Taxonomy of bacterial viruses: establishment of tailed virus genera and the other Caudovirales

Maniloff, Jack; Ackermann, Hans-Wolfgang

doi:10.1007/s007050050442

Cited by 127 publications

(93 citation statements)

References 19 publications

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“…The phage also had tail fibres whose length was at least 86 nm. According to the ICTV classification, wR1-37 belongs to the order Caudovirales and the family Myoviridae (Ackermann, 2003;Maniloff & Ackermann, 1998). In Bradley's classification, wR1-37 belongs to the A1 morphotype (Bradley, 1967).…”

Section: Wr1-37 Belongs To the Myoviridaementioning

confidence: 99%

Yersiniophage ϕR1-37 is a tailed bacteriophage having a 270 kb DNA genome with thymidine replaced by deoxyuridine

et al. 2005

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Yersiniophage wR1-37 is a tailed bacteriophage having a 270 kb DNA genome with thymidine replaced by deoxyuridine Bacteriophage wR1-37 was isolated based on its ability to infect strain YeO3-R1, a virulenceplasmid-cured O antigen-negative derivative of Yersinia enterocolitica serotype O : 3. In this study, the phage receptor was found to be a structure in the outer core hexasaccharide of Y. enterocolitica O : 3 LPS. The phage receptor was present in the outer core of strains of many other Y. enterocolitica serotypes, but also in some Yersinia intermedia strains. Surprisingly, the receptor structure resided in the O antigen of Yersinia pseudotuberculosis O : 9. Electron microscopy demonstrated that wR1-37 particles have an icosahedral head of 88 nm, a short neck of 10 nm, a long contractile tail of 236 nm, and tail fibres of at least 86 nm. This implies that the phage belongs to the order Caudovirales and the family Myoviridae in the ICTV (International Committee for Taxonomy of Viruses) classification. wR1-37 was found to have a lytic life cycle, with eclipse and latent periods of 40 and 50 min, respectively, and a burst size of~80 p.f.u. per infected cell. Restriction digestions and PFGE showed that the wR1-37 genome was dsDNA and~270 kb in size. Enzymically hydrolysed DNA was subjected to HPLC-MS/MS analysis, which demonstrated that the wR1-37 genome is composed of DNA in which thymidine (T) is >99 % replaced by deoxyuridine (dU). The only organisms known to have similar DNA are the Bacillus subtilis-specific bacteriophages PBS1 and PBS2. N-terminal amino acid sequences of four major structural proteins did not show any similarity to (viral) protein sequences in databases, indicating that close relatives of wR1- 37 have not yet been characterized. Genes for two of the structural proteins, p24 and p46, were identified from the partially sequenced wR1-37 genome. INTRODUCTIONYersinia enterocolitica is a Gram-negative bacterium of the family Enterobacteriaceae. The species includes over 30 serotypes, a number of which are human pathogens (Wauters et al., 1991). While the major pathogenic serotypes in Europe, Canada, Japan and South Africa are O : 3 and O : 9; in the United States serotype O : 8 is more prevalent. Y. enterocolitica is widely distributed in nature, swine being the major reservoir of the pathogenic strains (Bottone, 1997).Bacteriophages are the most abundant organisms on Earth, and it is estimated that for each microbial isolate at least 10 different phages can be found (Hendrix, 2002;Pedulla et al., 2003). A number of phages infecting the members of the genus Yersinia have been isolated (Baker & Farmer, 1982;Popp et al., 2000;Stevenson & Airdrie, 1984), but relatively few have been characterized in more detail. Y. enterocolitica O : 3-specific phage wYeO3-12 has been shown to be closely related to Escherichia coli phages T3 and T7 (Pajunen et al., 2000(Pajunen et al., , 2001. Likewise, Yersinia pestis phage wA1122 was recently found to be a close relative of T7 (Garcia et al., 2003a). Bacteriophage...

