Temperature Dependence of Collateral Activity of Thermostable Recombinant CRISPR Nucleases Cas12b Obtained by One-Step Purification with Metal-Chelate Chromatography after Heterologous Expression
Main Article Content
Abstract
Thermostable CRISPR/Cas nucleases are considered as promising enzymes for development of next-generation DNA diagnostics by coupling loop-mediated isothermal amplification of nucleic acids (LAMP) with selective CRISPR/Cas detection of specific amplicons. In this paper, we present the results of testing the collateral activity of CRISPR nuclease AapCas12b and three variants of CRISPR nuclease BrCas12b (wild type and two mutants) obtained using simplified purification in the typical temperature range of LAMP - from 56°C to 72°C. It was shown that the use of one-step metal-chelate chromatography by excluding a stage of enzymatic removal of N-terminal sequences translated together with the target protein allows for obtaining recombinant CRISPR nucleases BrCas12b with a sufficiently high level of collateral activity. Temperature dependences of collateral activity differed among the studied BrCas12b variants. The obtained results can be useful in selecting thermostable CRISPR nucleases Cas12b for development of test systems based on a combination of LAMP and CRISPR/Cas detection.
Article Details
References
- van der Oost, J., Westra, E.R., Jackson, R.N., Wiedenheft, B. (2014) Unravelling the structural and mechanistic basis of CRISPR-Cas systems. Nature Review Microbiology, 12(7), 479-492. DOI
- Kaminski, M.M., Abudayyeh, O.O., Gootenberg, J.S., Zhang, F., Collins, J.J. (2021) CRISPR-based diagnostics. Nature Biomedical Engineering, 5(7), 643-656. DOI
- Fapohunda, F.O., Qiao, S., Pan, Y., Wang, H., Liu, Y., Chen, Q., Lu, P.(2022) CRISPR Cas system: A strategic approach in detection of nucleic acids. Microbiological Research, 259, 127000. DOI
- Gootenberg, J.S., Abudayyeh, O.O., Lee, J.W., Essletzbichler, P., Dy, A.J., Joung, J., Verdine, V., Donghia, N., Daringer, N.M., Freije, C.A., Myhrvold, C., Bhattacharyya, R.P., Livny, J., Regev, A., Koonin, E.V., Hung, D.T., Sabeti, P.C.,Collins, J.J., Zhang, F. (2017) Nucleic acid detection with CRISPR-Cas13a/C2c2. Science, 356(6336), 438-442. DOI
- Chen, J.S., Ma, E., Harrington, L.B., Da Costa, M., Tian, X., Palefsky, J.M., Doudna, J.A. (2018) CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science, 360(6387), 436-439. DOI
- Piepenburg, O., Williams, C.H., Stemple, D.L., Armes, N.A. (2006) DNA detection using recombination proteins. PLoS Biology, 4(7), e204. DOI
- Khmeleva, S. A., Ptitsyn, K. G., Kurbatov, L. K., Timoshenko, O. S.,Suprun, E. V., Radko, S. P., Lisitsa, A. V. (2024) Biosensing platforms forDNA diagnostics based on CRISPR/Cas nucleases: towards the detection of nucleic acids at the level of single molecules in non-laboratory settings. Biomeditsinskaya Khimiya, 70(5), 287-303. DOI
- Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., Watanab,e K., Amino, N., Hase, T. (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Research, 28(12), e63. DOI
- Joung, J., Ladha, A., Saito, M., Kim, N.G., Woolley, A.E., Segel, M., Barretto, R.P.J., Ranu, A., Macrae, R.K., Faure, G., Ioannidi, E.I., Krajeski, R.N., Bruneau, R., Huang, M.W., Yu, X.G., Li, J.Z., Walker, B.D., Hung, D.T.,Greninger, A.L., Jerome, K.R., Gootenberg, J.S., Abudayyeh, O.O., Zhang, F.(2020) Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing. The New England Journal of Medicine, 383(15), 1492-1494. DOI
