1
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Kariyawasam NL, Ploetz EA, Swint-Kruse L, Smith PE. Simulated pressure changes in LacI suggest a link between hydration and functional conformational changes. Biophys Chem 2024; 304:107126. [PMID: 37924711 PMCID: PMC10842697 DOI: 10.1016/j.bpc.2023.107126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023]
Abstract
The functions of many proteins are associated with interconversions among conformational substates. However, these substates can be difficult to measure experimentally, and determining contributions from hydration changes can be especially difficult. Here, we assessed the use of pressure perturbations to sample the substates accessible to the Escherichia coli lactose repressor protein (LacI) in various liganded forms. In the presence of DNA, the regulatory domain of LacI adopts an Open conformation that, in the absence of DNA, changes to a Closed conformation. Increasing the simulation pressure prevented the transition from an Open to a Closed conformation, in a similar manner to the binding of DNA and anti-inducer, ONPF. The results suggest the hydration of specific residues play a significant role in determining the population of different LacI substates and that simulating pressure perturbation could be useful for assessing the role of hydration changes that accompany functionally-relevant amino acid substitutions.
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Affiliation(s)
- Nilusha L Kariyawasam
- Department of Chemistry, 213 CBC Building, 1212 Mid-Campus Dr. North, Kansas State University, Manhattan, KS 66506, USA
| | - Elizabeth A Ploetz
- Department of Chemistry, 213 CBC Building, 1212 Mid-Campus Dr. North, Kansas State University, Manhattan, KS 66506, USA
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, MSN 3030, 3901 Rainbow Blvd, The University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Paul E Smith
- Department of Chemistry, 213 CBC Building, 1212 Mid-Campus Dr. North, Kansas State University, Manhattan, KS 66506, USA.
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2
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Weeramange CJ, Fairlamb MS, Singh D, Fenton AW, Swint‐Kruse L. The strengths and limitations of using biolayer interferometry to monitor equilibrium titrations of biomolecules. Protein Sci 2020; 29:1018-1034. [PMID: 31943488 PMCID: PMC7096710 DOI: 10.1002/pro.3827] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/03/2020] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Every method used to quantify biomolecular interactions has its own strengths and limitations. To quantify protein-DNA binding affinities, nitrocellulose filter binding assays with 32 P-labeled DNA quantify Kd values from 10-12 to 10-8 M but have several technical limitations. Here, we considered the suitability of biolayer interferometry (BLI), which monitors association and dissociation of a soluble macromolecule to an immobilized species; the ratio koff /kon determines Kd . However, for lactose repressor protein (LacI) and an engineered repressor protein ("LLhF") binding immobilized DNA, complicated kinetic curves precluded this analysis. Thus, we determined whether the amplitude of the BLI signal at equilibrium related linearly to the fraction of protein bound to DNA. A key question was the effective concentration of immobilized DNA. Equilibrium titration experiments with DNA concentrations below Kd (equilibrium binding regime) must be analyzed differently than those with DNA near or above Kd (stoichiometric binding regime). For ForteBio streptavidin tips, the most frequent effective DNA concentration was ~2 × 10-9 M. Although variation occurred among different lots of sensor tips, binding events with Kd ≥ 10-8 M should reliably be in the equilibrium binding regime. We also observed effects from multi-valent interactions: Tetrameric LacI bound two immobilized DNAs whereas dimeric LLhF did not. We next used BLI to quantify the amount of inducer sugars required to allosterically diminish protein-DNA binding and to assess the affinity of fructose-1-kinase for the DNA-LLhF complex. Overall, when experimental design corresponded with appropriate data interpretation, BLI was convenient and reliable for monitoring equilibrium titrations and thereby quantifying a variety of binding interactions.
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Affiliation(s)
- Chamitha J. Weeramange
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansas CityKansas
| | - Max S. Fairlamb
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansas CityKansas
| | - Dipika Singh
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansas CityKansas
| | - Aron W. Fenton
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansas CityKansas
| | - Liskin Swint‐Kruse
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansas CityKansas
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3
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Du M, Kodner S, Bai L. Enhancement of LacI binding in vivo. Nucleic Acids Res 2019; 47:9609-9618. [PMID: 31396617 PMCID: PMC6765135 DOI: 10.1093/nar/gkz698] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/11/2019] [Accepted: 07/30/2019] [Indexed: 11/30/2022] Open
Abstract
Transcription factors (TFs) bind to specific sequences in DNA to regulate transcription. Despite extensive measurements of TFs’ dissociation constant (Kd) in vitro, their apparent Kdin vivo are usually unknown. LacI, a bacterial TF, is often used to artificially recruit proteins onto eukaryotic genomes. As LacI binds tightly to its recognition site (LacO) in vitro with a Kd about 10 picomolar (pM), it is often assumed that LacI also has high affinity to LacO in vivo. In this work, we measured LacI binding in living yeast cells using a fluorescent repressor operator system and found an apparent Kd of ∼0.6 μM, four orders of magnitude higher than that in vitro. By genetically altering (i) GFP-LacI structure, (ii) GFP-LacI stability, (iii) chromosome accessibility and (iv) LacO sequence, we reduced the apparent Kd to <10 nM. It turns out that the GFP tagging location and the fusion protein stability have a large effect on LacI binding, but surprisingly, chromosome accessibility only plays a mild role. These findings contribute to our quantitative understanding of the features that affect the apparent Kd of TF in cells. They also provide guidance for future design of more specific chromosomal recruitment through high-affinity TFs.
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Affiliation(s)
- Manyu Du
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.,Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Seth Kodner
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.,Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA
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4
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Tungtur S, Schwingen KM, Riepe JJ, Weeramange CJ, Swint-Kruse L. Homolog comparisons further reconcile in vitro and in vivo correlations of protein activities by revealing over-looked physiological factors. Protein Sci 2019; 28:1806-1818. [PMID: 31351028 DOI: 10.1002/pro.3695] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/10/2019] [Accepted: 07/22/2019] [Indexed: 12/22/2022]
Abstract
To bridge biological and biochemical disciplines, the relationship between in vitro protein biochemical function and in vivo activity must be established. Such studies can (a) help determine whether properties measured in simple, dilute solutions extrapolate to the complex in vivo conditions and (b) illuminate cryptic biological factors that are new avenues for study. We have explored the in vivo-in vitro relationship for chimeras built from LacI/GalR transcription regulators. In prior studies of individual chimeras, amino acid changes that altered in vitro DNA binding affinity exhibited correlated changes in in vivo transcription repression. However, discrepancies arose when the two datasets were compared to each other: Although their DNA binding domains were identical and their in vitro binding affinities spanned the same range, their in vivo repression ranges differed by >50-fold. Here, we determined that the presence of endogenous ligand for one chimera further exacerbated the offset, but that different abilities to simultaneously bind and "loop" two DNA operators resolves the discrepancy. Indeed, results suggest that the lac operon can be looped by even weakly interacting repressor dimers. For looping-competent repressors, we measured in vitro binding to the secondary operator. Surprisingly, this was largely insensitive to amino acid changes in the repressor protein, which reflects altered specificity; this supports the emerging view that the locations of specificity determining positions can be unique to each protein homolog. In aggregate, this work illustrates how a comparative approach can enrich understanding of the in vivo-in vitro relationship and suggest unexpected avenues for future study.