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Section: Wr1-37 Belongs To the Myoviridaementioning

confidence: 99%

Yersiniophage ϕR1-37 is a tailed bacteriophage having a 270 kb DNA genome with thymidine replaced by deoxyuridine

et al. 2005

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Section: Introductionmentioning

confidence: 99%

“…This protein is also conserved to a lesser extent in T4-like bacteriophages in the family Myoviridae (Davison 1992). Indeed, the perceived utilization of a similar enzyme complex for packaging DNA into preformed capsids by HVs and by members of the order Caudovirales, of which the family Myoviridae is a member (Maniloff & Ackermann 1998), may indicate a common evolutionary origin for these viruses of animals and bacteria.In terms of formal taxa, the family Alloherpesviridae consists of one genus (Ictalurivirus), which contains the species Ictalurid herpesvirus 1 (represented by IcHV1), and the species Cyprinid herpesvirus 3 (represented by CyHV3), which has not been assigned to a genus (www.ictvonline.org). It also contains several fish and amphibian viruses that have not been assigned to any taxa: acipenserid HV 1 (AciHV1), acipenserid HV 2 (AciHV2), anguillid HV 1 (AngHV1), cyprinid HV 1 (CyHV1), and cyprinid HV 2 (CyHV2), esocid HV 1 (EsHV1), percid HV 1 (PeHV1), pleuronectid HV 1 (PlHV1), RaHV1, RaHV2, and salmonid HV 1 (SalHV1), and salmonid HV 2 (SalHV2) (Davison et al 2005a).…”

mentioning

confidence: 99%

Phylogenetic relationships in the family Alloherpesviridae

Waltzek¹,

Kelley²,

Alfaro³

et al. 2009

Dis. Aquat. Org.

127

146

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Phylogenetic relationships among herpesviruses (HVs) of mammals, birds, and reptiles have been studied extensively, whereas those among other HVs are relatively unexplored. We have reconstructed the phylogenetic relationships among 13 fish and amphibian HVs using maximum likelihood and Bayesian analyses of amino acid sequences predicted from parts of the DNA polymerase and terminase genes. The relationships among 6 of these viruses were confirmed using the partial DNA polymerase data plus the complete sequences of the terminase, helicase, and triplex protein genes; the position of these viruses among all other sequenced HVs was also investigated using the complete terminase gene. The results established the monophyly of the fish and amphibian HVs (Alloherpesviridae) separate from the HVs of mammals, birds, and reptiles (Herpesviridae) and the single recognized HV of bivalve mollusks (Malacoherpesviridae) in the order Herpesvirales. Two major clades in the family Alloherpesviridae were recognized: one consisting of viruses from cyprinid and anguillid hosts and the other of viruses from ictalurid, salmonid, acipenserid, and ranid hosts. A comparison of virus and host phylogenies suggested that closely related HVs in this family may have coevolved with their hosts, whereas significant codiversification was not apparent for the more distantly related viruses.KEY WORDS: Alloherpesviridae · Fish herpesviruses · Frog herpesviruses · Phylogeny · Coevolution· DNA polymerase · Terminase Resale or republication not permitted without written consent of the publisherDis Aquat Org 84: [179][180][181][182][183][184][185][186][187][188][189][190][191][192][193][194] 2009 pesviridae, divided into the subfamilies Alphaherpesvirinae, Betaherpesvirinae, and Gammaherpesvirinae) containing mammalian, avian, and reptilian viruses, one (Alloherpesviridae) containing fish and amphibian viruses, and one (Malacoherpesviridae) containing a single virus, OsHV1. The taxonomic structure of the family Herpesviridae has been well established phylogenetically, and the viruses are characterized by approximately 43 homologous genes that were presumably inherited from a common ancestor (McGeoch et al. 2006). The erection of the 2 new families was driven by the findings that these viruses are but tenuously related to the fish and amphibian HVs, which share at least 13 homologous genes with each other (Aoki et al. 2007), and that OsHV1 is related only marginally to all other HVs (Davison et al. 2005b). Indeed, the best, and perhaps only, sequence-based evidence supporting a common ancestry for all HVs resides in a single gene, that encoding the putative ATPase subunit of terminase (hereafter terminase; an enzyme complex involved in packaging DNA into capsids), in which 5 regions are conserved (Davison 1992(Davison , 2002. This protein is also conserved to a lesser extent in T4-like bacteriophages in the family Myoviridae (Davison 1992). Indeed, the perceived utilization of a similar enzyme complex for packaging DNA into preformed capsids...

