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Bieber P, Borduas-Dedekind N. High-speed cryo-microscopy reveals that ice-nucleating proteins of Pseudomonas syringae trigger freezing at hydrophobic interfaces. SCIENCE ADVANCES 2024; 10:eadn6606. [PMID: 38959312 PMCID: PMC11221516 DOI: 10.1126/sciadv.adn6606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/22/2024] [Indexed: 07/05/2024]
Abstract
Ice-nucleating proteins (INpro) trigger the freezing of supercooled water droplets relevant to atmospheric, biological, and technological applications. The high ice nucleation activity of INpro isolated from the bacteria Pseudomonas syringae could be linked to the aggregation of proteins at the bacterial membrane or at the air-water interface (AWI) of droplets. Here, we imaged freezing onsets, providing direct evidence of these proposed mechanisms. High-speed cryo-microscopy identified the onset location of freezing in droplets between two protein-repellent glass slides. INpro from sterilized P. syringae (Snomax) statistically favored nucleation at the AWI of the droplets. Removing cellular fragments by filtration or adding surfactants increased the frequency of nucleation events at the AWI. On the other hand, cultivated intact bacteria cells or lipid-free droplets nucleated ice without an affinity to the AWI. Overall, we provide visual evidence that INpro from P. syringae trigger freezing at hydrophobic interfaces, such as the AWI or the bacterial membrane, with important mechanistic implications for applications of INpro.
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2
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Schwidetzky R, de Almeida Ribeiro I, Bothen N, Backes AT, DeVries AL, Bonn M, Fröhlich-Nowoisky J, Molinero V, Meister K. Functional aggregation of cell-free proteins enables fungal ice nucleation. Proc Natl Acad Sci U S A 2023; 120:e2303243120. [PMID: 37943838 PMCID: PMC10655213 DOI: 10.1073/pnas.2303243120] [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: 02/28/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023] Open
Abstract
Biological ice nucleation plays a key role in the survival of cold-adapted organisms. Several species of bacteria, fungi, and insects produce ice nucleators (INs) that enable ice formation at temperatures above -10 °C. Bacteria and fungi produce particularly potent INs that can promote water crystallization above -5 °C. Bacterial INs consist of extended protein units that aggregate to achieve superior functionality. Despite decades of research, the nature and identity of fungal INs remain elusive. Here, we combine ice nucleation measurements, physicochemical characterization, numerical modeling, and nucleation theory to shed light on the size and nature of the INs from the fungus Fusarium acuminatum. We find ice-binding and ice-shaping activity of Fusarium IN, suggesting a potential connection between ice growth promotion and inhibition. We demonstrate that fungal INs are composed of small 5.3 kDa protein subunits that assemble into ice-nucleating complexes that can contain more than 100 subunits. Fusarium INs retain high ice-nucleation activity even when only the ~12 kDa fraction of size-excluded proteins are initially present, suggesting robust pathways for their functional aggregation in cell-free aqueous environments. We conclude that the use of small proteins to build large assemblies is a common strategy among organisms to create potent biological INs.
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Affiliation(s)
- Ralph Schwidetzky
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Mainz55128, Germany
| | | | - Nadine Bothen
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz55128, Germany
| | - Anna T. Backes
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz55128, Germany
| | - Arthur L. DeVries
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Mischa Bonn
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Mainz55128, Germany
| | | | - Valeria Molinero
- Department of Chemistry, The University of Utah, Salt Lake City, UT84112
| | - Konrad Meister
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Mainz55128, Germany
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID83725
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3
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Eufemio RJ, de Almeida Ribeiro I, Sformo TL, Laursen GA, Molinero V, Fröhlich-Nowoisky J, Bonn M, Meister K. Lichen species across Alaska produce highly active and stable ice nucleators. BIOGEOSCIENCES (ONLINE) 2023; 20:2805-2812. [PMID: 38818347 PMCID: PMC11138219 DOI: 10.5194/bg-20-2805-2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Forty years ago, lichens were identified as extraordinary biological ice nucleators (INs) that enable ice formation at temperatures close to 0°C. By employing INs, lichens thrive in freezing environments that surpass the physiological limits of other vegetation, thus making them the majority of vegetative biomass in northern ecosystems. Aerosolized lichen INs might further impact cloud glaciation and have the potential to alter atmospheric processes in a warming Arctic. Despite the ecological importance and formidable ice nucleation activities, the abundance, diversity, sources, and role of ice nucleation in lichens remain poorly understood. Here, we investigate the ice nucleation capabilities of lichens collected from various ecosystems across Alaska. We find ice-nucleating activity in lichen to be widespread, particularly in the coastal rainforest of Southeast Alaska. Across 29 investigated lichen, all species show ice nucleation temperatures above -15 °C and ~30% initiate freezing at temperatures above -6 °C. Concentration series of lichen ice nucleation assays in combination with statistical analysis reveal that the lichens contain two subpopulations of INs, similar to previous observations in bacteria. However, unlike the bacterial INs, the lichen INs appear as independent subpopulations resistant to freeze-thaw cycles and against temperature treatment. The ubiquity and high stability of the lichen INs suggest that they can impact local atmospheric processes and that ice nucleation activity is an essential trait for their survival in cold environments.
