1
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Wu J, Liang C, Li Y, Zeng Y, Sun X, Jiang P, Chen W, Xiong D, Jin J, Tang S. Engineering and application of LacI mutants with stringent expressions. Microb Biotechnol 2024; 17:e14427. [PMID: 38465475 PMCID: PMC10926051 DOI: 10.1111/1751-7915.14427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 03/12/2024] Open
Abstract
Optimal transcriptional regulatory circuits are expected to exhibit stringent control, maintaining silence in the absence of inducers while exhibiting a broad induction dynamic range upon the addition of effectors. In the Plac /LacI pair, the promoter of the lac operon in Escherichia coli is characterized by its leakiness, attributed to the moderate affinity of LacI for its operator target. In response to this limitation, the LacI regulatory protein underwent engineering to enhance its regulatory properties. The M7 mutant, carrying I79T and N246S mutations, resulted in the lac promoter displaying approximately 95% less leaky expression and a broader induction dynamic range compared to the wild-type LacI. An in-depth analysis of each mutation revealed distinct regulatory profiles. In contrast to the wild-type LacI, the M7 mutant exhibited a tighter binding to the operator sequence, as evidenced by surface plasmon resonance studies. Leveraging the capabilities of the M7 mutant, a high-value sugar biosensor was constructed. This biosensor facilitated the selection of mutant galactosidases with approximately a seven-fold improvement in specific activity for transgalactosylation. Consequently, this advancement enabled enhanced biosynthesis of galacto-oligosaccharides (GOS).
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Affiliation(s)
- Jieyuan Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial ResourcesInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Chaoning Liang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial ResourcesInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Yufei Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial ResourcesInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yueting Zeng
- School of Life SciencesHebei UniversityBaodingChina
| | - Xu Sun
- Beijing Key Laboratory of Plant Resources Research and DevelopmentBeijing Technology and Business UniversityBeijingChina
| | - Peixia Jiang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial ResourcesInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Wei Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial ResourcesInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Dandan Xiong
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial ResourcesInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jian‐Ming Jin
- Beijing Key Laboratory of Plant Resources Research and DevelopmentBeijing Technology and Business UniversityBeijingChina
| | - Shuang‐Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial ResourcesInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Asensio‐Calavia A, Ceballos‐Munuera Á, Méndez‐Pérez A, Álvarez B, Fernández LÁ. A tuneable genetic switch for tight control of tac promoters in Escherichia coli boosts expression of synthetic injectisomes. Microb Biotechnol 2024; 17:e14328. [PMID: 37608576 PMCID: PMC10832536 DOI: 10.1111/1751-7915.14328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/24/2023] Open
Abstract
Biosafety of engineered bacteria as living therapeutics requires a tight regulation to control the specific delivery of protein effectors, maintaining minimum leakiness in the uninduced (OFF) state and efficient expression in the induced (ON) state. Here, we report a three repressors (3R) genetic circuit that tightly regulates the expression of multiple tac promoters (Ptac) integrated in the chromosome of E. coli and drives the expression of a complex type III secretion system injectisome for therapeutic protein delivery. The 3R genetic switch is based on the tetracycline repressor (TetR), the non-inducible lambda repressor cI (ind-) and a mutant lac repressor (LacIW220F ) with higher activity. The 3R switch was optimized with different protein translation and degradation signals that control the levels of LacIW220F . We demonstrate the ability of an optimized switch to fully repress the strong leakiness of the Ptac promoters in the OFF state while triggering their efficient activation in the ON state with anhydrotetracycline (aTc), an inducer suitable for in vivo use. The implementation of the optimized 3R switch in the engineered synthetic injector E. coli (SIEC) strain boosts expression of injectisomes upon aTc induction, while maintaining a silent OFF state that preserves normal growth in the absence of the inducer. Since Ptac is a commonly used promoter, the 3R switch may have multiple applications for tight control of protein expression in E. coli. In addition, the modularity of the 3R switch may enable its tuning for the control of Ptac promoters with different inducers.
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Affiliation(s)
- Alejandro Asensio‐Calavia
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
| | - Álvaro Ceballos‐Munuera
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
- Programa de Doctorado en Biociencias MolecularesUniversidad Autónoma de Madrid (UAM)MadridSpain
| | - Almudena Méndez‐Pérez
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
- Programa de Doctorado en Biociencias MolecularesUniversidad Autónoma de Madrid (UAM)MadridSpain
| | - Beatriz Álvarez
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
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4
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Romanuka J, Folkers GE, Gnida M, Kovačič L, Wienk H, Kaptein R, Boelens R. Genetic switching by the Lac repressor is based on two-state Monod-Wyman-Changeux allostery. Proc Natl Acad Sci U S A 2023; 120:e2311240120. [PMID: 38019859 DOI: 10.1073/pnas.2311240120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
High-resolution NMR spectroscopy enabled us to characterize allosteric transitions between various functional states of the dimeric Escherichia coli Lac repressor. In the absence of ligands, the dimer exists in a dynamic equilibrium between DNA-bound and inducer-bound conformations. Binding of either effector shifts this equilibrium toward either bound state. Analysis of the ternary complex between repressor, operator DNA, and inducer shows how adding the inducer results in allosteric changes that disrupt the interdomain contacts between the inducer binding and DNA binding domains and how this in turn leads to destabilization of the hinge helices and release of the Lac repressor from the operator. Based on our data, the allosteric mechanism of the induction process is in full agreement with the well-known Monod-Wyman-Changeux model.
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Affiliation(s)
- Julija Romanuka
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Manuel Gnida
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Lidija Kovačič
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Robert Kaptein
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
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5
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Abstract
Recent progress in DNA synthesis and sequencing technology has enabled systematic studies of protein function at a massive scale. We explore a deep mutational scanning study that measured the transcriptional repression function of 43,669 variants of the Escherichia coli LacI protein. We analyze structural and evolutionary aspects that relate to how the function of this protein is maintained, including an in-depth look at the C-terminal domain. We develop a deep neural network to predict transcriptional repression mediated by the lac repressor of Escherichia coli using experimental measurements of variant function. When measured across 10 separate training and validation splits using 5,009 single mutations of the lac repressor, our best-performing model achieved a median Pearson correlation of 0.79, exceeding any previous model. We demonstrate that deep representation learning approaches, first trained in an unsupervised manner across millions of diverse proteins, can be fine-tuned in a supervised fashion using lac repressor experimental datasets to more effectively predict a variant's effect on repression. These findings suggest a deep representation learning model may improve the prediction of other important properties of proteins.
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Affiliation(s)
- Alexander S Garruss
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138
- Program in Bioinformatics and Integrative Genomics, Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115
| | - Katherine M Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Boston, MA 02139
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138
- Program in Bioinformatics and Integrative Genomics, Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115
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6
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Tack DS, Tonner PD, Pressman A, Olson ND, Levy SF, Romantseva EF, Alperovich N, Vasilyeva O, Ross D. The genotype-phenotype landscape of an allosteric protein. Mol Syst Biol 2021; 17:e10179. [PMID: 33784029 PMCID: PMC8009258 DOI: 10.15252/msb.202010179] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 12/18/2022] Open
Abstract
Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here, we report the large-scale measurement of the genotype-phenotype landscape for an allosteric protein: the lac repressor from Escherichia coli, LacI. Using a method that combines long-read and short-read DNA sequencing, we quantitatively measure the dose-response curves for nearly 105 variants of the LacI genetic sensor. The resulting data provide a quantitative map of the effect of amino acid substitutions on LacI allostery and reveal systematic sequence-structure-function relationships. We find that in many cases, allosteric phenotypes can be quantitatively predicted with additive or neural-network models, but unpredictable changes also occur. For example, we were surprised to discover a new band-stop phenotype that challenges conventional models of allostery and that emerges from combinations of nearly silent amino acid substitutions.
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Affiliation(s)
- Drew S Tack
- National Institute of Standards and TechnologyGaithersburgMDUSA
| | - Peter D Tonner
- National Institute of Standards and TechnologyGaithersburgMDUSA
| | - Abe Pressman
- National Institute of Standards and TechnologyGaithersburgMDUSA
| | - Nathan D Olson
- National Institute of Standards and TechnologyGaithersburgMDUSA
| | - Sasha F Levy
- SLAC National Accelerator LaboratoryMenlo ParkCAUSA
- Joint Initiative for Metrology in BiologyStanfordCAUSA
| | | | - Nina Alperovich
- National Institute of Standards and TechnologyGaithersburgMDUSA
| | - Olga Vasilyeva
- National Institute of Standards and TechnologyGaithersburgMDUSA
| | - David Ross
- National Institute of Standards and TechnologyGaithersburgMDUSA
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7
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Becker NA, Peters JP, Schwab TL, Phillips WJ, Wallace JP, Clark KJ, Maher LJ. Characterization of Gene Repression by Designed Transcription Activator-like Effector Dimer Proteins. Biophys J 2020; 119:2045-2054. [PMID: 33091377 PMCID: PMC7732741 DOI: 10.1016/j.bpj.2020.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 11/18/2022] Open
Abstract
Gene regulation by control of transcription initiation is a fundamental property of living cells. Much of our understanding of gene repression originated from studies of the Escherichia coli lac operon switch, in which DNA looping plays an essential role. To validate and generalize principles from lac for practical applications, we previously described artificial DNA looping driven by designed transcription activator-like effector dimer (TALED) proteins. Because TALE monomers bind the idealized symmetrical lac operator sequence in two orientations, our prior studies detected repression due to multiple DNA loops. We now quantitatively characterize gene repression in living E. coli by a collection of individual TALED loops with systematic loop length variation. Fitting of a thermodynamic model allows unequivocal demonstration of looping and comparison of the engineered TALED repression system with the natural lac repressor system.
