Harnessing the native type I-B CRISPR-Cas for genome editing in a polyploid archaeon

Feiyue Cheng; Luyao Gong; Dahe Zhao; Haibo Yang; Jian Zhou; Ming Li; Hua Xiang

doi:10.1016/j.jgg.2017.09.010

Volume 44 Issue 11

Nov. 2017

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2017 > 44(11): 541-548

PDF( 2015 KB)

Harnessing the native type I-B CRISPR-Cas for genome editing in a polyploid archaeon

doi: 10.1016/j.jgg.2017.09.010

Feiyue Cheng^{a, b},
Luyao Gong^{a, b},
Dahe Zhao^{a, b},
Haibo Yang^{a, b},
Jian Zhou^a,
Ming Li^a,
Hua Xiang^{a, b}

a
State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
b
University of Chinese Academy of Sciences, Beijing 100049, China

More Information

Corresponding author: E-mail address: lim_im@im.ac.cn (Ming Li); E-mail address: xiangh@im.ac.cn (Hua Xiang)
Received Date: 2017-07-23
Accepted Date: 2017-09-25
Rev Recd Date: 2017-09-18

Available Online: 2017-11-02

Publish Date: 2017-11-20

Abstract

Abstract

Research on CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated protein) systems has led to the revolutionary CRISPR/Cas9 genome editing technique. However, for most archaea and half of bacteria, exploitation of their native CRISPR-Cas machineries may be more straightforward and convenient. In this study, we harnessed the native type I-B CRISPR-Cas system for precise genome editing in the polyploid haloarchaeon Haloarcula hispanica. After testing different designs, the editing tool was optimized to be a single plasmid that carries both the self-targeting mini-CRISPR and a 600–800 bp donor. Significantly, chromosomal modifications, such as gene deletion, gene tagging or single nucleotide substitution, were precisely introduced into the vast majority of the transformants. Moreover, we showed that simultaneous editing of two genomic loci could also be readily achieved by one step. In summary, our data demonstrate that the haloarchaeal CRISPR-Cas system can be harnessed for genome editing in this polyploid archaeon, and highlight the convenience and efficiency of the native CRISPR-based genome editing strategy.
- CRISPR-Cas,
- Genome editing,
- Polyploid

FullText(HTML)

References(49)

