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Wang L, Zhang M, Teng H, Wang Z, Wang S, Li P, Wu J, Yang L, Xu G. Rationally introducing non-canonical amino acids to enhance catalytic activity of LmrR for Henry reaction. BIORESOUR BIOPROCESS 2024; 11:26. [PMID: 38647789 PMCID: PMC10992053 DOI: 10.1186/s40643-024-00744-w] [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: 12/28/2023] [Accepted: 02/19/2024] [Indexed: 04/25/2024] Open
Abstract
The use of enzymes to catalyze Henry reaction has advantages of mild reaction conditions and low contamination, but low enzyme activity of promiscuous catalysis limits its application. Here, rational design was first performed to identify the key amino acid residues in Henry reaction catalyzed by Lactococcal multidrug resistance Regulator (LmrR). Further, non-canonical amino acids were introduced into LmrR, successfully obtaining variants that enhanced the catalytic activity of LmrR. The best variant, V15CNF, showed a 184% increase in enzyme activity compared to the wild type, and was 1.92 times more effective than the optimal natural amino acid variant, V15F. Additionally, this variant had a broad substrate spectrum, capable of catalyzing reactions between various aromatic aldehydes and nitromethane, with product yielded ranging from 55 to 99%. This study improved enzymatic catalytic activity by enhancing affinity between the enzyme and substrates, while breaking limited types of natural amino acid residues by introducing non-canonical amino acids into the enzyme, providing strategies for molecular modifications.
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Affiliation(s)
- Lan Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Mengting Zhang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Haidong Teng
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Zhe Wang
- Huadong Medicine Co., Ltd, Hangzhou, 310011, Zhejiang, China
| | - Shulin Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Pengcheng Li
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Gang Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China.
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2
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Corbeski I, Horn V, van der Valk RA, le Paige U, Dame RT, van Ingen H. Microscale Thermophoresis Analysis of Chromatin Interactions. Methods Mol Biol 2024; 2819:357-379. [PMID: 39028515 DOI: 10.1007/978-1-0716-3930-6_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Architectural DNA-binding proteins are key to the organization and compaction of genomic DNA inside cells. The activity of architectural proteins is often subject to further modulation and regulation through the interaction with a diverse array of other protein factors. Detailed knowledge on the binding modes involved is crucial for our understanding of how these protein-protein and protein-DNA interactions shape the functional landscape of chromatin in all kingdoms of life: bacteria, archaea, and eukarya.Microscale thermophoresis (MST) is a biophysical technique for the study of biomolecular interactions. It has seen increasing application in recent years thanks to its solution-based nature, rapid application, modest sample demand, and the sensitivity of the thermophoresis effect to binding events.Here, we describe the use of MST in the study of chromatin interactions. The emphasis lies on the wide range of ways in which these experiments are set up and the diverse types of information they reveal. These aspects are illustrated with four very different systems: the sequence-dependent DNA compaction by architectural protein HMfB, the sequential binding of core histone complexes to histone chaperone APLF, the impact of the nucleosomal context on the recognition of histone modifications, and the binding of a viral peptide to the nucleosome. Special emphasis is given to the key steps in the design, execution, and analysis of MST experiments in the context of the provided examples.