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Affiliation(s)
- Nicole A Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Justin P Peters
- Department of Chemistry and Biochemistry, University of Northern Iowa, Cedar Falls, Iowa
| | - Tanya L Schwab
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - William J Phillips
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Jordan P Wallace
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota.
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8
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Lai SN, Zhou X, Ouyang X, Zhou H, Liang Y, Xia J, Zheng B. Artificial Cells Capable of Long-Lived Protein Synthesis by Using Aptamer Grafted Polymer Hydrogel. ACS Synth Biol 2020; 9:76-83. [PMID: 31880928 DOI: 10.1021/acssynbio.9b00338] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Herein we report a new type of artificial cells capable of long-term protein expression and regulation. We constructed the artificial cells by grafting anti-His-tag aptamer into the polymer backbone of the hydrogel particles, and then immobilizing the His-tagged proteinaceous factors of the transcription and translation system into the hydrogel particles. Long-term protein expression for at least 16 days was achieved by continuously flowing feeding buffer through the artificial cells. The effect of various metal ions on the protein expression in the artificial cells was investigated. Utilizing the lac operator-repressor system, we could regulate the expression level of eGFP in the artificial cells by controlling the β-D-1-thiogalatopyranoside (IPTG) concentration in the feeding buffer. The artificial cells based on the aptamer grafted hydrogel provide a useful platform for gene circuit engineering, metabolic engineering, drug delivery, and biosensors.
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Affiliation(s)
- Sze Nga Lai
- Department of Chemistry , The Chinese University of Hong Kong , Sha Tin , Hong Kong
| | - Xiaoyu Zhou
- Department of Chemistry , The Chinese University of Hong Kong , Sha Tin , Hong Kong
- Department of Biomedical Sciences , City University of Hong Kong , 83 Tat Chee Avenue , Kowloon , Hong Kong
| | - Xiaofei Ouyang
- Department of Chemistry , The Chinese University of Hong Kong , Sha Tin , Hong Kong
| | - Hui Zhou
- Department of Chemistry , The Chinese University of Hong Kong , Sha Tin , Hong Kong
| | - Yujie Liang
- Department of Chemistry , The Chinese University of Hong Kong , Sha Tin , Hong Kong
| | - Jiang Xia
- Department of Chemistry , The Chinese University of Hong Kong , Sha Tin , Hong Kong
| | - Bo Zheng
- Department of Chemistry , The Chinese University of Hong Kong , Sha Tin , Hong Kong
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9
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Chure G, Razo-Mejia M, Belliveau NM, Einav T, Kaczmarek ZA, Barnes SL, Lewis M, Phillips R. Predictive shifts in free energy couple mutations to their phenotypic consequences. Proc Natl Acad Sci U S A 2019; 116:18275-18284. [PMID: 31451655 PMCID: PMC6744869 DOI: 10.1073/pnas.1907869116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Mutation is a critical mechanism by which evolution explores the functional landscape of proteins. Despite our ability to experimentally inflict mutations at will, it remains difficult to link sequence-level perturbations to systems-level responses. Here, we present a framework centered on measuring changes in the free energy of the system to link individual mutations in an allosteric transcriptional repressor to the parameters which govern its response. We find that the energetic effects of the mutations can be categorized into several classes which have characteristic curves as a function of the inducer concentration. We experimentally test these diagnostic predictions using the well-characterized LacI repressor of Escherichia coli, probing several mutations in the DNA binding and inducer binding domains. We find that the change in gene expression due to a point mutation can be captured by modifying only the model parameters that describe the respective domain of the wild-type protein. These parameters appear to be insulated, with mutations in the DNA binding domain altering only the DNA affinity and those in the inducer binding domain altering only the allosteric parameters. Changing these subsets of parameters tunes the free energy of the system in a way that is concordant with theoretical expectations. Finally, we show that the induction profiles and resulting free energies associated with pairwise double mutants can be predicted with quantitative accuracy given knowledge of the single mutants, providing an avenue for identifying and quantifying epistatic interactions.
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Affiliation(s)
- Griffin Chure
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Manuel Razo-Mejia
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Nathan M Belliveau
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Tal Einav
- Department of Physics, California Institute of Technology, Pasadena, CA 91125
| | - Zofii A Kaczmarek
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Stephanie L Barnes
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Mitchell Lewis
- Department of Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Rob Phillips
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;
- Department of Physics, California Institute of Technology, Pasadena, CA 91125
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10
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Tempestini A, Monico C, Gardini L, Vanzi F, Pavone FS, Capitanio M. Sliding of a single lac repressor protein along DNA is tuned by DNA sequence and molecular switching. Nucleic Acids Res 2018; 46:5001-5011. [PMID: 29584872 PMCID: PMC6007606 DOI: 10.1093/nar/gky208] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 03/06/2018] [Accepted: 03/09/2018] [Indexed: 01/12/2023] Open
Abstract
In any living cell, genome maintenance is carried out by DNA-binding proteins that recognize specific sequences among a vast amount of DNA. This includes fundamental processes such as DNA replication, DNA repair, and gene expression and regulation. Here, we study the mechanism of DNA target search by a single lac repressor protein (LacI) with ultrafast force-clamp spectroscopy, a sub-millisecond and few base-pair resolution technique based on laser tweezers. We measure 1D-diffusion of proteins on DNA at physiological salt concentrations with 20 bp resolution and find that sliding of LacI along DNA is sequence dependent. We show that only allosterically activated LacI slides along non-specific DNA sequences during target search, whereas the inhibited conformation does not support sliding and weakly interacts with DNA. Moreover, we find that LacI undergoes a load-dependent conformational change when it switches between sliding and strong binding to the target sequence. Our data reveal how DNA sequence and molecular switching regulate LacI target search process and provide a comprehensive model of facilitated diffusion for LacI.
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Affiliation(s)
- Alessia Tempestini
- LENS—European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Italy
| | - Carina Monico
- LENS—European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Lucia Gardini
- LENS—European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- National Institute of Optics—National Research Council, Largo Fermi 6, 50125 Florence, Italy
| | - Francesco Vanzi
- LENS—European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- Department of Biology, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Francesco S Pavone
- LENS—European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Italy
- National Institute of Optics—National Research Council, Largo Fermi 6, 50125 Florence, Italy
- International Center of Computational Neurophotonics, Via Nello Carrara 1, 50019 Sesto Fiorentino (FI), Italy
| | - Marco Capitanio
- LENS—European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Italy
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11
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Kipper K, Eremina N, Marklund E, Tubasum S, Mao G, Lehmann LC, Elf J, Deindl S. Structure-guided approach to site-specific fluorophore labeling of the lac repressor LacI. PLoS One 2018; 13:e0198416. [PMID: 29856839 PMCID: PMC5983854 DOI: 10.1371/journal.pone.0198416] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/19/2018] [Indexed: 11/26/2022] Open
Abstract
The lactose operon repressor protein LacI has long served as a paradigm of the bacterial transcription factors. However, the mechanisms whereby LacI rapidly locates its cognate binding site on the bacterial chromosome are still elusive. Single-molecule fluorescence imaging approaches are well suited for the study of these mechanisms but rely on a functionally compatible fluorescence labeling of LacI. Particularly attractive for protein fluorescence labeling are synthetic fluorophores due to their small size and favorable photophysical characteristics. Synthetic fluorophores are often conjugated to natively occurring cysteine residues using maleimide chemistry. For a site-specific and functionally compatible labeling with maleimide fluorophores, the target protein often needs to be redesigned to remove unwanted native cysteines and to introduce cysteines at locations better suited for fluorophore attachment. Biochemical screens can then be employed to probe for the functional activity of the redesigned protein both before and after dye labeling. Here, we report a mutagenesis-based redesign of LacI to enable a functionally compatible labeling with maleimide fluorophores. To provide an easily accessible labeling site in LacI, we introduced a single cysteine residue at position 28 in the DNA-binding headpiece of LacI and replaced two native cysteines with alanines where derivatization with bulky substituents is known to compromise the protein’s activity. We find that the redesigned LacI retains a robust activity in vitro and in vivo, provided that the third native cysteine at position 281 is retained in LacI. In a total internal reflection microscopy assay, we observed individual Cy3-labeled LacI molecules bound to immobilized DNA harboring the cognate O1 operator sequence, indicating that the dye-labeled LacI is functionally active. We have thus been able to generate a functional fluorescently labeled LacI that can be used to unravel mechanistic details of LacI target search at the single molecule level.
