1
|
Lopes JC, Kinasz CT, Luiz AMC, Kreusch MG, Duarte RTD. Frost fighters: unveiling the potential of microbial antifreeze proteins in biotech innovation. J Appl Microbiol 2024; 135:lxae140. [PMID: 38877650 DOI: 10.1093/jambio/lxae140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/30/2024] [Accepted: 06/13/2024] [Indexed: 06/16/2024]
Abstract
Polar environments pose extreme challenges for life due to low temperatures, limited water, high radiation, and frozen landscapes. Despite these harsh conditions, numerous macro and microorganisms have developed adaptive strategies to reduce the detrimental effects of extreme cold. A primary survival tactic involves avoiding or tolerating intra and extracellular freezing. Many organisms achieve this by maintaining a supercooled state by producing small organic compounds like sugars, glycerol, and amino acids, or through increasing solute concentration. Another approach is the synthesis of ice-binding proteins, specifically antifreeze proteins (AFPs), which hinder ice crystal growth below the melting point. This adaptation is crucial for preventing intracellular ice formation, which could be lethal, and ensuring the presence of liquid water around cells. AFPs have independently evolved in different species, exhibiting distinct thermal hysteresis and ice structuring properties. Beyond their ecological role, AFPs have garnered significant attention in biotechnology for potential applications in the food, agriculture, and pharmaceutical industries. This review aims to offer a thorough insight into the activity and impacts of AFPs on water, examining their significance in cold-adapted organisms, and exploring the diversity of microbial AFPs. Using a meta-analysis from cultivation-based and cultivation-independent data, we evaluate the correlation between AFP-producing microorganisms and cold environments. We also explore small and large-scale biotechnological applications of AFPs, providing a perspective for future research.
Collapse
Affiliation(s)
- Joana Camila Lopes
- Laboratory of Molecular Ecology and Extremophiles, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina-Campus Reitor João David Ferreira Lima, s/n Trindade, Florianópolis, SC 88040-900, Brazil
- Postgraduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Campus Reitor João David Ferreira Lima, s/n Trindade, Florianópolis, SC 88040-900, Brazil
| | - Camila Tomazini Kinasz
- Laboratory of Molecular Ecology and Extremophiles, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina-Campus Reitor João David Ferreira Lima, s/n Trindade, Florianópolis, SC 88040-900, Brazil
- Postgraduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Campus Reitor João David Ferreira Lima,, s/n Trindade, Florianópolis, SC 88040-900, Brazil
| | - Alanna Maylle Cararo Luiz
- Laboratory of Molecular Ecology and Extremophiles, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina-Campus Reitor João David Ferreira Lima, s/n Trindade, Florianópolis, SC 88040-900, Brazil
- Postgraduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Campus Reitor João David Ferreira Lima,, s/n Trindade, Florianópolis, SC 88040-900, Brazil
| | - Marianne Gabi Kreusch
- Laboratory of Molecular Ecology and Extremophiles, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina-Campus Reitor João David Ferreira Lima, s/n Trindade, Florianópolis, SC 88040-900, Brazil
| | - Rubens Tadeu Delgado Duarte
- Laboratory of Molecular Ecology and Extremophiles, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina-Campus Reitor João David Ferreira Lima, s/n Trindade, Florianópolis, SC 88040-900, Brazil
- Postgraduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Campus Reitor João David Ferreira Lima,, s/n Trindade, Florianópolis, SC 88040-900, Brazil
| |
Collapse
|
2
|
Barts N, Bhatt RH, Toner C, Meyer WK, Durrant JD, Kohl KD. Functional convergence in gastric lysozymes of foregut-fermenting rodents, ruminants, and primates is not attributed to convergent molecular evolution. Comp Biochem Physiol B Biochem Mol Biol 2024; 271:110949. [PMID: 38341948 DOI: 10.1016/j.cbpb.2024.110949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/28/2024] [Accepted: 01/28/2024] [Indexed: 02/13/2024]
Abstract
Convergent evolution is a widespread phenomenon. While there are many examples of convergent evolution at the phenotypic scale, convergence at the molecular level has been more difficult to identify. A classic example of convergent evolution across scales is that of the digestive lysozyme found in ruminants and Colobine monkeys. These herbivorous species rely on foregut fermentation, which has evolved to function more optimally under acidic conditions. Here, we explored if rodents with similar dietary strategies and digestive morphologies have convergently evolved a lysozyme with digestive functions. At the phenotypic level, we find that rodents with bilocular stomach morphologies exhibited a lysozyme that maintained higher relative activities at low pH values, similar to the lysozymes of ruminants and Colobine monkeys. Additionally, the lysozyme of Peromyscus leucopus shared a similar predicted protonation state as that observed in previously identified digestive lysozymes. However, we found limited evidence of positive selection acting on the lysozyme gene in foregut-fermenting species and did not identify patterns of convergent molecular evolution in this gene. This study emphasizes that phenotypic convergence need not be the result of convergent genetic modifications, and we encourage further exploration into the mechanisms regulating convergence across biological scales.
Collapse
Affiliation(s)
- Nick Barts
- Department of Biological and Clinical Sciences, University of Central Missouri, Warrensburg, MO, USA; Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Roshni H Bhatt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA. https://twitter.com/RoshniBhatt3
| | - Chelsea Toner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA. https://twitter.com/sorrywm
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA. https://twitter.com/KevinDKohl
| |
Collapse
|
3
|
Hadi Z, Ahmadi E, Shams-Esfandabadi N, Davoodian N, Shirazi A, Moradian M. Polyvinyl alcohol addition to freezing extender can improve the post-thaw quality, longevity and in vitro fertility of ram epididymal spermatozoa. Cryobiology 2024; 114:104853. [PMID: 38301951 DOI: 10.1016/j.cryobiol.2024.104853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/18/2023] [Accepted: 01/24/2024] [Indexed: 02/03/2024]
Abstract
Recovering and cryopreserving epididymal spermatozoa are suitable methods for preserving the genetic potential of livestock and endangered species. Regarding encouraging reports on the use of polyvinyl alcohol (PVA) in cryopreserving various cell types, we conducted this study to examine the impact of PVA on the post-thaw quality, longevity, and in vitro fertility of ram epididymal sperm. In the first experiment, ram epididymal spermatozoa were frozen in extenders containing 6 % glycerol and 0, 0.5, 1, 2, 5, 10, or 15 mg/ml of PVA. Polyvinyl alcohol at concentrations of 0.5, 1, and 2 mg/ml improved the motility and functional membrane integrity (FMI) of the sperm compared with the control group (P < 0.05). In the second experiment, we investigated whether PVA could partially substitute glycerol in the freezing extender. PVA was added at 0, 0.5, 1, and 2 mg/ml to the extenders containing 1 % or 2 % glycerol. After thawing, the sperm motility parameters of the group containing 1 mg/ml PVA and 2 % glycerol were significantly higher than those of the un-supplemented groups (P < 0.05). In the third experiment, the effect of PVA on the post-thaw sperm longevity were examined. Sperm were frozen in 3 extenders: one containing 6 % glycerol and 1 mg/ml PVA (Gly6P1), another containing 2 % glycerol and 1 mg/ml PVA (Gly2P1), and a control extender with 6 % glycerol. After thawing, the quality of the sperm was evaluated. Sperm were then diluted in human tubal fluid (HTF) and incubated at 37 °C for 3 h. Afterwards, the quality of the sperm was evaluated once more. The presence of PVA in the freezing extender improved motility parameters and FMI. Additionally, PVA-containing groups had lower proportions of capacitated and acrosome reacted sperm compared with the control group (P < 0.05). The Gly6P1 group performed better than the other two groups (P < 0.05). In the fourth experiment, sperm from the Gly6P1 and Control groups were used in the IVF process immediately after thawing (T0) and after a 3-h incubation at 37 °C in HTF (T3). Cleavage, blastocyst and hatching rates in both groups were similar at T0, but they were lower in the Control group at T3 (P < 0.05). In conclusion, PVA as an additive to the freezing extender significantly improves post-thaw motility, viability, acrosome integrity, longevity, and fertile lifespan of ram epididymal spermatozoa.
Collapse
Affiliation(s)
- Zeinab Hadi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran; Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran
| | - Ebrahim Ahmadi
- Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran.
| | - Naser Shams-Esfandabadi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran; Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran
| | - Najmeh Davoodian
- Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran
| | - Abolfazl Shirazi
- Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran; Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Midya Moradian
- Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran
| |
Collapse
|
4
|
Diao Y, Hao T, Liu X, Yang H. Advances in single ice crystal shaping materials: From nature to synthesis and applications in cryopreservation. Acta Biomater 2024; 174:49-68. [PMID: 38040076 DOI: 10.1016/j.actbio.2023.11.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/23/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
Antifreeze (glyco) proteins [AF(G)Ps], which are widely present in various extreme microorganisms, can control the formation and growth of ice crystals. Given the significance of cryogenic technology in biomedicine, climate science, electronic energy, and other fields of research, scientists are quite interested in the development and synthesis high-efficiency bionic antifreeze protein materials, particularly to reproduce their dynamic ice shaping (DIS) characteristics. Single ice crystal shaping materials, a promising class of ice-controlling materials, can alter the morphology and growth rate of ice crystals at low temperatures. This review aims to highlight the development of single ice crystal shaping materials and provide a brief comparison between a series of natural and bionic synthetic materials with DIS ability, which include AF(G)Ps, polymers, salts, and nanomaterials. Additionally, we summarize their applications in cryopreservation. Finally, this paper presents the current challenges and prospects encountered in developing high-efficiency and practical single ice crystal shaping materials. STATEMENT OF SIGNIFICANCE: The formation and growth of ice crystals hold a significant importance to an incredibly broad range of fields. Therefore, the design and fabrication of the single ice crystal shaping materials have gained the increasing popularity due to its key role in dynamic ice shaping (DIS) characteristics. Especially, single ice crystal shaping materials are considered one of the most promising candidates as ice inhibitors, presenting tremendous prospects for enhancing cryopreservation. In this work, we focus on the molecular characteristics, structure-function relationships, and DIS mechanisms of typical natural and biomimetic synthetic materials. This review may provide inspiration for the design and preparation of single ice crystal shaping materials and give guidance for the development of effective cryopreservation agent.
