Structural and Genetic Analyses Reveal a Key Role in Prophage Excision for the TorI Response Regulator Inhibitor

Elantak, Latifa; Ansaldi, Mireille; Guerlesquin, Françoise; Méjean, Vincent; Morelli, Xavier

doi:10.1074/jbc.m507409200

Cited by 19 publications

(40 citation statements)

References 38 publications

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“…2, black line), which was consistent with the solution structure of TorI (8). To analyze whether structural changes occurred upon interaction of TorI with DnaJ, we monitored the effect of DnaJ on the structural conformation of TorI by adding low quantities of DnaJ (TorI/DnaJ ratio 25:0.8 or 25:0.2).…”

Section: Resultssupporting

confidence: 60%

“…The perturbed residues congregate onto one face of the TorI protein surface opposite the TorI DNA-binding site, which we have previously mapped (Fig. 5, B and C) (8). Indeed, none of the residues involved in the interaction with DNA were perturbed upon DnaJ binding.…”

Section: Tori Is Transiently Protected From Limited Proteolysis In Thmentioning

confidence: 65%

“…In addition to the integrase protein, prophage excision from the chromosome requires additional proteins, which are classed as recombination directionality factors (RDFs) 3 (7). TorI is the RDF of KplE1 and is essential for prophage excision (8). It is encoded by the torI gene, which is located upstream of the 3Ј core sequence that marks the end of the prophage (6).…”

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confidence: 99%

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DnaJ (Hsp40 Protein) Binding to Folded Substrate Impacts KplE1 Prophage Excision Efficiency

Puvirajesinghe

Elantak

Lignon

et al. 2012

Journal of Biological Chemistry

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Background: DnaJ positively modulates KplE1 prophage excision and is involved in lysogeny escape. Results: The recombination directionality factor TorI, from KplE1 prophage, interacts with the DnaJ chaperone, and they protect each other from limited trypsin digestion. Conclusion: DnaJ stabilizes TorI recombination directionality factor conformation. Significance: DnaJ cochaperone can bind folded substrates and induces the conformational stabilization of the TorI protein.

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Section: Resultssupporting

confidence: 60%

Section: Tori Is Transiently Protected From Limited Proteolysis In Thmentioning

confidence: 65%

mentioning

confidence: 99%

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DnaJ (Hsp40 Protein) Binding to Folded Substrate Impacts KplE1 Prophage Excision Efficiency

Puvirajesinghe

Elantak

Lignon

et al. 2012

Journal of Biological Chemistry

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“…Each time, the KplE1 prophage was excised as soon as the allele was acquired. Moreover, a Km R insertion between the yfdO and yfdP genes (strain LCB984), which is functional for site-specific recombination when the torI gene is overexpressed (35), was not excised in the presence of BCM (Fig. S3A), indicating that transcription was affected by the insertion of the resistance cassette that contains an intrinsic terminator.…”

Section: Resultsmentioning

confidence: 99%

Transcription termination controls prophage maintenance in Escherichia coli genomes

Menouni

Champ

Espinosa

et al. 2013

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

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Prophages represent a large fraction of prokaryotic genomes and often provide new functions to their hosts, in particular virulence and fitness. How prokaryotic cells maintain such gene providers is central for understanding bacterial genome evolution by horizontal transfer. Prophage excision occurs through site-specific recombination mediated by a prophage-encoded integrase. In addition, a recombination directionality factor (or excisionase) directs the reaction toward excision and prevents the phage genome from being reintegrated. In this work, we describe the role of the transcription termination factor Rho in prophage maintenance through control of the synthesis of transcripts that mediate recombination directionality factor expression and, thus, excisive recombination. We show that Rho inhibition by bicyclomycin allows for the expression of prophage genes that lead to excisive recombination. Thus, besides its role in the silencing of horizontally acquired genes, Rho also maintains lysogeny of defective and functional prophages.bacteriophage | transduction | transcriptional regulation

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“…The N-terminal end has been predicted to contain an HTH motif presumed to be involved in DNA binding (32). Since the HTH motif, according to the secondary structure prediction of the Cox proteins using JPRED, is preceded by a ␤-strand and followed by two ␤-strands, the Cox proteins most likely belong to the wingedhelix family of prokaryotic excisionases (15,31,33) and the DNA binding domain of the Mu repressor (19). The identity within different immunity repressor classes was mirrored by the variation of the Cox protein.…”

Section: Vol 188 2006 Immunity and Integration Sites Of P2-like Phamentioning

confidence: 99%

Evolution of Immunity and Host Chromosome Integration Site of P2-Like Coliphages

et al. 2006

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The amount and distribution of variation in the genomic region containing the genes in the lytic-lysogenic genetic switch and the sequence that determines the integration site into the host chromosome were analyzed for 38 P2-like phages from Escherichia coli. The genetic switch consists of two convergent mutually exclusive promoters, Pe and Pc, and two repressors, C and Cox. The immunity repressor C blocks the early Pe promoter, leading to the establishment of lysogeny. The Cox repressor blocks expression of Pc, allowing lytic growth. Phylogenetic analyses showed that the C and Cox proteins were distributed into seven distinct classes. The phylogenetic relationship differed between the two proteins, and we showed that homologous recombination plays a major role in creating alterations in the genetic switch, leading to new immunity classes. Analyses of the host integration site for these phages resulted in the discovery of a previously unknown site, and there were at least four regular integration sites. Interestingly, we found no case where phages of the same immunity class had different host attachment sites. The evolution of immunity and integration sites is complex, since it involves interactions both between the phages themselves and between phages and hosts, and often, both regulatory proteins and target DNA must change.P2-like phages are a group of related temperate phages that grow on ␥-proteobacteria and share common traits such as morphology, control of lytic versus lysogenic growth, and noninducibility by UV light (for a recent review, see reference 26). Temperate phages have the ability to reproduce by two alternative life cycles: the lytic or the lysogenic cycle. In the latter life cycle, the phage genome integrates into a specific location on the host chromosome, and most phage genes are turned off by the phage-encoded immunity repressor C. P2-like phages are prevalent in Escherichia coli strains; about 30% of the strains in the ECOR collection (28) contain P2-like prophages (27). P2-like phages that are found in other ␥-proteobacteria are more distantly related to P2 than those found in E. coli, and it seems as if the evolution of the P2-like phages tracks the evolution of their respective hosts (26; A. S. Nilsson, unpublished data). An analysis of the DNA sequence of the late structural genes of 18 P2-like isolates that grow on E. coli showed that these genes are at least 96% identical to the genes of P2 (25). Thus, these P2-like coliphages might be considered different isolates of P2, but they have been shown to have different immunities, based on their capacity to grow on bacteria lysogenized with different P2-like phages (6,9,14) and to integrate at at least two different sites in the host chromosome (22,38). Phage 186 is a more distantly related E. coli phage, and its immunity repressor, cI, differs in size and sequence from the C repressors of the P2-like coliphages in this study. In fact, both cI and Apl (the equivalent of Cox) of phage 186 are more related to the cI and Cox repressors of Ha...

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Structural and Genetic Analyses Reveal a Key Role in Prophage Excision for the TorI Response Regulator Inhibitor

Cited by 19 publications

References 38 publications

DnaJ (Hsp40 Protein) Binding to Folded Substrate Impacts KplE1 Prophage Excision Efficiency

DnaJ (Hsp40 Protein) Binding to Folded Substrate Impacts KplE1 Prophage Excision Efficiency

Transcription termination controls prophage maintenance in Escherichia coli genomes

Evolution of Immunity and Host Chromosome Integration Site of P2-Like Coliphages

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