1
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Grabowska J, Kuffel A, Zielkiewicz J. Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice. J Chem Phys 2024; 160:095101. [PMID: 38445741 DOI: 10.1063/5.0187663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
Using molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water, which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation and distance relative to the surface of ice, which enables the effective binding (via hydrogen bonds) of the molecule with the nascent ice surface. Our results show that the final adsorption of the AFP III molecule on the surface of ice is not achieved by chaotic diffusion movements, but it is preceded by a remote, water-mediated interaction between the IBS and the surface of ice. The key factor that determines the existence of this interaction is the ability of water molecules to spontaneously form large, high-volume aggregates that can be anchored to both the IBS of the AFP molecule and the surface of ice. The results presented in this work for AFP III are in full agreement with the ones obtained by us previously for hyperactive CfAFP, which indicates that the mechanism of the remote interaction of these molecules with ice remains unchanged despite significant differences in the molecular structure of their ice binding sites. For that reason, we can expect that also other types of AFPs interact with the ice surface according to an analogous mechanism.
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Affiliation(s)
- Joanna Grabowska
- Faculty of Chemistry, Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Anna Kuffel
- Faculty of Chemistry, Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Jan Zielkiewicz
- Faculty of Chemistry, Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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2
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Procházková L, Remias D, Nedbalová L, Raymond JA. A DUF3494 ice-binding protein with a root cap domain in a streptophyte glacier ice alga. FRONTIERS IN PLANT SCIENCE 2024; 14:1306511. [PMID: 38250448 PMCID: PMC10796529 DOI: 10.3389/fpls.2023.1306511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024]
Abstract
Ice-binding proteins (IBPs) of the DUF3494 type have been found in many ice-associated unicellular photoautotrophs, including chlorophytes, haptophytes, diatoms and a cyanobacterium. Unrelated IBPs have been found in many land plants (streptophytes). Here we looked for IBPs in two streptophyte algae that grow only on glaciers, a group in which IBPs have not previously been examined. The two species, Ancylonema nordenskioeldii and Ancylonema. alaskanum, belong to the class Zygnematophyceae, whose members are the closest relatives to all land plants. We found that one of them, A. nordenskioeldii, expresses a DUF3494-type IBP that is similar to those of their chlorophyte ancestors and that has not previously been found in any streptophytes. The protein is unusual in having what appears to be a perfect array of TXT motifs that have been implicated in water or ice binding. The IBP strongly binds to ice and almost certainly has a role in mitigating the daily freeze-thaw cycles that the alga is exposed to during late summer. No IBP was found in the second species, A. alaskanum, which may rely more on glycerol production for its freeze-thaw tolerance. The IBP is also unusual in having a 280-residue domain with a β sandwich structure (which we designate as the DPH domain) that is characteristic of root cap proteins of land plants, and that may have a role in forming IBP oligomers. We also examined existing transcriptome data obtained from land plants to better understand the tissue and temperature dependence of expression of this domain.
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Affiliation(s)
| | - Daniel Remias
- Department of Environment and Biodiversity, Paris Lodron University Salzburg, Salzburg, Austria
| | | | - James A. Raymond
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
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3
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Vance TDR. Ice Isn't the Only Crystal in Town: Structure Determination of Ice-Binding Proteins via X-Ray Crystallography. Methods Mol Biol 2024; 2730:35-62. [PMID: 37943449 DOI: 10.1007/978-1-0716-3503-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Ice-binding proteins (IBPs) are proteins that have the remarkable ability to bind to ice, and their study has intrigued researchers for decades. This chapter explores the importance of structural biology in understanding IBPs and highlights the significant contributions of IBPs to the field of structural biology. The structures of various IBPs from different organisms have been elucidated, revealing key elements involved in ice binding. Structural biology techniques, including nuclear magnetic resonance (NMR) spectroscopy, transmission electron cryo-microscopy (cryo-EM), and X-ray crystallography, play crucial roles in solving protein structures. This article focuses on X-ray crystallography as a tool for investigating IBP structures, providing insights into its theoretical and practical aspects, experimental workflows, and common pitfalls to avoid.
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Affiliation(s)
- Tyler D R Vance
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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4
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Silva Júnior RA, Desenzi R, Ramires MMS, Souza AF, Donato MAM, Peixoto CA, Nascimento T, Bartolomeu CC, Batista AM. Effects of antifreeze protein from Lolium perenne L. ( LpAFP) in the vitrification of in vitro-produced bovine embryos. ZYGOTE 2023; 31:468-474. [PMID: 37366027 DOI: 10.1017/s0967199423000333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
In the present study, the cryoprotective effects of Lolium perenne antifreeze protein (LpAFP) on the vitrification of bovine embryos were evaluated. In vitro-produced blastocysts were divided into two groups: the control group (CG) without the addition of LpAFP and the treatment group (TG) with the addition of 500 ng/ml of LpAFP in the equilibrium and vitrification solution. Vitrification was carried out by transferring the blastocysts to the equilibrium solution [7.5% ethylene glycol (EG) and 7.5% dimethyl sulfoxide (DMSO)] for 2 min and then to the vitrification solution (15% EG, 15% DMSO and 0.5M sucrose). The blastocysts were deposited on a cryotop device and submerged in liquid nitrogen. Warming was carried out in three steps in solutions with different sucrose concentrations (1.0, 0.5, and 0.0 M, respectively). Embryos were evaluated for re-expansion/hatching, the total cell count, and ultrastructural analysis. There was no significant difference in the re-expansion rate 24 h after warming; however, there was variation (P < 0.05) in the hatching rate in the TG and the total number of cells 24 h after warming was higher in the TG (114.87 ± 7.24) when compared with the CG (91.81 ± 4.94). The ultrastructural analysis showed changes in organelles related to the vitrification process but, in the TG, there was less damage to mitochondria and rough endoplasmic reticulum compared with the CG. In conclusion, the addition of 500 ng/ml of LpAFP during the vitrification of in vitro-produced bovine embryos improved the hatching rate and total cell number of blastocysts after warming and mitigated intracellular damage.
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Affiliation(s)
- R A Silva Júnior
- Laboratório de Biotécnicas Aplicadas à Reprodução, Departamento de Medicina Veterinária, Universidade Federal Rural de Pernambuco, Recife, Pernambuco, Brazil
| | - R Desenzi
- Laboratório de Biotécnicas Aplicadas à Reprodução, Departamento de Medicina Veterinária, Universidade Federal Rural de Pernambuco, Recife, Pernambuco, Brazil
| | - M M S Ramires
- Departamento de Zootecnia, Universidade Federal Rural de Pernambuco, Recife, Pernambuco, Brazil
| | - A F Souza
- Departamento de Zootecnia, Universidade Federal Rural de Pernambuco, Recife, Pernambuco, Brazil
| | - M A M Donato
- Departamento de Histologia e Embriologia, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - C A Peixoto
- Laboratory of Ultrastructure, Aggeu Magalhães Institute (IAM), Recife, PE, Brazil; National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM, CNPq), Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - T Nascimento
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - C C Bartolomeu
- Laboratório de Biotécnicas Aplicadas à Reprodução, Departamento de Medicina Veterinária, Universidade Federal Rural de Pernambuco, Recife, Pernambuco, Brazil
| | - A M Batista
- Laboratório de Biotécnicas Aplicadas à Reprodução, Departamento de Medicina Veterinária, Universidade Federal Rural de Pernambuco, Recife, Pernambuco, Brazil
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5
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Zielkiewicz J. Mechanism of antifreeze protein functioning and the "anchored clathrate water" concept. J Chem Phys 2023; 159:085101. [PMID: 37622597 DOI: 10.1063/5.0158590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
In liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case, the interactions of water molecules with the protein surface shift the equilibrium of the process. In this paper, we analyze the structural properties of the solvation water in antifreeze proteins (AFPs). The results of molecular dynamics analysis with the use of various parameters related to the structure of solvation water on the protein surface are presented. We found that in the vicinity of the active region responsible for the binding of AFPs to ice, the equilibrium is clearly shifted toward the formation of "ice-like aggregates," and the solvation water has a more ordered ice-like structure. We have demonstrated that a reduction in the tendency to create "ice-like aggregates" results in a significant reduction in the antifreeze activity of the protein. We conclude that shifting the equilibrium in favor of the formation of "ice-like aggregates" in the solvation water in the active region is a prerequisite for the biological functionality of AFPs, at least for AFPs having a well-defined ice binding area. In addition, our results fully confirm the validity of the "anchored clathrate water" concept, formulated by Garnham et al. [Proc. Natl. Acad. Sci. U. S. A. 108, 7363 (2011)].
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Affiliation(s)
- Jan Zielkiewicz
- Faculty of Chemistry, Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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6
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Farag H, Peters B. Engulfment Avalanches and Thermal Hysteresis for Antifreeze Proteins on Supercooled Ice. J Phys Chem B 2023. [PMID: 37294871 DOI: 10.1021/acs.jpcb.3c01089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Antifreeze proteins (AFPs) bind to the ice-water surface and prevent ice growth at temperatures below 0 °C through a Gibbs-Thomson effect. Each adsorbed AFP creates a metastable depression on the surface that locally resists ice growth, until ice engulfs the AFP. We recently predicted the susceptibility to engulfment as a function of AFP size, distance between AFPs, and supercooling [ J. Chem. Phys. 2023, 158, 094501]. For an ensemble of AFPs adsorbed on the ice surface, the most isolated AFPs are the most susceptible, and when an isolated AFP gets engulfed, its former neighbors become more isolated and more susceptible to engulfment. Thus, an initial engulfment event can trigger an avalanche of subsequent engulfment events, leading to a sudden surge of unrestrained ice growth. This work develops a model to predict the supercooling at which the first engulfment event will occur for an ensemble of randomly distributed AFP pinning sites on an ice surface. Specifically, we formulate an inhomogeneous survival probability that accounts for the AFP coverage, the distribution of AFP neighbor distances, the resulting ensemble of engulfment rates, the ice surface area, and the cooling rate. We use the model to predict thermal hysteresis trends and compare with experimental data.
