Complete nucleotide sequence and genome analysis of bacteriophage BFK20 — A lytic phage of the industrial producer Brevibacterium flavum

Bukovská, Gabriela; Klučár, Ľuboš; Vlček, Čestmı́r; Adamovic, Jan; Turña, Ján; Timko, Jozef

doi:10.1016/j.virol.2005.12.010

Cited by 33 publications

(26 citation statements)

References 82 publications

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“…Using this equation, the length of the tails in PH15 and CNPH82 corresponds to 155 nm (TMP, 1,034 amino acids), which correlates well with our estimation from the electron micrographs. Similar calculations of tail length based on TMP size have also been made for phages that are unrelated to (11,44,62,81,82).…”

Section: Resultsmentioning

confidence: 82%

First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

Daniel¹,

Bonnen

Fischetti³

2007

J Bacteriol

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Staphylococcus epidermidis is an important opportunistic pathogen causing nosocomial infections and is often associated with infections in patients with implanted prosthetic devices. A number of virulence determinants have been identified in S. epidermidis, which are typically acquired through horizontal gene transfer. Due to the high recombination potential, bacteriophages play an important role in these transfer events. Knowledge of phage genome sequences provides insights into phage-host biology and evolution. We present the complete genome sequence and a molecular characterization of two S. epidermidis phages, PH15 (PH15) and CNPH82 (CNPH82). Both phages belonged to the Siphoviridae family and produced stable lysogens. The PH15 and CNPH82 genomes displayed high sequence homology; however, our analyses also revealed important functional differences. The PH15 genome contained two introns, and in vivo splicing of phage mRNAs was demonstrated for both introns. Secondary structures for both introns were also predicted and showed high similarity to those of Streptococcus thermophilus phage 2972 introns. An additional finding was differential superinfection inhibition between the two phages that corresponded with differences in nucleotide sequence and overall gene content within the lysogeny module. We conducted phylogenetic analyses on all known Siphoviridae, which showed PH15 and CNPH82 clustering with Staphylococcus aureus, creating a novel clade within the S. aureus group and providing a higher overall resolution of the siphophage branch of the phage proteomic tree than previous studies. Until now, no S. epidermidis phage genome sequences have been reported in the literature, and thus this study represents the first complete genomic and molecular description of two S. epidermidis phages.Staphylococcus epidermidis, a member of the novobiocin-susceptible coagulase-negative staphylococci, is an important opportunistic pathogen and a major cause of nosocomial infections (42, 55). S. epidermidis predominantly colonizes the mucous membranes, groin, and axillar areas, as well as the cutaneous system of human body, with bacterial counts of up to 10 to 10 3 CFU/cm 2 (26). S. epidermidis is usually considered a harmless commensal microorganism; however, infections can occur in immunocompromised individuals and in patients with indwelling or implanted medical devices such as prosthetic heart valves and joint prostheses, where the staphylococci penetrate cutaneous and mucosal barriers (79). With the increasing use of such devices in medical practice, several million people are affected by complications arising from S. epidermidis infections (49). The widespread use of various antimicrobial agents, including penicillins, macrolides, aminoglycosides, and semisynthetic penicillins such as methicillin, has now led to the emergence of multiple-drug-resistant S. epidermidis strains (21, 72).Two S. epidermidis genomes have been sequenced: those of the non-biofilm-forming, non-infection-associated strain ATCC 12228 and the infecti...

