1
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Baugh AC, Momany C, Neidle EL. Versatility and Complexity: Common and Uncommon Facets of LysR-Type Transcriptional Regulators. Annu Rev Microbiol 2023; 77:317-339. [PMID: 37285554 DOI: 10.1146/annurev-micro-050323-040543] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
LysR-type transcriptional regulators (LTTRs) form one of the largest families of bacterial regulators. They are widely distributed and contribute to all aspects of metabolism and physiology. Most are homotetramers, with each subunit composed of an N-terminal DNA-binding domain followed by a long helix connecting to an effector-binding domain. LTTRs typically bind DNA in the presence or absence of a small-molecule ligand (effector). In response to cellular signals, conformational changes alter DNA interactions, contact with RNA polymerase, and sometimes contact with other proteins. Many are dual-function repressor-activators, although different modes of regulation may occur at multiple promoters. This review presents an update on the molecular basis of regulation, the complexity of regulatory schemes, and applications in biotechnology and medicine. The abundance of LTTRs reflects their versatility and importance. While a single regulatory model cannot describe all family members, a comparison of similarities and differences provides a framework for future study.
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Affiliation(s)
- Alyssa C Baugh
- Department of Microbiology, University of Georgia, Athens, Georgia, USA;
| | - Cory Momany
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, USA
| | - Ellen L Neidle
- Department of Microbiology, University of Georgia, Athens, Georgia, USA;
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2
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Pu W, Chen J, Liu P, Shen J, Cai N, Liu B, Lei Y, Wang L, Ni X, Zhang J, Liu J, Zhou Y, Zhou W, Ma H, Wang Y, Zheng P, Sun J. Directed evolution of linker helix as an efficient strategy for engineering LysR-type transcriptional regulators as whole-cell biosensors. Biosens Bioelectron 2023; 222:115004. [PMID: 36516630 DOI: 10.1016/j.bios.2022.115004] [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: 06/02/2022] [Revised: 11/17/2022] [Accepted: 12/08/2022] [Indexed: 12/13/2022]
Abstract
Whole-cell biosensors based on transcriptional regulators are powerful tools for rapid measurement, high-throughput screening, dynamic metabolic regulation, etc. To optimize the biosensing performance of transcriptional regulator, its effector-binding domain is commonly engineered. However, this strategy is encumbered by the limitation of diversifying such a large domain and the risk of affecting effector specificity. Molecular dynamics simulation of effector binding of LysG (an LysR-type transcriptional regulator, LTTR) suggests the crucial role of the short linker helix (LH) connecting effector- and DNA-binding domains in protein conformational change. Directed evolution of LH efficiently produced LysG variants with extended operational range and unaltered effector specificity. The whole-cell biosensor based on the best LysGE58V variant outperformed the wild-type LysG in enzyme high-throughput screening and dynamic regulation of l-lysine biosynthetic pathway. LH mutations are suggested to affect DNA binding and facilitate transcriptional activation upon effector binding. LH engineering was also successfully applied to optimize another LTTR BenM for biosensing. Since LTTRs represent the largest family of prokaryotic transcriptional regulators with highly conserved structures, LH engineering is an efficient and universal strategy for development and optimization of whole-cell biosensors.
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Affiliation(s)
- Wei Pu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jiuzhou Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Pi Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; BioDesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jie Shen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Ningyun Cai
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Baoyan Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; BioDesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yu Lei
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lixian Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xiaomeng Ni
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jie Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jiao Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yingyu Zhou
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Wenjuan Zhou
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Hongwu Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China; BioDesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
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3
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Breisch J, Schumm C, Poehlein A, Daniel R, Averhoff B. The carnitine degradation pathway of Acinetobacter baumannii and its role in virulence. Environ Microbiol 2022; 24:4437-4448. [PMID: 35652489 DOI: 10.1111/1462-2920.16075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 11/30/2022]
Abstract
The opportunistic human pathogen Acinetobacter baumannii can grow with carnitine but its metabolism, regulation and role in virulence remained elusive. Recently, we identified a carnitine transporter encoded by a gene closely associated with potential carnitine degradation genes. Among those is a gene coding for a putative d-malate dehydrogenase (Mdh). Deletion of the mdh gene led to a loss of growth with carnitine but not l-malate; growth with d-malate was strongly reduced. Therefore, it is hypothesized that d-malate is formed during carnitine oxidation and further oxidized to CO2 and pyruvate and, that not, as previously suggested, l-malate is the product and funnelled directly into the TCA cycle. Mutant analyses revealed that the hydrolase in this cluster funnels acetylcarnitine into the degradation pathway by deacetylation. A transcriptional regulator CarR bound in a concentration-dependent manner to the intergenic region between the mdh gene, the first gene of the carnitine catabolic operon and the carR gene in the presence and absence of carnitine. Both carnitine and d-malate induced CarR-dependent expression of the carnitine operon. Infection studies with Galleria mellonella larvae demonstrated a strong increase in virulence by addition of carnitine indicating that carnitine degradation plays a pivotal role in virulence of A. baumannii.
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Affiliation(s)
- Jennifer Breisch
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Clemens Schumm
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Beate Averhoff
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
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4
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Javanpour AA, Liu CC. Evolving Small-Molecule Biosensors with Improved Performance and Reprogrammed Ligand Preference Using OrthoRep. ACS Synth Biol 2021; 10:2705-2714. [PMID: 34597502 DOI: 10.1021/acssynbio.1c00316] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Genetically encoded biosensors are valuable for the optimization of small-molecule biosynthesis pathways, because they transduce the production of small-molecule ligands into a readout compatible with high-throughput screening or selection in vivo. However, engineering biosensors with appropriate response functions and ligand preferences remains challenging. Here, we show that the continuous hypermutation system, OrthoRep, can be effectively applied to evolve biosensors with a high dynamic range, reprogrammed activity toward desired noncognate ligands, and proper operational range for coupling to biosynthetic pathways. In particular, we encoded the allosteric transcriptional factor, BenM, on OrthoRep such that the propagation of host yeast cells resulted in BenM's rapid and continuous diversification. When these cells were subjected to cycles of culturing and sorting on BenM activity in the presence and absence of its cognate ligand, muconic acid, or the noncognate ligand, adipic acid, we obtained multiple BenM variants that respond to their corresponding ligands. These biosensors outperform previously engineered BenM-based biosensors by achieving a substantially greater dynamic range (up to ∼180-fold induction) and broadened operational range. The expression of select BenM variants in the presence of a muconic acid biosynthetic pathway demonstrated sensitive biosensor activation without saturating response, which should enable pathway and host engineering for higher production of muconic and adipic acids. Given the streamlined manner in which high-performance and versatile biosensors were evolved using OrthoRep, this study provides a template for generating custom biosensors for metabolic pathway engineering and other biotechnology goals.
