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Kim H, Kim S, Jung Y, Han J, Yun JH, Chang I, Lee W. Probing the Folding-Unfolding Transition of a Thermophilic Protein, MTH1880. PLoS One 2016; 11:e0145853. [PMID: 26766214 PMCID: PMC4713090 DOI: 10.1371/journal.pone.0145853] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
The folding mechanism of typical proteins has been studied widely, while our understanding of the origin of the high stability of thermophilic proteins is still elusive. Of particular interest is how an atypical thermophilic protein with a novel fold maintains its structure and stability under extreme conditions. Folding-unfolding transitions of MTH1880, a thermophilic protein from Methanobacterium thermoautotrophicum, induced by heat, urea, and GdnHCl, were investigated using spectroscopic techniques including circular dichorism, fluorescence, NMR combined with molecular dynamics (MD) simulations. Our results suggest that MTH1880 undergoes a two-state N to D transition and it is extremely stable against temperature and denaturants. The reversibility of refolding was confirmed by spectroscopic methods and size exclusion chromatography. We found that the hyper-stability of the thermophilic MTH1880 protein originates from an extensive network of both electrostatic and hydrophobic interactions coordinated by the central β-sheet. Spectroscopic measurements, in combination with computational simulations, have helped to clarify the thermodynamic and structural basis for hyper-stability of the novel thermophilic protein MTH1880.
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Affiliation(s)
- Heeyoun Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Sangyeol Kim
- Department of Physics, Pusan National University, Busan, 609–735, Korea
- Center for Proteome Biophysics, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 711–873, Korea
| | - Youngjin Jung
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Jeongmin Han
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Ji-Hye Yun
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Iksoo Chang
- Center for Proteome Biophysics, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 711–873, Korea
- Department of Brain and Cognitive Sciences, DGIST, Daegu, 711–873, Korea
| | - Weontae Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
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Amoroso A, Boudet J, Berzigotti S, Duval V, Teller N, Mengin-Lecreulx D, Luxen A, Simorre JP, Joris B. A peptidoglycan fragment triggers β-lactam resistance in Bacillus licheniformis. PLoS Pathog 2012; 8:e1002571. [PMID: 22438804 PMCID: PMC3305447 DOI: 10.1371/journal.ppat.1002571] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Accepted: 01/24/2012] [Indexed: 01/29/2023] Open
Abstract
To resist to β-lactam antibiotics Eubacteria either constitutively synthesize a β-lactamase or a low affinity penicillin-binding protein target, or induce its synthesis in response to the presence of antibiotic outside the cell. In Bacillus licheniformis and Staphylococcus aureus, a membrane-bound penicillin receptor (BlaR/MecR) detects the presence of β-lactam and launches a cytoplasmic signal leading to the inactivation of BlaI/MecI repressor, and the synthesis of a β-lactamase or a low affinity target. We identified a dipeptide, resulting from the peptidoglycan turnover and present in bacterial cytoplasm, which is able to directly bind to the BlaI/MecI repressor and to destabilize the BlaI/MecI-DNA complex. We propose a general model, in which the acylation of BlaR/MecR receptor and the cellular stress induced by the antibiotic, are both necessary to generate a cell wall-derived coactivator responsible for the expression of an inducible β-lactam-resistance factor. The new model proposed confirms and emphasizes the role of peptidoglycan degradation fragments in bacterial cell regulation.
