The phi X 174 (or
Escherichia virus | |
---|---|
![]() | |
Electron micrograph of phage | |
Virus classification ![]() | |
(unranked): | Virus |
Realm: | Monodnaviria |
Kingdom: | Sangervirae |
Phylum: | Phixviricota |
Class: | Malgrandaviricetes |
Order: | Petitvirales |
Family: | Microviridae |
Genus: | Sinsheimervirus |
Species: | Escherichia virus
|
![](https://upload.wikimedia.org/wikipedia/commons/thumb/5/52/PhiX174.jpg/225px-PhiX174.jpg)
![](https://upload.wikimedia.org/wikipedia/commons/thumb/b/b4/Sinsheimervirus_virion.jpg/225px-Sinsheimervirus_virion.jpg)
Genome
editThis bacteriophage has a [+] sense circular single-stranded DNA genome of 5,386 nucleotides.[10] The genome GC-content is 44% and 95% of nucleotides belong to coding genes. Because of the balance base pattern of the genome, it is used as the control DNA for Illumina sequencers.[citation needed]
Genes
editThe first half of the
Phage
Transcriptome
editIn 2020, the transcriptome of
Proteins
editProtein | Copies | Function[17] |
---|---|---|
A | — | Nicks RF DNA to initiate rolling circle replication; ligates ends of linear phage DNA to form single-stranded circular DNA |
A* | — | Inhibits host cell DNA replication; blocks superinfecting phage; not essential |
B | 60 in procapsid | Internal scaffolding protein involved in procapsid assembly |
C | — | DNA packaging |
D | 240 in procapsid | External scaffolding protein involved in procapsid assembly |
E | — | Host cell lysis |
F | 60 in virion | Major capsid protein |
G | 60 in virion | Major spike protein |
H | 12 in virion | DNA pilot protein (or minor spike protein) |
J | 60 in virion | Binds to new single-stranded phage DNA; accompanies phage DNA into procapsid |
K | — | Optimizes burst size; not essential |
Proteome
editIdentification of all
Infection Cycle
editInfection begins when G protein binds to lipopolysaccharides on the bacterial host cell surface. H protein (or the DNA Pilot Protein) pilots the viral genome through the bacterial membrane of E.coli bacteria[18] most likely via a predicted N-terminal transmembrane domain helix.[19] However, it has become apparent that H protein is a multifunctional protein.[20] This is the only viral capsid protein of
The DNA is ejected through a hydrophilic channel at the 5-fold vertex.[22] It is understood that H protein resides in this area but experimental evidence has not verified its exact location. Once inside the host bacterium, replication of the [+] ssDNA genome proceeds via negative sense DNA intermediate. This is done as the phage genome supercoils and the secondary structure formed by such supercoiling attracts a primosome protein complex. This translocates once around the genome and synthesizes a [−]ssDNA from the positive original genome. [+]ssDNA genomes to package into viruses are created from this by a rolling circle mechanism. This is the mechanism by which the double stranded supercoiled genome is nicked on the positive strand by a virus-encoded A protein, also attracting a bacterial DNA polymerase (DNAP) to the site of cleavage. DNAP uses the negative strand as a template to make positive sense DNA. As it translocates around the genome it displaces the outer strand of already-synthesised DNA, which is immediately coated by SSBP proteins. The A protein cleaves the complete genome every time it recognises the origin sequence.[citation needed]
As D protein is the most abundant gene transcript, it is the most protein in the viral procapsid. Similarly, gene transcripts for F, J, and G are more abundant than for H as the stoichiometry for these structural proteins is 5:5:5:1. The primosomes are protein complexes which attach/bind the enzyme helicase on the template. Primosomes gives RNA primers for DNA synthesis to strands.[citation needed]
Phylogenetics and diversity
editUses
editExperimental evolution
editBiotechnology
editSynthetic Biology
editThe
See also
editReferences
edit- ^ Lacković, Zdravko; Toljan, Karlo (20 December 2020). "Vladimir Sertić: forgotten pioneer of virology and bacteriophage therapy". Notes and Records: the Royal Society Journal of the History of Science. 74 (4): 567–578. doi:10.1098/rsnr.2019.0010. ISSN 0035-9149. PMC 7653334. PMID 33177747.
