Escherichia virus T4 is a species of bacteriophages that infects Escherichia coli bacteria. It is a double-stranded DNA virus in the subfamily Tevenvirinae of the family Straboviridae. T4 is capable of undergoing only a lytic life cycle and not the lysogenic life cycle. The species was formerly named T-even bacteriophage, a name which also encompasses, among other strains (or isolates), Enterobacteria phage T2, Enterobacteria phage T4 and Enterobacteria phage T6.
Use in research Dating back to the 1940s and continuing today, T-even phages are considered the best studied model organisms. T-even phages are among the largest and highest complexity virus, being made up of around 300 genes. T-even viruses also use hydroxymethylcytosine (HMC) in place of cytosine as part of their DNA.
Genome and structure The T4 virus's double-stranded DNA genome is about 169 kbp long and encodes 289 proteins. The T4 genome is terminally redundant. Upon DNA replication, long multi-genome length concatemers are formed, perhaps by a rolling circle mechanism of replication. When packaged, the concatemer is cut at unspecific positions of the same length, leading to several genomes that represent circular permutations of the original. The T4 genome bears eukaryote-like intron sequences.
Translation The Shine-Dalgarno sequence GAGG dominates in virus T4 early genes, whereas the sequence GGAG is a target for the T4 endonuclease RegB that initiates the early mRNA degradation.
Virus particle structure
T4 is a relatively large virus, at approximately 90 nm wide and 200 nm long (most viruses range from 25 to 200 nm in length). The DNA genome is held in an icosahedral head, also known as a capsid. The T4's tail is hollow so that it can pass its nucleic acid into the cell it is infecting after attachment. Myoviridae phages like T4 have complex contractile tail structures with a large number of proteins involved in the tail assembly and function. The tail fibres are also important in recognizing host cell surface receptors, so they determine if a bacterium is within the virus's host range.
The structure of the 6 megadalton T4 baseplate that comprises 127 polypeptide chains of 13 different proteins (gene products 5, 5.4, 6, 7, 8, 9, 10, 11, 12, 25, 27, 48 and 53) has recently been described in atomic detail. An atomic model of the proximal region of the tail tube formed by gp54 and the main tube protein gp19 have also been created. The tape measure protein gp29 is present in the baseplate-tail tube complexes, but it could not be modeled.
During assembly of the bacteriophage (phage) T4 virion, the morphogenetic proteins encoded by the phage genes interact with each other in a characteristic sequence. Maintaining an appropriate balance in the amounts of each of these proteins produced during viral infection appears to be critical for normal phage T4 morphogenesis. Phage T4 encoded proteins that determine virion structure include major structural components, minor structural components and non-structural proteins that catalyze specific steps in the morphogenesis sequence. Phage T4 morphogenesis is divided into three independent pathways: the head, the tail and the long tail fibres as detailed by Yap and Rossman.
Infection process The T4 virus initiates an Escherichia coli infection by binding OmpC porin proteins and lipopolysaccharide (LPS) on the surface of E. coli cells with its long tail fibers (LTF). A recognition signal is sent through the LTFs to the baseplate. This unravels the short tail fibers (STF) that bind irreversibly to the E. coli cell surface. The baseplate changes conformation and the tail sheath contracts, causing GP5 at the end of the tail tube to puncture the outer membrane of the cell. The lysozyme domain of GP5 is activated and degrades the periplasmic peptidoglycan layer. The remaining part of the membrane is degraded and then DNA from the head of the virus can travel through the tail tube and enter the E. coli cell.
In 1952, Hershey and Chase provided key evidence that the phage DNA, as distinct from protein, enters the host bacterial cell upon infection and is thus the genetic material of the phage. This finding suggested that DNA is, in general, the genetic material of different organisms.
Reproduction The lytic life cycle (from entering a bacterium to its destruction) takes approximately 30 minutes (at 37 °C). Virulent bacteriophages multiply in their bacterial host immediately after entry. After the number of progeny phages reach a certain amount, they cause the host to lyse or break down, therefore they would be released and infect new host cells. The process of host lyses and release is called the lytic cycle. Lytic cycle is a cycle of viral reproduction that involves the destruction of the infected cell and its membrane. This cycle involves a virus that overtakes the host cell and its machinery to reproduce. Therefore, the virus must go through 5 stages in order to reproduce and infect the host cell: Adsorption and penetration (starting immediately) Arrest of host gene expression (starting immediately) Enzyme synthesis (starting after 5 minutes) DNA replication (starting after 10 minutes) Formation of new virus particles (starting after 12 minutes) After the life cycle is complete, the host cell bursts open and ejects the newly built viruses into the environment, destroying the host cell. T4 has a burst size of approximately 100–150 viral particles per infected host.