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Affiliation(s)
- Ivan Corbeski
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Velten Horn
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- CSL Behring, Hattersheim, Germany
| | - Ramon A van der Valk
- Kavli Institute of NanoScience, Department of Bionanoscience, Faculty of Applied Sciences, TU Delft, Delft, The Netherlands
| | - Ulric le Paige
- Structure and Dynamics of Biomolecules, Department of Chemistry, Ecole Normale Supérieure - Paris Sciences et Lettres, Paris, France
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Hugo van Ingen
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
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3
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Zhang J, Wu YF, Tang ST, Chen J, Rosen BP, Zhao FJ. A PadR family transcriptional repressor controls transcription of a trivalent metalloid resistance operon of Azospirillum halopraeferens strain Au 4. Environ Microbiol 2022; 24:5139-5150. [PMID: 35880613 DOI: 10.1111/1462-2920.16147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/28/2022]
Abstract
Methylarsenite [MAs(III)] is a highly toxic arsenical produced by some microbes as an antibiotic. In this study, we demonstrate that a PadR family transcriptional regulator, PadRars , from Azospirillum halopraeferens strain Au 4 directly binds to the promoter region of the arsenic resistance (ars) operon (consisting of padRars , arsV, and arsW) and represses transcription of arsV and arsW genes involved in MAs(III) resistance. Quantitative reverse transcriptase PCR and transcriptional reporter assays showed that transcription of the ars operon is induced strongly by MAs(III) and less strongly by arsenite and antimonite. Electrophoretic mobility shift assays with recombinant PadRars showed that it represses transcription of the ars operon by binding to two inverted-repeat sequences within the ars promoter. PadRars has two conserved cysteine pairs, Cys56/57 and Cys133/134; mutation of the first pair to serine abolished the transcriptional response of the ars operon to trivalent metalloids, suggesting that Cys56/57 form a binding site for trivalent metalloids. Either C133S or C134S derivative responses to MAs(III) but not As(III) or Sb(III), suggesting that it is a third ligand to trivalent metalloids. PadRars represents a new type of repressor proteins regulating transcription of an ars operon involved in the resistance to trivalent metalloids, especially MAs(III). This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jun Zhang
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yi-Fei Wu
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shi-Tong Tang
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jian Chen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Barry P Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Fang-Jie Zhao
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
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4
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Shao J, Kuiper BP, Thunnissen AMWH, Cool RH, Zhou L, Huang C, Dijkstra BW, Broos J. The Role of Tryptophan in π Interactions in Proteins: An Experimental Approach. J Am Chem Soc 2022; 144:13815-13822. [PMID: 35868012 PMCID: PMC9354243 DOI: 10.1021/jacs.2c04986] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
In proteins, the amino acids Phe, Tyr, and especially
Trp are frequently
involved in π interactions such as π–π, cation−π,
and CH−π bonds. These interactions are often crucial
for protein structure and protein–ligand binding. A powerful
means to study these interactions is progressive fluorination of these
aromatic residues to modulate the electrostatic component of the interaction.
However, to date no protein expression platform is available to produce
milligram amounts of proteins labeled with such fluorinated amino
acids. Here, we present a Lactococcus lactis Trp
auxotroph-based expression system for efficient incorporation (≥95%)
of mono-, di-, tri-, and tetrafluorinated, as well as a methylated
Trp analog. As a model protein we have chosen LmrR, a dimeric multidrug
transcriptional repressor protein from L. lactis. LmrR binds aromatic drugs, like daunomycin and riboflavin, between
Trp96 and Trp96′ in the dimer interface. Progressive fluorination
of Trp96 decreased the affinity for the drugs 6- to 70-fold, clearly
establishing the importance of electrostatic π–π
interactions for drug binding. Presteady state kinetic data of the
LmrR–drug interaction support the enthalpic nature of the interaction,
while high resolution crystal structures of the labeled protein–drug
complexes provide for the first time a structural view of the progressive
fluorination approach. The L. lactis expression system
was also used to study the role of Trp68 in the binding of riboflavin
by the membrane-bound riboflavin transport protein RibU from L. lactis. Progressive fluorination of Trp68 revealed a
strong electrostatic component that contributed 15–20% to the
total riboflavin-RibU binding energy.