- ^ a b Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, et al. (February 1977). "Nucleotide sequence of bacteriophage phi X174 DNA". Nature. 265 (5596): 687–95. Bibcode:1977Natur.265..687S. doi:10.1038/265687a0. PMID 870828. S2CID 4206886.
- ^ Fiers W, Sinsheimer RL (October 1962). "The structure of the DNA of bacteriophage phi-X174. III. Ultracentrifugal evidence for a ring structure". Journal of Molecular Biology. 5 (4): 424–34. doi:10.1016/S0022-2836(62)80031-X. PMID 13945085.
- ^ National Library of Medicine Profiles in Science. The Arthur Kornberg Papers. "Creating Life in the Test Tube," 1959-1970. link[non-primary source needed]
- ^ Goulian M, Kornberg A, Sinsheimer RL (December 1967). "Enzymatic synthesis of DNA, XXIV. Synthesis of infectious phage phi-X174 DNA". Proceedings of the National Academy of Sciences of the United States of America. 58 (6): 2321–8. Bibcode:1967PNAS...58.2321G. doi:10.1073/pnas.58.6.2321. JSTOR 58720. PMC 223838. PMID 4873588.
- ^ Wickner S, Hurwitz J (October 1974). "Conversion of phiX174 viral DNA to double-stranded form by purified Escherichia coli proteins". Proceedings of the National Academy of Sciences of the United States of America. 71 (10): 4120–4. doi:10.1073/pnas.71.10.4120. PMC 434340. PMID 4610569.
- ^ Smith HO, Hutchison CA, Pfannkoch C, Venter JC (December 2003). "Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides". Proceedings of the National Academy of Sciences of the United States of America. 100 (26): 15440–5. Bibcode:2003PNAS..10015440S. doi:10.1073/pnas.2237126100. JSTOR 3149024. PMC 307586. PMID 14657399.
- ^ Cherwa JE, Organtini LJ, Ashley RE, Hafenstein SL, Fane BA (September 2011). "In VITRO ASSEMBLY of the øX174 procapsid from external scaffolding protein oligomers and early pentameric assembly intermediates". Journal of Molecular Biology. 412 (3): 387–96. doi:10.1016/j.jmb.2011.07.070. PMID 21840317.
- ^ a b c Jaschke PR, Lieberman EK, Rodriguez J, Sierra A, Endy D (December 2012). "A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast". Virology. 434 (2): 278–84. doi:10.1016/j.virol.2012.09.020. PMID 23079106.
- ^ a b c Enterobacteria phage phiX174 sensu lato, complete genome. "Complete genome: accession NC_001422", National Center for Biotechnology Information. Retrieved on 30 January 2016.
- ^ Baas PD, Liewerink H, van Teeffelen HA, van Mansfeld AD, van Boom JH, Jansz HS (June 1987). "Alteration of the ATG start codon of the A protein of bacteriophage phi X174 into an ATT codon yields a viable phage indicating that A protein is not essential for phi X174 reproduction". FEBS Letters. 218 (1): 119–25. doi:10.1016/0014-5793(87)81030-x. PMID 2954853. S2CID 24174007.
- ^ Hecht A, Glasgow J, Jaschke PR, Bawazer LA, Munson MS, Cochran JR, et al. (April 2017). "Measurements of translation initiation from all 64 codons in E. coli". Nucleic Acids Research. 45 (7): 3615–3626. doi:10.1093/nar/gkx070. PMC 5397182. PMID 28334756.
- ^ a b 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.
- ^ a b c Wright BW, Ruan J, Molloy MP, Jaschke PR (November 2020). "Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction". ACS Synthetic Biology. 9 (11): 3079–3090. doi:10.1021/acssynbio.0c00323. PMID 33044064. S2CID 222300240.
