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Short SE, Zamorano M, Aranzaez-Ríos C, Lee-Estevez M, Díaz R, Quiñones J, Ulloa-Rodríguez P, Villalobos EF, Bravo LA, Graether SP, Farías JG. Novel Apoplastic Antifreeze Proteins of Deschampsia antarctica as Enhancer of Common Cell Freezing Media for Cryobanking of Genetic Resources, a Preliminary Study. Biomolecules 2024; 14:174. [PMID: 38397411 PMCID: PMC10886522 DOI: 10.3390/biom14020174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Antifreeze proteins (AFPs) are natural biomolecules found in cold-adapted organisms that lower the freezing point of water, allowing survival in icy conditions. These proteins have the potential to improve cryopreservation techniques by enhancing the quality of genetic material postthaw. Deschampsia antarctica, a freezing-tolerant plant, possesses AFPs and is a promising candidate for cryopreservation applications. In this study, we investigated the cryoprotective properties of AFPs from D. antarctica extracts on Atlantic salmon spermatozoa. Apoplastic extracts were used to determine ice recrystallization inhibition (IRI), thermal hysteresis (TH) activities and ice crystal morphology. Spermatozoa were cryopreserved using a standard cryoprotectant medium (C+) and three alternative media supplemented with apoplastic extracts. Flow cytometry was employed to measure plasma membrane integrity (PMI) and mitochondrial membrane potential (MMP) postthaw. Results showed that a low concentration of AFPs (0.05 mg/mL) provided significant IRI activity. Apoplastic extracts from D. antarctica demonstrated a cryoprotective effect on salmon spermatozoa, with PMI comparable to the standard medium. Moreover, samples treated with apoplastic extracts exhibited a higher percentage of cells with high MMP. These findings represent the first and preliminary report that suggests that AFPs derived from apoplastic extracts of D. antarctica have the potential to serve as cryoprotectants and could allow the development of novel freezing media.
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Affiliation(s)
- Stefania E. Short
- Department of Chemical Engineering, Universidad de La Frontera, Av. Francisco Salazar 01145, P.O. Box 54D, Temuco 4811230, Chile; (S.E.S.); (M.Z.); (C.A.-R.)
| | - Mauricio Zamorano
- Department of Chemical Engineering, Universidad de La Frontera, Av. Francisco Salazar 01145, P.O. Box 54D, Temuco 4811230, Chile; (S.E.S.); (M.Z.); (C.A.-R.)
| | - Cristian Aranzaez-Ríos
- Department of Chemical Engineering, Universidad de La Frontera, Av. Francisco Salazar 01145, P.O. Box 54D, Temuco 4811230, Chile; (S.E.S.); (M.Z.); (C.A.-R.)
| | - Manuel Lee-Estevez
- Faculty of Health Sciences, Universidad Autónoma de Chile, Av. Alemania 1090, Temuco 4810101, Chile;
| | - Rommy Díaz
- Faculty of Agricultural and Environmental Sciences, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco 4811230, Chile; (R.D.); (J.Q.)
| | - John Quiñones
- Faculty of Agricultural and Environmental Sciences, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco 4811230, Chile; (R.D.); (J.Q.)
| | - Patricio Ulloa-Rodríguez
- Department of Agronomical Sciences, Universidad Católica del Maule, Av. Carmen 684, Curicó 3341695, Chile;
| | - Elías Figueroa Villalobos
- Nucleus of Research in Food Production, Faculty of Natural Resources, Universidad Católica de Temuco, Manuel Montt 056, Temuco 4813302, Chile;
| | - León A. Bravo
- Department of Agronomical Sciences and Natural Resources, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco 4811230, Chile;
| | - Steffen P. Graether
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada;
| | - Jorge G. Farías
- Department of Chemical Engineering, Universidad de La Frontera, Av. Francisco Salazar 01145, P.O. Box 54D, Temuco 4811230, Chile; (S.E.S.); (M.Z.); (C.A.-R.)
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2
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Melnik BS, Glukhova KA, Sokolova (Voronova) EA, Balalaeva IV, Garbuzynskiy SO, Finkelstein AV. Physics of Ice Nucleation and Antinucleation: Action of Ice-Binding Proteins. Biomolecules 2023; 14:54. [PMID: 38254654 PMCID: PMC10813080 DOI: 10.3390/biom14010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/09/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Ice-binding proteins are crucial for the adaptation of various organisms to low temperatures. Some of these, called antifreeze proteins, are usually thought to inhibit growth and/or recrystallization of ice crystals. However, prior to these events, ice must somehow appear in the organism, either coming from outside or forming inside it through the nucleation process. Unlike most other works, our paper is focused on ice nucleation and not on the behavior of the already-nucleated ice, its growth, etc. The nucleation kinetics is studied both theoretically and experimentally. In the theoretical section, special attention is paid to surfaces that bind ice stronger than water and thus can be "ice nucleators", potent or relatively weak; but without them, ice cannot be nucleated in any way in calm water at temperatures above -30 °C. For experimental studies, we used: (i) the ice-binding protein mIBP83, which is a previously constructed mutant of a spruce budworm Choristoneura fumiferana antifreeze protein, and (ii) a hyperactive ice-binding antifreeze protein, RmAFP1, from a longhorn beetle Rhagium mordax. We have shown that RmAFP1 (but not mIBP83) definitely decreased the ice nucleation temperature of water in test tubes (where ice originates at much higher temperatures than in bulk water and thus the process is affected by some ice-nucleating surfaces) and, most importantly, that both of the studied ice-binding proteins significantly decreased the ice nucleation temperature that had been significantly raised in the presence of potent ice nucleators (CuO powder and ice-nucleating bacteria Pseudomonas syringae). Additional experiments on human cells have shown that mIBP83 is concentrated in some cell regions of the cooled cells. Thus, the ice-binding protein interacts not only with ice, but also with other sites that act or potentially may act as ice nucleators. Such ice-preventing interaction may be the crucial biological task of ice-binding proteins.
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Affiliation(s)
- Bogdan S. Melnik
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
| | - Ksenia A. Glukhova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
| | - Evgeniya A. Sokolova (Voronova)
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia (I.V.B.)
| | - Irina V. Balalaeva
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia (I.V.B.)
| | - Sergiy O. Garbuzynskiy
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.G.); (S.O.G.)
- Faculty of Biotechnology, Lomonosov Moscow State University, 142290 Pushchino, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119192 Moscow, Russia
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3
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Pushkareva E, Elster J, Becker B. Metagenomic Analysis of Antarctic Biocrusts Unveils a Rich Range of Cold-Shock Proteins. Microorganisms 2023; 11:1932. [PMID: 37630492 PMCID: PMC10459675 DOI: 10.3390/microorganisms11081932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Microorganisms inhabiting Antarctic biocrusts develop several strategies to survive extreme environmental conditions such as severe cold and drought. However, the knowledge about adaptations of biocrusts microorganisms are limited. Here, we applied metagenomic sequencing to study biocrusts from east Antarctica. Biocrusts were dominated by cyanobacteria, actinobacteria and proteobacteria. Furthermore, the results provided insights into the presence and abundance of cold shock proteins (Csp), cold shock domain A proteins (CsdA), and antifreeze proteins (AFP) in these extreme environments. The metagenomic analysis revealed a high number of CsdA across the samples. The majority of the Csp recorded in the studied biocrusts were Csp A, C, and E. In addition, CsdA, Csp, and AFP primarily originated from proteobacteria and actinobacteria.
