Pub Date : 2024-05-24DOI: 10.1021/acssynbio.4c00145
Deniz Durmusoglu, Daniel J. Haller, Ibrahim S. Al’Abri, Katie Day, Carmen Sands, Andrew Clark, Adriana San-Miguel, Ruben Vazquez-Uribe, Morten O. A. Sommer and Nathan C. Crook*,
Saccharomyces boulardii (Sb) is an emerging probiotic chassis for delivering biomolecules to the mammalian gut, offering unique advantages as the only eukaryotic probiotic. However, precise control over gene expression and gut residence time in Sb have remained challenging. To address this, we developed five ligand-responsive gene expression systems and repaired galactose metabolism in Sb, enabling inducible gene expression in this strain. Engineering these systems allowed us to construct AND logic gates, control the surface display of proteins, and turn on protein production in the mouse gut in response to dietary sugar. Additionally, repairing galactose metabolism expanded Sb’s habitat within the intestines and resulted in galactose-responsive control over gut residence time. This work opens new avenues for precise dosing of therapeutics by Sb via control over its in vivo gene expression levels and localization within the gastrointestinal tract.
{"title":"Programming Probiotics: Diet-Responsive Gene Expression and Colonization Control in Engineered S. boulardii","authors":"Deniz Durmusoglu, Daniel J. Haller, Ibrahim S. Al’Abri, Katie Day, Carmen Sands, Andrew Clark, Adriana San-Miguel, Ruben Vazquez-Uribe, Morten O. A. Sommer and Nathan C. Crook*, ","doi":"10.1021/acssynbio.4c00145","DOIUrl":"10.1021/acssynbio.4c00145","url":null,"abstract":"<p ><i>Saccharomyces boulardii</i> (<i>Sb</i>) is an emerging probiotic chassis for delivering biomolecules to the mammalian gut, offering unique advantages as the only eukaryotic probiotic. However, precise control over gene expression and gut residence time in <i>Sb</i> have remained challenging. To address this, we developed five ligand-responsive gene expression systems and repaired galactose metabolism in <i>Sb</i>, enabling inducible gene expression in this strain. Engineering these systems allowed us to construct AND logic gates, control the surface display of proteins, and turn on protein production in the mouse gut in response to dietary sugar. Additionally, repairing galactose metabolism expanded <i>Sb</i>’s habitat within the intestines and resulted in galactose-responsive control over gut residence time. This work opens new avenues for precise dosing of therapeutics by <i>Sb</i> via control over its <i>in vivo</i> gene expression levels and localization within the gastrointestinal tract.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141089633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-24DOI: 10.1021/acssynbio.4c00059
João Rainha, Joana L. Rodrigues* and Lígia R. Rodrigues,
Curcumin, a natural polyphenol derived from turmeric, has attracted immense interest due to its diverse pharmacological properties. Traditional extraction methods from Curcuma longa plants present limitations in meeting the growing demand for this bioactive compound, giving significance to its production by genetically modified microorganisms. Herein, we have developed an engineered Saccharomyces cerevisiae to produce curcumin from glucose. A pathway composed of the 4-hydroxyphenylacetate 3-monooxygenase oxygenase complex from Pseudomonas aeruginosa and Salmonella enterica, caffeic acid O-methyltransferase from Arabidopsis thaliana, feruloyl-CoA synthetase from Pseudomonas paucimobilis, and diketide-CoA synthase and curcumin synthase from C. longa was introduced in a p-coumaric acid overproducing S. cerevisiae strain. This strain produced 240.1 ± 15.1 μg/L of curcumin. Following optimization of phenylpropanoids conversion, a strain capable of producing 4.2 ± 0.6 mg/L was obtained. This study reports for the first time the successful de novo production of curcumin in S. cerevisiae.
