{"title":"Engineering Yarrowia lipolytica as a yeast cell factory for the de novo production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate)","authors":"Jinming Liu, Jia Yan, Zhiyong Cui, Qingsheng Qi","doi":"10.1016/j.synbio.2025.09.002","DOIUrl":"10.1016/j.synbio.2025.09.002","url":null,"abstract":"<div><div>The oleaginous yeast <em>Yarrowia lipolytica</em> presents a promising chassis for the production of biodegradable plastic polyhydroxyalkanoates (PHAs) due to its advantages in precursor supply capabilities and cost-effective substrate utilization. However, <em>Y. lipolytica</em> has primarily been engineered for the synthesis of homopolymeric PHAs, such as poly (3-hydroxybutyrate) (P3HB), which have limited material properties and application potential. In this study, the succinate dehydrogenase-deficient <em>Y. lipolytica</em> strains were utilized as hosts for the de novo biosynthesis of copolymer poly (3-hydroxybutyrate-co-4-hydroxybutyrate) (P34HB). By employing a strategy of subcellular partitioning, poly (4-hydroxybutyrate) (P4HB) was synthesized in the cytoplasm using 4-hydrobutyrate (4HB) derived from mitochondrial sources as a monomer. We then introduced the biosynthetic pathway for 3-hydroxybutyryl-CoA to facilitate P34HB accumulation. Importantly, the ratio of 4HB monomer in P34HB could be adjusted from 9.17 mol% to 45.26 mol% by varying medium components and carbon sources. Under fed-batch fermentation conditions in a 5 L bioreactor, the engineered strain achieved a P34HB titer of 18.61 g/L representing 19.18 % of cell dry weight (CDW). This study not only demonstrates the potential of <em>Y. lipolytica</em> for P34HB synthesis, but also expands the monomer pool available for PHAs in yeast cell factories.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"11 ","pages":"Pages 152-160"},"PeriodicalIF":4.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145096566","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}
Yanmei Liu, Zizhen Liang, Yanyun Jing , Yanrui Ye, Xiaofeng Yang, Zhanglin Lin
{"title":"An efficient CRISPR-Cas12a tool for iterative genome editing, streamlined minimization, and payload engineering of Pseudomonas phage S1","authors":"Yanmei Liu, Zizhen Liang, Yanyun Jing , Yanrui Ye, Xiaofeng Yang, Zhanglin Lin","doi":"10.1016/j.synbio.2025.09.019","DOIUrl":"10.1016/j.synbio.2025.09.019","url":null,"abstract":"<div><div>The ability to precisely engineer phage genomes is critical for advancing phage-based biotechnology and therapeutic development. Here, we present a high-efficiency, scarless CRISPR-Cas12a genome editing method for a virulent <em>Pseudomonas aeruginosa</em> phage vB_PaeM_SCUT-S1 (S1). Using a two-plasmid system, we achieved near-complete efficiency in gene deletion, point mutation, gene insertion, and replacement. Iterative deletions enabled the identification of 27 non-essential, 16 quasi-essential, and seven essential genes, and culminated in the largest genome reduction (13.9 kb) reported for a <em>P. aeruginosa</em> phage. The minimized phage mutant S1_200L retained infectivity and supported integration of large exogenous gene cassettes (e.g., <em>lacZ</em>, <em>lys009</em>). This system offers a versatile and high-throughput approach for phage genome engineering and rational design of functional phages for synthetic biology and antimicrobial applications.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"11 ","pages":"Pages 268-276"},"PeriodicalIF":4.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145325257","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":"Thank you Reviewers","authors":"","doi":"10.1016/S2405-805X(26)00057-8","DOIUrl":"10.1016/S2405-805X(26)00057-8","url":null,"abstract":"","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"11 ","pages":"Pages I-IV"},"PeriodicalIF":4.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147420496","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}
Tao Sun , Mei-Li Sun , Lu Lin , Jian Gao , Rodrigo Ledesma-Amaro , Kaifeng Wang , Xiao-Jun Ji