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Affiliation(s)
- Jinfeng Shao
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Bastiaan P Kuiper
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Andy-Mark W H Thunnissen
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Robbert H Cool
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Liang Zhou
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Chenxi Huang
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Bauke W Dijkstra
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jaap Broos
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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5
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Characterization of the DNA Binding Domain of StbA, A Key Protein of A New Type of DNA Segregation System. J Mol Biol 2022; 434:167752. [PMID: 35868361 DOI: 10.1016/j.jmb.2022.167752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 11/21/2022]
Abstract
Low-copy-number plasmids require sophisticated genetic devices to achieve efficient segregation of plasmid copies during cell division. Plasmid R388 uses a unique segregation mechanism, based on StbA, a small multifunctional protein. StbA is the key protein in a segregation system not involving a plasmid-encoded NTPase partner, it regulates the expression of several plasmid operons, and it is the main regulator of plasmid conjugation. The mechanisms by which StbA, together with the centromere-like sequence stbS, achieves segregation, is largely uncharacterized. To better understand the molecular basis of R388 segregation, we determined the crystal structure of the conserved N-terminal domain of StbA to 1.9 Å resolution. It folds into an HTH DNA-binding domain, structurally related to that of the PadR subfamily II of transcriptional regulators. StbA is organized in two domains. Its N-terminal domain carries the specific stbS DNA binding activity. A truncated version of StbA, deleted of its C-terminal domain, displays only partial activities in vivo, indicating that the non-conserved C-terminal domain is required for efficient segregation and subcellular plasmid positioning. The structure of StbA DNA-binding domain also provides some insight into how StbA monomers cooperate to repress transcription by binding to the stbDR and to form the segregation complex with stbS.
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6
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Kim J, Park J, Choi Z, Hong M. Structure-based molecular characterization of the LltR transcription factor from Listeria monocytogenes. Biochem Biophys Res Commun 2022; 600:142-149. [PMID: 35219103 DOI: 10.1016/j.bbrc.2022.02.067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 12/18/2022]
Abstract
Listeria monocytogenes is a psychrotrophic food-borne pathogenic bacterium that causes listeriosis. Due to its unusual adaptation, an ability to grow at extended temperatures ranging from 4 to 45 °C, L. monocytogenes is notoriously hard to control in food-manufacturing processes. In addition, the growing number of antibiotic-resistant L. monocytogenes strains have made listeriosis steadily refractory to clinical treatments and can lead to serious life-threatening diseases, such as sepsis and meningitis, in immunocompromised persons and neonates. Transcription factors that belong to the PadR family play a key role in bacterial survival against unfavorable environmental stresses. The LltR protein from L. monocytogenes was identified as a PadR-type transcription factor and was shown to be required for bacterial growth adaptation at low temperatures. Despite the functional significance of LltR in listeria survival and pathogenesis, our molecular understanding of the LltR-mediated transcriptional regulation is highly limited. Here, we report the crystal structure of LltR and reveal the operator DNA recognition mechanism used by LltR. LltR dimerizes into an isosceles triangle-like shape and requires a winged helix-turn-helix motif for dsDNA recognition. Indeed, LltR and putative operator dsDNA binding was observed and suggests a transcriptional repression of the llfR-lmo0600-lmo0601 operon by direct interaction between the LltR transcription factor and its promoter region. Structure-based comparative and mutational analyses showed that LltR interacts with dsDNA via a unique strategy that combines both LltR-specific and PadR family-common mechanisms.
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Affiliation(s)
- Junghun Kim
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea
| | - Jaewan Park
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea
| | - Zion Choi
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea
| | - Minsun Hong
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea.
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7
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Chordia S, Narasimhan S, Lucini Paioni A, Baldus M, Roelfes G. In Vivo Assembly of Artificial Metalloenzymes and Application in Whole-Cell Biocatalysis*. Angew Chem Int Ed Engl 2021; 60:5913-5920. [PMID: 33428816 PMCID: PMC7986609 DOI: 10.1002/anie.202014771] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Indexed: 12/14/2022]
Abstract
We report the supramolecular assembly of artificial metalloenzymes (ArMs), based on the Lactococcal multidrug resistance regulator (LmrR) and an exogeneous copper(II)-phenanthroline complex, in the cytoplasm of E. coli cells. A combination of catalysis, cell-fractionation, and inhibitor experiments, supplemented with in-cell solid-state NMR spectroscopy, confirmed the in-cell assembly. The ArM-containing whole cells were active in the catalysis of the enantioselective Friedel-Crafts alkylation of indoles and the Diels-Alder reaction of azachalcone with cyclopentadiene. Directed evolution resulted in two different improved mutants for both reactions, LmrR_A92E_M8D and LmrR_A92E_V15A, respectively. The whole-cell ArM system required no engineering of the microbial host, the protein scaffold, or the cofactor to achieve ArM assembly and catalysis. We consider this a key step towards integrating abiological catalysis with biosynthesis to generate a hybrid metabolism.