- Teng, F., Cui, T., Feng, G., Guo, L., Xu, K., Gao, Q., Li, T., Li, J., Zhou,Q., Li, W. (2018) Repurposing CRISPR-Cas12b for mammalian genome engineering. Cell Discovery, 27(4), 63. DOI
- Tian, Y., Liu, R.R., Xian, W.D., Xiong, M., Xiao, M., Li, W.J. (2020) A novel thermal Cas12b from a hot spring bacterium with high target mismatch tolerance and robust DNA cleavage efficiency. International Journal of Biological Macromolecules, 147, 376-384. DOI
- Nan, X., Hardinge, P., Hoehn, S., Dighe, S.N., Ukeri, J., Pease, D.F., Griffin, J., Warrington, J.I., Saud, Z., Hottinger, E., Webster, G., Jones, D., Kille, P., Weightman, A., Stanton, R., Castell, O.K., Murray, J.A.H., Jurkowski, T.P.(2023) VarLOCK: sequencing-independent, rapid detection of SARS-CoV-2 variants of concern for point-of-care testing, qPCR pipelines and national wastewater surveillance. Scientific Reports, 13(1), 20832. DOI
- Nguyen, L.T., Macaluso, N.C., Pizzano, B.L.M., Cash, M.N., Spacek, J., Karasek, J., Miller, M.R., Lednicky, J.A., Dinglasan, R.R., Salemi, M., Jain,P.K. (2022) A thermostable Cas12b from Brevibacillus leverages one-potdiscrimination of SARS-CoV-2 variants of concern. EBio Medicine, 77, 103926. DOI
- Nguyen, L.T., Rananaware, S.R., Yang, L.G., Macaluso, N.C., Ocana-Ortiz, J.E., Meister, K.S., Pizzano, B.L.M., Sandoval, L.S.W., Hautamaki, R.C., Fang,Z.R., Joseph, S.M., Shoemaker, G.M., Carman, D.R., Chang, L., Rakestraw,N.R., Zachary, J.F., Guerra, S., Perez, A., Jain, P.K. (2023) Engineering high lythermostable Cas12b via de novo structural analyses for one-pot detection of nucleic acids. Cell Reports Medicine, 4(5), 101037. DOI
- Kurbatov, L.K., Radko, S.P., Kravchenko, S.V., Kiseleva, O. I., Durmanov, N.D., Lisitsa, A. V. (2020) Single Stage Purification of CRISPR/Cas13a Nucleasevia Metal-Chelating Chromatography Following Heterologous Expression with the Preservation of Collateral Ribonuclease Activity. Applied Biochemistry andMicrobiology, 56(6), 671–677. DOI
- Kurbatov, L. K., Radko, S. P., Khmeleva, S. A., Ptitsyn, K. G., Timoshenko,O. S., Lisitsa, A. V. (2024) Application of DETECTR for Selective Detection of Bacterial Phytopathogen Dickeya solani Using Recombinant CRISPR-Nuclease Cas12a Obtained by Single-Stage Chromatographic Purification. Applied Biochemistry and Microbiology, 60(1), 17-25. DOI
- Habimana, J.D., Mukama, O., Chen, G., Chen, M., Amissah, O.B., Wang,L., Liu, Y., Sun, Y., Li, A.L., Deng, S., Huang, J., Yan, X.X., Rutaganda, T.,Mutangana, D., Wu, L.P., Huang, R., Li, Z. (2023) Harnessing enhanced CRISPR/Cas12a trans-cleavage activity with extended reporters and reductants for early diagnosis of Helicobacter pylori, the causative agent of peptic ulcersand stomach cancer. Biosensors and Bioelectronics, 222, 114939. DOI
- Ptitsyn, K. G, Khmeleva, S. A, Kurbatov, L. K, Timoshenko, O. S, Suprun, E. A, Radko, S. P, Lisitsa, A. V. (2024). Lamp Primer Designing Software: The Overview. Biomedical Chemistry: Research and Methods, 7(4), e00226. DOI
- Kurbatov, L. K., Radko, S. P, Khmeleva, S. A., Timoshenko, O. S. Lisitsa,A. V. (2022) Standardization of Recombinant CRISPR/Cas13a-nuclease Preparations by Using RNase A of Known Activity. Biomedical Chemistry:Research and Methods, 5(4), e00177. DOI
- Hand, T.H., Das, A., Li, H. (2019). Directed evolution studies of athermophilic Type II-C Cas9. Methods in Enzymology, 616, 265–288. DOI
- Kumar, S., Tsai, C.J., Nussinov, R. (2000) Factors enhancing protein thermostability. Protein Engineering, 13(3), 179–191. DOI
