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Hansen T, Lee J, Reicher N, Ovadia G, Guo S, Guo W, Liu J, Braslavsky I, Rudich Y, Davies PL. Ice nucleation proteins self-assemble into large fibres to trigger freezing at near 0 °C. eLife 2023; 12:RP91976. [PMID: 38109272 PMCID: PMC10727499 DOI: 10.7554/elife.91976] [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] [Indexed: 12/20/2023] Open
Abstract
In nature, frost can form at a few degrees below 0 °C. However, this process requires the assembly of tens of thousands of ice-like water molecules that align together to initiate freezing at these relatively high temperatures. Water ordering on this scale is mediated by the ice nucleation proteins (INPs) of common environmental bacteria like Pseudomonas syringae and Pseudomonas borealis. However, individually, these 100 kDa proteins are too small to organize enough water molecules for frost formation, and it is not known how giant, megadalton-sized multimers, which are crucial for ice nucleation at high sub-zero temperatures, form. The ability of multimers to self-assemble was suggested when the transfer of an INP gene into Escherichia coli led to efficient ice nucleation. Here, we demonstrate that a positively charged subdomain at the C-terminal end of the central β-solenoid of the INP is crucial for multimerization. Truncation, relocation, or change of the charge of this subdomain caused a catastrophic loss of ice nucleation ability. Cryo-electron tomography of the recombinant E. coli showed that the INP multimers form fibres that are ~5 nm across and up to 200 nm long. A model of these fibres as an overlapping series of antiparallel dimers can account for all their known properties and suggests a route to making cell-free ice nucleators for biotechnological applications.
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Affiliation(s)
- Thomas Hansen
- Department of Biomedical and Molecular Sciences, Queen’s UniversityKingstonCanada
| | - Jocelyn Lee
- Department of Biomedical and Molecular Sciences, Queen’s UniversityKingstonCanada
| | - Naama Reicher
- Department of Earth and Planetary Sciences, The Weizmann Institute of ScienceRehovotIsrael
| | - Gil Ovadia
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science, and Nutrition, The Hebrew University of JerusalemRehovotIsrael
| | - Shuaiqi Guo
- Department of Microbial Pathogenesis, Yale University School of MedicineNew HavenUnited States
| | - Wangbiao Guo
- Department of Microbial Pathogenesis, Yale University School of MedicineNew HavenUnited States
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University School of MedicineNew HavenUnited States
| | - Ido Braslavsky
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science, and Nutrition, The Hebrew University of JerusalemRehovotIsrael
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, The Weizmann Institute of ScienceRehovotIsrael
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen’s UniversityKingstonCanada
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Hansen T, Lee JC, Reicher N, Ovadia G, Guo S, Guo W, Liu J, Braslavsky I, Rudich Y, Davies PL. Ice nucleation proteins self-assemble into large fibres to trigger freezing at near 0 °C. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551873. [PMID: 37577566 PMCID: PMC10418271 DOI: 10.1101/2023.08.03.551873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
In nature, frost can form at a few degrees below 0 °C. However, this process requires the assembly of tens of thousands of ice-like water molecules that align together to initiate freezing at these relatively high temperatures. Water ordering on this scale is mediated by the ice nucleation proteins of common environmental bacteria like Pseudomonas syringae and P. borealis. However, individually, these 100-kDa proteins are too small to organize enough water molecules for frost formation, and it is not known how giant, megadalton-sized multimers, which are crucial for ice nucleation at high sub-zero temperatures, form. The ability of multimers to self-assemble was suggested when the transfer of an ice nucleation protein gene into Escherichia coli led to efficient ice nucleation. Here we demonstrate that a positively-charged sub-domain at the C-terminal end of the central beta-solenoid of the ice nucleation protein is crucial for multimerization. Truncation, relocation, or change of the charge of this subdomain caused a catastrophic loss of ice nucleation ability. Cryo-electron tomography of the recombinant E. coli showed that the ice nucleation protein multimers form fibres that are ~ 5 nm across and up to 200 nm long. A model of these fibres as an overlapping series of antiparallel dimers can account for all their known properties and suggests a route to making cell-free ice nucleators for biotechnological applications.
