Engineering Microbiology最新文献

Engineering thermotolerant microbial strains via TrRCC1 overexpression for efficient bioethanol production 通过TrRCC1过表达工程耐热微生物菌株高效生产生物乙醇

Engineering Microbiology Pub Date : 2025-06-01 DOI: 10.1016/j.engmic.2025.100212

Tingting Chen, Xiao He, Xinyan Zhang, Tian Tian, Jian Cheng, Tingting Long, Yonghao Li

{"title":"Engineering thermotolerant microbial strains via TrRCC1 overexpression for efficient bioethanol production","authors":"Tingting Chen, Xiao He, Xinyan Zhang, Tian Tian, Jian Cheng, Tingting Long, Yonghao Li","doi":"10.1016/j.engmic.2025.100212","DOIUrl":"10.1016/j.engmic.2025.100212","url":null,"abstract":"<div><div>Efficient conversion of corn stover to bioethanol via simultaneous saccharification and fermentation (SSF) is a promising strategy for sustainable biofuel production. A major current barrier to this process is the limited thermotolerance of <em>Saccharomyces cerevisiae</em>, which hampers its performance under the high-temperature conditions required for efficient SSF. In this study, we identified <em>TrRCC1</em>, a gene from <em>Trichoderma reesei</em>, as a candidate for improving microbial stress resistance. Overexpression of <em>TrRCC1</em> in both <em>T. reesei</em> Rut C30 and <em>S. cerevisiae</em> BY4741 significantly enhanced thermotolerance. In <em>T. reesei</em> Rut C30, <em>TrRCC1</em> overexpression improved heat resistance and increased cellulase production by 2.5-fold compared to the wild-type strain. In <em>S. cerevisiae</em> BY4741, <em>TrRCC1</em> overexpression resulted in enhanced thermotolerance and a 21.8 % increase in ethanol production during SSF of corn stover. The ethanol concentration achieved in the SSF process with <em>TrRCC1</em>-overexpressing <em>S. cerevisiae</em> was 44.1 g/L, which was a notable improvement over control strain production. These findings highlight the potential of <em>TrRCC1</em> as a key gene for engineering microbial strains with improved stress resistance to enhance the efficiency of bioethanol production from lignocellulosic biomass.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 2","pages":"Article 100212"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144230932","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

Functional heterologous expression of the reversible Cu-decarboxylase from the lichen, Cladonia uncialis 地衣中可逆cu脱羧酶的功能异源表达

Engineering Microbiology Pub Date : 2025-06-01 DOI: 10.1016/j.engmic.2025.100211

Harman Gill, John L. Sorensen

{"title":"Functional heterologous expression of the reversible Cu-decarboxylase from the lichen, Cladonia uncialis","authors":"Harman Gill, John L. Sorensen","doi":"10.1016/j.engmic.2025.100211","DOIUrl":"10.1016/j.engmic.2025.100211","url":null,"abstract":"<div><div>Despite the isolation of over 1000 known bioactive lichen mycobiont-derived secondary metabolites (SMs), understanding the genetic basis of their biosynthesis remains elusive. Biosynthetic gene clusters (BGCs) have been tentatively linked to chemical structures, with core genes such as polyketide synthases (PKSs) surrounded by accessory genes like decarboxylases. In this study, we focused on a decarboxylase gene from the genome of the lichen <em>cladonia uncialis</em> (named as <em>Cu</em>-decarboxylase) to elucidate its role in SM biosynthesis. A 963 bp gene was cloned from <em>C. uncialis</em> and expressed in <em>Escherichia coli</em> (BL21(DE3) cells using the pQE80L expression vector. The resulting 35 kDa protein was purified by applying a Ni<sup>+</sup>-NTA column using an FPLC system. Functional activity assays revealed the decarboxylation and reversible carboxylation of resorcinol to 2,4-dihydroxybenzoic acid and orcinol to orsellinic acid. This suggests a potential role for this <em>Cu</em>-decarboxylase in SM biosynthesis.</div><div>Furthermore, the lack of activity on substrates like anthranilic acid and aniline highlighted the importance of the phenolic OH group in facilitating these reactions. The 3D protein structure was predicted with AlphaFold3, based on sequence similarity with a known decarboxylases and revealed the importance of a zinc cofactor for the catalytic activity of the enzyme. The optimization of the reaction conditions, particularly for orsellinic acid production from orcinol, may enhance conversion rates and offer a viable route for industrial-scale production of bioactive compounds. This study marks the first known instance of functional heterologous expression of a non-codon-optimized gene isolated from lichen in <em>E. coli</em>.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 2","pages":"Article 100211"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144230931","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