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Affiliation(s)
- Ekaterina Pushkareva
- Department of Biology, Botanical Institute, University of Cologne, Zulpicher Str. 47B, 50674 Cologne, Germany;
| | - Josef Elster
- Institute of Botany, Academy of Sciences of the Czech Republic, Dukelska 135, 37982 Trebon, Czech Republic;
- Centre for Polar Ecology, University of South Bohemia, Na Zlate Stoce 3, 37005 Ceske Budejovice, Czech Republic
| | - Burkhard Becker
- Department of Biology, Botanical Institute, University of Cologne, Zulpicher Str. 47B, 50674 Cologne, Germany;
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Byanju B, Sen S, Mansell T, Lamsal BP. Evaluation of corn steep liquor as fermentation media for recombinant Lactococcus lactis producing antifreeze proteins. J Sci Food Agric 2023; 103:2512-2521. [PMID: 36661481 DOI: 10.1002/jsfa.12461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/15/2023] [Accepted: 01/20/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Corn processing byproducts corn steep liquor (CSL), and thin stillage were evaluated as growth media for recombinant Lactococcus lactis modified to produce antifreeze proteins (AFPs) that could have important food and non-food applications. The AFP III sequence from ocean pout was cloned into a shuttle vector to make an expression vector that facilitated the production of recombinant AFP III in Lactococcus lactis. Light CSL from yellow dent corn and thin stillage from the industrial corn bioethanol process were optimized as fermentation media with a combination of the following additives and trace elements: disodium-β-glycerophosphate (DG), tryptone (T), ascorbic acid (AA), iron (Fe), zinc (Zn), and magnesium (Mg). The growth of wild-type and recombinant Lactococcus lactis strains were compared over a 72 h period in 96-well plates and 250 mL shake flasks. RESULTS The corn coproducts media consisting of 50% (v/v) light steep in water supplemented with DG-5 g L-1 , T-5 g L-1 , AA-0.5 g L-1 , and Zn-4 ppm resulted in best growth and was considered as the best-optimized media. The addition of additives and trace elements better supported the growth of both wild-type and recombinant Lactococcus lactis strains compared to control media without any additives. Respective fermentation supernatants were frozen to -20 °C, and the time to supercool and freeze was compared. A distinct supercooling effect was observed for the supernatants from recombinant strains thus, extending the time and temperature of supercooling and freezing. The maximum time of supercooling extended was 17.55 ± 4.45 min for thin stillage followed by M17 media (17.25 ± 4.45 min), Kent Corporation CSL (10.80 ± 2.12 min), and yellow dent CSL (6.9 ± 0.85 min) when fermented with recombinant Lactococcus lactis strains. CONCLUSION The supplemented corn coproduct-based media enhanced the growth of both wild-type and recombinant Lactococcus lactis strains. These optimized media can replace or supplement more expensive media (e.g. M17), potentially reducing cost. The fermentation supernatants exhibited longer times to supercool, and freeze compared to control supernatants, indicating potential use as antifreeze compounds in frozen food and non-food applications. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Bibek Byanju
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, USA
| | - Swastik Sen
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Thomas Mansell
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Buddhi P Lamsal
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, USA
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5
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Hotaling S, Desvignes T, Sproul JS, Lins LSF, Kelley JL. Pathways to polar adaptation in fishes revealed by long-read sequencing. Mol Ecol 2023; 32:1381-1397. [PMID: 35561000 DOI: 10.1111/mec.16501] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/31/2022] [Accepted: 05/05/2022] [Indexed: 11/28/2022]
Abstract
Long-read sequencing is driving a new reality for genome science in which highly contiguous assemblies can be produced efficiently with modest resources. Genome assemblies from long-read sequences are particularly exciting for understanding the evolution of complex genomic regions that are often difficult to assemble. In this study, we utilized long-read sequencing data to generate a high-quality genome assembly for an Antarctic eelpout, Ophthalmolycus amberensis, the first for the globally distributed family Zoarcidae. We used this assembly to understand how O. amberensis has adapted to the harsh Southern Ocean and compared it to another group of Antarctic fishes: the notothenioids. We showed that selection has largely acted on different targets in eelpouts relative to notothenioids. However, we did find some overlap; in both groups, genes involved in membrane structure, thermal tolerance and vision have evidence of positive selection. We found evidence for historical shifts of transposable element activity in O. amberensis and other polar fishes, perhaps reflecting a response to environmental change. We were specifically interested in the evolution of two complex genomic loci known to underlie key adaptations to polar seas: haemoglobin and antifreeze proteins (AFPs). We observed unique evolution of the haemoglobin MN cluster in eelpouts and related fishes in the suborder Zoarcoidei relative to other Perciformes. For AFPs, we identified the first species in the suborder with no evidence of afpIII sequences (Cebidichthys violaceus) in the genomic region where they are found in all other Zoarcoidei, potentially reflecting a lineage-specific loss of this cluster. Beyond polar fishes, our results highlight the power of long-read sequencing to understand genome evolution.
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Affiliation(s)
- Scott Hotaling
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - John S Sproul
- Department of Biology, University of Nebraska Omaha, Omaha, Nebraska, USA
| | - Luana S F Lins
- Australian National Insect Collection, CSIRO, Canberra, Australia
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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Tas RP, Hendrix MMRM, Voets IK. Nanoscopy of single antifreeze proteins reveals that reversible ice binding is sufficient for ice recrystallization inhibition but not thermal hysteresis. Proc Natl Acad Sci U S A 2023; 120:e2212456120. [PMID: 36595705 DOI: 10.1073/pnas.2212456120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antifreeze proteins (AFPs) bind ice to reduce freezing temperatures and arrest ice crystal ripening, making AFPs essential for the survival of many organisms in ice-laden environments and attractive as biocompatible antifreezes in many applications. While their activity was identified over 50 years ago, the physical mechanisms through which they function are still debated because experimental insights at the molecular scale remain elusive. Here, we introduce subzero nanoscopy by the design and incorporation of a freezing stage on a commercial super-resolution setup to resolve the interfacial dynamics of single AFPs with ice crystal surfaces. Using this method, we demonstrate irreversible binding and immobilization (i.e., pinning) of individual proteins to the ice/water interface. Surprisingly, pinning is lost and adsorption becomes reversible when freezing point depression activity, but not ice recrystallization inhibition, is eliminated by a single mutation in the ice-binding site of the AFP. Our results provide direct experimental evidence for the adsorption-inhibition paradigm, pivotal to all theoretical descriptions of freezing point depression activity, but also reveal that reversible binding to ice must be accounted for in an all-inclusive model for AFP activity. These mechanistic insights into the relation between interfacial interactions and activity further our understanding and may serve as leading principles in the future design of highly potent, biocompatible antifreezes with tunable affinity.
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7
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Delesky EA, Garcia LF, Lobo AJ, Mikofsky RA, Dowdy ND, Wallat JD, Miyake GM, Srubar WV. Bioinspired Threonine-Based Polymers with Potent Ice Recrystallization Inhibition Activity. ACS Appl Polym Mater 2022; 4:7934-7942. [PMID: 36714526 PMCID: PMC9881732 DOI: 10.1021/acsapm.2c01496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Ice growth mitigation is a pervasive challenge for multiple industries. In nature, ice-binding proteins (IBPs) demonstrate potent ice growth prevention through ice recrystallization inhibition (IRI). However, IBPs are expensive, difficult to produce in large quantities, and exhibit minimal resilience to nonphysiological environmental stressors, such as pH. For these reasons, researchers have turned to bioinspired polymeric materials that mimic IBP behavior. To date, however, no synthetic polymer has rivaled the ability of native IBPs to display IRI activity at ultralow nanomolar concentrations. In this work, we study the IRI activity of peptides and polypeptides inspired by common ice-binding residues of IBPs to inform the synthesis and characterization of a potent bioinspired polymer that mimics IBP behavior. We show first that the threonine polypeptide (pThr) displays the best IRI activity in phosphate-buffered saline (PBS). Second, we use pThr as a molecular model to synthesize and test a bioinspired polymer, poly(2-hydroxypropyl methacrylamide) (pHPMA). We show that pHPMA exhibits potent IRI activity in neutral PBS at ultralow concentrations (0.01 mg/mL). pHPMA demonstrates potent IRI activity at low molecular weights (2.3 kDa), with improved activity at higher molecular weights (32.8 kDa). These results substantiate that pHPMA is a robust molecule that mitigates ice crystal growth at concentrations similar to native IBPs.
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Affiliation(s)
- Elizabeth A Delesky
- Materials Science and Engineering Program, University of Colorado Boulder, Boulder, Colorado 80309-0428, United States
| | - Luis F Garcia
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Aparna J Lobo
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309-0428, United States
| | - Rebecca A Mikofsky
- Materials Science and Engineering Program, University of Colorado Boulder, Boulder, Colorado 80309-0428, United States
| | - Nicolas D Dowdy
- Materials Science and Engineering Program, University of Colorado Boulder, Boulder, Colorado 80309-0428, United States
| | - Jaqueline D Wallat
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, Colorado 80309-0428, United States
| | - Garret M Miyake
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Wil V Srubar
- Materials Science and Engineering Program and Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, Colorado 80309-0428, United States
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8
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Juurakko CL, Bredow M, diCenzo GC, Walker VK. Cold-inducible promoter-driven knockdown of Brachypodium antifreeze proteins confers freezing and phytopathogen susceptibility. Plant Direct 2022; 6:e449. [PMID: 36172079 PMCID: PMC9467863 DOI: 10.1002/pld3.449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/12/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
The model forage crop, Brachypodium distachyon, has a cluster of ice recrystallization inhibition (BdIRI) genes, which encode antifreeze proteins that function by adsorbing to ice crystals and inhibiting their growth. The genes were targeted for knockdown using a cold-induced promoter from rice (prOsMYB1R35) to drive miRNA. The transgenic lines showed no apparent pleiotropic developmental defects but had reduced antifreeze activity as assessed by assays for ice-recrystallization inhibition, thermal hysteresis, electrolyte leakage, and leaf infrared thermography. Strikingly, the number of cold-acclimated transgenic plants that survived freezing at -8°C was reduced by half or killed entirely, depending on the line, compared with cold-acclimated wild type plants. In addition, more leaf damage was apparent at subzero temperatures in knockdowns after infection with an ice nucleating pathogen, Pseudomonas syringae. Although antifreeze proteins have been studied for almost 60 years, this is the first unequivocal demonstration of their function by knockdown in any organism, and their dual contribution to freeze protection as well as pathogen susceptibility, independent of obvious developmental defects. These proteins are thus of potential interest in a wide range of biotechnological applications from cryopreservation, to frozen product additives, to the engineering of transgenic crops with enhanced pathogen and freezing tolerance.
