Engineering Microbiology最新文献

Pathway reprogramming and catalytic network engineering for the production of bioactive aspertetranones from deep-sea Aspergillus versicolor ADS-F20 深海杂色曲霉ADS-F20生产生物活性阿斯特戊酮的途径重编程和催化网络工程

Engineering Microbiology

Pub Date : 2026-01-02 DOI: 10.1016/j.engmic.2025.100259

Peiyuan Feng , Moli Sang , Wei Zhang

Aspertetranones are a unique class of marine fungal meroditerpenoids characterized by a highly oxygenated, linear 6/6/6/6 tetracyclic core fused to an α-pyrone scaffold. Although the pathway of aspertetranone biosynthesis in Aspergillus ochraceopetaliformis has been partially elucidated, the full potential of these compounds remains untapped. The structural diversity and enzyme promiscuity of tailoring reactions offer unexplored opportunities for the generation of bioactive derivatives through combinatorial biosynthesis. In this study, we identified the atn biosynthetic gene cluster responsible for aspertetranone production in deep-sea-derived Aspergillus versicolor ADS-F20. Through the systematic heterologous expression of 12 key genes in Aspergillus oryzae, the full pathway reconstitution and targeted biosynthesis of 17 metabolites were achieved, thus expanding the known chemical space of meroterpenoids. Notably, bioactivity screening identified compound 6 as having potent antibacterial and antifungal activities against Vibrio vulnificus ATCC 27562 (MIC = 4.50 μg/mL) and Phytophthora nicotianae (MIC = 9.01 μg/mL). Compound 11 demonstrated broad-spectrum anticancer and cytotoxic effects against the K-562, MCF7, and PATU8988T cell lines. This study underscores the power of pathway reprogramming and catalytic network engineering as versatile strategies for expanding the structural and functional diversity of biosynthetic pathway components.

阿斯特戊酮类化合物是一类独特的海洋真菌甲基萜类化合物，其特征是一个高氧、线性的6/6/6/6四环核心与α-吡酮支架融合。虽然阿斯特丁酮在赭曲霉中的生物合成途径已部分阐明，但这些化合物的全部潜力尚未开发。裁剪反应的结构多样性和酶的混杂性为通过组合生物合成产生生物活性衍生物提供了未开发的机会。在这项研究中，我们鉴定了深海来源的花色曲霉ADS-F20中负责阿斯特丁酮生产的atn生物合成基因簇。通过12个关键基因在米曲霉中的系统异源表达，实现了17种代谢物的全途径重构和靶向生物合成，从而扩大了已知的美罗萜类化合物的化学空间。生物活性筛选表明，化合物6对创伤弧菌ATCC 27562 （MIC = 4.50 μg/mL）和烟草疫霉（MIC = 9.01 μg/mL）具有较强的抗菌和抗真菌活性。化合物11对K-562、MCF7和PATU8988T细胞系具有广谱的抗癌和细胞毒作用。这项研究强调了途径重编程和催化网络工程作为扩展生物合成途径组分结构和功能多样性的通用策略的力量。

{"title":"Pathway reprogramming and catalytic network engineering for the production of bioactive aspertetranones from deep-sea Aspergillus versicolor ADS-F20","authors":"Peiyuan Feng , Moli Sang , Wei Zhang","doi":"10.1016/j.engmic.2025.100259","DOIUrl":"10.1016/j.engmic.2025.100259","url":null,"abstract":"<div><div>Aspertetranones are a unique class of marine fungal meroditerpenoids characterized by a highly oxygenated, linear 6/6/6/6 tetracyclic core fused to an α-pyrone scaffold. Although the pathway of aspertetranone biosynthesis in <em>Aspergillus ochraceopetaliformis</em> has been partially elucidated, the full potential of these compounds remains untapped. The structural diversity and enzyme promiscuity of tailoring reactions offer unexplored opportunities for the generation of bioactive derivatives through combinatorial biosynthesis. In this study, we identified the <em>atn</em> biosynthetic gene cluster responsible for aspertetranone production in deep-sea-derived <em>Aspergillus versicolor</em> ADS-F20. Through the systematic heterologous expression of 12 key genes in <em>Aspergillus oryzae</em>, the full pathway reconstitution and targeted biosynthesis of 17 metabolites were achieved, thus expanding the known chemical space of meroterpenoids. Notably, bioactivity screening identified compound <strong>6</strong> as having potent antibacterial and antifungal activities against <em>Vibrio vulnificus</em> ATCC 27562 (MIC = 4.50 μg/mL) and <em>Phytophthora nicotianae</em> (MIC = 9.01 μg/mL). Compound <strong>11</strong> demonstrated broad-spectrum anticancer and cytotoxic effects against the K-562, MCF7, and PATU8988T cell lines. This study underscores the power of pathway reprogramming and catalytic network engineering as versatile strategies for expanding the structural and functional diversity of biosynthetic pathway components.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"6 2","pages":"Article 100259"},"PeriodicalIF":0.0,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145950281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetically encoded biosensors enabled high-throughput screening of microbial cell factories 基因编码的生物传感器实现了微生物细胞工厂的高通量筛选

