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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
Dissecting host–microbe interactions with modern functional genomics 利用现代功能基因组学剖析宿主与微生物之间的相互作用。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-10-04 DOI: 10.1016/j.mib.2024.102554
Baylee J Russell , Manasvi Verma , Nolan K Maier , Marco Jost
{"title":"Dissecting host–microbe interactions with modern functional genomics","authors":"Baylee J Russell ,&nbsp;Manasvi Verma ,&nbsp;Nolan K Maier ,&nbsp;Marco Jost","doi":"10.1016/j.mib.2024.102554","DOIUrl":"10.1016/j.mib.2024.102554","url":null,"abstract":"<div><div>Interrogation of host–microbe interactions has long been a source of both basic discoveries and benefits to human health. Here, we review the role that functional genomics approaches have played in such efforts, with an emphasis on recent examples that have harnessed technological advances to provide mechanistic insight at increased scale and resolution. Finally, we discuss how concurrent innovations in model systems and genetic tools have afforded opportunities to interrogate additional types of host–microbe relationships, such as those in the mammalian gut. Bringing these innovations together promises many exciting discoveries ahead.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"82 ","pages":"Article 102554"},"PeriodicalIF":5.9,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142377768","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
Iron–sulfur Rrf2 transcription factors: an emerging versatile platform for sensing stress 铁硫 Rrf2 转录因子：感知压力的新兴多功能平台
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-09-24 DOI: 10.1016/j.mib.2024.102543
Rajdeep Banerjee , Isabel Askenasy , Erin L Mettert , Patricia J Kiley
{"title":"Iron–sulfur Rrf2 transcription factors: an emerging versatile platform for sensing stress","authors":"Rajdeep Banerjee ,&nbsp;Isabel Askenasy ,&nbsp;Erin L Mettert ,&nbsp;Patricia J Kiley","doi":"10.1016/j.mib.2024.102543","DOIUrl":"10.1016/j.mib.2024.102543","url":null,"abstract":"<div><div>The widespread family of Rrf2 transcription factors has emerged as having prominent roles in diverse bacterial functions. These proteins share an overall common structure to sense and respond to stress signals. In many known cases, signaling occurs through iron–sulfur cluster cofactors. Recent research has highlighted distinct characteristics of individual family members that have enabled the Rrf2 family as a whole to sense a diverse array of stresses and subsequently alter gene expression to maintain homeostasis. Here, we review unique traits of four Rrf2 family members (IscR, NsrR, RisR, and RirA), which include iron–sulfur ligation schemes, stress-sensing mechanisms, protein conformation changes, and differential gene regulation, that allow these transcription factors to rapidly respond to environmental cues routinely encountered by bacteria.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"82 ","pages":"Article 102543"},"PeriodicalIF":5.9,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142314593","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
Predicting the evolution of antibiotic resistance 预测抗生素耐药性的演变
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-09-18 DOI: 10.1016/j.mib.2024.102542
Fernanda Pinheiro
{"title":"Predicting the evolution of antibiotic resistance","authors":"Fernanda Pinheiro","doi":"10.1016/j.mib.2024.102542","DOIUrl":"10.1016/j.mib.2024.102542","url":null,"abstract":"<div><p>Predicting the evolution of antibiotic resistance is critical for realizing precision antibiotic therapies. How exactly to achieve such predictions is a theoretical challenge. Insights from mathematical models that reflect future behavior of microbes under antibiotic stress can inform intervention protocols. However, this requires going beyond heuristic approaches by modeling ecological and evolutionary responses linked to metabolic pathways and cellular functions. Developing such models is now becoming possible due to increasing data availability from systematic experiments with microbial systems. Here, I review recent theoretical advances promising building blocks to piece together a predictive theory of antibiotic resistance evolution. I focus on the conceptual framework of eco-evolutionary response models grounded on quantitative laws of bacterial physiology. These forward-looking models can predict previously unknown behavior of bacteria upon antibiotic exposure. With current developments covering mostly the case of ribosome-targeting antibiotics, I write this Opinion piece as an invitation to generalize the principles discussed here to a broader range of drugs and context dependencies.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"82 ","pages":"Article 102542"},"PeriodicalIF":5.9,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1369527424001188/pdfft?md5=c5a40650bac522618648ffd0caa862ca&pid=1-s2.0-S1369527424001188-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142238846","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
Molecular architecture and function of the bacterial stressosome 细菌应激体的分子结构和功能
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-09-12 DOI: 10.1016/j.mib.2024.102541
Ziyi Zhao , Fahimeh Hajiahmadi , Maryam S Alehashem , Allison H Williams
