ACS Synthetic Biology最新文献

Characterization of Rationally Designed CRISPR/Cas9-Based DNA Methyltransferases with Distinct Methyltransferase and Gene Silencing Activities in Human Cell Lines and Primary Human T Cells.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-02-03 DOI: 10.1021/acssynbio.4c00569

Rosa Selenia Guerra-Resendez, Samantha LeGoff Lydon, Alex J Ma, Guy C Bedford, Daniel R Reed, Sunghwan Kim, Erik R Terán, Tomoki Nishiguchi, Mario Escobar, Andrew R DiNardo, Isaac B Hilton

{"title":"Characterization of Rationally Designed CRISPR/Cas9-Based DNA Methyltransferases with Distinct Methyltransferase and Gene Silencing Activities in Human Cell Lines and Primary Human T Cells.","authors":"Rosa Selenia Guerra-Resendez, Samantha LeGoff Lydon, Alex J Ma, Guy C Bedford, Daniel R Reed, Sunghwan Kim, Erik R Terán, Tomoki Nishiguchi, Mario Escobar, Andrew R DiNardo, Isaac B Hilton","doi":"10.1021/acssynbio.4c00569","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00569","url":null,"abstract":"Nuclease-deactivated Cas (dCas) proteins can be used to recruit epigenetic effectors, and this class of epigenetic editing technologies has revolutionized the ability to synthetically control the mammalian epigenome and transcriptome. DNA methylation is one of the most important and well-characterized epigenetic modifications in mammals, and while many different forms of dCas-based DNA methyltransferases (dCas-DNMTs) have been developed for programmable DNA methylation, these tools are frequently poorly tolerated and/or lowly expressed in mammalian cell types. Further, the use of dCas-DNMTs has largely been restricted to cell lines, which limits mechanistic insights in karyotypically normal contexts and hampers translational utility in the longer term. Here, we extend previous insights into the rational design of the catalytic core of the mammalian DNMT3A methyltransferase and test three dCas9-DNMT3A/3L variants across different human cell lines and in primary donor-derived human T cells. We find that mutations within the catalytic core of DNMT3A stabilize the expression of dCas9-DNMT3A/3L fusion proteins in Jurkat T cells without sacrificing DNA methylation or gene-silencing performance. We also show that these rationally engineered mutations in DNMT3A alter DNA methylation profiles at loci targeted with dCas9-DNMT3A/3L in cell lines and donor-derived human T cells. Finally, we leverage the transcriptionally repressive effects of dCas9-DNMT3A/3L variants to functionally link the expression of a key immunomodulatory transcription factor to cytokine secretion in donor-derived T cells. Overall, our work expands the synthetic biology toolkit for epigenetic editing and provides a roadmap for the use of engineered dCas-based DNMTs in primary mammalian cell types.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078034","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

Harnessing Non-standard Nucleic Acids for Highly Sensitive Icosaplex (20-Plex) Detection of Microbial Threats for Environmental Surveillance.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-02-03 DOI: 10.1021/acssynbio.4c00619

Hinako Kawabe, Luran Manfio, Sebastian Magana Pena, Nicolette A Zhou, Kevin M Bradley, Cen Chen, Chris McLendon, Steven A Benner, Karen Levy, Zunyi Yang, Jorge A Marchand, Erica R Fuhrmeister

{"title":"Harnessing Non-standard Nucleic Acids for Highly Sensitive Icosaplex (20-Plex) Detection of Microbial Threats for Environmental Surveillance.","authors":"Hinako Kawabe, Luran Manfio, Sebastian Magana Pena, Nicolette A Zhou, Kevin M Bradley, Cen Chen, Chris McLendon, Steven A Benner, Karen Levy, Zunyi Yang, Jorge A Marchand, Erica R Fuhrmeister","doi":"10.1021/acssynbio.4c00619","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00619","url":null,"abstract":"Environmental surveillance and clinical diagnostics heavily rely on the polymerase chain reaction (PCR) for target detection. A growing list of microbial threats warrants new PCR-based detection methods that are highly sensitive, specific, and multiplexable. Here, we introduce a PCR-based icosaplex (20-plex) assay for detecting 18 enteropathogen and two antimicrobial resistance genes. This multiplexed PCR assay leverages the self-avoiding molecular recognition system (SAMRS) to avoid primer dimer formation, the artificially expanded genetic information system (AEGIS) for amplification specificity, and next-generation sequencing for amplicon identification. Using parallelized multitarget TaqMan Array Cards (TAC) to benchmark performance of the 20-plex assay on wastewater, soil, and human stool samples, we found 90% agreement on positive calls and 89% agreement on negative calls. Additionally, we show how long-read and short-read sequencing information from the 20-plex can be used to further classify allelic variants of genes and distinguish subspecies. The strategy presented offers sensitive, affordable, and robust multiplex detection that can be used to support efforts in wastewater-based epidemiology, environmental monitoring, and human/animal diagnostics.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078035","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

