EcoSal Plus最新文献_第3页

Repeat-Unit Elongations To Produce Bacterial Complex Long Polysaccharide Chains, an O-Antigen Perspective. 从 O 抗原的角度看重复单位延伸产生细菌复合长多糖链

EcoSal Plus Pub Date : 2023-12-12 Epub Date: 2023-01-09 DOI: 10.1128/ecosalplus.esp-0020-2022

Yaoqin Hong, Dalong Hu, Anthony D Verderosa, Jilong Qin, Makrina Totsika, Peter R Reeves

{"title":"Repeat-Unit Elongations To Produce Bacterial Complex Long Polysaccharide Chains, an O-Antigen Perspective.","authors":"Yaoqin Hong, Dalong Hu, Anthony D Verderosa, Jilong Qin, Makrina Totsika, Peter R Reeves","doi":"10.1128/ecosalplus.esp-0020-2022","DOIUrl":"10.1128/ecosalplus.esp-0020-2022","url":null,"abstract":"The O-antigen, a long polysaccharide that constitutes the distal part of the outer membrane-anchored lipopolysaccharide, is one of the critical components in the protective outer membrane of Gram-negative bacteria. Most species produce one of the structurally diverse O-antigens, with nearly all the polysaccharide components having complex structures made by the Wzx/Wzy pathway. This pathway produces repeat-units of mostly 3-8 sugars on the cytosolic face of the cytoplasmic membrane that is translocated by Wzx flippase to the periplasmic face and polymerized by Wzy polymerase to give long-chain polysaccharides. The Wzy polymerase is a highly diverse integral membrane protein typically containing 10-14 transmembrane segments. Biochemical evidence confirmed that Wzy polymerase is the sole driver of polymerization, and recent progress also began to demystify its interacting partner, Wzz, shedding some light to speculate how the proteins may operate together during polysaccharide biogenesis. However, our knowledge of how the highly variable Wzy proteins work as part of the O-antigen processing machinery remains poor. Here, we discuss the progress to the current understanding of repeat-unit polymerization and propose an updated model to explain the formation of additional short chain O-antigen polymers found in the lipopolysaccharide of diverse Gram-negative species and their importance in the biosynthetic process.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00202022"},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10729934/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9871090","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

DNA Segregation in Enterobacteria. 肠杆菌的 DNA 分离。

EcoSal Plus Pub Date : 2023-12-12 Epub Date: 2023-05-09 DOI: 10.1128/ecosalplus.esp-0038-2020

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

引用次数: 0

An Overview of Diverse Strategies To Inactivate Enterobacteriaceae-Targeting Bacteriophages. 灭活肠杆菌属靶向噬菌体的多种策略概述

EcoSal Plus Pub Date : 2023-12-12 Epub Date: 2023-01-18 DOI: 10.1128/ecosalplus.esp-0019-2022

Sada Raza, Mateusz Wdowiak, Jan Paczesny

引用次数: 0

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

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":" ","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":"10054128","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

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