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Affiliation(s)
- Kalle Kipper
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Nadja Eremina
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Emil Marklund
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sumera Tubasum
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Guanzhong Mao
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Laura Christina Lehmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail:
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12
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Becker NA, Schwab TL, Clark KJ, Maher LJ. Bacterial gene control by DNA looping using engineered dimeric transcription activator like effector (TALE) proteins. Nucleic Acids Res 2018; 46:2690-2696. [PMID: 29390154 PMCID: PMC5861415 DOI: 10.1093/nar/gky047] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/07/2018] [Accepted: 01/18/2018] [Indexed: 01/04/2023] Open
Abstract
Genetic switches must alternate between states whose probabilities are dependent on regulatory signals. Classical examples of transcriptional control in bacteria depend on repressive DNA loops anchored by proteins whose structures are sensitive to small molecule inducers or co-repressors. We are interested in exploiting these natural principles to engineer artificial switches for transcriptional control of bacterial genes. Here, we implement designed homodimeric DNA looping proteins ('Transcription Activator-Like Effector Dimers'; TALEDs) for this purpose in living bacteria. Using well-studied FKBP dimerization domains, we build switches that mimic regulatory characteristics of classical Escherichia coli lactose, galactose and tryptophan operon promoters, including induction or co-repression by small molecules. Engineered DNA looping using TALEDs is thus a new approach to tuning gene expression in bacteria. Similar principles may also be applicable for gene control in eukaryotes.
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Affiliation(s)
- Nicole A Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA
| | - Tanya L Schwab
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA
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13
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Gebhardt MJ, Jacobson RK, Shuman HA. Seeing red; the development of pON.mCherry, a broad-host range constitutive expression plasmid for Gram-negative bacteria. PLoS One 2017; 12:e0173116. [PMID: 28257493 PMCID: PMC5336243 DOI: 10.1371/journal.pone.0173116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/15/2017] [Indexed: 01/16/2023] Open
Abstract
The development of plasmid-mediated gene expression control in bacteria revolutionized the field of bacteriology. Many of these expression control systems rely on the addition of small molecules, generally metabolites or non-metabolized analogs thereof, to the growth medium to induce expression of the genes of interest. The paradigmatic example of an expression control system is the lac system from Escherichia coli, which typically relies on the Ptac promoter and the Lac repressor, LacI. In many cases, however, constitutive gene expression is desired, and other experimental approaches require the coordinated control of multiple genes. While multiple systems have been developed for use in E. coli and its close relatives, the utility and/or functionality of these tools does not always translate to other species. For example, for the Gram-negative pathogen, Legionella pneumophila, a causative agent of Legionnaires' Disease, the aforementioned Ptac system represents the only well-established expression control system. In order to enhance the tools available to study bacterial gene expression in L. pneumophila, we developed a plasmid, pON.mCherry, which confers constitutive gene expression from a mutagenized LacI binding site. We demonstrate that pON.mCherry neither interferes with other plasmids harboring an intact LacI-Ptac expression system nor alters the growth of Legionella species during intracellular growth. Furthermore, the broad-host range plasmid backbone of pON.mCherry allows constitutive gene expression in a wide variety of Gram-negative bacterial species, making pON.mCherry a useful tool for the greater research community.
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Affiliation(s)
- Michael J. Gebhardt
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
| | - Rachael K. Jacobson
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
| | - Howard A. Shuman
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
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14
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Fuglestad B, Stetz MA, Belnavis Z, Wand AJ. Solution NMR investigation of the response of the lactose repressor core domain dimer to hydrostatic pressure. Biophys Chem 2017; 231:39-44. [PMID: 28249763 DOI: 10.1016/j.bpc.2017.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/21/2017] [Accepted: 02/22/2017] [Indexed: 11/19/2022]
Abstract
Previous investigations of the sensitivity of the lac repressor to high-hydrostatic pressure have led to varying conclusions. Here high-pressure solution NMR spectroscopy is used to provide an atomic level view of the pressure induced structural transition of the lactose repressor regulatory domain (LacI* RD) bound to the ligand IPTG. As the pressure is raised from ambient to 3kbar the native state of the protein is converted to a partially unfolded form. Estimates of rotational correlation times using transverse optimized relaxation indicates that a monomeric state is never reached and that the predominate form of the LacI* RD is dimeric throughout this pressure change. Spectral analysis suggests that the pressure-induced transition is localized and is associated with a volume change of approximately -115mlmol-1 and an average pressure dependent change in compressibility of approximately 30mlmol-1kbar-1. In addition, a subset of resonances emerge at high-pressures indicating the presence of a non-native but folded alternate state.
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Affiliation(s)
- Brian Fuglestad
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, 905 Stellar-Chance Laboratories, 422 Curie Blvd, Philadelphia, PA 19104-6059, USA
| | - Matthew A Stetz
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, 905 Stellar-Chance Laboratories, 422 Curie Blvd, Philadelphia, PA 19104-6059, USA
| | - Zachary Belnavis
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, 905 Stellar-Chance Laboratories, 422 Curie Blvd, Philadelphia, PA 19104-6059, USA
| | - A Joshua Wand
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, 905 Stellar-Chance Laboratories, 422 Curie Blvd, Philadelphia, PA 19104-6059, USA.
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15
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Abstract
Confined water often exhibits anomalous properties not observable in the bulk phase. Although water in hydrophobic confinement has been the focus of intense investigation, the behavior of water confined between hydrophilic surfaces, which are more frequently found in biological systems, has not been fully explored. Here, we investigate using molecular dynamics simulations dynamical properties of the water confined in hydrophilic protein-protein and protein-DNA interfaces. We find that the interfacial water exhibits glassy slow relaxations even at 300 K. In particular, the rotational dynamics show a logarithmic decay that was observed in glass-forming liquids at deeply supercooled states. We argue that such slow water dynamics are indeed induced by the hydrophilic binding surfaces, which is in opposition to the picture that the hydration water slaves protein motions. Our results will significantly impact the view on the role of water in biomolecular interactions.
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Affiliation(s)
- Song-Ho Chong
- Department of Chemistry, Sookmyung Women's University , Cheongpa-ro 47-gil 100, Yongsan-Ku, Seoul 04310, Korea
| | - Sihyun Ham
- Department of Chemistry, Sookmyung Women's University , Cheongpa-ro 47-gil 100, Yongsan-Ku, Seoul 04310, Korea
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16
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Lloyd-Price J, Startceva S, Kandavalli V, Chandraseelan JG, Goncalves N, Oliveira SMD, Häkkinen A, Ribeiro AS. Dissecting the stochastic transcription initiation process in live Escherichia coli. DNA Res 2016; 23:203-14. [PMID: 27026687 PMCID: PMC4909308 DOI: 10.1093/dnares/dsw009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/11/2016] [Indexed: 02/01/2023] Open
Abstract
We investigate the hypothesis that, in Escherichia coli, while the concentration of RNA polymerases differs in different growth conditions, the fraction of RNA polymerases free for transcription remains approximately constant within a certain range of these conditions. After establishing this, we apply a standard model-fitting procedure to fully characterize the in vivo kinetics of the rate-limiting steps in transcription initiation of the Plac/ara-1 promoter from distributions of intervals between transcription events in cells with different RNA polymerase concentrations. We find that, under full induction, the closed complex lasts ∼788 s while subsequent steps last ∼193 s, on average. We then establish that the closed complex formation usually occurs multiple times prior to each successful initiation event. Furthermore, the promoter intermittently switches to an inactive state that, on average, lasts ∼87 s. This is shown to arise from the intermittent repression of the promoter by LacI. The methods employed here should be of use to resolve the rate-limiting steps governing the in vivo dynamics of initiation of prokaryotic promoters, similar to established steady-state assays to resolve the in vitro dynamics.
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Affiliation(s)
- Jason Lloyd-Price
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland
| | - Sofia Startceva
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland
| | - Vinodh Kandavalli
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland
| | - Jerome G Chandraseelan
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland
| | - Nadia Goncalves
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland
| | - Samuel M D Oliveira
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland
| | - Antti Häkkinen
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland
| | - Andre S Ribeiro
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, PO Box 553, Office TC336, 33101 Tampere, Finland
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17
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Sun L, Tabaka M, Hou S, Li L, Burdzy K, Aksimentiev A, Maffeo C, Zhang X, Holyst R. The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study. PLoS One 2016; 11:e0152002. [PMID: 27008630 PMCID: PMC4805274 DOI: 10.1371/journal.pone.0152002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/06/2016] [Indexed: 11/30/2022] Open
Abstract
LacI is commonly used as a model to study the protein-DNA interaction and gene regulation. The headpiece of the lac-repressor (LacI) protein is an ideal system for investigation of nonspecific binding of the whole LacI protein to DNA. The hinge region of the headpiece has been known to play a key role in the specific binding of LacI to DNA, whereas its role in nonspecific binding process has not been elucidated. Here, we report the results of explicit solvent molecular dynamics simulation and continuum electrostatic calculations suggesting that the hinge region strengthens the nonspecific interaction, accounting for up to 50% of the micro-dissociation free energy of LacI from DNA. Consequently, the rate of microscopic dissociation of LacI from DNA is reduced by 2~3 orders of magnitude in the absence of the hinge region. We find the hinge region makes an important contribution to the electrostatic energy, the salt dependence of electrostatic energy, and the number of salt ions excluded from binding of the LacI-DNA complex.
