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The promise of CRISPR-associated transposons for bacterial functional genomics crispr相关转座子在细菌功能基因组学中的应用前景。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-01 DOI: 10.1016/j.mib.2024.102563
Amy B Banta , Rodrigo A Cuellar , Nischala Nadig , Bryce C Davis , Jason M Peters
{"title":"The promise of CRISPR-associated transposons for bacterial functional genomics","authors":"Amy B Banta ,&nbsp;Rodrigo A Cuellar ,&nbsp;Nischala Nadig ,&nbsp;Bryce C Davis ,&nbsp;Jason M Peters","doi":"10.1016/j.mib.2024.102563","DOIUrl":"10.1016/j.mib.2024.102563","url":null,"abstract":"<div><div>CRISPR-associated transposons (CASTs) are naturally occurring amalgamations of CRISPR-Cas machinery and Tn<em>7</em>-like transposons that direct site-specific integration of transposon DNA via programmable guide RNAs. Although the mechanisms of CAST-based transposition have been well studied at the molecular and structural level, CASTs have yet to be broadly applied to bacterial genome engineering and systematic gene phenotyping (i.e. functional genomics) — likely due to their relatively recent discovery. Here, we describe the function and applications of CASTs, focusing on well-characterized systems, including the type I-F CAST from <em>Vibrio cholerae</em> (VcCAST) and type V-K CAST from <em>Scytonema hofmanni</em> (ShCAST). Further, we discuss the potentially transformative impact of targeted transposition on bacterial functional genomics by proposing genome-scale extensions of existing CAST tools.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"Article 102563"},"PeriodicalIF":5.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779649","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
Corrigendum to “Innovative and potential treatments for fungal central nervous system infections” [Curr Opin Microbiol 76 (2023) 102397] “真菌性中枢神经系统感染的创新和潜在治疗方法”的更正[现行微生物学杂志76(2023)102397]。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-01 DOI: 10.1016/j.mib.2025.102583
Marta Reguera-Gomez , Michael R. Dores , Luis R. Martinez
{"title":"Corrigendum to “Innovative and potential treatments for fungal central nervous system infections” [Curr Opin Microbiol 76 (2023) 102397]","authors":"Marta Reguera-Gomez ,&nbsp;Michael R. Dores ,&nbsp;Luis R. Martinez","doi":"10.1016/j.mib.2025.102583","DOIUrl":"10.1016/j.mib.2025.102583","url":null,"abstract":"","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"Article 102583"},"PeriodicalIF":5.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Innovative approaches in the discovery of terpenoid natural products 发现萜类天然产物的创新方法。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-01 DOI: 10.1016/j.mib.2024.102575
Shu Cheng , Xinghuan Wang , Zixin Deng , Tiangang Liu
{"title":"Innovative approaches in the discovery of terpenoid natural products","authors":"Shu Cheng ,&nbsp;Xinghuan Wang ,&nbsp;Zixin Deng ,&nbsp;Tiangang Liu","doi":"10.1016/j.mib.2024.102575","DOIUrl":"10.1016/j.mib.2024.102575","url":null,"abstract":"<div><div>As a class of natural compounds ubiquitous in nature, diverse terpenoids exhibit a broad spectrum of applications in human endeavors. The efficient discovery of novel terpenoids and the establishment of a terpene library for broad utilization represent pressing challenges in terpenoid natural product research. Various microbial platforms offer abundant precursors for terpene biosynthesis from diverse sources. Leveraging artificial intelligence for enzyme function prediction and screening can facilitate the identification of terpenoid synthesis components with innovative mechanisms. Automated high-throughput bio-foundry workstations can expedite the construction of terpenoid libraries, providing substantial time and labor savings. The integration of multiple strategies promises to yield substantial advancements in the exploration of valuable terpenoids.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"Article 102575"},"PeriodicalIF":5.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142871628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Dirammox (direct ammonia oxidation) to nitrogen (N2): discovery, current status, and perspectives 地拉莫克斯（氨直接氧化）制氮（N2）：发现、现状和前景。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-01 DOI: 10.1016/j.mib.2024.102565
Ji-Guo Qiu , Shuang-Jiang Liu