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Affiliation(s)
- Sudheer Tungtur
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Kristen M Schwingen
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Joshua J Riepe
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Chamitha J Weeramange
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
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5
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Fernandez M, Plumbridge J. Complex synergistic amino acid-nucleotide interactions contribute to the specificity of NagC operator recognition and induction. MICROBIOLOGY-SGM 2019; 165:792-803. [PMID: 31107208 DOI: 10.1099/mic.0.000814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
NagC is a transcription factor that represses genes involved in N-acetylglucosamine catabolism in Escherichia coli. Repression by NagC is relieved by interaction with GlcNAc6P, the product of transport of GlcNAc into the cell. The DNA-binding domain of NagC contains a classic helix-turn-helix (HTH) motif, but specific operator recognition requires, in addition, an adjacent linker sequence, which is thought to form an extended wing. Sequences in the linker region are required to distinguish NagC-binding sites from those of its paralogue, Mlc. In investigating the contribution of the HTH to operator recognition, we have identified mutations in the first two positions of the recognition helix of the DNA-binding motif of NagC, which change NagC from being a repressor, which binds in the absence of the inducing signal (GlcNAc6P), to one whose binding is enhanced by GlcNAc6P. In this case GlcNAc6P behaves as a co-repressor rather than an inducer for NagC. The NagC mutants exhibiting this paradoxical behaviour have basic amino acids, arginine or lysine, at two critical positions of the recognition helix. Introducing a third amino acid change converts NagC back to a protein, which represses in the absence of GlcNAc6P. The triple mutant also effectively represses a modified NagC operator that is not repressed by wild-type NagC, showing that this form of NagC is a more promiscuous DNA binder. Specific recognition of the NagC operator thus involves a modulation of basic amino acid-DNA interactions, which affects the ability to discriminate against other permissive sites.
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Affiliation(s)
- Marion Fernandez
- UMR8261,CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13, rue P. et M. Curie, 75005 Paris, France
| | - Jacqueline Plumbridge
- UMR8261,CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13, rue P. et M. Curie, 75005 Paris, France
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6
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Seckfort D, Montgomery Pettitt B. Price of disorder in the lac repressor hinge helix. Biopolymers 2019; 110:e23239. [PMID: 30485404 PMCID: PMC6335174 DOI: 10.1002/bip.23239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/12/2018] [Accepted: 10/04/2018] [Indexed: 12/26/2022]
Abstract
The Lac system of genes has been pivotal in understanding gene regulation. When the lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The structure of this region of the protein is well understood when it is in this bound conformation, but less so when it is not. Structural studies show that this region is flexible. Our simulations show this region is extremely flexible in solution; however, a high concentration of salt can help kinetically trap the hinge helix. Thermodynamically, disorder is more favorable without the DNA present.
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Affiliation(s)
- Danielle Seckfort
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas
| | - B Montgomery Pettitt
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas
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7
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Darlington APS, Kim J, Jiménez JI, Bates DG. Engineering Translational Resource Allocation Controllers: Mechanistic Models, Design Guidelines, and Potential Biological Implementations. ACS Synth Biol 2018; 7:2485-2496. [PMID: 30346148 DOI: 10.1021/acssynbio.8b00029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of orthogonal ribosomes in combination with dynamic resource allocation controllers is a promising approach for relieving the negative effects of cellular resource limitations on the modularity of synthetic gene circuits. Here, we develop a detailed mechanistic model of gene expression and resource allocation, which when simplified to a tractable level of complexity, allows the rational design of translational resource allocation controllers. Analysis of this model reveals a fundamental design trade-off: that reducing coupling acts to decrease gene expression. Through a sensitivity analysis of the experimentally tunable controller parameters, we identify how each controller design parameter affects the overall closed-loop behavior of the system, leading to a detailed set of design guidelines for optimally managing this trade-off. On the basis of our designs, we evaluated a number of alternative potential experimental implementations of the proposed system using commonly available biological components. Finally, we show that the controller is capable of dynamically allocating ribosomes as needed to restore modularity in a number of more complex synthetic circuits, such as the repressilator, and activation cascades composed of multiple interacting modules.
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Affiliation(s)
- Alexander P. S. Darlington
- Warwick Integrative Synthetic Biology Centre, School of Engineering, University of Warwick, Coventry CV4 7AL, U.K
| | - Juhyun Kim
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, U.K
| | - José I. Jiménez
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, U.K
| | - Declan G. Bates
- Warwick Integrative Synthetic Biology Centre, School of Engineering, University of Warwick, Coventry CV4 7AL, U.K
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8
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Schaerli Y, Jiménez A, Duarte JM, Mihajlovic L, Renggli J, Isalan M, Sharpe J, Wagner A. Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution. Mol Syst Biol 2018; 14:e8102. [PMID: 30201776 PMCID: PMC6129954 DOI: 10.15252/msb.20178102] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 08/15/2018] [Accepted: 08/15/2018] [Indexed: 12/22/2022] Open
Abstract
Phenotypic variation is the raw material of adaptive Darwinian evolution. The phenotypic variation found in organismal development is biased towards certain phenotypes, but the molecular mechanisms behind such biases are still poorly understood. Gene regulatory networks have been proposed as one cause of constrained phenotypic variation. However, most pertinent evidence is theoretical rather than experimental. Here, we study evolutionary biases in two synthetic gene regulatory circuits expressed in Escherichia coli that produce a gene expression stripe-a pivotal pattern in embryonic development. The two parental circuits produce the same phenotype, but create it through different regulatory mechanisms. We show that mutations cause distinct novel phenotypes in the two networks and use a combination of experimental measurements, mathematical modelling and DNA sequencing to understand why mutations bring forth only some but not other novel gene expression phenotypes. Our results reveal that the regulatory mechanisms of networks restrict the possible phenotypic variation upon mutation. Consequently, seemingly equivalent networks can indeed be distinct in how they constrain the outcome of further evolution.
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Affiliation(s)
- Yolanda Schaerli
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Alba Jiménez
- Systems Biology Program, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain
| | - José M Duarte
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Ljiljana Mihajlovic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | | | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - James Sharpe
- Systems Biology Program, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Spain
- EMBL Barcelona European Molecular Biology Laboratory, Barcelona, Spain
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- The Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, NM, USA
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9
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Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes. Nat Commun 2018; 9:695. [PMID: 29449554 PMCID: PMC5814443 DOI: 10.1038/s41467-018-02898-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 01/08/2018] [Indexed: 11/08/2022] Open
Abstract
Introduction of synthetic circuits into microbes creates competition between circuit and host genes for shared cellular resources, such as ribosomes. This can lead to the emergence of unwanted coupling between the expression of different circuit genes, complicating the design process and potentially leading to circuit failure. By expressing a synthetic 16S rRNA with altered specificity, we can partition the ribosome pool into host-specific and circuit-specific activities. We show mathematically and experimentally that the effects of resource competition can be alleviated by targeting genes to different ribosomal pools. This division of labour can be used to increase flux through a metabolic pathway. We develop a model of cell physiology which is able to capture these observations and use it to design a dynamic resource allocation controller. When implemented, this controller acts to decouple genes by increasing orthogonal ribosome production as the demand for translational resources by a synthetic circuit increases.
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10
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Xu JS, Hewitt MN, Gulati JS, Cruz MA, Zhan H, Liu S, Matthews KS. Lactose repressor hinge domain independently binds DNA. Protein Sci 2018; 27:839-847. [PMID: 29318690 PMCID: PMC5866929 DOI: 10.1002/pro.3372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 01/02/2018] [Accepted: 01/02/2018] [Indexed: 12/29/2022]
Abstract
The short 8-10 amino acid "hinge" sequence in lactose repressor (LacI), present in other LacI/GalR family members, links DNA and inducer-binding domains. Structural studies of full-length or truncated LacI-operator DNA complexes demonstrate insertion of the dimeric helical "hinge" structure at the center of the operator sequence. This association bends the DNA ∼40° and aligns flanking semi-symmetric DNA sites for optimal contact by the N-terminal helix-turn-helix (HtH) sequences within each dimer. In contrast, the hinge region remains unfolded when bound to nonspecific DNA sequences. To determine ability of the hinge helix alone to mediate DNA binding, we examined (i) binding of LacI variants with deletion of residues 1-50 to remove the HtH DNA binding domain or residues 1-58 to remove both HtH and hinge domains and (ii) binding of a synthetic peptide corresponding to the hinge sequence with a Val52Cys substitution that allows reversible dimer formation via a disulfide linkage. Binding affinity for DNA is orders of magnitude lower in the absence of the helix-turn-helix domain with its highly positive charge. LacI missing residues 1-50 binds to DNA with ∼4-fold greater affinity for operator than for nonspecific sequences with minimal impact of inducer presence; in contrast, LacI missing residues 1-58 exhibits no detectable affinity for DNA. In oxidized form, the dimeric hinge peptide alone binds to O1 and nonspecific DNA with similarly small difference in affinity; reduction to monomer diminished binding to both O1 and nonspecific targets. These results comport with recent reports regarding LacI hinge interaction with DNA sequences.
