EcoSal Plus最新文献

{"title":"Transcription activation in <i>Escherichia coli</i> and <i>Salmonella</i>.","authors":"Stephen J W Busby, Douglas F Browning","doi":"10.1128/ecosalplus.esp-0039-2020","DOIUrl":"10.1128/ecosalplus.esp-0039-2020","url":null,"abstract":"<p><p>Promoter-specific activation of transcript initiation provides an important regulatory device in <i>Escherichia coli</i> and <i>Salmonella</i>. Here, we describe the different mechanisms that operate, focusing on how they have evolved to manage the \"housekeeping\" bacterial transcription machinery. Some mechanisms involve assisting the bacterial DNA-dependent RNA polymerase or replacing or remodeling one of its subunits. Others are directed to chromosomal DNA, improving promoter function, or relieving repression. We discuss how different activators work together at promoters and how the present complex network of transcription factors evolved.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00392020"},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11636354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139722108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nutrition of Escherichia coli within the intestinal microbiome","authors":"Sudhir Doranga, K. A. Krogfelt, Paul S. Cohen, Tyrrell Conway","doi":"10.1128/ecosalplus.esp-0006-2023","DOIUrl":"https://doi.org/10.1128/ecosalplus.esp-0006-2023","url":null,"abstract":"ABSTRACT In this chapter, we update our 2004 review of “The Life of Commensal Escherichia coli in the Mammalian Intestine” (https://doi.org/10.1128/ecosalplus.8.3.1.2), with a change of title that reflects the current focus on “Nutrition of E. coli within the Intestinal Microbiome.” The earlier part of the previous two decades saw incremental improvements in understanding the carbon and energy sources that E. coli and Salmonella use to support intestinal colonization. Along with these investigations of electron donors came a better understanding of the electron acceptors that support the respiration of these facultative anaerobes in the gastrointestinal tract. Hundreds of recent papers add to what was known about the nutrition of commensal and pathogenic enteric bacteria. The fact that each biotype or pathotype grows on a different subset of the available nutrients suggested a mechanism for succession of commensal colonizers and invasion by enteric pathogens. Competition for nutrients in the intestine has also come to be recognized as one basis for colonization resistance, in which colonized strain(s) prevent colonization by a challenger. In the past decade, detailed investigations of fiber- and mucin-degrading anaerobes added greatly to our understanding of how complex polysaccharides support the hundreds of intestinal microbiome species. It is now clear that facultative anaerobes, which usually cannot degrade complex polysaccharides, live in symbiosis with the anaerobic degraders. This concept led to the “restaurant hypothesis,” which emphasizes that facultative bacteria, such as E. coli, colonize the intestine as members of mixed biofilms and obtain the sugars they need for growth locally through cross-feeding from polysaccharide-degrading anaerobes. Each restaurant represents an intestinal niche. Competition for those niches determines whether or not invaders are able to overcome colonization resistance and become established. Topics centered on the nutritional basis of intestinal colonization and gastrointestinal health are explored here in detail.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"3 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139438248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The rise, fall, and resurgence of phage therapy for urinary tract infection","authors":"J. Zulk, K. Patras, A. Maresso","doi":"10.1128/ecosalplus.esp-0029-2023","DOIUrl":"https://doi.org/10.1128/ecosalplus.esp-0029-2023","url":null,"abstract":"ABSTRACT In the face of rising antimicrobial resistance, bacteriophage therapy, also known as phage therapy, is seeing a resurgence as a potential treatment for bacterial infections including urinary tract infection (UTI). Primarily caused by uropathogenic Escherichia coli, the 400 million UTI cases annually are major global healthcare burdens and a primary cause of antibiotic prescriptions in the outpatient setting. Phage therapy has several potential advantages over antibiotics including the ability to disrupt bacterial biofilms and synergize with antimicrobial treatments with minimal side effects or impacts on the microbiota. Phage therapy for UTI treatment has shown generally favorable results in recent animal models and human case reports. Ongoing clinical trials seek to understand the efficacy of phage therapy in individuals with asymptomatic bacteriuria and uncomplicated cystitis. A possible challenge for phage therapy is the development of phage resistance in bacteria during treatment. While resistance frequently develops in vitro and in vivo, resistance can come with negative consequences for the bacteria, leaving them susceptible to antibiotics and other environmental conditions and reducing their overall virulence. “Steering” bacteria toward phage resistance outcomes that leave them less fit or virulent is especially useful in the context of UTI where poorly adherent or slow-growing bacteria are likely to be flushed from the system. In this article, we describe the history of phage therapy in treating UTI and its current resurgence, the state of its clinical use, and an outlook on how well-designed phage therapy could be used to “steer” bacteria toward less virulent and antimicrobial-susceptible states.