Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Protocol
  • Published:

Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli

Nature Protocols volume 8, pages 1694–1707 (2013)Cite this article

Subjects

Abstract

Gene knockout experiments are often essential in functional genomics and metabolic engineering studies. However, repeated multiple gene knockout experiments are laborious, time consuming and sometimes impossible to perform for those genes that are essential for cell function. Small regulatory RNAs (sRNAs) are short noncoding RNAs in prokaryotes that can finely control the expression of target genes in trans at the post-transcriptional level. Here we describe the protocol for synthetic sRNA-based gene expression control, including sRNA design principles. Customized synthetic sRNAs consist of a scaffold and a target-binding sequence, and they can be created by simply replacing an existing target-binding sequence with one that is complementary to the target mRNA to be repressed, while retaining the scaffold. Our plasmid-based synthetic sRNA system does not require chromosomal modifications, and it enables one to perform high-throughput studies on the effects of knockdowns on host cell physiology, and it further allows the simultaneous screening of target genes in different Escherichia coli strains for applications in metabolic engineering and synthetic biology. Once an sRNA scaffold-harboring plasmid is constructed, customized synthetic sRNAs can be made within 3–4 d; after this time, the synthetic sRNAs can be applied to the desired experiments.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Mode of trans-acting and Hfq-dependent sRNA action.
Figure 2: Construction of customized synthetic sRNA plasmid library.
Figure 3: Schematic illustration of potential applications of tailor-made synthetic sRNAs.
Figure 4: Schematics of the template plasmid producing sRNAs, and of the dual regulatory expression system.
Figure 5: Design and construction of synthetic sRNAs (anti-lacZ as an example).

Similar content being viewed by others

References

  1. Warner, J.R. et al. Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides. Nat. Biotechnol. 28, 856–862 (2010).

    Article  CAS  Google Scholar 

  2. Wang, H.H. et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature 460, 894–898 (2009).

    Article  CAS  Google Scholar 

  3. Sandoval, N.R. et al. Strategy for directing combinatorial genome engineering in Escherichia coli. Proc. Natl. Acad. Sci. USA 109, 10540–10545 (2012).

    Article  CAS  Google Scholar 

  4. Lee, S.Y., Lee, K.M., Chan, H.N. & Steinbüchel, A. Comparison of recombinant Escherichia coli strains for synthesis and accumulation of poly-(3-hydroxybutyric acid) and morphological changes. Biotechnol. Bioeng. 44, 1337–1347 (1994).

    Article  CAS  Google Scholar 

  5. Desai, S.K. & Gallivan, J.P. Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J. Am. Chem. Soc. 126, 13247–13254 (2004).

    Article  CAS  Google Scholar 

  6. Nomura, Y. & Yokobayashi, Y. Reengineering a natural riboswitch by dual genetic selection. J. Am. Chem. Soc. 129, 13814–13815 (2007).

    Article  CAS  Google Scholar 

  7. Jin, Y. & Huang, J.D. Engineering a portable riboswitch-LacP hybrid device for two-way gene regulation. Nucleic Acids Res. 39, e131 (2011).

    Article  CAS  Google Scholar 

  8. Sun, X., Zhulin, I. & Wartell, R.M. Predicted structure and phyletic distribution of the RNA-binding protein Hfq. Nucleic Acids Res. 30, 3663–3671 (2002).

    Article  Google Scholar 

  9. Hershberg, R., Altuvia, S. & Margalit, H. A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res. 31, 1813 (2003).

    Article  CAS  Google Scholar 

  10. Win, M.N. & Smolke, C.D. Higher-order cellular information processing with synthetic RNA devices. Science 322, 456–460 (2008).

    Article  CAS  Google Scholar 

  11. Man, S. et al. Artificial trans-encoded small non-coding RNAs specifically silence the selected gene expression in bacteria. Nucleic Acids Res. 39, e50 (2011).

    Article  CAS  Google Scholar 

  12. Urban, J.H. & Vogel, J. Translational control and target recognition by Escherichia coli small RNAs in vivo. Nucleic Acids Res. 35, 1018–1037 (2007).

    Article  CAS  Google Scholar 

  13. Na, D. et al. Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat. Biotechnol. 31, 170–174 (2013).

    Article  CAS  Google Scholar 

  14. Gottesman, S. The small RNA regulators of Escherichia coli: roles and mechanisms. Annu. Rev. Microbiol. 58, 303–328 (2004).