Superoxide-mediated O2 activation drives radical cyclization in ergot alkaloid biosynthesis 超氧化物介导的O2活化驱动麦角生物碱生物合成中的自由基环化

Engineering Microbiology Pub Date : 2025-06-01 DOI: 10.1016/j.engmic.2025.100207

Yuanyuan Jiang , Zhong Li , Shengying Li

引用次数: 0

The Kongming defense: Host-pathogen battles take a new face 孔明防御：宿主-病原体的战斗有了新的面貌

Engineering Microbiology Pub Date : 2025-06-01 DOI: 10.1016/j.engmic.2025.100209

Dongchun Ni

引用次数: 0

Cytochrome P450-catalyzed allylic oxidation of pentalenene to 1-deoxypentalenic acid in pentalenolactone biosynthesis 五烯内酯生物合成中细胞色素p450催化烯丙基氧化五烯烯生成1-脱氧五烯酸

Engineering Microbiology Pub Date : 2025-06-01 DOI: 10.1016/j.engmic.2025.100206

Jing Li , Chengde Zhang , Shiwen Wu , Jiao Xue , Ke Chen , Zixin Deng , Dongqing Zhu

引用次数: 0

Production of dicarboxylates from ω-amino acids using a cofactor- and co-substrate-free in vitro biosynthetic system 利用无辅助因子和无共底物的体外生物合成系统从ω-氨基酸生产二羧酸盐

Engineering Microbiology Pub Date : 2025-05-17 DOI: 10.1016/j.engmic.2025.100210

Jinxin Yan , Hui Zhang , Hongxu Zhang , Hairong Yu , Wenjia Tian , Mingyuan Liu , Weikang Sun , Leilei Guo , Xiaoxu Tan , Kaiyu Gao , Tianyi Jiang , Chuanjuan Lü , Qianjin Kang , Wensi Meng , Cuiqing Ma , Chao Gao , Ping Xu

{"title":"Production of dicarboxylates from ω-amino acids using a cofactor- and co-substrate-free in vitro biosynthetic system","authors":"Jinxin Yan , Hui Zhang , Hongxu Zhang , Hairong Yu , Wenjia Tian , Mingyuan Liu , Weikang Sun , Leilei Guo , Xiaoxu Tan , Kaiyu Gao , Tianyi Jiang , Chuanjuan Lü , Qianjin Kang , Wensi Meng , Cuiqing Ma , Chao Gao , Ping Xu","doi":"10.1016/j.engmic.2025.100210","DOIUrl":"10.1016/j.engmic.2025.100210","url":null,"abstract":"<div><div>Dicarboxylates are valuable platform compounds with a broad range of applications. The <em>in vitro</em> biosynthetic system used to produce dicarboxylates from ω-amino acids via the natural pathway requires costly cofactors and co-substrates, which restricts its economic feasibility of use. In this study, we designed a cofactor- and co-substrate-free artificial pathway for the production of dicarboxylates from ω-amino acids. Only three enzymes (viz., amine oxidase from <em>Kluyveromyces marxianus</em> DMKU3-1042, xanthine oxidase from bovine milk, and catalase from <em>Aspergillus niger</em>) were required for dicarboxylate production. Succinate (0.79 g g<sup>-1</sup>), glutarate (0.83 g g<sup>-1</sup>), and adipate (0.77 g g<sup>-1</sup>) were produced in high yields from the corresponding ω-amino acids through the <em>in vitro</em> biosynthetic system with the artificial pathway. Glutarate could also be produced from <span>l</span>-lysine by further introducing <span>l</span>-lysine monooxygenase and 5-aminovaleramide amidohydrolase from <em>Pseudomonas putida</em> KT2440 into the <em>in vitro</em> biosynthetic system, with the cofactor- and co-substrate-free system achieving a product yield of 0.63 g g<sup>-1</sup>. Considering its desirable characteristics, this artificial pathway-based <em>in vitro</em> biosynthetic system may be a promising alternative for dicarboxylate production from biotechnologically produced ω-amino acids.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 3","pages":"Article 100210"},"PeriodicalIF":0.0,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144272099","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

