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Mutagenesis techniques for evolutionary engineering of microbes - exploiting CRISPR-Cas, oligonucleotides, recombinases, and polymerases. 微生物进化工程的突变技术--利用 CRISPR-Cas、寡核苷酸、重组酶和聚合酶。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-01 Epub Date: 2024-03-15 DOI: 10.1016/j.tim.2024.02.006
Anna Zimmermann, Julian E Prieto-Vivas, Karin Voordeckers, Changhao Bi, Kevin J Verstrepen
{"title":"Mutagenesis techniques for evolutionary engineering of microbes - exploiting CRISPR-Cas, oligonucleotides, recombinases, and polymerases.","authors":"Anna Zimmermann, Julian E Prieto-Vivas, Karin Voordeckers, Changhao Bi, Kevin J Verstrepen","doi":"10.1016/j.tim.2024.02.006","DOIUrl":"10.1016/j.tim.2024.02.006","url":null,"abstract":"<p><p>The natural process of evolutionary adaptation is often exploited as a powerful tool to obtain microbes with desirable traits. For industrial microbes, evolutionary engineering is often used to generate variants that show increased yields or resistance to stressful industrial environments, thus obtaining superior microbial cell factories. However, even in large populations, the natural supply of beneficial mutations is typically low, which implies that obtaining improved microbes is often time-consuming and inefficient. To overcome this limitation, different techniques have been developed that boost mutation rates. While some of these methods simply increase the overall mutation rate across a genome, others use recent developments in DNA synthesis, synthetic biology, and CRISPR-Cas techniques to control the type and location of mutations. This review summarizes the most important recent developments and methods in the field of evolutionary engineering in model microorganisms. It discusses how both in vitro and in vivo approaches can increase the genetic diversity of the host, with a special emphasis on in vivo techniques for the optimization of metabolic pathways for precision fermentation.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"884-901"},"PeriodicalIF":14.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140140787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Supramolecular assemblies in bacterial immunity: an emerging paradigm. 细菌免疫中的超分子组装：一种新兴范式。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-01 Epub Date: 2024-06-27 DOI: 10.1016/j.tim.2024.06.003
Leighton Payne, Simon Jackson, Rafael Pinilla-Redondo
{"title":"Supramolecular assemblies in bacterial immunity: an emerging paradigm.","authors":"Leighton Payne, Simon Jackson, Rafael Pinilla-Redondo","doi":"10.1016/j.tim.2024.06.003","DOIUrl":"10.1016/j.tim.2024.06.003","url":null,"abstract":"<p><p>The study of bacterial immune systems has recently gained momentum, revealing a fascinating trend: many systems form large supramolecular assemblies. Here, we examine the potential mechanisms underpinning the evolutionary success of these structures, draw parallels to eukaryotic immunity, and offer fresh perspectives to stimulate future research into bacterial immunity.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"828-831"},"PeriodicalIF":14.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141470971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Adaptive strategies and ecological roles of phages in habitats under physicochemical stress. 理化压力下生境中噬菌体的适应策略和生态作用。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-01 Epub Date: 2024-03-02 DOI: 10.1016/j.tim.2024.02.002
Dan Huang, Rong Xia, Chengyi Chen, Jingqiu Liao, Linxing Chen, Dongsheng Wang, Pedro J J Alvarez, Pingfeng Yu
{"title":"Adaptive strategies and ecological roles of phages in habitats under physicochemical stress.","authors":"Dan Huang, Rong Xia, Chengyi Chen, Jingqiu Liao, Linxing Chen, Dongsheng Wang, Pedro J J Alvarez, Pingfeng Yu","doi":"10.1016/j.tim.2024.02.002","DOIUrl":"10.1016/j.tim.2024.02.002","url":null,"abstract":"<p><p>Bacteriophages (phages) play a vital role in ecosystem functions by influencing the composition, genetic exchange, metabolism, and environmental adaptation of microbial communities. With recent advances in sequencing technologies and bioinformatics, our understanding of the ecology and evolution of phages in stressful environments has substantially expanded. Here, we review the impact of physicochemical environmental stress on the physiological state and community dynamics of phages, the adaptive strategies that phages employ to cope with environmental stress, and the ecological effects of phage-host interactions in stressful environments. Specifically, we highlight the contributions of phages to the adaptive evolution and functioning of microbiomes and suggest that phages and their hosts can maintain a mutualistic relationship in response to environmental stress. In addition, we discuss the ecological consequences caused by phages in stressful environments, encompassing biogeochemical cycling. Overall, this review advances an understanding of phage ecology in stressful environments, which could inform phage-based strategies to improve microbiome performance and ecosystem resilience and resistance in natural and engineering systems.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"902-916"},"PeriodicalIF":14.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140022666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cancer-associated SNPs in bacteria: lessons from Helicobacter pylori. 细菌中与癌症相关的 SNPs：幽门螺旋杆菌的启示。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-01 Epub Date: 2024-03-13 DOI: 10.1016/j.tim.2024.02.001
