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Camsund D, Jaramillo A, Lindblad P. Engineering of a Promoter Repressed by a Light-Regulated Transcription Factor in Escherichia coli. BIODESIGN RESEARCH 2021; 2021:9857418. [PMID: 37849950 PMCID: PMC10521638 DOI: 10.34133/2021/9857418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/23/2021] [Indexed: 10/19/2023] Open
Abstract
Light-regulated gene expression systems allow controlling gene expression in space and time with high accuracy. Contrary to previous synthetic light sensors that incorporate two-component systems which require localization at the plasma membrane, soluble one-component repression systems provide several advantageous characteristics. Firstly, they are soluble and able to diffuse across the cytoplasm. Secondly, they are smaller and of lower complexity, enabling less taxing expression and optimization of fewer parts. Thirdly, repression through steric hindrance is a widespread regulation mechanism that does not require specific interaction with host factors, potentially enabling implementation in different organisms. Herein, we present the design of the synthetic promoter PEL that in combination with the light-regulated dimer EL222 constitutes a one-component repression system. Inspired by previously engineered synthetic promoters and the Escherichia coli lacZYA promoter, we designed PEL with two EL222 operators positioned to hinder RNA polymerase binding when EL222 is bound. PEL is repressed by EL222 under conditions of white light with a light-regulated repression ratio of five. Further, alternating conditions of darkness and light in cycles as short as one hour showed that repression is reversible. The design of the PEL-EL222 system herein presented could aid the design and implementation of analogous one-component optogenetic repression systems. Finally, we compare the PEL-EL222 system with similar systems and suggest general improvements that could optimize and extend the functionality of EL222-based as well as other one-component repression systems.
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Affiliation(s)
- Daniel Camsund
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
- Molecular Systems Biology, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, UK
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Institute for Integrative Systems Biology (I2SysBio), CSIC – Universitat de València, 46980 Paterna, Spain
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
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Deter HS, Abualrahi AH, Jadhav P, Schweer EK, Ogle CT, Butzin NC. Proteolytic Queues at ClpXP Increase Antibiotic Tolerance. ACS Synth Biol 2020; 9:95-103. [PMID: 31860281 DOI: 10.1021/acssynbio.9b00358] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Antibiotic tolerance is a widespread phenomenon that renders antibiotic treatments less effective and facilitates antibiotic resistance. Here we explore the role of proteases in antibiotic tolerance, short-term population survival of antibiotics, using queueing theory (i.e., the study of waiting lines), computational models, and a synthetic biology approach. Proteases are key cellular components that degrade proteins and play an important role in a multidrug tolerant subpopulation of cells, called persisters. We found that queueing at the protease ClpXP increases antibiotic tolerance ∼80 and ∼60 fold in an E. coli population treated with ampicillin and ciprofloxacin, respectively. There does not appear to be an effect on antibiotic persistence, which we distinguish from tolerance based on population decay. These results demonstrate that proteolytic queueing is a practical method to probe proteolytic activity in bacterial tolerance and related genes, while limiting the unintended consequences frequently caused by gene knockout and overexpression.