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Affiliation(s)
- Shreyans Chordia
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Siddarth Narasimhan
- NMR Spectroscopy groupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8, 3584CHUtrechtThe Netherlands
- Current address: Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryMeyerhofstraße 169117HeidelbergGermany
| | - Alessandra Lucini Paioni
- NMR Spectroscopy groupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8, 3584CHUtrechtThe Netherlands
| | - Marc Baldus
- NMR Spectroscopy groupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8, 3584CHUtrechtThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
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8
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Chordia S, Narasimhan S, Lucini Paioni A, Baldus M, Roelfes G. In Vivo Assembly of Artificial Metalloenzymes and Application in Whole‐Cell Biocatalysis**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014771] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shreyans Chordia
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Siddarth Narasimhan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
- Current address: Structural and Computational Biology Unit European Molecular Biology Laboratory Meyerhofstraße 1 69117 Heidelberg Germany
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Marc Baldus
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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9
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Mejías SH, Roelfes G, Browne WR. Impact of binding to the multidrug resistance regulator protein LmrR on the photo-physics and -chemistry of photosensitizers. Phys Chem Chem Phys 2020; 22:12228-12238. [PMID: 32432253 DOI: 10.1039/d0cp01755h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Light activated photosensitizers generate reactive oxygen species (ROS) that interfere with cellular components and can induce cell death, e.g., in photodynamic therapy (PDT). The effect of cellular components and especially proteins on the photochemistry and photophysics of the sensitizers is a key aspect in drug design and the correlating cellular response with the generation of specific ROS species. Here, we show the complex range of effects of binding of photosensitizer to a multidrug resistance protein, produced by bacteria, on the formers reactivity. We show that recruitment of drug like molecules by LmrR (Lactococcal multidrug resistance Regulator) modifies their photophysical properties and their capacity to induce oxidative stress especially in 1O2 generation, including rose bengal (RB), protoporphyrin IX (PpIX), bodipy, eosin Y (EY), riboflavin (RBF), and rhodamine 6G (Rh6G). The range of neutral and charged dyes with different exited redox potentials, are broadly representative of the dyes used in PDT.
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Affiliation(s)
- Sara H Mejías
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Wesley R Browne
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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10
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Structure-based functional analysis of a PadR transcription factor from Streptococcus pneumoniae and characteristic features in the PadR subfamily-2. Biochem Biophys Res Commun 2020; 532:251-257. [PMID: 32868077 DOI: 10.1016/j.bbrc.2020.08.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 11/24/2022]
Abstract
Since the first discovery of phenolic acid decarboxylase transcriptional regulator (PadR), its homologs have been identified mostly in bacterial species and constitute the PadR family. PadR family members commonly contain a winged helix-turn-helix (wHTH) motif and function as a transcription factor. However, the PadR family members are varied in terms of molecular size and structure. As a result, they are divided into PadR subfamily-1 and PadR subfamily-2. PadR subfamily-2 proteins have been reported in some pathogenic bacteria, including Listeria monocytogenes and Streptococcus pneumoniae, and implicated in drug resistance processes. Despite the growing numbers of known PadR family proteins and their critical functions in bacteria survival, biochemical and biophysical studies of the PadR subfamily-2 are limited. Here, we report the crystal structure of a PadR subfamily-2 member from Streptococcus pneumoniae (SpPadR) at a 2.40 Å resolution. SpPadR forms a dimer using its N-terminal and C-terminal helices. The two wHTH motifs of a SpPadR dimer expose their positively charged residues presumably to interact with DNA. Our structure-based mutational and biochemical study indicates that SpPadR specifically recognizes a palindromic nucleotide sequence upstream of its encoding region as a transcriptional regulator. Furthermore, comparative structural analysis of diverse PadR family members combined with a modeling study highlights the structural and regulatory features of SpPadR that are canonical to the PadR family or specific to the PadR subfamily-2.
