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Tsai MJ, Wang JR, Yang CD, Kao KC, Huang WL, Huang HY, Tseng CP, Huang HD, Ho SY. PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli. Sci Rep 2018; 8:951. [PMID: 29343727 PMCID: PMC5772556 DOI: 10.1038/s41598-017-18648-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/13/2017] [Indexed: 02/04/2023] Open
Abstract
Cyclic AMP receptor protein (CRP), a global regulator in Escherichia coli, regulates more than 180 genes via two roles: activation and repression. Few methods are available for predicting the regulatory roles from the binding sites of transcription factors. This work proposes an accurate method PredCRP to derive an optimised model (named PredCRP-model) and a set of four interpretable rules (named PredCRP-ruleset) for predicting and analysing the regulatory roles of CRP from sequences of CRP-binding sites. A dataset consisting of 169 CRP-binding sites with regulatory roles strongly supported by evidence was compiled. The PredCRP-model, using 12 informative features of CRP-binding sites, and cooperating with a support vector machine achieved a training and test accuracy of 0.98 and 0.93, respectively. PredCRP-ruleset has two activation rules and two repression rules derived using the 12 features and the decision tree method C4.5. This work further screened and identified 23 previously unobserved regulatory interactions in Escherichia coli. Using quantitative PCR for validation, PredCRP-model and PredCRP-ruleset achieved a test accuracy of 0.96 (=22/23) and 0.91 (=21/23), respectively. The proposed method is suitable for designing predictors for regulatory roles of all global regulators in Escherichia coli. PredCRP can be accessed at https://github.com/NctuICLab/PredCRP.
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Affiliation(s)
- Ming-Ju Tsai
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Jyun-Rong Wang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chi-Dung Yang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Kuo-Ching Kao
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Wen-Lin Huang
- Department and Institute of Industrial Engineering and Management, Minghsin University of Science and Technology, Hsinchu, Taiwan
| | - Hsi-Yuan Huang
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Ching-Ping Tseng
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan. .,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.
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Ishihama A, Shimada T, Yamazaki Y. Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors. Nucleic Acids Res 2016; 44:2058-74. [PMID: 26843427 PMCID: PMC4797297 DOI: 10.1093/nar/gkw051] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/20/2016] [Indexed: 01/25/2023] Open
Abstract
Bacterial genomes are transcribed by DNA-dependent RNA polymerase (RNAP), which achieves gene selectivity through interaction with sigma factors that recognize promoters, and transcription factors (TFs) that control the activity and specificity of RNAP holoenzyme. To understand the molecular mechanisms of transcriptional regulation, the identification of regulatory targets is needed for all these factors. We then performed genomic SELEX screenings of targets under the control of each sigma factor and each TF. Here we describe the assembly of 156 SELEX patterns of a total of 116 TFs performed in the presence and absence of effector ligands. The results reveal several novel concepts: (i) each TF regulates more targets than hitherto recognized; (ii) each promoter is regulated by more TFs than hitherto recognized; and (iii) the binding sites of some TFs are located within operons and even inside open reading frames. The binding sites of a set of global regulators, including cAMP receptor protein, LeuO and Lrp, overlap with those of the silencer H-NS, suggesting that certain global regulators play an anti-silencing role. To facilitate sharing of these accumulated SELEX datasets with the research community, we compiled a database, ‘Transcription Profile of Escherichia coli’ (www.shigen.nig.ac.jp/ecoli/tec/).
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Affiliation(s)
- Akira Ishihama
- Micro-Nano Technology Research Center, Hosei University, Koganei, Tokyo, 184-8584, Japan
| | - Tomohiro Shimada
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuda, Yokohama 226-8503, Japan
| | - Yukiko Yamazaki
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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Le VH, Yanney M, McGuire M, Sygula A, Lewis EA. Thermodynamics of host-guest interactions between fullerenes and a buckycatcher. J Phys Chem B 2014; 118:11956-64. [PMID: 25248285 PMCID: PMC4199543 DOI: 10.1021/jp5087152] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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1H NMR and isothermal
titration calorimetry (ITC) experiments
were employed to obtain reliable thermodynamic data for the formation
of the 1:1 inclusion complexes of fullerenes C60 and C70 with the buckycatcher (C60H28). NMR
measurements were done in toluene-d8 and
chlorobenzene-d5 at 288, 298, and 308
K, while the ITC titrations were performed in toluene, chlorobenzene, o-dichlorobenzene, anisole, and 1,1,2,2-tetrachloroethane
at temperatures from 278 to 323 K. The association constants, Ka, obtained with both techniques are in very
good agreement. The thermodynamic data obtained by ITC indicate that
generally the host–guest association is enthalpy-driven. Interestingly,
the entropy contributions are, with rare exceptions, slightly stabilizing
or close to zero. Neither ΔH nor ΔS is constant over the temperature range studied, and these
thermodynamic functions exhibit classical enthalpy/entropy compensation.
