Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants
Abstract
Tight control and multifactorial regulation of gene expression are important challenges in genetic engineering and are critical for the development of regulatory circuits. In meeting these challenges we will facilitate transgene expression regulation and support the fine-tuning of metabolic pathways to avoid the accumulation of undesired intermediates. By employing the endoribonuclease Csy4 and its recognition sequence from Pseudomonas aeruginosa and manipulating 5'UTR of mRNA, we developed a two-component expression–repression system to tightly control synthesis of transgene products. We demonstrated that this regulatory device was functional in monocotyledonous and dicotyledonous plant species, and showed that it can be used to repress transgene expression by >400-fold and to synchronize transgene repression. In addition to tissue-specific transgene repression, this system offers stimuli-dependent expression control. Here, we identified 54 orthologous systems from various bacteria, using a bioinformatics approach and then validated in planta the activity for a few of those systems, demonstrating the potential diversity of such a two-component repressor system.
- Authors:
-
[1];
[1];
[2];
- Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
- Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering, Dept. of Chemical and Biomolecular Engineering
- Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division; Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
- Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division; Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology; National Inst. of Applied Sciences (INSA), Lyon (France)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1361519
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- ACS Synthetic Biology
- Additional Journal Information:
- Journal Volume: 6; Journal Issue: 5; Journal ID: ISSN 2161-5063
- Publisher:
- American Chemical Society (ACS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; CRISPR/Cas9; Csy4; endoribonuclease; gene regulation; synthetic biology; two-component repressor system
Citation Formats
Liang, Yan, Richardson, Sarah, Yan, Jingwei, Benites, Veronica T., Cheng-Yue, Clarabelle, Tran, Thu, Mortimer, Jenny, Mukhopadhyay, Aindrila, Keasling, Jay D., Scheller, Henrik V., and Loqué, Dominique. Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants. United States: N. p., 2017.
Web. doi:10.1021/acssynbio.6b00295.
Liang, Yan, Richardson, Sarah, Yan, Jingwei, Benites, Veronica T., Cheng-Yue, Clarabelle, Tran, Thu, Mortimer, Jenny, Mukhopadhyay, Aindrila, Keasling, Jay D., Scheller, Henrik V., & Loqué, Dominique. Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants. United States. https://doi.org/10.1021/acssynbio.6b00295
Liang, Yan, Richardson, Sarah, Yan, Jingwei, Benites, Veronica T., Cheng-Yue, Clarabelle, Tran, Thu, Mortimer, Jenny, Mukhopadhyay, Aindrila, Keasling, Jay D., Scheller, Henrik V., and Loqué, Dominique. Tue .
"Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants". United States. https://doi.org/10.1021/acssynbio.6b00295. https://www.osti.gov/servlets/purl/1361519.
@article{osti_1361519,
title = {Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants},
author = {Liang, Yan and Richardson, Sarah and Yan, Jingwei and Benites, Veronica T. and Cheng-Yue, Clarabelle and Tran, Thu and Mortimer, Jenny and Mukhopadhyay, Aindrila and Keasling, Jay D. and Scheller, Henrik V. and Loqué, Dominique},
abstractNote = {Tight control and multifactorial regulation of gene expression are important challenges in genetic engineering and are critical for the development of regulatory circuits. In meeting these challenges we will facilitate transgene expression regulation and support the fine-tuning of metabolic pathways to avoid the accumulation of undesired intermediates. By employing the endoribonuclease Csy4 and its recognition sequence from Pseudomonas aeruginosa and manipulating 5'UTR of mRNA, we developed a two-component expression–repression system to tightly control synthesis of transgene products. We demonstrated that this regulatory device was functional in monocotyledonous and dicotyledonous plant species, and showed that it can be used to repress transgene expression by >400-fold and to synchronize transgene repression. In addition to tissue-specific transgene repression, this system offers stimuli-dependent expression control. Here, we identified 54 orthologous systems from various bacteria, using a bioinformatics approach and then validated in planta the activity for a few of those systems, demonstrating the potential diversity of such a two-component repressor system.},
doi = {10.1021/acssynbio.6b00295},
journal = {ACS Synthetic Biology},
number = 5,
volume = 6,
place = {United States},
year = {Tue Jan 17 00:00:00 EST 2017},
month = {Tue Jan 17 00:00:00 EST 2017}
}
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Works referenced in this record:
Targeted transcriptional repression using a chimeric TALE-SRDX repressor protein
journal, December 2011
- Mahfouz, Magdy M.; Li, Lixin; Piatek, Marek
- Plant Molecular Biology, Vol. 78, Issue 3
Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency
journal, January 2015
- Eudes, Aymerick; Sathitsuksanoh, Noppadon; Baidoo, Edward E. K.
