Bacteriophage T4

Abstract

Bacteriophage T4 and its host bacterium, , can be considered among the earliest model organisms – biological systems that attract large numbers of investigators who, because of technical or conceptual advantages of the system, use the system to investigate processes and mechanisms of general significance in biology. Beginning in the mid‐twentieth century, studies focused on bacteriophage T4 revealed essential features of the molecular nature of genes and genomes, mechanism and fidelity of DNA replication, genetic recombination, DNA repair, control of gene expression, genome organisation, assembly of complex macromolecular structures and pre‐emption of cell metabolism by virus infection. Although much of the molecular biology research community has moved on to eukaryotic model organisms, such as yeast, nematode worms, fruitflies, the plant , zebrafish and mice, bacteriophage T4 still presents the best opportunities for understanding at the molecular level DNA replication and recombination, and macromolecular assembly. In addition, T4 and related phages are being used in investigations of bacteriophage therapy. Finally, recent analyses of DNA packaging and morphogenesis have suggested applications of T4 as a gene delivery vehicle.

Key Concepts

  • Bacteriophage T4 presents numerous technical advantages as a model for studying virus reproduction or gene organisation and expression.
  • Bacteriophage T4 is representative of a large group of closely related phages found in varied environments worldwide.
  • Bacteriophage T4 is a virulent phage, which always lyses and kills its host bacterium.
  • The T4 virion has a complex multiprotein structure with a contractile tail that serves both for adsorption to host cells and for intracellular delivery of the viral genome.
  • Bacteriophage T4 contains a large, linear double‐stranded DNA genome, with chemical modifications of its cytosine residues.
  • The T4 genome is circularly permuted and terminally redundant with respect to base sequence; these features protect against information loss during replication of a linear DNA.
  • The T4 genome encodes numerous enzymes, used to support replication of the viral genome and to synthesise deoxyribonucleotides to support the enormous rate of DNA accumulation in infected cells.
  • T4 uses host cell RNA polymerase for transcription of its own genes, but it modifies the bacterial enzyme, both to prevent its transcription of bacterial genes after infection and to contribute towards a timed viral gene transcription program.
  • T4 morphogenesis involves separate subassembly pathways for viral heads, tails, tail baseplates and fibres, with the substructures assembling spontaneously.

Keywords: bacteriophage; genetics; molecular biology; viruses; enzymes; model organisms; macromolecular assembly

Figure 1. A model of the T4 virion, with its tail contracted, based on image reconstruction from electron microscopic images. The elongated icosahedral head (in grey) contains four exterior proteins and within its interior, DNA and six different proteins. The collar and portal structure (in orange and blue) contains six proteins. The whiskers (not shown), which are attached to the collar, contain one protein. The contractile tail sheath (in green) contains multiple copies of one ATP‐binding protein. The tail tube (in pink) contains one protein. The complex tail baseplate (in red, yellow and blue) contains a central hub, with eight proteins, and six surrounding wedges, each with six proteins. The six short tail fibres (in purple) contain four proteins each. The six long‐tail fibres (in light blue) contain four proteins each. Reproduced with permission from Leiman et al. (2004) © Elsevier.
Figure 2. Generation of a population of linear DNA molecules that are circularly permuted and terminally redundant with respect to base sequence, by cutting of a concatemeric replication intermediate. In this scheme, the genome is depicted as the alphabet. If the cutting mechanism recognises slightly more than one genome length, each resultant DNA molecule has two letters (as schematised) repeated at the beginning and end of the molecule.
Figure 3. (a) A one‐step growth curve for bacteriophage T4 infecting . B at 37 °C. Blue circles, infective centres; red circles, intracellular phages; see text for details. PFU, plaque‐forming unit. (b) A chronology of major events in T4 infection. The precise times of expression of genes within the major temporal classes vary somewhat with individual genes, as shown. Under some conditions, lysis may occur later than 30 min after infection; under those conditions, replication, transcription, translation and viral assembly continue until lysis. Reproduced with permission from Mathews in Karam JD (ed.) (1994)©American Society for Microbiology.
Figure 4. Overview of the T4 developmental programme. Reproduced with permission from Mathews in Karam JD (ed.) (1994)© American Society for Microbiology.
Figure 5. Assembly of the T4 DNA polymerase holoenzyme. (a) Reaction of gp43 DNA polymerase with two different forms of the gp44/62 clamp loader. (b) Kinetic analysis of interactions involved in assembly and disassembly of the holoenzyme and its complex with DNA. Three‐dimensional structures of the proteins and rate constants for individual steps are shown. Reproduced with permission from Perumall SK, Ren W, Lee T‐H, and Benkovic SJ (2013) © the National Academy of Sciences of the USA.
Figure 6. T4 assembly pathway, showing the role of portal. (a) The dodecameric portal (magenta) is assembled on the inner membrane of . . The portal acts as an initiator for head assembly, leading to copolymerisation of the major capsid protein gp23 and scaffolding proteins. (b) A symmetry mismatch is created between the fivefold capsid and the dodecameric portal. (c) gp21 protease catalyses maturation cleavages with release of the prohead from the membrane and degradation of the scaffolding proteins. (d) The pentameric gp17 packaging motor assembles at the portal, and DNA packaging begins. The prohead expands when it is 25% filled with DNA (e). Packaging continues until the head is filled with the 172‐kbp genome (f). The packaging motor dissociates (g), and neck proteins (gp13, gp14 and gp15) assemble on the portal (h). Tails and tail fibres, which have been assembled by independent pathways, assemble to produce the complete virion (i). Reproduced with permission from Padilla‐Sanchez et al. (2014) © Elsevier.
Figure 7. Details of T4 head assembly. The portal vertex initiates head assembly. gp23, the major head protein, assembles around a scaffolding core into a prohead. Proteolytic removal of the core creates an empty unexpanded prohead. (a) The packaging machine–DNA complex docks on portal and initiates packaging. (b) After partial head filling, the prohead expands. (c) When the head is full, the packaging machine cuts DNA and dissociates. (d) Neck proteins assemble at the portal. (e) Accessory proteins, Hoc and Soc, bind to gp23 molecules in the head, preparing it for joining to the tail. Reproduced with permission from Yap and Rossmann (2014) © Future Medicine Ltd.
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Mathews, Christopher K(Aug 2015) Bacteriophage T4. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000784.pub4]