Engineering Microbiology

Pub Date : 2025-12-24 DOI: 10.1016/j.engmic.2025.100258

Jin Wang , Xueyan Liu , Longqian Zhao , Yue Zhang , Meng Wang

Genetically encoded biosensors provide powerful tools for coupling desired phenotypes to detectable outputs and have been extensively developed to detect a wide range of natural and unnatural products. When integrated with diverse high-throughput screening (HTS) approaches, these biosensors enable efficient product-driven screening across various throughputs, thereby expediting the engineering and optimization of microbial cell factories to produce various target compounds. For effective HTS of microbial cell factories, biosensors need to possess certain crucial characteristics. The performance features of biosensors significantly influence their application potential in HTS and can be precisely engineered through synthetic biology strategies. Furthermore, to ensure biosensor-driven HTS, additional engineering and optimizations of the biosensors are often required to increase the success rate and reduce false positives in the screening process. This review discusses the essential features of genetically encoded biosensors designed for HTS and then summarizes the latest advances in biosensor engineering for HTS purposes via synthetic biology strategies. Following this, the challenges and optimization of biosensors to adapt to different HTS processes are also discussed and exemplified. Finally, the key concerns and research prospects of developing biosensors for HTS applications are highlighted. Overall, this review provides comprehensive guidance on the engineering of genetically encoded biosensors and their applications in HTS for developing microbial cell factories to produce diverse target compounds.

遗传编码的生物传感器为将所需表型与可检测输出相耦合提供了强大的工具，并已广泛开发用于检测各种天然和非天然产品。当与各种高通量筛选（HTS）方法集成时，这些生物传感器可以在各种吞吐量中实现高效的产品驱动筛选，从而加快微生物细胞工厂的工程和优化，以生产各种目标化合物。为了实现微生物细胞工厂的高效高温超导，生物传感器需要具备某些关键特性。生物传感器的性能特征显著影响其在高温超导领域的应用潜力，并可通过合成生物学策略进行精确设计。此外，为了确保生物传感器驱动的HTS，通常需要对生物传感器进行额外的工程和优化，以提高筛选过程中的成功率并减少误报。本文综述了用于HTS的基因编码生物传感器的基本特征，并从合成生物学的角度总结了用于HTS的生物传感器工程的最新进展。在此之后，还讨论并举例说明了适应不同高温高温过程的生物传感器的挑战和优化。最后，对高温超导应用生物传感器的研究前景进行了展望。综上所述，本文对基因编码生物传感器的工程设计及其在HTS中的应用提供了全面的指导，以开发微生物细胞工厂来生产多种目标化合物。

{"title":"Genetically encoded biosensors enabled high-throughput screening of microbial cell factories","authors":"Jin Wang , Xueyan Liu , Longqian Zhao , Yue Zhang , Meng Wang","doi":"10.1016/j.engmic.2025.100258","DOIUrl":"10.1016/j.engmic.2025.100258","url":null,"abstract":"<div><div>Genetically encoded biosensors provide powerful tools for coupling desired phenotypes to detectable outputs and have been extensively developed to detect a wide range of natural and unnatural products. When integrated with diverse high-throughput screening (HTS) approaches, these biosensors enable efficient product-driven screening across various throughputs, thereby expediting the engineering and optimization of microbial cell factories to produce various target compounds. For effective HTS of microbial cell factories, biosensors need to possess certain crucial characteristics. The performance features of biosensors significantly influence their application potential in HTS and can be precisely engineered through synthetic biology strategies. Furthermore, to ensure biosensor-driven HTS, additional engineering and optimizations of the biosensors are often required to increase the success rate and reduce false positives in the screening process. This review discusses the essential features of genetically encoded biosensors designed for HTS and then summarizes the latest advances in biosensor engineering for HTS purposes via synthetic biology strategies. Following this, the challenges and optimization of biosensors to adapt to different HTS processes are also discussed and exemplified. Finally, the key concerns and research prospects of developing biosensors for HTS applications are highlighted. Overall, this review provides comprehensive guidance on the engineering of genetically encoded biosensors and their applications in HTS for developing microbial cell factories to produce diverse target compounds.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"6 1","pages":"Article 100258"},"PeriodicalIF":0.0,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145886453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Advances in microbial mevalonolactone production: from fermentative mevalonate accumulation to downstream lactonization 微生物甲羟戊酸内酯生产的进展：从发酵甲羟戊酸积累到下游内酯化

Engineering Microbiology

Pub Date : 2025-12-24 DOI: 10.1016/j.engmic.2025.100257

Hao Tang , Lihong Yin , Yiwen Jiang , Teng Xu , Ting Xue , Meimei Fu , Jianghao Chen , Jinshan Guo

Mevalonolactone (MVAL) is a high-value feedstock for the cosmetic industry, with (R)-(-)-MVAL as the sole bioactive enantiomer. Chemical synthesis, which is the traditional method for MVAL production, is hindered by cumbersome procedures, low chiral purity, and sensitivity to humidity. Microbial fermentation via fermentative mevalonate (MVA) accumulation followed by in vitro acid-catalyzed lactonization has emerged as a promising alternative for producing optically pure (R)-(-)-MVAL. Strategies for MVA overproduction in microbial systems are reviewed, including the selection of chassis strains and enzymes for the MVA biosynthetic pathway, metabolic engineering approaches for strain improvement, optimization of fermentation processes, and downstream processes for MVA-to-MVAL lactonization. Finally, prospects for advancing microbial MVAL production are discussed.

