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SALMONELLA CRISPR-Cas SİSTEMİ’NİN TEMEL ÖZELLİKLERİ

Year 2023, Volume: 14 Issue: 2, 72 - 78, 01.09.2023

Özge Erdoğan

https://doi.org/10.38137/vftd.1208878

Abstract

Son yıllarda keşfedilen CRISPR-Cas sistemi, CRISPR dizileri (düzenli aralıklarla bölünmüş palindromik tekrar kümeleri) ve Cas (CRISPR ilişkili proteinler) genlerinden oluşmaktadır. 1987 yılında bu tekrar kümeleri ilk olarak Escherichia coli’de keşfedilmiş ancak fonksiyonları tanımlanamamıştır. Günümüzde Salmonella da dahil olmak üzere bakteri genomlarının yaklaşık % 45'inde bulunan CRISPR-Cas sisteminin bakterilerin nükleik asit tabanlı adaptif bağışıklık sisteminin temel bileşenleri olduğu bilinmektedir. CRISPR-Cas bölgelerinin analizine dayalı çalışmaların son yıllarda oldukça artması, CRISPR tabanlı teknolojilerin ve uygulamaların çoğalması bu alanda yapılan çalışmaların etkinliğini de giderek artırmaktadır. Bu derlemede CRISPR-Cas sistemi ve Salmonella’da mevcut olan CRISPR bölge özellikleri ile kullanım alanları hakkında bilgi verilecektir

