EcoSal Plus最新文献

{"title":"The <i>E. coli</i> CRISPR-Cas conundrum: are they functional immune systems or genomic singularities?","authors":"Edward G Dudley","doi":"10.1128/ecosalplus.esp-0040-2020","DOIUrl":"https://doi.org/10.1128/ecosalplus.esp-0040-2020","url":null,"abstract":"<p><p>The discovery and subsequent characterization and applications of CRISPR-Cas is one of the most fascinating scientific stories from the past two decades. While first identified in <i>Escherichia coli</i>, this microbial workhorse often took a back seat to other bacteria during the early race to detail CRISPR-Cas function as an adaptive immune system. This was not a deliberate slight, but the result of early observations that the CRISPR-Cas systems found in <i>E. coli</i> were not robust phage defense systems as first described in <i>Streptococcus thermophilus</i>. This apparent lack of activity was discovered to result from transcriptional repression by the nucleoid protein H-NS. Despite extensive evidence arguing against such roles, some studies still present <i>E. coli</i> CRISPR-Cas systems in the context of anti-phage and/or anti-plasmid activities. Here, the studies that led to our understanding of its cryptic nature are highlighted, along with ongoing research to uncover potential alternative functions in <i>E. coli</i>.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00402020"},"PeriodicalIF":0.0,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810786","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":"Siderophore cephalosporins.","authors":"Malcolm G P Page","doi":"10.1128/ecosalplus.esp-0015-2022","DOIUrl":"https://doi.org/10.1128/ecosalplus.esp-0015-2022","url":null,"abstract":"<p><p>Siderophore cephalosporins are designed to exploit bacterial nutrient uptake systems to gain accelerated uptake across the outer membrane of Gram-negative bacteria. They contain iron (III) binding motifs that allow them to form complexes that will be recognized as potential substrates by iron-siderophore transport systems. Research during the last five decades has culminated in the approval for clinical use of the siderophore cephalosporin cefiderocol, which incorporates accumulated learning from investigations of structural features that enhance resistance toward hydrolysis by β-lactamases, that promote bacterial membrane permeability, and that confer long pharmacokinetic half-life in the human host.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00152022"},"PeriodicalIF":0.0,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794939","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":"Spatio-temporal organization of the <i>E. coli</i> chromosome from base to cellular length scales.","authors":"Sonya K Royzenblat, Lydia Freddolino","doi":"10.1128/ecosalplus.esp-0001-2022","DOIUrl":"10.1128/ecosalplus.esp-0001-2022","url":null,"abstract":"<p><p><i>Escherichia coli</i> has been a vital model organism for studying chromosomal structure, thanks, in part, to its small and circular genome (4.6 million base pairs) and well-characterized biochemical pathways. Over the last several decades, we have made considerable progress in understanding the intricacies of the structure and subsequent function of the <i>E. coli</i> nucleoid. At the smallest scale, DNA, with no physical constraints, takes on a shape reminiscent of a randomly twisted cable, forming mostly random coils but partly affected by its stiffness. This ball-of-spaghetti-like shape forms a structure several times too large to fit into the cell. Once the physiological constraints of the cell are added, the DNA takes on overtwisted (negatively supercoiled) structures, which are shaped by an intricate interplay of many proteins carrying out essential biological processes. At shorter length scales (up to about 1 kb), nucleoid-associated proteins organize and condense the chromosome by inducing loops, bends, and forming bridges. Zooming out further and including cellular processes, topological domains are formed, which are flanked by supercoiling barriers. At the megabase-scale both large, highly self-interacting regions (macrodomains) and strong contacts between distant but co-regulated genes have been observed. At the largest scale, the nucleoid forms a helical ellipsoid. In this review, we will explore the history and recent advances that pave the way for a better understanding of <i>E. coli</i> chromosome organization and structure, discussing the cellular processes that drive changes in DNA shape, and what contributes to compaction and formation of dynamic structures, and in turn how bacterial chromatin affects key processes such as transcription and replication.