Targeted DNA degradation using a CRISPR device stably carried in the host genome

Nature Communications

Volumn 6, Issue , 2015, Pages

  Caliando, Brian J ^a   Voigt, Christopher A ^a  

^a Massachusetts Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PLASMID DNA; BACTERIAL DNA; PHOTOPROTEIN; RED FLUORESCENT PROTEIN;

CYTOLOGY; DNA; GENETIC ENGINEERING; GENOME;

APOPTOSIS; ARTICLE; BIOCHEMISTRY; CELL DENSITY; CELL GROWTH; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONTROLLED STUDY; DNA DEGRADATION; DNA REPLICATION ORIGIN; DNA SEQUENCE; ENVIRONMENT; GENE TARGETING; GENETIC STABILITY; GENOME; LOSS OF FUNCTION MUTATION; NONHUMAN; PROTEIN EXPRESSION; CELL DEATH; CELL PROLIFERATION; CHEMISTRY; CRISPR CAS SYSTEM; ESCHERICHIA COLI; GENETIC ENGINEERING; GENETIC PROCEDURES; GENETIC TRANSCRIPTION; KINETICS; METABOLISM; PLASMID; PROMOTER REGION; TIME FACTOR;

CELL DEATH; CELL PROLIFERATION; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-CAS SYSTEMS; DNA, BACTERIAL; ESCHERICHIA COLI; GENETIC ENGINEERING; GENETIC TECHNIQUES; GENOME; KINETICS; LUMINESCENT PROTEINS; PLASMIDS; PROMOTER REGIONS, GENETIC; TIME FACTORS; TRANSCRIPTION, GENETIC;

EID: 84930197469     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms7989     Document Type: Article

References (69)

