ACS Synthetic Biology最新文献_第10页

Metabolic Engineering of Clostridium tyrobutyricum for High-Yield n-Butanol Production by Increasing Intracellular Reducing Equivalent with NADPH-Dependent 3-Hydroxybutyryl-CoA Dehydrogenase 利用依赖nadph的3-羟基丁基辅酶a脱氢酶增加细胞内还原当量以高产正丁醇生产酪氨酸丁酸梭菌的代谢工程

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-05-22 DOI: 10.1021/acssynbio.5c0021810.1021/acssynbio.5c00218

Jun Feng, Qingke Wang, Xiaolong Guo, Jialei Hu, Geng Wang, Li Lu, Zhen Qin, Hongxin Fu, Jufang Wang and Shang-Tian Yang*,

{"title":"Metabolic Engineering of Clostridium tyrobutyricum for High-Yield n-Butanol Production by Increasing Intracellular Reducing Equivalent with NADPH-Dependent 3-Hydroxybutyryl-CoA Dehydrogenase","authors":"Jun Feng, Qingke Wang, Xiaolong Guo, Jialei Hu, Geng Wang, Li Lu, Zhen Qin, Hongxin Fu, Jufang Wang and Shang-Tian Yang*, ","doi":"10.1021/acssynbio.5c0021810.1021/acssynbio.5c00218","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00218https://doi.org/10.1021/acssynbio.5c00218","url":null,"abstract":"Clostridium tyrobutyricum was engineered to overexpress adhE2 encoding the aldehyde/alcohol dehydrogenase and an exogenous NADPH-dependent 3-hydroxybutyryl-CoA dehydrogenase from Clostridium kluyveri (Ckhbd) for n-butanol production. In general, large amounts of butyrate, acetate, and ethanol are also produced from glucose when butanol biosynthesis is hindered by limited intracellular NADH pools. In silico flux balance analysis showed that coupling NADP+/NADPH turnover with butanol production increased the reducing equivalent supply and butanol selectivity over ethanol and acids, thus increasing butanol production from glucose. This was verified with the coexpression of Ckhbd and adhE2 in C. tyrobutyricum wild type (WT), Ack, ΔhydA, and Δcat1 strains. Except for the Δcat1 strains, strains coexpressing Ckhbd showed significant (>5%) increase in reducing equivalents, 50–60% increase in butanol production (butanol yield: 0.24–0.28 vs. 0.15–0.18 g/g), and 2.5- to 4.5-fold increases in butanol/ethanol and alcohols/acids ratios due to increased flux from acetyl-CoA to butyryl-CoA and reducing equivalents compared to the strains expressing only adhE2. In the presence of methyl viologen, the strain Ack-adhE2-Ckhbd produced the highest butanol yield of 0.36 g/g, ∼88% of the theoretical yield from glucose, which was among the highest yields reported for known solventogenic clostridia.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"14 6","pages":"2341–2353 2341–2353"},"PeriodicalIF":3.7,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320726","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

CRISPR-Based Regulation for High-Throughput Screening 基于crispr的高通量筛选调控

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-05-22 DOI: 10.1021/acssynbio.5c0007610.1021/acssynbio.5c00076

Lingling Jiao, Qi Zhou and Dongchang Sun*,

{"title":"CRISPR-Based Regulation for High-Throughput Screening","authors":"Lingling Jiao, Qi Zhou and Dongchang Sun*, ","doi":"10.1021/acssynbio.5c0007610.1021/acssynbio.5c00076","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00076https://doi.org/10.1021/acssynbio.5c00076","url":null,"abstract":"CRISPR technology has revolutionized genome editing by enabling precise, permanent modifications to genetic material. To circumvent the irreversible alterations associated with traditional CRISPR methods and facilitate research on both essential and nonessential genes, CRISPR interference or inhibition (CRISPRi) and CRISPR activation (CRISPRa) were developed. The gene-silencing approach leverages an inactivated Cas effector protein paired with guide RNA to obstruct transcription initiation or elongation, while the gene-activation approach exploits the programmability of CRISPR to activate gene expression. Recent advances in CRISPRi technology, in combination with other technologies (e.g., biosensing, sequencing), have significantly expanded its applications, allowing for genome-wide high-throughput screening (HTS) to identify genetic determinants of phenotypes. These screening strategies have been applied in biomedicine, industry, and basic research. This review explores the CRISPR regulation mechanisms, offers an overview of the workflow for genome-wide CRISPR-based regulation for screens, and highlights its superior suitability for HTS across biomedical and industrial applications. Finally, we discuss the limitations of current CRISPRi/a HTS screening methods and envision future directions in CRISPR-mediated HTS research, considering its potential for broader application across diverse fields.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"14 6","pages":"1890–1904 1890–1904"},"PeriodicalIF":3.7,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320725","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