Keywords

CRISPR Moleküler tiplendirme Salmonella

References

  • Barrangou, R. & Dudley, E. G. (2016). CRISPR-based typing and next-generation tracking technologies. Annual Review of Food Science and Technology, 7, 395–411.
  • Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A. & Horvath, P. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science, 315, 1709–1712.
  • Barrangou, R. & Marraffini, L. A. (2014). CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity. Molecular Cell, 54, 234- 244.
  • Barrangou, R. & van der Oost, J. (2013). CRISPR-Cas systems: RNA-mediated adaptive immunity in bacteria and archaea. Heidelberg, Germany: Springer; 2013. https://doi.org/10.1007/978-3-642-34657-6.
  • Deveau, H., Barrangou, R., Garneau, J. E., Labonté, J., Fremaux, C., Boyaval, P., Romeo, D. A., Horvath, P. & Moineau, S. (2008). Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. Journal of Bacteriology, 190 (4), 1390–1400.
  • DiMarzio, M. J., Shariat, N., Kariyawasam, S., Barrangou, R. & Dudley, E. G. (2013). Antibiotic resistance in Salmonella Typhimurium associates with CRISPR sequence type. Antimicrobial Agents and Chemotherapy, 57, 4282–4289.
  • Fabre, L., Zhang, J., Guigon, G., Le Hello, S., Guibert, V., Accou-Demartin, M., de Romans, S., Lim, C., Roux, C., Passet, V., Diancourt, L., Guibourdenche, M., Issenhuth-Jeanjean, S., Achtman, M., Brisse, S., Sola, C. & Weill, F. X. (2012). CRISPR typing and subtyping for Improved Laboratory Surveillance of Salmonella Infections. PLoS One, 7 (5), e36995.
  • Fricke, W. F., Mammel, M. K., McDermott, P. F., Tartera, C., White, D. G., Leclerc, J. E., Ravel, J. & Cebula, T. A. (2011). Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution. Journal of Bacteriology, 193, 3556–3568.
  • Grissa, I., Vergnaud, G. & Pourcel, C. (2007). The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics, 8, 172.
  • Haft, D. H., Selengut, J., Mongodin, E. F. & Nelson, K. E. (2005). A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Computational Biology, 1, e60.
  • Horvath, P. & Barrangou, R. (2010). CRISPR/Cas, the immune system of bacteria and archaea. Science, 327, 167–170.
  • Horvath, P., Romero, D. A., Coûté-Monvoisin, A. C., Richards, M., Deveau, H., Moineau, S., Boyaval, P., Fremaux, C. & Barrangou, R. (2008). Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. Journal of Bacteriology, 190 (4), 1401–1412.
  • Jansen, R., Embden, J. D., Gaastra, W. & Schouls, L. M. (2002). Identification of genes that are associated with DNA repeats in prokaryotes. Molecular Microbiology, 43, 1565–1575.
  • Jiang, F. & Doudna, J. A. (2015). The structural biology of CRISPR-Cas systems. Structural Biology, 30, 100-111.
  • Karimi, Z., Ahmadi, A., Najafi, A. & Ranjbar, R. (2018). Bacterial CRISPR Regions: General Features and their Potential for Epidemiological Molecular Typing Studies. The Open Microbiology Journal, 12, 59-70.
  • Kunin, V., Sorek, R. & Hugenholtz, P. (2007). Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biology, 8 (4), R61.
  • Liu, F., Barrangou, R., Gerner-Smidt, P., Ribot, E. M., Knabel, S. J. & Dudley, E. G. (2011a). Novel virulence gene and clustered regularly interspaced short palindromic repeat (CRISPR) multilocus sequence typing scheme for subtyping of the major serovars of Salmonella enterica subsp. Enterica. Applied and Environmental Microbiology, 77, 1946–1956.
  • Makarova K. S., Grishin N. V., Shabalala S. A., Wolf, Y. I. & Koonin, E. V. (2006). A putative RNA-interference-based immune system in prokaryotes: computational analysis of shahypothetical mechanisms of action. Biology Direct, 1, 7.