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"11 14","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139438684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Infection biology of Salmonella enterica","authors":"Jing Han, Nesreen H. Aljahdali, Shaohua Zhao, Hailin Tang, H. Harbottle, Maria Hoffmann, Jonathan G. Frye, S. Foley","doi":"10.1128/ecosalplus.esp-0001-2023","DOIUrl":"https://doi.org/10.1128/ecosalplus.esp-0001-2023","url":null,"abstract":"ABSTRACT Salmonella enterica is the leading cause of bacterial foodborne illness in the USA, with an estimated 95% of salmonellosis cases due to the consumption of contaminated food products. Salmonella can cause several different disease syndromes, with the most common being gastroenteritis, followed by bacteremia and typhoid fever. Among the over 2,600 currently identified serotypes/serovars, some are mostly host-restricted and host-adapted, while the majority of serotypes can infect a broader range of host species and are associated with causing both livestock and human disease. Salmonella serotypes and strains within serovars can vary considerably in the severity of disease that may result from infection, with some serovars that are more highly associated with invasive disease in humans, while others predominantly cause mild gastroenteritis. These observed clinical differences may be caused by the genetic make-up and diversity of the serovars. Salmonella virulence systems are very complex containing several virulence-associated genes with different functions that contribute to its pathogenicity. The different clinical syndromes are associated with unique groups of virulence genes, and strains often differ in the array of virulence traits they display. On the chromosome, virulence genes are often clustered in regions known as Salmonella pathogenicity islands (SPIs), which are scattered throughout different Salmonella genomes and encode factors essential for adhesion, invasion, survival, and replication within the host. Plasmids can also carry various genes that contribute to Salmonella pathogenicity. For example, strains from several serovars associated with significant human disease, including Choleraesuis, Dublin, Enteritidis, Newport, and Typhimurium, can carry virulence plasmids with genes contributing to attachment, immune system evasion, and other roles. The goal of this comprehensive review is to provide key information on the Salmonella virulence, including the contributions of genes encoded in SPIs and plasmids during Salmonella pathogenesis.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"69 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139387303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Research on phage λ: a lucky choice","authors":"D. Lewis, S. Adhya","doi":"10.1128/ecosalplus.esp-0014-2023","DOIUrl":"https://doi.org/10.1128/ecosalplus.esp-0014-2023","url":null,"abstract":"ABSTRACT Bacteriophage λ is a paradigm in the field of gene regulation and one of the best-understood systems in genetic regulatory biology. A so-called Genetic Switch determines the mechanisms by which λ transitions to its dual lifestyles—lytic or lysogenic. When λ initiates the lysogenic lifestyle, the phage-encoded CI repressor binds cooperatively to multi-partite operators in a defined pattern that autoregulates repression of phage lytic promoters as well as activation of the lysogenic promoter. The study of this genetic switch and related earlier research on phage λ revealed the main principles of gene expression and regulation in molecular biology. This article describes the underlying molecular details of λ lysogeny, as it is currently understood.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138946709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA Segregation in Enterobacteria.","authors":"François Cornet, Corentin Blanchais, Romane Dusfour-Castan, Alix Meunier, Valentin Quebre, Hicham Sekkouri Alaoui, François Boudsoq, Manuel Campos, Estelle Crozat, Catherine Guynet, Franck Pasta, Philippe Rousseau, Bao Ton Hoang, Jean-Yves Bouet","doi":"10.1128/ecosalplus.esp-0038-2020","DOIUrl":"10.1128/ecosalplus.esp-0038-2020","url":null,"abstract":"<p><p>DNA segregation ensures that cell offspring receive at least one copy of each DNA molecule, or replicon, after their replication. This important cellular process includes different phases leading to the physical separation of the replicons and their movement toward the future daughter cells. Here, we review these phases and processes in enterobacteria with emphasis on the molecular mechanisms at play and their controls.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"1 1","pages":"eesp00382020"},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10729935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42472568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterizing the Pathogenic Potential of Crohn's Disease-Associated Adherent-Invasive <i>Escherichia coli</i>.","authors":"Megan T Zangara, Lena Darwish, Brian K Coombes","doi":"10.1128/ecosalplus.esp-0018-2022","DOIUrl":"10.1128/ecosalplus.esp-0018-2022","url":null,"abstract":"<p><p>The microbiome of Crohn's disease (CD) patients is composed of a microbial community that is considered dysbiotic and proinflammatory in nature. The overrepresentation of <i>Enterobacteriaceae</i> species is a common feature of the CD microbiome, and much attention has been given to understanding the pathogenic role this feature plays in disease activity. Over 2 decades ago, a new <i>Escherichia coli</i> subtype called adherent-invasive <i>E. coli</i> (AIEC) was isolated and linked to ileal Crohn's disease. Since the isolation of the first AIEC strain, additional AIEC strains have been isolated from both inflammatory bowel disease (IBD) patients and non-IBD individuals using the original <i>in vitro</i> phenotypic characterization methods. Identification of a definitive molecular marker of the AIEC pathotype has been elusive; however, significant advancements have been made in understanding the genetic, metabolic, and virulence determinants of AIEC infection biology. Here, we review the current knowledge of AIEC pathogenesis to provide additional, objective measures that could be considered in defining AIEC and their pathogenic potential.