Benzer (1955 – 1959) developed a system for studying the fine structure of the gene using bacteriophage T4 mutants defective in the rIIA and rIIB genes.Benzer S. "Adventures in the rII region" in Phage and the Origins of Molecular Biology (2007) Edited by John Cairns, Gunther S. Stent, and James D. Watson, Cold Spring Harbor Laboratory of Quantitative Biology, Cold Spring Harbor, Long Island, New York The techniques employed were complementation tests and crosses to detect recombination, particularly between deletion mutations. These genetic experiments led to the finding of a unique linear order of mutational sites within the genes. This result provided strong evidence for the key idea that the gene has a linear structure equivalent to a length of DNA with many sites that can independently mutate.
Adsorption and penetration
Just like all other viruses, even phages do not randomly attach to the surface of their host; instead, they "search" and bind to receptors, specific protein structures, found on the surface of the host. These receptors vary with the phage; teichoic acid, cell wall proteins and lipopolysaccharides, flagella, and pili all can serve as receptors for the phage to bind to. For the T-even phage to infect its host and begin its life cycle, it must enter the first process of infection, adsorption of the phage to the bacterial cell. Adsorption is a value characteristic of the phage-host pair, and the adsorption of the phage on the host cell surface is illustrated as a 2-stage process: reversible and irreversible. It involves the phage's tail structure that begins when the phage's tail fibres help bind the phage to the appropriate receptor of its host. This process is reversible. One or more of the components of the base plate mediates the reversible process of binding of the phage to a bacterium.
Penetration is also a value characteristic of phage-host infection that involves the injection of the phages genetic material inside the bacterium. Penetration of nucleic acid takes place after the irreversible adsorption phase. Mechanisms involving penetration of the phage's nucleic acid are specific for each phage. This penetration mechanism can involve electrochemical membrane potential, ATP molecules, enzymatic splitting of peptidoglycan layer, or all three of these factors can be vital for the penetration of the nucleic acid inside the bacterial cell. Studies have been done on the T2 bacteriophage (T4-like phage) mechanism of penetration, and it has been shown that the phage's tail does not penetrate inside the bacterial cell wall, and penetration of this phage involves electrochemical membrane potential on the inner membrane.
Replication and packaging Virus T4 genome is synthesized within the host cell using rolling circle replication. The time it takes for DNA replication in a living cell was measured as the rate of virus T4 DNA elongation in virus-infected E. coli. During the period of exponential DNA increase at 37 °C, the rate was 749 nucleotides per second. The mutation rate per base pair per replication during virus T4 DNA synthesis is 1.7 per 10−8,Drake JW (1970) The Molecular Basis of Mutation. Holden-Day, San Francisco a highly accurate DNA copying mechanism, with only 1 error in 300 copies. The virus also codes for unique DNA repair mechanisms. The T4 phage head is assembled empty around a scaffolding protein, which is later degraded. Consequently, the DNA needs to enter the prohead through a tiny pore, which is achieved by a hexamer of gp17 interacting with DNA first, which also serves as a motor and nuclease. The T4 DNA packaging motor has been found to load DNA into virus capsids at a rate up to 2000 base pairs per second. The power involved, if scaled up in size, would be equivalent to that of an average automobile engine.
Release The final step in viral reproduction and multiplication is determined by the release of virions from the host cell. The release of the virions occurs after the breakage of the bacterial plasma membrane. Nonenveloped viruses lyse the host cell which is characterized by viral proteins attacking the peptidoglycan or membrane. The lysis of the bacteria occurs when the capsids inside the cell release the enzyme lysozyme which break down the cell wall. The released bacteriophages infect other cells, and the viral multiplication cycle is repeated within those cells.
Multiplicity reactivation
Multiplicity reactivation (MR) is the process by which two or more virus genomes, each containing inactivating genome damage, can interact within an infected cell to form a viable virus genome. Salvador Luria, while studying UV irradiated virus T4 in 1946, discovered MR and proposed that the observed reactivation of damaged virus occurs by a recombination mechanism.(see refs.) This preceded the confirmation of DNA as the genetic material in 1952 in related virus T2 by the Hershey–Chase experiment.
As remembered by Luria (1984,Salvador E. Luria. A Slot Machine, A Broken Test Tube: An Autobiography. Harper & Row, New York: 1984. Pp. 228. (USA and Canada) pg. 97) the discovery of reactivation of irradiated virus (referred to as "multiplicity reactivation") immediately started a flurry of activity in the study of repair of radiation damage within the early phage group (reviewed by Bernstein in 1981). It turned out later that the repair of damaged virus by mutual help that Luria had discovered was only one special case of DNA repair. Cells of all types, not just, bacteria and their viruses, but all organisms studied, including humans, are now known to have complex biochemical processes for repairing DNA damages (see DNA repair). DNA repair processes are also now recognized as playing critical roles in protecting against aging, cancer, and infertility.