)T cells through cleavage of membrane ***17 inhibition led to elevated CD122 expression and enhanced response to IL-2 and IL-15 stimulation in both mouse and human CD8^(+)T ***,inhibition of ADAM17 in CD8^(+)T cells improved the efficacy of chimeric antigen receptor(CAR)T cells in solid *** findings reveal a critical post-translational regulation in CD8^(+)T cells,providing a potential therapeutic strategy of targeting ADAM17 for effective anti-tumor immunity.

关键词： immunity stimulation involvement

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Abiotic transformation of chlorinated organics at the active surface of iron-bearing minerals in soils and sediments

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Science China Technological Sciences 2024年第10期67卷 2991-3008页

作者： LI XuXin YAN Chen ZENG YuXi LI WenBin PENG TianWei SONG Biao ZHOU ChengYun College of Environmental Science and Engineering Hunan University key laboratory of Environmental biology and Pollution Control (Hunan University) Ministry of Education

Chlorinated organic compounds are emerging pollutants of widespread concern because of their toxicity, bioaccumulation,persistence, and lack of adequate regulatory measures. Their abiotic transformation, facilitated by iron-bearing minerals, is critical to their natural dissipation in soils and sediments. However, further exploration is needed to understand their underlying mechanisms and potential engineering applications under different redox conditions. This paper reviews the abiotic transformation behaviors and mechanisms of chlorinated organics at the active surface of iron-bearing minerals under anoxic and oxic conditions and summarizes the strategies for enhancing the abiotic transformation efficiency of chlorinated organics. The abiotic transformation rate under oxic conditions can be a few orders of magnitude higher than that under anoxic conditions. Under anoxic conditions, chlorinated organics undergo reductive dechlorination through reductive elimination, hydrogenolysis, dehydrohalogenation, and nucleophilic substitution. A close relationship between the abiotic transformation of chlorinated organics and the production of hydroxyl radicals by iron-bearing minerals under oxic conditions was discovered. synthetic active iron-bearing minerals, carbonaceous materials, and biological synergy can facilitate abiotic dechlorination under anoxic conditions. Meanwhile, the regulation of redox conditions, the introduction of ligands, and the utilization of coexisting anions are proposed to enhance oxidative degradation. This study is expected to improve the comprehension of the abiotic degradation of chlorinated organics mediated by iron-bearing minerals and provide the theoretical foundation for developing new approaches aimed at addressing chlorinated organic pollution.

关键词： chlorinated organic compounds iron-bearing minerals dechlorination degradation remediation

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An integrative database and its application for plant synthetic biology research

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Plant Communications 2024年第5期5卷 123-133页

作者： Chenfei Tian Jianhua Li Yuhan Wu Guangyi Wang Yixin Zhang Xiaowei Zhang Yuwei Sun Yong Wang CAS-key laboratory of synthetic biology CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200032China University of Chinese Academy of Sciences Beijing 100039China College of Life Science Jilin Agricultural UniversityChangchun 130118China

Plant synthetic biology research requires diverse bioparts that facilitate the redesign and construction of new-to-nature biological devices or systems in *** by few well-characterized bioparts for plant chassis,the development of plant synthetic biology lags behind that of its microbial ***,we constructed a web-based Plant synthetic BioDatabase(PSBD),which currently categorizes 1677 catalytic bioparts and 384 regulatory elements and provides information on 309 species and 850 *** bioinformatics tools including local BLAST,chem similarity,phylogenetic analysis,and visual strength are provided to assist with the rational design of genetic circuits for manipulation of gene expression in *** demonstrated the utility of the PSBD by functionally characterizing taxadiene synthase 2 and its quan-titative regulation in tobacco *** powerful synthetic devices were then assembled to amplify the transcriptional signals,enabling enhanced expression ofﬂavivirus non-structure 1 proteins in *** PSBD is expected to be an integrative and user-centered platform that provides a one-stop service for diverse applications in plant synthetic biology research.

