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Bacillus virus phi29
open-in-new
<h2 id="history">History</h2> <p>In 1965, <a href="/facts/United_States/P0sCdLe5">American</a> <a href="/facts/Microbiologist/cqEyJwNK">microbiologist</a> Dr. Bernard Reilly discovered the Φ29 phage in Dr. John Spizizen's lab at the <a href="/facts/University_of_Minnesota/vN1uQvP5">University of Minnesota</a>.<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a><a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a> Due to its small size and complex morphology, it has become an ideal model for the study of many processes in <a href="/facts/Molecular_biology/YgqU35ub">molecular biology</a>, such as <a href="/facts/Morphogenesis/zHJh8Eae">morphogenesis</a>, viral <a href="/facts/DNA_packaging/FRGf11FC">DNA packaging</a>, viral replication, and <a href="/facts/Transcription_(biology)/bDgp9HDN">transcription</a>.<a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a><a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a> </p> <h2 id="structure">Structure</h2> <p>The structure of Φ29 is composed of seven main <a href="/facts/Protein/Jxmagu3E">proteins</a>: the terminal protein (p3), the head or <a href="/facts/Capsid/hm7V6Ewm">capsid protein</a> (p8), the head or capsid fiber protein (p8.5), the distal tail knob (p9), the portal or connector protein (p10), the tail tube or lower collar proteins (p11), and the tail fibers or appendage proteins (p12*).<a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a> </p><p>The main difference between Φ29's structure and that of other phages is its use of pRNA in its DNA packaging motor.<a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a> </p> <h3>DNA packaging motor</h3> <p>The Φ29 DNA packaging motor packages the phage genome into the <a href="/facts/Procapsid/hm7V6Ewm">procapsid</a> during viral replication.<a class="footnote-ref" id="fnref:18" href="#fn:18"><sup>18</sup></a> The Φ29 packaging motor is structurally composed of the procapsid and the connector proteins, which interact with the pRNA, the packaging <a href="/facts/Enzyme/DSI1Fh7y">enzyme</a> (gp16), and the packaging <a href="/facts/Substrate_(chemistry)/6MnaV19h">substrate</a> (genomic DNA-gp3).<a class="footnote-ref" id="fnref:19" href="#fn:19"><sup>19</sup></a> Because the process of genome packaging is <a href="/facts/Energy/wd8PrQM7">energy</a>-intensive, it must be facilitated by an <a href="/facts/Adenosine_triphosphate/nB9bwgcU">ATP</a>-powered motor that converts <a href="/facts/Chemical_energy/Y3VP3Ifq">chemical energy</a> to <a href="/facts/Mechanical_energy/gI4oMzoY">mechanical energy</a> through <a href="/facts/ATP_hydrolysis/940XnJMX">ATP hydrolysis</a>.<a class="footnote-ref" id="fnref:20" href="#fn:20"><sup>20</sup></a><a class="footnote-ref" id="fnref:21" href="#fn:21"><sup>21</sup></a> The Φ29 packaging motor is able to generate approximately 57 <a href="/facts/Piconewton/Ral9XgNl">piconewtons</a> (pN) of <a href="/facts/Force/LNAUWMwK">force</a>, making it one of the most powerful biomotors studied to date.<a class="footnote-ref" id="fnref:22" href="#fn:22"><sup>22</sup></a> </p> <h3>pRNA</h3> <p>The Φ29 pRNA is a highly versatile <a href="/facts/Molecule/N9ljSfFq">molecule</a> that can <a href="/facts/Polymerization/1hmBz7Ur">polymerize</a> into <a href="/facts/Dimer_(chemistry)/mU64PnEq">dimers</a>, <a href="/facts/Trimer_(chemistry)/ws3JkjuQ">trimers</a>, <a href="/facts/Tetramer/qeUFnwC4">tetramers</a>, <a href="/facts/Pentamer/JUdMmxlg">pentamers</a>, and <a href="/facts/Hexamer/v7oDY8zu">hexamers</a>.<a class="footnote-ref" id="fnref:23" href="#fn:23"><sup>23</sup></a> Early studies such as Anderson (1990) and Trottier (1998) hypothesized that pRNA formed intermolecular hexamers, but these studies had a solely <a href="/facts/Genetics/bu8wne0A">genetic</a> basis rather than a <a href="/facts/Microscopy/GpHlElDS">microscopy</a> based approach.