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Permeabilisation of the Outer Membrane of Escherichia coli for Enhanced Transport of Complex Molecules 大肠杆菌外膜的通透性增强了复杂分子的运输
IF 5.7 2区 生物学
Microbial Biotechnology Pub Date : 2025-03-09 DOI: 10.1111/1751-7915.70122
Ivan Casas-Rodrigo, Tobias Vornholt, Kathrin Castiglione, Tania Michelle Roberts, Markus Jeschek, Thomas R. Ward, Sven Panke
{"title":"Permeabilisation of the Outer Membrane of Escherichia coli for Enhanced Transport of Complex Molecules","authors":"Ivan Casas-Rodrigo,&nbsp;Tobias Vornholt,&nbsp;Kathrin Castiglione,&nbsp;Tania Michelle Roberts,&nbsp;Markus Jeschek,&nbsp;Thomas R. Ward,&nbsp;Sven Panke","doi":"10.1111/1751-7915.70122","DOIUrl":"https://doi.org/10.1111/1751-7915.70122","url":null,"abstract":"<p>The bacterial envelope plays a critical role in maintaining essential cellular functions by selectively regulating import and export. The selectivity of this envelope can restrict the utilisation of externally provided compounds, thereby restricting the functional space of cellular engineering. This study systematically investigates the potential of large pore outer membrane proteins (OMPs) to enhance outer membrane permeability for diverse challenging compounds. We focus on the general porin OmpF, which facilitates the diffusion of water and small molecules, and specific OMP transporters FhuA and FepA, which mediate the translocation of small hydrophilic compounds. Through comprehensive characterisation, we evaluate the effects of recombinant expression of OMPs and engineered variants for small and hydrophilic compounds, aromatic molecules and bulky molecules and apply our findings to address two critical contemporary transport challenges: the uptake of large metal-containing cofactors for artificial metalloenzymes and non-permeant fluorescent Halo-ligands for in vivo protein labelling. Notably, we demonstrate significant improvements in ArM-catalysis and labelling. This study provides a practical guide for designing experiments that include outer-membrane-transport-limiting steps. This study highlights the potential of engineered OMPs to overcome the limitations imposed by the cell envelope, enabling the incorporation of complex molecules and expanding the frontiers of cellular engineering.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70122","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143581580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Permeabilisation of the Outer Membrane of Escherichia coli for Enhanced Transport of Complex Molecules 大肠杆菌外膜的通透性增强了复杂分子的运输
IF 5.7 2区 生物学
Microbial Biotechnology Pub Date : 2025-03-09 DOI: 10.1111/1751-7915.70122
Ivan Casas-Rodrigo, Tobias Vornholt, Kathrin Castiglione, Tania Michelle Roberts, Markus Jeschek, Thomas R. Ward, Sven Panke
{"title":"Permeabilisation of the Outer Membrane of Escherichia coli for Enhanced Transport of Complex Molecules","authors":"Ivan Casas-Rodrigo,&nbsp;Tobias Vornholt,&nbsp;Kathrin Castiglione,&nbsp;Tania Michelle Roberts,&nbsp;Markus Jeschek,&nbsp;Thomas R. Ward,&nbsp;Sven Panke","doi":"10.1111/1751-7915.70122","DOIUrl":"https://doi.org/10.1111/1751-7915.70122","url":null,"abstract":"<p>The bacterial envelope plays a critical role in maintaining essential cellular functions by selectively regulating import and export. The selectivity of this envelope can restrict the utilisation of externally provided compounds, thereby restricting the functional space of cellular engineering. This study systematically investigates the potential of large pore outer membrane proteins (OMPs) to enhance outer membrane permeability for diverse challenging compounds. We focus on the general porin OmpF, which facilitates the diffusion of water and small molecules, and specific OMP transporters FhuA and FepA, which mediate the translocation of small hydrophilic compounds. Through comprehensive