EcoSal Plus最新文献_第7页

Mechanisms of Type I-E and I-F CRISPR-Cas Systems in Enterobacteriaceae. 肠杆菌科 I-E 型和 I-F 型 CRISPR-Cas 系统的机制。

EcoSal Plus Pub Date : 2019-02-01 DOI: 10.1128/ecosalplus.ESP-0008-2018

Chaoyou Xue, Dipali G Sashital

{"title":"Mechanisms of Type I-E and I-F CRISPR-Cas Systems in Enterobacteriaceae.","authors":"Chaoyou Xue, Dipali G Sashital","doi":"10.1128/ecosalplus.ESP-0008-2018","DOIUrl":"10.1128/ecosalplus.ESP-0008-2018","url":null,"abstract":"CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against invasion by bacteriophages and other mobile genetic elements. Short fragments of invader DNA are stored as immunological memories within CRISPR (clustered regularly interspaced short palindromic repeat) arrays in the host chromosome. These arrays provide a template for RNA molecules that can guide CRISPR-associated (Cas) proteins to specifically neutralize viruses upon subsequent infection. Over the past 10 years, our understanding of CRISPR-Cas systems has benefited greatly from a number of model organisms. In particular, the study of several members of the Gram-negative Enterobacteriaceae family, especially Escherichia coli and Pectobacterium atrosepticum, have provided significant insights into the mechanisms of CRISPR-Cas immunity. In this review, we provide an overview of CRISPR-Cas systems present in members of the Enterobacteriaceae. We also detail the current mechanistic understanding of the type I-E and type I-F CRISPR-Cas systems that are commonly found in enterobacteria. Finally, we discuss how phages can escape or inactivate CRISPR-Cas systems and the measures bacteria can enact to counter these types of events.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368399/pdf/nihms-1004596.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36980852","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

Architecture, Function, and Substrates of the Type II Secretion System. II型分泌系统的结构、功能和底物。

EcoSal Plus Pub Date : 2019-02-01 DOI: 10.1128/ecosalplus.ESP-0034-2018

Konstantin V Korotkov, Maria Sandkvist

{"title":"Architecture, Function, and Substrates of the Type II Secretion System.","authors":"Konstantin V Korotkov, Maria Sandkvist","doi":"10.1128/ecosalplus.ESP-0034-2018","DOIUrl":"https://doi.org/10.1128/ecosalplus.ESP-0034-2018","url":null,"abstract":"The type II secretion system (T2SS) delivers toxins and a range of hydrolytic enzymes, including proteases, lipases, and carbohydrate-active enzymes, to the cell surface or extracellular space of Gram-negative bacteria. Its contribution to survival of both extracellular and intracellular pathogens as well as environmental species of proteobacteria is evident. This dynamic, multicomponent machinery spans the entire cell envelope and consists of a cytoplasmic ATPase, several inner membrane proteins, a periplasmic pseudopilus, and a secretin pore embedded in the outer membrane. Despite the trans-envelope configuration of the T2S nanomachine, proteins to be secreted engage with the system first once they enter the periplasmic compartment via the Sec or TAT export system. Thus, the T2SS is specifically dedicated to their outer membrane translocation. The many sequence and structural similarities between the T2SS and type IV pili suggest a common origin and argue for a pilus-mediated mechanism of secretion. This minireview describes the structures, functions, and interactions of the individual T2SS components and the general architecture of the assembled T2SS machinery and briefly summarizes the transport and function of a growing list of T2SS exoproteins. Recent advances in cryo-electron microscopy, which have led to an increased understanding of the structure-function relationship of the secretin channel and the pseudopilus, are emphasized.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1128/ecosalplus.ESP-0034-2018","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36562024","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: 43

Type V Secretion in Gram-Negative Bacteria. 革兰氏阴性菌的V型分泌。

EcoSal Plus Pub Date : 2019-02-01 DOI: 10.1128/ecosalplus.ESP-0031-2018

Harris D Bernstein

{"title":"Type V Secretion in Gram-Negative Bacteria.","authors":"Harris D Bernstein","doi":"10.1128/ecosalplus.ESP-0031-2018","DOIUrl":"https://doi.org/10.1128/ecosalplus.ESP-0031-2018","url":null,"abstract":"Type V, or \"autotransporter,\" secretion is a term used to refer to several simple protein export pathways that are found in a wide range of Gram-negative bacteria. Autotransporters are generally single polypeptides that consist of an extracellular (\"passenger\") domain and a β barrel domain that anchors the protein to the outer membrane (OM). Although it was originally proposed that the passenger domain is secreted through a channel formed solely by the covalently linked β barrel domain, experiments performed primarily on the type Va, or \"classical,\" autotransporter pathway have challenged this hypothesis. Several lines of evidence strongly suggest that both the secretion of the passenger domain and the membrane integration of the β barrel domain are catalyzed by the barrel assembly machinery (Bam) complex, a conserved hetero-oligomer that plays an essential role in the assembly of most integral OM proteins. The secretion reaction appears to be driven at least in part by the folding of the passenger domain in the extracellular space. Although many aspects of autotransporter biogenesis remain to be elucidated, it will be especially interesting to determine whether the different classes of proteins that fall under the type V rubric-most of which have not been examined in detail-are assembled by the same basic mechanism as classical autotransporters.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1128/ecosalplus.ESP-0031-2018","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37189300","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: 15