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“…Escherichia coli phage T7 is a member of the Podoviridae family of the Caudovirales (tailed phages) order (2). T7 is composed of an icosahedral capsid with a 20-nm short tail at one of the vertices (3,4).…”

mentioning

confidence: 99%

Structure of the receptor-binding carboxy-terminal domain of bacteriophage T7 tail fibers

Garcia-Doval

Raaij

2012

Proc. Natl. Acad. Sci. U.S.A.

103

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The six bacteriophage T7 tail fibers, homo-trimers of gene product 17, are thought to be responsible for the first specific, albeit reversible, attachment to Escherichia coli lipopolysaccharide. The protein trimer forms kinked fibers comprised of an amino-terminal tail-attachment domain, a slender shaft, and a carboxyl-terminal domain composed of several nodules. Previously, we expressed, purified, and crystallized a carboxyl-terminal fragment comprising residues 371-553. Here, we report the structure of this protein trimer, solved using anomalous diffraction and refined at 2 Å resolution. Amino acids 371-447 form a tapered pyramid with a triangular cross-section composed of interlocked β-sheets from each of the three chains. The triangular pyramid domain has three α-helices at its narrow end, which are connected to a carboxyl-terminal three-blade β-propeller tip domain by flexible loops. The monomers of this tip domain each contain an eight-stranded β-sandwich. The exact topology of the β-sandwich fold is novel, but similar to that of knob domains of other viral fibers and the phage Sf6 needle. Several host-range change mutants have been mapped to loops located on the top of this tip domain, suggesting that this surface of the tip domain interacts with receptors on the cell surface.bacterial viruses | caudovirales | crystallography | infection | Podoviridae B acteriophages (bacterial viruses or phages) are important biological model systems and, because of the high specificity for their host bacteria, have found application in phage typing, food security, and phage therapy (1). Escherichia coli phage T7 is a member of the Podoviridae family of the Caudovirales (tailed phages) order (2). T7 is composed of an icosahedral capsid with a 20-nm short tail at one of the vertices (3, 4). The capsid is formed by the shell protein gene product (gp) 10 and encloses a DNA of 40 kb. A cylindrical structure composed of gp14, gp15, and gp16 is present inside the capsid (5), attached to the special vertex formed by the connector, a circular dodecamer of gp8 (6). Gp11 and gp12 form the tail; gp13, gp6.7, and gp7.3 have also been shown to be part of the virion and to be necessary for infection, although their location has not been established (7,8). Although extensive electron microscopy studies have been performed on phage T7 (3-6, 9), crystallographic studies have so far been limited to its nonstructural proteins.The main portion of the tail is composed of gp12, a large protein of which six copies are present (10); the small gp11 protein is also located in the tail (5). Attached to the tail are six fibers, each containing three copies of the gp17 protein. T7 tail fibers are elongated homo-trimers, which are responsible for initial, reversible, host cell recognition. A second, irreversible, decisionmaking interaction with the bacterial membrane is presumably mediated by one or more of the tail-tube proteins. DNA transfer into the host is then mediated by an extension formed by gp14-16 (7, 8, 11). Previously, we have reported t...

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Taxonomy of bacterial viruses: establishment of tailed virus genera and the other Caudovirales

Cited by 127 publications

References 19 publications

Yersiniophage ϕR1-37 is a tailed bacteriophage having a 270 kb DNA genome with thymidine replaced by deoxyuridine

Yersiniophage ϕR1-37 is a tailed bacteriophage having a 270 kb DNA genome with thymidine replaced by deoxyuridine

Phylogenetic relationships in the family Alloherpesviridae

Structure of the receptor-binding carboxy-terminal domain of bacteriophage T7 tail fibers

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