CRISPR-interference-based modulation of mobile genetic elements in bacteria

Synthetic Biology

Volumn 4, Issue 1, 2019, Pages

  Nyerges, Ákos ^a   Bálint, Balázs ^a,b   Cseklye, Judit ^b   Nagy, István ^a,b   Pál, Csaba ^a   Feher, Tamás ^a  

^a INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

^b SEQOMICS BIOTECHNOLOGY LTD   (Hungary)

Author keywords

CRISPR mediated gene silencing; decreased mutation rate; genome stability; repression of transposition; transposable element

Indexed keywords

ESCHERICHIA COLI; GENES; SYNTHETIC BIOLOGY;

GENE SILENCING; GENOME STABILITY; MUTATION RATES; REPRESSION OF TRANSPOSITION; TRANSPOSABLE ELEMENTS;

DNA;

EID: 85068534271     PISSN: 19397267     EISSN: 23977000     Source Type: Journal    
DOI: 10.1093/synbio/ysz008     Document Type: Article

References (58)

1. Endy, D. (2005) Foundations for engineering biology. Nature, 438, 449-453.
2. Renda, B.A., Hammerling, M.J., Barrick, J.E. (2014) Engineering reduced evolutionary potential for synthetic biology. Mol. Biosyst., 10, 1668-1678.
3. Bull, J.J., Barrick, J.E. (2017) Arresting evolution. Trends Genet., 33, 910-920.
4. Tyo, K.E., Ajikumar, P.K., Stephanopoulos, G. (2009) Stabilized gene duplication enables long-termselection-free heterologous pathway expression. Nat. Biotechnol., 27, 760-765.
5. Jack, B.R., Leonard, S.P., Mishler, D.M., Renda, B.A., Leon, D., Suarez, G.A., Barrick, J.E. (2015) Predicting the genetic stability of engineered DNA sequences with the EFM calculator. ACS Synth. Biol., 4, 939-943.
6. Sleight, S.C., Bartley, B.A., Lieviant, J.A., Sauro, H.M. (2010) Designing and engineering evolutionary robust genetic circuits. J. Biol. Eng., 4, 12.
7. Yang, S., Sleight, S.C., Sauro, H.M. (2013) Rationally designed bidirectional promoter improves the evolutionary stability of synthetic genetic circuits. Nucleic Acids Res., 41, e33.
8. Harris, R.S., Feng, G., Ross, K.J., Sidhu, R., Thulin, C., Longerich, S., Szigety, S.K., Winkler, M.E., Rosenberg, S.M. (1997) Mismatch repair protein MutL becomes limiting during stationary-phase mutation. Genes Dev., 11, 2426-2437.
9. Kamiya, H., Iida, E., Murata-Kamiya, N., Yamamoto, Y., Miki, T., Harashima, H. (2003) Suppression of spontaneous and hydrogen peroxide-induced mutations by a MutT-type nucleotide pool sanitization enzyme, the Escherichia coli Orf135 protein. Genes Cells, 8, 941-950.
10. Csorgo, B., Feher, T., Timar, E., Blattner, F.R., Posfai, G., (2012) Low-mutation-rate, reduced-genome Escherichia coli: An improved host for faithful maintenance of engineered genetic constructs. Microb. Cell Fact., 11, 11.
11. Deatherage, D.E., Leon, D., Rodriguez, A.E., Omar, S.K., Barrick, J.E. (2018) Directed evolution of Escherichia coli with lower-than-natural plasmid mutation rates. Nucleic Acids Res., 46, 9236-9250.
12. Vapnek, D., Alton, N.K., Bassett, C.L., Kushner, S.R. (1976) Amplification in Escherichia coli of enzymes involved in genetic recombination: Construction of hybrid ColE1 plasmids carrying the structural gene for exonuclease I. Proc. Natl. Acad. Sci. USA, 73, 3492-3496.
13. Troester, H., Bub, S., Hunziker, A., Trendelenburg, M.F. (2000) Stability of DNA repeats in Escherichia coli dam mutant strains indicates a Dam methylation-dependent DNA deletion process. Gene, 258, 95-108.
14. Rugbjerg, P., Myling-Petersen, N., Porse, A., Sarup-Lytzen, K., Sommer, M.O.A. (2018) Diverse genetic error modes constrain large-scale bio-based production. Nat. Commun., 9, 787.
15. Mahillon, J., Chandler, M. (1998) Insertion sequences. Microbiol. Mol. Biol. Rev., 62, 725-774.
16. Feher, T., Cseh, B., Umenhoffer, K., Karcagi, I., Posfai, G. (2006) Characterization of cycA mutants of Escherichia coli. An assay for measuring in vivomutation rates. Mutat. Res., 595, 184-190.