characterisation, we evaluate the effects of recombinant expression of OMPs and engineered variants for small and hydrophilic compounds, aromatic molecules and bulky molecules and apply our findings to address two critical contemporary transport challenges: the uptake of large metal-containing cofactors for artificial metalloenzymes and non-permeant fluorescent Halo-ligands for in vivo protein labelling. Notably, we demonstrate significant improvements in ArM-catalysis and labelling. This study provides a practical guide for designing experiments that include outer-membrane-transport-limiting steps. This study highlights the potential of engineered OMPs to overcome the limitations imposed by the cell envelope, enabling the incorporation of complex molecules and expanding the frontiers of cellular engineering.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70122","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143581508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Characterisation of the Self-Sufficient Cytochrome P450 CYP116B234 From Rhodococcus globerulus and Its Suggested Native Role in 2-Hydroxyphenylacetic Acid Metabolism 球状红球菌自给细胞色素P450 CYP116B234的特性及其在2-羟基苯乙酸代谢中的天然作用
IF 5.7 2区 生物学
Microbial Biotechnology Pub Date : 2025-03-08 DOI: 10.1111/1751-7915.70125
Simran Kundral, Hannah Beamish, Peter D. Giang, Lauren J. Salisbury, Amanda S. Nouwens, Sunil K. Khare, Paul V. Bernhardt, Jeffrey R. Harmer, Stephen G. Bell, James J. De Voss
{"title":"Characterisation of the Self-Sufficient Cytochrome P450 CYP116B234 From Rhodococcus globerulus and Its Suggested Native Role in 2-Hydroxyphenylacetic Acid Metabolism","authors":"Simran Kundral,&nbsp;Hannah Beamish,&nbsp;Peter D. Giang,&nbsp;Lauren J. Salisbury,&nbsp;Amanda S. Nouwens,&nbsp;Sunil K. Khare,&nbsp;Paul V. Bernhardt,&nbsp;Jeffrey R. Harmer,&nbsp;Stephen G. Bell,&nbsp;James J. De Voss","doi":"10.1111/1751-7915.70125","DOIUrl":"https://doi.org/10.1111/1751-7915.70125","url":null,"abstract":"<p>Cytochromes P450 (P450s) are exceptional biocatalysts that enable the selective oxidation of unactivated C–H bonds using molecular oxygen. Typically, auxiliary redox partner proteins deliver electrons from NAD(P)H to the P450, enabling oxygen activation. However, associating native redox partners with P450s can be challenging, particularly when they are genomically separated. Self-sufficient P450s, where the P450 heme domain is naturally fused to redox partners, represent a simpler, single-protein system. Here, we present CYP116B234, a novel self-sufficient P450 from <i>Rhodococcus globerulus</i>, comprising fused heme and phthalate-family oxygenase reductase (PFOR) domains. The gene encoding CYP116B234 was codon-optimised for heterologous expression in <i>E. coli</i> and subsequently purified to homogeneity. Spectroelectrochemical analysis and electron paramagnetic resonance spectroscopy were performed to determine the redox potentials of the heme and associated Fe–S and FMN cofactors of the PFOR domain. CYP116B234 binds and efficiently oxidises the substituted aromatic compound 2-hydroxyphenylacetic acid (2-HPA) to homogentisic acid. Quantitative proteomics revealed the expression of CYP116B234 in <i>R. globerulus</i> grown on 2-HPA, suggesting a role in initiating 2-HPA degradation. This study presents a new addition to the self-sufficient CYP116 family and provides evidence for their native function.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70125","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Characterisation of the Self-Sufficient Cytochrome P450 CYP116B234 From Rhodococcus globerulus and Its Suggested Native Role in 2-Hydroxyphenylacetic Acid Metabolism 球状红球菌自给细胞色素P450 CYP116B234的特性及其在2-羟基苯乙酸代谢中的天然作用
IF 5.7 2区 生物学
Microbial Biotechnology Pub Date : 2025-03-08 DOI: 10.1111/1751-7915.70125
