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Engineering natural molecule-triggered genetic control systems for tunable gene-and cell-based therapies

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synthetic and Systems Biotechnology 2023年第3期8卷 416-426页

作者： Xinyi Wang Xuantong Zhou Liping Kang Yuqin Lai Haifeng Ye synthetic biology and Biomedical Engineering laboratory Biomedical Synthetic Biology Research CenterShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityDongchuan Road 500Shanghai 200241China

The ability to precisely control activities of engineered designer cells provides a novel strategy for modern precision *** adjustable gene-and cell-based precision therapies are recognized as next generation ***,the translation of these controllable therapeutics into clinical practice is severely hampered by the lack of safe and highly specific genetic switches controlled by triggers that are nontoxic and side-effect ***,natural products derived from plants have been extensively explored as trigger molecules to control genetic switches and synthetic gene networks for multiple *** controlled genetic switches could be further introduced into mammalian cells to obtain synthetic designer cells for adjustable and fine tunable cell-based precision *** this review,we introduce various available natural molecules that were engineered to control genetic switches for controllable transgene expression,complex logic computation,and therapeutic drug delivery to achieve precision *** also discuss current challenges and prospects in translating these natural molecule-controlled genetic switches developed for biomedical applications from the laboratory to the clinic.

关键词： Mammalian synthetic biology Natural molecules Genetic switches Gene-and cell-based therapy Precision medicine

Improving cooperativity of transcription activators by oligomerization domains in mammalian cells

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synthetic and Systems Biotechnology 2023年第1期8卷 114-120页

作者： Xinmao Chen Ziming Liu Chunbo Lou Ying Guan Qi Ouyang Yanhui Xiang School of Physics Peking UniversityBeijing100871China Department of Chemical Engineering Tsinghua UniversityBeijing100871China 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 SciencesShenzhen518055China

Cooperative activation is critical for the applications of synthetic biology in mammalian *** this study,we have developed cooperative transcription factor by fusing oligomerization domain in mammalian ***,we demonstrated that two oligomerized domains(CI434 and CI)successfully improved transcription factor cooperativity in bacterial cells but failed to increase cooperativity in mammalian cells,possibly because the additional mammalian activation domain disrupted their oligomerization ***,we chose a different type of oligomerized domain(CarHC),whose ability to oligomerize is not dependent on its C-terminal domains,to fuse with a transcription factor(RpaR)and activation domain(VTR3),forming a potential cooperative transcription activator RpaR-CarH-VTR3 for mammalian regulatory *** with RpaR-VTR3,the cooperativity of RpaR-CarH-VTR3 was significantly improved with higher Hill coefficient and a narrower input range in the inducible switch system in mammalian ***,a mathematical model based on statistical mechanics model was developed and the simulation results supported the hypothesis that the tetramer of the CarH domain in mammalian cells was the reason for the cooperative capacity of RpaR-CarH-VTR3.

关键词： activation narrow cooperative

Role of vitamin D receptor in the regulation of CYP3A gene expression

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Acta Pharmaceutica Sinica B 2019年第6期9卷 1087-1098页

作者： Xuan Qin Xin Wang Shanghai key laboratory of regulatory biology Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China

Vitamin D3(VD3)is a multifunctional nutrient which can be either synthesized or absorbed from the *** plays a pivotal role in systemic calcium and phosphate homeostasis,as well as in various physiological and pathological ***3 is converted to the active form,1α,25-dihydroxy vitamin D3(1,25-D3),by cytochrome P4502R1(CYP2R1)/CYP27A1 and CYP27B1 sequentially,and deactivated by multiple enzymes including *** the other hand,1,25-D3 is capable of activating the transcription of CYP3A genes in humans,mice and *** vitamin D receptor(VDR)-mediated transactivation of human CYP3A4 and CYP3A5 resembles that known for pregnane X receptor(PXR).Activated VDR forms a heterodimer with retinoid X receptorα(RXRα),recruits co-activators,translocates to the cell nucleus,binds to the specific vitamin D responsive elements(VDRE),and activates the gene *** mice,intestinal Cyp3a11 mRNA levels,but not those of hepatic CYP3As,were induced by in vivo administration of VDR and PXR *** rats,intestinal Cyp3a1 and Cyp3a2mRNAs were induced by 1,25-D3 or lithocholic acid(LCA),whereas hepatic Cyp3a2,but not Cyp3a1and Cyp3a9,was modulated to 1,25-D3 *** general,the VDR-mediated regulation of CYP3A presents species and organ specificity.