Mevalonolactone （MVAL）是化妆品行业的高价值原料，(R)-(-)-MVAL是唯一具有生物活性的对映体。化学合成是生产MVAL的传统方法，但由于程序繁琐、手性纯度低、对湿度敏感等问题，阻碍了MVAL的生产。微生物发酵通过发酵甲羟戊酸（MVA）积累，然后体外酸催化内酯化已成为生产光学纯(R)-(-)- mval的一种有前途的替代方法。综述了微生物系统中MVA过量生产的策略，包括MVA生物合成途径的基础菌株和酶的选择，菌株改良的代谢工程方法，发酵过程的优化以及MVA到mval内酯化的下游工艺。最后，对推进微生物MVAL生产的前景进行了展望。

引用次数: 0

Advances in polyethylene biodegradation and bioconversion: Microbial, enzymatic, and biotechnological insights 聚乙烯生物降解和生物转化的进展：微生物、酶和生物技术的见解

Engineering Microbiology

Pub Date : 2025-12-20 DOI: 10.1016/j.engmic.2025.100255

Jie Qiao , Luxuan Wu , Xiaoru Ma , Anni Li , Yannan Tian , Hailong Lin , Dongsheng Guo , Xiujuan Li

Polyethylene (PE) is one of the most widely used plastics worldwide and is valued for its versatility, durability, and cost-effectiveness. However, the chemical stability of PE combined with its widespread use makes it a persistent environmental pollutant that contributes to the accumulation of plastic waste in terrestrial and marine ecosystems. The escalating issue of plastic pollution has underscored the importance of developing sustainable solutions, of which PE biodegradation has emerged as a promising avenue for mitigating the environmental burden of recalcitrant polyolefins. This review systematically summarizes the recent advances in the biodegradation and bioconversion of PE, focusing on methods for evaluating degradation efficiency, the mechanisms by which microorganisms and enzymes contribute to PE degradation, and the microbial and enzymatic resources identified to date. In addition, we discuss physicochemical strategies that enhance degradation efficiency and their integration with biological approaches, as well as the potential applications of emerging biotechnological tools in PE degradation. The integration of cutting-edge biotechnological tools such as synthetic biology and machine learning with traditional biodegradation methods holds great potential for accelerating PE degradation rates and achieving more sustainable plastic waste management.

聚乙烯（PE）是世界上使用最广泛的塑料之一，因其多功能性、耐用性和成本效益而受到重视。然而，聚乙烯的化学稳定性及其广泛使用使其成为一种持久性环境污染物，有助于在陆地和海洋生态系统中积累塑料废物。不断升级的塑料污染问题强调了开发可持续解决方案的重要性，其中PE生物降解已成为减轻顽固性聚烯烃环境负担的有希望的途径。本文系统地综述了聚乙烯生物降解和生物转化的最新进展，重点介绍了降解效率的评价方法、微生物和酶对聚乙烯降解的作用机制以及迄今为止发现的微生物和酶资源。此外，我们还讨论了提高降解效率的物理化学策略及其与生物方法的结合，以及新兴生物技术工具在PE降解中的潜在应用。将合成生物学和机器学习等尖端生物技术工具与传统生物降解方法相结合，在加快PE降解速度和实现更可持续的塑料废物管理方面具有巨大潜力。

{"title":"Advances in polyethylene biodegradation and bioconversion: Microbial, enzymatic, and biotechnological insights","authors":"Jie Qiao , Luxuan Wu , Xiaoru Ma , Anni Li , Yannan Tian , Hailong Lin , Dongsheng Guo , Xiujuan Li","doi":"10.1016/j.engmic.2025.100255","DOIUrl":"10.1016/j.engmic.2025.100255","url":null,"abstract":"<div><div>Polyethylene (PE) is one of the most widely used plastics worldwide and is valued for its versatility, durability, and cost-effectiveness. However, the chemical stability of PE combined with its widespread use makes it a persistent environmental pollutant that contributes to the accumulation of plastic waste in terrestrial and marine ecosystems. The escalating issue of plastic pollution has underscored the importance of developing sustainable solutions, of which PE biodegradation has emerged as a promising avenue for mitigating the environmental burden of recalcitrant polyolefins. This review systematically summarizes the recent advances in the biodegradation and bioconversion of PE, focusing on methods for evaluating degradation efficiency, the mechanisms by which microorganisms and enzymes contribute to PE degradation, and the microbial and enzymatic resources identified to date. In addition, we discuss physicochemical strategies that enhance degradation efficiency and their integration with biological approaches, as well as the potential applications of emerging biotechnological tools in PE degradation. The integration of cutting-edge biotechnological tools such as synthetic biology and machine learning with traditional biodegradation methods holds great potential for accelerating PE degradation rates and achieving more sustainable plastic waste management.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"6 1","pages":"Article 100255"},"PeriodicalIF":0.0,"publicationDate":"2025-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145928178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Modulation of Hachiman defence by a type II toxin-antitoxin system via balancing trade-off between the fitness cost and antiphage activity II型毒素-抗毒素系统通过适应成本和抗噬菌体活性之间的平衡权衡来调节Hachiman防御