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11
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Villarino L, Chordia S, Alonso-Cotchico L, Reddem E, Zhou Z, Thunnissen AMWH, Maréchal JD, Roelfes G. Cofactor Binding Dynamics Influence the Catalytic Activity and Selectivity of an Artificial Metalloenzyme. ACS Catal 2020; 10:11783-11790. [PMID: 33101759 PMCID: PMC7574625 DOI: 10.1021/acscatal.0c01619] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/11/2020] [Indexed: 12/20/2022]
Abstract
We present an artificial metalloenzyme based on the transcriptional regulator LmrR that exhibits dynamics involving the positioning of its abiological metal cofactor. The position of the cofactor, in turn, was found to be related to the preferred catalytic reactivity, which is either the enantioselective Friedel-Crafts alkylation of indoles with β-substituted enones or the tandem Friedel-Crafts alkylation/enantioselective protonation of indoles with α-substituted enones. The artificial metalloenzyme could be specialized for one of these catalytic reactions introducing a single mutation in the protein. The relation between cofactor dynamics and activity and selectivity in catalysis has not been described for natural enzymes and, to date, appears to be particular for artificial metalloenzymes.
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Affiliation(s)
- Lara Villarino
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Shreyans Chordia
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Lur Alonso-Cotchico
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Eswar Reddem
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Zhi Zhou
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Andy Mark W. H. Thunnissen
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193,
Cerdanyola del Vallés, Barcelona, Spain
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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12
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Park SC, Song WS, Yoon SI. Apo structure of the transcriptional regulator PadR from Bacillus subtilis: Structural dynamics and conserved Y70 residue. Biochem Biophys Res Commun 2020; 530:215-221. [PMID: 32828288 DOI: 10.1016/j.bbrc.2020.06.135] [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: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 11/24/2022]
Abstract
PadR is a bacterial transcriptional regulator that controls the expression of phenolic acid decarboxylase (PadC) in response to phenolic acids to prevent their toxic effects. During transcriptional repression, PadR associates with the operator sequence at the promoter site of the padC gene. However, when phenolic acids are present, PadR directly binds the phenolic acids and undergoes an interdomain rearrangement to dissociate from the operator DNA. To further examine the structural dynamics of PadR, we determined the apo structure of Bacillus subtilis PadR. Apo-PadR exhibits significant interdomain flexibility and adopts structures that are similar to the phenolic acid-bound PadR structures but distinct from the DNA-bound structure, suggesting that apo-PadR can bind phenolic acids without substantial structural rearrangement. Furthermore, we identified the Y70 residue of PadR as the most conserved residue in the PadR family. PadR Y70 displays similar conformations irrespective of the associated partners, and its conformation is conserved in diverse PadR family members. The Y70 residue is surrounded by the key DNA-binding entities of PadR and is required to optimally arrange them for operator DNA recognition by PadR. PadR Y70 also plays a critical role in protein stability based on the results of a denaturation assay. These observations suggest that PadR Y70 is a canonical residue of the PadR family that contributes to protein stability and DNA binding.