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Affiliation(s)
- Hossam Farag
- Nuclear, Plasma, and Radiological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Baron Peters
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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7
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Kamat K, Naullage PM, Molinero V, Peters B. Oriented attachment kinetics for rod-like particles at a flat surface: Buffon's needle at the nanoscale. J Chem Phys 2022; 157:214113. [PMID: 36511557 DOI: 10.1063/5.0124531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The adsorption of large rod-like molecules or crystallites on a flat crystal face, similar to Buffon's needle, requires the rods to "land," with their binding sites in precise orientational alignment with matching sites on the surface. An example is provided by long, helical antifreeze proteins (AFPs), which bind at specific facets and orientations on the ice surface. The alignment constraint for adsorption, in combination with the loss in orientational freedom as the molecule diffuses toward the surface, results in an entropic barrier that hinders the adsorption. Prior kinetic models do not factor in the complete geometry of the molecule, nor explicitly enforce orientational constraints for adsorption. Here, we develop a diffusion-controlled adsorption theory for AFP molecules binding at specific orientations to flat ice surfaces. We formulate the diffusion equation with relevant boundary conditions and present analytical solutions to the attachment rate constant. The resulting rate constant is a function of the length and aspect ratio of the AFP, the distance threshold associated with binding, and solvent conditions such as temperature and viscosity. These results and methods of calculation may also be useful for predicting the kinetics of crystal growth through oriented attachment.
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Affiliation(s)
- Kartik Kamat
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Pavithra M Naullage
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Valeria Molinero
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Baron Peters
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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8
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Yang F, Jiang W, Chen X, Chen X, Wu J, Huang J, Cai X, Wang S. Identification of Novel Antifreeze Peptides from Takifugu obscurus Skin and Molecular Mechanism in Inhibiting Ice Crystal Growth. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14148-14156. [PMID: 36314886 DOI: 10.1021/acs.jafc.2c04393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Foodborne hydrolyzed antifreeze peptides have been widely used in the food industry and the biomedical field. However, the components of hydrolyzed peptides are complex and the molecular mechanism remains unclear. This study focused on identification and mechanism analysis of novel antifreeze peptides from Takifugu obscurus skin by traditional methods and computer-assisted techniques. Results showed that three peptides (EGPRAGGAPG, GDAGPSGPAGPTG, and GEAGPAGPAG) possessed cryoprotection via reducing the freezing point and inhibiting ice crystal growth. Molecular docking confirmed that the cryoprotective property was related to peptide structure, especially α-helix, and hydrogen bond sites. Moreover, the antifreeze peptides were double-faces, which controlled ice crystals while affecting the arrangement of surrounding water molecules, thus exhibiting a strong antifreeze activity. This investigation deepens the comprehension of the mechanism of antifreeze peptides at molecular scale, and the novel efficient antifreeze peptides can be developed in antifreeze materials design and applied in food industry.
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Affiliation(s)
- Fujia Yang
- College of Chemical Engineering, Fuzhou University, Fuzhou350108, P.R. China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Wenting Jiang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Xu Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Xuan Chen
- College of Chemical Engineering, Fuzhou University, Fuzhou350108, P.R. China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Jinhong Wu
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai200240, P.R. China
| | - Jianlian Huang
- Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing of Ministry of Agriculture and Rural Affairs, Xiamen361022, P.R. China
- Fujian Anjoy Foods Co. Ltd., Xiamen361022, P.R. China
| | - Xixi Cai
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Shaoyun Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
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9
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Arai T, Yamauchi A, Yang Y, Singh SM, Sasaki YC, Tsuda S. Adsorption of ice-binding proteins onto whole ice crystal surfaces does not necessarily confer a high thermal hysteresis activity. Sci Rep 2022; 12:15443. [PMID: 36104389 PMCID: PMC9474881 DOI: 10.1038/s41598-022-19803-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Many psychrophilic microorganisms synthesize ice-binding proteins (IBPs) to survive the cold. The functions of IBPs are evaluated by the effect of the proteins on the nonequilibrium water freezing-point depression, which is called “thermal hysteresis (TH)”, and the inhibitory effect of the proteins on the growth of larger ice crystals, which is called “ice recrystallization inhibition (IRI)”. To obtain mechanical insight into the two activities, we developed a modified method of ice affinity purification and extracted two new IBP isoforms from Psychromyces glacialis, an Arctic glacier fungus. One isoform was found to be an approximately 25 kDa protein (PsgIBP_S), while the other is a 28 kDa larger protein (PsgIBP_L) that forms an intermolecular dimer. Their TH activities were less than 1 °C at millimolar concentrations, implying that both isoforms are moderately active but not hyperactive IBP species. It further appeared that both isoforms exhibit high IRI activity even at submicromolar concentrations. Furthermore, the isoforms can bind to the whole surface of a hemispherical single ice crystal, although such ice-binding was generally observed for hyperactive IBP species. These results suggest that the binding ability of IBPs to whole ice crystal surfaces is deficient for hyperactivity but is crucial for significant IRI activity.
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10
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Water-organizing motif continuity is critical for potent ice nucleation protein activity. Nat Commun 2022; 13:5019. [PMID: 36028506 PMCID: PMC9418140 DOI: 10.1038/s41467-022-32469-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/29/2022] [Indexed: 12/02/2022] Open
Abstract
Bacterial ice nucleation proteins (INPs) can cause frost damage to plants by nucleating ice formation at high sub-zero temperatures. Modeling of Pseudomonas borealis INP by AlphaFold suggests that the central domain of 65 tandem sixteen-residue repeats forms a beta-solenoid with arrays of outward-pointing threonines and tyrosines, which may organize water molecules into an ice-like pattern. Here we report that mutating some of these residues in a central segment of P. borealis INP, expressed in Escherichia coli, decreases ice nucleation activity more than the section’s deletion. Insertion of a bulky domain has the same effect, indicating that the continuity of the water-organizing repeats is critical for optimal activity. The ~10 C-terminal coils differ from the other 55 coils in being more basic and lacking water-organizing motifs; deletion of this region eliminates INP activity. We show through sequence modifications how arrays of conserved motifs form the large ice-nucleating surface required for potency. Ice nucleation proteins have the same tandemly arrayed water-organizing motifs seen in some antifreeze proteins, but on a larger scale. The authors show that mutation, interruption, and truncation of these arrays reduce ice nucleation activity indicating that the two protein types share a common mechanism.
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11
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Yu H, Zhang Q, Zhuang W. Comparative analysis of hydration layer reorientation dynamics of antifreeze protein and protein cytochrome P450. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2203038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Antifreeze proteins (AFPs) inhibit ice re-crystallization by a mechanism remaining largely elusive. Dynamics of AFPs’ hydration water and its involvement in the antifreeze activity have not been identified conclusively. We herein, by simulation and theory, examined the water reorientation dynamics in the first hydration layer of an AFP from the spruce budworm, Choristoneura fumiferana, compared with a protein cytochrome P450 (CYP). The increase of potential acceptor water molecules around donor water molecules leads to the acceleration of hydrogen bond exchange between water molecules. Therefore, the jump reorientation of water molecules around the AFP active region is accelerated. Due to the mutual coupling and excitation of hydrogen bond exchange, with the acceleration of hydrogen bond exchange, the rearrangement of the hydrogen bond network and the frame reorientation of water are accelerated. Therefore, the water reorientation dynamics of AFP is faster than that of CYP. The results of this study provide a new physical image of antifreeze protein and a new understanding of the antifreeze mechanism of antifreeze proteins.
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Affiliation(s)
- Hongfeng Yu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhang
- College of Chemistry and Material Sciences, Inner Mongolia Minzu University, Tongliao 028043, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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12
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Brachypodium Antifreeze Protein Gene Products Inhibit Ice Recrystallisation, Attenuate Ice Nucleation, and Reduce Immune Response. PLANTS 2022; 11:plants11111475. [PMID: 35684248 PMCID: PMC9182837 DOI: 10.3390/plants11111475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/17/2022]
Abstract
Antifreeze proteins (AFPs) from the model crop, Brachypodium distachyon, allow freeze survival and attenuate pathogen-mediated ice nucleation. Intriguingly, Brachypodium AFP genes encode two proteins, an autonomous AFP and a leucine-rich repeat (LRR). We present structural models which indicate that ice-binding motifs on the ~13 kDa AFPs can “spoil” nucleating arrays on the ~120 kDa bacterial ice nucleating proteins used to form ice at high sub-zero temperatures. These models are consistent with the experimentally demonstrated decreases in ice nucleating activity by lysates from wildtype compared to transgenic Brachypodium lines. Additionally, the expression of Brachypodium LRRs in transgenic Arabidopsis inhibited an immune response to pathogen flagella peptides (flg22). Structural models suggested that this was due to the affinity of the LRR domains to flg22. Overall, it is remarkable that the Brachypodium genes play multiple distinctive roles in connecting freeze survival and anti-pathogenic systems via their encoded proteins’ ability to adsorb to ice as well as to attenuate bacterial ice nucleation and the host immune response.
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13
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Chen X, Wu J, Li X, Yang F, Huang D, Huang J, Wang S, Guyonnet V. Snow flea antifreeze peptide for cryopreservation of lactic acid bacteria. NPJ Sci Food 2022; 6:10. [PMID: 35115563 PMCID: PMC8813996 DOI: 10.1038/s41538-022-00128-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/10/2022] [Indexed: 01/10/2023] Open
Abstract
Cryogenic machining is one of the most commonly used techniques for processing and preserving in food industry, and traditional antifreeze agents cannot regulate the mechanical stress damage caused by ice crystals formed during recrystallization or thawing. In this study, we successfully developed an express system of a novel recombinant snow flea antifreeze peptide (rsfAFP), which has significant ice recrystallization inhibition ability, thermal hysteresis activity and alters ice nucleation, thus regulating extracellular ice crystal morphology and recrystallization. We showed that rsfAFP improved the survival rate, acid-producing ability, freezing stability, and cellular metabolism activity of Streptococcus thermophilus. We further showed that rsfAFP interacts with the membrane and ice crystals to cover the outer layer of cells, forming a dense protective layer that maintains the physiological functions of S. thermophilus under freezing stress. These findings provide the scientific basis for using rsfAFP as an effective antifreeze agent for lactic acid bacteria cryopreservation or other frozen food.
