Article Review: Editing genome of Toxoplasma gondii by CRISPR/Cas9 system | ||
| Journal of University of Anbar for Pure Science | ||
| Article 15, Volume 14, Issue 2, August 2020, Pages 16-21 PDF (490.98 K) | ||
| Document Type: Review Paper | ||
| DOI: 10.37652/juaps.2022.172354 | ||
| Author | ||
| Musafer H. Al-Ardi* | ||
| The General Directorate for Education / Al-Qadisiyah, Ministry of education – Iraq | ||
| Abstract | ||
| It is well known that finding out the genetic information of any organism helps in understanding how performs its metabolism, and knowing the extent of the effect that gene modification affects the performance of these functions. Many techniques have been used to editing genome of parasites such as Zinc fingers and Transcription activator-like effector nucleases (TALENs), But the development of clustered regularly interspaced short palindromic repeats/ CRISPR-associated (CRISPR Cas9) system created the quantum leap in this area, as this technique relies on identifying the portion to be modified using a guide from Guide RNAs (gRNA) that identifies this part very accurately. Not only that, but the enzyme present with it called CAS9 works as a molecular scissor to cut DNA at this part and allow the required modification.Since 2014, the date on which the first article about use CRISPR/Cas9 in the editing of Toxoplasma gondii genome was published, after that continued, developed new methods and protocols that facilitate the researchers work, we will attempt in this paper to review some of these major achievements. | ||
| Keywords | ||
| Toxoplasma gondii; CRISPR/Cas9; Editing genome; genome manipulation | ||
| References | ||
|
[1] Jinek, M., Chylinski, K. and Fonfara, I. (2012). A programmable dual- RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 337; 816–821.
[2] Ishino, Y., Shinagawa, H., Makino, K., Amemura, M. and Nakata, A. (1987). “Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product”. Journal of Bacteriology. 169; 5429–5433.
[3] Barrangou, R, Christophe, F., Hélène, D., Melissa, R., Patrick, B.; Sylvain, M.; Dennis, A. and Philippe, H.(2007). “CRISPR provides acquired resistance against viruses in prokaryotes”. Science. 315(5819); 1709–1712.
[4] Cong, L., Ran, F. and Cox, D. (2013). “Multiplex genome engineering using CRISPR/Cas systems”. Science. 339; 819–823.
[5] Hsu, P., Lander, E. and F. Zhang. (2012) “Development and applications of CRISPR-Cas9 for genome engineering”. Cell. 157(6); 1262–1278.
[6] Xingliang, M., Qunyu, Z., Qinlong, Z.,Wei, L., Yan, C.; Rong, Q., Bin, W., Zhongfang, Y., Heying, L., Yuru, L., Yongyao, X., Rongxin, S., Shuifu, C., Zhi, W, Yuanling, C.,Jingxin, G., Letian, C., Xiucai, Z., Zhicheng, D. and Yao-Guang, L.(2015). “A robust CRISPR/Cas9 system for convenient high efficiency multiplex genome editing in monocot and dicot plants”, Molecular Plant. 8;1274–1284.
[7] Dominguez, A., Lim, W. and Qi, L. (2016). “Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation”, Nat. Rev. Mol. Cell Biology.17(1); 5–15.
[8] Komor, A., Kim, Y., Packer, M., Zuris, J. and Liu, D. (2016). “Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage”, Nature. 533(7603) ; 420-424.
[9] Hu, J, Miller, S., Geertz, M., Tang, W,Chen, L.; Sun, N.; Zeina, C.; Gao, X.; Rees, H.; Lin, Z. and Liu, D. (2018).“Evolved Cas9 variants with broad PAM compatibility and high DNA specificity”. Nature. 556(7699),57-63.
[10] Yang, N, Wang, R. and Zhao,Y.(2017). “Revolutionize genetic studies and crop improvement with high-throughput and genome-cale CRISPR/Cas9 gene editing technology”. Molecular Plant. 10 (9); 1141–1143.
[11] Gao, Y., Zhang, Y., Zhang, D., Dai, X., Estelle, M. and Zhao,Y. (2017). “Auxin binding protein 1 (ABP1) is not required for either auxin signaling or Arabidopsis development”. Proceedings of the National Academy of Sciences.112 (7) ; 2275–2280.
[12] Tang, X., Lowder, L., Zhang, T.,Malzahn, A.; Zheng, X.; Voytas, D.; Zhong, Z.; Chen, Y.; Ren, Q.; Li, Q.; Kirkland, E.; Zhang, Y. and Qi., Y.(2017). “A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants”. Nature Plants. 3; 17103.
[13] Mali, P., Yang, L, Esvelt, K., Aach, J., Guell, M.; Di Carlo, J.; Norville, E. and Church. M. (2013). “RNA-guided human genome engineering via Cas9”. Science. 339 (6121);823–826.