    Article  CAS  Google Scholar 

  15. Repoila, F. & Darfeuille, F. Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects. Biol. Cell 101, 117–131 (2009).

    Article  CAS  Google Scholar 

  16. Storz, G., Opdyke, J. & Zhang, A. Controlling mRNA stability and translation with small, noncoding RNAs. Curr. Opin. Microbiol. 7, 140–144 (2004).

    Article  CAS  Google Scholar 

  17. Moll, I., Afonyushkin, T., Vytvytska, O., Kaberdin, V.R. & Bläsi, U. Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs. RNA 9, 1308–1314 (2003).

    Article  CAS  Google Scholar 

  18. Aiba, H. Mechanism of RNA silencing by Hfq-binding small RNAs. Curr. Opin. Microbiol. 10, 134–139 (2007).

    Article  CAS  Google Scholar 

  19. Delebecque, C.J., Lindner, A.B., Silver, P.A. & Aldaye, F.A. Organization of intracellular reactions with rationally designed RNA assemblies. Science 333, 470–474 (2011).

    Article  CAS  Google Scholar 

  20. Kang, Z., Wang, X., Li, Y., Wang, Q. & Qi, Q. Small RNA RyhB as a potential tool used for metabolic engineering in Escherichia coli. Biotechnol. Lett. 34, 527–531 (2012).

    Article  CAS  Google Scholar 

  21. Sharma, V., Yamamura, A. & Yokobayashi, Y. Engineering artificial small RNAs for conditional gene silencing in Escherichia coli. ACS Synth. Biol. 1, 6–13 (2012).

    Article  CAS  Google Scholar 

  22. Liang, J.C., Bloom, R.J. & Smolke, C.D. Engineering biological systems with synthetic RNA molecules. Mol. Cell 43, 915–926 (2011).

    Article  CAS  Google Scholar 

  23. Duckert, P., Brunak, S. & Blom, N. Prediction of proprotein convertase cleavage sites. Protein Eng. Des. Sel. 17, 107–112 (2004).

    Article  CAS  Google Scholar 

  24. McDaniel, R. & Weiss, R. Advances in synthetic biology: on the path from prototypes to applications. Curr. Opin. Biotechnol. 16, 476–483 (2005).

    Article  CAS  Google Scholar 

  25. Landrain, T.E., Carrera, J., Kirov, B., Rodrigo, G. & Jaramillo, A. Modular model-based design for heterologous bioproduction in bacteria. Curr. Opin. Biotechnol. 20, 272–279 (2009).

    Article  CAS  Google Scholar 

  26. McDaniel, R., Endy, D. & Weiss, R. Foundations for engineering biology. Nature 438, 449–453 (2005).

    Article  Google Scholar 

  27. Na, D., Lee, S. & Lee, D. Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with a desired expression level in prokaryotes. BMC Syst. Biol. 4, 71 (2010).

    Article  Google Scholar 

  28. Jana, N.K., Roy, S., Bhattacharyya, B. & Mandal, N.C. Amino acid changes in the repressor of bacteriophage lambda due to temperature-sensitive mutations in its cI gene and the structure of a highly temperature-sensitive mutant repressor. Protein Eng. 12, 225–233 (1999).

    Article  CAS  Google Scholar 

  29. Zhang, R., Ou, H.Y. & Zhang, C.T. DEG: a database of essential genes. Nucleic Acids Res. 32, D271–272 (2004).

    Article  CAS  Google Scholar 

  30. Markham, N. & Zuker, M. UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol. 453, 3–31 (2008).

    Article  CAS  Google Scholar 

  31. Nolan, T., Hands, E.R. & Bustin, A.S. Quantification of mRNA using real-time RT-PCR. Nat. Protoc. 1, 1559–1582 (2006).

    Article  CAS  Google Scholar 

  32. Mahmood, T. & Yang, P.-C. Western blot: technique, theory, and trouble shooting. N. Am. J. Med. Sci. 4, 429–434 (2012).

    Article  Google Scholar 

  33. Sambrook, J. & Russell, D. Molecular Cloning: a Laboratory Manual (Cold Spring Harbor Laboratory Press, 2001).

  34. Schägger, H. Tricine–SDS-PAGE. Nat. Protoc. 1, 16–22 (2006).

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by the Technology Development Program to Solve Climate Changes on Systems Metabolic Engineering for Biorefineries (NRF-2012-C1AAA001-2012M1A2A2026556) and the Intelligent Synthetic Biology Center through the Global Frontier Project (2011-0031963) of the Ministry of Science, ICT and Future Planning through the National Research Foundation of Korea. This protocol paper describes the detailed strategies and step-by-step procedures for the work reported in our previous paper.

