Skip to main content
Log in

Engineering Escherichia coli BL21 genome to improve the heptanoic acid tolerance by using CRISPR-Cas9 system

  • Research Paper
  • Published:
Biotechnology and Bioprocess Engineering Aims and scope Submit manuscript

Abstract

Acid tolerance is one of the critical factors to determine the quality of the industrial production strains. Therefore, we have investigated the introduction of the acid tolerance genes into the genome of Escherichia coli BL21 by using CRISPR-Cas9 system. The dsrA and rcsB genes of E. coli K-12, which are involved in the heptanoic acid tolerance, were inserted into the genome of E. coli BL21 without scar. The native transcription unit (TU) of dsrA and the synthetic TU of rcsB were integrated in E. coli BL21 genome. We found that the position of genomic coordinate of 1,300,270 was more efficient to integrate dsrA and rcsB than genomic coordinate of 3,876,428. Furthermore, the rcsB was successfully expressed in the resulting engineered strains (i.e., rcsB+ or dsrA+rcsB+ strains). The engineered strains expressing dsrA and/or rcsB showed the higher survival rate and specific growth rate under n-heptanoic acid stress than wild-type E. coli BL21. These results indicate that the newly introduced acid-tolerance systems were active in the E. coli BL21 strain.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Desbois, A. P. and V. J. Smith (2010) Antibacterial free fatty acids: activities, mechanisms of action and biotechnological potential. Appl. Microbiol. Biotechnol. 85: 1629–1642.

    Article  CAS  Google Scholar 

  2. Jarboe, L. R., L. A. Royce, and P. Liu (2013) Understanding biocatalyst inhibition by carboxylic acids. Front. Microbiol. 4: 272.

    Article  Google Scholar 

  3. Lee, S. Y. and H. U. Kim (2015) Systems strategies for developing industrial microbial strains. Nat. Biotechnol. 33: 1061–1072.

    Article  CAS  Google Scholar 

  4. Lease, R. A., D. Smith, K. McDonough, and M. Belfort (2004) The small noncoding DsrA RNA is an acid resistance regulator in Escherichia coli. J. Bacteriol. 186: 6179–6185.

    Article  CAS  Google Scholar 

  5. Johnson, M. D., N. A. Burton, B. Gutierrez, K. Painter, and P. A. Lund (2011) RcsB is required for inducible acid resistance in Escherichia coli and acts at gadE-dependent and -independent promoters. J. Bacteriol. 193: 3653–3656.

    Article  CAS  Google Scholar 

  6. Woo, J. -M., J. -W. Kim, J. -W. Song, L. M. Blank, and J. -B. Park (2016) Activation of the glutamic acid-dependent acid resistance system in Escherichia coli BL21(DE3) leads to increase of the fatty acid biotransformation activity. PLoS One 11: e0163265.

    Article  Google Scholar 

  7. Castanie-Cornet, M. P., K. Cam, B. Bastiat, A. Cros, P. Bordes, and C. Gutierrez (2010) Acid stress response in Escherichia coli: Mechanism of regulation of gadA transcription by RcsB and GadE. Nucleic Acids Res. 38: 3546–3554.

    Article  CAS  Google Scholar 

  8. Gaida, S. M., M. A. Al-Hinai, D. C. Indurthi, S. A. Nicolaou, and E. T. Papoutsakis (2013) Synthetic tolerance: three noncoding small RNAs, DsrA, ArcZ and RprA, acting supra-additively against acid stress. Nucleic Acids Res. 41: 8726–8737.

    Article  CAS  Google Scholar 

  9. Cho, S. W., S. Kim, Y. Kim, J. Kweon, H. S. Kim, S. Bae, and J. S. Kim (2014) Analysis of off-target effects of CRISPR/Casderived RNA-guided endonucleases and nickases. Genome Res. 24: 132–141.

    Article  CAS  Google Scholar 

  10. Riesenberg, D. (1991) High-cell-density cultivation of Escherichia coli. Curr. Opin. Biotechnol. 2: 380–384.

    Article  CAS  Google Scholar 

  11. Jiang, Y., B. Chen, C. Duan, B. Sun, J. Yang, and S. Yang (2015) Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system. Appl. Environ. Microbiol. 81: 2506–2514.

