Insight into the Molecular Mechanism of the Transposon-encoded Type I-F CRISPR-Cas System

Overview

Journal J Genet Eng Biotechnol

Specialty Biotechnology

Date 2023 May 16

PMID 37191877

Authors

Amnah Alalmaie

Saousen Diaf

Raed Khashan

Affiliations

Soon will be listed here.

Abstract

CRISPR-Cas9 is a popular gene-editing tool that allows researchers to introduce double-strand breaks to edit parts of the genome. CRISPR-Cas9 system is used more than other gene-editing tools because it is simple and easy to customize. However, Cas9 may produce unintended double-strand breaks in DNA, leading to off-target effects. There have been many improvements in the CRISPR-Cas system to control the off-target effect and improve the efficiency. The presence of a nuclease-deficient CRISPR-Cas system in several bacterial Tn7-like transposons inspires researchers to repurpose to direct the insertion of Tn7-like transposons instead of cleaving the target DNA, which will eventually limit the risk of off-target effects. Two transposon-encoded CRISPR-Cas systems have been experimentally confirmed. The first system, found in Tn7 like-transposon (Tn6677), is associated with the variant type I-F CRISPR-Cas system. The second one, found in Tn7 like-transposon (Tn5053), is related to the variant type V-K CRISPR-Cas system. This review describes the molecular and structural mechanisms of DNA targeting by the transposon-encoded type I-F CRISPR-Cas system, from assembly around the CRISPR-RNA (crRNA) to the initiation of transposition.

References

Haurwitz R, Jinek M, Wiedenheft B, Zhou K, Doudna J . Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science. 2010; 329(5997):1355-8. PMC: 3133607. DOI: 10.1126/science.1192272. View

Peters J, Makarova K, Shmakov S, Koonin E . Recruitment of CRISPR-Cas systems by Tn7-like transposons. Proc Natl Acad Sci U S A. 2017; 114(35):E7358-E7366. PMC: 5584455. DOI: 10.1073/pnas.1709035114. View

Zheng Y, Li J, Wang B, Han J, Hao Y, Wang S . Endogenous Type I CRISPR-Cas: From Foreign DNA Defense to Prokaryotic Engineering. Front Bioeng Biotechnol. 2020; 8:62. PMC: 7064716. DOI: 10.3389/fbioe.2020.00062. View

Parks A, Peters J . Tn7 elements: engendering diversity from chromosomes to episomes. Plasmid. 2008; 61(1):1-14. PMC: 2614081. DOI: 10.1016/j.plasmid.2008.09.008. View

Jore M, Lundgren M, van Duijn E, Bultema J, Westra E, Waghmare S . Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol. 2011; 18(5):529-36. DOI: 10.1038/nsmb.2019. View

Hare S, Gupta S, Valkov E, Engelman A, Cherepanov P . Retroviral intasome assembly and inhibition of DNA strand transfer. Nature. 2010; 464(7286):232-6. PMC: 2837123. DOI: 10.1038/nature08784. View

Jasin M, Haber J . The democratization of gene editing: Insights from site-specific cleavage and double-strand break repair. DNA Repair (Amst). 2016; 44:6-16. PMC: 5529214. DOI: 10.1016/j.dnarep.2016.05.001. View

Dyda F, Hickman A, Jenkins T, Engelman A, Craigie R, Davies D . Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science. 1994; 266(5193):1981-6. DOI: 10.1126/science.7801124. View

Harrison S, Aggarwal A . DNA recognition by proteins with the helix-turn-helix motif. Annu Rev Biochem. 1990; 59:933-69. DOI: 10.1146/annurev.bi.59.070190.004441. View

10.

May E, Craig N . Switching from cut-and-paste to replicative Tn7 transposition. Science. 1996; 272(5260):401-4. DOI: 10.1126/science.272.5260.401. View

11.

Lichtenstein C, Brenner S . Unique insertion site of Tn7 in the E. coli chromosome. Nature. 1982; 297(5867):601-3. DOI: 10.1038/297601a0. View

12.

Jansen R, van Embden J, Gaastra W, Schouls L . Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol. 2002; 43(6):1565-75. DOI: 10.1046/j.1365-2958.2002.02839.x. View

13.

Hidalgo-Cantabrana C, Goh Y, Barrangou R . Characterization and Repurposing of Type I and Type II CRISPR-Cas Systems in Bacteria. J Mol Biol. 2018; 431(1):21-33. DOI: 10.1016/j.jmb.2018.09.013. View

14.

Mohanraju P, Makarova K, Zetsche B, Zhang F, Koonin E, van der Oost J . Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science. 2016; 353(6299):aad5147. DOI: 10.1126/science.aad5147. View

15.

Vo P, Ronda C, Klompe S, Chen E, Acree C, Wang H . CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering. Nat Biotechnol. 2020; 39(4):480-489. PMC: 10583764. DOI: 10.1038/s41587-020-00745-y. View

16.

Sternberg S, Haurwitz R, Doudna J . Mechanism of substrate selection by a highly specific CRISPR endoribonuclease. RNA. 2012; 18(4):661-72. PMC: 3312554. DOI: 10.1261/rna.030882.111. View

17.

Torres-Ruiz R, Rodriguez-Perales S . CRISPR-Cas9: A Revolutionary Tool for Cancer Modelling. Int J Mol Sci. 2015; 16(9):22151-68. PMC: 4613301. DOI: 10.3390/ijms160922151. View

18.

Park J, Tsai A, Mehrotra E, Petassi M, Hsieh S, Ke A . Structural basis for target site selection in RNA-guided DNA transposition systems. Science. 2021; 373(6556):768-774. PMC: 9080059. DOI: 10.1126/science.abi8976. View

19.

Makarova K, Wolf Y, Koonin E . Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?. CRISPR J. 2019; 1(5):325-336. PMC: 6636873. DOI: 10.1089/crispr.2018.0033. View

20.

Abudayyeh O, Gootenberg J, Konermann S, Joung J, Slaymaker I, Cox D . C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016; 353(6299):aaf5573. PMC: 5127784. DOI: 10.1126/science.aaf5573. View