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Affiliation(s)
| | - Melissa Bredow
- Department of BiologyQueen's UniversityKingstonOntarioCanada
- Present address:
Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIowaUSA
| | | | - Virginia K. Walker
- Department of BiologyQueen's UniversityKingstonOntarioCanada
- School of Environmental StudiesQueen's UniversityKingstonOntarioCanada
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9
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Kumar V, Kashyap P, Kumar S, Thakur V, Kumar S, Singh D. Multiple Adaptive Strategies of Himalayan Iodobacter sp. PCH194 to High-Altitude Stresses. Front Microbiol 2022; 13:881873. [PMID: 35875582 PMCID: PMC9298515 DOI: 10.3389/fmicb.2022.881873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/01/2022] [Indexed: 11/24/2022] Open
Abstract
Bacterial adaption to the multiple stressed environments of high-altitude niches in the Himalayas is intriguing and is of considerable interest to biotechnologists. Previously, we studied the culturable and unculturable metagenome microbial diversity from glacial and kettle lakes in the Western Himalayas. In this study, we explored the adaptive strategies of a unique Himalayan eurypsychrophile Iodobacter sp. PCH194, which can synthesize polyhydroxybutyrate (PHB) and violacein pigment. Whole-genome sequencing and analysis of Iodobacter sp. PCH194 (4.58 Mb chromosome and three plasmids) revealed genetic traits associated with adaptive strategies for cold/freeze, nutritional fluctuation, defense against UV, acidic pH, and the kettle lake's competitive environment. Differential proteome analysis suggested the adaptive role of chaperones, ribonucleases, secretion systems, and antifreeze proteins under cold stress. Antifreeze activity inhibiting the ice recrystallization at −9°C demonstrated the bacterium's survival at subzero temperature. The bacterium stores carbon in the form of PHB under stress conditions responding to nutritional fluctuations. However, violacein pigment protects the cells from UV radiation. Concisely, genomic, proteomic, and physiological studies revealed the multiple adaptive strategies of Himalayan Iodobacter to survive the high-altitude stresses.
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Affiliation(s)
- Vijay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Prakriti Kashyap
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Subhash Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC), Ghaziabad, India
| | - Vikas Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC), Ghaziabad, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Dharam Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC), Ghaziabad, India
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10
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Béliveau C, Gagné P, Picq S, Vernygora O, Keeling CI, Pinkney K, Doucet D, Wen F, Spencer Johnston J, Maaroufi H, Boyle B, Laroche J, Dewar K, Juretic N, Blackburn G, Nisole A, Brunet B, Brandão M, Lumley L, Duan J, Quan G, Lucarotti CJ, Roe AD, Sperling FAH, Levesque RC, Cusson M. The Spruce Budworm Genome: Reconstructing the Evolutionary History of Antifreeze Proteins. Genome Biol Evol 2022; 14:evac087. [PMID: 35668612 PMCID: PMC9210311 DOI: 10.1093/gbe/evac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/27/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Insects have developed various adaptations to survive harsh winter conditions. Among freeze-intolerant species, some produce "antifreeze proteins" (AFPs) that bind to nascent ice crystals and inhibit further ice growth. Such is the case of the spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae), a destructive North American conifer pest that can withstand temperatures below -30°C. Despite the potential importance of AFPs in the adaptive diversification of Choristoneura, genomic tools to explore their origins have until now been limited. Here we present a chromosome-scale genome assembly for C. fumiferana, which we used to conduct comparative genomic analyses aimed at reconstructing the evolutionary history of tortricid AFPs. The budworm genome features 16 genes homologous to previously reported C. fumiferana AFPs (CfAFPs), 15 of which map to a single region on chromosome 18. Fourteen of these were also detected in five congeneric species, indicating Choristoneura AFP diversification occurred before the speciation event that led to C. fumiferana. Although budworm AFPs were previously considered unique to the genus Choristoneura, a search for homologs targeting recently sequenced tortricid genomes identified seven CfAFP-like genes in the distantly related Notocelia uddmanniana. High structural similarity between Notocelia and Choristoneura AFPs suggests a common origin, despite the absence of homologs in three related tortricids. Interestingly, one Notocelia AFP formed the C-terminus of a "zonadhesin-like" protein, possibly representing the ancestral condition from which tortricid AFPs evolved. Future work should clarify the evolutionary path of AFPs between Notocelia and Choristoneura and assess the role of the "zonadhesin-like" protein as precursor of tortricid AFPs.
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Affiliation(s)
- Catherine Béliveau
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
| | - Patrick Gagné
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
| | - Sandrine Picq
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
| | - Oksana Vernygora
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - Christopher I Keeling
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, Quebec, Canada
| | - Kristine Pinkney
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | - Daniel Doucet
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | - Fayuan Wen
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington DC, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, 2475 College Station, Texas, USA
| | - Halim Maaroufi
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Brian Boyle
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Jérôme Laroche
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Ken Dewar
- Quantitative Life Sciences, McGill University, Montreal, Quebec, Canada
| | - Nikoleta Juretic
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Gwylim Blackburn
- Pacific Forestry Centre, Natural Resources Canada, Victoria, British Columbia, Canada
| | - Audrey Nisole
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
| | - Bryan Brunet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Marcelo Brandão
- Laboratório de Biologia Integrativa e Sistêmica - CBMEG/UNICAMP, Campinas, Brazil
| | - Lisa Lumley
- Alberta Biodiversity Monitoring Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jun Duan
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Guoxing Quan
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | | | - Amanda D Roe
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Roger C Levesque
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Michel Cusson
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, Quebec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
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11
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Soussana TN, Weissman H, Rybtchinski B, Drori R. Adsorption-Inhibition of Clathrate Hydrates by Self-Assembled Nanostructures. Chemphyschem 2021; 22:2182-2189. [PMID: 34407283 DOI: 10.1002/cphc.202100463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/11/2021] [Indexed: 11/11/2022]
Abstract
The mechanism by which safranine O (SFO), an ice growth inhibitor, halts the growth of single crystal tetrahydrofuran (THF) clathrate hydrates was explored using microfluidics coupled with cold stages and fluorescence microscopy. THF hydrates grown in SFO solutions exhibited morphology changes and were shaped as truncated octahedrons or hexagons. Fluorescence microscopy and microfluidics demonstrated that SFO binds to the surface of THF hydrates on specific crystal planes. Cryo-TEM experiments of aqueous solutions containing millimolar concentrations of SFO exhibited the formation of bilayered lamellae with an average thickness of 4.2±0.2 nm covering several μm2 . Altogether, these results indicate that SFO forms supramolecular lamellae in solution, which might bind to the surface of the hydrate and inhibit further growth. As an ice and hydrate inhibitor, SFO may bind to the surface of these crystals via ordered water molecules near its amine and methyl groups, similar to some antifreeze proteins.
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Affiliation(s)
- Tamar Nicole Soussana
- Department of Chemistry and Biochemistry, Yeshiva University, 245 Lexington Avenue, New York, NY, 10016, USA
| | - Haim Weissman
- Department of Organic Chemistry, Weizmann Institute of Science, 234 Hertzel Street, PO Box 26, Rehovot, 7610001, Israel
| | - Boris Rybtchinski
- Department of Organic Chemistry, Weizmann Institute of Science, 234 Hertzel Street, PO Box 26, Rehovot, 7610001, Israel
| | - Ran Drori
- Department of Chemistry and Biochemistry, Yeshiva University, 245 Lexington Avenue, New York, NY, 10016, USA
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12
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Sampaio-Pinto V, Janssen J, Chirico N, Serra M, Alves PM, Doevendans PA, Voets IK, Sluijter JPG, van Laake LW, van Mil A. A Roadmap to Cardiac Tissue-Engineered Construct Preservation: Insights from Cells, Tissues, and Organs. Adv Mater 2021; 33:e2008517. [PMID: 34048090 DOI: 10.1002/adma.202008517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/15/2021] [Indexed: 06/12/2023]
Abstract
Worldwide, over 26 million patients suffer from heart failure (HF). One strategy aspiring to prevent or even to reverse HF is based on the transplantation of cardiac tissue-engineered (cTE) constructs. These patient-specific constructs aim to closely resemble the native myocardium and, upon implantation on the diseased tissue, support and restore cardiac function, thereby preventing the development of HF. However, cTE constructs off-the-shelf availability in the clinical arena critically depends on the development of efficient preservation methodologies. Short- and long-term preservation of cTE constructs would enable transportation and direct availability. Herein, currently available methods, from normothermic- to hypothermic- to cryopreservation, for the preservation of cardiomyocytes, whole-heart, and regenerative materials are reviewed. A theoretical foundation and recommendations for future research on developing cTE construct specific preservation methods are provided. Current research suggests that vitrification can be a promising procedure to ensure long-term cryopreservation of cTE constructs, despite the need of high doses of cytotoxic cryoprotective agents. Instead, short-term cTE construct preservation can be achieved at normothermic or hypothermic temperatures by administration of protective additives. With further tuning of these promising methods, it is anticipated that cTE construct therapy can be brought one step closer to the patient.