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Affiliation(s)
- Lili Sun
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Sen Hou
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, South Carolina, 29634, United States of America
| | - Krzysztof Burdzy
- Department of Mathematics, University of Washington, Seattle, Washington, 98195–4350, United States of America
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Christopher Maffeo
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Xuzhu Zhang
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Robert Holyst
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
- * E-mail:
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18
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Sun L, Tabaka M, Hou S, Li L, Burdzy K, Aksimentiev A, Maffeo C, Zhang X, Holyst R. The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study. PLoS One 2016; 11:e0152002. [PMID: 27008630 DOI: 10.1371/joumal.pone.0152002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/06/2016] [Indexed: 05/27/2023] Open
Abstract
LacI is commonly used as a model to study the protein-DNA interaction and gene regulation. The headpiece of the lac-repressor (LacI) protein is an ideal system for investigation of nonspecific binding of the whole LacI protein to DNA. The hinge region of the headpiece has been known to play a key role in the specific binding of LacI to DNA, whereas its role in nonspecific binding process has not been elucidated. Here, we report the results of explicit solvent molecular dynamics simulation and continuum electrostatic calculations suggesting that the hinge region strengthens the nonspecific interaction, accounting for up to 50% of the micro-dissociation free energy of LacI from DNA. Consequently, the rate of microscopic dissociation of LacI from DNA is reduced by 2~3 orders of magnitude in the absence of the hinge region. We find the hinge region makes an important contribution to the electrostatic energy, the salt dependence of electrostatic energy, and the number of salt ions excluded from binding of the LacI-DNA complex.
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Affiliation(s)
- Lili Sun
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Sen Hou
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, South Carolina, 29634, United States of America
| | - Krzysztof Burdzy
- Department of Mathematics, University of Washington, Seattle, Washington, 98195-4350, United States of America
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Christopher Maffeo
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Xuzhu Zhang
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Robert Holyst
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
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19
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Abstract
The specificity of protein-DNA interactions can be determined directly by sequencing the bound and unbound fractions in a standard binding reaction. The procedure is easy and inexpensive, and the accuracy can be high for thousands of sequences assayed in parallel. From the measurements, simple models of specificity, such as position weight matrices, can be assessed for their accuracy and more complex models developed if useful. Those may provide more accurate predictions of in vivo binding sites and can help us to understand the details of recognition. As an example, we demonstrate new information gained about the binding of lac repressor. One can apply the same method to combinations of factors that bind simultaneously to a single DNA and determine both the specificity of the individual factors and the cooperativity between them.
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20
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Perez PJ, Clauvelin N, Grosner MA, Colasanti AV, Olson WK. What controls DNA looping? Int J Mol Sci 2014; 15:15090-108. [PMID: 25167135 PMCID: PMC4200792 DOI: 10.3390/ijms150915090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/11/2014] [Accepted: 08/19/2014] [Indexed: 01/15/2023] Open
Abstract
The looping of DNA provides a means of communication between sequentially distant genomic sites that operate in tandem to express, copy, and repair the information encoded in the DNA base sequence. The short loops implicated in the expression of bacterial genes suggest that molecular factors other than the naturally stiff double helix are involved in bringing the interacting sites into close spatial proximity. New computational techniques that take direct account of the three-dimensional structures and fluctuations of protein and DNA allow us to examine the likely means of enhancing such communication. Here, we describe the application of these approaches to the looping of a 92 base-pair DNA segment between the headpieces of the tetrameric Escherichia coli Lac repressor protein. The distortions of the double helix induced by a second protein--the nonspecific nucleoid protein HU--increase the computed likelihood of looping by several orders of magnitude over that of DNA alone. Large-scale deformations of the repressor, sequence-dependent features in the DNA loop, and deformability of the DNA operators also enhance looping, although to lesser degrees. The correspondence between the predicted looping propensities and the ease of looping derived from gene-expression and single-molecule measurements lends credence to the derived structural picture.
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Affiliation(s)
- Pamela J Perez
- BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Nicolas Clauvelin
- BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Michael A Grosner
- BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Andrew V Colasanti
- BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Wilma K Olson
- BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
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21
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Mazumder M, McMillen DR. Design and characterization of a dual-mode promoter with activation and repression capability for tuning gene expression in yeast. Nucleic Acids Res 2014; 42:9514-22. [PMID: 25056312 PMCID: PMC4132757 DOI: 10.1093/nar/gku651] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/03/2014] [Accepted: 07/08/2014] [Indexed: 11/15/2022] Open
Abstract
Modularity in controlling gene expression artificially is becoming an essential aspect of synthetic biology. Artificial transcriptional control of gene expression is one of the most well-developed methods for the design of novel synthetic regulatory networks. Such networks are intended to help understand natural cellular phenomena and to enable new biotechnological applications. Promoter sequence manipulation with cis-regulatory elements is a key approach to control gene expression transcriptionally. Here, we have designed a promoter that can be both activated and repressed, as a contribution to the library of synthetic biological 'parts'. Starting with the minimal cytochrome C (minCYC) promoter in yeast, we incorporated five steroid hormone responsive elements (SHREs) and one lac operator site, respectively, upstream and downstream of the TATA box. This allows activation through the testosterone-responsive androgen receptor, and repression through the LacI repressor. Exposure to varying concentrations of testosterone (to vary activation) and IPTG (to vary repression) demonstrated the ability to tune the promoter's output curve over a wide range. By integrating activating and repressing signals, the promoter permits a useful form of signal integration, and we are optimistic that it will serve as a component in future regulatory networks, including feedback controllers.
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Affiliation(s)
- Mostafizur Mazumder
- Department of Chemical and Physical Sciences and Impact Centre, University of Toronto Mississauga, 3359 Mississauga Rd., Mississauga, ON L5L 1C6, Canada
| | - David R McMillen
- Department of Chemical and Physical Sciences and Impact Centre, University of Toronto Mississauga, 3359 Mississauga Rd., Mississauga, ON L5L 1C6, Canada
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22
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Choudhary K, Oehler S, Narang A. Protein distributions from a stochastic model of the lac operon of E. coli with DNA looping: analytical solution and comparison with experiments. PLoS One 2014; 9:e102580. [PMID: 25055040 PMCID: PMC4108355 DOI: 10.1371/journal.pone.0102580] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 06/20/2014] [Indexed: 11/19/2022] Open
Abstract
Although noisy gene expression is widely accepted, its mechanisms are subjects of debate, stimulated largely by single-molecule experiments. This work is concerned with one such study, in which Choi et al., 2008, obtained real-time data and distributions of Lac permease in E. coli. They observed small and large protein bursts in strains with and without auxiliary operators. They also estimated the size and frequency of these bursts, but these were based on a stochastic model of a constitutive promoter. Here, we formulate and solve a stochastic model accounting for the existence of auxiliary operators and DNA loops. We find that DNA loop formation is so fast that small bursts are averaged out, making it impossible to extract their size and frequency from the data. In contrast, we can extract not only the size and frequency of the large bursts, but also the fraction of proteins derived from them. Finally, the proteins follow not the negative binomial distribution, but a mixture of two distributions, which reflect the existence of proteins derived from small and large bursts.
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Affiliation(s)
- Krishna Choudhary
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology, Delhi, India
| | - Stefan Oehler
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology, Delhi, India
| | - Atul Narang
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology, Delhi, India
- * E-mail:
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23
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Biton YY, Kumar S, Dunlap D, Swigon D. Lac repressor mediated DNA looping: Monte Carlo simulation of constrained DNA molecules complemented with current experimental results. PLoS One 2014; 9:e92475. [PMID: 24800809 PMCID: PMC4011716 DOI: 10.1371/journal.pone.0092475] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 02/23/2014] [Indexed: 11/30/2022] Open
Abstract
Tethered particle motion (TPM) experiments can be used to detect time-resolved loop formation in a single DNA molecule by measuring changes in the length of a DNA tether. Interpretation of such experiments is greatly aided by computer simulations of DNA looping which allow one to analyze the structure of the looped DNA and estimate DNA-protein binding constants specific for the loop formation process. We here present a new Monte Carlo scheme for accurate simulation of DNA configurations subject to geometric constraints and apply this method to Lac repressor mediated DNA looping, comparing the simulation results with new experimental data obtained by the TPM technique. Our simulations, taking into account the details of attachment of DNA ends and fluctuations of the looped subsegment of the DNA, reveal the origin of the double-peaked distribution of RMS values observed by TPM experiments by showing that the average RMS value for anti-parallel loop types is smaller than that of parallel loop types. The simulations also reveal that the looping probabilities for the anti-parallel loop types are significantly higher than those of the parallel loop types, even for loops of length 600 and 900 base pairs, and that the correct proportion between the heights of the peaks in the distribution can only be attained when loops with flexible Lac repressor conformation are taken into account. Comparison of the in silico and in vitro results yields estimates for the dissociation constants characterizing the binding affinity between O1 and Oid DNA operators and the dimeric arms of the Lac repressor.