- ^ Jaschke PR, Dotson GA, Hung KS, Liu D, Endy D (November 2019). "Definitive demonstration by synthesis of genome annotation completeness". Proceedings of the National Academy of Sciences of the United States of America. 116 (48): 24206–24213. doi:10.1073/pnas.1905990116. PMC 6883844. PMID 31719208.
- ^ Logel DY, Jaschke PR (August 2020). "A high-resolution map of bacteriophage ϕX174 transcription". Virology. 547: 47–56. doi:10.1016/j.virol.2020.05.008. PMID 32560904. S2CID 219459208.
- ^ Fane BA, Brentlinger KL, Burch AD, Chen M, Hafenstein S, Moore E, Novak CR, Uchiyama A (2006). "ɸX174 et al., the Microviridae". In Calender R (ed.). The Bacteriophages (2nd ed.). New York: Oxford Univ. Press. p. 130. ISBN 978-0195148503.
- ^ Jazwinski SM, Lindberg AA, Kornberg A (July 1975). "The lipopolysaccharide receptor for bacteriophage phiX174 and S13". Virology. 66 (1): 268–82. doi:10.1016/0042-6822(75)90197-x. PMID 1094681.
- ^ Tusnády GE, Simon I (September 2001). "The HMMTOP transmembrane topology prediction server". Bioinformatics. 17 (9): 849–50. doi:10.1093/bioinformatics/17.9.849. PMID 11590105.
- ^ Cherwa JE, Young LN, Fane BA (March 2011). "Uncoupling the functions of a multifunctional protein: the isolation of a DNA pilot protein mutant that affects particle morphogenesis". Virology. 411 (1): 9–14. doi:10.1016/j.virol.2010.12.026. PMID 21227478.
- ^ Ruboyianes MV, Chen M, Dubrava MS, Cherwa JE, Fane BA (October 2009). "The expression of N-terminal deletion DNA pilot proteins inhibits the early stages of phiX174 replication". Journal of Virology. 83 (19): 9952–6. doi:10.1128/JVI.01077-09. PMC 2748053. PMID 19640994.
- ^ McKenna R, Xia D, Willingmann P, Ilag LL, Krishnaswamy S, Rossmann MG, et al. (January 1992). "Atomic structure of single-stranded DNA bacteriophage phi X174 and its functional implications". Nature. 355 (6356): 137–43. Bibcode:1992Natur.355..137M. doi:10.1038/355137a0. PMC 4167681. PMID 1370343.
- ^ Rokyta DR, Burch CL, Caudle SB, Wichman HA (February 2006). "Horizontal gene transfer and the evolution of microvirid coliphage genomes". Journal of Bacteriology. 188 (3): 1134–42. doi:10.1128/JB.188.3.1134-1142.2006. PMC 1347346. PMID 16428417.
- ^ Wichman HA, Brown CJ (August 2010). "Experimental evolution of viruses: Microviridae as a model system". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365 (1552): 2495–501. doi:10.1098/rstb.2010.0053. PMC 2935103. PMID 20643739.
- ^ "Using a PhiX Control for HiSeq® Sequencing Runs". Illumina. Archived from the original on 9 January 2019. Retrieved 8 January 2019.
- ^ "PPE-Info – Standard Details". wwwn.cdc.gov. Retrieved 8 February 2019.
- ^ Christakos KJ, Chapman JA, Fane BA, Campos SK (January 2016). "PhiXing-it, displaying foreign peptides on bacteriophage
Φ X174". Virology. 488: 242–8. doi:10.1016/j.virol.2015.11.021. PMC 6191337. PMID 26655242. - ^ Ando H, Lemire S, Pires DP, Lu TK (September 2015). "Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing". Cell Systems. 1 (3): 187–196. doi:10.1016/j.cels.2015.08.013. PMC 4785837. PMID 26973885.
External links
edit- Goodsell D (February 2000). "Bacteriophage phiX174". Molecule of the Month. RCSB-PDB.