Nonlinear Classifiers Based on DNA Logic Circuits for Cancer Diagnosis 基于DNA逻辑电路的非线性分类器用于癌症诊断

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-05-22 DOI: 10.1021/acssynbio.5c0012910.1021/acssynbio.5c00129

Chunlin Chen, Zhixiang Yin, Shiyin Li, Wenhui Lian and Zhen Tang*,

{"title":"Nonlinear Classifiers Based on DNA Logic Circuits for Cancer Diagnosis","authors":"Chunlin Chen, Zhixiang Yin, Shiyin Li, Wenhui Lian and Zhen Tang*, ","doi":"10.1021/acssynbio.5c0012910.1021/acssynbio.5c00129","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00129https://doi.org/10.1021/acssynbio.5c00129","url":null,"abstract":"DNA logical circuits can be applied to accurate classification of cancer status, benefiting from their excellent biocompatibility and parallelism. However, the existing cancer diagnosis models based on DNA logic circuits mainly adopt a linear structure, which makes it difficult to fully capture the complex nonlinear distribution characteristics in the disease data. In addition, DNA logic circuits cannot directly sense the expression levels of microRNAs (miRNAs). Here, we constructed a nonlinear classifier based on DNA logic circuits with the random forest algorithm. The classifier can directly sense the expression level of miRNAs in serum samples without isolating specific miRNAs and transmit the signals to the logic classification module and complete the nonlinear classification of cancer status. We validated the classification performance of the constructed nonlinear classifiers by using miRNA expression level samples to diagnose adenocarcinoma, ductal and lobular neoplasms, and squamous cell carcinoma with accuracies of 95.4%, 96.6%, and 97.2%, respectively. The classification results generated using the nonlinear classifiers based on DNA logic circuits showed a strong agreement with the actual disease states labeled in TCGA, as well as with the random forest algorithm, and had high parallelism and stability in the multiclassification of three different cancers. This work shows the great potential of DNA logic circuit-based nonlinear classifiers in cancer diagnosis, which provides a new approach to design efficient, accurate, and intelligent integrated disease diagnosis schemes.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"14 6","pages":"2208–2218 2208–2218"},"PeriodicalIF":3.7,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320727","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

Formation of Polyphasic RNP Granules by Intrinsically Disordered Qβ Coat Proteins and Hairpin-Containing RNA 内在无序Qβ外壳蛋白和含发夹RNA形成多相RNP颗粒

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-05-21 DOI: 10.1021/acssynbio.4c0089110.1021/acssynbio.4c00891

Naor Granik, Sarah Goldberg and Roee Amit*,

{"title":"Formation of Polyphasic RNP Granules by Intrinsically Disordered Qβ Coat Proteins and Hairpin-Containing RNA","authors":"Naor Granik, Sarah Goldberg and Roee Amit*, ","doi":"10.1021/acssynbio.4c0089110.1021/acssynbio.4c00891","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00891https://doi.org/10.1021/acssynbio.4c00891","url":null,"abstract":"RNA–protein (RNP) granules are fundamental components in cells, where they perform multiple crucial functions. Many RNP granules form via phase separation driven by protein–protein, protein–RNA, and RNA–RNA interactions. Notably, associated proteins frequently contain intrinsically disordered regions (IDRs) that can associate with multiple partners. Previously, we showed that synthetic RNA molecules containing multiple hairpin coat-protein binding sites can phase-separate, forming granules capable of selectively incorporating proteins inside. Here, we expand this platform by introducing a phage coat protein with a known IDR that facilitates protein–protein interactions. We show that the coat protein phase-separates on its own in vivo and that introduction of hairpin-containing RNA molecules can lead to dissolvement of the protein granules. We further demonstrate via multiple assays that RNA valency, determined by the number of hairpins present on the RNA, leads to distinctly different phase behaviors, effectively forming a polyphasic, programmable RNP granule. Moreover, by incorporating the gene for a blue fluorescent protein into the RNA, we demonstrate a phase-dependent boost of protein titer. These insights not only shed light on the behavior of natural granules but also hold profound implications for the biotechnology field, offering a blueprint for engineering cellular compartments with tailored functionalities.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"14 6","pages":"2081–2093 2081–2093"},"PeriodicalIF":3.7,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320662","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

