EcoSal Plus最新文献_第3页

Characterizing the Pathogenic Potential of Crohn's Disease-Associated Adherent-Invasive Escherichia coli. 确定克罗恩病相关粘附侵袭性大肠埃希菌的致病潜能。

EcoSal Plus Pub Date : 2023-12-12 Epub Date: 2023-05-17 DOI: 10.1128/ecosalplus.esp-0018-2022

Megan T Zangara, Lena Darwish, Brian K Coombes

{"title":"Characterizing the Pathogenic Potential of Crohn's Disease-Associated Adherent-Invasive Escherichia coli.","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":"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 Enterobacteriaceae 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 Escherichia coli subtype called adherent-invasive E. coli (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 in vitro 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.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","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":"9509596","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}

引用次数: 0

The EcoCyc Database (2023). EcoCyc数据库(2023)。

EcoSal Plus Pub Date : 2023-12-12 Epub Date: 2023-05-11 DOI: 10.1128/ecosalplus.esp-0002-2023

Peter D Karp, Suzanne Paley, Ron Caspi, Anamika Kothari, Markus Krummenacker, Peter E Midford, Lisa R Moore, Pallavi Subhraveti, Socorro Gama-Castro, Victor H Tierrafria, Paloma Lara, Luis Muñiz-Rascado, César Bonavides-Martinez, Alberto Santos-Zavaleta, Amanda Mackie, Gwanggyu Sun, Travis A Ahn-Horst, Heejo Choi, Markus W Covert, Julio Collado-Vides, Ian Paulsen

{"title":"The EcoCyc Database (2023).","authors":"Peter D Karp, Suzanne Paley, Ron Caspi, Anamika Kothari, Markus Krummenacker, Peter E Midford, Lisa R Moore, Pallavi Subhraveti, Socorro Gama-Castro, Victor H Tierrafria, Paloma Lara, Luis Muñiz-Rascado, César Bonavides-Martinez, Alberto Santos-Zavaleta, Amanda Mackie, Gwanggyu Sun, Travis A Ahn-Horst, Heejo Choi, Markus W Covert, Julio Collado-Vides, Ian Paulsen","doi":"10.1128/ecosalplus.esp-0002-2023","DOIUrl":"10.1128/ecosalplus.esp-0002-2023","url":null,"abstract":"EcoCyc is a bioinformatics database available online at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists and for biologists who work with related microorganisms. The database includes information pages on each E. coli gene product, metabolite, reaction, operon, and metabolic pathway. The database also includes information on the regulation of gene expression, E. coli gene essentiality, and nutrient conditions that do or do not support the growth of E. coli. 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 online. 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 are also available. This review outlines the data content of EcoCyc and of the procedures by which this content is generated.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"1 1","pages":"eesp00022023"},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10729931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47779970","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}

引用次数: 0

Cell cycle-coordinated maintenance of the Vibrio bipartite genome 细胞周期协调维持弧菌双组基因组

EcoSal Plus Pub Date : 2023-11-22 DOI: 10.1128/ecosalplus.esp-0008-2022

Théophile Niault, Jakub Czarnecki, Morgan Lambérioux, D. Mazel, Marie-Eve Val

引用次数: 0

Structure, Assembly, and Function of Flagella Responsible for Bacterial Locomotion. 细菌运动中鞭毛的结构、组装和功能。

EcoSal Plus Pub Date : 2023-06-01 DOI: 10.1128/ecosalplus.esp-0011-2023

T. Minamino, M. Kinoshita

{"title":"Structure, Assembly, and Function of Flagella Responsible for Bacterial Locomotion.","authors":"T. Minamino, M. Kinoshita","doi":"10.1128/ecosalplus.esp-0011-2023","DOIUrl":"https://doi.org/10.1128/ecosalplus.esp-0011-2023","url":null,"abstract":"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 Salmonella enterica 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 Salmonella flagella.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"1 1","pages":"eesp00112023"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46739585","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}

引用次数: 0

A Brief History of Plasmids. 质粒简史

EcoSal Plus Pub Date : 2022-12-15 Epub Date: 2022-04-04 DOI: 10.1128/ecosalplus.esp-0028-2021

Donald R Helinski

{"title":"A Brief History of Plasmids.","authors":"Donald R Helinski","doi":"10.1128/ecosalplus.esp-0028-2021","DOIUrl":"10.1128/ecosalplus.esp-0028-2021","url":null,"abstract":"In the late 1950s, a number of laboratories took up the study of plasmids once the discovery was made that extrachromosomal antibiotic resistance (R) factors are the responsible agents for the transmissibility of multiple antibiotic resistance among the enterobacteria. The use of incompatibility for the classification of plasmids is now widespread. It seems clear now on the basis of the limited studies to date that the number of incompatibility groups of plasmids will likely be extremely large when one includes plasmids obtained from bacteria that are normal inhabitants of poorly studied natural environments. The presence of both linear chromosomes and linear plasmids is now established for several Streptomyces species. One of the more fascinating developments in plasmid biology was the discovery of linear plasmids in the 1980s. A remarkable feature of the Ti plasmids of Agrobacterium tumefaciens is the presence of two DNA transfer systems. A definitive demonstration that plasmids consisted of duplex DNA came from interspecies conjugal transfer of plasmids followed by separation of plasmid DNA from chromosomal DNA by equilibrium buoyant density centrifugation. The formation of channels for DNA movement and the actual steps involved in DNA transport offer many opportunities for the discovery of proteins with novel activities and for establishing fundamentally new concepts of macromolecular interactions between DNA and specific proteins, membranes, and the peptidoglycan matrix.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"10 1","pages":"eESP00282021"},"PeriodicalIF":0.0,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10729939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10394341","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}

