Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System

Molecular Cell

Volumn 69, Issue 1, 2018, Pages 146-157.e3

  Marshall, Ryan ^a   Maxwell, Colin S ^b   Collins, Scott P ^b   Jacobsen, Thomas ^b   Luo, Michelle L ^b   Begemann, Matthew B ^c   Gray, Benjamin N ^c   January, Emma ^c   Singer, Anna ^c   He, Yonghua ^c   Beisel, Chase L ^b   Noireaux, Vincent ^a  

^a University of Minnesota   (United States)

^b North Carolina State University   (United States)

^c Benson Hill Inc   (United States)

Author keywords

Cas9; Cascade; Cpf1; PAM; prototyping; synthetic biology; TXTL

Indexed keywords

BACTERIAL PROTEIN; BACTERIAL RNA; CPF1 PROTEIN; CRISPR ASSOCIATED PROTEIN; GREEN FLUORESCENT PROTEIN; GUIDE RNA; HLA ANTIGEN; LINEAR DNA; NUCLEASE; PLASMID DNA; RIBONUCLEOPROTEIN; RNA POLYMERASE; UNCLASSIFIED DRUG; BACTERIAL DNA; ENDONUCLEASE;

5' UNTRANSLATED REGION; ARTICLE; ASSAY; BINDING SITE; CELL FREE SYSTEM; CELL FREE TRANSCRIPTION TRANSLATION SYSTEM; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONTROLLED STUDY; CRISPR CAS SYSTEM; DNA BINDING; DNA CLEAVAGE; ESCHERICHIA COLI; FLUORESCENCE; GENE REPRESSION; NONHUMAN; PAM ASSAY; PLASMID; POLYMERASE CHAIN REACTION; PROMOTER REGION; PROTEIN PURIFICATION; QUANTITATIVE ANALYSIS; SANGER SEQUENCING; STAPHYLOCOCCUS AUREUS; TRANSIENT EXPRESSION; GENETIC ENGINEERING; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; ORYZA; PROCEDURES; PROTEIN SYNTHESIS;

CELL-FREE SYSTEM; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-CAS SYSTEMS; DNA, BACTERIAL; ENDONUCLEASES; ESCHERICHIA COLI; GENETIC ENGINEERING; ORYZA; PROTEIN BIOSYNTHESIS; RNA, GUIDE; TRANSCRIPTION, GENETIC;

EID: 85040126791     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2017.12.007     Document Type: Article

References (63)