Analysis of single-cell RNA sequencing data to examine the gastric inflammation-to-cancer transition and evaluation of the effect of probiotic on precancerous lesions 单细胞RNA测序数据分析胃炎症-癌转化及益生菌对癌前病变影响的评价

Engineering Microbiology Pub Date : 2025-05-09 DOI: 10.1016/j.engmic.2025.100208

Minmin Hu , Shiyang Xu , Ruofei Xu , Xiangjie Qi , Xiaofeng Yu , Jinqi Wang , Yige Li , Yangyang Liu , Guiran Xi , Junbao Yu , Mei Shi

{"title":"Analysis of single-cell RNA sequencing data to examine the gastric inflammation-to-cancer transition and evaluation of the effect of probiotic on precancerous lesions","authors":"Minmin Hu , Shiyang Xu , Ruofei Xu , Xiangjie Qi , Xiaofeng Yu , Jinqi Wang , Yige Li , Yangyang Liu , Guiran Xi , Junbao Yu , Mei Shi","doi":"10.1016/j.engmic.2025.100208","DOIUrl":"10.1016/j.engmic.2025.100208","url":null,"abstract":"<div><div>Gastric cancer (GC) is the fifth most prevalent malignancy globally. However, its heterogeneity and asymptomatic early-stage development hinder timely diagnosis and effective treatment. Here, we employed single-cell RNA sequencing to delineate the transitional features of pit mucous cells (PMCs) during the gastritis-to-cancer transition and identified 100 core genes. Characterization of the gene set revealed the role of ribosomal protein small subunit and ribosomal protein large subunit in inflammation-to-cancer transition, which promoted ribonucleoprotein complex biogenesis and cytoplasmic translation. External validation using independent cohorts confirmed that this core gene set discriminated disease progression (AUC > 0.7) and was significantly enriched in GC tissues (<em>p</em> < 0.01). Moreover, we evaluated the therapeutic intervention effects of <em>C. butyricum</em> and synbiotics (Weichanghao®) using a rat model of gastritis and demonstrated the targeted suppression of inflammation-to-cancer transition genes. Our findings establish the basis for early diagnosis of GC through PMC-driven molecular dynamics. Additionally, we propose microbiota-based strategies to prevent the inflammation-to-cancer transition in preneoplastic stages. Furthermore, our results highlight that dysbiosis of the gastric microbiome can be addressed using probiotic supplementations and the core gene set may provide labeling for the evaluation of probiotics-based treatment.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 3","pages":"Article 100208"},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144205430","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 synthetic microbial ecosystems approach for studying ecological interactions and their influencing factors 合成微生物生态系统方法研究生态相互作用及其影响因素的进展

Engineering Microbiology Pub Date : 2025-03-26 DOI: 10.1016/j.engmic.2025.100205

Wei Jiang , Sumeng Wang , Fei Gu , Xiaoya Yang , Qingsheng Qi , Quanfeng Liang

{"title":"Advances in synthetic microbial ecosystems approach for studying ecological interactions and their influencing factors","authors":"Wei Jiang , Sumeng Wang , Fei Gu , Xiaoya Yang , Qingsheng Qi , Quanfeng Liang","doi":"10.1016/j.engmic.2025.100205","DOIUrl":"10.1016/j.engmic.2025.100205","url":null,"abstract":"<div><div>Investigating ecological interactions within microbial ecosystems is essential for enhancing our comprehension of key ecological issues, such as community stability, keystone species identification, and the manipulation of community structures. However, exploring these interactions proves challenging within complex natural ecosystems. With advances in synthetic biology, the design of synthetic microbial ecosystems has received increasing attention due to their reduced complexity and enhanced controllability. Various ecological relationships, including commensalism, amensalism, mutualism, competition, and predation have been established within synthetic ecosystems. These relationships are often context-dependent and shaped by physical and chemical environmental factors, as well as by interacting populations and surrounding species. This review consolidates current knowledge of synthetic microbial ecosystems and factors influencing their ecological dynamics. A deeper understanding of how these ecosystems function and respond to different variables will advance our understanding of microbial-community interactions.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 2","pages":"Article 100205"},"PeriodicalIF":0.0,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143881878","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

