EcoSal Plus Pub Date : 2025-10-01 DOI: 10.1128/ecosalplus.esp-0006-2025

Deborah M Hinton

引用次数: 0

Bacteriophage T4 genome packaging: mechanism and application. 噬菌体T4基因组包装：机制与应用。

EcoSal Plus Pub Date : 2025-10-01 DOI: 10.1128/ecosalplus.esp-0004-2025

Venigalla B Rao

{"title":"Bacteriophage T4 genome packaging: mechanism and application.","authors":"Venigalla B Rao","doi":"10.1128/ecosalplus.esp-0004-2025","DOIUrl":"10.1128/ecosalplus.esp-0004-2025","url":null,"abstract":"It has been a 45-year journey studying genome packaging of a single virus, the tailed bacteriophage T4. T4, then and now, remains a powerful model for understanding viruses, particularly tailed phages, the most abundant and widely distributed organisms on Earth. The biochemistry, structure, and single-molecule dynamics of the T4 DNA packaging motor have been teased out. Packaging ~171 kb genomic DNA into a 120 × 86 nm prolate icosahedral head in a few minutes, the T4 packaging motor is the fastest and most powerful motor known. It is also the most promiscuous, allowing packaging of any double-stranded DNA regardless of sequence or length into various head (capsid) assemblies: unexpanded prohead, expanded prohead, or mature head. These studies established the basic architecture of an ATP-powered viral genome packaging machine consisting of a pentameric packaging motor attached to the dodecameric portal vertex of the capsid shell. Furthermore, it opened new avenues to engineer and repurpose the packaging machine for the delivery of genes, proteins, and protein-nucleic acid complexes into human cells. The biggest challenge now is to translate this knowledge into the design of future phage-vectored gene therapy platforms that allow engineered phages to interact with human cells and make appropriate genetic and metabolic corrections to alleviate disease. This possibility was unimaginable when we started but evolved through lessons learned by examining the intricate machinery of the phage T4 life cycle.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00042025"},"PeriodicalIF":0.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145198825","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

The bacteriophage T4 replisome: a model system for understanding DNA replication mechanisms. T4噬菌体：理解DNA复制机制的模型系统。

EcoSal Plus Pub Date : 2025-09-16 DOI: 10.1128/ecosalplus.esp-0010-2025

Michelle M Spiering, Stephen J Benkovic

引用次数: 0

The bacteriophage T4 homologous recombination system: mechanism, applications, conservation, and environmental significance. 噬菌体T4同源重组体系：机制、应用、保护及环境意义

EcoSal Plus Pub Date : 2025-09-16 DOI: 10.1128/ecosalplus.esp-0003-2025

Scott W Morrical

{"title":"The bacteriophage T4 homologous recombination system: mechanism, applications, conservation, and environmental significance.","authors":"Scott W Morrical","doi":"10.1128/ecosalplus.esp-0003-2025","DOIUrl":"https://doi.org/10.1128/ecosalplus.esp-0003-2025","url":null,"abstract":"The homologous recombination (HR) system of bacteriophage T4 plays critical, direct roles in the replication and repair of the phage genome. This review covers the classic, UvsX-dependent HR pathway in T4, focusing on recent findings on the mechanisms of central HR proteins UvsX, UvsY, and Gp32, plus the key helicase and nuclease enzymes that affect HR and promote its coupling to T4 recombination-dependent replication and repair processes. The T4 HR pathways are paradigmatic, since they are highly conserved in all orders of viral and cellular life. Therefore, the study of T4 recombination is highly relevant to biomedicine and to environmental microbiology. At the same time, the tractability of the T4 recombination system for biochemical studies has led to the development of novel, isothermal DNA amplification technologies based on the activities of UvsX, UvsY, and Gp32, which are discussed herein. Globally, the recent revolution in metagenomics has demonstrated that T4-like phages, most encoding the genes and proteins of the T4 HR system, are abundant and widespread in the environment, where they play important roles in the dynamics of diverse microbiomes, from the earth's oceans to the animal gut. Accordingly, we discuss the conservation of T4 HR genes in representatives of T4-like jumbo phages and cyanophages. As a paradigm for HR in diverse organisms, as a source of novel technologies, and as a window on the importance of bacteriophages in the environment, the T4 HR system continues to provide new insights and reagents for a better understanding of life on earth.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00032025"},"PeriodicalIF":0.0,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145069202","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

