Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Its Current Applicatıons in Microbial Diagnosis

Emre Taşkın; Özlem Kutlu; Cüneyt Kuru; Yeliz Eski

doi:10.34084/bshr.596146

Derleme

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Its Current Applicatıons in Microbial Diagnosis

Yıl 2019, Cilt: 3 Sayı: 3, 154 - 160, 31.12.2019

Emre Taşkın Özlem Kutlu Cüneyt Kuru Yeliz Eski

https://doi.org/10.34084/bshr.596146

Öz

Conventional
diagnostic methods have been used successfully for a long time in infectious
diseases. Besides conventional microbiologic diagnosis methods, new methods are
being developed for advanced accuracy, cost-effectiveness and ease of
application. Prokaryotic immune system has defense types of innate, adaptive
and cell suicide (programmed death). A part of prokaryotic adaptive immune
system named CRISPR-Cas is under intensive research recently as a novel
bacterial diagnostic system. CRISPR-Cas system can be used as a
biotechnological method and can be classified in genetic based bacterial
diagnostic methods. CRISPR-Cas system classification is based on included Cas
protein type and the target nucleic acid type (DNA or RNA). CRISPR-Cas locus in
prokaryotic cells consists of two main parts which are repeat sequences and
spacer sequences. Sequences which constitutes the adaptive immunity are spacer
sequences that are acquired from invading agents after survival of the prokaryote
from the attack. In CRISPR-Cas system cas genes are in charge of
cleaving foreign nucleic acid to defense prokaryotic cell itself. Currently new
systems like SHERLOCK, DETECTR and HUDSON are developed as variations of CRISPR-Cas
system by different research groups. Also, as a gene editing tool CRISPR-Cas
system is highly effective in setting up knock-out and knock-in systems and in
experiments which require gene regulation either in the transcriptional and
post-transcriptional level. CRISPR-Cas system is planned to be used in
producing therapeutic antiviral drugs. Considering current data, CRISPR-Cas is
a promising bacterial diagnostic system with all its advantages of rapidity,
lower cost, accuracy and simple application protocol.