Optimizing the CRISPR/Cas9 system for gene editing in Yarrowia lipolytica 脂溶耶氏菌基因编辑CRISPR/Cas9系统的优化

Engineering Microbiology Pub Date : 2025-03-18 DOI: 10.1016/j.engmic.2025.100193

Jianhui Liu , Yamin Zhu , Jin Hou

{"title":"Optimizing the CRISPR/Cas9 system for gene editing in Yarrowia lipolytica","authors":"Jianhui Liu , Yamin Zhu , Jin Hou","doi":"10.1016/j.engmic.2025.100193","DOIUrl":"10.1016/j.engmic.2025.100193","url":null,"abstract":"<div><div><em>Yarrowia lipolytica</em> is a promising host for producing valuable chemicals owing to its robustness and metabolic versatility. Efficient genome editing tools are essential for advancing its biotechnological applications. Although CRISPR/Cas9 technology has been applied in <em>Y. lipolytica</em>, achieving a consistently high editing performance remains challenging owing to the low homologous recombination efficiency and variability in system components. In this study, we optimized CRISPR/Cas9-mediated genome editing in <em>Y. lipolytica</em> to enhance its editing efficiency. Using the RNA polymerase III promoter <em>SCR1-tRNA</em> for sgRNA expression, we achieved a gene disruption efficiency of 92.5 %. The tRNA-sgRNA architecture enabled a dual gene disruption efficiency of 57.5 %. <em>KU70</em> deletion in the Cas9 system increased the integration efficiency to 92.5 %, and <em>Rad52</em> and <em>Sae2</em> overexpression boosted homologous recombination. The introduction of Cas9<sup>D147Y, P411T</sup> (iCas9) enhanced the efficiency of both gene disruption and genome integration. This study provides a powerful tool for efficient gene editing in <em>Y. lipolytica</em>, which will accelerate the construction of yeast cell factories.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 2","pages":"Article 100193"},"PeriodicalIF":0.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143643980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Carbon sequestration pathways in microorganisms: Advances, strategies, and applications 微生物中的碳固存途径：进展、策略和应用

Engineering Microbiology Pub Date : 2025-03-08 DOI: 10.1016/j.engmic.2025.100196

Shupeng Ruan , Yuchen Jiang , Aoxue Wang , Xinying Zhang , Ying Lin , Shuli Liang

{"title":"Carbon sequestration pathways in microorganisms: Advances, strategies, and applications","authors":"Shupeng Ruan , Yuchen Jiang , Aoxue Wang , Xinying Zhang , Ying Lin , Shuli Liang","doi":"10.1016/j.engmic.2025.100196","DOIUrl":"10.1016/j.engmic.2025.100196","url":null,"abstract":"<div><div>In recent years, industrial activities have significantly increased atmospheric CO<sub>2</sub> levels, exacerbating global warming. Carbon reduction involves implementing measures to minimize CO<sub>2</sub> emissions from human activities and achieve a balance between carbon absorption and emissions. Therefore, effective reduction of CO<sub>2</sub> emissions is crucial. Conventional physical and chemical methods for CO₂ fixation frequently cause secondary environmental pollution. As a result, utilizing microorganisms for CO<sub>2</sub> fixation has gained considerable interest. This review provides an overview of the natural pathways for microbial CO<sub>2</sub> fixation, recent advancements in artificial CO<sub>2</sub> fixation, and strategies for enhancing the efficiency of microbial CO<sub>2</sub> fixation. We also discuss the conversion of CO<sub>2</sub> into diverse metabolic products and high-value chemicals. By identifying efficient carbon fixation pathways for microorganisms, this review aims to lay the foundation for the biological production of high-value chemicals using CO<sub>2</sub> as a raw material.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 2","pages":"Article 100196"},"PeriodicalIF":0.0,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143642867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0