EcoSal Plus (ESP) is the authoritative online review journal that publishes an ever-growing body of expert reviews covering virtually all aspects of Escherichia coli , Salmonella , and other members of the order Enterobacterales and their use as model microbes for biological explorations. This review will cover the history of ESP, starting with its origins as multi-volume printed books entitled Escherichia coli and Salmonella: Cellular and Molecular Biology that became “the Bible” for information on the physiology, metabolism, genetics, and other aspects of E. coli and Salmonella . After two printed editions, this resource moved online as EcoSal in an era when electronic publishing was still in its infancy. Progress in establishing EcoSal was slow due to technical issues of online publishing and difficulties in recruiting authors to produce new material. This venture was relaunched in 2013 as EcoSal Plus in a completely new web platform that was much more user (and author) friendly and with an expanded scope to include other members of the order Enterobacterales. EcoSal Plus will be ending as a standalone publication but will merge with Microbiology and Molecular Biology Reviews to continue providing high-quality, authoritative reviews on E. coli , Salmonella , and related organisms.
Immediately after infection of Escherichia coli , bacteriophage T4 begins to reprogram the host’s transcriptional machinery, first by chemical modification and then by producing factors that alter the specificity of RNA polymerase (RNAP). This leads to the temporal expression of three classes of T4 transcripts: early, middle, and late. For early transcription, the Alt protein, which is present in the phage head, is injected with the DNA and subsequently ADP-ribosylates RNAP, providing an advantage for T4 early promoters over host promoters. For middle and late transcription, T4 utilizes phage-encoded factors to either reconfigure or replace the primary specificity subunit, σ 70 , of RNAP, respectively. In both cases, the phage relies on several processes to maximize the efficiency of these phage-created, alternative σ’s. This review summarizes older biochemical, genetic, and structural work that elucidated many of the elegant mechanisms of this transcriptional takeover and focuses on the more recent cryo-EM structures of the complete transcription machines that allow us to visualize the processes.
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.
The bacteriophage T4 replisome is a complex molecular machine responsible for DNA replication in the T4 phage. It consists of multiple proteins that work together to ensure efficient and accurate replication of the phage genome. The replisome comprises DNA polymerases, helicase, primase, and other accessory proteins, which coordinate leading- and lagging-strand synthesis. Extensive research over the years, including protein analysis, enzyme kinetics, and structural investigations, has provided insights into the organization and function of these proteins, along with their dynamics and coordination at the replication fork. The T4 replisome serves as a useful model system for understanding molecular fidelity, enzymatic interplay, and fundamental principles of DNA replication.
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.
