ACS Synthetic Biology最新文献

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Efficient Simulation of Viral Transduction and Propagation for Biomanufacturing. 高效模拟生物制造中的病毒转导和传播。
IF 3.7 2区 生物学
ACS Synthetic Biology Pub Date : 2024-10-18 Epub Date: 2024-09-24 DOI: 10.1021/acssynbio.4c00227
Francesco Destro, Richard D Braatz
{"title":"Efficient Simulation of Viral Transduction and Propagation for Biomanufacturing.","authors":"Francesco Destro, Richard D Braatz","doi":"10.1021/acssynbio.4c00227","DOIUrl":"10.1021/acssynbio.4c00227","url":null,"abstract":"<p><p>The design of biomanufacturing platforms based on viral transduction and/or propagation poses significant challenges at the intersection between synthetic biology and process engineering. This paper introduces vitraPro, a software toolkit composed of a multiscale model and an efficient numeric technique that can be leveraged for determining genetic and process designs that optimize transduction-based biomanufacturing platforms and viral amplification processes. Viral infection and propagation for up to two viruses simultaneously can be simulated through the model, considering viruses in either the lytic or lysogenic stage, during batch, perfusion, or continuous operation. The model estimates the distribution of the viral genome(s) copy number in the cell population, which is an indicator of transduction efficiency and viral genome stability. The infection age distribution of the infected cells is also calculated, indicating how many cells are in an infection stage compatible with recombinant product expression or viral amplification. The model can also consider the presence of defective interfering particles in the system, which can severely compromise the productivity of biomanufacturing processes. Model benchmarking and validation are demonstrated for case studies of the baculovirus expression vector system and influenza A propagation in suspension cultures.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306534","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}
引用次数: 0
Energy Aware Technology Mapping of Genetic Logic Circuits. 遗传逻辑电路的能量感知技术映射
IF 3.7 2区 生物学
ACS Synthetic Biology Pub Date : 2024-10-18 Epub Date: 2024-10-08 DOI: 10.1021/acssynbio.4c00395
Erik Kubaczka, Maximilian Gehri, Jérémie J M Marlhens, Tobias Schwarz, Maik Molderings, Nicolai Engelmann, Hernan G Garcia, Christian Hochberger, Heinz Koeppl
{"title":"Energy Aware Technology Mapping of Genetic Logic Circuits.","authors":"Erik Kubaczka, Maximilian Gehri, Jérémie J M Marlhens, Tobias Schwarz, Maik Molderings, Nicolai Engelmann, Hernan G Garcia, Christian Hochberger, Heinz Koeppl","doi":"10.1021/acssynbio.4c00395","DOIUrl":"10.1021/acssynbio.4c00395","url":null,"abstract":"<p><p>Energy and its dissipation are fundamental to all living systems, including cells. Insufficient abundance of energy carriers─as caused by the additional burden of artificial genetic circuits─shifts a cell's priority to survival, also impairing the functionality of the genetic circuit. Moreover, recent works have shown the importance of energy expenditure in information transmission. Despite living organisms being non-equilibrium systems, non-equilibrium models capable of accounting for energy dissipation and non-equilibrium response curves are not yet employed in genetic design automation (GDA) software. To this end, we introduce Energy Aware Technology Mapping, the automated design of genetic logic circuits with respect to energy efficiency and functionality. The basis for this is an energy aware non-equilibrium steady state model of gene expression, capturing characteristics like energy dissipation─which we link to the entropy production rate─and transcriptional bursting, relevant to eukaryotes as well as prokaryotes. Our evaluation shows that a genetic logic circuit's functional performance and energy efficiency are disjoint optimization goals. For our benchmark, energy efficiency improves by 37.2% on average when comparing to functionally optimized variants. We discover a linear increase in energy expenditure and overall protein expression with the circuit size, where Energy Aware Technology Mapping allows for designing genetic logic circuits with the energetic costs of circuits that are one to two gates smaller. Structural variants improve this further, while results show the Pareto dominance among structures of a single Boolean function. By incorporating energy demand into the design, Energy Aware Technology Mapping enables energy efficiency by design. This extends current GDA tools and complements approaches coping with burden <i>in vivo</i>.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11494706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386362","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}