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Affiliation(s)
- Xu Chen
- College of Biological Science and Engineering, Fuzhou University, 350108, Fuzhou, Fujian, China.,College of Chemical Engineering, Fuzhou University, 350108, Fuzhou, Fujian, China
| | - Jinhong Wu
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Xiaozhen Li
- College of Biological Science and Engineering, Fuzhou University, 350108, Fuzhou, Fujian, China
| | - Fujia Yang
- College of Biological Science and Engineering, Fuzhou University, 350108, Fuzhou, Fujian, China.,College of Chemical Engineering, Fuzhou University, 350108, Fuzhou, Fujian, China
| | - Dan Huang
- Fujian Provincial Key Laboratory of Frozen Processed Aquatic Products, 361022, Xiamen, China.,Fujian Anjoy Food Co. Ltd, 361022, Xiamen, China
| | - Jianlian Huang
- Fujian Provincial Key Laboratory of Frozen Processed Aquatic Products, 361022, Xiamen, China.,Fujian Anjoy Food Co. Ltd, 361022, Xiamen, China
| | - Shaoyun Wang
- College of Biological Science and Engineering, Fuzhou University, 350108, Fuzhou, Fujian, China.
| | - Vincent Guyonnet
- FFI Consulting Ltd, 2488 Lyn Road, Brockville, ON, K6V 5T3, Canada
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14
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Kamat K, Naullage PM, Molinero V, Peters B. Diffusion Attachment Model for Long Helical Antifreeze Proteins to Ice. Biomacromolecules 2021; 23:513-519. [PMID: 34928587 DOI: 10.1021/acs.biomac.1c01247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Some of the most potent antifreeze proteins (AFPs) are approximately rigid helical structures that bind with one side in contact with the ice surface at specific orientations. These AFPs take random orientations in solution; however, most orientations become sterically inaccessible as the AFP approaches the ice surface. The effect of these inaccessible orientations on the rate of adsorption of AFP to ice has never been explored. Here, we present a diffusion-controlled theory of adsorption kinetics that accounts for these orientational restrictions to predict a rate constant for adsorption (kon, in m/s) as a function of the length and width of the AFP molecules. We find that kon decreases with length and diameter of the AFP and is almost proportional to the inverse of the area of the binding surface. We demonstrate that the restricted orientations create an entropic barrier to AFP adsorption, which we compute to be approximately 7 kBT for most AFPs and up to 9 kBT for Maxi, the largest known AFP. We compare the entropic resistance 1/kon to resistances for diffusion through boundary layers and across typical distances in the extracellular matrix and find that these entropic and diffusion resistances could become comparable in the small confined spaces of biological environments.
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Affiliation(s)
- Kartik Kamat
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Pavithra M Naullage
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112, United States
| | - Valeria Molinero
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112, United States
| | - Baron Peters
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry and Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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15
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Baskaran A, Kaari M, Venugopal G, Manikkam R, Joseph J, Bhaskar PV. Anti freeze proteins (Afp): Properties, sources and applications - A review. Int J Biol Macromol 2021; 189:292-305. [PMID: 34419548 DOI: 10.1016/j.ijbiomac.2021.08.105] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022]
Abstract
Extreme cold marine and freshwater temperatures (below 4 °C) induce massive deterioration to the cell membranes of organisms resulting in the formation of ice crystals, consequently causing organelle damage or cell death. One of the adaptive mechanisms organisms have evolved to thrive in cold environments is the production of antifreeze proteins with the functional capabilities to withstand frigid temperatures. Antifreeze proteins are extensively identified in different cold-tolerant species and they facilitate the persistence of cold-adapted organisms by decreasing the freezing point of their body fluids. Various structurally diverse types of antifreeze proteins detected possess the ability to modify ice crystal growth by thermal hysteresis and ice recrystallization inhibition. The unique properties of antifreeze proteins have made them a promising resource in industry, biomedicine, food storage and cryobiology. This review collates the findings of the various studies carried out in the past and the recent developments observed in the properties, functional mechanisms, classification, distinct sources and the ever-increasing applications of antifreeze proteins. This review also summarizes the possibilities of the way forward to identify new avenues of research on anti-freeze proteins.
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Affiliation(s)
- Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Gopikrishnan Venugopal
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India.
| | - Jerrine Joseph
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Parli V Bhaskar
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama 403804, Goa, India
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16
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Stevens CA, Bachtiger F, Kong XD, Abriata LA, Sosso GC, Gibson MI, Klok HA. A minimalistic cyclic ice-binding peptide from phage display. Nat Commun 2021; 12:2675. [PMID: 33976148 PMCID: PMC8113477 DOI: 10.1038/s41467-021-22883-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 04/01/2021] [Indexed: 11/09/2022] Open
Abstract
Developing molecules that emulate the properties of naturally occurring ice-binding proteins (IBPs) is a daunting challenge. Rather than relying on the (limited) existing structure-property relationships that have been established for IBPs, here we report the use of phage display for the identification of short peptide mimics of IBPs. To this end, an ice-affinity selection protocol is developed, which enables the selection of a cyclic ice-binding peptide containing just 14 amino acids. Mutational analysis identifies three residues, Asp8, Thr10 and Thr14, which are found to be essential for ice binding. Molecular dynamics simulations reveal that the side chain of Thr10 hydrophobically binds to ice revealing a potential mechanism. To demonstrate the biotechnological potential of this peptide, it is expressed as a fusion ('Ice-Tag') with mCherry and used to purify proteins directly from cell lysate.
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Affiliation(s)
- Corey A Stevens
- Laboratoire des Polymères, Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Fabienne Bachtiger
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK
| | - Xu-Dong Kong
- Laboratory of Therapeutic Proteins and Peptides, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Luciano A Abriata
- Protein Production and Structure Core Facility and Laboratory for Biomolecular Modeling, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gabriele C Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK
| | - Matthew I Gibson
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK.,Warwick Medical School, University of Warwick, Coventry, UK
| | - Harm-Anton Klok
- Laboratoire des Polymères, Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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17
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Khan NMMU, Arai T, Tsuda S, Kondo H. Characterization of microbial antifreeze protein with intermediate activity suggests that a bound-water network is essential for hyperactivity. Sci Rep 2021; 11:5971. [PMID: 33727595 PMCID: PMC7966756 DOI: 10.1038/s41598-021-85559-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/03/2021] [Indexed: 12/27/2022] Open
Abstract
Antifreeze proteins (AFPs) inhibit ice growth by adsorbing onto specific ice planes. Microbial AFPs show diverse antifreeze activity and ice plane specificity, while sharing a common molecular scaffold. To probe the molecular mechanisms responsible for AFP activity, we here characterized the antifreeze activity and crystal structure of TisAFP7 from the snow mold fungus Typhula ishikariensis. TisAFP7 exhibited intermediate activity, with the ability to bind the basal plane, compared with a hyperactive isoform TisAFP8 and a moderately active isoform TisAFP6. Analysis of the TisAFP7 crystal structure revealed a bound-water network arranged in a zigzag pattern on the surface of the protein's ice-binding site (IBS). While the three AFP isoforms shared the water network pattern, the network on TisAFP7 IBS was not extensive, which was likely related to its intermediate activity. Analysis of the TisAFP7 crystal structure also revealed the presence of additional water molecules that form a ring-like network surrounding the hydrophobic side chain of a crucial IBS phenylalanine, which might be responsible for the increased adsorption of AFP molecule onto the basal plane. Based on these observations, we propose that the extended water network and hydrophobic hydration at IBS together determine the TisAFP activity.
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Affiliation(s)
- N M-Mofiz Uddin Khan
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.,Department of Chemistry, Dhaka University of Engineering and Technology, Gazipur Gazipur, 1700, Bangladesh
| | - Tatsuya Arai
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Sakae Tsuda
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1, Tsukisamu-Higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.,OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8563, Japan
| | - Hidemasa Kondo
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan. .,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1, Tsukisamu-Higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
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18
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Gruneberg AK, Graham LA, Eves R, Agrawal P, Oleschuk RD, Davies PL. Ice recrystallization inhibition activity varies with ice-binding protein type and does not correlate with thermal hysteresis. Cryobiology 2021; 99:28-39. [PMID: 33529683 DOI: 10.1016/j.cryobiol.2021.01.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/07/2021] [Accepted: 01/23/2021] [Indexed: 01/06/2023]
Abstract
Ice-binding proteins (IBPs) inhibit the growth of ice through surface adsorption. In some freeze-resistant fishes and insects, circulating IBPs serve as antifreeze proteins to stop ice growth by lowering the freezing point. Plants are less able to avoid freezing and some use IBPs to minimize the damage caused in the frozen state by ice recrystallization, which is the growth of large ice grains at the expense of small ones. Here we have accurately and reproducibly measured the ice recrystallization inhibition (IRI) activity of over a dozen naturally occurring IBPs from fishes, insects, plants, and microorganisms using a modified 'splat' method on serial dilutions of IBPs whose concentrations were determined by amino acid analysis. The endpoint of IRI, which was scored as the lowest protein concentration at which no recrystallization was observed, varied for the different IBPs over two orders of magnitude from 1000 nM to 5 nM. Moreover, there was no apparent correlation between their IRI levels and reported antifreeze activities. IBPs from insects and fishes had similar IRI activity, even though the insect IBPs are typically 10x more active in freezing point depression. Plant IBPs had weak antifreeze activity but were more effective at IRI. Bacterial IBPs involved in ice adhesion showed both strong freezing point depression and IRI. Two trends did emerge, including that basal plane binding IBPs correlated with stronger IRI activity and larger IBPs had higher IRI activity.