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Affiliation(s)
- Rosemary J. Eufemio
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID 83725, USA
- Biomolecular Sciences Graduate Programs, Boise State University, Boise, ID 83725, USA
| | | | - Todd L. Sformo
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Gary A. Laursen
- High Latitude Mycological Research Institute, University of Montana, Missoula, MT 59801, USA
| | | | | | - Mischa Bonn
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Konrad Meister
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID 83725, USA
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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4
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Tomalty HE, Graham LA, Walker VK, Davies PL. Chilling injury in human kidney tubule cells after subzero storage is not mitigated by antifreeze protein addition. Cryobiology 2023:S0011-2240(23)00034-2. [PMID: 37164251 DOI: 10.1016/j.cryobiol.2023.05.002] [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: 12/02/2022] [Revised: 03/26/2023] [Accepted: 05/06/2023] [Indexed: 05/12/2023]
Abstract
By preventing freezing, antifreeze proteins (AFPs) can permit cells and organs to be stored at subzero temperatures. As metabolic rates decrease with decreasing temperature, subzero static cold storage (SZ-SCS) could provide more time for tissue matching and potentially lead to fewer discarded organs. Human kidneys are generally stored for under 24 h and the tubule epithelium is known to be particularly sensitive to static cold storage (SCS). Here, telomerase-immortalized proximal-tubule epithelial cells from humans, which closely resemble their progenitors, were used as a proxy to assess the potential benefit of SZ-SCS for kidneys. The effects of hyperactive AFPs from a beetle and Cryostasis Storage Solution were compared to University of Wisconsin Solution at standard SCS temperatures (4 °C) and at -6 °C for up to six days. Although the AFPs helped guard against freezing, lower storage temperatures under these conditions were not beneficial. Compared to cells at 4 °C, those stored at -6 °C showed decreased viability as well as increased lactate dehydrogenase release and apoptosis. This suggests that this kidney cell type might be prone to chilling injury and that the addition of AFPs to enable SZ-SCS may not be effective for increasing storage times.
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Affiliation(s)
- Heather E Tomalty
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
| | - Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
| | - Virginia K Walker
- Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
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5
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Lindow S. History of Discovery and Environmental Role of Ice Nucleating Bacteria. PHYTOPATHOLOGY 2023; 113:605-615. [PMID: 36122194 DOI: 10.1094/phyto-07-22-0256-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The phenomenon of biological ice nucleation that is exhibited by a variety of bacteria is a fascinating phenotype, which has been shown to incite frost damage to frost-sensitive plants and has been proposed to contribute to atmospheric processes that affect the water cycle and earth's radiation balance. This review explores the several possible drivers for the evolutionary origin of the ice nucleation phenotype. These bacteria and the gene required for this phenotype have also been exploited in processes as diverse as reporter gene assays to assess environmentally responsive gene expression in various plant pathogenic and environmental bacteria and in the detection of foodborne human pathogens when coupled with host-specific bacteriophage, whereas ice nucleating bacteria themselves have been exploited in the production of artificial snow for recreation and oil exploration and in the process of freezing of various food products. This review also examines the historical development of our understanding of ice nucleating bacteria, details of the genetic determinants of ice nucleation, and features of the aggregates of membrane-bound ice nucleation protein necessary for catalyzing ice. Lastly, this review also explores the role of these bacteria in limiting the supercooling ability of plants and the strategies and limitations of avoiding plant frost damage by managing these bacterial populations by bactericides, antagonistic bacteria, or cultural control strategies.
