1
|
Graham LA, Davies PL. Fish antifreeze protein origin in sculpins by frameshifting within a duplicated housekeeping gene. FEBS J 2024. [PMID: 38923815 DOI: 10.1111/febs.17205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/25/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Antifreeze proteins (AFPs) are found in a variety of marine cold-water fishes where they prevent freezing by binding to nascent ice crystals. Their diversity (types I, II, III and antifreeze glycoproteins), as well as their scattered taxonomic distribution hint at their complex evolutionary history. In particular, type I AFPs appear to have arisen in response to the Late Cenozoic Ice Age that began ~ 34 million years ago via convergence in four different groups of fish that diverged from lineages lacking this AFP. The progenitor of the alanine-rich α-helical type I AFPs of sculpins has now been identified as lunapark, an integral membrane protein of the endoplasmic reticulum. Following gene duplication and loss of all but three of the 15 exons, the final exon, which encoded a glutamate- and glutamine-rich segment, was converted to an alanine-rich sequence by a combination of frameshifting and mutation. Subsequent gene duplications produced numerous isoforms falling into four distinct groups. The origin of the flounder type I AFP is quite different. Here, a small segment from the original antiviral protein gene was amplified and the rest of the coding sequence was lost, while the gene structure was largely retained. The independent origins of type I AFPs with up to 83% sequence identity in flounder and sculpin demonstrate strong convergent selection at the level of protein sequence for alanine-rich single alpha helices that bind to ice. Recent acquisition of these AFPs has allowed sculpins to occupy icy seawater niches with reduced competition and predation from other teleost species.
Collapse
Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| |
Collapse
|
2
|
Sirotinskaya V, Bar Dolev M, Yashunsky V, Bahari L, Braslavsky I. Extended Temperature Range of the Ice-Binding Protein Activity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7395-7404. [PMID: 38527127 PMCID: PMC11008235 DOI: 10.1021/acs.langmuir.3c03710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024]
Abstract
Ice-binding proteins (IBPs) are expressed in various organisms for several functions, such as protecting them from freezing and freeze injuries. Via adsorption on ice surfaces, IBPs depress ice growth and recrystallization and affect nucleation and ice shaping. IBPs have shown promise in mitigating ice growth under moderate supercooling conditions, but their functionality under cryogenic conditions has been less explored. In this study, we investigate the impact of two types of antifreeze proteins (AFPs): type III AFP from fish and a hyperactive AFP from an insect, the Tenebrio molitor AFP, in vitrified dimethylsulfoxide (DMSO) solutions. We report that these AFPs depress devitrification at -80 °C. Furthermore, in cases where devitrification does occur, AFPs depress ice recrystallization during the warming stage. The data directly demonstrate that AFPs are active at temperatures below the regime of homogeneous nucleation. This research paves the way for exploring AFPs as potential enhancers of cryopreservation techniques, minimizing ice-growth-related damage, and promoting advancements in this vital field.
Collapse
Affiliation(s)
- Vera Sirotinskaya
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Maya Bar Dolev
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
- Faculty
of Biotechnology and Food Engineering, Technion, Haifa 3200003, Israel
| | - Victor Yashunsky
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
- The
Swiss Institute for Dryland Environmental and Energy Research, Ben Gurion University, Beer-Sheva 84105, Israel
| | - Liat Bahari
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Ido Braslavsky
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
| |
Collapse
|
3
|
Grabowska J, Kuffel A, Zielkiewicz J. Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice. J Chem Phys 2024; 160:095101. [PMID: 38445741 DOI: 10.1063/5.0187663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
Using molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water, which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation and distance relative to the surface of ice, which enables the effective binding (via hydrogen bonds) of the molecule with the nascent ice surface. Our results show that the final adsorption of the AFP III molecule on the surface of ice is not achieved by chaotic diffusion movements, but it is preceded by a remote, water-mediated interaction between the IBS and the surface of ice. The key factor that determines the existence of this interaction is the ability of water molecules to spontaneously form large, high-volume aggregates that can be anchored to both the IBS of the AFP molecule and the surface of ice. The results presented in this work for AFP III are in full agreement with the ones obtained by us previously for hyperactive CfAFP, which indicates that the mechanism of the remote interaction of these molecules with ice remains unchanged despite significant differences in the molecular structure of their ice binding sites. For that reason, we can expect that also other types of AFPs interact with the ice surface according to an analogous mechanism.
Collapse
Affiliation(s)
- Joanna Grabowska
- Faculty of Chemistry, Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Anna Kuffel
- Faculty of Chemistry, Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Jan Zielkiewicz
- Faculty of Chemistry, Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| |
Collapse
|
4
|
Nam Y, Nguyen DL, Hoang T, Kim B, Lee JH, Do H. Engineered ice-binding protein (FfIBP) shows increased stability and resistance to thermal and chemical denaturation compared to the wildtype. Sci Rep 2024; 14:3234. [PMID: 38331970 PMCID: PMC10853241 DOI: 10.1038/s41598-024-53864-w] [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: 11/13/2023] [Accepted: 02/06/2024] [Indexed: 02/10/2024] Open
Abstract
Many polar organisms produce antifreeze proteins (AFPs) and ice-binding proteins (IBPs) to protect themselves from ice formation. As IBPs protect cells and organisms, the potential of IBPs as natural or biological cryoprotective agents (CPAs) for the cryopreservation of animal cells, such as oocytes and sperm, has been explored to increase the recovery rate after freezing-thawing. However, only a few IBPs have shown success in cryopreservation, possibly because of the presence of protein denaturants, such as dimethyl sulfoxide, alcohols, or ethylene glycol, in freezing buffer conditions, rendering the IBPs inactive. Therefore, we investigated the thermal and chemical stability of FfIBP isolated from Antarctic bacteria to assess its suitability as a protein-based impermeable cryoprotectant. A molecular dynamics (MD) simulation identified and generated stability-enhanced mutants (FfIBP_CC1). The results indicated that FfIBP_CC1 displayed enhanced resistance to denaturation at elevated temperatures and chemical concentrations, compared to wildtype FfIBP, and was functional in known CPAs while retaining ice-binding properties. Given that FfIBP shares an overall structure similar to DUF3494 IBPs, which are recognized as the most widespread IBP family, these findings provide important structural information on thermal and chemical stability, which could potentially be applied to other DUF3494 IBPs for future protein engineering.
Collapse
Affiliation(s)
- Yewon Nam
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Dieu Linh Nguyen
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Trang Hoang
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Bogeun Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea.
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea.
| |
Collapse
|
5
|
Yang Y, Yamauchi A, Tsuda S, Kuramochi M, Mio K, Sasaki YC, Arai T. The ice-binding site of antifreeze protein irreversibly binds to cell surface for its hypothermic protective function. Biochem Biophys Res Commun 2023; 682:343-348. [PMID: 37837755 DOI: 10.1016/j.bbrc.2023.10.015] [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: 09/20/2023] [Accepted: 10/03/2023] [Indexed: 10/16/2023]
Abstract
Antifreeze proteins (AFPs) are multifunctional polypeptides that adsorb onto ice crystals to inhibit their growth and onto cells to protect them from nonfreezing hypothermic damage. However, the mechanism by which AFP exerts its hypothermic cell protective (HCP) function remains uncertain. Here, we assessed the HCP function of three types of fish-derived AFPs (type I, II, and III AFPs) against human T-lymphoblastic lymphoma by measuring the survival rate (%) of the cells after preservation at 4 °C for 24 h. All AFPs improved the survival rate in a concentration-dependent manner, although the HCP efficiency was inferior for type III AFP compared to other AFPs. In addition, after point mutations were introduced into the ice-binding site (IBS) of a type III AFP, HCP activity was dramatically increased, suggesting that the IBS of AFP is involved in cell adsorption. Significantly, high HCP activity was observed for a mutant that exhibited poorer antifreeze activity, indicating that AFP exerts HCP- and ice-binding functions through a different mechanism. We next incubated the cells in an AFP-containing solution, replaced it with pure EC solution, and then preserved the cells, showing that no significant reduction in the cell survival rate occurred for type I and II AFPs even after replacement. Thus, these AFPs irreversibly bind to the cells at 4 °C, and only tightly adsorbed AFP molecules contribute towards the cell-protection function.
