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Ma Z, Chang R, Zhu L, Zhu D, Deng Y, Guo X, Cheng Z, Chen X. Metabolic Engineering of Corynebacterium glutamicum for Highly Efficient Production of Ectoine. ACS Synth Biol 2024; 13:2081-2090. [PMID: 38607270 DOI: 10.1021/acssynbio.4c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Ectoine is a compatible solute that functions as a cell protector from various stresses, protecting cells and stabilizing biomolecules, and is widely used in medicine, cosmetics, and biotechnology. Microbial fermentation has been widely used for the large-scale production of ectoine, and a number of fermentation strategies have been developed to increase the ectoine yield, reduce production costs, and simplify the production process. Here, Corynebacterium glutamicum was engineered for ectoine production by heterologous expression of the ectoine biosynthesis operon ectBAC gene from Halomonas elongata, and a series of genetic modifications were implemented. This included introducing the de3 gene from Escherichia coli BL21 (DE3) to express the T7 promoter, eliminating the lysine transporter protein lysE to limit lysine production, and performing a targeted mutation lysCS301Y on aspartate kinase to alleviate feedback inhibition of lysine. The new engineered strain Ect10 obtained an ectoine titer of 115.87 g/L in an optimized fed-batch fermentation, representing the highest ectoine production level in C. glutamicum and achieving the efficient production of ectoine in a low-salt environment.
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Affiliation(s)
- Zhi Ma
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Renjie Chang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Linjiang Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Dianhao Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yanfeng Deng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xinying Guo
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Ziyi Cheng
- Department of Mechanical & Industrial Engineering, University of Toronto, 5 King's College Road, Toronto, Ontario M5S 3G8, Canada
| | - Xiaolong Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
- Quzhou Eco-Industrial Innovation Institute, Zhejiang University of Technology, Quzhou 324003, PR China
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2
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Panuszko A, Szymczak M, Dłużewska J, Godlewska J, Kuffel A, Bruździak P. Effect of ectoine on hydration spheres of peptides-spectroscopic studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 306:123590. [PMID: 37922848 DOI: 10.1016/j.saa.2023.123590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/10/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
In this paper, we use FTIR spectroscopy to characterize the hydration water of ectoine, its interactions with two peptides-diglycine and NAGMA, and the properties of water molecules in the hydration spheres of both peptides changed by the presence of the osmolyte. We found that the interaction of ectoine with the peptide hydration shells had no effect on its own hydration sphere. However, the enhanced hydration layer of the osmolyte influences the hydration shells of both peptides and does so in a different way for both peptides: (1) the interfacial interaction of the NAGMA peptide and ectoine hydration spheres strengthened the hydration shell of this peptide; (2) the inclusion of water molecules from the ectoine hydration sphere into the diglycine hydration sphere had only a marginally enhancing effect. Since ectoine is being used in more and more biopharmaceutical products and cosmetics, knowledge of the properties of its hydration shell and its effect on the hydration shell of other molecules is extremely relevant to understanding its protective mechanism.
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Affiliation(s)
- Aneta Panuszko
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk, 80-233, Poland.
| | - Marek Szymczak
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk, 80-233, Poland
| | - Julia Dłużewska
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk, 80-233, Poland
| | - Julia Godlewska
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk, 80-233, Poland
| | - Anna Kuffel
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk, 80-233, Poland
| | - Piotr Bruździak
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk, 80-233, Poland
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Ma Z, Wu C, Zhu L, Chang R, Ma W, Deng Y, Chen X. Bioactivity profiling of the extremolyte ectoine as a promising protectant and its heterologous production. 3 Biotech 2022; 12:331. [PMID: 36311375 PMCID: PMC9606177 DOI: 10.1007/s13205-022-03370-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022] Open
Abstract
Ectoine is a compatible solutes that is diffusely dispersed in bacteria and archaea. It plays a significant role as protectant against various external pressures, such as high temperature, high osmolarity, dryness and radiation, in cells. Ectoine can be utilized in cosmetics due to its properties of moisturizing and antiultraviolet. It can also be used in the pharmaceutical industry for treating various diseases. Therefore, strong protection of ectoine creates a high commercial value. Its current market value is approximately US$1000 kg-1. However, traditional ectoine production in high-salinity media causes high costs of equipment loss and wastewater treatment. There is a growing attention to reduce the salinity of the fermentation broth without sacrificing the production of ectoine. Thus, heterologous production of ectoine in nonhalophilic microorganisms may represent the new generation of the industrial production of ectoine. In this review, we summarized and discussed the biological activities of ectoine on cell and human health protection and its heterologous production.