Collapse
Affiliation(s)
- Yunhe Diao
- School of Materials Science and Engineering, Zhengzhou University, 450001 Zhengzhou, Henan, China
| | - Tongtong Hao
- School of Materials Science and Engineering, Beijing Institute of Technology, 100081 Beijing, China
| | - Xuying Liu
- School of Materials Science and Engineering, Zhengzhou University, 450001 Zhengzhou, Henan, China
| | - Huige Yang
- School of Materials Science and Engineering, Zhengzhou University, 450001 Zhengzhou, Henan, China..
| |
Collapse
|
5
|
Ali F, Kumar H, Alghamdi W, Kateb FA, Alarfaj FK. Recent Advances in Machine Learning-Based Models for Prediction of Antiviral Peptides. ARCHIVES OF COMPUTATIONAL METHODS IN ENGINEERING : STATE OF THE ART REVIEWS 2023; 30:1-12. [PMID: 37359746 PMCID: PMC10148704 DOI: 10.1007/s11831-023-09933-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/19/2023] [Indexed: 06/28/2023]
Abstract
Viruses have killed and infected millions of people across the world. It causes several chronic diseases like COVID-19, HIV, and hepatitis. To cope with such diseases and virus infections, antiviral peptides (AVPs) have been applied in the design of drugs. Keeping in view the significant role in pharmaceutical industry and other research fields, identification of AVPs is highly indispensable. In this connection, experimental and computational methods were proposed to identify AVPs. However, more accurate predictors for boosting AVPs identification are highly desirable. This work presents a thorough study and reports the available predictors of AVPs. We explained applied datasets, feature representation approaches, classification algorithms, and evaluation parameters of performance. In this study, the limitations of the existing studies and the best methods were emphasized. Provided the pros and cons of the applied classifiers. The future insights demonstrate efficient feature encoding approaches, best feature optimization schemes, and effective classification techniques that can improve the performance of novel method for accurate prediction of AVPs.
Collapse
Affiliation(s)
- Farman Ali
- Sarhad University of Science and Information Technology Peshawar, Mardan Campus, Khyber Pakhtunkhwa, Pakistan
| | - Harish Kumar
- Department of Computer Science, College of Computer Science, King Khalid University, Abha, Saudi Arabia
| | - Wajdi Alghamdi
- Department of Information Technology, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Faris A. Kateb
- Department of Information Technology, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Fawaz Khaled Alarfaj
- Department of Management Information Systems, King Faisal University, Hufof, Saudi Arabia
| |
Collapse
|
6
|
Watanabe YY, Payne NL. Thermal sensitivity of metabolic rate mirrors biogeographic differences between teleosts and elasmobranchs. Nat Commun 2023; 14:2054. [PMID: 37045817 PMCID: PMC10097821 DOI: 10.1038/s41467-023-37637-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 03/24/2023] [Indexed: 04/14/2023] Open
Abstract
Environmental temperature affects physiological functions, representing a barrier for the range expansions of ectothermic species. To understand the link between thermal physiology and biogeography, a key question is whether among-species thermal sensitivity of metabolic rates is mechanistically constrained or buffered through physiological remodeling over evolutionary time. The former conception, the Universal Temperature Dependence hypothesis, predicts similar among- and within-species thermal sensitivity. The latter conception, the Metabolic Cold Adaptation hypothesis, predicts lower among-species thermal sensitivity than within-species sensitivity. Previous studies that tested these hypotheses for fishes overwhelmingly investigated teleosts with elasmobranchs understudied. Here, we show that among-species thermal sensitivity of resting metabolic rates is lower than within-species sensitivity in teleosts but not in elasmobranchs. Further, species richness declines with latitude more rapidly in elasmobranchs than in teleosts. Metabolic Cold Adaptation exhibited by teleosts might underpin their high diversity at high latitudes, whereas the inflexible thermal sensitivity approximated by Universal Temperature Dependence of elasmobranchs might explain their low diversity at high latitudes.
Collapse
Affiliation(s)
- Yuuki Y Watanabe
- National Institute of Polar Research, Tachikawa, Tokyo, Japan.
- Department of Polar Science, The Graduate University for Advanced Studies, SOKENDAI, Tachikawa, Tokyo, Japan.
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama, Kanagawa, Japan.
| | - Nicholas L Payne
- School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| |
Collapse
|
7
|
Liu M, Chen C, Liang L, Yu C, Guo B, Zhang H, Qiu Y, Zhang H, Yao F, Li J. A biocompatible cell cryoprotectant based on sulfoxide-containing amino acids: mechanism and application. J Mater Chem B 2023; 11:2504-2517. [PMID: 36852742 DOI: 10.1039/d3tb00005b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The preservation of cells at cryogenic temperatures requires the presence of cryoprotectants (CPAs). Dimethyl sulfoxide (DMSO), as a state-of-the-art CPA, is widely used for the storage of many types of cells. However, its intrinsic toxicity is still an obstacle for its applications in clinical practice. Herein, we report a DMSO analogue, L-methionine sulfoxide (Met(O)-OH), as a CPA for cell cryopreservation. The molecular-level cryopreservation roles of Met(O)-OH were investigated by experiments and molecular dynamics simulations. The results also found that Met(O)-OH showed high ice recrystallization inhibition (IRI) activity and the ice crystals in Met(O)-OH solution tend to be relatively round and smooth; moreover, the ice size was significantly reduced to 30.26 μm compared with pure water (135.87 μm) or DMSO solution (45.08 μm). At the molecular level, Met(O)-OH could stably bind the surface of the ice crystals and form more stable hydrogen bonds with ice compared with L-methionine. Moreover, Met(O)-OH could significantly reduce the damage to cells caused by osmotic shock and did not change the cell viability even at high concentration (4%). Based on these results, nucleated L929 cells and anuclear sheep red blood cells (SRBCs) were used as cell models to investigate the cryopreservation activity of Met(O)-OH. The results suggested that, under the optimum protocol, Met(O)-OH showed an effective post-thaw survival efficiency with ultrarapid freezing, and the post-thaw survival efficiency of L929 cells reached 84.0%. This work opens up the possibility for an alternative to traditional toxic CPA DMSO, and provides insights for the development of DMSO analogues with non-toxic/low toxicity for cell cryoprotection applications.
Collapse
Affiliation(s)
- Min Liu
- Department of Polymer Science, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Changhong Chen
- Department of Polymer Science, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Lei Liang
- Department of Polymer Science, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Chaojie Yu
- Department of Polymer Science, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Bingyan Guo
- Department of Polymer Science, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Haitao Zhang
- Department of Polymer Science, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Yuwei Qiu
- Department of Polymer Science, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Hong Zhang
- Department of Polymer Science, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China. .,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
| | - Fanglian Yao
- Department of Polymer Science, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China. .,Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Junjie Li
- Department of Polymer Science, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China. .,Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
| |
Collapse
|
8
|
Farag H, Peters B. Free energy barriers for anti-freeze protein engulfment in ice: Effects of supercooling, footprint size, and spatial separation. J Chem Phys 2023; 158:094501. [PMID: 36889941 DOI: 10.1063/5.0131983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Anti-freeze proteins (AFPs) protect organisms at freezing conditions by attaching to the ice surface and arresting its growth. Each adsorbed AFP locally pins the ice surface, resulting in a metastable dimple for which the interfacial forces counteract the driving force for growth. As supercooling increases, these metastable dimples become deeper, until metastability is lost in an engulfment event where the ice irreversibly swallows the AFP. Engulfment resembles nucleation in some respects, and this paper develops a model for the "critical profile" and free energy barrier for the engulfment process. Specifically, we variationally optimize the ice-water interface and estimate the free energy barrier as a function of the supercooling, the AFP footprint size, and the distance to neighboring AFPs on the ice surface. Finally, we use symbolic regression to derive a simple closed-form expression for the free energy barrier as a function of two physically interpretable, dimensionless parameters.
Collapse
Affiliation(s)
- Hossam Farag
- Nuclear, Plasma, and Radiological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Baron Peters
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| |
Collapse
|
9
|
Akhondzadeh S, Farshad A, Rostamzadeh J, Sharafi M. Effects of Antifreeze Protein Type I and Glycerol in Diluents on Cryopreserved Goat Epididymal Sperm. Biopreserv Biobank 2023; 21:65-73. [PMID: 35426727 DOI: 10.1089/bio.2021.0150] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The effect of antifreeze protein (AFP) as a cryoprotectant used in different concentrations of glycerol on post-thaw quality of epididymal sperm was investigated. Sperm were isolated from 50 testicles, obtained from 25 healthy mature goat bucks, with progressive motility >80%, and total morphological abnormalities <10% were pooled in each replication. The semen samples were diluted with Tris-citrate-fructose-soybean lecithin extender containing different concentration of AFP [0 μg/mL (A0), 5 μg/mL (A5), 10 μg/mL (A10)]. Each concentration of AFP was added in an extender containing either 7% (G7) or 5% (G5) glycerol. Post-thaw total and progressive motility were found to be higher (p < 0.05) in groups A5G5 and A5G7. Plasma membrane integrity, sperm acrosome integrity, DNA integrity, acrosome intact sperm, and mitochondrial membrane potential were found to be higher (p < 0.05) in groups A5G5 and A10G5. Sperm viability was found to be higher (p < 0.05) in group A5G5, while lipid peroxidation was recorded lower (p < 0.05) in groups A5G5 and A5G7. Regarding the apoptosis occurrence, the results demonstrate higher (p < 0.05) live post-thawed spermatozoa for groups containing 5 μg/mL AFP with 5% and 7% glycerol in addition to the lowest (p < 0.05) value for groups containing 0 μg/mL AFP with 5% and 7% glycerol. Based on these results, the present study concludes that the addition of 5 μg/mL AFP in combination with 5% glycerol in freezing extender improves the post-thaw quality, structure, and function parameters for buck spermatozoa.
Collapse
Affiliation(s)
- Saeed Akhondzadeh
- Laboratory of Reproduction Biology, Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Kurdistan, Iran
| | - Abbas Farshad
- Laboratory of Reproduction Biology, Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Kurdistan, Iran
| | - Jalal Rostamzadeh
- Laboratory of Reproduction Biology, Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Kurdistan, Iran
| | - Mohsen Sharafi
- Department of Embryology at Reproductive Biomedicine Research Center, Royan Institute for Reproductive, ACECR, Tehran, Iran
| |
Collapse
|
10
|
Jaiswal AN, Vagga A. Cryopreservation: A Review Article. Cureus 2022; 14:e31564. [DOI: 10.7759/cureus.31564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/16/2022] [Indexed: 11/17/2022] Open
|
11
|
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.