Collapse
Affiliation(s)
- Yue Yang
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Akari Yamauchi
- Hibernation Metabolism, Physiology and Development Group, Institute of Low Temperature Science, Hokkaido University, Sapporo, 060-0819, Japan
| | - Sakae Tsuda
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan; AIST-UTokyo Advanced Operando Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, 277-0882, Japan
| | - Masahiro Kuramochi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, 316-8511, Japan
| | - Kazuhiro Mio
- AIST-UTokyo Advanced Operando Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, 277-0882, Japan
| | - Yuji C Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan; AIST-UTokyo Advanced Operando Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, 277-0882, Japan
| | - Tatsuya Arai
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan; AIST-UTokyo Advanced Operando Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, 277-0882, Japan.
| |
Collapse
|
6
|
Scholl CL, Holmstrup M, Graham LA, Davies PL. Polyproline type II helical antifreeze proteins are widespread in Collembola and likely originated over 400 million years ago in the Ordovician Period. Sci Rep 2023; 13:8880. [PMID: 37264058 DOI: 10.1038/s41598-023-35983-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023] Open
Abstract
Antifreeze proteins (AFPs) bind to ice crystals to prevent organisms from freezing. A diversity of AFP folds has been found in fish and insects, including alpha helices, globular proteins, and several different beta solenoids. But the variety of AFPs in flightless arthropods, like Collembola, has not yet been adequately assessed. Here, antifreeze activity was shown to be present in 18 of the 22 species of Collembola from cold or temperate zones. Several methods were used to characterize these AFPs, including isolation by ice affinity purification, MALDI mass spectrometry, amino acid composition analysis, tandem mass spectrometry sequencing, transcriptome sequencing, and bioinformatic investigations of sequence databases. All of these AFPs had a high glycine content and were predicted to have the same polyproline type II helical bundle fold, a fold unique to Collembola. These Hexapods arose in the Ordovician Period with the two orders known to produce AFPs diverging around 400 million years ago during the Andean-Saharan Ice Age. Therefore, it is likely that the AFP arose then and persisted in many lineages through the following two ice ages and intervening warm periods, unlike the AFPs of fish which arose independently during the Cenozoic Ice Age beginning ~ 30 million years ago.
Collapse
Affiliation(s)
- Connor L Scholl
- Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, ON, K7L3N6, Canada
| | - Martin Holmstrup
- Section of Terrestrial Ecology, Department of Ecoscience, Aarhus University, C.F. Møllers Allé 4, 8000, Aarhus C, Denmark
- Arctic Research Center, Aarhus University, Ny Munkegade 114, 8000, Aarhus C, Denmark
| | - Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, ON, K7L3N6, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, ON, K7L3N6, Canada.
| |
Collapse
|
7
|
Hotaling S, Desvignes T, Sproul JS, Lins LSF, Kelley JL. Pathways to polar adaptation in fishes revealed by long-read sequencing. Mol Ecol 2023; 32:1381-1397. [PMID: 35561000 DOI: 10.1111/mec.16501] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/31/2022] [Accepted: 05/05/2022] [Indexed: 11/28/2022]
Abstract
Long-read sequencing is driving a new reality for genome science in which highly contiguous assemblies can be produced efficiently with modest resources. Genome assemblies from long-read sequences are particularly exciting for understanding the evolution of complex genomic regions that are often difficult to assemble. In this study, we utilized long-read sequencing data to generate a high-quality genome assembly for an Antarctic eelpout, Ophthalmolycus amberensis, the first for the globally distributed family Zoarcidae. We used this assembly to understand how O. amberensis has adapted to the harsh Southern Ocean and compared it to another group of Antarctic fishes: the notothenioids. We showed that selection has largely acted on different targets in eelpouts relative to notothenioids. However, we did find some overlap; in both groups, genes involved in membrane structure, thermal tolerance and vision have evidence of positive selection. We found evidence for historical shifts of transposable element activity in O. amberensis and other polar fishes, perhaps reflecting a response to environmental change. We were specifically interested in the evolution of two complex genomic loci known to underlie key adaptations to polar seas: haemoglobin and antifreeze proteins (AFPs). We observed unique evolution of the haemoglobin MN cluster in eelpouts and related fishes in the suborder Zoarcoidei relative to other Perciformes. For AFPs, we identified the first species in the suborder with no evidence of afpIII sequences (Cebidichthys violaceus) in the genomic region where they are found in all other Zoarcoidei, potentially reflecting a lineage-specific loss of this cluster. Beyond polar fishes, our results highlight the power of long-read sequencing to understand genome evolution.
Collapse
Affiliation(s)
- Scott Hotaling
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - John S Sproul
- Department of Biology, University of Nebraska Omaha, Omaha, Nebraska, USA
| | - Luana S F Lins
- Australian National Insect Collection, CSIRO, Canberra, Australia
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| |
Collapse
|
8
|
Ghalamara S, Coscueta ER, Silva S, Brazinha C, Pereira CD, Pintado ME. Integrated ultrafiltration, nanofiltration, and reverse osmosis pilot process to produce bioactive protein/peptide fractions from sardine cooking effluent. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 317:115344. [PMID: 35642813 DOI: 10.1016/j.jenvman.2022.115344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/06/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Sardine cooking effluents contain a high level of organic matter, such as proteins and lipids, which allows them to be forward into a chain exploiting high added-value compounds attained from these effluents, increasing their economic value while reducing their environmental effect. Thus, the purpose of this work was to develop an innovative pilot-scale integrated membrane process, with or without enzymatic hydrolysis, to obtain fractions with high protein/peptide and low NaCl contents, as well as optimized bioactive properties. The research strategy followed involved the use of ultrafiltration (UF) and nanofiltration (NF) technologies of the pretreated sardine cooking effluent followed by reverse osmosis (RO) at a pilot scale levels. Moreover, it allowed for the attainment of fractions rich in protein/peptides that might be used in the food, pharmaceutical, or cosmetic industries, particularly after RO, as they present a lower NaCl content. The RO retentate (hydrolyzed sample) coupled with UF and NF resulted in the fractions with the best bioactive properties (higher antioxidant capacity and antimicrobial activity) of all the analyzed samples. Overall, the current work demonstrated the feasibility of exploiting liquid by-products as a source of functional components as well as reinforcing this strategy's potential relevance in future effective management strategies for this type of effluents.