{"title":"De Novo Biosynthesis of Curcumin in Saccharomyces cerevisiae","authors":"João Rainha, Joana L. Rodrigues* and Lígia R. Rodrigues, ","doi":"10.1021/acssynbio.4c00059","DOIUrl":"10.1021/acssynbio.4c00059","url":null,"abstract":"<p >Curcumin, a natural polyphenol derived from turmeric, has attracted immense interest due to its diverse pharmacological properties. Traditional extraction methods from <i>Curcuma longa</i> plants present limitations in meeting the growing demand for this bioactive compound, giving significance to its production by genetically modified microorganisms. Herein, we have developed an engineered <i>Saccharomyces cerevisiae</i> to produce curcumin from glucose. A pathway composed of the 4-hydroxyphenylacetate 3-monooxygenase oxygenase complex from <i>Pseudomonas aeruginosa</i> and <i>Salmonella enterica</i>, caffeic acid <i>O</i>-methyltransferase from <i>Arabidopsis thaliana</i>, feruloyl-CoA synthetase from <i>Pseudomonas paucimobilis</i>, and diketide-CoA synthase and curcumin synthase from <i>C. longa</i> was introduced in a <i>p-</i>coumaric acid overproducing <i>S. cerevisiae</i> strain. This strain produced 240.1 ± 15.1 μg/L of curcumin. Following optimization of phenylpropanoids conversion, a strain capable of producing 4.2 ± 0.6 mg/L was obtained. This study reports for the first time the successful <i>de novo</i> production of curcumin in <i>S. cerevisiae</i>.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acssynbio.4c00059","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141092350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-23DOI: 10.1021/acssynbio.4c00230
Calvin Lam*,
Bottom-up approaches are becoming increasingly popular for studying multicellular self-organization and development. In contrast to the classic top-down approach, where parts of the organization/developmental process are broken to understand the process, the goal is to build the process to understand it. For example, synthetic circuits have been built to understand how cell–cell communication and differential adhesion can drive multicellular development. The majority of current bottom-up efforts focus on using activatory circuits to engineer and understand development, but efforts with inhibitory circuits have been minimal. Yet, inhibitory circuits are ubiquitous and vital to native developmental processes. Thus, inhibitory circuits are a crucial yet poorly studied facet of bottom-up multicellular development. To demonstrate the potential of inhibitory circuits for building and developing multicellular structures, several synthetic inhibitory circuits that combine engineered cell–cell communication and differential adhesion were designed, and then examined for synthetic development capability using a previously validated in silico framework. These designed inhibitory circuits can build a variety of patterned, self-organized structures and even morphological oscillations. These results support that inhibitory circuits can be powerful tools for building, studying, and understanding developmental processes.
{"title":"Mathematical and In Silico Analysis of Synthetic Inhibitory Circuits That Program Self-Organizing Multicellular Structures","authors":"Calvin Lam*, ","doi":"10.1021/acssynbio.4c00230","DOIUrl":"10.1021/acssynbio.4c00230","url":null,"abstract":"<p >Bottom-up approaches are becoming increasingly popular for studying multicellular self-organization and development. In contrast to the classic top-down approach, where parts of the organization/developmental process are broken to understand the process, the goal is to build the process to understand it. For example, synthetic circuits have been built to understand how cell–cell communication and differential adhesion can drive multicellular development. The majority of current bottom-up efforts focus on using activatory circuits to engineer and understand development, but efforts with inhibitory circuits have been minimal. Yet, inhibitory circuits are ubiquitous and vital to native developmental processes. Thus, inhibitory circuits are a crucial yet poorly studied facet of bottom-up multicellular development. To demonstrate the potential of inhibitory circuits for building and developing multicellular structures, several synthetic inhibitory circuits that combine engineered cell–cell communication and differential adhesion were designed, and then examined for synthetic development capability using a previously validated in silico framework. These designed inhibitory circuits can build a variety of patterned, self-organized structures and even morphological oscillations. These results support that inhibitory circuits can be powerful tools for building, studying, and understanding developmental processes.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141089632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Electroactive bacteria, exemplified by Shewanella oneidensis MR-1, have garnered significant attention due to their unique extracellular electron-transfer (EET) capabilities, which are crucial for energy recovery and pollutant conversion. However, the practical application of MR-1 is constrained by its EET efficiency, a key limiting factor, due to the complexity of research methodologies and the challenges associated with the practical use of gene editing tools. To address this challenge, a novel gene integration system, INTEGRATE, was developed, utilizing CRISPR-mediated transposase technologies for precise genomic insertion within the S. oneidensis MR-1 genome. This system facilitated the insertion of extensive gene segments at different sites of the Shewanella genome with an efficiency approaching 100%. The inserted cargo genes could be kept stable on the genome after continuous cultivation. The enhancement of the organism’s EET efficiency was realized through two primary strategies: the integration of the phenazine-1-carboxylic acid synthesis gene cluster to augment EET efficiency and the targeted disruption of the SO3350 gene to promote anodic biofilm development. Collectively, our findings highlight the potential of utilizing the INTEGRATE system for strategic genomic alterations, presenting a synergistic approach to augment the functionality of electroactive bacteria within bioelectrochemical systems.