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Affiliation(s)
- Yoav Y. Biton
- Department of Mathematics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
| | - Sandip Kumar
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - David Dunlap
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - David Swigon
- Department of Mathematics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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24
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Hammar P, Walldén M, Fange D, Persson F, Baltekin Ö, Ullman G, Leroy P, Elf J. Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation. Nat Genet 2014; 46:405-8. [PMID: 24562187 PMCID: PMC6193529 DOI: 10.1038/ng.2905] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 01/31/2014] [Indexed: 12/21/2022]
Abstract
Transcription factors mediate gene regulation by site-specific binding to chromosomal operators. It is commonly assumed that the level of repression is determined solely by the equilibrium binding of a repressor to its operator. However, this assumption has not been possible to test in living cells. Here we have developed a single-molecule chase assay to measure how long an individual transcription factor molecule remains bound at a specific chromosomal operator site. We find that the lac repressor dimer stays bound on average 5 min at the native lac operator in Escherichia coli and that a stronger operator results in a slower dissociation rate but a similar association rate. Our findings do not support the simple equilibrium model. The discrepancy with this model can, for example, be accounted for by considering that transcription initiation drives the system out of equilibrium. Such effects need to be considered when predicting gene activity from transcription factor binding strengths.
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Affiliation(s)
- Petter Hammar
- Department for Cell and Molecular biology, Science for Life Laboratory, Uppsala University, Sweden
| | - Mats Walldén
- Department for Cell and Molecular biology, Science for Life Laboratory, Uppsala University, Sweden
| | - David Fange
- Department for Cell and Molecular biology, Science for Life Laboratory, Uppsala University, Sweden
| | - Fredrik Persson
- Department for Cell and Molecular biology, Science for Life Laboratory, Uppsala University, Sweden
| | - Özden Baltekin
- Department for Cell and Molecular biology, Science for Life Laboratory, Uppsala University, Sweden
| | - Gustaf Ullman
- Department for Cell and Molecular biology, Science for Life Laboratory, Uppsala University, Sweden
| | - Prune Leroy
- Department for Cell and Molecular biology, Science for Life Laboratory, Uppsala University, Sweden
| | - Johan Elf
- Department for Cell and Molecular biology, Science for Life Laboratory, Uppsala University, Sweden
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25
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Abstract
The millions of protein sequences generated by genomics are expected to transform protein engineering and personalized medicine. To achieve these goals, tools for predicting outcomes of amino acid changes must be improved. Currently, advances are hampered by insufficient experimental data about nonconserved amino acid positions. Since the property “nonconserved” is identified using a sequence alignment, we designed experiments to recapitulate that context: Mutagenesis and functional characterization was carried out in 15 LacI/GalR homologs (rows) at 12 nonconserved positions (columns). Multiple substitutions were made at each position, to reveal how various amino acids of a nonconserved column were tolerated in each protein row. Results showed that amino acid preferences of nonconserved positions were highly context-dependent, had few correlations with physico-chemical similarities, and were not predictable from their occurrence in natural LacI/GalR sequences. Further, unlike the “toggle switch” behaviors of conserved positions, substitutions at nonconserved positions could be rank-ordered to show a “rheostatic”, progressive effect on function that spanned several orders of magnitude. Comparisons to various sequence analyses suggested that conserved and strongly co-evolving positions act as functional toggles, whereas other important, nonconserved positions serve as rheostats for modifying protein function. Both the presence of rheostat positions and the sequence analysis strategy appear to be generalizable to other protein families and should be considered when engineering protein modifications or predicting the impact of protein polymorphisms.
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Affiliation(s)
- Sarah Meinhardt
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Michael W. Manley
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Daniel J. Parente
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, United States of America
- * E-mail:
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Marklund EG, Mahmutovic A, Berg OG, Hammar P, van der Spoel D, Fange D, Elf J. Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models. Proc Natl Acad Sci U S A 2013; 110:19796-801. [PMID: 24222688 PMCID: PMC3856812 DOI: 10.1073/pnas.1307905110] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Transcription factors search for specific operator sequences by alternating rounds of 3D diffusion with rounds of 1D diffusion (sliding) along the DNA. The details of such sliding have largely been beyond direct experimental observation. For this purpose we devised an analytical formulation of umbrella sampling along a helical coordinate, and from extensive and fully atomistic simulations we quantified the free-energy landscapes that underlie the sliding dynamics and dissociation kinetics for the LacI dimer. The resulting potential of mean force distributions show a fine structure with an amplitude of 1 k(B)T for sliding and 12 k(B)T for dissociation. Based on the free-energy calculations the repressor slides in close contact with DNA for 8 bp on average before making a microscopic dissociation. By combining the microscopic molecular-dynamics calculations with Brownian simulation including rotational diffusion from the microscopically dissociated state we estimate a macroscopic residence time of 48 ms at the same DNA segment and an in vitro sliding distance of 240 bp. The sliding distance is in agreement with previous in vitro sliding-length estimates. The in vitro prediction for the macroscopic residence time also compares favorably to what we measure by single-molecule imaging of nonspecifically bound fluorescently labeled LacI in living cells. The investigation adds to our understanding of transcription-factor search kinetics and connects the macro-/mesoscopic rate constants to the microscopic dynamics.
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Affiliation(s)
- Erik G. Marklund
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Anel Mahmutovic
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Otto G. Berg
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Petter Hammar
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - David van der Spoel
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - David Fange
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
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Wang X, Yang JG, Chen L, Wang JL, Cheng Q, Dixon R, Wang YP. Using synthetic biology to distinguish and overcome regulatory and functional barriers related to nitrogen fixation. PLoS One 2013; 8:e68677. [PMID: 23935879 PMCID: PMC3723869 DOI: 10.1371/journal.pone.0068677] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/07/2013] [Indexed: 01/14/2023] Open
Abstract
Biological nitrogen fixation is a complex process requiring multiple genes working in concert. To date, the Klebsiella pneumoniae nif gene cluster, divided into seven operons, is one of the most studied systems. Its nitrogen fixation capacity is subject to complex cascade regulation and physiological limitations. In this report, the entire K. pneumoniae nif gene cluster was reassembled as operon-based BioBrick parts in Escherichia coli. It provided ~100% activity of native K. pneumoniae system. Based on the expression levels of these BioBrick parts, a T7 RNA polymerase-LacI expression system was used to replace the σ(54)-dependent promoters located upstream of nif operons. Expression patterns of nif operons were critical for the maximum activity of the recombinant system. By mimicking these expression levels with variable-strength T7-dependent promoters, ~42% of the nitrogenase activity of the σ(54)-dependent nif system was achieved in E. coli. When the newly constructed T7-dependent nif system was challenged with different genetic and physiological conditions, it bypassed the original complex regulatory circuits, with minor physiological limitations. Therefore, we have successfully replaced the nif regulatory elements with a simple expression system that may provide the first step for further research of introducing nif genes into eukaryotic organelles, which has considerable potentials in agro-biotechnology.
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Affiliation(s)
- Xia Wang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Jian-Guo Yang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Li Chen
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Ji-Long Wang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Qi Cheng
- Biotechnology Research Institute, Chinese Academy of Agriculture Science, Beijing, China
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- * E-mail: (RD); (YPW)
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
- * E-mail: (RD); (YPW)
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Rodrigo G, Kirov B, Shen S, Jaramillo A. Theoretical and experimental analysis of the forced LacI-AraC oscillator with a minimal gene regulatory model. Chaos 2013; 23:025109. [PMID: 23822507 DOI: 10.1063/1.4809786] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Oscillatory dynamics have been observed in multiple cellular functions and synthetic constructs; and here, we study the behavior of a synthetic oscillator under temporal perturbations. We use a minimal model, involving a single transcription factor with delayed self-repression and enzymatic degradation, together with a first-order perturbative approach, to derive an analytical expression for the power spectrum of the system, which characterizes its response to external forces and molecular noise. Experimentally, we force and monitor the dynamics of the LacI-AraC oscillator in single cells during long time intervals by constructing a microfluidics device. Pulse dynamics of IPTG with different periods serve to perturb this system. Due to the resonance of the system, we predict theoretically and confirm experimentally the dependence on the forcing frequency of the variability in gene expression with time and the synchronization of the population to the input signal. The reported results show that the engineering of gene circuits can provide test cases for dynamical models, which could be further exploited in synthetic biology.