Promises and Challenges of the Type Three Secretion System Injectisome as an Antivirulence Target. 将第三类分泌系统注射体作为抗病毒目标的前景与挑战

EcoSal Plus Pub Date : 2019-02-01 DOI: 10.1128/ecosalplus.ESP-0032-2018

Alyssa C Fasciano, Lamyaa Shaban, Joan Mecsas

{"title":"Promises and Challenges of the Type Three Secretion System Injectisome as an Antivirulence Target.","authors":"Alyssa C Fasciano, Lamyaa Shaban, Joan Mecsas","doi":"10.1128/ecosalplus.ESP-0032-2018","DOIUrl":"10.1128/ecosalplus.ESP-0032-2018","url":null,"abstract":"Antibiotic resistance is a major public health threat that has stimulated the scientific community to search for nontraditional therapeutic targets. Because virulence, but not the growth, of many Gram-negative bacterial pathogens depends on the multicomponent type three secretion system injectisome (T3SSi), the T3SSi has been an attractive target for identifying small molecules, peptides, and monoclonal antibodies that inhibit its function to render the pathogen avirulent. While many small-molecule lead compounds have been identified in whole-cell-based high-throughput screens (HTSs), only a few protein targets of these compounds are known; such knowledge is an important step to developing more potent and specific inhibitors. Evaluation of the efficacy of compounds in animal studies is ongoing. Some efforts involving the development of antibodies and vaccines that target the T3SSi are further along and include an antibody that is currently in phase II clinical trials. Continued research into these antivirulence therapies, used alone or in combination with traditional antibiotics, requires combined efforts from both pharmaceutical companies and academic labs.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6367940/pdf/nihms-1002889.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36966819","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 TAM: A Translocation and Assembly Module of the β-Barrel Assembly Machinery in Bacterial Outer Membranes. TAM:细菌外膜β-桶式组装机制的易位和组装模块。

EcoSal Plus Pub Date : 2019-02-01 DOI: 10.1128/ecosalplus.ESP-0036-2018

Christopher J Stubenrauch, Trevor Lithgow

引用次数: 19

Invasive Nontyphoidal Salmonella Disease in Africa. 非洲侵袭性非伤寒沙门氏菌病。

EcoSal Plus Pub Date : 2019-01-01 DOI: 10.1128/ecosalplus.ESP-0007-2018

James J Gilchrist, Calman A MacLennan

{"title":"Invasive Nontyphoidal Salmonella Disease in Africa.","authors":"James J Gilchrist, Calman A MacLennan","doi":"10.1128/ecosalplus.ESP-0007-2018","DOIUrl":"https://doi.org/10.1128/ecosalplus.ESP-0007-2018","url":null,"abstract":"Nontyphoidal salmonellae (NTS) are a major cause of invasive (iNTS) disease in sub-Saharan Africa, manifesting as bacteremia and meningitis. Available epidemiological data indicate that iNTS disease is endemic in much of the region. Antimicrobial resistance is common and case fatality rates are high. There are well-characterized clinical associations with iNTS disease, including young age, HIV infection, malaria, malnutrition, anemia, and sickle cell disease. However, the clinical presentation of iNTS disease is often with fever alone, so clinical diagnosis is impossible without blood culture confirmation. No vaccine is currently available, making this a priority area for global health research. Over the past ten years, it has emerged that iNTS disease in Africa is caused by distinct pathovars of Salmonella Typhimurium, belonging to sequence type ST313, and Salmonella Enteritidis. These are characterized by genome degradation and appear to be adapting to an invasive lifestyle. Investigation of rare patients with primary immunodeficiencies has suggested a key role for interferon gamma-mediated immunity in host defense against NTS. This concept has been supported by recent population-based host genetic studies in African children. In contrast, immunoepidemiological studies from Africa indicate an important role for antibody for protective immunity, supporting the development of antibody-inducing vaccines against iNTS disease. With candidate O-antigen-based vaccines due to enter clinical trials in the near future, research efforts should focus on understanding the relative contributions of antibody and cell-mediated immunity to protection against iNTS disease in humans.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1128/ecosalplus.ESP-0007-2018","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36864950","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: 66