引用次数: 0

Identifying Bacterial Lineages in Salmonella by Flow Cytometry. 通过流式细胞仪识别沙门氏菌中的细菌系。

EcoSal Plus Pub Date : 2022-12-15 Epub Date: 2022-02-04 DOI: 10.1128/ecosalplus.ESP-0018-2021

Rocío Fernández-Fernández, David R Olivenza, María Antonia Sánchez-Romero

引用次数: 0

A Career's Work, the l-Arabinose Operon: How It Functions and How We Learned It. l-阿拉伯糖操作子：它是如何运作的，我们又是如何学习的？

EcoSal Plus Pub Date : 2022-12-15 Epub Date: 2021-08-18 DOI: 10.1128/ecosalplus.ESP-0012-2021

Robert Schleif

{"title":"A Career's Work, the l-Arabinose Operon: How It Functions and How We Learned It.","authors":"Robert Schleif","doi":"10.1128/ecosalplus.ESP-0012-2021","DOIUrl":"10.1128/ecosalplus.ESP-0012-2021","url":null,"abstract":"Very few labs have had the good fortune to have been able to focus for more than 50 years on a relatively narrow research topic and to be in a field in which both basic knowledge and the research technology and methods have progressed as rapidly as they have in molecular biology. My research group, first at Brandeis University and then at Johns Hopkins University, has had this opportunity. In this review, therefore, I will describe largely the work from my laboratory that has spanned this period and which was carried out by 40 plus graduate students, several postdoctoral associates, my technician, and me. In addition to presenting the scientific findings or results, I will place many of the topics in scientific context and, because we needed to develop a good many of the experimental methods behind our findings, I will also describe some of these methods and their importance. Also included will be occasional comments on how the research community or my research group functioned. Because a wide variety of approaches were used throughout our work, no ideal organization of this review is apparent. Therefore, I have chosen to use a hybrid structure in which there are six sections. Within each of the sections, experiments and findings will be described roughly in chronological order. Frequent cross references between parts and sections will be made because some findings and experimental approaches could logically have been described in more than one place.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"10 1","pages":"eESP00122021"},"PeriodicalIF":0.0,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10729937/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10458589","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}

引用次数: 0

Correction for Sande and Whitfield, "Capsules and Extracellular Polysaccharides in Escherichia coli and Salmonella". 对 Sande 和 Whitfield "大肠杆菌和沙门氏菌的胶囊和胞外多糖 "的更正。

EcoSal Plus Pub Date : 2022-12-15 Epub Date: 2022-05-09 DOI: 10.1128/ecosalplus.esp-0007-2022

Caitlin Sande, Chris Whitfield

引用次数: 0

Hypermodified DNA in Viruses of E. coli and Salmonella. 大肠杆菌和沙门氏菌病毒中的超修饰DNA。

EcoSal Plus Pub Date : 2021-12-15 Epub Date: 2021-09-28 DOI: 10.1128/ecosalplus.ESP-0028-2019

Geoffrey Hutinet, Yan-Jiun Lee, Valérie de Crécy-Lagard, Peter R Weigele

{"title":"Hypermodified DNA in Viruses of E. coli and Salmonella.","authors":"Geoffrey Hutinet, Yan-Jiun Lee, Valérie de Crécy-Lagard, Peter R Weigele","doi":"10.1128/ecosalplus.ESP-0028-2019","DOIUrl":"10.1128/ecosalplus.ESP-0028-2019","url":null,"abstract":"The DNA in bacterial viruses collectively contains a rich, yet relatively underexplored, chemical diversity of nucleobases beyond the canonical adenine, guanine, cytosine, and thymine. Herein, we review what is known about the genetic and biochemical basis for the biosynthesis of complex DNA modifications, also called DNA hypermodifications, in the DNA of tailed bacteriophages infecting Escherichia coli and Salmonella enterica. These modifications, and their diversification, likely arose out of the evolutionary arms race between bacteriophages and their cellular hosts. Despite their apparent diversity in chemical structure, the syntheses of various hypermodified bases share some common themes. Hypermodifications form through virus-directed synthesis of noncanonical deoxyribonucleotide triphosphates, direct modification DNA, or a combination of both. Hypermodification enzymes are often encoded in modular operons reminiscent of biosynthetic gene clusters observed in natural product biosynthesis. The study of phage-hypermodified DNA provides an exciting opportunity to expand what is known about the enzyme-catalyzed chemistry of nucleic acids and will yield new tools for the manipulation and interrogation of DNA.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eESP00282019"},"PeriodicalIF":0.0,"publicationDate":"2021-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11163837/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39728487","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}

引用次数: 0

Localization, Assembly, and Activation of the Escherichia coli Cell Division Machinery. 大肠杆菌细胞分裂机制的定位、组装和激活。

EcoSal Plus Pub Date : 2021-12-15 Epub Date: 2021-12-13 DOI: 10.1128/ecosalplus.ESP-0022-2021

Petra Anne Levin, Anuradha Janakiraman

引用次数: 0