- Plant Biotechnology Journal, Vol. 13, Issue 9
Stringent control of transgene expression in Arabidopsis thaliana using the Top10 promoter system
journal, March 2000
- Love, John; Scott, Amie C.; Thompson, William F.
- The Plant Journal, Vol. 21, Issue 6
Both the constitutive Cauliflower Mosaic Virus 35S and tissue-specific AGAMOUS enhancers activate transcription autonomously in Arabidopsis thaliana
journal, August 2010
- Singer, Stacy D.; Cox, Kerik D.; Liu, Zongrang
- Plant Molecular Biology, Vol. 74, Issue 3
mRNA localization: message on the move
journal, April 2001
- Jansen, Ralf-Peter
- Nature Reviews Molecular Cell Biology, Vol. 2, Issue 4
A nuclear micrococcal-sensitive, ATP-dependent exoribonuclease degrades uncapped but not capped RNA substratesx
journal, May 1991
- Murthy, K. G. K.; Park, P.; Manley, J. L.
- Nucleic Acids Research, Vol. 19, Issue 10
An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3
journal, May 2011
- Sashital, Dipali G.; Jinek, Martin; Doudna, Jennifer A.
- Nature Structural & Molecular Biology, Vol. 18, Issue 6
The effect of intron location on intron-mediated enhancement of gene expression in Arabidopsis: Intron position affects enhancement
journal, November 2004
- Rose, Alan B.
- The Plant Journal, Vol. 40, Issue 5
Sequence- and Structure-Specific RNA Processing by a CRISPR Endonuclease
journal, September 2010
- Haurwitz, R. E.; Jinek, M.; Wiedenheft, B.
- Science, Vol. 329, Issue 5997, p. 1355-1358
ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering
journal, July 2013
- Gaj, Thomas; Gersbach, Charles A.; Barbas, Carlos F.
- Trends in Biotechnology, Vol. 31, Issue 7, p. 397-405
Detecting microRNA binding and siRNA off-target effects from expression data
journal, November 2008
- van Dongen, Stijn; Abreu-Goodger, Cei; Enright, Anton J.
- Nature Methods, Vol. 5, Issue 12
Cell-to-cell and long-distance siRNA movement in plants: mechanisms and biological implications
journal, October 2011
- Brosnan, Christopher Andrew; Voinnet, Olivier
- Current Opinion in Plant Biology, Vol. 14, Issue 5
PlantGDB: a resource for comparative plant genomics
journal, December 2007
- Duvick, J.; Fu, A.; Muppirala, U.
- Nucleic Acids Research, Vol. 36, Issue Database
A highly efficient transient protoplast system for analyzing defence gene expression and protein–protein interactions in rice
journal, July 2006
- Chen, Songbiao; Tao, Lizen; Zeng, Lirong
- Molecular Plant Pathology, Vol. 7, Issue 5
Isolation of a strong Arabidopsis guard cell promoter and its potential as a research tool
journal, January 2008
- Yang, Yingzhen; Costa, Alex; Leonhardt, Nathalie
- Plant Methods, Vol. 4, Issue 1
PlantGDB, plant genome database and analysis tools
journal, January 2004
- Dong, Q.
- Nucleic Acids Research, Vol. 32, Issue 90001
RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors
journal, November 2014
- Piatek, Agnieszka; Ali, Zahir; Baazim, Hatoon
- Plant Biotechnology Journal, Vol. 13, Issue 4
Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA: Mechanism of CRISPR RNA cleavage
journal, April 2012
- Haurwitz, Rachel E.; Sternberg, Samuel H.; Doudna, Jennifer A.