  • Medina-Aparicio, L., Dávila, S., Rebollar-Flores, J. E., Calva, E. & Hernández-Lucas, I. (2018). The CRISPR-Cas system in Enterobacteriaceae. Pathogens and Disease, 76.
  • Mojica, F. J., Díez-Villaseñor, C., García-Martínez, J. & Almendros, C. (2009). Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology, 155, 733-740.
  • Nishimasu, H., Ran, F. A., Hsu P. D., Konermann, S., Dohmae, N., Shehata, S. I., Ishitani, R., Zhang, F. & Nureki, O. (2014). Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Cell, 156, 935-949.
  • Oliveira, S. D., Santos, L. R., Schuch, D. M., Silva, A. B., Salle, C. T. & Canal, C. W. (2002). Detection and identification of Salmonellas from poultry related samples by PCR. Veterinary Microbiology, 87, 25-35.
  • Pettengill, J. B., Timme, R. E., Barrangou, R., Toro, M., Allard, M. W., Strain, E., Musser, S. M. & Brown, E. W. (2014). The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica. Peer J, 2, e340.
  • Rath, D., Amlinger, L., Rath, A. & Lundgren, M. (2015). The CRISPR-Cas immune system: Biology, mechanisms and applications. Biochimie, 117, 119-128.
  • Richards, A. K., Hopkins, B. A. & Shariat, N. W. (2020). Conserved CRISPR arrays in Salmonella enterica serovar Infantis can serve as qPCR targets to detect Infantis in mixed serovar populations. Letters in Applied Microbiology, 71 (2), 138-145.
  • Savic, N. & Schwank, G. (2016). Advances in therapeutic CRISPR/Cas9 genome editing. Translational Research, 168, 15-21.
  • Shariat, N., DiMarzio, M. J., Yin, S., Dettinger, L., Sandt, C. H., Lute, J. R., Barrangou, R. & Dudley, E. G. (2013a). The combination of CRISPR-MVLST and PFGE provides increased discriminatory power for differentiating human clinical isolates of Salmonella 173. entericasubsp. enterica. Applied and Environmental Microbiology, 77, 1946–1956.
  • Shariat, N., Kirchner, M. K., Sandt, C. H., Trees, E., Barrangou, R. & Dudley, E. G. (2013b). Subtyping of Salmonella enterica serovar Newport outbreak isolates by CRISPR-MVLST and determination of the relationship between CRISPR-MVLST and PFGE results. Journal of Clinical Microbiology, 51, 2328-2336.
  • Shariat, N., Sandt, C. H., DiMarzio, M. J., Barrangou, R. & Dudley, E. G. (2013c). CRISPR-MVLSTsubtyping of Salmonella enterica subsp. Enterica serovars Typhimurium and Heidelberg and application in identifying outbreak isolates. BMC Microbiology, 13, 254.
  • Shariat, N., Timme, R. E., Pettengill, J. B., Barrangou, R. & Dudley, E. G. (2015). Characterization and evolution of Salmonella CRISPR-Cas systems. Microbiology, 161, 374-386.
  • Sorek, R., Lawrence, C. M., Wiedenheft, B. (2013). CRISPR mediated adaptive immune systems in Bacteria and Archaea. Annual Review of Biochemistry, 82, 237–66.
  • Touchon, M. & Rocha, E. P. (2010). The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS One, 5, e11126.
  • Xie, X., Hu, Y., Xu, Y., Yin, K., Li, Y., Chen, Y., Xia, J., Xu, L., Liu, Z., Geng, S., Li, Q., Jiao, X., Chen, X. & Pan, Z. (2017). Genetic analysis of Salmonella enterica Molecular typing and subtyping of Salmonella by identification of the variable nucleotide sequences of the CRISPR loci serovar Gallinarum biovar Pullorum based on characterization and evolution of CRISPR sequence. Veterinary Microbiology, 203, 81–87.
  • Vosik, D., Tewari, D., Dettinger, L., M’ikanatha, N. M., Shariat, N. W. (2018). CRISPR Typing and Antibiotic Resistance Correlates with Polyphyletic Distribution in Human Isolates of Salmonella Kentucky. Foodborne Pathogenes and Disease, 15 (2), 101-108.