{"title":"Molecular architecture and function of the bacterial stressosome","authors":"Ziyi Zhao ,&nbsp;Fahimeh Hajiahmadi ,&nbsp;Maryam S Alehashem ,&nbsp;Allison H Williams","doi":"10.1016/j.mib.2024.102541","DOIUrl":"10.1016/j.mib.2024.102541","url":null,"abstract":"<div><p>The bacterial stressosome is a supramolecular multiprotein complex that acts as a critical signal integration and transduction hub, orchestrating cellular responses to environmental stimuli. Recent studies have resolved near-atomic stressosome structures from various bacterial species, revealing assemblies that should be capable of altering their configuration in response to external changes. Further genetic, biochemical, and cell biology research has elucidated interactions and phosphorylation status within the stressosome complex as well as its subcellular localization and mobility within living cells. These insights enhance our comprehension of the stressosome pathways and their roles in directing various survival responses during environmental stress.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"82 ","pages":"Article 102541"},"PeriodicalIF":5.9,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142173305","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
Is Cryptococcus neoformans a pleomorphic fungus? 新生隐球菌是一种多形真菌吗？
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-09-10 DOI: 10.1016/j.mib.2024.102539
Jessica CS Brown , Elizabeth R Ballou
{"title":"Is Cryptococcus neoformans a pleomorphic fungus?","authors":"Jessica CS Brown ,&nbsp;Elizabeth R Ballou","doi":"10.1016/j.mib.2024.102539","DOIUrl":"10.1016/j.mib.2024.102539","url":null,"abstract":"<div><p>Improved understanding of the human fungal pathogen <em>Cryptococcus neoformans,</em> classically described as a basidiomycete budding yeast, has revealed new infection-relevant single cell morphologies <em>in vivo</em> and <em>in vitro</em>. Here, we ask whether these morphologies constitute true morphotypes, requiring updated classification of <em>C. neoformans</em> as a pleomorphic fungus. We profile recent discoveries of <em>C. neoformans</em> seed cells and titan cells and provide a framework for determining whether these and other recently described single-cell morphologies constitute true morphotypes. We demonstrate that multiple <em>C. neoformans</em> single-cell morphologies are transcriptionally distinct, stable, heritable, and associated with active growth and therefore should be considered true morphotypes in line with the classification in other well-studied fungi. We conclude that <em>C. neoformans</em> is a pleomorphic fungus with an important capacity for morphotype switching that underpins pathogenesis.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"82 ","pages":"Article 102539"},"PeriodicalIF":5.9,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1369527424001152/pdfft?md5=81c0fd0affe38894e43d774b7273774c&pid=1-s2.0-S1369527424001152-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142163311","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
Biofilms as more than the sum of their parts: lessons from developmental biology 生物膜不仅仅是各部分的总和：从发育生物学中汲取的教训。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-09-05 DOI: 10.1016/j.mib.2024.102537
Georgia R Squyres , Dianne K Newman
{"title":"Biofilms as more than the sum of their parts: lessons from developmental biology","authors":"Georgia R Squyres ,&nbsp;Dianne K Newman","doi":"10.1016/j.mib.2024.102537","DOIUrl":"10.1016/j.mib.2024.102537","url":null,"abstract":"<div><p>Although our understanding of both bacterial cell physiology and the complex behaviors exhibited by bacterial biofilms is expanding rapidly, we cannot yet sum the behaviors of individual cells to understand or predict biofilm behavior. This is both because cell physiology in biofilms is different from planktonic growth and because cell behavior in biofilms is spatiotemporally patterned. We use developmental biology as a guide to examine this phenotypic patterning, discussing candidate cues that may encode spatiotemporal information and possible roles for phenotypic patterning in biofilms. We consider other questions that arise from the comparison between biofilm and eukaryotic development, including what defines normal biofilm development and the nature of biofilm cell types and fates. We conclude by discussing what biofilm development can tell us about developmental processes, emphasizing the additional challenges faced by bacteria in biofilm development compared with their eukaryotic counterparts.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"82 ","pages":"Article 102537"},"PeriodicalIF":5.9,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145363","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
Insights into Alphaproteobacterial regulators of cell envelope remodeling 细胞膜重塑的阿尔法蛋白细菌调控因子透视
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2024-09-03 DOI: 10.1016/j.mib.2024.102538
Bryan Lakey , François Alberge , Timothy J Donohue
{"title":"Insights into Alphaproteobacterial regulators of cell envelope remodeling","authors":"Bryan Lakey ,&nbsp;François Alberge ,&nbsp;Timothy J Donohue","doi":"10.1016/j.mib.2024.102538","DOIUrl":"10.1016/j.mib.2024.102538","url":null,"abstract":"<div><p>The cell envelope is at the center of many processes essential for bacterial lifestyles. In addition to giving bacteria shape and delineating it from the environment, it contains macromolecules important for energy transduction, cell division, protection against toxins, biofilm formation, or virulence. Hence, many systems coordinate different processes within the cell envelope to ensure function and integrity. Two-component systems have been identified as crucial regulators of cell envelope functions over the last few years. In this review, we summarize the new information obtained on the regulation of cell envelope biosynthesis and homeostasis in α-proteobacteria<em>,</em> as well as newly identified targets that coordinate the processes in the cell envelope.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"81 ","pages":"Article 102538"},"PeriodicalIF":5.9,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142129993","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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