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Affiliation(s)
- Vasco Sampaio-Pinto
- Department of Cardiology, Experimental Cardiology Laboratory, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Jasmijn Janssen
- Department of Cardiology, Experimental Cardiology Laboratory, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Nino Chirico
- Department of Cardiology, Experimental Cardiology Laboratory, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Margarida Serra
- IBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Paula M Alves
- IBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Pieter A Doevendans
- Department of Cardiology, Experimental Cardiology Laboratory, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
- Netherlands Heart Institute, P.O. Box 19258, Utrecht, 3501 DG, The Netherlands
| | - Ilja K Voets
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry & Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology (TUE), Groene Loper 3, Eindhoven, 5612 AE, The Netherlands
| | - Joost P G Sluijter
- Department of Cardiology, Experimental Cardiology Laboratory, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Linda W van Laake
- Department of Cardiology, Experimental Cardiology Laboratory, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Alain van Mil
- Department of Cardiology, Experimental Cardiology Laboratory, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
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13
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William N, Acker JP. High Sub-Zero Organ Preservation: A Paradigm of Nature-Inspired Strategies. Cryobiology 2021; 102:15-26. [PMID: 33905707 DOI: 10.1016/j.cryobiol.2021.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/18/2021] [Accepted: 04/11/2021] [Indexed: 01/03/2023]
Abstract
The field of organ preservation is filled with advancements that have yet to see widespread clinical translation, with some of the more notable strategies deriving their inspiration from nature. While static cold storage (SCS) at 2 °C to 4 °C is the current state-of-the-art, it contributes to the current shortage of transplantable organs due to the limited preservation times it affords combined with the limited ability of marginal grafts (i.e. those at risk for post-transplant dysfunction or primary non-function) to tolerate SCS. The era of storage solution optimization to minimize SCS-induced hypothermic injury has plateaued in its improvements, resulting in a shift towards the use of machine perfusion systems to oxygenate organs at normothermic, sub-normothermic, or hypothermic temperatures, as well as the use of sub-zero storage temperatures to leverage the protection brought forth by a reduction in metabolic demand. Many of the rigors that organs are subjected to at low sub-zero temperatures (-80 °C to -196 °C) commonly used for mammalian cell preservation have yet to be surmounted. Therefore, this article focuses on an intermediate temperature range (0 °C to -20 °C), where much success has been seen in the past two decades. The mechanisms leveraged by organisms capable of withstanding prolonged periods at these temperatures through either avoiding or tolerating the formation of ice has provided a foundation for some of the more promising efforts. This article therefore aims to contextualize the translation of these strategies into the realm of mammalian organ preservation.
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Affiliation(s)
- Nishaka William
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2R3, Canada.
| | - Jason P Acker
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2R3, Canada; Centre for Innovation, Canadian Blood Services, 8249 114th Street, Edmonton, AB, T6G 2R8, Canada.
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14
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Sun S, Ding H, Wang D, Han S. Identifying Antifreeze Proteins Based on Key Evolutionary Information. Front Bioeng Biotechnol 2020; 8:244. [PMID: 32274383 PMCID: PMC7113384 DOI: 10.3389/fbioe.2020.00244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/09/2020] [Indexed: 01/08/2023] Open
Abstract
Antifreeze proteins are important antifreeze materials that have been widely used in industry, including in cryopreservation, de-icing, and food storage applications. However, the quantity of some commercially produced antifreeze proteins is insufficient for large-scale industrial applications. Further, many antifreeze proteins have properties such as cytotoxicity, severely hindering their applications. Understanding the mechanisms underlying the protein-ice interactions and identifying novel antifreeze proteins are, therefore, urgently needed. In this study, to uncover the mechanisms underlying protein-ice interactions and provide an efficient and accurate tool for identifying antifreeze proteins, we assessed various evolutionary features based on position-specific scoring matrices (PSSMs) and evaluated their importance for discriminating of antifreeze and non-antifreeze proteins. We then parsimoniously selected seven key features with the highest importance. We found that the selected features showed opposite tendencies (regarding the conservation of certain amino acids) between antifreeze and non-antifreeze proteins. Five out of the seven features had relatively high contributions to the discrimination of antifreeze and non-antifreeze proteins, as revealed by a principal component analysis, i.e., the conservation of the replacement of Cys, Trp, and Gly in antifreeze proteins by Ala, Met, and Ala, respectively, in the related proteins, and the conservation of the replacement of Arg in non-antifreeze proteins by Ser and Arg in the related proteins. Based on the seven parsimoniously selected key features, we established a classifier using support vector machine, which outperformed the state-of-the-art tools. These results suggest that understanding evolutionary information is crucial to designing accurate automated methods for discriminating antifreeze and non-antifreeze proteins. Our classifier, therefore, is an efficient tool for annotating new proteins with antifreeze functions based on sequence information and can facilitate their application in industry.
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Affiliation(s)
- Shanwen Sun
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Hui Ding
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Donghua Wang
- Department of General Surgery, Heilongjiang Province Land Reclamation Headquarters General Hospital, Harbin, China
| | - Shuguang Han
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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15
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Białkowska A, Majewska E, Olczak A, Twarda-Clapa A. Ice Binding Proteins: Diverse Biological Roles and Applications in Different Types of Industry. Biomolecules 2020; 10:E274. [PMID: 32053888 DOI: 10.3390/biom10020274] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/02/2020] [Accepted: 02/07/2020] [Indexed: 02/06/2023] Open
Abstract
More than 80% of Earth’s surface is exposed periodically or continuously to temperatures below 5 °C. Organisms that can live in these areas are called psychrophilic or psychrotolerant. They have evolved many adaptations that allow them to survive low temperatures. One of the most interesting modifications is production of specific substances that prevent living organisms from freezing. Psychrophiles can synthesize special peptides and proteins that modulate the growth of ice crystals and are generally called ice binding proteins (IBPs). Among them, antifreeze proteins (AFPs) inhibit the formation of large ice grains inside the cells that may damage cellular organelles or cause cell death. AFPs, with their unique properties of thermal hysteresis (TH) and ice recrystallization inhibition (IRI), have become one of the promising tools in industrial applications like cryobiology, food storage, and others. Attention of the industry was also caught by another group of IBPs exhibiting a different activity—ice-nucleating proteins (INPs). This review summarizes the current state of art and possible utilizations of the large group of IBPs.
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16
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Bissoyi A, Reicher N, Chasnitsky M, Arad S, Koop T, Rudich Y, Braslavsky I. Ice Nucleation Properties of Ice-binding Proteins from Snow Fleas. Biomolecules 2019; 9:E532. [PMID: 31557956 DOI: 10.3390/biom9100532] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/15/2019] [Accepted: 09/19/2019] [Indexed: 01/11/2023] Open
Abstract
Ice-binding proteins (IBPs) are found in many organisms, such as fish and hexapods, plants, and bacteria that need to cope with low temperatures. Ice nucleation and thermal hysteresis are two attributes of IBPs. While ice nucleation is promoted by large proteins, known as ice nucleating proteins, the smaller IBPs, referred to as antifreeze proteins (AFPs), inhibit the growth of ice crystals by up to several degrees below the melting point, resulting in a thermal hysteresis (TH) gap between melting and ice growth. Recently, we showed that the nucleation capacity of two types of IBPs corresponds to their size, in agreement with classical nucleation theory. Here, we expand this finding to additional IBPs that we isolated from snow fleas (the arthropod Collembola), collected in northern Israel. Chemical analyses using circular dichroism and Fourier-transform infrared spectroscopy data suggest that these IBPs have a similar structure to a previously reported snow flea antifreeze protein. Further experiments reveal that the ice-shell purified proteins have hyperactive antifreeze properties, as determined by nanoliter osmometry, and also exhibit low ice-nucleation activity in accordance with their size.
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17
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Surís-Valls R, Voets IK. The Impact of Salts on the Ice Recrystallization Inhibition Activity of Antifreeze (Glyco)Proteins. Biomolecules 2019; 9:biom9080347. [PMID: 31390745 PMCID: PMC6724029 DOI: 10.3390/biom9080347] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 11/16/2022] Open
Abstract
Antifreeze (glyco)proteins (AF(G)Ps) have received increasing attention as potential cryopreservation agents since their discovery in the 1970s. While cryopreservation strategies for specific cells (such as red blood cells) are successful and widely implemented, preservation of other cell types, tissues and whole organs remains challenging. This is due to the multifactorial nature of the freeze-thaw damage, the complexity of preserving biological matter and the (country-to-country) variability of the employed procedures and regulations. AF(G)Ps are well-known for their ability to modulate ice crystal growth morphology and ice recrystallization inhibition (IRI), both of which are considered key contributors to freeze-thaw damage. To date, however, the impact of AF(G)Ps on cell survival remains at best partially understood as conflicting results on the benefits or disadvantages of including AF(G)P in cryopreservation strategies remain unelucidated. We hypothesize that variability in the additives in the cryopreservation media contributes to the observed discrepancies. To critically examine this idea, we monitored the inhibition of ice recrystallization by AF(G)P in the presence of various salts using a quantitative analysis of optical microscopy images via the Lifshitz-Slyozov-Wagner (LSW) theory for Oswald ripening. We found that the addition of salts, which are used in culture and cryopreservation media, enhances the IRI activity of AF(G)Ps, and that the magnitude of the enhancement was in line with the Hofmeister series. The size of ice crystals grown in AFGP1–5 and type III AFP samples containing chloride, phosphate and citrate ions were statistically smaller after 90 min of incubation than crystals grown in the absence of these salts. The ice recrystallization rates (kd) of AFGP1–5 and type III AFP samples prepared at a fixed overall ionic strength of 100 mM progressively decreased following the Hofmeister series for anions. Our results demonstrate that the performance of AF(G)Ps is significantly influenced by additives present in common cryopreservation media. It is thus important to conduct excipient compatibility experiments to identify potential incompatibilities between additives and AF(G)Ps in cryopreservation formulations.
