ACS Synthetic Biology最新文献_第4页

Construction of Chitinase Complexes Using Self-Assembly Systems for Efficient Hydrolysis of Chitin. 利用自组装系统构建几丁质酶复合物，以高效水解几丁质。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-11-20 DOI: 10.1021/acssynbio.4c00613

Zhewei Shen, Yuchen Pan, Yuansheng Liu, Houhui Song, Chenggang Xu

{"title":"Construction of Chitinase Complexes Using Self-Assembly Systems for Efficient Hydrolysis of Chitin.","authors":"Zhewei Shen, Yuchen Pan, Yuansheng Liu, Houhui Song, Chenggang Xu","doi":"10.1021/acssynbio.4c00613","DOIUrl":"10.1021/acssynbio.4c00613","url":null,"abstract":"Chitin biomass is the second most abundant natural polysaccharide after cellulose on the earth, yet its recalcitrance to degrade and utilize severely limits its application. However, many microorganisms, such as Serratia marcescen, can secrete a range of free chitinases to degrade chitin, though their activity is typically insufficient to meet industrial demands. In this study, we employed self-assembly systems, named SpyTag/SpyCatcher and SnoopTag/SnoopCatcher, to modularize the molecular design of CHB, ChiB, ChiC, and CBP21 derived from S. marcescens ATCC14756, and we successfully constructed a variety of chitinase complexes. The assembled complexes showed higher chitinolytic activity and stability, compared to free chitinase mixture. Moreover, the distinct arrangements and combinations of chitinases within these complexes led to varied activities, suggesting that the spatial proximity and substrate channeling effects contribute to the synergy of chitinase complexes. The findings lay a solid technical foundation for the application of chitinosome in the industrial production of N-acetylglucosamine and chitooligosaccharides.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"4143-4153"},"PeriodicalIF":3.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680307","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 Diagnostics for Quantification and Rapid Diagnosis of Myotonic Dystrophy Type 1 Repeat Expansion Disorders. 用于定量和快速诊断肌营养不良 1 型重复扩增症的 CRISPR 诊断技术。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-11-20 DOI: 10.1021/acssynbio.4c00265

Koji Asano, Kazuto Yoshimi, Kohei Takeshita, Satomi Mitsuhashi, Yuta Kochi, Rika Hirano, Zong Tingyu, Saeko Ishida, Tomoji Mashimo

{"title":"CRISPR Diagnostics for Quantification and Rapid Diagnosis of Myotonic Dystrophy Type 1 Repeat Expansion Disorders.","authors":"Koji Asano, Kazuto Yoshimi, Kohei Takeshita, Satomi Mitsuhashi, Yuta Kochi, Rika Hirano, Zong Tingyu, Saeko Ishida, Tomoji Mashimo","doi":"10.1021/acssynbio.4c00265","DOIUrl":"10.1021/acssynbio.4c00265","url":null,"abstract":"Repeat expansion disorders, exemplified by myotonic dystrophy type 1 (DM1), present challenges in diagnostic quantification because of the variability and complexity of repeat lengths. Traditional diagnostic methods, including PCR and Southern blotting, exhibit limitations in sensitivity and specificity, necessitating the development of innovative approaches for precise and rapid diagnosis. Here, we introduce a CRISPR-based diagnostic method, REPLICA (repeat-primed locating of inherited disease by Cas3), for the quantification and rapid diagnosis of DM1. This method, using in vitro-assembled CRISPR-Cas3, demonstrates superior sensitivity and specificity in quantifying CTG repeat expansion lengths, correlated with disease severity. We also validate the robustness and accuracy of CRISPR diagnostics in quantitatively diagnosing DM1 using patient genomes. Furthermore, we optimize a REPLICA-based assay for point-of-care-testing using lateral flow test strips, facilitating rapid screening and detection. In summary, REPLICA-based CRISPR diagnostics offer precise and rapid detection of repeat expansion disorders, promising personalized treatment strategies.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"3926-3935"},"PeriodicalIF":3.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680308","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

Metabolic Perturbations to an Escherichia coli-based Cell-Free System Reveal a Trade-off between Transcription and Translation. 对基于大肠杆菌的无细胞系统的代谢干扰揭示了转录与翻译之间的权衡。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-11-20 DOI: 10.1021/acssynbio.4c00361