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
| | - Ezequiel R Coscueta
- 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, Department of Chemistry, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Carlos D Pereira
- Instituto Politécnico de Coimbra - Escola Superior Agraria (IPC/ESAC), Bencanta, 3045-601, Coimbra, Portugal
| | - Manuela E 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
|
9
|
Graham LA, Gauthier SY, Davies PL. Origin of an antifreeze protein gene in response to Cenozoic climate change. Sci Rep 2022; 12:8536. [PMID: 35595816 PMCID: PMC9122973 DOI: 10.1038/s41598-022-12446-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Antifreeze proteins (AFPs) inhibit ice growth within fish and protect them from freezing in icy seawater. Alanine-rich, alpha-helical AFPs (type I) have independently (convergently) evolved in four branches of fishes, one of which is a subsection of the righteye flounders. The origin of this gene family has been elucidated by sequencing two loci from a starry flounder, Platichthys stellatus, collected off Vancouver Island, British Columbia. The first locus had two alleles that demonstrated the plasticity of the AFP gene family, one encoding 33 AFPs and the other allele only four. In the closely related Pacific halibut, this locus encodes multiple Gig2 (antiviral) proteins, but in the starry flounder, the Gig2 genes were found at a second locus due to a lineage-specific duplication event. An ancestral Gig2 gave rise to a 3-kDa "skin" AFP isoform, encoding three Ala-rich 11-a.a. repeats, that is expressed in skin and other peripheral tissues. Subsequent gene duplications, followed by internal duplications of the 11 a.a. repeat and the gain of a signal sequence, gave rise to circulating AFP isoforms. One of these, the "hyperactive" 32-kDa Maxi likely underwent a contraction to a shorter 3.3-kDa "liver" isoform. Present day starry flounders found in Pacific Rim coastal waters from California to Alaska show a positive correlation between latitude and AFP gene dosage, with the shorter allele being more prevalent at lower latitudes. This study conclusively demonstrates that the flounder AFP arose from the Gig2 gene, so it is evolutionarily unrelated to the three other classes of type I AFPs from non-flounders. Additionally, this gene arose and underwent amplification coincident with the onset of ocean cooling during the Cenozoic ice ages.
Collapse
Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Sherry Y Gauthier
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada.
| |
Collapse
|
10
|
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
|
11
|
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
|
12
|
Baskaran A, Kaari M, Venugopal G, Manikkam R, Joseph J, Bhaskar PV. Anti freeze proteins (Afp): Properties, sources and applications - A review. Int J Biol Macromol 2021; 189:292-305. [PMID: 34419548 DOI: 10.1016/j.ijbiomac.2021.08.105] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022]
Abstract
Extreme cold marine and freshwater temperatures (below 4 °C) induce massive deterioration to the cell membranes of organisms resulting in the formation of ice crystals, consequently causing organelle damage or cell death. One of the adaptive mechanisms organisms have evolved to thrive in cold environments is the production of antifreeze proteins with the functional capabilities to withstand frigid temperatures. Antifreeze proteins are extensively identified in different cold-tolerant species and they facilitate the persistence of cold-adapted organisms by decreasing the freezing point of their body fluids. Various structurally diverse types of antifreeze proteins detected possess the ability to modify ice crystal growth by thermal hysteresis and ice recrystallization inhibition. The unique properties of antifreeze proteins have made them a promising resource in industry, biomedicine, food storage and cryobiology. This review collates the findings of the various studies carried out in the past and the recent developments observed in the properties, functional mechanisms, classification, distinct sources and the ever-increasing applications of antifreeze proteins. This review also summarizes the possibilities of the way forward to identify new avenues of research on anti-freeze proteins.
Collapse
Affiliation(s)
- Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Gopikrishnan Venugopal
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India.
| | - Jerrine Joseph
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Parli V Bhaskar
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama 403804, Goa, India
| |
Collapse
|
13
|
Prediction and analysis of antifreeze proteins. Heliyon 2021; 7:e07953. [PMID: 34604556 PMCID: PMC8473546 DOI: 10.1016/j.heliyon.2021.e07953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/28/2021] [Accepted: 09/03/2021] [Indexed: 11/20/2022] Open
Abstract
Antifreeze proteins (AFPs) are proteins that protect cellular fluids and body fluids from freezing by inhibiting the nucleation and growth of ice crystals and preventing ice recrystallization, thereby contributing to the maintenance of life in living organisms. They exist in fish, insects, microorganisms, and fungi. However, the number of known AFPs is currently limited, and it is essential to construct a reliable dataset of AFPs and develop a bioinformatics tool to predict AFPs. In this work, we first collected AFPs sequences from UniProtKB considering the reliability of annotations and, based on these datasets, developed a prediction system using random forest. We achieved accuracies of 0.961 and 0.947 for non-redundant sequences with less than 90% and 30% identities and achieved the accuracy of 0.953 for representative sequences for each species. Using the ability of random forest, we identified the sequence features that contributed to the prediction. Some sequence features were common to AFPs from different species. These features include the Cys content, Ala-Ala content, Trp-Gly content, and the amino acids' distribution related to the disorder propensity. The computer program and the dataset developed in this work are available from the GitHub site: https://github.com/ryomiya/Prediction-and-analysis-of-antifreeze-proteins.
Collapse
|
14
|
Graham LA, Davies PL. Horizontal Gene Transfer in Vertebrates: A Fishy Tale. Trends Genet 2021; 37:501-503. [PMID: 33714557 DOI: 10.1016/j.tig.2021.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 11/25/2022]
Abstract
The recent assembly of the herring genome suggests this fish acquired its antifreeze protein gene by horizontal transfer and then passed a copy on to the smelt. The direction of gene transfer is confirmed by some accompanying transposable elements and by the breakage of gene synteny.
Collapse
Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada.
| |
Collapse
|
15
|
Gruneberg AK, Graham LA, Eves R, Agrawal P, Oleschuk RD, Davies PL. Ice recrystallization inhibition activity varies with ice-binding protein type and does not correlate with thermal hysteresis. Cryobiology 2021; 99:28-39. [PMID: 33529683 DOI: 10.1016/j.cryobiol.2021.01.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/07/2021] [Accepted: 01/23/2021] [Indexed: 01/06/2023]
Abstract
Ice-binding proteins (IBPs) inhibit the growth of ice through surface adsorption. In some freeze-resistant fishes and insects, circulating IBPs serve as antifreeze proteins to stop ice growth by lowering the freezing point. Plants are less able to avoid freezing and some use IBPs to minimize the damage caused in the frozen state by ice recrystallization, which is the growth of large ice grains at the expense of small ones. Here we have accurately and reproducibly measured the ice recrystallization inhibition (IRI) activity of over a dozen naturally occurring IBPs from fishes, insects, plants, and microorganisms using a modified 'splat' method on serial dilutions of IBPs whose concentrations were determined by amino acid analysis. The endpoint of IRI, which was scored as the lowest protein concentration at which no recrystallization was observed, varied for the different IBPs over two orders of magnitude from 1000 nM to 5 nM. Moreover, there was no apparent correlation between their IRI levels and reported antifreeze activities. IBPs from insects and fishes had similar IRI activity, even though the insect IBPs are typically 10x more active in freezing point depression. Plant IBPs had weak antifreeze activity but were more effective at IRI. Bacterial IBPs involved in ice adhesion showed both strong freezing point depression and IRI. Two trends did emerge, including that basal plane binding IBPs correlated with stronger IRI activity and larger IBPs had higher IRI activity.