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Affiliation(s)
- Romà Surís-Valls
- Laboratory of Self-Organizing Soft Matter, Laboratory of Macro-Organic Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, The Netherlands
| | - Ilja K Voets
- Laboratory of Self-Organizing Soft Matter, Laboratory of Macro-Organic Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, The Netherlands.
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18
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Biggs CI, Stubbs C, Graham B, Fayter AER, Hasan M, Gibson MI. Mimicking the Ice Recrystallization Activity of Biological Antifreezes. When is a New Polymer "Active"? Macromol Biosci 2019; 19:e1900082. [PMID: 31087781 PMCID: PMC6828557 DOI: 10.1002/mabi.201900082] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/26/2019] [Indexed: 01/16/2023]
Abstract
Antifreeze proteins and ice-binding proteins have been discovered in a diverse range of extremophiles and have the ability to modulate the growth and formation of ice crystals. Considering the importance of cryoscience across transport, biomedicine, and climate science, there is significant interest in developing synthetic macromolecular mimics of antifreeze proteins, in particular to reproduce their property of ice recrystallization inhibition (IRI). This activity is a continuum rather than an "on/off" property and there may be multiple molecular mechanisms which give rise to differences in this observable property; the limiting concentrations for ice growth vary by more than a thousand between an antifreeze glycoprotein and poly(vinyl alcohol), for example. The aim of this article is to provide a concise comparison of a range of natural and synthetic materials that are known to have IRI, thus providing a guide to see if a new synthetic mimic is active or not, including emerging materials which are comparatively weak compared to antifreeze proteins, but may have technological importance. The link between activity and the mechanisms involving either ice binding or amphiphilicity is discussed and known materials assigned into classes based on this.
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Affiliation(s)
- Caroline I Biggs
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Ben Graham
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Alice E R Fayter
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Muhammad Hasan
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Medical School, , University of Warwick, Coventry, CV4 7AL, UK
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19
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Her C, Yeh Y, Krishnan VV. The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy. Biomolecules 2019; 9:biom9060235. [PMID: 31213033 PMCID: PMC6628104 DOI: 10.3390/biom9060235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 12/13/2022] Open
Abstract
The primary sequence of antifreeze glycoproteins (AFGPs) is highly degenerate, consisting of multiple repeats of the same tripeptide, Ala–Ala–Thr*, in which Thr* is a glycosylated threonine with the disaccharide beta-d-galactosyl-(1,3)-alpha-N-acetyl-d-galactosamine. AFGPs seem to function as intrinsically disordered proteins, presenting challenges in determining their native structure. In this work, a different approach was used to elucidate the three-dimensional structure of AFGP8 from the Arctic cod Boreogadussaida and the Antarctic notothenioid Trematomusborchgrevinki. Dimethyl sulfoxide (DMSO), a non-native solvent, was used to make AFGP8 less dynamic in solution. Interestingly, DMSO induced a non-native structure, which could be determined via nuclear magnetic resonance (NMR) spectroscopy. The overall three-dimensional structures of the two AFGP8s from two different natural sources were different from a random coil ensemble, but their “compactness” was very similar, as deduced from NMR measurements. In addition to their similar compactness, the conserved motifs, Ala–Thr*–Pro–Ala and Ala–Thr*–Ala–Ala, present in both AFGP8s, seemed to have very similar three-dimensional structures, leading to a refined definition of local structural motifs. These local structural motifs allowed AFGPs to be considered functioning as effectors, making a transition from disordered to ordered upon binding to the ice surface. In addition, AFGPs could act as dynamic linkers, whereby a short segment folds into a structural motif, while the rest of the AFGPs could still be disordered, thus simultaneously interacting with bulk water molecules and the ice surface, preventing ice crystal growth.
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Affiliation(s)
- Cheenou Her
- Department of Chemistry, California State University, Fresno, CA 93740, USA.
| | - Yin Yeh
- Department of Applied Science, University of California, Davis, CA 95616, USA.
| | - Viswanathan V Krishnan
- Department of Chemistry, California State University, Fresno, CA 93740, USA.
- Department Medical Pathology and Laboratory Medicine, Davis School of Medicine, University of California, Davis, CA 95616, USA.
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20
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Chasnitsky M, Braslavsky I. Ice-binding proteins and the applicability and limitations of the kinetic pinning model. Philos Trans A Math Phys Eng Sci 2019; 377:20180391. [PMID: 30982449 PMCID: PMC6501913 DOI: 10.1098/rsta.2018.0391] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Ice-binding proteins (IBPs) are unique molecules that bind to and are active on the interface between two phases of water: ice and liquid water. This property allows them to affect ice growth in multiple ways: shaping ice crystals, suppressing the freezing point, inhibiting recrystallization and promoting nucleation. Advances in the protein's production technologies make these proteins promising agents for medical applications among others. Here, we focus on a special class of IBPs that suppress freezing by causing thermal hysteresis (TH): antifreeze proteins (AFPs). The kinetic pinning model describes the dynamics of a growing ice face with proteins binding to it, which eventually slow it down to a halt. We use the kinetic pinning model, with some adjustments made, to study the TH dependence on the solution's concentration of AFPs by fitting the model to published experimental data. We find this model describes the activity of (moderate) type III AFPs well, but is inadequate for the (hyperactive) Tenebrio molitor AFPs. We also find the engulfment resistance to be a key parameter, which depends on the protein's size. Finally, we explain intuitively how TH depends on the seeding time of the ice crystal in the protein solution. Using this insight, we explain the discrepancy in TH measurements between different assays. This article is part of the theme issue 'The physics and chemistry of ice: scaffolding across scales, from the viability of life to the formation of planets'.
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21
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Yamazaki A, Nishimiya Y, Tsuda S, Togashi K, Munehara H. Freeze Tolerance in Sculpins (Pisces; Cottoidea) Inhabiting North Pacific and Arctic Oceans: Antifreeze Activity and Gene Sequences of the Antifreeze Protein. Biomolecules 2019; 9:biom9040139. [PMID: 30959891 PMCID: PMC6523315 DOI: 10.3390/biom9040139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/28/2019] [Accepted: 04/03/2019] [Indexed: 11/16/2022] Open
Abstract
Many marine species inhabiting icy seawater produce antifreeze proteins (AFPs) to prevent their body fluids from freezing. The sculpin species of the superfamily Cottoidea are widely found from the Arctic to southern hemisphere, some of which are known to express AFP. Here we clarified DNA sequence encoding type I AFP for 3 species of 2 families (Cottidae and Agonidae) belonging to Cottoidea. We also examined antifreeze activity for 3 families and 32 species of Cottoidea (Cottidae, Agonidae, and Rhamphocottidae). These fishes were collected in 2013–2015 from the Arctic Ocean, Alaska, Japan. We could identify 8 distinct DNA sequences exhibiting a high similarity to those reported for Myoxocephalus species, suggesting that Cottidae and Agonidae share the same DNA sequence encoding type I AFP. Among the 3 families, Rhamphocottidae that experience a warm current did not show antifreeze activity. The species inhabiting the Arctic Ocean and Northern Japan that often covered with ice floe showed high activity, while those inhabiting Alaska, Southern Japan with a warm current showed low/no activity. These results suggest that Cottoidea acquires type I AFP gene before dividing into Cottidae and Agonidae, and have adapted to each location with optimal antifreeze activity level.
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Affiliation(s)
- Aya Yamazaki
- Nanae Fresh-Water Station, Field Science Center for Northern Biosphere, Hokkaido University, Nanae Town Kameda-gun 041-1105, Japan.
| | - Yoshiyuki Nishimiya
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo 062-8517, Japan.
| | - Sakae Tsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo 062-8517, Japan.
| | - Koji Togashi
- Graduate School of Environmental Sciences, Hokkaido University, Sapporo 060-0810, Japan.
| | - Hiroyuki Munehara
- Usujiri Fisheries Station, Field Science Center of Northern Biosphere, Hokkaido University, Hakodate 041-1613, Japan.