- The EMBO Journal, Vol. 31, Issue 12
Synthetic biology to access and expand nature's chemical diversity
journal, February 2016
- Smanski, Michael J.; Zhou, Hui; Claesen, Jan
- Nature Reviews Microbiology, Vol. 14, Issue 3
Tight regulation of plant immune responses by combining promoter and suicide exon elements
journal, July 2015
- Gonzalez, Tania L.; Liang, Yan; Nguyen, Bao N.
- Nucleic Acids Research, Vol. 43, Issue 14
Identification of an essential upstream element in the nopaline synthase promoter by stable and transient assays
journal, August 1987
- Ebert, P. R.; Ha, S. B.; An, G.
- Proceedings of the National Academy of Sciences, Vol. 84, Issue 16
Stringent repression and homogeneous de-repression by tetracycline of a modified CaMV 35S promoter in intact transgenic tobacco plants.
journal, May 1992
- Gatz, C.; Frohberg, C.; Wendenburg, R.
- The Plant Journal, Vol. 2, Issue 3
CRISPR-Cas systems for editing, regulating and targeting genomes
journal, March 2014
- Sander, Jeffry D.; Joung, J. Keith
- Nature Biotechnology, Vol. 32, Issue 4
Controlling gene expression in plants using synthetic zinc finger transcription factors
journal, December 2002
- Stege, Justin T.; Guan, Xuen; Ho, Thao
- The Plant Journal, Vol. 32, Issue 6
Localization, Ion Channel Regulation, and Genetic Interactions during Abscisic Acid Signaling of the Nuclear mRNA Cap-Binding Protein, ABH1
journal, November 2002
- Hugouvieux, Véronique; Murata, Yoshiyuki; Young, Jared J.
- Plant Physiology, Vol. 130, Issue 3
Transgene regulation in plants by alternative splicing of a suicide exon
journal, February 2012
- Hickey, Scott F.; Sridhar, Malathy; Westermann, Alexander J.
- Nucleic Acids Research, Vol. 40, Issue 10
Small molecules that interact with RNA : riboswitch‐based gene control and its involvement in metabolic regulation in plants and algae
journal, June 2014
- Bocobza, Samuel E.; Aharoni, Asaph
- The Plant Journal, Vol. 79, Issue 4
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
journal, January 2002
- Lescot, M.
- Nucleic Acids Research, Vol. 30, Issue 1
Gene silencing in plants using artificial microRNAs and other small RNAs: Engineering small RNA-mediated gene silencing
journal, February 2008
- Ossowski, Stephan; Schwab, Rebecca; Weigel, Detlef
- The Plant Journal, Vol. 53, Issue 4
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
journal, January 2007
- Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine
- BMC Bioinformatics, Vol. 8, Issue 1
KEGG as a reference resource for gene and protein annotation
journal, October 2015
- Kanehisa, Minoru; Sato, Yoko; Kawashima, Masayuki
- Nucleic Acids Research, Vol. 44, Issue D1
A transcription activation system for regulated gene expression in transgenic plants
journal, January 1998
- Moore, I.; Galweiler, L.; Grosskopf, D.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 1
Computational discovery of soybean promoter cis -regulatory elements for the construction of soybean cyst nematode-inducible synthetic promoters
journal, June 2014
- Liu, Wusheng; Mazarei, Mitra; Peng, Yanhui
- Plant Biotechnology Journal, Vol. 12, Issue 8
An mRNA Cap Binding Protein, ABH1, Modulates Early Abscisic Acid Signal Transduction in Arabidopsis
journal, August 2001
- Hugouvieux, Véronique; Kwak, June M.; Schroeder, Julian I.
