DNA PACKAGING IN dsDNA BACTERIOPHAGES

Black, Lindsay W.

doi:10.1146/annurev.mi.43.100189.001411

Cited by 391 publications

(256 citation statements)

References 247 publications

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“…We also observed submolar fragments of both PH15 and CNPH82 DNAs after heating the restriction endonuclease digestion mixture (data not shown), suggesting that both phages belonged to the pac-type group. In this group of phages, which typically have circularly permuted linear chromosomes, packaging of concatemeric phage DNA is initiated processively in a headful manner after the terminase cuts the DNA at a pac site (5).…”

Section: Resultsmentioning

confidence: 99%

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: 99%

First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

Daniel¹,

Bonnen

Fischetti³

2007

J Bacteriol

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“…The resulting DNA structure, thought to involve concentric loops of DNA arranged at decreasing radii about a single axis, is referred to as an ''inverse spool''. Alternative models of the packed DNA structure have also been proposed, 21 but the asymmetric cryoelectron microscopy structures described above strongly support the inverse spool model. In one of the original models of the energetics of viral DNA packing, 14 the DNA is assumed to be packed tightly into an inverse spool, with strands touching each other so that they are locally aligned on a square lattice, with an interstrand separation d ¼ 2 nm.…”

Section: Dna Virusesmentioning

confidence: 90%

“…Many authors speculate that the DNA may actually be bent so tightly that it forms 1808 kinks. 9,21 The mathematical models described above are complemented by computer simulations that aim to show how the DNA arranges itself into a spool during packing [34][35][36][37][38] or how it moves out of the capsid during ejection. 39,40 Simulations present plausible scenarios for the details of packing and ejection, but their most interesting features are tied to assumptions that may or may not be correct in biological situations.…”

Section: Dna Virusesmentioning

confidence: 99%

Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity

et al. 2006

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The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA persistence length. Similarly, eukaryotic DNA is packed in DNA-protein complexes (nucleosomes) in which DNA is tightly bent around protein spools. DNA is also tightly bent by many proteins that regulate transcription, resulting in a variation in gene expression that is amenable to quantitative analysis. In these cases, DNA loops are formed with lengths that are comparable to or smaller than the DNA persistence length. The aim of this review is to describe the physical forces associated with tightly bent DNA in all of these settings and to explore the biological consequences of such bending, as increasingly accessible by single-molecule techniques.

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“…It is the only protein that shows sequence similarity with most of the mycobacteriophages sequenced so far, suggesting that it is highly conserved among them. The terminase gene, transporting DNA into the proheads prior to attachment of the tail (54)(55)(56), is located close to the structural gene operon and far from the physical end of the genome, more than 20 kbp. This is also observed in the genomes of cluster A myobacteriophages (13,30,(56)(57)(58).…”

Section: Discussionmentioning

confidence: 99%

The First Structure of a Mycobacteriophage, the Mycobacterium abscessus subsp. bolletii Phage Araucaria

Sassi

Bebeacua

Drancourt

et al. 2013

J Virol

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The unique characteristics of the waxy mycobacterial cell wall raise questions about specific structural features of their bacteriophages. No structure of any mycobacteriophage is available, although ϳ3,500 have been described to date. To fill this gap, we embarked in a genomic and structural study of a bacteriophage from Mycobacterium abscessus subsp. bolletii, a member of the Mycobacterium abscessus group. This opportunistic pathogen is responsible for respiratory tract infections in patients with lung disorders, particularly cystic fibrosis. M. abscessus subsp. bolletii was isolated from respiratory tract specimens, and bacteriophages were observed in the cultures. We report here the genome annotation and characterization of the M. abscessus subsp. bolletii prophage Araucaria, as well as the first single-particle electron microscopy reconstruction of the whole virion. Araucaria belongs to Siphoviridae and possesses a 64-kb genome containing 89 open reading frames (ORFs), among which 27 could be annotated with certainty. Although its capsid and connector share close similarity with those of several phages from Gram-negative (Gram ؊ ) or Gram ؉ bacteria, its most distinctive characteristic is the helical tail decorated by radial spikes, possibly host adhesion devices, according to which the phage name was chosen. Its host adsorption device, at the tail tip, assembles features observed in phages binding to protein receptors, such as phage SPP1. All together, these results suggest that Araucaria may infect its mycobacterial host using a mechanism involving adhesion to cell wall saccharides and protein, a feature that remains to be further explored.

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DNA PACKAGING IN dsDNA BACTERIOPHAGES

Cited by 391 publications

References 247 publications

First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity

The First Structure of a Mycobacteriophage, the Mycobacterium abscessus subsp. bolletii Phage Araucaria

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