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22
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Abstract
The antifreeze protein (AFP) activity is explained using two models. The first model is using ice binding and the second is using antiice
structuralization of water molecules. The description of AFP function using anti-ice structuralization of water molecules is less
explored. Therefore, it is of interest to explain AFP function using this model. Protein folding is often described using models where
hydrophobic residues move away from water getting buried and hydrophilic residues are exposed to the surface. Thus, the 3D Gauss
function stretched on the protein molecule describes the hydrophobicity distribution in a protein molecule. Small antifreeze proteins
(less than 150 residues) are often represented by structures with hydrophobic core. Large antifreeze proteins (above 200 residues)
contain solenoid (modular repeats). The hydrophobic field of solenoid show different distribution with linear propagation of the bands
of different hydrophobicity level having high and low hydrophobicity that is propagated parallel to the long axis of solenoid. This
specific ordering of hydrophobicity implies water molecules ordering different from ice. We illustrate this phenomenon using two antifreeze
proteins to describe the hypothesis.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and telemedicine, Jagiellonian University - Medical College, Lazarza 16, 31-530 Krakow, Poland.,Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Lojasiewicza 11, 30-348 Krakow, Poland
| | - Mateusz Banach
- Department of Bioinformatics and telemedicine, Jagiellonian University - Medical College, Lazarza 16, 31-530 Krakow, Poland.,Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Lojasiewicza 11, 30-348 Krakow, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University - Medical College, Kopernika 7, 31-034 Krakow, Poland
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23
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Kim HJ, Lee JH, Hur YB, Lee CW, Park SH, Koo BW. Marine Antifreeze Proteins: Structure, Function, and Application to Cryopreservation as a Potential Cryoprotectant. Mar Drugs 2017; 15:md15020027. [PMID: 28134801 PMCID: PMC5334608 DOI: 10.3390/md15020027] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/20/2017] [Indexed: 11/16/2022] Open
Abstract
Antifreeze proteins (AFPs) are biological antifreezes with unique properties, including thermal hysteresis(TH),ice recrystallization inhibition(IRI),and interaction with membranes and/or membrane proteins. These properties have been utilized in the preservation of biological samples at low temperatures. Here, we review the structure and function of marine-derived AFPs, including moderately active fish AFPs and hyperactive polar AFPs. We also survey previous and current reports of cryopreservation using AFPs. Cryopreserved biological samples are relatively diverse ranging from diatoms and reproductive cells to embryos and organs. Cryopreserved biological samples mainly originate from mammals. Most cryopreservation trials using marine-derived AFPs have demonstrated that addition of AFPs can improve post-thaw viability regardless of freezing method (slow-freezing or vitrification), storage temperature, and types of biological sample type.
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Affiliation(s)
- Hak Jun Kim
- Department of Chemistry, Pukyong National University, Busan 48513, Korea.
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Young Baek Hur
- Tidal Flat Research Institute, National Fisheries Research and Development Institute, Gunsan, Jeonbuk 54014, Korea.
| | - Chang Woo Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Sun-Ha Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Bon-Won Koo
- Department of Chemistry, Pukyong National University, Busan 48513, Korea.
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24
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Abstract
The mechanism of ice nucleation at the molecular level remains largely unknown. Nature endows antifreeze proteins (AFPs) with the unique capability of controlling ice formation. However, the effect of AFPs on ice nucleation has been under debate. Here we report the observation of both depression and promotion effects of AFPs on ice nucleation via selectively binding the ice-binding face (IBF) and the non-ice-binding face (NIBF) of AFPs to solid substrates. Freezing temperature and delay time assays show that ice nucleation is depressed with the NIBF exposed to liquid water, whereas ice nucleation is facilitated with the IBF exposed to liquid water. The generality of this Janus effect is verified by investigating three representative AFPs. Molecular dynamics simulation analysis shows that the Janus effect can be established by the distinct structures of the hydration layer around IBF and NIBF. Our work greatly enhances the understanding of the mechanism of AFPs at the molecular level and brings insights to the fundamentals of heterogeneous ice nucleation.
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Affiliation(s)
- Kai Liu
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Chunlei Wang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People's Republic of China;
| | - Ji Ma
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, People's Republic of China
| | - Guosheng Shi
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People's Republic of China
| | - Xi Yao
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Haiping Fang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People's Republic of China
| | - Yanlin Song
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Jianjun Wang
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China;
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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25
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Bar Dolev M, Bernheim R, Guo S, Davies PL, Braslavsky I. Putting life on ice: bacteria that bind to frozen water. J R Soc Interface 2016; 13:20160210. [PMID: 27534698 PMCID: PMC5014055 DOI: 10.1098/rsif.2016.0210] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/19/2016] [Indexed: 11/12/2022] Open
Abstract
Ice-binding proteins (IBPs) are typically small, soluble proteins produced by cold-adapted organisms to help them avoid ice damage by either resisting or tolerating freezing. By contrast, the IBP of the Antarctic bacterium Marinomonas primoryensis is an extremely long, 1.5 MDa protein consisting of five different regions. The fourth region, a 34 kDa domain, is the only part that confers ice binding. Bioinformatic studies suggest that this IBP serves as an adhesin that attaches the bacteria to ice to keep it near the top of the water column, where oxygen and nutrients are available. Using temperature-controlled cells and a microfluidic apparatus, we show that M. primoryensis adheres to ice and is only released when melting occurs. Binding is dependent on the mobility of the bacterium and the functionality of the IBP domain. A polyclonal antibody raised against the IBP region blocks bacterial ice adhesion. This concept may be the basis for blocking biofilm formation in other bacteria, including pathogens. Currently, this IBP is the only known example of an adhesin that has evolved to bind ice.
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Affiliation(s)
- Maya Bar Dolev
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Reut Bernheim
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Shuaiqi Guo
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Ido Braslavsky
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
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26
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Cid FP, Rilling JI, Graether SP, Bravo LA, Mora MDLL, Jorquera MA. Properties and biotechnological applications of ice-binding proteins in bacteria. FEMS Microbiol Lett 2016; 363:fnw099. [PMID: 27190285 DOI: 10.1093/femsle/fnw099] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2016] [Indexed: 01/04/2023] Open
Abstract
Ice-binding proteins (IBPs), such as antifreeze proteins (AFPs) and ice-nucleating proteins (INPs), have been described in diverse cold-adapted organisms, and their potential applications in biotechnology have been recognized in various fields. Currently, both IBPs are being applied to biotechnological processes, primarily in medicine and the food industry. However, our knowledge regarding the diversity of bacterial IBPs is limited; few studies have purified and characterized AFPs and INPs from bacteria. Phenotypically verified IBPs have been described in members belonging to Gammaproteobacteria, Actinobacteria and Flavobacteriia classes, whereas putative IBPs have been found in Gammaproteobacteria, Alphaproteobacteria and Bacilli classes. Thus, the main goal of this minireview is to summarize the current information on bacterial IBPs and their application in biotechnology, emphasizing the potential application in less explored fields such as agriculture. Investigations have suggested the use of INP-producing bacteria antagonists and AFPs-producing bacteria (or their AFPs) as a very attractive strategy to prevent frost damages in crops. UniProt database analyses of reported IBPs (phenotypically verified) and putative IBPs also show the limited information available on bacterial IBPs and indicate that major studies are required.
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Affiliation(s)
- Fernanda P Cid
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco 4811230, Chile
| | - Joaquín I Rilling
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco 4811230, Chile
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Leon A Bravo
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Forestales, Universidad de la Frontera, Temuco 4811230, Chile
| | - María de La Luz Mora
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Milko A Jorquera
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
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27
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Yang R, Zhang C, Gao R, Zhang L. An Effective Antifreeze Protein Predictor with Ensemble Classifiers and Comprehensive Sequence Descriptors. Int J Mol Sci 2015; 16:21191-214. [PMID: 26370959 PMCID: PMC4613249 DOI: 10.3390/ijms160921191] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 08/18/2015] [Accepted: 08/26/2015] [Indexed: 12/03/2022] Open
Abstract
Antifreeze proteins (AFPs) play a pivotal role in the antifreeze effect of overwintering organisms. They have a wide range of applications in numerous fields, such as improving the production of crops and the quality of frozen foods. Accurate identification of AFPs may provide important clues to decipher the underlying mechanisms of AFPs in ice-binding and to facilitate the selection of the most appropriate AFPs for several applications. Based on an ensemble learning technique, this study proposes an AFP identification system called AFP-Ensemble. In this system, random forest classifiers are trained by different training subsets and then aggregated into a consensus classifier by majority voting. The resulting predictor yields a sensitivity of 0.892, a specificity of 0.940, an accuracy of 0.938 and a balanced accuracy of 0.916 on an independent dataset, which are far better than the results obtained by previous methods. These results reveal that AFP-Ensemble is an effective and promising predictor for large-scale determination of AFPs. The detailed feature analysis in this study may give useful insights into the molecular mechanisms of AFP-ice interactions and provide guidance for the related experimental validation. A web server has been designed to implement the proposed method.
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Affiliation(s)
- Runtao Yang
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
| | - Chengjin Zhang
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
- School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai 264209, China.
| | - Rui Gao
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
| | - Lina Zhang
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
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28
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Pucciarelli S, Devaraj RR, Mancini A, Ballarini P, Castelli M, Schrallhammer M, Petroni G, Miceli C. Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences. Microb Ecol 2015; 70:484-97. [PMID: 25704316 PMCID: PMC4494151 DOI: 10.1007/s00248-015-0568-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 01/08/2015] [Indexed: 05/23/2023]
Abstract
We report the characterization of the bacterial consortium associated to Euplotes focardii, a strictly psychrophilic marine ciliate that was maintained in laboratory cultures at 4 °C after its first isolation from Terra Nova Bay, in Antarctica. By Illumina genome analyser, we obtained 11,179 contigs of potential prokaryotic origin and classified them according to the NCBI's prokaryotic attributes table. The majority of these sequences correspond to either Bacteroidetes (16 %) or Proteobacteria (78 %). The latter were dominated by gamma- (39 %, including sequences related to the pathogenic genus Francisella), and alpha-proteobacterial (30 %) sequences. Analysis of the Pfam domain family and Gene Ontology term variation revealed that the most frequent terms that appear unique to this consortium correspond to proteins involved in "transmembrane transporter activity" and "oxidoreductase activity". Furthermore, we identified genes that encode for enzymes involved in the catabolism of complex substance for energy reserves. We also characterized members of the transposase and integrase superfamilies, whose role in bacterial evolution is well documented, as well as putative antifreeze proteins. Antibiotic treatments of E. focardii cultures delayed the cell division of the ciliate. To conclude, our results indicate that this consortium is largely represented by bacteria derived from the original Antarctic sample and may contribute to the survival of E. focardii in laboratory condition. Furthermore, our results suggest that these bacteria may have a more general role in E. focardii survival in its natural cold and oxidative environment.