Collapse
|
12
|
Choi HW, Jang H. Application of Nanoparticles and Melatonin for Cryopreservation of Gametes and Embryos. Curr Issues Mol Biol 2022; 44:4028-4044. [PMID: 36135188 PMCID: PMC9497981 DOI: 10.3390/cimb44090276] [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: 08/17/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Cryopreservation of gametes and embryos, a technique widely applied in human infertility clinics and to preserve desirable genetic traits of livestock, has been developed over 30 years as a component of the artificial insemination process. A number of researchers have conducted studies to reduce cell toxicity during cryopreservation using adjuvants leading to higher gamete and embryo survival rates. Melatonin and Nanoparticles are novel cryoprotectants and recent studies have investigated their properties such as regulating oxidative stresses, lipid peroxidation, and DNA fragmentation in order to protect gametes and embryos during vitrification. This review presented the current status of cryoprotectants and highlights the novel biomaterials such as melatonin and nanoparticles that may improve the survivability of gametes and embryos during this process.
Collapse
Affiliation(s)
- Hyun-Woo Choi
- Department of Animal Science, Jeonbuk National University, Jeonju 54896, Korea
| | - Hoon Jang
- Department of Life Sciences, Jeonbuk National University, Jeonju 54896, Korea
- Correspondence: ; Tel.: +82-63-270-3359
| |
Collapse
|
13
|
Martínez-Jiménez M, Benavides AL. The liquidus temperature curve of aqueous methanol mixtures: a numerical simulation study. J Chem Phys 2022; 157:104502. [DOI: 10.1063/5.0099751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The liquidus temperature curve that characterizes the boundary between the liquid methanol/water mixture and its coexistence with ice Ih is determined using the direct-coexistence method. Several methanol concentrations and pressures of 0.1 MPa, 50 MPa, and 100 MPa are considered. In this study, we used the TIP4P/Ice model for water and two different models for methanol: OPLS and OPLS/2016, using the geometric rule for the Lennard-Jones cross interactions. We compared our simulation results with available experimental data and found that this combination of models reproduces reasonably well the liquidus curve for methanol mole fractions up to xm=0.3 at p=0.1 MPa. The freezing point depression of these mixtures is calculated and compared to experimental results. We also analyzed the effect of pressure on the liquidus curve, and we found that both models also reproduce qualitatively well the experimental decreasing of the liquidus temperatures as the pressure increases.
Collapse
Affiliation(s)
| | - Ana Laura Benavides
- Ingeniería Física, Universidad de Guanajuato División de Ciencias e Ingenierías Campus León, Mexico
| |
Collapse
|
14
|
Gerber L, MacSween CE, Staples JF, Gamperl AK. Cold-induced metabolic depression in cunner (Tautogolabrus adspersus): A multifaceted cellular event. PLoS One 2022; 17:e0271086. [PMID: 35917356 PMCID: PMC9345476 DOI: 10.1371/journal.pone.0271086] [Citation(s) in RCA: 4] [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: 02/21/2022] [Accepted: 06/22/2022] [Indexed: 11/19/2022] Open
Abstract
Metabolic depression and dormancy (i.e., stopping/greatly reducing activity and feeding) are strategies used by many animals to survive winter conditions characterized by food shortages and cold temperatures. However, controversy exists on whether the reduced metabolism of some fishes at cold temperatures is due to dormancy alone, or also involves active metabolic depression. Thus, we acclimated winter-dormant cunner [Tautogolabrus adspersus, a north temperate wrasse which in Newfoundland is at the northern limit of its distribution] and winter-active Atlantic salmon (Salmo salar) to winter (0°C; 8h light: 16h dark) and summer (10°C; 16h light: 8 h dark) conditions, and measured the thermal sensitivity of ATP-producing and O2-consuming processes in isolated liver mitochondria and hepatocytes when exposed in vitro to temperatures from 20 to 0°C and 10 to 0°C, respectively. We found that: 1) liver mitochondrial State 3 respiration and hepatocyte O2 consumption in cunner were only ~ one-third and two-thirds of that measured in salmon, respectively, at all measurement temperatures; 2) cunner mitochondria also have proton conductance and leak respiration (State 4) values that are only approximately one-third of those in salmon; 3) the mitochondria of cunner show a dramatic reduction in respiratory control ratio (from ~ 8 to 3), and a much greater drop in State 3 respiration, between 10 and 5°C (Q10 values in 10- and 0°C-acclimated fish of 14.5 and 141.2, respectively), as compared with salmon (3.9 and 9.6, respectively); and 4) lowering temperature from 5 to 0°C resulted in ~ 40 and 30% reductions in hepatocyte O2 consumption due to non-mitochondrial respiration and Na+-K+-ATPase activity, respectively, in cunner, but not in salmon. Collectively, these results highlight the intrinsic capacity for metabolic depression in hepatocytes and mitochondria of cunner, and clearly suggest that several cellular processes play a role in the reduced metabolic rates exhibited by some fishes at cold temperatures.
Collapse
Affiliation(s)
- Lucie Gerber
- Department of Ocean Sciences, Memorial University of Newfoundland and Labrador, St. John’s, NL, Canada
| | - Courtney E. MacSween
- Department of Ocean Sciences, Memorial University of Newfoundland and Labrador, St. John’s, NL, Canada
| | - James F. Staples
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - A. Kurt Gamperl
- Department of Ocean Sciences, Memorial University of Newfoundland and Labrador, St. John’s, NL, Canada
- * E-mail:
| |
Collapse
|
15
|
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.
Collapse
|
16
|
Davies PL. Reflections on antifreeze proteins and their evolution. Biochem Cell Biol 2022; 100:282-291. [PMID: 35580352 DOI: 10.1139/bcb-2022-0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The discovery of radically different antifreeze proteins (AFPs) in fishes during the 1970s and 1980s suggested that these proteins had recently and independently evolved to protect teleosts from freezing in icy seawater. Early forays into the isolation and characterization of AFP genes in these fish showed they were massively amplified, often in long tandem repeats. The work of many labs in the 1980s onward led to the discovery and characterization of AFPs in other kingdoms, such as insects, plants, and many different microorganisms. The distinct ice-binding property that these ice-binding proteins (IBPs) share has facilitated their purification through adsorption to ice, and the ability to produce recombinant versions of IBPs has enabled their structural characterization and the mapping of their ice-binding sites (IBSs) using site-directed mutagenesis. One hypothesis for their ice affinity is that the IBS organizes surface waters into an ice-like pattern that freezes the protein onto ice. With access now to a rapidly expanding database of genomic sequences, it has been possible to trace the origins of some fish AFPs through the process of gene duplication and divergence, and to even show the horizontal transfer of an AFP gene from one species to another.
Collapse
Affiliation(s)
- Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| |
Collapse
|
17
|
Guerreiro BM, Consiglio AN, Rubinsky B, Powell-Palm MJ, Freitas F. Enhanced Control over Ice Nucleation Stochasticity Using a Carbohydrate Polymer Cryoprotectant. ACS Biomater Sci Eng 2022; 8:1852-1859. [PMID: 35380422 DOI: 10.1021/acsbiomaterials.2c00075] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metastable supercooling has emerged as a transformative technique for ice-free biopreservation, but issues of stability inherent to the stochastic nature of ice formation have thus far limited its translation out of the laboratory. In this work, we explore the influence of the bio-based carbohydrate polymer FucoPol on aqueous supercooling using an isochoric nucleation detection technique. We show that FucoPol, a high-molecular-weight, fucose-rich polysaccharide, which has previously been shown to reduce average ice crystal sizes after nucleation, also induces a concentration-dependent stabilization of metastable supercooled water, as evidenced by both a significant reduction in nucleation stochasticity (i.e., the spread in temperatures over which the system will nucleate upon cooling) and a corresponding increase in the predicted induction time of nucleation. FucoPol is found to confine the stochasticity of ice nucleation to a narrow, well-defined band of temperatures roughly one-third as wide as that of pure water under identical conditions. Importantly, this substantial reduction in stochasticity is accompanied by only a minimal (<1 °C) change in the average nucleation temperature, suggesting that this effect is distinct from colligative freezing point depression. Reducing and characterizing the stochasticity of aqueous supercooling is essential to the engineering design of practical biopreservation protocols, and the results reported herein suggest that high-viscosity polymer systems may provide a powerful and largely unexplored lever by which to manipulate metastable-equilibrium phase change kinetics at subzero temperatures.
Collapse
Affiliation(s)
- Bruno M Guerreiro
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica 2819-516, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica 2819-516, Portugal.,LAQV-REQUIMTE, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica 2829-516, Portugal.,CENIMAT/I3N, Department of Physics, School of Science and Technology, NOVA University Lisbon, Caparica 2829-516, Portugal
| | - Anthony N Consiglio
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley 94720, California, United States
| | - Boris Rubinsky
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley 94720, California, United States
| | - Matthew J Powell-Palm
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley 94720, California, United States
| | - Filomena Freitas
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica 2819-516, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica 2819-516, Portugal
| |
Collapse
|
18
|
Sreter JA, Foxall TL, Varga K. Intracellular and Extracellular Antifreeze Protein Significantly Improves Mammalian Cell Cryopreservation. Biomolecules 2022; 12:669. [PMID: 35625597 PMCID: PMC9139014 DOI: 10.3390/biom12050669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/23/2022] [Accepted: 04/29/2022] [Indexed: 12/03/2022] Open
Abstract
Cell cryopreservation is an essential part of the biotechnology, food, and health care industries. There is a need to develop more effective, less toxic cryoprotective agents (CPAs) and methods, especially for mammalian cells. We investigated the impact of an insect antifreeze protein from Anatolica polita (ApAFP752) on mammalian cell cryopreservation using the human embryonic kidney cell line HEK 293T. An enhanced green fluorescent protein (EGFP)-tagged antifreeze protein, EGFP-ApAFP752, was transfected into the cells and the GFP was used to determine the efficiency of transfection. AFP was assessed for its cryoprotective effects intra- and extracellularly and both simultaneously at different concentrations with and without dimethyl sulfoxide (DMSO) at different concentrations. Comparisons were made to DMSO or medium alone. Cells were cryopreserved at -196 °C for ≥4 weeks. Upon thawing, cellular viability was determined using trypan blue, cellular damage was assessed by lactate dehydrogenase (LDH) assay, and cellular metabolism was measured using a metabolic activity assay (MTS). The use of this AFP significantly improved cryopreserved cell survival when used with DMSO intracellularly. Extracellular AFP also significantly improved cell survival when included in the DMSO freezing medium. Intra- and extracellular AFP used together demonstrated the most significantly increased cryoprotection compared to DMSO alone. These findings present a potential method to improve the viability of cryopreserved mammalian cells.
