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Schindl A, Hagen ML, Cooley I, Jäger CM, Warden AC, Zelzer M, Allers T, Croft AK. Ion-combination specific effects driving the enzymatic activity of halophilic alcohol dehydrogenase 2 from Haloferax volcanii in aqueous ionic liquid solvent mixtures. RSC SUSTAINABILITY 2024; 2:2559-2580. [PMID: 39211508 PMCID: PMC11353702 DOI: 10.1039/d3su00412k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 06/30/2024] [Indexed: 09/04/2024]
Abstract
Biocatalysis in ionic liquids enables novel routes for bioprocessing. Enzymes derived from extremophiles promise greater stability and activity under ionic liquid (IL) influence. Here, we probe the enzyme alcohol dehydrogenase 2 from the halophilic archaeon Haloferax volcanii in thirteen different ion combinations for relative activity and analyse the results against molecular dynamics (MD) simulations of the same IL systems. We probe the ionic liquid property space based on ion polarizability and molecular electrostatic potential. Using the radial distribution functions, survival probabilities and spatial distribution functions of ions, we show that cooperative ion-ion interactions determine ion-protein interactions, and specifically, strong ion-ion interactions equate to higher enzymatic activity if neither of the ions interact strongly with the protein surface. We further demonstrate a tendency for cations interacting with the protein surface to be least detrimental to enzymatic activity if they show a low polarizability when combined with small hydrophilic anions. We also find that the IL ion influence is not mitigated by the surplus of negatively charged residues of the halophilic enzyme. This is shown by free energy landscape analysis in root mean square deviation and distance variation plots of active site gating residues (Trp43 and His273) demonstrating no protection of specific structural elements relevant to preserving enzymatic activity. On the other hand, we observe a general effect across all IL systems that a tight binding of water at acidic residues is preferentially interrupted at these residues through the increased presence of potassium ions. Overall, this study demonstrates a co-ion interaction dependent influence on allosteric surface residues controlling the active/inactive conformation of halophilic alcohol dehydrogenase 2 and the necessity to engineer ionic liquid systems for enzymes that rely on the integrity of functional surface residues regardless of their halophilicity or thermophilicity for use in bioprocessing.
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Affiliation(s)
- Alexandra Schindl
- Sustainable Process Technologies Group, Department of Chemical and Environmental Engineering, University of Nottingham Nottingham NG7 2RD UK
- School of Pharmacy, University of Nottingham, University Park Campus Nottingham NG7 2RD UK
- School of Life Sciences, University of Nottingham, Queen's Medical Centre Nottingham NG7 2UH UK
- School of Molecular and Cellular Biology, University of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds Leeds LS2 9JT UK
| | - M Lawrence Hagen
- Sustainable Process Technologies Group, Department of Chemical and Environmental Engineering, University of Nottingham Nottingham NG7 2RD UK
| | - Isabel Cooley
- Department of Chemical Engineering, Loughborough University LE11 3TU UK
| | - Christof M Jäger
- Sustainable Process Technologies Group, Department of Chemical and Environmental Engineering, University of Nottingham Nottingham NG7 2RD UK
- Data Science and Modelling, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg Pepparedsleden 1 SE-431 83 Mölndal Sweden
| | - Andrew C Warden
- CSIRO Environment, Commonwealth Scientific and Industrial Research Organization (CSIRO), Research and Innovation Park Acton Canberra ACT 2600 Australia
- Advanced Engineering Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Research and Innovation Park Acton Canberra ACT 2600 Australia
| | - Mischa Zelzer
- School of Pharmacy, University of Nottingham, University Park Campus Nottingham NG7 2RD UK
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre Nottingham NG7 2UH UK
| | - Anna K Croft
- Department of Chemical Engineering, Loughborough University LE11 3TU UK
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2
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Subramaniam P, Michael HSR, Subiramanian SR, Karthikeyan N, Natarajan M, Sivaraman RK, Anguraj A, Kumar CR. Reduction of oxidative rancidification of fungal melanin-coated films in pork lard preservation in trading. Int Microbiol 2024:10.1007/s10123-024-00585-9. [PMID: 39167295 DOI: 10.1007/s10123-024-00585-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 08/13/2024] [Accepted: 08/13/2024] [Indexed: 08/23/2024]
Abstract
Storage of meat has always been challenging due to its deterioration caused by oxidative rancidity and microbial activity, especially in trading. The melanin-coated film acts as a potent antioxidant, prevents the oxidation of fatty acids, and neutralizes the reactive oxygen species (ROS) helping to withstand or perpetuate the oxidative stress of meat. This study emphasizes the production of fungal melanin extracted from Curvularia lunata and the preparation of two different melanin film combinations of gelatin/melanin and agar/melanin at 0.1% and 0.5% formulation for rancidity stability of coated pork lard. Interpretations revealed the delayed rancidity in both peroxide and acid values with 5.76% in 0.5% agar-coated melanin up to the 11th day which was supported by arithmetical analysis showing p < 0.05 are statistically significant. Further, upon testing the brine shrimp assay for melanin toxicity, 7% were in a mortal state at 1000 µg/mL concentration, considered zero lethality. This result implies that modified coatings, particularly when trading meats, that include fungal melanin can effectively prevent the oxidation of pork lard.
