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Genome reprogramming for synthetic biology

Kylie Standage-Beier,Xiao Wang

Frontiers of Chemical Science and Engineering 2017, Volume 11, Issue 1,   Pages 37-45 doi: 10.1007/s11705-017-1618-2

Abstract: The ability to go from a digitized DNA sequence to a predictable biological function is central to syntheticbiology.Recent development of new programmable tools to reengineer genomes has spurred myriad advances in syntheticbiology.Advanced DNA synthesis and assembly methods have also enabled the construction of fully synthetic organisms

Keywords： CRISPR     genome engineering     synthetic biology     rational design    

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Designer enzyme for green materials innovation: Lactate-polymerizing enzyme as a key catalyst

Seiichi Taguchi

Frontiers of Chemical Science and Engineering 2017, Volume 11, Issue 1,   Pages 139-142 doi: 10.1007/s11705-017-1636-0

Abstract: typical topic of synthetic biology.

Keywords： synthetic biology     enzyme evolutionary engineering     polyhydroxyalkanoate    

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Improving prodeoxyviolacein production via multiplex SCRaMbLE iterative cycles

Juan Wang, Bin Jia, Zexiong Xie, Yunxiang Li, Yingjin Yuan

Frontiers of Chemical Science and Engineering 2018, Volume 12, Issue 4,   Pages 806-814 doi: 10.1007/s11705-018-1739-2

Abstract:

The synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) system

Keywords： synthetic biology     genome rearrangement     prodeoxyviolacein     SCRaMbLE     Saccharomyces cerevisiae    

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

Frontiers of Chemical Science and Engineering 2022, Volume 16, Issue 8,   Pages 1281-1289 doi: 10.1007/s11705-022-2141-7

Abstract: 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 production. Here, we developed a mobile CRISPR-Cas9 based anti-phage system for bacteriophages defense in E. coli. Two conjugative plasmids pGM1 (phosphoglucomutase 1) and pGM2 carrying one and two guide RNAs, respectively, were designed to defend against a filamentous phage. The results showed that the pGM1 and pGM2 could decrease the phage infection rate to 1.6% and 0.2% respectively in infected cells. For preventing phage infection in E. coli, the pGM2 decreased the phage infection rate to 0.1%, while pGM1 failed to block phage infection. Sequence verification revealed that point mutations in protospacer or protospacer adjacent motif sequences of the phage genome caused loss of the defense function. These results support the potential application of MCBAS in E. coli cell factories to defend against phage infections.

Keywords： phage infections     anti-phage     CRISPR-Cas9     conjugative transfer     synthetic biology    

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An Additive Manufacturing Approach that Enables the Field Deployment of Synthetic Biosensors Article

Daniel Wolozny, John R. Lake, Paul G. Movizzo, Zhicheng Long, Warren C. Ruder

Engineering 2019, Volume 5, Issue 1,   Pages 173-180 doi: 10.1016/j.eng.2018.12.001

Abstract:

The tools of synthetic biology can be used to engineer living biosensors that report the presenceHere, we describe the development of a biosensing system consisting of a synthetic biological circuit

Keywords： Synthetic biology     Additive manufacturing     Biosensors    

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Dendritic cell vaccines in cancer immunotherapy: from biology to translational medicine

Hongmei Xu, Xuetao Cao

Frontiers of Medicine 2011, Volume 5, Issue 4,   Pages 323-332 doi: 10.1007/s11684-011-0172-4

Abstract:
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Synthetically engineered microbes reveal interesting principles of cooperation

Michael D. Dressler,Corey J. Clark,Chelsea A. Thachettu,Yasmine Zakaria,Omar Tonsi Eldakar,Robert P. Smith

Frontiers of Chemical Science and Engineering 2017, Volume 11, Issue 1,   Pages 3-14 doi: 10.1007/s11705-016-1605-z

Abstract: Over the past decade, synthetic biology has emerged as a powerful tool to study social dynamics.bacterial pathogens require cooperation to infect the host and survive, the principles developed using syntheticbiology offer promise of developing novel tools and strategies to treat infections, which may reduceverify existing, and develop novel, theories that may govern cooperative behaviors at all levels of biology

