Active protection by bacteriophages T3 and T7 againstE. coli B-and K-specific restriction of their DNA

Krüger, Detlev H.; Schroeder, Cornelia; Hansen, Sigrid; Rosenthal, H. A.

doi:10.1007/bf01036001

Cited by 68 publications

(43 citation statements)

References 40 publications

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“…Phage T4 e.g. protects its free genomic ends from degradation by exonucleases with the help of small DNA-binding proteins [43], phage T7 possesses an anti-restriction system that inhibits the activity of the bacterial restriction endonuclease by prevention of its binding to the phage DNA [44,45]. Phage JWAlpha also harbors a gene (gp24) that might play a role in a putative anti-restriction system.…”

Section: Resultsmentioning

confidence: 99%

First genome sequences of Achromobacter phages reveal new members of the N4 family

Wittmann

Dreiseikelmann

Rohde

et al. 2014

Virol J

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BackgroundMulti-resistant Achromobacter xylosoxidans has been recognized as an emerging pathogen causing nosocomially acquired infections during the last years. Phages as natural opponents could be an alternative to fight such infections. Bacteriophages against this opportunistic pathogen were isolated in a recent study. This study shows a molecular analysis of two podoviruses and reveals first insights into the genomic structure of Achromobacter phages so far.MethodsGrowth curve experiments and adsorption kinetics were performed for both phages. Adsorption and propagation in cells were visualized by electron microscopy. Both phage genomes were sequenced with the PacBio RS II system based on single molecule, real-time (SMRT) technology and annotated with several bioinformatic tools. To further elucidate the evolutionary relationships between the phage genomes, a phylogenomic analysis was conducted using the genome Blast Distance Phylogeny approach (GBDP).ResultsIn this study, we present the first detailed analysis of genome sequences of two Achromobacter phages so far. Phages JWAlpha and JWDelta were isolated from two different waste water treatment plants in Germany. Both phages belong to the Podoviridae and contain linear, double-stranded DNA with a length of 72329 bp and 73659 bp, respectively. 92 and 89 putative open reading frames were identified for JWAlpha and JWDelta, respectively, by bioinformatic analysis with several tools. The genomes have nearly the same organization and could be divided into different clusters for transcription, replication, host interaction, head and tail structure and lysis. Detailed annotation via protein comparisons with BLASTP revealed strong similarities to N4-like phages.ConclusionsAnalysis of the genomes of Achromobacter phages JWAlpha and JWDelta and comparisons of different gene clusters with other phages revealed that they might be strongly related to other N4-like phages, especially of the Escherichia group. Although all these phages show a highly conserved genomic structure and partially strong similarities at the amino acid level, some differences could be identified. Those differences, e.g. the existence of specific genes for replication or host interaction in some N4-like phages, seem to be interesting targets for further examination of function and specific mechanisms, which might enlighten the mechanism of phage establishment in the host cell after infection.

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Section: Resultsmentioning

confidence: 99%

First genome sequences of Achromobacter phages reveal new members of the N4 family

Wittmann

Dreiseikelmann

Rohde

et al. 2014

Virol J

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“…Similar anti-restriction and anti-modification activities of the Ocr protein have been determined against the IA to ID families (34,35). Ocr was found to act as an anti-restriction protein against all four families but was only effective as an anti-modification protein against the IA and ID families (16,19,30). …”

Section: Resultsmentioning

confidence: 99%

Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance

McMahon

Roberts

Johnson

et al. 2009

Nucleic Acids Research

105

113

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The ardA gene, found in many prokaryotes including important pathogenic species, allows associated mobile genetic elements to evade the ubiquitous Type I DNA restriction systems and thereby assist the spread of resistance genes in bacterial populations. As such, ardA contributes to a major healthcare problem. We have solved the structure of the ArdA protein from the conjugative transposon Tn916 and find that it has a novel extremely elongated curved cylindrical structure with defined helical grooves. The high density of aspartate and glutamate residues on the surface follow a helical pattern and the whole protein mimics a 42-base pair stretch of B-form DNA making ArdA by far the largest DNA mimic known. Each monomer of this dimeric structure comprises three alpha–beta domains, each with a different fold. These domains have the same fold as previously determined proteins possessing entirely different functions. This DNA mimicry explains how ArdA can bind and inhibit the Type I restriction enzymes and we demonstrate that 6 different ardA from pathogenic bacteria can function in Escherichia coli hosting a range of different Type I restriction systems.

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“…The T3 and T7 genomes were also resistant to the type I restriction enzyme EcoKI (28,29,72,73) because of SAMases and the downstream locations of the first recognition sequences, 5490 to 5502 and 15161 to 15173, respectively, from gene 3 (Table 3). Four Salmonella type 1 restriction enzymes (StySBI, StySPI, StySKI, and StySBLI) have been identified in S. enterica serovar Typhimurium, S. enterica serovar Potsdam, S. enterica serovar Kaduna, and S. enterica serovar Blegdam, respectively (46,75,76).…”

Section: Vol 74 2008 Characterization Of a T7-like Virus (Sg-jl2) 6973mentioning

confidence: 99%

Characterization of a T7-Like Lytic Bacteriophage (φSG-JL2) of Salmonella enterica Serovar Gallinarum Biovar Gallinarum

Kwon

Cho²,

Kim

et al. 2008

Appl Environ Microbiol

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SG-JL2 is a newly discovered lytic bacteriophage infecting Salmonella enterica serovar Gallinarum biovar Gallinarum but is nonlytic to a rough vaccine strain of serovar Gallinarum biovar Gallinarum (SG-9R), S. enterica serovar Enteritidis, S. enterica serovar Typhimurium, and S. enterica serovar Gallinarum biovar Pullorum. The SG-JL2 genome is 38,815 bp in length (GC content, 50.9%; 230-bp-long direct terminal repeats), and 55 putative genes may be transcribed from the same strand. Functions were assigned to 30 genes based on high amino acid similarity to known proteins. Most of the expected proteins except tail fiber (31.9%) and the overall organization of the genomes were similar to those of yersiniophage YeO3-12. SG-JL2 could be classified as a new T7-like virus and represents the first serovar Gallinarum biovar Gallinarum phage genome to be sequenced. On the basis of intraspecific ratios of nonsynonymous to synonymous nucleotide changes (Pi[a]/Pi[s]), gene 2 encoding the host RNA polymerase inhibitor displayed Darwinian positive selection. Pretreatment of chickens with SG-JL2 before intratracheal challenge with wild-type serovar Gallinarum biovar Gallinarum protected most birds from fowl typhoid. Therefore, SG-JL2 may be useful for the differentiation of serovar Gallinarum biovar Gallinarum from other Salmonella serotypes, prophylactic application in fowl typhoid control, and understanding of the vertical evolution of T7-like viruses.

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Active protection by bacteriophages T3 and T7 againstE. coli B-and K-specific restriction of their DNA

Cited by 68 publications

References 40 publications

First genome sequences of Achromobacter phages reveal new members of the N4 family

First genome sequences of Achromobacter phages reveal new members of the N4 family

Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance

Characterization of a T7-Like Lytic Bacteriophage (φSG-JL2) of Salmonella enterica Serovar Gallinarum Biovar Gallinarum

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