ACS Synthetic Biology最新文献

{"title":"Correction to “One-Step Multi-Fragment Assembly and Targeted Genomic Integration in Corynebacterium glutamicum”","authors":"Xiaoyu Wang, Siqi Yang, Xiaojie Zhou, Jiao Zhu, Fenghui Qian, Yu Jiang, Sheng Yang","doi":"10.1021/acssynbio.6c00666","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00666","url":null,"abstract":"","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4380–4380"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210941","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}

{"title":"Harnessing Yeast Mitochondria for the Sustainable Production of High-Value Chemicals","authors":"Jie Sheng,&nbsp;Xiaochun Zheng","doi":"10.1021/acssynbio.6c00350","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00350","url":null,"abstract":"<p>In microbial cytoplasmic reaction compartments, competitive pathways and metabolic interactions often hinder the efficient synthesis of target compounds. In contrast, eukaryotic cells can control metabolic complexity by utilizing organelles to segregate biochemical pathways. Mitochondria, known as the “powerhouses of the cell,” are rich in a unique set of enzymes, intermediate metabolites, and cofactors that can be exploited for metabolic engineering. However, wider application of mitochondria in metabolic engineering is limited by an insufficient understanding of their unique metabolic traits, the lack of efficient genetic tools, and the difficulty of balancing cell growth and product accumulation. This review outlines yeast mitochondria-related aspects, including their intrinsic properties, mechanisms of protein synthesis and import, recognition and screening of mitochondrial signal peptides, and potential advantages of using mitochondria alone or mitochondria collaborating with other organelles to produce high-value chemicals. Additionally, we discuss challenges in mitochondrial engineering and provide an outlook on future priorities.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"3911–3928"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210995","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}

{"title":"Engineered Calprotectin-Responsive Probiotics for Inflammatory Bowel Disease Treatment","authors":"Fan Yang,&nbsp;Lina He,&nbsp;Xian Lin,&nbsp;Xindi Huang,&nbsp;Yuefeng Hu,&nbsp;Min Chen,&nbsp;Zhiyong Wu,&nbsp;Jiayang Xi,&nbsp;Xiaoxiao Lu,&nbsp;Mengke Li,&nbsp;Yangbo Hu","doi":"10.1021/acssynbio.6c00347","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00347","url":null,"abstract":"<p>Inflammatory bowel disease (IBD) is a complex intestinal disorder for which effective treatment options remain limited. The modulation of gut microbiota balance using probiotics holds promise as a therapeutic approach to restore intestinal microenvironment homeostasis. However, the clinical translation of conventional probiotics is constrained by the suboptimal therapeutic efficacy. Here, we constructed a recombinant <em>Escherichia coli</em> Nissle 1917 strain (EcN-CR-IL2) based on an optimized calprotectin-responsive <em>ykgMO</em> promoter to achieve inflammation-dependent expression of the immunomodulatory cytokine interleukin-2 (IL-2), which selectively expands regulatory T cells to suppress aberrant intestinal inflammation. The optimized promoter achieved approximately 100-fold greater induction than the native <em>ykgMO</em> promoter and responded robustly to calprotectin both in vitro and in a DSS-induced murine colitis model in vivo. Oral administration of EcN-CR-IL2 significantly alleviated colitis symptoms in both prophylactic and therapeutic settings, suppressed proinflammatory cytokine levels, restored intestinal barrier integrity, and shifted gut microbiota composition toward a more homeostatic profile. Importantly, the therapeutic output of EcN-CR-IL2 correlated with local calprotectin levels, enabling on-demand modulation of anti-inflammatory effects in response to disease progression. This study presents a probiotic delivery system that combines real-time sensing of a clinically validated biomarker with autonomous therapeutic production, providing a new approach for the treatment of chronic intestinal inflammatory diseases.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4145–4156"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149211020","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}