Keywords： synthetic biology     engineered bacteria     cooperation     cheater     quorum sensing    

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Engineering of

Ruizhao Wang,Xiaoli Gu,Mingdong Yao,Caihui Pan,Hong Liu,Wenhai Xiao,Ying Wang,Yingjin Yuan

Frontiers of Chemical Science and Engineering 2017, Volume 11, Issue 1,   Pages 89-99 doi: 10.1007/s11705-017-1628-0

Abstract: The conversion of -carotene to astaxanthin is a complex pathway network, in which two steps of hydroxylation and two steps of ketolation are catalyzed by -carotene hydroxylase (CrtZ) and -carotene ketolase (CrtW) respectively. Here, astaxanthin biosynthesis pathway was constructed in by introducing heterologous CrtZ and CrtW into an existing high -carotene producing strain. Both genes and were codon optimized and expressed under the control of constitutive promoters. Through combinatorial expression of CrtZ and CrtW from diverse species, nine strains in dark red were visually chosen from thirty combinations. In all the selected strains, strain SyBE_Sc118060 with CrtW from DC263 and CrtZ from sp. strain PC-1 achieved the highest astaxanthin yield of 3.1 mg/g DCW. Protein phylogenetic analysis shows that the shorter evolutionary distance of CrtW is, the higher astaxanthin titer is. Further, when the promoter of in strain SyBE_Sc118060 was replaced from FBA1p to TEF1p, the astaxanthin yield was increased by 30.4% (from 3.4 to 4.5 mg/g DCW). In the meanwhile, 33.5-fold increase on transcription level and 39.1-fold enhancement on the transcriptional ratio of to were observed at early exponential phase in medium with 4% (w/v) glucose. Otherwise, although the ratio of to were increased at mid-, late-exponential phases in medium with 2% (w/v) glucose, the transcription level of both and were actually decreased during the whole time course, consequently leading to no significant improvement on astaxanthin production. Finally, through high cell density fed-batch fermentation using a carbon source restriction strategy, the production of astaxanthin in a 5-L bioreactor reached to 81.0 mg/L, which was the highest astaxanthin titer reported in yeast. This study provides a reference to greatly enhance desired compounds accumulation by employing the key enzyme(s) in microbes.

Keywords： synthetic biology     astaxanthin     β-carotene hydroxylase     β-carotene ketolase     Saccharomyces    

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Microbial Medicine Industry: Current Status and Future Trends

Yu Qing, Huang Tingting, Deng Zixin

Strategic Study of CAE 2021, Volume 23, Issue 5,   Pages 69-78 doi: 10.15302/J-SSCAE-2021.05.009

Abstract:

The microbial sourced natural products possess diverse structures and excellent activities, implying great potentials for clinical application. This study systematically analyzes the current status of the microbial medicine industry in China and summarizes the development trends of the industry from the aspects of microbial strain resource utilization, excellent strain screening, fermentation process optimization, strain engineering, and new microbial medicine development. This aims to facilitate major breakthroughs and industrial upgrades for China’s microbial medicine industry. Although China’s microbial medicine industry has solid resource and technical foundations, it still lags behind the international advanced level. Considering the opportunities and challenges, we propose several suggestions for promoting China’s microbial medicine industry: constructing large-scale scientific facilities for microbial medicine, strengthening basic research and independent technology development, establishing a talent cultivation system, and formulating systematic industrial incentives.

Keywords： microbial medicine     development trend     biological activity     microbial metabolism     synthetic biology    

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A method for Absolute Protein Expression Quantity Measurement Employing Insulator RiboJ Article

Hongbin Yu, Zheng Wang, Hanyue Xu, Jiusi Guo, Qingge Ma, Xiangxu Mu, Yunzi Luo

Engineering 2018, Volume 4, Issue 6,   Pages 881-887 doi: 10.1016/j.eng.2018.09.012

Abstract: absolute protein expression quantity for a specific promoter is necessary in the fields of both molecular biologyand synthetic biology.measurement of the absolute protein expression quantity for a promoter, however, has been unsuccessful in syntheticbiology.

