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Fricke PM, Gries ML, Mürköster M, Höninger M, Gätgens J, Bott M, Polen T. The l-rhamnose-dependent regulator RhaS and its target promoters from Escherichia coli expand the genetic toolkit for regulatable gene expression in the acetic acid bacterium Gluconobacter oxydans. Front Microbiol 2022; 13:981767. [PMID: 36060754 PMCID: PMC9429829 DOI: 10.3389/fmicb.2022.981767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/13/2022] [Indexed: 11/25/2022] Open
Abstract
For regulatable target gene expression in the acetic acid bacterium (AAB) Gluconobacter oxydans only recently the first plasmids became available. These systems solely enable AraC- and TetR-dependent induction. In this study we showed that the l-rhamnose-dependent regulator RhaS from Escherichia coli and its target promoters PrhaBAD, PrhaT, and PrhaSR could also be used in G. oxydans for regulatable target gene expression. Interestingly, in contrast to the responsiveness in E. coli, in G. oxydans RhaS increased the expression from PrhaBAD in the absence of l-rhamnose and repressed PrhaBAD in the presence of l-rhamnose. Inserting an additional RhaS binding site directly downstream from the −10 region generating promoter variant PrhaBAD(+RhaS-BS) almost doubled the apparent RhaS-dependent promoter strength. Plasmid-based PrhaBAD and PrhaBAD(+RhaS-BS) activity could be reduced up to 90% by RhaS and l-rhamnose, while a genomic copy of PrhaBAD(+RhaS-BS) appeared fully repressed. The RhaS-dependent repression was largely tunable by l-rhamnose concentrations between 0% and only 0.3% (w/v). The RhaS-PrhaBAD and the RhaS-PrhaBAD(+RhaS-BS) systems represent the first heterologous repressible expression systems for G. oxydans. In contrast to PrhaBAD, the E. coli promoter PrhaT was almost inactive in the absence of RhaS. In the presence of RhaS, the PrhaT activity in the absence of l-rhamnose was weak, but could be induced up to 10-fold by addition of l-rhamnose, resulting in a moderate expression level. Therefore, the RhaS-PrhaT system could be suitable for tunable low-level expression of difficult enzymes or membrane proteins in G. oxydans. The insertion of an additional RhaS binding site directly downstream from the E. coli PrhaT −10 region increased the non-induced expression strength and reversed the regulation by RhaS and l-rhamnose from inducible to repressible. The PrhaSR promoter appeared to be positively auto-regulated by RhaS and this activation was increased by l-rhamnose. In summary, the interplay of the l-rhamnose-binding RhaS transcriptional regulator from E. coli with its target promoters PrhaBAD, PrhaT, PrhaSR and variants thereof provide new opportunities for regulatable gene expression in G. oxydans and possibly also for simultaneous l-rhamnose-triggered repression and activation of target genes, which is a highly interesting possibility in metabolic engineering approaches requiring redirection of carbon fluxes.
