EcoSal Plus最新文献_第7页

Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica. 反式作用小核糖核酸及其对大肠杆菌和肠炎沙门氏菌基因表达的影响

EcoSal Plus Pub Date : 2020-03-01 DOI: 10.1128/ecosalplus.ESP-0030-2019

Jens Hör, Gianluca Matera, Jörg Vogel, Susan Gottesman, Gisela Storz

{"title":"Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica.","authors":"Jens Hör, Gianluca Matera, Jörg Vogel, Susan Gottesman, Gisela Storz","doi":"10.1128/ecosalplus.ESP-0030-2019","DOIUrl":"10.1128/ecosalplus.ESP-0030-2019","url":null,"abstract":"The last few decades have led to an explosion in our understanding of the major roles that small regulatory RNAs (sRNAs) play in regulatory circuits and the responses to stress in many bacterial species. Much of the foundational work was carried out with Escherichia coli and Salmonella enterica serovar Typhimurium. The studies of these organisms provided an overview of how the sRNAs function and their impact on bacterial physiology, serving as a blueprint for sRNA biology in many other prokaryotes. They also led to the development of new technologies. In this chapter, we first summarize how these sRNAs were identified, defining them in the process. We discuss how they are regulated and how they act and provide selected examples of their roles in regulatory circuits and the consequences of this regulation. Throughout, we summarize the methodologies that were developed to identify and study the regulatory RNAs, most of which are applicable to other bacteria. Newly updated databases of the known sRNAs in E. coli K-12 and S. enterica Typhimurium SL1344 serve as a reference point for much of the discussion and, hopefully, as a resource for readers and for future experiments to address open questions raised in this review.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112153/pdf/nihms-1551392.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37772749","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

Chromosomal Organization and Regulation of Genetic Function in Escherichia coli Integrates the DNA Analog and Digital Information. 大肠杆菌的染色体组织和遗传功能调控整合了 DNA 模拟信息和数字信息。

EcoSal Plus Pub Date : 2020-02-01 DOI: 10.1128/ecosalplus.ESP-0016-2019

Andrew Travers, Georgi Muskhelishvili

{"title":"Chromosomal Organization and Regulation of Genetic Function in Escherichia coli Integrates the DNA Analog and Digital Information.","authors":"Andrew Travers, Georgi Muskhelishvili","doi":"10.1128/ecosalplus.ESP-0016-2019","DOIUrl":"10.1128/ecosalplus.ESP-0016-2019","url":null,"abstract":"In this article, we summarize our current understanding of the bacterial genetic regulation brought about by decades of studies using the Escherichia coli model. It became increasingly evident that the cellular genetic regulation system is organizationally closed, and a major challenge is to describe its circular operation in quantitative terms. We argue that integration of the DNA analog information (i.e., the probability distribution of the thermodynamic stability of base steps) and digital information (i.e., the probability distribution of unique triplets) in the genome provides a key to understanding the organizational logic of genetic control. During bacterial growth and adaptation, this integration is mediated by changes of DNA supercoiling contingent on environmentally induced shifts in intracellular ionic strength and energy charge. More specifically, coupling of dynamic alterations of the local intrinsic helical repeat in the structurally heterogeneous DNA polymer with structural-compositional changes of RNA polymerase holoenzyme emerges as a fundamental organizational principle of the genetic regulation system. We present a model of genetic regulation integrating the genomic pattern of DNA thermodynamic stability with the gene order and function along the chromosomal OriC-Ter axis, which acts as a principal coordinate system organizing the regulatory interactions in the genome.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11168577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37642536","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

EnvZ/OmpR Two-Component Signaling: An Archetype System That Can Function Noncanonically. EnvZ/OmpR 双组分信号：可发挥非典型功能的原型系统

EcoSal Plus Pub Date : 2020-01-01 DOI: 10.1128/ecosalplus.ESP-0001-2019

Linda J Kenney, Ganesh S Anand

{"title":"EnvZ/OmpR Two-Component Signaling: An Archetype System That Can Function Noncanonically.","authors":"Linda J Kenney, Ganesh S Anand","doi":"10.1128/ecosalplus.ESP-0001-2019","DOIUrl":"10.1128/ecosalplus.ESP-0001-2019","url":null,"abstract":"Two-component regulatory systems represent the major paradigm for signal transduction in prokaryotes. The simplest systems are composed of a sensor kinase and a response regulator. The sensor is often a membrane protein that senses a change in environmental conditions and is autophosphorylated by ATP on a histidine residue. The phosphoryl group is transferred onto an aspartate of the response regulator, which activates the regulator and alters its output, usually resulting in a change in gene expression. In this review, we present a historical view of the archetype EnvZ/OmpR two-component signaling system, and then we provide a new view of signaling based on our recent experiments. EnvZ responds to cytoplasmic signals that arise from changes in the extracellular milieu, and OmpR acts canonically (requiring phosphorylation) to regulate the porin genes and noncanonically (without phosphorylation) to activate the acid stress response. Herein, we describe how insights gleaned from stimulus recognition and response in EnvZ are relevant to nearly all sensor kinases and response regulators.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7192543/pdf/nihms-1062097.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37597224","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