Year 2023, Volume: 14 Issue: 2, 72 - 78, 01.09.2023

Özge Erdoğan

https://doi.org/10.38137/vftd.1208878

Abstract

The CRISPR-Cas system, discovered in recent years, consists of CRISPR sequences (clusters of regularly spaced palindromic repeats) and Cas (CRISPR-associated proteins) genes. These repeat clusters were first discovered in Escherichia coli in 1987, but their function has not been defined. It is known that the CRISPR-Cas system, which is present in approximately 45% of bacterial genomes, including Salmonella, is the essential component of the nucleic acid-based adaptive immune system of bacteria. The increase in studies based on the analysis of CRISPR-Cas regions and the proliferation of CRISPR-based technologies and applications increase the effectiveness of studies in this field. In this review, information will be given about the CRISPR-Cas system and the CRISPR region features and usage areas in Salmonella.

Keywords

CRISPR Molecular typing Salmonella

References

  • Barrangou, R. & Dudley, E. G. (2016). CRISPR-based typing and next-generation tracking technologies. Annual Review of Food Science and Technology, 7, 395–411.
  • Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A. & Horvath, P. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science, 315, 1709–1712.
  • Barrangou, R. & Marraffini, L. A. (2014). CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity. Molecular Cell, 54, 234- 244.
  • Barrangou, R. & van der Oost, J. (2013). CRISPR-Cas systems: RNA-mediated adaptive immunity in bacteria and archaea. Heidelberg, Germany: Springer; 2013. https://doi.org/10.1007/978-3-642-34657-6.
  • Deveau, H., Barrangou, R., Garneau, J. E., Labonté, J., Fremaux, C., Boyaval, P., Romeo, D. A., Horvath, P. & Moineau, S. (2008). Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. Journal of Bacteriology, 190 (4), 1390–1400.
  • DiMarzio, M. J., Shariat, N., Kariyawasam, S., Barrangou, R. & Dudley, E. G. (2013). Antibiotic resistance in Salmonella Typhimurium associates with CRISPR sequence type. Antimicrobial Agents and Chemotherapy, 57, 4282–4289.
  • Fabre, L., Zhang, J., Guigon, G., Le Hello, S., Guibert, V., Accou-Demartin, M., de Romans, S., Lim, C., Roux, C., Passet, V., Diancourt, L., Guibourdenche, M., Issenhuth-Jeanjean, S., Achtman, M., Brisse, S., Sola, C. & Weill, F. X. (2012). CRISPR typing and subtyping for Improved Laboratory Surveillance of Salmonella Infections. PLoS One, 7 (5), e36995.
  • Fricke, W. F., Mammel, M. K., McDermott, P. F., Tartera, C., White, D. G., Leclerc, J. E., Ravel, J. & Cebula, T. A. (2011). Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution. Journal of Bacteriology, 193, 3556–3568.
  • Grissa, I., Vergnaud, G. & Pourcel, C. (2007). The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics, 8, 172.
  • Haft, D. H., Selengut, J., Mongodin, E. F. & Nelson, K. E. (2005). A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Computational Biology, 1, e60.
  • Horvath, P. & Barrangou, R. (2010). CRISPR/Cas, the immune system of bacteria and archaea. Science, 327, 167–170.
  • Horvath, P., Romero, D. A., Coûté-Monvoisin, A. C., Richards, M., Deveau, H., Moineau, S., Boyaval, P., Fremaux, C. & Barrangou, R. (2008). Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. Journal of Bacteriology, 190 (4), 1401–1412.
  • Jansen, R., Embden, J. D., Gaastra, W. & Schouls, L. M. (2002). Identification of genes that are associated with DNA repeats in prokaryotes. Molecular Microbiology, 43, 1565–1575.
  • Jiang, F. & Doudna, J. A. (2015). The structural biology of CRISPR-Cas systems. Structural Biology, 30, 100-111.
  • Karimi, Z., Ahmadi, A., Najafi, A. & Ranjbar, R. (2018). Bacterial CRISPR Regions: General Features and their Potential for Epidemiological Molecular Typing Studies. The Open Microbiology Journal, 12, 59-70.
  • Kunin, V., Sorek, R. & Hugenholtz, P. (2007). Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biology, 8 (4), R61.
  • Liu, F., Barrangou, R., Gerner-Smidt, P., Ribot, E. M., Knabel, S. J. & Dudley, E. G. (2011a). Novel virulence gene and clustered regularly interspaced short palindromic repeat (CRISPR) multilocus sequence typing scheme for subtyping of the major serovars of Salmonella enterica subsp. Enterica. Applied and Environmental Microbiology, 77, 1946–1956.