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The AraC/XylS Protein MxiE and Its Coregulator IpgC Control a Negative Feedback Loop in the Transcriptional Cascade That Regulates Type III Secretion in Shigella flexneri. J Bacteriol 2022; 204:e0013722. [PMID: 35703565 DOI: 10.1128/jb.00137-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the AraC family of transcriptional regulators (AFTRs) control the expression of many genes important to cellular processes, including virulence. In Shigella species, the type III secretion system (T3SS), a key determinant for host cell invasion, is regulated by the three-tiered VirF/VirB/MxiE transcriptional cascade. Both VirF and MxiE belong to the AFTRs and are characterized as positive transcriptional regulators. Here, we identify a novel regulatory activity for MxiE and its coregulator IpgC, which manifests as a negative feedback loop in the VirF/VirB/MxiE transcriptional cascade. Our findings show that MxiE and IpgC downregulate the virB promoter and, hence, VirB protein production, thus decreasing VirB-dependent promoter activity at ospD1, one of the nearly 50 VirB-dependent genes. At the virB promoter, regions required for negative MxiE- and IpgC-dependent regulation were mapped and found to be coincident with regions required for positive VirF-dependent regulation. In tandem, negative MxiE- and IpgC-dependent regulation of the virB promoter only occurred in the presence of VirF, suggesting that MxiE and IpgC can function to counter VirF activation of the virB promoter. Lastly, MxiE and IpgC do not downregulate another VirF-activated promoter, icsA, demonstrating that this negative feedback loop targets the virB promoter. Our study provides insight into a mechanism that may reprogram Shigella virulence gene expression following type III secretion and provides the impetus to examine if MxiE and IpgC homologs in other important bacterial pathogens, such as Burkholderia pseudomallei and Salmonella enterica serovars Typhimurium and Typhi, coordinate similar negative feedback loops. IMPORTANCE The large AraC family of transcriptional regulators (AFTRs) control virulence gene expression in many bacterial pathogens. In Shigella species, the AraC/XylS protein MxiE and its coregulator IpgC positively regulate the expression of type III secretion system genes within the three-tiered VirF/VirB/MxiE transcriptional cascade. Our findings suggest a negative feedback loop in the VirF/VirB/MxiE cascade, in which MxiE and IpgC counter VirF-dependent activation of the virB promoter, thus making this the first characterization of negative MxiE- and IpgC-dependent regulation. Our study provides insight into a mechanism that likely reprograms Shigella virulence gene expression following type III secretion, which has implications for other important bacterial pathogens with functional homologs of MxiE and IpgC.
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Picard HR, Schwingen KS, Green LM, Shis DL, Egan SM, Bennett MR, Swint-Kruse L. Allosteric regulation within the highly interconnected structural scaffold of AraC/XylS homologs tolerates a wide range of amino acid changes. Proteins 2022; 90:186-199. [PMID: 34369028 PMCID: PMC8671227 DOI: 10.1002/prot.26206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 01/03/2023]
Abstract
To create bacterial transcription "circuits" for biotechnology, one approach is to recombine natural transcription factors, promoters, and operators. Additional novel functions can be engineered from existing transcription factors such as the E. coli AraC transcriptional activator, for which binding to DNA is modulated by binding L-arabinose. Here, we engineered chimeric AraC/XylS transcription activators that recognized ara DNA binding sites and responded to varied effector ligands. The first step, identifying domain boundaries in the natural homologs, was challenging because (i) no full-length, dimeric structures were available and (ii) extremely low sequence identities (≤10%) among homologs precluded traditional assemblies of sequence alignments. Thus, to identify domains, we built and aligned structural models of the natural proteins. The designed chimeric activators were assessed for function, which was then further improved by random mutagenesis. Several mutational variants were identified for an XylS•AraC chimera that responded to benzoate; two enhanced activation to near that of wild-type AraC. For an RhaR•AraC chimera, a variant with five additional substitutions enabled transcriptional activation in response to rhamnose. These five changes were dispersed across the protein structure, and combinatorial experiments testing subsets of substitutions showed significant non-additivity. Combined, the structure modeling and epistasis suggest that the common AraC/XylS structural scaffold is highly interconnected, with complex intra-protein and inter-domain communication pathways enabling allosteric regulation. At the same time, the observed epistasis and the low sequence identities of the natural homologs suggest that the structural scaffold and function of transcriptional regulation are nevertheless highly accommodating of amino acid changes.