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Affiliation(s)
- Alex A. Javanpour
- Department of Biomedical Engineering, University of California, Irvine, California 92697, United States
- Center for Synthetic Biology, University of California, Irvine, California 92697, United States
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, California 92697, United States
- Center for Synthetic Biology, University of California, Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697, United States
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5
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Giannopoulou EA, Senda M, Koentjoro MP, Adachi N, Ogawa N, Senda T. Crystal structure of the full-length LysR-type transcription regulator CbnR in complex with promoter DNA. FEBS J 2021; 288:4560-4575. [PMID: 33576566 DOI: 10.1111/febs.15764] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/03/2021] [Accepted: 02/11/2021] [Indexed: 12/01/2022]
Abstract
LysR-type transcription regulators (LTTRs) comprise one of the largest families of transcriptional regulators in bacteria. They are typically homo-tetrameric proteins and interact with promoter DNA of ~ 50-60 bp. Earlier biochemical studies have suggested that LTTR binding to promoter DNA bends the DNA and, upon inducer binding, the bend angle of the DNA is reduced through a quaternary structure change of the tetrameric LTTR, leading to the activation of transcription. To date, crystal structures of full-length LTTRs, DNA-binding domains (DBD) with their target DNAs, and the regulatory domains with and without inducer molecules have been reported. However, these crystal structures have not provided direct evidence of the quaternary structure changes of LTTRs or of the molecular mechanism underlying these changes. Here, we report the first crystal structure of a full-length LTTR, CbnR, in complex with its promoter DNA. The crystal structure showed that, in the absence of bound inducer molecules, the four DBDs of the tetrameric CbnR interact with the promoter DNA, bending the DNA by ~ 70°. Structural comparison between the DNA-free and DNA-bound forms demonstrates that the quaternary structure change of the tetrameric CbnR required for promoter region-binding arises from relative orientation changes of the three domains in each subunit. The mechanism of the quaternary structure change caused by inducer binding is also discussed based on the present crystal structure, affinity analysis between CbnR and the promoter DNA, and earlier mutational studies on CbnR. DATABASE: Atomic coordinates and structure factors for the full-length Cupriavidus necator NH9 CbnR in complex with promoter DNA are available in the Protein Data Bank under the accession code 7D98.
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Affiliation(s)
- Evdokia-Anastasia Giannopoulou
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
| | - Miki Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
| | - Maharani Pertiwi Koentjoro
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan.,The United Graduate School of Agricultural Science, Gifu University, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
| | - Naoto Ogawa
- The United Graduate School of Agricultural Science, Gifu University, Japan.,Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), Tsukuba, Japan
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6
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Wolański M, Krawiec M, Schwarz PN, Stegmann E, Wohlleben W, Buchmann A, Gross H, Eitel M, Koch P, Botas A, Méndez C, Núñez LE, Morís F, Cortés J, Zakrzewska‐Czerwińska J. A novel LysR-type regulator negatively affects biosynthesis of the immunosuppressant brasilicardin. Eng Life Sci 2021; 21:4-18. [PMID: 33531886 PMCID: PMC7837296 DOI: 10.1002/elsc.202000038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/29/2020] [Accepted: 10/08/2020] [Indexed: 11/16/2022] Open
Abstract
Brasilicardin A (BraA) is a promising immunosuppressive compound produced naturally by the pathogenic bacterium Nocardia terpenica IFM 0406. Heterologous host expression of brasilicardin gene cluster showed to be efficient to bypass the safety issues, low production levels and lack of genetic tools related with the use of native producer. Further improvement of production yields requires better understanding of gene expression regulation within the BraA biosynthetic gene cluster (Bra-BGC); however, the only so far known regulator of this gene cluster is Bra12. In this study, we discovered the protein LysRNt, a novel member of the LysR-type transcriptional regulator family, as a regulator of the Bra-BGC. Using in vitro approaches, we identified the gene promoters which are controlled by LysRNt within the Bra-BGC. Corresponding genes encode enzymes involved in BraA biosynthesis as well as the key Bra-BGC regulator Bra12. Importantly, we provide in vivo evidence that LysRNt negatively affects production of brasilicardin congeners in the heterologous host Amycolatopsis japonicum. Finally, we demonstrate that some of the pathway related metabolites, and their chemical analogs, can interact with LysRNt which in turn affects its DNA-binding activity.
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Affiliation(s)
| | - Michał Krawiec
- Faculty of BiotechnologyUniversity of WrocławWrocławPoland
| | - Paul N. Schwarz
- Department of Microbiology and BiotechnologyInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
| | - Evi Stegmann
- Department of Microbiology and BiotechnologyInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- German Centre for Infection Research (DZIF)Partner Site TübingenTübingenGermany
| | - Wolfgang Wohlleben
- Department of Microbiology and BiotechnologyInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- German Centre for Infection Research (DZIF)Partner Site TübingenTübingenGermany
| | - Anina Buchmann
- German Centre for Infection Research (DZIF)Partner Site TübingenTübingenGermany
- Department of Pharmaceutical BiologyInstitute of Pharmaceutical SciencesUniversity of TübingenTübingenGermany
- Present address:
Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Harald Gross
- German Centre for Infection Research (DZIF)Partner Site TübingenTübingenGermany
- Department of Pharmaceutical BiologyInstitute of Pharmaceutical SciencesUniversity of TübingenTübingenGermany
| | - Michael Eitel
- Department of Pharmaceutical ChemistryInstitute of Pharmaceutical SciencesUniversity of TübingenTübingenGermany
| | - Pierre Koch
- Department of Pharmaceutical ChemistryInstitute of Pharmaceutical SciencesUniversity of TübingenTübingenGermany
| | - Alma Botas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de AsturiasUniversidad de OviedoOviedoSpain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de AsturiasUniversidad de OviedoOviedoSpain
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7
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Snoek T, Chaberski EK, Ambri F, Kol S, Bjørn SP, Pang B, Barajas JF, Welner DH, Jensen MK, Keasling JD. Evolution-guided engineering of small-molecule biosensors. Nucleic Acids Res 2020; 48:e3. [PMID: 31777933 PMCID: PMC6943132 DOI: 10.1093/nar/gkz954] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/06/2019] [Accepted: 10/24/2019] [Indexed: 11/14/2022] Open
Abstract
Allosteric transcription factors (aTFs) have proven widely applicable for biotechnology and synthetic biology as ligand-specific biosensors enabling real-time monitoring, selection and regulation of cellular metabolism. However, both the biosensor specificity and the correlation between ligand concentration and biosensor output signal, also known as the transfer function, often needs to be optimized before meeting application needs. Here, we present a versatile and high-throughput method to evolve prokaryotic aTF specificity and transfer functions in a eukaryote chassis, namely baker's yeast Saccharomyces cerevisiae. From a single round of mutagenesis of the effector-binding domain (EBD) coupled with various toggled selection regimes, we robustly select aTF variants of the cis,cis-muconic acid-inducible transcription factor BenM evolved for change in ligand specificity, increased dynamic output range, shifts in operational range, and a complete inversion-of-function from activation to repression. Importantly, by targeting only the EBD, the evolved biosensors display DNA-binding affinities similar to BenM, and are functional when ported back into a prokaryotic chassis. The developed platform technology thus leverages aTF evolvability for the development of new host-agnostic biosensors with user-defined small-molecule specificities and transfer functions.