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Affiliation(s)
- Ponnusamy Subramaniam
- PG and Research Centre in Botany, Arignar Anna Government Arts College, Namakkal, India
| | - Helan Soundra Rani Michael
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamil Nadu, India.
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Coimbatore, Tamil Nadu, India.
| | - Shri Ranjini Subiramanian
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Coimbatore, Tamil Nadu, India
| | - Naresh Karthikeyan
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Coimbatore, Tamil Nadu, India
| | - Mani Natarajan
- Department of Mathematics, Sri Ramakrishna College of Arts & Science, Coimbatore, Tamil Nadu, India
| | - Rathish Kumar Sivaraman
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Coimbatore, Tamil Nadu, India
| | - Aswini Anguraj
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Coimbatore, Tamil Nadu, India
| | - Charu Ramesh Kumar
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Coimbatore, Tamil Nadu, India
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3
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Herrero‐Alfonso P, Pejenaute A, Millet O, Ortega‐Quintanilla G. Electrostatics introduce a trade-off between mesophilic stability and adaptation in halophilic proteins. Protein Sci 2024; 33:e5003. [PMID: 38747380 PMCID: PMC11094771 DOI: 10.1002/pro.5003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/22/2024] [Accepted: 04/12/2024] [Indexed: 05/19/2024]
Abstract
Extremophile organisms have adapted to extreme physicochemical conditions. Halophilic organisms, in particular, survive at very high salt concentrations. To achieve this, they have engineered the surface of their proteins to increase the number of short, polar and acidic amino acids, while decreasing large, hydrophobic and basic residues. While these adaptations initially decrease protein stability in the absence of salt, they grant halophilic proteins remarkable stability in environments with extremely high salt concentrations, where non-adapted proteins unfold and aggregate. The molecular mechanisms by which halophilic proteins achieve this, however, are not yet clear. Here, we test the hypothesis that the halophilic amino acid composition destabilizes the surface of the protein, but in exchange improves the stability in the presence of salts. To do that, we have measured the folding thermodynamics of various protein variants with different degrees of halophilicity in the absence and presence of different salts, and at different pH values to tune the ionization state of the acidic amino acids. Our results show that halophilic amino acids decrease the stability of halophilic proteins under mesophilic conditions, but in exchange improve salt-induced stabilization and solubility. We also find that, in contrast to traditional assumptions, contributions arising from hydrophobic effect and preferential ion exclusion are more relevant for haloadaptation than electrostatics. Overall, our findings suggest a trade-off between folding thermodynamics and halophilic adaptation to optimize proteins for hypersaline environments.
