EcoSal PlusPub Date : 2025-07-24DOI: 10.1128/ecosalplus.esp-0002-2024
Jaan Männik, Jaana Männik, Chathuddasie Amarasinghe, Mu-Hung Chang, Maxim O Lavrentovich
{"title":"The role of macromolecular crowders in the formation and compaction of the <i>Escherichia coli</i> nucleoid.","authors":"Jaan Männik, Jaana Männik, Chathuddasie Amarasinghe, Mu-Hung Chang, Maxim O Lavrentovich","doi":"10.1128/ecosalplus.esp-0002-2024","DOIUrl":"https://doi.org/10.1128/ecosalplus.esp-0002-2024","url":null,"abstract":"<p><p>The chromosomal DNA of <i>Escherichia coli</i> is approximately a thousand times longer than the linear dimensions of the cell it occupies. Nevertheless, it fills only about one-half of the cytosolic volume of the cell. The volume pervaded by the chromosomal DNA is known as nucleoid. The nucleoid is a ribosome-depleted region that behaves as a distinct liquid-like phase within the cytosol. In most bacteria, including <i>E. coli</i>, which lack membrane-enclosed organelles, the phase separation between the nucleoid and the ribosome-rich cytosolic fraction represents the most prominent organizational principle of the cell's cytosolic interior. This review explores the mechanisms driving nucleoid phase separation, including the roles of DNA-binding proteins, supercoiling, and active DNA looping. Recent studies highlight macromolecular crowding as the dominant factor governing this spatial organization. The main focus of this review is on experimental and theoretical works-ranging from <i>in vitro</i> and <i>in vivo</i> studies to polymer physics-based models-that elucidate how macromolecular crowding drives nucleoid phase formation and regulates DNA compaction <i>in E. coli</i>.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00022024"},"PeriodicalIF":0.0,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697905","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}
EcoSal PlusPub Date : 2025-07-02DOI: 10.1128/ecosalplus.esp-0018-2023
Nicola Holden, Jeri Barak
{"title":"Microbe-plant interactions of <i>Escherichia coli</i> and <i>Salmonella</i>.","authors":"Nicola Holden, Jeri Barak","doi":"10.1128/ecosalplus.esp-0018-2023","DOIUrl":"https://doi.org/10.1128/ecosalplus.esp-0018-2023","url":null,"abstract":"<p><p><i>Escherichia coli</i> and non-typhoidal <i>Salmonella enterica</i> are capable of persisting and growing in a wide range of environments. Although best known for their interactions and pathogenic phenotypes in warm-blooded animal hosts, they can be located in a diversity of hosts and habitats. This capability has led to foodborne illness arising from multiple sources, including crop plants. It raises key questions about the bacterial traits and adaptations that permit this degree of flexibility. By describing plant features and the associated environments, we illustrate the underlying physiological basis that enables <i>E. coli</i>, including Shiga toxin-producing <i>E. coli,</i> and <i>S. enterica</i> to colonize plant hosts. We follow the distinct stages of the interactions and the different considerations to understand how they will play out and the resulting outcome for the bacteria. Knowledge of the processes involved lays the foundation for understanding and managing real-life scenarios in agriculture and food production and allows predictions for the bacterial responses in the plant environment under changing climatic conditions.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00182023"},"PeriodicalIF":0.0,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144539534","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}
EcoSal PlusPub Date : 2025-06-30DOI: 10.1128/ecosalplus.esp-0011-2024
Viktoria Van Nederveen, Angela R Melton-Celsa
{"title":"Enteroaggregative <i>Escherichia coli</i> (EAEC).","authors":"Viktoria Van Nederveen, Angela R Melton-Celsa","doi":"10.1128/ecosalplus.esp-0011-2024","DOIUrl":"https://doi.org/10.1128/ecosalplus.esp-0011-2024","url":null,"abstract":"<p><p>A cause of diarrhea worldwide, enteroaggregative <i>Escherichia coli</i> (or EAEC) is one of six diarrheagenic <i>E. coli</i> pathotypes. EAEC strains are heterogeneic in terms of virulence factors, adhere strongly to epithelial cells, and produce a strong biofilm. It is the characteristic aggregative adherence on epithelial cells that was both the gold standard of clinical identification and the source of the appellation \"aggregative.