Engineering Microbiology

Pub Date : 2025-12-19 DOI: 10.1016/j.engmic.2025.100254

Xuhui Tian, Ruyi Zheng, Xin Li, Suping Jiang, Fang Wang, Yulong Shen, Qunxin She

Hachiman systems provide innate antiphage immunity across prokaryotic domains. The system encodes a HamA nuclease and a HamB helicase both of which exhibit great diversity in sequence. Phylogenetic analyses of HamA and HamB proteins revealed similar phylogenetic trees for both proteins, falling into three major types. Close examination of one of the subclades identified a distinct subfamily in which most of these Hachiman systems stands alone, however, Hachiman in the Streptococcus genus is combined with PezAT, a distinct pneumococcal epsilon zeta toxin-antitoxin system, yielding the Pez-Ham system. Investigation of a S. thermophilus Pez-Ham system revealed that only the Hachiman system is required for mediating antiphage defence. Biochemical characterization of encoded proteins, i.e., HamA or HamB individually or in protein complex revealed that the HamA nuclease is inactive alone, but upon the formation of heterologous dimer with HamB, the resulting protein complex effectively cleaves DNAs of various forms with a broad specificity (5′-CNNNG-3′), and the nuclease activity is greatly facilitated by ATP-binding in HamB and to a less degree by ATP hydrolysis. Genetic investigations further showed, while the Pez system did not function in antiphage immunity in Escherichia coli, the system repressed the expression of Hachiman, and thereby balancing the trade-off between the fitness cost and the effectiveness of antiphage defence.

Hachiman系统提供跨原核结构域的先天性抗噬菌体免疫。该系统编码一个HamB核酸酶和一个HamB解旋酶，这两个酶在序列上都表现出很大的多样性。对HamA和HamB蛋白的系统发育分析显示，这两种蛋白的系统发育树相似，可分为三种主要类型。对其中一个亚分支的仔细检查发现了一个独特的亚家族，其中大多数Hachiman系统是单独存在的，然而，链球菌属的Hachiman与PezAT（一种独特的肺炎球菌epsilon zeta毒素-抗毒素系统）结合在一起，产生了PezAT - ham系统。对嗜热链球菌Pez-Ham系统的研究表明，只有Hachiman系统是介导抗噬菌体防御所必需的。对编码蛋白（即HamA或HamB单独或在蛋白质复合物中）的生化表征表明，HamA核酸酶单独无活性，但当与HamB形成异源二聚体时，所产生的蛋白质复合物能以广泛的特异性（5 ' -CNNNG-3 '）有效地切割各种形式的dna，并且HamB中的ATP结合极大地促进了核酸酶的活性，而ATP水解则在较小程度上促进了酶的活性。遗传学研究进一步表明，虽然Pez系统在大肠杆菌的抗噬菌体免疫中不起作用，但该系统抑制了Hachiman的表达，从而平衡了适应度成本和抗噬菌体防御效果之间的权衡。

{"title":"Modulation of Hachiman defence by a type II toxin-antitoxin system via balancing trade-off between the fitness cost and antiphage activity","authors":"Xuhui Tian, Ruyi Zheng, Xin Li, Suping Jiang, Fang Wang, Yulong Shen, Qunxin She","doi":"10.1016/j.engmic.2025.100254","DOIUrl":"10.1016/j.engmic.2025.100254","url":null,"abstract":"<div><div>Hachiman systems provide innate antiphage immunity across prokaryotic domains. The system encodes a HamA nuclease and a HamB helicase both of which exhibit great diversity in sequence. Phylogenetic analyses of HamA and HamB proteins revealed similar phylogenetic trees for both proteins, falling into three major types. Close examination of one of the subclades identified a distinct subfamily in which most of these Hachiman systems stands alone, however, Hachiman in the <em>Streptococcus</em> genus is combined with PezAT, a distinct pneumococcal epsilon zeta toxin-antitoxin system, yielding the Pez-Ham system. Investigation of a <em>S. thermophilus</em> Pez-Ham system revealed that only the Hachiman system is required for mediating antiphage defence. Biochemical characterization of encoded proteins, i.e., HamA or HamB individually or in protein complex revealed that the HamA nuclease is inactive alone, but upon the formation of heterologous dimer with HamB, the resulting protein complex effectively cleaves DNAs of various forms with a broad specificity (5′-CNNNG-3′), and the nuclease activity is greatly facilitated by ATP-binding in HamB and to a less degree by ATP hydrolysis. Genetic investigations further showed, while the Pez system did not function in antiphage immunity in <em>Escherichia coli</em>, the system repressed the expression of Hachiman, and thereby balancing the trade-off between the fitness cost and the effectiveness of antiphage defence.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"6 1","pages":"Article 100254"},"PeriodicalIF":0.0,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145928177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization of Bacillus subtilis phages PJNB030, PJNB031, and PJNB032 reveals wall teichoic acid as a key receptor determinant 枯草芽孢杆菌噬菌体PJNB030、PJNB031和PJNB032的鉴定表明壁磷壁酸是一个关键的受体决定因素