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Affiliation(s)
- Joseph S Xu
- Department of BioSciences, MS-140, Rice University, Houston, Texas, 77251
| | - Madeleine N Hewitt
- Department of BioSciences, MS-140, Rice University, Houston, Texas, 77251
| | - Jaskeerat S Gulati
- Department of BioSciences, MS-140, Rice University, Houston, Texas, 77251
| | - Matthew A Cruz
- Department of BioSciences, MS-140, Rice University, Houston, Texas, 77251
| | - Hongli Zhan
- Department of BioSciences, MS-140, Rice University, Houston, Texas, 77251
| | - Shirley Liu
- Department of BioSciences, MS-140, Rice University, Houston, Texas, 77251
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11
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Sengupta R, Capp MW, Shkel IA, Record MT. The mechanism and high-free-energy transition state of lac repressor-lac operator interaction. Nucleic Acids Res 2017; 45:12671-12680. [PMID: 29036376 PMCID: PMC5727403 DOI: 10.1093/nar/gkx862] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/22/2017] [Indexed: 01/06/2023] Open
Abstract
Significant, otherwise-unavailable information about mechanisms and transition states (TS) of protein folding and binding is obtained from solute effects on rate constants. Here we characterize TS for lac repressor(R)–lac operator(O) binding by analyzing effects of RO-stabilizing and RO-destabilizing solutes on association (ka) and dissociation (kd) rate constants. RO-destabilizing solutes (urea, KCl) reduce ka comparably (urea) or more than (KCl) they increase kd, demonstrating that they destabilize TS relative to reactants and RO, and that TS exhibits most of the Coulombic interactions between R and O. Strikingly, three solutes which stabilize RO by favoring burial/dehydration of amide oxygens and anionic phosphate oxygens all reduce kd without affecting ka significantly. The lack of stabilization of TS by these solutes indicates that O phosphates remain hydrated in TS and that TS preferentially buries aromatic carbons and amide nitrogens while leaving amide oxygens exposed. In our proposed mechanism, DNA-binding-domains (DBD) of R insert in major grooves of O pre-TS, forming most Coulombic interactions of RO and burying aromatic carbons. Nucleation of hinge helices creates TS, burying sidechain amide nitrogens. Post-TS, hinge helices assemble and the DBD-hinge helix-O-DNA module docks on core repressor, partially dehydrating phosphate oxygens and tightening all interfaces to form RO.
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Affiliation(s)
- Rituparna Sengupta
- Program in Biophysics, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael W Capp
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Irina A Shkel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - M Thomas Record
- Program in Biophysics, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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12
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Bartosik AA, Glabski K, Kulinska A, Lewicka E, Godziszewska J, Markowska A, Jagura-Burdzy G. Convenient broad-host-range unstable vectors for studying stabilization cassettes in diverse bacteria. BMC Microbiol 2016; 16:59. [PMID: 27044351 PMCID: PMC4820964 DOI: 10.1186/s12866-016-0674-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/17/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Low-copy-number vectors of potential wide application in biotechnology need to encode stabilization modules ensuring their stable inheritance. The efficiency of stabilization may vary depending on the plasmid host so a thorough analysis of stabilization functions is required before use. RESULTS To facilitate such analysis highly unstable, mobilizable, broad-host-range (BHR) vectors based on RK2 replicon were constructed. The vectors are suitable for testing of various stabilization functions, including plasmid and chromosomal partitioning cassettes encoding ParB homologues capable of spreading on DNA. The xylE or lacZ reporter systems facilitate easy monitoring of plasmid segregation. CONCLUSION The range of BHR vectors with different reporter cassettes and alternative mobilization systems expands their application in diverse bacterial species.
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Affiliation(s)
- Aneta A. Bartosik
- />Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Krzysztof Glabski
- />Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Anna Kulinska
- />Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
- />Present address: Faculty of Chemistry, Institute of Biotechnology, Warsaw University of Technology, Warsaw, Poland
| | - Ewa Lewicka
- />Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Jolanta Godziszewska
- />Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
- />Present address: Faculty of Human Nutrition and Consumer Sciences, Laboratory of Food Chemistry, Warsaw University of Life Sciences, Warsaw, Poland
| | - Aleksandra Markowska
- />Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
- />Present address: Pulawska 255A/4, 02-740 Warsaw, Poland
| | - Grazyna Jagura-Burdzy
- />Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
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13
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Bondos SE, Swint-Kruse L, Matthews KS. Flexibility and Disorder in Gene Regulation: LacI/GalR and Hox Proteins. J Biol Chem 2015; 290:24669-77. [PMID: 26342073 DOI: 10.1074/jbc.r115.685032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
To modulate transcription, a variety of input signals must be sensed by genetic regulatory proteins. In these proteins, flexibility and disorder are emerging as common themes. Prokaryotic regulators generally have short, flexible segments, whereas eukaryotic regulators have extended regions that lack predicted secondary structure (intrinsic disorder). Two examples illustrate the impact of flexibility and disorder on gene regulation: the prokaryotic LacI/GalR family, with detailed information from studies on LacI, and the eukaryotic family of Hox proteins, with specific insights from investigations of Ultrabithorax (Ubx). The widespread importance of structural disorder in gene regulatory proteins may derive from the need for flexibility in signal response and, particularly in eukaryotes, in protein partner selection.
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Affiliation(s)
- Sarah E Bondos
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Liskin Swint-Kruse
- the Department of Biochemistry and Molecular Biology, the University of Kansas Medical Center, Kansas City, Kansas 66160, and
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14
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Vujanac M, Iyer VS, Sengupta M, Ajdic D. Regulation of Streptococcus mutans PTS Bio by the transcriptional repressor NigR. Mol Oral Microbiol 2015; 30:280-94. [PMID: 25580872 DOI: 10.1111/omi.12093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2014] [Indexed: 11/29/2022]
Abstract
Streptococcus mutans is implicated in human dental caries, and the carbohydrate metabolism of this organism plays an important role in the formation of this disease. Carbohydrate transport and metabolism are essential for the survival of S. mutans in the oral cavity. It is known that a unique phosphoenolpyruvate-sugar phosphotransferase system PTS(B) (io) of S. mutans UA159 is expressed in sucrose-grown biofilms (Mol Oral Microbiol 28: 2013; 114). In this study we analyzed the transcriptional regulation of the operon (O(B) (io) ) encoding the PTS(B) (io) and showed that it was repressed by NigR, a LacI-like transcriptional regulator. Using electro-mobility shift assay, we described two operators to which NigR bound with different affinities. We also identified the transcriptional start site and showed that one of the operators overlaps with the promoter and presumably represses initiation of transcription. Mutational analyses revealed the key nucleotides in the operators required for high-affinity binding of NigR. PTS(B) (io) is expressed in S. mutans biofilms so understanding its regulation may provide improved strategies for caries treatment and prevention.
