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Characterizing the Pathogenic Potential of Crohn's Disease-Associated Adherent-Invasive Escherichia coli. 克罗恩病相关粘附侵袭性大肠杆菌致病潜力的鉴定。
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 <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}
引用次数: 0
The Mar, Sox, and Rob Systems. Mar、Sox和Rob系统。
EcoSal Plus Pub Date : 2023-12-12 Epub Date: 2023-04-04 DOI: 10.1128/ecosalplus.esp-0010-2022
Lon M Chubiz
{"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}
引用次数: 0
Structure, Assembly, and Function of Flagella Responsible for Bacterial Locomotion. 负责细菌运动的鞭毛的结构、组装和功能。
EcoSal Plus Pub Date : 2023-12-12 Epub Date: 2023-06-01 DOI: 10.1128/ecosalplus.esp-0011-2023
Tohru Minamino, Miki Kinoshita
{"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}
引用次数: 0
The Mar, Sox, and Rob Systems. Mar、Sox 和 Rob 系统。
EcoSal Plus Pub Date : 2023-12-12 Epub Date: 2023-04-04 DOI: 10.1128/ecosalplus.esp-0010-2022
Lon M Chubiz
{"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}
引用次数: 0
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":"<p><p>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.</p>","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
{"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":" ","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":"9509599","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
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
{"title":"An Overview of Diverse Strategies To Inactivate <i>Enterobacteriaceae</i>-Targeting Bacteriophages.","authors":"Sada Raza, Mateusz Wdowiak, Jan Paczesny","doi":"10.1128/ecosalplus.esp-0019-2022","DOIUrl":"10.1128/ecosalplus.esp-0019-2022","url":null,"abstract":"<p><p>Bacteriophages are viruses that infect bacteria and thus threaten industrial processes relying on the production executed by bacterial cells. Industries bear huge economic losses due to such recurring and resilient infections. Depending on the specificity of the process, there is a need for appropriate methods of bacteriophage inactivation, with an emphasis on being inexpensive and high efficiency. In this review, we summarize the reports on antiphagents, i.e., antibacteriophage agents on inactivation of bacteriophages. We focused on bacteriophages targeting the representatives of the <i>Enterobacteriaceae</i> family, as its representative, <i>Escherichia coli</i>, is most commonly used in the bio-industry. The review is divided into sections dealing with bacteriophage inactivation by physical factors, chemical factors, and nanotechnology-based solutions.</p>","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00192022"},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10729933/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9493773","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 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":"<p><p>EcoCyc is a bioinformatics database available online 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 is 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 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.</p>","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 <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":" ","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":"<p><p>EcoCyc is a bioinformatics database available online 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 is 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 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.</p>","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
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