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Enhancing whole yeast genome rearrangements through multiple LoxPsym sequences

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Science China(Life Sciences) 2024年第9期67卷 2045-2047页

作者： Bing-Zhi Li ying-jin yuan Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300072China Frontiers Research Institute for Synthetic Biology Tianjin UniversityTianjin 300072China

Genomic rearrangements play a significant role in disease,evolution,and tumorigenesis(Mani and Chinnaiyan,2010).While single nucleotide polymorphisms(SNPs)and small insertions/deletions contribute substantially to gen... 详细信息

关键词： insertion sequences

Enhancement of polymyxin B1 production by an artificial microbial consortium of Paenibacillus polymyxa and recombinant Corynebacterium glutamicum producing precursor amino acids

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Synthetic and Systems Biotechnology 2024年第1期9卷 176-185页

作者： Hui-Zhong Sun Si-Yu Wei Qiu-Man Xu Wei Shang Qing Li jing-Sheng Cheng ying-jin yuan Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityYaguan Road 135Jinnan DistrictTianjin300350PR China Tianjin Key Laboratory of Animal and Plant Resistance College of Life ScienceTianjin Normal UniversityBinshuixi Road 393Xiqing DistrictTianjin300387PR China Department of Pharmaceutical School of Chemical Engineering and TechnologyTianjin UniversityYaguan Road 135Jinnan DistrictTianjin300350PR China

Polymyxin B,produced by Paenibacillus polymyxa,is used as the last line of defense *** this study,exogenous mixture of precursor amino acids increased the level and proportion of polymyxin B1 in the total of polymyxin B analogs of *** CJX518-AC(PPAC)from 0.15 g/L and 61.8%to 0.33 g/L and 79.9%,*** co-culture of strain PPAC and recombinant Corynebacterium glutamicum-leu01,which produces high levels of threonine,leucine,and isoleucine,increased polymyxin B1 production to 0.64 g/*** strains PPAC and ***-leu01 simultaneously inoculated into an optimized medium with 20 g/L peptone,polymyxin B1 production was increased to 0.97 g/***,the polymyxin B1 production in the co-culture of strains PPAC and ***-leu01 increased to 2.21 g/L after optimized inoculation ratios and fermentation medium with 60 g/L *** study provides a new strategy to improve polymyxin B1 production.

关键词： Polymyxin Co-culture Paenibacillus polymyxa Corynebacterium glutamicum Medium optimization Metabolic precursors

Mobile CRISPR-Cas9 based anti-phage system in E. coli

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Frontiers of Chemical Science and Engineering 2022年第8期16卷 1281-1289页

作者： Zhou Cao Yuxin Ma Bin Jia ying-jin yuan Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering(Ministry of Education) Tianjin UniversityTianjin 300072China Collaborative Innovation Center of Chemical Science and Engineering(Tianjin) School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300072China

Escherichia coli is one of the most important microbial cell factories,but infection by bacteriophages in the environment may have a huge impact on its application in industrial ***,we developed a mobile CRISPR-Cas9 based anti-phage system for bacteriophages defense in *** conjugative plasmids pGM1(phosphoglucomutase 1)and pGM2 carrying one and two guide RNAs,respectively,were designed to defend against a filamentous *** results showed that the pGM1 and pGM2 could decrease the phage infection rate to 1.6%and 0.2%respectively in infected *** preventing phage infection in ***,the pGM2 decreased the phage infection rate to 0.1%,while pGM1 failed to block phage *** verification revealed that point mutations in protospacer or protospacer adjacent motif sequences of the phage genome caused loss of the defense *** results support the potential application of MCBAS in *** cell factories to defend against phage infections.