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Affiliation(s)
- M Vujanac
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - V S Iyer
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - M Sengupta
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - D Ajdic
- Miller School of Medicine, University of Miami, Miami, FL, USA
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15
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Gatti-Lafranconi P, Dijkman WP, Devenish SRA, Hollfelder F. A single mutation in the core domain of the lac repressor reduces leakiness. Microb Cell Fact 2013; 12:67. [PMID: 23834731 PMCID: PMC3722110 DOI: 10.1186/1475-2859-12-67] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 06/29/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The lac operon provides cells with the ability to switch from glucose to lactose metabolism precisely when necessary. This metabolic switch is mediated by the lac repressor (LacI), which in the absence of lactose binds to the operator DNA sequence to inhibit transcription. Allosteric rearrangements triggered by binding of the lactose isomer allolactose to the core domain of the repressor impede DNA binding and lift repression. In Nature, the ability to detect and respond to environmental conditions comes at the cost of the encoded enzymes being constitutively expressed at low levels. The readily-switched regulation provided by LacI has resulted in its widespread use for protein overexpression, and its applications in molecular biology represent early examples of synthetic biology. However, the leakiness of LacI that is essential for the natural function of the lac operon leads to an increased energetic burden, and potentially toxicity, in heterologous protein production. RESULTS Analysis of the features that confer promiscuity to the inducer-binding site of LacI identified tryptophan 220 as a target for saturation mutagenesis. We found that phenylalanine (similarly to tryptophan) affords a functional repressor that is still responsive to IPTG. Characterisation of the W220F mutant, LacIWF, by measuring the time dependence of GFP production at different IPTG concentrations and at various incubation temperatures showed a 10-fold reduction in leakiness and no decrease in GFP production. Cells harbouring a cytotoxic protein under regulatory control of LacIWF showed no decrease in viability in the early phases of cell growth. Changes in responsiveness to IPTG observed in vivo are supported by the thermal shift assay behaviour of purified LacIWF with IPTG and operator DNA. CONCLUSIONS In LacI, long-range communications are responsible for the transmission of the signal from the inducer binding site to the DNA binding domain and our results are consistent with the involvement of position 220 in modulating these. The mutation of this single tryptophan residue to phenylalanine generated an enhanced repressor with a 10-fold decrease in leakiness. By minimising the energetic burden and cytotoxicity caused by leakiness, LacIWF constitutes a useful switch for protein overproduction and synthetic biology.
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Affiliation(s)
| | - Willem P Dijkman
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Sean RA Devenish
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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16
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Meyer S, Ramot R, Kishore Inampudi K, Luo B, Lin C, Amere S, Wilson CJ. Engineering alternate cooperative-communications in the lactose repressor protein scaffold. Protein Eng Des Sel 2013; 26:433-43. [DOI: 10.1093/protein/gzt013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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17
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Kim S, Broströmer E, Xing D, Jin J, Chong S, Ge H, Wang S, Gu C, Yang L, Gao YQ, Su XD, Sun Y, Xie XS. Probing allostery through DNA. Science 2013; 339:816-9. [PMID: 23413354 DOI: 10.1126/science.1229223] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Allostery is well documented for proteins but less recognized for DNA-protein interactions. Here, we report that specific binding of a protein on DNA is substantially stabilized or destabilized by another protein bound nearby. The ternary complex's free energy oscillates as a function of the separation between the two proteins with a periodicity of ~10 base pairs, the helical pitch of B-form DNA, and a decay length of ~15 base pairs. The binding affinity of a protein near a DNA hairpin is similarly dependent on their separation, which-together with molecular dynamics simulations-suggests that deformation of the double-helical structure is the origin of DNA allostery. The physiological relevance of this phenomenon is illustrated by its effect on gene expression in live bacteria and on a transcription factor's affinity near nucleosomes.
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Affiliation(s)
- Sangjin Kim
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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18
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Bréchemier-Baey D, Domínguez-Ramírez L, Plumbridge J. The linker sequence, joining the DNA-binding domain of the homologous transcription factors, Mlc and NagC, to the rest of the protein, determines the specificity of their DNA target recognition inEscherichia coli. Mol Microbiol 2012; 85:1007-19. [DOI: 10.1111/j.1365-2958.2012.08158.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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19
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Maity TS, Jha RK, Strauss CEM, Dunbar J. Exploring the sequence-function relationship in transcriptional regulation by the lac O1 operator. FEBS J 2012; 279:2534-43. [PMID: 22594825 DOI: 10.1111/j.1742-4658.2012.08635.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding how binding of a transcription factor to an operator is influenced by the operator sequence is an ongoing quest. It facilitates discovery of alternative binding sites as well as tuning of transcriptional regulation. We investigated the behavior of the Escherichia coli Lac repressor (LacI) protein with a large set of lac O(1) operator variants. The 114 variants examined contained a mean of 2.9 (range 0-4) mutations at positions -4, -2, +2 and +4 in the minimally required 17 bp operator. The relative affinity of LacI for the operators was examined by quantifying expression of a GFP reporter gene and Rosetta structural modeling. The combinations of mutations in the operator sequence created a wide range of regulatory behaviors. We observed variations in the GFP fluorescent signal among the operator variants of more than an order of magnitude under both uninduced and induced conditions. We found that a single nucleotide change may result in changes of up to six- and 12-fold in uninduced and induced GFP signals, respectively. Among the four positions mutated, we found that nucleotide G at position -4 is strongly correlated with strong repression. By Rosetta modeling, we found a significant correlation between the calculated binding energy and the experimentally observed transcriptional repression strength for many operators. However, exceptions were also observed, underscoring the necessity for further improvement in biophysical models of protein-DNA interactions.
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Affiliation(s)
- Tuhin S Maity
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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20
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Quan S, Ray JCJ, Kwota Z, Duong T, Balázsi G, Cooper TF, Monds RD. Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli. PLoS Genet 2012; 8:e1002444. [PMID: 22253602 PMCID: PMC3257284 DOI: 10.1371/journal.pgen.1002444] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 11/16/2011] [Indexed: 01/22/2023] Open
Abstract
Adaptation to novel environments is often associated with changes in gene regulation. Nevertheless, few studies have been able both to identify the genetic basis of changes in regulation and to demonstrate why these changes are beneficial. To this end, we have focused on understanding both how and why the lactose utilization network has evolved in replicate populations of Escherichia coli. We found that lac operon regulation became strikingly variable, including changes in the mode of environmental response (bimodal, graded, and constitutive), sensitivity to inducer concentration, and maximum expression level. In addition, some classes of regulatory change were enriched in specific selective environments. Sequencing of evolved clones, combined with reconstruction of individual mutations in the ancestral background, identified mutations within the lac operon that recapitulate many of the evolved regulatory changes. These mutations conferred fitness benefits in environments containing lactose, indicating that the regulatory changes are adaptive. The same mutations conferred different fitness effects when present in an evolved clone, indicating that interactions between the lac operon and other evolved mutations also contribute to fitness. Similarly, changes in lac regulation not explained by lac operon mutations also point to important interactions with other evolved mutations. Together these results underline how dynamic regulatory interactions can be, in this case evolving through mutations both within and external to the canonical lactose utilization network.
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Affiliation(s)
- Selwyn Quan
- Bio-X Program, Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - J. Christian J. Ray
- Department of Systems Biology–Unit 950, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Zakari Kwota
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Trang Duong
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Gábor Balázsi
- Department of Systems Biology–Unit 950, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Tim F. Cooper
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Russell D. Monds
- Bio-X Program, Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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21
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Sakaguchi-Mikami A, Taniguchi A, Sode K, Yamazaki T. Construction of a novel glucose-sensing molecule based on a substrate-binding protein for intracellular sensing. Biotechnol Bioeng 2010; 108:725-33. [PMID: 21404246 DOI: 10.1002/bit.23006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 09/14/2010] [Accepted: 10/20/2010] [Indexed: 01/29/2023]
Abstract
A novel transcriptional regulator responding to glucose was designed with a substrate-binding protein (SBP) as a probe towards intracellular sensing system for glucose in mammalian cells. A chimeric protein of an SBP for glucose (GBP) and a LacI-type regulator, LacI (SLCP(GL) ), was designed, constructed and characterized using Escherichia coli recombinant protein. We report that SLCP(GL) has a glucose-specific binding ability and an operator-sequence specific DNA-binding ability. The loss of its DNA-binding ability in the presence of glucose suggests a role as a transcriptional regulator in vitro. The glucose-dependent gene regulation function of SLCP(GL) in cells was investigated using mammalian cells co-transfected with SLCP(GL) and Lac operator-fused luciferase gene constructs. The luciferase activity of the transfected cells increased with the glucose concentration in the medium, showing that the expression of the luciferase gene is regulated by SLCP(GL) , which can dissociate from DNA in a glucose concentration-dependent manner. Therefore, we demonstrated that SLCP(GL) functions as a glucose-sensitive transcriptional regulator in mammalian cells. These results reveal the possibility of developing an SBP-based regulator as a probe of intracellular sensing and gene regulation system for mammalian cells in response to a desired ligands depending on the SBP ligand specificity.