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Affiliation(s)
- Hunter R. Picard
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160
| | - Kristen S. Schwingen
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160
| | - Lisa M. Green
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160
| | - David L. Shis
- Department of Biosciences and Department of Bioengineering, Rice University, Houston, TX 77005
| | - Susan M. Egan
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045
| | - Matthew R. Bennett
- Department of Biosciences and Department of Bioengineering, Rice University, Houston, TX 77005
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160,To whom correspondence should be addressed: ; 913-588-0399
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Improved Dynamic Range of a Rhamnose-Inducible Promoter for Gene Expression in Burkholderia spp. Appl Environ Microbiol 2021; 87:e0064721. [PMID: 34190606 DOI: 10.1128/aem.00647-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A diverse genetic toolkit is critical for understanding bacterial physiology and genotype-phenotype relationships. Inducible promoter systems are an integral part of this toolkit. In Burkholderia and related species, the l-rhamnose-inducible promoter is among the first choices due to its tight control and the lack of viable alternatives. To improve upon its maximum activity and dynamic range, we explored the effect of promoter system modifications in Burkholderia cenocepacia with a LacZ-based reporter. By combining the bacteriophage T7 gene 10 stem-loop and engineered rhaI transcription factor-binding sites, we obtained a rhamnose-inducible system with a 6.5-fold and 3.0-fold increases in maximum activity and dynamic range, respectively, compared to the native promoter. We then added the modified promoter system to pSCrhaB2 and pSC201, common genetic tools used for plasmid-based and chromosome-based gene expression, respectively, in Burkholderia, creating pSCrhaB2plus and pSC201plus. We demonstrated the utility of pSCrhaB2plus for gene expression in B. thailandensis, B. multivorans, and B. vietnamiensis and used pSC201plus to control highly expressed essential genes from the chromosome of B. cenocepacia. The utility of the modified system was demonstrated as we recovered viable mutants to control ftsZ, rpoBC, and rpsF, whereas the unmodified promoter was unable to control rpsF. The modified expression system allowed control of an essential gene depletion phenotype at lower levels of l-rhamnose, the inducer. pSCRhaB2plus and pSC201plus are expected to be valuable additions to the genetic toolkit for Burkholderia and related species. IMPORTANCE Species of Burkholderia are dually recognized as being of attractive biotechnological potential but also opportunistic pathogens for immunocompromised individuals. Understanding the genotype-phenotype relationship is critical for synthetic biology approaches in Burkholderia to disentangle pathogenic from beneficial traits. A diverse genetic toolkit, including inducible promoters, is the foundation for these investigations. Thus, we sought to improve on the commonly used rhamnose-inducible promoter system. Our modifications resulted in both higher levels of heterologous protein expression and broader control over highly expressed essential genes in B. cenocepacia. The significance of our work is in expanding the genetic toolkit to enable more comprehensive studies into Burkholderia and related bacteria.
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Backbone Interactions Between Transcriptional Activator ExsA and Anti-Activator ExsD Facilitate Regulation of the Type III Secretion System in Pseudomonas aeruginosa. Sci Rep 2020; 10:9881. [PMID: 32555263 PMCID: PMC7303211 DOI: 10.1038/s41598-020-66555-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 05/20/2020] [Indexed: 12/20/2022] Open
Abstract
The type III secretion system (T3SS) is a pivotal virulence mechanism of many Gram-negative bacteria. During infection, the syringe-like T3SS injects cytotoxic proteins directly into the eukaryotic host cell cytoplasm. In Pseudomonas aeruginosa, expression of the T3SS is regulated by a signaling cascade involving the proteins ExsA, ExsC, ExsD, and ExsE. The AraC-type transcription factor ExsA activates transcription of all T3SS-associated genes. Prior to host cell contact, ExsA is inhibited through direct binding of the anti-activator protein ExsD. Host cell contact triggers secretion of ExsE and sequestration of ExsD by ExsC to cause the release of ExsA. ExsA does not bind ExsD through the canonical ligand binding pocket of AraC-type proteins. Using site-directed mutagenesis and a specific in vitro transcription assay, we have now discovered that backbone interactions between the amino terminus of ExsD and the ExsA beta barrel constitute a pivotal part of the ExsD-ExsA interface. Follow-up bacterial two-hybrid experiments suggest additional contacts create an even larger protein–protein interface. The discovered role of the amino terminus of ExsD in ExsA binding explains how ExsC might relieve the ExsD-mediated inhibition of T3SS gene expression, because the same region of ExsD interacts with ExsC following host cell contact.