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Affiliation(s)
- Tim Snoek
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Evan K Chaberski
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Francesca Ambri
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stefan Kol
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Sara P Bjørn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Bo Pang
- Joint BioEnergy Institute, Emeryville, CA, USA
| | | | - Ditte H Welner
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.,Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA, USA.,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
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8
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Ambri F, D’Ambrosio V, Di Blasi R, Maury J, Jacobsen SAB, McCloskey D, Jensen MK, Keasling JD. High-Resolution Scanning of Optimal Biosensor Reporter Promoters in Yeast. ACS Synth Biol 2020; 9:218-226. [PMID: 31935067 DOI: 10.1021/acssynbio.9b00333] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Small-molecule binding allosteric transcription factors (aTFs) derived from bacteria enable real-time monitoring of metabolite abundances, high-throughput screening of genetic designs, and dynamic control of metabolism. Yet, engineering of reporter promoter designs of prokaryotic aTF biosensors in eukaryotic cells is complex. Here we investigate the impact of aTF binding site positions at single-nucleotide resolution in >300 reporter promoter designs in Saccharomyces cerevisiae. From this we identify biosensor output landscapes with transient and distinct aTF binding site position effects for aTF repressors and activators, respectively. Next, we present positions for tunable reporter promoter outputs enabling metabolite-responsive designs for a total of four repressor-type and three activator-type aTF biosensors with dynamic output ranges up to 8- and 26-fold, respectively. This study highlights aTF binding site positions in reporter promoters as key for successful biosensor engineering and that repressor-type aTF biosensors allows for more flexibility in terms of choice of binding site positioning compared to activator-type aTF biosensors.
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Affiliation(s)
- Francesca Ambri
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Vasil D’Ambrosio
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Roberto Di Blasi
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Jerome Maury
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | | | - Douglas McCloskey
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Jay. D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen 518055, China
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9
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Liu Q, Hassan KA, Ashwood HE, Gamage HKAH, Li L, Mabbutt BC, Paulsen IT. Regulation of the aceI multidrug efflux pump gene in Acinetobacter baumannii. J Antimicrob Chemother 2019; 73:1492-1500. [PMID: 29481596 PMCID: PMC5961012 DOI: 10.1093/jac/dky034] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/15/2018] [Indexed: 01/17/2023] Open
Abstract
Objectives To investigate the function of AceR, a putative transcriptional regulator of the chlorhexidine efflux pump gene aceI in Acinetobacter baumannii. Methods Chlorhexidine susceptibility and chlorhexidine induction of aceI gene expression were determined by MIC and quantitative real-time PCR, respectively, in A. baumannii WT and ΔaceR mutant strains. Recombinant AceR was prepared as both a full-length protein and as a truncated protein, AceR (86–299), i.e. AceRt, which has the DNA-binding domain deleted. The binding interaction of the purified AceR protein and its putative operator region was investigated by electrophoretic mobility shift assays and DNase I footprinting assays. The binding of AceRt with its putative ligand chlorhexidine was examined using surface plasmon resonance and tryptophan fluorescence quenching assays. Results MIC determination assays indicated that the ΔaceI and ΔaceR mutant strains both showed lower resistance to chlorhexidine than the parental strain. Chlorhexidine-induced expression of aceI was abolished in a ΔaceR background. Electrophoretic mobility shift assays and DNase I footprinting assays demonstrated chlorhexidine-stimulated binding of AceR with two sites upstream of the putative aceI promoter. Surface plasmon resonance and tryptophan fluorescence quenching assays suggested that the purified ligand-binding domain of the AceR protein was able to bind with chlorhexidine with high affinity. Conclusions This study provides strong evidence that AceR is an activator of aceI gene expression when challenged with chlorhexidine. This study is the first characterization, to our knowledge, of a regulator controlling expression of a PACE family multidrug efflux pump.
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Affiliation(s)
- Qi Liu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Karl A Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Heather E Ashwood
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Hasinika K A H Gamage
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Liping Li
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Bridget C Mabbutt
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
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10
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Kim Y, Chhor G, Tsai CS, Winans JB, Jedrzejczak R, Joachimiak A, Winans SC. Crystal structure of the ligand-binding domain of a LysR-type transcriptional regulator: transcriptional activation via a rotary switch. Mol Microbiol 2019; 110:550-561. [PMID: 30168204 DOI: 10.1111/mmi.14115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/20/2018] [Accepted: 08/26/2018] [Indexed: 11/29/2022]
Abstract
LysR-type transcriptional regulators (LTTRs) generally bind to target promoters in two conformations, depending on the availability of inducing ligands. OccR is an LTTR that regulates the octopine catabolism operon of Agrobacterium tumefaciens. OccR binds to a site located between the divergent occQ and occR promoters. Octopine triggers a conformational change that activates the occQ promoter, and does not affect autorepression. This change shortens the length of bound DNA and relaxes a high-angle DNA bend. Here, we describe the crystal structure of the ligand-binding domain (LBD) of OccR apoprotein and holoprotein. Pairs of LBDs form dimers with extensive hydrogen bonding, while pairs of dimers interact via a single helix, creating a tetramer interface. Octopine causes a 70° rotation of each dimer with respect to the opposite dimer, precisely at the tetramer interface. We modeled the DNA binding domain (DBD), linker helix and bound DNA onto the apoprotein and holoprotein. The two DBDs of the modeled apoprotein lie far apart and the bound DNA between them has a high-angle DNA bend. In contrast, the two DBDs of the holoprotein lie closer to each other, with a low DNA bend angle. This inter-dimer pivot fully explains earlier studies of this LTTR.