Collapse
Affiliation(s)
- Jonathan A. Sreter
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA;
| | - Thomas L. Foxall
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA;
| | - Krisztina Varga
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA;
| |
Collapse
|
19
|
Box ICH, Matthews BJ, Marshall KE. Molecular evidence of intertidal habitats selecting for repeated ice-binding protein evolution in invertebrates. J Exp Biol 2022; 225:274373. [PMID: 35258616 DOI: 10.1242/jeb.243409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/20/2021] [Indexed: 12/21/2022]
Abstract
Ice-binding proteins (IBPs) have evolved independently in multiple taxonomic groups to improve their survival at sub-zero temperatures. Intertidal invertebrates in temperate and polar regions frequently encounter sub-zero temperatures, yet there is little information on IBPs in these organisms. We hypothesized that there are far more IBPs than are currently known and that the occurrence of freezing in the intertidal zone selects for these proteins. We compiled a list of genome-sequenced invertebrates across multiple habitats and a list of known IBP sequences and used BLAST to identify a wide array of putative IBPs in those invertebrates. We found that the probability of an invertebrate species having an IBP was significantly greater in intertidal species than in those primarily found in open ocean or freshwater habitats. These intertidal IBPs had high sequence similarity to fish and tick antifreeze glycoproteins and fish type II antifreeze proteins. Previously established classifiers based on machine learning techniques further predicted ice-binding activity in the majority of our newly identified putative IBPs. We investigated the potential evolutionary origin of one putative IBP from the hard-shelled mussel Mytilus coruscus and suggest that it arose through gene duplication and neofunctionalization. We show that IBPs likely readily evolve in response to freezing risk and that there is an array of uncharacterized IBPs, and highlight the need for broader laboratory-based surveys of the diversity of ice-binding activity across diverse taxonomic and ecological groups.
Collapse
Affiliation(s)
- Isaiah C H Box
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, CanadaV6T 1Z4
| | - Benjamin J Matthews
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, CanadaV6T 1Z4
| | - Katie E Marshall
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, CanadaV6T 1Z4
| |
Collapse
|
20
|
Gharib G, Saeidiharzand S, Sadaghiani AK, Koşar A. Antifreeze Proteins: A Tale of Evolution From Origin to Energy Applications. Front Bioeng Biotechnol 2022; 9:770588. [PMID: 35186912 PMCID: PMC8851421 DOI: 10.3389/fbioe.2021.770588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/31/2021] [Indexed: 11/19/2022] Open
Abstract
Icing and formation of ice crystals is a major obstacle against applications ranging from energy systems to transportation and aviation. Icing not only introduces excess thermal resistance, but it also reduces the safety in operating systems. Many organisms living under harsh climate and subzero temperature conditions have developed extraordinary survival strategies to avoid or delay ice crystal formation. There are several types of antifreeze glycoproteins with ice-binding ability to hamper ice growth, ice nucleation, and recrystallization. Scientists adopted similar approaches to utilize a new generation of engineered antifreeze and ice-binding proteins as bio cryoprotective agents for preservation and industrial applications. There are numerous types of antifreeze proteins (AFPs) categorized according to their structures and functions. The main challenge in employing such biomolecules on industrial surfaces is the stabilization/coating with high efficiency. In this review, we discuss various classes of antifreeze proteins. Our particular focus is on the elaboration of potential industrial applications of anti-freeze polypeptides.
Collapse
Affiliation(s)
- Ghazaleh Gharib
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul, Turkey
- Sabanci University Nanotechnology and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano-Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
| | - Shaghayegh Saeidiharzand
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul, Turkey
- Sabanci University Nanotechnology and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
| | - Abdolali K. Sadaghiani
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul, Turkey
- Sabanci University Nanotechnology and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano-Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
- *Correspondence: Abdolali K. Sadaghiani, ; Ali Koşar,
| | - Ali Koşar
- Faculty of Engineering and Natural Sciences (FENS), Sabanci University, Istanbul, Turkey
- Sabanci University Nanotechnology and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano-Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
- *Correspondence: Abdolali K. Sadaghiani, ; Ali Koşar,
| |
Collapse
|
21
|
Ghalamara S, Silva S, Brazinha C, Pintado M. Structural diversity of marine anti-freezing proteins, properties and potential applications: a review. BIORESOUR BIOPROCESS 2022; 9:5. [PMID: 38647561 PMCID: PMC10992025 DOI: 10.1186/s40643-022-00494-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/08/2022] [Indexed: 11/10/2022] Open
Abstract
Cold-adapted organisms, such as fishes, insects, plants and bacteria produce a group of proteins known as antifreeze proteins (AFPs). The specific functions of AFPs, including thermal hysteresis (TH), ice recrystallization inhibition (IRI), dynamic ice shaping (DIS) and interaction with membranes, attracted significant interest for their incorporation into commercial products. AFPs represent their effects by lowering the water freezing point as well as preventing the growth of ice crystals and recrystallization during frozen storage. The potential of AFPs to modify ice growth results in ice crystal stabilizing over a defined temperature range and inhibiting ice recrystallization, which could minimize drip loss during thawing, improve the quality and increase the shelf-life of frozen products. Most cryopreservation studies using marine-derived AFPs have shown that the addition of AFPs can increase post-thaw viability. Nevertheless, the reduced availability of bulk proteins and the need of biotechnological techniques for industrial production, limit the possible usage in foods. Despite all these drawbacks, relatively small concentrations are enough to show activity, which suggests AFPs as potential food additives in the future. The present work aims to review the results of numerous investigations on marine-derived AFPs and discuss their structure, function, physicochemical properties, purification and potential applications.
Collapse
Affiliation(s)
- Soudabeh Ghalamara
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Sara Silva
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Carla Brazinha
- LAQV/Requimte, Faculdade de Ciências E Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516, Caparica, Portugal
| | - Manuela Pintado
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal.
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Baloh P, Hanlon R, Anderson C, Dolan E, Pacholik G, Stinglmayr D, Burkart J, Felgitsch L, Schmale DG, Grothe H. Seasonal ice nucleation activity of water samples from alpine rivers and lakes in Obergurgl, Austria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149442. [PMID: 34426361 DOI: 10.1016/j.scitotenv.2021.149442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Heterogeneous ice nucleation plays an important role in many environmental processes such as ice cloud formation, freezing of water bodies or biological freeze protection in the cryosphere. New information is needed about the seasonal availability, nature, and activity of ice nucleating particles (INPs) in alpine environments. These INPs trigger the phase transition from liquid water to solid ice at elevated subzero temperatures. We collected water samples from a series of alpine rivers and lakes (two valleys and their rivers, an artificial pond, and a natural lake system) in Obergurgl, Austria in June 2016, July 2016, November 2016, and May 2017. Each alpine river and lake was sampled multiple times across different seasons, depending on site access during different times of the year. Water samples were filtered through a 0.22 μm membrane filter to separate microbial INPs from the water, and both fractions were analyzed for ice nucleation activity (INA) by an emulsion freezing method. Microorganisms were cultured from the filters, and the cultures then analyzed for INA. Portions of the filtered samples were concentrated by lyophilization to observe potential enhancement of INA. Two sediment samples were taken as reference points for inorganic INPs. Sub-micron INPs were observed in all of the alpine water sources studied, and a seasonal shift to a higher fraction of microbial ice nucleators cultured on selective media was observed during the winter collections. Particles larger than 0.22 μm showed INA, and microbes were cultured from this fraction. Results from 60 samples gave evidence of a seasonal change in INA, presence of submicrometer INPs, and show the abundance of culturable microorganisms, with late spring and early summer showing the most active biological INPs. With additional future research on this topic ski resorts could make use of such knowledge of geographical and seasonal trends of microbial INPs in freshwater habitats in order to improve the production of artificial snow.
Collapse
Affiliation(s)
- Philipp Baloh
- Institute of Materials Chemistry, TU Wien, Vienna, Austria
| | - Regina Hanlon
- School of Plant and Environmental Sciences, Blacksburg, VA, USA
| | | | - Eoin Dolan
- Institute of Materials Chemistry, TU Wien, Vienna, Austria
| | | | | | - Julia Burkart
- Institute of Materials Chemistry, TU Wien, Vienna, Austria; Faculty of Physics, University of Vienna, Vienna, Austria
| | | | - David G Schmale
- School of Plant and Environmental Sciences, Blacksburg, VA, USA
| | - Hinrich Grothe
- Institute of Materials Chemistry, TU Wien, Vienna, Austria.
| |
Collapse
|
24
|
Lu C, Qiu J, Zhao W, Sakai E, Zhang G, Nobe R, Kudo M, Komiyama T. Low-temperature adaptive conductive hydrogel based on ice structuring proteins/CaCl 2 anti-freeze system as wearable strain and temperature sensor. Int J Biol Macromol 2021; 188:534-541. [PMID: 34390749 DOI: 10.1016/j.ijbiomac.2021.08.060] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/27/2021] [Accepted: 08/08/2021] [Indexed: 12/24/2022]
Abstract
Conductive hydrogels as wearable devices meet the basic demands of mechanical flexibility and smart sensing. However, achieving anti-freeze property in conductive hydrogels is still challengeable. Here, a novel anti-freezing system based on ice structuring proteins and CaCl2 was introduced to enable a conductive hydrogel with low-temperature adaptability. Both formation of ice nuclei and ice growth of the hydrogel at sub-zero temperature could be inhibited. Supported by the anti-freeze system, the hydrogel revealed good flexibility (890% at -20 °C), recovery and conductivity (0.50 S/m at -20 °C) at both room temperature and sub-zero temperature. The low-temperature adaptability enabled the hydrogel to be used as strain and temperature sensors at both room temperature and sub-zero temperature. The anti-freeze system in this work is expected to open up a new avenue to promote the conductive hydrogel with low-temperature adaptability.