17. Hall, B.G. (1998) Activation of the bgl operon by adaptive mutation. Mol. Biol. Evol., 15, 1-5.
18. Halliday, J.A., Glickman, B.W. (1991) Mechanisms of spontaneous mutation in DNA repair-proficient Escherichia coli. Mutat. Res., 250, 55-71.
19. Chao, L., Vargas, C., Spear, B.B., Cox, E.C. (1983) Transposable elements asmutator genes in evolution. Nature, 303, 633-635.
20. Feher, T., Bogos, B., Mehi, O., Fekete, G., Csorgo, B., Kovacs, K., Posfai, G., Papp, B., Hurst, L.D., Pal, C. (2012) Competition between transposable elements and mutator genes in bacteria. Mol. Biol. Evol., 29, 3153-3159.
21. Orgel, L.E., Crick, F.H. (1980) Selfish DNA: The ultimate parasite. Nature, 284, 604-607.
22. Schneider, D., Lenski, R.E. (2004) Dynamics of insertion sequence elements during experimental evolution of bacteria. Res. Microbiol., 155, 319-327.
23. Pósfai, G., Plunkett, G., Fehér, T., Frisch, D., Keil, G.M., Umenhoffer, K., Kolisnychenko, V., Stahl, B., Sharma, S.S., de Arruda, M. et al. (2006) Emergent properties of reduced-genome Escherichia coli. Science, 312, 1044-1046.
24. Umenhoffer, K., Draskovits, G., Nyerges, Á ., Karcagi, I., Bogos, B., Tmá r, E., Csö rg}o, B., Herczeg, R., Nagy, I., Fehé r, T. et al., (2017) Genome-wide abolishment of mobile genetic elements using genome shuffling and CRISPR/Cas-assisted MAGE allows the efficient stabilization of a bacterial chassis. ACS Synth. Biol., 6, 1471-1483.
25. Park, M.K., Lee, S.H., Yang, K.S., Jung, S.C., Lee, J.H., Kim, S.C. (2014) Enhancing recombinant protein production with an Escherichia coli host strain lacking insertion sequences. Appl. Microbiol. Biotechnol., 98, 6701-6713.
26. Choi, J.W., Yim, S.S., Kim, M.J., Jeong, K.J. (2015) Enhanced production of recombinant proteins with Corynebacterium glutamicum by deletion of insertion sequences (IS elements). Microb. Cell Fact., 14, 207.
27. Suarez, G.A., Renda, B.A., Dasgupta, A., Barrick, J.E. (2017) Reduced mutation rate and increased transformability of transposon-free Acinetobacter baylyi ADP1-ISx. Appl. Environ. Microbiol., 83, e01025-17.
28. Jansen, R., Embden, J.D., Gaastra, W., Schouls, L.M. (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol., 43, 1565-1575.
29. Mojica, F.J., Diez-Villasenor, C., Soria, E., Juez, G. (2000) Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol. Microbiol., 36, 244-246.
30. Niu, D., Wei, H.J., Lin, L., George, H., Wang, T., Lee, I.H., Zhao, H.Y., Wang, Y., Kan, Y., Shrock, E. et al. (2017) Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science, 357, 1303-1307.
31. Yang, L., Guell, M., Niu, D., George, H., Lesha, E., Grishin, D., Aach, J., Shrock, E., Xu, W., Poci, J. et al. (2015) Genome-wide inactivation of porcine endogenous retroviruses (PERVs). Science, 350, 1101-1104.
32. Banno, S., Nishida, K., Arazoe, T., Mitsunobu, H., Kondo, A. (2018) Deaminase-mediated multiplex genome editing in Escherichia coli. Nat. Microbiol., 3, 423-429.
33. Shapiro, R.S., Chavez, A., Collins, J.J. (2018) CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms. Nat. Rev. Microbiol., 16, 333-339.
34. Bikard, D., Jiang, W., Samai, P., Hochschild, A., Zhang, F., Marraffini, L.A. (2013) Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res., 41, 7429-7437.
35. Cress, B.F., Toparlak, O.D., Guleria, S., Lebovich, M., Stieglitz, J.T., Englaender, J.A., Jones, J.A., Linhardt, R.J., Koffas, M.A. (2015) CRISPathBrick: Modular combinatorial assembly of type II-A CRISPR arrays for dCas9-mediated multiplex transcriptional repression in E. coli. ACS Synth. Biol., 4, 987-1000.
36. Blattner, F.R., Plunkett, G., Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1462.