{"title":"A Single Mutation Enhancing the DNA-Binding Affinity of Cra Redirects Metabolism for High-Yield Succinate Production in Escherichia coli","authors":"Wan-Fang Wei,&nbsp;Ruo-Lin Wang,&nbsp;Ying Huang,&nbsp;Meng-Ying Tang,&nbsp;Kai-Zhi Jia,&nbsp;Wei-Ping Wang,&nbsp;Wei Zhao,&nbsp;Xiao-Nan Liu,&nbsp;Li-Wen Zhu","doi":"10.1021/acssynbio.6c00579","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00579","url":null,"abstract":"<p>Rational engineering of transcription factors is an attractive strategy to modulate microbial metabolism. This study demonstrated its effectiveness through a key mutation (R60A) in the understudied linker region of the global transcription factor Cra. Transcriptional and enzymatic analyses revealed that R60A upregulated multiple genes and enhanced several key enzyme activities in central carbon metabolism, including the direct Cra targets <em>pck</em> and <em>aceB</em>, which were selected for further mechanistic investigation. In vitro binding assays confirmed that R60A bound to the promoter regions of these genes with enhanced affinity. Molecular docking analysis predicted that the top-ranked binding poses of the WT and R60A complexes differ in DNA placement, with an altered set of predicted hydrogen-bond contacts. This mutation altered the central carbon metabolism, leading to improved CO₂ fixation and succinate biosynthesis. Coupled with an optimized exponential feeding strategy that precisely controlled the specific growth rate, this approach achieved a high succinate titer of 100.8 g/L. Our work suggests a possible role for linker-mediated geometric modulation of DNA binding by Cra and presents an integrated metabolic and process engineering strategy for efficient succinate production.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4360–4370"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149211000","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}

{"title":"Developing a 4-Helix Bundle Protein Engineering Platform for Isolating Rare-Earth Elements","authors":"Joshua A. Mancini,&nbsp;Selemon Bekele,&nbsp;Emily Koerner,&nbsp;Douglas H. Pike,&nbsp;Karen Holley,&nbsp;Zhifeng Kuang,&nbsp;Maya Rao,&nbsp;Hao-Bo Guo,&nbsp;Patricia Legler,&nbsp;Jinny Liu,&nbsp;Blake Stamps,&nbsp;Baxter Huntington,&nbsp;Sushil R. Kanel,&nbsp;Alexander Perminov,&nbsp;Rajiv Berry,&nbsp;Justin C. Biffinger,&nbsp;Nancy Kelley-Loughnane,&nbsp;Martha Carter-Gerakines,&nbsp;Chia-Suei Hung","doi":"10.1021/acssynbio.5c00950","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00950","url":null,"abstract":"<p>Rare-earth elements (REEs) are crucial for sustainable industrial processes, but current extraction methods are environmentally damaging. Our research explores using proteins that bind REEs as a potentially eco-friendly alternative for purification. Lanmodulin (LanM) is a natural protein known for its extremely strong (picomolar) affinity for REEs. However, LanM’s disordered structure makes it challenging for engineering. To overcome this, we developed a protein engineering platform based on the stable 4-Helix Bundle (4HB) framework, which has 3 helix-loop-helix regions. We incorporated the core REE-binding segments, a helix-loop-helix region, from native LanM (specifically, LanM loop1 into the 4HB’s second loop) in prearranged optimal REE-binding configuration. The 4HB platform underwent engineering to eliminate off-target REE binding as well and was then rationally designed for specificity towards REEs with smaller ionic radii. This resulted in successful REE binding with nanomolar affinities. Furthermore, we employed machine learning and molecular dynamics to customize REE-binding loops for individual REE selectivity. Crucially, we demonstrated that the 4HB framework is reusable and capable of binding and releasing REEs under mild, environmentally friendly conditions.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"3983–3992"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210977","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}

