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Annual review of microbiology最新文献

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Small RNAs, Large Networks: Posttranscriptional Regulons in Gram-Negative Bacteria. 小RNA，大网络：革兰氏阴性菌中的转录后调控子。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2023-09-15 Epub Date: 2023-03-21 DOI: 10.1146/annurev-micro-041320-025836
Kai Papenfort, Sahar Melamed
{"title":"Small RNAs, Large Networks: Posttranscriptional Regulons in Gram-Negative Bacteria.","authors":"Kai Papenfort,&nbsp;Sahar Melamed","doi":"10.1146/annurev-micro-041320-025836","DOIUrl":"10.1146/annurev-micro-041320-025836","url":null,"abstract":"<p><p>Small regulatory RNA (sRNAs) are key mediators of posttranscriptional gene control in bacteria. Assisted by RNA-binding proteins, a single sRNA often modulates the expression of dozens of genes, and thus sRNAs frequently adopt central roles in regulatory networks. Posttranscriptional regulation by sRNAs comes with several unique features that cannot be achieved by transcriptional regulators. However, for optimal network performance, transcriptional and posttranscriptional control mechanisms typically go hand-in-hand. This view is reflected by the ever-growing class of mixed network motifs involving sRNAs and transcription factors, which are ubiquitous in biology and whose regulatory properties we are beginning to understand. In addition, sRNA activity can be antagonized by base-pairing with sponge RNAs, adding yet another layer of complexity to these networks. In this article, we summarize the regulatory concepts underlying sRNA-mediated gene control in bacteria and discuss how sRNAs shape the output of a network, focusing on several key examples.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"77 ","pages":"23-43"},"PeriodicalIF":10.5,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10626414","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: 13
Past, Present, and Future of Extracytoplasmic Function σ Factors: Distribution and Regulatory Diversity of the Third Pillar of Bacterial Signal Transduction. 胞外功能σ因子的过去、现在和未来：细菌信号转导第三支柱的分布和调节多样性。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2023-09-15 Epub Date: 2023-07-12 DOI: 10.1146/annurev-micro-032221-024032
Thorsten Mascher
{"title":"Past, Present, and Future of Extracytoplasmic Function σ Factors: Distribution and Regulatory Diversity of the Third Pillar of Bacterial Signal Transduction.","authors":"Thorsten Mascher","doi":"10.1146/annurev-micro-032221-024032","DOIUrl":"10.1146/annurev-micro-032221-024032","url":null,"abstract":"<p><p>Responding to environmental cues is a prerequisite for survival in the microbial world. Extracytoplasmic function σ factors (ECFs) represent the third most abundant and by far the most diverse type of bacterial signal transduction. While archetypal ECFs are controlled by cognate anti-σ factors, comprehensive comparative genomics efforts have revealed a much higher abundance and regulatory diversity of ECF regulation than previously appreciated. They have also uncovered a diverse range of anti-σ factor-independent modes of controlling ECF activity, including fused regulatory domains and phosphorylation-dependent mechanisms. While our understanding of ECF diversity is comprehensive for well-represented and heavily studied bacterial phyla-such as <i>Proteobacteria</i>, <i>Firmicutes</i>, and Actinobacteria (phylum <i>Actinomycetota</i>)-our current knowledge about ECF-dependent signaling in the vast majority of underrepresented phyla is still far from complete. In particular, the dramatic extension of bacterial diversity in the course of metagenomic studies represents both a new challenge and an opportunity in expanding the world of ECF-dependent signal transduction.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"77 ","pages":"625-644"},"PeriodicalIF":10.5,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10280875","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: 2
Mobile Genetic Element Flexibility as an Underlying Principle to Bacterial Evolution. 可移动遗传元件的灵活性是细菌进化的基本原理。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2023-09-15 Epub Date: 2023-07-12 DOI: 10.1146/annurev-micro-032521-022006
Alexandra J Weisberg, Jeff H Chang