1. Abudayyeh, O.O., Gootenberg, J.S., Konermann, S., Joung, J., Slaymaker, I.M., Cox, D.B., Shmakov, S., Makarova, K.S., Semenova, E., Minakhin, L., et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science, 353, 2016, aaf5573.
2. Barrangou, R., Doudna, J.A., Applications of CRISPR technologies in research and beyond. Nat. Biotechnol. 34 (2016), 933–941.
3. Begemann, M.B., Gray, B.N., January, E., Gordon, G.C., He, Y., Liu, H., Wu, X., Brutnell, T.P., Mockler, T.C., Oufattole, M., Precise insertion and guided editing of higher plant genomes using Cpf1 CRISPR nucleases. Sci. Rep., 7, 2017, 11606.
4. Bikard, D., Jiang, W., Samai, P., Hochschild, A., Zhang, F., Marraffini, L.A., Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 41 (2013), 7429–7437.
5. Bondy-Denomy, J., Garcia, B., Strum, S., Du, M., Rollins, M.F., Hidalgo-Reyes, Y., Wiedenheft, B., Maxwell, K.L., Davidson, A.R., Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins. Nature 526 (2015), 136–139.
6. Boyle, E.A., Andreasson, J.O.L., Chircus, L.M., Sternberg, S.H., Wu, M.J., Guegler, C.K., Doudna, J.A., Greenleaf, W.J., High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding. Proc. Natl. Acad. Sci. USA 114 (2017), 5461–5466.
7. Carlson, E.D., Gan, R., Hodgman, C.E., Jewett, M.C., Cell-free protein synthesis: applications come of age. Biotechnol. Adv. 30 (2012), 1185–1194.
8. Caschera, F., Noireaux, V., Synthesis of 2.3 mg/ml of protein with an all Escherichia coli cell-free transcription-translation system. Biochimie 99 (2014), 162–168.
9. Chappell, J., Jensen, K., Freemont, P.S., Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology. Nucleic Acids Res. 41 (2013), 3471–3481.
10. Chen, B., Guan, J., Huang, B., Imaging specific genomic DNA in living cells. Annu. Rev. Biophys. 45 (2016), 1–23.
11. Dominguez, A.A., Lim, W.A., Qi, L.S., Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat. Rev. Mol. Cell Biol. 17 (2016), 5–15.
12. Dudley, Q.M., Karim, A.S., Jewett, M.C., Cell-free metabolic engineering: biomanufacturing beyond the cell. Biotechnol. J. 10 (2015), 69–82.
13. Fineran, P.C., Gerritzen, M.J., Suárez-Diez, M., Künne, T., Boekhorst, J., van Hijum, S.A., Staals, R.H., Brouns, S.J., Degenerate target sites mediate rapid primed CRISPR adaptation. Proc. Natl. Acad. Sci. USA 111 (2014), E1629–E1638.
14. Fonfara, I., Le Rhun, A., Chylinski, K., Makarova, K.S., Lécrivain, A.L., Bzdrenga, J., Koonin, E.V., Charpentier, E., Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res. 42 (2014), 2577–2590.
15. Fonfara, I., Richter, H., Bratovič M., Le Rhun, A., Charpentier, E., The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature 532 (2016), 517–521.
16. Garamella, J., Marshall, R., Rustad, M., Noireaux, V., The all E. coli TX-TL toolbox 2.0: a platform for cell-free synthetic biology. ACS Synth. Biol. 5 (2016), 344–355.
17. Gilbert, L.A., Horlbeck, M.A., Adamson, B., Villalta, J.E., Chen, Y., Whitehead, E.H., Guimaraes, C., Panning, B., Ploegh, H.L., Bassik, M.C., et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159 (2014), 647–661.
18. 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., et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356 (2017), 438–442.
19. Harrington, L.B., Doxzen, K.W., Ma, E., Liu, J.J., Knott, G.J., Edraki, A., Garcia, B., Amrani, N., Chen, J.S., Cofsky, J.C., et al. A broad-spectrum inhibitor of CRISPR-Cas9. Cell 170 (2017), 1224–1233.e15.
20. Hockenberry, A.J., Jewett, M.C., Synthetic in vitro circuits. Curr. Opin. Chem. Biol. 16 (2012), 253–259.
21. Hynes, A.P., Rousseau, G.M., Lemay, M.L., Horvath, P., Romero, D.A., Fremaux, C., Moineau, S., An anti-CRISPR from a virulent streptococcal phage inhibits Streptococcus pyogenes Cas9. Nat. Microbiol. 2 (2017), 1374–1380.
22. Jewett, M.C., Calhoun, K.A., Voloshin, A., Wuu, J.J., Swartz, J.R., An integrated cell-free metabolic platform for protein production and synthetic biology. Mol. Syst. Biol., 4, 2008, 220.