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Affiliation(s)
- Youngchang Kim
- Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory, Argonne, IL, 60439, USA.,Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Gekleng Chhor
- Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Ching-Sung Tsai
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - James B Winans
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Robert Jedrzejczak
- Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory, Argonne, IL, 60439, USA.,Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL, 60439, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Stephen C Winans
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
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DbdR, a New Member of the LysR Family of Transcriptional Regulators, Coordinately Controls Four Promoters in the Thauera aromatica AR-1 3,5-Dihydroxybenzoate Anaerobic Degradation Pathway. Appl Environ Microbiol 2019; 85:AEM.02295-18. [PMID: 30389770 DOI: 10.1128/aem.02295-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 10/24/2018] [Indexed: 12/27/2022] Open
Abstract
The facultative anaerobe Thauera aromatica strain AR-1 uses 3,5-dihydroxybenzoate (3,5-DHB) as a sole carbon and energy source under anoxic conditions using an unusual oxidative strategy to overcome aromatic ring stability. A 25-kb gene cluster organized in four main operons encodes the anaerobic degradation pathway for this aromatic. The dbdR gene coding for a LysR-type transcriptional regulator (LTTR), which is present at the foremost end of the cluster, is required for anaerobic growth on 3,5-DHB and for the expression of the main pathway operons. A model structure of DbdR showed conserved key residues for effector binding with its closest relative TsaR for p-toluenesulfonate degradation. We found that DbdR controlled expression of three promoters upstream from the operons coding for the three main steps of the pathway. While one of them (P orf20 ) was only active in the presence of 3,5-DHB, the other two (P dbhL and P orf18 ) showed moderate basal levels that were further induced in the presence of the pathway substrate, which needed be converted to hydroxyhydroquinone to activate transcription. Both basal and induced activities were strictly dependent on DbdR, which was also required for transcription from its own promoter. DbdR basal expression was moderately high and, unlike most LTTR, increased 2-fold in response to the presence of the effector. DbdR was found to be a tetramer in solution, producing a single retardation complex in binding assays with the three enzymatic promoters, consistent with its tetrameric structure. The three promoters had a conserved organization with a clear putative primary (regulatory) binding site and a putative secondary (activating) binding site positioned at the expected distances from the transcription start site. In contrast, two protein-DNA complexes were observed for the P dbdR promoter, which also showed significant sequence divergence from those of the three other promoters. Taken together, our results show that a single LTTR coordinately controls expression of the entire 3,5-DHB anaerobic degradation pathway in Thauera aromatica AR-1, allowing a fast and optimized response to the presence of the aromatic.IMPORTANCE Thauera aromatica AR-1 is a facultative anaerobe that is able to use 3,5-dihydroxybenzoat (3,5-DHB) as the sole carbon and energy source in a process that is dependent on nitrate respiration. We have shown that a single LysR-type regulator with unusual properties, DbdR, controls the expression of the pathway in response to the presence of the substrate; unlike other regulators of the family, DbdR does not repress but activates its own synthesis and is able to bind and activate three promoters directing the synthesis of the pathway enzymes. The promoter architecture is conserved among the three promoters but deviates from that of typical LTTR-dependent promoters. The substrate must be metabolized to an intermediate compound to activate transcription, which requires basal enzyme levels to always be present. The regulatory network present in this strain is designed to allow basal expression of the enzymatic machinery, which would rapidly metabolize the substrate when exposed to it, thus rendering the effector molecule. Once activated, the regulator induces the synthesis of the entire pathway through a positive feedback, increasing expression from all the target promoters to allow maximum growth.
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12
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Rhodes KA, Somprasong N, Podnecky NL, Mima T, Chirakul S, Schweizer HP. Molecular determinants of Burkholderia pseudomallei BpeEF-OprC efflux pump expression. MICROBIOLOGY-SGM 2018; 164:1156-1167. [PMID: 30024368 DOI: 10.1099/mic.0.000691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Burkholderia pseudomallei, the cause of melioidosis, is intrinsically resistant to many antibiotics. Acquired multidrug resistance, including resistance to doxycycline and co-trimoxazole used for melioidosis eradication phase therapy, is mainly attributed to constitutive expression of the BpeEF-OprC efflux pump. Constitutive expression of this pump is caused by mutations affecting two highly similar LysR-type transcriptional regulators (LTTR), BpeT and BpeS, but their interaction with the regulatory region governing BpeEF-OprC expression has not yet been studied. The bpeE-bpeF-oprC genes are distally located in the llpE-bpeE-bpeF-oprC operon. The llpE gene encodes a putative lipase/esterase of unknown function. We show that in a bpeT mutant llpE is constitutively co-transcribed with bpeE-bpeF-oprC. As expected from previous studies with B. cenocepacia, deletion of llpE does not affect antibiotic efflux. Using transcriptional bpeE'-lacZ fusions, we demonstrate that the 188 bp bpeT-llpE intergenic region located between bpeT and the llpE-bpeE-bpeF-oprC operon contains regulatory elements needed for control of bpeT and llpE-bpeE-bpeF-oprC operon expression. By native polyacrylamide gel electrophoresis and electrophoretic mobility shift assays with purified recombinant BpeT and BpeS proteins, we show BpeT and BpeS form oligomers that share a 14 bp binding site overlapping the essential region required for llpE-bpeE-bpeF-oprC expression. The binding site contains the conserved T-N11-A LTTR box motif involved in binding of LysR proteins, which in concert with two other possible LTTR boxes may mediate BpeT and BpeS regulation of BpeEF-OprC expression. These studies form the basis for further investigation of BpeEF-OprC expression and regulation at the molecular level by yet unknown external stimuli.