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Affiliation(s)
- Audrey K Gruneberg
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada
| | - Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada
| | - Robert Eves
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada
| | - Prashant Agrawal
- Department of Chemistry, Queen's University. 90 Bader Lane, Kingston, Ontario, K7L2S8, Canada
| | - Richard D Oleschuk
- Department of Chemistry, Queen's University. 90 Bader Lane, Kingston, Ontario, K7L2S8, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada.
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19
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Deng J, Apfelbaum E, Drori R. Ice Growth Acceleration by Antifreeze Proteins Leads to Higher Thermal Hysteresis Activity. J Phys Chem B 2020; 124:11081-11088. [PMID: 33232147 DOI: 10.1021/acs.jpcb.0c08119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Since some antifreeze proteins and glycoproteins (AF(G)Ps) cannot directly bind to all ice crystal planes, they change ice crystal morphology by minimizing the area of the crystal planes to which they cannot bind until crystal growth is halted. Previous studies found that growth along the c-axis (perpendicular to the basal plane, the crystal plane to which these AF(G)Ps cannot bind) is accelerated by some AF(G)Ps, while growth of other planes is inhibited. The effects of this growth acceleration on crystal morphology and on the thermal hysteresis activity are unknown to date. Understanding these effects will elucidate the mechanism of ice growth inhibition by AF(G)Ps. Using cold stages and an infrared laser, ice growth velocities and crystal morphologies in AF(G)P solutions were measured. Three types of effects on growth velocity were found: concentration-dependent acceleration, concentration-independent acceleration, and concentration-dependent deceleration. Quantitative crystal morphology measurements in AF(G)P solutions demonstrated that the adsorption rate of the proteins to ice plays a major role in determining the morphology of the bipyramidal crystal. These results demonstrate that faster adsorption rates generate bipyramidal crystals with diminished basal surfaces at higher temperatures compared to slower adsorption rates. The acceleration of growth along the c-axis generates crystals with smaller basal surfaces at higher temperatures leading to increased growth inhibition of the entire crystal.
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Affiliation(s)
- Jinzi Deng
- Department of Chemistry and Biochemistry, Yeshiva University, New York, New York 10016, United States
| | - Elana Apfelbaum
- Department of Chemistry and Biochemistry, Yeshiva University, New York, New York 10016, United States
| | - Ran Drori
- Department of Chemistry and Biochemistry, Yeshiva University, New York, New York 10016, United States
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20
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Sformo TL, Raymond JA. An ice-binding protein from an Arctic population of American dunegrass, Leymus mollis. F1000Res 2020; 9:648. [PMID: 32765842 PMCID: PMC7383708 DOI: 10.12688/f1000research.24328.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/06/2020] [Indexed: 11/20/2022] Open
Abstract
Several cold-hardy grasses have been shown to have ice-binding proteins (IBPs) that protect against freeze-thaw injury. Here, we looked for IBP activity in an Alaskan coastal grass,
Leymus mollis (Pooidae), that had not previously been examined. Rhizome tissue had strong ice-structuring and ice recrystallization inhibiting (IRI) activities, indicating the probable presence of IBPs. The gene sequence of an IBP was obtained. The sequence encoded a 118-amino acid IRI domain composed of eight repeats and that was 80% identical to the IRI domain of the IBP of perennial ryegrass
Lolium perenne. The predicted 3D structure of the IRI domain had eight beta-roll coils like those in
L. perenne IBP
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Affiliation(s)
- Todd L Sformo
- Department of Wildlife Management, North Slope Borough, Utqiaġvik, Alaska, 99723, USA.,Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, 99775, USA
| | - James A Raymond
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, 89154, USA
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21
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Chen X, Shi X, Cai X, Yang F, Li L, Wu J, Wang S. Ice-binding proteins: a remarkable ice crystal regulator for frozen foods. Crit Rev Food Sci Nutr 2020; 61:3436-3449. [PMID: 32715743 DOI: 10.1080/10408398.2020.1798354] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Ice crystal growth during cold storage presents a quality problem in frozen foods. The development of appropriate technical conditions and ingredient formulations is an effective method for frozen food manufacturers to inhibit ice crystals generated during storage and distribution. Ice-binding proteins (IBPs) have great application potential as ice crystal growth inhibitors. The ability of IBPs to retard the growth of ice crystals suggests that IBPs can be used as a natural ice conditioner for a variety of frozen products. In this review, we first discussed the damage caused by ice crystals in frozen foods during freezing and frozen storage. Next, the methods and technologies for production, purification and evaluation of IBPs were summarized. Importantly, the present review focused on the characteristics, structural diversity and mechanisms of IBPs, and the application advances of IBPs in food industry. Finally, the challenges and future perspectives of IBPs are also discussed. This review may provide a better understanding of IBPs and their applications in frozen products, providing some valuable information for further research and application of IBPs.
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Affiliation(s)
- Xu Chen
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian, China.,College of Chemical Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Xiaodan Shi
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian, China
| | - Xixi Cai
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian, China
| | - Fujia Yang
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian, China.,College of Chemical Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Ling Li
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian, China
| | - Jinhong Wu
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shaoyun Wang
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian, China
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22
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Carrot ‘antifreeze’ protein has an irregular ice-binding site that confers weak freezing point depression but strong inhibition of ice recrystallization. Biochem J 2020; 477:2179-2192. [DOI: 10.1042/bcj20200238] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 11/17/2022]
Abstract
Ice-binding proteins (IBPs) are found in many biological kingdoms where they protect organisms from freezing damage as antifreeze agents or inhibitors of ice recrystallization. Here, the crystal structure of recombinant IBP from carrot (Daucus carota) has been solved to a resolution of 2.3 Å. As predicted, the protein is a structural homologue of a plant polygalacturonase-inhibiting protein forming a curved solenoid structure with a leucine-rich repeat motif. Unexpectedly, close examination of its surface did not reveal any large regions of flat, regularly spaced hydrophobic residues that characterize the ice-binding sites (IBSs) of potent antifreeze proteins from freeze-resistant fish and insects. An IBS was defined by site-directed mutagenesis of residues on the convex surface of the carrot solenoid. This imperfect site is reminiscent of the irregular IBS of grass ‘antifreeze’ protein. Like the grass protein, the carrot IBP has weak freezing point depression activity but is extremely active at nanomolar concentrations in inhibiting ice recrystallization. Ice crystals formed in the presence of both plant proteins grow slowly and evenly in all directions. We suggest that this slow, controlled ice growth is desirable for freeze tolerance. The fact that two plant IBPs have evolved very different protein structures to affect ice in a similar manner suggests this pattern of weak freezing point depression and strong ice recrystallization inhibition helps their host to tolerate freezing rather than to resist it.
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23
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Ice Binding Proteins: Diverse Biological Roles and Applications in Different Types of Industry. Biomolecules 2020; 10:biom10020274. [PMID: 32053888 PMCID: PMC7072191 DOI: 10.3390/biom10020274] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [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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24
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Cho SM, Kim S, Cho H, Lee H, Lee JH, Lee H, Park H, Kang S, Choi HG, Lee J. Type II Ice-Binding Proteins Isolated from an Arctic Microalga Are Similar to Adhesin-Like Proteins and Increase Freezing Tolerance in Transgenic Plants. PLANT & CELL PHYSIOLOGY 2019; 60:2744-2757. [PMID: 31418793 DOI: 10.1093/pcp/pcz162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 08/11/2019] [Indexed: 06/10/2023]
Abstract
Microalgal ice-binding proteins (IBPs) in the polar region are poorly understood at the genome-wide level, although they are important for cold adaptation. Through the transcriptome study with the Arctic green alga Chloromonas sp. KNF0032, we identified six Chloromonas IBP genes (CmIBPs), homologous with the previously reported IBPs from Antarctic snow alga CCMP681 and Antarctic Chloromonas sp. They were organized with multiple exon/intron structures and low-temperature-responsive cis-elements in their promoters and abundantly expressed at low temperature. The biological functions of three representative CmIBPs (CmIBP1, CmIBP2 and CmIBP3) were tested using in vitro analysis and transgenic plant system. CmIBP1 had the most effective ice recrystallization inhibition (IRI) activities in both in vitro and transgenic plants, and CmIBP2 and CmIBP3 had followed. All transgenic plants grown under nonacclimated condition were freezing tolerant, and especially 35S::CmIBP1 plants were most effective. After cold acclimation, only 35S::CmIBP2 plants showed slightly increased freezing tolerance. Structurally, the CmIBPs were predicted to have β-solenoid forms with parallel β-sheets and repeated TXT motifs. The repeated TXT structure of CmIBPs appears similar to the AidA domain-containing adhesin-like proteins from methanogens. We have shown that the AidA domain has IRI activity as CmIBPs and phylogenetic analysis also supported that the AidA domains are monophyletic with ice-binding domain of CmIBPs, and these results suggest that CmIBPs are a type of modified adhesins.