关键词： Vitamin D3 VDR CYP3A Transactivation Pharmacokinetic Drug metabolism

Genomic landscape of gastric cancer： molecular classification and potential targets

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Science China(Life Sciences) 2017年第2期60卷 126-137页

作者： Jiawei Guo Weiwei Yu Hui Su Xiufeng Pang Shanghai key laboratory of regulatory biology Institute of Biomedical Sciences and School of Life Sciences East China Normal University Shanghai 200241 China

Gastric cancer imposes a considerable health burden worldwide, and its mortality ranks as the second highest for all types of cancers. The limited knowledge of the molecular mechanisms underlying gastric cancer tumorigenesis hinders the development of therapeutic strategies. However, ongoing collaborative sequencing efforts facilitate molecular classification and unveil the genomic landscape of gastric cancer. Several new drivers and tumorigenic pathways in gastric cancer, including chromatin remodeling genes, Rho A-related pathways, TP53 dysregulation, activation of receptor tyrosine kinases, stem cell pathways and abnormal DNA methylation, have been revealed. These newly identified genomic alterations await translation into clinical diagnosis and targeted therapies. Considering that loss-of-function mutations are intractable, synthetic lethality could be employed when discussing feasible therapeutic strategies. Although many challenges remain to be tackled, we are optimistic regarding improvements in the prognosis and treatment of gastric cancer in the near future.

关键词： gastric cancer chromatin remodeling RhoA p53 receptor tyrosine kinase DNA methylation

New food sources and production systems:a comparison of international regulations and China’s advancements in novel foods with synthetic biology

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Food Science and Human Wellness 2024年第5期13卷 2519-2542页

作者： Xin Liu Di Wu Yi Shao Yongning Wu key laboratory for Deep Processing of Major Grain and Oil(The Chinese Ministry of Education) College of Food Science and EngineeringWuhan Polytechnic UniversityWuhan 430023China Institute for Global Food Security School of Biological SciencesBelfast B795DLUnited Kingdom NHC key laboratory of Food Safety Risk Assessment China National Center for Food Safety Risk AssessmentBeijing 100021China Department of Nutrition and Food Safety Peking Union Medical CollegeResearch Unit of Food SafetyChinese Academy of Medical SciencesBeijing 100021China

The global shift towards sustainable food systems has sparked innovations in food sources and production systems,including cell-based meat,plant-based food products,precision fermentation,and 3D food *** advancements pose regulatory challenges and opportunities,with China emerging as a critical player in adopting and regulating new food *** review explores the international landscape of new food sources and production systems(NFPS),focusing on China’s role and regulatory approaches compared to global *** this comparative analysis,we aim to contribute to the ongoing dialogue on food safety regulation,offering insights and recommendations for policymakers,industry stakeholders,and researchers engaged in the global food system’s *** comprehensive overview underscores the dynamic nature of regulatory frameworks governing NFPS,highlighting the international efforts to ensure food safety,consumer protection,and the sustainable evolution of the food industry.

关键词： New food sources Food production system Food safety International regulation synthetic biology China

Towards understanding the mechanism of n-hexane tolerance in Synechocystis *** 6803

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中国化学工程学报:英文版 2023年第7期59卷 128-134页

作者： Tao Sun Shubin Li Guangsheng Pei Lei Chen Weiwen Zhang laboratory of synthetic Microbiology School of Chemical Engineering&TechnologyTianjin UniversityTianjin 300072China Frontier Science Center for synthetic biology&key laboratory of Systems Bioengineering Ministry of Education of ChinaTianjin 300072China Center for Biosafety Research and Strategy Tianjin UniversityTianjin 300072China

synthetic biology efforts have also led to the development of photosynthetic cyanobacteria as"autotrophic cell factories"for biosynthesis of various biofuels directly from CO_(2).However,the low tolerance to toxicity of biofuels has restricted the economic application of cyanobacterial *** this study,RNAseq transcriptomics was employed to reveal stress responses to exogenous n-hexane in Synechocystis *** *** enrichment analysis of the transcriptomic data showed that signal transduction systems were induced *** further identify regulatory genes related to n-hexane tolerance,a library of transcriptional regulators(TRs)deletion mutants was then screened for their roles in nhexane *** results showed that a knockout mutant of slr0724 that encodes an Hta R suppressor protein was more tolerant to n-hexane than the wild type,indicating the involvement of slr0724 in nhexane *** study provides the foundation for better understanding the cellular responses to n-hexane in Synechocystis *** 6803,which could contribute to the further engineering of nhexane tolerance in cyanobacteria.

