Regulation of bacteriophage Mu transposition

Toussaint, Ariane; Gama, M.-J.; Laachouch, Jamal E; Maenhaut-Michel, G.; Mhammedi-Alaoui, A

doi:10.1007/bf01435237

Cited by 18 publications

(16 citation statements)

References 74 publications

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“…Rather, morphology and protein homology suggest the PSAHS6-like phages are modular hybrids composed of a siphovirus-like non-contractile tail fused to a myovirus Mu-like head ( Figure 5B ). Protein homology suggested the PSAHS6-like phages replicate by Mu-type transposition, which implies obligate integration into their host genomes and the capacity to remain as prophages in a host lysogen (Toussaint et al, 1994). The PSAHS6-like genomes contain numerous Mu-like conserved proteins localized in the two canonical Mu regions (Morgan et al, 2002): (i) head formation among the late genes and (ii) transposition and replication functions among the early genes ( Figure 5A ).…”

Section: Resultsmentioning

confidence: 99%

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept

et al. 2017

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Viruses influence the ecology and evolutionary trajectory of microbial communities. Yet our understanding of their roles in ecosystems is limited by the paucity of model systems available for hypothesis generation and testing. Further, virology is limited by the lack of a broadly accepted conceptual framework to classify viral diversity into evolutionary and ecologically cohesive units. Here, we introduce genomes, structural proteomes, and quantitative host range data for eight Pseudoalteromonas phages isolated from Helgoland (North Sea, Germany) and use these data to advance a genome-based viral operational taxonomic unit (OTU) definition. These viruses represent five new genera and inform 498 unaffiliated or unannotated protein clusters (PCs) from global virus metagenomes. In a comparison of previously sequenced Pseudoalteromonas phage isolates (n = 7) and predicted prophages (n = 31), the eight phages are unique. They share a genus with only one other isolate, Pseudoalteromonas podophage RIO-1 (East Sea, South Korea) and two Pseudoalteromonas prophages. Mass-spectrometry of purified viral particles identified 12–20 structural proteins per phage. When combined with 3-D structural predictions, these data led to the functional characterization of five previously unidentified major capsid proteins. Protein functional predictions revealed mechanisms for hijacking host metabolism and resources. Further, they uncovered a hybrid sipho-myovirus that encodes genes for Mu-like infection rarely described in ocean systems. Finally, we used these data to evaluate a recently introduced definition for virus populations that requires members of the same population to have >95% average nucleotide identity across at least 80% of their genes. Using physiological traits and genomics, we proposed a conceptual model for a viral OTU definition that captures evolutionarily cohesive and ecologically distinct units. In this trait-based framework, sensitive hosts are considered viral niches, while host ranges and infection efficiencies are tracked as viral traits. Quantitative host range assays revealed conserved traits within virus OTUs that break down between OTUs, suggesting the defined units capture niche and fitness differentiation. Together these analyses provide a foundation for model system-based hypothesis testing that will improve our understanding of marine copiotrophs, as well as phage–host interactions on the ocean particles and aggregates where Pseudoalteromonas thrive.

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Section: Resultsmentioning

confidence: 99%

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept

et al. 2017

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“…1 It amplifies its genome by multiple rounds of replicative transposition, a process also responsible for the spreading of many bacterial transposable elements. 2 In this lytic/derepressed configuration, the replication functions are expressed from the early lytic promoter pE. Alternatively, Mu can reside as a latent prophage, integrated at a random location in the host genome.…”

Section: Introductionmentioning

confidence: 99%

Control of Bacteriophage Mu Lysogenic Repression

Ranquet

Toussaint

Jong

et al. 2005

Journal of Molecular Biology

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“…This predator of Escherichia coli has the ability to integrate randomly into the host genome, often leading to mutations in the host, and to transduce variable amounts of heterogeneous host DNA (53). These traits, characteristic of the transposable phages, make it an extraordinary resource for genetic research.…”

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confidence: 99%

Complete Sequence and Evolutionary Genomic Analysis of the Pseudomonas aeruginosa Transposable Bacteriophage D3112

2004

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Bacteriophage D3112 represents one of two distinct groups of transposable phage found in the clinically relevant, opportunistic pathogen Pseudomonas aeruginosa. To further our understanding of transposable phage in P. aeruginosa, we have sequenced the complete genome of D3112. The genome is 37,611 bp, with an overall G؉C content of 65%. We have identified 53 potential open reading frames, including three genes (the c repressor gene and early genes A and B) that have been previously characterized and sequenced. The organization of the putative coding regions corresponds to published genetic and transcriptional maps and is very similar to that of enterobacteriophage Mu. In contrast, the International Committee on Taxonomy of Viruses has classified D3112 as a -like phage on the basis of its morphology. Similarity-based analyses identified 27 open reading frames with significant matches to proteins in the NCBI databases. Forty-eight percent of these were similar to Mu-like phage and prophage sequences, including proteins responsible for transposition, transcriptional regulation, virion morphogenesis, and capsid formation. The tail proteins were highly similar to prophage sequences in Escherichia coli and phage Phi12 from Staphylococcus aureus, while proteins at the right end were highly similar to proteins in Xylella fastidiosa. We performed phylogenetic analyses to understand the evolutionary relationships of D3112 with respect to Mu-like versus -like bacteriophages. Different results were obtained from similarity-based versus phylogenetic analyses in some instances. Overall, our findings reveal a highly mosaic structure and suggest that extensive horizontal exchange of genetic material played an important role in the evolution of D3112.

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Regulation of bacteriophage Mu transposition

Cited by 18 publications

References 74 publications

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept

Control of Bacteriophage Mu Lysogenic Repression

Complete Sequence and Evolutionary Genomic Analysis of the Pseudomonas aeruginosa Transposable Bacteriophage D3112

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