1. Arkin, A. Setting the standard in synthetic biology. Nat. Biotechnol. 26, 771-774 (2008).
2. Molin, S. et al. Suicidal genetic elements and their use in biological containment of bacteria. Annu. Rev. Microbiol. 47, 139-166 (1993).
3. Isaacs, F. J. et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nat. Biotechnol. 22, 841-847 (2004).
4. Callura, J. M., Dwyer, D. J., Isaacs, F. J., Cantor, C. R. & Collins, J. J. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proc. Natl Acad. Sci. USA 107, 15898-15903 (2010).
5. Curtiss, R. et al. Salmonella enterica serovar typhimurium strains with regulated delayed attenuation in vivo. Infect. Immun. 77, 1071-1082 (2009).
6. Kong, W. et al. Regulated programmed lysis of recombinant Salmonella in host tissues to release protective antigens and confer biological containment. Proc. Natl Acad. Sci. USA 105, 9361-9366 (2008).
7. You, L., Cox, R. S., Weiss, R. & Arnold, F. H. Programmed population control by cell-cell communication and regulated killing. Nature 428, 868-871 (2004).
8. Ahrenholtz, I., Lorenz, M. G. & Wackernagel, W. A conditional suicide system in Escherichia coli based on the intracellular degradation of DNA. Appl. Environ. Microbiol. 60, 3746-3751 (1994).
9. Djordjevic, G. M., O'Sullivan, D. J., Walker, S. A., Conkling, M. A. & Klaenhammer, T. R. A triggered-suicide system designed as a defense against bacteriophages. J. Bacteriol. 179, 6741-6748 (1997).
10. Andersen, J. T., Schäfer, T., Jørgensen, P. L. & Møller, S. Using inactivated microbial biomass as fertilizer: the fate of antibiotic resistance genes in the environment. Res. Microbiol. 152, 823-833 (2001).
11. Nielsen, K. M., Johnsen, P. J., Bensasson, D. & Daffonchio, D. Release and persistence of extracellular DNA in the environment. Environ. Biosafety Res. 6, 37-53 (2007).
12. Recorbet, G., Picard, C., Normand, P. & Simonet, P. Kinetics of the persistence of chromosomal DNA from genetically engineered Escherichia coli introduced into soil. Appl. Environ. Microbiol. 59, 4289-4294 (1993).
13. Daniel, R. The metagenomics of soil. Nat. Rev. Microbiol. 3, 470-478 (2005).
14. Thiel, C. S. et al. Functional activity of plasmid DNA after entry into the atmosphere of earth investigated by a new biomarker stability assay for ballistic spaceflight experiments. PLoS ONE 9, e112979 (2014).
15. Gibson, D. G. et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52-56 (2010).
16. Gibson, D. G. et al. Complete chemical synthesis, assembly, and cloning of a mycoplasma genitalium genome. Science 319, 1215-1220 (2008).
17. Lartigue, C. et al. Genome Transplantation in bacteria: changing one species to another. Science 317, 632-638 (2007).
18. Trevors, J. T. Plasmid curing in bacteria. FEMS Microbiol. Lett. 32, 149-157 (1986).
19. Charlton, H. R., Relton, J. M. & Slater, N. K. H. Characterisation of a generic monoclonal antibody harvesting system for adsorption of DNA by depth filters and various membranes. Bioseparation 8, 281-291 (1999).
20. Prazeres, D. M. F., Ferreira, G. N. M., Monteiro, G. A., Cooney, C. L. & Cabral, J. M. S. Large-scale production of pharmaceutical-grade plasmid DNA for gene therapy: problems and bottlenecks. Trends Biotechnol. 17, 169-174 (1999).
21. Ng, P. & Mitra, G. Removal of DNA contaminants from therapeutic protein preparations. J. Chromatogr. A 658, 459-463 (1994).
22. Makarova, K. S. et al. Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 9, 467-477 (2011).
23. Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709-1712 (2007).
24. Marraffini, L. A. & Sontheimer, E. J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322, 1843-1845 (2008).
25. Brouns, S. J. J. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960-964 (2008).
26. Haurwitz, R. E., Jinek, M., Wiedenheft, B., Zhou, K. & Doudna, J. A. Sequenceand structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355-1358 (2010).
27. Garside, E. L. et al. Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases. RNA 18, 2020-2028 (2012).
28. Niewoehner, O., Jinek, M. & Doudna, J. A. Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Nucleic Acids Res. 42, 1341-1353 (2014).
29. Deltcheva, E. et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471, 602-607 (2011).
30. Hatoum-Aslan, A., Maniv, I. & Marraffini, L. A. Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site. Proc. Natl Acad. Sci. USA 108, 21218-21222 (2011).
31. Jore, M. M. et al. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat. Struct. Mol. Biol. 18, 529-536 (2011).
32. Westra, E. R. et al. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol. Cell 46, 595-605 (2012).
33. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).
34. Deveau, H. et al. Phage response to CRISPR-encoded resistance in streptococcus thermophilus. J. Bacteriol. 190, 1390-1400 (2008).
35. Mojica, F. J. M., Diéz-Villasenõr, C., García-Martínez, J. & Almendros, C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155, 733-740 (2009).
36. Sashital, D. G., Wiedenheft, B. & Doudna, J. A. Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol. Cell 46, 606-615 (2012).
37. Westra, E. R. et al. Type I-E CRISPR-Cas systems discriminate target from nontarget DNA through base pairing-independent PAM recognition. PLoS Genet. 9, e1003742 (2013).
38. Semenova, E. et al. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc. Natl Acad. Sci. USA 108, 10098-10103 (2011).
39. Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequencespecific control of gene expression. Cell 152, 1173-1183 (2013).
40. Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 31, 233-239 (2013).
41. Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823 (2013).
42. Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823-826 (2013).
43. Bikard, D. et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 41, 7429-7437 (2013).
44. Citorik, R. J., Mimee, M. & Lu, T. K. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat. Biotechnol. 32, 1141-1145 (2014).
45. Gomaa, A. A. et al. Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems. MBio 5, e00928-e01013 (2014).
46. Garneau, J. E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67-71 (2010).
47. Datsenko, K. A. et al. Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat. Commun. 3, 945 (2012).
48. Bikard, D. et al. Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nat. Biotechnol. 32, 1146-1150 (2014).
49. Westra, E. R. et al. CRISPR-Cas systems preferentially target the leading regions of MOBF conjugative plasmids. RNA Biol. 10, 749-761 (2013).
50. Yosef, I., Goren, M. G., Kiro, R., Edgar, R. & Qimron, U. High-temperature protein G is essential for activity of the Escherichia coli clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system. Proc. Natl Acad. Sci. USA 108, 20136-20141 (2011).
51. Brophy, J. A. N. & Voigt, C. A. Principles of genetic circuit design. Nat. Methods 11, 508-520 (2014).
52. Sinkunas, T. et al. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system. EMBO J. 30, 1335-1342 (2011).
53. Beloglazova, N. et al. Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference. EMBO J. 30, 4616-4627 (2011).
54. Lutz, R. & Bujard, H. Independent and tight regulation of transcriptional units in Escherichia Coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 25, 1203-1210 (1997).
55. Kittleson, J. T., Cheung, S. & Anderson, J. C. Rapid optimization of gene dosage in E. coli using DIAL strains. J. Biol. Eng. 5, 10 (2011).
56. Shizuya, H. et al. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl Acad. Sci. USA 89, 8794-8797 (1992).
57. Balan, A. & Schenberg, A. C. G. A conditional suicide system for Saccharomyces cerevisiae relying on the intracellular production of the Serratia marcescens nuclease. Yeast 22, 203-212 (2005).
58. Li, Q. & Wu, Y.-J. A fluorescent, genetically engineered microorganism that degrades organophosphates and commits suicide when required. Appl. Microbiol. Biotechnol. 82, 749-756 (2009).
59. Moe-Behrens, G. H. G., Davis, R. & Haynes, K. A. Preparing synthetic biology for the world. Front. Microbiol. 4 (2013).
60. National Institutes of Health. Guidelines for Research Involving Recombinant or Synthetic Nucleic Acid Molecules (2013).
61. Brenner, S. Bacteriophage tales. Curr. Biol. 7, R736-R737 (1997).
62. Gullo, K. Ex-Dow scientist who stole secrets gets 7 years, 3 months prison. Bloomberg Businessweek. http://www.bloomberg.com/news/articles/2011-12-21/ex-dow-scientist-gets-more-than-seven-years-in-prison-for-stealing-secrets (2011).
63. Stanton, B. C. et al. Genomic mining of prokaryotic repressors for orthogonal logic gates. Nat. Chem. Biol. 10, 99-105 (2014).
64. Wright, O., Stan, G.-B. & Ellis, T. Building-in biosafety for synthetic biology. Microbiology 159, 1221-1235 (2013).
65. Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640-6645 (2000).
66. Hirano, N. et al. Site-specific recombination system based on actinophage TG1 integrase for gene integration into bacterial genomes. Appl. Microbiol. Biotechnol. 89, 1877-1884 (2011).
67. Yang, L. et al. Permanent genetic memory with41-byte capacity. Nat. Methods 11, 1261-1266 (2014).
68. Thomason, L. C., Costantino, N. & Court, D. L. in Current Protocols in Molecular Biology (John Wiley & Sons, Inc., 2001).
69. Vieira, J. & Messing, J. Production of Single-Stranded Plasmid DNA. Methods Enzymol 153, 3-11 (1987).