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Hirooka K, Tamano A. Bacillus subtilis highly efficient protein expression systems that are chromosomally integrated and controllable by glucose and rhamnose. Biosci Biotechnol Biochem 2018; 82:1942-1954. [PMID: 30010487 DOI: 10.1080/09168451.2018.1497945] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
To achieve rhamnose-inducible efficient protein expression in Bacillus subtilis, we assembled the strong promoters of B. subtilis cdd and ylbP genes and the regulatory region (PrhaEW) of B. subtilis rhaEWRBMA operon, whose transcription is induced by rhamnose and repressed by glucose, to produce various hybrid constructs. These constructs were evaluated using B. subtilis strains carrying a fusion of each construct to the gene encoding a mutated green fluorescent protein in the chromosome. When these strains were cultivated in the presence of glucose or rhamnose, the strain carrying a fusion of a partial PrhaEW region, lacking the intrinsic Shine-Dalgarno (SD) sequence, and the ylbP SD sequence most strictly controlled the promoter activity depending on sugar species. Moreover, the strain carrying a fusion of the cdd core promoter and the ylbP SD sequence showed the highest promoter activity when it was cultivated in the presence of glucose until the late stationary phase. Abbreviations: RNAP: RNA polymerase; cre: catabolite-responsive element; SD: Shine-Dalgarno; PAGE: polyacrylamide gel electrophoresis; GFP: green fluorescent protein; OD600: optical density at 600 nm; LB: Luria-Bertani; a.u.: arbitrary unit; SDS: sodium dodecyl sulfate.
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Affiliation(s)
- Kazutake Hirooka
- a Department of Biotechnology, Faculty of Life Science and Biotechnology , Fukuyama University , Fukuyama Hiroshima , Japan
| | - Ayaka Tamano
- a Department of Biotechnology, Faculty of Life Science and Biotechnology , Fukuyama University , Fukuyama Hiroshima , Japan
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7
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Lange MD, Farmer BD, Declercq AM, Peatman E, Decostere A, Beck BH. Sickeningly Sweet: L-rhamnose stimulates Flavobacterium columnare biofilm formation and virulence. JOURNAL OF FISH DISEASES 2017; 40:1613-1624. [PMID: 28581211 DOI: 10.1111/jfd.12629] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/07/2017] [Accepted: 02/09/2017] [Indexed: 06/07/2023]
Abstract
Flavobacterium columnare, the causative agent of columnaris disease, causes substantial mortality worldwide in numerous freshwater finfish species. Due to its global significance and impact on the aquaculture industry continual efforts to better understand basic mechanisms that contribute to disease are urgently needed. The current work sought to evaluate the effect of L-rhamnose on the growth characteristics of F. columnare. While we initially did not observe any key changes during the total growth of F. columnare isolates tested when treated with L-rhamnose, it soon became apparent that the difference lies in the ability of this carbohydrate to facilitate the formation of biofilms. The addition of different concentrations of L-rhamnose consistently promoted the development of biofilms among different F. columnare isolates; however, it does not appear to be sufficient as a sole carbon source for biofilm growth. Our data also suggest that iron acquisition machinery is required for biofilm development. Finally, the addition of different concentrations of L-rhamnose to F. columnare prior to a laboratory challenge increased mortality rates in channel catfish (Ictalurus punctatus) as compared to controls. These results provide further evidence that biofilm formation is an integral virulence factor in the initiation of disease in fish.