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Section: Resultsmentioning

confidence: 82%

First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

Daniel¹,

Bonnen

Fischetti³

2007

J Bacteriol

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“…Subsequently, it could be shown that this is due to an induction of the CGP3 prophage in C. glutamicum. Upon induction, the CGP3 DNA becomes excised from the genome and exists as a doublestranded DNA phage with cohesive ends, like the majority of other known corynephages (2,22,24,30). Until now, the CGP3 prophage DNA (ϳ187 kbp) was supposed to exist exclusively as a genomic island integrated into the C. glutamicum genome.…”

Section: Discussionmentioning

confidence: 99%

Population Heterogeneity inCorynebacterium glutamicumATCC 13032 Caused by Prophage CGP3

et al. 2008

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The genome of Corynebacterium glutamicum type strain ATCC 13032 (accession number BX927147) contains three prophages, CGP1, CGP2, and CGP3. We recently observed that many genes within the CGP3 prophage region have increased mRNA levels in a dtxR deletion mutant that lacks the master regulator of iron homeostasis (J. Wennerhold and M. Bott, J. Bacteriol. 188:2907-2918, 2006). Here, we provide evidence that this effect is due to the increased induction of the prophage CGP3 in the dtxR mutant, possibly triggered by DNA damage caused by elevated intracellular iron concentrations. Upon induction, the CGP3 prophage region is excised from the genome and forms a circular double-stranded DNA molecule. Using quantitative real-time PCR, an average copy number of about 0.1 per chromosome was determined for circular CGP3 DNA in wild-type C. glutamicum. This copy number increased about 15-fold in the dtxR mutant. In order to visualize the CGP3 DNA within single cells, a derivative of the wild type was constructed that contained an array of tet operators integrated within the CGP3 region and a plasmid-encoded YFP-TetR fusion protein. As expected, one to two fluorescent foci that represented the chromosomally integrated CGP3 prophage were detected in the majority of cells. However, in a small fraction (2 to 4%) of the population, 4 to 10 CGP3 DNA molecules could be observed in a single cell. Interestingly, the presence of many CGP3 copies in a cell often was accompanied by an efflux of chromosomal DNA, indicating the lysis of the corresponding cell. However, evidence for the formation of functional infective CGP3 phage particles could not be obtained.

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“…The 36.5-kb prophage genome has a GϩC content of 52.2% and encodes 43 predicted proteins. Its closest sequence matches at the amino acid level were with deduced structural proteins of the lytic phage BFK20 of "Brevibacterium flavum" (52). However, its genome organization resembles that of phages infecting low-GϩC gram-positive bacteria, and several of its proteins show weak sequence similarities with these phages (50).…”

Section: Prophage-like Element In the Genome Of C Diphtheriaementioning

confidence: 99%

“…The SSIs are loaded mainly with transposable elements and genes of unknown function, although several enzymes and proteins of a diverse functional context are also encoded on the islands (415,416). SSI-8 includes a gene region with deduced amino acid sequence similarity to proteins of the lytic corynephage BFK20 from the industrial amino acid producer "Brevibacterium flavum" (52). By means of a precise genome excision method based on the Cre/loxP recombination system, the 11 SSIs were individually deleted from the C. glutamicum R genome (415,416).…”

Section: Corynebacterium Comparative Genome Analysismentioning

confidence: 99%

“…Genomic island CEGI-3 (40.4 kb) is flanked by a 26-bp direct repeat element and encodes an integrase at the 5Ј junction (494). Seven of the 50 predicted genes of CEGI-3 encode proteins similar to late proteins of the lytic bacteriophage BFK20 (52). A high content of genes coding for hypothetical proteins and the similarity to the genome of bacteriophage BFK20 indicate that CEGI-3 is a likely prophage island.…”

Section: Prophage-like Elements In the C Glutamicum Genomementioning

confidence: 99%

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Genomics ofActinobacteria: Tracing the Evolutionary History of an Ancient Phylum

Ventura

Canchaya

Tauch

et al. 2007

Microbiol Mol Biol Rev

946

638

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SUMMARY Actinobacteria constitute one of the largest phyla among Bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context.

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Complete nucleotide sequence and genome analysis of bacteriophage BFK20 — A lytic phage of the industrial producer Brevibacterium flavum

Cited by 33 publications

References 82 publications

First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

Population Heterogeneity inCorynebacterium glutamicumATCC 13032 Caused by Prophage CGP3

Genomics ofActinobacteria: Tracing the Evolutionary History of an Ancient Phylum

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