{"title":"Mobile Genetic Element Flexibility as an Underlying Principle to Bacterial Evolution.","authors":"Alexandra J Weisberg,&nbsp;Jeff H Chang","doi":"10.1146/annurev-micro-032521-022006","DOIUrl":"10.1146/annurev-micro-032521-022006","url":null,"abstract":"<p><p>Mobile genetic elements are key to the evolution of bacteria and traits that affect host and ecosystem health. Here, we use a framework of a hierarchical and modular system that scales from genes to populations to synthesize recent findings on mobile genetic elements (MGEs) of bacteria. Doing so highlights the role that emergent properties of flexibility, robustness, and genetic capacitance of MGEs have on the evolution of bacteria. Some of their traits can be stored, shared, and diversified across different MGEs, taxa of bacteria, and time. Collectively, these properties contribute to maintaining functionality against perturbations while allowing changes to accumulate in order to diversify and give rise to new traits. These properties of MGEs have long challenged our abilities to study them. Implementation of new technologies and strategies allows for MGEs to be analyzed in new and powerful ways.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"77 ","pages":"603-624"},"PeriodicalIF":10.5,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10280008","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: 3
Essential Amino Acid Metabolites as Chemical Mediators of Host-Microbe Interaction in the Gut. 必需氨基酸代谢产物作为肠道中宿主-微生物相互作用的化学介质。
IF 8.5 1区 生物学
Annual review of microbiology Pub Date : 2023-09-15 Epub Date: 2023-06-20 DOI: 10.1146/annurev-micro-032421-111819
Jessica R McCann, John F Rawls
{"title":"Essential Amino Acid Metabolites as Chemical Mediators of Host-Microbe Interaction in the Gut.","authors":"Jessica R McCann, John F Rawls","doi":"10.1146/annurev-micro-032421-111819","DOIUrl":"10.1146/annurev-micro-032421-111819","url":null,"abstract":"<p><p>Amino acids are indispensable substrates for protein synthesis in all organisms and incorporated into diverse aspects of metabolic physiology and signaling. However, animals lack the ability to synthesize several of them and must acquire these essential amino acids from their diet or perhaps their associated microbial communities. The essential amino acids therefore occupy a unique position in the health of animals and their relationships with microbes. Here we review recent work connecting microbial production and metabolism of essential amino acids to host biology, and the reciprocal impacts of host metabolism of essential amino acids on their associated microbes. We focus on the roles of the branched-chain amino acids (valine, leucine, and isoleucine) and tryptophan on host-microbe communication in the intestine of humans and other vertebrates. We then conclude by highlighting research questions surrounding the less-understood aspects of microbial essential amino acid synthesis in animal hosts.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"77 ","pages":"479-497"},"PeriodicalIF":8.5,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11188676/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10272294","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
The ChvG-ChvI Regulatory Network: A Conserved Global Regulatory Circuit Among the Alphaproteobacteria with Pervasive Impacts on Host Interactions and Diverse Cellular Processes. ChvG-ChvI调控网络：对宿主相互作用和多种细胞过程具有普遍影响的α-变形菌中的一个保守的全球调控回路。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2023-09-15 Epub Date: 2023-04-11 DOI: 10.1146/annurev-micro-120822-102714
Jennifer L Greenwich, Brynn C Heckel, Melene A Alakavuklar, Clay Fuqua
{"title":"The ChvG-ChvI Regulatory Network: A Conserved Global Regulatory Circuit Among the Alphaproteobacteria with Pervasive Impacts on Host Interactions and Diverse Cellular Processes.","authors":"Jennifer L Greenwich,&nbsp;Brynn C Heckel,&nbsp;Melene A Alakavuklar,&nbsp;Clay Fuqua","doi":"10.1146/annurev-micro-120822-102714","DOIUrl":"10.1146/annurev-micro-120822-102714","url":null,"abstract":"<p><p>The ChvG-ChvI two-component system is conserved among multiple <i>Alphaproteobacteria</i>. ChvG is a canonical two-component system sensor kinase with a single large periplasmic loop. Active ChvG directs phosphotransfer to its cognate response regulator ChvI, which controls transcription of target genes. In many alphaproteobacteria, ChvG is regulated by a third component, a periplasmic protein called ExoR, that maintains ChvG in an inactive state through direct interaction. Acidic pH stimulates proteolysis of ExoR, unfettering ChvG-ChvI to control its regulatory targets. Activated ChvI among different alphaproteobacteria controls a broad range of cellular processes, including symbiosis and virulence, exopolysaccharide production, biofilm formation, motility, type VI secretion, cellular metabolism, envelope composition, and growth. Low pH is a virulence signal in <i>Agrobacterium tumefaciens</i>, but in other systems, conditions that cause envelope stress may also generally activate ChvG-ChvI. There is mounting evidence that these regulators influence diverse aspects of bacterial physiology, including but not limited to host interactions.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"77 ","pages":"131-148"},"PeriodicalIF":10.5,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10282081","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: 2