Manisha Kapasiawala, Richard M Murray

{"title":"Metabolic Perturbations to an Escherichia coli-based Cell-Free System Reveal a Trade-off between Transcription and Translation.","authors":"Manisha Kapasiawala, Richard M Murray","doi":"10.1021/acssynbio.4c00361","DOIUrl":"10.1021/acssynbio.4c00361","url":null,"abstract":"Cell-free transcription-translation (TX-TL) systems have been used for diverse applications, but their performance and scope are limited by variability and poor predictability. To understand the drivers of this variability, we explored the effects of metabolic perturbations to anEscherichia coli (E. coli) Rosetta2 TX-TL system. We targeted three classes of molecules: energy molecules, in the form of nucleotide triphosphates (NTPs); central carbon \"fuel\" molecules, which regenerate NTPs; and magnesium ions (Mg2+). Using malachite green mRNA aptamer (MG aptamer) and destabilized enhanced green fluorescent protein (deGFP) as transcriptional and translational readouts, respectively, we report the presence of a trade-off between optimizing total protein yield and optimizing total mRNA yield, as measured by integrating the area under the curve for mRNA time-course dynamics. We found that a system's position along the trade-off curve is strongly determined by Mg2+ concentration, fuel type and concentration, and cell lysate preparation and that variability can be reduced by modulating these components. Our results further suggest that the trade-off arises from limitations in translation regulation and inefficient energy regeneration. This work advances our understanding of the effects of fuel and energy metabolism on TX-TL in cell-free systems and lays a foundation for improving TX-TL performance, lifetime, standardization, and prediction.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"3976-3990"},"PeriodicalIF":3.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680310","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

Genetically Modifying the Protein Matrix of Macroscopic Living Materials to Control Their Structure and Rheological Properties. 基因修饰宏观生命材料的蛋白质基质，控制其结构和流变特性。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-11-27 DOI: 10.1021/acssynbio.4c00336

Esther M Jimenez, Carlson Nguyen, Ahmad Shakeel, Robert Tesoriero, Marimikel Charrier, Alanna Stull, Caroline M Ajo-Franklin

{"title":"Genetically Modifying the Protein Matrix of Macroscopic Living Materials to Control Their Structure and Rheological Properties.","authors":"Esther M Jimenez, Carlson Nguyen, Ahmad Shakeel, Robert Tesoriero, Marimikel Charrier, Alanna Stull, Caroline M Ajo-Franklin","doi":"10.1021/acssynbio.4c00336","DOIUrl":"10.1021/acssynbio.4c00336","url":null,"abstract":"The field of engineering living materials (ELMs) seeks to engineer cells to form macroscopic materials with tailorable structures and properties. While the rheological properties of ELMs have been altered using synthetic biology methodology, the relationships connecting their sequence, structural, and rheological properties remain to be elucidated. Recently, our lab created centimeter-scale ELMs from Caulobacter crescentus that offer a platform to investigate this paradigm. Here, we explore how changing the elastin-like polypeptide (ELP) length within the protein matrix of this ELM impacts its microstructure and viscoelastic behavior. We demonstrate that shortening ELP produces fibers almost 2× thicker than other variants, resulting in a stiffer material at rest. Interestingly, the midlength ELP forms a complex structure with globules and multidirectional fibers with increased yield stress under flow conditions. Lengthening ELP creates thinner strands between cells with similar storage and loss moduli to those of the midlength ELP. This study begins to elucidate sequence-structure-property relationships in these ELMs and shows that they are complex with few parallels to other biocomposite models. Furthermore, it highlights that fine-tuning genetic sequences can create significant differences in rheological properties, uncovering new design principles of ELMs.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"3936-3947"},"PeriodicalIF":3.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724490","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

MIRA/PfAgo-Mediated Biosensor for Multiplex Human Enteroviruses Virus Typing Detection on HFMD.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-12-05 DOI: 10.1021/acssynbio.4c00545

Xuan Yang, Yue Wang, Chengming Xu, Zhiyi Liu, Yuanqi Guan, Fei Wang, Shuliang Chen, Yuan Wang, Yibin Cheng, Yanming Dong