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Affiliation(s)
- Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, 62032, Italy,
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29
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Wisniewski M, Neuner G, Gusta LV. The use of high-resolution infrared thermography (HRIT) for the study of ice nucleation and ice propagation in plants. J Vis Exp 2015:e52703. [PMID: 25992743 PMCID: PMC4542532 DOI: 10.3791/52703] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Freezing events that occur when plants are actively growing can be a lethal event, particularly if the plant has no freezing tolerance. Such frost events often have devastating effects on agricultural production and can also play an important role in shaping community structure in natural populations of plants, especially in alpine, sub-arctic, and arctic ecosystems. Therefore, a better understanding of the freezing process in plants can play an important role in the development of methods of frost protection and understanding mechanisms of freeze avoidance. Here, we describe a protocol to visualize the freezing process in plants using high-resolution infrared thermography (HRIT). The use of this technology allows one to determine the primary sites of ice formation in plants, how ice propagates, and the presence of ice barriers. Furthermore, it allows one to examine the role of extrinsic and intrinsic nucleators in determining the temperature at which plants freeze and evaluate the ability of various compounds to either affect the freezing process or increase freezing tolerance. The use of HRIT allows one to visualize the many adaptations that have evolved in plants, which directly or indirectly impact the freezing process and ultimately enables plants to survive frost events.
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Affiliation(s)
- Michael Wisniewski
- U.S Department of Agriculture, Agricultural Research Service (USDA-ARS), Kearneysville, WV;
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30
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Kuiper MJ, Morton CJ, Abraham SE, Gray-Weale A. The biological function of an insect antifreeze protein simulated by molecular dynamics. eLife 2015; 4. [PMID: 25951514 PMCID: PMC4442126 DOI: 10.7554/elife.05142] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 05/06/2015] [Indexed: 11/16/2022] Open
Abstract
Antifreeze proteins (AFPs) protect certain cold-adapted organisms from freezing to death by selectively adsorbing to internal ice crystals and inhibiting ice propagation. The molecular details of AFP adsorption-inhibition is uncertain but is proposed to involve the Gibbs–Thomson effect. Here we show by using unbiased molecular dynamics simulations a protein structure-function mechanism for the spruce budworm Choristoneura fumiferana AFP, including stereo-specific binding and consequential melting and freezing inhibition. The protein binds indirectly to the prism ice face through a linear array of ordered water molecules that are structurally distinct from the ice. Mutation of the ice binding surface disrupts water-ordering and abolishes activity. The adsorption is virtually irreversible, and we confirm the ice growth inhibition is consistent with the Gibbs–Thomson law. DOI:http://dx.doi.org/10.7554/eLife.05142.001 Water expands as it freezes. If this happens to the water inside plants and animals, the resulting ice crystals can rupture cells. To prevent this, many plants and animals that live in cold climates have evolved ‘antifreeze proteins’. When a small particle of ice first starts to form, the antifreeze proteins bind to it and prevent the water around it freezing, hence preventing the growth of an ice crystal. There are many different types of antifreeze protein, and some are more active than others. For example, some insects including the spruce budworm are exposed to extremely cold temperatures—sometimes below −30°C—and these insects have antifreeze proteins that are highly active. It is not fully understood how different antifreeze proteins interact with ice and prevent the growth of ice crystals. This is largely because, as yet, there are no experimental techniques that make it possible to see how antifreeze proteins and water molecules arrange themselves at the surface of a growing particle of ice. Instead, scientists have developed computer simulations to investigate this process. While many of these studies have provided valuable information, the computational methods used have only recently become powerful enough to analyze how the antifreeze proteins approach the surface of the ice particle. Kuiper et al. carried out simulations involving a highly active antifreeze protein from the spruce budworm. The results of these simulations revealed that this antifreeze protein does not bind directly to ice; instead, water molecules at the surface of the protein act as a bridge between the protein and the ice. These water molecules are highly ordered and though they have similarities with how water is structured in the ice, they are distinct from the ice lattice itself. Furthermore, this arrangement appears to be important for allowing the spruce budworm antifreeze protein to interact with the ice. This study provides detailed insights as to how a highly active antifreeze protein helps to prevent ice crystals forming. In the future, the computational simulations used here may be extended to study the dynamics of other antifreeze proteins, and also how crystals of other materials form. DOI:http://dx.doi.org/10.7554/eLife.05142.002
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Affiliation(s)
- Michael J Kuiper
- Victorian Life Sciences Computation Initiative, The University of Melbourne, Carlton, Australia
| | - Craig J Morton
- ACRF Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, Australia
| | - Sneha E Abraham
- School of Chemistry, The University of Melbourne, Melbourne, Australia
| | - Angus Gray-Weale
- School of Chemistry, The University of Melbourne, Melbourne, Australia
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31
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Meister K, Lotze S, Olijve LLC, DeVries AL, Duman JG, Voets IK, Bakker HJ. Investigation of the Ice-Binding Site of an Insect Antifreeze Protein Using Sum-Frequency Generation Spectroscopy. J Phys Chem Lett 2015; 6:1162-1167. [PMID: 26262966 DOI: 10.1021/acs.jpclett.5b00281] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We study the ice-binding site (IBS) of a hyperactive antifreeze protein from the beetle Dendroides canadensis (DAFP-1) using vibrational sum-frequency generation spectroscopy. We find that DAFP-1 accumulates at the air-water interface due to the hydrophobic character of its threonine-rich IBS while retaining its highly regular β-helical fold. We observe a narrow band at 3485 cm(-1) that we assign to the O-H stretch vibration of threonine hydroxyl groups of the IBS. The narrow character of the 3485 cm(-1) band suggests that the hydrogen bonds between the threonine residues at the IBS and adjacent water molecules are quite similar in strength, indicating that the IBS of DAFP-1 is extremely well-ordered, with the threonine side chains showing identical rotameric confirmations. The hydrogen-bonded water molecules do not form an ordered ice-like layer, as was recently observed for the moderate antifreeze protein type III. It thus appears that the antifreeze action of DAFP-1 does not require the presence of ordered water but likely results from the direct binding of its highly ordered array of threonine residues to the ice surface.
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Affiliation(s)
- Konrad Meister
- †FOM-Institute for Atomic and Molecular Physics AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Stephan Lotze
- †FOM-Institute for Atomic and Molecular Physics AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Luuk L C Olijve
- ‡Laboratory of Macromolecular and Organic Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Postbus 513, 5600 MB Eindhoven, The Netherlands
| | - Arthur L DeVries
- §Department of Animal Biology, University of Illinois at Urbana-Champaign, 515 Morrill Hall, Urbana, Illinois 61801, United States
| | - John G Duman
- ∥Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences Center, Notre Dame, Indiana 46556, United States
| | - Ilja K Voets
- ‡Laboratory of Macromolecular and Organic Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Postbus 513, 5600 MB Eindhoven, The Netherlands
| | - Huib J Bakker
- †FOM-Institute for Atomic and Molecular Physics AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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32
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Drori R, Celik Y, Davies PL, Braslavsky I. Ice-binding proteins that accumulate on different ice crystal planes produce distinct thermal hysteresis dynamics. J R Soc Interface 2015; 11:20140526. [PMID: 25008081 PMCID: PMC4233703 DOI: 10.1098/rsif.2014.0526] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ice-binding proteins that aid the survival of freeze-avoiding, cold-adapted organisms
by inhibiting the growth of endogenous ice crystals are called antifreeze proteins
(AFPs). The binding of AFPs to ice causes a separation between the melting point and
the freezing point of the ice crystal (thermal hysteresis, TH). TH produced by
hyperactive AFPs is an order of magnitude higher than that produced by a typical fish
AFP. The basis for this difference in activity remains unclear. Here, we have
compared the time dependence of TH activity for both hyperactive and moderately
active AFPs using a custom-made nanolitre osmometer and a novel microfluidics system.
We found that the TH activities of hyperactive AFPs were time-dependent, and that the
TH activity of a moderate AFP was almost insensitive to time. Fluorescence microscopy
measurement revealed that despite their higher TH activity, hyperactive AFPs from two
insects (moth and beetle) took far longer to accumulate on the ice surface than did a
moderately active fish AFP. An ice-binding protein from a bacterium that functions as
an ice adhesin rather than as an antifreeze had intermediate TH properties.