关键词： phage infections anti-phage CRISPR-Cas9,conjugative transfer synthetic biology

Biomanufacturing boosts the high-level development of economy and society

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Green Chemical Engineering 2023年第2期4卷 135-136页

作者： Chun Li An-Ping Zeng ying-jin yuan Key Lab for Industrial Biocatalysis Ministry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China Center for Synthetic&Systems Biology Department of Chemical EngineeringTsinghua UniversityBeijing100084China Center of Synthetic Biology and Integrated Bioengineering School of EngineeringWestlake UniversityHangzhou310030China Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering(Ministry of Education) Tianjin UniversityTianjin300072China School of Chemical Engineering and Technology Tianjin UniversityTianjin300072China

Global society requires new technologies for manufacturing essential chemicals for modern life that are decoupled from fossil ***,Green Chemical Engineering focuses on the areas of green and sustain-able development o... 详细信息

关键词： boost attractive chemicals

High production of fatty alcohols in Yarrowia lipolytica by coordination with glycolysis

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Science China Chemistry 2019年第8期62卷 1007-1016页

作者： jin-Lai Zhang ying-Xiu Cao Yang-Zi Peng Cong-Cong jin Qiu-Yan Bai Ruo-Si Zhang Duo Liu ying-jin yuan Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education) Tianjin University Tianjin 300072China Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) School of Chemical Engineering and Technology Tianjin UniversityTianjin 300072China

Fatty alcohol biosynthesis by oleaginous microbes was a promising alternative to the petroleum or other non-renewable resources-based process. However, low titer and yield hamper the further industrial and commercial applications. Here, we developed an efficient strategy to coordinate fatty alcohol with glycolysis which achieved a ‘pull-and-push’ effect to improve fatty alcohol production. Transcript profiling indicated that genes in carbohydrate metabolism were up-regulated significantly in response to high fatty alcohol production. Based on it, 11 glycolysis promoters were screening to express fatty acyl-CoA reductase(FAR) to relate the fatty alcohol production with the up-regulated carbohydrate metabolism, and the fatty alcohol production reached 557 mg/L when FAR was expressed by the promoter of PFBAin. RNA-seq and qRT-PCR analysis demonstrated that a ‘pull-and-push’ effect caused by the coordination system dynamically enhanced the product synthesis flux from top to bottom, which was also testified and intensified by doubled glucose concentration. After manipulating structural and regulatory genes of lipid metabolism, the final strain achieved up to 5.75 g/L fatty alcohol production from modified YPD medium(containing 91 g/L glucose) in shake flasks, which represented the highest titer reported to date. This work offered a feasible and effective reference for dynamic manipulation of fatty acid-derived chemicals synthesis.

关键词： fatty alcohol biosynthesis coordinative expression Yarrowia lipolytica fatty acyl-CoA reductase(FAR) metabolic engineering

Comparative lipidomic analysis of S. cerevisiae cells during industrial bioethanol fermentation

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Frontiers of Chemical Science and Engineering 2012年第4期6卷 461-469页

作者： Bin QIAO Hong-Chi TIAN ying-jin yuan Key Laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300072China

Variations in the composition and level of phospholipids （PLs） in yeast cells during industrial ethanol fermentation processes were analyzed. A comparative lipidomic method was used to investigate the changes in total cellular PLs during continuous and fed-batch/batch processes. The phospholipid metabolism in yeast changed during both processes, mainly due to the presence of longchain poly unsaturated fatty acids （PUFA） that contained phosphatidyglycerol （PG）, phosphatidylethanolamine （PE） and phosphatidylserine （PS）. The complexity of the media affected the growth of the yeast and the membrane composition. Yeast incorporated lots of exogenous saturated and PUFAs from the feedstock during the fermentations. During the continuous fermentation, there was an increase in PLs with shorter chains as the fermentation progressed and early in process there were more longchains. During the fed-batch/batch process, the PG species increased as the fermentation progressed. This is probably due to an inositol deficiency in the earlier part of the fermentation.