<a class="footnote-ref" id="fnref:24" href="#fn:24"><sup>24</sup></a><a class="footnote-ref" id="fnref:25" href="#fn:25"><sup>25</sup></a><a class="footnote-ref" id="fnref:26" href="#fn:26"><sup>26</sup></a> In the year 2000, a study by Simpson et al. employed <a href="/facts/Cryogenic_electron_microscopy/Hjbcf4Ec">cryo-electron microscopy</a> to determine that, <i><a href="/facts/In_vivo/kWcWyl6f">in vivo</a></i>, only a pentamer or smaller polymer could spatially fit in the virus.<a class="footnote-ref" id="fnref:27" href="#fn:27"><sup>27</sup></a> Ultimately, single isomorphous replacement with <a href="/facts/Anomalous_scattering/oQuTGrL5">anomalous scattering</a> (SIRAS) <a href="/facts/X-ray_crystallography/WtI0F5DN">crystallography</a> was used to determine that the <i>in vivo</i> structure is a tetramer ring.<a class="footnote-ref" id="fnref:28" href="#fn:28"><sup>28</sup></a> This discovery aligned with what was known about the structural geometry and necessary <a href="/facts/Flexibility/xlabLkfT">flexibility</a> of the packaging motor's three-way junction.<a class="footnote-ref" id="fnref:29" href="#fn:29"><sup>29</sup></a> When pRNA is in this tetramer ring form, it works as a part of the DNA packaging motor to transport DNA molecules to their destination location within the prohead capsule.<a class="footnote-ref" id="fnref:30" href="#fn:30"><sup>30</sup></a> Specifically, the functional domains of pRNA bind to the gp16 packaging enzyme and the structural connector molecule to aid in the translocation of DNA through the prohead channel.<a class="footnote-ref" id="fnref:31" href="#fn:31"><sup>31</sup></a> After DNA packaging is complete, the pRNA dissociates and is degraded.<a class="footnote-ref" id="fnref:32" href="#fn:32"><sup>32</sup></a> </p> <h2 id="genome-and-replication">Genome and replication</h2> <p>The Φ29 phage has a linear dsDNA genome consisting of 19,285 <a href="/facts/DNA_base/zj1Vl9Qh">bases</a>.<a class="footnote-ref" id="fnref:33" href="#fn:33"><sup>33</sup></a> Both <a href="/facts/5%2527_end/TIAXEQmY">5’ ends</a> of the genome are capped with a <a href="/facts/Covalent_bond/EzMLf3Pz">covalently bonded</a> terminal protein (p3) that complexes with <a href="/facts/DNA_polymerase/xtNLncBu">DNA polymerase</a> during replication.<a class="footnote-ref" id="fnref:34" href="#fn:34"><sup>34</sup></a><a class="footnote-ref" id="fnref:35" href="#fn:35"><sup>35</sup></a> </p><p>Φ29 is one of many phages with a <a href="/facts/%25CE%25A629_DNA_polymerase/CzckRUAS">DNA polymerase</a> that has a different structure and function compared to standard DNA <a href="/facts/Polymerase/hN2ECr7B">polymerases</a> in other organisms.<a class="footnote-ref" id="fnref:36" href="#fn:36"><sup>36</sup></a> Φ29 forms a replication complex involving the p3 terminal protein, the dAMP nucleotide, and its own DNA polymerase to synthesize DNA in a 5’ to <a href="/facts/3%25E2%2580%2599/TIAXEQmY">3’</a> direction. This replication process also employs a sliding-back mechanism towards the 3’ end of the genome that uses a repeating TTT motif to move the replication complex backward without altering the template sequence.<a class="footnote-ref" id="fnref:37" href="#fn:37"><sup>37</sup></a><a class="footnote-ref" id="fnref:38" href="#fn:38"><sup>38</sup></a> This allows the initiation of <a href="/facts/DNA_replication/wrU6RuR3">DNA replication</a> to be more accurate by having the polymerase complex check a specific sequence before beginning the elongation process.<a class="footnote-ref" id="fnref:39" href="#fn:39"><sup>39</sup></a><a class="footnote-ref" id="fnref:40" href="#fn:40"><sup>40</sup></a> </p> <h2 id="applications">Applications</h2> <h3>Nanoparticle assembly</h3> <p>Versatility in <a href="/facts/RNA/HxPeNfNj">RNA</a> structure and function provides the ability to assemble <a href="/facts/Nanoparticle/k8kNxX4E">nanoparticles</a> for nanomedicinal <a href="/facts/Therapy/2ytkGbgT">therapeutics</a>.