{"title":"Combining multiplex metabolic engineering with adaptive evolution strategies for high-level succinic acid production in Yarrowia lipolytica","authors":"Tao Sun , Mei-Li Sun , Lu Lin , Jian Gao , Rodrigo Ledesma-Amaro , Kaifeng Wang , Xiao-Jun Ji","doi":"10.1016/j.synbio.2025.08.011","DOIUrl":"10.1016/j.synbio.2025.08.011","url":null,"abstract":"<div><div>Succinic acid, an essential platform chemical with extensive utility in biodegradable materials, pharmaceuticals, and the food industry, faces challenges of high energy consumption and environmental pollution in traditional chemical synthesis. Here, we employed multiplex metabolic engineering and adaptive laboratory evolution to enhance succinic acid biosynthesis in <em>Y</em><em>arrowia lipolytica</em>. By attenuating succinate dehydrogenase (Sdh) activity, mitigating by-product accumulation, and enhancing the succinate synthesis pathway, engineered strains showed efficient succinic acid production from glycerol. The titer reached 130.99 g/L under unregulated pH conditions, translating to a yield of 0.35 g/g and a productivity of 0.70 g/(L·h). Subsequently, transporter engineering and adaptive evolution strategies were applied to enhance glucose utilization for succinic acid synthesis, yielding an evolved strain that eliminated the growth lag phase and produced 106.68 g/L succinic acid from glucose, which translated to a yield of 0.32 g/g and a productivity of 0.64 g/(L·h). Additionally, transcriptomic analysis and inverse metabolic engineering revealed that 4-hydroxyphenylpyruvate dioxygenase (4-Hppd) in the tyrosine degradation pathway partially restored the growth of Sdh-deficient strains on glucose, offering new insights for subsequent succinic acid biomanufacturing using <em>Y</em>. <em>lipolytica</em>.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"11 ","pages":"Pages 48-58"},"PeriodicalIF":4.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145027104","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}
Mark J. Calcott , Jonas Kröger , David F. Ackerley
{"title":"A rapid combinatorial assembly method for gene cluster characterisation illuminates glidobactin biosynthesis","authors":"Mark J. Calcott , Jonas Kröger , David F. Ackerley","doi":"10.1016/j.synbio.2025.09.010","DOIUrl":"10.1016/j.synbio.2025.09.010","url":null,"abstract":"<div><div>Heterologous expression of natural product gene clusters in tractable hosts offers great promise for achieving sustainable production of nature-inspired drugs. However, it is common for the roles of some genes in a cluster to be unclear, and this can make it difficult to identify the minimal gene set required to produce the desired molecule. Typically, the function of unknown genes is inferred by time-consuming reductionist techniques, e.g. single and multiple gene knockouts in the native producer, followed by phenotype analysis. Here, we instead present a rapid combinatorial method to assemble individual genes involved in glidobactin biosynthesis into a collection of partial or complete clusters in a heterologous host. Following up with mass spectrometry allowed identification of the minimum genes required for compound production. We applied this synthetic biology approach to characterise the glidobactin gene cluster, for which previous gene knockout studies had yielded conflicting results. In the process, we showed that an added intrinsic advantage of combinatorial assembly is the generation of multiple strains that produce potentially desirable analogues in addition to glidobactin.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"11 ","pages":"Pages 85-90"},"PeriodicalIF":4.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145061145","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}
Sihan Yang , Zupeng Cai , Natalie Chia , Jing Luo , Tilmann Weber , Kai Blin , Yaojun Tong
{"title":"CRISPy-web 3.0: A unified platform for multi-modal guide RNA design for CRISPR and TnpB genome editing applications","authors":"Sihan Yang , Zupeng Cai , Natalie Chia , Jing Luo , Tilmann Weber , Kai Blin , Yaojun Tong","doi":"10.1016/j.synbio.2025.10.003","DOIUrl":"10.1016/j.synbio.2025.10.003","url":null,"abstract":"<div><div>CRISPy-web is an interactive web-based platform designed for rational guide RNA design in CRISPR-Cas9-based genome editing systems. Here, we present CRISPy-web 3.0 (<span><span>https://crispy.secondarymetabolites.org/</span><svg><path></path></svg></span>), an upgraded and versatile version that extends its functionality beyond classical Cas9-based systems. This version integrates support for diverse genome editing systems, including Cas9, CRISPR interference (CRISPRi), and TnpB/ωRNA. The redesigned interface enables users to toggle between multiple editing modes, select target regions such as ORFs or 5′ UTRs, and visualize strand orientation, off-targets, and predicted mutation outcomes. It also incorporates scoring systems that evaluate guide RNA efficiency and specificity based on mismatch tolerance, positional context, and PAM requirements for CRISPR-Cas9-based applications. With an improved user interface design, enhanced backend scalability, and modular support for customizable inputs, CRISPy-web 3.0 provides a comprehensive and extensible platform for guide RNA design, enabling genome editing across a broader range of prokaryotic systems, including both CRISPR and TnpB.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"11 ","pages":"Pages 317-322"},"PeriodicalIF":4.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145416668","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}