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Affiliation(s)
- Katherine A Rhodes
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,3Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,2Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,†Present address: University of Arizona BIO5 Institute, Tucson, AZ 85721, USA
| | - Nawarat Somprasong
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,2Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,3Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Nicole L Podnecky
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,‡Present address: Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Tromsø, 9037 Tromsø, Norway
| | - Takehiko Mima
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,§Present address: Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Sunisa Chirakul
- 2Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,3Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Herbert P Schweizer
- 3Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,2Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
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13
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Housseini B Issa K, Phan G, Broutin I. Functional Mechanism of the Efflux Pumps Transcription Regulators From Pseudomonas aeruginosa Based on 3D Structures. Front Mol Biosci 2018; 5:57. [PMID: 29971236 PMCID: PMC6018408 DOI: 10.3389/fmolb.2018.00057] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/31/2018] [Indexed: 01/19/2023] Open
Abstract
Bacterial antibiotic resistance is a worldwide health problem that deserves important research attention in order to develop new therapeutic strategies. Recently, the World Health Organization (WHO) classified Pseudomonas aeruginosa as one of the priority bacteria for which new antibiotics are urgently needed. In this opportunistic pathogen, antibiotics efflux is one of the most prevalent mechanisms where the drug is efficiently expulsed through the cell-wall. This resistance mechanism is highly correlated to the expression level of efflux pumps of the resistance-nodulation-cell division (RND) family, which is finely tuned by gene regulators. Thus, it is worthwhile considering the efflux pump regulators of P. aeruginosa as promising therapeutical targets alternative. Several families of regulators have been identified, including activators and repressors that control the genetic expression of the pumps in response to an extracellular signal, such as the presence of the antibiotic or other environmental modifications. In this review, based on different crystallographic structures solved from archetypal bacteria, we will first focus on the molecular mechanism of the regulator families involved in the RND efflux pump expression in P. aeruginosa, which are TetR, LysR, MarR, AraC, and the two-components system (TCS). Finally, the regulators of known structure from P. aeruginosa will be presented.
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Affiliation(s)
- Karim Housseini B Issa
- Laboratoire de Cristallographie et RMN Biologiques (UMR 8015), Centre National de la Recherche Scientifique, Faculté de Pharmacie, Université Paris Descartes, Université Sorbonne Paris Cité, Paris, France
| | - Gilles Phan
- Laboratoire de Cristallographie et RMN Biologiques (UMR 8015), Centre National de la Recherche Scientifique, Faculté de Pharmacie, Université Paris Descartes, Université Sorbonne Paris Cité, Paris, France
| | - Isabelle Broutin
- Laboratoire de Cristallographie et RMN Biologiques (UMR 8015), Centre National de la Recherche Scientifique, Faculté de Pharmacie, Université Paris Descartes, Université Sorbonne Paris Cité, Paris, France
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14
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Koentjoro MP, Ogawa N. STRUCTURAL STUDIES OF TRANSCRIPTIONAL REGULATION BY LysR-TYPE TRANSCRIPTIONAL REGULATORS IN BACTERIA. ACTA ACUST UNITED AC 2018. [DOI: 10.7831/ras.6.105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Naoto Ogawa
- The United Graduate School of Agricultural Science, Gifu University
- Faculty of Agriculture, Shizuoka University
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15
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Mittal M, Singh AK, Kumaran S. Structural and biochemical characterization of ligand recognition by CysB, the master regulator of sulfate metabolism. Biochimie 2017; 142:112-124. [PMID: 28838607 DOI: 10.1016/j.biochi.2017.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/17/2017] [Indexed: 10/19/2022]
Abstract
CysB, a member of LysR-type transcriptional regulators, up-regulates the expression of genes associated with sulfate metabolism and cysteine biosynthesis. CysB is activated under sulfur limiting conditions by O-acetylserine (OAS) and N-acetylserine (NAS), but the activation mechanism of CysB remain unknown. Here, we report four crystal structures of ligand binding domains of CysB (CysB-LBD) in apo form and in complex with sulfate, OAS, and NAS. Our results show that CysB has two distinct allosteric ligand binding sites; a sulfate and NAS specific site-1 and a second, NAS and OAS specific site-2. All three ligands bind through the induced-fit mechanism. Surprisingly, OAS remodels the site-1 by binding to site-2, suggesting that site-1 and site-2 are coupled allosterically. Using DNA binding and site-directed mutagenesis approach, we show that OAS enhances NAS mediated activation and mutation at site-1 has no effect on site-2 mediated OAS activation. Results indicate that inducer binding triggered signals from OAS-Specific site-2 are relayed to DBD through site-1. Together, results presented here suggest that induced-fit binding and allosteric coupling between two ligand binding sites and DBD underlie the key feature of CysB activation. Further, this study provides first structural glimpse into recognition of inducer ligands by CysB and provides a general framework to understand how LTTR family regulators respond to dual activators.
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Affiliation(s)
- Monica Mittal
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology (IMTECH), G. N. Ramachandran Protein Center, Sector 39-A, Chandigarh, 160036, India
| | - Appu Kumar Singh
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology (IMTECH), G. N. Ramachandran Protein Center, Sector 39-A, Chandigarh, 160036, India
| | - S Kumaran
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology (IMTECH), G. N. Ramachandran Protein Center, Sector 39-A, Chandigarh, 160036, India.
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16
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Passaglia LMP. Bradyrhizobium elkanii nod regulon: insights through genomic analysis. Genet Mol Biol 2017; 40:703-716. [PMID: 28767122 PMCID: PMC5596368 DOI: 10.1590/1678-4685-gmb-2016-0228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 02/16/2017] [Indexed: 12/26/2022] Open
Abstract
A successful symbiotic relationship between soybean [Glycinemax (L.) Merr.] and Bradyrhizobium species requires expression of the bacterial structural nod genes that encode for the synthesis of lipochitooligosaccharide nodulation signal molecules, known as Nod factors (NFs). Bradyrhizobium diazoefficiens USDA 110 possesses a wide nodulation gene repertoire that allows NF assembly and modification, with transcription of the nodYABCSUIJnolMNOnodZ operon depending upon specific activators, i.e., products of regulatory nod genes that are responsive to signaling molecules such as flavonoid compounds exuded by host plant roots. Central to this regulatory circuit of nod gene expression are NodD proteins, members of the LysR-type regulator family. In this study, publicly available Bradyrhizobium elkanii sequenced genomes were compared with the closely related B. diazoefficiens USDA 110 reference genome to determine the similarities between those genomes, especially with regards to the nod operon and nod regulon. Bioinformatics analyses revealed a correlation between functional mechanisms and key elements that play an essential role in the regulation of nod gene expression. These analyses also revealed new genomic features that had not been clearly explored before, some of which were unique for some B. elkanii genomes.