引用次数: 0
Genetically Encoded Trensor Circuits Report HeLa Cell Treatment with Polyplexed Plasmid DNA and Small-Molecule Transfection Modulators. 用多聚质粒 DNA 和小分子转染调节剂处理 HeLa 细胞的基因编码 Trensor 电路报告。
IF 3.7 2区 生物学
ACS Synthetic Biology Pub Date : 2024-10-18 Epub Date: 2024-09-06 DOI: 10.1021/acssynbio.4c00148
Chileab Redwood-Sawyerr, Geoffrey Howe, Andalucia Evans Theodore, Darren N Nesbeth
{"title":"Genetically Encoded Trensor Circuits Report HeLa Cell Treatment with Polyplexed Plasmid DNA and Small-Molecule Transfection Modulators.","authors":"Chileab Redwood-Sawyerr, Geoffrey Howe, Andalucia Evans Theodore, Darren N Nesbeth","doi":"10.1021/acssynbio.4c00148","DOIUrl":"10.1021/acssynbio.4c00148","url":null,"abstract":"<p><p>HeLa cell transfection with plasmid DNA (pDNA) is widely used to materialize biologicals and as a preclinical test of nucleic acid-based vaccine efficacy. We sought to genetically encode mammalian transfection sensor (Trensor) circuits and test their utility in HeLa cells for detecting molecules and methods for their propensity to influence transfection. We intended these Trensor circuits to be triggered if their host cell was treated with polyplexed pDNA or certain small-molecule modulators of transfection. We prioritized three promoters, implicated by others in feedback responses as cells import and process foreign material and stably integrated each into the genomes of three different cell lines, each upstream of a green fluorescent protein (GFP) open reading frame within a transgene. All three Trensor circuits showed an increase in their GFP expression when their host HeLa cells were incubated with pDNA and the degraded polyamidoamine dendrimer reagent, SuperFect. We next experimentally demonstrated the modulation of PEI-mediated HeLa cell transient transfection by four different small molecules, with Trichostatin A (TSA) showing the greatest propensity to boost transgene expression. The Trensor circuit based on the <i>TRA2B</i> promoter (Trensor-T) was triggered by incubation with TSA alone and not the other three small molecules. These data suggest that mammalian reporter circuits could enable low-cost, high-throughput screening to identify novel transfection methods and reagents without the need to perform actual transfections requiring costly plasmids or expensive fluorescent labels.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11494703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142138545","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}
引用次数: 0
Bioproduction of 3-Hydroxypropionic Acid by Enhancing the Precursor Supply with a Hybrid Pathway and Cofactor Regeneration. 利用混合途径和辅助因子再生技术加强前体供应,实现 3-羟基丙酸的生物生产
IF 3.7 2区 生物学
ACS Synthetic Biology Pub Date : 2024-10-18 Epub Date: 2024-09-25 DOI: 10.1021/acssynbio.4c00427
Tingting Chen, Yufei Zhang, Junhua Yun, Mei Zhao, Cunsheng Zhang, Ziwei Chen, Hossain M Zabed, Wenjing Sun, Xianghui Qi
{"title":"Bioproduction of 3-Hydroxypropionic Acid by Enhancing the Precursor Supply with a Hybrid Pathway and Cofactor Regeneration.","authors":"Tingting Chen, Yufei Zhang, Junhua Yun, Mei Zhao, Cunsheng Zhang, Ziwei Chen, Hossain M Zabed, Wenjing Sun, Xianghui Qi","doi":"10.1021/acssynbio.4c00427","DOIUrl":"10.1021/acssynbio.4c00427","url":null,"abstract":"<p><p>3-Hydroxypropionic acid (3-HP) is one of the 12 valuable platform chemicals with versatile applications in the chemical, food, and cosmetic industries. However, the biosynthesis of 3-HP faces challenges due to the lack of robust chassis and the high costs associated with the fermentation process. To address these challenges, we made efforts to augment the robustness of 3-HP-producing chassis by exploiting metabolic regulation, controlling carbon flux, balancing cofactor generation, and optimizing fermentation conditions. First, the malonyl-CoA (MCA) pathway was recruited and rebalanced in <i>Escherichia coli</i>. Subsequently, a hybrid pathway integrating the Embden-Meyerhof-Parnas pathway with the nonoxidative glycolysis pathway was systematically modulated to enhance carbon flux to the MCA pathway, followed by fine-tuning NADPH regeneration. Then, by optimizing the fermentation conditions, 3-HP production was significantly improved, reaching 6.8 g/L. Finally, in a fed-batch experiment, the final chassis produced 42.8 g/L 3-HP, corresponding to a 0.4 mol/mol yield and 0.6 g/(L·h) productivity.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337271","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}