{"title":"Efficient Enhancement of Extracellular Electron Transfer in Shewanella oneidensis MR-1 via CRISPR-Mediated Transposase Technology","authors":"Wei-Qiang Lin, Zhou-Hua Cheng*, Qi-Zhong Wu, Jia-Qi Liu, Dong-Feng Liu* and Guo-Ping Sheng*, ","doi":"10.1021/acssynbio.4c00240","DOIUrl":"10.1021/acssynbio.4c00240","url":null,"abstract":"<p >Electroactive bacteria, exemplified by <i>Shewanella oneidensis</i> MR-1, have garnered significant attention due to their unique extracellular electron-transfer (EET) capabilities, which are crucial for energy recovery and pollutant conversion. However, the practical application of MR-1 is constrained by its EET efficiency, a key limiting factor, due to the complexity of research methodologies and the challenges associated with the practical use of gene editing tools. To address this challenge, a novel gene integration system, INTEGRATE, was developed, utilizing CRISPR-mediated transposase technologies for precise genomic insertion within the <i>S. oneidensis</i> MR-1 genome. This system facilitated the insertion of extensive gene segments at different sites of the <i>Shewanella</i> genome with an efficiency approaching 100%. The inserted cargo genes could be kept stable on the genome after continuous cultivation. The enhancement of the organism’s EET efficiency was realized through two primary strategies: the integration of the phenazine-1-carboxylic acid synthesis gene cluster to augment EET efficiency and the targeted disruption of the <i>SO3350</i> gene to promote anodic biofilm development. Collectively, our findings highlight the potential of utilizing the INTEGRATE system for strategic genomic alterations, presenting a synergistic approach to augment the functionality of electroactive bacteria within bioelectrochemical systems.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141079441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-23DOI: 10.1021/acssynbio.4c00068
Jure Tica, Haobin Chen, Shulei Luo, Manman Chen and Mark Isalan*,
Quorum sensing signals have evolved for population-level signaling in bacterial communities and are versatile tools for engineering cell–cell signaling in synthetic biology projects. Here, we characterize the spatial diffusion of a palette of quorum sensing signals and find that their diffusion in agar can be predicted from their molecular weight with a simple power law. We also engineer novel dual- and multi-input promoters that respond to quorum-sensing diffusive signals for use in engineered genetic systems. We engineer a promoter scaffold that can be adapted for activation and repression by multiple diffusers simultaneously. Lastly, we combine the knowledge on diffusion dynamics with the novel genetic components to build a new generation of spatial, stripe-forming systems with a simplified design, improved robustness, tuneability, and response time.
