Article

Genome Gating in Tailed Bacteriophage Capsids

Unité de Virologie Moléculaire et Structurale, Gif-sur-Yvette, France.
Advances in Experimental Medicine and Biology (Impact Factor: 1.96). 01/2012; 726:585-600. DOI: 10.1007/978-1-4614-0980-9_25
Source: PubMed

ABSTRACT

Written by leaders in their respective fields
Uses the best examples from bacteriophages and animal viruses, many causing infectious diseases of public health importance
Conveys state of the art knowledge of the topic generated by combining X-ray crystallography, high resolution electron microscopy, molecular genetics, biochemistry, and single molecule biophysics
A biological organism can be viewed as a collection of molecular machines well integrated to function as a self-replicating unit. One of the principal goals in biology is to be able to fully understand the mechanisms of an organism in atomic detail. Viruses offer the best opportunities to achieve this goal. Written by leaders in the respective fields, this book examines a variety of viral molecular machines, using the best examples from bacteriophages and animal viruses, many causing infectious diseases of public health importance. Beginning with the viral entry into a host cell, the book takes the reader through replication of the genome, assembly of structural components, genome packaging and maturation into an infectious virion. The book conveys the state of the art knowledge of the topic generated by combining X-ray crystallography, high resolution electron microscopy, molecular genetics, biochemistry, and single molecule biophysics. Viral Molecular Machines is not only a “must-have” book for virologists but it will also be broadly useful for molecular biologists in academia and industry as well as an educational tool for teaching graduate and upper level undergraduate students.

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    • "This protein, like that of other staphylococcal siphoviruses[9]contains an N-terminal lytic transglycosylase SLT domain and a Cterminal peptidase_M23. SEP9 encodes a head-tail connector and head-tail adapter are described to be involved in DNA packaging being localized inside the head shell, where the tail attaches[42]. SEP9 also encodes a virion-associated hydrolase with a N-terminal endopeptidase domain (gp16) and a preneck appendage protein (gp18) with a pectin-lyase like domain that could be involved in the degradation of extracellular polymers[11]. The presence of depolymerases may help the efficacy of some phages degrading biofilm matrix[11]. "
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    ABSTRACT: Relatively few phages (<10) of coagulase-negative staphylococci (CoNS) have been described. S. epidermidis phage vB_SepS_SEP9 is a siphovirus with a unique morphology as a staphylococcal phage, possessing a very long tail. Its genome is unique and unrelated to any phage genomes deposited in public databases. It appears to encode a nonfunctional integrase. Due to the not having a recognizable lysogeny module, the phage is unable lysogenize. The genome comprises 129 coding sequences (CDS), 46 of which have an assigned function and 59 are unique. Its unique morphology and genome led to the proposal of the establishment of a new Siphoviridae genus named “Sep9likevirus”.
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    • "packaging. In many bacteriophages the DNA packaging depends on their portal structure (Johnson and Chiu, 2007; Tavares et al., 2012). In the future it would be interesting to study the structure of the portal vertices of EL, and compare it to the ones of phiKZ, and other related phages. "
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    ABSTRACT: A unique feature of the Pseudomonas aeruginosa giant phage phiKZ is its way of genome packaging onto a spool-like protein structure, the inner body. Until recently, no similar structures have been detected in other phages. We have studied DNA packaging in P. aeruginosa phages EL and Lin68 using cryo-electron microscopy and revealed the presence of inner bodies. The shape and positioning of the inner body and the density of the DNA packaging in EL are different from those found in phiKZ and Lin68. This internal organization explains how the shorter EL genome is packed into a large EL capsid, which has the same external dimensions as the capsids of phiKZ and Lin68. The similarity in the structural organization in EL and other phiKZ-like phages indicates that EL is phylogenetically related to other phiKZ-like phages, and, despite the lack of detectable DNA homology, EL, phiKZ, and Lin68 descend from a common ancestor.
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    • "A switch back to nuclease activity in response to the level of DNA filling of the capsid achieves the dsDNA termination cut ending the packaging cycle. This cleavage is either sequence-specific or sequence-independent (headful packaging mechanism) depending on the viral system (7). "
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    ABSTRACT: The large terminase subunit is a central component of the genome packaging motor from tailed bacteriophages and herpes viruses. This two-domain enzyme has an N-terminal ATPase activity that fuels DNA translocation during packaging and a C-terminal nuclease activity required for initiation and termination of the packaging cycle. Here, we report that bacteriophage SPP1 large terminase (gp2) is a metal-dependent nuclease whose stability and activity are strongly and preferentially enhanced by Mn2+ ions. Mutation of conserved residues that coordinate Mn2+ ions in the nuclease catalytic site affect the metal-induced gp2 stabilization and impair both gp2-specific cleavage at the packaging initiation site pac and unspecific nuclease activity. Several of these mutations block also DNA encapsidation without affecting ATP hydrolysis or gp2 C-terminus binding to the procapsid portal vertex. The data are consistent with a mechanism in which the nuclease domain bound to the portal switches between nuclease activity and a coordinated action with the ATPase domain for DNA translocation. This switch of activities of the nuclease domain is critical to achieve the viral chromosome packaging cycle.
    Full-text · Article · Oct 2012 · Nucleic Acids Research
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