Simran Kundral, Hannah Beamish, Peter D. Giang, Lauren J. Salisbury, Amanda S. Nouwens, Sunil K. Khare, Paul V. Bernhardt, Jeffrey R. Harmer, Stephen G. Bell, James J. De Voss
{"title":"Characterisation of the Self-Sufficient Cytochrome P450 CYP116B234 From Rhodococcus globerulus and Its Suggested Native Role in 2-Hydroxyphenylacetic Acid Metabolism","authors":"Simran Kundral,&nbsp;Hannah Beamish,&nbsp;Peter D. Giang,&nbsp;Lauren J. Salisbury,&nbsp;Amanda S. Nouwens,&nbsp;Sunil K. Khare,&nbsp;Paul V. Bernhardt,&nbsp;Jeffrey R. Harmer,&nbsp;Stephen G. Bell,&nbsp;James J. De Voss","doi":"10.1111/1751-7915.70125","DOIUrl":"https://doi.org/10.1111/1751-7915.70125","url":null,"abstract":"<p>Cytochromes P450 (P450s) are exceptional biocatalysts that enable the selective oxidation of unactivated C–H bonds using molecular oxygen. Typically, auxiliary redox partner proteins deliver electrons from NAD(P)H to the P450, enabling oxygen activation. However, associating native redox partners with P450s can be challenging, particularly when they are genomically separated. Self-sufficient P450s, where the P450 heme domain is naturally fused to redox partners, represent a simpler, single-protein system. Here, we present CYP116B234, a novel self-sufficient P450 from <i>Rhodococcus globerulus</i>, comprising fused heme and phthalate-family oxygenase reductase (PFOR) domains. The gene encoding CYP116B234 was codon-optimised for heterologous expression in <i>E. coli</i> and subsequently purified to homogeneity. Spectroelectrochemical analysis and electron paramagnetic resonance spectroscopy were performed to determine the redox potentials of the heme and associated Fe–S and FMN cofactors of the PFOR domain. CYP116B234 binds and efficiently oxidises the substituted aromatic compound 2-hydroxyphenylacetic acid (2-HPA) to homogentisic acid. Quantitative proteomics revealed the expression of CYP116B234 in <i>R. globerulus</i> grown on 2-HPA, suggesting a role in initiating 2-HPA degradation. This study presents a new addition to the self-sufficient CYP116 family and provides evidence for their native function.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70125","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Deep-Learning-Based Approaches for Rational Design of Stapled Peptides With High Antimicrobial Activity and Stability 基于深度学习的高效抗菌肽合理设计方法
IF 5.7 2区 生物学
Microbial Biotechnology Pub Date : 2025-03-05 DOI: 10.1111/1751-7915.70121
Ruole Chen, Yuhao You, Yanchao Liu, Xin Sun, Tianyue Ma, Xingzhen Lao, Heng Zheng
{"title":"Deep-Learning-Based Approaches for Rational Design of Stapled Peptides With High Antimicrobial Activity and Stability","authors":"Ruole Chen,&nbsp;Yuhao You,&nbsp;Yanchao Liu,&nbsp;Xin Sun,&nbsp;Tianyue Ma,&nbsp;Xingzhen Lao,&nbsp;Heng Zheng","doi":"10.1111/1751-7915.70121","DOIUrl":"https://doi.org/10.1111/1751-7915.70121","url":null,"abstract":"<p>Antimicrobial peptides (AMPs) face stability and toxicity challenges in clinical use. Stapled modification enhances their stability and effectiveness, but its application in peptide design is rarely reported. This study built ten prediction models for stapled AMPs using deep and machine learning, tested their accuracy with an independent data set and wet lab experiments, and characterised stapled loop structures using structural, sequence and amino acid descriptors. AlphaFold improved stapled peptide structure prediction. The support vector machine model performed best, while two deep learning models achieved the highest accuracy of 1.0 on an external test set. Designed cysteine- and lysine-stapled peptides inhibited various bacteria with low concentrations and showed good serum stability and low haemolytic activity. This study highlights the potential of the deep learning method in peptide modification and design.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70121","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143554623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Engineering Genome-Free Bacterial Cells for Effective SARS-COV-2 Neutralisation 有效中和SARS-COV-2的工程无基因组细菌细胞