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Affiliation(s)
- Zhi Ma
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Chutian Wu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Linjiang Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Renjie Chang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Weilin Ma
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Yanfeng Deng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Xiaolong Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
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4
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Diaz A, Jothiraman HB, Ramakrishnan V. Effect of glycerol on free DNA: A molecular dynamics simulation study. J Mol Graph Model 2022; 114:108169. [DOI: 10.1016/j.jmgm.2022.108169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
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5
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Bowater RP, Bohálová N, Brázda V. Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids. Int J Mol Sci 2022; 23:ijms23116171. [PMID: 35682854 PMCID: PMC9180970 DOI: 10.3390/ijms23116171] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023] Open
Abstract
Cruciforms occur when inverted repeat sequences in double-stranded DNA adopt intra-strand hairpins on opposing strands. Biophysical and molecular studies of these structures confirm their characterization as four-way junctions and have demonstrated that several factors influence their stability, including overall chromatin structure and DNA supercoiling. Here, we review our understanding of processes that influence the formation and stability of cruciforms in genomes, covering the range of sequences shown to have biological significance. It is challenging to accurately sequence repetitive DNA sequences, but recent advances in sequencing methods have deepened understanding about the amounts of inverted repeats in genomes from all forms of life. We highlight that, in the majority of genomes, inverted repeats are present in higher numbers than is expected from a random occurrence. It is, therefore, becoming clear that inverted repeats play important roles in regulating many aspects of DNA metabolism, including replication, gene expression, and recombination. Cruciforms are targets for many architectural and regulatory proteins, including topoisomerases, p53, Rif1, and others. Notably, some of these proteins can induce the formation of cruciform structures when they bind to DNA. Inverted repeat sequences also influence the evolution of genomes, and growing evidence highlights their significance in several human diseases, suggesting that the inverted repeat sequences and/or DNA cruciforms could be useful therapeutic targets in some cases.
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Affiliation(s)
- Richard P. Bowater
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK;
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Correspondence:
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Khavani M, Mehranfar A, Vahid H. Application of amino acid ionic liquids for increasing the stability of DNA in long term storage. J Biomol Struct Dyn 2022:1-15. [PMID: 35467487 DOI: 10.1080/07391102.2022.2067239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The structural stability of DNA is important because of its biological activity. DNAs due to their inherent chemical properties are not stable in an aqueous solution, therefore, a long period of storage of DNA at the ambient condition in bioscience is of importance. Ionic liquids (ILs) as interesting alternatives compared to organic solvents and water due to their considerable properties can be used as new agents to increase the stability of DNA for a long period of storage. In this article, molecular dynamics (MD) simulations and quantum chemistry calculations were applied to investigate the effects of amino acid ionic liquids ([BMIM][Ala], [BMIM][Gly], [BMIM][Val], [BMIM][Pro] and [BMIM][Leu]) on the dynamical behavior and the structural stability of calf thymus DNA. Based on the obtained MD results ILs enter into the solvation shell of the DNA and push away the water molecules from the DNA surface. Structural analysis shows that [BMIM]+ cations can occupy the DNA minor groove without disturbing the double-helical structure of DNA. ILs due to strong electrostatic and van der Waals (vdW) interactions with the DNA structure contribute to the stability of the double-helical structure. Quantum chemistry calculations indicate that the interactions between the [BMIM]+ cation and DNA structure has an electrostatic character. Moreover, this cation forms a more stable complex with the CGCG region of the DNA in comparison with AATT base pairs. Overall, the results of this study can provide new insight into the application of ILs for maintaining DNA stability during long-term storage.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Khavani