关键词： lipidomics systems biology phospholipids,stirred-tank saccharomyces cerevisiae biorefinery engi-neering

Directed evolution of the fusion enzyme for improving astaxanthin biosynthesis in Saccharomyces cerevisiae

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Synthetic and Systems Biotechnology 2023年第1期8卷 46-53页

作者： Yong-Wen Ding Chuan-Zhen Lu Yan Zheng Han-Zhang Ma jin jin Bin Jia ying-jin yuan Frontier Science Center for Synthetic Biology(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China

catalyzed byβ-carotene hydroxylase(crtZ)andβ-carotene ketolase(crtW)decreases the content of the ***,we exploited directed evolution of the fusion of crtZ and crtW for improving astaxanthin biosynthesis in Saccharomyces *** results demonstrated that the fusion enzyme of crtZ-crtW with 2 X GGGGS peptides linker can effectively reduce the accumulation of intermediates and improves the content of *** with the control strain,the fusion enzyme of ketase and hydroxylase reduced zeaxanthin and canthaxanthin by 7 and 14 times and increased astaxanthin by 1.6 times,***,9 variant fusion mutants with improved astaxanthin production were generated through directed *** these dominant mutants generated a variant,L95S+I206L,which increased the astaxanthin content of 3.8 times than the control *** AlphaFold2 assisted structural analysis indicated that these two mutations alter the interaction between the substrate and the enzymes *** research provided an efficient idea to reduce the accumulation of the intermediate products in complex biosynthesis pathway.

关键词： Astaxanthin Directed evolution Fusion enzyme Saccharomyces cerevisiae Synthetic biology

Orthogonality of Redesigned tRNA Molecules with Three Stop Codons

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Chinese Journal of Chemistry 2022年第7期40卷 825-831页

作者： Zhao-Yang Zhang Dan-Ni Liao Yu-Xin Ma Bin Jia ying-jin yuan Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300072China Collaborative Innovation Center of Chemical Science and Engineering(Tianjin) Tianjin UniversityTianjin 300072China

The ability to expand genetic code in living cells has emerged as a powerful method with diverse ***,we design re-placement of the anticodons of *** tRNAs that recognize codons for 20 natural amino acids,with three anti-stop codons,resulting in a total of 60 engineered tRNA *** test these constructs one by one in ***,and found that six tRNAsCUA(tyrV,serX,hisR,trpT,glnV and leuX),two tRNAsUCA(trpT and leuX)and one tRNAUUA(tyrV)allowed efficient expression of Red Fluorescence Protein(RFP)with the presence of a corresponding stop codon in ***,we exploit the mutual orthogonality of tRNASer CUA,tRNATrpUCA and tRNATyrUUA with corresponding stop codons and demonstrated that the tRNASer CUA and the tRNATrp UCA can provide dynamic range and low ***,we show the TAG and TGA can not only be used as an"AND gate"circuit to control the translation of target gene,but also be used to control the translation of a prodeoxyviolacein(PDV)pathway and a reporter in ***,this work provides flexible tools for translational control and holds great potential to promote synthetic biology studies.

关键词： tRNA Orthogonality Synthetic biology Series control Parallel control Biosynthesis

Machine learning-aided scoring of synthesis difficulties for designer chromosomes

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Science China(Life Sciences) 2023年第7期66卷 1615-1625页

作者： Yan Zheng Kai Song Ze-Xiong Xie Ming-Zhe Han Fei Guo ying-jin yuan Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering Ministry of EducationTianjin UniversityTianjin300072China School of Chemical Engineering and Technology Tianjin UniversityTianjin300072China School of Computer Science and Engineering Central South UniversityChangsha410083China

Designer chromosomes are artificially synthesized ***,these chromosomes have numerous applications ranging from medical research to the development of ***,some chromosome fragments can interfere with the chemical synthesis of designer chromosomes and eventually limit the widespread use of this *** address this issue,this study aimed to develop an interpretable machine learning framework to predict and quantify the synthesis difficulties of designer chromosomes in *** the use of this framework,six key sequence features leading to synthesis difficulties were identified,and an e Xtreme Gradient Boosting model was established to integrate these *** predictive model achieved high-quality performance with an AUC of 0.895 in cross-validation and an AUC of 0.885 on an independent test *** on these results,the synthesis difficulty index(S-index)was proposed as a means of scoring and interpreting synthesis difficulties of chromosomes from prokaryotes to *** findings of this study emphasize the significant variability in synthesis difficulties between chromosomes and demonstrate the potential of the proposed model to predict and mitigate these difficulties through the optimization of the synthesis process and genome rewriting.

关键词： synthetic biology machine learning artificial chromosome chemical synthesis