关键词： plant synthetic biology bioparts bioinformatics tools regulation genetic circuits

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Genome-wide identifcation of the histone acetyltransferase gene family in Citrus clementina and its potential roles in citrate metabolism

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Food Quality and Safety 2024年第1期8卷 201-211页

作者： Xiahui Lin Yanna Shi Shengchao Liu Xincheng Liu Minglei Zhang Bo Zhang Shaojia Li Kunsong Chen College of Agriculture and Biotechnology Zhejiang UniversityZijingang CampusHangzhouChina Zhejiang Provincial key laboratory of Horticultural Plant Integrative biology Zhejiang UniversityZijingang CampusHangzhouChina The State Agriculture Ministry laboratory of Horticultural Plant Growth Development and Quality ImprovementZhejiang UniversityZijingang CampusHangzhouChina Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina Institute of Horticulture Jiangxi Academy of Agricultural SciencesNanchangChina

Histone acetyltransferase(HAT)catalyzes histone acetylation and is involved in plant growth and development and stress ***,37 CitHAT genes were identifed in Citrus *** physicochemical properties,chromosomal location,gene structure,conserved domain and motif,and cis-acting elements were *** were classifed into four subfamilies based on protein sequence homology,which was strongly supported by gene structure,conserved domain,and motif *** cis-acting elements in gene promoter regions were predicted to be associated with the regulation of plant growth,stress resistance,and response to *** and transcriptomic analyses of citrus callus with mock treatment and HAT inhibitor treatment revealed that increased citric acid content in inhibitor treatment may be attributed to differential expression of CitPEPCK2 and CitGS2,which may be due to the hypo-acetylation of histone *** expression patterns of CitHATs in citrus fruit development stages showed that CitHAG11 and CitHAG28 exhibited a negative correlation with citric acid *** study associates the potential function of histone acetyltransferases in citrate metabolism and extends the molecular mechanism of citrate metabolism in fruits.

关键词： Citrus histone acetyltransferases citric acid citrate metabolism histone acetylation.

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Single-cell transcriptome sequencing reveals the mechanism regulating rice plumule development

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The Crop Journal 2024年第3期12卷 688-697页

作者： Mingdong Zhu Meng Zhang Kunyong Huang Feifei Lu Hong Wang Shaolu Zhao Yinghong Yu Shaoqing Tang Haining Wu Peisong Hu Xiangjin Wei State key laboratory of Rice biology and Breeding China National Center for Rice ImprovementChina National Rice Research InstituteHangzhou 310006ZhejiangChina b State key laboratory of Hybrid Rice Hunan Rice Research InstituteHunan Academy of Agricultural SciencesChangsha 410125HunanChina Hunan Provincial key laboratory of Plant Functional Genomics and Developmental Regulation College of BiologyHunan UniversityChangsha 410082HunanChina Hubei University Wuhan 430062HubeiChina

Seed plumules comprise multiple developing tissues and are key sites for above-ground plant organ ***,the spatial expression of genes in developing rice seed plumules was characterized by single-cell transcriptome sequencing in Zhongjiazao 17,a popular Chinese indica rice *** 15 cell clusters,13 were assigned to cell types using marker genes and cluster-specific *** genes of multiple cell types were expressed in several clusters,suggesting a complex developmental *** genes for signaling by phytohormones such as abscisic acid were highly expressed in specific *** cis-elements in the promoters of genes specifically expressed in cell clusters were calculated,and some key hormone-related motifs were frequent in certain *** expression patterns of genes involved in rapid seed germination,seedling growth,and development were *** findings enhanced our understanding of cellular diversity and specialization within plumules of rice,a monocotyledonous model crop.

关键词： Rice Plumule Single-cell sequencing regulatory network

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Advancing CRISPR base editing technology through innovative strategies and ideas

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Science China Life Sciences 2024年

作者： Xiongwei Fan Yang Lei Liren Wang Xiushan Wu Dali Li The Center for Heart Development College of Life Science Hunan Normal University Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy Shanghai Key Laboratory of Regulatory Biology Institute of Biomedical Sciences and School of Life Sciences East China Normal University Guangdong Provincial key laboratory of Pathogenesis Targeted Prevention and Treatment of Heart Disease

The innovation of CRISPR/Cas gene editing technology has developed rapidly in recent years. It is widely used in the fields of disease animal model construction, biological breeding, disease diagnosis and screening, gene therapy, cell localization, cell lineage tracking, synthetic biology, information storage, etc. However, developing idealized editors in various fields is still a goal for future development. This article focuses on the development and innovation of non-DSB editors BE and PE in the platform-based CRISPR system. It first explains the application of ideas for improvement such as “substitution”, “combination”, “adaptation”, and “adjustment” in BE and PE development and then catalogues the ingenious inversions and leaps of thought reflected in the innovations made to CRISPR technology. It will then elaborate on the efforts currently being made to develop small editors to solve the problem of AAV overload and summarize the current application status of editors for in vivo gene modification using AAV as a delivery system. Finally, it summarizes the inspiration brought by CRISPR/Cas innovation and assesses future prospects for development of an idealized editor.