Collapse
Affiliation(s)
- Audrey K Gruneberg
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada
| | - Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada
| | - Robert Eves
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada
| | - Prashant Agrawal
- Department of Chemistry, Queen's University. 90 Bader Lane, Kingston, Ontario, K7L2S8, Canada
| | - Richard D Oleschuk
- Department of Chemistry, Queen's University. 90 Bader Lane, Kingston, Ontario, K7L2S8, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada.
| |
Collapse
|
16
|
Scholl CL, Tsuda S, Graham LA, Davies PL. Crystal waters on the nine polyproline type II helical bundle springtail antifreeze protein from Granisotoma rainieri match the ice lattice. FEBS J 2021; 288:4332-4347. [PMID: 33460499 DOI: 10.1111/febs.15717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/18/2020] [Accepted: 01/11/2021] [Indexed: 01/03/2023]
Abstract
A springtail (Collembola) identified as Granisotoma rainieri was collected from snow in Hokkaido, Japan, in late winter when nighttime temperatures were below zero. Extracts of these arthropods showed antifreeze activity by shaping ice crystals and stopping their growth. The glycine-rich proteins responsible for this freezing point depression were isolated by ice-affinity purification and had principal masses of ~ 6.9 and 9.6 kDa. We identified a transcript for a 9.6-kDa component and produced it as a His-tagged recombinant protein for structural analysis. Its crystal structure was solved to a resolution of 1.21 Å and revealed a polyproline type II helical bundle, similar to the six-helix Hypogastrura harveyi AFP, but with nine helices organized into two layers held together by an extensive network of hydrogen bonds. One of the layers is flat, regular, and hydrophobic and likely serves as the ice-binding side. Although this surface makes close protein-protein contacts with its symmetry mate in the crystal, it has bound chains of waters present that resemble those on the basal and primary prism planes of ice. Molecular dynamic simulations indicate most of these crystal waters would preferentially occupy these sites if exposed to bulk solvent in the absence of the symmetry mate. These prepositioned waters lend further support to the ice-binding mechanism in which AFPs organize ice-like waters on one surface to adsorb to ice. DATABASES: Structural data are available in the Protein Data Bank under the accession number 7JJV. Transcript data are available in GenBank under accession numbers MT780727, MT780728, MT780729, MT780730, MT780731 and MT985982.
Collapse
Affiliation(s)
- Connor L Scholl
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Sakae Tsuda
- Bioproduction Research Institute, National Institute of Advanced Science and Technology (AIST), Sapporo, Japan
| | - Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| |
Collapse
|
17
|
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
|
18
|
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
|
19
|
Dorant Y, Cayuela H, Wellband K, Laporte M, Rougemont Q, Mérot C, Normandeau E, Rochette R, Bernatchez L. Copy number variants outperform SNPs to reveal genotype–temperature association in a marine species. Mol Ecol 2020; 29:4765-4782. [DOI: 10.1111/mec.15565] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Yann Dorant
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Hugo Cayuela
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Kyle Wellband
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Claire Mérot
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Rémy Rochette
- Department of Biology University of New Brunswick Saint John NB Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| |
Collapse
|
20
|
Graham LA, Boddington ME, Holmstrup M, Davies PL. Antifreeze protein complements cryoprotective dehydration in the freeze-avoiding springtail Megaphorura arctica. Sci Rep 2020; 10:3047. [PMID: 32080305 PMCID: PMC7033094 DOI: 10.1038/s41598-020-60060-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 01/31/2020] [Indexed: 12/03/2022] Open
Abstract
The springtail, Megaphorura arctica, is freeze-avoiding and survives sub-zero temperatures by cryoprotective dehydration. At the onset of dehydration there is some supercooling of body fluids, and the danger of inoculative freezing, which would be lethal. To see if the springtails are protected by antifreeze proteins in this pre-equilibrium phase, we examined extracts from cold-acclimated M. arctica and recorded over 3 °C of freezing point depression. Proteins responsible for this antifreeze activity were isolated by ice affinity. They comprise isoforms ranging from 6.5 to 16.9 kDa, with an amino acid composition dominated by glycine (>35 mol%). Tryptic peptide sequences were used to identify the mRNA sequence coding for the smallest isoform. This antifreeze protein sequence has high similarity to one characterized in Hypogastrura harveyi, from a different springtail order. If these two antifreeze proteins are true homologs, we suggest their origin dates back to the Permian glaciations some 300 million years ago.
Collapse
Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Marie E Boddington
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Martin Holmstrup
- Section of Terrestrial Ecology, Department of Bioscience, Aarhus University, Vejlsøvej 25, 8600, Silkeborg, Denmark
- Arctic Research Center, Aarhus University, Ny Munkegade 114, 8000, Aarhus C, Denmark
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.
| |
Collapse
|
21
|
Ice Binding Proteins: Diverse Biological Roles and Applications in Different Types of Industry. Biomolecules 2020; 10:biom10020274. [PMID: 32053888 PMCID: PMC7072191 DOI: 10.3390/biom10020274] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/02/2020] [Accepted: 02/07/2020] [Indexed: 02/06/2023] Open
Abstract
More than 80% of Earth’s surface is exposed periodically or continuously to temperatures below 5 °C. Organisms that can live in these areas are called psychrophilic or psychrotolerant. They have evolved many adaptations that allow them to survive low temperatures. One of the most interesting modifications is production of specific substances that prevent living organisms from freezing. Psychrophiles can synthesize special peptides and proteins that modulate the growth of ice crystals and are generally called ice binding proteins (IBPs). Among them, antifreeze proteins (AFPs) inhibit the formation of large ice grains inside the cells that may damage cellular organelles or cause cell death. AFPs, with their unique properties of thermal hysteresis (TH) and ice recrystallization inhibition (IRI), have become one of the promising tools in industrial applications like cryobiology, food storage, and others. Attention of the industry was also caught by another group of IBPs exhibiting a different activity—ice-nucleating proteins (INPs). This review summarizes the current state of art and possible utilizations of the large group of IBPs.
Collapse
|
22
|
Berger T, Meister K, DeVries AL, Eves R, Davies PL, Drori R. Synergy between Antifreeze Proteins Is Driven by Complementary Ice-Binding. J Am Chem Soc 2019; 141:19144-19150. [DOI: 10.1021/jacs.9b10905] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Tehilla Berger
- Department of Chemistry and Biochemistry, Yeshiva University, New York, New York 10016, United States
| | - Konrad Meister
- Max-Planck Institute for Polymer Research, Mainz D-55128, Germany
| | - Arthur L. DeVries
- Department of Animal Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Robert Eves
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Peter L. Davies
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Ran Drori
- Department of Chemistry and Biochemistry, Yeshiva University, New York, New York 10016, United States
| |
Collapse
|
23
|
Abstract
Antifreeze proteins (AFPs) protect marine fishes from freezing in icy seawater. They evolved relatively recently, most likely in response to the formation of sea ice and Cenozoic glaciations that occurred less than 50 million years ago, following a greenhouse Earth event. Based on their diversity, AFPs have independently evolved on many occasions to serve the same function, with some remarkable examples of convergent evolution at the structural level, and even instances of lateral gene transfer. For some AFPs, the progenitor gene is recognizable. The intense selection pressure exerted by icy seawater, which can rapidly kill unprotected fish, has led to massive AFP gene amplification, as well as some partial gene duplications that have increased the size and activity of the antifreeze. The many protein evolutionary processes described in Gordon H. Dixon's Essays in Biochemistry article will be illustrated here by examples from studies on AFPs. Abbreviations: AFGP: antifreeze glycoproteins; AFP: antifreeze proteins; GHD: Gordon H. Dixon; SAS: sialic acid synthase; TH: thermal hysteresis.