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Affiliation(s)
- Sun Cheol Park
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Wan Seok Song
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea; Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Sung-Il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea; Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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13
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Structural and DNA-binding studies of the PadR-like transcriptional regulator BC1756 from Bacillus cereus. Biochem Biophys Res Commun 2019; 515:607-613. [PMID: 31178139 DOI: 10.1016/j.bbrc.2019.05.141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 05/22/2019] [Indexed: 02/03/2023]
Abstract
Transcription factors that belong to the PadR family play an essential role in the transcriptional regulation of diverse biological processes by recognizing their cognate palindromic DNA sequences. Bacillus cereus harbors a gene that encodes a PadR-like protein (bcPLP; BC1756). bcPLP has not been structurally characterized, and it remains unelucidated how bcPLP interacts with a specific DNA sequence to function as a transcription factor. To provide structural insights into DNA recognition by bcPLP, we performed a structural study and a DNA-binding analysis of bcPLP. The crystal structure of bcPLP was determined at 1.92 Å resolution. bcPLP consists of two domains, an N-terminal domain (NTD) and a C-terminal domain (CTD), and forms a homodimer mainly using the CTD. In the structure, bcPLP contains a highly positively charged elongated patch in the NTD that serves as a putative DNA-binding site. Indeed, an electrophoresis mobility shift assay and a fluorescence polarization assay showed that bcPLP specifically recognizes a palindromic DNA sequence upstream of the bcPLP-encoding region. Moreover, based on our mutagenesis and modeling studies, we demonstrate that bcPLP interacts with dsDNA primarily using the Y19, Y41, P64, and K66 residues in the NTD.
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Hauf S, Möller L, Fuchs S, Halbedel S. PadR-type repressors controlling production of a non-canonical FtsW/RodA homologue and other trans-membrane proteins. Sci Rep 2019; 9:10023. [PMID: 31296881 PMCID: PMC6624303 DOI: 10.1038/s41598-019-46347-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 06/27/2019] [Indexed: 01/02/2023] Open
Abstract
The Gram-positive bacterium Listeria monocytogenes occurs ubiquitously in the environment and infects humans upon ingestion. It encodes four PadR-like repressors, out of which LftR has been characterized previously and was shown to control gene expression in response to the antibiotic aurantimycin produced by other environmental bacteria. To better understand the PadR regulons of L. monocytogenes, we performed RNA-sequencing with mutants of the other three repressors LadR, LstR and Lmo0599. We show that LadR is primarily responsible for the regulation of the mdrL gene, encoding an efflux pump, while LstR and Lmo0599 mainly regulate their own operons. The lstR operon contains the lmo0421 gene, encoding a homolog of the RodA/FtsW protein family. However, this protein does not possess such functionality, as we demonstrate here. The lmo0599 operon contains two additional genes coding for the hypothetical trans-membrane proteins lmo0600 and lmo0601. A striking phenotype of the lmo0599 mutant is its impaired growth at refrigeration temperature. In light of these and other results we suggest that Lmo0599 should be renamed and propose LltR (listerial low temperature regulator) as its new designation. Based on the nature of the PadR target genes we assume that these repressors collectively respond to compounds acting on the cellular envelope.
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Affiliation(s)
- Samuel Hauf
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Burgstrasse 37, 38855, Wernigerode, Germany
| | - Lars Möller
- ZBS 4 - Advanced Light and Electron Microscopy, Robert Koch Institute, Nordufer 20, 13353, Berlin, Germany
| | - Stephan Fuchs
- FG13 Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Burgstrasse 37, 38855, Wernigerode, Germany
| | - Sven Halbedel
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Burgstrasse 37, 38855, Wernigerode, Germany.