Author information

Author notes

  1. Dokyun Na

    Present address: Present address: Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada.,

  2. Seung Min Yoo and Dokyun Na: These authors equally contributed to this work.

Authors and Affiliations

  1. Department of Chemical and Biomolecular Engineering (The World Class University Program), Metabolic and Biomolecular Engineering National Research Laboratory, BioProcess Engineering Research Center, Bioinformatics Research Center, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea

    Seung Min Yoo, Dokyun Na & Sang Yup Lee

Authors
  1. Seung Min Yoo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dokyun Na
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sang Yup Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

D.N. and S.Y.L. conceived the project. S.M.Y. and D.N. performed all experiments and developed the experimental protocol. S.Y.L. supervised the project. All authors wrote the paper together and approved the final manuscript.

Corresponding author

Correspondence to Sang Yup Lee.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Figure 1

Scaffold selection for the construction of effective synthetic sRNAs. (a) Most sRNAs possess a consensus sequence that is able to recruit the Hfq protein. The left figure illustrates the process of analyzing sequence features of discovered sRNAs in E. coli and the selection of three candidate scaffolds from MicC, MicF and SgrS sRNAs. The respective scaffolds were fused with a sequence complementary to the TIR of DsRed2 mRNA in order to build anti-DsRed2 synthetic sRNAs with different scaffolds. The graph on the right shows that the three scaffolds are highly efficient (>90%) in repressing DsRed2 translation and that the MicC scaffold showed the highest repression efficiency. Consequently, the MicC scaffold was selected to be the synthetic sRNA scaffold. “C”, no synthetic sRNA; “-”, a scaffold without the DsRed2 targeting sequence; “+”, a scaffold with the DsRed2 targeting sequence. (b) Identification of effective mRNA binding regions and sRNA lengths are identified. The graph on the right shows repressed DsRed2 expression by synthetic sRNAs targeting different regions in the mRNA, as indicated in the left figure. “A” denotes the same anti-DsRed2 synthetic sRNA with a MicC scaffold used in (a). The TIR, denoted by a green bar, was estimated using a previously published algorithm27. (Reprinted from ref. 13; please see details there.) (PDF 316 kb)

Supplementary Figure 2

Testing the specificities of synthetic sRNA by using the web-based tools TargetRNA2 and RNAPredator. (a) TargetRNA2. Input information in the indicated boxes: select the target genome to search to E. coli (named ‘Replicon’), input the whole sequence of the synthetic sRNA (named ‘sRNA sequence’) – in this example anti-lacZ, enter ‘24’ in ‘Target parameters’, and then ‘Submit’. (b) Predicted target mRNAs for the anti-lacZ synthetic sRNA by TargetRNA2. (c) Predicted target mRNAs for the anti-lacZ synthetic sRNA by RNAPredator. (PDF 278 kb)

Supplementary Figure 3

Binding free energy–dependent repression capabilities of different anti-lacZ synthetic sRNA. (a) Primers for the anti-lacZ synthetic sRNAs with different binding free energies were designed. (b) The tunability of repression with respect to binding energy was investigated for lacZα (MITRegistry, BBa_I732006) and its corresponding synthetic sRNAs. The LacZ expression levels were measured according to the standard β-galactosidase assay in E. coli DH5α strain by α-complementation33. (Reprinted from ref. 13; please see details there.) (PDF 455 kb)

Supplementary Figure 4

Vector map of the pWAS plasmid. (a) This figure illustrates the brief structure of the pWAS plasmid and indicates promoters, coding sequences, synthetic sRNAs, etc. (b) The vector sequence is available in the Supplementary Data file, where the locations of relevant genetic components in the plasmid are listed. (PDF 136 kb)

Supplementary Discussion

Computational design of synthetic sRNAs and high-throughput library construction. (PDF 154 kb)

Supplementary Data

Sequence of the pWAS vector. (TXT 85 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yoo, S., Na, D. & Lee, S. Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli. Nat Protoc 8, 1694–1707 (2013). https://doi.org/10.1038/nprot.2013.105

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nprot.2013.105

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research