EcoSal Plus最新文献_第5页

Iron Transport and Metabolism in Escherichia, Shigella, and Salmonella. 埃希氏菌、志贺氏菌和沙门氏菌中的铁转运和代谢。

EcoSal Plus Pub Date : 2021-12-15 DOI: 10.1128/ecosalplus.ESP-0034-2020

Alexandra R Mey, Camilo Gómez-Garzón, Shelley M Payne

{"title":"Iron Transport and Metabolism in Escherichia, Shigella, and Salmonella.","authors":"Alexandra R Mey, Camilo Gómez-Garzón, Shelley M Payne","doi":"10.1128/ecosalplus.ESP-0034-2020","DOIUrl":"https://doi.org/10.1128/ecosalplus.ESP-0034-2020","url":null,"abstract":"Iron is an essential element for Escherichia, Salmonella, and Shigella species. The acquisition of sufficient amounts of iron is difficult in many environments, including the intestinal tract, where these bacteria usually reside. Members of these genera have multiple iron transport systems to transport both ferrous and ferric iron. These include transporters for free ferrous iron, ferric iron associated with chelators, and heme. The numbers and types of transport systems in any species reflect the diversity of niches that it can inhabit. Many of the iron transport genes are found on mobile genetic elements or pathogenicity islands, and there is evidence of the spread of the genes among different species and pathotypes. This is notable among the pathogenic members of the genera in which iron transport systems acquired by horizontal gene transfer allow the bacteria to overcome host innate defenses that act to restrict the availability of iron to the pathogen. The need for iron is balanced by the need to avoid iron overload since excess iron is toxic to the cell. Genes for iron transport and metabolism are tightly regulated and respond to environmental cues, including iron availability, oxygen, and temperature. Master regulators, the iron sensor Fur and the Fur-regulated small RNA (sRNA) RyhB, coordinate the expression of iron transport and cellular metabolism genes in response to the availability of iron.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"9 2","pages":"eESP00342020"},"PeriodicalIF":0.0,"publicationDate":"2021-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8865473/pdf/nihms-1780222.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10462647","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: 18

Dynamics of Proteins and Macromolecular Machines in Escherichia coli. 大肠杆菌中蛋白质和大分子机器的动力学。

EcoSal Plus Pub Date : 2021-12-15 Epub Date: 2021-06-01 DOI: 10.1128/ecosalplus.ESP-0011-2020

Maxime Leroux, Nicolas Soubry, Rodrigo Reyes-Lamothe

引用次数: 0

Knowns and Unknowns of Vitamin B₆ Metabolism in Escherichia coli. 大肠杆菌中维生素B6代谢的已知和未知。

EcoSal Plus Pub Date : 2021-04-01 DOI: 10.1128/ecosalplus.ESP-0004-2021

Angela Tramonti, Caterina Nardella, Martino L di Salvo, Anna Barile, Federico D'Alessio, Valérie de Crécy-Lagard, Roberto Contestabile

{"title":"Knowns and Unknowns of Vitamin B6 Metabolism in Escherichia coli.","authors":"Angela Tramonti, Caterina Nardella, Martino L di Salvo, Anna Barile, Federico D'Alessio, Valérie de Crécy-Lagard, Roberto Contestabile","doi":"10.1128/ecosalplus.ESP-0004-2021","DOIUrl":"https://doi.org/10.1128/ecosalplus.ESP-0004-2021","url":null,"abstract":"Vitamin B6 is an ensemble of six interconvertible vitamers: pyridoxine (PN), pyridoxamine (PM), pyridoxal (PL), and their 5'-phosphate derivatives, PNP, PMP, and PLP. Pyridoxal 5'-phosphate is a coenzyme in a variety of enzyme reactions concerning transformations of amino and amino acid compounds. This review summarizes all known and putative PLP-binding proteins found in the Escherichia coli MG1655 proteome. PLP can have toxic effects since it contains a very reactive aldehyde group at its 4' position that easily forms aldimines with primary and secondary amines and reacts with thiols. Most PLP is bound either to the enzymes that use it as a cofactor or to PLP carrier proteins, protected from the cellular environment but at the same time readily transferable to PLP-dependent apoenzymes. E. coli and its relatives synthesize PLP through the seven-step deoxyxylulose-5-phosphate (DXP)-dependent pathway. Other bacteria synthesize PLP in a single step, through a so-called DXP-independent pathway. Although the DXP-dependent pathway was the first to be revealed, the discovery of the widespread DXP-independent pathway determined a decline of interest in E. coli vitamin B6 metabolism. In E. coli, as in most organisms, PLP can also be obtained from PL, PN, and PM, imported from the environment or recycled from protein turnover, via a salvage pathway. Our review deals with all aspects of vitamin B6 metabolism in E. coli, from transcriptional to posttranslational regulation. A critical interpretation of results is presented, in particular, concerning the most obscure aspects of PLP homeostasis and delivery to PLP-dependent enzymes.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8995791/pdf/nihms-1780781.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25533630","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: 9