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Affiliation(s)
- M D Lange
- Harry K. Dupree Stuttgart National Aquaculture Research Center, U.S. Department of Agriculture, Agricultural Research Service, Stuttgart, AR, USA
| | - B D Farmer
- Harry K. Dupree Stuttgart National Aquaculture Research Center, U.S. Department of Agriculture, Agricultural Research Service, Stuttgart, AR, USA
| | - A M Declercq
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
- Stress Physiology Research Group, Department of Bio-analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - E Peatman
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - A Decostere
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - B H Beck
- Aquatic Animal Health Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Auburn, AL, USA
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Hjelm A, Karyolaimos A, Zhang Z, Rujas E, Vikström D, Slotboom DJ, de Gier JW. Tailoring Escherichia coli for the l-Rhamnose P BAD Promoter-Based Production of Membrane and Secretory Proteins. ACS Synth Biol 2017; 6:985-994. [PMID: 28226208 DOI: 10.1021/acssynbio.6b00321] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Membrane and secretory protein production in Escherichia coli requires precisely controlled production rates to avoid the deleterious saturation of their biogenesis pathways. On the basis of this requirement, the E. coli l-rhamnose PBAD promoter (PrhaBAD) is often used for membrane and secretory protein production since PrhaBAD is thought to regulate protein production rates in an l-rhamnose concentration-dependent manner. By monitoring protein production in real-time in E. coli wild-type and an l-rhamnose catabolism deficient mutant, we demonstrate that the l-rhamnose concentration-dependent tunability of PrhaBAD-mediated protein production is actually due to l-rhamnose consumption rather than regulating production rates. Using this information, a RhaT-mediated l-rhamnose transport and l-rhamnose catabolism deficient double mutant was constructed. We show that this mutant enables the regulation of PrhaBAD-based protein production rates in an l-rhamnose concentration-dependent manner and that this is critical to optimize membrane and secretory protein production yields. The high precision of protein production rates provided by the PrhaBAD promoter in an l-rhamnose transport and catabolism deficient background could also benefit other applications in synthetic biology.
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Affiliation(s)
- Anna Hjelm
- Department
of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Alexandros Karyolaimos
- Department
of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Zhe Zhang
- Department
of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Edurne Rujas
- Department
of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | | | - Dirk Jan Slotboom
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9712 CP Groningen, The Netherlands
| | - Jan-Willem de Gier
- Department
of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
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Marschall L, Sagmeister P, Herwig C. Tunable recombinant protein expression in E. coli: promoter systems and genetic constraints. Appl Microbiol Biotechnol 2017; 101:501-512. [PMID: 27999902 PMCID: PMC5566544 DOI: 10.1007/s00253-016-8045-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 11/26/2016] [Accepted: 11/29/2016] [Indexed: 12/11/2022]
Abstract
Tuning of transcription is a promising strategy to overcome challenges associated with a non-suitable expression rate like outgrowth of segregants, inclusion body formation, metabolic burden and inefficient translocation. By adjusting the expression rate-even on line-to purposeful levels higher product titres and more cost-efficient production processes can be achieved by enabling culture long-term stability and constant product quality. Some tunable systems are registered for patents or already commercially available. Within this contribution, we discuss the induction mechanisms of various Escherichia coli inherent promoter systems with respect to their tunability and review studies using these systems for expression tuning. According to the current level of knowledge, some promoter systems were successfully used for expression tuning, and in some cases, analytical evidence on single-cell level is still pending. However, only a few studies using tunable strains apply a suitable process control strategy. So far, expression tuning has only gathered little attention, but we anticipate that expression tuning harbours great potential for enabling and optimizing the production of a broad spectrum of products in E. coli.
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Affiliation(s)
- Lukas Marschall
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Vienna, Austria
| | | | - Christoph Herwig
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Vienna, Austria.
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna University of Technology, Gumpendorferstrasse 1a/166-4, A-1060, Vienna, Austria.