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Affiliation(s)
- Sung Mi Cho
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Sanghee Kim
- Division of Polar Life Sciences, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Hojin Cho
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Polar Science, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Hyoungseok Lee
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Polar Science, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Polar Science, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Horim Lee
- Department of Biotechnology, Duksung Women's University, Seoul 01369, Republic of Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Polar Science, University of Science and Technology, Daejeon 34113, Republic of Korea
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Seunghyun Kang
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Han-Gu Choi
- Division of Polar Life Sciences, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Jungeun Lee
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Polar Science, University of Science and Technology, Daejeon 34113, Republic of Korea
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25
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Berger T, Meister K, DeVries AL, Eves R, Davies PL, Drori R. Synergy between Antifreeze Proteins Is Driven by Complementary Ice-Binding. J Am Chem Soc 2019; 141:19144-19150. [DOI: 10.1021/jacs.9b10905] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Tehilla Berger
- Department of Chemistry and Biochemistry, Yeshiva University, New York, New York 10016, United States
| | - Konrad Meister
- Max-Planck Institute for Polymer Research, Mainz D-55128, Germany
| | - Arthur L. DeVries
- Department of Animal Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Robert Eves
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Peter L. Davies
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Ran Drori
- Department of Chemistry and Biochemistry, Yeshiva University, New York, New York 10016, United States
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26
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Surís-Valls R, Voets IK. Peptidic Antifreeze Materials: Prospects and Challenges. Int J Mol Sci 2019; 20:E5149. [PMID: 31627404 PMCID: PMC6834126 DOI: 10.3390/ijms20205149] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 12/28/2022] Open
Abstract
Necessitated by the subzero temperatures and seasonal exposure to ice, various organisms have developed a remarkably effective means to survive the harsh climate of their natural habitats. Their ice-binding (glyco)proteins keep the nucleation and growth of ice crystals in check by recognizing and binding to specific ice crystal faces, which arrests further ice growth and inhibits ice recrystallization (IRI). Inspired by the success of this adaptive strategy, various approaches have been proposed over the past decades to engineer materials that harness these cryoprotective features. In this review we discuss the prospects and challenges associated with these advances focusing in particular on peptidic antifreeze materials both identical and akin to natural ice-binding proteins (IBPs). We address the latest advances in their design, synthesis, characterization and application in preservation of biologics and foods. Particular attention is devoted to insights in structure-activity relations culminating in the synthesis of de novo peptide analogues. These are sequences that resemble but are not identical to naturally occurring IBPs. We also draw attention to impactful developments in solid-phase peptide synthesis and 'greener' synthesis routes, which may aid to overcome one of the major bottlenecks in the translation of this technology: unavailability of large quantities of low-cost antifreeze materials with excellent IRI activity at (sub)micromolar concentrations.
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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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27
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Kaleda A, Haleva L, Sarusi G, Pinsky T, Mangiagalli M, Bar Dolev M, Lotti M, Nardini M, Braslavsky I. Saturn-Shaped Ice Burst Pattern and Fast Basal Binding of an Ice-Binding Protein from an Antarctic Bacterial Consortium. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:7337-7346. [PMID: 30198719 DOI: 10.1021/acs.langmuir.8b01914] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ice-binding proteins (IBPs) bind to ice crystals and control their growth, enabling host organisms to adapt to subzero temperatures. By binding to ice, IBPs can affect the shape and recrystallization of ice crystals. The shapes of ice crystals produced by IBPs vary and are partially due to which ice planes the IBPs are bound to. Previously, we have described a bacterial IBP found in the metagenome of the symbionts of Euplotes focardii ( EfcIBP). EfcIBP shows remarkable ice recrystallization inhibition activity. As recrystallization inhibition of IBPs and other materials are important to the cryopreservation of cells and tissues, we speculate that the EfcIBP can play a future role as an ice recrystallization inhibitor in cryopreservation applications. Here we show that EfcIBP results in a Saturn-shaped ice burst pattern, which may be due to the unique ice-plane affinity of the protein that we elucidated using the fluorescent-based ice-plane affinity analysis. EfcIBP binds to ice at a speed similar to that of other moderate IBPs (5 ± 2 mM-1 s-1); however, it is unique in that it binds to the basal and previously unobserved pyramidal near-basal planes, while other moderate IBPs typically bind to the prism and pyramidal planes and not basal or near-basal planes. These insights into EfcIBP allow a better understanding of the recrystallization inhibition for this unique protein.
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Affiliation(s)
- Aleksei Kaleda
- 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
- Department of Chemistry and Biotechnology, School of Science , Tallinn University of Technology , Ehitajate tee 5 , 19086 Tallinn , Estonia
| | - Lotem Haleva
- 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
| | - Guy Sarusi
- 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
| | - Tova Pinsky
- 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
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - 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
| | - Marina Lotti
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Marco Nardini
- Department of Biosciences , University of Milano , Via Celoria 26 , 20133 Milan , Italy
| | - 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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Tomalty HE, Graham LA, Eves R, Gruneberg AK, Davies PL. Laboratory-Scale Isolation of Insect Antifreeze Protein for Cryobiology. Biomolecules 2019; 9:biom9050180. [PMID: 31075842 PMCID: PMC6572240 DOI: 10.3390/biom9050180] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/02/2022] Open
Abstract
Micromolar concentrations of hyperactive antifreeze proteins (AFPs) from insects can prevent aqueous solutions from freezing down to at least −6 °C. To explore cryopreservation of cells, tissues and organs at these temperatures without ice formation, we have developed a protocol to reliably produce ultrapure Tenebrio molitor AFP from cold-acclimated beetle larvae reared in the laboratory. The AFP was prepared from crude larval homogenates through five cycles of rotary ice-affinity purification, which can be completed in one day. Recovery of the AFP at each step was >90% and no impurities were detected in the final product. The AFP is a mixture of isoforms that are more active in combination than any one single component. Toxicity testing of the purified AFP in cell culture showed no inhibition of cell growth. The production process can easily be scaled up to industrial levels, and the AFP used in cryobiology applications was recovered for reuse in good yield and with full activity.
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Affiliation(s)
- Heather E Tomalty
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Robert Eves
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Audrey K Gruneberg
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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29
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Vance TDR, Bayer-Giraldi M, Davies PL, Mangiagalli M. Ice-binding proteins and the 'domain of unknown function' 3494 family. FEBS J 2019; 286:855-873. [PMID: 30680879 DOI: 10.1111/febs.14764] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/03/2019] [Accepted: 01/22/2019] [Indexed: 02/03/2023]
Abstract
Ice-binding proteins (IBPs) control the growth and shape of ice crystals to cope with subzero temperatures in psychrophilic and freeze-tolerant organisms. Recently, numerous proteins containing the domain of unknown function (DUF) 3494 were found to bind ice crystals and, hence, are classified as IBPs. DUF3494 IBPs constitute today the most widespread of the known IBP families. They can be found in different organisms including bacteria, yeasts and microalgae, supporting the hypothesis of horizontal transfer of its gene. Although the 3D structure is always a discontinuous β-solenoid with a triangular cross-section and an adjacent alpha-helix, DUF3494 IBPs present very diverse activities in terms of the magnitude of their thermal hysteresis and inhibition of ice recrystallization. The proteins are secreted into the environments around the host cells or are anchored on their cell membranes. This review covers several aspects of this new class of IBPs, which promise to leave their mark on several research fields including structural biology, protein biochemistry and cryobiology.
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Affiliation(s)
- Tyler D R Vance
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Maddalena Bayer-Giraldi
- Department of Glaciology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
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30
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Combined molecular dynamics and neural network method for predicting protein antifreeze activity. Proc Natl Acad Sci U S A 2018; 115:13252-13257. [PMID: 30530650 DOI: 10.1073/pnas.1814945115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Antifreeze proteins (AFPs) are a diverse class of proteins that depress the kinetically observable freezing point of water. AFPs have been of scientific interest for decades, but the lack of an accurate model for predicting AFP activity has hindered the logical design of novel antifreeze systems. To address this, we perform molecular dynamics simulation for a collection of well-studied AFPs. By analyzing both the dynamic behavior of water near the protein surface and the geometric structure of the protein, we introduce a method that automatically detects the ice binding face of AFPs. From these data, we construct a simple neural network that is capable of quantitatively predicting experimentally observed thermal hysteresis from a trio of relevant physical variables. The model's accuracy is tested against data for 17 known AFPs and 5 non-AFP controls.
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31
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Baier T, Kros D, Feiner RC, Lauersen KJ, Müller KM, Kruse O. Engineered Fusion Proteins for Efficient Protein Secretion and Purification of a Human Growth Factor from the Green Microalga Chlamydomonas reinhardtii. ACS Synth Biol 2018; 7:2547-2557. [PMID: 30296377 DOI: 10.1021/acssynbio.8b00226] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Light-driven recombinant protein (RP) production in eukaryotic microalgae offers a sustainable alternative to other established cell-culture systems. RP production via secretion into the culture medium enables simple product separation from the cells adding a layer of process value in addition to the algal biomass, which can be separately harvested. For the model microalga Chlamydomonas reinhardtii, a broad range of molecular tools have been established to enable heterologous gene expression; however, low RP production levels and unreliable purification from secretion concepts have been reported. Domesticated C. reinhardtii strains used for genetic engineering are often cell-wall deficient. These strains nevertheless secrete cell-wall components such as insoluble (hydroxy)proline-rich glycoproteins into the culture media, which hinder downstream purification processes. Here, we attempted to overcome limitations in secretion titers and improve protein purification by combining fusion partners that enhance RP secretion and enable alternative aqueous two-phase (ATPS) RP extraction from the culture medium. Protein fusions were strategically designed to contain a stably folded peptide, which enhanced secretion capacities and gave insights into (some) regulatory mechanisms responsible for this process in the algal host. The elevated protein titers mediated by this fusion were then successfully applied in combination with a fungal hydrophobin tag, which enabled protein purification from the complex microalgal extracellular environment by ATPS, to yield functional recombinant human epidermal growth factor (hEGF) from the algal host.