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, Aalto, Finland.,Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California, USA
| | - Aliyeh Mehranfar
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, Aalto, Finland
| | - Hossein Vahid
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, Aalto, Finland.,Department of Applied Physics, Aalto University, Aalto, Finland
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Dai T, Wang Y, Yang G. Visualization of DNA Damage and Protection by Atomic Force Microscopy in Liquid. Int J Mol Sci 2022; 23:ijms23084388. [PMID: 35457204 PMCID: PMC9025965 DOI: 10.3390/ijms23084388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
DNA damage is closely related to cancer and many aging-related diseases. Peroxynitrite is a strong oxidant, thus a typical DNA damage agent, and is a major mediator of the inflammation-associated pathogenesis. For the first time, we directly visualized the process of DNA damage by peroxynitrite and DNA protection by ectoine via atomic force microscopy in liquid. We found that the persistence length of DNA decreases significantly by adding a small amount of peroxynitrite, but the observed DNA chains are still intact. Specifically, the persistence length of linear DNA in a low concentration of peroxynitrite (0 µM to 200 µM) solution decreases from about 47 nm to 4 nm. For circular plasmid DNA, we observed the enhanced superhelices of plasmid DNA due to the chain soften. When the concentration of peroxynitrite was above 300 µM, we observed the fragments of DNA. Interestingly, we also identified single-stranded DNAs during the damage process, which is also confirmed by ultraviolet spectroscopy. However, if we added 500 mM ectoine to the high concentration PN solution, almost no DNA fragments due to double strand breaks were observed because of the protection of ectoine. This protection is consistent with the similar effect for DNA damage caused by ionizing radiation and oxygenation. We ascribe DNA protection to the preferential hydration of ectoine.
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Affiliation(s)
| | - Yanwei Wang
- Correspondence: (Y.W.); (G.Y.); Tel.: +86-577-8668-9033 (Y.W. & G.Y.); Fax: +86-577-8668-9010 (Y.W. & G.Y.)
| | - Guangcan Yang
- Correspondence: (Y.W.); (G.Y.); Tel.: +86-577-8668-9033 (Y.W. & G.Y.); Fax: +86-577-8668-9010 (Y.W. & G.Y.)
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Miranda-Quintana RA, Smiatek J. Electronic Properties of Protein Destabilizers and Stabilizers: Implications for Preferential Binding and Exclusion Mechanisms. J Phys Chem B 2021; 125:11857-11868. [PMID: 34672590 DOI: 10.1021/acs.jpcb.1c06295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We study the electronic properties of low-weight organic co-solutes by means of conceptual density functional theory calculations. Our results highlight the important role of certain chemical reactivity descriptors such as chemical hardness, electronegativity, nucleofugality, and the electrofugality as important criteria to classify protein stabilizers and destabilizers. Our results imply Lewis basic properties with lower chemical hardness for stabilizers, while destabilizers show higher Lewis acidity with higher chemical hardness. Further consideration of analytical calculations in terms of transfer energies reveals the crucial role of co-solute-protein interactions which significantly change the interaction pattern of the stabilizing or destabilizing species. The corresponding outcomes connect statistical thermodynamics with the electronic properties of co-solutes and also allow us to define general principles for strong stabilizers and destabilizers.