Collapse
Affiliation(s)
- Peter L Davies
- a Department of Biomedical and Molecular Sciences , Queen's University , Kingston , Canada
| | - Laurie A Graham
- a Department of Biomedical and Molecular Sciences , Queen's University , Kingston , Canada
| |
Collapse
|
24
|
Ice cream structure modification by ice-binding proteins. Food Chem 2018; 246:164-171. [DOI: 10.1016/j.foodchem.2017.10.152] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 10/26/2017] [Accepted: 10/31/2017] [Indexed: 11/22/2022]
|
25
|
Ammar AY, El Nahas AF, Mahmoud S, Barakat ME, Hassan AM. Characterization of type IV antifreeze gene in Nile tilapia (Oreochromis niloticus) and influence of cold and hot weather on its expression and some immune-related genes. FISH PHYSIOLOGY AND BIOCHEMISTRY 2018; 44:515-525. [PMID: 29234908 DOI: 10.1007/s10695-017-0450-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 11/22/2017] [Indexed: 06/07/2023]
Abstract
The aim of this work is to study the effect of the thermal stress of ambient temperature during winter and summer on the expression of type IV antifreeze gene (ANF IV) in different tissues of Nile tilapia (Oreochromis niloticus) as well as some immune-related genes. At first, genomic ANF IV gene was characterized from one fish; 124 amino acids were identified with 92.7% similarity with that on the gene bank. Expression of ANF IV and immune-related genes were done twice, once at the end of December (winter sample, temperature 14 °C) and the other at August (summer sample, temperature 36 °C). Assessment of ANF IV gene expression in different organs of fish was done; splenic mRNA was used for assessment of immune-related gene transcripts (CXCl2 chemokine, cc-chemokine, INF-3A, and MHC IIβ). Winter expression analysis of AFP IV in O. niloticus revealed significant upregulation of mRNA transcript levels in the intestine, gills, skin, spleen, liver, and brain with 324.03-, 170.06-, 107.63-, 97.61-, 94.35-, and 27.85-folds, respectively. Furthermore, upregulation in the gene was observed in some organs during summer: in the liver, gills, skin, intestine, and brain with lower levels compared with winter. The level of expression of immune-related genes in winter is significantly higher than summer in all assessed genes. Cc-chemokine gene expression was the most affected in both winter and summer. Variable expression profile of ANF IV in different organs and in different seasons together with its amino acid similarity of N-terminal and C-terminal with apolipoprotein (lipid binder) and form of high-density lipoprotein (HDL) suggests a different role for this protein which may be related to lipid metabolism.
Collapse
Affiliation(s)
- Asmma Y Ammar
- Biotechnology department, Animal Health Research Institute, Kafr El Sheikh, Egypt
| | - Abeer F El Nahas
- Animal Husbandry and Animal Wealth Department, Faculty of Veterinary Medicine, Alexandria University, Edfina, Behera, 22758, Egypt.
| | - Shawky Mahmoud
- Department of Physiology, Faculty of Veterinary Medicine, Kafer El Sheikh University, Kafr El Sheikh, Egypt
| | - Mohamed E Barakat
- Biotechnology Department, Animal Health Research Institute, Kafer El Sheik, Egypt
| | - Asmaa M Hassan
- Biotechnology department, Animal Health Research Institute, Kafr El Sheikh, Egypt
| |
Collapse
|
26
|
Cid FP, Maruyama F, Murase K, Graether SP, Larama G, Bravo LA, Jorquera MA. Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere. Extremophiles 2018; 22:537-552. [PMID: 29492666 DOI: 10.1007/s00792-018-1015-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/18/2018] [Indexed: 11/28/2022]
Abstract
Genome analyses are being used to characterize plant growth-promoting (PGP) bacteria living in different plant compartiments. In this context, we have recently isolated bacteria from the phyllosphere of an Antarctic plant (Deschampsia antarctica) showing ice recrystallization inhibition (IRI), an activity related to the presence of antifreeze proteins (AFPs). In this study, the draft genomes of six phyllospheric bacteria showing IRI activity were sequenced and annotated according to their functional gene categories. Genome sizes ranged from 5.6 to 6.3 Mbp, and based on sequence analysis of the 16S rRNA genes, five strains were identified as Pseudomonas and one as Janthinobacterium. Interestingly, most strains showed genes associated with PGP traits, such as nutrient uptake (ammonia assimilation, nitrogen fixing, phosphatases, and organic acid production), bioactive metabolites (indole acetic acid and 1-aminocyclopropane-1-carboxylate deaminase), and antimicrobial compounds (hydrogen cyanide and pyoverdine). In relation with IRI activity, a search of putative AFPs using current bioinformatic tools was also carried out. Despite that genes associated with reported AFPs were not found in these genomes, genes connected to ice-nucleation proteins (InaA) were found in all Pseudomonas strains, but not in the Janthinobacterium strain.
Collapse
Affiliation(s)
- Fernanda P Cid
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
| | - Kazunori Murase
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Giovanni Larama
- Department of Mathematical Engineering, Universidad de La Frontera, Temuco, Chile
| | - Leon A Bravo
- Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Forestales, Universidad de la Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Milko A Jorquera
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile.
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile.
| |
Collapse
|
27
|
Mahatabuddin S, Tsuda S. Applications of Antifreeze Proteins: Practical Use of the Quality Products from Japanese Fishes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1081:321-337. [PMID: 30288717 DOI: 10.1007/978-981-13-1244-1_17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Numerous embryonic ice crystals are generated in water at the moment of freezing. These crystals grow and merge together to form an ice block that can be generally observed. Antifreeze protein (AFP) is capable of binding to the embryonic ice crystals, inhibiting such an ice block formation. Fish-derived AFP additionally binds to membrane lipid bilayers to prolong the lifetime of cells. These unique abilities of AFP have been studied extensively for the development of advanced techniques, such as ice recrystallization inhibitors, freeze-tolerant gels, cell preservation fluids, and high-porosity ceramics, for which mass-preparation method of the quality product of AFP utilizing fish muscle homogenates made a significant contribution. In this chapter, we present both fundamental and advanced information of fish AFPs that have been especially discovered from mid-latitude sea area, which will provide a hint to develop more advanced techniques applicable in both medical and industrial fields.
Collapse
Affiliation(s)
- Sheikh Mahatabuddin
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Sakae Tsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.
| |
Collapse
|
28
|
Soyano K, Mushirobira Y. The Mechanism of Low-Temperature Tolerance in Fish. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1081:149-164. [DOI: 10.1007/978-981-13-1244-1_9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
29
|
Deller RC, Carter BM, Zampetakis I, Scarpa F, Perriman AW. The effect of surface charge on the thermal stability and ice recrystallization inhibition activity of antifreeze protein III (AFP III). Biochem Biophys Res Commun 2017; 495:1055-1060. [PMID: 29137985 DOI: 10.1016/j.bbrc.2017.11.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 11/10/2017] [Indexed: 10/18/2022]
Abstract
The aim of this study was to examine the effect of chemical cationization on the structure and function of antifreeze protein III (AFP III) over an extreme temperature range (-40°C to +90°C) using far-UV synchrotron radiation circular dichroism (SRCD) and ice recrystallization inhibition (IRI) assays. Chemical cationization was able to produce a modified AFP III with a net cationic charge at physiological pH that had enhanced resistance to denaturation at elevated temperatures, with no immediate negative impact on protein structure at subzero temperatures. Furthermore, cationized AFP III retained an IRI activity similar to that of native AFP III. Consequently, chemical cationization may provide a pathway to the development of more robust antifreeze proteins as supplementary cryoprotectants in the cryopreservation of clinically relevant cells.