Engineering Microbiology

Pub Date : 2025-12-19 DOI: 10.1016/j.engmic.2025.100253

Jiaoyang Song , Ming Hu , Min Zhao , Shengqing Luo , Yibao Chen , Yuqing Liu , Yingjun Li

Bacillus subtilis is widely used in industrial fermentation and probiotic applications; however, phage contamination poses a substantial economic threat. To address this, we isolated three phages (PJNB030, PJNB031, and PJNB032) from a contaminated B. subtilis fermentation broth and characterized their biological properties. Phenotypic analyses indicated broad pH stability (pH 4–10), variable thermal tolerance, and differential UV sensitivity. Replication kinetics revealed latent periods of 10–20 min and burst sizes ranging from 50 to 73 PFU/cell. Genomic sequencing identified linear dsDNA genomes (64–165 kb) with GC content ranging from 33.5 to 47.4%. Phylogenomic and comparative genomic analyses revealed that these phages were located on distinct branches. Deletion of pgcA (which encodes α-phosphoglucomutase) rendered cells completely resistant to PJNB031 and PJNB032, whereas it reduced PJNB030 infectivity (plaque formation efficiency) by approximately six orders of magnitude. Adsorption assays confirmed that the binding of PJNB031 and PJNB032 to ΔpgcA mutants was abolished, whereas PJNB030 retained partial adsorption capacity. In conclusion, this study identified wall teichoic acid as the primary receptor for these phages and established pgcA deletion as an effective strategy for engineering phage-resistant B. subtilis strains. Our findings provide critical insights into the mitigation of phage contamination in industrial bioprocesses.

枯草芽孢杆菌广泛应用于工业发酵和益生菌领域；然而，噬菌体污染构成了巨大的经济威胁。为了解决这一问题，我们从被污染的枯草芽孢杆菌发酵液中分离出三种噬菌体（PJNB030、PJNB031和PJNB032），并对它们的生物学特性进行了表征。表型分析表明其pH稳定（pH 4-10），耐热性不同，紫外线敏感性不同。复制动力学显示潜伏期为10-20分钟，爆发大小为50至73 PFU/细胞。基因组测序鉴定出线性dsDNA基因组（64-165 kb）， GC含量在33.5 ~ 47.4%之间。系统基因组学和比较基因组学分析显示，这些噬菌体位于不同的分支上。pgcA（编码α-磷酸葡萄糖糖化酶）的缺失使细胞对PJNB031和PJNB032完全耐药，而PJNB030的感染性（斑块形成效率）降低了大约6个数量级。吸附实验证实PJNB031和PJNB032与ΔpgcA突变体的结合被消除，而PJNB030保留了部分吸附能力。综上所述，本研究确定壁苔酸是这些噬菌体的主要受体，并确定pgcA缺失是一种有效的工程策略，可用于抗噬菌体枯草芽孢杆菌菌株。我们的研究结果为减轻工业生物过程中噬菌体污染提供了重要的见解。

{"title":"Characterization of Bacillus subtilis phages PJNB030, PJNB031, and PJNB032 reveals wall teichoic acid as a key receptor determinant","authors":"Jiaoyang Song , Ming Hu , Min Zhao , Shengqing Luo , Yibao Chen , Yuqing Liu , Yingjun Li","doi":"10.1016/j.engmic.2025.100253","DOIUrl":"10.1016/j.engmic.2025.100253","url":null,"abstract":"<div><div><em>Bacillus subtilis</em> is widely used in industrial fermentation and probiotic applications; however, phage contamination poses a substantial economic threat. To address this, we isolated three phages (PJNB030, PJNB031, and PJNB032) from a contaminated <em>B. subtilis</em> fermentation broth and characterized their biological properties. Phenotypic analyses indicated broad pH stability (pH 4–10), variable thermal tolerance, and differential UV sensitivity. Replication kinetics revealed latent periods of 10–20 min and burst sizes ranging from 50 to 73 PFU/cell. Genomic sequencing identified linear dsDNA genomes (64–165 kb) with GC content ranging from 33.5 to 47.4%. Phylogenomic and comparative genomic analyses revealed that these phages were located on distinct branches. Deletion of <em>pgcA</em> (which encodes α-phosphoglucomutase) rendered cells completely resistant to PJNB031 and PJNB032, whereas it reduced PJNB030 infectivity (plaque formation efficiency) by approximately six orders of magnitude. Adsorption assays confirmed that the binding of PJNB031 and PJNB032 to Δ<em>pgcA</em> mutants was abolished, whereas PJNB030 retained partial adsorption capacity. In conclusion, this study identified wall teichoic acid as the primary receptor for these phages and established <em>pgcA</em> deletion as an effective strategy for engineering phage-resistant <em>B. subtilis</em> strains. Our findings provide critical insights into the mitigation of phage contamination in industrial bioprocesses.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"6 1","pages":"Article 100253"},"PeriodicalIF":0.0,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145928176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gdx mediates low-affinity Cs⁺/H⁺ antiport and confers cesium resistance in Escherichia coli Gdx介导低亲和力Cs + /H +反端口，并在大肠杆菌中赋予铯抗性

Engineering Microbiology

Pub Date : 2025-12-18 DOI: 10.1016/j.engmic.2025.100251

Daiki Kojima , Masahiro Ito

Following the Fukushima Daiichi nuclear power plant accident, radioactive cesium was released into the environment, prompting intensified efforts to identify cesium-resistant microorganisms. During these studies, we isolated a cesium-resistant Escherichia coli strain, designated ZX-1, which exhibits remarkable tolerance to cesium concentrations exceeding 700 mM. As no prior reports of cesium-resistant E. coli exist, this finding suggests the presence of a previously unrecognized resistance mechanism. This study aims to elucidate the molecular basis of cesium resistance in ZX-1.