The ΔCp values
calculated from the temperature dependence of the calorimetric ΔH values are negative for the association of both fullerenes
with the buckycatcher in toluene. The negative ΔCp values are consistent with some desolvation
of the host-cavity and the guest in the inclusion complexes, C60@C60H28 and C70@C60H28.
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Affiliation(s)
- Vu H Le
- Department of Chemistry, Mississippi State University , Mississippi State, Mississippi 39762, United States
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King NM, Prabu-Jeyabalan M, Bandaranayake RM, Nalam MNL, Nalivaika EA, Özen A, Haliloǧlu T, Yılmaz NK, Schiffer CA. Extreme entropy-enthalpy compensation in a drug-resistant variant of HIV-1 protease. ACS Chem Biol 2012; 7:1536-46. [PMID: 22712830 DOI: 10.1021/cb300191k] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of HIV-1 protease inhibitors has been the historic paradigm of rational structure-based drug design, where structural and thermodynamic analyses have assisted in the discovery of novel inhibitors. While the total enthalpy and entropy change upon binding determine the affinity, often the thermodynamics are considered in terms of inhibitor properties only. In the current study, profound changes are observed in the binding thermodynamics of a drug-resistant variant compared to wild-type HIV-1 protease, irrespective of the inhibitor bound. This variant (Flap+) has a combination of flap and active site mutations and exhibits extremely large entropy-enthalpy compensation compared to wild-type protease, 5-15 kcal/mol, while losing only 1-3 kcal/mol in total binding free energy for any of six FDA-approved inhibitors. Although entropy-enthalpy compensation has been previously observed for a variety of systems, never have changes of this magnitude been reported. The co-crystal structures of Flap+ protease with four of the inhibitors were determined and compared with complexes of both the wild-type protease and another drug-resistant variant that does not exhibit this energetic compensation. Structural changes conserved across the Flap+ complexes, which are more pronounced for the flaps covering the active site, likely contribute to the thermodynamic compensation. The finding that drug-resistant mutations can profoundly modulate the relative thermodynamic properties of a therapeutic target independent of the inhibitor presents a new challenge for rational drug design.
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Affiliation(s)
- Nancy M. King
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Moses Prabu-Jeyabalan
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Rajintha M. Bandaranayake
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Madhavi N. L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Ayşegül Özen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Türkan Haliloǧlu
- Polymer Research Center and Department
of Chemical Engineering, Bogazici University, TR-34342, Bebek, Istanbul, Turkey
| | - Neşe Kurt Yılmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
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Ishihama A. Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks. FEMS Microbiol Rev 2010; 34:628-45. [DOI: 10.1111/j.1574-6976.2010.00227.x] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Xie F, Turvey SE, Williams MA, Mor G, Von Dadelszen P. REVIEW ARTICLE: Toll-Like Receptor Signaling and Pre-Eclampsia. Am J Reprod Immunol 2009; 63:7-16. [DOI: 10.1111/j.1600-0897.2009.00745.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Energetic contributions to the initiation of transcription in E. coli. Biophys Chem 2008; 138:91-8. [PMID: 18834656 DOI: 10.1016/j.bpc.2008.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Revised: 09/02/2008] [Accepted: 09/03/2008] [Indexed: 11/21/2022]
Abstract
The thermodynamics of RNA polymerase (RNAP) binding to a 108 base pair (bp) synthetic promoter with consensus sequences at the -35 and -10 bp binding regions upstream from the transcription start point were determined using isothermal titration calorimetry (ITC). The binding constant at 25 degrees C is 2.37+/-0.18x10(7) M(-1), which is reduced to 0.17+/-0.06x10(7) M(-1) with mutations in the -10 bp region but remained the same with mutations in the -35 binding region. The binding reactions were enthalpically-driven with exothermic binding enthalpies ranging from -57+/-6 kJ mol(-1) at 15 degrees C to -271+/-20 kJ mol(-1) at 35 degrees C yielding a large binding heat capacity change of -10.7+/-1.9 kJ mol(-1) K(-1), indicating a conformational change upon binding to the RNAP. Differential scanning calorimetry (DSC) scans of the thermal unfolding of RNAP and the promoter-RNAP complex exhibited an unfolding transition at 55.5+/-0.6 degrees C and at 58.9+/-0.5 degrees C for the RNAP but only one transition at 60.5+/-1.1 degrees C for the complex with van't Hoff enthalpy to transition enthalpy ratios of, resp., 3.2+/-0.3 and 4.3+/-0.5. The single transition of the complex results from a shift to 60.5 degrees C of the low temperature transition upon promoter binding to the structural unit unfolding at the lower temperature in RNAP. The large transition enthalpy ratios indicate that the sigma, alpha, alpha, beta, and beta' subunits unfold as almost independent entities. The dissociation thermodynamics of short transcription "bubble" duplexes of 7 promoters sequenced from -1 to -12 bp were determined from ITC and DSC measurements. The free energy change of the promoter binding to the RNAP and the free energy requirement for formation of the transcription bubble at the low promoter concentrations in the cell are sufficient to drive the initiation of transcription through the isomerization of the closed to the open form step of the RNAP-promoter complex.