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Affiliation(s)
- Akane Sakaguchi-Mikami
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Namiki, Tsukuba, 305-0044 Ibaraki, Japan
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22
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Pan Y, Nussinov R. Lysine120 interactions with p53 response elements can allosterically direct p53 organization. PLoS Comput Biol 2010; 6:e1000878. [PMID: 20700496 PMCID: PMC2916859 DOI: 10.1371/journal.pcbi.1000878] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Accepted: 07/08/2010] [Indexed: 01/02/2023] Open
Abstract
p53 can serve as a paradigm in studies aiming to figure out how allosteric perturbations in transcription factors (TFs) triggered by small changes in DNA response element (RE) sequences, can spell selectivity in co-factor recruitment. p53-REs are 20-base pair (bp) DNA segments specifying diverse functions. They may be located near the transcription start sites or thousands of bps away in the genome. Their number has been estimated to be in the thousands, and they all share a common motif. A key question is then how does the p53 protein recognize a particular p53-RE sequence among all the similar ones? Here, representative p53-REs regulating diverse functions including cell cycle arrest, DNA repair, and apoptosis were simulated in explicit solvent. Among the major interactions between p53 and its REs involving Lys120, Arg280 and Arg248, the bps interacting with Lys120 vary while the interacting partners of other residues are less so. We observe that each p53-RE quarter site sequence has a unique pattern of interactions with p53 Lys120. The allosteric, DNA sequence-induced conformational and dynamic changes of the altered Lys120 interactions are amplified by the perturbation of other p53-DNA interactions. The combined subtle RE sequence-specific allosteric effects propagate in the p53 and in the DNA. The resulting amplified allosteric effects far away are reflected in changes in the overall p53 organization and in the p53 surface topology and residue fluctuations which play key roles in selective co-factor recruitment. As such, these observations suggest how similar p53-RE sequences can spell the preferred co-factor binding, which is the key to the selective gene transactivation and consequently different functional effects.
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Affiliation(s)
- Yongping Pan
- Basic Science Program, Science Applications International Corporation-Frederick, Inc., Center for Cancer Research Nanobiology Program, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Basic Science Program, Science Applications International Corporation-Frederick, Inc., Center for Cancer Research Nanobiology Program, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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23
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Lymperopoulos K, Crawford R, Torella JP, Heilemann M, Hwang LC, Holden SJ, Kapanidis AN. Single-molecule DNA biosensors for protein and ligand detection. Angew Chem Int Ed Engl 2010; 49:1316-20. [PMID: 20077444 DOI: 10.1002/anie.200904597] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Konstantinos Lymperopoulos
- Biological Physics Research Group, Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, United Kingdom
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24
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Lymperopoulos K, Crawford R, Torella J, Heilemann M, Hwang L, Holden S, Kapanidis A. Einzelmolekül-DNA-Biosensoren zur Detektion von Proteinen und Liganden. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200904597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Comparing the functional roles of nonconserved sequence positions in homologous transcription repressors: implications for sequence/function analyses. J Mol Biol 2009; 395:785-802. [PMID: 19818797 DOI: 10.1016/j.jmb.2009.10.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 10/01/2009] [Accepted: 10/02/2009] [Indexed: 11/21/2022]
Abstract
The explosion of protein sequences deduced from genetic code has led to both a problem and a potential resource: Efficient data use requires interpreting the functional impact of sequence change without experimentally characterizing each protein variant. Several groups have hypothesized that interpretation could be aided by analyzing the sequences of naturally occurring homologues. To that end, myriad sequence/function analyses have been developed to predict which conserved, semi-conserved, and nonconserved positions are functionally important. These positions must be discriminated from the nonconserved positions that are functionally silent. However, the assumptions that underlie sequence analyses are based on experimental results that are sparse and usually designed to address different questions. Here, we use three homologues from a test family common to bioinformatics-the LacI/GalR transcription repressors-to test a common assumption: If a position is functionally important for one family member, it has similar importance in all homologues. We generated experimental sequence/function information for each nonconserved position in the 18 amino acids that link the DNA-binding and regulatory domains of three LacI/GalR homologues. We find that the functional importance of each position is preserved among the three linkers, albeit to different degrees. We also find that every linker position contributes to function, which has twofold implications. (1) Since the linker positions range from highly conserved to semi-conserved to nonconserved and contribute to affinity, selectivity, and allosteric response, we assert that sequence/function analyses must identify positions in the LacI/GalR linkers to be qualified as "successful". Many analyses overlook this region since most of the residues do not directly contact ligand. (2) No position in the LacI/GalR linker is functionally silent. This finding is inconsistent with another underlying principle of many analyses: Using sequence sets to discriminate important from non-contributing positions obligates silent positions, which denotes that most homologues tolerate a variety of amino acid substitutions at the position without functional change. Instead, additional combinatorial mutants in the LacI/GalR linkers show that particular substitutions can be silent in a context-dependent manner. Thus, specific permutations of sequence change (rather than change at silent positions) would facilitate neutral drift during evolution. Finally, the combinatorial mutants also reveal functional synergy between semi- and nonconserved positions. Such functional relationships would be missed by analyses that rely primarily upon co-evolution.
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26
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Swint-Kruse L, Matthews KS. Allostery in the LacI/GalR family: variations on a theme. Curr Opin Microbiol 2009; 12:129-37. [PMID: 19269243 DOI: 10.1016/j.mib.2009.01.009] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 01/22/2009] [Accepted: 01/26/2009] [Indexed: 12/21/2022]
Abstract
The lactose repressor protein (LacI) was among the very first genetic regulatory proteins discovered, and more than 1000 members of the bacterial LacI/GalR family are now identified. LacI has been the prototype for understanding how transcription is controlled using small metabolites to modulate protein association with specific DNA sites. This understanding has been greatly expanded by the study of other LacI/GalR homologues. A general picture emerges in which the conserved fold provides a scaffold for multiple types of interactions - including oligomerization, small molecule binding, and protein-protein binding - that in turn influence target DNA binding and thereby regulate mRNA production. Although many different functions have evolved from this basic scaffold, each homologue retains functional flexibility: For the same protein, different small molecules can have disparate impact on DNA binding and hence transcriptional outcome. In turn, binding to alternative DNA sequences may impact the degree of allosteric response. Thus, this family exhibits a symphony of variations by which transcriptional control is achieved.
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Affiliation(s)
- Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, 66160, United States.
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27
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Chen H, Su X, Neoh KG, Choe WS. Context-dependent adsorption behavior of cyclic and linear peptides on metal oxide surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:1588-1593. [PMID: 19170646 DOI: 10.1021/la8030304] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Peptides with specific binding affinity to inorganic materials bridge biological systems with synthetic inorganic materials. Many inorganic-binding peptides were isolated using combinatorial peptide libraries without a good understanding of the interaction mechanism, which thus hinders the practical application of these peptides. Besides the amino acid composition, peptides' structure (e.g., cyclic structure constrained by disulfide bond) is believed to play an important role in their binding behavior. A cyclic peptide STB1 (-CHKKPSKSC-) was previously identified to electrostatically bind to TiO2 and SiO2. In the present study, the binding behavior (affinity and conformation) of STB1 and its linear version LSTB1 (-AHKKPSKSA-) on a TiO2 or SiO2 surface was investigated in three different contexts (i.e., free peptides, phage particles displaying peptides, and LacI-peptide fusion protein) using quartz crystal microbalance with energy dissipation measurement (QCM-D). The binding kinetics of STB1 and LSTB1 in the context of fusion protein to either metal oxide was quantitatively analyzed. LSTB1 showed similar binding behavior on both TiO2 and SiO2 surfaces. In the context of phage-displayed and LacI-hosted peptides, STB1 was found to have weaker binding affinity than LSTB1 for either metal oxide, but it was able to distinguish between SiO2 and TiO2. This is probably because LSTB1 has a much more flexible structure than STB1, as shown by the molecular dynamics simulation. The structural flexibility of LSTB1 enables it to explore a wider range of conformations to maximize its interaction with TiO2 and SiO2.