\" To understand EAEC in the continuum with other pathogenic <i>E. coli</i>, we discuss the overlap of EAEC with other diarrheagenic <i>E. coli</i> and extraintestinal pathogenic <i>E. coli</i> isolates. Due to the increased use of molecular techniques for the identification of EAEC, the use of various PCR markers and DNA sequencing for EAEC identification and how that correlates to the phenotypic definition is discussed. Aspects of EAEC pathogenesis, including an overview of virulence factors, such as the five aggregative adherence fimbriae (AAF) and SPATEs (serine protease autotransporters of Enterobacteriaceae), will be explored. The advantages and limitations of various EAEC animal models and what is known about human immunity and host factors that influence infection outcomes are outlined. This review includes a synthesis of new discoveries published for the EAEC field, including non-AAF fimbrial adhesins, additional information about post-infection sequelae, and new EAEC models.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00112024"},"PeriodicalIF":0.0,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144526914","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}
EcoSal PlusPub Date : 2025-04-30DOI: 10.1128/ecosalplus.esp-0019-2024
Peter D Karp, Suzanne Paley, Ron Caspi, Anamika Kothari, Markus Krummenacker, Peter E Midford, Lisa R Moore, Pallavi Subhraveti, Socorro Gama-Castro, Víctor H Tierrafria, Paloma Lara, Luis Muñiz-Rascado, César Bonavides-Martinez, Alberto Santos-Zavaleta, Amanda Mackie, Gwanggyu Sun, Travis A Ahn-Horst, Heejo Choi, Riley Juenemann, Cyrus N M Knudsen, Markus W Covert, Julio Collado-Vides, Ian Paulsen
{"title":"The EcoCyc database (2025).","authors":"Peter D Karp, Suzanne Paley, Ron Caspi, Anamika Kothari, Markus Krummenacker, Peter E Midford, Lisa R Moore, Pallavi Subhraveti, Socorro Gama-Castro, Víctor H Tierrafria, Paloma Lara, Luis Muñiz-Rascado, César Bonavides-Martinez, Alberto Santos-Zavaleta, Amanda Mackie, Gwanggyu Sun, Travis A Ahn-Horst, Heejo Choi, Riley Juenemann, Cyrus N M Knudsen, Markus W Covert, Julio Collado-Vides, Ian Paulsen","doi":"10.1128/ecosalplus.esp-0019-2024","DOIUrl":"10.1128/ecosalplus.esp-0019-2024","url":null,"abstract":"<p><p>EcoCyc is a bioinformatics database (DB) available at EcoCyc.org that describes the genome and the biochemical machinery of <i>Escherichia coli</i> K-12 MG1655. The long-term goal of the project was to describe the complete molecular catalog of the <i>E. coli</i> cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of <i>E. coli</i>. EcoCyc is an electronic reference source for <i>E. coli</i> biologists and for biologists who work with related microorganisms. The database includes information pages on each <i>E. coli</i> gene product, metabolite, reaction, operon, and metabolic pathway. The database also includes information on the regulation of gene expression, <i>E. coli</i> gene essentiality, and nutrient conditions that do or do not support the growth of <i>E. coli</i>. The website and downloadable software contain tools for the analysis of high-throughput data sets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc and can be executed via EcoCyc.org. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. Data generated from a whole-cell model that is parameterized from the latest data on EcoCyc is also available. This review outlines the data content of EcoCyc and the procedures by which this content is generated.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00192024"},"PeriodicalIF":0.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143989974","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}
EcoSal PlusPub Date : 2025-04-09DOI: 10.1128/ecosalplus.esp-0040-2020
Edward G Dudley
{"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}
EcoSal PlusPub Date : 2025-04-07DOI: 10.1128/ecosalplus.esp-0015-2022
Malcolm G P Page
{"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}
EcoSal PlusPub Date : 2024-12-12Epub Date: 2024-06-12DOI: 10.1128/ecosalplus.esp-0001-2022
Sonya K Royzenblat, Lydia Freddolino
{"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}
EcoSal PlusPub Date : 2024-12-12Epub Date: 2024-07-18DOI: 10.1128/ecosalplus.esp-0004-2023
Garima Bansal, Mostafa Ghanem, Khandra T Sears, James E Galen, Sharon M Tennant
{"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}
EcoSal PlusPub Date : 2024-12-12Epub Date: 2024-01-31DOI: 10.1128/ecosalplus.esp-0003-2023
Janay I Little, Pradip K Singh, Jinlei Zhao, Shakeera Dunn, Hanover Matz, Michael S Donnenberg
{"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}
EcoSal PlusPub Date : 2024-12-12Epub Date: 2024-05-20DOI: 10.1128/ecosalplus.esp-0025-2022
Selene F H Shore, Florian H Leinberger, Elizabeth M Fozo, Bork A Berghoff
{"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}