  • Makarova K. S., Grishin N. V., Shabalala S. A., Wolf, Y. I. & Koonin, E. V. (2006). A putative RNA-interference-based immune system in prokaryotes: computational analysis of shahypothetical mechanisms of action. Biology Direct, 1, 7.
  • Medina-Aparicio, L., Dávila, S., Rebollar-Flores, J. E., Calva, E. & Hernández-Lucas, I. (2018). The CRISPR-Cas system in Enterobacteriaceae. Pathogens and Disease, 76.
  • Mojica, F. J., Díez-Villaseñor, C., García-Martínez, J. & Almendros, C. (2009). Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology, 155, 733-740.
  • Nishimasu, H., Ran, F. A., Hsu P. D., Konermann, S., Dohmae, N., Shehata, S. I., Ishitani, R., Zhang, F. & Nureki, O. (2014). Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Cell, 156, 935-949.
  • Oliveira, S. D., Santos, L. R., Schuch, D. M., Silva, A. B., Salle, C. T. & Canal, C. W. (2002). Detection and identification of Salmonellas from poultry related samples by PCR. Veterinary Microbiology, 87, 25-35.
  • Pettengill, J. B., Timme, R. E., Barrangou, R., Toro, M., Allard, M. W., Strain, E., Musser, S. M. & Brown, E. W. (2014). The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica. Peer J, 2, e340.
  • Rath, D., Amlinger, L., Rath, A. & Lundgren, M. (2015). The CRISPR-Cas immune system: Biology, mechanisms and applications. Biochimie, 117, 119-128.
  • Richards, A. K., Hopkins, B. A. & Shariat, N. W. (2020). Conserved CRISPR arrays in Salmonella enterica serovar Infantis can serve as qPCR targets to detect Infantis in mixed serovar populations. Letters in Applied Microbiology, 71 (2), 138-145.
  • Savic, N. & Schwank, G. (2016). Advances in therapeutic CRISPR/Cas9 genome editing. Translational Research, 168, 15-21.
  • Shariat, N., DiMarzio, M. J., Yin, S., Dettinger, L., Sandt, C. H., Lute, J. R., Barrangou, R. & Dudley, E. G. (2013a). The combination of CRISPR-MVLST and PFGE provides increased discriminatory power for differentiating human clinical isolates of Salmonella 173. entericasubsp. enterica. Applied and Environmental Microbiology, 77, 1946–1956.
  • Shariat, N., Kirchner, M. K., Sandt, C. H., Trees, E., Barrangou, R. & Dudley, E. G. (2013b). Subtyping of Salmonella enterica serovar Newport outbreak isolates by CRISPR-MVLST and determination of the relationship between CRISPR-MVLST and PFGE results. Journal of Clinical Microbiology, 51, 2328-2336.
  • Shariat, N., Sandt, C. H., DiMarzio, M. J., Barrangou, R. & Dudley, E. G. (2013c). CRISPR-MVLSTsubtyping of Salmonella enterica subsp. Enterica serovars Typhimurium and Heidelberg and application in identifying outbreak isolates. BMC Microbiology, 13, 254.
  • Shariat, N., Timme, R. E., Pettengill, J. B., Barrangou, R. & Dudley, E. G. (2015). Characterization and evolution of Salmonella CRISPR-Cas systems. Microbiology, 161, 374-386.
  • Sorek, R., Lawrence, C. M., Wiedenheft, B. (2013). CRISPR mediated adaptive immune systems in Bacteria and Archaea. Annual Review of Biochemistry, 82, 237–66.
  • Touchon, M. & Rocha, E. P. (2010). The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS One, 5, e11126.
  • Xie, X., Hu, Y., Xu, Y., Yin, K., Li, Y., Chen, Y., Xia, J., Xu, L., Liu, Z., Geng, S., Li, Q., Jiao, X., Chen, X. & Pan, Z. (2017). Genetic analysis of Salmonella enterica Molecular typing and subtyping of Salmonella by identification of the variable nucleotide sequences of the CRISPR loci serovar Gallinarum biovar Pullorum based on characterization and evolution of CRISPR sequence. Veterinary Microbiology, 203, 81–87.
  • Vosik, D., Tewari, D., Dettinger, L., M’ikanatha, N. M., Shariat, N. W. (2018). CRISPR Typing and Antibiotic Resistance Correlates with Polyphyletic Distribution in Human Isolates of Salmonella Kentucky. Foodborne Pathogenes and Disease, 15 (2), 101-108.
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Details

Primary Language Turkish
Subjects Veterinary Sciences, Veterinary Microbiology
Journal Section Review
Authors

Özge Erdoğan 0000-0003-1721-1579

Publication Date September 1, 2023
Acceptance Date August 11, 2023
Published in Issue Year 2023 Volume: 14 Issue: 2

Cite

APA Erdoğan, Ö. (2023). SALMONELLA CRISPR-Cas SİSTEMİ’NİN TEMEL ÖZELLİKLERİ. Veteriner Farmakoloji Ve Toksikoloji Derneği Bülteni, 14(2), 72-78. https://doi.org/10.38137/vftd.1208878
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