Anahtar Kelimeler

CRISPR-Cas, Bacterial diagnosis, microbiology, biotechnology

Kaynakça

1. Barrangou R, Marraffini LA. CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol Cell. 24 Nisan 2014;54(2):234-44.
2. Ishino Y, Krupovic M, Forterre P. History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology. J Bacteriol. 01 2018;200(7).
3. Mojica FJ, Juez G, Rodríguez-Valera F. Transcription at different salinities of Haloferax mediterranei sequences adjacent to partially modified PstI sites. Mol Microbiol. Ağustos 1993;9(3):613-21.
4. Mojica FJM, Díez-Villaseñor C, García-Martínez J, Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol. Şubat 2005;60(2):174-82.
5. Price AA, Grakoui A, Weiss DS. Harnessing the Prokaryotic Adaptive Immune System as a Eukaryotic Antiviral Defense. Trends Microbiol. Nisan 2016;24(4):294-306.
6. van Soolingen D, de Haas PE, Hermans PW, Groenen PM, van Embden JD. Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology of Mycobacterium tuberculosis. J Clin Microbiol. Ağustos 1993;31(8):1987-95.
7. Savitskaya EE, Musharova OS, Severinov KV. Diversity of CRISPR-Cas-Mediated Mechanisms of Adaptive Immunity in Prokaryotes and Their Application in Biotechnology. Biochemistry Mosc. Temmuz 2016;81(7):653-61.
8. Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, vd. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 2015;13(11):722-36.
9. Anders C, Niewoehner O, Duerst A, Jinek M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature. Eylül 2014;513(7519):569-73.
10. Szczelkun MD, Tikhomirova MS, Sinkunas T, Gasiunas G, Karvelis T, Pschera P, vd. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. PNAS. 08 Temmuz 2014;111(27):9798-803.
11. Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature. Mart 2014;507(7490):62-7.
12. Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct. 16 Mart 2006;1:7.
13. Haft DH, Selengut J, Mongodin EF, Nelson KE. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol. Kasım 2005;1(6):e60.
14. Makarova KS, Aravind L, Wolf YI, Koonin EV. Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct. 14 Temmuz 2011;6:38.
15. Wiedenheft B, Sternberg SH, Doudna JA. RNA-guided genetic silencing systems in bacteria and archaea. Nature. 15 Şubat 2012;482(7385):331-8.
16. Beloglazova N, Petit P, Flick R, Brown G, Savchenko A, Yakunin AF. Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference. EMBO J. 16 Kasım 2011;30(22):4616-27.
17. Rath D, Amlinger L, Rath A, Lundgren M. The CRISPR-Cas immune system: biology, mechanisms and applications. Biochimie. Ekim 2015;117:119-28.
18. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, vd. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 23 Mart 2007;315(5819):1709-12.
19. Sampson TR, Saroj SD, Llewellyn AC, Tzeng Y-L, Weiss DS. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature. 09 Mayıs 2013;497(7448):254-7.
20. Sampson TR, Napier BA, Schroeder MR, Louwen R, Zhao J, Chin C-Y, vd. A CRISPR-Cas system enhances envelope integrity mediating antibiotic resistance and inflammasome evasion. Proc Natl Acad Sci USA. 29 Temmuz 2014;111(30):11163-8.
21. Price AA, Sampson TR, Ratner HK, Grakoui A, Weiss DS. Cas9-mediated targeting of viral RNA in eukaryotic cells. Proc Natl Acad Sci USA. 12 Mayıs 2015;112(19):6164-9.
22. Sashital DG. Pathogen detection in the CRISPR–Cas era. Genome Med [Internet]. 24 Nisan 2018 [a.yer 28 Haziran 2019];10. Erişim adresi: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937823/
23. Geraldi A, Giri-Rachman EA. Synthetic biology-based portable in vitro diagnostic platforms. Alexandria Journal of Medicine. 01 Aralık 2018;54(4):423-8.
24. East-Seletsky A, O’Connell MR, Knight SC, Burstein D, Cate JHD, Tjian R, vd. Two Distinct RNase Activities of CRISPR-C2c2 Enable Guide RNA Processing and RNA Detection. Nature. 13 Ekim 2016;538(7624):270-3.
25. Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, vd. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 28 Nisan 2017;356(6336):438-42.
26. Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, vd. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 27 2018;360(6387):436-9.
27. Myhrvold C, Freije CA, Gootenberg JS, Abudayyeh OO, Metsky HC, Durbin AF, vd. Field-deployable viral diagnostics using CRISPR-Cas13. Science. 27 Nisan 2018;360(6387):444-8.
28. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, vd. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 28 Şubat 2013;152(5):1173-83.
29. Bikard D, Jiang W, Samai P, Hochschild A, Zhang F, Marraffini LA. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. Ağustos 2013;41(15):7429-37.
30. Choudhary E, Thakur P, Pareek M, Agarwal N. Gene silencing by CRISPR interference in mycobacteria. Nat Commun. 25 Şubat 2015;6:6267.
31. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, vd. CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes. Cell. 18 Temmuz 2013;154(2):442-51.
32. Sharma A, Toepfer CN, Ward T, Wasson L, Agarwal R, Conner DA, vd. CRISPR/Cas9 Mediated Fluorescent Tagging of Endogenous Proteins in Human Pluripotent Stem Cells. Curr Protoc Hum Genet. 24 Ocak 2018;96:21.11.1-21.11.20.
33. Lokko Y, Heijde M, Schebesta K, Scholtès P, Van Montagu M, Giacca M. Biotechnology and the bioeconomy—Towards inclusive and sustainable industrial development. New Biotechnology. 25 Ocak 2018;40:5-10.

Düzenli Aralıklarla Bölünmüş Palindromik Tekrar Kümelerinin (CRISPR) Güncel Mikrobiyal Tanıda Kullanımı

