T7 phage

Last updated
Bacteriophage T7 Structural Model at Atomic Resolution Bacteriophage T7 7-24-2021 ps.tif
Bacteriophage T7 Structural Model at Atomic Resolution
Escherichia virus T7
Phage T7.png
Virus classification OOjs UI icon edit-ltr.svg
(unranked): Virus
Realm: Duplodnaviria
Kingdom: Heunggongvirae
Phylum: Uroviricota
Class: Caudoviricetes
Order: Caudovirales
Family: Autographiviridae
Genus: Teseptimavirus
Species:
Escherichia virus T7

Bacteriophage T7 (or the T7 phage) is a bacteriophage, a virus that infects bacteria. It infects most strains of Escherichia coli and relies on these hosts to propagate. Bacteriophage T7 has a lytic life cycle, meaning that it destroys the cell it infects. It also possesses several properties that make it an ideal phage for experimentation: its purification and concentration have produced consistent values in chemical analyses; [2] it can be rendered noninfectious by exposure to UV light; [3] and it can be used in phage display to clone RNA binding proteins. [3]

Contents

Discovery

In a 1945 study by Demerec and Fano, [4] T7 was used to describe one of the seven phage types (T1 to T7) that grow lytically on Escherichia coli. [5] Although all seven phages were numbered arbitrarily, phages with odd numbers, or T-odd phages, were later discovered to share morphological and biochemical features that distinguish them from T-even phages. [6] Before being physically referred to as T7, the phage was used in prior experiments. German-American biophysicist Max Delbrück worked with the same virus in the late 1930s, calling it phage δ, and French-Canadian microbiologist Félix d'Herelle likely studied its close relative in the 1920s. [7] [5]

Hosts

T7 grows on rough strains of Escherichia coli (i.e. those without full-length O-antigen polysaccharide on their surface) and some other enteric bacteria, but close relatives also infect smooth and even capsulated strains. [8]

Virion structure

Colored microphotography of a T7 virion with its six tail fibers that are folded back against its capsid. The fibers extend as the virus locates a suitable host. 51639 web T7 microphotography colored.jpg
Colored microphotography of a T7 virion with its six tail fibers that are folded back against its capsid. The fibers extend as the virus locates a suitable host.
Annotated schematic drawing of a Enterobacteria phage T7 virion (cross section and side view) T7likevirus virion.jpg
Annotated schematic drawing of a Enterobacteria phage T7 virion (cross section and side view)

The virus has complex structural symmetry, with a capsid of the phage that is icosahedral (twenty faces) with an inner diameter of 55  nm and a tail 19 nm in diameter and 28.5 nm long attached to the capsid. [9] The ejection of proteins from the capsid upon infection causes the virus to change structure when it enters the cell. [10]

Genome

The genome of phage T7 [11] was among the first completely sequenced genomes and was published in 1983. [12] The head of the phage particle contains the roughly 40 kbp dsDNA genome which encodes 55 proteins. [13] The genome features numerous overlapping genes [14] that were partially removed through 'refactoring' the genome to produce T7.1. [15]

T7 phage genome.png

Life cycle

T7 has a life cycle of 17 min at 37˚C, i.e. the time from infection to the lysis of the host cell when new phages are released. Due to the short latent period, most physiological studies are conducted at 30˚C where infected cells lyse after 30 min. However, high-fitness strains of T7 have been isolated with a latent period of only ~11 min at 37˚C growing under optimal conditions in rich media results. This adapted phage can undergo an effective expansion of its population by more than 1013 in one hour of growth. [16]

Infection of host bacteria

T7 infecting a host cell. Schematic drawing with annotations. Structure of T7 phage.svg
T7 infecting a host cell. Schematic drawing with annotations.
Tomograms of a T7 virion in action. T7 is using its fibers to "walk" across the cell surface and finally infect the cell. 51640 web T7 caught in the act.jpg
Tomograms of a T7 virion in action. T7 is using its fibers to "walk" across the cell surface and finally infect the cell.
Reproduction cycle of T7, in total T7cycle3.jpg
Reproduction cycle of T7, in total
Replication machinery of T7, details Phage T7 replication machinery.png
Replication machinery of T7, details