Ancient Antibiotics, Ancient Resistance. 古老的抗生素，古老的抵抗力。

EcoSal Plus Pub Date : 2021-03-01 DOI: 10.1128/ecosalplus.ESP-0027-2020

Nicholas Waglechner, Elizabeth J Culp, Gerard D Wright

{"title":"Ancient Antibiotics, Ancient Resistance.","authors":"Nicholas Waglechner, Elizabeth J Culp, Gerard D Wright","doi":"10.1128/ecosalplus.ESP-0027-2020","DOIUrl":"10.1128/ecosalplus.ESP-0027-2020","url":null,"abstract":"As the spread of antibiotic resistance threatens our ability to treat infections, avoiding the return of a preantibiotic era requires the discovery of new drugs. While therapeutic use of antibiotics followed by the inevitable selection of resistance is a modern phenomenon, these molecules and the genetic determinants of resistance were in use by environmental microbes long before humans discovered them. In this review, we discuss evidence that antibiotics and resistance were present in the environment before anthropogenic use, describing techniques including direct sampling of ancient DNA and phylogenetic analyses that are used to reconstruct the past. We also pay special attention to the ecological and evolutionary forces that have shaped the natural history of antibiotic biosynthesis, including a discussion of competitive versus signaling roles for antibiotics, proto-resistance, and substrate promiscuity of biosynthetic and resistance enzymes. Finally, by applying an evolutionary lens, we describe concepts governing the origins and evolution of biosynthetic gene clusters and cluster-associated resistance determinants. These insights into microbes' use of antibiotics in nature, a game they have been playing for millennia, can provide inspiration for discovery technologies and management strategies to combat the growing resistance crisis.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11163840/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25501260","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

Role of Plasmids in the Ecology and Evolution of "High-Risk" Extraintestinal Pathogenic Escherichia coli Clones. 质粒在 "高风险 "肠道外致病性大肠杆菌克隆的生态学和进化中的作用。

EcoSal Plus Pub Date : 2021-02-01 DOI: 10.1128/ecosalplus.ESP-0013-2020

Timothy J Johnson

引用次数: 0

Peptidoglycan: Structure, Synthesis, and Regulation. 肽聚糖：结构、合成和调节。

EcoSal Plus Pub Date : 2021-01-01 DOI: 10.1128/ecosalplus.ESP-0010-2020

Shambhavi Garde, Pavan Kumar Chodisetti, Manjula Reddy

{"title":"Peptidoglycan: Structure, Synthesis, and Regulation.","authors":"Shambhavi Garde, Pavan Kumar Chodisetti, Manjula Reddy","doi":"10.1128/ecosalplus.ESP-0010-2020","DOIUrl":"10.1128/ecosalplus.ESP-0010-2020","url":null,"abstract":"Peptidoglycan is a defining feature of the bacterial cell wall. Initially identified as a target of the revolutionary beta-lactam antibiotics, peptidoglycan has become a subject of much interest for its biology, its potential for the discovery of novel antibiotic targets, and its role in infection. Peptidoglycan is a large polymer that forms a mesh-like scaffold around the bacterial cytoplasmic membrane. Peptidoglycan synthesis is vital at several stages of the bacterial cell cycle: for expansion of the scaffold during cell elongation and for formation of a septum during cell division. It is a complex multifactorial process that includes formation of monomeric precursors in the cytoplasm, their transport to the periplasm, and polymerization to form a functional peptidoglycan sacculus. These processes require spatio-temporal regulation for successful assembly of a robust sacculus to protect the cell from turgor and determine cell shape. A century of research has uncovered the fundamentals of peptidoglycan biology, and recent studies employing advanced technologies have shed new light on the molecular interactions that govern peptidoglycan synthesis. Here, we describe the peptidoglycan structure, synthesis, and regulation in rod-shaped bacteria, particularly Escherichia coli, with a few examples from Salmonella and other diverse organisms. We focus on the pathway of peptidoglycan sacculus elongation, with special emphasis on discoveries of the past decade that have shaped our understanding of peptidoglycan biology.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11168573/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38773322","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

Mechanisms of Theta Plasmid Replication in Enterobacteria and Implications for Adaptation to Its Host. 肠杆菌中Theta质粒复制的机制及其对宿主的适应意义

EcoSal Plus Pub Date : 2020-11-01 DOI: 10.1128/ecosalplus.ESP-0026-2019

Jay W Kim, Vega Bugata, Gerardo Cortés-Cortés, Giselle Quevedo-Martínez, Manel Camps