Host Evolution Improves Genetic Circuit Function in Complex Growth Environments 宿主进化在复杂生长环境中改善遗传回路功能

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-05-20 DOI: 10.1021/acssynbio.5c0016810.1021/acssynbio.5c00168

Joanna T. Zhang*, Andrew Lezia, Philip Emmanuele, Muyao Wu, Elina C. Olson, Aayush Somani, Adam M. Feist and Jeff Hasty,

{"title":"Host Evolution Improves Genetic Circuit Function in Complex Growth Environments","authors":"Joanna T. Zhang*, Andrew Lezia, Philip Emmanuele, Muyao Wu, Elina C. Olson, Aayush Somani, Adam M. Feist and Jeff Hasty, ","doi":"10.1021/acssynbio.5c0016810.1021/acssynbio.5c00168","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00168https://doi.org/10.1021/acssynbio.5c00168","url":null,"abstract":"The systematic design of genetic circuits with predictable behaviors in complex environments remains a significant challenge. Here, we engineered a population control circuit and used a combination of evolutionary and rational engineering approaches to enhance Escherichia coli for robust genetic circuit behavior in nontraditional growth environments. We utilized adaptive laboratory evolution (ALE) on E. coli MG1655 in minimal media with a sole carbon source and saw improved dynamics of the circuit after host evolution. Additionally, we applied ALE to E. coli Nissle, a probiotic strain, in a more complex medium environment with added reactive oxygen species (ROS) stress. In combination with directed mutagenesis and high-throughput microfluidic screening, we observed restored circuit function and improved tolerance of the circuit components. These findings serve as a framework for the optimization of relevant bacterial host strains for improved growth and gene circuit performance in complex environments.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"14 6","pages":"2270–2282 2270–2282"},"PeriodicalIF":3.7,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320659","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

Digitizing the Blue Light-Activated T7 RNA Polymerase System with a tet-Controlled Riboregulator 数字化蓝光激活的T7 RNA聚合酶系统与一个tet控制的核糖调节器

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-05-19 DOI: 10.1021/acssynbio.5c0014210.1021/acssynbio.5c00142

Sara Baldanta, and , Guillermo Rodrigo*,

{"title":"Digitizing the Blue Light-Activated T7 RNA Polymerase System with a tet-Controlled Riboregulator","authors":"Sara Baldanta,  and , Guillermo Rodrigo*, ","doi":"10.1021/acssynbio.5c0014210.1021/acssynbio.5c00142","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00142https://doi.org/10.1021/acssynbio.5c00142","url":null,"abstract":"Optogenetic systems offer precise control over gene expression, but leaky activity in the dark limits their dynamic range and, consequently, their applicability. Here, we enhanced an optogenetic system based on a split T7 RNA polymerase fused to blue-light-inducible Magnets by incorporating a tet-controlled riboregulatory module. This module exploits the photosensitivity of anhydrotetracycline and the designability of synthetic small RNAs to digitize light-controlled gene expression, implementing a repressive action over the translation of a polymerase fragment gene that is relieved with blue light. Our engineered system exhibited 13-fold improvement in dynamic range upon blue light exposure, which even raised to 23-fold improvement when using cells preadapted to chemical induction. As a functional demonstration, we implemented light-controlled antibiotic resistance in bacteria. Such integration of regulatory layers represents a suitable strategy for engineering better circuits for light-based biotechnological applications.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"14 6","pages":"2393–2399 2393–2399"},"PeriodicalIF":3.7,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acssynbio.5c00142","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320569","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

PERRC: Protease Engineering with Reactant Residence Time Control 蛋白酶工程与反应物停留时间控制

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-05-19 DOI: 10.1021/acssynbio.5c0015410.1021/acssynbio.5c00154

Sage Nelson, Jokent Gaza, Seyednima Ajayebi, Ronald Masse, Raymond Pho, Cianna Scutero, Samantha Martinusen, Lawton Long, Amor Menezes, Alberto Perez and Carl Denard*,

