NinR- and Red-Mediated Phage-Prophage Marker Rescue Recombination in <i>Escherichia coli</i>

Hayes, Sidney; Asai, Kengo; Chu, Audrey; Hayes, Connie

doi:10.1534/genetics.105.042341

Cited by 6 publications

(28 citation statements)

References 76 publications

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“…The same result was seen for Y836 recA host cells infected with imm 434 versions of NinR + ΔNinL and ΔNinR ΔNinL phages (Table 2, lines 2–3 in [18]). The GrpD55 locus was suggested linked to dnaB [36], and Horbay [37] subsequently determined by sequence analysis that it represented two missense mutations within dnaB .…”

Section: Resultssupporting

confidence: 74%

“…The plasmid version containing intact O / ori λ, with cI from imm λ, reduced the plaque diameter of all four assayed rep λ phages but the version with a hybrid imm λ-imm434 cI gene did not. λvir was inhibited for plating at 30° in cells with multiple copies of the O / ori λ plasmid version with cI from imm λ, while λ imm 434 cI was not inhibited, suggesting λvir plating remains sensitive to high CI repressor concentration (we made a similar observation with another cI + plasmid [18]). …”

Section: Resultssupporting

confidence: 57%

“…Previously, we confirmed that theta-mode ori λ-dependent prophage replication initiation, which requires P interaction with, and loading of, DnaB, was inhibited if the host carried the dnaB -GrpD55 mutation, yet there was no obvious influence of this allele on E. coli DNA propagation [18]. Herein, we observed that both theta-mode replication from ori λ, and its manifestation, i.e., the Replicative Killing of induced cells (dependent upon triggering theta-mode replication from a trapped, defective λ prophage) was prevented in cells with plasmids exhibiting IP.…”

Section: Discussionmentioning

confidence: 58%

“…A map of the cryptic lambda prophage in strain Y836 is drawn in Fig. 4A.bLysogenic strains show the prophage within the cell by “( )” bordering the prophage.cThe NinR region deleted by Δnin5 removes λ bases 40,503–43,307, i.e., ren-ninA – ninI (including orf -ninC and rap-ninH ); the NinL region substituted by bio 275 replaces genes int-xis-hin-exo-bet-gam-kil , representing λ bases 27,731–∼33,303 [18].…”

Section: Resultsmentioning

confidence: 99%

“…Refer to Hayes et al. [18] for detailed hybridization methodology, and for comparing the effect of a cI + repressor expressed from a plasmid on prophage induction, the influence of host recombination defects on replication initiation from ori λ from the prophage in Y836 cells, and the inhibition of replication initiation from ori λ by host mutations.…”

Section: Resultsmentioning

confidence: 99%

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A CI-Independent Form of Replicative Inhibition: Turn Off of Early Replication of Bacteriophage Lambda

2012

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Several earlier studies have described an unusual exclusion phenotype exhibited by cells with plasmids carrying a portion of the replication region of phage lambda. Cells exhibiting this inhibition phenotype (IP) prevent the plating of homo-immune and hybrid hetero-immune lambdoid phages. We have attempted to define aspects of IP, and show that it is directed to repλ phages. IP was observed in cells with plasmids containing a λ DNA fragment including oop, encoding a short OOP micro RNA, and part of the lambda origin of replication, oriλ, defined by iteron sequences ITN1-4 and an adjacent high AT-rich sequence. Transcription of the intact oop sequence from its promoter, pO is required for IP, as are iterons ITN3–4, but not the high AT-rich portion of oriλ. The results suggest that IP silencing is directed to theta mode replication initiation from an infecting repλ genome, or an induced repλ prophage. Phage mutations suppressing IP, i.e., Sip, map within, or adjacent to cro or in O, or both. Our results for plasmid based IP suggest the hypothesis that there is a natural mechanism for silencing early theta-mode replication initiation, i.e. the buildup of λ genomes with oop + oriλ+ sequence.

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Section: Resultssupporting

confidence: 74%

Section: Resultssupporting

confidence: 57%

Section: Discussionmentioning

confidence: 58%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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A CI-Independent Form of Replicative Inhibition: Turn Off of Early Replication of Bacteriophage Lambda

2012

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Systematic classification of the His-Me finger superfamily

Jabłońska

Matelska

Steczkiewicz

et al. 2017

Nucleic Acids Research

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The His-Me finger endonucleases, also known as HNH or ββα-metal endonucleases, form a large and diverse protein superfamily. The His-Me finger domain can be found in proteins that play an essential role in cells, including genome maintenance, intron homing, host defense and target offense. Its overall structural compactness and non-specificity make it a perfectly-tailored pathogenic module that participates on both sides of inter- and intra-organismal competition. An extremely low sequence similarity across the superfamily makes it difficult to identify and classify new His-Me fingers. Using state-of-the-art distant homology detection methods, we provide an updated and systematic classification of His-Me finger proteins. In this work, we identified over 100 000 proteins and clustered them into 38 groups, of which three groups are new and cannot be found in any existing public domain database of protein families. Based on an analysis of sequences, structures, domain architectures, and genomic contexts, we provide a careful functional annotation of the poorly characterized members of this superfamily. Our results may inspire further experimental investigations that should address the predicted activity and clarify the potential substrates, to provide more detailed insights into the fundamental biological roles of these proteins.

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Temperate Phages Acquire DNA from Defective Prophages by Relaxed Homologous Recombination: The Role of Rad52-Like Recombinases

et al. 2014

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Bacteriophages (or phages) dominate the biosphere both numerically and in terms of genetic diversity. In particular, genomic comparisons suggest a remarkable level of horizontal gene transfer among temperate phages, favoring a high evolution rate. Molecular mechanisms of this pervasive mosaicism are mostly unknown. One hypothesis is that phage encoded recombinases are key players in these horizontal transfers, thanks to their high efficiency and low fidelity. Here, we associate two complementary in vivo assays and a bioinformatics analysis to address the role of phage encoded recombinases in genomic mosaicism. The first assay allowed determining the genetic determinants of mosaic formation between lambdoid phages and Escherichia coli prophage remnants. In the second assay, recombination was monitored between sequences on phage λ, and allowed to compare the performance of three different Rad52-like recombinases on the same substrate. We also addressed the importance of homologous recombination in phage evolution by a genomic comparison of 84 E. coli virulent and temperate phages or prophages. We demonstrate that mosaics are mainly generated by homology-driven mechanisms that tolerate high substrate divergence. We show that phage encoded Rad52-like recombinases act independently of RecA, and that they are relatively more efficient when the exchanged fragments are divergent. We also show that accessory phage genes orf and rap contribute to mosaicism. A bioinformatics analysis strengthens our experimental results by showing that homologous recombination left traces in temperate phage genomes at the borders of recently exchanged fragments. We found no evidence of exchanges between virulent and temperate phages of E. coli. Altogether, our results demonstrate that Rad52-like recombinases promote gene shuffling among temperate phages, accelerating their evolution. This mechanism may prove to be more general, as other mobile genetic elements such as ICE encode Rad52-like functions, and play an important role in bacterial evolution itself.

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NinR- and Red-Mediated Phage-Prophage Marker Rescue Recombination in Escherichia coli

Cited by 6 publications

References 76 publications

A CI-Independent Form of Replicative Inhibition: Turn Off of Early Replication of Bacteriophage Lambda

A CI-Independent Form of Replicative Inhibition: Turn Off of Early Replication of Bacteriophage Lambda

Systematic classification of the His-Me finger superfamily

Temperate Phages Acquire DNA from Defective Prophages by Relaxed Homologous Recombination: The Role of Rad52-Like Recombinases

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