The T7 phage recognizes certain receptors on the surface of E. coli cells, and binds to the cell surface by its viral tail fibers. In some strains of T7, the tail fibers are replaced with tail-spikes that degrade the O- or K-antigens on the cell surface by way of enzymatic activity. [5]

The adsorption and penetration process use lysozymes to create an opening within the peptidoglycan layer of the bacterial cell wall, allowing transfer of the viral DNA into the bacterium. The short, stubby tail of the T7-like phage is too short to span the cell envelope and, in order to eject the phage genome into the cell at the initiation of infection, virion proteins must first make a channel from the tip of the tail into the cell cytoplasm. [17] The phage also releases five proteins needed to begin replication of the viral genome and cleave the host genome. [18] T7 bacteriophage has been evolved to override several of the host bacteria's defenses including the peptidoglycan cell wall and the CRISPR system. [18] Once the T7 phage has inserted the viral genome, the process of DNA replication of the host genome is halted and replication of viral genome begins. [19]

Under optimal conditions, the T7 phage can complete the lytic process within 25 minutes, leading to the death of the E. coli host cell. At the time of lysis, the virus can produce over 100 progeny. [18]

Components

Gp5 (encoded by gene gp5) is the T7 DNA polymerase. T7 DNA polymerase uses E. coli's endogenous thioredoxin, a REDOX protein, as a sliding DNA clamp during phage DNA replication (though thioredoxin normally has a different function). The sliding clamp functions to hold the polymerase onto the DNA, which increases the rate of synthesis. [20]

DNA replication and repair

Phage T7 has the simplest known DNA replisome, consisting of a helicase and primase that reside in a single polypeptide chain that forms a hexamer in the presence of DNA and ATP or dTTP. T7 DNA polymerase, assisted by E. coli thioredoxin, performs both leading and lagging-strand DNA synthesis.

In phage T7, DNA double-strand breaks are likely repaired by insertion of a patch of donor DNA into a gap at the break site. [21] This repair of double-strand breaks is facilitated by the gene 2.5 protein that promotes the annealing of homologous complementary strands of DNA. [22]

Replicative intermediates

The replicating intracellular DNA of phage T7, when stretched out after cell lysis, is usually longer than the mature phage chromosome (11 to 15 μM) and can occur in the form of highly concatenated linear strands up to 66 times the length of the mature phage chromosome. [23] The replicating DNA can also be seen in the form of coiled ring structures that appear to correspond to multiply looped DNA configurations in which superhelical twists, necessary for compaction of the DNA, were relieved by strand nicking upon cell lysis. [23]

Applications in molecular biology

The T7 promoter sequence is used extensively in molecular biology due to its extremely high affinity for T7 RNA polymerase and thus high level of expression. [3] [2]

T7 has been used as a model in synthetic biology. Chan et al. (2005) "refactored" the genome of T7, replacing approximately 12 kbp of its genome with engineered DNA. [15] The engineered DNA was designed to be easier to work with in a number of ways: individual functional elements were separated by restriction endonuclease sites for simple modification, and overlapping protein coding domains were separated and, where necessary, modified by single base pair silent mutations.

Related Research Articles

<span class="mw-page-title-main">Bacteriophage</span> Virus that infects and replicates within bacteria

A bacteriophage, also known informally as a phage, is a virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν, meaning "to devour". Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have structures that are either simple or elaborate. Their genomes may encode as few as four genes and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm.

<span class="mw-page-title-main">Lambda phage</span> Bacteriophage that infects Escherichia coli

Enterobacteria phage λ is a bacterial virus, or bacteriophage, that infects the bacterial species Escherichia coli. It was discovered by Esther Lederberg in 1950. The wild type of this virus has a temperate life cycle that allows it to either reside within the genome of its host through lysogeny or enter into a lytic phase, during which it kills and lyses the cell to produce offspring. Lambda strains, mutated at specific sites, are unable to lysogenize cells; instead, they grow and enter the lytic cycle after superinfecting an already lysogenized cell.