IF 5.7 2区 生物学
Microbial Biotechnology Pub Date : 2025-03-05 DOI: 10.1111/1751-7915.70109
Yutong Yin, Chang Liu, Xianglin Ji, Yun Wang, Juthathip Mongkolsapaya, Gavin R. Screaton, Zhanfeng Cui, Wei E. Huang
{"title":"Engineering Genome-Free Bacterial Cells for Effective SARS-COV-2 Neutralisation","authors":"Yutong Yin,&nbsp;Chang Liu,&nbsp;Xianglin Ji,&nbsp;Yun Wang,&nbsp;Juthathip Mongkolsapaya,&nbsp;Gavin R. Screaton,&nbsp;Zhanfeng Cui,&nbsp;Wei E. Huang","doi":"10.1111/1751-7915.70109","DOIUrl":"https://doi.org/10.1111/1751-7915.70109","url":null,"abstract":"<p>The COVID-19 pandemic has caused unparalleled impacts on global social dynamics, healthcare systems and economies, highlighting the urgent need for effective interventions to address current challenges and future pandemic preparedness. This study introduces a novel virus neutralisation platform based on SimCells (~1 μm) and mini-SimCells (100–200 nm), which are chromosome-free and non-replicating bacteria from an LPS-free <i>Escherichia coli</i> strain (ClearColi). SimCells and mini-SimCells were engineered to display nanobodies on their surface, specifically targeting the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein – a critical immunogenic fragment essential for viral entry into host cells. It was demonstrated that nanobody-expressing SimCells achieved over 90% blocking efficiency against synthesised RBD from both the original Wuhan and the B.1.351 (Beta) variant using competitive enzyme-linked immunosorbent assay (ELISA) assay. More importantly, live virus neutralisation assays demonstrated that NB6 nanobody-presenting mini-SimCells effectively neutralised the live SARS-CoV-2 Victoria variant with an IC50 of 2.95 × 10<sup>9</sup> ± 1.40 × 10<sup>8</sup> mini-SimCells/mL. Similarly, VE nanobody-presenting mini-SimCells effectively neutralised the B.1.351 (Beta) variant of the SARS-CoV-2 virus with an IC50 of 5.68 × 10<sup>9</sup> ± 9.94 × 10<sup>8</sup> mini-SimCells/mL. The mini-SimCells successfully protected Vero cells, a cell line derived from the kidney of an African green monkey, from infection by the live virus of SARS-CoV-2 and its variants. These results suggest that SimCell-based neutralisation offers a promising strategy for the prevention and treatment of SARS-CoV-2, and potentially other viral infections.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70109","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143554454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Deep-Learning-Based Approaches for Rational Design of Stapled Peptides With High Antimicrobial Activity and Stability 基于深度学习的高效抗菌肽合理设计方法
IF 5.7 2区 生物学
Microbial Biotechnology Pub Date : 2025-03-05 DOI: 10.1111/1751-7915.70121
Ruole Chen, Yuhao You, Yanchao Liu, Xin Sun, Tianyue Ma, Xingzhen Lao, Heng Zheng
{"title":"Deep-Learning-Based Approaches for Rational Design of Stapled Peptides With High Antimicrobial Activity and Stability","authors":"Ruole Chen,&nbsp;Yuhao You,&nbsp;Yanchao Liu,&nbsp;Xin Sun,&nbsp;Tianyue Ma,&nbsp;Xingzhen Lao,&nbsp;Heng Zheng","doi":"10.1111/1751-7915.70121","DOIUrl":"https://doi.org/10.1111/1751-7915.70121","url":null,"abstract":"<p>Antimicrobial peptides (AMPs) face stability and toxicity challenges in clinical use. Stapled modification enhances their stability and effectiveness, but its application in peptide design is rarely reported. This study built ten prediction models for stapled AMPs using deep and machine learning, tested their accuracy with an independent data set and wet lab experiments, and characterised stapled loop structures using structural, sequence and amino acid descriptors. AlphaFold improved stapled peptide structure prediction. The support vector machine model performed best, while two deep learning models achieved the highest accuracy of 1.0 on an external test set. Designed cysteine- and lysine-stapled peptides inhibited various bacteria with low concentrations and showed good serum stability and low haemolytic activity. This study highlights the potential of the deep learning method in peptide modification and design.