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10
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Kelly CL, Liu Z, Yoshihara A, Jenkinson SF, Wormald MR, Otero J, Estévez A, Kato A, Marqvorsen MHS, Fleet GWJ, Estévez RJ, Izumori K, Heap JT. Synthetic Chemical Inducers and Genetic Decoupling Enable Orthogonal Control of the rhaBAD Promoter. ACS Synth Biol 2016; 5:1136-1145. [PMID: 27247275 DOI: 10.1021/acssynbio.6b00030] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
External control of gene expression is crucial in synthetic biology and biotechnology research and applications, and is commonly achieved using inducible promoter systems. The E. coli rhamnose-inducible rhaBAD promoter has properties superior to more commonly used inducible expression systems, but is marred by transient expression caused by degradation of the native inducer, l-rhamnose. To address this problem, 35 analogues of l-rhamnose were screened for induction of the rhaBAD promoter, but no strong inducers were identified. In the native configuration, an inducer must bind and activate two transcriptional activators, RhaR and RhaS. Therefore, the expression system was reconfigured to decouple the rhaBAD promoter from the native rhaSR regulatory cascade so that candidate inducers need only activate the terminal transcription factor RhaS. Rescreening the 35 compounds using the modified rhaBAD expression system revealed several promising inducers. These were characterized further to determine the strength, kinetics, and concentration-dependence of induction; whether the inducer was used as a carbon source by E. coli; and the modality (distribution) of induction among populations of cells. l-Mannose was found to be the most useful orthogonal inducer, providing an even greater range of induction than the native inducer l-rhamnose, and crucially, allowing sustained induction instead of transient induction. These findings address the key limitation of the rhaBAD expression system and suggest it may now be the most suitable system for many applications.
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Affiliation(s)
- Ciarán L. Kelly
- Centre
for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K
| | - Zilei Liu
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K
| | - Akihide Yoshihara
- International
Institute of Rare Sugar Research and Education, Kagawa University, Miki, Kagawa 761-0795, Japan
| | - Sarah F. Jenkinson
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K
| | - Mark R. Wormald
- Glycobiology
Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, U.K
| | - Jose Otero
- Departamento
de Química Orgánica and Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Amalia Estévez
- Departamento
de Química Orgánica and Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Atsushi Kato
- Department
of Hospital Pharmacy, University of Toyama, Toyama 930-0194, Japan
| | - Mikkel H. S. Marqvorsen
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K
| | - George W. J. Fleet
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K
| | - Ramón J. Estévez
- Departamento
de Química Orgánica and Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Ken Izumori
- International
Institute of Rare Sugar Research and Education, Kagawa University, Miki, Kagawa 761-0795, Japan
| | - John T. Heap
- Centre
for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K
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11
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Liu Z, Yoshihara A, Kelly C, Heap JT, Marqvorsen MHS, Jenkinson SF, Wormald MR, Otero JM, Estévez A, Kato A, Fleet GWJ, Estévez RJ, Izumori K. 6-Deoxyhexoses froml-Rhamnose in the Search for Inducers of the Rhamnose Operon: Synergy of Chemistry and Biotechnology. Chemistry 2016; 22:12557-65. [PMID: 27439720 DOI: 10.1002/chem.201602482] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Zilei Liu
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; Oxford OX1 3TA UK
- Glycobiology Institute; Department of Biochemistry; University of Oxford; Oxford OX1 3QU UK
| | - Akihide Yoshihara
- International Institute of Rare Sugar Research and Education; Kagawa University; Miki Kagawa 761-0795 Japan
| | - Ciarán Kelly
- Centre for Synthetic Biology and Innovation; Department of Life Sciences; Imperial College; London SW7 2AZ UK
| | - John T. Heap
- Centre for Synthetic Biology and Innovation; Department of Life Sciences; Imperial College; London SW7 2AZ UK
| | - Mikkel H. S. Marqvorsen
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; Oxford OX1 3TA UK
| | - Sarah F. Jenkinson
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; Oxford OX1 3TA UK
| | - Mark R. Wormald
- Glycobiology Institute; Department of Biochemistry; University of Oxford; Oxford OX1 3QU UK
| | - José M. Otero
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Amalia Estévez
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Atsushi Kato
- Department of Hospital Pharmacy; University of Toyama; Toyama 930-0194 Japan
| | - George W. J. Fleet
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; Oxford OX1 3TA UK
| | - Ramón J. Estévez
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Ken Izumori
- International Institute of Rare Sugar Research and Education; Kagawa University; Miki Kagawa 761-0795 Japan