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Affiliation(s)
- Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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17
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Ribavirin suppresses bacterial virulence by targeting LysR-type transcriptional regulators. Sci Rep 2016; 6:39454. [PMID: 27991578 PMCID: PMC5171790 DOI: 10.1038/srep39454] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 11/23/2016] [Indexed: 12/30/2022] Open
Abstract
Targeting bacterial virulence mechanisms without compromising bacterial growth is a promising strategy to prevent drug resistance. LysR-type transcriptional regulators (LTTRs) possess structural conservation across bacterial species and regulate virulence in numerous pathogens, making them attractive targets for antimicrobial agents. We targeted AphB, a Vibrio cholerae LTTR, which regulates the expression of genes encoding cholera toxin and toxin-co-regulated pilus for inhibitor designing. Since AphB ligand is unknown, we followed a molecular fragment-based approach for ligand designing using FDA-approved drugs and subsequent screen to identify molecules that exhibited high-affinity binding to AphB ligand-binding pocket. Among the identified compounds, ribavirin, an anti-viral drug, antagonized AphB functions. Ribavirin perturbed Vibrio cholerae pathogenesis in animal models. The inhibitory effects of the drug was limited to the bacteria expressing wild type AphB, but not its constitutively active mutant (AphBN100E), which represents the ligand-bound state, suggesting that ribavirin binds to the active site of AphB to exert its inhibitory role and there exists no AphB-independent mechanism of its action. Similarly, ribavirin suppressed the functions of Salmonella Typhi LTTR Hrg, indicating its broad spectrum efficacy. Moreover, ribavirin did not affect the bacterial viability in culture. This study cites an example of drug repurposing for anti-infective therapy.
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18
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Crystal Structure of Fad35R from Mycobacterium tuberculosis H37Rv in the Apo-State. PLoS One 2015; 10:e0124333. [PMID: 25938298 PMCID: PMC4418694 DOI: 10.1371/journal.pone.0124333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 03/04/2015] [Indexed: 11/19/2022] Open
Abstract
Fad35R from Mycobacterium tuberculosis binds to the promoter site of Fad35 operon and its DNA binding activities are reduced in the presence of tetracycline and palmitoyl-CoA. We resolved the crystal structure of Fad35R using single-wavelength anomalous diffraction method (SAD). Fad35R comprises canonical DNA binding domain (DBD) and ligand binding domain (LBD), but displays several distinct structural features. Two recognition helices of two monomers in the homodimer are separated by ~ 48 Å and two core triangle-shaped ligand binding cavities are well exposed to solvent. Structural comparison with DesT and QacR structures suggests that ligand binding-induced movement of α7, which adopts a straight conformation in the Fad35R, may be crucial to switch the conformational states between repressive and derepressive forms. Two DBDs are packed asymmetrically, creating an alternative dimer interface which coincides with the possible tetramer interface that connects the two canonical dimers. Quaternary state of alternative dimer mimics a closed-state structure in which two recognition helices are distanced at ~ 35 Å and ligand binding pockets are inaccessible. Results of biophysical studies indicate that Fad35R has the propensity to oligomerize in solution in the presence of tetracycline. We present the first structure of a FadR homologue from mycobacterium and the structure reveals DNA and ligand binding features of Fad35R and also provides a view on alternative quaternary states that mimic open and closed forms of the regulator.
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19
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Vadlamani G, Thomas MD, Patel TR, Donald LJ, Reeve TM, Stetefeld J, Standing KG, Vocadlo DJ, Mark BL. The β-lactamase gene regulator AmpR is a tetramer that recognizes and binds the D-Ala-D-Ala motif of its repressor UDP-N-acetylmuramic acid (MurNAc)-pentapeptide. J Biol Chem 2014; 290:2630-43. [PMID: 25480792 DOI: 10.1074/jbc.m114.618199] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inducible expression of chromosomal AmpC β-lactamase is a major cause of β-lactam antibiotic resistance in the Gram-negative bacteria Pseudomonas aeruginosa and Enterobacteriaceae. AmpC expression is induced by the LysR-type transcriptional regulator (LTTR) AmpR, which activates ampC expression in response to changes in peptidoglycan (PG) metabolite levels that occur during exposure to β-lactams. Under normal conditions, AmpR represses ampC transcription by binding the PG precursor UDP-N-acetylmuramic acid (MurNAc)-pentapeptide. When exposed to β-lactams, however, PG catabolites (1,6-anhydroMurNAc-peptides) accumulate in the cytosol, which have been proposed to competitively displace UDP-MurNAc-pentapeptide from AmpR and convert it into an activator of ampC transcription. Here we describe the molecular interactions between AmpR (from Citrobacter freundii), its DNA operator, and repressor UDP-MurNAc-pentapeptide. Non-denaturing mass spectrometry revealed AmpR to be a homotetramer that is stabilized by DNA containing the T-N11-A LTTR binding motif and revealed that it can bind four repressor molecules in an apparently stepwise manner. A crystal structure of the AmpR effector-binding domain bound to UDP-MurNAc-pentapeptide revealed that the terminal D-Ala-D-Ala motif of the repressor forms the primary contacts with the protein. This observation suggests that 1,6-anhydroMurNAc-pentapeptide may convert AmpR into an activator of ampC transcription more effectively than 1,6-anhydroMurNAc-tripeptide (which lacks the D-Ala-D-Ala motif). Finally, small angle x-ray scattering demonstrates that the AmpR·DNA complex adopts a flat conformation similar to the LTTR protein AphB and undergoes only a slight conformational change when binding UDP-MurNAc-pentapeptide. Modeling the AmpR·DNA tetramer bound to UDP-MurNAc-pentapeptide predicts that the UDP-MurNAc moiety of the repressor participates in modulating AmpR function.
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Affiliation(s)
| | | | | | | | | | | | - Kenneth G Standing
- Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and
| | - David J Vocadlo
- the Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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Isolation and characterization of mutant Sinorhizobium meliloti NodD1 proteins with altered responses to luteolin. J Bacteriol 2013; 195:3714-23. [PMID: 23772067 DOI: 10.1128/jb.00309-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
NodD1, a member of the NodD family of LysR-type transcriptional regulators (LTTRs), mediates nodulation (nod) gene expression in the soil bacterium Sinorhizobium meliloti in response to the plant-secreted flavonoid luteolin. We used genetic screens and targeted approaches to identify NodD1 residues that show altered responses to luteolin during the activation of nod gene transcription. Here we report four types of NodD1 mutants. Type I (NodD1 L69F, S104L, D134N, and M193I mutants) displays reduced or no activation of nod gene expression. Type II (NodD1 K205N) is constitutively active but repressed by luteolin. Type III (NodD1 L280F) demonstrates enhanced activity with luteolin compared to that of wild-type NodD1. Type IV (NodD1 D284N) shows moderate constitutive activity yet can still be induced by luteolin. In the absence of luteolin, many mutants display a low binding affinity for nod gene promoter DNA in vitro. Several mutants also show, as does wild-type NodD1, increased affinity for nod gene promoters with added luteolin. All of the NodD1 mutant proteins can homodimerize and heterodimerize with wild-type NodD1. Based on these data and the crystal structures of several LTTRs, we present a structural model of wild-type NodD1, identifying residues important for inducer binding, protein multimerization, and interaction with RNA polymerase at nod gene promoters.
