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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
How do bacteria tune transcription termination efficiency? 细菌如何调节转录终止效率？
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-10-17 DOI: 10.1016/j.mib.2024.102557
Kathryn Julia Dierksheide , Robert A. Battaglia , Gene-Wei Li
{"title":"How do bacteria tune transcription termination efficiency?","authors":"Kathryn Julia Dierksheide ,&nbsp;Robert A. Battaglia ,&nbsp;Gene-Wei Li","doi":"10.1016/j.mib.2024.102557","DOIUrl":"10.1016/j.mib.2024.102557","url":null,"abstract":"<div><div>Bacterial operons often contain intergenic transcription terminators that terminate some, but not all, RNA polymerase molecules. In these operons, the level of terminator readthrough determines downstream gene expression and helps establish protein ratios among co-regulated genes. Despite its critical role in maintaining stoichiometric gene expression, terminator strength remains difficult to predict from DNA sequence. The necessary features of a major class of bacterial terminators — intrinsic terminators — have been known for half a century, but a strong sequence–function model has yet to be developed. Here, we summarize high-throughput approaches for probing the sequence determinants of intrinsic termination efficiency and discuss the impact of <em>trans</em>-acting factors on this sequence–function relationship. Building on the main lessons from these studies, we map out the experimental challenges that must be circumvented to establish a quantitative model for termination efficiency.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"82 ","pages":"Article 102557"},"PeriodicalIF":5.9,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142445866","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
Temperature structuring of microbial communities on a global scale 全球微生物群落的温度结构
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-10-17 DOI: 10.1016/j.mib.2024.102558
Martina Dal Bello , Clare I Abreu
{"title":"Temperature structuring of microbial communities on a global scale","authors":"Martina Dal Bello ,&nbsp;Clare I Abreu","doi":"10.1016/j.mib.2024.102558","DOIUrl":"10.1016/j.mib.2024.102558","url":null,"abstract":"<div><div>Temperature is a fundamental physical constraint regulating key aspects of microbial life. Protein binding, membrane fluidity, central dogma processes, and metabolism are all tightly controlled by temperature, such that growth rate profiles across taxa and environments follow the same general curve. An open question in microbial ecology is how the effects of temperature on individual traits scale up to determine community structure and function at planetary scales. Here, we review recent theoretical and experimental efforts to connect physiological responses to the outcome of species interactions, the assembly of microbial communities, and their function as temperature changes. We identify open questions in the field and define a roadmap for future studies.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"82 ","pages":"Article 102558"},"PeriodicalIF":5.9,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142445868","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
Tapping the treasure trove of atypical phages 挖掘非典型噬菌体的宝库。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-10-10 DOI: 10.1016/j.mib.2024.102555
Simon Roux , Vivek K Mutalik
{"title":"Tapping the treasure trove of atypical phages","authors":"Simon Roux ,&nbsp;Vivek K Mutalik","doi":"10.1016/j.mib.2024.102555","DOIUrl":"10.1016/j.mib.2024.102555","url":null,"abstract":"<div><div>With advancements in genomics technologies, a vast diversity of ‘atypical’ phages, that is, with single-stranded DNA or RNA genomes, are being uncovered from different ecosystems. Though these efforts have revealed the existence and prevalence of these nonmodel phages, computational approaches often fail to associate these phages with their specific bacterial host(s), while the lack of methods to isolate these phages has limited our ability to characterize infectivity pathways and new gene function. In this review, we call for the development of generalizable experimental methods to better capture this understudied viral diversity via isolation and study them through gene-level characterization and engineering. Establishing a diverse set of new ‘atypical’ phage model systems has the potential to provide many new biotechnologies, including potential uses of these atypical phages in halting the spread of antibiotic resistance and engineering of microbial communities for beneficial outcomes.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"82 ","pages":"Article 102555"},"PeriodicalIF":5.9,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399683","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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