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Affiliation(s)
- Ramón Alain Miranda-Quintana
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany
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Wittmar J, Ohle C, Kunte J, Brand I. Effect of Ectoine on the Conformation and Hybridization of dsDNA in Monolayer Films: A Spectroelectrochemical Study. ChemElectroChem 2021. [DOI: 10.1002/celc.202100816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Julia Wittmar
- Department of Chemistry University of Oldenburg 26111 Oldenburg Germany
- Institute of Cell Dynamics and Imaging Westfälische Wilhelms Universität Münster 48149 Münster Germany
| | - Corina Ohle
- Division Biodeterioration and Reference Organisms Bundesanstalt für Materialforschung und -prüfung BAM 12205 Berlin Germany
- Deutsche Akkreditierungsstelle GmbH (DAkkS) Spittelmarkt 10 10117 Berlin Germany
| | - Jörg Kunte
- Division Biodeterioration and Reference Organisms Bundesanstalt für Materialforschung und -prüfung BAM 12205 Berlin Germany
| | - Izabella Brand
- Department of Chemistry University of Oldenburg 26111 Oldenburg Germany
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10
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Rasteniene A, Gruskiene R, Sereikaite J. Interaction of ectoine and hydroxyectoine with protein: fluorescence study. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01527-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Oprzeska-Zingrebe EA, Smiatek J. Interactions of a DNA G-quadruplex with TMAO and urea: a molecular dynamics study on co-solute compensation mechanisms. Phys Chem Chem Phys 2021; 23:1254-1264. [PMID: 33355575 DOI: 10.1039/d0cp05356b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We study the individual and combined influence of TMAO and urea on a basket-type DNA G-quadruplex by means of atomistic molecular dynamics (MD) simulations. In combination with the Kirkwood-Buff theory of solutions, we propose a simple mechanism to elucidate the impact of TMAO and urea on the G-quadruplex. Our results reveal the importance of the molecular accumulation around the DNA in terms of stabilizing or destabilizing effects. The results for mixtures show only a weak interaction between both co-solutes, which highlights the additivity of contributions. Despite the fact, that TMAO can to some extent compensate the adverse impact of urea on the G-quadruplex structure, the destabilizing influence is not completely eliminated. This observation opens the door for further research on selective stabilization of DNA G-quadruplexes by modulating the concentrations of TMAO and urea in solution.
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Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany.
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Wittmar J, Meyer S, Sieling T, Kunte J, Smiatek J, Brand I. What Does Ectoine Do to DNA? A Molecular-Scale Picture of Compatible Solute-Biopolymer Interactions. J Phys Chem B 2020; 124:7999-8011. [PMID: 32816487 DOI: 10.1021/acs.jpcb.0c05273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Compatible solutes accumulate in the cytoplasm of halophilic microorganisms, enabling their survival in a high-salinity environment. Ectoine is such a compatible solute. It is a zwitterionic molecule that strongly interacts with surrounding water molecules and changes the dynamics of the local hydration shell. Ectoine interacts with biomolecules such as lipids, proteins, and DNA. The molecular interaction between ectoine and biomolecules, in particular the interaction between ectoine and DNA, is far from being understood. In this paper, we describe molecular aspects of the interaction between ectoine and double-stranded DNA (dsDNA). Two 20 base pairs-long dsDNA fragments were immobilized on a gold surface via a thiol-tether. The interaction between the dsDNA monolayers with diluted and concentrated ectoine solutions was examined by means of X-ray photoelectron and polarization modulation infrared reflection absorption spectroscopies (PM IRRAS). Experimental results indicate that the ability of ectoine to bind water reduces the strength of hydrogen bonds formed to the ribose-phosphate backbone in the dsDNA. In diluted (0.1 M) ectoine solution, DNA interacts predominantly with water molecules. The sugar-phosphate backbone is involved in the formation of strong hydrogen bonds to water, which, over time, leads to a reorientation of the planes of nucleic acid bases. This reorientation destabilizes the strength of hydrogen bonds between the bases and leads to a partial dehybridization of the dsDNA. In concentrated ectoine solution (2.5 M), almost all water molecules interact with ectoine. Under this condition, ectoine is able to interact directly with DNA. Density functional theory (DFT) calculations demonstrate that the direct interaction involves the nitrogen atoms in ectoine and phosphate groups in the DNA molecule. The results of the quantum-chemical calculations show that rearrangements in the ribose-phosphate backbone, caused by a direct interaction with ectoine, facilitates contacts between the O atom in the phosphate group and H atoms in a nucleic acid base. In the PM IRRA spectra, an increase in the number of IR absorption modes in the base pair frequency region proves that the hydrogen bonds between bases become weaker. Thus, a sequence of reorientations caused by interaction with ectoine leads to a breakdown of hydrogen bonds between bases in the double helix.