- Cell, Vol. 106, Issue 4
Endogenous microRNA can be broadly exploited to regulate transgene expression according to tissue, lineage and differentiation state
journal, November 2007
- Brown, Brian D.; Gentner, Bernhard; Cantore, Alessio
- Nature Biotechnology, Vol. 25, Issue 12
Fine‐tuning levels of heterologous gene expression in plants by orthogonal variation of the untranslated regions of a nonreplicating transient expression system
journal, March 2014
- Meshcheriakova, Yulia A.; Saxena, Pooja; Lomonossoff, George P.
- Plant Biotechnology Journal, Vol. 12, Issue 6
Transactivated and chemically inducible gene expression in plants
journal, February 2006
- Moore, Ian; Samalova, Marketa; Kurup, Smita
- The Plant Journal, Vol. 45, Issue 4
Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor
journal, March 1999
- Kasuga, Mie; Liu, Qiang; Miura, Setsuko
- Nature Biotechnology, Vol. 17, Issue 3
Characterization of the interaction of plant transcription factors using a bacterial repressor protein.
journal, December 1991
- Frohberg, C.; Heins, L.; Gatz, C.
- Proceedings of the National Academy of Sciences, Vol. 88, Issue 23
Antisense Down-Regulation of 4CL Expression Alters Lignification, Tree Growth, and Saccharification Potential of Field-Grown Poplar
journal, August 2010
- Voelker, Steven L.; Lachenbruch, Barbara; Meinzer, Frederick C.
- Plant Physiology, Vol. 154, Issue 2
Cinnamate-4-Hydroxylase Expression in Arabidopsis (Regulation in Response to Development and the Environment)
journal, March 1997
- Bell-Lelong, D. A.; Cusumano, J. C.; Meyer, K.
- Plant Physiology, Vol. 113, Issue 3
Heritable endogenous gene regulation in plants with designed polydactyl zinc finger transcription factors
journal, September 2002
- Guan, Xuen; Stege, Justin; Kim, Myoung
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 20
A multiplexed miRNA and transgene expression platform for simultaneous repression and expression of protein coding sequences
journal, January 2016
- Seyhan, Attila A.
- Molecular BioSystems, Vol. 12, Issue 1
The cap and poly(A) tail function synergistically to regulate mRNA translational efficiency.
journal, November 1991
- Gallie, D. R.
- Genes & Development, Vol. 5, Issue 11
Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells
journal, May 2014
- Nissim, Lior; Perli, Samuel D.; Fridkin, Alexandra
- Molecular Cell, Vol. 54, Issue 4
Engineering Translational Activators with CRISPR-Cas System
journal, October 2015
- Du, Pei; Miao, Chensi; Lou, Qiuli
- ACS Synthetic Biology, Vol. 5, Issue 1
Controlling mRNA stability and translation with the CRISPR endoribonuclease Csy4
journal, September 2015
- Borchardt, Erin K.; Vandoros, Leonidas A.; Huang, Michael
- RNA, Vol. 21, Issue 11
A 28 nt long synthetic 5′UTR (synJ) as an enhancer of transgene expression in dicotyledonous plants
journal, November 2012
- Kanoria, Shaveta; Burma, Pradeep Kumar
- BMC Biotechnology, Vol. 12, Issue 1
A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation
journal, August 2015
- Lowder, Levi G.; Zhang, Dengwei; Baltes, Nicholas J.
- Plant Physiology, Vol. 169, Issue 2
Characteristics of Plant Essential Genes Allow for within- and between-Species Prediction of Lethal Mutant Phenotypes
journal, August 2015
- Lloyd, John P.; Seddon, Alexander E.; Moghe, Gaurav D.
- The Plant Cell, Vol. 27, Issue 8
Mechanism of substrate selection by a highly specific CRISPR endoribonuclease
journal, February 2012
- Sternberg, S. H.; Haurwitz, R. E.; Doudna, J. A.
- RNA, Vol. 18, Issue 4
Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana
journal, December 1998
- Clough, Steven J.; Bent, Andrew F.