Are Bacteria Leaky? Mechanisms of Metabolite Externalization in Bacterial Cross-Feeding. 细菌泄漏吗？细菌交叉喂养中代谢产物外部化的机制。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2023-09-15 Epub Date: 2023-06-07 DOI: 10.1146/annurev-micro-032521-023815
James B McKinlay
{"title":"Are Bacteria Leaky? Mechanisms of Metabolite Externalization in Bacterial Cross-Feeding.","authors":"James B McKinlay","doi":"10.1146/annurev-micro-032521-023815","DOIUrl":"10.1146/annurev-micro-032521-023815","url":null,"abstract":"<p><p>The metabolism of a bacterial cell stretches beyond its boundaries, often connecting with the metabolism of other cells to form extended metabolic networks that stretch across communities, and even the globe. Among the least intuitive metabolic connections are those involving cross-feeding of canonically intracellular metabolites. How and why are these intracellular metabolites externalized? Are bacteria simply leaky? Here I consider what it means for a bacterium to be leaky, and I review mechanisms of metabolite externalization from the context of cross-feeding. Despite common claims, diffusion of most intracellular metabolites across a membrane is unlikely. Instead, passive and active transporters are likely involved, possibly purging excess metabolites as part of homeostasis. Re-acquisition of metabolites by a producer limits the opportunities for cross-feeding. However, a competitive recipient can stimulate metabolite externalization and initiate a positive-feedback loop of reciprocal cross-feeding.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"77 ","pages":"277-297"},"PeriodicalIF":10.5,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10627458","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: 3
License to Clump: Secretory IgA Structure-Function Relationships Across Scales. Clump许可证：跨量表的分泌IgA结构-功能关系。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2023-09-15 DOI: 10.1146/annurev-micro-032521-041803
Alyson Hockenberry, Emma Slack, Beth M Stadtmueller
{"title":"License to Clump: Secretory IgA Structure-Function Relationships Across Scales.","authors":"Alyson Hockenberry, Emma Slack, Beth M Stadtmueller","doi":"10.1146/annurev-micro-032521-041803","DOIUrl":"10.1146/annurev-micro-032521-041803","url":null,"abstract":"<p><p>Secretory antibodies are the only component of our adaptive immune system capable of attacking mucosal pathogens topologically outside of our bodies. All secretory antibody classes are (<i>a</i>) relatively resistant to harsh proteolytic environments and (<i>b</i>) polymeric. Recent elucidation of the structure of secretory IgA (SIgA) has begun to shed light on SIgA functions at the nanoscale. We can now begin to unravel the structure-function relationships of these molecules, for example, by understanding how the bent conformation of SIgA enables robust cross-linking between adjacent growing bacteria. Many mysteries remain, such as the structural basis of protease resistance and the role of noncanonical bacteria-IgA interactions. In this review, we explore the structure-function relationships of IgA from the nano- to the metascale, with a strong focus on how the seemingly banal \"license to clump\" can have potent effects on bacterial physiology and colonization.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"77 ","pages":"645-668"},"PeriodicalIF":10.5,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10650413","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
Factors Affecting Variation of the Human Gut Phageome. 影响人类肠道形态变异的因素。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2023-09-15 Epub Date: 2023-07-12 DOI: 10.1146/annurev-micro-032421-105754
Ciara A Tobin, Colin Hill, Andrey N Shkoporov