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Affiliation(s)
- Julia Wittmar
- Department of Chemistry, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg, Germany
| | - Susann Meyer
- Biodeterioration and Reference Organisms, Bundesanstalt für Materialforschung und -prüfung BAM, 12205 Berlin, Germany
| | - Thorben Sieling
- Department of Chemistry, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg, Germany
| | - Jörg Kunte
- Biodeterioration and Reference Organisms, Bundesanstalt für Materialforschung und -prüfung BAM, 12205 Berlin, Germany
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Izabella Brand
- Department of Chemistry, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg, Germany
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Solomun T, Hahn MB, Smiatek J. Raman Spectroscopic Signature of Ectoine Conformations in Bulk Solution and Crystalline State. Chemphyschem 2020; 21:1945-1950. [PMID: 32628316 PMCID: PMC7540454 DOI: 10.1002/cphc.202000457] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/06/2020] [Indexed: 01/29/2023]
Abstract
Recent crystallographic results revealed conformational changes of zwitterionic ectoine upon hydration. By means of confocal Raman spectroscopy and density functional theory calculations, we present a detailed study of this transformation process as part of a Fermi resonance analysis. The corresponding findings highlight that all resonant couplings are lifted upon exposure to water vapor as a consequence of molecular binding processes. The importance of the involved molecular groups for water binding and conformational changes upon hydration is discussed. Our approach further shows that the underlying rapid process can be reversed by carbon dioxide saturated atmospheres. For the first time, we also confirm that the conformational state of ectoine in aqueous bulk solution coincides with crystalline ectoine in its dihydrate state, thereby highlighting the important role of a few bound water molecules.
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Affiliation(s)
- Tihomir Solomun
- Bundesanstalt für Materialforschung und -prüfung (BAM)12205BerlinGermany
| | - Marc Benjamin Hahn
- Bundesanstalt für Materialforschung und -prüfung (BAM)12205BerlinGermany
- Freie Universität BerlinInstitut für Experimentalphysik14195BerlinGermany
| | - Jens Smiatek
- Institut für ComputerphysikUniversität Stuttgart70569StuttgartGermany
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14
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Hahn MB, Smales GJ, Seitz H, Solomun T, Sturm H. Ectoine interaction with DNA: influence on ultraviolet radiation damage. Phys Chem Chem Phys 2020; 22:6984-6992. [PMID: 32188961 DOI: 10.1039/d0cp00092b] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Ectoine is a small zwitterionic osmolyte and compatible solute, which does not interfere with cell metabolism even at molar concentrations. Plasmid DNA (pUC19) was irradiated with ultraviolet radiation (UV-C at 266 nm) under quasi physiological conditions (PBS) and in pure water in the presence and absence of ectoine (THP(B)) and hydroxyectoine (THP(A)). Different types of UV induced DNA damage were analysed: DNA single-strand breaks (SSBs), abasic sites and cyclobutane pyrimidine dimers (CPDs). A complex interplay between these factors was observed with respect to the nature and occurrence of DNA damage with 266 nm photons. In PBS, the cosolutes showed efficient protection against base damage, whilst in pure water, a dramatic shift from SSB damage to base damage was observed when cosolutes were added. To test whether these effects are caused by ectoine binding to DNA, further experiments were conducted: small-angle X-ray scattering (SAXS), surface-plasmon resonance (SPR) measurements and Raman spectroscopy. The results show, for the first time, a close interaction between ectoine and DNA. This is in stark contrast to the assumption made by preferential exclusion models, which are often used to interpret the behaviour of compatible solutes within cells and with biomolecules. It is tentatively proposed that the alterations of UV damage to DNA are attributed to ectoine influence on nucleobases through the direct interaction between ectoine and DNA.