<span class="mw-page-title-main">Lytic cycle</span> Cycle of viral reproduction

The lytic cycle is one of the two cycles of viral reproduction, the other being the lysogenic cycle. The lytic cycle results in the destruction of the infected cell and its membrane. Bacteriophages that can only go through the lytic cycle are called virulent phages.

<i>Escherichia virus T4</i> Species of bacteriophage

Escherichia virus T4 is a species of bacteriophages that infect 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, Enterobacteria phage T2, Enterobacteria phage T4 and Enterobacteria phage T6.

<i>Podoviridae</i> Family of viruses

Podoviridae was a family of bacteriophage in the order Caudovirales often associated with T-7 like phages. The family and order Caudoviraleshave now been abolished, with the term podovirus now used to refer to the morphology of viruses in this former family. There were 130 species in this family, assigned to 3 subfamilies and 52 genera. This family was characterized by having very short, noncontractile tails. Many former phages in the former family Podoviriade are now classified in the Autographiviridae

Microviridae is a family of bacteriophages with a single-stranded DNA genome. The name of this family is derived from the ancient Greek word μικρός (mikrós), meaning "small". This refers to the size of their genomes, which are among the smallest of the DNA viruses. Enterobacteria, intracellular parasitic bacteria, and spiroplasma serve as natural hosts. There are 22 species in this family, divided among seven genera and two subfamilies.

<span class="mw-page-title-main">Viral replication</span> Formation of biological viruses during the infection process

Viral replication is the formation of biological viruses during the infection process in the target host cells. Viruses must first get into the cell before viral replication can occur. Through the generation of abundant copies of its genome and packaging these copies, the virus continues infecting new hosts. Replication between viruses is greatly varied and depends on the type of genes involved in them. Most DNA viruses assemble in the nucleus while most RNA viruses develop solely in cytoplasm.

<span class="mw-page-title-main">M13 bacteriophage</span> Species of virus

M13 is one of the Ff phages, a member of the family filamentous bacteriophage (inovirus). Ff phages are composed of circular single-stranded DNA (ssDNA), which in the case of the m13 phage is 6407 nucleotides long and is encapsulated in approximately 2700 copies of the major coat protein p8, and capped with about 5 copies each of four different minor coat proteins. The minor coat protein p3 attaches to the receptor at the tip of the F pilus of the host Escherichia coli. The life cycle is relatively short, with the early phage progeny exiting the cell ten minutes after infection. Ff phages are chronic phage, releasing their progeny without killing the host cells. The infection causes turbid plaques in E. coli lawns, of intermediate opacity in comparison to regular lysis plaques. However, a decrease in the rate of cell growth is seen in the infected cells. The replicative form of M13 is circular double-stranded DNA similar to plasmids that are used for many recombinant DNA processes, and the virus has also been used for phage display, directed evolution, nanostructures and nanotechnology applications.

<span class="mw-page-title-main">Phi X 174</span> A single-stranded DNA virus that infects bacteria

The phi X 174 bacteriophage is a single-stranded DNA (ssDNA) virus that infects Escherichia coli. This virus was isolated in 1935 by Nicolas Bulgakov in Félix d'Hérelle's laboratory at the Pasteur Institute, from samples collected in Paris sewers. Its characterization and the study of its replication mechanism were carried out from the 1950s onwards. It was the first DNA-based genome to be sequenced. This work was completed by Fred Sanger and his team in 1977. In 1962, Walter Fiers and Robert Sinsheimer had already demonstrated the physical, covalently closed circularity of ΦX174 DNA. Nobel prize winner Arthur Kornberg used ΦX174 as a model to first prove that DNA synthesized in a test tube by purified enzymes could produce all the features of a natural virus, ushering in the age of synthetic biology. In 1972–1974, Jerard Hurwitz, Sue Wickner, and Reed Wickner with collaborators identified the genes required to produce the enzymes to catalyze conversion of the single stranded form of the virus to the double stranded replicative form. In 2003, it was reported by Craig Venter's group that the genome of ΦX174 was the first to be completely assembled in vitro from synthesized oligonucleotides. The ΦX174 virus particle has also been successfully assembled in vitro. In 2012, it was shown how its highly overlapping genome can be fully decompressed and still remain functional.