RNA-seq analysis comparing ZX-1 with its parental strain, the commercial E. coli Mach1™, revealed constitutive upregulation of the guanidinium exporter gene gdx in ZX-1. Reanalysis of the whole-genome sequence identified a 20-bp deletion upstream of the gdx open reading frame, likely disrupting formation of the guanidinium riboswitch P2 loop and resulting in constitutive gdx expression.

To evaluate gdx function, the gene was cloned into the expression vector pBAD24 and expressed in E. coli. The resulting gdx-expressing strain exhibited even greater cesium resistance than ZX-1. Functional assays demonstrated that this strain mediates not only guanidinium/H⁺ antiport activity but also Cs⁺/H⁺ antiport activity. Cesium resistance was further enhanced in the presence of guanidinium, consistent with riboswitch-mediated induction of gdx.

Collectively, these findings provide evidence for a novel cesium efflux mechanism in E. coli and uncover an unexpected role of the guanidinium exporter Gdx in cesium export. These insights may facilitate the discovery of additional cesium-resistant microorganisms and broaden the potential for future applications.

福岛第一核电站事故发生后，放射性铯被释放到环境中，促使人们加强了识别抗铯微生物的努力。在这些研究中，我们分离出一株铯耐药大肠杆菌，命名为ZX-1，它对铯浓度超过700 mM表现出显著的耐受性。由于之前没有关于铯耐药大肠杆菌的报道，这一发现表明存在一种以前未被认识到的耐药机制。本研究旨在阐明ZX-1耐铯的分子基础。将ZX-1与其亲本菌株（商业大肠杆菌Mach1™）进行RNA-seq分析，发现ZX-1中的胍输出基因gdx组成上调。对全基因组序列的重新分析发现，gdx开放阅读框上游有一个20bp的缺失，可能破坏了胍核糖开关P2环的形成，导致了gdx的组成性表达。为了评估gdx的功能，我们将该基因克隆到表达载体pBAD24中，并在大肠杆菌中表达。表达gdx的菌株表现出比ZX-1更强的抗铯能力。功能测试表明，该菌株不仅介导胍+ /H +的反端口活性，还介导Cs + /H +的反端口活性。在胍的存在下，对铯的抗性进一步增强，这与核糖体开关介导的gdx诱导一致。总的来说，这些发现为大肠杆菌中新的铯外排机制提供了证据，并揭示了胍出口基因Gdx在铯出口中的意想不到的作用。这些见解可能有助于发现更多的抗铯微生物，并扩大未来应用的潜力。

{"title":"Gdx mediates low-affinity Cs⁺/H⁺ antiport and confers cesium resistance in Escherichia coli","authors":"Daiki Kojima , Masahiro Ito","doi":"10.1016/j.engmic.2025.100251","DOIUrl":"10.1016/j.engmic.2025.100251","url":null,"abstract":"<div><div>Following the Fukushima Daiichi nuclear power plant accident, radioactive cesium was released into the environment, prompting intensified efforts to identify cesium-resistant microorganisms. During these studies, we isolated a cesium-resistant <em>Escherichia coli</em> strain, designated ZX-1, which exhibits remarkable tolerance to cesium concentrations exceeding 700 mM. As no prior reports of cesium-resistant <em>E. coli</em> exist, this finding suggests the presence of a previously unrecognized resistance mechanism. This study aims to elucidate the molecular basis of cesium resistance in ZX-1.</div><div>RNA-seq analysis comparing ZX-1 with its parental strain, the commercial <em>E. coli</em> Mach1™, revealed constitutive upregulation of the guanidinium exporter gene <em>gdx</em> in ZX-1. Reanalysis of the whole-genome sequence identified a 20-bp deletion upstream of the <em>gdx</em> open reading frame, likely disrupting formation of the guanidinium riboswitch P2 loop and resulting in constitutive <em>gdx</em> expression.</div><div>To evaluate <em>gdx</em> function, the gene was cloned into the expression vector pBAD24 and expressed in <em>E. coli</em>. The resulting <em>gdx</em>-expressing strain exhibited even greater cesium resistance than ZX-1. Functional assays demonstrated that this strain mediates not only guanidinium/H⁺ antiport activity but also Cs⁺/H⁺ antiport activity. Cesium resistance was further enhanced in the presence of guanidinium, consistent with riboswitch-mediated induction of <em>gdx</em>.</div><div>Collectively, these findings provide evidence for a novel cesium efflux mechanism in <em>E. coli</em> and uncover an unexpected role of the guanidinium exporter Gdx in cesium export. These insights may facilitate the discovery of additional cesium-resistant microorganisms and broaden the potential for future applications.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"6 1","pages":"Article 100251"},"PeriodicalIF":0.0,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145928175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phase variation in Bacteroides fragilis governs susceptibility to a microvirus and drives its evolution 脆弱拟杆菌的阶段变异控制着对微病毒的易感性并驱动其进化