Yıl 2019, Cilt: 3 Sayı: 3, 154 - 160, 31.12.2019

Emre Taşkın Özlem Kutlu Cüneyt Kuru Yeliz Eski

https://doi.org/10.34084/bshr.596146

Öz

Bulaşıcı hastalıklarda geleneksel tanı yöntemleri uzun
zamandır başarıyla kullanılmaktadır. Geleneksel mikrobiyolojik tanı
yöntemlerinin yanı sıra, gelişmiş doğruluk, maliyet etkinliği ve uygulama
kolaylığı için yeni yöntemler geliştirilmektedir. Prokaryotik bağışıklık
sistemi tipleri doğuştan gelen, adaptif ve programlı hücre ölümüdür. Son
zamanlarda yeni bir bakteriyel tanı sistemi olarak CRISPR-Cas adlı system prokaryotik
adaptif bağışıklık sisteminin bir parçasıdır ve yoğun olarak araştırılmaktadır.
CRISPR-Cas sistemi, genetik tabanlı bakteriyel tanı yöntemlerinde
sınıflandırılabilir ve aynı zamanda biyoteknolojik bir yöntem olarak da kullanılmaktadır.
CRISPR-Cas sisteminin sınıflandırılması, Cas protein tipine ve hedef nükleik
asit tipine (DNA veya RNA) göre yapılmaktadır. Prokaryotik hücrelerde
CRISPR-Cas lokusu, tekrarlayan diziler ve spacer diziler olarak iki ana
bölümden oluşur. Spacer diziler prokaryotun saldırıdan sağkalımından sonra
istilacı ajanların genomundan bakteriye geçen dizilerdir. CRISPR-Cas sisteminde
cas genleri prokaryotik hücrenin kendisini korumak için yabancı nükleik
asidi parçalayan enzimlerdir. CRISPR-Cas sisteminin varyasyonları olarak Şu
anda SHERLOCK, DETECTR ve HUDSON gibi yeni sistemler, farklı araştırma grupları
tarafından geliştirilmektedir. Ayrıca CRISPR-Cas sistemi, knock-out ve knock-in
sistemlerinin oluşturulmasında, transkripsiyon ve transkripsiyon sonrası
seviyede gen regülasyonu gerektiren deneylerde oldukça etkilidir. CRISPR-Cas
sisteminin terapötik antiviral ilaçların üretilmesinde kullanılması da planlanmaktadır.
Mevcut veriler göz önüne alındığında, CRISPR-Cas, hız, düşük maliyet, yüksek
doğruluk ve basit uygulama protokolü avantajları ile umut verici bir bakteriyel
tanı sistemidir.