{"title":"Engineering Psl Polysaccharide Biofilms as Living Bioflocculants for Dye Decolorization","authors":"Xinyu Zhou,&nbsp;Zhiqiang Cao,&nbsp;Zhen Chang,&nbsp;Zhanqing Cao,&nbsp;Xiaoli Zhou,&nbsp;Anming Xu,&nbsp;Weiliang Dong,&nbsp;Min Jiang","doi":"10.1021/acssynbio.6c00391","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00391","url":null,"abstract":"<p>Decolorization remains a major challenge in the treatment of dye-containing wastewater. Here, we engineered <em>Escherichia coli</em> with a chromosomally integrated minimal Psl polysaccharide synthesis operon, <em>pslA-G</em>, to create a Psl biofilm-based living bioflocculant enabling autonomous dye capture, sedimentation, and controllable recovery. The engineered bioflocculant exhibited rapid self-flocculation, achieving approximately 85% sedimentation within 8 h. The bioflocculant mediated the removal of Reactive Red 24, Acid Orange 7, and Congo red in a dye-dependent manner, achieving its highest removal efficiency of approximately 90% for Congo red. Importantly, dye-loaded aggregates could be disassembled via PslG-triggered Psl polysaccharide hydrolysis, enabling controlled dye release. This work establishes a proof-of-concept living bioflocculation approach that integrates capture, sedimentation, and recovery for potential dye wastewater treatment.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4199–4206"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149211019","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}

{"title":"Engineered Orthogonal Translation Systems from Metagenomic Libraries Expand the Genetic Code","authors":"Kosuke Seki,&nbsp;Michael T. A. Nguyen,&nbsp;Petar I. Penev,&nbsp;Jillian F. Banfield,&nbsp;Farren J. Isaacs,&nbsp;Michael C. Jewett","doi":"10.1021/acssynbio.6c00373","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00373","url":null,"abstract":"<p>Genetic code expansion with noncanonical amino acids (ncAAs) opens new opportunities for the design and engineering of proteins by broadening their chemical repertoire. Unfortunately, ncAA incorporation into proteins is limited both by a small collection of orthogonal aminoacyl-tRNA synthetases (aaRSs) and tRNAs and by low-throughput methods to discover them. Here, we report the discovery, characterization, and engineering of a UGA suppressing orthogonal translation system mined from metagenomic data. We develop an integrated computational and experimental pipeline based on cell-free gene expression to screen the orthogonality of &gt;200 tRNAs, test &gt;1,250 combinations of aaRS/tRNA pairs, and identify the AP1 TrpRS/tRNA^Trp_UCA as an orthogonal pair that natively encodes tryptophan at the UGA codon. We demonstrate that the AP1 TrpRS/tRNA^Trp_UCA is highly active in cell-free and cellular contexts. We then use <em>Ochre</em>, a genomically recoded <em>Escherichia coli</em> strain that lacks UAG and UGA codons, to engineer an AP1 TrpRS variant capable of 5-hydroxytryptophan incorporation at an open UGA codon. We anticipate that our strategy of integrating metagenomic bioprospecting with cell-free screening and cell-based engineering will accelerate the discovery and optimization of orthogonal translation systems for genetic code expansion.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4157–4171"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210936","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}

{"title":"High-Yield Xylitol Production from l-Arabinose via Simultaneous Glucose Co-Utilization and Chromosomal Pathway Integration in Escherichia coli","authors":"Xudong Xu,&nbsp;Jialin Zhu,&nbsp;Jikun Xia,&nbsp;Ziyan Liew,&nbsp;Mian Li,&nbsp;Jianping Lin,&nbsp;Lidan Ye,&nbsp;Mianbin Wu","doi":"10.1021/acssynbio.6c00247","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00247","url":null,"abstract":"<p><span>l</span>-arabinose, a valuable C5 pentose sugar in xylose mother liquor (a low-cost cellulose hydrolysis byproduct), remains underutilized due to costly separation requirements, resulting in significant waste of fermentable carbon resources. In this study, <em>Escherichia coli</em> W3110 was systematically engineered to efficiently convert <span>l</span>-arabinose into xylitol, a low-calorie sweetener with significant commercial value. Firstly, the <span>l</span>-arabinose metabolic network was reconstructed and glucose catabolic repression was alleviated through coordinated pathway modifications, enabling simultaneous utilization of both <span>l</span>-arabinose and glucose. Subsequently, a xylitol synthesis module consisting of <span>l</span>-arabinose isomerase (AraA), <span>l</span>-xylulose reductase (LXR), and <span>d</span>-psicose-3-epimerase (DPE) was systematically optimized via gene arrangement, promoter and RBS engineering. The optimized pathway was integrated into the <em>E. coli</em> W3110 genome at the IS5 locus using MUCICAT technology, generating a plasmid-free production strain and reducing plasmid-segregation concerns. Fed-batch fermentation in a 3 L bioreactor yielded 64.07 g/L xylitol at a productivity of 1.46 g/L/h with 90.77% <span>l</span>-arabinose conversion in 44 h. This achievement overcomes two critical metabolic bottlenecks: (1) glucose catabolite repression, which normally prevents pentose utilization in the presence of glucose, and (2) the successful stoichiometric balancing of three enzymatic steps (AraA, LXR, DPE). The engineered strain achieves simultaneous glucose-arabinose co-metabolism, and glucose co-utilization supports xylitol formation in a manner consistent with an endogenous reducing-power contribution, thereby eliminating the requirement for exogenous glycerol supplementation in the optimized process. This work establishes a defined-substrate engineering platform for <span>l</span>-arabinose-to-xylitol conversion and provides a strategic basis for future evaluation using complex industrial carbohydrate streams.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4050–4059"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210959","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}