Sijia Wang , Qiyao Zhu , Chuan Liu , Huina Dong , Miaomiao Xia , Zhaoxia Jin , Dawei Zhang
{"title":"Engineering riboflavin-overproducing Bacillus subtilis via pathway gene overexpression","authors":"Sijia Wang , Qiyao Zhu , Chuan Liu , Huina Dong , Miaomiao Xia , Zhaoxia Jin , Dawei Zhang","doi":"10.1016/j.synbio.2025.09.005","DOIUrl":"10.1016/j.synbio.2025.09.005","url":null,"abstract":"<div><div>Overexpression of genes at key metabolic nodes frequently enhances the yield of target products. However, this often leads to widespread issues with growth defect and plasmid instability. This study utilizes the riboflavin over-producer <em>Bacillus subtilis</em> U3 as a model to systematically investigate the impact of overexpressing riboflavin operon genes on strain growth and plasmid structural instability. Overexpression of genes in rib operon enhances target product yields by 13.2 % in U3, but the engineered strains suffer growth defects and plasmid instability. Frameshift mutations in the <em>ribD</em> gene were found to significantly reduce the loss of operon gene fragments by 16.7 %. Furthermore, this study investigates the application of the Respiration Activity Monitoring System (RAMOS) in evaluating the growth of metabolically engineered strains. RAMOS serves as a medium optimization tool and pre-fermentation screening platform. Specifically, guanine supplementation increased biomass by 11.1 % in <em>zwf</em>-overexpressing strains, whereas histidine, uracil, and tryptophan supplementation could improve the biomass of <em>purF</em>-overexpressing strain by 71.1 %. This approach provides a methodological framework for resolving growth defects in metabolic engineering.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"11 ","pages":"Pages 91-101"},"PeriodicalIF":4.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145061146","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}
Ai-Tong Jiang , Guang-Qing Du , Xu-Yang Huang , Zheng-Zi Ji , Si-Riguleng Qian , Lin-Xia Liu , Da-Wei Zhang
{"title":"Enhanced microbial production of pyridoxine (Vitamin B6) in Bacillus subtilis via pathway and process optimization","authors":"Ai-Tong Jiang , Guang-Qing Du , Xu-Yang Huang , Zheng-Zi Ji , Si-Riguleng Qian , Lin-Xia Liu , Da-Wei Zhang","doi":"10.1016/j.synbio.2025.09.014","DOIUrl":"10.1016/j.synbio.2025.09.014","url":null,"abstract":"<div><div>Vitamin B<sub>6</sub> refers to a family of water-soluble B vitamin, which is essential for various physiological functions, including amino acid metabolism, neurotransmitter synthesis, and hemoglobin synthesis. The biosynthesis of pyridoxine (PN), a commercial form of vitamin B<sub>6</sub>, through microbial fermentation has garnered widespread attention owing to its environmentally friendly and safe production methods, as well as its mild reaction conditions. However, the low yield of natural strains limits their application. This study focused on constructing a high-yielding strain of PN through pathway engineering and process optimization. Firstly, five key deoxyxylulose-5-phosphate-dependent pathway genes (<em>epd</em>, <em>pdxB</em>, <em>serC</em>, <em>pdxA</em>, and <em>pdxJ</em>) were overexpressed in <em>Bacillus subtilis</em> ARTP, which improved the PN titer by 3.2-fold to 2.9 mg/L. Subsequently, <em>pdxST</em> genes involved in the DXP-independent pathway were screened from various strains. Ribosome binding site (RBS) sequences were optimized to regulate their expression, which further increased the PN titer to 24.6 mg/L. Finally, systematic medium optimization was identified as a critical strategy for enhancing PN biosynthesis, leading to a remarkable 1.8-fold improvement in PN production. Under optimized fermentation conditions, the engineered strain achieved a PN titer of 174.6 mg/L in fed-batch fermentation, which represents the highest level reported to date in <em>B</em>. <em>subtilis</em>. Overall, this study presents an effective strategy combining pathway engineering and medium optimization for significantly improving PN production, offering valuable insights for the industrial development of PN biosynthesis.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"11 ","pages":"Pages 216-225"},"PeriodicalIF":4.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145220362","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}