Anahtar Kelimeler

CRISPR-Cas, Mikrobiyal tanı, Mikrobiyoloji, Biyoteknoloji

Kaynakça

1. Barrangou R, Marraffini LA. CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol Cell. 24 Nisan 2014;54(2):234-44.
2. Ishino Y, Krupovic M, Forterre P. History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology. J Bacteriol. 01 2018;200(7).
3. Mojica FJ, Juez G, Rodríguez-Valera F. Transcription at different salinities of Haloferax mediterranei sequences adjacent to partially modified PstI sites. Mol Microbiol. Ağustos 1993;9(3):613-21.
4. Mojica FJM, Díez-Villaseñor C, García-Martínez J, Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol. Şubat 2005;60(2):174-82.
5. Price AA, Grakoui A, Weiss DS. Harnessing the Prokaryotic Adaptive Immune System as a Eukaryotic Antiviral Defense. Trends Microbiol. Nisan 2016;24(4):294-306.
6. van Soolingen D, de Haas PE, Hermans PW, Groenen PM, van Embden JD. Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology of Mycobacterium tuberculosis. J Clin Microbiol. Ağustos 1993;31(8):1987-95.
7. Savitskaya EE, Musharova OS, Severinov KV. Diversity of CRISPR-Cas-Mediated Mechanisms of Adaptive Immunity in Prokaryotes and Their Application in Biotechnology. Biochemistry Mosc. Temmuz 2016;81(7):653-61.
8. Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, vd. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 2015;13(11):722-36.
9. Anders C, Niewoehner O, Duerst A, Jinek M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature. Eylül 2014;513(7519):569-73.
10. Szczelkun MD, Tikhomirova MS, Sinkunas T, Gasiunas G, Karvelis T, Pschera P, vd. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. PNAS. 08 Temmuz 2014;111(27):9798-803.
11. Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature. Mart 2014;507(7490):62-7.
12. Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct. 16 Mart 2006;1:7.
13. Haft DH, Selengut J, Mongodin EF, Nelson KE. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol. Kasım 2005;1(6):e60.
14. Makarova KS, Aravind L, Wolf YI, Koonin EV. Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct. 14 Temmuz 2011;6:38.
15. Wiedenheft B, Sternberg SH, Doudna JA. RNA-guided genetic silencing systems in bacteria and archaea. Nature. 15 Şubat 2012;482(7385):331-8.
16. Beloglazova N, Petit P, Flick R, Brown G, Savchenko A, Yakunin AF. Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference. EMBO J. 16 Kasım 2011;30(22):4616-27.
17. Rath D, Amlinger L, Rath A, Lundgren M. The CRISPR-Cas immune system: biology, mechanisms and applications. Biochimie. Ekim 2015;117:119-28.
18. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, vd. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 23 Mart 2007;315(5819):1709-12.
19. Sampson TR, Saroj SD, Llewellyn AC, Tzeng Y-L, Weiss DS. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature. 09 Mayıs 2013;497(7448):254-7.
20. Sampson TR, Napier BA, Schroeder MR, Louwen R, Zhao J, Chin C-Y, vd. A CRISPR-Cas system enhances envelope integrity mediating antibiotic resistance and inflammasome evasion. Proc Natl Acad Sci USA. 29 Temmuz 2014;111(30):11163-8.
21. Price AA, Sampson TR, Ratner HK, Grakoui A, Weiss DS. Cas9-mediated targeting of viral RNA in eukaryotic cells. Proc Natl Acad Sci USA. 12 Mayıs 2015;112(19):6164-9.
22. Sashital DG. Pathogen detection in the CRISPR–Cas era. Genome Med [Internet]. 24 Nisan 2018 [a.yer 28 Haziran 2019];10. Erişim adresi: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937823/
23. Geraldi A, Giri-Rachman EA. Synthetic biology-based portable in vitro diagnostic platforms. Alexandria Journal of Medicine. 01 Aralık 2018;54(4):423-8.
24. East-Seletsky A, O’Connell MR, Knight SC, Burstein D, Cate JHD, Tjian R, vd. Two Distinct RNase Activities of CRISPR-C2c2 Enable Guide RNA Processing and RNA Detection. Nature. 13 Ekim 2016;538(7624):270-3.
25. Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, vd. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 28 Nisan 2017;356(6336):438-42.
26. Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, vd. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 27 2018;360(6387):436-9.
27. Myhrvold C, Freije CA, Gootenberg JS, Abudayyeh OO, Metsky HC, Durbin AF, vd. Field-deployable viral diagnostics using CRISPR-Cas13. Science. 27 Nisan 2018;360(6387):444-8.
28. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, vd. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 28 Şubat 2013;152(5):1173-83.
29. Bikard D, Jiang W, Samai P, Hochschild A, Zhang F, Marraffini LA. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. Ağustos 2013;41(15):7429-37.
30. Choudhary E, Thakur P, Pareek M, Agarwal N. Gene silencing by CRISPR interference in mycobacteria. Nat Commun. 25 Şubat 2015;6:6267.
31. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, vd. CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes. Cell. 18 Temmuz 2013;154(2):442-51.
32. Sharma A, Toepfer CN, Ward T, Wasson L, Agarwal R, Conner DA, vd. CRISPR/Cas9 Mediated Fluorescent Tagging of Endogenous Proteins in Human Pluripotent Stem Cells. Curr Protoc Hum Genet. 24 Ocak 2018;96:21.11.1-21.11.20.
33. Lokko Y, Heijde M, Schebesta K, Scholtès P, Van Montagu M, Giacca M. Biotechnology and the bioeconomy—Towards inclusive and sustainable industrial development. New Biotechnology. 25 Ocak 2018;40:5-10.

Toplam 33 adet kaynakça vardır.

Ayrıntılar

Birincil Dil	İngilizce
Konular	Klinik Tıp Bilimleri (Diğer)
Bölüm	Derleme
Yazarlar	Emre Taşkın 0000-0002-4092-3489 Özlem Kutlu 0000-0002-3769-2536 Cüneyt Kuru Bu kişi benim 0000-0002-8055-0891 Yeliz Eski Bu kişi benim 0000-0002-7187-4261
Yayımlanma Tarihi	31 Aralık 2019
Kabul Tarihi	21 Ağustos 2019
Yayımlandığı Sayı	Yıl 2019 Cilt: 3 Sayı: 3

Kaynak Göster

AMA	Taşkın E, Kutlu Ö, Kuru C, Eski Y. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Its Current Applicatıons in Microbial Diagnosis. J Biotechnol and Strategic Health Res. Aralık 2019;3(3):154-160. doi:10.34084/bshr.596146

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