CRISPR RNA
{{Short description|RNA transcript from the CRISPR locus}}
CRISPR RNA or crRNA is a RNA transcript from the CRISPR locus.{{Cite journal |last1=Gasiunas |first1=Giedrius |last2=Barrangou |first2=Rodolphe |last3=Horvath |first3=Philippe |last4=Siksnys |first4=Virginijus |date=2012-09-25 |title=Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria |journal=Proceedings of the National Academy of Sciences |language=en |volume=109 |issue=39 |pages=E2579-86 |doi=10.1073/pnas.1208507109 |issn=0027-8424 |pmc=3465414 |pmid=22949671|doi-access=free }} CRISPR-Cas (clustered, regularly interspaced short palindromic repeats - CRISPR associated systems) is an adaptive immune system found in bacteria and archaea to protect against mobile genetic elements, like viruses, plasmids, and transposons.{{Cite journal |last1=Faure |first1=Guilhem |last2=Shmakov |first2=Sergey A. |last3=Yan |first3=Winston X. |last4=Cheng |first4=David R. |last5=Scott |first5=David A. |last6=Peters |first6=Joseph E. |last7=Makarova |first7=Kira S. |last8=Koonin |first8=Eugene V. |date=August 2019 |title=CRISPR–Cas in mobile genetic elements: counter-defence and beyond |journal=Nature Reviews Microbiology |language=en |volume=17 |issue=8 |pages=513–525 |doi=10.1038/s41579-019-0204-7 |pmid=31165781 |s2cid=174809341 |issn=1740-1534|pmc=11165670 }} The CRISPR locus contains a series of repeats interspaced with unique spacers. These unique spacers can be acquired from MGEs.
File:13 Hegasy CRISPR pre crRNA Wiki E CCBYSA.png
Pre-crRNA is formed after the transcription of the CRISPR locus and before being processed by Cas proteins. Mature crRNA transcripts contain a partial conserved section of repeat and a sequence of spacer that is complementary to the target DNA.{{Cite journal |last1=Karvelis |first1=Tautvydas |last2=Gasiunas |first2=Giedrius |last3=Miksys |first3=Algirdas |last4=Barrangou |first4=Rodolphe |last5=Horvath |first5=Philippe |last6=Siksnys |first6=Virginijus |date=2013-05-01 |title=crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus |journal=RNA Biology |volume=10 |issue=5 |pages=841–851 |doi=10.4161/rna.24203 |issn=1547-6286 |pmc=3737341 |pmid=23535272}} crRNA forms an effector complex with a single nuclease or multiple Cas proteins called a Cascade (CRISPR-associated complex for antiviral defense). Once the effector complex is formed a Cas nuclease or single effector protein will cause interference guided by the crRNA match.{{Cite journal |last1=Jinek |first1=Martin |last2=Chylinski |first2=Krzysztof |last3=Fonfara |first3=Ines |last4=Hauer |first4=Michael |last5=Doudna |first5=Jennifer A. |last6=Charpentier |first6=Emmanuelle |date=2012-08-17 |title=A programmable dual RNA-guided DNA endonuclease in adaptive bacterial immunity |journal=Science |volume=337 |issue=6096 |pages=816–821 |doi=10.1126/science.1225829 |issn=0036-8075 |pmc=6286148 |pmid=22745249|bibcode=2012Sci...337..816J }}
Function
= Type-I =
Type-I CRISPR systems are characterized by Cas3, a nuclease-helicase 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.{{Cite journal |last1=Sinkunas |first1=Tomas |last2=Gasiunas |first2=Giedrius |last3=Fremaux |first3=Christophe |last4=Barrangou |first4=Rodolphe |last5=Horvath |first5=Philippe |last6=Siksnys |first6=Virginijus |date=2011-04-06 |title=Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system |journal=The EMBO Journal |volume=30 |issue=7 |pages=1335–1342 |doi=10.1038/emboj.2011.41 |issn=0261-4189 |pmc=3094125 |pmid=21343909}}
Typically in the Cascade, Cas6 generates the mature crRNAs while Cas5 and Cas7 process and stabilize the crRNA.{{Cite journal |last1=Brendel |first1=Jutta |last2=Stoll |first2=Britta |last3=Lange |first3=Sita J. |last4=Sharma |first4=Kundan |last5=Lenz |first5=Christof |last6=Stachler |first6=Aris-Edda |last7=Maier |first7=Lisa-Katharina |last8=Richter |first8=Hagen |last9=Nickel |first9=Lisa |last10=Schmitz |first10=Ruth A. |last11=Randau |first11=Lennart |last12=Allers |first12=Thorsten |last13=Urlaub |first13=Henning |last14=Backofen |first14=Rolf |last15=Marchfelder |first15=Anita |date=2014-03-07 |title=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 |journal=The Journal of Biological Chemistry |volume=289 |issue=10 |pages=7164–7177 |doi=10.1074/jbc.M113.508184 |issn=0021-9258 |pmc=3945376 |pmid=24459147|doi-access=free }}
