Baylee J Russell , Manasvi Verma , Nolan K Maier , Marco Jost
{"title":"Dissecting host–microbe interactions with modern functional genomics","authors":"Baylee J Russell , Manasvi Verma , Nolan K Maier , 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}
{"title":"Iron–sulfur Rrf2 transcription factors: an emerging versatile platform for sensing stress","authors":"Rajdeep Banerjee , Isabel Askenasy , Erin L Mettert , 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}
{"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}
Ziyi Zhao , Fahimeh Hajiahmadi , Maryam S Alehashem , Allison H Williams
{"title":"Molecular architecture and function of the bacterial stressosome","authors":"Ziyi Zhao , Fahimeh Hajiahmadi , Maryam S Alehashem , 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}
{"title":"Is Cryptococcus neoformans a pleomorphic fungus?","authors":"Jessica CS Brown , 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}
{"title":"Biofilms as more than the sum of their parts: lessons from developmental biology","authors":"Georgia R Squyres , 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}
Bryan Lakey , François Alberge , Timothy J Donohue
{"title":"Insights into Alphaproteobacterial regulators of cell envelope remodeling","authors":"Bryan Lakey , François Alberge , 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}
Madeleine Delbeau , Ruby Froom , Robert Landick , Seth A Darst , Elizabeth A Campbell
{"title":"The yin and yang of the universal transcription factor NusG","authors":"Madeleine Delbeau , Ruby Froom , Robert Landick , Seth A Darst , Elizabeth A Campbell","doi":"10.1016/j.mib.2024.102540","DOIUrl":"10.1016/j.mib.2024.102540","url":null,"abstract":"<div><p>RNA polymerase (RNAP), the central enzyme of transcription, intermittently pauses during the elongation stage of RNA synthesis. Pausing provides an opportunity for regulatory events such as nascent RNA folding or the recruitment of transregulators. NusG (Spt5 in eukaryotes and archaea) regulates RNAP pausing and is the only transcription factor conserved across all cellular life. NusG is a multifunctional protein: its N-terminal domain (NGN) binds to RNAP, and its C-terminal KOW domain in bacteria interacts with transcription regulators such as ribosomes and termination factors. In <em>Escherichia coli</em>, NusG acts as an antipausing factor. However, recent studies have revealed that NusG has distinct transcriptional regulatory roles specific to bacterial clades with clinical implications. Here, we focus on NusG’s dual roles in the regulation of pausing.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"81 ","pages":"Article 102540"},"PeriodicalIF":5.9,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142122814","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}
{"title":"From dusty shelves toward the spotlight: growing evidence for Ap4A as an alarmone in maintaining RNA stability and proteostasis","authors":"Megan KM Young, Jue D Wang","doi":"10.1016/j.mib.2024.102536","DOIUrl":"10.1016/j.mib.2024.102536","url":null,"abstract":"<div><p>Bacteria thrive in diverse environments and must withstand various stresses. A key stress response mechanism is the reprogramming of macromolecular biosynthesis and metabolic processes through alarmones — signaling nucleotides that accumulate intracellularly in response to metabolic stress. Diadenosine tetraphosphate (Ap4A), a putative alarmone, is produced in a noncanonical reaction by universally conserved aminoacyl-tRNA synthetases. Ap4A is ubiquitous across all domains of life and accumulates during heat and oxidative stress. Despite its early discovery in 1966, Ap4A’s alarmone status remained inconclusive. Recent discoveries identified Ap4A as a precursor to RNA 5′ caps in <em>Escherichia coli</em>. Additionally, Ap4A was found to directly bind to and allosterically inhibit the purine biosynthesis enzyme inosine 5′-monophosphate dehydrogenase, regulating guanosine triphosphate levels and enabling heat resistance in <em>Bacillus subtilis</em>. These findings, along with previous research, strongly suggest that Ap4A plays a crucial role as an alarmone, warranting further investigation to fully elucidate its functions.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"81 ","pages":"Article 102536"},"PeriodicalIF":5.9,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142095703","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}
{"title":"Horizontal gene transfer and beyond: the delivery of biological matter by bacterial membrane vesicles to host and bacterial cells","authors":"Alice X Wen , Christophe Herman","doi":"10.1016/j.mib.2024.102525","DOIUrl":"10.1016/j.mib.2024.102525","url":null,"abstract":"<div><p>Membrane vesicles (MVs) are produced in all domains of life. In eukaryotes, extracellular vesicles have been shown to mediate the horizontal transfer of biological material between cells [1]. Therefore, bacterial MVs are also thought to mediate horizontal material transfer to host cells and other bacteria, especially in the context of cell stress. In this review, we discuss the mechanisms of bacterial MV production, evidence that their contents can be trafficked to host cells and other bacteria, and the biological relevance of horizontal material transfer by bacterial MVs.</p></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"81 ","pages":"Article 102525"},"PeriodicalIF":5.9,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142077455","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}