Collapse
Affiliation(s)
- Chunyin Lu
- Department of Machine Intelligence and Systems Engineering, Faculty of Systems Science and Technology, Akita Prefectural University, Yurihonjo 015-0055, Japan
| | - Jianhui Qiu
- Department of Machine Intelligence and Systems Engineering, Faculty of Systems Science and Technology, Akita Prefectural University, Yurihonjo 015-0055, Japan.
| | - Wei Zhao
- Department of Machine Intelligence and Systems Engineering, Faculty of Systems Science and Technology, Akita Prefectural University, Yurihonjo 015-0055, Japan
| | - Eiichi Sakai
- Department of Machine Intelligence and Systems Engineering, Faculty of Systems Science and Technology, Akita Prefectural University, Yurihonjo 015-0055, Japan
| | - Guohong Zhang
- Department of Machine Intelligence and Systems Engineering, Faculty of Systems Science and Technology, Akita Prefectural University, Yurihonjo 015-0055, Japan
| | - Rie Nobe
- Ecological Material Development Section, Akita Industrial Technology Center, Akita 010-1623, Japan
| | - Makoto Kudo
- Ecological Material Development Section, Akita Industrial Technology Center, Akita 010-1623, Japan
| | - Takao Komiyama
- Department of Machine Intelligence and Systems Engineering, Faculty of Systems Science and Technology, Akita Prefectural University, Yurihonjo 015-0055, Japan
| |
Collapse
|
25
|
Ptak-Kaczor M, Banach M, Stapor K, Fabian P, Konieczny L, Roterman I. Solubility and Aggregation of Selected Proteins Interpreted on the Basis of Hydrophobicity Distribution. Int J Mol Sci 2021; 22:ijms22095002. [PMID: 34066830 PMCID: PMC8125953 DOI: 10.3390/ijms22095002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 11/30/2022] Open
Abstract
Protein solubility is based on the compatibility of the specific protein surface with the polar aquatic environment. The exposure of polar residues to the protein surface promotes the protein’s solubility in the polar environment. The aquatic environment also influences the folding process by favoring the centralization of hydrophobic residues with the simultaneous exposure to polar residues. The degree of compatibility of the residue distribution, with the model of the concentration of hydrophobic residues in the center of the molecule, with the simultaneous exposure of polar residues is determined by the sequence of amino acids in the chain. The fuzzy oil drop model enables the quantification of the degree of compatibility of the hydrophobicity distribution observed in the protein to a form fully consistent with the Gaussian 3D function, which expresses an idealized distribution that meets the preferences of the polar water environment. The varied degrees of compatibility of the distribution observed with the idealized one allow the prediction of preferences to interactions with molecules of different polarity, including water molecules in particular. This paper analyzes a set of proteins with different levels of hydrophobicity distribution in the context of the solubility of a given protein and the possibility of complex formation.
Collapse
Affiliation(s)
- Magdalena Ptak-Kaczor
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Medyczna 7, 30-688 Kraków, Poland; (M.P.-K.); (M.B.)
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Medyczna 7, 30-688 Kraków, Poland; (M.P.-K.); (M.B.)
| | - Katarzyna Stapor
- Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland; (K.S.); (P.F.)
| | - Piotr Fabian
- Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland; (K.S.); (P.F.)
| | - Leszek Konieczny
- Chair of Medical Biochemistry—Jagiellonian University—Medical College, Kopernika 7, 31-034 Kraków, Poland;
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Medyczna 7, 30-688 Kraków, Poland; (M.P.-K.); (M.B.)
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
- Correspondence:
| |
Collapse
|
26
|
Liu Z, Wang Y, Zheng X, Jin S, Liu S, He Z, Xiang JF, Wang J. Bioinspired Crowding Inhibits Explosive Ice Growth in Antifreeze Protein Solutions. Biomacromolecules 2021; 22:2614-2624. [PMID: 33945264 DOI: 10.1021/acs.biomac.1c00331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antifreeze (glyco)proteins (AF(G)Ps) are naturally evolved ice inhibitors incomparable to any man-made materials, thus, they are gaining intensive interest for cryopreservation and beyond. AF(G)Ps depress the freezing temperature (Tf) noncolligatively below the melting temperature (Tm), generating a thermal hysteresis (TH) gap, within which the ice growth is arrested. However, the ice crystals have been reported to undergo a retaliatory and explosive growth beyond the TH gap, which is lethal to living organisms. Although intensive research has been carried to inhibit such an explosive ice growth, no satisfactory strategy has been discovered until now. Here, we report that crowded solutions mimicking an extracellular matrix (ECM), in which AF(G)Ps are located, can completely inhibit the explosive ice growth. The crowded solutions are the condensates of liquid-liquid phase separation consisting of polyethylene glycol (PEG) and sodium citrate (SC), which possess a nanoscale network and strong hydrogen bond (HB) forming ability, completely different to crowded solutions made of single components, that is, PEG or SC. Due to these unique features, the dynamics of the water is significantly slowed down, and the energy needed for breaking the HB between water molecules is distinctly increased; consequently, ice growth is inhibited as the rate of water molecules joining the ice is substantially reduced. The present work not only opens a new avenue for cryopreservation, but also suggests that the ECM of cold-hardy organisms, which also exhibit great water confining properties, may have a positive effect in protecting the living organisms from freezing damage.
Collapse
Affiliation(s)
- Zhang Liu
- Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Yan Wang
- School of Medicine, Shihezi University, Shihezi, Xinjiang 832000, People's Republic of China
| | - Xia Zheng
- Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Shenglin Jin
- Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Shuo Liu
- Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Zhiyuan He
- Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Jun-Feng Xiang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,CAS Research/Education Center for Excellence in Molecular Sciences, and Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Jianjun Wang
- Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.,School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| |
Collapse
|
27
|
Choi SR, Lee J, Seo YJ, Kong HS, Kim M, Jin E, Lee JR, Lee JH. Molecular basis of ice-binding and cryopreservation activities of type III antifreeze proteins. Comput Struct Biotechnol J 2021; 19:897-909. [PMID: 33598104 PMCID: PMC7851773 DOI: 10.1016/j.csbj.2021.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 01/08/2023] Open
Abstract
The QAE2ACT and SP ACT mutants showed full TH and IRI activities. Active AFPs effectively preserved intact follicle and prevented DSB damage. Active AFPs exhibited unique structural feature in the first 310 helix of the IBS. Unique structure of the IBS determines TH, IRI, and cryopreservation activities.
Antifreeze proteins (AFPs) can inhibit the freezing of body fluid at subzero temperatures to promote the survival of various organisms living in polar regions. Type III AFPs are categorized into three subgroups, QAE1, QAE2, and SP isoforms, based on differences in their isoelectric points. We determined the thermal hysteresis (TH), ice recrystallization inhibition (IRI), and cryopreservation activity of three isoforms of the notched-fin eelpout AFP and their mutant constructs and characterized their structural and dynamic features using NMR. The QAE1 isoform is the most active among the three classes of III AFP isoforms, and the mutants of inactive QAE2 and SP isoforms, QAE2ACT and SPACT, displayed the full TH and IRI activities with resepect to QAE1 isoform. Cryopreservation studies using mouse ovarian tissue revealed that the QAE1 isoform and the active mutants, QAE2ACT and SPACT, more effectively preserved intact follicle morphology and prevented DNA double-strand break damage more efficiently than the inactive isoforms. It was also found that all active AFPs, QAE1, QAE2ACT, and SPACT, formed unique H-bonds with the first 310 helix, an interaction that plays an important role in the formation of anchored clathrate water networks for efficient binding to the primary prism and pyramidal planes of ice crystals, which was disrupted in the inactive isoforms. Our studies provide valuable insights into the molecular mechanism of the TH and IRI activity, as well as the cryopreservation efficiency, of type III AFPs.
Collapse
Key Words
- AFP, Antifreeze protein
- Antifreeze protein
- CPA, cryoprotective agent
- Cryopreservation
- D-PBS, Dulbecco’s phosphate-buffered saline
- DMSO, dimethyl sulfoxide
- DSB, double-strand break
- EG, ethylene glycol
- H-bond, hydrogen bond
- IBP, ice-binding protein
- IBS, ice-binding surface
- IRI, ice recrystallization inhibition
- Ice crystallization inhibition
- NMR
- OT, ovarian tissue
- QAE, quaternary-amino-ethyl
- RT, room temperature
- SP, sulfopropyl
- TH, thermal hysteresis
- TUNEL, terminal deoxynucleotidyl transferase dUTP nick end labelling
- Thermal hysteresis
- nfeAFP, notched-fin eelpout AFP
- wt, wild-type
Collapse
Affiliation(s)
- Seo-Ree Choi
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Gyeongnam 52828, Republic of Korea
| | - Jaewang Lee
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Gyeonggi 13620, Republic of Korea.,Department of Biomedical Laboratory Science, Eulji University, Gyeonggi 13135, Republic of Korea
| | - Yeo-Jin Seo
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Gyeongnam 52828, Republic of Korea
| | - Hyun Sun Kong
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Gyeonggi 13620, Republic of Korea
| | - Minjae Kim
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea
| | - EonSeon Jin
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Jung Ryeol Lee
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Gyeonggi 13620, Republic of Korea.,Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Joon-Hwa Lee
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Gyeongnam 52828, Republic of Korea
| |
Collapse
|
28
|
Cryopreservation of Stem Cells. Stem Cells 2021. [DOI: 10.1007/978-981-16-1638-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
29
|
Kwan CS, Cerullo AR, Braunschweig AB. Design and Synthesis of Mucin-Inspired Glycopolymers. Chempluschem 2020; 85:2704-2721. [PMID: 33346954 DOI: 10.1002/cplu.202000637] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/08/2020] [Indexed: 12/11/2022]
Abstract
Mucins are bottlebrush biopolymers that are glycoproteins on the surfaces of cells and as hydrogels secreted inside and outside the body. Mucin function in biology includes cell-cell recognition, signaling, protection, adhesion, and lubrication. Because of their attractive and diverse properties, mucins have recently become the focus of synthetic efforts by researchers who hope to understand and emulate these biomaterials. This review is focused on the development of methodologies for preparing mucin-inspired synthetic oligomers and glycopolymers, including solid-phase synthesis, polymerization of glycosylated monomers, and post-polymerization grafting of glycans to polymer chains. How these synthetic mucins have been used in health applications is discussed. Natural mucins are formed from a conserved set of monomers that are combined into chains of different sequences and lengths to achieve materials with widely diverse properties. Adopting this design paradigm from natural mucins could lead to next-generation bioinspired synthetic materials.
