Replication of Mu prophages lacking the central strong gyrase site

Twenty Years of Collaboration to Sort out Phage Mu Replication and Its Dependence on the Mu Central Gyrase Binding Site

For 20 years, the intricacies in bacteriophage Mu replication and its regulation were elucidated in collaboration between Ariane Toussaint and her co-workers in the Laboratory of Genetics at the Université Libre de Bruxelles, and the groups of Martin Pato and N. Patrick Higgins in the US. Here, to honor Martin Pato’s scientific passion and rigor, we tell the history of this long-term sharing of results, ideas and experiments between the three groups, and Martin’s final discovery of a very unexpected step in the initiation of Mu replication, the joining of Mu DNA ends separated by 38 kB with the assistance of the host DNA gyrase.

Deep sequencing reveals new roles for MuB in transposition immunity and target-capture, and redefines the insular Ter region of E. coli

Background

The target capture protein MuB is responsible for the high efficiency of phage Mu transposition within the E. coli genome. However, some targets are off-limits, such as regions immediately outside the Mu ends (cis-immunity) as well as the entire ~ 37 kb genome of Mu (Mu genome immunity). Paradoxically, MuB is responsible for cis-immunity and is also implicated in Mu genome immunity, but via different mechanisms. This study was undertaken to dissect the role of MuB in target choice in vivo.

Results

We tracked Mu transposition from six different starting locations on the E. coli genome, in the presence and absence of MuB. The data reveal that Mu’s ability to sample the entire genome during a single hop in a clonal population is independent of MuB, and that MuB is responsible for cis-immunity, plays a minor role in Mu genome immunity, and facilitates insertions into transcriptionally active regions. Unexpectedly, transposition patterns in the absence of MuB have helped extend the boundaries of the insular Ter segment of the E. coli genome.

Conclusions

The results in this study demonstrate unambiguously the operation of two distinct mechanisms of Mu target immunity, only one of which is wholly dependent on MuB. The study also reveals several interesting and hitherto unknown aspects of Mu target choice in vivo, particularly the role of MuB in facilitating the capture of promoter and translation start site targets, likely by displacing macromolecular complexes engaged in gene expression. So also, MuB facilitates transposition into the restricted Ter region of the genome.

Mu-driven transposition of recombinant mini-Mu unit DNA in the Corynebacterium glutamicum chromosome

A dual-component Mu-transposition system was modified for the integration/amplification of genes in Corynebacterium. The system consists of two types of plasmids: (i) a non-replicative integrative plasmid that contains the transposing mini-Mu(LR) unit bracketed by the L/R Mu ends or the mini-Mu(LER) unit, which additionally contains the enhancer element, E, and (ii) an integration helper plasmid that expresses the transposition factor genes for MuA and MuB. Efficient transposition in the C. glutamicum chromosome (≈ 2 × 10⁻⁴ per cell) occurred mainly through the replicative pathway via cointegrate formation followed by possible resolution. Optimizing the E location in the mini-Mu unit significantly increased the efficiency of Mu-driven intramolecular transposition–amplification in C. glutamicum as well as in gram-negative bacteria. The new C. glutamicum genome modification strategy that was developed allows the consequent independent integration/amplification/fixation of target genes at high copy numbers. After integration/amplification of the first mini-Mu(LER) unit in the C. glutamicum chromosome, the E-element, which is bracketed by lox-like sites, is excised by Cre-mediated fashion, thereby fixing the truncated mini-Mu(LR) unit in its position for the subsequent integration/amplification of new mini-Mu(LER) units. This strategy was demonstrated using the genes for the citrine and green fluorescent proteins, yECitrine and yEGFP, respectively.

Transposable Phage Mu

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.