Bodo Linz, Heinrich Sticht, Nicole Tegtmeyer, Steffen Backert
{"title":"Cancer-associated SNPs in bacteria: lessons from Helicobacter pylori.","authors":"Bodo Linz, Heinrich Sticht, Nicole Tegtmeyer, Steffen Backert","doi":"10.1016/j.tim.2024.02.001","DOIUrl":"10.1016/j.tim.2024.02.001","url":null,"abstract":"<p><p>Several single-nucleotide polymorphisms (SNPs) in human chromosomes are known to predispose to cancer. However, cancer-associated SNPs in bacterial pathogens were unknown until discovered in the stomach pathogen Helicobacter pylori. Those include an alanine-threonine polymorphism in the EPIYA-B phosphorylation motif of the injected effector protein CagA that affects cancer risk by modifying inflammatory responses and loss of host cell polarity. A serine-to-leucine change in serine protease HtrA is associated with boosted proteolytic cleavage of epithelial junction proteins and introduction of DNA double-strand breaks (DSBs) in host chromosomes, which co-operatively elicit malignant alterations. In addition, H. pylori genome-wide association studies (GWAS) identified several other SNPs potentially associated with increased gastric cancer (GC) risk. Here we discuss the clinical importance, evolutionary origin, and functional advantage of the H. pylori SNPs. These exciting new data highlight cancer-associated SNPs in bacteria, which should be explored in more detail in future studies.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"847-857"},"PeriodicalIF":14.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140132656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rethinking microbially driven methane formation in mangrove wetlands. 重新思考红树林湿地中微生物驱动的甲烷形成。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-01 Epub Date: 2024-06-18 DOI: 10.1016/j.tim.2024.06.002
Ruiwen Hu, Zhili He, Cheng Wang
{"title":"Rethinking microbially driven methane formation in mangrove wetlands.","authors":"Ruiwen Hu, Zhili He, Cheng Wang","doi":"10.1016/j.tim.2024.06.002","DOIUrl":"10.1016/j.tim.2024.06.002","url":null,"abstract":"<p><p>Mangrove wetlands contribute to climate change mitigation through efficient carbon burial, yet microbial methanogenesis offsets these climate benefits. We review the diversity of methanogenic microorganisms in mangrove sediments, present the unrecognized role of bacteria on methanogenesis, and highlight the significance of distinguishing various methanogenic pathways to assess mangrove climate benefits.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"832-835"},"PeriodicalIF":14.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141427625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploiting cAMP signaling in Mycobacterium tuberculosis for drug discovery. 利用结核分枝杆菌中的 cAMP 信号来发现药物。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-09-01 Epub Date: 2024-02-14 DOI: 10.1016/j.tim.2024.01.008
Dipak Kathayat, Brian C VanderVen
{"title":"Exploiting cAMP signaling in Mycobacterium tuberculosis for drug discovery.","authors":"Dipak Kathayat, Brian C VanderVen","doi":"10.1016/j.tim.2024.01.008","DOIUrl":"10.1016/j.tim.2024.01.008","url":null,"abstract":"<p><p>Mycobacterium tuberculosis (Mtb) replicates within host macrophages by adapting to the stressful and nutritionally constrained environments in these cells. Exploiting these adaptations for drug discovery has revealed that perturbing cAMP signaling can restrict Mtb growth in macrophages. Specifically, compounds that agonize or stimulate the bacterial enzyme, Rv1625c/Cya, induce cAMP synthesis and this interferes with the ability of Mtb to metabolize cholesterol. In murine tuberculosis (TB) infection models, Rv1625c/Cya agonists contribute to reducing relapse and shortening combination treatments, highlighting the therapeutic potential for this class of compounds. More recently, cAMP signaling has been implicated in regulating fatty acid utilization by Mtb. Thus, a new model is beginning to emerge in which cAMP regulates the utilization of host lipids by Mtb during infection, and this could provide new targets for TB drug development. Here, we summarize the current understanding of cAMP signaling in Mtb with a focus on our understanding of how cAMP signaling impacts Mtb physiology during infection. We also discuss additional cAMP-related drug targets in Mtb and other bacterial pathogens that may have therapeutic potential.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"874-883"},"PeriodicalIF":14.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11322422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139742051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Bacillus lipopeptides as key players in rhizosphere chemical ecology. 芽孢杆菌脂肽是根圈化学生态学中的关键角色。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-08-29 DOI: 10.1016/j.tim.2024.08.001
Guillaume Balleux, Monica Höfte, Anthony Arguelles-Arias, Magali Deleu, Marc Ongena