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Affiliation(s)
- Thomas Baier
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Dana Kros
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Rebecca C. Feiner
- Bielefeld University, Faculty of Technology, Cellular and Molecular Biotechnology, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Kyle J. Lauersen
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Kristian M. Müller
- Bielefeld University, Faculty of Technology, Cellular and Molecular Biotechnology, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Olaf Kruse
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
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32
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Growth suppression of ice crystal basal face in the presence of a moderate ice-binding protein does not confer hyperactivity. Proc Natl Acad Sci U S A 2018; 115:7479-7484. [PMID: 29967176 DOI: 10.1073/pnas.1807461115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ice-binding proteins (IBPs) affect ice crystal growth by attaching to crystal faces. We present the effects on the growth of an ice single crystal caused by an ice-binding protein from the sea ice microalga Fragilariopsis cylindrus (fcIBP) that is characterized by the widespread domain of unknown function 3494 (DUF3494) and known to cause a moderate freezing point depression (below 1 °C). By the application of interferometry, bright-field microscopy, and fluorescence microscopy, we observed that the fcIBP attaches to the basal faces of ice crystals, thereby inhibiting their growth in the c direction and resulting in an increase in the effective supercooling with increasing fcIBP concentration. In addition, we observed that the fcIBP attaches to prism faces and inhibits their growth. In the event that the effective supercooling is small and crystals are faceted, this process causes an emergence of prism faces and suppresses crystal growth in the a direction. When the effective supercooling is large and ice crystals have developed into a dendritic shape, the suppression of prism face growth results in thinner dendrite branches, and growth in the a direction is accelerated due to enhanced latent heat dissipation. Our observations clearly indicate that the fcIBP occupies a separate position in the classification of IBPs due to the fact that it suppresses the growth of basal faces, despite its moderate freezing point depression.
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33
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Bredow M, Tomalty HE, Smith L, Walker VK. Ice and anti-nucleating activities of an ice-binding protein from the annual grass, Brachypodium distachyon. PLANT, CELL & ENVIRONMENT 2018; 41:983-992. [PMID: 28035668 DOI: 10.1111/pce.12889] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 05/15/2023]
Abstract
Plants exposed to sub-zero temperatures face unique challenges that threaten their survival. The growth of ice crystals in the extracellular space can cause cellular dehydration, plasma membrane rupture and eventual cell death. Additionally, some pathogenic bacteria cause tissue damage by initiating ice crystal growth at high sub-zero temperatures through the use of ice-nucleating proteins (INPs), presumably to access nutrients from lysed cells. An annual species of brome grass, Brachypodium distachyon (Bd), produces an ice-binding protein (IBP) that shapes ice with a modest depression of the freezing point (~0.1 °C at 1 mg/mL), but high ice-recrystallization inhibition (IRI) activity, allowing ice crystals to remain small at near melting temperatures. This IBP, known as BdIRI, is unlike other characterized IBPs with a single ice-binding face, as mutational analysis indicates that BdIRI adsorbs to ice on two faces. BdIRI also dramatically attenuates the nucleation of ice by bacterial INPs (up to -2.26 °C). This 'anti-nucleating' activity is significantly higher than previously documented for any IBP.
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Affiliation(s)
- Melissa Bredow
- Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Heather E Tomalty
- Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Lindsay Smith
- Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Virginia K Walker
- Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada
- Department of Biomedical and Molecular Sciences, and School of Environmental Studies, Queen's University, Kingston, Ontario, K7L 3N6, Canada
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34
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Zhang L, Jin Q, Luo J, Wu J, Wang S, Wang Z, Gong S, Zhang W, Lan X. Intracellular Expression of Antifreeze Peptides in Food Grade Lactococcus lactis and Evaluation of Their Cryoprotective Activity. J Food Sci 2018; 83:1311-1320. [PMID: 29660758 DOI: 10.1111/1750-3841.14117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 02/11/2018] [Accepted: 02/13/2018] [Indexed: 02/06/2023]
Abstract
Antifreeze peptides can protect living organisms from low temperatures by preventing damage or killing due to ice crystal formation between cells. Therefore, antifreeze peptides can be used as a low temperature protectant for cryopreservation of cells and tissues, and also in food production. In this study, a recombinant SF-P gene was constructed and inserted into pNZ8149 to construct a food grade expression vector, which was then electroporated into Lactococcus lactis NZ3900. The expression of the target protein was induced using Nisin, and the optimal expression condition was determined to be a pH of 6.0, Nisin concentration of 25 ng/mL, temperature of 37 °C, and incubation time of 6 hr. Compared to the strain NZ3900 and the recombinant strain SF-P1 without addition of Nisin, the recombinant strain SF-P2 showed the highest cell survival and thermal hysteresis activity, and had a reduction in the changes of activities of extracellular and intracellular lactate dehydrogenase and β-galactosidase after freezing. Moreover, analysis by SEM showed that SF-P2 cells were more completely and regularly shaped than other strains, displayed no obvious leakage of cell contents, and had an intact boundary between cells after freezing. These results indicate that the recombinant strain SF-P2 has a protective effect against freezing. This paper presents a food grade expression system for an antifreeze peptide SF-P using L. lactis as a host, and shows that the intracellular expression of antifreeze peptide could protect the cellular integrity and physiological functions of L. lactis. PRACTICAL APPLICATION The recombinant Lactococcus lactis with intracellular expression of antifreeze peptides SF-P could reduce the damage of bacteria cells induced by freezing or freeze drying, so, it could be applied in the process of freezing food without separation, such as the manufacture of yoghurt ice cream, frozen dough, and so on.
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Affiliation(s)
- Li Zhang
- Dept. of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong Univ., Shanghai, 200240, China
| | - Quan Jin
- Dept. of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong Univ., Shanghai, 200240, China
| | - Jing Luo
- Dept. of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong Univ., Shanghai, 200240, China
| | - Jinhong Wu
- Dept. of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong Univ., Shanghai, 200240, China
| | - Shaoyun Wang
- College of Biological Science and Technology, Fuzhou Univ., Fuzhou, 350108, China
| | - Zhengwu Wang
- Dept. of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong Univ., Shanghai, 200240, China
| | - Shengxiang Gong
- Dept. of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong Univ., Shanghai, 200240, China
| | - Wei Zhang
- Dept. of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong Univ., Shanghai, 200240, China
| | - Xiaohong Lan
- Dept. of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong Univ., Shanghai, 200240, China
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35
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Cid FP, Maruyama F, Murase K, Graether SP, Larama G, Bravo LA, Jorquera MA. Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere. Extremophiles 2018; 22:537-552. [PMID: 29492666 DOI: 10.1007/s00792-018-1015-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/18/2018] [Indexed: 11/28/2022]
Abstract
Genome analyses are being used to characterize plant growth-promoting (PGP) bacteria living in different plant compartiments. In this context, we have recently isolated bacteria from the phyllosphere of an Antarctic plant (Deschampsia antarctica) showing ice recrystallization inhibition (IRI), an activity related to the presence of antifreeze proteins (AFPs). In this study, the draft genomes of six phyllospheric bacteria showing IRI activity were sequenced and annotated according to their functional gene categories. Genome sizes ranged from 5.6 to 6.3 Mbp, and based on sequence analysis of the 16S rRNA genes, five strains were identified as Pseudomonas and one as Janthinobacterium. Interestingly, most strains showed genes associated with PGP traits, such as nutrient uptake (ammonia assimilation, nitrogen fixing, phosphatases, and organic acid production), bioactive metabolites (indole acetic acid and 1-aminocyclopropane-1-carboxylate deaminase), and antimicrobial compounds (hydrogen cyanide and pyoverdine). In relation with IRI activity, a search of putative AFPs using current bioinformatic tools was also carried out. Despite that genes associated with reported AFPs were not found in these genomes, genes connected to ice-nucleation proteins (InaA) were found in all Pseudomonas strains, but not in the Janthinobacterium strain.
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Affiliation(s)
- Fernanda P Cid
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
| | - Kazunori Murase
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Giovanni Larama
- Department of Mathematical Engineering, Universidad de La Frontera, Temuco, Chile
| | - Leon A Bravo
- Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Forestales, Universidad de la Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Milko A Jorquera
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile.
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile.
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36
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Affiliation(s)
- Alexander G. Shtukenberg
- Department of Chemistry and Molecular
Design Institute, New York University, 100 Washington Square East, New York City, New York 10003, United States
| | - Michael D. Ward
- Department of Chemistry and Molecular
Design Institute, New York University, 100 Washington Square East, New York City, New York 10003, United States
| | - Bart Kahr
- Department of Chemistry and Molecular
Design Institute, New York University, 100 Washington Square East, New York City, New York 10003, United States
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37
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Wang C, Pakhomova S, Newcomer ME, Christner BC, Luo BH. Structural basis of antifreeze activity of a bacterial multi-domain antifreeze protein. PLoS One 2017; 12:e0187169. [PMID: 29108002 PMCID: PMC5673226 DOI: 10.1371/journal.pone.0187169] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/13/2017] [Indexed: 01/05/2023] Open
Abstract
Antifreeze proteins (AFPs) enhance the survival of organisms inhabiting cold environments by affecting the formation and/or structure of ice. We report the crystal structure of the first multi-domain AFP that has been characterized. The two ice binding domains are structurally similar. Each consists of an irregular β-helix with a triangular cross-section and a long α-helix that runs parallel on one side of the β-helix. Both domains are stabilized by hydrophobic interactions. A flat plane on the same face of each domain’s β-helix was identified as the ice binding site. Mutating any of the smaller residues on the ice binding site to bulkier ones decreased the antifreeze activity. The bulky side chain of Leu174 in domain A sterically hinders the binding of water molecules to the protein backbone, partially explaining why antifreeze activity by domain A is inferior to that of domain B. Our data provide a molecular basis for understanding differences in antifreeze activity between the two domains of this protein and general insight on how structural differences in the ice-binding sites affect the activity of AFPs.
