Advertisement

Biotechnology Letters

, Volume 41, Issue 10, pp 1147–1154 | Cite as

Quorum-sensing based small RNA regulation for dynamic and tuneable gene expression

  • Shao-Heng Bao
  • Wen-Ying Li
  • Chang-Jun Liu
  • Dong-Yi ZhangEmail author
  • Er MengEmail author
Original Research Paper

Abstract

Objectives

Developing a dynamic regulation strategy is an essential step in establishing an automatic control system for manipulating metabolic fluxes and cellular behaviors. To broaden the extent of the application, a system that can generally control any gene of interest is demanded.

Results

Through characterization and optimization, the strategy repressed the immediate expression incrementally from 0 to 90% during culturing. Moreover, by changing single base pair in the lux box of the Plux promoter, the degree of repression of the target genomic gene was tuned to a difference of 70%. This strategy is expected to control metabolic flux without disrupting cell growth.

Conclusions

We engineered bacterial small RNA to develop a pathway-independent strategy that can dynamically repress the expression of any gene at the posttranscription level.

Keywords

Bacterial small RNA Dynamic regulation Pathway independent Quorum sensing Tuneable regulation 

Abbreviations

E. coli

Escherichia coli

AHL

3-Oxohexanoylhomoserine lactone

sRNA

Small RNA

sfGFP

Super-folded green fluorescent protein

TBS

Target binding sequence

QS

Quorum sensing

OPPS

Octaprenyl pyrophosphate synthase

GOI

Gene of interest

Notes

Acknowledgements

This work was supported by the National Natural Science Foundation of China under Grant Number 81703400 (to Dr. E. Meng). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Author contributions

EM, D-YZ and S-HB designed the appropriate technology routes. S-HB conducted main experiments including plasmid and strain construction, shake flask fermentation and western blot experiments. EM, W-YL, C-JL and D-YZ participated in the establishment of mathematic models. EM and D-YZ supervised the project and S-HB wrote the paper. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare they have no competing interests.

Supplementary material

10529_2019_2719_MOESM1_ESM.docx (91 kb)
Supplementary material 1 (DOCX 90 kb)

References

  1. Asai K, Fujisaki S, Nishimura Y, Nishino T, Okada K, Nakagawa T, Kawamukai M, Matsuda H (1994) The identification of Escherichia coli ispB (cel) gene encoding the octaprenyl diphosphate synthase. Biochem Biophys Res Commun 202:340–345.  https://doi.org/10.1006/bbrc.1994.1933 CrossRefGoogle Scholar
  2. Balagadde FK, Song H, Ozaki J, Collins CH, Barnet M, Arnold FH, Quake SR, You L (2008) A synthetic Escherichia coli predator-prey ecosystem. Mol Syst Biol 4:187.  https://doi.org/10.1038/msb.2008.24 CrossRefGoogle Scholar
  3. Cataldi TR, Bianco G, Palazzo L, Quaranta V (2007) Occurrence of N-acyl-L-homoserine lactones in extracts of some Gram-negative bacteria evaluated by gas chromatography-mass spectrometry. Anal Biochem 361:226–235.  https://doi.org/10.1016/j.ab.2006.11.037 CrossRefGoogle Scholar
  4. Gupta A, Reizman IM, Reisch CR, Prather KL (2017) Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit. Nat Biotechnol 35:273–279.  https://doi.org/10.1038/nbt.3796 CrossRefGoogle Scholar
  5. Kim EM, Woo HM, Tian T, Yilmaz S, Javidpour P, Keasling JD, Lee TS (2017) Autonomous control of metabolic state by a quorum sensing (QS)-mediated regulator for bisabolene production in engineered E. coli. Metab Eng 44:325–336.  https://doi.org/10.1016/j.ymben.2017.11.004 CrossRefGoogle Scholar
  6. Kimura Y, Tashiro Y, Saito K, Kawai-Noma S, Umeno D (2016) Directed evolution of Vibrio fischeri LuxR signal sensitivity. J Biosci Bioeng 122:533–538.  https://doi.org/10.1016/j.jbiosc.2016.04.010 CrossRefGoogle Scholar
  7. Liu CJ, Jiang H, Wu L, Zhu LY, Meng E, Zhang DY (2017) OEPR Cloning: an efficient and seamless cloning strategy for large- and multi-fragments. Sci Rep 7:44648.  https://doi.org/10.1038/srep44648 CrossRefGoogle Scholar
  8. Markham NR, Zuker M (2008) UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol (Clifton, NJ) 453:3–31.  https://doi.org/10.1007/978-1-60327-429-6_1 CrossRefGoogle Scholar
  9. Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, Hasty J (2011) A sensing array of radically coupled genetic ‘biopixels’. Nature 481:39–44.  https://doi.org/10.1038/nature10722 CrossRefGoogle Scholar
  10. Scott SR, Hasty J (2016) Quorum sensing communication modules for microbial consortia. ACS Synth Biol 5:969–977.  https://doi.org/10.1021/acssynbio.5b00286 CrossRefGoogle Scholar
  11. Soma Y, Hanai T (2015) Self-induced metabolic state switching by a tunable cell density sensor for microbial isopropanol production. Metab Eng 30:7–15.  https://doi.org/10.1016/j.ymben.2015.04.005 CrossRefGoogle Scholar
  12. Taylor ND, Garruss AS, Moretti R, Chan S, Arbing MA, Cascio D, Rogers JK, Isaacs FJ, Kosuri S, Baker D, Fields S, Church GM, Raman S (2016) Engineering an allosteric transcription factor to respond to new ligands. Nat Methods 13:177–183.  https://doi.org/10.1038/nmeth.3696 CrossRefGoogle Scholar
  13. You L, Cox RS 3rd, Weiss R, Arnold FH (2004) Programmed population control by cell-cell communication and regulated killing. Nature 428:868–871.  https://doi.org/10.1038/nature02491 CrossRefGoogle Scholar
  14. Zeng W, Du P, Lou Q, Wu L, Zhang HM, Lou C, Wang H, Ouyang Q (2017) Rational design of an ultrasensitive quorum-sensing switch. ACS Synth Biol 6:1445–1452.  https://doi.org/10.1021/acssynbio.6b00367 CrossRefGoogle Scholar
  15. Zhang F, Carothers JM, Keasling JD (2012) Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 30:354–359.  https://doi.org/10.1038/nbt.2149 CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Research Center of Biological Information, College of Arts and SciencesNational University of Defense TechnologyChangshaPeople’s Republic of China
  2. 2.School of Life SciencesHunan University of Science and TechnologyXiangtanPeople’s Republic of China

Personalised recommendations