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Affiliation(s)
- Guillermo Rodrigo
- Institute of Systems and Synthetic Biology (iSSB), CNRS, F-91000 Évry, France
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Semsey S, Jauffred L, Csiszovszki Z, Erdőssy J, Stéger V, Hansen S, Krishna S. The effect of LacI autoregulation on the performance of the lactose utilization system in Escherichia coli. Nucleic Acids Res 2013; 41:6381-90. [PMID: 23658223 PMCID: PMC3711431 DOI: 10.1093/nar/gkt351] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The lactose operon of Escherichia coli is a paradigm system for quantitative understanding of gene regulation in prokaryotes. Yet, none of the many mathematical models built so far to study the dynamics of this system considered the fact that the Lac repressor regulates its own transcription by forming a transcriptional roadblock at the O3 operator site. Here we study the effect of autoregulation on intracellular LacI levels and also show that cAMP-CRP binding does not affect the efficiency of autoregulation. We built a mathematical model to study the role of LacI autoregulation in the lactose utilization system. Previously, it has been argued that negative autoregulation can significantly reduce noise as well as increase the speed of response. We show that the particular molecular mechanism, a transcriptional roadblock, used to achieve self-repression in the lac system does neither. Instead, LacI autoregulation balances two opposing states, one that allows quicker response to smaller pulses of external lactose, and the other that minimizes production costs in the absence of lactose.
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Affiliation(s)
- Szabolcs Semsey
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA, Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100 Gödöllő, Hungary and National Centre for Biological Sciences, Bangalore 560065, India
- *To whom correspondence should be addressed. Tel: +91 80 23666001/02; Fax: +91 80 23636662;
| | - Liselotte Jauffred
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA, Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100 Gödöllő, Hungary and National Centre for Biological Sciences, Bangalore 560065, India
| | - Zsolt Csiszovszki
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA, Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100 Gödöllő, Hungary and National Centre for Biological Sciences, Bangalore 560065, India
| | - János Erdőssy
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA, Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100 Gödöllő, Hungary and National Centre for Biological Sciences, Bangalore 560065, India
| | - Viktor Stéger
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA, Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100 Gödöllő, Hungary and National Centre for Biological Sciences, Bangalore 560065, India
| | - Sabine Hansen
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA, Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100 Gödöllő, Hungary and National Centre for Biological Sciences, Bangalore 560065, India
| | - Sandeep Krishna
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA, Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100 Gödöllő, Hungary and National Centre for Biological Sciences, Bangalore 560065, India
- Correspondence may also be addressed to Szabolcs Semsey. Tel: +45 24942613; Fax: +45 35325425;
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Loth K, Gnida M, Romanuka J, Kaptein R, Boelens R. Sliding and target location of DNA-binding proteins: an NMR view of the lac repressor system. J Biomol NMR 2013; 56:41-49. [PMID: 23568265 DOI: 10.1007/s10858-013-9723-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 03/15/2013] [Indexed: 06/02/2023]
Abstract
In non-specific lac headpiece-DNA complexes selective NMR line broadening is observed that strongly depends on length and composition of the DNA fragments. This broadening involves amide protons found in the non-specific lac-DNA structure to be interacting with the DNA phosphate backbone, and can be ascribed to DNA sliding of the protein along the DNA. This NMR exchange broadening has been used to estimate the 1D diffusion constant for sliding along non-specific DNA. The observed 1D diffusion constant of 4×10(-12) cm(2)/s is two orders of magnitude smaller than derived from previous kinetic experiments, but falls in the range of values determined more recently using single molecule methods. This strongly supports the notion that sliding could play at most a minor role in the association kinetics of binding of lac repressor to lac operator and that other processes such as hopping and intersegment transfer contribute to facilitate the DNA recognition process.
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Affiliation(s)
- Karine Loth
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Abstract
The E. coli Lac repressor is the classic textbook example of a protein that attaches to widely spaced sites along a genome and forces the intervening DNA into a loop. The short loops implicated in the regulation of the lac operon suggest the involvement of factors other than DNA and repressor in gene control. The molecular simulations presented here examine two likely structural contributions to the in-vivo looping of bacterial DNA: the distortions of the double helix introduced upon association of the highly abundant, nonspecific nucleoid protein HU and the large-scale deformations of the repressor detected in low-resolution experiments. The computations take account of the three-dimensional arrangements of nucleotides and amino acids found in crystal structures of DNA with the two proteins, the natural rest state and deformational properties of protein-free DNA, and the constraints on looping imposed by the conformation of the repressor and the orientation of bound DNA. The predicted looping propensities capture the complex, chain-length-dependent variation in repression efficacy extracted from gene expression studies and in vitro experiments and reveal unexpected chain-length-dependent variations in the uptake of HU, the deformation of repressor, and the folding of DNA. Both the opening of repressor and the presence of HU, at levels approximating those found in vivo, enhance the probability of loop formation. HU affects the global organization of the repressor and the opening of repressor influences the levels of HU binding to DNA. The length of the loop determines whether the DNA adopts antiparallel or parallel orientations on the repressor, whether the repressor is opened or closed, and how many HU molecules bind to the loop. The collective behavior of proteins and DNA is greater than the sum of the parts and hints of ways in which multiple proteins may coordinate the packaging and processing of genetic information.
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Affiliation(s)
- Luke Czapla
- Department of Chemistry & Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Michael A. Grosner
- Department of Chemistry & Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - David Swigon
- Department of Mathematics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Wilma K. Olson
- Department of Chemistry & Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
- BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
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Abstract
CytR is a transcription regulator from the LacI family, present in some gamma-proteobacteria including Escherichia coli and known not only for its cellular role, control of transport and utilization of nucleosides, but for a number of unusual structural properties. The present study addressed three related problems: structure of CytR-binding sites and motifs, their evolutionary conservation, and identification of new members of the CytR regulon. While the majority of CytR-binding sites are imperfect inverted repeats situated between binding sites for another transcription factor, CRP, other architectures were observed, in particular, direct repeats. While the similarity between sites for different genes in one genome is rather low, and hence the consensus motif is weak, there is high conservation of orthologous sites in different genomes (mainly in the Enterobacteriales) arguing for the presence of specific CytR-DNA contacts. On larger evolutionary distances candidate CytR sites may migrate but the approximate distance between flanking CRP sites tends to be conserved, which demonstrates that the overall structure of the CRP-CytR-DNA complex is gene-specific. The analysis yielded candidate CytR-binding sites for orthologs of known regulon members in less studied genomes of the Enterobacteriales and Vibrionales and identified a new candidate member of the CytR regulon, encoding a transporter named NupT (YcdZ).
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Affiliation(s)
- Natalia V. Sernova
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences (IITP RAS), Moscow, Russia
| | - Mikhail S. Gelfand
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences (IITP RAS), Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M.V.Lomonosov Moscow State University, Moscow, Russia
- * E-mail:
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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35
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Fedonin GG, Rakhmaninova AB, Korostelev ID, Laĭkova ON, Gel'fand MS. [Machine learning study of DNA binding by transcription factors from the LacI family]. Mol Biol (Mosk) 2011; 45:724-737. [PMID: 21954606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We studied 1372 LacI-family transcription factors and their 4484 DNA binding sites using machine learning algorithms and feature selection techniques. The Naive Bayes classifier and Logistic Regression were used to predict binding sites given transcription factor sequences and to classify factor-site pairs on binding and non-binding ones. Prediction accuracy was estimated using 10-fold cross-validation. Experiments showed that the best prediction of nucleotide densities at selected site positions is obtained using only a few key protein sequence positions. These positions are stably selected by the forward feature selection based on the mutual information of factor-site position pairs.
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Abstract
Few proteins have had such a strong impact on a field, as the lac repressor and λ repressor have had in Molecular Biology in bacteria. The genes required for lactose utilization are negatively regulated; the lac repressor binds to an upstream operator blocking the transcription of the enzymes necessary for lactose utilization. A similar switch regulates the virus life cycle; λ repressor binds to an operator site and blocks transcription of the phage genes necessary for lytic development. It is now 50 years since Jacob and Monod first proposed a model for gene regulation, which survives essentially unchanged in contemporary textbooks. Jacob, F. & Monod, J. (1961). Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318-356. This model provides a cogent depiction of how a set of genes can be coordinately transcribed in response to environmental conditions and regulates metabolic events in the cell. A historical perspective that illustrates the role these two repressor molecules played and their contribution to our understanding of gene regulation is presented.
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Affiliation(s)
- Mitchell Lewis
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
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37
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Xu J, Liu KW, Matthews KS, Biswal SL. Monitoring DNA binding to Escherichia coli lactose repressor using quartz crystal microbalance with dissipation. Langmuir 2011; 27:4900-4905. [PMID: 21410208 DOI: 10.1021/la200056h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Lactose repressor protein (LacI) functions as a negative transcription regulator in Escherichia coli by binding to the operator DNA sequence. Our understanding of the immobilized LacI function and the effect of ligand binding on the conformation of LacI-DNA complexes remains poorly understood. Here, we have examined the difference in functionality of wild-type and mutant LacI binding to the target DNA using quartz crystal microbalance with dissipation (QCM-D). To direct the orientation of LacI binding to the gold surface, residue 334 was substituted with cysteine (T334C) to generate a sulfur-gold linkage. Position 334 is located on the surface opposite the DNA-binding domain and remote from the site for inducer binding. With T334C immobilized on the gold surface, our sensors successfully detect operator binding as well as the release of the operator DNA from the repressor in the presence of inducer isopropyl-β-D-thiogalactoside (IPTG). Besides the natural operator DNA sequence (O(1)), a symmetric high-affinity DNA sequence (O(sym)), and a non-specific DNA (O(ns)) sequence with low affinity were also used. In addition, the impact of anti-inducer o-nitrophenyl-beta-d-fucoside (ONPF), which stabilizes LacI operator binding, was examined. The results from immobilized mutant LacI are in good agreement with known solution parameters for LacI-ligand interactions, demonstrating that QCM-D provides a rapid and efficient measurement of DNA binding and impact of ligands upon binding for this complex oligomeric protein.
