Engineering Microbiology最新文献

Optimizing the CRISPR/Cas9 system for gene editing in Yarrowia lipolytica

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

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

Modification of essential factors mediating post-translational processing for high-quality protein expression in Penicillium

Engineering Microbiology Pub Date : 2025-03-01 DOI: 10.1016/j.engmic.2025.100194

Demin Guo , Shengfang Zhao , Jie Chen, Shuhui Han, Yangtao Li, Yu Chen, Shengbiao Hu, Yibo Hu

{"title":"Modification of essential factors mediating post-translational processing for high-quality protein expression in Penicillium","authors":"Demin Guo , Shengfang Zhao , Jie Chen, Shuhui Han, Yangtao Li, Yu Chen, Shengbiao Hu, Yibo Hu","doi":"10.1016/j.engmic.2025.100194","DOIUrl":"10.1016/j.engmic.2025.100194","url":null,"abstract":"<div><div>The formation of mature proteins requires complex post-translational modification and processing. Efficient post-translational processing machinery is beneficial for the high-quality expression of proteins. To comprehensively evaluate the role of post-translational mediating factors (PTMFs) in protein synthesis, two reporter strains expressing a homologous protein, Amy15A, and a heterologous protein, TaEG, were constructed in <em>Penicillium oxalicum</em>. Three PTMFs including a conserved basic leucine zipper transcription factor, HacA; an endoplasmic reticulum chaperone-binding protein, BipA; and a protein disulfide isomerase, PdiA, were individually overexpressed in the both reporter strains. The findings showed that overexpression of these PTMFs enhanced the enzymatic activity of both homologous and heterologous proteins. However, sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis revealed that, upon overexpression of the PTMFs, heterologous protein secretion remained stable or slightly increased, whereas that of homologous proteins remained unchanged or decreased. Neither the vegetative growth rate nor reporter transcription levels accounted for these variations in protein production or enzymatic activity. Conclusively, this study suggests that PTMFs play a positive role in protein expression and can be leveraged to optimize filamentous fungal chassis cells in the future.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 1","pages":"Article 100194"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143610266","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

Erratum to “In vitro characterization of a nitro-forming oxygenase involved in 3-(trans-2’-aminocyclopropyl)alanine biosynthesis” [Engineering Microbiology 2 (2022) 100007]

Engineering Microbiology Pub Date : 2025-03-01 DOI: 10.1016/j.engmic.2025.100195

Linlin Pang , Weijing Niu , Yuwei Duan , Liujie Huo , Aiying Li , Jiequn Wu , Youming Zhang , Xiaoying Bian , Guannan Zhong

引用次数: 0

Establishment and improvement of genetic manipulation tools for Fusobacterium nucleatum

Engineering Microbiology Pub Date : 2025-02-08 DOI: 10.1016/j.engmic.2025.100192

Zhiwei Guan , Hailong Wang , Qiang Feng

{"title":"Establishment and improvement of genetic manipulation tools for Fusobacterium nucleatum","authors":"Zhiwei Guan , Hailong Wang , Qiang Feng","doi":"10.1016/j.engmic.2025.100192","DOIUrl":"10.1016/j.engmic.2025.100192","url":null,"abstract":"<div><div>An imbalance in oral microbial homeostasis is significantly associated with the onset and progression of several systemic diseases. <em>Fusobacterium nucleatum</em>, a ubiquitous periodontitis-causing bacterium in the oral cavity, is frequently detected in focal sites and contributes to the pathogenesis of many extraoral diseases, including cancers, cardiovascular diseases, and adverse pregnancy outcomes (APOs). <em>F. nucleatum</em> is one of the few oral anaerobes that can be cultured purely <em>in vitro</em> and is a ‘model species’ for studying the impact of oral health on systemic health. The establishment and development of genetic manipulation tools for <em>F. nucleatum</em> and the construction of pathogenic gene-disrupted strains are important strategies for studying the pathogenicity of <em>F. nucleatum</em>. Here, we review the establishment and development of the genetic manipulation systems for <em>F. nucleatum</em> and summarize the characteristics of various genetic manipulation tools, such as suicide plasmid-based systems for gene inactivation, replicable plasmid-based systems controlling gene expression, and transposon-based random mutagenesis systems. Notably, we summarize and analyze their applications in the study of the pathogenic mechanisms of <em>F. nucleatum</em>. We hope to provide reference information and ideas for future research on genetic manipulation tools and the pathogenic mechanisms of <em>F. nucleatum</em> and other <em>Fusobacterium</em> species.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 1","pages":"Article 100192"},"PeriodicalIF":0.0,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143421876","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

The gut virome and human health: From diversity to personalized medicine

Engineering Microbiology Pub Date : 2025-02-07 DOI: 10.1016/j.engmic.2025.100191

Rahul Harikumar Lathakumari, Leela Kakithakara Vajravelu, Anusha Gopinathan, Poornima Baskar Vimala, Vishnupriya Panneerselvam, Sujith Sri Surya Ravi, Jayaprakash Thulukanam

