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Title: Jungle Express is a versatile repressor system for tight transcriptional control

Tightly regulated promoters are essential for numerous biological applications, where strong inducibility, portability, and scalability are desirable. Current systems are often incompatible with large-scale fermentations due to high inducer costs and strict media requirements. Here, we describe the bottom-up engineering of ‘Jungle Express’, an expression system that enables efficient gene regulation in diverse proteobacteria. This system is guided by EilR, a multidrug-binding repressor with high affinity to its optimized operator and cationic dyes that act as powerful inducers at negligible costs. In E. coli, the engineered promoters exhibit minimal basal transcription and are inducible over four orders of magnitude by 1 µM crystal violet, reaching expression levels exceeding those of the strongest current bacterial systems. Further, we provide molecular insights into specific interactions of EilR with its operator and with two inducers. The versatility of Jungle Express opens the way for tightly controlled and efficient gene expression that is not restricted to host organism, substrate, or scale.
Authors:
 [1] ;  [2] ;  [3] ;  [2] ;  [4] ;  [4] ;  [2] ; ORCiD logo [5] ; ORCiD logo [5] ; ORCiD logo [5] ;  [6] ;  [7]
  1. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Univ. of Basel (Switzerland). Inst. of Botany
  2. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division
  3. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); San Francisco State Univ., CA (United States). Dept. of Biology
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
  5. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division
  6. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
  7. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Biology and Biotechnology Division
Publication Date:
Grant/Contract Number:
AC02-05CH11231; AC52-07NA27344; SC3GM096943
Type:
Published Article
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 9; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Research Org:
Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Univ. of Basel (Switzerland)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); National Inst. of Health (NIH) (United States); Howard Hughes Medical Inst. (United States); Swiss National Science Foundation (SNSF)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; applied microbiology; synthetic biology; transcriptional regulatory elements
OSTI Identifier:
1467933
Alternate Identifier(s):
OSTI ID: 1477413

Ruegg, Thomas L., Pereira, Jose H., Chen, Joseph C., DeGiovanni, Andy, Novichkov, Pavel, Mutalik, Vivek K., Tomaleri, Giovani P., Singer, Steven W., Hillson, Nathan J., Simmons, Blake A., Adams, Paul D., and Thelen, Michael P.. Jungle Express is a versatile repressor system for tight transcriptional control. United States: N. p., Web. doi:10.1038/s41467-018-05857-3.
Ruegg, Thomas L., Pereira, Jose H., Chen, Joseph C., DeGiovanni, Andy, Novichkov, Pavel, Mutalik, Vivek K., Tomaleri, Giovani P., Singer, Steven W., Hillson, Nathan J., Simmons, Blake A., Adams, Paul D., & Thelen, Michael P.. Jungle Express is a versatile repressor system for tight transcriptional control. United States. doi:10.1038/s41467-018-05857-3.
Ruegg, Thomas L., Pereira, Jose H., Chen, Joseph C., DeGiovanni, Andy, Novichkov, Pavel, Mutalik, Vivek K., Tomaleri, Giovani P., Singer, Steven W., Hillson, Nathan J., Simmons, Blake A., Adams, Paul D., and Thelen, Michael P.. 2018. "Jungle Express is a versatile repressor system for tight transcriptional control". United States. doi:10.1038/s41467-018-05857-3.
@article{osti_1467933,
title = {Jungle Express is a versatile repressor system for tight transcriptional control},
author = {Ruegg, Thomas L. and Pereira, Jose H. and Chen, Joseph C. and DeGiovanni, Andy and Novichkov, Pavel and Mutalik, Vivek K. and Tomaleri, Giovani P. and Singer, Steven W. and Hillson, Nathan J. and Simmons, Blake A. and Adams, Paul D. and Thelen, Michael P.},
abstractNote = {Tightly regulated promoters are essential for numerous biological applications, where strong inducibility, portability, and scalability are desirable. Current systems are often incompatible with large-scale fermentations due to high inducer costs and strict media requirements. Here, we describe the bottom-up engineering of ‘Jungle Express’, an expression system that enables efficient gene regulation in diverse proteobacteria. This system is guided by EilR, a multidrug-binding repressor with high affinity to its optimized operator and cationic dyes that act as powerful inducers at negligible costs. In E. coli, the engineered promoters exhibit minimal basal transcription and are inducible over four orders of magnitude by 1 µM crystal violet, reaching expression levels exceeding those of the strongest current bacterial systems. Further, we provide molecular insights into specific interactions of EilR with its operator and with two inducers. The versatility of Jungle Express opens the way for tightly controlled and efficient gene expression that is not restricted to host organism, substrate, or scale.},
doi = {10.1038/s41467-018-05857-3},
journal = {Nature Communications},
number = ,
volume = 9,
place = {United States},
year = {2018},
month = {9}
}

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