Modular architecture of the T4 phage superfamily: A conserved core genome and a plastic periphery

Comeau, A.; Bertrand, Claire; Letarov, Andrei V.; Tétart, Françoise; Krisch, Henry

doi:10.1016/j.virol.2006.12.031

Cited by 135 publications

(173 citation statements)

References 56 publications

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“…Similar acidic and hydrophobic motifs are located at the C-ends of gp55 homologues of other T4-family phages (with the possible exception of nt-1 and 65) (Comeau et al, 2007;Filée et al, 2006;Nolan et al, 2006;. Amino acid sequence is generally more divergent among putative gp33 homologues, especially at their N-ends but, with the exception of phages nt-1 and 65, they present similar hydrophobic and acidic 4-to 6-residue C-terminal elements (Supplemental Figure 1).…”

Section: The Functional Asymmetry Of Gp55 and Gp33 Interactions With mentioning

confidence: 74%

Dissection of the Bacteriophage T4 Late Promoter Complex

Nechaev

Geiduschek

2008

Journal of Molecular Biology

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Activated transcription of the bacteriophage T4 late genes is generated by a mechanism that stands apart from the common modalities of transcriptional regulation: the activator gp45 is the viral replisome's sliding clamp; two sliding clamp-binding proteins, gp33 and gp55, replace the host RNA polymerase (RNAP) σ subunit. We have mutagenized, reconfigured and selectively disrupted individual interactions of the sliding clamp with gp33 and gp55 and have monitored effects on transcription. The C-terminal sliding clamp-binding epitopes of gp33 and gp55 are perfectly interchangeable, but the functions of these two RNAP-sliding clamp connections differ, with only the gp33-gp45 linkage essential for activation. Formation of transcription-ready promoter complexes by the sliding clamp-activated wild-type T4 RNAP resists competition by high concentrations of the polyanion heparin. This avid formation of promoter complexes requires both linkages of the T4 late RNAP to the sliding clamp. Preopening the promoter compensates for loss of the gp55-gp45 but not the gp33-gp45 linkage. We interpret these findings in relation to the common model of transcriptional initiation in bacteria and highlight the roles of individual interactions of the promoter complex.

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Section: The Functional Asymmetry Of Gp55 and Gp33 Interactions With mentioning

confidence: 74%

Dissection of the Bacteriophage T4 Late Promoter Complex

Nechaev

Geiduschek

2008

Journal of Molecular Biology

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“…1; also, see Table S1 in the supplemental material) with relatively low levels of disruption separated by regions of a more hyperplastic character. The division of phage genomes into syntenic blocks and hyperplastic regions was found to be a useful means of describing vertical descent in the presence of significant amounts of horizontal transfer in the analysis of KZ-related and T4 genomes (11,17,23). The OBP/EL syntenic blocks were similar to syntenic blocks between EL and KZ (23) and among 2012-1, KZ, and EL (52).…”

Section: Resultsmentioning

confidence: 97%

Complete Genome Sequence of the Giant Virus OBP and Comparative Genome Analysis of the Diverse ϕKZ-Related Phages