Nevertheless, the accumulation of this ice adhesion protein and the two hyperactive
AFPs on the basal plane of ice is distinct and extensive, but not detectable for
moderately active AFPs. Basal ice plane binding is the distinguishing feature of
antifreeze hyperactivity, which is not strictly needed in fish that require only
approximately 1°C of TH. Here, we found a correlation between the accumulation
kinetics of the hyperactive AFP at the basal plane and the time sensitivity of the
measured TH.
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Affiliation(s)
- Ran Drori
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yeliz Celik
- Department of Physics and Astronomy, Ohio University, Athens, OH, USA
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Ido Braslavsky
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel Department of Physics and Astronomy, Ohio University, Athens, OH, USA
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33
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Meister K, Strazdaite S, DeVries AL, Lotze S, Olijve LL, Voets IK, Bakker HJ. Observation of ice-like water layers at an aqueous protein surface. Proc Natl Acad Sci U S A 2014; 111:17732-6. [PMID: 25468976 DOI: 10.1073/pnas.1414188111] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We study the properties of water at the surface of an antifreeze protein with femtosecond surface sum frequency generation spectroscopy. We find clear evidence for the presence of ice-like water layers at the ice-binding site of the protein in aqueous solution at temperatures above the freezing point. Decreasing the temperature to the biological working temperature of the protein (0 °C to -2 °C) increases the amount of ice-like water, while a single point mutation in the ice-binding site is observed to completely disrupt the ice-like character and to eliminate antifreeze activity. Our observations indicate that not the protein itself but ordered ice-like water layers are responsible for the recognition and binding to ice.
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34
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Banerjee R, Chakraborti P, Bhowmick R, Mukhopadhyay S. Distinct molecular features facilitating ice-binding mechanisms in hyperactive antifreeze proteins closely related to an Antarctic sea ice bacterium. J Biomol Struct Dyn 2014; 33:1424-41. [PMID: 25190099 DOI: 10.1080/07391102.2014.952665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Antifreeze proteins or ice-binding proteins (IBPs) facilitate the survival of certain cellular organisms in freezing environment by inhibiting the growth of ice crystals in solution. Present study identifies orthologs of the IBP of Colwellia sp. SLW05, which were obtained from a wide range of taxa. Phylogenetic analysis on the basis of conserved regions (predicted as the 'ice-binding domain' [IBD]) present in all the orthologs, separates the bacterial and archaeal orthologs from that of the eukaryotes'. Correspondence analysis pointed out that the bacterial and archaeal IBDs have relatively higher average hydrophobicity than the eukaryotic members. IBDs belonging to bacterial as well as archaeal AFPs contain comparatively more strands, and therefore are revealed to be under higher evolutionary selection pressure. Molecular docking studies prove that the ice crystals form more stable complex with the bacterial as well as archaeal proteins than the eukaryotic orthologs. Analysis of the docked structures have traced out the ice-binding sites (IBSs) in all the orthologs which continue to facilitate ice-binding activity even after getting mutated with respect to the well-studied IBSs of Typhula ishikariensis and notably, all these mutations performing ice-binding using 'anchored clathrate mechanism' have been found to prefer polar and hydrophilic amino acids. Horizontal gene transfer studies point toward a strong selection pressure favoring independent evolution of the IBPs in some polar organisms including prokaryotes as well as eukaryotes because these proteins facilitate the polar organisms to acclimatize to the adversities in their niche, thus safeguarding their existence.
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Affiliation(s)
- Rachana Banerjee
- a Department of Biophysics, Molecular Biology and Bioinformatics , University of Calcutta , 92, A.P.C. Road, Kolkata 700009 , India
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Do H, Kim SJ, Kim HJ, Lee JH. Structure-based characterization and antifreeze properties of a hyperactive ice-binding protein from the Antarctic bacterium Flavobacterium frigoris PS1. ACTA ACUST UNITED AC 2014; 70:1061-73. [PMID: 24699650 DOI: 10.1107/s1399004714000996] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 01/15/2014] [Indexed: 11/10/2022]
Abstract
Ice-binding proteins (IBPs) inhibit ice growth through direct interaction with ice crystals to permit the survival of polar organisms in extremely cold environments. FfIBP is an ice-binding protein encoded by the Antarctic bacterium Flavobacterium frigoris PS1. The X-ray crystal structure of FfIBP was determined to 2.1 Å resolution to gain insight into its ice-binding mechanism. The refined structure of FfIBP shows an intramolecular disulfide bond, and analytical ultracentrifugation and analytical size-exclusion chromatography show that it behaves as a monomer in solution. Sequence alignments and structural comparisons of IBPs allowed two groups of IBPs to be defined, depending on sequence differences between the α2 and α4 loop regions and the presence of the disulfide bond. Although FfIBP closely resembles Leucosporidium (recently re-classified as Glaciozyma) IBP (LeIBP) in its amino-acid sequence, the thermal hysteresis (TH) activity of FfIBP appears to be tenfold higher than that of LeIBP. A comparison of the FfIBP and LeIBP structures reveals that FfIBP has different ice-binding residues as well as a greater surface area in the ice-binding site. Notably, the ice-binding site of FfIBP is composed of a T-A/G-X-T/N motif, which is similar to the ice-binding residues of hyperactive antifreeze proteins. Thus, it is proposed that the difference in TH activity between FfIBP and LeIBP may arise from the amino-acid composition of the ice-binding site, which correlates with differences in affinity and surface complementarity to the ice crystal. In conclusion, this study provides a molecular basis for understanding the antifreeze mechanism of FfIBP and provides new insights into the reasons for the higher TH activity of FfIBP compared with LeIBP.
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Affiliation(s)
- Hackwon Do
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea
| | - Soon-Jong Kim
- Department of Chemistry, Mokpo National University, Chonnam 534-729, Republic of Korea
| | - Hak Jun Kim
- Department of Chemistry, Pukyong National University, Busan 608-739, Republic of Korea
| | - Jun Hyuck Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea
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Abstract
Antifreeze proteins (AFPs) bind to ice crystal surfaces and thus inhibit the ice growth. The mechanism for how AFPs suppress freezing is commonly modeled as an adsorption-inhibition process by the Gibbs-Thomson effect. Here we develop an improved adsorption-inhibition model for AFP action based on the thermodynamics of impurity adsorption on the crystal surfaces. We demonstrate the derivation of a realistic relationship between surface protein coverage and the protein concentration. We show that the improved model provides a quantitatively better fit to the experimental antifreeze activities of AFPs from distinct structural classes, including fish and insect AFPs, in a wide range of concentrations. Our theoretical results yielded the adsorption coefficients of the AFPs on ice, suggesting that, despite the distinct difference in their antifreeze activities and structures, the affinities of the AFPs to ice are very close and the mechanism of AFP action is a kinetically controlled, reversible process. The applications of the model to more complex systems along with its potential limitations are also discussed.
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Affiliation(s)
- Sen Wang
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California 90032
- Visiting scholar from the Molecular Imaging Program, Stanford University, Stanford, California 94305
| | - Natapol Amornwittawat
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California 90032
| | - Xin Wen
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California 90032
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Zhao X, Ma Z, Yin M. Using support vector machine and evolutionary profiles to predict antifreeze protein sequences. Int J Mol Sci 2012; 13:2196-2207. [PMID: 22408447 PMCID: PMC3292016 DOI: 10.3390/ijms13022196] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 01/29/2012] [Accepted: 01/29/2012] [Indexed: 11/16/2022] Open
Abstract
Antifreeze proteins (AFPs) are ice-binding proteins. Accurate identification of new AFPs is important in understanding ice-protein interactions and creating novel ice-binding domains in other proteins. In this paper, an accurate method, called AFP_PSSM, has been developed for predicting antifreeze proteins using a support vector machine (SVM) and position specific scoring matrix (PSSM) profiles. This is the first study in which evolutionary information in the form of PSSM profiles has been successfully used for predicting antifreeze proteins. Tested by 10-fold cross validation and independent test, the accuracy of the proposed method reaches 82.67% for the training dataset and 93.01% for the testing dataset, respectively. These results indicate that our predictor is a useful tool for predicting antifreeze proteins. A web server (AFP_PSSM) that implements the proposed predictor is freely available.
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Affiliation(s)
- Xiaowei Zhao
- College of Computer Science and Information Technology, Northeast Normal University, 2555 Jingyue Street, Changchun 130117, China; E-Mail:
- Key Laboratory of Intelligent Information Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
- College of Life Science, Northeast Normal University, 5268 Renmin Street, Changchun 130024, China
| | - Zhiqiang Ma
- College of Computer Science and Information Technology, Northeast Normal University, 2555 Jingyue Street, Changchun 130117, China; E-Mail:
- Key Laboratory of Intelligent Information Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
- College of Life Science, Northeast Normal University, 5268 Renmin Street, Changchun 130024, China
- Authors to whom correspondence should be addressed; E-Mails: (Z.M.); (M.Y.); Tel./Fax: +86-0431-8453-6338 (Z.M.; M.Y.)
| | - Minghao Yin
- College of Computer Science and Information Technology, Northeast Normal University, 2555 Jingyue Street, Changchun 130117, China; E-Mail:
- Key Laboratory of Intelligent Information Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
- Authors to whom correspondence should be addressed; E-Mails: (Z.M.); (M.Y.); Tel./Fax: +86-0431-8453-6338 (Z.M.; M.Y.)
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