Engineering Microbiology

Pub Date : 2025-12-18 DOI: 10.1016/j.engmic.2025.100252

Pan Huang , Meiqi Du , Yanqiu Liu , Zhenhao Han , Qian Wan , Fuming Liang , Wenyuan Han

The interaction and co-evolution between human gut bacteria and their phages shape the dynamic gut microbiome, exerting a significant impact on human health. However, the underlying mechanisms are largely unexplored. In particular, a bacteria-phage interaction model of the Bacteroidota phylum and the Microviridae phages is lacking, limiting our understanding of their ecological roles in human gut. In this study, we isolated a Bacteroidota-infecting Microviridae phage φHBP1 from human feces. Infection of its host Bacteroides fragilis with φHBP1 drives multiple genomic structural variations, which are correlated with host resistance to φHBP1. In turn, our phage evolution assay in B. fragilis H1 obtained φHBP1 mutants that carry mutations within the capsid and pilot proteins and can reinfect the resistant bacterial population. Together, our findings provide novel insights into an antagonistic co-evolution mechanism between gut phage and bacteria, and hold important implications for diversifying phages through evolution to target resistant bacteria in phage therapy.

人类肠道细菌及其噬菌体之间的相互作用和共同进化塑造了动态肠道微生物群，对人类健康产生重大影响。然而，潜在的机制在很大程度上尚未被探索。特别是，缺乏拟杆菌门和微病毒科噬菌体的细菌-噬菌体相互作用模型，限制了我们对它们在人类肠道中的生态作用的理解。在这项研究中，我们从人类粪便中分离出一株感染拟杆菌的微病毒科噬菌体φHBP1。其宿主脆弱拟杆菌（Bacteroides fragilis）感染φHBP1引发多种基因组结构变异，这些变异与宿主对φHBP1的抗性相关。反过来，我们在脆弱芽孢杆菌H1噬菌体进化实验中获得了φHBP1突变体，这些突变体在衣壳和先导蛋白内携带突变，并且可以重新感染耐药菌群。总之，我们的研究结果为肠道噬菌体和细菌之间的拮抗共同进化机制提供了新的见解，并对噬菌体通过进化来靶向噬菌体治疗中的耐药细菌而使噬菌体多样化具有重要意义。

{"title":"Phase variation in Bacteroides fragilis governs susceptibility to a microvirus and drives its evolution","authors":"Pan Huang , Meiqi Du , Yanqiu Liu , Zhenhao Han , Qian Wan , Fuming Liang , Wenyuan Han","doi":"10.1016/j.engmic.2025.100252","DOIUrl":"10.1016/j.engmic.2025.100252","url":null,"abstract":"<div><div>The interaction and co-evolution between human gut bacteria and their phages shape the dynamic gut microbiome, exerting a significant impact on human health. However, the underlying mechanisms are largely unexplored. In particular, a bacteria-phage interaction model of the Bacteroidota phylum and the <em>Microviridae</em> phages is lacking, limiting our understanding of their ecological roles in human gut. In this study, we isolated a Bacteroidota-infecting <em>Microviridae</em> phage φHBP1 from human feces. Infection of its host <em>Bacteroides fragilis</em> with φHBP1 drives multiple genomic structural variations, which are correlated with host resistance to φHBP1. In turn, our phage evolution assay in <em>B. fragilis</em> H1 obtained φHBP1 mutants that carry mutations within the capsid and pilot proteins and can reinfect the resistant bacterial population. Together, our findings provide novel insights into an antagonistic co-evolution mechanism between gut phage and bacteria, and hold important implications for diversifying phages through evolution to target resistant bacteria in phage therapy.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"6 1","pages":"Article 100252"},"PeriodicalIF":0.0,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145886454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unraveling microbial life from a high-altitude hydrothermal system in the Andes plateau and their potential for nitrogen transformations 揭示安第斯高原高海拔热液系统中的微生物生命及其氮转化的潜力

Engineering Microbiology

Pub Date : 2025-09-29 DOI: 10.1016/j.engmic.2025.100242

Coral Pardo-Esté , Juan Castro-Severyn , Jacqueline Aldridge , Diego Alvarez-Saravia , Lenka Kurte , Polette Aguilar-Muñoz , Pablo Paquis , Vilma Pérez , David Medina , Wade H Jeffrey , Verónica Molina , Martha B Hengst