<a class="footnote-ref" id="fnref:41" href="#fn:41"><sup>41</sup></a> The pRNA in bacteriophage Φ29 can use its three-way junction in order to self-assemble into nanoparticles.<a class="footnote-ref" id="fnref:42" href="#fn:42"><sup>42</sup></a> </p><p>One major challenge of using pRNA-derived nanoparticles is <a href="/facts/Large-scale_production/31Cmgjuc">large-scale production</a>, as most industries are currently unequipped to handle industrial pRNA synthesis.<a class="footnote-ref" id="fnref:43" href="#fn:43"><sup>43</sup></a> This is primarily because RNA nanotechnology is still an emerging field that lacks industrial application and manufacturing optimization of small RNAs.<a class="footnote-ref" id="fnref:44" href="#fn:44"><sup>44</sup></a> </p> <h3>Drug delivery</h3> <p>Φ29’s DNA packaging system, using pRNA, incorporates a motor for the delivery of therapeutic molecules like <a href="/facts/Ribozyme/yvcl3ygp">ribozymes</a> and <a href="/facts/Aptamer/3UvhuQP4">aptamers</a>.<a class="footnote-ref" id="fnref:45" href="#fn:45"><sup>45</sup></a> The small size of pRNA-derived nanoparticles also helps to deliver <a href="/facts/Drug/FFFUI9n4">drugs</a> in tight spaces like <a href="/facts/Blood_vessel/FG3GjPNW">blood vessels</a>.<a class="footnote-ref" id="fnref:46" href="#fn:46"><sup>46</sup></a> </p><p>The main difficulty in using aptamer-based drug delivery is sourcing unique aptamers and other <a href="/facts/Multimers/ukuyKJfj">multimers</a> for specific treatments for <a href="/facts/Disease/55eeQlGL">diseases</a> that potentially degrade therapeutic multimers and nanoparticles <i>in vivo.</i><a class="footnote-ref" id="fnref:47" href="#fn:47"><sup>47</sup></a> Nanoparticles need to be stabilized as delivery mechanisms in order to adapt to microenvironments that may result in loss of therapeutic cargo.<a class="footnote-ref" id="fnref:48" href="#fn:48"><sup>48</sup></a> </p> <h3>Triple-negative breast cancer treatment</h3> <p><a href="/facts/Triple-negative_breast_cancer/RJD05EcH">Triple-negative breast cancer</a> (TNBC) is an aggressive form of <a href="/facts/Breast_cancer/6hME580v">breast cancer</a> that accounts for ten to fifteen percent of all breast cancer cases.<a class="footnote-ref" id="fnref:49" href="#fn:49"><sup>49</sup></a> <a href="/facts/Chemotherapy/fWTLbaUT">Chemotherapy</a> is the only viable current treatment for TNBC because the loss of target receptors inherent to the disease causes <a href="/facts/Cancer_cell/HXSQQjhw">cancer cells</a> to resist therapeutic <a href="/facts/Pharmaceuticals/h9mhwWP2">pharmaceuticals</a>.<a class="footnote-ref" id="fnref:50" href="#fn:50"><sup>50</sup></a> </p><p>The three-way junction in the Φ29 DNA packaging motor can help sensitize TNBC cells to chemotherapy using a <a href="/facts/SiRNA/891ytkD9">siRNA</a> drug delivery mechanism to inhibit TNBC growth and volume.<a class="footnote-ref" id="fnref:51" href="#fn:51"><sup>51</sup></a> This treatment can also be combined with anti-cancer drugs like <a href="/facts/Doxorubicin/4XuC2ajQ">Doxorubicin</a> to enhance therapeutic effects.<a class="footnote-ref" id="fnref:52" href="#fn:52"><sup>52</sup></a> </p> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/Bacteriophage/L2Ll0T3q">Bacteriophage</a></li> <li><a href="/facts/Bacteriophage_pRNA/0qWbFmbu">Bacteriophage pRNA</a></li> <li><a href="/facts/%25CE%25A629_DNA_polymerase/CzckRUAS">Φ29 DNA polymerase</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Meijer, Wilfried J. J.; Horcajadas, José A.; Salas, Margarita (2001). "φ29 Family of Phages". Microbiology and Molecular Biology Reviews. 65 (2): 261–287. doi:10.1128/MMBR.65.2.261-287.2001. ISSN 1092-2172. PMC 99027. PMID 11381102. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99027" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99027</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Ackermann, Hans-W. (1998). "Tailed Bacteriophages: The Order Caudovirales". Advances in Virus Research. 51: 135–201. doi:10.1016/S0065-3527(08)60785-X. ISBN 978-0-12-039851-5. ISSN 0065-3527. PMC 7173057. PMID 9891587. <a href="978-0-12-039851-5" target="_blank">978-0-12-039851-5</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Bacteriophage : genetics and molecular biology. Stephen Mc Grath, Douwe van Sinderen. Norfolk, UK: Caister Academic Press. 2007. ISBN 978-1-904455-14-1. OCLC 86168751.{{cite book}}: CS1 maint: others (link) <a href="978-1-904455-14-1" target="_blank">978-1-904455-14-1</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Camacho, Ana; Jimenez, Fernando; Torre, Javier; Carrascosa, Jose L.; Mellado, Rafael P.; Vinuela, Eladio; Salas, Margarita; Vasquez, Cesar (February 1977). "Assembly of Bacillus subtilis Phage Phi29. 1. Mutants in the Cistrons Coding for the Structural Proteins". European Journal of Biochemistry. 73 (1): 39–55. doi:10.1111/j.1432-1033.1977.tb11290.x. ISSN 0014-2956. PMID 402269. <a href="https://doi.org/10.1111%2Fj.1432-1033.1977.tb11290.x" target="_blank">https://doi.org/10.1111%2Fj.1432-1033.1977.tb11290.x</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Meijer, Wilfried J. J.; Horcajadas, José A.; Salas, Margarita (2001). "φ29 Family of Phages". Microbiology and Molecular Biology Reviews. 65 (2): 261–287. doi:10.1128/MMBR.65.2.261-287.2001. ISSN 1092-2172. PMC 99027. PMID 11381102. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99027" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99027</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Ackermann, Hans-W. (1998). "Tailed Bacteriophages: The Order Caudovirales". Advances in Virus Research. 51: 135–201. doi:10.1016/S0065-3527(08)60785-X. ISBN 978-0-12-039851-5. ISSN 0065-3527. PMC 7173057. PMID 9891587. <a href="978-0-12-039851-5" target="_blank">978-0-12-039851-5</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Lee, Tae Jin; Schwartz, Chad; Guo, Peixuan (2009-10-01). "Construction of Bacteriophage Phi29 DNA Packaging Motor and its Applications in Nanotechnology and Therapy". Annals of Biomedical Engineering. 37 (10): 2064–2081. doi:10.1007/s10439-009-9723-0. ISSN 1573-9686. PMC 2855900. PMID 19495981. <a href="https://doi.org/10.1007/s10439-009-9723-0" target="_blank">https://doi.org/10.1007/s10439-009-9723-0</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Shu, Yi; Wang, Hongzhi; Seremi, Bahar; Guo, Peixuan (2022), "Fabrication Methods for RNA Nanoparticle Assembly Based on Bacteriophage Phi29 pRNA Structural Features", RNA Nanotechnology and Therapeutics, pp. 141–157, doi:10.1201/9781003001560-21, ISBN 978-1-003-00156-0, retrieved 2022-11-01 <a href="978-1-003-00156-0" target="_blank">978-1-003-00156-0</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Ye, Xin; Hemida, Maged; Zhang, Huifang M.; Hanson, Paul; Ye, Qiu; Yang, Decheng (2012). "Current advances in Phi29 pRNA biology and its application in drug delivery: Current advances in Phi29 pRNA biology and its application". Wiley Interdisciplinary Reviews: RNA. 3 (4): 469–481. doi:10.1002/wrna.1111. PMID 22362726. S2CID 12631001. <a href="https://doi.org/10.1002%2Fwrna.1111" target="_blank">https://doi.org/10.1002%2Fwrna.1111</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Zhang, Long; Mu, Chaofeng; Zhang, Tinghong; Yang, Dejun; Wang, Chenou; Chen, Qiong; Tang, Lin; Fan, Luhui; Liu, Cong; Shen, Jianliang; Li, Huaqiong (2021-01-07). "Development of targeted therapy therapeutics to sensitize triple-negative breast cancer chemosensitivity utilizing bacteriophage phi29 derived packaging RNA". Journal of Nanobiotechnology. 19 (1): 13. doi:10.1186/s12951-020-00758-4. ISSN 1477-3155. PMC 7792131. PMID 33413427. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7792131" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7792131</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Errington, Jeffery; van der Aart, Lizah T (2020-05-11). "Microbe Profile: Bacillus subtilis: model organism for cellular development, and industrial workhorse". Microbiology. 166 (5): 425–427. doi:10.1099/mic.0.000922. ISSN 1350-0872. PMC 7376258. PMID 32391747. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7376258" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7376258</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Reilly, Bernard E.; Spizizen, John (1965). "Bacteriophage Deoxyribonucleate Infection of Competent Bacillus subtilis1". Journal of Bacteriology. 89 (3): 782–790. doi:10.1128/jb.89.3.782-790.1965. ISSN 0021-9193. PMC 277537. PMID 14273661. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC277537" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC277537</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>Salas, Margarita (2007-10-01). "40 Years with Bacteriophage ø29". Annual Review of Microbiology. 61 (1): 1–22. doi:10.1146/annurev.micro.61.080706.093415. ISSN 0066-4227. PMID 17441785. <a href="https://doi.org/10.1146%2Fannurev.micro.61.080706.093415" target="_blank">https://doi.org/10.1146%2Fannurev.micro.61.080706.093415</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>Salas, Margarita (2007-10-01). "40 Years with Bacteriophage ø29". Annual Review of Microbiology. 61 (1): 1–22. doi:10.1146/annurev.micro.61.080706.093415. ISSN 0066-4227. PMID 17441785. <a href="https://doi.org/10.1146%2Fannurev.micro.61.080706.093415" target="_blank">https://doi.org/10.1146%2Fannurev.micro.61.080706.093415</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> <li id="fn:15"><p>"About | Virology". University of Minnesota. Archived from the original on 2022-11-01. Retrieved 2022-10-31. <a href="https://web.archive.org/web/20221101001301/https://virology.umn.edu/about" target="_blank">https://web.archive.org/web/20221101001301/https://virology.umn.edu/about</a> <a href="#fnref:15" class="footnote-back-ref">↩</a></p></li> <li id="fn:16"><p>Lee, Tae Jin; Schwartz, Chad; Guo, Peixuan (2009-10-01). "Construction of Bacteriophage Phi29 DNA Packaging Motor and its Applications in Nanotechnology and Therapy". Annals of Biomedical Engineering. 37 (10): 2064–2081. doi:10.1007/s10439-009-9723-0. ISSN 1573-9686. PMC 2855900. PMID 19495981. <a href="https://doi.org/10.1007/s10439-009-9723-0" target="_blank">https://doi.org/10.1007/s10439-009-9723-0</a> <a href="#fnref:16" class="footnote-back-ref">↩</a></p></li> <li id="fn:17"><p>Lee, Tae Jin; Schwartz, Chad; Guo, Peixuan (2009-10-01). "Construction of Bacteriophage Phi29 DNA Packaging Motor and its Applications in Nanotechnology and Therapy". Annals of Biomedical Engineering. 37 (10): 2064–2081. doi:10.1007/s10439-009-9723-0. ISSN 1573-9686. PMC 2855900. PMID 19495981. <a href="https://doi.org/10.1007/s10439-009-9723-0" target="_blank">https://doi.org/10.1007/s10439-009-9723-0</a> <a href="#fnref:17" class="footnote-back-ref">↩</a></p></li> <li id="fn:18"><p>Lee, Tae Jin; Schwartz, Chad; Guo, Peixuan (2009-10-01). "Construction of Bacteriophage Phi29 DNA Packaging Motor and its Applications in Nanotechnology and Therapy". Annals of Biomedical Engineering. 37 (10): 2064–2081. doi:10.1007/s10439-009-9723-0. ISSN 1573-9686. PMC 2855900. PMID 19495981. <a href="https://doi.org/10.1007/s10439-009-9723-0" target="_blank">https://doi.org/10.1007/s10439-009-9723-0</a> <a href="#fnref:18" class="footnote-back-ref">↩</a></p></li> <li id="fn:19"><p>Lee, Tae Jin; Schwartz, Chad; Guo, Peixuan (2009-10-01). "Construction of Bacteriophage Phi29 DNA Packaging Motor and its Applications in Nanotechnology and Therapy". 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