{"title":"Engineering Tunable, Low Latency Spatial Computation with Dual Input Quorum Sensing Promoters","authors":"Jure Tica, Haobin Chen, Shulei Luo, Manman Chen and Mark Isalan*, ","doi":"10.1021/acssynbio.4c00068","DOIUrl":"10.1021/acssynbio.4c00068","url":null,"abstract":"<p >Quorum sensing signals have evolved for population-level signaling in bacterial communities and are versatile tools for engineering cell–cell signaling in synthetic biology projects. Here, we characterize the spatial diffusion of a palette of quorum sensing signals and find that their diffusion in agar can be predicted from their molecular weight with a simple power law. We also engineer novel dual- and multi-input promoters that respond to quorum-sensing diffusive signals for use in engineered genetic systems. We engineer a promoter scaffold that can be adapted for activation and repression by multiple diffusers simultaneously. Lastly, we combine the knowledge on diffusion dynamics with the novel genetic components to build a new generation of spatial, stripe-forming systems with a simplified design, improved robustness, tuneability, and response time.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acssynbio.4c00068","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141089631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cadaverine is a critical C5 monomer for the production of polyamides. Pyridoxal 5′-phosphate (PLP), as a crucial cofactor for the key enzyme lysine decarboxylase in the cadaverine biosynthesis pathway, has seen a persistent shortage, leading to limitations in cadaverine production. To address this issue, a dual-pathway strategy was implemented, synergistically enhancing both endogenous and heterologous PLP synthesis modules and resulting in improved PLP synthesis. Subsequently, a growth-stage-dependent molecular switch was introduced to balance the precursor competition between PLP synthesis and cell growth. Additionally, a PLP sensor-based negative feedback circuit was constructed by integrating a newly identified PLP-responsive promoter PygjH and an arabinose-regulated system, dynamically regulating the expression of the PLP synthetic genes and preventing excessive intracellular PLP accumulation. The optimal strain, L18, cultivated in the minimal medium AM1, demonstrated cadaverine production with a titer, yield, and productivity of 64.03 g/L, 0.23 g/g glucose, and 1.33 g/L/h, respectively. This represents the highest titer reported to date in engineered Escherichia coli by fed-batch fermentation in a minimal medium.
{"title":"Fine-Tuning Pyridoxal 5′-Phosphate Synthesis in Escherichia coli for Cadaverine Production in Minimal Culture Media","authors":"Cunping Liu, Cong Gao, Longfei Song, Xiaomin Li, Xiulai Chen, Jing Wu, Wei Song, Wanqing Wei and Liming Liu*, ","doi":"10.1021/acssynbio.4c00102","DOIUrl":"10.1021/acssynbio.4c00102","url":null,"abstract":"<p >Cadaverine is a critical C5 monomer for the production of polyamides. Pyridoxal 5′-phosphate (PLP), as a crucial cofactor for the key enzyme lysine decarboxylase in the cadaverine biosynthesis pathway, has seen a persistent shortage, leading to limitations in cadaverine production. To address this issue, a dual-pathway strategy was implemented, synergistically enhancing both endogenous and heterologous PLP synthesis modules and resulting in improved PLP synthesis. Subsequently, a growth-stage-dependent molecular switch was introduced to balance the precursor competition between PLP synthesis and cell growth. Additionally, a PLP sensor-based negative feedback circuit was constructed by integrating a newly identified PLP-responsive promoter P<sub>ygjH</sub> and an arabinose-regulated system, dynamically regulating the expression of the PLP synthetic genes and preventing excessive intracellular PLP accumulation. The optimal strain, L18, cultivated in the minimal medium AM1, demonstrated cadaverine production with a titer, yield, and productivity of 64.03 g/L, 0.23 g/g glucose, and 1.33 g/L/h, respectively. This represents the highest titer reported to date in engineered <i>Escherichia coli</i> by fed-batch fermentation in a minimal medium.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141064400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-18DOI: 10.1021/acssynbio.4c00325
Arik Shams, Alexandria Fischer, Anastasia Bodnar and Melinda Kliegman*,
{"title":"Correction to “Perspectives on Genetically Engineered Microorganisms and Their Regulation in the United States”","authors":"Arik Shams, Alexandria Fischer, Anastasia Bodnar and Melinda Kliegman*, ","doi":"10.1021/acssynbio.4c00325","DOIUrl":"10.1021/acssynbio.4c00325","url":null,"abstract":"","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acssynbio.4c00325","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140954863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-17DOI: 10.1021/acssynbio.4c00125
Irene Komera, Xiulai Chen, Liming Liu and Cong Gao*,
Microbial synthetic epigenetics offers significant opportunities for the design of synthetic biology tools by leveraging reversible gene control mechanisms without altering DNA sequences. However, limited understanding and a lack of technologies for thorough analysis of the mechanisms behind epigenetic modifications have hampered their utilization in biotechnological applications. In this review, we explore advancements in developing epigenetic-based synthetic gene regulatory tools at both transcriptional and post-transcriptional levels. Furthermore, we examine strategies developed to construct epigenetic-based circuits that provide controllable and stable gene regulation, aiming to boost the performance of microbial chassis cells. Finally, we discuss the current challenges and perspectives in the development of synthetic epigenetic tools.