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Affiliation(s)
- Steven Lindow
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
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Hartmann S, Ling M, Dreyer LSA, Zipori A, Finster K, Grawe S, Jensen LZ, Borck S, Reicher N, Drace T, Niedermeier D, Jones NC, Hoffmann SV, Wex H, Rudich Y, Boesen T, Šantl-Temkiv T. Structure and Protein-Protein Interactions of Ice Nucleation Proteins Drive Their Activity. Front Microbiol 2022; 13:872306. [PMID: 35783412 PMCID: PMC9247515 DOI: 10.3389/fmicb.2022.872306] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Microbially-produced ice nucleating proteins (INpro) are unique molecular structures with the highest known catalytic efficiency for ice formation. Airborne microorganisms utilize these proteins to enhance their survival by reducing their atmospheric residence times. INpro also have critical environmental effects including impacts on the atmospheric water cycle, through their role in cloud and precipitation formation, as well as frost damage on crops. INpro are ubiquitously present in the atmosphere where they are emitted from diverse terrestrial and marine environments. Even though bacterial genes encoding INpro have been discovered and sequenced decades ago, the details of how the INpro molecular structure and oligomerization foster their unique ice-nucleation activity remain elusive. Using machine-learning based software AlphaFold 2 and trRosetta, we obtained and analysed the first ab initio structural models of full length and truncated versions of bacterial INpro. The modeling revealed a novel beta-helix structure of the INpro central repeat domain responsible for ice nucleation activity. This domain consists of repeated stacks of two beta strands connected by two sharp turns. One beta-strand is decorated with a TxT amino acid sequence motif and the other strand has an SxL[T/I] motif. The core formed between the stacked beta helix-pairs is unusually polar and very distinct from previous INpro models. Using synchrotron radiation circular dichroism, we validated the β-strand content of the central repeat domain in the model. Combining the structural model with functional studies of purified recombinant INpro, electron microscopy and modeling, we further demonstrate that the formation of dimers and higher-order oligomers is key to INpro activity. Using computational docking of the new INpro model based on rigid-body algorithms we could reproduce a previously proposed homodimer structure of the INpro CRD with an interface along a highly conserved tyrosine ladder and show that the dimer model agrees with our functional data. The parallel dimer structure creates a surface where the TxT motif of one monomer aligns with the SxL[T/I] motif of the other monomer widening the surface that interacts with water molecules and therefore enhancing the ice nucleation activity. This work presents a major advance in understanding the molecular foundation for bacterial ice-nucleation activity.
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Affiliation(s)
| | - Meilee Ling
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | - Lasse S. A. Dreyer
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | - Assaf Zipori
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Kai Finster
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
| | - Sarah Grawe
- Institute for Tropospheric Research, Leipzig, Germany
| | - Lasse Z. Jensen
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | - Stella Borck
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | - Naama Reicher
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Taner Drace
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
| | | | - Nykola C. Jones
- Department of Physics and Astronomy, The Institute for Storage Ring Facilities, Aarhus University, Aarhus, Denmark
| | - Søren V. Hoffmann
- Department of Physics and Astronomy, The Institute for Storage Ring Facilities, Aarhus University, Aarhus, Denmark
| | - Heike Wex
- Institute for Tropospheric Research, Leipzig, Germany
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Thomas Boesen
- Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Center and Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
- Thomas Boesen,
| | - Tina Šantl-Temkiv
- Department of Biology, Microbiology Section, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
- *Correspondence: Tina Šantl-Temkiv,
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Lukas M, Schwidetzky R, Eufemio RJ, Bonn M, Meister K. Toward Understanding Bacterial Ice Nucleation. J Phys Chem B 2022; 126:1861-1867. [PMID: 35084861 PMCID: PMC8919256 DOI: 10.1021/acs.jpcb.1c09342] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Bacterial ice nucleators
(INs) are among the most effective ice
nucleators known and are relevant for freezing processes in agriculture,
the atmosphere, and the biosphere. Their ability to facilitate ice
formation is due to specialized ice-nucleating proteins (INPs) anchored
to the outer bacterial cell membrane, enabling the crystallization
of water at temperatures up to −2 °C. In this Perspective,
we highlight the importance of functional aggregation of INPs for
the exceptionally high ice nucleation activity of bacterial ice nucleators.
We emphasize that the bacterial cell membrane, as well as environmental
conditions, is crucial for a precise functional INP aggregation. Interdisciplinary
approaches combining high-throughput droplet freezing assays with
advanced physicochemical tools and protein biochemistry are needed
to link changes in protein structure or protein–water interactions
with changes on the functional level.
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Affiliation(s)
- Max Lukas
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | | | | | - Mischa Bonn
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Konrad Meister
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany.,University of Alaska Southeast, Juneau, Alaska 99801, United States
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Mael LE, Peiker G, Busse HL, Grassian VH. Temperature-Dependent Liquid Water Structure for Individual Micron-Sized, Supercooled Aqueous Droplets with Inclusions. J Phys Chem A 2021; 125:10742-10749. [PMID: 34928159 DOI: 10.1021/acs.jpca.1c08331] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein, we measure the water structure for individual micron-sized droplets of water, salt water, and water containing biologically and marine relevant atmospheric inclusions as a function of temperature. Individual droplets, formed on a hydrophobic substrate, are analyzed with micro-Raman spectroscopy. Analysis of the Raman spectra in the O-H stretching region shows that the equilibrium of partially and fully hydrogen-bonding water interactions change as temperature decreases up until there is a phase transition to form ice. Using these temperature-dependent measurements, the thermodynamic parameters for the interchange between partially and fully hydrogen-bonded water (PHW ⇄ FHW) for different supercooled droplets (water, salt water, and water containing biologically and marine relevant atmospheric inclusions) have been determined.
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Affiliation(s)
- Liora E Mael
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92037, United States
| | - Gordon Peiker
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92037, United States
| | - Heidi L Busse
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92037, United States
| | - Vicki H Grassian
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92037, United States
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