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Affiliation(s)
- Chen Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Svetlana Pakhomova
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Marcia E. Newcomer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Brent C. Christner
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Department of Microbiology and Cell Science, Biodiversity Institute, University of Florida, Gainesville, Florida, United States of America
| | - Bing-Hao Luo
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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38
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Banach M, Konieczny L, Roterman I. Why do antifreeze proteins require a solenoid? Biochimie 2017; 144:74-84. [PMID: 29054801 DOI: 10.1016/j.biochi.2017.10.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/12/2017] [Indexed: 12/21/2022]
Abstract
Proteins whose presence prevents water from freezing in living organisms at temperatures below 0 °C are referred to as antifreeze proteins. This group includes molecules of varying size (from 30 to over 300 aa) and variable secondary/supersecondary conformation. Some of these proteins also contain peculiar structural motifs called solenoids. We have applied the fuzzy oil drop model in the analysis of four categories of antifreeze proteins: 1 - very small proteins, i.e. helical peptides (below 40 aa); 2 - small globular proteins (40-100 aa); 3 - large globular proteins (>100 aa) and 4 - proteins containing solenoids. The FOD model suggests a mechanism by which antifreeze proteins prevent freezing. In accordance with this theory, the presence of the protein itself produces an ordering of water molecules which counteracts the formation of ice crystals. This conclusion is supported by analysis of the ordering of hydrophobic and hydrophilic residues in antifreeze proteins, revealing significant variability - from perfect adherence to the fuzzy oil drop model through structures which lack a clearly defined hydrophobic core, all the way to linear arrangement of alternating local minima and maxima propagating along the principal axis of the solenoid (much like in amyloids). The presented model - alternative with respect to the ice docking model - explains the antifreeze properties of compounds such as saccharides and fatty acids. The fuzzy oil drop model also enables differentiation between amyloids and antifreeze proteins.
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Affiliation(s)
- M Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College, Lazarza 16, 31-530, Krakow, Poland
| | - L Konieczny
- Chair of Medical Biochemistry, Jagiellonian University, Medical College, Kopernika 7, 31-034, Krakow, Poland
| | - I Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College, Lazarza 16, 31-530, Krakow, Poland.
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39
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Qihong Z, Jie L, Xiao X, Qian X, Wei G, Jichen X. PicW orthologs from spruce with differential freezing tolerance expressed in Escherichia coli. Int J Biol Macromol 2017; 101:595-602. [PMID: 28315763 DOI: 10.1016/j.ijbiomac.2017.03.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 03/09/2017] [Accepted: 03/13/2017] [Indexed: 12/19/2022]
Abstract
Spruce can grow at an extra low temperature (LT), and is inferred with important antifreezing gene resources. The research here identified 4 different spruce varieties, named as PicW1, PicW2, PicM and PicK. Sequence alignment showed base-substitution and deficiency mutations among them with sequence identity between 97.61% and 99.25%. Each gene was transferred into E. coli, where protein was induced by IPTG (isopropyl-β-d-thiogalactoside). Strains cultured at -5°C showed the lethal dose 50% (LD-50) between 53h and 57h for the transgenic strains, but 35h for the control. Strains cultivated at -20°C showed the LD-50 between 38h and 44h for the transgenic strains, but 25h for the control. Further, the soluble gene proteins were extracted and purified for Differential Scanning Calorimeter (DSC) test, which showed characteristic thermal hysteresis (TH) value of 0.77°C (PicW1), 0.78°C (PicW2), 0.72°C (PicM), and 0.86°C (PicK) respectively, significantly higher than the value of 0.05°C of the control (BSA). Summarily, four homologous proteins showed good antifreeze property with the range from high to low as PicK>PicW2>PicW1>PicM. It suggested that they can be used as resources for genetic engineering of plant cold tolerance.
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Affiliation(s)
- Zhao Qihong
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China.
| | - Liu Jie
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China.
| | - Xu Xiao
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China
| | - Xu Qian
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China
| | - Gao Wei
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China
| | - Xu Jichen
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China.
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40
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Zhao B, Cohen Stuart MA, Hall CK. Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the β-solenoid structure formed by a silk-like polypeptide. PLoS Comput Biol 2017; 13:e1005446. [PMID: 28329017 PMCID: PMC5388506 DOI: 10.1371/journal.pcbi.1005446] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 04/11/2017] [Accepted: 03/08/2017] [Indexed: 11/22/2022] Open
Abstract
The β roll molecules with sequence (GAGAGAGQ)10 stack via hydrogen bonding to form fibrils which have been themselves been used to make viral capsids of DNA strands, supramolecular nanotapes and pH-responsive gels. Accelerated molecular dynamics (aMD) simulations are used to investigate the unfolding of a stack of two β roll molecules, (GAGAGAGQ)10, to shed light on the folding mechanism by which silk-inspired polypeptides form fibrils and to identify the dominant forces that keep the silk-inspired polypeptide in a β roll configuration. Our study shows that a molecule in a stack of two β roll molecules unfolds in a step-wise fashion mainly from the C terminal. The bottom template is found to play an important role in stabilizing the β roll structure of the molecule on top by strengthening the hydrogen bonds in the layer that it contacts. Vertical hydrogen bonds within the β roll structure are considerably weaker than lateral hydrogen bonds, signifying the importance of lateral hydrogen bonds in stabilizing the β roll structure. Finally, an intermediate structure was found containing a β hairpin and an anti-parallel β sheet consisting of strands from the top and bottom molecules, revealing the self-healing ability of the β roll stack.
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Affiliation(s)
- Binwu Zhao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, United States
| | - Martien A. Cohen Stuart
- Laboratory of Physical Chemistry & Colloid Science, Wageningen University, NL, Wageningen, The Netherlands
| | - Carol K. Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, United States
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41
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CryoProtect: A Web Server for Classifying Antifreeze Proteins from Nonantifreeze Proteins. J CHEM-NY 2017. [DOI: 10.1155/2017/9861752] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Antifreeze protein (AFP) is an ice-binding protein that protects organisms from freezing in extremely cold environments. AFPs are found across a diverse range of species and, therefore, significantly differ in their structures. As there are no consensus sequences available for determining the ice-binding domain of AFPs, thus the prediction and characterization of AFPs from their sequence is a challenging task. This study addresses this issue by predicting AFPs directly from sequence on a large set of 478 AFPs and 9,139 non-AFPs using machine learning (e.g., random forest) as a function of interpretable features (e.g., amino acid composition, dipeptide composition, and physicochemical properties). Furthermore, AFPs were characterized using propensity scores and important physicochemical properties via statistical and principal component analysis. The predictive model afforded high performance with an accuracy of 88.28% and results revealed that AFPs are likely to be composed of hydrophobic amino acids as well as amino acids with hydroxyl and sulfhydryl side chains. The predictive model is provided as a free publicly available web server called CryoProtect for classifying query protein sequence as being either AFP or non-AFP. The data set and source code are for reproducing the results which are provided on GitHub.
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42
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Bredow M, Vanderbeld B, Walker VK. Ice-binding proteins confer freezing tolerance in transgenic Arabidopsis thaliana. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:68-81. [PMID: 27317906 PMCID: PMC5253476 DOI: 10.1111/pbi.12592] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/30/2016] [Accepted: 06/10/2016] [Indexed: 05/07/2023]
Abstract
Lolium perenne is a freeze-tolerant perennial ryegrass capable of withstanding temperatures below -13 °C. Ice-binding proteins (IBPs) presumably help prevent damage associated with freezing by restricting the growth of ice crystals in the apoplast. We have investigated the expression, localization and in planta freezing protection capabilities of two L. perenne IBP isoforms, LpIRI2 and LpIRI3, as well as a processed IBP (LpAFP). One of these isoforms, LpIRI2, lacks a conventional signal peptide and was assumed to be a pseudogene. Nevertheless, both LpIRI2 and LpIRI3 transcripts were up-regulated following cold acclimation. LpIRI2 also demonstrated ice-binding activity when produced recombinantly in Escherichia coli. Both the LpIRI3 and LpIRI2 isoforms appeared to accumulate in the apoplast of transgenic Arabidopsis thaliana plants. In contrast, the fully processed isoform, LpAFP, remained intracellular. Transgenic plants expressing either LpIRI2 or LpIRI3 showed reduced ion leakage (12%-39%) after low-temperature treatments, and significantly improved freezing survival, while transgenic LpAFP-expressing lines did not confer substantial subzero protection. Freeze protection was further enhanced by with the introduction of more than one IBP isoform; ion leakage was reduced 26%-35% and 10% of plants survived temperatures as low as -8 °C. Our results demonstrate that apoplastic expression of multiple L. perenne IBP isoforms shows promise for providing protection to crops susceptible to freeze-induced damage.
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Affiliation(s)
| | | | - Virginia K. Walker
- Department of BiologyQueen's UniversityKingstonONCanada
- Department of Biomedical and Molecular Sciences and School of Environmental StudiesQueen's UniversityKingstonONCanada
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43
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Bredow M, Walker VK. Ice-Binding Proteins in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:2153. [PMID: 29312400 PMCID: PMC5744647 DOI: 10.3389/fpls.2017.02153] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 12/05/2017] [Indexed: 05/04/2023]
Abstract
Sub-zero temperatures put plants at risk of damage associated with the formation of ice crystals in the apoplast. Some freeze-tolerant plants mitigate this risk by expressing ice-binding proteins (IBPs), that adsorb to ice crystals and modify their growth. IBPs are found across several biological kingdoms, with their ice-binding activity and function uniquely suited to the lifestyle they have evolved to protect, be it in fishes, insects or plants. While IBPs from freeze-avoidant species significantly depress the freezing point, plant IBPs typically have a reduced ability to lower the freezing temperature. Nevertheless, they have a superior ability to inhibit the recrystallization of formed ice. This latter activity prevents ice crystals from growing larger at temperatures close to melting. Attempts to engineer frost-hardy plants by the controlled transfer of IBPs from freeze-avoiding fish and insects have been largely unsuccessful. In contrast, the expression of recombinant IBP sequences from freeze-tolerant plants significantly reduced electrolyte leakage and enhanced freezing survival in freeze-sensitive plants. These promising results have spurred additional investigations into plant IBP localization and post-translational modifications, as well as a re-evaluation of IBPs as part of the anti-stress and anti-pathogen axis of freeze-tolerant plants. Here we present an overview of plant freezing stress and adaptation mechanisms and discuss the potential utility of IBPs for the generation of freeze-tolerant crops.