<span class="mw-page-title-main">Bacteriophage MS2</span> Species of virus

Bacteriophage MS2, commonly called MS2, is an icosahedral, positive-sense single-stranded RNA virus that infects the bacterium Escherichia coli and other members of the Enterobacteriaceae. MS2 is a member of a family of closely related bacterial viruses that includes bacteriophage f2, bacteriophage Qβ, R17, and GA.

P1 is a temperate bacteriophage that infects Escherichia coli and some other bacteria. When undergoing a lysogenic cycle the phage genome exists as a plasmid in the bacterium unlike other phages that integrate into the host DNA. P1 has an icosahedral head containing the DNA attached to a contractile tail with six tail fibers. The P1 phage has gained research interest because it can be used to transfer DNA from one bacterial cell to another in a process known as transduction. As it replicates during its lytic cycle it captures fragments of the host chromosome. If the resulting viral particles are used to infect a different host the captured DNA fragments can be integrated into the new host's genome. This method of in vivo genetic engineering was widely used for many years and is still used today, though to a lesser extent. P1 can also be used to create the P1-derived artificial chromosome cloning vector which can carry relatively large fragments of DNA. P1 encodes a site-specific recombinase, Cre, that is widely used to carry out cell-specific or time-specific DNA recombination by flanking the target DNA with loxP sites.

<span class="mw-page-title-main">T7 DNA polymerase</span> Enzyme

T7 DNA polymerase is an enzyme used during the DNA replication of the T7 bacteriophage. During this process, the DNA polymerase “reads” existing DNA strands and creates two new strands that match the existing ones. The T7 DNA polymerase requires a host factor, E. coli thioredoxin, in order to carry out its function. This helps stabilize the binding of the necessary protein to the primer-template to improve processivity by more than 100-fold, which is a feature unique to this enzyme. It is a member of the Family A DNA polymerases, which include E. coli DNA polymerase I and Taq DNA polymerase.

<span class="mw-page-title-main">Bacteriophage Qbeta</span> Species of virus

Bacteriophage Qbeta, commonly referred to as Qbeta or Qβ, is a species consisting of several strains of positive-strand RNA virus which infects bacteria that have F-pili, most commonly Escherichia coli. Its linear genome is packaged into an icosahedral capsid with a diameter of 28 nm. Bacteriophage Qβ enters its host cell after binding to the side of the F-pilus.

<span class="mw-page-title-main">Bacteriophage P2</span> Species of virus

Bacteriophage P2, scientific name Peduovirus P2, is a temperate phage that infects E. coli. It is a tailed virus with a contractile sheath and is thus classified in the genus Peduovirus, family Peduoviridae within class Caudoviricetes. This genus of viruses includes many P2-like phages as well as the satellite phage P4.

Phikmvvirus is a genus of viruses that infect bacteria. There are currently 16 species in this genus including the type species Pseudomonas virus phiKMV. Bacteriophage phiKMV and its relatives are known to be highly virulent phages, producing large clear plaques on a susceptible host. The only reported exception is phage LKA1, which yields small plaques surrounded by a halo. While all other P. aeruginosa-specific phikmvviruses use the Type IV pili as primary receptor, LKA1 particles attach to the bacterial lipopolysaccharide layer.

Enquatrovirus is a genus of bacteriophages in the order Caudovirales, in the family Podoviridae. Bacteria serve as natural hosts. There is currently only one species in this genus: the type species Escherichia virus N4.