{"title":"PERRC: Protease Engineering with Reactant Residence Time Control","authors":"Sage Nelson, Jokent Gaza, Seyednima Ajayebi, Ronald Masse, Raymond Pho, Cianna Scutero, Samantha Martinusen, Lawton Long, Amor Menezes, Alberto Perez and Carl Denard*, ","doi":"10.1021/acssynbio.5c0015410.1021/acssynbio.5c00154","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00154https://doi.org/10.1021/acssynbio.5c00154","url":null,"abstract":"Proteases with engineered specificity hold great potential for targeted therapeutics, protein circuit construction, and biotechnology applications. However, many proteases exhibit broad substrate specificity, limiting their use in such applications. Engineering protease specificity remains challenging because evolving a protease to recognize a new substrate, without counterselecting against its native substrate, often results in high residual activity on the original substrate. To address this, we developed Protease Engineering with Reactant Residence Time Control (PERRC), a platform that exploits the correlation between endoplasmic reticulum (ER) retention sequence strength and ER residence time. PERRC allows precise control over the stringency of protease evolution by adjusting counterselection to selection substrate ratios. Using PERRC, we evolved an orthogonal tobacco etch virus protease variant, TEVESNp, that selectively cleaves a substrate (ENLYFES) that differs by only one amino acid from its parent sequence (ENLYFQS). TEVESNp exhibits a remarkable 65-fold preference for the evolved substrate, marking the first example of an engineered orthogonal protease driven by such a slight difference in substrate recognition. Furthermore, TEVESNp functions as a competent protease for constructing orthogonal protein circuits in bacteria, and molecular dynamics simulations analysis reveals subtle yet functionally significant active site rearrangements. PERRC is a modular dual-substrate display system that facilitates precise engineering of protease specificity.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"14 6","pages":"2241–2253 2241–2253"},"PeriodicalIF":3.7,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320626","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

Genetic Toggle Switch in Plants 植物的基因开关

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-05-19 DOI: 10.1021/acssynbio.4c0077710.1021/acssynbio.4c00777

Tessema K. Kassaw, Wenlong Xu, Christopher S. Zalewski, Katherine Kiwimagi, Ron Weiss, Mauricio S. Antunes, Ashok Prasad* and June I. Medford*,

{"title":"Genetic Toggle Switch in Plants","authors":"Tessema K. Kassaw, Wenlong Xu, Christopher S. Zalewski, Katherine Kiwimagi, Ron Weiss, Mauricio S. Antunes, Ashok Prasad* and June I. Medford*, ","doi":"10.1021/acssynbio.4c0077710.1021/acssynbio.4c00777","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00777https://doi.org/10.1021/acssynbio.4c00777","url":null,"abstract":"In synthetic biology, genetic components are assembled to make transcriptional units, and transcriptional units are assembled into circuits to perform specific and predictable functions of a genetic device. Genetic devices have been described in bacteria, mammalian cell cultures, and small organoids, yet the development of programmable genetic circuits for devices in plants has lagged. Programmable genetic devices require defining the component’s quantitative functions. Because plants have long life spans, studies often use transient analysis to define quantitative functions, while verification in stably engineered plants is often neglected and largely unknown. This raises the question if unique attributes of plants, such as environmental sensitivity, developmental plasticity, or alternation of generations, adversely impact predictability of plant genetic circuits and devices. Alternatively, it is also possible that genetic elements to produce predictable genetic devices for plants require rigorous characterization with detailed mathematical modeling. Here, we use plant genetic elements with quantitatively characterized transfer functions and developed in silico models to guide their assembly into a genetic device: a toggle switch or a mutually inhibitory gene-regulatory device. Our approach allows for computational selection of plant genetic components and iterative refinement of the circuit if the desired genetic functions are not initially achieved. We show that our computationally selected genetic circuit functions as predicted in stably engineered plants, including through tissue and organ differentiation. Developing abilities to produce predictable and programmable plant genetic devices opens the prospect of predictably engineering plant’s unique abilities in sustainable human and environmental systems.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"14 6","pages":"1988–2001 1988–2001"},"PeriodicalIF":3.7,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320567","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

Optimization of a Cas12a-Driven Synthetic Gene Regulatory Network System. cas12a驱动合成基因调控网络系统的优化