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Fic E, Górecki A, Wasylewski Z. Fluorescence quenching studies of conformational changes induced by cAMP and DNA binding to heterodimer of cyclic AMP receptor protein from Escherichia coli. Protein J 2008; 26:457-66. [PMID: 17505875 DOI: 10.1007/s10930-007-9085-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In Escherichia coli, cyclic AMP receptor protein (CRP) is known to regulate the transcription of about 100 genes. The signal to activate CRP is the binding of cyclic AMP. In this study the fluorescence quenching measurements were used to observe conformational changes in the structure of CRP after binding of cAMP and DNA. We used the constructed CRP heterodimer, which contains only a single Trp13 residue localized in the N-terminal domain of one CRP subunit. We propose that apo-CRP subunits exist in a solution in one conformational state and it changes after the ligand binding. We also suggest that the signal transmission upon binding of cAMP is possible not only from the N-terminal domain to C-terminal domain but also in the opposite direction after binding of specific DNA sequence, both with and without cAMP. Thereby it can influence on the CRP's interaction with RNA polymerase and the genes expression.
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Affiliation(s)
- Ewelina Fic
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7 str, Krakow, 30-387, Poland.
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Ramprakesh J, Schwarz FP. Energetic differences between the specific binding of a 40bp DNA duplex and the lac promoter to lac repressor protein. Arch Biochem Biophys 2005; 438:162-73. [PMID: 15916747 DOI: 10.1016/j.abb.2005.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Revised: 04/22/2005] [Accepted: 04/26/2005] [Indexed: 11/27/2022]
Abstract
The energetics of LRP binding to a 104 bp lac promoter determined from ITC measurements were compared to the energetics of binding to a shorter 40 bp DNA duplex with the 21 bp promoter binding site sequence. The promoter binding affinity of 2.47 +/- 0.0 1x 10(7) M(-1) was higher than the DNA binding affinity of 1.81 +/- 0.67 x 10(7) M(-1) while the binding enthalpy of -804 +/- 41 kJ mol(-1) was lower than that of the DNA binding enthalpy of -145 +/- 16 kJ mol(-1) at 298.15 K. Both the promoter and DNA binding reactions were exothermic in phosphate buffer but endothermic in Tris buffer that showed the transfer of four protons to LRP in the former reaction but only two in the latter. A more complicated dependence of these parameters on temperature was observed for promoter binding. These energetic differences are attributable to additional LRP-promoter interactions from wrapping of the promoter around the LRP.
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Affiliation(s)
- Jayanthi Ramprakesh
- Center for Advanced Research in Biotechnology/National Institute of Standards and Technology, Rockville, MD 20850, USA
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Tworzydło M, Polit A, Mikołajczak J, Wasylewski Z. Fluorescence quenching and kinetic studies of conformational changes induced by DNA and cAMP binding to cAMP receptor protein from Escherichia coli. FEBS J 2005; 272:1103-16. [PMID: 15720385 DOI: 10.1111/j.1742-4658.2005.04540.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Cyclic AMP receptor protein (CRP) regulates the expression of more then 100 genes in Escherichia coli. It is known that the allosteric activation of CRP by cAMP involves a long-distance signal transmission from the N-terminal cAMP-binding domain to the C-terminal domain of CRP responsible for the interactions with specific sequences of DNA. In this report we have used a CRP mutant containing a single Trp13 located in the N-terminal domain of the protein. We applied the iodide and acrylamide fluorescence quenching method in order to study how different DNA sequences and cAMP binding induce the conformational changes in the CRP molecule. The results presented provide evidence for the occurrence of a long-distance conformational signal transduction within the protein from the C-terminal DNA-binding domain to the N-terminal domain of CRP. This conformational signal transmission depends on the promoter sequence. We also used the stopped-flow and Forster resonance energy transfer between labeled Cys178 of CRP and fluorescently labeled DNA sequences to study the kinetics of DNA-CRP interactions. The results thus obtained lead to the conclusion that CRP can exist in several conformational states and that their distribution is affected by binding of both the cAMP and of specific DNA sequences.
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Affiliation(s)
- Magdalena Tworzydło
- Department of Physical Biochemistry, Faculty of Biotechnology, Jagiellonian University, Kraków, Poland
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