Repair of transposable phage Mu DNA insertions begins only when the E. coli replisome collides with the transpososome

We report a new cellular interaction between the infecting transposable phage Mu and the host Escherichia coli replication machinery during repair of Mu insertions, which involves filling-in of short target gaps on either side of the insertion, concomitant with degradation of extraneous long flanking DNA (FD) linked to Mu. Using the FD as a marker to follow repair, we find that after transposition into the chromosome, the unrepaired Mu is indefinitely stable until the replication fork arrives at the insertion site, whereupon the FD is rapidly degraded. When the fork runs into a Mu target gap, a double strand end (DSE) will result; we demonstrate fork-dependent DSEs proximal to Mu. These findings suggest that Pol III stalled at the transpososome is exploited for co-ordinated repair of both target gaps flanking Mu without replicating the intervening 37 kb of Mu, disassembling the stable transpososome in the process. This work is relevant to all transposable elements, including retroviral elements like HIV-1, which share with Mu the common problem of repair of their flanking target gaps.

Transposable prophage Mu is organized as a stable chromosomal domain of E. coli

The E. coli chromosome is compacted by segregation into 400–500 supercoiled domains by both active and passive mechanisms, for example, transcription and DNA-protein association. We find that prophage Mu is organized as a stable domain bounded by the proximal location of Mu termini L and R, which are 37 kbp apart on the Mu genome. Formation/maintenance of the Mu ‘domain’ configuration, reported by Cre-loxP recombination and 3C (chromosome conformation capture), is dependent on a strong gyrase site (SGS) at the center of Mu, the Mu L end and MuB protein, and the E. coli nucleoid proteins IHF, Fis and HU. The Mu domain was observed at two different chromosomal locations tested. By contrast, prophage λ does not form an independent domain. The establishment/maintenance of the Mu domain was promoted by low-level transcription from two phage promoters, one of which was domain dependent. We propose that the domain confers transposition readiness to Mu by fostering topological requirements of the reaction and the proximity of Mu ends. The potential benefits to the host cell from a subset of proteins expressed by the prophage may in turn help its long-term stability.

A majority of sequenced bacterial genomes harbor prophage sequences. Some prophages are viable, while others have decayed from accumulating mutations and genome rearrangements. Prophages, including defective ones, can contribute important biological properties such as antibiotic resistance, toxins, and serum resistance that increase the survival and ecological range of their hosts. We show in this study that the 37 kbp transposable prophage Mu exists in a unique configuration we call the ‘Mu domain’, where its two ends are paired, segregating the Mu sequences from those of the host chromosome. This is the largest stable chromosomal domain in E. coli mapped to date. The Mu domain configuration promotes low-level transcription from an early prophage promoter, which controls the expression of several genes, not all essential for phage growth. Some non-essential genes include DNA repair functions. We suggest 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.

The Mu story: how a maverick phage moved the field forward

This article traces the pioneering contributions of phage Mu to our current knowledge of how movable elements move/transpose. Mu provided the first molecular evidence of insertion elements in E. coli, postulated by McClintock to control gene activity in maize in the pre-DNA era. An early Mu-based model successfully explained all the DNA rearrangements associated with transposition, providing a blueprint for navigating the deluge of accumulating reports on transposable element activity. Amplification of the Mu genome via transposition meant that its transposition frequencies were orders of magnitude greater than any rival, so it was only natural that the first in vitro system for transposition was established for Mu. These experiments unraveled the chemistry of the phosphoryl transfer reaction of transposition, and shed light on the nucleoprotein complexes within which they occur. They hastened a similar analysis of other transposons and ushered in the structural era where many transpososomes were crystallized. While it was a lucky break that the mechanism of HIV DNA integration turned out to be similar to that of Mu, it is no accident that current drugs for HIV integrase inhibitors owe their discovery to trailblazing experiments done with Mu. Shining the light on how movable elements restructure genomes, Mu has also given of itself generously to understanding the genome.

Bacteriophage Mu targets the trinucleotide sequence CGG

Target specificity for bacteriophage Mu was studied using a new phage derivative that enabled cloning of Mu-host junctions from phage DNA. Insertions distributed throughout the chromosome showed no orientation bias with respect to transcription or replication polarity. Genes with a high frequency of the triplet CGG were preferred targets.