Collapse
Affiliation(s)
- Chak-Shing Kwan
- The Advanced Science Research Center at the, Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA.,Department of Chemistry and Biochemistry, Hunter College, 695 Park Ave, New York, NY, 10065, USA
| | - Antonio R Cerullo
- The Advanced Science Research Center at the, Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA.,Department of Chemistry and Biochemistry, Hunter College, 695 Park Ave, New York, NY, 10065, USA.,The PhD program in Biochemistry, Graduate Center of the City University of New York, 365 5th Ave, New York, NY, 10016, USA
| | - Adam B Braunschweig
- The Advanced Science Research Center at the, Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA.,Department of Chemistry and Biochemistry, Hunter College, 695 Park Ave, New York, NY, 10065, USA.,The PhD program in Biochemistry, Graduate Center of the City University of New York, 365 5th Ave, New York, NY, 10016, USA.,The PhD program in Chemistry, Graduate Center of the City University of New York, 365 5th Ave, New York, NY, 10016, USA
| |
Collapse
|
30
|
Hobbs RS, Hall JR, Graham LA, Davies PL, Fletcher GL. Antifreeze protein dispersion in eelpouts and related fishes reveals migration and climate alteration within the last 20 Ma. PLoS One 2020; 15:e0243273. [PMID: 33320906 PMCID: PMC7737890 DOI: 10.1371/journal.pone.0243273] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 11/18/2020] [Indexed: 12/31/2022] Open
Abstract
Antifreeze proteins inhibit ice growth and are crucial for the survival of supercooled fish living in icy seawater. Of the four antifreeze protein types found in fishes, the globular type III from eelpouts is the one restricted to a single infraorder (Zoarcales), which is the only clade know to have antifreeze protein-producing species at both poles. Our analysis of over 60 unique antifreeze protein gene sequences from several Zoarcales species indicates this gene family arose around 18 Ma ago, in the Northern Hemisphere, supporting recent data suggesting that the Arctic Seas were ice-laden earlier than originally thought. The Antarctic was subject to widespread glaciation over 30 Ma and the Notothenioid fishes that produce an unrelated antifreeze glycoprotein extensively exploited the adjoining seas. We show that species from one Zoarcales family only encroached on this niche in the last few Ma, entering an environment already dominated by ice-resistant fishes, long after the onset of glaciation. As eelpouts are one of the dominant benthic fish groups of the deep ocean, they likely migrated from the north to Antarctica via the cold depths, losing all but the fully active isoform gene along the way. In contrast, northern species have retained both the fully active (QAE) and partially active (SP) isoforms for at least 15 Ma, which suggests that the combination of isoforms is functionally advantageous.
Collapse
Affiliation(s)
- Rod S. Hobbs
- Department of Ocean Sciences, Memorial University of Newfoundland, St John’s, Newfoundland, Canada
| | - Jennifer R. Hall
- Aquatic Research Cluster, CREAIT Network, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Laurie A. Graham
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
- * E-mail:
| | - Peter L. Davies
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Garth L. Fletcher
- Department of Ocean Sciences, Memorial University of Newfoundland, St John’s, Newfoundland, Canada
| |
Collapse
|
31
|
Lin J, Sun-Waterhouse D, Tang R, Cui C, Wang W, Xiong J. The effect of γ-[Glu] (1≤n≤5)-Gln on the physicochemical characteristics of frozen dough and the quality of baked bread. Food Chem 2020; 343:128406. [PMID: 33406571 DOI: 10.1016/j.foodchem.2020.128406] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/09/2020] [Accepted: 10/12/2020] [Indexed: 11/25/2022]
Abstract
This study was the first to examine the effects of γ-[Glu](1≤n≤5)-Gln (GGP, a taste enhancer; added at 0.5% or 5.0%) on the breadmaking using frozen dough. γ-[Glu](1≤n≤5)-Gln was produced using the method established in our research center. The addition of GGP at either level increased yeast viability, freezable water content and storage and loss moduli, decreased the free sulfhydryl content of dough during the frozen storage and freeze-thaw cycles, and improved the microstructure of frozen dough and texture of the baked bread. The addition of GGP at 0.5% led to a dough having the highest extensibility, and most complete and uniform starch-gluten network, and a baked bread crumb with the lowest hardness, best texture, and most uniform organization. These results indicated that GGP has great potential as a food-derived cryoprotectant/antifreeze agent for the baking industry.
Collapse
Affiliation(s)
- Junjie Lin
- College of Food Science and Technology, South China University of Technology, Guangzhou 510640, China
| | - Dongxiao Sun-Waterhouse
- College of Food Science and Technology, South China University of Technology, Guangzhou 510640, China
| | - Runmei Tang
- College of Food Science and Technology, South China University of Technology, Guangzhou 510640, China
| | - Chun Cui
- College of Food Science and Technology, South China University of Technology, Guangzhou 510640, China; Guangdong Wei-Wei Biotechnology Co., Ltd, Guangzhou 510640, China.
| | - Wei Wang
- College of Food Science and Technology, South China University of Technology, Guangzhou 510640, China
| | - Jian Xiong
- College of Food Science and Technology, South China University of Technology, Guangzhou 510640, China
| |
Collapse
|
32
|
Shi M, Zhang Q, Li Y, Zhang W, Liao L, Cheng Y, Jiang Y, Huang X, Duan Y, Xia L, Ye W, Wang Y, Xia XQ. Global gene expression profile under low-temperature conditions in the brain of the grass carp (Ctenopharyngodon idellus). PLoS One 2020; 15:e0239730. [PMID: 32976524 PMCID: PMC7518592 DOI: 10.1371/journal.pone.0239730] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 09/13/2020] [Indexed: 01/29/2023] Open
Abstract
Grass carp is an important commercial fish widely cultivated in China. A wide range of temperatures, particularly extremely low temperatures, have dramatic effects on the aquaculture of this teleost. However, relatively few studies have characterized the molecular responses of grass carp exposed to acute cooling in natural environment. Here, we investigated the transcriptome profiles of the grass carp brain in response to cooling. Through regulation pattern analyses, we identified 2,513 differentially expressed genes (DEGs) that responded to moderate cold stress (12°C), while 99 DEGs were induced by severe low temperature (4°C).The pathway analyses revealed that the DEGs sensitive to moderate cold were largely enriched in steroid biosynthesis, spliceosome, translation, protein metabolism, phagosome, gap junction and estrogen signaling pathways. Additionally, we discerned genes most likely involved in low temperature tolerance, of which the MAPK signaling pathway was dominantly enriched. Further examination and characterization of the candidate genes may help to elucidate the mechanisms underpinning extreme plasticity to severe cold stress in grass carp.
Collapse
Affiliation(s)
- Mijuan Shi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Qiangxiang Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongming Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Lanjie Liao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yingyin Cheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yanxin Jiang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Huang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - You Duan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weidong Ye
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yaping Wang
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- * E-mail: (XQX); (YW)
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: (XQX); (YW)
| |
Collapse
|
33
|
Kashyap P, Kumar S, Singh D. Performance of antifreeze protein HrCHI4 from Hippophae rhamnoides in improving the structure and freshness of green beans upon cryopreservation. Food Chem 2020; 320:126599. [DOI: 10.1016/j.foodchem.2020.126599] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 02/18/2020] [Accepted: 03/10/2020] [Indexed: 01/26/2023]
|
34
|
Mier P, Andrade-Navarro MA. MAGA: A Supervised Method to Detect Motifs From Annotated Groups in Alignments. Evol Bioinform Online 2020; 16:1176934320916199. [PMID: 32425492 PMCID: PMC7218316 DOI: 10.1177/1176934320916199] [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] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/10/2020] [Indexed: 11/17/2022] Open
Abstract
Multiple sequence alignments are usually phylogenetically driven. They are studied in the framework of evolution. But sometimes, it is interesting to study residue conservation at positions unconstrained by evolutionary rules. We present a supervised method to access a layer of information difficult to appreciate visually when many protein sequences are aligned. This new tool (MAGA; http://cbdm-01.zdv.uni-mainz.de/~munoz/maga/) locates positions in multiple sequence alignments differentially conserved in manually defined groups of sequences.
Collapse
Affiliation(s)
- Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, Mainz 55128, Germany
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, Mainz 55128, Germany
| |
Collapse
|
35
|
Usman M, Khan S, Lee JA. AFP-LSE: Antifreeze Proteins Prediction Using Latent Space Encoding of Composition of k-Spaced Amino Acid Pairs. Sci Rep 2020; 10:7197. [PMID: 32345989 PMCID: PMC7188683 DOI: 10.1038/s41598-020-63259-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/26/2020] [Indexed: 02/06/2023] Open
Abstract
Species living in extremely cold environments resist the freezing conditions through antifreeze proteins (AFPs). Apart from being essential proteins for various organisms living in sub-zero temperatures, AFPs have numerous applications in different industries. They possess very small resemblance to each other and cannot be easily identified using simple search algorithms such as BLAST and PSI-BLAST. Diverse AFPs found in fishes (Type I, II, III, IV and antifreeze glycoproteins (AFGPs)), are sub-types and show low sequence and structural similarity, making their accurate prediction challenging. Although several machine-learning methods have been proposed for the classification of AFPs, prediction methods that have greater reliability are required. In this paper, we propose a novel machine-learning-based approach for the prediction of AFP sequences using latent space learning through a deep auto-encoder method. For latent space pruning, we use the output of the auto-encoder with a deep neural network classifier to learn the non-linear mapping of the protein sequence descriptor and class label. The proposed method outperformed the existing methods, yielding excellent results in comparison. A comprehensive ablation study is performed, and the proposed method is evaluated in terms of widely used performance measures. In particular, the proposed method demonstrated a high Matthews correlation coefficient of 0.52, F-score of 0.49, and Youden’s index of 0.81 on an independent test dataset, thereby outperforming the existing methods for AFP prediction.