微生物合成表观遗传学在不改变 DNA 序列的情况下利用可逆的基因控制机制,为设计合成生物学工具提供了重要机会。然而,由于对表观遗传修饰机制的了解有限,而且缺乏对其进行透彻分析的技术,因此阻碍了表观遗传修饰在生物技术领域的应用。在本综述中,我们将探讨在转录和转录后水平上开发基于表观遗传的合成基因调控工具的进展。此外,我们还研究了构建基于表观遗传学的电路的策略,这些电路可提供可控和稳定的基因调控,旨在提高微生物底盘细胞的性能。最后,我们讨论了当前合成表观遗传工具开发所面临的挑战和前景。
{"title":"Microbial Synthetic Epigenetic Tools Design and Applications","authors":"Irene Komera, Xiulai Chen, Liming Liu and Cong Gao*, ","doi":"10.1021/acssynbio.4c00125","DOIUrl":"10.1021/acssynbio.4c00125","url":null,"abstract":"<p >Microbial synthetic epigenetics offers significant opportunities for the design of synthetic biology tools by leveraging reversible gene control mechanisms without altering DNA sequences. However, limited understanding and a lack of technologies for thorough analysis of the mechanisms behind epigenetic modifications have hampered their utilization in biotechnological applications. In this review, we explore advancements in developing epigenetic-based synthetic gene regulatory tools at both transcriptional and post-transcriptional levels. Furthermore, we examine strategies developed to construct epigenetic-based circuits that provide controllable and stable gene regulation, aiming to boost the performance of microbial chassis cells. Finally, we discuss the current challenges and perspectives in the development of synthetic epigenetic tools.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140954895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-17DOI: 10.1021/acssynbio.4c00006
Xian Fu, and , Yue Shen*,
Substantial improvements in DNA sequencing and synthesis technologies and increased understanding of genome biology have empowered the development of synthetic genomics. The ability to design and construct engineered living cells boosted up by synthetic chromosomes provides opportunities to tackle enormous current and future challenges faced by humanity and the planet. Here we review the progresses, considerations, challenges, and future direction of the “design–build–test–learn” cycle used in synthetic genomics. We also discuss future applications enabled by synthetic genomics as this emerging field shapes and revolutionizes biomanufacturing and biomedicine.
DNA 测序和合成技术的巨大进步以及对基因组生物学认识的加深,推动了合成基因组学的发展。通过合成染色体设计和构建工程活细胞的能力,为解决人类和地球当前和未来面临的巨大挑战提供了机遇。在此,我们回顾了合成基因组学中 "设计-构建-测试-学习 "循环的进展、注意事项、挑战和未来方向。我们还将讨论合成基因组学的未来应用,因为这一新兴领域将塑造并彻底改变生物制造和生物医学。
{"title":"Synthetic Genomics: Repurposing Biological Systems for Applications in Engineering Biology","authors":"Xian Fu, and , Yue Shen*, ","doi":"10.1021/acssynbio.4c00006","DOIUrl":"10.1021/acssynbio.4c00006","url":null,"abstract":"<p >Substantial improvements in DNA sequencing and synthesis technologies and increased understanding of genome biology have empowered the development of synthetic genomics. The ability to design and construct engineered living cells boosted up by synthetic chromosomes provides opportunities to tackle enormous current and future challenges faced by humanity and the planet. Here we review the progresses, considerations, challenges, and future direction of the “design–build–test–learn” cycle used in synthetic genomics. We also discuss future applications enabled by synthetic genomics as this emerging field shapes and revolutionizes biomanufacturing and biomedicine.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acssynbio.4c00006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140954896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-15DOI: 10.1021/acssynbio.4c00104