{"title":"Mechanisms of Theta Plasmid Replication in Enterobacteria and Implications for Adaptation to Its Host.","authors":"Jay W Kim, Vega Bugata, Gerardo Cortés-Cortés, Giselle Quevedo-Martínez, Manel Camps","doi":"10.1128/ecosalplus.ESP-0026-2019","DOIUrl":"10.1128/ecosalplus.ESP-0026-2019","url":null,"abstract":"Plasmids are autonomously replicating sequences that help cells adapt to diverse stresses. Theta plasmids are the most frequent plasmid class in enterobacteria. They co-opt two host replication mechanisms: replication at oriC, a DnaA-dependent pathway leading to replisome assembly (theta class A), and replication fork restart, a PriA-dependent pathway leading to primosome assembly through primer extension and D-loop formation (theta classes B, C, and D). To ensure autonomy from the host's replication and to facilitate copy number regulation, theta plasmids have unique mechanisms of replication initiation at the plasmid origin of replication (ori). Tight plasmid copy number regulation is essential because of the major and direct impact plasmid gene dosage has on gene expression. The timing of plasmid replication and segregation are also critical for optimizing plasmid gene expression. Therefore, we propose that plasmid replication needs to be understood in its biological context, where complex origins of replication (redundant origins, mosaic and cointegrated replicons), plasmid segregation, and toxin-antitoxin systems are often present. Highlighting their tight functional integration with ori function, we show that both partition and toxin-antitoxin systems tend to be encoded in close physical proximity to the ori in a large collection of Escherichia coli plasmids. We also propose that adaptation of plasmids to their host optimizes their contribution to the host's fitness while restricting access to broad genetic diversity, and we argue that this trade-off between adaptation to host and access to genetic diversity is likely a determinant factor shaping the distribution of replicons in populations of enterobacteria.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7724965/pdf/nihms-1636126.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38629114","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

Prokaryotic Organelles: Bacterial Microcompartments in E. coli and Salmonella. 原核生物细胞器：大肠杆菌和沙门氏菌中的细菌微隔。

EcoSal Plus Pub Date : 2020-10-01 DOI: 10.1128/ecosalplus.ESP-0025-2019

Katie L Stewart, Andrew M Stewart, Thomas A Bobik

{"title":"Prokaryotic Organelles: Bacterial Microcompartments in E. coli and Salmonella.","authors":"Katie L Stewart, Andrew M Stewart, Thomas A Bobik","doi":"10.1128/ecosalplus.ESP-0025-2019","DOIUrl":"10.1128/ecosalplus.ESP-0025-2019","url":null,"abstract":"Bacterial microcompartments (MCPs) are proteinaceous organelles consisting of a metabolic pathway encapsulated within a selectively permeable protein shell. Hundreds of species of bacteria produce MCPs of at least nine different types, and MCP metabolism is associated with enteric pathogenesis, cancer, and heart disease. This review focuses chiefly on the four types of catabolic MCPs (metabolosomes) found in Escherichia coli and Salmonella: the propanediol utilization (pdu), ethanolamine utilization (eut), choline utilization (cut), and glycyl radical propanediol (grp) MCPs. Although the great majority of work done on catabolic MCPs has been carried out with Salmonella and E. coli, research outside the group is mentioned where necessary for a comprehensive understanding. Salient characteristics found across MCPs are discussed, including enzymatic reactions and shell composition, with particular attention paid to key differences between classes of MCPs. We also highlight relevant research on the dynamic processes of MCP assembly, protein targeting, and the mechanisms that underlie selective permeability. Lastly, we discuss emerging biotechnology applications based on MCP principles and point out challenges, unanswered questions, and future directions.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7552817/pdf/nihms-1626342.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38469310","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

Bacteriophage Infections of Biofilms of Health Care-Associated Pathogens: Klebsiella pneumoniae. 卫生保健相关病原体：肺炎克雷伯菌生物膜的噬菌体感染。

EcoSal Plus Pub Date : 2020-10-01 DOI: 10.1128/ecosalplus.ESP-0029-2019

Ariel J Santiago, Rodney M Donlan

{"title":"Bacteriophage Infections of Biofilms of Health Care-Associated Pathogens: Klebsiella pneumoniae.","authors":"Ariel J Santiago, Rodney M Donlan","doi":"10.1128/ecosalplus.ESP-0029-2019","DOIUrl":"10.1128/ecosalplus.ESP-0029-2019","url":null,"abstract":"Members of the family Enterobacteriaceae, such as Klebsiella pneumoniae, are considered both serious and urgent public health threats. Biofilms formed by these health care-associated pathogens can lead to negative and costly health outcomes. The global spread of antibiotic resistance, coupled with increased tolerance to antimicrobial treatments in biofilm-associated bacteria, highlights the need for novel strategies to overcome treatment hurdles. Bacteriophages (phages), or viruses that infect bacteria, have reemerged as one such potential strategy. Virulent phages are capable of infecting and killing their bacterial hosts, in some cases producing depolymerases that are able to hydrolyze biofilms. Phage therapy does have its limitations, however, including potential narrow host ranges, development of bacterial resistance to infection, and the potential spread of phage-encoded virulence genes. That being said, advances in phage isolation, screening, and genome sequencing tools provide an upside in overcoming some of these limitations and open up the possibilities of using phages as effective biofilm control agents.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10242522/pdf/nihms-1901609.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9951989","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

Escherichia coli Residency in the Gut of Healthy Human Adults. 健康成年人肠道中的大肠埃希氏菌残留物

EcoSal Plus Pub Date : 2020-09-01 DOI: 10.1128/ecosalplus.ESP-0003-2020

Jonathan N V Martinson, Seth T Walk

引用次数: 0