Tagliani A.

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Synthetic promoters went green: MinSyns bridge thegap between tunable expression and synthetic biologyin plantsAndrea Tagliani *Department of Biosciences, Università degli Studi di Milano, 20133 Milan, Italy*Corresponding author: E-mail: andrea.tagliani@unimi.itPrecise control of gene expression is critical to allow the designof tunable synthetic gene circuits. To date, our ability to pre-cisely predict orthogonal expression in plants lags well behindthat of animals and bacteria. This is largely because traditionalattempts to characterize plant promoters have found few reli-able sequence patterns. Even the TATA box is found in a minor-ity of plant promoters (1). As a result, plant biologists are stillrelying on a set of promoters that are not completely orthogonaland that often cannot ensure homogenous expression betweendifferent tissues; moreover, the length of these promoters, thelocal DNA environment of the insertion and other unknown fac-tors often do not allow for tunable and specific expression.Recently, where classical approaches aimed at characteriz-ing a discrete set of cis elements in plant promoters have failedto provide a comprehensive answer, machine learning helpedresearchers to blaze a new path for synthetic promoter design.In a paper published in Nucleic Acid Research, Cai et al. (2) devel-oped a set of minimal synthetic promoters (MinSyns) by miningfrom typical promoters used in plant biology a set of rules bywhich, through a computational approach, the researcherswere able to build a set of small standardized cis-regulatory ele-ments (CREs) exploitable for green synthetic biology.The main fodder for the author’s machine learning approachconsisted not of plant promoters, but of sequences derived frompathogenic plant viruses, which are widely used in plant biologyto drive constitutive expression. They found that small CREsfrom a set of these promoters are regulated by an endogenousplant transcription factor. Indeed, deletion experiments con-firmed the importance of these CREs in regulating expression.The authors used the experimentally determined strength ofthese CREs to generate a quantitative score for each. They thendeveloped a script, which randomly assembles minimal pro-moters composed of few CREs for which a score is assigned,based on the relative promoter strength. Using luciferase-basedreporter assays, the authors first confirmed that their MinSyn li-brary could be exploited to tune transient expression in plantprotoplasts.The authors then selected four MinSyns for further charac-terization in transgenic plants. MinSyn promoters predictablydrove the constitutive expression of GUS or YFP in stable trans-genic lines of Arabidopsis thaliana, Brassica rapa and Nicotiana ben-thamiana plants. Finally, the authors demonstrated that it ispossible to build synthetic genetic circuits from MinSyns, allow-ing tunable expression of two genes and variable expressionpatterns depending on the number of cognate binding sites foran orthogonal TF.The novelty of this work lies in the organisms themselves.Due to their capacity to produce secondary metabolites andphotosynthetic abilities, plants are arguably the most suitablechassis for the production of drugs, sustainable foods, biofuelsand bioplastics (3, 4). Yet, tunable expression in plants hasremained elusive, due to poor characterization of plant pro-moters. This work has important implications for the potentialto develop a set of reliable promoters with predictable outputsfor plants.Conflict of interest statement. None declared.References1.Morton,T., Petricka,J., Corcoran,D.L., Li,S., Winter,C.M.,Carda,A., Benfey,P.N., Ohler,U. and Megraw,M. (2014)Submitted: 9 November 2020; Received (in revised form): 11 November 2020; Accepted: 16 November 2020VC The Author(s) 2020. Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/),which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.1Synthetic Biology, 2020, 5(1): ysaa027doi: 10.1093/synbio/ysaa027Advance Access Publication Date: 27 November 2020Synthetic Biology NewsDownloaded from https://academic.oup.com/synbio/article/5/1/ysaa027/6007534 by Biblioteca Biologica user on 04 June 2024Paired-end analysis of transcription start sites in Arabidopsisreveals plant-specific promoter signatures. Plant Cell, 26,2746–2760.2.Cai,Y.M., Kallam,K., Tidd,H., Gendarini,G., Salzman,A. andPatron,N.J. (2020) Rational design of minimal synthetic pro-moters for plants. Nucleic Acids Res., 48, 11845–11856.3.Fesenko,E. and Edwards,R. (2014) Plant synthetic biology: anew platform for industrial biotechnology. J. Exp. Bot., 65,1927–1937.4.Roell,M.S. and Zurbriggen,M.D. (2020) The impact of syntheticbiology for future agriculture and nutrition. Curr. Opin.Biotechnol., 61, 102–109.2 | Synthetic Biology, 2020, Vol. 5, No. 1Downloaded from https://academic.oup.com/synbio/article/5/1/ysaa027/6007534 by Biblioteca Biologica user on 04 June 2024

Synthetic promoters went green: MinSyns bridge the gap between tunable expression and synthetic biology in plants

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Synthetic promoters went green: MinSyns bridge the gap between tunable expression and synthetic biology in plants

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