{"title":"MIRA/PfAgo-Mediated Biosensor for Multiplex Human Enteroviruses Virus Typing Detection on HFMD.","authors":"Xuan Yang, Yue Wang, Chengming Xu, Zhiyi Liu, Yuanqi Guan, Fei Wang, Shuliang Chen, Yuan Wang, Yibin Cheng, Yanming Dong","doi":"10.1021/acssynbio.4c00545","DOIUrl":"10.1021/acssynbio.4c00545","url":null,"abstract":"Hand, foot, and mouth disease (HFMD), caused by enteroviruses, mostly including EV71, CVA6, CVA10, and CVA16, is an acute infectious disease commonly found in children. Due to no approved antiviral therapies and available vaccines, except for EV71, developing accurate diagnostic methods of HFMD is essential for controlling its spread and mitigating its impact on public health. Here, we create a MIRA-HEV-PAND multiple nucleic acid typing method that utilizes PfAgo to identify enterovirus type A pathogens (EV71, CVA6, CVA10, and CVA16) and universal type EVU. The MDC (minimum detection concentration) level of MIRA-HEV-PAND is within the range of 1.66 aM (1.0 copy/μL), which was matched to that of qPCR assays and even more sensitive up to 10%. Importantly, the MIRA-HEV-PAND method exhibits higher sensitivity and less time-consuming efficiency compared to the approach that combines PCR amplification instead of MIRA amplification. Meanwhile, though the quintuple and single-tube multiple MIRA-HEV-PAND detection system can be used for one viral target or multiple viral target detection, the single-tube detection system detects more efficiently and rapidly than the quintuple-tube multiple detection system. Moreover, the diagnostic results obtained by evaluating clinical samples using MIRA-HEV-PAND show a complete consistency of 100% with qPCR assays. The MIRA-HEV-PAND method can screen a wider range of target regions using low-cost guide DNA without being limited to PAM sequences, compared to the MARPLES based on the CRISPR-Cas12a. The utilization of this correlation can be beneficial for the application of molecular testing for clinical diagnoses and the study of human enteroviruses A infection and virus typing on an epidemiological scale.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"4119-4130"},"PeriodicalIF":3.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142783350","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

Toward a Quadruplet Codon Mitochondrial Genetic Code.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-12-04 DOI: 10.1021/acssynbio.4c00630

Michael L Pigula, Yahui Ban, Peter G Schultz

引用次数: 0

Control Intracellular Protein Condensates with Light.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-12-02 DOI: 10.1021/acssynbio.4c00305

Manjia Li, Weiqi Huang, Liting Duan, Fei Sun

{"title":"Control Intracellular Protein Condensates with Light.","authors":"Manjia Li, Weiqi Huang, Liting Duan, Fei Sun","doi":"10.1021/acssynbio.4c00305","DOIUrl":"10.1021/acssynbio.4c00305","url":null,"abstract":"Protein phase transitions are gaining traction among biologists for their wide-ranging roles in biological regulation. However, achieving precise control over these phenomena in vivo remains a formidable task. Optogenetic techniques present us with a potential means to control protein phase behavior with spatiotemporal precision. This review delves into the design of optogenetic tools, particularly those aimed at manipulating protein phase transitions in complex biological systems. We begin by discussing the pivotal roles of subcellular phase transitions in physiological and pathological processes. Subsequently, we offer a thorough examination of the evolution of optogenetic tools and their applications in regulating these protein phase behaviors. Furthermore, we highlight the tailored design of optogenetic tools for controlling protein phase transitions and the construction of synthetic condensates using these innovative techniques. In the long run, the development of optogenetic tools not only holds the potential to elucidate the roles of protein phase transitions in various physiological processes but also to antagonize pathological ones to reinstate cellular homeostasis, thus bringing about novel therapeutic strategies. The integration of optogenetic techniques into the study of protein phase transitions represents a significant step forward in our understanding and manipulation of biology at the subcellular level.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"3799-3811"},"PeriodicalIF":3.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764676","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

Automated Design of Oligopools and Rapid Analysis of Massively Parallel Barcoded Measurements.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-12-06 DOI: 10.1021/acssynbio.4c00661

Ayaan Hossain, Daniel P Cetnar, Travis L LaFleur, James R McLellan, Howard M Salis