Escherichia virus CC31, formerly known as Enterobacter virus CC31, is a dsDNA bacteriophage of the subfamily Tevenvirinae responsible for infecting the bacteria family of Enterobacteriaceae. It is one of two discovered viruses of the genus Karamvirus, diverging away from the previously discovered T4virus, as a clonal complex (CC). CC31 was first isolated from Escherichia coli B strain S/6/4 and is primarily associated with Escherichia, even though is named after Enterobacter.

<i>Duplodnaviria</i> Realm of viruses

Duplodnaviria is a realm of viruses that includes all double-stranded DNA viruses that encode the HK97 fold major capsid protein. The HK97 fold major capsid protein is the primary component of the viral capsid, which stores the viral deoxyribonucleic acid (DNA). Viruses in the realm also share a number of other characteristics, such as an icosahedral capsid, an opening in the viral capsid called a portal, a protease enzyme that empties the inside of the capsid prior to DNA packaging, and a terminase enzyme that packages viral DNA into the capsid.

Bacteriophage AP205 is a plaque-forming bacteriophage that infects Acinetobacter bacteria. Bacteriophage AP205 is a protein-coated virus with a positive single-stranded RNA genome. It is a member of the family Fiersviridae, consisting of particles that infect Gram-negative bacteria such as E. coli.

<span class="mw-page-title-main">Integration host factor</span>

The integration host factor (IHF) is a bacterial DNA binding protein complex that facilitates genetic recombination, replication, and transcription by binding to specific DNA sequences and bending the DNA. It also facilitates the integration of foreign DNA into the host genome. It is a heterodimeric complex composed of two homologous subunits IHFalpha and IHFbeta.