Keywords： RiboJ     Promoter measurement     Synthetic biology    

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Industry 5.0—The Relevance and Implications of Bionics and Synthetic Biology Artical

Peter Sachsenmeier

Engineering 2016, Volume 2, Issue 2,   Pages 225-229 doi: 10.1016/J.ENG.2016.02.015

Abstract: Bionics (the imitation or abstraction of the “inventions of nature) and, to an even greater extent, syntheticbiology, will be as relevant to engineering development and industry as the silicon chip was over theSynthetic biology is also used for the development of second-generation biofuels and for harvesting theAlthough synthetic biology will be as pervasive and transformative in the next 50 years as digitizationbiology are discussed.

Keywords： Bionics     Synthetic biology     Bio-engineering     Biological sensors     Biofuels     Bio weapons     Virtual evolution     Protocells    

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Rational Design of and Mechanism Insight into an Efficient Antifreeze Peptide for Cryopreservation

Haishan Qi,Yihang Gao,Lin Zhang,Zhongxin Cui,Xiaojie Sui,Jianfan Ma,Jing Yang,Zhiquan Shu,Lei Zhang,

Engineering doi: 10.1016/j.eng.2023.01.015

Abstract: up a new avenue for designing antifreeze materials and provides peptide-based functional modules for syntheticbiology.

Keywords： Evolution analysis     Ice recrystallization inhibition     Molecular dynamics simulation     Cryopreservation     Syntheticbiology    

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Construction, characterization and application of a genome-wide promoter library in

Ting Yuan,Yakun Guo,Junkai Dong,Tianyi Li,Tong Zhou,Kaiwen Sun,Mei Zhang,Qingyu Wu,Zhen Xie,Yizhi Cai,Limin Cao,Junbiao Dai

Frontiers of Chemical Science and Engineering 2017, Volume 11, Issue 1,   Pages 107-116 doi: 10.1007/s11705-017-1621-7

Abstract: 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 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.

Keywords： synthetic biology     yeast     promoter activity     metabolic engineering     xylose utilization    

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Engineering the Biosynthesis of Caffeic Acid in Saccharomyces cerevisiae with Heterologous Enzyme Combinations Article

Lanqing Liu, Hong Liu, Wei Zhang, Mingdong Yao, Bingzhi Li, Duo Liu, Yingjin Yuan

Engineering 2019, Volume 5, Issue 2,   Pages 287-295 doi: 10.1016/j.eng.2018.11.029

Abstract:

Engineering the biosynthesis of plant-derived natural products in microbes presents several challenges, especially when the expression and activation of the plant cytochrome P450 enzyme is required. By recruiting two enzymes—HpaB and HpaC—from several bacteria, we constructed functional 4-hydroxyphenylacetate 3-hydroxylase (4HPA3H) in Saccharomyces cerevisiae to take on a role similar to that of the plant-derived cytochrome P450 enzyme and produce caffeic acid. Along with a common tyrosine ammonia lyase (TAL), the different combinations of HpaB and HpaC presented varied capabilities in producing the target product, caffeic acid, from the substrate, L-tyrosine. The highest production of caffeic acid was obtained with the enzyme combination of HpaB from Pseudomonas aeruginosa and HpaC from Salmonella enterica, which yielded up to 289.4 ± 4.6 mg·L−1 in shake-flask cultivation. The compatibility of heterologous enzymes within a yeast chassis was effectively improved, as the caffeic acid production was increased by 40 times from the initial yield. Six key amino acid residues around the flavin adenine dinucleotide (FAD) binding domain in HpaB from Pseudomonas aeruginosa were distinguished from those other HpaBs, and might play critical roles in affecting enzyme activity. We have thus established an effective approach to construct a highly efficient yeast system to synthesize non-native hydroxylated phenylpropanoids.