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Affiliation(s)
- Jia Xu
- Department of Biochemistry and Cell Biochemistry, Rice University, Houston, Texas 77005, USA
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Brody Y, Neufeld N, Bieberstein N, Causse SZ, Böhnlein EM, Neugebauer KM, Darzacq X, Shav-Tal Y. The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing. PLoS Biol 2011; 9:e1000573. [PMID: 21264352 PMCID: PMC3019111 DOI: 10.1371/journal.pbio.1000573] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 11/19/2010] [Indexed: 01/01/2023] Open
Abstract
Kinetic analysis shows that RNA polymerase elongation kinetics are not modulated by co-transcriptional splicing and that post-transcriptional splicing can proceed at the site of transcription without the presence of the polymerase. RNA processing events that take place on the transcribed pre-mRNA include capping, splicing, editing, 3′ processing, and polyadenylation. Most of these processes occur co-transcriptionally while the RNA polymerase II (Pol II) enzyme is engaged in transcriptional elongation. How Pol II elongation rates are influenced by splicing is not well understood. We generated a family of inducible gene constructs containing increasing numbers of introns and exons, which were stably integrated in human cells to serve as actively transcribing gene loci. By monitoring the association of the transcription and splicing machineries on these genes in vivo, we showed that only U1 snRNP localized to the intronless gene, consistent with a splicing-independent role for U1 snRNP in transcription. In contrast, all snRNPs accumulated on intron-containing genes, and increasing the number of introns increased the amount of spliceosome components recruited. This indicates that nascent RNA can assemble multiple spliceosomes simultaneously. Kinetic measurements of Pol II elongation in vivo, Pol II ChIP, as well as use of Spliceostatin and Meayamycin splicing inhibitors showed that polymerase elongation rates were uncoupled from ongoing splicing. This study shows that transcription elongation kinetics proceed independently of splicing at the model genes studied here. Surprisingly, retention of polyadenylated mRNA was detected at the transcription site after transcription termination. This suggests that the polymerase is released from chromatin prior to the completion of splicing, and the pre-mRNA is post-transcriptionally processed while still tethered to chromatin near the gene end. The pre-mRNA emerging from RNA polymerase II during eukaryotic transcription undergoes a series of processing events. These include 5′-capping, intron excision and exon ligation during splicing, 3′-end processing, and polyadenylation. Processing events occur co-transcriptionally, meaning that a variety of enzymes assemble on the pre-mRNA while the polymerase is still engaged in transcription. The concept of co-transcriptional mRNA processing raises questions about the possible coupling between the transcribing polymerase and the processing machineries. Here we examine how the co-transcriptional assembly of the splicing machinery (the spliceosome) might affect the elongation kinetics of the RNA polymerase. Using live-cell microscopy, we followed the kinetics of transcription of genes containing increasing numbers of introns and measured the recruitment of transcription and splicing factors. Surprisingly, a sub-set of splicing factors was recruited to an intronless gene, implying that there is a polymerase-coupled scanning mechanism for intronic sequences. There was no difference in polymerase elongation rates on genes with or without introns, suggesting that the spliceosome does not modulate elongation kinetics. Experiments including inhibition of splicing or transcription, together with stochastic computational simulation, demonstrated that pre-mRNAs can be retained on the gene when polymerase termination precedes completion of splicing. Altogether we show that polymerase elongation kinetics are not affected by splicing events on the emerging pre-mRNA, that increased splicing leads to more splicing factors being recruited to the mRNA, and that post-transcriptional splicing can proceed at the site of transcription in the absence of the polymerase.
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Affiliation(s)
- Yehuda Brody
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Noa Neufeld
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Nicole Bieberstein
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sebastien Z. Causse
- Functional Imaging of Transcription, Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, CNRS, UMR8197, Paris, France
| | - Eva-Maria Böhnlein
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Karla M. Neugebauer
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Xavier Darzacq
- Functional Imaging of Transcription, Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, CNRS, UMR8197, Paris, France
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
- * E-mail:
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Bond LM, Peters JP, Becker NA, Kahn JD, Maher LJ. Gene repression by minimal lac loops in vivo. Nucleic Acids Res 2010; 38:8072-82. [PMID: 21149272 PMCID: PMC3001091 DOI: 10.1093/nar/gkq755] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 08/09/2010] [Accepted: 08/09/2010] [Indexed: 01/25/2023] Open
Abstract
The inflexibility of double-stranded DNA with respect to bending and twisting is well established in vitro. Understanding apparent DNA physical properties in vivo is a greater challenge. Here, we exploit repression looping with components of the Escherichia coli lac operon to monitor DNA flexibility in living cells. We create a minimal system for testing the shortest possible DNA repression loops that contain an E. coli promoter, and compare the results to prior experiments. Our data reveal that loop-independent repression occurs for certain tight operator/promoter spacings. When only loop-dependent repression is considered, fits to a thermodynamic model show that DNA twisting limits looping in vivo, although the apparent DNA twist flexibility is 2- to 4-fold higher than in vitro. In contrast, length-dependent resistance to DNA bending is not observed in these experiments, even for the shortest loops constraining <0.4 persistence lengths of DNA. As observed previously for other looping configurations, loss of the nucleoid protein heat unstable (HU) markedly disables DNA looping in vivo. Length-independent DNA bending energy may reflect the activities of architectural proteins and the structure of the DNA topological domain. We suggest that the shortest loops are formed in apical loops rather than along the DNA plectonemic superhelix.
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Affiliation(s)
- Laura M. Bond
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
| | - Justin P. Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
| | - Nicole A. Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
| | - Jason D. Kahn
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
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40
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Newell CA, Gray JC. Binding of lac repressor-GFP fusion protein to lac operator sites inserted in the tobacco chloroplast genome examined by chromatin immunoprecipitation. Nucleic Acids Res 2010; 38:e145. [PMID: 20484380 PMCID: PMC2919732 DOI: 10.1093/nar/gkq413] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 04/29/2010] [Accepted: 05/04/2010] [Indexed: 11/12/2022] Open
Abstract
Chromatin immunoprecipitation (ChIP) has been used to detect binding of DNA-binding proteins to sites in nuclear and mitochondrial genomes. Here, we describe a method for detecting protein-binding sites on chloroplast DNA, using modifications to the nuclear ChIP procedures. The method was developed using the lac operator (lacO)/lac repressor (LacI) system from Escherichia coli. The lacO sequences were integrated into a single site between the rbcL and accD genes in tobacco plastid DNA and homoplasmic transplastomic plants were crossed with transgenic tobacco plants expressing a nuclear-encoded plastid-targeted GFP-LacI fusion protein. In the progeny, the GFP-LacI fusion protein could be visualized in living tissues using confocal microscopy, and was found to co-localize with plastid nucleoids. Isolated chloroplasts from the lacO/GFP-LacI plants were lysed, treated with micrococcal nuclease to digest the DNA to fragments of approximately 600 bp and incubated with antibodies to GFP and protein A-Sepharose. PCR analysis on DNA extracted from the immunoprecipitate demonstrated IPTG (isopropylthiogalactoside)-sensitive binding of GFP-LacI to lacO. Binding of GFP-LacI to endogenous sites in plastid DNA showing sequence similarity to lacO was also detected, but required reversible cross-linking with formaldehyde. This may provide a general method for the detection of binding sites on plastid DNA for specific proteins.
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Affiliation(s)
| | - John C. Gray
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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Abstract
The protein-DNA complex, involved in the lac operon of enteric bacteria, is paradigmatic in understanding the extent of DNA bending and plasticity due to interactions with protein assemblies acting as DNA regulators. For the lac operon, two classes of structures have been proposed: 1), with the protein tetramer lying away from the DNA loop (wrapped-away model); and 2), with the protein tetramer lying inside the DNA loop (wrapped-around model). A recently developed electrostatic analytical model shows that the size and net charge of the Lac protein tetramer allow the bending of DNA, which is consistent with another wrapped-around model from the literature. Coarse-grained models, designed based on this observation, are extensively investigated and show three kinds of wrapped-around arrangements of DNA and a lower propensity for wrapped-away configurations. Molecular dynamics simulations of an all-atom model, built on the basis of the most tightly collapsed coarse-grained model, show that most of the DNA double-helical architecture is maintained in the region between O3 and O1 DNA operators, that the DNA distortion is concentrated in the chain beyond the O1 operator, and that the protein tetramer can adapt the N-terminal domains to the DNA tension.
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Affiliation(s)
- Giovanni La Penna
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo-Metallici, Sesto Fiorentino, Florence, Italy.