Biology of host-dependent restriction-modification in prokaryotes. 原核生物寄主依赖性限制性修饰生物学。

EcoSal Plus Pub Date : 2025-08-26 DOI: 10.1128/ecosalplus.esp-0014-2022

Brian P Anton, Robert Blumenthal, James B Eaglesham, Iwona Mruk, Richard J Roberts, Shuang-Yong Xu, Peter R Weigele, Elisabeth A Raleigh

{"title":"Biology of host-dependent restriction-modification in prokaryotes.","authors":"Brian P Anton, Robert Blumenthal, James B Eaglesham, Iwona Mruk, Richard J Roberts, Shuang-Yong Xu, Peter R Weigele, Elisabeth A Raleigh","doi":"10.1128/ecosalplus.esp-0014-2022","DOIUrl":"10.1128/ecosalplus.esp-0014-2022","url":null,"abstract":"Understanding the mechanisms that modulate horizontal genetic exchange in prokaryotes is a key problem in biology. DNA entry is limited by resident host-dependent restriction-modification (RM) systems (HDRM), which are present in most prokaryotic genomes. This review specifically focuses on the biological functions of HDRM, rather than detailed enzyme mechanisms. DNA in each cell carries epigenetic marks imposed by host-modifying enzymes (HDM), most often not only base methylation but also additions to the phosphodiester backbone. The pattern of base and backbone modifications is read by host-restriction enzymes (HDR). Broadly, HDRM systems read the pattern of chemical modifications to DNA at host-determined (HD) sites to regulate the fate of incoming mobile DNA. An inappropriate pattern may be restricted either due to the absence of protective modification or its presence; the latter activity is mediated by modification-dependent restriction enzymes (MDRE). Most often, restriction occurs via nuclease-mediated degradation, but it can also act via other mechanisms that prevent the initiation of replication. Like other genome-defense systems, HDRM systems are highly diverse and somewhat modular. The basic functions required for action in vivo and the protein domains responsible for each function are addressed here. Particularly under-studied among the latter are the interaction domains that control the launch of highly toxic activities such as HDR. These have been evolutionarily shuffled to build a variety of classical RM systems as well as more divergent systems.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00142022"},"PeriodicalIF":0.0,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144946893","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

Post-transcriptional control during T4 infection. T4感染期间的转录后控制。

EcoSal Plus Pub Date : 2025-08-06 DOI: 10.1128/ecosalplus.esp-0009-2025

Jinshil Kim, Bokyung Son

引用次数: 0

The role of macromolecular crowders in the formation and compaction of the Escherichia coli nucleoid. 大分子挤压剂在大肠杆菌类核形成和压实中的作用。

EcoSal Plus Pub Date : 2025-07-24 DOI: 10.1128/ecosalplus.esp-0002-2024

Jaan Männik, Jaana Männik, Chathuddasie Amarasinghe, Mu-Hung Chang, Maxim O Lavrentovich

{"title":"The role of macromolecular crowders in the formation and compaction of the Escherichia coli nucleoid.","authors":"Jaan Männik, Jaana Männik, Chathuddasie Amarasinghe, Mu-Hung Chang, Maxim O Lavrentovich","doi":"10.1128/ecosalplus.esp-0002-2024","DOIUrl":"https://doi.org/10.1128/ecosalplus.esp-0002-2024","url":null,"abstract":"The chromosomal DNA of Escherichia coli is approximately a thousand times longer than the linear dimensions of the cell it occupies. Nevertheless, it fills only about one-half of the cytosolic volume of the cell. The volume pervaded by the chromosomal DNA is known as nucleoid. The nucleoid is a ribosome-depleted region that behaves as a distinct liquid-like phase within the cytosol. In most bacteria, including E. coli, which lack membrane-enclosed organelles, the phase separation between the nucleoid and the ribosome-rich cytosolic fraction represents the most prominent organizational principle of the cell's cytosolic interior. This review explores the mechanisms driving nucleoid phase separation, including the roles of DNA-binding proteins, supercoiling, and active DNA looping. Recent studies highlight macromolecular crowding as the dominant factor governing this spatial organization. The main focus of this review is on experimental and theoretical works-ranging from in vitro and in vivo studies to polymer physics-based models-that elucidate how macromolecular crowding drives nucleoid phase formation and regulates DNA compaction in E. coli.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00022024"},"PeriodicalIF":0.0,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697905","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