Keywords： Saccharomyces cerevisiae     Caffeic acid     Heterologous enzyme     Cytochrome P450     Synthetic biology    

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Cytokine storm and translating IL-6 biology into effective treatments for COVID-19

Frontiers of Medicine doi: 10.1007/s11684-023-1044-4

Abstract: As of May 3, 2023, the coronavirus disease 2019 (COVID-19) pandemic has resulted in more than 760 million confirmed cases and over 6.9 million deaths. Several patients have developed pneumonia, which can deteriorate into acute respiratory distress syndrome. The primary etiology may be attributed to cytokine storm, which is triggered by the excessive release of proinflammatory cytokines and subsequently leads to immune dysregulation. Considering that high levels of interleukin-6 (IL-6) have been detected in several highly pathogenic coronavirus-infected diseases, such as severe acute respiratory syndrome in 2002, the Middle East respiratory syndrome in 2012, and COVID-19, the IL-6 pathway has emerged as a key in the pathogenesis of this hyperinflammatory state. Thus, we review the history of cytokine storm and the process of targeting IL-6 signaling to elucidate the pivotal role played by tocilizumab in combating COVID-19.

Keywords： SARS-CoV-2     COVID-19     cytokine storm     interleukin-6     tocilizumab    

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Title Author Date Type Operation

Genome reprogramming for synthetic biology

Kylie Standage-Beier,Xiao Wang

Journal Article

Designer enzyme for green materials innovation: Lactate-polymerizing enzyme as a key catalyst

Seiichi Taguchi

Journal Article

Improving prodeoxyviolacein production via multiplex SCRaMbLE iterative cycles

Juan Wang, Bin Jia, Zexiong Xie, Yunxiang Li, Yingjin Yuan

Journal Article

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

Journal Article

An Additive Manufacturing Approach that Enables the Field Deployment of Synthetic Biosensors

Daniel Wolozny, John R. Lake, Paul G. Movizzo, Zhicheng Long, Warren C. Ruder

Journal Article

Dendritic cell vaccines in cancer immunotherapy: from biology to translational medicine

Hongmei Xu, Xuetao Cao

Journal Article

Synthetically engineered microbes reveal interesting principles of cooperation

Michael D. Dressler,Corey J. Clark,Chelsea A. Thachettu,Yasmine Zakaria,Omar Tonsi Eldakar,Robert P. Smith

Journal Article

Engineering of

Ruizhao Wang,Xiaoli Gu,Mingdong Yao,Caihui Pan,Hong Liu,Wenhai Xiao,Ying Wang,Yingjin Yuan

Journal Article

Microbial Medicine Industry: Current Status and Future Trends

Yu Qing, Huang Tingting, Deng Zixin

Journal Article

A method for Absolute Protein Expression Quantity Measurement Employing Insulator RiboJ

Hongbin Yu, Zheng Wang, Hanyue Xu, Jiusi Guo, Qingge Ma, Xiangxu Mu, Yunzi Luo

Journal Article

Industry 5.0—The Relevance and Implications of Bionics and Synthetic Biology

Peter Sachsenmeier

Journal Article

Rational Design of and Mechanism Insight into an Efficient Antifreeze Peptide for Cryopreservation

Haishan Qi,Yihang Gao,Lin Zhang,Zhongxin Cui,Xiaojie Sui,Jianfan Ma,Jing Yang,Zhiquan Shu,Lei Zhang,

Journal Article

Construction, characterization and application of a genome-wide promoter library in

Ting Yuan,Yakun Guo,Junkai Dong,Tianyi Li,Tong Zhou,Kaiwen Sun,Mei Zhang,Qingyu Wu,Zhen Xie,Yizhi Cai,Limin Cao,Junbiao Dai

Journal Article

Engineering the Biosynthesis of Caffeic Acid in Saccharomyces cerevisiae with Heterologous Enzyme Combinations

Lanqing Liu, Hong Liu, Wei Zhang, Mingdong Yao, Bingzhi Li, Duo Liu, Yingjin Yuan

Journal Article

Cytokine storm and translating IL-6 biology into effective treatments for COVID-19

Journal Article