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Affiliation(s)
- Pablo Herrero‐Alfonso
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences CIC bioGUNEBizkaia Science and Technology ParkDerioSpain
| | - Alba Pejenaute
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences CIC bioGUNEBizkaia Science and Technology ParkDerioSpain
- Tekniker, Basque Research and Technology Alliance (BRTA)EibarSpain
| | - Oscar Millet
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences CIC bioGUNEBizkaia Science and Technology ParkDerioSpain
| | - Gabriel Ortega‐Quintanilla
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences CIC bioGUNEBizkaia Science and Technology ParkDerioSpain
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
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4
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Young IN, Jimenez VM. Short communication: Investigating optimal laboratory growth conditions of Gracilibacillus halotolerans in media supplemented with salt. J Microbiol Methods 2024; 219:106892. [PMID: 38311183 DOI: 10.1016/j.mimet.2024.106892] [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] [Received: 12/22/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Gracilibacillus halotolerans, a new and relatively unstudied extremophile, extracted from the Great Salt Lake USA, survives in an extreme saline environment. Uncovering optimal laboratory growth conditions can be useful to improve treatment strategies against antibiotic resistance and biofilm formation. In the current study, G. halotolerans growth optimization was tested to determine the ideal saline concentration. In addition, a variety of G. halotolerans'-derived survival strategies were reviewed. The major findings of the current study includes the optimal laboratory growth condition for G. halotolerans that requires the supplement of 5% NaCl. In addition, optimal growth was observed up to 72 h in Luria Bertani (LB) broth. Identifying the optimal laboratory growth conditions for G. halotolerans will standardize growth methods, reduce laboratory cost, and can improve future investigations of extremophile bacteria as model organisms to combat antibiotic resistance, biofilm, and other persister cell characteristics that negatively affect research and clinical settings.
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Affiliation(s)
- Isaac N Young
- Department of Biomedical Sciences, Noorda College of Osteopathic Medicine 2162 S 180 E, Provo, UT 84606, United States of America
| | - Victor M Jimenez
- Department of Biomedical Sciences, Noorda College of Osteopathic Medicine 2162 S 180 E, Provo, UT 84606, United States of America; Department of Pharmacy, Roseman University of Health Sciences, 10920 S River Front Pkwy, South Jordan, UT 84095, United States of America.
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Amangeldina A, Tan ZW, Berezovsky IN. Living in trinity of extremes: Genomic and proteomic signatures of halophilic, thermophilic, and pH adaptation. Curr Res Struct Biol 2024; 7:100129. [PMID: 38327713 PMCID: PMC10847869 DOI: 10.1016/j.crstbi.2024.100129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Since nucleic acids and proteins of unicellular prokaryotes are directly exposed to extreme environmental conditions, it is possible to explore the genomic-proteomic compositional determinants of molecular mechanisms of adaptation developed by them in response to harsh environmental conditions. Using a wealth of currently available complete genomes/proteomes we were able to explore signatures of adaptation to three environmental factors, pH, salinity, and temperature, observing major trends in compositions of their nucleic acids and proteins. We derived predictors of thermostability, halophilic, and pH adaptations and complemented them by the principal components analysis. We observed a clear difference between thermophilic and salinity/pH adaptations, whereas latter invoke seemingly overlapping mechanisms. The genome-proteome compositional trade-off reveals an intricate balance between the work of base paring and base stacking in stabilization of coding DNA and r/tRNAs, and, at the same time, universal requirements for the stability and foldability of proteins regardless of the nucleotide biases. Nevertheless, we still found hidden fingerprints of ancient evolutionary connections between the nucleotide and amino acid compositions indicating their emergence, mutual evolution, and adjustment. The evolutionary perspective on the adaptation mechanisms is further studied here by means of the comparative analysis of genomic/proteomic traits of archaeal and bacterial species. The overall picture of genomic/proteomic signals of adaptation obtained here provides a foundation for future engineering and design of functional biomolecules resistant to harsh environments.