Microbe-plant interactions of Escherichia coli and Salmonella. 大肠杆菌和沙门氏菌的微生物-植物相互作用。

EcoSal Plus Pub Date : 2025-07-02 DOI: 10.1128/ecosalplus.esp-0018-2023

Nicola Holden, Jeri Barak

引用次数: 0

Enteroaggregative Escherichia coli (EAEC). 大肠杆菌肠聚合(EAEC)。

EcoSal Plus Pub Date : 2025-06-30 DOI: 10.1128/ecosalplus.esp-0011-2024

Viktoria Van Nederveen, Angela R Melton-Celsa

{"title":"Enteroaggregative Escherichia coli (EAEC).","authors":"Viktoria Van Nederveen, Angela R Melton-Celsa","doi":"10.1128/ecosalplus.esp-0011-2024","DOIUrl":"https://doi.org/10.1128/ecosalplus.esp-0011-2024","url":null,"abstract":"A cause of diarrhea worldwide, enteroaggregative Escherichia coli (or EAEC) is one of six diarrheagenic E. coli pathotypes. EAEC strains are heterogeneic in terms of virulence factors, adhere strongly to epithelial cells, and produce a strong biofilm. It is the characteristic aggregative adherence on epithelial cells that was both the gold standard of clinical identification and the source of the appellation \"aggregative.\" To understand EAEC in the continuum with other pathogenic E. coli, we discuss the overlap of EAEC with other diarrheagenic E. coli and extraintestinal pathogenic E. coli isolates. Due to the increased use of molecular techniques for the identification of EAEC, the use of various PCR markers and DNA sequencing for EAEC identification and how that correlates to the phenotypic definition is discussed. Aspects of EAEC pathogenesis, including an overview of virulence factors, such as the five aggregative adherence fimbriae (AAF) and SPATEs (serine protease autotransporters of Enterobacteriaceae), will be explored. The advantages and limitations of various EAEC animal models and what is known about human immunity and host factors that influence infection outcomes are outlined. This review includes a synthesis of new discoveries published for the EAEC field, including non-AAF fimbrial adhesins, additional information about post-infection sequelae, and new EAEC models.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00112024"},"PeriodicalIF":0.0,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144526914","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

The EcoCyc database (2025). EcoCyc数据库（2025）。

EcoSal Plus Pub Date : 2025-04-30 DOI: 10.1128/ecosalplus.esp-0019-2024

Peter D Karp, Suzanne Paley, Ron Caspi, Anamika Kothari, Markus Krummenacker, Peter E Midford, Lisa R Moore, Pallavi Subhraveti, Socorro Gama-Castro, Víctor H Tierrafria, Paloma Lara, Luis Muñiz-Rascado, César Bonavides-Martinez, Alberto Santos-Zavaleta, Amanda Mackie, Gwanggyu Sun, Travis A Ahn-Horst, Heejo Choi, Riley Juenemann, Cyrus N M Knudsen, Markus W Covert, Julio Collado-Vides, Ian Paulsen

{"title":"The EcoCyc database (2025).","authors":"Peter D Karp, Suzanne Paley, Ron Caspi, Anamika Kothari, Markus Krummenacker, Peter E Midford, Lisa R Moore, Pallavi Subhraveti, Socorro Gama-Castro, Víctor H Tierrafria, Paloma Lara, Luis Muñiz-Rascado, César Bonavides-Martinez, Alberto Santos-Zavaleta, Amanda Mackie, Gwanggyu Sun, Travis A Ahn-Horst, Heejo Choi, Riley Juenemann, Cyrus N M Knudsen, Markus W Covert, Julio Collado-Vides, Ian Paulsen","doi":"10.1128/ecosalplus.esp-0019-2024","DOIUrl":"10.1128/ecosalplus.esp-0019-2024","url":null,"abstract":"EcoCyc is a bioinformatics database (DB) 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 was 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 via EcoCyc.org. 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 is also available. This review outlines the data content of EcoCyc and the procedures by which this content is generated.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":" ","pages":"eesp00192024"},"PeriodicalIF":0.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143989974","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

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