引用次数: 0
Disentangling the Regulatory Response of Agrobacterium tumefaciens CHLDO to Glyphosate for Engineering Whole-Cell Phosphonate Biosensors. 解密农杆菌 CHLDO 对草甘膦的调控反应,以设计全细胞膦酸盐生物传感器。
IF 3.7 2区 生物学
ACS Synthetic Biology Pub Date : 2024-10-18 Epub Date: 2024-09-30 DOI: 10.1021/acssynbio.4c00497
Fiorella Masotti, Nicolas Krink, Nicolas Lencina, Natalia Gottig, Jorgelina Ottado, Pablo I Nikel
{"title":"Disentangling the Regulatory Response of <i>Agrobacterium tumefaciens</i> CHLDO to Glyphosate for Engineering Whole-Cell Phosphonate Biosensors.","authors":"Fiorella Masotti, Nicolas Krink, Nicolas Lencina, Natalia Gottig, Jorgelina Ottado, Pablo I Nikel","doi":"10.1021/acssynbio.4c00497","DOIUrl":"10.1021/acssynbio.4c00497","url":null,"abstract":"<p><p>Phosphonates (PHTs), organic compounds with a stable C-P bond, are widely distributed in nature. Glyphosate (GP), a synthetic PHT, is extensively used in agriculture and has been linked to various human health issues and environmental damage. Given the prevalence of GP, developing cost-effective, on-site methods for GP detection is key for assessing pollution and reducing exposure risks. We adopted <i>Agrobacterium tumefaciens</i> CHLDO, a natural GP degrader, as a host and the source of genetic parts for constructing PHT biosensors. In this bacterial species, the <i>phn</i> gene cluster, encoding the C-P lyase pathway, is regulated by the PhnF transcriptional repressor. We selected the <i>phnG</i> promoter, which displays a dose-dependent response to GP, to build a set of whole-cell biosensors. Through stepwise genetic optimization of the transcriptional cascade, we created a whole-cell biosensor capable of detecting GP in the 0.25-50 μM range in various samples, including soil and water.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11494704/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337282","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}
引用次数: 0
An Automated Cell-Free Workflow for Transcription Factor Engineering. 转录因子工程的无细胞自动工作流程。
IF 3.7 2区 生物学
ACS Synthetic Biology Pub Date : 2024-10-18 Epub Date: 2024-10-07 DOI: 10.1021/acssynbio.4c00471
Holly M Ekas, Brenda Wang, Adam D Silverman, Julius B Lucks, Ashty S Karim, Michael C Jewett
{"title":"An Automated Cell-Free Workflow for Transcription Factor Engineering.","authors":"Holly M Ekas, Brenda Wang, Adam D Silverman, Julius B Lucks, Ashty S Karim, Michael C Jewett","doi":"10.1021/acssynbio.4c00471","DOIUrl":"10.1021/acssynbio.4c00471","url":null,"abstract":"<p><p>The design and optimization of metabolic pathways, genetic systems, and engineered proteins rely on high-throughput assays to streamline design-build-test-learn cycles. However, assay development is a time-consuming and laborious process. Here, we create a generalizable approach for the tailored optimization of automated cell-free gene expression (CFE)-based workflows, which offers distinct advantages over in vivo assays in reaction flexibility, control, and time to data. Centered around designing highly accurate and precise transfers on the Echo Acoustic Liquid Handler, we introduce pilot assays and validation strategies for each stage of protocol development. We then demonstrate the efficacy of our platform by engineering transcription factor-based biosensors. As a model, we rapidly generate and assay libraries of 127 MerR and 134 CadR transcription factor variants in 3682 unique CFE reactions in less than 48 h to improve limit of detection, selectivity, and dynamic range for mercury and cadmium detection. This was achieved by assessing a panel of ligand conditions for sensitivity (to 0.1, 1, 10 μM Hg and 0, 1, 10, 100 μM Cd for MerR and CadR, respectively) and selectivity (against Ag, As, Cd, Co, Cu, Hg, Ni, Pb, and Zn). We anticipate that our Echo-based, cell-free approach can be used to accelerate multiple design workflows in synthetic biology.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11494693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379448","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}