References

  1. ↑ Padilla-Sanchez, Victor (2021-07-10), Bacteriophage T7 Structural Model at Atomic Resolution, doi:10.5281/zenodo.5133295 , retrieved 2021-07-24
  2. 1 2 Studier, F. William (1969-11-01). "The genetics and physiology of bacteriophage T7". Virology. 39 (3): 562–574. doi:10.1016/0042-6822(69)90104-4. ISSN   0042-6822. PMID   4902069.
  3. 1 2 3 Teesalu, Tambet; Sugahara, Kazuki N.; Ruoslahti, Erkki (1 January 2012). "Mapping of Vascular ZIP Codes by Phage Display". In Wittrup, K. Dane; Verdine, Gregory L. (eds.). Methods in Enzymology. Academic Press. pp. 35–56. doi:10.1016/B978-0-12-396962-0.00002-1. PMID   22230564.
  4. ↑ Demerec, M; Fano, U (15 March 1945). "Bacteriophage-Resistant Mutants in Escherichia coli". Genetics. 30 (2): 119–136. doi:10.1093/genetics/30.2.119. PMC   1209279 . PMID   17247150.
  5. 1 2 3 Häuser, Roman; Blasche, Sonja; Dokland, Terje; Haggård-Ljungquist, Elisabeth; von Brunn, Albrecht; Salas, Margarita; Casjens, Sherwood; Molineux, Ian; Uetz, Peter (2012). "Bacteriophage Protein–Protein Interactions". Advances in Virus Research. 83: 219–298. doi:10.1016/B978-0-12-394438-2.00006-2. PMC   3461333 . PMID   22748812.
  6. ↑ Cammack, Richard; Atwood, Teresa; Campbell, Peter; Parish, Howard; Smith, Anthony; Vella, Frank; Stirling, John, eds. (2006). Oxford Dictionary of Biochemistry and Molecular Biology. Oxford University Press. doi:10.1093/acref/9780198529170.001.0001. ISBN   9780191727641.
  7. ↑ D'Herelle, Félix (1926). The Bacteriophage and Its Behavior. Baltimore, MD: Williams & Wilkins. doi:10.5962/bhl.title.7308. LCCN   26009494. OCLC   2394374.
  8. ↑ Molineux, Ian J. (2006). "Chapter 20: The T7 group". In Calendar, Richard Lane (ed.). The Bacteriophages (2nd ed.). Oxford: Oxford University Press. p. 277. ISBN   9780195148503.
  9. ↑ "Teseptimavirus ~ ViralZone page". viralzone.expasy.org. Retrieved 18 November 2019.
  10. ↑ Molineux, Ian J.; Panja, Debabrata (March 2013). "Popping the cork: mechanisms of phage genome ejection". Nature Reviews Microbiology. 11 (3): 194–204. doi:10.1038/nrmicro2988. ISSN   1740-1534. PMID   23385786. S2CID   205498472.
  11. ↑ "Genome of bacteriophage T7". 9 September 2004. Retrieved 18 May 2011.
  12. ↑ Dunn, John J.; Studier, F. William; Gottesman, M. (June 1983). "Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements". Journal of Molecular Biology. 166 (4): 477–535. doi:10.1016/S0022-2836(83)80282-4. PMID   6864790.
  13. ↑ "Uniprot: reference proteome of bacteriophage T7".
  14. ↑ Wright, Bradley W.; Molloy, Mark P.; Jaschke, Paul R. (5 October 2021). "Overlapping genes in natural and engineered genomes". Nature Reviews Genetics. 23 (3): 154–168. doi:10.1038/s41576-021-00417-w. ISSN   1471-0064. PMC   8490965 . PMID   34611352.
  15. 1 2 Chan, Leon Y; Kosuri, Sriram; Endy, Drew (January 2005). "Refactoring bacteriophage T7". Molecular Systems Biology. 1 (1). doi:10.1038/msb4100025. PMC   1681472 . PMID   16729053.
  16. ↑ Heineman, Richard H.; Bull, James J. (July 2007). "Testing Optimality With Experimental Evolution: Lysis Time in a Bacteriophage". Evolution. 61 (7): 1695–1709. doi:10.1111/j.1558-5646.2007.00132.x. PMC   1974807 . PMID   17598749.
  17. ↑ Chang, Chung-Yu; Kemp, Priscilla; Molineux, Ian J. (March 2010). "Gp15 and gp16 cooperate in translocating bacteriophage T7 DNA into the infected cell". Virology. 398 (2): 176–186. doi:10.1016/j.virol.2009.12.002. PMC   2825023 . PMID   20036409.
  18. 1 2 3 Qimron, Udi; Tabor, Stanley; Richardson, Charles C. "New Details about Bacteriophage T7-Host Interactions". Archived from the original on 17 August 2011.
  19. ↑ Kulczyk, A.W.; Richardson, C.C. (2016). "The Replication System of Bacteriophage T7". The Enzymes. 39: 89–136. doi:10.1016/bs.enz.2016.02.001. PMID   27241928.
  20. ↑ Jeffery, Constance J. (January 1999). "Moonlighting proteins". Trends in Biochemical Sciences. 24 (1): 8–11. doi:10.1016/S0968-0004(98)01335-8. ISSN   0968-0004. PMID   10087914.
  21. ↑ Lai, Ying‐Ta; Masker, Warren (April 2000). "Repair of double‐strand breaks by incorporation of a molecule of homologous DNA". Molecular Microbiology. 36 (2): 437–446. doi:10.1046/j.1365-2958.2000.01861.x. PMID   10792729.
  22. ↑ Yu, Man; Masker, Warren (15 March 2001). "T7 Single Strand DNA Binding Protein but Not T7 Helicase Is Required for DNA Double Strand Break Repair". Journal of Bacteriology. 183 (6): 1862–1869. doi:10.1128/JB.183.6.1862-1869.2001. PMC   95080 . PMID   11222583.
  23. 1 2 Bernstein, Carol; Bernstein, Harris (June 1974). "Coiled Rings of DNA Released from Cells Infected with Bacteriophages T7 or T4 or from Uninfected Escherichia coli". Journal of Virology. 13 (6): 1346–1355. doi:10.1128/JVI.13.6.1346-1355.1974. PMC   355455 . PMID   4598784.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.