Collapse
Affiliation(s)
- R C Deller
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - B M Carter
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - I Zampetakis
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK; Bristol Composites Institute (ACCIS), University of Bristol, Bristol, BS8 1TR, UK
| | - F Scarpa
- Bristol Composites Institute (ACCIS), University of Bristol, Bristol, BS8 1TR, UK
| | - A W Perriman
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
| |
Collapse
|
30
|
Kim HJ, Lee JH, Hur YB, Lee CW, Park SH, Koo BW. Marine Antifreeze Proteins: Structure, Function, and Application to Cryopreservation as a Potential Cryoprotectant. Mar Drugs 2017; 15:md15020027. [PMID: 28134801 PMCID: PMC5334608 DOI: 10.3390/md15020027] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/20/2017] [Indexed: 11/16/2022] Open
Abstract
Antifreeze proteins (AFPs) are biological antifreezes with unique properties, including thermal hysteresis(TH),ice recrystallization inhibition(IRI),and interaction with membranes and/or membrane proteins. These properties have been utilized in the preservation of biological samples at low temperatures. Here, we review the structure and function of marine-derived AFPs, including moderately active fish AFPs and hyperactive polar AFPs. We also survey previous and current reports of cryopreservation using AFPs. Cryopreserved biological samples are relatively diverse ranging from diatoms and reproductive cells to embryos and organs. Cryopreserved biological samples mainly originate from mammals. Most cryopreservation trials using marine-derived AFPs have demonstrated that addition of AFPs can improve post-thaw viability regardless of freezing method (slow-freezing or vitrification), storage temperature, and types of biological sample type.
Collapse
Affiliation(s)
- Hak Jun Kim
- Department of Chemistry, Pukyong National University, Busan 48513, Korea.
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Young Baek Hur
- Tidal Flat Research Institute, National Fisheries Research and Development Institute, Gunsan, Jeonbuk 54014, Korea.
| | - Chang Woo Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Sun-Ha Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Bon-Won Koo
- Department of Chemistry, Pukyong National University, Busan 48513, Korea.
| |
Collapse
|
31
|
Choi SR, Seo YJ, Kim M, Eo Y, Ahn HC, Lee AR, Park CJ, Ryu KS, Cheong HK, Lee SS, Jin E, Lee JH. NMR study of the antifreeze activities of active and inactive isoforms of a type III antifreeze protein. FEBS Lett 2016; 590:4202-4212. [PMID: 27718246 DOI: 10.1002/1873-3468.12451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/23/2016] [Accepted: 09/30/2016] [Indexed: 11/06/2022]
Abstract
The quaternary-amino-ethyl 1 (QAE1) isoforms of type III antifreeze proteins (AFPs) prevent the growth of ice crystals within organisms living in polar regions. We determined the antifreeze activity of wild-type and mutant constructs of the Japanese notched-fin eelpout (Zoarces elongates Kner) AFP8 (nfeAFP8) and characterized the structural and dynamics properties of their ice-binding surface using NMR. We found that the three constructs containing the V20G mutation were incapable of stopping the growth of ice crystals and exhibited structural changes, as well as increased conformational flexibility, in the first 310 helix (residues 18-22) of the sequence. Our results suggest that the inactive nfeAFP8s are incapable of anchoring water molecules due to the unusual and flexible backbone conformation of their primary prism plane-binding surface.
Collapse
Affiliation(s)
- Seo-Ree Choi
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, Korea
| | - Yeo-Jin Seo
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, Korea
| | - Minjae Kim
- Department of Life Science, Hanyang University, Seoul, Korea
| | - Yumi Eo
- College of Pharmacy, Dongguk University, Gyeonggi, Korea
| | - Hee-Chul Ahn
- College of Pharmacy, Dongguk University, Gyeonggi, Korea
| | - Ae-Ree Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, Korea
| | | | | | | | - Shim Sung Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, Korea
| | - EonSeon Jin
- Department of Life Science, Hanyang University, Seoul, Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, Korea.,Division of Magnetic Resonance, KBSI, Chungbuk, Korea
| |
Collapse
|
32
|
Leiter A, Rau S, Winger S, Muhle-Goll C, Luy B, Gaukel V. Influence of heating temperature, pressure and pH on recrystallization inhibition activity of antifreeze protein type III. J FOOD ENG 2016. [DOI: 10.1016/j.jfoodeng.2016.04.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
33
|
Affiliation(s)
- Maya Bar Dolev
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agricultural, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; ,
| | - Ido Braslavsky
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agricultural, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; ,
| | - Peter L. Davies
- Department of Biomedical and Molecular Science, Queen's University, Kingston, Ontario K7L 3N6, Canada;
| |
Collapse
|
34
|
Yoshida K, Baron AQR, Uchiyama H, Tsutsui S, Yamaguchi T. Structure and collective dynamics of hydrated anti-freeze protein type III from 180 K to 298 K by X-ray diffraction and inelastic X-ray scattering. J Chem Phys 2016; 144:134505. [PMID: 27059578 DOI: 10.1063/1.4944987] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigated hydrated antifreeze protein type III (AFP III) powder with a hydration level h (=mass of water/mass of protein) of 0.4 in the temperature range between 180 K and 298 K using X-ray diffraction and inelastic X-ray scattering (IXS). The X-ray diffraction data showed smooth, largely monotonic changes between 180 K and 298 K without freezing water. Meanwhile, the collective dynamics observed by IXS showed a strong change in the sound velocity at 180 K, after being largely temperature independent at higher temperatures (298-220 K). We interpret this change in terms of the dynamic transition previously discussed using other probes including THz IR absorption spectroscopy and incoherent elastic and quasi-elastic neutron scattering. This finding suggests that the dynamic transition of hydrated proteins is observable on the subpicosecond time scale as well as nano- and pico-second scales, both in collective dynamics from IXS and single particle dynamics from neutron scattering. Moreover, it is most likely that the dynamic transition of hydrated AFP III is not directly correlated with its hydration structure.
Collapse
Affiliation(s)
- Koji Yoshida
- Department of Chemistry, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Alfred Q R Baron
- Materials Dynamics Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hiroshi Uchiyama
- Research and Utilization Division, Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Satoshi Tsutsui
- Research and Utilization Division, Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Toshio Yamaguchi
- Department of Chemistry, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| |
Collapse
|
35
|
Lauersen KJ, Huber I, Wichmann J, Baier T, Leiter A, Gaukel V, Kartushin V, Rattenholl A, Steinweg C, von Riesen L, Posten C, Gudermann F, Lütkemeyer D, Mussgnug JH, Kruse O. Investigating the dynamics of recombinant protein secretion from a microalgal host. J Biotechnol 2015; 215:62-71. [DOI: 10.1016/j.jbiotec.2015.05.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/24/2015] [Accepted: 05/04/2015] [Indexed: 02/07/2023]
|
36
|
Sun T, Gauthier SY, Campbell RL, Davies PL. Revealing Surface Waters on an Antifreeze Protein by Fusion Protein Crystallography Combined with Molecular Dynamic Simulations. J Phys Chem B 2015; 119:12808-15. [PMID: 26371748 DOI: 10.1021/acs.jpcb.5b06474] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antifreeze proteins (AFPs) adsorb to ice through an extensive, flat, relatively hydrophobic surface. It has been suggested that this ice-binding site (IBS) organizes surface waters into an ice-like clathrate arrangement that matches and fuses to the quasi-liquid layer on the ice surface. On cooling, these waters join the ice lattice and freeze the AFP to its ligand. Evidence for the generality of this binding mechanism is limited because AFPs tend to crystallize with their IBS as a preferred protein-protein contact surface, which displaces some bound waters. Type III AFP is a 7 kDa globular protein with an IBS made up two adjacent surfaces. In the crystal structure of the most active isoform (QAE1), the part of the IBS that docks to the primary prism plane of ice is partially exposed to solvent and has clathrate waters present that match this plane of ice. The adjacent IBS, which matches the pyramidal plane of ice, is involved in protein-protein crystal contacts with few surface waters. Here we have changed the protein-protein contacts in the ice-binding region by crystallizing a fusion of QAE1 to maltose-binding protein. In this 1.9 Å structure, the IBS that fits the pyramidal plane of ice is exposed to solvent. By combining crystallography data with MD simulations, the surface waters on both sides of the IBS were revealed and match well with the target ice planes. The waters on the pyramidal plane IBS were loosely constrained, which might explain why other isoforms of type III AFP that lack the prism plane IBS are less active than QAE1. The AFP fusion crystallization method can potentially be used to force the exposure to solvent of the IBS on other AFPs to reveal the locations of key surface waters.