引用次数: 0
Bacterial Living Therapeutics with Engineered Protein Secretion Circuits to Eliminate Breast Cancer Cells. 利用工程化蛋白质分泌回路消灭乳腺癌细胞的细菌活体疗法。
IF 3.7 2区 生物学
ACS Synthetic Biology Pub Date : 2024-10-18 Epub Date: 2024-10-05 DOI: 10.1021/acssynbio.3c00723
Gozeel Binte Shahid, Recep Erdem Ahan, Julian Ostaku, Urartu Ozgur Safak Seker
{"title":"Bacterial Living Therapeutics with Engineered Protein Secretion Circuits to Eliminate Breast Cancer Cells.","authors":"Gozeel Binte Shahid, Recep Erdem Ahan, Julian Ostaku, Urartu Ozgur Safak Seker","doi":"10.1021/acssynbio.3c00723","DOIUrl":"10.1021/acssynbio.3c00723","url":null,"abstract":"<p><p>Cancer therapy can be limited by potential side effects, and bacteria-based living cancer therapeutics have gained scientific interest in recent years. However, the full potential of bacteria as therapeutics has yet to be explored due to engineering challenges. In this study, we present a bacterial device designed to specifically target and eliminate breast cancer cells. We have engineered <i>Escherichia coli</i> (<i>E. coli</i>) to bind to HER2 receptors on breast cancer cells while also secreting a toxin, HlyE, which is a pore-forming protein. The binding of <i>E. coli</i> to HER2 is facilitated by a nanobody expressed on the bacteria's surface <i>via</i> the Ag43 autotransporter protein system. Our findings demonstrate that the nanobody efficiently binds to HER2+ cells <i>in vitro</i>, and we have utilized the YebF secretion tag to secrete HlyE and kill the target cancer cells. Overall, our results highlight the potential of our engineered bacteria as an innovative strategy for breast cancer treatment.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378776","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}
引用次数: 0
Engineering Living Material for Controlled Fragrance Release Utilizing Kluyveromyces marxianus CBS6556 and Adaptive Hydrogel. 利用 Kluyveromyces marxianus CBS6556 和自适应水凝胶制造可控香味释放的生物材料。
IF 3.7 2区 生物学
ACS Synthetic Biology Pub Date : 2024-10-18 Epub Date: 2024-08-05 DOI: 10.1021/acssynbio.4c00229
Yichen Yuan, Bofan Yu, Xinzhi Zhou, He Qiao, Jiazhang Lian, Xuye Lang, Yuan Yao
{"title":"Engineering Living Material for Controlled Fragrance Release Utilizing <i>Kluyveromyces marxianus</i> CBS6556 and Adaptive Hydrogel.","authors":"Yichen Yuan, Bofan Yu, Xinzhi Zhou, He Qiao, Jiazhang Lian, Xuye Lang, Yuan Yao","doi":"10.1021/acssynbio.4c00229","DOIUrl":"10.1021/acssynbio.4c00229","url":null,"abstract":"<p><p>The demand for controllable fragrance materials is substantial owing to their potential to impart enduring scents in a variety of applications. However, the practical application of such materials has been limited by challenges in tunable morphogenesis, structural variability, and adaptability to diverse conditions. In our study, we introduce a hybrid living material that integrates a genetically engineered strain of <i>Kluyveromyces marxianus</i> CBS6556 with an adaptive hydrogel. The engineered <i>K. marxianus</i> achieved temperature stability in 2-phenylethanol (2-PE) and 2-phenylethyl acetate (2-PEAc) production by expressing relevant genes in the 2-PE metabolic pathway using the high-temperature preferential promoter SSE1. The enhanced water retention capacity supports the metabolic activities of the encapsulated yeast cells, ensuring their survival and functionality over an extended period. Fragrance-releasing living material (FLM) is designed to controllably emit fragrance 2-PE by adjusting the microbial concentration within the hydrogel matrix. The FLM exhibits versatile adhesion capabilities, effectively binding to a spectrum of surfaces such as wood, textiles, and glass as well as to natural substrates like leaves. This adaptability enhances the material's applicability across various settings. Furthermore, FLM can be crafted into various forms, including microbeads, fibers, and films. This research opens up new horizons for controlled fragrance release of living materials.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141887492","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}