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Lee C, Kim MI, Park J, Hong M. Structure-based molecular characterization and regulatory mechanism of the LftR transcription factor from Listeria monocytogenes: Conformational flexibilities and a ligand-induced regulatory mechanism. PLoS One 2019; 14:e0215017. [PMID: 30970033 PMCID: PMC6457526 DOI: 10.1371/journal.pone.0215017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/25/2019] [Indexed: 12/28/2022] Open
Abstract
Listeria monocytogenes is a foodborne pathogen that causes listeriosis and can lead to serious clinical problems, such as sepsis and meningitis, in immunocompromised patients and neonates. Due to a growing number of antibiotic-resistant L. monocytogenes strains, listeriosis can steadily become refractory to antibiotic treatment. To develop novel therapeutics against listeriosis, the drug resistance mechanism of L. monocytogenes needs to be determined. The transcription factor LftR from L. monocytogenes regulates the expression of a putative multidrug resistance transporter, LieAB, and belongs to the PadR-2 subfamily of the PadR family. Despite the functional significance of LftR, our molecular understanding of the transcriptional regulatory mechanism for LftR and even for the PadR-2 subfamily is highly limited. Here, we report the crystal structure of LftR, which forms a dimer and protrudes two winged helix-turn-helix motifs for DNA recognition. Structure-based mutational and comparative analyses showed that LftR interacts with operator DNA through a LftR-specific mode as well as a common mechanism used by the PadR family. Moreover, the LftR dimer harbors one intersubunit cavity in the center of the dimeric structure as a putative ligand-binding site. Finally, conformational flexibilities in the LftR dimer and in the cavity suggest that a ligand-induced regulatory mechanism would be used by the LftR transcription factor.
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Affiliation(s)
- Choongdeok Lee
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Meong Il Kim
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Jaewan Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Minsun Hong
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
- * E-mail:
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Kwak YM, Park SC, Na H, Kang SG, Lee G, Ko H, Kim P, Oh B, Yoon S. Crystal structure of the VanR transcription factor and the role of its unique α‐helix in effector recognition. FEBS J 2018; 285:3786-3800. [DOI: 10.1111/febs.14629] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/03/2018] [Accepted: 08/07/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Yun Mi Kwak
- Division of Biomedical Convergence College of Biomedical Science Kangwon National University Chuncheon Korea
| | - Sun Cheol Park
- Division of Biomedical Convergence College of Biomedical Science Kangwon National University Chuncheon Korea
| | - Hye‐won Na
- Division of Biomedical Convergence College of Biomedical Science Kangwon National University Chuncheon Korea
| | - Seung Goo Kang
- Division of Biomedical Convergence College of Biomedical Science Kangwon National University Chuncheon Korea
| | - Geun‐Shik Lee
- College of Veterinary Medicine Kangwon National University Chuncheon Korea
| | - Hyun‐Jeong Ko
- Laboratory of Microbiology and Immunology College of Pharmacy Kangwon National University Chuncheon Korea
| | - Pyeung‐Hyeun Kim
- Department of Molecular Bioscience School of Biomedical Science Kangwon National University Chuncheon Korea
| | - Byung‐Chul Oh
- Lee Gil Ya Cancer and Diabetes Institute College of Medicine Gachon University Incheon Korea
| | - Sung‐il Yoon
- Division of Biomedical Convergence College of Biomedical Science Kangwon National University Chuncheon Korea
- Institute of Bioscience and Biotechnology Kangwon National University Chuncheon Korea
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Park SC, Kwak YM, Song WS, Hong M, Yoon SI. Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR. Nucleic Acids Res 2018; 45:13080-13093. [PMID: 29136175 PMCID: PMC5728393 DOI: 10.1093/nar/gkx1055] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 10/19/2017] [Indexed: 12/24/2022] Open
Abstract
The PadR family is a large group of transcriptional regulators that function as environmental sensors. PadR negatively controls the expression of phenolic acid decarboxylase, which detoxifies harmful phenolic acids. To identify the mechanism by which PadR regulates phenolic acid-mediated gene expression, we performed structural and mutational studies of effector and operator recognition by Bacillus subtilis PadR. PadR contains an N-terminal winged helix-turn-helix (wHTH) domain (NTD) and a C-terminal homodimerization domain (CTD) and dimerizes into a dolmen shape. The PadR dimer interacts with the palindromic sequence of the operator DNA using the NTD. Two tyrosine residues and a positively charged residue in the NTD provide major DNA-binding energy and are highly conserved in the PadR family, suggesting that these three residues represent the canonical DNA-binding motif of the PadR family. PadR directly binds a phenolic acid effector molecule using a unique interdomain pocket created between the NTD and the CTD. Although the effector-binding site of PadR is positionally segregated from the DNA-binding site, effector binding to the interdomain pocket causes PadR to be rearranged into a DNA binding-incompatible conformer through an allosteric interdomain-reorganization mechanism.