Mei Tang, Xianhao Xu, Yanfeng Liu, Jianghua Li, Guocheng Du, Xueqin Lv and Long Liu*,
Betulinic acid (BA) is a lupane-type triterpenoid with potent anticancer and anti-HIV activities. Its great potential in clinical applications necessitates the development of an efficient strategy for BA synthesis. This study attempted to achieve efficient BA biosynthesis in Saccharomyces cerevisiae using systematic metabolic engineering strategies. First, a de novo BA biosynthesis pathway in S. cerevisiae was constructed, which yielded a titer of 14.01 ± 0.21 mg/L. Then, by enhancing the BA synthesis pathway and dynamic inhibition of the competitive pathway, a greater proportion of the metabolic flow was directed toward BA synthesis, achieving a titer of 88.07 ± 5.83 mg/L. Next, acetyl-CoA and NADPH supply was enhanced, which increased the BA titer to 166.43 ± 1.83 mg/L. Finally, another BA synthesis pathway in the peroxisome was constructed. Dual regulation of the peroxisome and cytoplasmic metabolism increased the BA titer to 210.88 ± 4.76 mg/L. Following fed-batch fermentation process modification, the BA titer reached 682.29 ± 8.16 mg/L. Overall, this work offers a guide for building microbial cell factories that are capable of producing terpenoids with efficiency.
白桦脂酸(BA)是一种羽扇豆型三萜类化合物,具有很强的抗癌和抗艾滋病毒活性。由于白桦脂酸在临床应用中的巨大潜力,有必要开发一种高效的白桦脂酸合成策略。本研究试图利用系统的代谢工程策略在酿酒酵母中实现高效的 BA 生物合成。首先,在酿酒酵母中构建了一条全新的 BA 生物合成途径,该途径产生的滴度为 14.01 ± 0.21 mg/L。然后,通过增强 BA 合成途径和动态抑制竞争途径,将更大比例的代谢流导向 BA 合成,使滴度达到 88.07 ± 5.83 mg/L。接着,乙酰-CoA 和 NADPH 的供应量增加,使 BA 滴度增至 166.43 ± 1.83 mg/L。最后,在过氧化物酶体中构建了另一条合成 BA 的途径。过氧物酶体和细胞质代谢的双重调节将 BA 滴度提高到 210.88 ± 4.76 mg/L。经过饲料批量发酵工艺改造后,BA 滴度达到了 682.29 ± 8.16 mg/L。总之,这项工作为建立能够高效生产萜类化合物的微生物细胞工厂提供了指导。
{"title":"Combinatorial Metabolic Engineering for Improving Betulinic Acid Biosynthesis in Saccharomyces cerevisiae","authors":"Mei Tang, Xianhao Xu, Yanfeng Liu, Jianghua Li, Guocheng Du, Xueqin Lv and Long Liu*, ","doi":"10.1021/acssynbio.4c00104","DOIUrl":"10.1021/acssynbio.4c00104","url":null,"abstract":"<p >Betulinic acid (BA) is a lupane-type triterpenoid with potent anticancer and anti-HIV activities. Its great potential in clinical applications necessitates the development of an efficient strategy for BA synthesis. This study attempted to achieve efficient BA biosynthesis in <i>Saccharomyces cerevisiae</i> using systematic metabolic engineering strategies. First, a <i>de novo</i> BA biosynthesis pathway in <i>S. cerevisiae</i> was constructed, which yielded a titer of 14.01 ± 0.21 mg/L. Then, by enhancing the BA synthesis pathway and dynamic inhibition of the competitive pathway, a greater proportion of the metabolic flow was directed toward BA synthesis, achieving a titer of 88.07 ± 5.83 mg/L. Next, acetyl-CoA and NADPH supply was enhanced, which increased the BA titer to 166.43 ± 1.83 mg/L. Finally, another BA synthesis pathway in the peroxisome was constructed. Dual regulation of the peroxisome and cytoplasmic metabolism increased the BA titer to 210.88 ± 4.76 mg/L. Following fed-batch fermentation process modification, the BA titer reached 682.29 ± 8.16 mg/L. Overall, this work offers a guide for building microbial cell factories that are capable of producing terpenoids with efficiency.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140943139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}