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00012022"},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11636183/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141305697","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":"Genetic engineering of <i>Salmonella</i> spp. for novel vaccine strategies and therapeutics.","authors":"Garima Bansal, Mostafa Ghanem, Khandra T Sears, James E Galen, Sharon M Tennant","doi":"10.1128/ecosalplus.esp-0004-2023","DOIUrl":"10.1128/ecosalplus.esp-0004-2023","url":null,"abstract":"<p><p><i>Salmonella enterica</i> is a diverse species that infects both humans and animals. <i>S. enterica</i> subspecies <i>enterica</i> consists of more than 1,500 serovars. Unlike typhoidal <i>Salmonella</i> serovars which are human host-restricted, non-typhoidal <i>Salmonella</i> (NTS) serovars are associated with foodborne illnesses worldwide and are transmitted via the food chain. Additionally, NTS serovars can cause disease in livestock animals causing significant economic losses. <i>Salmonella</i> is a well-studied model organism that is easy to manipulate and evaluate in animal models of infection. Advances in genetic engineering approaches in recent years have led to the development of <i>Salmonella</i> vaccines for both humans and animals. In this review, we focus on current progress of recombinant live-attenuated <i>Salmonella</i> vaccines, their use as a source of antigens for parenteral vaccines, their use as live-vector vaccines to deliver foreign antigens, and their use as therapeutic cancer vaccines in humans. We also describe development of live-attenuated <i>Salmonella</i> vaccines and live-vector vaccines for use in animals.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00042023"},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11636237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141633036","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":"Type IV pili of <i>Enterobacteriaceae</i> species.","authors":"Janay I Little, Pradip K Singh, Jinlei Zhao, Shakeera Dunn, Hanover Matz, Michael S Donnenberg","doi":"10.1128/ecosalplus.esp-0003-2023","DOIUrl":"10.1128/ecosalplus.esp-0003-2023","url":null,"abstract":"<p><p>Type IV pili (T4Ps) are surface filaments widely distributed among bacteria and archaea. T4Ps are involved in many cellular functions and contribute to virulence in some species of bacteria. Due to the diversity of T4Ps, different properties have been observed for homologous proteins that make up T4Ps in various organisms. In this review, we highlight the essential components of T4Ps, their functions, and similarities to related systems. We emphasize the unique T4Ps of enteric pathogens within the <i>Enterobacteriaceae</i> family, which includes pathogenic strains of <i>Escherichia coli</i> and <i>Salmonella</i>. These include the bundle-forming pilus (BFP) of enteropathogenic <i>E. coli</i> (EPEC), longus (Lng) and colonization factor III (CFA/III) of enterotoxigenic <i>E. coli</i> (ETEC), T4P of <i>Salmonella enterica</i> serovar Typhi, Colonization Factor Citrobacter (CFC) of <i>Citrobacter rodentium</i>, T4P of <i>Yersinia pseudotuberculosis</i>, a ubiquitous T4P that was characterized in enterohemorrhagic <i>E. coli</i> (EHEC), and the R64 plasmid thin pilus. Finally, we highlight areas for further study.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00032023"},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11636386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139641811","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":"Type I toxin-antitoxin systems in bacteria: from regulation to biological functions.","authors":"Selene F H Shore, Florian H Leinberger, Elizabeth M Fozo, Bork A Berghoff","doi":"10.1128/ecosalplus.esp-0025-2022","DOIUrl":"10.1128/ecosalplus.esp-0025-2022","url":null,"abstract":"<p><p>Toxin-antitoxin systems are ubiquitous in the prokaryotic world and widely distributed among chromosomes and mobile genetic elements. Several different toxin-antitoxin system types exist, but what they all have in common is that toxin activity is prevented by the cognate antitoxin. In type I toxin-antitoxin systems, toxin production is controlled by an RNA antitoxin and by structural features inherent to the toxin messenger RNA. Most type I toxins are small membrane proteins that display a variety of cellular effects. While originally discovered as modules that stabilize plasmids, chromosomal type I toxin-antitoxin systems may also stabilize prophages, or serve important functions upon certain stress conditions and contribute to population-wide survival strategies. Here, we will describe the intricate RNA-based regulation of type I toxin-antitoxin systems and discuss their potential biological functions.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00252022"},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11636113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141065100","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":"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}