Transposable Prophage Mu Is Organized as a Stable Chromosomal Domain of E. coli

Saha, Rudra P.; Lou, Zheng; Meng, Luke; Harshey, Rasika M.

doi:10.1371/journal.pgen.1003902

Cited by 26 publications

(27 citation statements)

References 85 publications

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“…The SGS site was seen to be important in maintaining the Mu prophage as a separate and stable chromosomal domain of E. coli (85). In the prophage, the two Mu ends are paired, segregating Mu into an independent chromosomal domain (Fig.…”

Section: The Central Sgs Site and Mu End Pairingmentioning

confidence: 99%

“…MuB might provide a NAP-like function (88). It is proposed that the Mu domain provides long-term survival benefits to both the prophage and the host: to the prophage in bestowing transposition-ready topological properties unique to the Mu reaction, and to the host in contributing extraneous DNA housekeeping functions (85). …”

Section: The Central Sgs Site and Mu End Pairingmentioning

confidence: 99%

“…DNA gyrase binds at the SGS and initiates processive introduction of supercoils, leading to the extrusion of a novel nucleoid domain comprising the Mu genome in its entirety, aligning the L and R ends to promote transpososome (MuA) assembly. ( B ) A model for the structure of a Mu prophage and for Mu genome immunity, taken from (85, 106). The model proposes that segregation of Mu into a separate domain as shown in (A) is sealed by either the Mu transpososome assembled on the ends, or by nucleoid associated proteins (NAPs).…”

Section: Figmentioning

confidence: 99%

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Transposable Phage Mu

Harshey

2014

Microbiol Spectr

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Transposable phage Mu has played a major role in elucidating the mechanism of movement of mobile DNA elements. The high efficiency of Mu transposition has facilitated a detailed biochemical dissection of the reaction mechanism, as well as of protein and DNA elements that regulate transpososome assembly and function. The deduced phosphotransfer mechanism involves in-line orientation of metal ion-activated hydroxyl groups for nucleophilic attack on reactive diester bonds, a mechanism that appears to be used by all transposable elements examined to date. A crystal structure of the Mu transpososome is available. Mu differs from all other transposable elements in encoding unique adaptations that promote its viral lifestyle. These adaptations include multiple DNA (enhancer, SGS) and protein (MuB, HU, IHF) elements that enable efficient Mu end synapsis, efficient target capture, low target specificity, immunity to transposition near or into itself, and efficient mechanisms for recruiting host repair and replication machineries to resolve transposition intermediates. MuB has multiple functions, including target capture and immunity. The SGS element promotes gyrase-mediated Mu end synapsis, and the enhancer, aided by HU and IHF, participates in directing a unique topological architecture of the Mu synapse. The function of these DNA and protein elements is important during both lysogenic and lytic phases. Enhancer properties have been exploited in the design of mini-Mu vectors for genetic engineering. Mu ends assembled into active transpososomes have been delivered directly into bacterial, yeast, and human genomes, where they integrate efficiently, and may prove useful for gene therapy.

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Section: The Central Sgs Site and Mu End Pairingmentioning

confidence: 99%

Section: The Central Sgs Site and Mu End Pairingmentioning

confidence: 99%

Section: Figmentioning

confidence: 99%

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Transposable Phage Mu

Harshey

2014

Microbiol Spectr

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“…The Mu bacteriophage seems to recruit the gyrase enzyme of the Escherichia coli host to supercoil the 37-kbp bacteriophage genome and juxtapose the ends to catalyze transpositional replication (6). Barriers to the free diffusion of supercoils appear to exist in this large domain, although their composition is unknown (7).…”

mentioning

confidence: 99%

DNA supercoiling: A regulatory signal for the λ repressor

Ding¹,

Manzo²,

Fulcrand

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Topoisomerases, polymerases, and the chirality introduced by the binding of histones or nucleoid-associated proteins affect DNA supercoiling in vivo. However, supercoiling is not just a by-product of DNA metabolism. Supercoiling is an indicator of cell health, it modifies the accessibility of chromatin, and coordinates the transcription of genes. This suggests that regulatory, proteinmediated loops in DNA may sense supercoiling of the genome in which they are embedded. The λ repressor (CI) maintains the quiescent (lysogenic) transcriptome of bacteriophage λ in infected Escherichia coli. CI-mediated looping prevents overexpression of the repressor protein to preserve sensitivity to conditions that trigger virulence (lysis). Experiments were performed to assess how well the CI-mediated DNA loop traps superhelicity and determine whether supercoiling enhances CI-mediated DNA looping. CI oligomers partitioned plasmids into topological domains and prevented the passage of supercoiling between them. Furthermore, in single DNA molecules stretched and twisted with magnetic tweezers, levels of superhelical density confined in CI-mediated DNA loops ranged from −15% or +11%. Finally, in DNA under tensions that may occur in vivo, supercoiling lowered the free energy of loop formation and was essential for DNA looping. Supercoiling-enhanced looping can influence the maintenance of lysogeny in the λ repressor system; it can encode sensitivity to the energy level of the cell and creates independent topological domains of distinct superhelical density.DNA looping | DNA supercoiling | bacteriophage λ repressor | magnetic tweezer | transcription

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“…It is involved in other site-specific recombination systems [Corcoran and Dorman, 2009;Dorman and Higgins, 1987;Eisenstein et al, 1987], in transposition [Haniford, 2006;Makris et al, 1990;Saha et al, 2013], plasmid replication [Biek and Cohen, 1989;Fekete et al, 2006;Filutowicz and Appelt, 1988], and conjugation-mediated plasmid transfer [Karl et al, 2001;Wil-liams and Schildbach, 2007]. IHF also makes many important contributions to transcription control (see below).…”

Section: Dna Bending Specialist Ihfmentioning

confidence: 99%

Function of Nucleoid-Associated Proteins in Chromosome Structuring and Transcriptional Regulation

Dorman¹

2014

Microb Physiol

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Nucleoid-associated proteins typically are abundant, low-molecular-mass polypeptides that bind DNA and alter its shape and its ability to participate in transactions such as transcription. Some can bind RNA and influence the gene expression profile of the cell at a posttranscriptional level. They also have the potential to model and remodel the structure of the nucleoid, contributing to chromosome packaging within the cell. Some nucleoid-associated proteins have been implicated in the facilitation of chromosome evolution through their ability to silence transcription, allowing new genes to be integrated into the nucleoid both physically and in a regulatory sense. The dynamic composition of the population of nucleoid-associated proteins in model bacteria such as Escherichia coli and Salmonella enterica links nucleoid structure and the global regulation of gene expression, enhancing microbial competitive fitness and survival in complex environments.

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Transposable Prophage Mu Is Organized as a Stable Chromosomal Domain of E. coli

Cited by 26 publications

References 85 publications

Transposable Phage Mu

Transposable Phage Mu

DNA supercoiling: A regulatory signal for the λ repressor

Function of Nucleoid-Associated Proteins in Chromosome Structuring and Transcriptional Regulation

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