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Affiliation(s)
- Marc Benjamin Hahn
- Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany. and Bundesanstalt für Materialforschung und -prüfung (BAM), 12205 Berlin, Germany
| | - Glen J Smales
- Bundesanstalt für Materialforschung und -prüfung (BAM), 12205 Berlin, Germany
| | - Harald Seitz
- Universität Potsdam, Institut für Biochemie und Biologie, 14476 Potsdam, Germany and Fraunhofer Institute for Cell Therapy and Immunology, 14476 Potsdam, Germany
| | - Tihomir Solomun
- Bundesanstalt für Materialforschung und -prüfung (BAM), 12205 Berlin, Germany
| | - Heinz Sturm
- Bundesanstalt für Materialforschung und -prüfung (BAM), 12205 Berlin, Germany
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15
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Hützler WM, Mossou E, Vollrath R, Kohagen M, El Ghrissi I, Grininger M, Zaccai G, Smiatek J, Oesterhelt D. Complex transitions between dihydrate and anhydrate forms of ectoine – unexpected behavior of a highly hygroscopic compatible solute in the solid state. CrystEngComm 2020. [DOI: 10.1039/c9ce01599j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystallizing the compatible solute ectoine from water yields a metastable dihydrate that readily degrades to a highly hygroscopic anhydrate at ambient conditions; this strange behavior is examined and a rationale is presented.
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Affiliation(s)
- Wilhelm Maximilian Hützler
- Institute of Organic Chemistry and Chemical Biology
- Buchmann Institute for Molecular Life Sciences
- Goethe-University Frankfurt
- 60438 Frankfurt am Main
- Germany
| | | | - Ronnald Vollrath
- Department of Membrane Biochemistry
- Max-Planck-Institute of Biochemistry
- 82152 Martinsried
- Germany
| | - Miriam Kohagen
- Institute for Computational Physics
- University of Stuttgart
- 70569 Stuttgart
- Germany
| | | | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology
- Buchmann Institute for Molecular Life Sciences
- Goethe-University Frankfurt
- 60438 Frankfurt am Main
- Germany
| | - Giuseppe Zaccai
- Institute Laue-Langevin
- 38042 Grenoble Cedex 9
- France
- Univ. Grenoble Alpes
- CNRS
| | - Jens Smiatek
- Institute for Computational Physics
- University of Stuttgart
- 70569 Stuttgart
- Germany
| | - Dieter Oesterhelt
- Department of Membrane Biochemistry
- Max-Planck-Institute of Biochemistry
- 82152 Martinsried
- Germany
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Pica A, Graziano G. Effect of sodium thiocyanate and sodium perchlorate on poly(N-isopropylacrylamide) collapse. Phys Chem Chem Phys 2019; 22:189-195. [PMID: 31799525 DOI: 10.1039/c9cp05706d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The T(collapse) of poly(N-isopropylacrylamide), PNIPAM, shows a nonlinear dependence on the concentration of NaSCN or NaClO4; in the case of NaClO4, for example, at very low concentrations of the salt, T(collapse) increases with the concentration, while it has an opposite trend at higher NaClO4 concentrations [J. Am. Chem. Soc., 2005, 127, 14505]. These puzzling experimental data can be rationalized by considering that low charge density and poorly hydrated ions, such as thiocyanate and perchlorate, interact preferentially with the surface of the polymer, and cause an increase of the magnitude of the energetic term that stabilizes swollen conformations at low salt concentrations. However, as both swollen and collapsed PNIPAM conformations are accessible to such ions in view of their large conformational freedom, the difference in the number of ions bound to PNIPAM surface upon collapse changes little on increasing the salt concentration. Thus, the energetic term that favors swollen conformations increases with salt concentration to a lesser extent than the solvent-excluded volume term (linked to the density increase caused by salt addition to water), that favors collapsed conformations, leading to a nonlinear trend of T(collapse).