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Affiliation(s)
- Sun Cheol Park
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Yun Mi Kwak
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Wan Seok Song
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Minsun Hong
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Sung-Il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea.,Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
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Corbeski I, Horn V, van der Valk RA, le Paige UB, Dame RT, van Ingen H. Microscale Thermophoresis Analysis of Chromatin Interactions. Methods Mol Biol 2018; 1837:177-197. [PMID: 30109612 DOI: 10.1007/978-1-4939-8675-0_11] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Architectural DNA-binding proteins are key to the organization and compaction of genomic DNA inside cells. The activity of architectural proteins is often subject to further modulation and regulation through the interaction with a diverse array of other protein factors. Detailed knowledge on the binding modes involved is crucial for our understanding of how these protein-protein and protein-DNA interactions shape the functional landscape of chromatin in all kingdoms of life: bacteria, archaea, and eukarya.Microscale thermophoresis (MST) is a biophysical technique that has seen increasing application in the study of biomolecular interactions thanks to its solution-based nature, its rapid application, modest sample demand, and the sensitivity of the thermophoresis effect to binding events. Here, we describe the use of MST in the study of chromatin interactions, with emphasis on the wide range of ways in which these experiments are set up and the diverse types of information they reveal. These aspects are illustrated with four very different systems: the sequence-dependent DNA compaction by architectural protein HMfB; the sequential binding of core histone complexes to histone chaperone APLF; the impact of the nucleosomal context on the recognition of histone modifications; and the binding of a LANA-derived peptide to nucleosome core. Special emphasis is given to the key steps in the design, execution, and analysis of MST experiments in the context of the provided examples.
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Affiliation(s)
- Ivan Corbeski
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Velten Horn
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Ulric B le Paige
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry and Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Hugo van Ingen
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
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Takeuchi K, Imai M, Shimada I. Dynamic equilibrium on DNA defines transcriptional regulation of a multidrug binding transcriptional repressor, LmrR. Sci Rep 2017; 7:267. [PMID: 28325892 PMCID: PMC5428041 DOI: 10.1038/s41598-017-00257-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/14/2017] [Indexed: 11/09/2022] Open
Abstract
LmrR is a multidrug binding transcriptional repressor that controls the expression of a major multidrug transporter, LmrCD, in Lactococcus lactis. Promiscuous compound ligations reduce the affinity of LmrR for the lmrCD operator by several fold to release the transcriptional repression; however, the affinity reduction is orders of magnitude smaller than that of typical transcriptional repressors. Here, we found that the transcriptional regulation of LmrR is achieved through an equilibrium between the operator-bound and non-specific DNA-adsorption states in vivo. The effective dissociation constant of LmrR for the lmrCD operator under the equilibrium is close to the endogenous concentration of LmrR, which allows a substantial reduction of LmrR occupancy upon compound ligations. Therefore, LmrR represents a dynamic type of transcriptional regulation of prokaryotic multidrug resistance systems, where the small affinity reduction induced by compounds is coupled to the functional relocalization of the repressor on the genomic DNA via nonspecific DNA adsorption.
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Affiliation(s)
- Koh Takeuchi
- Biomedicinal Information Research Center & Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Aomi 2-3-26, Koto-ku, Tokyo, 135-0064, Japan.,PRESTO, JST, Aomi 2-3-26, Koto-ku, Tokyo, 135-0064, Japan
| | - Misaki Imai
- Research and Development Department, Japan Biological Informatics Consortium, Aomi 2-3-26, Koto-ku, Tokyo, 135-0064, Japan
| | - Ichio Shimada
- Biomedicinal Information Research Center & Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Aomi 2-3-26, Koto-ku, Tokyo, 135-0064, Japan. .,Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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