关键词： Transcriptome n-Hexane tolerance Metabolomics Synechocystis

Construction, characterization and application of a genomewide promoter library in Saccharomyces cerevisiae

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Frontiers of Chemical Science and Engineering 2017年第1期11卷 107-116页

作者： Ting Yuan Yakun Guo Junkai Dong Tianyi Li Tong Zhou Kaiwen Sun Mei Zhang Qingyu Wu Zhen Xie Yizhi Cai Limin Cao Junbiao Dai MOE key laboratory of Bioinformatics and Centre for synthetic and Systems biology School of Life Sciences Tsinghua University Beijing 100084 China College of Life Sciences Capital Normal University Beijing 100048 China MOE key laboratory of Bioinformatics and Bioinformatics Division Center for Synthetic and Systems Biology TNLIST/Department of Automation Tsinghua University Beijing 100084 China School of Biological Sciences The King's Buildings University of Edinburgh Edinburgh EH9 3BF UK

Promoters are critical elements to control gene expression but could behave differently under various growth conditions. Here we report the construction of a genome-wide promoter library, in which each native promoter in Saccharomyces cerevisiae was cloned upstream of a yellow fluorescent protein （YFP） reporter gene. Nine libraries were arbitrarily defined and assembled in bacteria. The resulting pools of promoters could be prepared and transformed into a yeast strain either as centromeric plasmids or integrated into a genomic locus upon enzymatic treatment. Using fluorescence activated cell sorting, we classified the yeast strains based on YFP fluorescence intensity and arbitrarily divided the entire library into 12 bins, representing weak to strong promoters. Several strong promoters were identified from the most active bins and their activities were assayed under different growth conditions. Finally, these promoters were applied to drive the expression of genes in xylose utilization to improve fermentation efficiency. Together, this library could provide a quick solution to identify and utilize desired promoters under user-defined growth conditions.

关键词： synthetic biology yeast promoter activity,metabolic engineering xylose utilization

Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae

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Science China(Life Sciences) 2014年第1期57卷 52-58页

作者： LI YingXue LIU XueNing WANG XiaoWo ZHANG XueGong MOE key laboratory of Bioinformatics Bioinformatics Division and Center for Synthetic and Systems Biology TNLIST/Department of Automation Tsinghua University School of Life Sciences Tsinghua University

Recent studies have found many antisense non-coding transcripts at the opposite strand of some protein-coding *** yeast,it was reported that such antisense transcripts play regulatory roles for their partner genes by forming a feedback loop with the protein-coding *** not all coding genes have accompanying antisense transcripts,it would be interesting to know whether there are sequence signatures in a coding gene that are decisive or associated with the existence of such antisense *** collected all the annotated antisense transcripts in the yeast Saccharomyces cerevisiae,analyzed sequence motifs around the genes with antisense partners,and classified genes with and without accompanying antisense transcripts by using machine learning *** weak but statistically significant sequence features are detected,which indicates that there are sequence signatures around the protein-coding genes that may be decisive or indicative for the existence of accompanying antisense transcripts.

关键词： antisense transcript pattern recognition motif finding yeast

High-throughput,microscopy-based screening and quantification of genetic elements

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mLife 2023年第4期2卷 450-461页

作者： Rongrong Zhang Yajia Huang Mei Li Lei Wang Bing Li Aiguo Xia Ye Li Shuai Yang Fan Jin CAS key laboratory of Quantitative Engineering biology Shenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina Shenzhen synthetic biology Infrastructure Shenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina Chengdu Documentation and Information Center Chinese Academy of SciencesChengduChina

synthetic biology relies on the screening and quantification of genetic components to assemble sophisticated gene circuits with specific *** is a powerful tool for characterizing complex cellular phenotypes with increasing spatial and temporal resolution to library screening of genetic ***-based assays are powerful tools for characterizing cellular phenotypes with spatial and temporal resolution and can be applied to large-scale samples for library screening of genetic ***,strategies for high-throughput microscopy experiments remain ***,we present a high-throughput,microscopy-based platform that can simultaneously complete the preparation of an 8×12-well agarose pad plate,allowing for the screening of 96 independent strains or experimental conditions in a single *** this platform,we screened a library of natural intrinsic promoters from Pseudomonas aeruginosa and identified a small subset of robust promoters that drives stable levels of gene expression under varying growth ***,the platform allowed for single-cell measurement of genetic elements over time,enabling the identification of complex and dynamic phenotypes to map genotype in high *** expected that the platform could be employed to accelerate the identification and characterization of genetic elements in various biological systems,as well as to understand the relationship between cellular phenotypes and internal states,including genotypes and gene expression programs.

关键词： characterization methods high-throughput robust genetic elements synthetic biology