{"title":"The gut virome and human health: From diversity to personalized medicine","authors":"Rahul Harikumar Lathakumari, Leela Kakithakara Vajravelu, Anusha Gopinathan, Poornima Baskar Vimala, Vishnupriya Panneerselvam, Sujith Sri Surya Ravi, Jayaprakash Thulukanam","doi":"10.1016/j.engmic.2025.100191","DOIUrl":"10.1016/j.engmic.2025.100191","url":null,"abstract":"<div><div>The human gut virome plays a crucial role in the gut and overall health; its diversity and regulatory functions influence bacterial populations, metabolism, and immune responses. Bacteriophages (phages) and eukaryotic viruses within the gut microbiome contribute to these processes, and recent advancements in sequencing technologies and bioinformatics have greatly expanded our understanding of the gut virome. These advances have led to the development of phage-based therapeutics, diagnostics, and artificial intelligence-driven precision medicine. The emerging field of phageomics shows promise for delivering personalized phage therapies that combat antimicrobial resistance by specifically targeting pathogenic bacteria while preserving beneficial microbes. Moreover, CRISPR-Cas systems delivered via phages have shown success in selectively targeting antibiotic resistance genes and enhancing treatment effectiveness. Phage-based diagnostics are highly sensitive in detecting bacterial pathogens, offering significant benefits for human health and zoonotic disease surveillance. This synthesis of the current knowledge highlights the pivotal role of the gut virome in regulating microbial communities and its transformative potential in personalized medicine, emphasizing its importance in advancing therapeutic and diagnostic strategies for improving health outcomes.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 1","pages":"Article 100191"},"PeriodicalIF":0.0,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143427563","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

Activating cryptic biosynthetic gene clusters via ACTIMOT

Engineering Microbiology Pub Date : 2025-01-24 DOI: 10.1016/j.engmic.2025.100190

Xiaoying Bian

引用次数: 0

Applications of bacteriophages in precision engineering of the human gut microbiome

Engineering Microbiology Pub Date : 2025-01-06 DOI: 10.1016/j.engmic.2025.100189

Xiaoxian Kuang , Juntao Shen , Linggang Zheng , Yi Duan , Yingfei Ma , Elaine Lai-Han Leung , Lei Dai

引用次数: 0

Engineering Microbiology Pub Date : 2025-01-01 DOI: 10.1016/j.engmic.2024.100188

Zhiwei Deng, Zhenbo Yuan, Zhengshan Luo, Yijian Rao

引用次数: 0

Complexity of antibiotic resistance and its impact on gut microbiota dynamics

Engineering Microbiology Pub Date : 2024-12-30 DOI: 10.1016/j.engmic.2024.100187

H. Shayista , M.N. Nagendra Prasad , S. Niranjan Raj , Ashwini Prasad , S. Lakshmi , H.K. Ranjini , K. Manju , Ravikumara , Raghuraj Singh Chouhan , Olga Y. Khohlova , Olga V. Perianova , Syed Baker

{"title":"Complexity of antibiotic resistance and its impact on gut microbiota dynamics","authors":"H. Shayista , M.N. Nagendra Prasad , S. Niranjan Raj , Ashwini Prasad , S. Lakshmi , H.K. Ranjini , K. Manju , Ravikumara , Raghuraj Singh Chouhan , Olga Y. Khohlova , Olga V. Perianova , Syed Baker","doi":"10.1016/j.engmic.2024.100187","DOIUrl":"10.1016/j.engmic.2024.100187","url":null,"abstract":"<div><div>The present review explores the influence of the gut microbiota on antibiotic resistance dynamics, particularly those associated with dysbiosis. The improper use of antibiotics can induce resistance in pathogens through various pathways, which is a topic of increasing interest within the scientific community. This review highlights the importance of microbial diversity, gut metabolism, and inflammatory responses against the dysbiosis due to the action of antibiotics. Additionally, it examines how secondary metabolites secreted by pathogens can serve as biomarkers for the early detection of antibiotic resistance. Although significant progress has been made in this field, key research gaps persist, including the need for a deeper understanding of the long-term effects of antibiotic-induced dysbiosis and the specific mechanisms driving the evolution of resistance in gut bacteria. Based on these considerations, this review systematically analyzed studies from PubMed, Web of Science, Embase, Cochrane Library, and Scopus up to July 2024. This study aimed to explore the dynamics of the interactions between gut microbiota and antibiotic resistance, specifically examining how microbial composition influences the development of resistance mechanisms. By elucidating these relationships, this review provides insights into management strategies for drug resistance and improves our understanding of microbial contributions to host health.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 1","pages":"Article 100187"},"PeriodicalIF":0.0,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143099238","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