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Affiliation(s)
- Andrea Pica
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, Grenoble, France
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Kou SB, Lou YY, Zhou KL, Wang BL, Lin ZY, Shi JH. In vitro exploration of interaction behavior between calf thymus DNA and fenhexamid with the help of multi-spectroscopic methods and molecular dynamics simulations. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.112067] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Brands S, Schein P, Castro-Ochoa KF, Galinski EA. Hydroxyl radical scavenging of the compatible solute ectoine generates two N-acetimides. Arch Biochem Biophys 2019; 674:108097. [DOI: 10.1016/j.abb.2019.108097] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/26/2019] [Accepted: 09/02/2019] [Indexed: 11/16/2022]
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Oprzeska-Zingrebe EA, Smiatek J. Some Notes on the Thermodynamic Accuracy of Coarse-Grained Models. Front Mol Biosci 2019; 6:87. [PMID: 31552269 PMCID: PMC6746972 DOI: 10.3389/fmolb.2019.00087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/27/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ewa Anna Oprzeska-Zingrebe
- Institute for Computational Physics, Theoretical Chemical Physics, University of Stuttgart, Stuttgart, Germany
| | - Jens Smiatek
- Institute for Computational Physics, Theoretical Chemical Physics, University of Stuttgart, Stuttgart, Germany
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20
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Oprzeska-Zingrebe EA, Smiatek J. Aqueous Mixtures of Urea and Trimethylamine-N-oxide: Evidence for Kosmotropic or Chaotropic Behavior? J Phys Chem B 2019; 123:4415-4424. [PMID: 31046272 DOI: 10.1021/acs.jpcb.9b02598] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Trimethylamine-N-oxide (TMAO) and urea are commonly produced in many extremophilic microorganisms that live in harsh environments. In view of high temperature, high pressure, or high salt content, TMAO is known as a protein structure stabilizer, whereas urea destabilizes protein structures even under ambient conditions. Despite clear evidence, destabilizers are often regarded as chaotropes, meaning water-structure breakers, whereas kosmotropes as water-structure makers are classified as stabilizers. Using atomistic molecular dynamics simulations, we study aqueous mixtures of TMAO and urea in various biologically relevant concentrations to gain insight into the molecular details of their mutual cross-interactions and their influence on water dynamics and structure. Our results for binary and ternary solutions in combination with different mixing ratios show that both co-solutes strengthen the water network in terms of dynamic and structural aspects. Slight differences in the water binding behavior between both species result in only negligible compensation effects. The outcomes of our simulations thus question the validity and the ill-considered use of attributes like kosmotropic or chaotropic substances for stabilizers and destabilizers.
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Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics , University of Stuttgart , D-70569 Stuttgart , Germany.,Helmholtz-Institute Münster: Ionics in Energy Storage (HIMS-IEK 12) , Forschungszentrum Jülich GmbH , D-48149 Münster , Germany
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21
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Chen B, Wang Y, Yang G. The promotion and suppression of DNA charge neutralization by the cosolute ectoine. RSC Adv 2019; 9:41050-41057. [PMID: 35540047 PMCID: PMC9076405 DOI: 10.1039/c9ra09355a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/27/2019] [Indexed: 12/28/2022] Open
Abstract
Ectoine, a cosolute and osmolyte, is used by extremophilic microorganisms to maintain an osmotic equilibrium of cells with their surrounding medium under conditions of extreme salinity or thermal and pressure stresses. It is also considered a protectant of biomolecules such as protein and DNA in cells. In the present study, we investigate its influence on DNA charge neutralization and compaction through dynamic light scattering (DLS), atomic force microscopy (AFM) and single molecular magnetic tweezers (MT). We found that ectoine can promote DNA charge neutralization induced by multivalent cations at mild cosolute concentration in solution. When the concentration of ectoine is high enough, however, a mixed effect of promotion and suppression can be found under the same ionic conditions. In this case, the electrophoretic mobility (EM) of DNA is promoted in the region of low cation concentration, while suppressed in the region of high counterionic concentration. The charge neutralization of DNA by ectoine is also related to DNA compaction. The promotion and suppression of DNA compaction by ectoine was observed by AFM imaging. The condensed structure of DNA becomes more compact and then loose once more with the increasing concentration of ectoine. Meanwhile, the condensing forces of DNA measured by magnetic tweezers shows the same trend as does the DNA EM. We explained the experimental findings through the combined effect of two intrinsic features of ectoine, preferential exclusion and enhancement of the dielectric constant of the medium. Ectoine can promote DNA charge neutralization at mild cosolute concentration in solution. When the concentration of ectoine is high enough, however, a mixing effect of promotion and suppression can be found in the same ionic condition.![]()
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Affiliation(s)
- Benteng Chen
- Department of Physics
- Wenzhou University
- Wenzhou
- China
| | - Yanwei Wang
- Department of Physics
- Wenzhou University
- Wenzhou
- China
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