EcoSal Plus Pub Date : 2019-01-01 DOI: 10.1128/ecosalplus.ESP-0030-2018

Denis Duché, Laetitia Houot

{"title":"Similarities and Differences between Colicin and Filamentous Phage Uptake by Bacterial Cells.","authors":"Denis Duché, Laetitia Houot","doi":"10.1128/ecosalplus.ESP-0030-2018","DOIUrl":"https://doi.org/10.1128/ecosalplus.ESP-0030-2018","url":null,"abstract":"Gram-negative bacteria have evolved a complex envelope to adapt and survive in a broad range of ecological niches. This physical barrier is the first line of defense against noxious compounds and viral particles called bacteriophages. Colicins are a family of bactericidal proteins produced by and toxic to Escherichia coli and closely related bacteria. Filamentous phages have a complex structure, composed of at least five capsid proteins assembled in a long thread-shaped particle, that protects the viral DNA. Despite their difference in size and complexity, group A colicins and filamentous phages both parasitize multiprotein complexes of their sensitive host for entry. They first bind to a receptor located at the surface of the target bacteria before specifically recruiting components of the Tol system to cross the outer membrane and find their way through the periplasm. The Tol system is thought to use the proton motive force of the inner membrane to maintain outer membrane integrity during the life cycle of the cell. This review describes the sequential docking mechanisms of group A colicins and filamentous phages during their uptake by their bacterial host, with a specific focus on the translocation step, promoted by interactions with the Tol system.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1128/ecosalplus.ESP-0030-2018","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36885427","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: 11

Aminoglycoside Revival: Review of a Historically Important Class of Antimicrobials Undergoing Rejuvenation. 氨基糖苷类药物的复兴:历史上一类重要抗菌剂的回顾。

EcoSal Plus Pub Date : 2018-11-01 DOI: 10.1128/ecosalplus.ESP-0002-2018

Alisa W Serio, Tiffany Keepers, Logan Andrews, Kevin M Krause

{"title":"Aminoglycoside Revival: Review of a Historically Important Class of Antimicrobials Undergoing Rejuvenation.","authors":"Alisa W Serio, Tiffany Keepers, Logan Andrews, Kevin M Krause","doi":"10.1128/ecosalplus.ESP-0002-2018","DOIUrl":"https://doi.org/10.1128/ecosalplus.ESP-0002-2018","url":null,"abstract":"Aminoglycosides are cidal inhibitors of bacterial protein synthesis that have been utilized for the treatment of serious bacterial infections for almost 80 years. There have been approximately 15 members of this class approved worldwide for the treatment of a variety of infections, many serious and life threatening. While aminoglycoside use declined due to the introduction of other antibiotic classes such as cephalosporins, fluoroquinolones, and carbapenems, there has been a resurgence of interest in the class as multidrug-resistant pathogens have spread globally. Furthermore, aminoglycosides are recommended as part of combination therapy for empiric treatment of certain difficult-to-treat infections. The development of semisynthetic aminoglycosides designed to overcome common aminoglycoside resistance mechanisms, and the shift to once-daily dosing, has spurred renewed interest in the class. Plazomicin is the first new aminoglycoside to be approved by the FDA in nearly 40 years, marking the successful start of a new campaign to rejuvenate the class.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1128/ecosalplus.ESP-0002-2018","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36690676","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: 64

The EcoCyc Database. EcoCyc 数据库。

EcoSal Plus Pub Date : 2018-11-01 DOI: 10.1128/ecosalplus.ESP-0006-2018

Peter D Karp, Wai Kit Ong, Suzanne Paley, Richard Billington, Ron Caspi, Carol Fulcher, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Peter E Midford, Pallavi Subhraveti, Socorro Gama-Castro, Luis Muñiz-Rascado, César Bonavides-Martinez, Alberto Santos-Zavaleta, Amanda Mackie, Julio Collado-Vides, Ingrid M Keseler, Ian Paulsen

{"title":"The EcoCyc Database.","authors":"Peter D Karp, Wai Kit Ong, Suzanne Paley, Richard Billington, Ron Caspi, Carol Fulcher, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Peter E Midford, Pallavi Subhraveti, Socorro Gama-Castro, Luis Muñiz-Rascado, César Bonavides-Martinez, Alberto Santos-Zavaleta, Amanda Mackie, Julio Collado-Vides, Ingrid M Keseler, Ian Paulsen","doi":"10.1128/ecosalplus.ESP-0006-2018","DOIUrl":"10.1128/ecosalplus.ESP-0006-2018","url":null,"abstract":"EcoCyc is a bioinformatics database available 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 E. coli gene essentiality and on nutrient conditions that do or do not support the growth of E. coli. The website and downloadable software contain tools for 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. 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":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6504970/pdf/nihms-1017975.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36646760","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 Introduction to the Structure and Function of the Catalytic Core Enzyme of Escherichia coli RNA Polymerase. 大肠杆菌RNA聚合酶催化核心酶的结构和功能介绍。

EcoSal Plus Pub Date : 2018-08-01 DOI: 10.1128/ecosalplus.ESP-0004-2018

Catherine Sutherland, Katsuhiko S Murakami

引用次数: 25