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Affiliation(s)
- Melissa Bredow
- Department of Biology, Queen’s University, Kingston, ON, Canada
- *Correspondence: Melissa Bredow,
| | - Virginia K. Walker
- Department of Biomedical and Molecular Sciences, and School of Environmental Studies, Queen’s University, Kingston, ON, Canada
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Mangiagalli M, Bar‐Dolev M, Tedesco P, Natalello A, Kaleda A, Brocca S, Pascale D, Pucciarelli S, Miceli C, Braslavsky I, Lotti M. Cryo‐protective effect of an ice‐binding protein derived from Antarctic bacteria. FEBS J 2016; 284:163-177. [DOI: 10.1111/febs.13965] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/31/2016] [Accepted: 11/14/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Marco Mangiagalli
- Department of Biotechnology and Biosciences State University of Milano‐Bicocca Italy
| | - 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 Israel
| | - Pietro Tedesco
- Institute of Protein Biochemistry National Research Council Naples Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences State University of Milano‐Bicocca Italy
| | - Aleksei Kaleda
- 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 Food Processing Faculty of Chemical and Materials Technology Tallinn University of Technology Estonia
| | - Stefania Brocca
- Department of Biotechnology and Biosciences State University of Milano‐Bicocca Italy
| | - Donatella Pascale
- Institute of Protein Biochemistry National Research Council Naples Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine University of Camerino Italy
| | - Cristina Miceli
- School of Biosciences and Veterinary Medicine University of Camerino Italy
| | - 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
| | - Marina Lotti
- Department of Biotechnology and Biosciences State University of Milano‐Bicocca Italy
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45
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Bredow M, Vanderbeld B, Walker VK. Knockdown of Ice-Binding Proteins in Brachypodium distachyon Demonstrates Their Role in Freeze Protection. PLoS One 2016; 11:e0167941. [PMID: 27959937 PMCID: PMC5154533 DOI: 10.1371/journal.pone.0167941] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/22/2016] [Indexed: 11/18/2022] Open
Abstract
Sub-zero temperatures pose a major threat to the survival of cold-climate perennials. Some of these freeze-tolerant plants produce ice-binding proteins (IBPs) that offer frost protection by restricting ice crystal growth and preventing expansion-induced lysis of the plasma membranes. Despite the extensive in vitro characterization of such proteins, the importance of IBPs in the freezing stress response has not been investigated. Using the freeze-tolerant grass and model crop, Brachypodium distachyon, we characterized putative IBPs (BdIRIs) and generated the first 'IBP-knockdowns'. Seven IBP sequences were identified and expressed in Escherichia coli, with all of the recombinant proteins demonstrating moderate to high levels of ice-recrystallization inhibition (IRI) activity, low levels of thermal hysteresis (TH) activity (0.03-0.09°C at 1 mg/mL) and apparent adsorption to ice primary prism planes. Following plant cold acclimation, IBPs purified from wild-type B. distachyon cell lysates similarly showed high levels of IRI activity, hexagonal ice-shaping, and low levels of TH activity (0.15°C at 0.5 mg/mL total protein). The transfer of a microRNA construct to wild-type plants resulted in the attenuation of IBP activity. The resulting knockdown mutant plants had reduced ability to restrict ice-crystal growth and a 63% reduction in TH activity. Additionally, all transgenic lines were significantly more vulnerable to electrolyte leakage after freezing to -10°C, showing a 13-22% increase in released ions compared to wild-type. IBP-knockdown lines also demonstrated a significant decrease in viability following freezing to -8°C, with some lines showing only two-thirds the survival seen in control lines. These results underscore the vital role IBPs play in the development of a freeze-tolerant phenotype and suggests that expression of these proteins in frost-susceptible plants could be valuable for the production of more winter-hardy crops.
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Affiliation(s)
- Melissa Bredow
- Department of Biology, Queen’s University, Kingston, ON, Canada
| | | | - Virginia K. Walker
- Department of Biology, Queen’s University, Kingston, ON, Canada
- Department of Biomedical and Molecular Sciences, and School of Environmental Studies, Queen’s University, Kingston, ON, Canada
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46
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Kim EJ, Lee JH, Lee SG, Han SJ. Improving thermal hysteresis activity of antifreeze protein from recombinant Pichia pastoris by removal of N-glycosylation. Prep Biochem Biotechnol 2016; 47:299-304. [DOI: 10.1080/10826068.2016.1244682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Eun Jae Kim
- Division of Life Sciences, Korea Polar Research Institute, Korea Institute of Ocean Science and Technology, Incheon, South Korea
- Department of Polar Sciences, University of Science and Technology, Yuseong-gu, Daejeon, South Korea
| | - Jun Hyuck Lee
- Division of Life Sciences, Korea Polar Research Institute, Korea Institute of Ocean Science and Technology, Incheon, South Korea
- Department of Polar Sciences, University of Science and Technology, Yuseong-gu, Daejeon, South Korea
| | - Sung Gu Lee
- Division of Life Sciences, Korea Polar Research Institute, Korea Institute of Ocean Science and Technology, Incheon, South Korea
- Department of Polar Sciences, University of Science and Technology, Yuseong-gu, Daejeon, South Korea
| | - Se Jong Han
- Division of Life Sciences, Korea Polar Research Institute, Korea Institute of Ocean Science and Technology, Incheon, South Korea
- Department of Polar Sciences, University of Science and Technology, Yuseong-gu, Daejeon, South Korea
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47
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Haleva L, Celik Y, Bar-Dolev M, Pertaya-Braun N, Kaner A, Davies PL, Braslavsky I. Microfluidic Cold-Finger Device for the Investigation of Ice-Binding Proteins. Biophys J 2016; 111:1143-1150. [PMID: 27653473 PMCID: PMC5034346 DOI: 10.1016/j.bpj.2016.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 06/27/2016] [Accepted: 08/01/2016] [Indexed: 11/30/2022] Open
Abstract
Ice-binding proteins (IBPs) bind to ice crystals and control their structure, enlargement, and melting, thereby helping their host organisms to avoid injuries associated with ice growth. IBPs are useful in applications where ice growth control is necessary, such as cryopreservation, food storage, and anti-icing. The study of an IBP's mechanism of action is limited by the technological difficulties of in situ observations of molecules at the dynamic interface between ice and water. We describe herein a new, to our knowledge, apparatus designed to generate a controlled temperature gradient in a microfluidic chip, called a microfluidic cold finger (MCF). This device allows growth of a stable ice crystal that can be easily manipulated with or without IBPs in solution. Using the MCF, we show that the fluorescence signal of IBPs conjugated to green fluorescent protein is reduced upon freezing and recovers at melting. This finding strengthens the evidence for irreversible binding of IBPs to their ligand, ice. We also used the MCF to demonstrate the basal-plane affinity of several IBPs, including a recently described IBP from Rhagium inquisitor. Use of the MCF device, along with a temperature-controlled setup, provides a relatively simple and robust technique that can be widely used for further analysis of materials at the ice/water interface.
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Affiliation(s)
- Lotem Haleva
- Institute of Biochemistry, Food Science and Nutrition, 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, Ohio; Department of Physics and Physical Sciences, Marshall University, Huntington, West Virginia
| | - Maya Bar-Dolev
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Avigail Kaner
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Ido Braslavsky
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel; Department of Physics and Astronomy, Ohio University, Athens, Ohio.
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48
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Affiliation(s)
- Maya Bar Dolev
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agricultural, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; ,
| | - Ido Braslavsky
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agricultural, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; ,
| | - Peter L. Davies
- Department of Biomedical and Molecular Science, Queen's University, Kingston, Ontario K7L 3N6, Canada;
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49
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Zhao B, Cohen Stuart MA, Hall CK. Dock 'n roll: folding of a silk-inspired polypeptide into an amyloid-like beta solenoid. SOFT MATTER 2016; 12:3721-9. [PMID: 26947809 PMCID: PMC4913789 DOI: 10.1039/c6sm00169f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Polypeptides containing the motif ((GA)mGX)n occur in silk and have a strong tendency to self-assemble. For example, polypeptides containing (GAGAGAGX)n, where X = G or H have been observed to form filaments; similar sequences but with X = Q have been used in the design of coat proteins (capsids) for artificial viruses. The structure of the (GAGAGAGX)m filaments has been proposed to be a stack of peptides in a β roll structure with the hydrophobic side chains pointing outwards (hydrophobic shell). Another possible configuration, a β roll or β solenoid structure which has its hydrophobic side chains buried inside (hydrophobic core) was, however, overlooked. We perform ground state analysis as well as atomic-level molecular dynamics simulations, both on single molecules and on two-molecule stacks of the silk-inspired sequence (GAGAGAGQ)10, to decide whether the hydrophobic core or the hydrophobic shell configuration is the most stable one. We find that a stack of two hydrophobic core molecules is energetically more favorable than a stack of two hydrophobic shell molecules. A shell molecule initially placed in a perfect β roll structure tends to rotate its strands, breaking in-plane hydrogen bonds and forming out-of-plane hydrogen bonds, while a core molecule stays in the β roll structure. The hydrophobic shell structure has type II' β turns whereas the core configuration has type II β turns; only the latter secondary structure agrees well with solid-state NMR experiments on a similar sequence (GA)15. We also observe that the core stack has a higher number of intra-molecular hydrogen bonds and a higher number of hydrogen bonds between stack and water than the shell stack. Hence, we conclude that the hydrophobic core configuration is the most likely structure. In the stacked state, each peptide has more intra-molecular hydrogen bonds than a single folded molecule, which suggests that stacking provides the extra stability needed for molecules to reach the folded state.
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Affiliation(s)
- Binwu Zhao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA.
| | - Martien A Cohen Stuart
- Laboratory of Physical Chemistry & Colloid Science, Wageningen University, PO Box 8083, NL, 6700 EK, The Netherlands
| | - Carol K Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA.
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50
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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] [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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