Collapse
Affiliation(s)
- Tianjun Sun
- Department of Biomedical and Molecular Sciences, Queen's University , Kingston, Ontario, Canada
| | - Sherry Y Gauthier
- Department of Biomedical and Molecular Sciences, Queen's University , Kingston, Ontario, Canada
| | - Robert L Campbell
- Department of Biomedical and Molecular Sciences, Queen's University , Kingston, Ontario, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University , Kingston, Ontario, Canada
| |
Collapse
|
37
|
Choi YG, Park CJ, Kim HE, Seo YJ, Lee AR, Choi SR, Lee SS, Lee JH. Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase. JOURNAL OF BIOMOLECULAR NMR 2015; 61:137-150. [PMID: 25575834 DOI: 10.1007/s10858-014-9895-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 12/30/2014] [Indexed: 06/04/2023]
Abstract
Antifreeze proteins (AFPs) are found in a variety of cold-adapted (psychrophilic) organisms to promote survival at subzero temperatures by binding to ice crystals and decreasing the freezing temperature of body fluids. The type III AFPs are small globular proteins that consist of one α-helix, three 3(10)-helices, and two β-strands. Sialic acids play important roles in a variety of biological functions, such as development, recognition, and cell adhesion and are synthesized by conserved enzymatic pathways that include sialic acid synthase (SAS). SAS consists of an N-terminal catalytic domain and a C-terminal antifreeze-like (AFL) domain, which is similar to the type III AFPs. Despite having very similar structures, AFL and the type III AFPs exhibit very different temperature-dependent stability and activity. In this study, we have performed backbone dynamics analyses of a type III AFP (HPLC12 isoform) and the AFL domain of human SAS (hAFL) at various temperatures. We also characterized the structural/dynamic properties of the ice-binding surfaces by analyzing the temperature gradient of the amide proton chemical shift and its correlation with chemical shift deviation from random coil. The dynamic properties of the two proteins were very different from each other. While HPLC12 was mostly rigid with a few residues exhibiting slow motions, hAFL showed fast internal motions at low temperature. Our results provide insight into the molecular basis of thermostability and structural flexibility in homologous psychrophilic HPLC12 and mesophilic hAFL proteins.
Collapse
Affiliation(s)
- Yong-Geun Choi
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju, Gyeongnam, 660-701, Republic of Korea
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Gaukel V, Leiter A, Spieß WE. Synergism of different fish antifreeze proteins and hydrocolloids on recrystallization inhibition of ice in sucrose solutions. J FOOD ENG 2014. [DOI: 10.1016/j.jfoodeng.2014.05.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
39
|
Bildanova LL, Salina EA, Shumny VK. Main properties and evolutionary features of antifreeze proteins. ACTA ACUST UNITED AC 2013. [DOI: 10.1134/s207905971301005x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
40
|
Brödel A, Raymond J, Duman J, Bier F, Kubick S. Functional evaluation of candidate ice structuring proteins using cell-free expression systems. J Biotechnol 2013. [DOI: 10.1016/j.jbiotec.2012.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
41
|
Haridas V, Naik S. Natural macromolecular antifreeze agents to synthetic antifreeze agents. RSC Adv 2013. [DOI: 10.1039/c3ra00081h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
|
42
|
Graham LA, Li J, Davidson WS, Davies PL. Smelt was the likely beneficiary of an antifreeze gene laterally transferred between fishes. BMC Evol Biol 2012; 12:190. [PMID: 23009612 PMCID: PMC3499448 DOI: 10.1186/1471-2148-12-190] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 08/20/2012] [Indexed: 12/26/2022] Open
Abstract
Background Type II antifreeze protein (AFP) from the rainbow smelt, Osmerus mordax, is a calcium-dependent C-type lectin homolog, similar to the AFPs from herring and sea raven. While C-type lectins are ubiquitous, type II AFPs are only found in a few species in three widely separated branches of teleost fishes. Furthermore, several other non-homologous AFPs are found in intervening species. We have previously postulated that this sporadic distribution has resulted from lateral gene transfer. The alternative hypothesis, that the AFP evolved from a lectin present in a shared ancestor and that this gene was lost in most species, is not favored because both the exon and intron sequences are highly conserved. Results Here we have sequenced and annotated a 160 kb smelt BAC clone containing a centrally-located AFP gene along with 14 other genes. Quantitative PCR indicates that there is but a single copy of this gene within the smelt genome, which is atypical for fish AFP genes. The corresponding syntenic region has been identified and searched in a number of other species and found to be devoid of lectin or AFP sequences. Unlike the introns of the AFP gene, the intronic sequences of the flanking genes are not conserved between species. As well, the rate and pattern of mutation in the AFP gene are radically different from those seen in other smelt and herring genes. Conclusions These results provide stand-alone support for an example of lateral gene transfer between vertebrate species. They should further inform the debate about genetically modified organisms by showing that gene transfer between ‘higher’ eukaryotes can occur naturally. Analysis of the syntenic regions from several fishes strongly suggests that the smelt acquired the AFP gene from the herring.
Collapse
Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | | | | | | |
Collapse
|
43
|
Garnham CP, Nishimiya Y, Tsuda S, Davies PL. Engineering a naturally inactive isoform of type III antifreeze protein into one that can stop the growth of ice. FEBS Lett 2012; 586:3876-81. [PMID: 23017208 DOI: 10.1016/j.febslet.2012.09.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 09/09/2012] [Accepted: 09/14/2012] [Indexed: 11/26/2022]
Abstract
Type III antifreeze proteins (AFPs) can be sub-divided into three classes of isoforms. SP and QAE2 isoforms can slow, but not stop, the growth of ice crystals by binding to pyramidal ice planes. The other class (QAE1) binds both pyramidal and primary prism planes and is able to halt the growth of ice. Here we describe the conversion of a QAE2 isoform into a fully-active QAE1-like isoform by changing four surface-exposed residues to develop a primary prism plane binding site. Molecular dynamics analyses suggest that the basis for gain in antifreeze activity is the formation of ice-like waters on the mutated protein surface.