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70121","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143554406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Engineering Genome-Free Bacterial Cells for Effective SARS-COV-2 Neutralisation 有效中和SARS-COV-2的工程无基因组细菌细胞
IF 5.7 2区 生物学
Microbial Biotechnology Pub Date : 2025-03-05 DOI: 10.1111/1751-7915.70109
Yutong Yin, Chang Liu, Xianglin Ji, Yun Wang, Juthathip Mongkolsapaya, Gavin R. Screaton, Zhanfeng Cui, Wei E. Huang
{"title":"Engineering Genome-Free Bacterial Cells for Effective SARS-COV-2 Neutralisation","authors":"Yutong Yin,&nbsp;Chang Liu,&nbsp;Xianglin Ji,&nbsp;Yun Wang,&nbsp;Juthathip Mongkolsapaya,&nbsp;Gavin R. Screaton,&nbsp;Zhanfeng Cui,&nbsp;Wei E. Huang","doi":"10.1111/1751-7915.70109","DOIUrl":"https://doi.org/10.1111/1751-7915.70109","url":null,"abstract":"<p>The COVID-19 pandemic has caused unparalleled impacts on global social dynamics, healthcare systems and economies, highlighting the urgent need for effective interventions to address current challenges and future pandemic preparedness. This study introduces a novel virus neutralisation platform based on SimCells (~1 μm) and mini-SimCells (100–200 nm), which are chromosome-free and non-replicating bacteria from an LPS-free <i>Escherichia coli</i> strain (ClearColi). SimCells and mini-SimCells were engineered to display nanobodies on their surface, specifically targeting the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein – a critical immunogenic fragment essential for viral entry into host cells. It was demonstrated that nanobody-expressing SimCells achieved over 90% blocking efficiency against synthesised RBD from both the original Wuhan and the B.1.351 (Beta) variant using competitive enzyme-linked immunosorbent assay (ELISA) assay. More importantly, live virus neutralisation assays demonstrated that NB6 nanobody-presenting mini-SimCells effectively neutralised the live SARS-CoV-2 Victoria variant with an IC50 of 2.95 × 10<sup>9</sup> ± 1.40 × 10<sup>8</sup> mini-SimCells/mL. Similarly, VE nanobody-presenting mini-SimCells effectively neutralised the B.1.351 (Beta) variant of the SARS-CoV-2 virus with an IC50 of 5.68 × 10<sup>9</sup> ± 9.94 × 10<sup>8</sup> mini-SimCells/mL. The mini-SimCells successfully protected Vero cells, a cell line derived from the kidney of an African green monkey, from infection by the live virus of SARS-CoV-2 and its variants. These results suggest that SimCell-based neutralisation offers a promising strategy for the prevention and treatment of SARS-CoV-2, and potentially other viral infections.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70109","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143554622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Enabling Access to Novel Bacterial Biosynthetic Potential From ONT Draft Genomic Data 从ONT基因组数据草案中获得新的细菌生物合成潜力
IF 5.7 2区 生物学
Microbial Biotechnology Pub Date : 2025-03-04 DOI: 10.1111/1751-7915.70104
Marco A. Campos-Magaña, Vitor A. P. Martins dos Santos, Luis Garcia-Morales