Collapse
Affiliation(s)
- Muhammad Usman
- Department of Computer Engineering, Chosun University, Gwangju, 61452, Republic of Korea
| | - Shujaat Khan
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jeong-A Lee
- Department of Computer Engineering, Chosun University, Gwangju, 61452, Republic of Korea.
| |
Collapse
|
36
|
Sun WS, Jang H, Kwon HJ, Kim KY, Ahn SB, Hwang S, Lee SG, Lee JH, Hwang IS, Lee JW. The protective effect of Leucosporidium-derived ice-binding protein (LeIBP) on bovine oocytes and embryos during vitrification. Theriogenology 2020; 151:137-143. [PMID: 32361180 DOI: 10.1016/j.theriogenology.2020.04.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/08/2020] [Accepted: 04/11/2020] [Indexed: 12/30/2022]
Abstract
Ice-binding proteins (IBPs) facilitate organism survival under extreme conditions by inhibiting thermal hysteresis and ice recrystallization. IBPs have been widely used as cryoprotectants to cryopreserve mammalian gametes and embryos. In the present study, we evaluated the protective effects of an Arctic yeast, Leucosporidium sp. AY30 derived ice-binding protein (LeIBP), on the vitrification of bovine metaphase II (MII) oocytes and embryos. When oocytes and embryos were frozen using the two-step vitrification method, the survival rate was significantly increased in the presence of LeIBP. The LeIBP supplementation decreased the levels of intracellular reactive oxygen species (ROS) and enhanced mitochondrial functions in the vitrified-warmed oocytes. Furthermore, LeIBP improved the developmental potential and suppressed apoptosis of the embryos derived from vitrified-warmed oocytes. Collectively, these data indicate that LeIBP can be used as a promising cryoprotectant to prevent cryoinjury during vitrification in bovine oocytes.
Collapse
Affiliation(s)
- Wu-Sheng Sun
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Hoon Jang
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Hyo Jin Kwon
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Ki Young Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Soo Bin Ahn
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Seongsoo Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Wanju, 55365, South Korea
| | - Sung Gu Lee
- Department of Polar Bioconvergence Research, Division of life Science, Korea Polar Research Institute, Incheon, 21990, South Korea
| | - Jun Hyuck Lee
- Department of Polar Bioconvergence Research, Division of life Science, Korea Polar Research Institute, Incheon, 21990, South Korea
| | - In-Sul Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Wanju, 55365, South Korea.
| | - Jeong-Woong Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea.
| |
Collapse
|
37
|
Xiang H, Yang X, Ke L, Hu Y. The properties, biotechnologies, and applications of antifreeze proteins. Int J Biol Macromol 2020; 153:661-675. [PMID: 32156540 DOI: 10.1016/j.ijbiomac.2020.03.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 01/30/2023]
Abstract
By natural selection, organisms evolve different solutions to cope with extremely cold weather. The emergence of an antifreeze protein gene is one of the most momentous solutions. Antifreeze proteins possess an importantly functional ability for organisms to survive in cold environments and are widely found in various cold-tolerant species. In this review, we summarize the origin of antifreeze proteins, describe the diversity of their species-specific properties and functions, and highlight the related biotechnology on the basis of both laboratory tests and bioinformatics analysis. The most recent advances in the applications of antifreeze proteins are also discussed. We expect that this systematic review will contribute to the comprehensive knowledge of antifreeze proteins to readers.
Collapse
Affiliation(s)
- Hong Xiang
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology
| | - Xiaohu Yang
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology
| | - Lei Ke
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology
| | - Yong Hu
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology.
| |
Collapse
|
38
|
Antifreeze protein from Anatolia polita (ApAFP914) improved outcome of vitrified in vitro sheep embryos. Cryobiology 2020; 93:109-114. [PMID: 32032586 DOI: 10.1016/j.cryobiol.2020.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/02/2020] [Accepted: 02/03/2020] [Indexed: 01/25/2023]
Abstract
Embryo cryopreservation is an important tool to preserve endangered species. As a cryoprotectant for mouse oocytes, antifreeze protein from Anatolica polita (ApAFP914) has demonstrated utility. In the present study, the effects of controlled slow freezing and vitrification methods on the survival rate of sheep oocytes fertilized in vitro after freezing-thawing were compared. Different ApAFP914 concentrations were added to the vitrification liquid for exploring the effect of antifreeze protein on the warmed embryos. The results showed that the survival and hatching rates of in vitro derived embryos were significantly higher than that of the slow freezing method. Furthermore, among the cryopreserved embryos at different developmental stages, the survival and hatching rates of the expanded blastocyst were significantly higher than those of the blastocysts, early blastocysts and morula. The survival and the hatching rates of the fast-growing embryos were both significantly higher than that of the slow-growing embryos. Additionally, treatment of ApAFP914 (5-30 μg/mL) did not increase the freezing efficiency of the 6-6.5 d embryos. However, addition of 10 μg/mL of ApAFP914 significantly increased the hatching rate of slow-growing embryos. In conclusion, our study suggests that the vitrification is better than the slow freezing method for the conservation of in vitro sheep embryos, and supplementation of ApAFP914 (10 μg/mL) significantly increased the hatching rate of slow-growing embryos after cryopreservation.
Collapse
|
39
|
Her C, Yeh Y, Krishnan VV. The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy. Biomolecules 2019; 9:biom9060235. [PMID: 31213033 PMCID: PMC6628104 DOI: 10.3390/biom9060235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 12/13/2022] Open
Abstract
The primary sequence of antifreeze glycoproteins (AFGPs) is highly degenerate, consisting of multiple repeats of the same tripeptide, Ala–Ala–Thr*, in which Thr* is a glycosylated threonine with the disaccharide beta-d-galactosyl-(1,3)-alpha-N-acetyl-d-galactosamine. AFGPs seem to function as intrinsically disordered proteins, presenting challenges in determining their native structure. In this work, a different approach was used to elucidate the three-dimensional structure of AFGP8 from the Arctic cod Boreogadussaida and the Antarctic notothenioid Trematomusborchgrevinki. Dimethyl sulfoxide (DMSO), a non-native solvent, was used to make AFGP8 less dynamic in solution. Interestingly, DMSO induced a non-native structure, which could be determined via nuclear magnetic resonance (NMR) spectroscopy. The overall three-dimensional structures of the two AFGP8s from two different natural sources were different from a random coil ensemble, but their “compactness” was very similar, as deduced from NMR measurements. In addition to their similar compactness, the conserved motifs, Ala–Thr*–Pro–Ala and Ala–Thr*–Ala–Ala, present in both AFGP8s, seemed to have very similar three-dimensional structures, leading to a refined definition of local structural motifs. These local structural motifs allowed AFGPs to be considered functioning as effectors, making a transition from disordered to ordered upon binding to the ice surface. In addition, AFGPs could act as dynamic linkers, whereby a short segment folds into a structural motif, while the rest of the AFGPs could still be disordered, thus simultaneously interacting with bulk water molecules and the ice surface, preventing ice crystal growth.
Collapse
Affiliation(s)
- Cheenou Her
- Department of Chemistry, California State University, Fresno, CA 93740, USA.
| | - Yin Yeh
- Department of Applied Science, University of California, Davis, CA 95616, USA.
| | - Viswanathan V Krishnan
- Department of Chemistry, California State University, Fresno, CA 93740, USA.
- Department Medical Pathology and Laboratory Medicine, Davis School of Medicine, University of California, Davis, CA 95616, USA.
| |
Collapse
|
40
|
Qiu Y, Hudait A, Molinero V. How Size and Aggregation of Ice-Binding Proteins Control Their Ice Nucleation Efficiency. J Am Chem Soc 2019; 141:7439-7452. [DOI: 10.1021/jacs.9b01854] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yuqing Qiu
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0580, United States
| | - Arpa Hudait
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0580, United States
| | - Valeria Molinero
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0580, United States
| |
Collapse
|
41
|
Yamazaki A, Nishimiya Y, Tsuda S, Togashi K, Munehara H. Freeze Tolerance in Sculpins (Pisces; Cottoidea) Inhabiting North Pacific and Arctic Oceans: Antifreeze Activity and Gene Sequences of the Antifreeze Protein. Biomolecules 2019; 9:biom9040139. [PMID: 30959891 PMCID: PMC6523315 DOI: 10.3390/biom9040139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/28/2019] [Accepted: 04/03/2019] [Indexed: 11/16/2022] Open
Abstract
Many marine species inhabiting icy seawater produce antifreeze proteins (AFPs) to prevent their body fluids from freezing. The sculpin species of the superfamily Cottoidea are widely found from the Arctic to southern hemisphere, some of which are known to express AFP. Here we clarified DNA sequence encoding type I AFP for 3 species of 2 families (Cottidae and Agonidae) belonging to Cottoidea. We also examined antifreeze activity for 3 families and 32 species of Cottoidea (Cottidae, Agonidae, and Rhamphocottidae). These fishes were collected in 2013–2015 from the Arctic Ocean, Alaska, Japan. We could identify 8 distinct DNA sequences exhibiting a high similarity to those reported for Myoxocephalus species, suggesting that Cottidae and Agonidae share the same DNA sequence encoding type I AFP. Among the 3 families, Rhamphocottidae that experience a warm current did not show antifreeze activity. The species inhabiting the Arctic Ocean and Northern Japan that often covered with ice floe showed high activity, while those inhabiting Alaska, Southern Japan with a warm current showed low/no activity. These results suggest that Cottoidea acquires type I AFP gene before dividing into Cottidae and Agonidae, and have adapted to each location with optimal antifreeze activity level.
Collapse
Affiliation(s)
- Aya Yamazaki
- Nanae Fresh-Water Station, Field Science Center for Northern Biosphere, Hokkaido University, Nanae Town Kameda-gun 041-1105, Japan.
| | - Yoshiyuki Nishimiya
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo 062-8517, Japan.
| | - Sakae Tsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo 062-8517, Japan.
| | - Koji Togashi
- Graduate School of Environmental Sciences, Hokkaido University, Sapporo 060-0810, Japan.
| | - Hiroyuki Munehara
- Usujiri Fisheries Station, Field Science Center of Northern Biosphere, Hokkaido University, Hakodate 041-1613, Japan.
| |
Collapse
|
42
|
Akbar S, Hayat M, Kabir M, Iqbal M. iAFP-gap-SMOTE: An Efficient Feature Extraction Scheme Gapped Dipeptide Composition is Coupled with an Oversampling Technique for Identification of Antifreeze Proteins. LETT ORG CHEM 2019. [DOI: 10.2174/1570178615666180816101653] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Antifreeze proteins (AFPs) perform distinguishable roles in maintaining homeostatic conditions of living organisms and protect their cell and body from freezing in extremely cold conditions. Owing to high diversity in protein sequences and structures, the discrimination of AFPs from non- AFPs through experimental approaches is expensive and lengthy. It is, therefore, vastly desirable to propose a computational intelligent and high throughput model that truly reflects AFPs quickly and accurately. In a sequel, a new predictor called “iAFP-gap-SMOTE” is proposed for the identification of AFPs. Protein sequences are expressed by adopting three numerical feature extraction schemes namely; Split Amino Acid Composition, G-gap di-peptide Composition and Reduce Amino Acid alphabet composition. Usually, classification hypothesis biased towards majority class in case of the imbalanced dataset. Oversampling technique Synthetic Minority Over-sampling Technique is employed in order to increase the instances of the lower class and control the biasness. 10-fold cross-validation test is applied to appraise the success rates of “iAFP-gap-SMOTE” model. After the empirical investigation, “iAFP-gap-SMOTE” model obtained 95.02% accuracy. The comparison suggested that the accuracy of” iAFP-gap-SMOTE” model is higher than that of the present techniques in the literature so far. It is greatly recommended that our proposed model “iAFP-gap-SMOTE” might be helpful for the research community and academia.