23. Jiang, W., Bikard, D., Cox, D., Zhang, F., Marraffini, L.A., RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 31 (2013), 233–239.
24. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A., Charpentier, E., A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337 (2012), 816–821.
25. Kanter, G., Yang, J., Voloshin, A., Levy, S., Swartz, J.R., Levy, R., Cell-free production of scFv fusion proteins: an efficient approach for personalized lymphoma vaccines. Blood 109 (2007), 3393–3399.
26. Karvelis, T., Gasiunas, G., Young, J., Bigelyte, G., Silanskas, A., Cigan, M., Siksnys, V., Rapid characterization of CRISPR-Cas9 protospacer adjacent motif sequence elements. Genome Biol., 16, 2015, 253.
27. Karvelis, T., Gasiunas, G., Siksnys, V., Methods for decoding Cas9 protospacer adjacent motif (PAM) sequences: a brief overview. Methods 121-122 (2017), 3–8.
28. Karzbrun, E., Tayar, A.M., Noireaux, V., Bar-Ziv, R.H., Synthetic biology. Programmable on-chip DNA compartments as artificial cells. Science 345 (2014), 829–832.
29. Kim, E., Koo, T., Park, S.W., Kim, D., Kim, K., Cho, H.Y., Song, D.W., Lee, K.J., Jung, M.H., Kim, S., et al. In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni. Nat. Commun., 8, 2017, 14500.
30. Kleinstiver, B.P., Prew, M.S., Tsai, S.Q., Topkar, V.V., Nguyen, N.T., Zheng, Z., Gonzales, A.P., Li, Z., Peterson, R.T., Yeh, J.R., et al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523 (2015), 481–485.
31. Kleinstiver, B.P., Tsai, S.Q., Prew, M.S., Nguyen, N.T., Welch, M.M., Lopez, J.M., McCaw, Z.R., Aryee, M.J., Joung, J.K., Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells. Nat. Biotechnol. 34 (2016), 869–874.
32. Komor, A.C., Badran, A.H., Liu, D.R., CRISPR-based technologies for the manipulation of eukaryotic genomes. Cell 168 (2017), 20–36.
33. Koonin, E.V., Makarova, K.S., Zhang, F., Diversity, classification and evolution of CRISPR-Cas systems. Curr. Opin. Microbiol. 37 (2017), 67–78.
34. Leenay, R.T., Beisel, C.L., Deciphering, communicating, and engineering the CRISPR PAM. J. Mol. Biol. 429 (2017), 177–191.
35. Leenay, R.T., Maksimchuk, K.R., Slotkowski, R.A., Agrawal, R.N., Gomaa, A.A., Briner, A.E., Barrangou, R., Beisel, C.L., Identifying and visualizing functional PAM diversity across CRISPR-Cas systems. Mol. Cell 62 (2016), 137–147.
36. Levy, A., Goren, M.G., Yosef, I., Auster, O., Manor, M., Amitai, G., Edgar, R., Qimron, U., Sorek, R., CRISPR adaptation biases explain preference for acquisition of foreign DNA. Nature 520 (2015), 505–510.
37. Luo, M.L., Mullis, A.S., Leenay, R.T., Beisel, C.L., Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression. Nucleic Acids Res. 43 (2015), 674–681.
38. Makarova, K.S., Wolf, Y.I., Alkhnbashi, O.S., Costa, F., Shah, S.A., Saunders, S.J., Barrangou, R., Brouns, S.J., Charpentier, E., Haft, D.H., et al. An updated evolutionary classification of CRISPR-Cas systems. Nat. Rev. Microbiol. 13 (2015), 722–736.
39. Marshall, R., Maxwell, C.S., Collins, S.P., Beisel, C.L., Noireaux, V., Short DNA containing χ sites enhances DNA stability and gene expression in E. coli cell-free transcription-translation systems. Biotechnol. Bioeng. 114 (2017), 2137–2141.
40. Mekler, V., Minakhin, L., Semenova, E., Kuznedelov, K., Severinov, K., Kinetics of the CRISPR-Cas9 effector complex assembly and the role of 3′-terminal segment of guide RNA. Nucleic Acids Res. 44 (2016), 2837–2845.
41. Mohanraju, P., Makarova, K.S., Zetsche, B., Zhang, F., Koonin, E.V., van der Oost, J., Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science, 353, 2016, aad5147.
42. Mulepati, S., Bailey, S., In vitro reconstitution of an Escherichia coli RNA-guided immune system reveals unidirectional, ATP-dependent degradation of DNA target. J. Biol. Chem. 288 (2013), 22184–22192.
43. Nelles, D.A., Fang, M.Y., O'Connell, M.R., Xu, J.L., Markmiller, S.J., Doudna, J.A., Yeo, G.W., Programmable RNA tracking in live cells with CRISPR/Cas9. Cell 165 (2016), 488–496.