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Affiliation(s)
- Thomas Hansen
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON Canada K7L 3N6
| | - Jocelyn C. Lee
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON Canada K7L 3N6
| | - Naama Reicher
- Department of Earth and Planetary Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gil Ovadia
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science, and Nutrition, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Shuaiqi Guo
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536
| | - Wangbiao Guo
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536
| | - Ido Braslavsky
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science, and Nutrition, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Peter L. Davies
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON Canada K7L 3N6
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Water-organizing motif continuity is critical for potent ice nucleation protein activity. Nat Commun 2022; 13:5019. [PMID: 36028506 PMCID: PMC9418140 DOI: 10.1038/s41467-022-32469-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/29/2022] [Indexed: 12/02/2022] Open
Abstract
Bacterial ice nucleation proteins (INPs) can cause frost damage to plants by nucleating ice formation at high sub-zero temperatures. Modeling of Pseudomonas borealis INP by AlphaFold suggests that the central domain of 65 tandem sixteen-residue repeats forms a beta-solenoid with arrays of outward-pointing threonines and tyrosines, which may organize water molecules into an ice-like pattern. Here we report that mutating some of these residues in a central segment of P. borealis INP, expressed in Escherichia coli, decreases ice nucleation activity more than the section’s deletion. Insertion of a bulky domain has the same effect, indicating that the continuity of the water-organizing repeats is critical for optimal activity. The ~10 C-terminal coils differ from the other 55 coils in being more basic and lacking water-organizing motifs; deletion of this region eliminates INP activity. We show through sequence modifications how arrays of conserved motifs form the large ice-nucleating surface required for potency. Ice nucleation proteins have the same tandemly arrayed water-organizing motifs seen in some antifreeze proteins, but on a larger scale. The authors show that mutation, interruption, and truncation of these arrays reduce ice nucleation activity indicating that the two protein types share a common mechanism.
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Roeters SJ, Golbek TW, Bregnhøj M, Drace T, Alamdari S, Roseboom W, Kramer G, Šantl-Temkiv T, Finster K, Pfaendtner J, Woutersen S, Boesen T, Weidner T. Ice-nucleating proteins are activated by low temperatures to control the structure of interfacial water. Nat Commun 2021; 12:1183. [PMID: 33608518 PMCID: PMC7895962 DOI: 10.1038/s41467-021-21349-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 01/22/2021] [Indexed: 11/17/2022] Open
Abstract
Ice-nucleation active (INA) bacteria can promote the growth of ice more effectively than any other known material. Using specialized ice-nucleating proteins (INPs), they obtain nutrients from plants by inducing frost damage and, when airborne in the atmosphere, they drive ice nucleation within clouds, which may affect global precipitation patterns. Despite their evident environmental importance, the molecular mechanisms behind INP-induced freezing have remained largely elusive. We investigate the structural basis for the interactions between water and the ice-nucleating protein InaZ from the INA bacterium Pseudomonas syringae. Using vibrational sum-frequency generation (SFG) and two-dimensional infrared spectroscopy, we demonstrate that the ice-active repeats of InaZ adopt a β-helical structure in solution and at water surfaces. In this configuration, interaction between INPs and water molecules imposes structural ordering on the adjacent water network. The observed order of water increases as the interface is cooled to temperatures close to the melting point of water. Experimental SFG data combined with molecular-dynamics simulations and spectral calculations show that InaZ reorients at lower temperatures. This reorientation can enhance water interactions, and thereby the effectiveness of ice nucleation. Ice-nucleating proteins promote ice formation at high sub-zero temperatures, but the mechanism is still unclear. The authors investigate a model ice-nucleating protein at the air-water interface using vibrational sum frequency generation spectroscopy and simulations, revealing its reorientation at low temperatures, which increases contact with water molecules and promotes their ordering.
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Affiliation(s)
- Steven J Roeters
- Department of Chemistry, Aarhus University, Aarhus C, Denmark.,Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Mikkel Bregnhøj
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Taner Drace
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Sarah Alamdari
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Winfried Roseboom
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Gertjan Kramer
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Tina Šantl-Temkiv
- Department of Biology, Aarhus University, Aarhus C, Denmark.,The Stellar Astrophysics Centre - SAC, Department of Physics and Astronomy, Aarhus University, Aarhus C, Denmark
| | - Kai Finster
- Department of Biology, Aarhus University, Aarhus C, Denmark.,The Stellar Astrophysics Centre - SAC, Department of Physics and Astronomy, Aarhus University, Aarhus C, Denmark
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Sander Woutersen
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Thomas Boesen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark.,Interdisciplinary Nanoscience Center - iNano, Aarhus University, Aarhus C, Denmark
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Aarhus C, Denmark. .,Department of Chemical Engineering, University of Washington, Seattle, WA, USA. .,Interdisciplinary Nanoscience Center - iNano, Aarhus University, Aarhus C, Denmark.
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