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Affiliation(s)
- Haibin Chen
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260
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28
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Meinhardt S, Swint-Kruse L. Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: bioinformatics-based predictions generate true positives and false negatives. Proteins 2008; 73:941-57. [PMID: 18536016 DOI: 10.1002/prot.22121] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In protein families, conserved residues often contribute to a common general function, such as DNA-binding. However, unique attributes for each homolog (e.g. recognition of alternative DNA sequences) must arise from variation in other functionally-important positions. The locations of these "specificity determinant" positions are obscured amongst the background of varied residues that do not make significant contributions to either structure or function. To isolate specificity determinants, a number of bioinformatics algorithms have been developed. When applied to the LacI/GalR family of transcription regulators, several specificity determinants are predicted in the 18 amino acids that link the DNA-binding and regulatory domains. However, results from alternative algorithms are only in partial agreement with each other. Here, we experimentally evaluate these predictions using an engineered repressor comprising the LacI DNA-binding domain, the LacI linker, and the GalR regulatory domain (LLhG). "Wild-type" LLhG has altered DNA specificity and weaker lacO(1) repression compared to LacI or a similar LacI:PurR chimera. Next, predictions of linker specificity determinants were tested, using amino acid substitution and in vivo repression assays to assess functional change. In LLhG, all predicted sites are specificity determinants, as well as three sites not predicted by any algorithm. Strategies are suggested for diminishing the number of false negative predictions. Finally, individual substitutions at LLhG specificity determinants exhibited a broad range of functional changes that are not predicted by bioinformatics algorithms. Results suggest that some variants have altered affinity for DNA, some have altered allosteric response, and some appear to have changed specificity for alternative DNA ligands.
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Affiliation(s)
- Sarah Meinhardt
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas 66160, USA
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29
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Francke C, Kerkhoven R, Wels M, Siezen RJ. A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1. BMC Genomics 2008; 9:145. [PMID: 18371204 PMCID: PMC2329647 DOI: 10.1186/1471-2164-9-145] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Accepted: 03/27/2008] [Indexed: 12/18/2022] Open
Abstract
Background A key problem in the sequence-based reconstruction of regulatory networks in bacteria is the lack of specificity in operator predictions. The problem is especially prominent in the identification of transcription factor (TF) specific binding sites. More in particular, homologous TFs are abundant and, as they are structurally very similar, it proves difficult to distinguish the related operators by automated means. This also holds for the LacI-family, a family of TFs that is well-studied and has many members that fulfill crucial roles in the control of carbohydrate catabolism in bacteria including catabolite repression. To overcome the specificity problem, a comprehensive footprinting approach was formulated to identify TF-specific operator motifs and was applied to the LacI-family of TFs in the model gram positive organism, Lactobacillus plantarum WCFS1. The main premise behind the approach is that only orthologous sequences that share orthologous genomic context will share equivalent regulatory sites. Results When the approach was applied to the 12 LacI-family TFs of the model species, a specific operator motif was identified for each of them. With the TF-specific operator motifs, potential binding sites were found on the genome and putative minimal regulons could be defined. Moreover, specific inducers could in most cases be linked to the TFs through phylogeny, thereby unveiling the biological role of these regulons. The operator predictions indicated that the LacI-family TFs can be separated into two subfamilies with clearly distinct operator motifs. They also established that the operator related to the 'global' regulator CcpA is not inherently distinct from that of other LacI-family members, only more degenerate. Analysis of the chromosomal position of the identified putative binding sites confirmed that the LacI-family TFs are mostly auto-regulatory and relate mainly to carbohydrate uptake and catabolism. Conclusion Our approach to identify specific operator motifs for different TF-family members is specific and in essence generic. The data infer that, although the specific operator motifs can be used to identify minimal regulons, experimental knowledge on TF activity especially is essential to determine complete regulons as well as to estimate the overlap between TF affinities.
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Affiliation(s)
- Christof Francke
- TI Food and Nutrition, P,O, Box 557, 6700AN Wageningen, The Netherlands.
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30
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Taraban M, Zhan H, Whitten AE, Langley DB, Matthews KS, Swint-Kruse L, Trewhella J. Ligand-induced conformational changes and conformational dynamics in the solution structure of the lactose repressor protein. J Mol Biol 2007; 376:466-81. [PMID: 18164724 DOI: 10.1016/j.jmb.2007.11.067] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 11/16/2007] [Accepted: 11/20/2007] [Indexed: 11/30/2022]
Abstract
We present here the results of a series of small-angle X-ray scattering studies aimed at understanding the role of conformational changes and structural flexibility in DNA binding and allosteric signaling in a bacterial transcription regulator, lactose repressor protein (LacI). Experiments were designed to detect possible conformational changes that occur when LacI binds either DNA or the inducer IPTG, or both. Our studies included the native LacI dimer of homodimers and a dimeric variant (R3), enabling us to probe conformational changes within the homodimers and distinguish them from those involving changes in the homodimer-homodimer relationships. The scattering data indicate that removal of operator DNA (oDNA) from R3 results in an unfolding and extension of the hinge helix that connects the LacI regulatory and DNA-binding domains. In contrast, only very subtle conformational changes occur in the R3 dimer-oDNA complex upon IPTG binding, indicative of small adjustments in the orientations of domains and/or subdomains within the structure. The binding of IPTG to native (tetrameric) LacI-oDNA complexes also appears to facilitate a modest change in the average homodimer-homodimer disposition. Notably, the crystal structure of the native LacI-oDNA complex differs significantly from the average solution conformation. The solution scattering data are best fit by an ensemble of structures that includes (1) approximately 60% of the V-shaped dimer of homodimers observed in the crystal structure and (2) approximately 40% of molecules with more "open" forms, such as those generated when the homodimers move with respect to each other about the tetramerization domain. In gene regulation, such a flexible LacI would be beneficial for the interaction of its two DNA-binding domains, positioned at the tips of the V, with the required two of three LacI operators needed for full repression.
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Affiliation(s)
- Marc Taraban
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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31
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van Dijk M, van Dijk ADJ, Hsu V, Boelens R, Bonvin AMJJ. Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility. Nucleic Acids Res 2006; 34:3317-25. [PMID: 16820531 PMCID: PMC1500871 DOI: 10.1093/nar/gkl412] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Intrinsic flexibility of DNA has hampered the development of efficient protein−DNA docking methods. In this study we extend HADDOCK (High Ambiguity Driven DOCKing) [C. Dominguez, R. Boelens and A. M. J. J. Bonvin (2003) J. Am. Chem. Soc.125, 1731–1737] to explicitly deal with DNA flexibility. HADDOCK uses non-structural experimental data to drive the docking during a rigid-body energy minimization, and semi-flexible and water refinement stages. The latter allow for flexibility of all DNA nucleotides and the residues of the protein at the predicted interface. We evaluated our approach on the monomeric repressor−DNA complexes formed by bacteriophage 434 Cro, the Escherichia coli Lac headpiece and bacteriophage P22 Arc. Starting from unbound proteins and canonical B-DNA we correctly predict the correct spatial disposition of the complexes and the specific conformation of the DNA in the published complexes. This information is subsequently used to generate a library of pre-bent and twisted DNA structures that served as input for a second docking round. The resulting top ranking solutions exhibit high similarity to the published complexes in terms of root mean square deviations, intermolecular contacts and DNA conformation. Our two-stage docking method is thus able to successfully predict protein−DNA complexes from unbound constituents using non-structural experimental data to drive the docking.