{"title":"Dirammox (direct ammonia oxidation) to nitrogen (N2): discovery, current status, and perspectives","authors":"Ji-Guo Qiu ,&nbsp;Shuang-Jiang Liu","doi":"10.1016/j.mib.2024.102565","DOIUrl":"10.1016/j.mib.2024.102565","url":null,"abstract":"<div><div>Microbial ammonia oxidation plays an important role in nitrogen (N<sub>2</sub>) cycling in natural and man-made systems. Heterotrophic microorganisms that oxidize ammonia were observed more than a century ago; however, the underlying molecular mechanism of ammonia oxidation is still mysterious. Dirammox (direct ammonia oxidation to N<sub>2</sub>) is a newly described heterotrophic ammonia oxidation process in which ammonia or its organic amine is oxidized into hydroxylamine and then directly converted to N<sub>2</sub> gas without the involvement of nitrite and nitrate. As demonstrated with <em>Alcaligenes</em> species, the conversion of ammonia to hydroxylamine is mediated by the <em>dnf</em> genes, and hydroxylamine conversion to N<sub>2</sub> is considered both a biotic and abiotic process. Dirammox is different from the N<sub>2</sub>-producing processes of nitrification–denitrification and anaerobic ammonia oxidation (anammox), in which nitrite or nitrate is involved. Here, we review the discovery of dirammox, progress toward understanding its genetics, biochemistry, physiology, and ecology, and future perspectives and directions.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"Article 102565"},"PeriodicalIF":5.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142812664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Dissecting S-itaconation at host–pathogen interactions with chemical proteomics tools 利用化学蛋白质组学工具分析宿主-病原体相互作用中的S-itaconation。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-01 DOI: 10.1016/j.mib.2025.102579
Zihua Liu , Chu Wang
{"title":"Dissecting S-itaconation at host–pathogen interactions with chemical proteomics tools","authors":"Zihua Liu ,&nbsp;Chu Wang","doi":"10.1016/j.mib.2025.102579","DOIUrl":"10.1016/j.mib.2025.102579","url":null,"abstract":"<div><div>The molecular essence of the battle between host and pathogens lies in the protein–protein or protein–metabolite interactions. Itaconate is one of the most upregulated immunometabolites, regulating immune responses through either noncovalent binding or covalent modification in the host. We herein briefly review recent progresses in the discoveries of physiological and pathological roles of itaconate and applications of chemical proteomic technologies in exploring itaconate modifications on cysteines (<em>S</em>-itaconation) at the interface of host–pathogen interactions. Key challenges are also proposed as future outlook.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"Article 102579"},"PeriodicalIF":5.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143022561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Animating insights into the biosynthesis of glycopeptide antibiotics 对糖肽抗生素生物合成的生动见解
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-12-01 DOI: 10.1016/j.mib.2024.102561
Athina Gavriilidou , Martina Adamek , Jens-Peter Rodler , Noel Kubach , Anna Voigtländer , Leon Kokkoliadis , Chambers C Hughes , Max J Cryle , Evi Stegmann , Nadine Ziemert
{"title":"Animating insights into the biosynthesis of glycopeptide antibiotics","authors":"Athina Gavriilidou ,&nbsp;Martina Adamek ,&nbsp;Jens-Peter Rodler ,&nbsp;Noel Kubach ,&nbsp;Anna Voigtländer ,&nbsp;Leon Kokkoliadis ,&nbsp;Chambers C Hughes ,&nbsp;Max J Cryle ,&nbsp;Evi Stegmann ,&nbsp;Nadine Ziemert","doi":"10.1016/j.mib.2024.102561","DOIUrl":"10.1016/j.mib.2024.102561","url":null,"abstract":"<div><div>The realm of natural product (NP) research is constantly expanding, with diverse applications in both medicine and industry. In this interdisciplinary field, scientists collaborate to investigate various aspects of NPs, including understanding the mode of action of these compounds, unraveling their biosynthetic pathways, studying evolutionary aspects, and biochemically characterizing the enzymes involved. However, this collaboration can be challenging as all parties involved come from very different backgrounds (such as microbiology, synthetic chemistry, biochemistry, or bioinformatics) and may not use the same terminology. Fortunately, contemporary technologies, such as videos, provide novel avenues for effective engagement. Recognizing the potency of visual stimuli in explaining complex processes, we envision a future where animations become more and more common in interdisciplinary communication, accompanying perspectives, and reviews. To demonstrate how such approaches can enhance the understanding of complex processes, we have animated the biosynthesis of the glycopeptide antibiotic vancomycin (https://youtu.be/TGAgC4c8hvo).</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"82 ","pages":"Article 102561"},"PeriodicalIF":5.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142745854","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
Important challenges to finding new leads for new antibiotics 寻找新型抗生素新线索的重要挑战
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-11-26 DOI: 10.1016/j.mib.2024.102562
Maya A Farha , Megan M Tu , Eric D Brown