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Metabolic plasticity of T cell fate decision

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Chinese Medical Journal 2024年第7期137卷 762-775页

作者： Xiaoli Pan Jiajia Wang Lianjun Zhang Guideng Li Bo Huang National key laboratory of Immunity and Inflammation Suzhou Institute of Systems MedicineChinese Academy of Medical Sciences&Peking Union Medical CollegeSuzhouJiangsu 215123China key laboratory of synthetic biology regulatory Element Suzhou Institute of Systems MedicineChinese Academy of Medical Sciences&Peking Union Medical CollegeSuzhouJiangsu 215123China Department of Immunology&National key laboratory of Medical Molecular biology Institute of Basic Medical SciencesChinese Academy of Medical Sciences(CAMS)&Peking Union Medical CollegeBeijing 100005China Department of Biochemistry&Molecular biology Tongji Medical CollegeHuazhong University of Science&TechnologyWuhanHubei 430030China

The efficacy of adaptive immune responses in cancer treatment relies heavily on the state of the T *** antigen exposure,T cells undergo metabolic reprogramming,leading to the development of functional effectors or memory ***,within the tumor microenvironment(TME),metabolic stress impairs CD8+T cell anti-tumor immunity,resulting in exhausted *** studies suggested that targeting T cell metabolism could offer promising therapeutic opportunities to enhance T cell *** this review,we provide a comprehensive summary of the intrinsic and extrinsic factors necessary for metabolic reprogramming during the development of effector and memory T cells in response to acute and chronic inflammatory ***,we delved into the different metabolic switches that occur during T cell exhaustion,exploring how prolonged metabolic stress within the TME triggers alterations in cellular metabolism and the epigenetic landscape that contribute to T cell exhaustion,ultimately leading to a persistently exhausted *** the intricate relationship between T cell metabolism and cancer immunotherapy can lead to the development of novel approaches to improve the efficacy of T cell-based treatments against cancer.

关键词： T cell immunotherapy T cell differentiation T cell exhaustion Metabolic reprogramming Tumor microenvironment

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A systematic understanding of microbial reductive dechlorination towards an improved “one health” soil bioremediation: A review and perspective

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Science China Technological Sciences 2024年第10期67卷 3009-3031页

作者： HE Yan LI ShuYao YUAN Jing CHENG Jie DOU JiBo YANG XueLing XU JianMing Zhejiang Provincial key laboratory of Agricultural Resources and Environment Institute of Soil and Water Resources and Environmental ScienceCollege of Environmental and Resource SciencesZhejiang University key laboratory of Environment Remediation and Ecological Health Ministry of Education Microbiome Network and Department of Agricultural biology Colorado State University Departments of Chemistry and Chemical & Biomolecular Engineering Institute for Functional Intelligent Materials (I-FIM)National University of Singapore

Chlorinated organic pollutants(COPs), both emerging and traditional, are typical persistent pollutants that harm soil health worldwide. Dechlorinators mediated reductive dechlorination is the optimal way to completely remove COPs from anaerobic soil through a redox reaction driven by electron transfer during microbial anaerobic respiration. Generally, the dechlorinated depletion of COPs in situ often interacts with multiple element biogeochemical activities, e.g., methanogenesis, sulfate reduction, iron reduction, and denitrification. Elucidating the relevance of biogeochemical cycles between COPs and multiple elements and the coupled mechanisms involved, thus, helps to develop effective pollution control strategies with the balance between pollution degradation and element cycles in heterogeneous soil, ultimately contributing to “one health” goal. In this review, we summarized the microbial-chemical coupling redox processes and the driving factors, elucidated the interspecies metabolites exchange and electron transfer mechanisms within COP-dechlorinating communities, and further proposed a detailed design, construction, and analysis framework of engineering COP-dechlorinating microbiomes via “top-down” selfassembly and “bottom-up” synthesis to pave the way from laboratory to practical field application. Especially, we delve into the major challenges and perspectives surrounding the design of state-of-the-art synthetic microbial communities. Our goal is to improve the understanding of the microbial-mediated coupling between reductive dechlorination and element biogeochemical cycling, with a particular focus on the implications for health-integrated soil bioremediation under the “one health” concept.

关键词： reductive dechlorination biogeochemical redox processes interspecies interaction synthetic microbiomes, anaerobic soils

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