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32
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Zhan H, Swint-Kruse L, Matthews KS. Extrinsic interactions dominate helical propensity in coupled binding and folding of the lactose repressor protein hinge helix. Biochemistry 2006; 45:5896-906. [PMID: 16669632 PMCID: PMC2701349 DOI: 10.1021/bi052619p] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A significant number of eukaryotic regulatory proteins are predicted to have disordered regions. Many of these proteins bind DNA, which may serve as a template for protein folding. Similar behavior is seen in the prokaryotic LacI/GalR family of proteins that couple hinge-helix folding with DNA binding. These hinge regions form short alpha-helices when bound to DNA but appear to be disordered in other states. An intriguing question is whether and to what degree intrinsic helix propensity contributes to the function of these proteins. In addition to its interaction with operator DNA, the LacI hinge helix interacts with the hinge helix of the homodimer partner as well as to the surface of the inducer-binding domain. To explore the hierarchy of these interactions, we made a series of substitutions in the LacI hinge helix at position 52, the only site in the helix that does not interact with DNA and/or the inducer-binding domain. The substitutions at V52 have significant effects on operator binding affinity and specificity, and several substitutions also impair functional communication with the inducer-binding domain. Results suggest that helical propensity of amino acids in the hinge region alone does not dominate function; helix-helix packing interactions appear to also contribute. Further, the data demonstrate that variation in operator sequence can overcome side chain effects on hinge-helix folding and/or hinge-hinge interactions. Thus, this system provides a direct example whereby an extrinsic interaction (DNA binding) guides internal events that influence folding and functionality.
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Affiliation(s)
- Hongli Zhan
- Department of Biochemistry and Cell Biology, MS 140, Rice University, Houston, TX 77005
- Department of Biochemistry and Molecular Biology, MS 3030, The University of Kansas Medical Center, Kansas City, KS 66160
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, MS 3030, The University of Kansas Medical Center, Kansas City, KS 66160
| | - Kathleen Shive Matthews
- Department of Biochemistry and Cell Biology, MS 140, Rice University, Houston, TX 77005
- W. M. Keck Center for Computational Biology, MS 140, Rice University, Houston, TX 77005
- To whom correspondence should be addressed. Telephone: 713−348−4871; Fax: 713−348−6149;
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Kim T, Balish RS, Heaton ACP, McKinney EC, Dhankher OP, Meagher RB. Engineering a root-specific, repressor-operator gene complex. PLANT BIOTECHNOLOGY JOURNAL 2005; 3:571-82. [PMID: 17147628 DOI: 10.1111/j.1467-7652.2005.00147.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Strong, tissue-specific and genetically regulated expression systems are essential tools in plant biotechnology. An expression system tool called a 'repressor-operator gene complex' (ROC) has diverse applications in plant biotechnology fields including phytoremediation, disease resistance, plant nutrition, food safety, and hybrid seed production. To test this concept, we assembled a root-specific ROC using a strategy that could be used to construct almost any gene expression pattern. When a modified E. coli lac repressor with a nuclear localization signal was expressed from a rubisco small subunit expression vector, S1pt::lacIn, LacIn protein was localized to the nuclei of leaf and stem cells, but not to root cells. A LacIn repressible Arabidopsis actin expression vector A2pot was assembled containing upstream bacterial lacO operator sequences, and it was tested for organ and tissue specificity using beta-glucuronidase (GUS) and mercuric ion reductase (merA) gene reporters. Strong GUS enzyme expression was restricted to root tissues of A2pot::GUS/S1pt::lacIn ROC plants, while GUS activity was high in all vegetative tissues of plants lacking the repressor. Repression of shoot GUS expression exceeded 99.9% with no evidence of root repression, among a large percentage of doubly transformed plants. Similarly, MerA was strongly expressed in the roots, but not the shoots of A2pot::merA/S1pt::lacIn plants, while MerA levels remained high in both shoots and roots of plants lacking repressor. Plants with MerA expression restricted to roots were approximately as tolerant to ionic mercury as plants constitutively expressing MerA in roots and shoots. The superiority of this ROC over the previously described root-specific tobacco RB7 promoter is demonstrated.
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Affiliation(s)
- Tehryung Kim
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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35
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Ramprakesh J, Schwarz FP. Energetic differences between the specific binding of a 40bp DNA duplex and the lac promoter to lac repressor protein. Arch Biochem Biophys 2005; 438:162-73. [PMID: 15916747 DOI: 10.1016/j.abb.2005.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Revised: 04/22/2005] [Accepted: 04/26/2005] [Indexed: 11/27/2022]
Abstract
The energetics of LRP binding to a 104 bp lac promoter determined from ITC measurements were compared to the energetics of binding to a shorter 40 bp DNA duplex with the 21 bp promoter binding site sequence. The promoter binding affinity of 2.47 +/- 0.0 1x 10(7) M(-1) was higher than the DNA binding affinity of 1.81 +/- 0.67 x 10(7) M(-1) while the binding enthalpy of -804 +/- 41 kJ mol(-1) was lower than that of the DNA binding enthalpy of -145 +/- 16 kJ mol(-1) at 298.15 K. Both the promoter and DNA binding reactions were exothermic in phosphate buffer but endothermic in Tris buffer that showed the transfer of four protons to LRP in the former reaction but only two in the latter. A more complicated dependence of these parameters on temperature was observed for promoter binding. These energetic differences are attributable to additional LRP-promoter interactions from wrapping of the promoter around the LRP.
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Affiliation(s)
- Jayanthi Ramprakesh
- Center for Advanced Research in Biotechnology/National Institute of Standards and Technology, Rockville, MD 20850, USA
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36
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Swint-Kruse L, Brown CS. Resmap: automated representation of macromolecular interfaces as two-dimensional networks. Bioinformatics 2005; 21:3327-8. [PMID: 15914544 DOI: 10.1093/bioinformatics/bti511] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED To aid detailed comparison of a large number of macromolecular structures, Resmap imports Protein Data Bank files and represents subunit/domain interfaces as two-dimensional networks. AVAILABILITY http://www.kumc.edu/biochemistry/resmap/. SUPPLEMENTARY INFORMATION Default definitions and directions for graphically managing networks are available at the same website.
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Affiliation(s)
- Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160, USA.
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37
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Santillán M, Mackey MC. Influence of catabolite repression and inducer exclusion on the bistable behavior of the lac operon. Biophys J 2004; 86:1282-92. [PMID: 14990461 PMCID: PMC1303969 DOI: 10.1016/s0006-3495(04)74202-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A mathematical model of the lac operon which includes all of the known regulatory mechanisms, including external-glucose-dependent catabolite repression and inducer exclusion, as well as the time delays inherent to transcription and translation, is presented. With this model we investigate the influence of external glucose, by means of catabolite repression and the regulation of lactose uptake, on the bistable behavior of this system.
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Affiliation(s)
- Moisés Santillán
- Centre for Nonlinear Dynamics, and Departments of Physiology, Physics, and Mathematics, McGill University, H3G 1Y6 Montreal, Quebec, Canada.
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Kalodimos CG, Boelens R, Kaptein R. Toward an integrated model of protein-DNA recognition as inferred from NMR studies on the Lac repressor system. Chem Rev 2004; 104:3567-86. [PMID: 15303828 DOI: 10.1021/cr0304065] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Gury J, Barthelmebs L, Tran NP, Diviès C, Cavin JF. Cloning, deletion, and characterization of PadR, the transcriptional repressor of the phenolic acid decarboxylase-encoding padA gene of Lactobacillus plantarum. Appl Environ Microbiol 2004; 70:2146-53. [PMID: 15066807 PMCID: PMC383121 DOI: 10.1128/aem.70.4.2146-2153.2004] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactobacillus plantarum displays a substrate-inducible padA gene encoding a phenolic acid decarboxylase enzyme (PadA) that is considered a specific chemical stress response to the inducing substrate. The putative regulator of padA was located in the padA locus based on its 52% identity with PadR, the padA gene transcriptional regulator of Pediococcus pentosaceus (L. Barthelmebs, B. Lecomte, C. Diviès, and J.-F. Cavin, J. Bacteriol. 182:6724-6731, 2000). Deletion of the L. plantarum padR gene clearly demonstrates that the protein it encodes is the transcriptional repressor of divergently oriented padA. The padR gene is cotranscribed with a downstream open reading frame (ORF1), the product of which may belong to a group of universal stress proteins (Usp). The padR deletion mutant overexpressed padA constitutively, and the padA promoter appears to be tightly regulated in this bacterium. Gel mobility shift assays using the padA gene promoter region and purified PadR expressed in Escherichia coli indicated that operator DNA binding by PadR was not eliminated by addition of p-coumarate. Gel mobility shift assays using partially purified extracts of native PadR protein from both phenolic acid-induced and noninduced L. plantarum cells demonstrate that inactivation of PadR by phenolic acids requires the integrity of L. plantarum and mediation by a specific protein absent in E. coli.