    Article  CAS  Google Scholar 

  12. Li, Y., Z. Lin, C. Huang, Y. Zhang, Z. Wang, Y. J. Tang, T. Chen, and X. Zhao (2015) Metabolic engineering of Escherichia coli using CRISPR-Cas9 meditated genome editing. Metab. Eng. 31: 13–21.

    Article  Google Scholar 

  13. Bassalo, M. C., A. D. Garst, A. L. Halweg-Edwards, W. C. Grau, D. W. Domaille, V. K. Mutalik, A. P. Arkin, and R. T. Gill (2016) Rapid and efficient one-step metabolic pathway integration in E. coli. ACS Synth. Biol. 5: 561–568.

    Article  CAS  Google Scholar 

  14. Trussart, M., E. Yus, S. Martinez, D. Bau, Y. O. Tahara, T. Pengo, M. Widjaja, S. Kretschmer, J. Swoger, S. Djordjevic, L. Turnbull, C. Whitchurch, M. Miyata, M. A. Marti-Renom, M. Lluch-Senar, and L. Serrano (2017) Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae. Nat. Commun. 8: 14665.

    Article  Google Scholar 

  15. Li, R., Y. Liu, T. Li, and C. Li (2016) 3Disease Browser: A web server for integrating 3D genome and disease-associated chromosome rearrangement data. Sci. Rep. 6: 34651.

    Article  CAS  Google Scholar 

  16. Vora, T., A. K. Hottes, and S. Tavazoie (2009) Protein occupancy landscape of a bacterial genome. Mol. Cell 35: 247–253.

    Article  CAS  Google Scholar 

  17. Bryant, J. A., L. E. Sellars, S. J. Busby, and D. J. Lee (2014) Chromosome position effects on gene expression in Escherichia coli K-12. Nucleic Acids Res. 42: 11383–11392.

    Article  CAS  Google Scholar 

  18. Benard, L. (2004) Inhibition of 5' to 3' mRNA degradation under stress conditions in Saccharomyces cerevisiae: from GCN4 to MET16. RNA 10: 458–468.

    Article  CAS  Google Scholar 

  19. Jang, H. -Y., K. Singha, H. -H. Kim, Y. -U. Kwon, and J. -B. Park (2016) Chemo-enzymatic synthesis of 11-hydroxyundecanoic acid and 1,11-undecanedioic acid from ricinoleic acid. Green Chem. 18: 1089–1095.

    Article  CAS  Google Scholar 

  20. Jeon, E. -Y., J. -H. Seo, W. -R. Kang, M. -J. Kim, J. -H. Lee, D. -K. Oh, and J. -B. Park (2016) Simultaneous enzyme/whole-cell biotransformation of plant oils into C9 carboxylic acids. ACS Catal. 6: 7547–7553.

    Article  CAS  Google Scholar 

  21. Koppireddi, S., J. -H. Seo, E. -Y. Jeon, P. S. Chowdhury, H. -Y. Jang, J. -B. Park, and Y. -U. Kwon (2016) Combined biocatalytic and chemical transformations of oleic acid to ω-hydroxynonanoic acid and α,ω-nonanedioic acid. Adv. Synth. Catal. 358: 3084–3092.

    Article  CAS  Google Scholar 

  22. Seo, J. H., H. -H. Kim, E. -Y. Jeon, Y. -H. Song, C. -S. Shin, and J. -B. Park (2016) Engineering of Baeyer-Villiger monooxygenase-based Escherichia coli biocatalyst for large scale biotransformation of ricinoleic acid into (Z)-11-(heptanoyloxy)undec-9-enoic acid. Sci. Rep. 6: 28223.

    Article  CAS  Google Scholar 

  23. Lee, N. -R., J. -Y. Yun, S. -M. Lee, and J. -B. Park (2015) Cyclohexanone-induced stress metabolism of Escherichia coli and Corynebacterium glutamicum. Biotechnol. Bioproc. Eng. 20: 1088–1098.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jin-Byung Park.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Seo, JH., Baek, SW., Lee, J. et al. Engineering Escherichia coli BL21 genome to improve the heptanoic acid tolerance by using CRISPR-Cas9 system. Biotechnol Bioproc E 22, 231–238 (2017). https://doi.org/10.1007/s12257-017-0158-4

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12257-017-0158-4

Keywords

Navigation