Enhanced Integration of Single-Cell Multi-Omics Data Using Graph Attention Networks. 利用图形注意网络增强单细胞多图像数据的整合。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-01-31 DOI: 10.1021/acssynbio.4c00864

Xingyu Liao, Yanyan Li, Shuangyi Li, Long Wen, Xingyi Li, Bin Yu

{"title":"Enhanced Integration of Single-Cell Multi-Omics Data Using Graph Attention Networks.","authors":"Xingyu Liao, Yanyan Li, Shuangyi Li, Long Wen, Xingyi Li, Bin Yu","doi":"10.1021/acssynbio.4c00864","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00864","url":null,"abstract":"The continuous advancement of single-cell multimodal omics (scMulti-omics) technologies offers unprecedented opportunities to measure various modalities, including RNA expression, protein abundance, gene perturbation, DNA methylation, and chromatin accessibility at single-cell resolution. These advances hold significant potential for breakthroughs by integrating diverse omics modalities. However, the data generated from different omics layers often face challenges due to high dimensionality, heterogeneity, and sparsity, which can adversely impact the accuracy and efficiency of data integration analyses. To address these challenges, we propose a high-precision analysis method called scMGAT (single-cell multiomics data analysis based on multihead graph attention networks). This method effectively coordinates reliable information across multiomics data sets using a multihead attention mechanism, allowing for better management of the heterogeneous characteristics inherent in scMulti-omics data. We evaluated scMGAT's performance on eight sets of real scMulti-omics data, including samples from both human and mouse. The experimental results demonstrate that scMGAT significantly enhances the quality of multiomics data and improves the accuracy of cell-type annotation compared to state-of-the-art methods. scMGAT is now freely accessible at https://github.com/Xingyu-Liao/scMGAT.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070726","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

Considerations for Domestication of Novel Strains of Filamentous Fungi.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-01-30 DOI: 10.1021/acssynbio.4c00672

Randi M Pullen, Stephen R Decker, Venkataramanan Subramanian, Meaghan J Adler, Alexander V Tobias, Matthew Perisin, Christian J Sund, Matthew D Servinsky, Mark T Kozlowski

{"title":"Considerations for Domestication of Novel Strains of Filamentous Fungi.","authors":"Randi M Pullen, Stephen R Decker, Venkataramanan Subramanian, Meaghan J Adler, Alexander V Tobias, Matthew Perisin, Christian J Sund, Matthew D Servinsky, Mark T Kozlowski","doi":"10.1021/acssynbio.4c00672","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00672","url":null,"abstract":"Fungi, especially filamentous fungi, are a relatively understudied, biotechnologically useful resource with incredible potential for commercial applications. These multicellular eukaryotic organisms have long been exploited for their natural production of useful commodity chemicals and proteins such as enzymes used in starch processing, detergents, food and feed production, pulping and paper making and biofuels production. The ability of filamentous fungi to use a wide range of feedstocks is another key advantage. As chassis organisms, filamentous fungi can express cellular machinery, and metabolic and signal transduction pathways from both prokaryotic and eukaryotic origins. Their genomes abound with novel genetic elements and metabolic processes that can be harnessed for biotechnology applications. Synthetic biology tools are becoming inexpensive, modular, and expansive while systems biology is beginning to provide the level of understanding required to design increasingly complex synthetic systems. This review covers the challenges of working in filamentous fungi and offers a perspective on the approaches needed to exploit fungi as microbial cell factories.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062250","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

Building the Future of Clinical Diagnostics: An Analysis of Potential Benefits and Current Barriers in CRISPR/Cas Diagnostics.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-01-29 DOI: 10.1021/acssynbio.4c00816

Jeanne E van Dongen, Loes I Segerink

引用次数: 0

Cell-Free Systems to Mimic and Expand Metabolism.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-01-29 DOI: 10.1021/acssynbio.4c00729