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Affiliation(s)
- Jérôme Gury
- Laboratoire de Microbiologie UMR UB/INRA 1232, ENSBANA, Université de Bourgogne, 21000 Dijon, France
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Swint-Kruse L, Matthews KS. Thermodynamics, protein modification, and molecular dynamics in characterizing lactose repressor protein: strategies for complex analyses of protein structure-function. Methods Enzymol 2004; 379:188-209. [PMID: 15051359 DOI: 10.1016/s0076-6879(04)79011-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Liskin Swint-Kruse
- Department of Biochemistry and Cell Biology, Rice University, Houston Texas 77005-1892, USA
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41
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Kalodimos CG, Bonvin AM, Salinas RK, Wechselberger R, Boelens R, Kaptein R. Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain. EMBO J 2002; 21:2866-76. [PMID: 12065400 PMCID: PMC126071 DOI: 10.1093/emboj/cdf318] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The lac repressor-operator system is a model system for understanding protein-DNA interactions and allosteric mechanisms in gene regulation. Despite the wealth of biochemical data provided by extensive mutations of both repressor and operator, the specific recognition mechanism of the natural lac operators by lac repressor has remained elusive. Here we present the first high-resolution structure of a dimer of the DNA-binding domain of lac repressor bound to its natural operator 01. The global positioning of the dimer on the operator is dramatically asymmetric, which results in a different pattern of specific contacts between the two sites. Specific recognition is accomplished by a combination of elongation and twist by 48 degrees of the right lac subunit relative to the left one, significant rearrangement of many side chains as well as sequence-dependent deformability of the DNA. The set of recognition mechanisms involved in the lac repressor-operator system is unique among other protein-DNA complexes and presents a nice example of the adaptability that both proteins and DNA exhibit in the context of their mutual interaction.
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Affiliation(s)
| | | | | | | | | | - Robert Kaptein
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, NL-3584 CH Utrecht, The Netherlands
Corresponding author e-mail:
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42
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Swint-Kruse L, Larson C, Pettitt BM, Matthews KS. Fine-tuning function: correlation of hinge domain interactions with functional distinctions between LacI and PurR. Protein Sci 2002; 11:778-94. [PMID: 11910022 PMCID: PMC2373529 DOI: 10.1110/ps.4050102] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
LacI and PurR are highly homologous proteins. Their functional units are homodimers, with an N-terminal DNA binding domain that comprises the helix-turn-helix (HTH), N-linker, and hinge regions from both monomers. Hinge structural changes are known to occur upon DNA dissociation but are difficult to monitor experimentally. The initial steps of hinge unfolding were therefore examined using molecular dynamics simulations, utilizing a truncated, chimeric protein comprising the LacI HTH/N-linker and PurR hinge. A terminal Gly-Cys-Gly was added to allow "dimerization" through disulfide bond formation. Simulations indicate that differences in LacI and PurR hinge primary sequence affect the quaternary structure of the hinge x hinge' interface. However, these alternate hinge orientations would be sterically restricted by the core domain. These results prompted detailed comparison of recently available DNA-bound structures for LacI and truncated LacI(1-62) with the PurR structure. Examination revealed that different N-linker and hinge contacts to the core domain of the partner monomer (which binds effector molecule) affect the juxtapositions of the HTH, N-linker, and hinge regions in the DNA binding domain. In addition, the two full-length repressors exhibit significant differences in the interactions between the core and the C-linker connection to the DNA binding domain. Both linkers and the hinge have been implicated in the allosteric response of these repressors. Intriguingly, one functional difference between these two proteins is that they exhibit opposite allosteric response to effector. Simulations and observed structural distinctions are correlated with mutational analysis and sequence information from the LacI/GalR family to formulate a mechanism for fine-tuning individual repressor function.
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Affiliation(s)
- Liskin Swint-Kruse
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA.
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43
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Abstract
In bacteria, coordinate expression of genes involved in lactose metabolism is regulated by the lac repressor and its DNA binding sequence, the lac operator. The lac operator-repressor complex can also be used to regulate gene expression in the laboratory mouse. In this review, I discuss the current state of murine trans-operons, and suggest ways this lac-based system might be used to build more advanced models of human diseases in the mouse.
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Affiliation(s)
- Heidi Scrable
- Department of Neuroscience, University of Virginia, Charlottesville, VA 22908, USA.
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44
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Eon S, Culard F, Sy D, Charlier M, Spotheim-Maurizot M. Radiation disrupts protein-DNA complexes through damage to the protein. The lac repressor-operator system. Radiat Res 2001; 156:110-7. [PMID: 11418079 DOI: 10.1667/0033-7587(2001)156[0110:rdpdct]2.0.co;2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Eon, S., Culard, F., Sy, D., Charlier, M. and Spotheim-Maurizot, M. Radiation Disrupts Protein-DNA Complexes through Damage to the Protein. The lac Repressor-Operator System. Radiat. Res. 156, 110-117 (2001). Binding of a protein to its cognate DNA sequence is a key step in the regulation of gene expression. If radiation damage interferes with protein-DNA recognition, the entire regulation process may be perturbed. We have studied the effect of gamma rays on a model regulatory system, the E. coli lactose repressor-operator complex. We have observed the disruption of the complex upon irradiation in aerated solution. The complex is completely restored by the addition of nonirradiated repressor, but not by the addition of nonirradiated DNA. Thus radiation disrupts the DNA-protein complex by affecting the binding ability of the protein. This interpretation is supported by the dramatic loss of binding ability of a free irradiated repressor toward nonirradiated DNA. Interestingly, the dose necessary for the disruption of the irradiated complex is higher than that for inducing the complete loss of the binding ability of the free irradiated repressor. This may be due to the protection of key amino acids by the bound DNA. As seen from calculations of the accessibility of amino acids to radiolytic OH(.), the protection is due to both masking and conformational effects.
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Affiliation(s)
- S Eon
- Centre de Biophysique Moléculaire-CNRS, Rue Charles-Sadron, F-45071 Orléans Cedex 2, France
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45
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Kalodimos CG, Folkers GE, Boelens R, Kaptein R. Strong DNA binding by covalently linked dimeric Lac headpiece: evidence for the crucial role of the hinge helices. Proc Natl Acad Sci U S A 2001; 98:6039-44. [PMID: 11353825 PMCID: PMC33418 DOI: 10.1073/pnas.101129898] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The combined structural and biochemical studies on Lac repressor bound to operator DNA have demonstrated the central role of the hinge helices in operator bending and the induction mechanism. We have constructed a covalently linked dimeric Lac-headpiece that binds DNA with four orders of magnitude higher affinity as compared with the monomeric form. This enabled a detailed biochemical and structural study of Lac binding to its cognate wild-type and selected DNA operators. The results indicate a profound contribution of hinge helices to the stability of the protein-DNA complex and highlight their central role in operator recognition. Furthermore, protein-DNA interactions in the minor groove appear to modulate hinge helix stability, thus accounting for affinity differences and protein-induced DNA bending among the various operator sites. Interestingly, the in vitro DNA-binding affinity of the reported dimeric Lac construct can de readily modulated by simple adjustment of redox conditions, thus rendering it a potential artificial gene regulator.
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Affiliation(s)
- C G Kalodimos
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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46
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Bell CE, Lewis M. The Lac repressor: a second generation of structural and functional studies. Curr Opin Struct Biol 2001; 11:19-25. [PMID: 11179887 DOI: 10.1016/s0959-440x(00)00180-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the past year, the crystal structure of a dimeric version of the Escherichia coli Lac repressor bound to operator DNA was determined at 2.6A resolution, providing a closer view of the operator-bound conformation of the repressor. Refined NMR studies of the DNA-binding portion of the repressor complexed to operator DNA have revealed further details of the unique DNA-binding interactions of the repressor. The structural studies have been complemented by continued biochemical studies, with the overall goal of understanding the mechanism of allosteric regulation.
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Affiliation(s)
- C E Bell
- The Johnson Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 37th and Hamilton Walk, Philadelphia, PA 19102-6059, USA
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