44. Pardee, K., Slomovic, S., Nguyen, P.Q., Lee, J.W., Donghia, N., Burrill, D., Ferrante, T., McSorley, F.R., Furuta, Y., Vernet, A., et al. Portable, on-demand biomolecular manufacturing. Cell 167 (2016), 248–259.e12.
45. Pattanayak, V., Lin, S., Guilinger, J.P., Ma, E., Doudna, J.A., Liu, D.R., High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat. Biotechnol. 31 (2013), 839–843.
46. Pawluk, A., Amrani, N., Zhang, Y., Garcia, B., Hidalgo-Reyes, Y., Lee, J., Edraki, A., Shah, M., Sontheimer, E.J., Maxwell, K.L., Davidson, A.R., Naturally occurring off-switches for CRISPR-Cas9. Cell 167 (2016), 1829–1838.e9.
47. Pawluk, A., Staals, R.H., Taylor, C., Watson, B.N., Saha, S., Fineran, P.C., Maxwell, K.L., Davidson, A.R., Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. Nat. Microbiol., 1, 2016, 16085.
48. Qi, L.S., Larson, M.H., Gilbert, L.A., Doudna, J.A., Weissman, J.S., Arkin, A.P., Lim, W.A., Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152 (2013), 1173–1183.
49. Rath, D., Amlinger, L., Hoekzema, M., Devulapally, P.R., Lundgren, M., Efficient programmable gene silencing by Cascade. Nucleic Acids Res. 43 (2015), 237–246.
50. Rauch, B.J., Silvis, M.R., Hultquist, J.F., Waters, C.S., McGregor, M.J., Krogan, N.J., Bondy-Denomy, J., Inhibition of CRISPR-Cas9 with bacteriophage proteins. Cell 168 (2017), 150–158.e10.
51. Schmidt, R., Bukau, B., Mogk, A., Principles of general and regulatory proteolysis by AAA+ proteases in Escherichia coli. Res. Microbiol. 160 (2009), 629–636.
52. Shin, J., Noireaux, V., Efficient cell-free expression with the endogenous E. Coli RNA polymerase and sigma factor 70. J. Biol. Eng., 4, 2010, 8.
53. Shin, J., Noireaux, V., An E. coli cell-free expression toolbox: application to synthetic gene circuits and artificial cells. ACS Synth. Biol. 1 (2012), 29–41.
54. Shmakov, S., Abudayyeh, O.O., Makarova, K.S., Wolf, Y.I., Gootenberg, J.S., Semenova, E., Minakhin, L., Joung, J., Konermann, S., Severinov, K., et al. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol. Cell 60 (2015), 385–397.
55. Sun, Z.Z., Yeung, E., Hayes, C.A., Noireaux, V., Murray, R.M., Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system. ACS Synth. Biol. 3 (2014), 387–397.
56. Swartz, J., Developing cell-free biology for industrial applications. J. Ind. Microbiol. Biotechnol. 33 (2006), 476–485.
57. Takahashi, M.K., Chappell, J., Hayes, C.A., Sun, Z.Z., Kim, J., Singhal, V., Spring, K.J., Al-Khabouri, S., Fall, C.P., Noireaux, V., et al. Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems. ACS Synth. Biol. 4 (2015), 503–515.
58. Takahashi, M.K., Hayes, C.A., Chappell, J., Sun, Z.Z., Murray, R.M., Noireaux, V., Lucks, J.B., Characterizing and prototyping genetic networks with cell-free transcription-translation reactions. Methods 86 (2015), 60–72.
59. Tayar, A.M., Karzbrun, E., Noireaux, V., Bar-Ziv, R.H., Propagating gene expression fronts in a one-dimensional coupled system of artificial cells. Nat. Phys. 11 (2015), 1037–1041.
60. Tsai, S.Q., Nguyen, N.T., Malagon-Lopez, J., Topkar, V.V., Aryee, M.J., Joung, J.K., CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets. Nat. Methods 14 (2017), 607–614.
61. Westra, E.R., van Erp, P.B., Künne, T., Wong, S.P., Staals, R.H., Seegers, C.L., Bollen, S., Jore, M.M., Semenova, E., Severinov, K., et al. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol. Cell 46 (2012), 595–605.
62. Zetsche, B., Gootenberg, J.S., Abudayyeh, O.O., Slaymaker, I.M., Makarova, K.S., Essletzbichler, P., Volz, S.E., Joung, J., van der Oost, J., Regev, A., et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163 (2015), 759–771.
63. Zetsche, B., Heidenreich, M., Mohanraju, P., Fedorova, I., Kneppers, J., DeGennaro, E.M., Winblad, N., Choudhury, S.R., Abudayyeh, O.O., Gootenberg, J.S., et al. Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. Nat. Biotechnol. 35 (2017), 31–34.