Blake J Rasor, Tobias J Erb

引用次数: 0

Do the Shuffle: Expanding the Synthetic Biology Toolkit for Shufflon-like Recombination Systems.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-01-27 DOI: 10.1021/acssynbio.4c00790

Jan Katalinić, Morgan Richards, Alex Auyang, James H Millett, Manjunatha Kogenaru, Nikolai Windbichler

引用次数: 0

CRISPR-Cas9 Cytidine-Base-Editor Mediated Continuous In Vivo Evolution in Aspergillus nidulans.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-01-26 DOI: 10.1021/acssynbio.4c00716

Yuan Tian, Qing Xu, Meng Pang, Youchu Ma, Zhiruo Zhang, Dongfang Zhang, Donghui Guo, Lupeng Wang, Qingbin Li, Yanling Li, Fanglong Zhao

{"title":"CRISPR-Cas9 Cytidine-Base-Editor Mediated Continuous In Vivo Evolution in Aspergillus nidulans.","authors":"Yuan Tian, Qing Xu, Meng Pang, Youchu Ma, Zhiruo Zhang, Dongfang Zhang, Donghui Guo, Lupeng Wang, Qingbin Li, Yanling Li, Fanglong Zhao","doi":"10.1021/acssynbio.4c00716","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00716","url":null,"abstract":"Filamentous fungi are important cell factories for producing chemicals, organic acids, and enzymes. Although several genome editing tools are available for filamentous fungi, few effectively enable continuous evolution for rational engineering of complex phenotype. Here, we present CRISPR-Cas9 cytidine-base-editor (CBE) assisted in vivo evolution by continuously delivering a combinatorial sgRNA library to filamentous fungi. The method was validated by targeting core genes of 46 natural product biosynthetic gene clusters in Aspergillus nidulans NRRL 8112 to eliminate fungal toxins via six rounds of evolution. NGS analysis revealed the average C-to-T conversion rates in the first, third, and sixth rounds were 2.02%, 5.25%, and 9.34%, respectively. Metabolic profiles of the evolved mutants exhibited significant changes, allowing for the isolation of clean-background strains with enhanced production of an antifungal compound Echinocandin B. This study demonstrates that CBE-mediated in vivo evolution greatly facilitates the iterative refinement of complex morphogenetic traits in filamentous fungi.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044907","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

Novel Isothermal Amplification Integrated with CRISPR/Cas13a and Its Applications for Ultrasensitive Detection of SARS-CoV-2. 新型CRISPR/Cas13a等温扩增技术及其在SARS-CoV-2超灵敏检测中的应用

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-01-21 DOI: 10.1021/acssynbio.4c00605

Jaemin Kim, Yo Rim Kim, Sang Mo Lee, Jinhwan Lee, Seoyoung Lee, Dongeun Yong, Hyun Gyu Park

{"title":"Novel Isothermal Amplification Integrated with CRISPR/Cas13a and Its Applications for Ultrasensitive Detection of SARS-CoV-2.","authors":"Jaemin Kim, Yo Rim Kim, Sang Mo Lee, Jinhwan Lee, Seoyoung Lee, Dongeun Yong, Hyun Gyu Park","doi":"10.1021/acssynbio.4c00605","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00605","url":null,"abstract":"We herein developed an ultrasensitive and rapid strategy to identify genomic nucleic acids by integrating a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 13a (Cas13a) into our recently developed isothermal technique, nicking and extension chain reaction system-based amplification (NESBA) reaction. In this technique, named CESBA, the NESBA reaction isothermally produces a large amount of RNA amplicons from the initial target genomic RNA (gRNA). The RNA amplicons bind to the crispr RNA (crRNA) and activate the collateral cleavage activity of Cas13a, which would then cleave the reporter probe nearby, consequently producing the final signals. Based on this design principle, we successfully detected SARS-CoV-2 gRNA as a model target very sensitively down to even a single copy (0.05 copies/μL) in both fluorescence- and lateral flow assay (LFA)-based modes with excellent specificity against other human coronaviruses (H-CoVs). We further validated the clinical applicability of CESBA by testing the 20 clinical samples with 100% clinical sensitivity and specificity. This work represents a potent and innovative strategy for the identification of genomic nucleic acids in molecular diagnostics, delivering exceptional levels of sensitivity.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996176","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

Microbial Production of Ectoine: A Review. 微生物生产依托碱的研究进展

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-01-20 DOI: 10.1021/acssynbio.4c00490

Ke Wang, Boya Cui, Yi Wang, Wei Luo

引用次数: 0