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"1 1","pages":"eesp00182022"},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10729932/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48769601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Mar, Sox, and Rob Systems.","authors":"Lon M Chubiz","doi":"10.1128/ecosalplus.esp-0010-2022","DOIUrl":"10.1128/ecosalplus.esp-0010-2022","url":null,"abstract":"<p><p>Environments inhabited by <i>Enterobacteriaceae</i> are diverse and often stressful. This is particularly true for <i>Escherichia coli</i> and <i>Salmonella</i> during host association in the gastrointestinal systems of animals. There, <i>E. coli</i> and <i>Salmonella</i> must survive exposure to various antimicrobial compounds produced or ingested by their host. A myriad of changes to cellular physiology and metabolism are required to achieve this feat. A central regulatory network responsible for sensing and responding to intracellular chemical stressors like antibiotics are the Mar, Sox, and Rob systems found throughout the <i>Enterobacteriaceae</i>. Each of these distinct regulatory networks controls expression of an overlapping set of downstream genes whose collective effects result in increased resistance to a wide array of antimicrobial compounds. This collection of genes is known as the <i>mar-sox-rob</i> regulon. This review will provide an overview of the <i>mar-sox-rob</i> regulon and molecular architecture of the Mar, Sox, and Rob systems.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"1 1","pages":"eesp00102022"},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10729928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47305824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure, Assembly, and Function of Flagella Responsible for Bacterial Locomotion.","authors":"Tohru Minamino, Miki Kinoshita","doi":"10.1128/ecosalplus.esp-0011-2023","DOIUrl":"10.1128/ecosalplus.esp-0011-2023","url":null,"abstract":"<p><p>Many motile bacteria use flagella for locomotion under a variety of environmental conditions. Because bacterial flagella are under the control of sensory signal transduction pathways, each cell is able to autonomously control its flagellum-driven locomotion and move to an environment favorable for survival. The flagellum of <i>Salmonella enterica</i> serovar Typhimurium is a supramolecular assembly consisting of at least three distinct functional parts: a basal body that acts as a bidirectional rotary motor together with multiple force generators, each of which serves as a transmembrane proton channel to couple the proton flow through the channel with torque generation; a filament that functions as a helical propeller that produces propulsion; and a hook that works as a universal joint that transmits the torque produced by the rotary motor to the helical propeller. At the base of the flagellum is a type III secretion system that transports flagellar structural subunits from the cytoplasm to the distal end of the growing flagellar structure, where assembly takes place. In recent years, high-resolution cryo-electron microscopy (cryoEM) image analysis has revealed the overall structure of the flagellum, and this structural information has made it possible to discuss flagellar assembly and function at the atomic level. In this article, we describe what is known about the structure, assembly, and function of <i>Salmonella</i> flagella.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00112023"},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10729930/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9705246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Mar, Sox, and Rob Systems.","authors":"Lon M Chubiz","doi":"10.1128/ecosalplus.esp-0010-2022","DOIUrl":"10.1128/ecosalplus.esp-0010-2022","url":null,"abstract":"<p><p>Environments inhabited by <i>Enterobacteriaceae</i> are diverse and often stressful. This is particularly true for <i>Escherichia coli</i> and <i>Salmonella</i> during host association in the gastrointestinal systems of animals. There, <i>E. coli</i> and <i>Salmonella</i> must survive exposure to various antimicrobial compounds produced or ingested by their host. A myriad of changes to cellular physiology and metabolism are required to achieve this feat. A central regulatory network responsible for sensing and responding to intracellular chemical stressors like antibiotics are the Mar, Sox, and Rob systems found throughout the <i>Enterobacteriaceae</i>. Each of these distinct regulatory networks controls expression of an overlapping set of downstream genes whose collective effects result in increased resistance to a wide array of antimicrobial compounds. This collection of genes is known as the <i>mar-sox-rob</i> regulon. This review will provide an overview of the <i>mar-sox-rob</i> regulon and molecular architecture of the Mar, Sox, and Rob systems.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00102022"},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10729928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9503297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}