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Affiliation(s)
- Ana Amoroso
- Centre d'Ingénierie des Protéines, Institut de Chimie B6A, Sart-Tilman, Université de Liège, Liège, Belgium
- Cátedra de Microbiología, Facultad de Farmacia y Bioquímica Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Julien Boudet
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF, Grenoble, France
| | - Stéphanie Berzigotti
- Centre d'Ingénierie des Protéines, Institut de Chimie B6A, Sart-Tilman, Université de Liège, Liège, Belgium
| | - Valérie Duval
- Centre d'Ingénierie des Protéines, Institut de Chimie B6A, Sart-Tilman, Université de Liège, Liège, Belgium
| | - Nathalie Teller
- Chimie Organique de Synthèse, Institut de Chimie B6A, Sart-Tilman. Université de Liège, Liège, Belgium
| | - Dominique Mengin-Lecreulx
- Université de Paris-Sud 11 and CNRS, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Laboratoire des Enveloppes Bactériennes et Antibiotiques, UMR 8619, Orsay, France
| | - André Luxen
- Chimie Organique de Synthèse, Institut de Chimie B6A, Sart-Tilman. Université de Liège, Liège, Belgium
| | - Jean-Pierre Simorre
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF, Grenoble, France
| | - Bernard Joris
- Centre d'Ingénierie des Protéines, Institut de Chimie B6A, Sart-Tilman, Université de Liège, Liège, Belgium
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Lee AJ, Clark RW, Youn H, Ponter S, Burstyn JN. Guanidine hydrochloride-induced unfolding of the three heme coordination states of the CO-sensing transcription factor, CooA. Biochemistry 2009; 48:6585-97. [PMID: 19594171 DOI: 10.1021/bi801827j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CooA is a heme-dependent CO-sensing transcription factor that has three observable heme coordination states. There is some evidence that each CooA heme state has a distinct protein conformation; the goal of this study was to characterize these conformations by measuring their structural stabilities through guanidine hydrochloride (GuHCl) denaturation. By studying the denaturation processes of the Fe(III) state of WT CooA and several variants, we were able to characterize independent unfolding processes for each domain of CooA. This information was used to compare the unfolding profiles of various CooA heme activation states [Fe(III), Fe(II), and Fe(II)-CO] to show that the heme coordination state changes the stability of the effector binding domain. A mechanism consistent with the data predicts that all CooA coordination states and variants undergo unfolding of the DNA-binding domain between 2 and 3 M GuHCl with a free energy of unfolding of approximately 17 kJ/mol, while unfolding of the heme domain is variable and dependent on the heme coordination state. The findings support a model in which changes in heme ligation alter the structural stability of the heme domain and dimer interface but do not alter the stability of the DNA-binding domain. These studies provide evidence that the domains of transcription factors are modular and that allosteric signaling occurs through changes in the relative positions of the protein domains without affecting the structure of the DNA-binding region.
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Affiliation(s)
- Andrea J Lee
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Boudet J, Duval V, Van Melckebeke H, Blackledge M, Amoroso A, Joris B, Simorre JP. Conformational and thermodynamic changes of the repressor/DNA operator complex upon monomerization shed new light on regulation mechanisms of bacterial resistance against beta-lactam antibiotics. Nucleic Acids Res 2007; 35:4384-95. [PMID: 17576674 PMCID: PMC1935004 DOI: 10.1093/nar/gkm448] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In absence of β-lactam antibiotics, BlaI and MecI homodimeric repressors negatively control the expression of genes involved in β-lactam resistance in Bacillus licheniformis and in Staphylococcus aureus. Subsequently to β-lactam presence, BlaI/MecI is inactivated by a single-point proteolysis that separates its N-terminal DNA-binding domain to its C-terminal domain responsible for its dimerization. Concomitantly to this proteolysis, the truncated repressor acquires a low affinity for its DNA target that explains the expression of the structural gene for resistance. To understand the loss of the high DNA affinity of the truncated repressor, we have determined the different dissociation constants of the system and solved the solution structure of the B. licheniformis monomeric repressor complexed to the semi-operating sequence OP1 of blaP (1/2OP1blaP) by using a de novo docking approach based on inter-molecular nuclear Overhauser effects and chemical-shift differences measured on each macromolecular partner. Although the N-terminal domain of the repressor is not subject to internal structural rearrangements upon DNA binding, the molecules adopt a tertiary conformation different from the crystallographic operator–repressor dimer complex, leading to a 30° rotation of the monomer with respect to a central axis extended across the DNA. These results open new insights for the repression and induction mechanisms of bacterial resistance to β-lactams.
