M13 bacteriophage
 | This article possibly contains original research. (May 2012) |
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| Escherichia virus M13 | |
|---|---|
| |
| Blue: Coat Protein pIII; Brown: Coat Protein pVI; Red: Coat Protein pVII; Limegreen: Coat Protein pVIII; Fuchsia: Coat Protein pIX; Purple: Single Stranded DNA | |
Virus classification 
| |
| (unranked): | Virus |
| Realm: | Monodnaviria |
| Kingdom: | Loebvirae |
| Phylum: | Hofneiviricota |
| Class: | Faserviricetes |
| Order: | Tubulavirales |
| Family: | Inoviridae |
| Genus: | Inovirus |
| Species: | Escherichia virus M13
|
M13 is a filamentous bacteriophage (inovirus) composed of circular single-stranded DNA (ssDNA) which is 6407 nucleotides long encapsidated in approximately 2700 copies of the major coat protein p8, and capped with about 5 copies each of four different minor coat proteins (p3 and p6 at one end and p7 and p9 at the other end).[1][2][3] The minor coat protein p3 attaches to the receptor at the tip of the F pilus of the host Escherichia coli. The life cycle of M13 is relatively short, with the early phage progeny exiting the cell ten minutes after infection. M13 is a chronic phage, releasing its progeny without killing the host cells. The infection causes turbid plaques in E. coli lawns, of intermediary opacity in comparison to regular lysis plaques. However, a decrease in the rate of cell growth is seen in the infected cells. M13 plasmids are used for many recombinant DNA processes, and the virus has also been used for phage display, directed evolution, nanostructures and nanotechnology applications.[4][5][6]
Phage particles
The phage coat is primarily assembled from a 50 amino acid protein called p8, which is encoded by gene 8 in the phage genome. For a wild type M13 particle, it takes approximately 2700 copies of p8 to make the coat about 900 nm long. The coat's dimensions are flexible though and the number of p8 copies adjusts to accommodate the size of the single stranded genome it packages.[7] The phage appear to be limited to approximately twice the natural DNA content. However, deletion of a phage protein (p3) prevents full escape from the host E. coli, and phage that are 10-20X the normal length with several copies of the phage genome can be seen shedding from the E. coli host.
At one end of the filament are five copies of the surface exposed protein (p9) and a more buried companion protein (p7). If p8 forms the shaft of the phage, p9 and p7 form the "blunt" end that is seen in micrographs. These proteins are very small, containing only 33 and 32 amino acids respectively, though some additional residues can be added to the N-terminal portion of each which are then presented on the outside of the coat. At the other end of the phage particle are five copies of the surface exposed (p3) and its less exposed accessory protein (p6). These form the rounded tip of the phage and are the first proteins to interact with the E. coli host during infection. Protein p3 is also the last point of contact with the host as new phage bud from the bacterial surface.
Replication in E. coli
Below are steps involved with replication of M13 in E. coli.
- Viral (+) strand DNA enters cytoplasm
- Complementary (-) strand is synthesized by bacterial enzymes
- DNA Gyrase, a type II topoisomerase, acts on double-stranded DNA and catalyzes formation of negative supercoils in double-stranded DNA
- Final product is parental replicative form (RF) DNA
- Transcription and translation of the viral genome begins by host resources, including p2.
- A phage protein, p2, nicks the (+) strand in the RF
- 3'-hydroxyl acts as a primer in the creation of new viral strand
- p2 circularizes displaced viral (+) strand DNA
- Pool of progeny double-stranded RF molecules produced
- Negative strand of RF is template of transcription
- mRNAs are translated into the phage proteins
Phage proteins in the cytoplasm are p2, p10 and p5, and they are part of the replication process of DNA. The other phage proteins are synthesized and inserted into the cytoplasmic or outer membranes.
- p5 dimers bind newly synthesized single-stranded DNA and prevent conversion to RF DNA. The timing and attenuation of p5 translation is essential.
- RF DNA synthesis continues and amount of p5 reaches critical concentration
- DNA replication switches to synthesis of single-stranded (+) viral DNA
- p5-DNA structures from about 800 nm long and 8 nm in diameter
- p5-DNA complex is substrate in phage assembly reaction
Research
George Smith, among others, showed that fragments of EcoRI endonuclease could be fused in the unique Bam site of f1 filamentous phage and thereby expressed in gene 3 whose protein p3 was externally accessible. M13 does not have this unique Bam site in gene 3. M13 had to be engineered to have accessible insertion sites, making it limited in its flexibility in handling different sized inserts. Because the M13 phage display system allows great flexibility in the location and number of recombinant proteins on the phage, it is a popular tool to construct or serve as a scaffold for nanostructures.[8] For example, the phage can be engineered to have a different protein on each end and along its length. This can be used to assemble structures like gold or cobalt oxide nano-wires for batteries[9] or to pack carbon nanotubes into straight bundles for use in photovoltaics.[10]
See also
References
- ^ Smeal, Steven W.; et al. (2017). "Simulation of the M13 life cycle I: Assembly of a genetically-structured deterministic chemical kinetic simulation". Virology. 500: 259–274. doi:10.1016/j.virol.2016.08.017. ISSN 0042-6822.