- The Plant Journal, Vol. 16, Issue 6, p. 735-743
Plant synthetic biology
journal, May 2015
- Liu, Wusheng; Stewart, C. Neal
- Trends in Plant Science, Vol. 20, Issue 5
Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants
journal, November 2006
- Sparkes, Imogen A.; Runions, John; Kearns, Anne
- Nature Protocols, Vol. 1, Issue 4
MicroRNA-mediated gene regulation: potential applications for plant genetic engineering
journal, June 2013
- Zhou, Man; Luo, Hong
- Plant Molecular Biology, Vol. 83, Issue 1-2
Design and construction of an in-plant activation cassette for transgene expression and recombinant protein production in plants
journal, April 2014
- Dugdale, Benjamin; Mortimer, Cara L.; Kato, Maiko
- Nature Protocols, Vol. 9, Issue 5
Retracted: An enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus
journal, February 2003
- Voinnet, Olivier; Rivas, Susana; Mestre, Pere
- The Plant Journal, Vol. 33, Issue 5
Control of gene expression in tobacco cells using a bacterial operator-repressor system.
journal, April 1992
- Wilde, R. J.; Shufflebottom, D.; Cooke, S.
- The EMBO Journal, Vol. 11, Issue 4
ppdb: plant promoter database version 3.0
journal, November 2013
- Hieno, Ayaka; Naznin, Hushna Ara; Hyakumachi, Mitsuro
- Nucleic Acids Research, Vol. 42, Issue D1
RNA processing enables predictable programming of gene expression
journal, September 2012
- Qi, Lei; Haurwitz, Rachel E.; Shao, Wenjun
- Nature Biotechnology, Vol. 30, Issue 10
The TRANSPLANTA collection of A rabidopsis lines: a resource for functional analysis of transcription factors based on their conditional overexpression
journal, February 2014
- Coego, Alberto; Brizuela, Esther; Castillejo, Pablo
- The Plant Journal, Vol. 77, Issue 6
RNAi for functional genomics in plants
journal, January 2010
- McGinnis, K. M.
- Briefings in Functional Genomics, Vol. 9, Issue 2
Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools
journal, June 2012
- Ham, T. S.; Dmytriv, Z.; Plahar, H.
- Nucleic Acids Research, Vol. 40, Issue 18
An in vivo, luciferase-based, Agrobacterium-infiltration assay system: implications for post-transcriptional gene silencing
journal, March 2006
- Cazzonelli, Christopher Ian; Velten, Jeff
- Planta, Vol. 224, Issue 3
Standards for plant synthetic biology: a common syntax for exchange of DNA parts
journal, July 2015
- Patron, Nicola J.; Orzaez, Diego; Marillonnet, Sylvestre
- New Phytologist, Vol. 208, Issue 1
Biotechnology and synthetic biology approaches for metabolic engineering of bioenergy crops
journal, June 2016
- Shih, Patrick M.; Liang, Yan; Loqué, Dominique
- The Plant Journal, Vol. 87, Issue 1
A chimeric transactivator allows tetracycline-responsive gene expression in whole plants
journal, April 1994
- Weinmann, Pamela; Gossen, Manfred; Hillen, Wolfgang
- The Plant Journal, Vol. 5, Issue 4
A library of synthetic transcription activator‐like effector‐activated promoters for coordinated orthogonal gene expression in plants
journal, April 2015
- Brückner, Kathleen; Schäfer, Petra; Weber, Ernst
- The Plant Journal, Vol. 82, Issue 4
Initiation factors that bind mRNA. A comparison of mammalian factors with wheat germ factors.
journal, April 1988
- Abramson, R. D.; Browning, K. S.; Dever, T. E.
- Journal of Biological Chemistry, Vol. 263, Issue 11
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- BMC Research Notes, Vol. 13, Issue 1
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- Liang, Yan; Eudes, Aymerick; Yogiswara, Sasha
- Biotechnology for Biofuels, Vol. 12, Issue 1
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journal, September 2018
- Mortimer, Jenny C.
- Experimental Biology and Medicine, Vol. 244, Issue 4
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journal, March 2019
- Gemmill, Darren; D’souza, Simmone; Meier-Stephenson, Vanessa
- Biochemistry and Cell Biology
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- Experimental Biology and Medicine, Vol. 244, Issue 4
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