= Type-II =
Type-II CRISPR systems{{Cite journal |last1=Makarova |first1=Kira S. |last2=Wolf |first2=Yuri I. |last3=Iranzo |first3=Jaime |last4=Shmakov |first4=Sergey A. |last5=Alkhnbashi |first5=Omer S. |last6=Brouns |first6=Stan J. J. |last7=Charpentier |first7=Emmanuelle |last8=Cheng |first8=David |last9=Haft |first9=Daniel H. |last10=Horvath |first10=Philippe |last11=Moineau |first11=Sylvain |last12=Mojica |first12=Francisco J. M. |last13=Scott |first13=David |last14=Shah |first14=Shiraz A. |last15=Siksnys |first15=Virginijus |date=February 2020 |title=Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants |journal=Nature Reviews Microbiology |language=en |volume=18 |issue=2 |pages=67–83 |doi=10.1038/s41579-019-0299-x |pmid=31857715 |pmc=8905525 |issn=1740-1534}} are characterized by the single signature nuclease Cas9.{{Cite journal |last1=Heler |first1=Robert |last2=Samai |first2=Poulami |last3=Modell |first3=Joshua W. |last4=Weiner |first4=Catherine |last5=Goldberg |first5=Gregory W. |last6=Bikard |first6=David |last7=Marraffini |first7=Luciano A. |date=2015-03-12 |title=Cas9 specifies functional viral targets during CRISPR-Cas adaptation |journal=Nature |volume=519 |issue=7542 |pages=199–202 |doi=10.1038/nature14245 |issn=0028-0836 |pmc=4385744 |pmid=25707807|bibcode=2015Natur.519..199H }} In type-II CRISPR systems crRNA and tracrRNA (trans-activating CRISPR RNA) can form a complex known as the guide RNA or gRNA.{{Cite journal |last1=Charpentier |first1=Emmanuelle |last2=Richter |first2=Hagen |last3=van der Oost |first3=John |last4=White |first4=Malcolm F. |date=2015-05-01 |title=Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity |journal=FEMS Microbiology Reviews |volume=39 |issue=3 |pages=428–441 |doi=10.1093/femsre/fuv023 |issn=0168-6445 |pmc=5965381 |pmid=25994611}} The crRNA within the gRNA is what matches up with the target sequence or protospacer after the PAM is found. Once the match is made Cas9 will make a double-stranded break.
= Type-III =
Type-III CRISPR systems are characterized by Cas10, an RNA cleaving protein.{{Cite journal |last1=Kolesnik |first1=Matvey V. |last2=Fedorova |first2=Iana |last3=Karneyeva |first3=Karyna A. |last4=Artamonova |first4=Daria N. |last5=Severinov |first5=Konstantin V. |date=2021-10-01 |title=Type III CRISPR-Cas Systems: Deciphering the Most Complex Prokaryotic Immune System |url=https://doi.org/10.1134/S0006297921100114 |journal=Biochemistry (Moscow) |language=en |volume=86 |issue=10 |pages=1301–1314 |doi=10.1134/S0006297921100114 |issn=1608-3040 |pmc=8527444 |pmid=34903162}} 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.
= Type-IV =
Type-IV CRISPR systems do not have an effector nuclease and are associated with plasmids and prophages. 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.{{Cite journal |last1=Pinilla-Redondo |first1=Rafael |last2=Mayo-Muñoz |first2=David |last3=Russel |first3=Jakob |last4=Garrett |first4=Roger A. |last5=Randau |first5=Lennart |last6=Sørensen |first6=Søren J. |last7=Shah |first7=Shiraz A. |date=2020-02-28 |title=Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids |journal=Nucleic Acids Research |volume=48 |issue=4 |pages=2000–2012 |doi=10.1093/nar/gkz1197 |issn=1362-4962 |pmc=7038947 |pmid=31879772}}
= Type-V =
Type-V CRISPR systems are characterized by Cas12, a nuclease that can cleave ssDNA, dsDNA, and RNA. 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.{{Cite journal |last1=Paul |first1=Bijoya |last2=Montoya |first2=Guillermo |date=February 2020 |title=CRISPR-Cas12a: Functional overview and applications |journal=Biomedical Journal |volume=43 |issue=1 |pages=8–17 |doi=10.1016/j.bj.2019.10.005 |issn=2319-4170 |pmc=7090318 |pmid=32200959}}
= Type-VI =
Type-VI CRISPR systems are characterized by Cas13, 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.{{Cite journal |last=O'Connell |first=Mitchell R. |date=2019-01-04 |title=Molecular Mechanisms of RNA Targeting by Cas13-containing Type VI CRISPR-Cas Systems |url=https://pubmed.ncbi.nlm.nih.gov/29940185/ |journal=Journal of Molecular Biology |volume=431 |issue=1 |pages=66–87 |doi=10.1016/j.jmb.2018.06.029 |issn=1089-8638 |pmid=29940185|s2cid=49414939 }}
References
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