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Toledo M, Santos C, Mendes J, Pelloso A, Beloti L, Crucello A, Favaro M, Santiago A, Schneider D, Saraiva A, Stach-Machado D, Souza A, Trivella D, Aparicio R, Tasic L, Azzoni A, Souza A. Small-angle X-ray scattering and in silico modeling approaches for the accurate functional annotation of an LysR-type transcriptional regulator. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:697-707. [DOI: 10.1016/j.bbapap.2012.12.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 12/24/2012] [Accepted: 12/26/2012] [Indexed: 01/31/2023]
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Momany C, Neidle EL. Defying stereotypes: the elusive search for a universal model of LysR-type regulation. Mol Microbiol 2012; 83:453-6. [PMID: 22235937 DOI: 10.1111/j.1365-2958.2011.07960.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
LysR-type transcriptional regulators (LTTRs) compose the largest family of homologous regulators in bacteria. Considering their prevalence, it is not surprising that LTTRs control diverse metabolic functions. Arguably, the most unexpected aspect of LTTRs is the paucity of available structural information. Solubility issues are notoriously problematic, and structural studies have only recently begun to flourish. In this issue of Molecular Microbiology, Taylor et al. (2012) present the structure of AphB, a LysR-type regulator of virulence in Vibrio cholerae. This contribution adds significantly to the group of known full-length atomic LTTR structures, which remains small. Importantly, this report also describes an active-form variant. Small conformational changes in the effector-binding domain translate to global reorganization of the DNA-binding domain. Emerging from these results is a model of theme-and-variation among LTTRs rather than a unified regulatory scheme. Despite common structural folds, LTTRs exhibit differences in oligomerization, promoter recognition and communication with RNA polymerase. Such variation mirrors the diversity in sequence and function associated with members of this very large family.
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Affiliation(s)
- Cory Momany
- Departments of Pharmaceutical and Biomedical Sciences Microbiology, University of Georgia, Athens, GA 30602, USA.
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The transcription factor AlsR binds and regulates the promoter of the alsSD operon responsible for acetoin formation in Bacillus subtilis. J Bacteriol 2011; 194:1100-12. [PMID: 22178965 DOI: 10.1128/jb.06425-11] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis forms acetoin under anaerobic fermentative growth conditions and as a product of the aerobic carbon overflow metabolism. Acetoin formation from pyruvate requires α-acetolactate synthase and acetolactate decarboxylase, both encoded by the alsSD operon. The alsR gene, encoding the LysR-type transcriptional regulator AlsR, was found to be essential for the in vivo expression of alsSD in response to anaerobic acetate accumulation, the addition of acetate, low pH, and the aerobic stationary phase. The expressions of the alsSD operon and the alsR regulatory gene were independent of other regulators of the anaerobic regulatory network, including ResDE, Fnr, and ArfM. A negative autoregulation of alsR was observed. In vitro transcription from the alsSD promoter using purified B. subtilis RNA polymerase required AlsR. DNA binding studies with purified recombinant AlsR in combination with promoter mutagenesis experiments identified a 19-bp high-affinity palindromic binding site (TAAT-N(11)-ATTA) at positions -76 to -58 (regulatory binding site [RBS]) and a low-affinity site (AT-N(11)-AT) at positions -41 to -27 (activator binding site [ABS]) upstream of the transcriptional start site of alsSD. The RBS and ABS were found to be essential for in vivo alsSD transcription. AlsR binding to both sites induced the formation of higher-order, transcription-competent complexes. The AlsR protein carrying the S100A substitution at the potential coinducer binding site still bound to the RBS and ABS. However, AlsR(S100A) failed to form the higher-order complex and to initiate in vivo and in vitro transcription. A model for AlsR promoter binding and transcriptional activation was deduced.
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Most mutant OccR proteins that are defective in positive control hold operator DNA in a locked high-angle bend. J Bacteriol 2011; 193:5442-9. [PMID: 21804007 DOI: 10.1128/jb.05352-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
OccR is a LysR-type transcriptional regulator of Agrobacterium tumefaciens that positively regulates the octopine catabolism operon of the Ti plasmid. Positive control of the occ genes occurs in response to octopine, a nutrient released from crown gall tumors. OccR also functions as an autorepressor in the presence or absence of octopine. OccR binds to a site between occQ and occR in the presence or absence of octopine, although octopine triggers a conformational change that shortens the DNA footprint and relaxes a DNA bend. In order to determine the roles of this conformational change in transcriptional activation, we isolated 11 OccR mutants that were defective in activation of the occQ promoter but were still capable of autorepression. The mutations in these mutants spanned most of the length of the protein. Two additional positive-control mutants were isolated using site-directed mutagenesis. Twelve mutant proteins displayed a high-angle DNA bend in the presence or absence of octopine. One mutant, the L26A mutant, showed ligand-responsive DNA binding similar to that of wild-type OccR and therefore must be impaired in a subsequent step in activation.
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Ruangprasert A, Craven SH, Neidle EL, Momany C. Full-Length Structures of BenM and Two Variants Reveal Different Oligomerization Schemes for LysR-Type Transcriptional Regulators. J Mol Biol 2010; 404:568-86. [DOI: 10.1016/j.jmb.2010.09.053] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 09/21/2010] [Accepted: 09/22/2010] [Indexed: 10/19/2022]
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Monferrer D, Tralau T, Kertesz MA, Dix I, Solà M, Usón I. Structural studies on the full-length LysR-type regulator TsaR from Comamonas testosteroni T-2 reveal a novel open conformation of the tetrameric LTTR fold. Mol Microbiol 2010; 75:1199-214. [PMID: 20059681 DOI: 10.1111/j.1365-2958.2010.07043.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
LysR-type transcriptional regulators (LTTRs) constitute the largest family of regulators in prokaryotes. The full-length structures of the LTTR TsaR from Comamonas testosteroni T-2 and its complex with the natural inducer para-toluensulfonate have been characterized by X-ray diffraction. Both ligand-free and complexed forms reveal a dramatically different quaternary structure from that of CbnR from Ralstonia eutropha, or a putative LysR-type regulator from Pseudomonas aeruginosa, the only other determined full-length structures of tetrameric LTTRs. Although all three show a head-to-head tetrameric ring, TsaR displays an open conformation, whereas CbnR and PA01-PR present additional contacts in opposing C-terminal domains that close the ring. Such large differences may be due to a broader structural versatility than previously assumed or either, reflect the intrinsic flexibility of tetrameric LTTRs. On the grounds of the sliding dimer hypothesis of LTTR activation, we propose a structural model in which the closed structures could reflect the conformation of a ligand-free LTTR, whereas inducer binding would bring about local changes to disrupt the interface linking the two compact C-terminal domains. This could lead to a TsaR-like, open structure, where the pairs of recognition helices are closer to each other by more than 10 A.
