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CRISPR RNA
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<h2 id="function">Function</h2> <h3>Type-I</h3> <p>Type-I CRISPR systems are characterized by <a href="/facts/Cas3/9khFCka6">Cas3</a>, a nuclease-<a href="/facts/Helicase/IemubWzR">helicase</a> protein, and the multi-subunit Cascade (CRISPR-associated complex for antiviral defense). The crRNA can form a complex with the Cas proteins in the Cascade and guide the complex to the target DNA sequence. Cas3 is recruited for the nuclease-helicase activity.<a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a> </p><p>Typically in the Cascade, Cas6 generates the mature crRNAs while Cas5 and Cas7 process and stabilize the crRNA.<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> </p> <h3>Type-II</h3> <p>Type-II CRISPR systems<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a> are characterized by the single signature nuclease <a href="/facts/Cas9/gDhwlw7I">Cas9</a>.<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a> In type-II CRISPR systems crRNA and <a href="/facts/Trans-activating_crRNA/d6r6gStk">tracrRNA</a> (trans-activating CRISPR RNA) can form a complex known as the guide RNA or <a href="/facts/Guide_RNA/tzh43P3A">gRNA</a>.<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a> The crRNA within the gRNA is what matches up with the target sequence or protospacer after the <a href="/facts/Protospacer_adjacent_motif/dHtb2Kjy">PAM</a> is found. Once the match is made Cas9 will make a double-stranded break. </p> <h3>Type-III</h3> <p>Type-III CRISPR systems are characterized by Cas10, an RNA cleaving protein.<a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a> Similar to type-I, a large subunit effector complex is formed and crRNA guides the complex to the target sequence. Cas6 helps to generate the mature crRNA.<a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a> </p> <h3>Type-IV</h3> <p>Type-IV CRISPR systems do not have an effector nuclease and are associated with <a href="/facts/Plasmid/yf59JVlA">plasmids</a> and <a href="/facts/Prophage/Ma9XpaLL">prophages</a>. A Cas6-like enzyme is associated with the maturation of the crRNA. Not all type-IV systems have a CRISPR locus and therefore do not have crRNA.<a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a> </p> <h3>Type-V</h3> <p>Type-V CRISPR systems are characterized by <a href="/facts/Cas12a/3abnuxHb">Cas12</a>, a nuclease that can cleave <a href="/facts/Ssdna/nB89Iauz">ssDNA</a>, dsDNA, and <a href="/facts/RNA/HxPeNfNj">RNA</a>.<a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a> Like Cas9, Cas12 is the single effector nuclease. Type-V systems process pre-crRNA without tracrRNA. The mature crRNA in complex with Cas12 target the DNA sequence of interest and cleave the DNA.<a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a> </p> <h3>Type-VI</h3> <p>Type-VI CRISPR systems are characterized by <a href="/facts/Cas13/VqRDofqC">Cas13</a>, a single effector protein that targets RNA. Like the type-V system, Cas13 can process the pre-crRNA without tracrRNA. The mature crRNA in complex with Cas13 guides the complex to the target RNA and degrades it.<a class="footnote-ref" id="fnref:18" href="#fn:18"><sup>18</sup></a> </p> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Gasiunas, Giedrius; Barrangou, Rodolphe; Horvath, Philippe; Siksnys, Virginijus (2012-09-25). "Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria". Proceedings of the National Academy of Sciences. 109 (39): E2579-86. doi:10.1073/pnas.1208507109. ISSN 0027-8424. PMC 3465414. PMID 22949671. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465414" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465414</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Faure, Guilhem; Shmakov, Sergey A.; Yan, Winston X.; Cheng, David R.; Scott, David A.; Peters, Joseph E.; Makarova, Kira S.; Koonin, Eugene V. (August 2019). "CRISPR–Cas in mobile genetic elements: counter-defence and beyond". Nature Reviews Microbiology. 17 (8): 513–525. doi:10.1038/s41579-019-0204-7. ISSN 1740-1534. PMC 11165670. PMID 31165781. S2CID 174809341. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165670" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165670</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Faure, Guilhem; Shmakov, Sergey A.; Yan, Winston X.; Cheng, David R.; Scott, David A.; Peters, Joseph E.; Makarova, Kira S.; Koonin, Eugene V. (August 2019). "CRISPR–Cas in mobile genetic elements: counter-defence and beyond". Nature Reviews Microbiology. 17 (8): 513–525. doi:10.1038/s41579-019-0204-7. ISSN 1740-1534. PMC 11165670. PMID 31165781. S2CID 174809341. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165670" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165670</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Karvelis, Tautvydas; Gasiunas, Giedrius; Miksys, Algirdas; Barrangou, Rodolphe; Horvath, Philippe; Siksnys, Virginijus (2013-05-01). "crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus". RNA Biology. 10 (5): 841–851. doi:10.4161/rna.24203. ISSN 1547-6286. PMC 3737341. PMID 23535272. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737341" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737341</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Karvelis, Tautvydas; Gasiunas, Giedrius; Miksys, Algirdas; Barrangou, Rodolphe; Horvath, Philippe; Siksnys, Virginijus (2013-05-01). "crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus". RNA Biology. 10 (5): 841–851. doi:10.4161/rna.24203. ISSN 1547-6286. PMC 3737341. PMID 23535272. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737341" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737341</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Gasiunas, Giedrius; Barrangou, Rodolphe; Horvath, Philippe; Siksnys, Virginijus (2012-09-25). "Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria". Proceedings of the National Academy of Sciences. 109 (39): E2579-86. doi:10.1073/pnas.1208507109. ISSN 0027-8424. PMC 3465414. PMID 22949671. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465414" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465414</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Jinek, Martin; Chylinski, Krzysztof; Fonfara, Ines; Hauer, Michael; Doudna, Jennifer A.; Charpentier, Emmanuelle (2012-08-17). "A programmable dual RNA-guided DNA endonuclease in adaptive bacterial immunity". Science. 337 (6096): 816–821. Bibcode:2012Sci...337..816J. doi:10.1126/science.1225829. ISSN 0036-8075. PMC 6286148. PMID 22745249. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6286148" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6286148</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Sinkunas, Tomas; Gasiunas, Giedrius; Fremaux, Christophe; Barrangou, Rodolphe; Horvath, Philippe; Siksnys, Virginijus (2011-04-06). "Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system". The EMBO Journal. 30 (7): 1335–1342. doi:10.1038/emboj.2011.41. ISSN 0261-4189. PMC 3094125. PMID 21343909. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094125" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094125</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Brendel, Jutta; Stoll, Britta; Lange, Sita J.; Sharma, Kundan; Lenz, Christof; Stachler, Aris-Edda; Maier, Lisa-Katharina; Richter, Hagen; Nickel, Lisa; Schmitz, Ruth A.; Randau, Lennart; Allers, Thorsten; Urlaub, Henning; Backofen, Rolf; Marchfelder, Anita (2014-03-07). "A Complex of Cas Proteins 5, 6, and 7 Is Required for the Biogenesis and Stability of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-derived RNAs (crRNAs) in Haloferax volcanii". The Journal of Biological Chemistry. 289 (10): 7164–7177. doi:10.1074/jbc.M113.508184. ISSN 0021-9258. PMC 3945376. 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"Type III CRISPR-Cas Systems: Deciphering the Most Complex Prokaryotic Immune System". Biochemistry (Moscow). 86 (10): 1301–1314. doi:10.1134/S0006297921100114. ISSN 1608-3040. PMC 8527444. PMID 34903162. <a href="https://doi.org/10.1134/S0006297921100114" target="_blank">https://doi.org/10.1134/S0006297921100114</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> <li id="fn:15"><p>Pinilla-Redondo, Rafael; Mayo-Muñoz, David; Russel, Jakob; Garrett, Roger A.; Randau, Lennart; Sørensen, Søren J.; Shah, Shiraz A. (2020-02-28). "Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids". Nucleic Acids Research. 48 (4): 2000–2012. doi:10.1093/nar/gkz1197. ISSN 1362-4962. PMC 7038947. PMID 31879772. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7038947" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7038947</a> <a href="#fnref:15" class="footnote-back-ref">↩</a></p></li> <li id="fn:16"><p>Makarova, Kira S.; Wolf, Yuri I.; Iranzo, Jaime; Shmakov, Sergey A.; Alkhnbashi, Omer S.; Brouns, Stan J. J.; Charpentier, Emmanuelle; Cheng, David; Haft, Daniel H.; Horvath, Philippe; Moineau, Sylvain; Mojica, Francisco J. M.; Scott, David; Shah, Shiraz A.; Siksnys, Virginijus (February 2020). "Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants". Nature Reviews Microbiology. 18 (2): 67–83. doi:10.1038/s41579-019-0299-x. ISSN 1740-1534. PMC 8905525. 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S2CID 49414939. <a href="https://pubmed.ncbi.nlm.nih.gov/29940185/" target="_blank">https://pubmed.ncbi.nlm.nih.gov/29940185/</a> <a href="#fnref:18" class="footnote-back-ref">↩</a></p></li> </ol>