引用次数: 0
Impact of Chromatin Organization and Epigenetics on CRISPR-Cas and TALEN Genome Editing. 染色质组织和表观遗传学对 CRISPR-Cas 和 TALEN 基因组编辑的影响。
IF 3.7 2区 生物学
ACS Synthetic Biology Pub Date : 2024-10-18 Epub Date: 2024-09-24 DOI: 10.1021/acssynbio.4c00099
Surbhi Jain, Guanhua Xun, Huimin Zhao
{"title":"Impact of Chromatin Organization and Epigenetics on CRISPR-Cas and TALEN Genome Editing.","authors":"Surbhi Jain, Guanhua Xun, Huimin Zhao","doi":"10.1021/acssynbio.4c00099","DOIUrl":"10.1021/acssynbio.4c00099","url":null,"abstract":"<p><p>DNA lies at the heart of the central dogma of life. Altering DNA can modify the flow of information in fundamental cellular processes such as transcription and translation. The ability to precisely manipulate DNA has led to remarkable advances in treating incurable human genetic ailments and has changed the landscape of biological research. Genome editors such as CRISPR-Cas nucleases and TALENs have become ubiquitous tools in basic and applied biological research and have been translated to the clinic to treat patients. The specificity and modularity of these genome editors have made it possible to efficiently engineer genomic DNA; however, underlying principles governing editing outcomes in eukaryotes are still being uncovered. Editing efficiency can vary from cell type to cell type for the same DNA target sequence, necessitating de novo design and validation efforts. Chromatin structure and epigenetic modifications have been shown to affect the activity of genome editors because of the role they play in hierarchical organization of the underlying DNA. Understanding the nuclear search mechanism of genome editors and their molecular interactions with higher order chromatin will lead to improved models for predicting precise genome editing outcomes. Insights from such studies will unlock the entire genome to be engineered for the creation of novel therapies to treat critical illnesses.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306535","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}
引用次数: 0
A Tunable Long Duration Pulse Generation Circuit in Mammalian Cells. 哺乳动物细胞中的可调长脉冲发生电路
IF 3.7 2区 生物学
ACS Synthetic Biology Pub Date : 2024-10-17 DOI: 10.1021/acssynbio.4c00368
Noreen Wauford, Georg Wachter, Katherine Kiwimagi, Ron Weiss
{"title":"A Tunable Long Duration Pulse Generation Circuit in Mammalian Cells.","authors":"Noreen Wauford, Georg Wachter, Katherine Kiwimagi, Ron Weiss","doi":"10.1021/acssynbio.4c00368","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00368","url":null,"abstract":"<p><p>Pulse generator circuits based on incoherent feed-forward logic have been developed in bacterial, yeast, and mammalian systems but are typically limited to production of short pulses lasting less than 1 day. To generate longer-lasting pulses, we introduce a feedback-based topology that induces multiday pulsatile gene expression with tunable duration and amplitude in mammalian cells. We constructed the circuit using the PERSIST platform, which consists of entirely post-transcriptional logic, because our experience suggests that this approach may attenuate long-term epigenetic silencing. To enable external regulation of PERSIST regulatory elements, we engineered inducer-stabilized CRISPR endoRNases that respond to FDA-approved drugs, generating small molecule responses with greater than 20-fold change. These inducer-responsive proteins were connected to a two-state cross-repression positive feedback topology to generate the pulse generator circuit architecture. We then optimized circuit design through chromosomal integration of circuit components at varying stoichiometries, resulting in a small library of circuits displaying tunable pulses lasting between two and 6 days in response to a single 24 h input of inducer. We expect that the small molecule-stabilized PERSIST proteins developed will serve as valuable components in the toolbox for post-transcriptional gene circuit development and that tunable post-transcriptional pulse generator circuits in mammalian cells will enable study of endogenous hysteretic gene networks and support advances in cell therapies and organoid engineering.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453362","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}
引用次数: 0
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