Control of the phoBR Regulon in Escherichia coli. phoBR调控子在大肠杆菌中的控制。

EcoSal Plus Pub Date : 2019-09-01 DOI: 10.1128/ecosalplus.ESP-0006-2019

Stewart G Gardner, William R McCleary

{"title":"Control of the phoBR Regulon in Escherichia coli.","authors":"Stewart G Gardner, William R McCleary","doi":"10.1128/ecosalplus.ESP-0006-2019","DOIUrl":"10.1128/ecosalplus.ESP-0006-2019","url":null,"abstract":"Phosphorus is required for many biological molecules and essential functions, including DNA replication, transcription of RNA, protein translation, posttranslational modifications, and numerous facets of metabolism. In order to maintain the proper level of phosphate for these processes, many bacteria adapt to changes in environmental phosphate levels. The mechanisms for sensing phosphate levels and adapting to changes have been extensively studied for multiple organisms. The phosphate response of Escherichia coli alters the expression of numerous genes, many of which are involved in the acquisition and scavenging of phosphate more efficiently. This review shares findings on the mechanisms by which E. coli cells sense and respond to changes in environmental inorganic phosphate concentrations by reviewing the genes and proteins that regulate this response. The PhoR/PhoB two-component signal transduction system is central to this process and works in association with the high-affinity phosphate transporter encoded by the pstSCAB genes and the PhoU protein. Multiple models to explain how this process is regulated are discussed.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"8 2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11573284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49084318","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

Plasmid Localization and Partition in Enterobacteriaceae. 肠杆菌科细菌中的质粒定位和分区。

EcoSal Plus Pub Date : 2019-06-01 DOI: 10.1128/ecosalplus.ESP-0003-2019

Jean-Yves Bouet, Barbara E Funnell

{"title":"Plasmid Localization and Partition in Enterobacteriaceae.","authors":"Jean-Yves Bouet, Barbara E Funnell","doi":"10.1128/ecosalplus.ESP-0003-2019","DOIUrl":"10.1128/ecosalplus.ESP-0003-2019","url":null,"abstract":"Plasmids are ubiquitous in the microbial world and have been identified in almost all species of bacteria that have been examined. Their localization inside the bacterial cell has been examined for about two decades; typically, they are not randomly distributed, and their positioning depends on copy number and their mode of segregation. Low-copy-number plasmids promote their own stable inheritance in their bacterial hosts by encoding active partition systems, which ensure that copies are positioned in both halves of a dividing cell. High-copy plasmids rely on passive diffusion of some copies, but many remain clustered together in the nucleoid-free regions of the cell. Here we review plasmid localization and partition (Par) systems, with particular emphasis on plasmids from Enterobacteriaceae and on recent results describing the in vivo localization properties and molecular mechanisms of each system. Partition systems also cause plasmid incompatibility such that distinct plasmids (with different replicons) with the same Par system cannot be stably maintained in the same cells. We discuss how partition-mediated incompatibility is a consequence of the partition mechanism.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"8 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11573283/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37319176","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 Twin-Arginine Pathway for Protein Secretion. 蛋白质分泌的双精氨酸途径

EcoSal Plus Pub Date : 2019-06-01 DOI: 10.1128/ecosalplus.ESP-0040-2018

Kelly M Frain, Jan Maarten van Dijl, Colin Robinson

引用次数: 0

Outer Membrane Protein Insertion by the β-barrel Assembly Machine. β桶组装机外膜蛋白插入。

EcoSal Plus Pub Date : 2019-03-01 DOI: 10.1128/ecosalplus.ESP-0035-2018

Dante P Ricci, Thomas J Silhavy

引用次数: 22

Therapeutic Approaches Targeting the Assembly and Function of Chaperone-Usher Pili. 针对伴侣纤毛虫组装和功能的治疗方法。