- ^ Rakonjac, Jasna; Das, Bhabatosh; Derda, Ratmir (2016). "Editorial: Filamentous Bacteriophage in Bio/Nano/Technology, Bacterial Pathogenesis and Ecology". Frontiers in Microbiology. 7. doi:10.3389/fmicb.2016.02109. ISSN 1664-302X. PMC 5179506. PMID 28066406.
{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link) - ^ Roux, Simon; Krupovic, Mart; Daly, Rebecca A.; Borges, Adair L.; Nayfach, Stephen; Schulz, Frederik; Sharrar, Allison; Matheus Carnevali, Paula B.; Cheng, Jan-Fang; Ivanova, Natalia N.; Bondy-Denomy, Joseph (2019). "Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes". Nature Microbiology. 4 (11): 1895–1906. doi:10.1038/s41564-019-0510-x. ISSN 2058-5276. PMC 6813254. PMID 31332386.
{{cite journal}}: CS1 maint: PMC format (link) - ^ Khalil AS, Ferrer JM, Brau RR, Kottmann ST, Noren CJ, Lang MJ, Belcher AM (March 2007). "Single M13 bacteriophage tethering and stretching". Proceedings of the National Academy of Sciences of the United States of America. 104 (12): 4892–7. doi:10.1073/pnas.0605727104. PMC 1829235. PMID 17360403.
- ^ Suthiwangcharoen N, Li T, Li K, Thompson P, You S, Wang Q (May 2011). "M13 bacteriophage-polymer nanoassemblies as drug delivery vehicles". Nano Research. 4 (5): 483–93. doi:10.1007/s12274-011-0104-2.
- ^ Esvelt KM, Carlson JC, Liu DR (April 2011). "A system for the continuous directed evolution of biomolecules". Nature. 472 (7344): 499–503. Bibcode:2011Natur.472..499E. doi:10.1038/nature09929. PMC 3084352. PMID 21478873.
- ^ Sattar, Sadia; Bennett, Nicholas J.; Wen, Wesley X.; Guthrie, Jenness M.; Blackwell, Len F.; Conway, James F.; Rakonjac, Jasna (2015). "Ff-nano, short functionalized nanorods derived from Ff (f1, fd, or M13) filamentous bacteriophage". Frontiers in Microbiology. 6. doi:10.3389/fmicb.2015.00316. ISSN 1664-302X. PMC 4403547. PMID 25941520.
{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link) - ^ Huang Y, Chiang CY, Lee SK, Gao Y, Hu EL, De Yoreo J, Belcher AM (July 2005). "Programmable assembly of nanoarchitectures using genetically engineered viruses". Nano Letters. 5 (7): 1429–34. Bibcode:2005NanoL...5.1429H. doi:10.1021/nl050795d. PMID 16178252.
- ^ Nam KT, Kim DW, Yoo PJ, Chiang CY, Meethong N, Hammond PT, et al. (May 2006). "Virus-enabled synthesis and assembly of nanowires for lithium ion battery electrodes". Science. 312 (5775): 885–8. Bibcode:2006Sci...312..885N. doi:10.1126/science.1122716. PMID 16601154.
- ^ Dang X, Yi H, Ham MH, Qi J, Yun DS, Ladewski R, et al. (April 2011). "Virus-templated self-assembled single-walled carbon nanotubes for highly efficient electron collection in photovoltaic devices". Nature Nanotechnology. 6 (6): 377–84. Bibcode:2011NatNa...6..377D. doi:10.1038/nnano.2011.50. PMID 21516089.
Further reading
- Barbas, Carlos F; Burton, Dennis R; Silverman, Gregg J (October 2004). Phage Display: A Laboratory Manual (1st ed.). Cold Spring Harbor Laboratory Press. ISBN 978-0-87969-740-2.
{{cite book}}: Unknown parameter|name-list-format=ignored (|name-list-style=suggested) (help) - Messing J (1993). "M13 Cloning Vehicles" (PDF). In Griffin H.G., Griffin A.M. (eds.). DNA Sequencing Protocols. Methods in Molecular Biology™. Methods in Molecular Biology. Vol. 23. Humana Press. pp. 9–22. doi:10.1385/0-89603-248-5:9. ISBN 0-89603-248-5. PMID 8220775. Archived from the original on 2012-02-19.
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