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Humily F, Partensky F, Six C, Farrant GK, Ratin M, Marie D, Garczarek L. A gene island with two possible configurations is involved in chromatic acclimation in marine Synechococcus. PLoS One 2013; 8:e84459. [PMID: 24391958 PMCID: PMC3877281 DOI: 10.1371/journal.pone.0084459] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/21/2013] [Indexed: 12/31/2022] Open
Abstract
Synechococcus, the second most abundant oxygenic phototroph in the marine environment, harbors the largest pigment diversity known within a single genus of cyanobacteria, allowing it to exploit a wide range of light niches. Some strains are capable of Type IV chromatic acclimation (CA4), a process by which cells can match the phycobilin content of their phycobilisomes to the ambient light quality. Here, we performed extensive genomic comparisons to explore the diversity of this process within the marine Synechococcus radiation. A specific gene island was identified in all CA4-performing strains, containing two genes (fciA/b) coding for possible transcriptional regulators and one gene coding for a phycobilin lyase. However, two distinct configurations of this cluster were observed, depending on the lineage. CA4-A islands contain the mpeZ gene, encoding a recently characterized phycoerythrobilin lyase-isomerase, and a third, small, possible regulator called fciC. In CA4-B islands, the lyase gene encodes an uncharacterized relative of MpeZ, called MpeW. While mpeZ is expressed more in blue light than green light, this is the reverse for mpeW, although only small phenotypic differences were found among chromatic acclimaters possessing either CA4 island type. This study provides novel insights into understanding both diversity and evolution of the CA4 process.
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Affiliation(s)
- Florian Humily
- Université Pierre et Marie Curie (Paris VI), Station Biologique, Roscoff, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7144, Oceanic Plankton group, Marine Phototrophic Prokaryotes team, Roscoff, France
| | - Frédéric Partensky
- Université Pierre et Marie Curie (Paris VI), Station Biologique, Roscoff, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7144, Oceanic Plankton group, Marine Phototrophic Prokaryotes team, Roscoff, France
| | - Christophe Six
- Université Pierre et Marie Curie (Paris VI), Station Biologique, Roscoff, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7144, Oceanic Plankton group, Marine Phototrophic Prokaryotes team, Roscoff, France
| | - Gregory K. Farrant
- Université Pierre et Marie Curie (Paris VI), Station Biologique, Roscoff, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7144, Oceanic Plankton group, Marine Phototrophic Prokaryotes team, Roscoff, France
| | - Morgane Ratin
- Université Pierre et Marie Curie (Paris VI), Station Biologique, Roscoff, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7144, Oceanic Plankton group, Marine Phototrophic Prokaryotes team, Roscoff, France
| | - Dominique Marie
- Université Pierre et Marie Curie (Paris VI), Station Biologique, Roscoff, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7144, Oceanic Plankton group, Marine Phototrophic Prokaryotes team, Roscoff, France
| | - Laurence Garczarek
- Université Pierre et Marie Curie (Paris VI), Station Biologique, Roscoff, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7144, Oceanic Plankton group, Marine Phototrophic Prokaryotes team, Roscoff, France
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Finely tuned regulation of the aromatic amine degradation pathway in Escherichia coli. J Bacteriol 2013; 195:5141-50. [PMID: 24013633 DOI: 10.1128/jb.00837-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
FeaR is an AraC family regulator that activates transcription of the tynA and feaB genes in Escherichia coli. TynA is a periplasmic topaquinone- and copper-containing amine oxidase, and FeaB is a cytosolic NAD-linked aldehyde dehydrogenase. Phenylethylamine, tyramine, and dopamine are oxidized by TynA to the corresponding aldehydes, releasing one equivalent of H2O2 and NH3. The aldehydes can be oxidized to carboxylic acids by FeaB, and (in the case of phenylacetate) can be further degraded to enter central metabolism. Thus, phenylethylamine can be used as a carbon and nitrogen source, while tyramine and dopamine can be used only as sources of nitrogen. Using genetic, biochemical and computational approaches, we show that the FeaR binding site is a TGNCA-N8-AAA motif that occurs in 2 copies in the tynA and feaB promoters. We show that the coactivator for FeaR is the product rather than the substrate of the TynA reaction. The feaR gene is upregulated by carbon or nitrogen limitation, which we propose reflects regulation of feaR by the cyclic AMP receptor protein (CRP) and the nitrogen assimilation control protein (NAC), respectively. In carbon-limited cells grown in the presence of a TynA substrate, tynA and feaB are induced, whereas in nitrogen-limited cells, only the tynA promoter is induced. We propose that tynA and feaB expression is finely tuned to provide the FeaB activity that is required for carbon source utilization and the TynA activity required for nitrogen and carbon source utilization.