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-05-16 Epub Date: 2025-05-02 DOI: 10.1021/acssynbio.5c00084

HyunJin Kang, John C Fitch, Reeba P Varghese, Curtis A Thorne, Darren A Cusanovich

{"title":"Optimization of a Cas12a-Driven Synthetic Gene Regulatory Network System.","authors":"HyunJin Kang, John C Fitch, Reeba P Varghese, Curtis A Thorne, Darren A Cusanovich","doi":"10.1021/acssynbio.5c00084","DOIUrl":"10.1021/acssynbio.5c00084","url":null,"abstract":"Gene regulatory networks, which control gene expression patterns in development and in response to stimuli, use regulatory logic modules to coordinate inputs and outputs. One example of a regulatory logic module is the gene regulatory cascade (GRC), where a series of transcription factor genes turn on in order. Synthetic biologists have derived artificial systems that encode regulatory rules, including GRCs. Furthermore, the development of single-cell approaches has enabled the discovery of gene regulatory modules in a variety of experimental settings. However, the tools available for validating these observations remain limited. Based on a synthetic GRC using DNA cutting-defective Cas9 (dCas9), we designed and implemented an alternative synthetic GRC utilizing DNA cutting-defective Cas12a (dCas12a). Comparing the ability of these two systems to express a fluorescent reporter, the dCas9 system was initially more active, while the dCas12a system was more streamlined. Investigating the influence of individual components of the systems identified nuclear localization as a major driver of differences in activity. Improving nuclear localization for the dCas12a system resulted in 1.5-fold more reporter-positive cells and a 15-fold increase in reporter intensity relative to the dCas9 system. We call this optimized system the \"Synthetic Gene Regulatory Network\" (SGRN, pronounced \"sojourn\").","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"1732-1744"},"PeriodicalIF":3.7,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12091039/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954130","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

A Robust and Orthogonal Far-Red Light Sensor for Gene Expression Control in Escherichia coli. 用于大肠杆菌基因表达控制的鲁棒正交远红光传感器。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-05-16 Epub Date: 2025-05-06 DOI: 10.1021/acssynbio.5c00044

Yueyang Sun, Mengran Xu, Baiyang Wang, Chenyang Xia, Zhiming He, Bowen Lu, Jiyun Cui, Qiancheng Liao, Qi Xu, Fei Gan

{"title":"A Robust and Orthogonal Far-Red Light Sensor for Gene Expression Control in Escherichia coli.","authors":"Yueyang Sun, Mengran Xu, Baiyang Wang, Chenyang Xia, Zhiming He, Bowen Lu, Jiyun Cui, Qiancheng Liao, Qi Xu, Fei Gan","doi":"10.1021/acssynbio.5c00044","DOIUrl":"10.1021/acssynbio.5c00044","url":null,"abstract":"Optogenetics has emerged as a powerful tool for regulating cellular processes due to its noninvasive nature and precise spatiotemporal control. Far-red light (FRL) has increasingly been used in the optogenetic control of mammalian cells due to its low toxicity and high tissue penetration. However, robust and orthogonal FRL sensors are lacking in bacteria. Here, we established an orthogonal FRL sensor in Escherichia coli with a maximum dynamic range exceeding 230-fold based on the RfpA-RfpC-RfpB (RfpABC) signaling system that regulates the far-red light photoacclimation (FaRLiP) in cyanobacteria. We identified a conserved DNA motif in the promoter sequences of the Chl f synthase gene and other genes in the FaRLiP gene clusters, termed the far-red light-regulatory (FLR) motif, which enables the light-responsive activation of gene expression through its interaction with RfpB. Based on the FLR motif, we simplified the FLR-containing promoters and characterized their activation abilities and dynamic ranges, which can be utilized in different synthetic biology scenarios. Additionally, one or two FLR motifs are present at other loci within the FaRLiP gene cluster, providing further FRL-inducible promoter resources. The FRL sensor exhibits effective activation and suppression under low-intensity FRL and white light, respectively, and remains functional in darkness. In conclusion, this study advances the understanding of the regulatory mechanisms of FaRLiP in cyanobacteria and provides robust and orthogonal FRL sensors for synthetic biology applications.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"1687-1700"},"PeriodicalIF":3.7,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954137","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