{"title":"Enabling Access to Novel Bacterial Biosynthetic Potential From ONT Draft Genomic Data","authors":"Marco A. Campos-Magaña,&nbsp;Vitor A. P. Martins dos Santos,&nbsp;Luis Garcia-Morales","doi":"10.1111/1751-7915.70104","DOIUrl":"https://doi.org/10.1111/1751-7915.70104","url":null,"abstract":"<p>Natural products comprise a wide diversity of compounds with a range of biological activities, including antibiotics, anti-inflammatory and anti-tumoral molecules. However, we can only access a small portion of these compounds due to various technical difficulties. We have herein developed a novel and efficient approach for accessing biosynthetic gene clusters (BGCs) that encode natural products from soil bacteria. The pipeline uses a combination of long-read sequencing, antiSMASH for BGC identification and Transformation-associated recombination (TAR) for cloning the BGCs. We hypothesized that a genome assembly using Oxford Nanopore Technology (ONT) sequencing could facilitate the detection of large BGCs at a relatively fast and low-cost DNA sequencing. Despite the relative low accuracy and sequence mistakes due to high GC content and sequence repetitions frequently found in BGC containing bacteria, we demonstrate that ONT long-read sequencing and antiSMASH are effective for identifying novel BGCs and enabling TAR cloning to isolate the BGC in a desired vector. We applied this pipeline on a previously non-sequenced myxobacteria <i>Aetherobacter fasciculatus</i> SBSr002. Our approach enabled us to clone a previously unknown BGC into a genome engineering-ready vector, illustrating the capabilities of this powerful and cost-effective strategy.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70104","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","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 Spread of the Mosquito-Transmitted West Nile Virus in North America and Europe 蚊子传播的西尼罗病毒在北美和欧洲的传播
IF 5.7 2区 生物学
Microbial Biotechnology Pub Date : 2025-03-04 DOI: 10.1111/1751-7915.70120
Harald Brüssow, Jordi Figuerola
{"title":"The Spread of the Mosquito-Transmitted West Nile Virus in North America and Europe","authors":"Harald Brüssow,&nbsp;Jordi Figuerola","doi":"10.1111/1751-7915.70120","DOIUrl":"https://doi.org/10.1111/1751-7915.70120","url":null,"abstract":"<p>West Nile virus (WNV) disease, a mosquito-transmitted Flavivirus infection, represents a substantial public health research interest. This virus was unknown in the Western hemisphere until it was introduced in 1999 into an immunologically naïve population. WNV caused an epizootic and epidemic in New York City. The infection then swept over North America, causing mass mortality in birds and cumulatively 60,000 human cases, half of whom were hospitalised, mostly with neurological symptoms. The virus closely resembled a goose virus isolated in Israel in 1998. Mosquitoes of the genus <i>Culex</i> were identified as the insect viral vectors. WNV can infect more than 300 bird species, but in the US, the American robin <i>(Turdus migratorius</i>) represented the ecologically most important bird viral reservoir. Mosquito-to-mosquito viral transmission might amplify the viral spread, and iatrogenic WNV transmission was also observed, leading to the screening of blood products. Compared with African WNV isolates, the New York WNV isolate NY99 showed a mutation in the nonstructural protein NS3 that increased its virulence in birds and was also observed in WNV outbreaks from Romania in 1996 and from Russia in 1999. During its spread across the US, NY99 acquired a mutation in the envelope gene E that favoured viral infection in the insect vector. Europe reported 1200 annual WNV cases in 2024, with a focus in Mediterranean countries, but a northward spread of the infection to Germany and The Netherlands was also noted. Global warming is likely to affect the geographical distribution of vector-borne infections such that people living in temperate climate areas might be increasingly exposed to these infections. Therefore, research on temperature effects on WNV transmission by <i>Culex</i> mosquitoes has become a recent focus of research. Pertinent climate aspects of WNV infections are retraced in the present review.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70120","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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