{"title":"Important challenges to finding new leads for new antibiotics","authors":"Maya A Farha ,&nbsp;Megan M Tu ,&nbsp;Eric D Brown","doi":"10.1016/j.mib.2024.102562","DOIUrl":"10.1016/j.mib.2024.102562","url":null,"abstract":"<div><div>Identification of new antibiotics remains a huge challenge. The last antibiotic of new chemical class and mechanism was discovered more than 30 years ago. Advances since have been largely incremental modifications to a limited number of chemical scaffolds. Discovering and developing truly new antibiotics is challenging: the science is complex, and the development process is time consuming and expensive. Herein, we focus on the discovery phase of modern antibacterial research and development. We argue that antibacterial discovery has been challenged by a poor understanding of bacterial permeability, by generic <em>in vitro</em> conventions that ignore the host, and by the inherent complexity of bacterial systems. Together, these factors have colluded to challenge modern, industrial, and reductionist approaches to antibiotic discovery. Nevertheless, advances in our understanding of many of these obstacles, including a new appreciation for the complexity of both host and pathogen biology, bode well for future efforts.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"Article 102562"},"PeriodicalIF":5.9,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142721726","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
Temporospatial control of topoisomerases by essential cellular processes 细胞基本过程对拓扑异构酶的时空控制
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-11-08 DOI: 10.1016/j.mib.2024.102559
Sora Kim, Monica S Guo
{"title":"Temporospatial control of topoisomerases by essential cellular processes","authors":"Sora Kim,&nbsp;Monica S Guo","doi":"10.1016/j.mib.2024.102559","DOIUrl":"10.1016/j.mib.2024.102559","url":null,"abstract":"<div><div>Topoisomerases are essential, ubiquitous enzymes that break and rejoin the DNA strand to control supercoiling. Because topoisomerases are DNA scissors, these enzymes are highly regulated to avoid excessive DNA cleavage, a vulnerability exploited by many antibiotics. Topoisomerase activity must be co-ordinated in time and space with transcription, replication, and cell division or else these processes stall, leading to genome loss. Recent work in <em>Escherichia coli</em> has revealed that topoisomerases do not act alone. Most topoisomerases interact with the essential process that they promote, a coupling that may stimulate topoisomerase activity precisely when and where cleavage is required. Surprisingly, in <em>E. coli</em> and most other bacteria, gyrase is not apparently regulated in this manner. We review how each <em>E. coli</em> topoisomerase is regulated, propose possible solutions to ‘the gyrase problem’, and conclude by highlighting how this regulation may present opportunities for antimicrobial development.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"82 ","pages":"Article 102559"},"PeriodicalIF":5.9,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Editorial overview: Human fungal pathogens: An increasing threat 编辑综述：人类真菌病原体：威胁与日俱增。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-10-23 DOI: 10.1016/j.mib.2024.102560
J. Christian Pérez
{"title":"Editorial overview: Human fungal pathogens: An increasing threat","authors":"J. Christian Pérez","doi":"10.1016/j.mib.2024.102560","DOIUrl":"10.1016/j.mib.2024.102560","url":null,"abstract":"","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"82 ","pages":"Article 102560"},"PeriodicalIF":5.9,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142496678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
It's complicated: relationships between integrative and conjugative elements and their bacterial hosts 这很复杂：整合元件和共轭元件与其细菌宿主之间的关系
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-10-18 DOI: 10.1016/j.mib.2024.102556
Alexa FS Gomberg, Alan D Grossman
{"title":"It's complicated: relationships between integrative and conjugative elements and their bacterial hosts","authors":"Alexa FS Gomberg,&nbsp;Alan D Grossman","doi":"10.1016/j.mib.2024.102556","DOIUrl":"10.1016/j.mib.2024.102556","url":null,"abstract":"<div><div>Integrative and conjugative elements (ICEs) are typically found integrated in a bacterial host chromosome. They can excise, replicate, and transfer from cell to cell. Many contain genes that confer phenotypes to host cells, including antibiotic resistances, specialized metabolisms, phage defense, and symbiosis or pathogenesis determinants. Recent studies revealed that at least three ICEs (ICE<em>clc</em>, Tn<em>916</em>, and Tn<em>Smu1</em>) cause growth arrest or death of host cells upon element activation. This review highlights the complex interactions between ICEs and their hosts, including the recent examples of the significant costs to host cells. We contrast two examples of killing, ICE<em>clc</em> and Tn<em>916</em>, in which killing, respectively, benefits or impairs conjugation and emphasize the importance of understanding the impacts of ICE–host relationships on conjugation. ICEs are typically only active in a small fraction of cells in a population, and we discuss how phenotypes normally occurring in a small subset of host cells can be uncovered.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"82 ","pages":"Article 102556"},"PeriodicalIF":5.9,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142445867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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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