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Small-molecule inhibitor of the Shigella flexneri master virulence regulator VirF. Infect Immun 2013; 81:4220-31. [PMID: 24002059 DOI: 10.1128/iai.00919-13] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
VirF is an AraC family transcriptional activator that is required for the expression of virulence genes associated with invasion and cell-to-cell spread by Shigella flexneri, including multiple components of the type three secretion system (T3SS) machinery and effectors. We tested a small-molecule compound, SE-1 (formerly designated OSSL_051168), which we had identified as an effective inhibitor of the AraC family proteins RhaS and RhaR, for its ability to inhibit VirF. Cell-based reporter gene assays with Escherichia coli and Shigella, as well as in vitro DNA binding assays with purified VirF, demonstrated that SE-1 inhibited DNA binding and transcription activation (likely by blocking DNA binding) by VirF. Analysis of mRNA levels using real-time quantitative reverse transcription-PCR (qRT-PCR) further demonstrated that SE-1 reduced the expression of the VirF-dependent virulence genes icsA, virB, icsB, and ipaB in Shigella. We also performed eukaryotic cell invasion assays and found that SE-1 reduced invasion by Shigella. The effect of SE-1 on invasion required preincubation of Shigella with SE-1, in agreement with the hypothesis that SE-1 inhibited the expression of VirF-activated genes required for the formation of the T3SS apparatus and invasion. We found that the same concentrations of SE-1 had no detectable effects on the growth or metabolism of the bacterial cells or the eukaryotic host cells, respectively, indicating that the inhibition of invasion was not due to general toxicity. Overall, SE-1 appears to inhibit transcription activation by VirF, exhibits selectivity toward AraC family proteins, and has the potential to be developed into a novel antibacterial agent.
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Skredenske JM, Koppolu V, Kolin A, Deng J, Kettle B, Taylor B, Egan SM. Identification of a small-molecule inhibitor of bacterial AraC family activators. ACTA ACUST UNITED AC 2013; 18:588-98. [PMID: 23364515 DOI: 10.1177/1087057112474690] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Protein members of the AraC family of bacterial transcriptional activators have great promise as targets for the development of novel antibacterial agents. Here, we describe an in vivo high-throughput screen to identify inhibitors of the AraC family activator protein RhaS. The screen used two Escherichia coli reporter fusions: one to identify potential RhaS inhibitors and a second to eliminate nonspecific inhibitors from consideration. One compound with excellent selectivity, OSSL_051168, was chosen for further study. OSSL_051168 inhibited in vivo transcription activation by the RhaS DNA-binding domain to the same extent as the full-length protein, indicating that this domain was the target of its inhibition. Growth curves showed that OSSL_051168 did not affect bacterial cell growth at the concentrations used in this study. In vitro DNA-binding assays with purified protein suggest that OSSL_051168 inhibits DNA binding by RhaS. In addition, we found that it inhibits DNA binding by a second AraC family protein, RhaR, which shares 30% amino acid identity with RhaS. OSSL_051168 did not have a significant impact on DNA binding by the non-AraC family proteins CRP and LacI, suggesting that the inhibition is likely specific for RhaS, RhaR, and possibly additional AraC family activator proteins.
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Affiliation(s)
- Jeff M Skredenske
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
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