[14] He, Y., Wang, R., Dai, X. and Zhao, Y. (2017). “On improving CRISPR for editing plant genes: ribozyme-mediated guide RNA production and fluorescence-based technology for isolating transgene-free mutants generated by CRISPR”. Molecular Biology and Translational Science.149; 151–166.
[15] Di Cristina, M. and Carruthers, V.B. (2018). “New and emerging uses of CRISPR/Cas9 to genetically manipulate apicomplexan parasites”. Parasitology. 145;1119–1126.
[16] Darde, M,Bouteille, B. and Pestre-Alexandre, M.(1988). “Isoenzymic characterization of seven strains of Toxoplasma gondii by iso- electrofocusing in polyacrylamide gels”. The American Journal of Tropical Medicine and Hygiene 39(6); 551-558.
[17] Darde, M. Bouteille, B. and Pestre-Alexandre,M. (1992). “Isoenzyme analysis of 35 Toxoplasma gondii isolates and the biological and epidemiological implications”. Journal of Parasitology. 78; 786-794
[18] Howe, D. and Sibley, L. (1995). “Toxoplasma gondii comprises 3 clonal lineages correlation of parasite genotype with human disease”. Journal of Infectious Diseases. vol.172, 1561-1566.
[19] Lehmann, T., Blackston, C.,Parmley, S., Remington, J. and Dubey,J. (2000). “Strain typing of Toxoplasma gondii: comparison of antigen-coding and housekeeping genes”. Journal of Parasitology. 86; 960-971.
[20] Ajzenberg, D.; Banuls, A.; Tibayrenc, M. and Darde, M. (2002). “Microsatellite analysis of Toxoplasma gondii shows considerable polymorphism structured into two main clonal groups”. International Journal for Parasitology. 32; 27-38.
[21] Grigg, M.; Bonnefoy, S., Hehl, A., Suzuki, Y. and Boothroyd, J. (2001). “Success and virulence in Toxoplasma as the result of sexual recombination between two distinct ancestries”. Science. 294;161-165.
[22] Su, C., Asis, K.; Peng, Z., Debashree, M, Daniel, A., Marie-Laure, D., Xing-Quan , Z, James, W. , Benjamin, M., Dubey, and L. Sibley, D.(2012). “Globally diverse Toxoplasma gondii isolates comprise six major clades originating from a small number of distinct ancestral lineages”. Proceedings of the National Academy of Sciencesdoi: 10.1073/pnas.1203190109.
[23] Wilson, R. and Williamson, H. (1997). “Extra chromosomal DNA in the Apicomplexa”. Microbiology and Molecular Biology. 61;1-16.
[24] Lau, Y.,Lee, W., Gudimella, R., Zhang, G., Ching, X. and Razali, R.(2016). “Deciphering the Draft Genome of Toxoplasma gondii RH Strain”, plos one. 11, (6); e0157901.
[25] Sibley,D. and Boothroyd, J.(1992) “Construction of a molecular karyotype for Toxoplasma gondii”, Molecular and Biochemical Parasitology. 51; 291-300.
[26] Khan, A., Taylor, S., Su, C., Mackey, A., Boyle, J., Cole, R. and Glover, D. (2005). “Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii”, Nucleic acids research. 33(9); 2980–2992.
[27] Pfefferkorn, L. and Pfefferkorn, E. (1980). “Toxoplasma gondii: genetic recombination between drug resistant mutants”. Experimental Parasitology. vol.50, 305-316.
[28] Jiménez-Ruiz, E. H. Eleanor, Wong, G., Pall, S. and Markus, M. (2014). “Advantages and Disadvantages of Conditional Systems for Characterization of Essential Genes in Toxoplasma gondii”. Parasitology. 141(11); 1390–1398.
[29] Ajioka, J., Fitzpatrick, J. and Reitter, C. (2001). “Toxoplasma gondii genomics: Shedding light on pathogenesis and chemotherapy”. Expert Reviews in molecular medicine.3(1); 1-19.
[30] Striepen, B., Crawford, M., Shaw, M.,Tilney, L.; Seeber, F. and Roos, D. (2000). “The plastid of Toxoplasma gondii is divided by association with the centrosomes”. The Journal of cell biology.151 (7) ; 1423–1434.
[31] Louis, M. and Kim, K. (2020). “Toxoplasma gondii The Model Apicomplexan: Perspectives and Methods”, Academic Press. 801.
[32] Yung, S. and Lang-Unnasch, N. (2004). “Targeting the toxoplasma gondii apicoplast for chemotherapy”. In: Lindsay, D. and Weiss L. (eds) “Opportunistic Infections: Toxoplasma, Sarcocystis, and MicrosporidiaSpringer, M.A. Boston.