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Pegram LM, Wendorff T, Erdmann R, Shkel I, Bellissimo D, Felitsky DJ, Record MT. Why Hofmeister effects of many salts favor protein folding but not DNA helix formation. Proc Natl Acad Sci U S A 2010; 107:7716-21. [PMID: 20385834 PMCID: PMC2867913 DOI: 10.1073/pnas.0913376107] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The majority ( approximately 70%) of surface buried in protein folding is hydrocarbon, whereas in DNA helix formation, the majority ( approximately 65%) of surface buried is relatively polar nitrogen and oxygen. Our previous quantification of salt exclusion from hydrocarbon (C) accessible surface area (ASA) and accumulation at amide nitrogen (N) and oxygen (O) ASA leads to a prediction of very different Hofmeister effects on processes that bury mostly polar (N, O) surface compared to the range of effects commonly observed for processes that bury mainly nonpolar (C) surface, e.g., micelle formation and protein folding. Here we quantify the effects of salts on folding of the monomeric DNA binding domain (DBD) of lac repressor (lac DBD) and on formation of an oligomeric DNA duplex. In accord with this prediction, no salt investigated has a stabilizing Hofmeister effect on DNA helix formation. Our ASA-based analyses of model compound data and estimates of the surface area buried in protein folding and DNA helix formation allow us to predict Hofmeister effects on these processes. We observe semiquantitative to quantitative agreement between these predictions and the experimental values, obtained from a novel separation of coulombic and Hofmeister effects. Possible explanations of deviations, including salt-dependent unfolded ensembles and interactions with other types of surface, are discussed.
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Affiliation(s)
- Laurel M Pegram
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Chen YF, Milstein JN, Meiners JC. Femtonewton entropic forces can control the formation of protein-mediated DNA loops. Phys Rev Lett 2010; 104:048301. [PMID: 20366742 DOI: 10.1103/physrevlett.104.048301] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Indexed: 05/29/2023]
Abstract
We show that minuscule entropic forces, on the order of 100 fN, can prevent the formation of DNA loops-a ubiquitous means of regulating the expression of genes. We observe a tenfold decrease in the rate of LacI-mediated DNA loop formation when a tension of 200 fN is applied to the substrate DNA, biasing the thermal fluctuations that drive loop formation and breakdown events. Conversely, once looped, the DNA-protein complex is insensitive to applied force. Our measurements are in excellent agreement with a simple polymer model of loop formation in DNA, and show that an antiparallel topology is the preferred LacI-DNA loop conformation for a generic loop-forming construct.
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Affiliation(s)
- Yih-Fan Chen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
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44
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Robeva R, Davies R, Hodge T, Enyedi A. Mathematical biology modules based on modern molecular biology and modern discrete mathematics. CBE Life Sci Educ 2010; 9:227-40. [PMID: 20810955 PMCID: PMC2931670 DOI: 10.1187/cbe.10-03-0019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 05/24/2010] [Accepted: 06/02/2010] [Indexed: 05/23/2023]
Abstract
We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to introduce students to mathematical methods beyond the interface of biology with calculus. Based on ongoing research, and designed to use the project-based-learning approach, the modules highlight applications of modern discrete mathematics and algebraic statistics to pressing problems in molecular biology. For the majority of projects, calculus is not a required prerequisite and, due to the modest amount of mathematical background needed for some of the modules, the materials can be used for an early introduction to mathematical modeling. At the same time, most modules are connected with topics in linear and abstract algebra, algebraic geometry, and probability, and they can be used as meaningful applied introductions into the relevant advanced-level mathematics courses. Open-source software is used to facilitate the relevant computations. As a detailed example, we outline a module that focuses on Boolean models of the lac operon network.
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Affiliation(s)
- Raina Robeva
- Department of Mathematical Sciences, Western Michigan University, Kalamazoo MI 49008, USA.
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Abstract
Transcriptional regulation is an essential component of all metabolic pathways. At the most basic level, a protein binds to a particular DNA sequence (operator) on the genome and either positively or negatively alters the level of transcription. Together, the protein and its operator form an epigenetic switch that regulates gene expression. In an effort to produce a 'better' switch, we have discovered novel facets of the lac operon that are responsible for optimal functionality. We have uncovered a relationship between operator binding affinity and inducibility and demonstrated that the operator DNA is not a passive component of a genetic switch; it is responsible for establishing binding affinity, specificity as well as translational efficiency. In addition, an operator's directionality can indirectly affect gene expression. Unraveling the basic properties of this classical epigenetic switch demonstrates that multiple factors must be optimized in designing a better switch.
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Affiliation(s)
| | - Mitchell Lewis
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 37th and Hamilton Walk, Philadelphia, PA 19104-6059, USA
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46
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Abstract
In allostery, a binding event at one site in a protein modulates the behavior of a distant site. Identifying residues that relay the signal between sites remains a challenge. We have developed predictive models using support-vector machines, a widely used machine-learning method. The training data set consisted of residues classified as either hotspots or non-hotspots based on experimental characterization of point mutations from a diverse set of allosteric proteins. Each residue had an associated set of calculated features. Two sets of features were used, one consisting of dynamical, structural, network, and informatic measures, and another of structural measures defined by Daily and Gray [1]. The resulting models performed well on an independent data set consisting of hotspots and non-hotspots from five allosteric proteins. For the independent data set, our top 10 models using Feature Set 1 recalled 68–81% of known hotspots, and among total hotspot predictions, 58–67% were actual hotspots. Hence, these models have precision P = 58–67% and recall R = 68–81%. The corresponding models for Feature Set 2 had P = 55–59% and R = 81–92%. We combined the features from each set that produced models with optimal predictive performance. The top 10 models using this hybrid feature set had R = 73–81% and P = 64–71%, the best overall performance of any of the sets of models. Our methods identified hotspots in structural regions of known allosteric significance. Moreover, our predicted hotspots form a network of contiguous residues in the interior of the structures, in agreement with previous work. In conclusion, we have developed models that discriminate between known allosteric hotspots and non-hotspots with high accuracy and sensitivity. Moreover, the pattern of predicted hotspots corresponds to known functional motifs implicated in allostery, and is consistent with previous work describing sparse networks of allosterically important residues. Allostery is the process whereby a molecule binds to one site in a protein and alters the function of a distant site. This phenomenon is ubiquitous, as proteins frequently must adapt their behavior to changes in the cellular milieu. The mechanism(s) underlying allostery remains incompletely understood. In particular, predictive models are needed that distinguish amino-acid residues that are critical to allostery, or “hotspots”, from non-hotspots. Here we have used data-mining approaches to infer rules that distinguish hotspots from non-hotspots. Starting with a data set of known hotspot and non-hotspot residues from a diverse set of allosteric proteins, the training data set, we applied machine learning to this data to “learn” models, or sets of rules, for distinguishing hotspots and non-hotspots by inferring associations between the classification (hotspot or non-hotspot) and an associated set of calculated attributes. Many models that showed the highest predictive power on the training data also exhibited high accuracy and sensitivity when applied to an independent data set. Moreover, the pattern of predicted hotspots in the proteins we studied was consistent with known structure/function relationships and previous work suggesting that a network of essential residues mediates the allosteric transition.
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Affiliation(s)
- Omar N. A. Demerdash
- Biophysics Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Medical Scientist Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael D. Daily
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Julie C. Mitchell
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Mathematics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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47
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Zhang Y, McEwen AE, Crothers DM, Levene SD. Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping. PLoS One 2006; 1:e136. [PMID: 17205140 PMCID: PMC1762422 DOI: 10.1371/journal.pone.0000136] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Accepted: 11/30/2006] [Indexed: 11/19/2022] Open
Abstract
Interactions of E. coli lac repressor (LacR) with a pair of operator sites on the same DNA molecule can lead to the formation of looped nucleoprotein complexes both in vitro and in vivo. As a major paradigm for loop-mediated gene regulation, parameters such as operator affinity and spacing, repressor concentration, and DNA bending induced by specific or non-specific DNA-binding proteins (e.g., HU), have been examined extensively. However, a complete and rigorous model that integrates all of these aspects in a systematic and quantitative treatment of experimental data has not been available. Applying our recent statistical-mechanical theory for DNA looping, we calculated repression as a function of operator spacing (58-156 bp) from first principles and obtained excellent agreement with independent sets of in-vivo data. The results suggest that a linear extended, as opposed to a closed v-shaped, LacR conformation is the dominant form of the tetramer in vivo. Moreover, loop-mediated repression in wild-type E. coli strains is facilitated by decreased DNA rigidity and high levels of flexibility in the LacR tetramer. In contrast, repression data for strains lacking HU gave a near-normal value of the DNA persistence length. These findings underscore the importance of both protein conformation and elasticity in the formation of small DNA loops widely observed in vivo, and demonstrate the utility of quantitatively analyzing gene regulation based on the mechanics of nucleoprotein complexes.
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Affiliation(s)
- Yongli Zhang
- Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- * To whom correspondence should be addressed. E-mail:
| | - Abbye E. McEwen
- Institute of Biomedical Sciences and Technology, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Donald M. Crothers
- Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Stephen D. Levene
- Institute of Biomedical Sciences and Technology, University of Texas at Dallas, Richardson, Texas, United States of America
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas, United States of America
- * To whom correspondence should be addressed. E-mail:
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