EcoSal Plus Pub Date : 2019-03-01 DOI: 10.1128/ecosalplus.ESP-0033-2018

John J Psonis, David G Thanassi

{"title":"Therapeutic Approaches Targeting the Assembly and Function of Chaperone-Usher Pili.","authors":"John J Psonis, David G Thanassi","doi":"10.1128/ecosalplus.ESP-0033-2018","DOIUrl":"10.1128/ecosalplus.ESP-0033-2018","url":null,"abstract":"The chaperone-usher (CU) pathway is a conserved secretion system dedicated to the assembly of a superfamily of virulence-associated surface structures by a wide range of Gram-negative bacteria. Pilus biogenesis by the CU pathway requires two specialized assembly components: a dedicated periplasmic chaperone and an integral outer membrane assembly and secretion platform termed the usher. The CU pathway assembles a variety of surface fibers, ranging from thin, flexible filaments to rigid, rod-like organelles. Pili typically act as adhesins and function as virulence factors that mediate contact with host cells and colonization of host tissues. Pilus-mediated adhesion is critical for early stages of infection, allowing bacteria to establish a foothold within the host. Pili are also involved in modulation of host cell signaling pathways, bacterial invasion into host cells, and biofilm formation. Pili are critical for initiating and sustaining infection and thus represent attractive targets for the development of antivirulence therapeutics. Such therapeutics offer a promising alternative to broad-spectrum antibiotics and provide a means to combat antibiotic resistance and treat infection while preserving the beneficial microbiota. A number of strategies have been taken to develop antipilus therapeutics, including vaccines against pilus proteins, competitive inhibitors of pilus-mediated adhesion, and small molecules that disrupt pilus biogenesis. Here we provide an overview of the function and assembly of CU pili and describe current efforts aimed at interfering with these critical virulence structures.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"8 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6422168/pdf/nihms-1006342.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37233432","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

Curli Biogenesis: Bacterial Amyloid Assembly by the Type VIII Secretion Pathway. Curli Biogenesis:细菌淀粉样蛋白通过VIII型分泌途径组装。

EcoSal Plus Pub Date : 2019-03-01 DOI: 10.1128/ecosalplus.ESP-0037-2018

Sujeet Bhoite, Nani van Gerven, Matthew R Chapman, Han Remaut

{"title":"Curli Biogenesis: Bacterial Amyloid Assembly by the Type VIII Secretion Pathway.","authors":"Sujeet Bhoite, Nani van Gerven, Matthew R Chapman, Han Remaut","doi":"10.1128/ecosalplus.ESP-0037-2018","DOIUrl":"https://doi.org/10.1128/ecosalplus.ESP-0037-2018","url":null,"abstract":"In 1989, Normark and coworkers reported on fibrous surface structures called curli on strains of Escherichia coli that were suspected of causing bovine mastitis. Subsequent work by many groups has revealed an elegant and highly regulated curli biogenesis pathway also referred to as the type VIII secretion system. Curli biogenesis is governed by two divergently transcribed operons, csgBAC and csgDEFG. The csgBAC operon encodes the structural subunits of curli, CsgA and CsgB, along with a chaperone-like protein, CsgC. The csgDEFG operon encodes the accessory proteins required for efficient transcription, secretion, and assembly of the curli fiber. CsgA and CsgB are secreted as largely unstructured proteins and transition to β-rich structures that aggregate into regular fibers at the cell surface. Since both of these proteins have been shown to be amyloidogenic in nature, the correct spatiotemporal synthesis of the curli fiber is of paramount importance for proper functioning and viability. Gram-negative bacteria have evolved an elegant machinery for the safe handling, secretion, and extracellular assembly of these amyloidogenic proteins.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"8 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1128/ecosalplus.ESP-0037-2018","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37074273","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: 36

Lipoproteins and Their Trafficking to the Outer Membrane. 脂蛋白及其向外膜的运输

EcoSal Plus Pub Date : 2019-03-01 DOI: 10.1128/ecosalplus.ESP-0038-2018

Marcin Grabowicz

{"title":"Lipoproteins and Their Trafficking to the Outer Membrane.","authors":"Marcin Grabowicz","doi":"10.1128/ecosalplus.ESP-0038-2018","DOIUrl":"10.1128/ecosalplus.ESP-0038-2018","url":null,"abstract":"Lipoproteins are produced by both Gram-positive and Gram-negative bacteria. Once secreted, lipoproteins are quickly acylated, anchoring them into the plasma membrane. Recent work has shown that Gram-positive bacteria are able to generate considerable diversity in the acylation of their lipoproteins, though the mechanisms involved are only just beginning to emerge. In Gram-negative organisms, most lipoproteins are subsequently trafficked to the outer membrane (OM). Lipoprotein trafficking is an essential pathway in these bacteria. At least one OM lipoprotein component is required by each of the essential machines that assemble the OM (such as the Bam and Lpt machines) and build the peptidoglycan cell wall (Lpo-penicillin-binding protein complexes). The Lol pathway has been the paradigm for OM lipoprotein trafficking: a complex of LolCDE extracts lipoproteins from the plasma membrane, LolA shuttles them through the periplasmic space, and LolB anchors them into the OM. The peptide signals responsible for OM-targeting via LolCDE have long been known for Escherichia coli. Remarkably, production of novel lipoprotein acyl forms in E. coli has reinforced the idea that lipid signals also contribute to OM targeting via LolCDE. Moreover, recent work has shown that lipoprotein trafficking can occur in E. coli without either LolA or LolB. Therefore, current evidence suggests that at least one additional, LolAB-independent route for OM lipoprotein trafficking exists. This chapter reviews the posttranslocation modifications of all lipoproteins, with a focus on the trafficking of lipoproteins to the OM of Gram-negative bacteria.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"8 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11573296/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37256757","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