{"title":"Automated Design of Oligopools and Rapid Analysis of Massively Parallel Barcoded Measurements.","authors":"Ayaan Hossain, Daniel P Cetnar, Travis L LaFleur, James R McLellan, Howard M Salis","doi":"10.1021/acssynbio.4c00661","DOIUrl":"10.1021/acssynbio.4c00661","url":null,"abstract":"Oligopool synthesis and next-generation sequencing enable the construction and characterization of large libraries of designed genetic parts and systems. As library sizes grow, it becomes computationally challenging to optimally design large numbers of primer binding sites, barcode sequences, and overlap regions to obtain efficient assemblies and precise measurements. We present the Oligopool Calculator, an end-to-end suite of algorithms and data structures that rapidly designs many thousands of oligonucleotides within an oligopool and rapidly analyzes many billions of barcoded sequencing reads. We introduce several novel concepts that greatly increase the design and analysis throughput, including orthogonally symmetric barcode design, adaptive decision trees for primer design, a Scry barcode classifier, and efficient read packing. We demonstrate the Oligopool Calculator's capabilities across computational benchmarks and real-data projects, including the design of over four million highly unique and compact barcodes in 1.2 h, the design of universal primer binding sites for one million 200-mer oligos in 15 min, and the analysis of about 500 million deep sequencing reads per hour, all on an 8-core desktop computer. Overall, the Oligopool Calculator accelerates the creative use of massively parallel experiments by eliminating the computational complexity of their design and analysis.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"4218-4232"},"PeriodicalIF":3.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142783348","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

Biosynthesis of Antimicrobial Ornithine-Containing Lacticin 481 Analogues by Use of a Combinatorial Biosynthetic Pathway in Escherichia coli.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-12-11 DOI: 10.1021/acssynbio.4c00650

Yanli Xu, Roos Reuvekamp, Oscar P Kuipers

{"title":"Biosynthesis of Antimicrobial Ornithine-Containing Lacticin 481 Analogues by Use of a Combinatorial Biosynthetic Pathway in Escherichia coli.","authors":"Yanli Xu, Roos Reuvekamp, Oscar P Kuipers","doi":"10.1021/acssynbio.4c00650","DOIUrl":"10.1021/acssynbio.4c00650","url":null,"abstract":"Lacticin 481, a ribosomally synthesized and post-translationally modified peptide (RiPP), exhibits antimicrobial activity, for which its characteristic lanthionine and methyllanthionine ring structures are essential. The post-translational introduction of (methyl)lanthionines in lacticin 481 is catalyzed by the enzyme LctM. In addition to macrocycle formation, various other post-translational modifications can enhance and modulate the chemical and functional diversity of antimicrobial peptides. The incorporation of noncanonical amino acids, occurring in many nonribosomal peptides (NRPs), is a valuable strategy to improve the properties of antimicrobial peptides. Ornithine, a noncanonical amino acid, can be integrated into RiPPs through the conversion of arginine residues by the newly characterized peptide arginase OspR. Recently, a flexible expression system was described for engineering lanthipeptides using the post-translational modification enzyme SyncM, which has a relaxed substrate specificity. This study demonstrates that SyncM is able to catalyze the production of active lacticin 481 by recognition of a designed hybrid leader peptide, which enables the incorporation of both ornithine and (methyl)lanthionine. Utilizing this hybrid leader peptide, the functional order was established for the production of active ornithine-containing lacticin 481 analogues at positions 8 and 12 in vivo. Furthermore, this study demonstrates that prior lanthionine (Lan) and methyllanthionine (MeLan) formation may preclude ornithine incorporation at specific sites of lacticin 481. The antibacterial activity of ornithine-containing lacticin 481 analogues was evaluated using Bacillus subtilis as the indicator strain. Overall, the synthetic biology pathway constructed here helped to elucidate aspects of the substrate preferences of OspR and SyncM, offering practical guidance to combine these modifications for further lantibiotic bioengineering.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"4209-4217"},"PeriodicalIF":3.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805527","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

Regulatory Components for Bacterial Cell-Free Systems Engineering. 无细胞细菌系统工程的监管组件。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-11-07 DOI: 10.1021/acssynbio.4c00574

Pao-Wan Lee, Sebastian J Maerkl

引用次数: 0