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Affiliation(s)
- Julien Boudet
- Institut de Biologie Structurale Jean-Pierre Ebel CEA-CNRS-UJF, 41 Avenue Jules Horowitz, 38027 Grenoble Cedex 1, France, Centre d’Ingénierie des Protéines, Institut de Chimie B6A, Université de Liège Sart-Tilman B4000, Belgium and Cátedra de Microbiología, Facultad de Farmacia y Bioquímica Universidad de Buenos Aires, Junín 954 (1113), Buenos Aires, Argentina
| | - Valérie Duval
- Institut de Biologie Structurale Jean-Pierre Ebel CEA-CNRS-UJF, 41 Avenue Jules Horowitz, 38027 Grenoble Cedex 1, France, Centre d’Ingénierie des Protéines, Institut de Chimie B6A, Université de Liège Sart-Tilman B4000, Belgium and Cátedra de Microbiología, Facultad de Farmacia y Bioquímica Universidad de Buenos Aires, Junín 954 (1113), Buenos Aires, Argentina
| | - Hélène Van Melckebeke
- Institut de Biologie Structurale Jean-Pierre Ebel CEA-CNRS-UJF, 41 Avenue Jules Horowitz, 38027 Grenoble Cedex 1, France, Centre d’Ingénierie des Protéines, Institut de Chimie B6A, Université de Liège Sart-Tilman B4000, Belgium and Cátedra de Microbiología, Facultad de Farmacia y Bioquímica Universidad de Buenos Aires, Junín 954 (1113), Buenos Aires, Argentina
| | - Martin Blackledge
- Institut de Biologie Structurale Jean-Pierre Ebel CEA-CNRS-UJF, 41 Avenue Jules Horowitz, 38027 Grenoble Cedex 1, France, Centre d’Ingénierie des Protéines, Institut de Chimie B6A, Université de Liège Sart-Tilman B4000, Belgium and Cátedra de Microbiología, Facultad de Farmacia y Bioquímica Universidad de Buenos Aires, Junín 954 (1113), Buenos Aires, Argentina
| | - Ana Amoroso
- Institut de Biologie Structurale Jean-Pierre Ebel CEA-CNRS-UJF, 41 Avenue Jules Horowitz, 38027 Grenoble Cedex 1, France, Centre d’Ingénierie des Protéines, Institut de Chimie B6A, Université de Liège Sart-Tilman B4000, Belgium and Cátedra de Microbiología, Facultad de Farmacia y Bioquímica Universidad de Buenos Aires, Junín 954 (1113), Buenos Aires, Argentina
| | - Bernard Joris
- Institut de Biologie Structurale Jean-Pierre Ebel CEA-CNRS-UJF, 41 Avenue Jules Horowitz, 38027 Grenoble Cedex 1, France, Centre d’Ingénierie des Protéines, Institut de Chimie B6A, Université de Liège Sart-Tilman B4000, Belgium and Cátedra de Microbiología, Facultad de Farmacia y Bioquímica Universidad de Buenos Aires, Junín 954 (1113), Buenos Aires, Argentina
| | - Jean-Pierre Simorre
- Institut de Biologie Structurale Jean-Pierre Ebel CEA-CNRS-UJF, 41 Avenue Jules Horowitz, 38027 Grenoble Cedex 1, France, Centre d’Ingénierie des Protéines, Institut de Chimie B6A, Université de Liège Sart-Tilman B4000, Belgium and Cátedra de Microbiología, Facultad de Farmacia y Bioquímica Universidad de Buenos Aires, Junín 954 (1113), Buenos Aires, Argentina
- *To whom correspondence should be addressed. +33-4-38785799+33-4-38785494
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