37. Jeong, H., Barbe, V., Lee, C.H., Vallenet, D., Yu, D.S., Choi, S.H., Couloux, A., Lee, S.W., Yoon, S.H., Cattolico, L. et al. (2009) Genome sequences of Escherichia coli B strains REL606 andx BL21(DE3). J. Mol. Biol., 394, 644-652.
38. Lutz, R., Bujard, H. (1997) 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.
39. Blumenthal, R.M., Gregory, S.A., Cooperider, J.S. (1985) Cloning of a restriction-modification system from Proteus vulgaris and its use in analyzing a methylase-sensitive phenotype in Escherichia coli. J. Bacteriol., 164, 501-509.
40. Sambrook, J., Fritch, E.F., Maniatis, T. (1987) Molecular Cloning. A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
41. Reese, M.G. (2001) Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput. Chem., 26, 51-56.
42. Sawers, R.G. (2005) Transcript analysis of Escherichia coli K-12 insertion element IS5. FEMS Microbiol. Lett., 244, 397-401.
43. Schwartz, E., Kroger, M., Rak, B. (1988) IS150: Distribution, nucleotide sequence and phylogenetic relationships of a new E. coli insertion element. Nucleic Acids Res., 16, 6789-6802.
44. Hall, B.G., Acar, H., Nandipati, A., Barlow, M. (2014) Growth rates made easy. Mol. Biol. Evol., 31, 232-238.
45. Robinson, M.D., McCarthy, D.J., Smyth, G.K. (2010) edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140.
46. Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., Smyth, G.K. (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res., 43, e47.
47. Sarkar, S., Ma, W.T., Sandri, G.H. (1992) On fluctuation analysis: A new, simple and efficient method for computing the expected number of mutants. Genetica, 85, 173-179.
48. Rosche, W.A., Foster, P.L. (2000) Determining mutation rates in bacterial populations. Methods, 20, 4-17.
49. Fernandez, C., Larhammar, D., Servenius, B., Rask, L., Peterson, P.A. (1986) Spontaneous insertions into cosmid vector-a warning. Gene, 42, 215-219.
50. Nakamura, K., Inouye, M. (1981) Inactivation of the Serratia marcescens gene for the lipoprotein in Escherichia coli by insertion sequences, IS1 and IS5; sequence analysis of junction points. Mol. Gen. Genet., 183, 107-114.
51. Prather, K.L., Edmonds, M.C., Herod, J.W. (2006) Identification and characterization of IS1 transposition in plasmid amplification mutants of E. coli clones producing DNA vaccines. Appl. Microbiol. Biotechnol., 73, 815-826.
52. Rood, J.I., Sneddon, M.K., Morrison, J.F. (1980) Instability in tyrR strains of plasmids carrying the tyrosine operon: Isolation and characterization of plasmid derivatives with insertions or deletions. J. Bacteriol., 144, 552-559.
53. Muller, J., Reinert, H., Malke, H. (1989) Streptokinase mutations relieving Escherichia coli K-12 (prlA4) of detriments caused by the wild-type skc gene. J. Bacteriol., 171, 2202-2208.
54. Rawat, P., Kumar, S., Pental, D., Burma, P.K. (2009) Inactivation of a transgene due to transposition of insertion sequence (IS136) of Agrobacteriumtumefaciens. J. Biosci., 34, 199-202.
55. Geng, P., Leonard, S.P., Mishler, D.M., Barrick, J.E. (2018) Synthetic genome defenses against selfish DNA elements stabilize engineered bacteria against evolutionary failure. ACS Synth. Biol., doi: 10.1021/acssynbio.8b00426.
56. Martinez-Garcia, E., Aparicio, T., Goni-Moreno, A., Fraile, S., de Lorenzo, V. (2015) SEVA 2.0: An update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities. Nucleic Acids Res., 43, D1183-D1189.
57. Silva-Rocha, R., Martinez-Garcia, E., Calles, B., Chavarria, M., Arce-Rodriguez, A., de Las Heras, A., Paez-Espino, A.D., Durante-Rodriguez, G., Kim, J., Nikel, P.I. et al. (2013) The Standard European Vector Architecture (SEVA): A coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res., 41, D666-D675.
58. Zhang, S., Voigt, C.A. (2018) Engineered dCas9 with reduced toxicity in bacteria: Implications for genetic circuit design. Nucleic Acids Res., 46, 11115-11125.