[33] Tjhin, E., Hayward, J., McFadden, G. and van Dooren, G.(2020). “Characterization of the apicoplast-localized enzyme TgUroD in Toxoplasma gondii reveals a key role of the apicoplast in heme biosynthesis”. The Journal of Biological Chemistry. 295(6); 1539‐1550.
[34] Flegontov, P., Michalek, J., Janouskovec, J., Lai, D., Jirku, M.; Hajduskova, E, Tomcala, A., Otto, T., Keeling, P. and Pain, A. (2015). “Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites”. Molecular biology and evolution.32; 1115-1131.
[35] Garbuz, T. and Arrizabalaga, G. (2017). “Lack of mitochondrial MutS homolog 1 in Toxoplasma gondii disrupts maintenance and fidelity of mitochondrial DNA and reveals metabolic plasticity”. PLoS ONE. 12(11); e0188040 [36] Lorenzi, H., Khan, A., Behnke, M., Namasivayam, S., Swapna, L, Hadjithomas, M., Karamycheva, S, Pinney, D., Brunk, B, and Ajioka,J. (2016). “Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii”. Nature Communication. 7;10147.
[37] Syn, G.,Anderson, D., Blackwell, J. and Jamieson, S.(2017). “Toxoplasma gondii Infection Is Associated with Mitochondrial Dysfunction in-Vitro. Front”. Cellular and infection microbiology. 7; 512.
[38] Zı´kova´, A, Hampl, V, Paris, Z., Tyc, J.and Lukesˇ, J. (2016). “Aerobic mitochondria of parasitic protists: Diverse genomes and complex functions”, Molecular and Biochemical Parasitology. 206; 46–57.
[39] Chen, H.; Guo, Y. and Qiu, Y. (2019).” Efficient genome engineering of Toxoplasma gondii using the TALEN technique”, Parasites Vectors. 12, 112.
[40] Zhao, G.; Pu, J. and Tang, B. (2016). “Coding mutations inNUS1contribute to Parkinson’s disease”. Proceedings of the national academy of sciences. 33(6);857‐862.
[41] Sidik, S.; Hackett, C.; Tran, F.; Westwood, N. and Lourido, S. (2014). “Efficient Genome Engineering of Toxoplasma gondii Using CRISPR/ Cas9”. PLoS ONE. 9)6); e 100450.
[42] Kirkman, L.; Lawrence, E. and Deitsch, K. (2014). “Malaria parasites utilize both homologous recombination and alternative end joining pathways to maintain genome integrity”. Nucleic Acids Research. 42; 370 –379
[43] Wang, J.; Huang, S.; Behnke, M.; Chen, K.; Shen, B. and Zhu, X. (2016). “The past, present, and future of genetic manipulation in Toxoplasma gondii”. Trends in Parasitology. 32;542–553.
[44] Shen, B.,Brown, K., Lee, T. and Sibley, L. (2014). “Efficient gene disruption in diverse strains of Toxoplasma gondii using CRISPR/CAS9”. Molecular biology. 5 (3); e01114-14.
[45] Behnke, M., Khan, A., Lauron, E., Jimah, J,Wang, Q. and Tolia, N.(2015). “Rhoptry Proteins ROP5 and ROP18 Are Major Murine Virulence Factors in Genetically Divergent South American Strains of Toxoplasma gondii”. PLoS Genetics. 11(8); e1005434.
[46] Zheng, J.; Jia, H. and Zheng, Y. (2015). “Knockout of leucine aminopeptidase in Toxoplasma gondii using CRISPR/Cas9”. International Journal for Parasitology. 45)2-3); 141‐148.
[47] Foroutan, M. and Ghaffarifar, F. (2018). “Calcium-dependent protein kinases are potential targets for Toxoplasma gondii vaccine”. Clinical and Experimental Vaccine Research. 7 (1) ; 24‐36.
[48] Long, S.,Wang, Q. and Sibley, L. (2016). “Analysis of non-canonical calcium dependent protein kinases in Toxoplasma gondii by targeted gene deletion using CRISPR/Cas9”. Infection and Immunity. 84, 1262–1273.
[49] Sidik, S.; Huet, D.; Ganesan, S.; Huynh, M.; Wang, T.; Nasamu, A.; Thiru, P.; Saeij, J.; Carruthers, V.; Niles, J. and Lourido, S.(2016). “Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes”. Cell. 166 (6);1423-1435.
[50] Sidik, S.; Huet, D. and Lourido,S.(2018).“CRISPR/Cas9-based genome-wide screening of Toxoplasma gondii”. Nature Protocol. 13(1); 307–323.
[51] Young, J.; Dominicus, C. and Wagener, J.(2019). “A CRISPR platform for targeted in vivo screens identifies Toxoplasma gondii virulence factors in mice”. Nature Communiication. 10; 3963.
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