Terrestrial hydrothermal systems provide a window for studying the biogeochemical interactions that occur in hot and gas-rich ecosystems resembling the conditions found in early life on Earth. The biogeochemical dynamics of the Andean hydrothermal systems in the Atacama Desert area are still understudied. Thus, we aimed to characterize the taxonomic composition and genomic potential of nitrogen transformations in a microbial community inhabiting a high-altitude hydrothermal system on the Altiplano Plateau of the Chilean Andes. Specifically, we sampled sediment and microbial mats in three ponds with water temperatures ranging from 42 to 64 °C. We found a high prevalence of photoheterotrophs, with differences in taxonomic composition and gene abundance between the microbial communities found in the sediment and microbial mats. Changes in physicochemical conditions, such as temperature and pH, and the concentrations of CO₂, CH₄ and Mn accounted for the variability in the microbial community structure. Our results indicated an enrichment of N-related genes associated with nitrate reduction, denitrification, and ammonia assimilation, suggesting a metabolically versatile community using nitrate, nitrite, and gaseous nitrogen species to assimilate ammonia into their biomass. This study contributes to our understanding of the taxonomy and functional microbial dynamics in a high-altitude thermal system, where ammonia assimilation is potentially critical for biomass formation, and particular environmental conditions favor adaptations to maintain biogeochemical cycles.

陆地热液系统为研究类似于地球早期生命条件的高温富气生态系统中发生的生物地球化学相互作用提供了一个窗口。阿塔卡马沙漠地区安第斯热液系统的生物地球化学动力学研究尚不充分。因此，我们旨在描述栖息在智利安第斯山脉Altiplano高原高海拔热液系统的微生物群落中氮转化的分类组成和基因组潜力。具体来说，我们在水温为42至64°C的三个池塘中取样了沉积物和微生物垫。我们发现，在沉积物和微生物席中发现的微生物群落在分类组成和基因丰度上存在差异，光异养生物普遍存在。温度、pH等理化条件以及CO2、CH4和Mn浓度的变化是微生物群落结构变化的主要原因。我们的研究结果表明，与硝酸盐还原、反硝化和氨同化相关的n相关基因富集，表明一个代谢多样的群落利用硝酸盐、亚硝酸盐和气态氮物种将氨同化到它们的生物量中。该研究有助于我们了解高海拔热系统中微生物的分类和功能动力学，其中氨同化对生物量的形成具有潜在的关键作用，并且特定的环境条件有利于维持生物地球化学循环。

{"title":"Unraveling microbial life from a high-altitude hydrothermal system in the Andes plateau and their potential for nitrogen transformations","authors":"Coral Pardo-Esté , Juan Castro-Severyn , Jacqueline Aldridge , Diego Alvarez-Saravia , Lenka Kurte , Polette Aguilar-Muñoz , Pablo Paquis , Vilma Pérez , David Medina , Wade H Jeffrey , Verónica Molina , Martha B Hengst","doi":"10.1016/j.engmic.2025.100242","DOIUrl":"10.1016/j.engmic.2025.100242","url":null,"abstract":"<div><div>Terrestrial hydrothermal systems provide a window for studying the biogeochemical interactions that occur in hot and gas-rich ecosystems resembling the conditions found in early life on Earth. The biogeochemical dynamics of the Andean hydrothermal systems in the Atacama Desert area are still understudied. Thus, we aimed to characterize the taxonomic composition and genomic potential of nitrogen transformations in a microbial community inhabiting a high-altitude hydrothermal system on the Altiplano Plateau of the Chilean Andes. Specifically, we sampled sediment and microbial mats in three ponds with water temperatures ranging from 42 to 64 °C. We found a high prevalence of photoheterotrophs, with differences in taxonomic composition and gene abundance between the microbial communities found in the sediment and microbial mats. Changes in physicochemical conditions, such as temperature and pH, and the concentrations of CO<sub>2</sub>, CH<sub>4</sub> and Mn accounted for the variability in the microbial community structure. Our results indicated an enrichment of N-related genes associated with nitrate reduction, denitrification, and ammonia assimilation, suggesting a metabolically versatile community using nitrate, nitrite, and gaseous nitrogen species to assimilate ammonia into their biomass. This study contributes to our understanding of the taxonomy and functional microbial dynamics in a high-altitude thermal system, where ammonia assimilation is potentially critical for biomass formation, and particular environmental conditions favor adaptations to maintain biogeochemical cycles.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 4","pages":"Article 100242"},"PeriodicalIF":0.0,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145519646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Archaeasins as a promising resource for developing next-generation antibiotics uncovered via deep learning 通过深度学习发现的古菌原是开发下一代抗生素的有前途的资源

Engineering Microbiology

Pub Date : 2025-09-23 DOI: 10.1016/j.engmic.2025.100241

Huan Du, Yang Liu

Fighting against antibiotic resistance has an unexpected ally, archaea. Despite the extensive exploration of antimicrobial peptides in bacteria and eukaryotes, the archaeal domain has been overlooked. A recent study employed deep learning to screen archaeasins. The synthesized versions showed a 93 % success rate against pathogens by depolarizing the cytoplasmic membrane, not the outer membrane. This highlights the promise and deep learning power of archaea for antibiotic discovery and the culture of uncultured archaea.

对抗抗生素耐药性有一个意想不到的盟友，古细菌。尽管在细菌和真核生物中广泛探索抗菌肽，但古细菌领域一直被忽视。最近的一项研究使用深度学习来筛选古细菌。合成版本显示，通过细胞质膜去极化，而不是外膜去极化，对病原体的成功率为93%。这凸显了古细菌在抗生素发现和未培养古细菌培养方面的前景和深度学习能力。

引用次数: 0