{"title":"Auxin-Activated Caspase 9 System (AuxiCasp9), a Suicide Switch for Engineered Cells","authors":"Satoshi Yoshimoto,&nbsp;Shigeo S. Sugano,&nbsp;Shinya Sakuma,&nbsp;Yoko Yamanishi,&nbsp;Kosuke Dodo","doi":"10.1021/acssynbio.6c00010","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00010","url":null,"abstract":"<p>Engineered cells incorporating synthetic gene circuits have been developed for therapeutic and diagnostic applications. However, cell proliferation and long-term engraftment may pose a risk of unpredictable toxicities. To address this issue, a suicide switch that can be selectively activated by exogenous stimuli has been developed as a regulatory system for engineered cells. However, the variety of reliable suicide switches is limited and insufficient for the orthogonal integration of multiple functions in engineered cells. This study developed auxin-activated caspase 9 (AuxiCasp9), a novel auxin-based suicide switch, by fusing the auxin receptor protein transport inhibitor response 1 (TIR1) carrying E7K/E10K/F74A mutations and auxin protein (Aux) to caspase 9. AuxiCasp9 exhibited cell death-inducing activity comparable to that of the established systems, inducible caspase 9 (iCasp9) and rapamycin-activated caspase 9 (RapaCasp9). Finally, we confirmed the orthogonality of AuxiCasp9 and iCasp9, suggesting the feasibility of multiplexed control of engineered cells.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"3959–3965"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210991","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}

{"title":"Membrane Formulation Impacts Vesicle-Based Artificial Cell Functions","authors":"Jordi Ventura-Cobos,&nbsp;Ángela Morellá-Aucejo,&nbsp;Bastiaan C. Buddingh’,&nbsp;Jan C. M. van Hest,&nbsp;Ramón Martínez-Máñez,&nbsp;Loai K. E. A. Abdelmohsen,&nbsp;Antoni Llopis-Lorente","doi":"10.1021/acssynbio.6c00401","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00401","url":null,"abstract":"<p>Engineering vesicle-based artificial cells capable of mimicking cellular processes is a central objective in synthetic biology. However, while giant unilamellar vesicles (GUVs) have become a popular artificial cell platform, the impact of fundamental design features remains obscure. Here, we assembled GUVs composed primarily of two phospholipids: POPC, a phosphatidylcholine widely employed in GUV preparation, and DOPC, a phosphatidylcholine with a lower melting temperature and higher fluidity. We found that the phospholipid mixture leads to an increase in average GUV size (compared to POPC only) without compromising GUV yield (in contrast to DOPC only). Moreover, we studied two artificial cell functions: enzyme-driven protein-membrane docking and protein expression. Artificial cells prepared from the phospholipid mixture exhibited enhanced relocation of proteins to the membrane and enhanced protein expression. Furthermore, our data allowed us to identify the limiting factor that underlies the observed differences in protein expression between membrane formulations: the efficiency of macromolecular encapsulation. Altogether, our study underscores the importance of membrane engineering as a powerful strategy for advancing the rational development of artificial cells with functional capabilities.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4217–4228"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210994","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}