{"title":"Factors Affecting Variation of the Human Gut Phageome.","authors":"Ciara A Tobin,&nbsp;Colin Hill,&nbsp;Andrey N Shkoporov","doi":"10.1146/annurev-micro-032421-105754","DOIUrl":"10.1146/annurev-micro-032421-105754","url":null,"abstract":"<p><p>The gut microbiome is a dense and metabolically active consortium of microorganisms and viruses located in the lower gastrointestinal tract of the human body. Bacteria and their viruses (phages) are the most abundant members of the gut microbiome. Investigating their biology and the interplay between the two is important if we are to understand their roles in human health and disease. In this review, we summarize recent advances in resolving the taxonomic structure and ecological functions of the complex community of phages in the human gut-the gut phageome. We discuss how age, diet, and geography can all have a significant impact on phageome composition. We note that alterations to the gut phageome have been observed in several diseases such as inflammatory bowel disease, irritable bowel syndrome, and colorectal cancer, and we evaluate whether these phageome changes can directly or indirectly contribute to disease etiology and pathogenesis. We also highlight how lack of standardization in studying the gut phageome has contributed to variation in reported results.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"77 ","pages":"363-379"},"PeriodicalIF":10.5,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10332136","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: 2
TonB-Dependent Transport Across the Bacterial Outer Membrane. TonB依赖性细菌外膜转运。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2023-09-15 Epub Date: 2023-03-21 DOI: 10.1146/annurev-micro-032421-111116
Augustinas Silale, Bert van den Berg
{"title":"TonB-Dependent Transport Across the Bacterial Outer Membrane.","authors":"Augustinas Silale,&nbsp;Bert van den Berg","doi":"10.1146/annurev-micro-032421-111116","DOIUrl":"10.1146/annurev-micro-032421-111116","url":null,"abstract":"<p><p>TonB-dependent transporters (TBDTs) are present in all gram-negative bacteria and mediate energy-dependent uptake of molecules that are too scarce or large to be taken up efficiently by outer membrane (OM) diffusion channels. This process requires energy that is derived from the proton motive force and delivered to TBDTs by the TonB-ExbBD motor complex in the inner membrane. Together with the need to preserve the OM permeability barrier, this has led to an extremely complex and fascinating transport mechanism for which the fundamentals, despite decades of research, are still unclear. In this review, we describe our current understanding of the transport mechanism of TBDTs, their potential role in the delivery of novel antibiotics, and the important contributions made by TBDT-associated (lipo)proteins.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"77 ","pages":"67-88"},"PeriodicalIF":10.5,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10626413","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: 5
The Origin of Metazoan Multicellularity: A Potential Microbial Black Swan Event. 后生动物多细胞性的起源：一个潜在的微生物黑天鹅事件。
IF 10.5 1区 生物学
Annual review of microbiology Pub Date : 2023-09-15 Epub Date: 2023-07-05 DOI: 10.1146/annurev-micro-032421-120023
Iñaki Ruiz-Trillo, Koryu Kin, Elena Casacuberta
{"title":"The Origin of Metazoan Multicellularity: A Potential Microbial Black Swan Event.","authors":"Iñaki Ruiz-Trillo,&nbsp;Koryu Kin,&nbsp;Elena Casacuberta","doi":"10.1146/annurev-micro-032421-120023","DOIUrl":"10.1146/annurev-micro-032421-120023","url":null,"abstract":"<p><p>The emergence of animals from their unicellular ancestors is a major evolutionary event. Thanks to the study of diverse close unicellular relatives of animals, we now have a better grasp of what the unicellular ancestor of animals was like. However, it is unclear how that unicellular ancestor of animals became the first animals. To explain this transition, two popular theories, the choanoblastaea and the synzoospore, have been proposed. We will revise and expose the flaws in these two theories while showing that, due to the limits of our current knowledge, the origin of animals is a biological black swan event. As such, the origin of animals defies retrospective explanations. Therefore, we should be extra careful not to fall for confirmation biases based on few data and, instead, embrace this uncertainty and be open to alternative scenarios. With the aim to broaden the potential explanations on how animals emerged, we here propose two novel and alternative scenarios. In any case, to find the answer to how animals evolved, additional data will be required, as will the hunt for microscopic creatures that are closely related to animals but have not yet been sampled and studied.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"77 ","pages":"499-516"},"PeriodicalIF":10.5,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10272793","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: 2
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