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Affiliation(s)
- Aidana Amangeldina
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore
| | - Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Igor N. Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore
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6
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Geraili Daronkola H, Vila Verde A. Prevalence and mechanism of synergistic carboxylate-cation-water interactions in halophilic proteins. Biophys J 2023; 122:2577-2589. [PMID: 37179455 PMCID: PMC10323026 DOI: 10.1016/j.bpj.2023.05.011] [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: 02/23/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023] Open
Abstract
The cytoplasmic proteins of some halophilic organisms remain stable and functional at multimolar concentrations of KCl, i.e., under conditions that most mesophilic proteins cannot withstand. Their stability arises from their unusual amino acid composition. The most dramatic difference between halophilic and mesophilic proteins is that the former are rich in acidic amino acids. It has been proposed that one of the evolutionary driving forces for this difference is the occurrence of synergistic interactions between multiple acidic amino acids at the surface of the protein, the potassium cations in solution, and water. We investigate this possibility with molecular dynamics simulations, using high-quality force fields for the protein-water, protein-ion, and ion-ion interactions. We create a rigorous thermodynamic definition of interactions between acidic amino acids on proteins that can be used to distinguish between synergistic, noninteracting and interfering interactions. Our results demonstrate that synergistic interactions between neighboring acidic amino acids in halophilic proteins are frequent at multimolar KCl concentration. Synergistic interactions have an electrostatic origin, and are associated with stronger water-to-carboxylate hydrogen bonds than for acidic amino acids without synergistic interactions. Synergistic interactions are not observed in minimal systems of carboxylates, indicating that the protein environment is critical for their emergence. Our results demonstrate that synergistic interactions are neither associated with rigid amino acid orientations nor with highly structured and slow moving water networks, as had been originally proposed. Moreover, synergistic interactions can also be found in unfolded protein conformations. However, because these conformations are only a small subset of the unfolded state ensemble, synergistic interactions should contribute to the net stabilization of the folded state.
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Affiliation(s)
- Hosein Geraili Daronkola
- Max Planck Institute of Colloids and Interfaces, Department of Theory & Bio-Systems, Potsdam, Germany
| | - Ana Vila Verde
- Max Planck Institute of Colloids and Interfaces, Department of Theory & Bio-Systems, Potsdam, Germany.
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7
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Knop JM, Mukherjee S, Jaworek MW, Kriegler S, Manisegaran M, Fetahaj Z, Ostermeier L, Oliva R, Gault S, Cockell CS, Winter R. Life in Multi-Extreme Environments: Brines, Osmotic and Hydrostatic Pressure─A Physicochemical View. Chem Rev 2023; 123:73-104. [PMID: 36260784 DOI: 10.1021/acs.chemrev.2c00491] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Elucidating the details of the formation, stability, interactions, and reactivity of biomolecular systems under extreme environmental conditions, including high salt concentrations in brines and high osmotic and high hydrostatic pressures, is of fundamental biological, astrobiological, and biotechnological importance. Bacteria and archaea are able to survive in the deep ocean or subsurface of Earth, where pressures of up to 1 kbar are reached. The deep subsurface of Mars may host high concentrations of ions in brines, such as perchlorates, but we know little about how these conditions and the resulting osmotic stress conditions would affect the habitability of such environments for cellular life. We discuss the combined effects of osmotic (salts, organic cosolvents) and hydrostatic pressures on the structure, stability, and reactivity of biomolecular systems, including membranes, proteins, and nucleic acids. To this end, a variety of biophysical techniques have been applied, including calorimetry, UV/vis, FTIR and fluorescence spectroscopy, and neutron and X-ray scattering, in conjunction with high pressure techniques. Knowledge of these effects is essential to our understanding of life exposed to such harsh conditions, and of the physical limits of life in general. Finally, we discuss strategies that not only help us understand the adaptive mechanisms of organisms that thrive in such harsh geological settings but could also have important ramifications in biotechnological and pharmaceutical applications.
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Affiliation(s)
- Jim-Marcel Knop
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Sanjib Mukherjee
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Michel W Jaworek
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Simon Kriegler
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Magiliny Manisegaran
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Zamira Fetahaj
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Lena Ostermeier
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Rosario Oliva
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany.,Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126Naples, Italy
| | - Stewart Gault
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, EH9 3FDEdinburgh, United Kingdom
| | - Charles S Cockell
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, EH9 3FDEdinburgh, United Kingdom
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
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