Xin-Yue Li , Kai Li , Feng-Li Zhang , Tomohisa Hasunuma , Akihiko Kondo , Lin Zhang , Xin-Qing Zhao , Feng-Wu Bai
{"title":"CRISPR-based synthetic biology toolkit development in Candida viswanthii and functional analysis of the stress responsive Ena1-like protein","authors":"Xin-Yue Li , Kai Li , Feng-Li Zhang , Tomohisa Hasunuma , Akihiko Kondo , Lin Zhang , Xin-Qing Zhao , Feng-Wu Bai","doi":"10.1016/j.synbio.2025.09.021","DOIUrl":"10.1016/j.synbio.2025.09.021","url":null,"abstract":"<div><div>Industrial strains from the <em>Candida</em> genus have been applied in production of enzymes, biochemicals, and single-cell protein. However, the synthetic biology manipulation tools for <em>Candida</em> species remain underdeveloped. In this study, a high-efficiency genome editing strategy for <em>C. viswanathii</em> was established by combining the CRISPR/Cas9 and Cre/loxP systems. This approach achieved 100 % editing efficiency and supported rapid iterative editing cycles within 6 days. The system enables iterative genomic modifications and was successfully applied for multiplex editing and multicopy gene integration up to 7 copies. Leveraging this platform, g144, an Ena1-like protein that exhibited differential expression during dodecanedioic acid (DDA) fermentation, was functionally characterized. The results showed that g144 lacks Na<sup>+</sup> transport activity, but both the disruption and overexpression strains showed increased sensitivity to alkaline pH and Na<sup>+</sup> stress, as well as a decrease in DDA production. The genome editing toolkit reported here benefits further applications of <em>Candida</em> strains for sustainable bioproduction.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"11 ","pages":"Pages 298-308"},"PeriodicalIF":4.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145362638","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}
Zhenyu Wang , Bangguo Fu , Huifang Zhang , Mengting Li , Xiwei Peng , Huanqing Niu , Yong Chen , Chenjie Zhu , Jia Liu , Dong Liu , Hanjie Ying
{"title":"Biofilm-based continuous secretion of human lysozyme through cell-surface display of FimH on Saccharomyces cerevisiae","authors":"Zhenyu Wang , Bangguo Fu , Huifang Zhang , Mengting Li , Xiwei Peng , Huanqing Niu , Yong Chen , Chenjie Zhu , Jia Liu , Dong Liu , Hanjie Ying","doi":"10.1016/j.synbio.2025.08.012","DOIUrl":"10.1016/j.synbio.2025.08.012","url":null,"abstract":"<div><div>Biofilms enhance microbial tolerance to harsh environments while preserving cellular activity over prolonged periods. Although biofilm-based continuous fermentation is widely applied for production of small-molecule chemicals, its application to macromolecular protein production has been rarely reported. Here, FimH, an adhesin from <em>E. coli</em> fimbriae that is employed for mannose-specific adherence and promotes biofilm formation, was displayed on the surface of <em>S. cerevisiae</em> using the anchoring proteins Sag1C, Sed1, Cwp2 and Ccw12, resulting in an 80–150 % enhancement in biofilm formation. Among them, Sed1 was the most effective, followed by Sag1C. A biofilm-based fermentation system for continuous secretion of human lysozyme (hLYZ) was established via cell-surface display of FimH in <em>S. cerevisiae</em>, achieving stable operation for over 350 h. The engineered strain BY4742-Sag1C-hlyz achieved an average extracellular hLYZ activity of 113.1 U/mL, significantly higher than the control BY4742-hlyz (41.6 U/mL), owing to enhanced cell adhesion that increased the total cell number in biofilm-based fermentation. Its productivity reached 2.36 U/mL/h, representing a 77.4 % increase compared with free-cell fermentation of BY4742-hlyz (1.33 U/mL/h). In conclusion, this study first achieved heterologous expression of a bacterial biofilm-forming gene in <em>S. cerevisiae</em>, enhancing biofilm formation and providing a reference for future expression of bacterial biofilm-related genes in yeast. Furthermore, biofilm-based fermentation enabled continuous secretion of hLYZ, highlighting a promising strategy for continuous production of recombinant proteins.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"11 ","pages":"Pages 28-36"},"PeriodicalIF":4.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144989537","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}