Collapse
Affiliation(s)
- Christopher P Garnham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | | | | | | |
Collapse
|
44
|
Desjardins M, Graham LA, Davies PL, Fletcher GL. Antifreeze protein gene amplification facilitated niche exploitation and speciation in wolffish. FEBS J 2012; 279:2215-30. [PMID: 22520964 DOI: 10.1111/j.1742-4658.2012.08605.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
During winter, the coastal waters of Newfoundland can be considered a 'freeze risk ecozone' for teleost fishes, where the shallower habitats pose a high (and the deeper habitats a low) risk of freezing. Atlantic (Anarhichas lupus) and spotted (Anarhichas minor) wolffish, which inhabit these waters, reside at opposite ends of this ecozone, with the Atlantic wolffish being the species facing the greatest risk, because of its shallower niche. In order to resist freezing, this species secretes five times the level of antifreeze protein (AFP) activity into the plasma than does the spotted wolffish. The main basis for this interspecific difference in AFP levels is gene dosage, as the Atlantic wolffish has approximately three times as many AFP gene copies as the spotted wolffish. In addition, AFP transcript levels in liver (the primary source of circulating AFPs) are several times higher in the Atlantic wolffish. One explanation for the difference in gene dosage and transcript levels is the presence of tandemly arrayed repeats in the latter, which make up two-thirds of its AFP gene pool. Such repeats are not present in the spotted wolffish. The available evidence indicates that the two species diverged from a common ancestor at a time when the ebb and flow of northern glaciations would have resulted in the emergence of shallow water 'freeze risk ecozones'. The results of this study suggest that the duplication/amplification of AFP genes in a subpopulation of ancestral wolffish would have facilitated the exploitation of this high-risk habitat, resulting in the divergence and evolution of modern-day Atlantic and spotted wolffish species.
Collapse
Affiliation(s)
- Mariève Desjardins
- Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, Canada
| | | | | | | |
Collapse
|
45
|
Hobbs RS, Shears MA, Graham LA, Davies PL, Fletcher GL. Isolation and characterization of type I antifreeze proteins from cunner, Tautogolabrus adspersus, order Perciformes. FEBS J 2011; 278:3699-710. [DOI: 10.1111/j.1742-4658.2011.08288.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
46
|
Garnham CP, Natarajan A, Middleton AJ, Kuiper MJ, Braslavsky I, Davies PL. Compound ice-binding site of an antifreeze protein revealed by mutagenesis and fluorescent tagging. Biochemistry 2010; 49:9063-71. [PMID: 20853841 DOI: 10.1021/bi100516e] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By binding to the surface of ice crystals, type III antifreeze protein (AFP) can depress the freezing point of fish blood to below that of freezing seawater. This 7-kDa globular protein is encoded by a multigene family that produces two major isoforms, SP and QAE, which are 55% identical. Disruptive mutations on the ice-binding site of type III AFP lower antifreeze activity but can also change ice crystal morphology. By attaching green fluorescent protein to different mutants and isoforms and by examining the binding of these fusion proteins to single-crystal ice hemispheres, we show that type III AFP has a compound ice-binding site. There are two adjacent, flat, ice-binding surfaces at 150° to each other. One binds the primary prism plane of ice; the other, a pyramidal plane. Steric mutations on the latter surface cause elongation of the ice crystal as primary prism plane binding becomes dominant. SP isoforms naturally have a greatly reduced ability to bind the prism planes of ice. Mutations that make the SP isoforms more QAE-like slow down the rate of ice growth. On the basis of these observations we postulate that other types of AFP also have compound ice-binding sites that enable them to bind to multiple planes of ice.
Collapse
|
47
|
Kelley JL, Aagaard JE, MacCoss MJ, Swanson WJ. Functional diversification and evolution of antifreeze proteins in the antarctic fish Lycodichthys dearborni. J Mol Evol 2010; 71:111-8. [PMID: 20686757 DOI: 10.1007/s00239-010-9367-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Accepted: 07/06/2010] [Indexed: 12/01/2022]
Abstract
Antifreeze proteins (AFPs) have independently evolved in many organisms. AFPs act by binding to ice crystals, effectively lowering the freezing point. AFPs are often at high copy number in a genome and diversity exists between copies. Type III antifreeze proteins are found in Arctic and Antarctic eel pouts, and have previously been shown to evolve under positive selection. Here we combine molecular and proteomic techniques to understand the molecular evolution and diversity of Type III antifreeze proteins in a single individual Antarctic fish Lycodichthys dearborni. Our expressed sequence tag (EST) screen reveals that at least seven different AFP variants are transcribed, which are ultimately translated into five different protein isoforms. The isoforms have identical 66 base pair signal sequences and different numbers of subsequent ice-binding domains followed by a stop codon. Isoforms with one ice-binding unit (monomer), two units (dimer), and multiple units (multimer) were present in the EST library. We identify a previously uncharacterized protein dimer, providing further evidence that there is diversity between Type III AFP isoforms, perhaps driven by positive selection for greater thermal hysteresis. Proteomic analysis confirms that several of these isoforms are translated and present in the liver. Our molecular evolution study shows that paralogs have diverged under positive selection. We hypothesize that antifreeze protein diversity is an important contributor to depressing the serum freezing point.
Collapse
Affiliation(s)
- Joanna L Kelley
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | | | | | | |
Collapse
|
48
|
Promoter analysis of a growth hormone transgene in Atlantic salmon. Theriogenology 2009; 72:62-71. [DOI: 10.1016/j.theriogenology.2009.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2008] [Revised: 02/03/2009] [Accepted: 02/05/2009] [Indexed: 11/30/2022]
|
49
|
Takamichi M, Nishimiya Y, Miura A, Tsuda S. Fully active QAE isoform confers thermal hysteresis activity on a defective SP isoform of type III antifreeze protein. FEBS J 2009; 276:1471-9. [PMID: 19187223 DOI: 10.1111/j.1742-4658.2009.06887.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Type III antifreeze protein is naturally expressed as a mixture of sulfopropyl-Sephadex (SP) and quaternary aminoethyl-Sephadex (QAE)-binding isoforms, whose sequence identity is approximately 55%. We studied the ice-binding properties of a SP isoform (nfeAFP6) and the differences from those of a QAE isoform (nfeAFP8); both of these isoforms have been identified from the Japanese fish Zoarces elongatus Kner. The two isoforms possessed ice-shaping ability, such as the creation of an ice bipyramid, but nfeAFP6 was unable to halt crystal growth and exhibited no thermal hysteresis activity. For example, the ice growth rate for nfeAFP6 was 1000-fold higher than that for nfeAFP8 when measured for 0.1 mm protein solution at 0.25 degrees C below the melting point. Nevertheless, nfeAFP6 exhibited full thermal hysteresis activity in the presence of only 1% nfeAFP8 (i.e. [nfeAFP8]/[nfeAFP6] = 0.01), the effectiveness of which was indistinguishable from that of nfeAFP8 alone. We also observed a burst of ice crystal growth from the tip of the ice bipyramid for both isoforms on lowering the temperature. These results suggest that the ice growth inhibitory activity of an antifreeze protein isoform lacking the active component is restored by the addition of a minute amount of the active isoform.
Collapse
Affiliation(s)
- Manabu Takamichi
- Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | | | | | | |
Collapse
|
50
|
Gauthier SY, Scotter AJ, Lin FH, Baardsnes J, Fletcher GL, Davies PL. A re-evaluation of the role of type IV antifreeze protein. Cryobiology 2008; 57:292-6. [DOI: 10.1016/j.cryobiol.2008.10.122] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 08/20/2008] [Accepted: 10/01/2008] [Indexed: 11/29/2022]
|