Cornelissen

Hardies

Shaburova

et al. 2012

J Virol

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The 283,757-bp double-stranded DNA genome of Pseudomonas fluorescens phage OBP shares a general genomic organization with Pseudomonas aeruginosa phage EL. Comparison of this genomic organization, assembled in syntenic genomic blocks interspersed with hyperplastic regions of the KZ-related phages, supports the proposed division in the "EL-like viruses," and the "phiKZ-like viruses" within a larger subfamily. Identification of putative early transcription promoters scattered throughout the hyperplastic regions explains several features of the KZ-related genome organization (existence of genomic islands) and evolution (multi-inversion in hyperplastic regions). When hidden Markov modeling was used, typical conserved core genes could be identified, including the portal protein, the injection needle, and two polypeptides with respective similarity to the 3=-5= exonuclease domain and the polymerase domain of the T4 DNA polymerase. While the N-terminal domains of the tail fiber module and peptidoglycan-degrading proteins are conserved, the observation of C-terminal catalytic domains typical for the different genera supports the further subdivision of the KZ-related phages. P seudomonas fluorescens phage OBP (vB_PflM_OBP) (30, 47) is member of a growing group of giant phages, isolated, to date, only from Pseudomonas species and represented by the completely sequenced and well-studied Pseudomonas aeruginosa myovirus KZ (9,18,19,[31][32][33]36,42). Three other phages encoding many proteins with similarity to KZ proteins have been completely sequenced: EL (23), 2012-1 (52), and PA3 (43). Krylov et al. (33) assigned 19 unsequenced Pseudomonas phages to this group. We refer to the group as KZ-related phages. Lavigne et al. (35) have argued that EL should be classified as a genus separate from KZ and 2012-1 based on its less extensive levels of similarity. By that criterion, PA3 belongs to the "phiKZ-like viruses" and the results reported here classify OBP as the second member of the possible genus EL-like viruses.OBP shares a number of definitive properties with the other KZ-related phages. Typically, KZ-related phages have a very large icosahedral head, ϳ122 nm in diameter, and a long (ϳ190-nm) contractile tail surrounded by fibers. A KZ-related phage head contains a proteinic inner body, which has been speculated to organize the packaged DNA (18, 32). The exceptionally large genomes of the KZ-related phages (between 211 and 317 kb of nonredundant sequence) are composed of circularly permuted and terminally redundant linear double-stranded DNAs as determined for KZ and 2012-1 (42, 52). The KZ-related genomes display a pronounced difference in GϩC content (between 36.8 and 48%) and all have markedly lower GϩC content than the chromosomes of their GC-rich Pseudomonas hosts (60 to 66% GϩC).This group of phages has numerous genes involved in nucleotide metabolism (e.g., thymidylate synthase, thymidylate kinase, ribonucleoside diphosphate reductase, subunit beta [NrdB], and dihydrofolate reductase) and at least six genes enco...

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“…The remainder of the genes, the noncore genes, is generally not found in all genomes in a group, and they are more likely to lack identified functions. Where functions are known for these genes, they typically provide accessory functions that appear to better adapt the phage to its ecological niche (56,68,264). In contrast to the dramatic horizontal movement of the noncore genes, the core genes of the T4 group were found to have congruent phylogenies (79)that is, they had not swapped horizontally-and a similar result was seen for the SPO1 group (261).…”

Section: Fig 1 Viruses Of the Ordermentioning

confidence: 88%

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Krupovìč

Prangishvili

Hendrix

et al. 2011

Microbiol Mol Biol Rev

216

176

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SUMMARY Prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet Earth with human beings (among others). However, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. An understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. The vast majority of characterized prokaryotic viruses belong to the order Caudovirales, double-stranded DNA (dsDNA) bacteriophages with tails. Consequently, these viruses have been studied (and reviewed) extensively from both genomic and functional perspectives. However, albeit numerous, tailed phages represent only a minor fraction of the prokaryotic virus diversity. Therefore, the knowledge which has been generated for this viral system does not offer a comprehensive view of the prokaryotic virosphere. In this review, we discuss all families of bacterial and archaeal viruses that contain more than one characterized member and for which evolutionary conclusions can be attempted by use of comparative genomic analysis. We focus on the molecular mechanisms of their genome evolution as well as on the relationships between different viral groups and plasmids. It becomes clear that evolutionary mechanisms shaping the genomes of prokaryotic viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the life cycle. We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions.

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Modular architecture of the T4 phage superfamily: A conserved core genome and a plastic periphery

Cited by 135 publications

References 56 publications

Dissection of the Bacteriophage T4 Late Promoter Complex

Dissection of the Bacteriophage T4 Late Promoter Complex

Complete Genome Sequence of the Giant Virus OBP and Comparative Genome Analysis of the Diverse ϕKZ-Related Phages

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

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