References

[1]	Barrangou, R., Fremaux, C., Deveau, H. et al. CRISPR provides acquired resistance against viruses in prokaryotes Science, 315 (2007),pp. 1709-1712
[2]	Barrangou, R., Marraffini, L.A. CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity Mol. Cell, 54 (2014),pp. 234-244
[3]	Breuert, S., Allers, T., Spohn, G. et al. Regulated polyploidy in halophilic archaea PLoS One, 1 (2006),p. e92
[4]	Brouns, S.J.J., Jore, M.M., Lundgren, M. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes Science, 321 (2008),pp. 960-964
[5]	Cai, S.F., Cai, L., Liu, H.L. et al. Appl. Environ. Microbiol., 78 (2012),pp. 1946-1952
[6]	Cai, S.F., Cai, L., Zhao, D.H. et al. Appl. Environ. Microbiol., 81 (2015),pp. 373-385
[7]	Carte, J., Pfister, N.T., Compton, M.M. et al. Binding and cleavage of CRISPR RNA by Cas6 RNA, 16 (2010),pp. 2181-2188
[8]	Cline, S.W., Lam, W.L., Charlebois, R.L. et al. Transformation methods for halophilic archaebacteria Can. J. Microbiol., 35 (1989),pp. 148-152
[9]	Cong, L., Ran, F.A., Cox, D. et al. Multiplex genome engineering using CRISPR/Cas systems Science, 339 (2013),pp. 819-823
[10]	Deltcheva, E., Chylinski, K., Sharma, C.M. et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III Nature, 471 (2011),pp. 602-607
[11]	DiCarlo, J.E., Norville, J.E., Mali, P. et al. Nucleic Acids Res., 41 (2013),pp. 4336-4343
[12]	Fischer, S., Maier, L.K., Stoll, B. et al. An archaeal immune system can detect multiple protospacer adjacent motifs (PAMs) to target invader DNA J. Biol. Chem., 287 (2012),pp. 33351-33363
[13]	Garneau, J.E., Dupuis, M.È., Villion, M. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA Nature, 468 (2010),pp. 67-71
[14]	Hale, C.R., Zhao, P., Olson, S. et al. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex Cell, 139 (2009),pp. 945-956
[15]	Haurwitz, R.E., Jinek, M., Wiedenheft, B. et al. Sequence- and structure-specific RNA processing by a CRISPR endonuclease Science, 329 (2010),pp. 1355-1358
[16]	Jiang, W.Y., Bikard, D., Cox, D. et al. RNA-guided editing of bacterial genomes using CRISPR-Cas systems Nat. Biotechnol., 31 (2013),pp. 233-239
[17]	Jinek, M., Chylinski, K., Fonfara, I. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity Science, 337 (2012),pp. 816-821
[18]	Kim, D., Kim, J., Hur, J.K. et al. Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells Nat. Biotechnol., 34 (2016),pp. 863-868
[19]	Kleinstiver, B.P., Tsai, S.Q., Prew, M.S. et al. Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells Nat. Biotechnol., 34 (2016),pp. 869-875
[20]	Li, M., Liu, H.L., Han, J. et al. J. Bacteriol., 195 (2013),pp. 867-875
[21]	Li, M., Gong, L.Y., Zhao, D.H. et al. The spacer size of I-B CRISPR is modulated by the terminal sequence of the protospacer Nucleic Acids Res., 45 (2017),pp. 4642-4654
[22]	Li, M., Wang, R., Xiang, H. Nucleic Acids Res., 42 (2014),pp. 7226-7235
[23]	Li, M., Wang, R., Zhao, D.H. et al. Nucleic Acids Res., 42 (2014),pp. 2483-2492
[24]	Li, Y.J., Pan, S.F., Zhang, Y. et al. Harnessing Type I and Type III CRISPR-Cas systems for genome editing Nucleic Acids Res., 44 (2016),p. e34
[25]	Liu, H.L., Han, J., Liu, X.Q. et al. J. Genet. Genomics, 38 (2011),pp. 261-269
[26]	Maier, L.K., Stachler, A.E., Saunders, S.J. et al. An active immune defense with a minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and without the Cas6 protein J. Biol. Chem., 290 (2015),pp. 4192-4201
[27]	Makarova, K.S., Wolf, Y.I., Alkhnbashi, O.S. et al. An updated evolutionary classification of CRISPR-Cas systems Nat. Rev. Microbiol., 13 (2015),pp. 722-736
[28]	Mali, P., Yang, L.H., Esvelt, K.M. et al. RNA-guided human genome engineering via Cas9 Science, 339 (2013),pp. 823-826
[29]	Marraffini, L.A., Sontheimer, E.J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA Science, 322 (2008),pp. 1843-1845
[30]	Marraffini, L.A., Sontheimer, E.J. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea Nat. Rev. Genet., 11 (2010),pp. 181-190
[31]	Plagens, A., Richter, H., Charpentier, E. et al. DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes FEMS Microbiol. Rev., 39 (2015),pp. 442-463
[32]	Pyne, M.E., Bruder, M.R., Moo-Young, M. et al. Harnessing heterologous and endogenous CRISPR-Cas machineries for efficient markerless genome editing in Clostridium Sci. Rep., 6 (2016),p. 25666
[33]	Sambrook, J., Fritsch, E.F., Maniatis, T.
[34]	Semenova, E., Jore, M.M., Datsenko, K.A. et al. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence Proc. Natl. Acad. Sci. U. S. A., 108 (2011),pp. 10098-10103
[35]	Shan, Q.W., Wang, Y.P., Li, J. et al. Targeted genome modification of crop plants using a CRISPR-Cas system Nat. Biotechnol., 31 (2013),pp. 686-688
[36]	Shmakov, S., Abudayyeh, O.O., Makarova, K.S. et al. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems Mol. Cell, 60 (2015),pp. 385-397
[37]	Shmakov, S., Smargon, A., Scott, D. et al. Diversity and evolution of class 2 CRISPR-Cas systems Nat. Rev. Microbiol., 15 (2017),pp. 169-182
[38]	Sorek, R., Kunin, V., Hugenholtz, P. CRISPR - a widespread system that provides acquired resistance against phages in bacteria and archaea Nat. Rev. Microbiol., 6 (2008),pp. 181-186
[39]	Stachler, A.E., Turgeman-Grott, I., Shtifman-Segal, E. et al. High tolerance to self-targeting of the genome by the endogenous CRISPR-Cas system in an archaeon Nucleic Acids Res., 45 (2017),pp. 5208-5216
[40]	Sternberg, S.H., Richter, H., Charpentier, E. et al. Adaptation in CRISPR-Cas systems Mol. Cell, 61 (2016),pp. 797-808
[41]	van der Oost, J., Jore, M.M., Westra, E.R. et al. CRISPR-based adaptive and heritable immunity in prokaryotes Trends biochem. Sci., 34 (2009),pp. 401-407
[42]	Wang, H.Y., Yang, H., Shivalila, C.S. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering Cell, 153 (2013),pp. 910-918
[43]	Wang, R., Li, M., Gong, L.Y. et al. Nucleic Acids Res., 44 (2016),pp. 4266-4277
[44]	Westra, E.R., Buckling, A., Fineran, P.C. CRISPR-Cas systems: beyond adaptive immunity Nat. Rev. Microbiol., 12 (2014),pp. 317-326
[45]	Westra, E.R., Semenova, E., Datsenko, K.A. et al. Type I-E CRISPR-Cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition PLoS Genet., 9 (2013),p. e1003742
[46]	Wiedenheft, B., van Duijn, E., Bultema, J. et al. RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions Proc. Natl. Acad. Sci. U. S. A., 108 (2011),pp. 10092-10097
[47]	Wu, Z.F., Liu, J.F., Yang, H.B. et al. Nucleic Acids Res., 42 (2014),pp. 2282-2294
[48]	Zerulla, K., Chimileski, S., Näther, D. et al. DNA as a phosphate storage polymer and the alternative advantages of polyploidy for growth or survival PLoS One, 9 (2014),p. e94819
[49]	Zetsche, B., Gootenberg, J.S., Abudayyeh, O.O. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system Cell, 163 (2015),pp. 759-771