{"title":"Bacillus lipopeptides as key players in rhizosphere chemical ecology.","authors":"Guillaume Balleux, Monica Höfte, Anthony Arguelles-Arias, Magali Deleu, Marc Ongena","doi":"10.1016/j.tim.2024.08.001","DOIUrl":"https://doi.org/10.1016/j.tim.2024.08.001","url":null,"abstract":"<p><p>Microbial natural products are widely explored for their therapeutic potential. Understanding the underlying evolutionary and adaptive forces driving their production remains a fundamental question in biology. Amphiphilic cyclic lipopeptides (CLPs), a prominent category of bacterial specialized metabolites, show strong antimicrobial activity, particularly against phytopathogens. It is thus assumed that these compounds are deployed by soil- or rhizosphere-dwelling bacteria as microbial weapons in competitive natural environments. Here, we challenge this reductionist perspective and present evidence that Bacillus CLPs are prominent chemical mediators of ecological interactions. They help Bacillus to communicate, compete, defend against predators, or cooperate and establish mutualistic relationships with other (micro)organisms. Additional parallel examples are highlighted in other genera, such as Pseudomonas. This broader perspective underscores the need for further investigation into the role of CLPs in shaping the adaptive strategies of key rhizobacterial species.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142112338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Toll-like receptor 4 - a multifunctional virus recognition receptor. Toll 样受体 4--一种多功能病毒识别受体。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-08-22 DOI: 10.1016/j.tim.2024.07.001
Elina Gerber-Tichet, Fabien P Blanchet, Karim Majzoub, Eric J Kremer
{"title":"Toll-like receptor 4 - a multifunctional virus recognition receptor.","authors":"Elina Gerber-Tichet, Fabien P Blanchet, Karim Majzoub, Eric J Kremer","doi":"10.1016/j.tim.2024.07.001","DOIUrl":"https://doi.org/10.1016/j.tim.2024.07.001","url":null,"abstract":"<p><p>Since the initial description of Toll receptors in Drosophila and their mammalian counterparts Toll-like receptors (TLRs), numerous fundamental and applied studies have explored their crucial role as sensors of pathogen-associated molecular patterns (PAMPs). Among the ten human TLRs, TLR4 is particularly well known for its ability to detect lipopolysaccharides (LPS), a component of the Gram-negative bacterial cell wall. In addition to its archetypal functions, TLR4 is also a versatile virus sensor. This review provides a background on the discovery of TLR4 and how this knowledge laid a foundation for characterization of its diverse roles in antiviral responses, examined through genetic, biochemical, structural, and immunological approaches. These advances have led to a deeper understanding of the molecular functions that enable TLR4 to orchestrate multi-nodal control by professional antigen-presenting cells (APCs) to initiate appropriate and regulated antiviral immune responses.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142047252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment. 用于加强生态评估的微生物、全生物体和生命之树 eDNA/eRNA。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-08-19 DOI: 10.1016/j.tim.2024.07.003
Lauren S J Cook, Andrew G Briscoe, Vera G Fonseca, Jens Boenigk, Guy Woodward, David Bass
{"title":"Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment.","authors":"Lauren S J Cook, Andrew G Briscoe, Vera G Fonseca, Jens Boenigk, Guy Woodward, David Bass","doi":"10.1016/j.tim.2024.07.003","DOIUrl":"https://doi.org/10.1016/j.tim.2024.07.003","url":null,"abstract":"<p><p>Microbial environmental DNA and RNA (collectively 'eNA') originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring. Incorporating holobiont and Tree of Life approaches into eNA analyses offers further holistic insight into the range of ecological interactions between microbes and other organisms, paving the way for advancing our understanding of, and ultimately manipulating ecosystem properties pertinent to environmental management, conservation, wildlife health, and food production.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142009515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Temperature sensing and virulence regulation in pathogenic bacteria. 致病细菌的温度感应和毒力调节。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-08-19 DOI: 10.1016/j.tim.2024.07.009
Davide Roncarati, Andrea Vannini, Vincenzo Scarlato
{"title":"Temperature sensing and virulence regulation in pathogenic bacteria.","authors":"Davide Roncarati, Andrea Vannini, Vincenzo Scarlato","doi":"10.1016/j.tim.2024.07.009","DOIUrl":"https://doi.org/10.1016/j.tim.2024.07.009","url":null,"abstract":"<p><p>Pathogenic bacteria can detect a variety of environmental signals, including temperature changes. While sudden and significant temperature variations act as danger signals that trigger a protective heat-shock response, minor temperature fluctuations typically signal to the pathogen that it has moved from one environment to another, such as entering a specific niche within a host during infection. These latter temperature fluctuations are utilized by pathogens to coordinate the expression of crucial virulence factors. Here, we elucidate the critical role of temperature in governing the expression of virulence factors in bacterial pathogens. Moreover, we outline the molecular mechanisms used by pathogens to detect temperature fluctuations, focusing on systems that employ proteins and nucleic acids as sensory devices. We also discuss the potential implications and the extent of the risk that climate change poses to human pathogenic diseases.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142009516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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