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Affiliation(s)
- Heather S Deter
- Department of Biology and Microbiology , South Dakota State University , Brookings , South Dakota 57006 , United States
| | - Alawiah H Abualrahi
- Department of Biology and Microbiology , South Dakota State University , Brookings , South Dakota 57006 , United States
| | - Prajakta Jadhav
- Department of Biology and Microbiology , South Dakota State University , Brookings , South Dakota 57006 , United States
| | - Elise K Schweer
- Department of Biology and Microbiology , South Dakota State University , Brookings , South Dakota 57006 , United States
| | | | - Nicholas C Butzin
- Department of Biology and Microbiology , South Dakota State University , Brookings , South Dakota 57006 , United States
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Brechun KE, Zhen D, Jaikaran A, Borisenko V, Kumauchi M, Hoff WD, Arndt KM, Woolley GA. Detection of Incorporation of p-Coumaric Acid into Photoactive Yellow Protein Variants in Vivo. Biochemistry 2019; 58:2682-2694. [DOI: 10.1021/acs.biochem.9b00279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Katherine E. Brechun
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Potsdam, Brandenburg 14476, Germany
| | - Danlin Zhen
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Anna Jaikaran
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Vitali Borisenko
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 Life Sciences East, Stillwater, Oklahoma 74078, United States
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 Life Sciences East, Stillwater, Oklahoma 74078, United States
| | - Katja M. Arndt
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Potsdam, Brandenburg 14476, Germany
| | - G. Andrew Woolley
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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Hughes RM. A compendium of chemical and genetic approaches to light-regulated gene transcription. Crit Rev Biochem Mol Biol 2018; 53:453-474. [PMID: 30040498 DOI: 10.1080/10409238.2018.1487382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
On-cue regulation of gene transcription is an invaluable tool for the study of biological processes and the development and integration of next-generation therapeutics. Ideal reagents for the precise regulation of gene transcription should be nontoxic to the host system, highly tunable, and provide a high level of spatial and temporal control. Light, when coupled with protein or small molecule-linked photoresponsive elements, presents an attractive means of meeting the demands of an ideal system for regulating gene transcription. In this review, we cover recent developments in the burgeoning field of light-regulated gene transcription, covering both genetically encoded and small-molecule based strategies for optical regulation of transcription during the period 2012 till present.
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Affiliation(s)
- Robert M Hughes
- a Department of Chemistry , East Carolina University , Greenville , NC , USA
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Strategies for the photo-control of endogenous protein activity. Curr Opin Struct Biol 2017; 45:53-58. [DOI: 10.1016/j.sbi.2016.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/13/2016] [Indexed: 11/21/2022]
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Optogenetic Inhibitor of the Transcription Factor CREB. ACTA ACUST UNITED AC 2016; 22:1531-1539. [PMID: 26590638 DOI: 10.1016/j.chembiol.2015.09.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/11/2015] [Accepted: 09/24/2015] [Indexed: 01/28/2023]
Abstract
Current approaches for optogenetic control of transcription do not mimic the activity of endogenous transcription factors, which act at numerous sites in the genome in a complex interplay with other factors. Optogenetic control of dominant negative versions of endogenous transcription factors provides a mechanism for mimicking the natural regulation of gene expression. Here we describe opto-DN-CREB, a blue-light-controlled inhibitor of the transcription factor CREB created by fusing the dominant negative inhibitor A-CREB to photoactive yellow protein (PYP). A light-driven conformational change in PYP prevents coiled-coil formation between A-CREB and CREB, thereby activating CREB. Optogenetic control of CREB function was characterized in vitro, in HEK293T cells, and in neurons where blue light enabled control of expression of the CREB targets NR4A2 and c-Fos. Dominant negative inhibitors exist for numerous transcription factors; linking these to optogenetic domains offers a general approach for spatiotemporal control of native transcriptional events.
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Kumar A, Ali AM, Woolley GA. Photo-control of DNA binding by an engrailed homeodomain-photoactive yellow protein hybrid. Photochem Photobiol Sci 2015. [PMID: 26204102 DOI: 10.1039/c5pp00160a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A photo-controlled version of the engrailed homeodomain (zENG) was created by inserting the homeodomain into a surface loop of a circularly permuted version of the photoactive yellow protein (cPYP). The two proteins fold independently as judged by NMR and fluorescence denaturation measurements. In the dark, the affinity of the zENG domain for its cognate DNA is inhibited >100-fold compared to wild-type zENG. Blue-light irradiation of the hybrid protein leads to enhanced conformational dynamics of the cPYP portion and a two-fold enhancement of the DNA binding affinity of the zENG domain. These results suggest that insertion into a surface loop of cPYP can be a general approach for conferring an initial level of photo-control on a given target protein. Focussed mutation/selection strategies may then be used to enhance the degree of photo-control.
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Affiliation(s)
- A Kumar
- Dept. of Chemistry, University of Toronto, 80 St. George St., Toronto, CanadaM5S 3H6.
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