Collapse
Affiliation(s)
- Shahid Akbar
- Department of Computer Science, Abdul Wali Khan University, Mardan, KP 23200, Pakistan
| | - Maqsood Hayat
- Department of Computer Science, Abdul Wali Khan University, Mardan, KP 23200, Pakistan
| | - Muhammad Kabir
- Department of Computer Science, Abdul Wali Khan University, Mardan, KP 23200, Pakistan
| | - Muhammad Iqbal
- Department of Computer Science, Abdul Wali Khan University, Mardan, KP 23200, Pakistan
| |
Collapse
|
43
|
Preparation, primary structure and antifreeze activity of antifreeze peptides from Scomberomorus niphonius skin. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2018.11.067] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
44
|
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.
Collapse
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
| |
Collapse
|
45
|
Zhao J, Johnson MA, Fisher R, Burke NAD, Stöver HDH. Synthetic Polyampholytes as Macromolecular Cryoprotective Agents. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:1807-1817. [PMID: 30134094 DOI: 10.1021/acs.langmuir.8b01602] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A series of polyampholytes based on different molar ratios on N, N-dimethylaminopropyl methacrylamide (DMAPMA), acrylic acid (AA), and optionally, N- tert-butylacrylamide ( t-BuAAm), were prepared by free radical copolymerization, and tested as DMSO-free cryoprotective agents for 3T3 fibroblast cells by using a standard freeze-rethaw protocol. Polybetaines prepared by reaction of DMAPMA homo and copolymers with 1,3-propane sultone were used as additional controls. Results showed strong effects of copolymer composition, molecular weight, polymer and NaCl concentrations, on post-thaw cell viability. Binary (DMAPMA/AA) copolymers showed best post-thaw cell viability of 70% at a 30/70 mol % ratio of DMAPMA/AA, which increased to 90% upon introduction of 9 mol % t-BuAAm while maintaining the 30/70 mol % cation/anion ratio. The use of acrylamide linkages in DMAPMA ensures absence of hydrolytic loss of cationic side chains. These polyampholytes were found to decrease ice crystal size and to form a polymer-rich, ice-free layer around cells, reducing damage from intercellular ice crystals during both freezing and thawing steps. These polyampholytes also dehydrate cells during freezing, which helps protect cells from intracellular ice damage. While cell viability immediately after thawing was high, subsequent culturing revealed poor attachment and long-term viability, which is attributed to residual cell damage from intracellular ice formation. Addition of 2 wt % DMSO or 1% BSA to the polymer-based freeze medium was found to mitigate this damage and result in post-thaw viabilities matching those achieved with 10 wt % DMSO.
Collapse
Affiliation(s)
- J Zhao
- Department of Chemistry and Chemical Biology , McMaster University , Hamilton , Ontario L8S 4M1 , Canada
| | - M A Johnson
- Department of Chemistry and Chemical Biology , McMaster University , Hamilton , Ontario L8S 4M1 , Canada
| | - R Fisher
- Department of Chemistry and Chemical Biology , McMaster University , Hamilton , Ontario L8S 4M1 , Canada
| | - N A D Burke
- Department of Chemistry and Chemical Biology , McMaster University , Hamilton , Ontario L8S 4M1 , Canada
| | - H D H Stöver
- Department of Chemistry and Chemical Biology , McMaster University , Hamilton , Ontario L8S 4M1 , Canada
| |
Collapse
|
46
|
Weng L, Stott SL, Toner M. Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation. Annu Rev Biomed Eng 2018; 21:1-31. [PMID: 30525930 DOI: 10.1146/annurev-bioeng-060418-052130] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Successful stabilization and preservation of biological materials often utilize low temperatures and dehydration to arrest molecular motion. Cryoprotectants are routinely employed to help the biological entities survive the physicochemical and mechanical stresses induced by cold or dryness. Molecular interactions between biomolecules, cryoprotectants, and water fundamentally determine the outcomes of preservation. The optimization of assays using the empirical approach is often limited in structural and temporal resolution, whereas classical molecular dynamics simulations can provide a cost-effective glimpse into the atomic-level structure and interaction of individual molecules that dictate macroscopic behavior. Computational research on biomolecules, cryoprotectants, and water has provided invaluable insights into the development of new cryoprotectants and the optimization of preservation methods. We describe the rapidly evolving state of the art of molecular simulations of these complex systems, summarize the molecular-scale protective and stabilizing mechanisms, and discuss the challenges that motivate continued innovation in this field.
Collapse
Affiliation(s)
- Lindong Weng
- Center for Engineering in Medicine and BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA; , , .,Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Shannon L Stott
- Center for Engineering in Medicine and BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA; , , .,Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Mehmet Toner
- Center for Engineering in Medicine and BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA; , , .,Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Shriners Hospital for Children, Boston, Massachusetts 02114, USA
| |
Collapse
|
47
|
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.
Collapse
|
48
|
Mao MG, Chen Y, Liu RT, Lü HQ, Gu J, Jiang ZQ, Jiang JL. Transcriptome from Pacific cod liver reveals types of apolipoproteins and expression analysis of AFP-IV, structural analogue with mammalian ApoA-I. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 28:204-212. [PMID: 30366214 DOI: 10.1016/j.cbd.2018.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/04/2018] [Indexed: 12/15/2022]
Abstract
Apolipoproteins (Apos), transporting the lipids through the lymphatic and circulatory systems, are associated with kinds of diseases. Additionally, type IV antifreeze protein (AFP-IV) was related evolutionarily with apolipoproteins. However, the information of Apos in fish was limited. In this study, ApoA-I, ApoA-I-2, ApoA-IV, Apo E, ApoB-100-like and AFP-IV were sequenced from Pacific cod (Gadus macrocephalus) liver transcriptome using Illumina HiSeq 2000, and their 3-D models were constructed based on the most confidence templates ever reported in mammals. Interestingly, the model of G. macrocephalus AFP-IV, named GmAFPIV, is quite similar to the structure of ApoA-I. GmAFPIV includes 689 bases with a complete open reading frame encoding 125 amino acids. Sequence alignment of GmAFPIV showed 30% to 50% similarity with that of other species except Gadus sp. Expression levels of GmAFPIV were found in a decreasing manner in liver, intestine, gill, brain and gonad. Heterologously expression of the GmAFPIV protein was expressed in Escherichia coli and purified to immunize New Zealand rabbits. The survivors of E. coli in 60 μg/mL of GmAFPIV are more than that in the 30 μg/mL group after stored in -20 °C and -80 °C, indicating high concentration of GmAFPIV could protect E. coli avoiding the damage from ice crystal. The subcellular localization of GmAFPIV showed that the green fluorescence was mainly observed in the cytoplasm, indicating GmAFPIV play roles in the cytoplasm. It was concluded that GmAFPIV may function not only as an antifreeze protein but also as an apolipoprotein transporting lipids in fish.
Collapse
Affiliation(s)
- Ming-Guang Mao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Applied Biology and Aquaculture in North China, Liaoning Province, College of Fisheries and Life Sciences, Dalian Ocean University, Dalian 116023, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yu Chen
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Applied Biology and Aquaculture in North China, Liaoning Province, College of Fisheries and Life Sciences, Dalian Ocean University, Dalian 116023, China
| | - Rui-Ting Liu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Applied Biology and Aquaculture in North China, Liaoning Province, College of Fisheries and Life Sciences, Dalian Ocean University, Dalian 116023, China
| | - Hui-Qian Lü
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Applied Biology and Aquaculture in North China, Liaoning Province, College of Fisheries and Life Sciences, Dalian Ocean University, Dalian 116023, China
| | - Jie Gu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Applied Biology and Aquaculture in North China, Liaoning Province, College of Fisheries and Life Sciences, Dalian Ocean University, Dalian 116023, China
| | - Zhi-Qiang Jiang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Applied Biology and Aquaculture in North China, Liaoning Province, College of Fisheries and Life Sciences, Dalian Ocean University, Dalian 116023, China
| | - Jie-Lan Jiang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Applied Biology and Aquaculture in North China, Liaoning Province, College of Fisheries and Life Sciences, Dalian Ocean University, Dalian 116023, China.
| |
Collapse
|
49
|
Properties of phase transition of ice binding protein from Arctic yeast (LeIBP) utilizing differential scanning calorimetry (DSC) and Raman spectroscopy. Cryobiology 2018; 85:33-38. [PMID: 30296411 DOI: 10.1016/j.cryobiol.2018.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/26/2018] [Accepted: 10/03/2018] [Indexed: 11/22/2022]
Abstract
Ice binding proteins (IBPs) have been attracting significant interest on account of their characteristic of inhibiting ice growth and recrystallization. Owing to their unique characteristics, IBPs have been studied for applications in food, pharmaceuticals, and medicine, as well as from a general scientific point of view. In this study, we have used differential scanning calorimetry (DSC) and Raman spectroscopy as tools to understand the ice binding activity of the Arctic-yeast-originating extracellular ice binding glycoprotein (LeIBP) isolated from Leucosporidium sp. AY30. From the DSC results, an increase in the specific heat capacity was confirmed for 1 mg/mL LeIBP, which suggested that additional heat flow was required for the change in temperature. In addition, the temperature corresponding to the phase change of the solution was measured, and Raman spectroscopy was carried out on the frozen and molten phases, respectively. From the results of Raman analysis, we confirmed that the helical vibrations related to the ice binding sites on LeIBP were dramatically suppressed when the LeIBP solution was frozen. Furthermore, principal component analysis (PCA) of the Raman spectra yielded the contrast factor between the freezing and melting states. Both DSC and Raman spectroscopy are widely used to study the ice binding activity and the structural changes associated with molecular vibrations in cryobiology.
Collapse
|
50
|
Weng L, Swei A, Toner M. Role of synthetic antifreeze agents in catalyzing ice nucleation. Cryobiology 2018; 84:91-94. [DOI: 10.1016/j.cryobiol.2018.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 01/17/2023]
|