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Affiliation(s)
- Dominique Monferrer
- IBMB-CSIC, Baldiri Reixach 15, Barcelona Science Park, 08028, Barcelona, Spain
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Zhou X, Lou Z, Fu S, Yang A, Shen H, Li Z, Feng Y, Bartlam M, Wang H, Rao Z. Crystal structure of ArgP from Mycobacterium tuberculosis confirms two distinct conformations of full-length LysR transcriptional regulators and reveals its function in DNA binding and transcriptional regulation. J Mol Biol 2009; 396:1012-24. [PMID: 20036253 DOI: 10.1016/j.jmb.2009.12.033] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 12/16/2009] [Accepted: 12/17/2009] [Indexed: 10/20/2022]
Abstract
Mycobacterium tuberculosis presents a challenging medical problem partly due to its persistent nonreplicative state. The inhibitor of chromosomal replication (iciA) protein encoded by M. tuberculosis has been suggested to inhibit chromosome replication initiation in vitro. However, iciA has also been identified as arginine permease (ArgP), a regulatory transcription factor for arginine outward transport. In order to understand the function of ArgP, we have determined its crystal structure by X-ray crystallography to a resolution of 2.7 A. ArgP is a member of the LysR-type transcriptional regulators (LTTRs) and forms a homodimer with each subunit containing two domains: a DNA binding domain (DBD) and a regulatory domain (RD). Two conformationally distinct subunits were identified: closed subunit and open subunit. This phenomenon was first observed in LTTR CbnR, but not in LTTR CrgA, and might be common in LTTRs. We identified two forms of dimers: DBD-type dimers and RD-type dimers. The former is confirmed in solution, and the latter is considered to form oligomers during function. We provide the first structural insights into the interaction of the extreme C-terminal residues with the DBD, which is confirmed by mutagenesis and analytical ultracentrifugation to be important for stability of the functional dimer. The structure serves as a model to suggest how three critical aspects, namely, DNA binding, homo-oligomerization, and interaction with RNAP, are mediated during regulation processing. A model is proposed for the LysR family of dimeric regulators.
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Affiliation(s)
- Xiaohong Zhou
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
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Mukherjee D, Saha RP, Chakrabarti P. Structural and unfolding features of HlyT, a tetrameric LysR type transcription regulator of Vibrio cholerae. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1134-41. [DOI: 10.1016/j.bbapap.2009.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 04/22/2009] [Accepted: 04/23/2009] [Indexed: 10/20/2022]
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29
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Craven SH, Ezezika OC, Haddad S, Hall RA, Momany C, Neidle EL. Inducer responses of BenM, a LysR-type transcriptional regulator fromAcinetobacter baylyiADP1. Mol Microbiol 2009; 72:881-94. [DOI: 10.1111/j.1365-2958.2009.06686.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Fischer R, Bleichrodt FS, Gerischer UC. Aromatic degradative pathways in Acinetobacter baylyi underlie carbon catabolite repression. MICROBIOLOGY-SGM 2008; 154:3095-3103. [PMID: 18832315 DOI: 10.1099/mic.0.2008/016907-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Carbon catabolite repression is an important mechanism allowing efficient carbon source utilization. In the soil bacterium Acinetobacter baylyi, this mechanism has been shown to apply to the aromatic degradative pathways for the substrates protocatechuate, p-hydroxybenzoate and vanillate. In this investigation, transcriptional fusions with the gene for luciferase in the gene clusters for the degradation of benzyl esters, anthranilate, benzoate, hydroxycinnamates and dicarboxylates (are, ant, ben, hca and dca genes) were constructed and established in the chromosome of A. baylyi. The respective strains revealed the presence of strong carbon catabolite repression at the transcriptional level. In all cases, succinate and acetate in combination had the strongest repressing effect, and pyruvate (or lactate in case of the ben and hca genes) allowed the highest expression when these carbon sources were supplied together with the respective inducer. The pattern of repression for the different cosubstrates was similar for all operons investigated and was also observed in the absence of the respective inducing compounds, indicating a mechanism that is independent of the respective specific regulators. Repression by acetate and succinate varied between 88 % for the hca genes and 99 % for the pca genes.
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Affiliation(s)
- Rita Fischer
- Institute for Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Fenja S Bleichrodt
- Institute for Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Ulrike C Gerischer
- Institute for Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
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Sainsbury S, Ren J, Saunders NJ, Stuart DI, Owens RJ. Crystallization and preliminary X-ray analysis of CrgA, a LysR-type transcriptional regulator from pathogenic Neisseria meningitidis MC58. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:797-801. [PMID: 18765907 PMCID: PMC2531262 DOI: 10.1107/s1744309108024068] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 07/29/2008] [Indexed: 05/26/2023]
Abstract
Although LysR-type regulators (LTTRs) represent the largest family of transcriptional regulators in bacteria, the full-length structure of only one annotated LTTR (CbnR) has been deposited in the PDB. CrgA, a LTTR from pathogenic Neisseria meningitidis MC58, which is up-regulated upon bacterial cell contact with human epithelial cells, has been cloned, purified and crystallized. Crystals of full-length CrgA were obtained after buffer screening with a thermal shift assay and concentration with 0.2 M NDSB-256. Data were collected from two crystal forms of full-length CrgA belonging to space groups P2(1)2(1)2(1) and P2(1), diffracting to 3.0 and 3.8 A resolution and consistent with the presence of between six and ten and between ten and 20 copies of CrgA in the asymmetric unit, respectively. In addition, diffraction data were collected to 2.3 A resolution from the selenomethionine derivative of the regulatory domain of CrgA. The crystals belonged to space group P2(1) and contained two molecules in the asymmetric unit.
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Affiliation(s)
- Sarah Sainsbury
- The Oxford Protein Production Facility and Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England.
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