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Lopes JC, Kinasz CT, Luiz AMC, Kreusch MG, Duarte RTD. Frost fighters: unveiling the potential of microbial antifreeze proteins in biotech innovation. J Appl Microbiol 2024; 135:lxae140. [PMID: 38877650 DOI: 10.1093/jambio/lxae140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/30/2024] [Accepted: 06/13/2024] [Indexed: 06/16/2024]
Abstract
Polar environments pose extreme challenges for life due to low temperatures, limited water, high radiation, and frozen landscapes. Despite these harsh conditions, numerous macro and microorganisms have developed adaptive strategies to reduce the detrimental effects of extreme cold. A primary survival tactic involves avoiding or tolerating intra and extracellular freezing. Many organisms achieve this by maintaining a supercooled state by producing small organic compounds like sugars, glycerol, and amino acids, or through increasing solute concentration. Another approach is the synthesis of ice-binding proteins, specifically antifreeze proteins (AFPs), which hinder ice crystal growth below the melting point. This adaptation is crucial for preventing intracellular ice formation, which could be lethal, and ensuring the presence of liquid water around cells. AFPs have independently evolved in different species, exhibiting distinct thermal hysteresis and ice structuring properties. Beyond their ecological role, AFPs have garnered significant attention in biotechnology for potential applications in the food, agriculture, and pharmaceutical industries. This review aims to offer a thorough insight into the activity and impacts of AFPs on water, examining their significance in cold-adapted organisms, and exploring the diversity of microbial AFPs. Using a meta-analysis from cultivation-based and cultivation-independent data, we evaluate the correlation between AFP-producing microorganisms and cold environments. We also explore small and large-scale biotechnological applications of AFPs, providing a perspective for future research.
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Affiliation(s)
- Joana Camila Lopes
- Laboratory of Molecular Ecology and Extremophiles, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina-Campus Reitor João David Ferreira Lima, s/n Trindade, Florianópolis, SC 88040-900, Brazil
- Postgraduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Campus Reitor João David Ferreira Lima, s/n Trindade, Florianópolis, SC 88040-900, Brazil
| | - Camila Tomazini Kinasz
- Laboratory of Molecular Ecology and Extremophiles, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina-Campus Reitor João David Ferreira Lima, s/n Trindade, Florianópolis, SC 88040-900, Brazil
- Postgraduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Campus Reitor João David Ferreira Lima,, s/n Trindade, Florianópolis, SC 88040-900, Brazil
| | - Alanna Maylle Cararo Luiz
- Laboratory of Molecular Ecology and Extremophiles, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina-Campus Reitor João David Ferreira Lima, s/n Trindade, Florianópolis, SC 88040-900, Brazil
- Postgraduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Campus Reitor João David Ferreira Lima,, s/n Trindade, Florianópolis, SC 88040-900, Brazil
| | - Marianne Gabi Kreusch
- Laboratory of Molecular Ecology and Extremophiles, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina-Campus Reitor João David Ferreira Lima, s/n Trindade, Florianópolis, SC 88040-900, Brazil
| | - Rubens Tadeu Delgado Duarte
- Laboratory of Molecular Ecology and Extremophiles, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina-Campus Reitor João David Ferreira Lima, s/n Trindade, Florianópolis, SC 88040-900, Brazil
- Postgraduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Campus Reitor João David Ferreira Lima,, s/n Trindade, Florianópolis, SC 88040-900, Brazil
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Němečková K, Mareš J, Procházková L, Culka A, Košek F, Wierzchos J, Nedbalová L, Dudák J, Tymlová V, Žemlička J, Kust A, Zima J, Nováková E, Jehlička J. Gypsum endolithic phototrophs under moderate climate (Southern Sicily): their diversity and pigment composition. Front Microbiol 2023; 14:1175066. [PMID: 37485515 PMCID: PMC10359912 DOI: 10.3389/fmicb.2023.1175066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/15/2023] [Indexed: 07/25/2023] Open
Abstract
In this study, we used microscopic, spectroscopic, and molecular analysis to characterize endolithic colonization in gypsum (selenites and white crystalline gypsum) from several sites in Sicily. Our results showed that the dominant microorganisms in these environments are cyanobacteria, including: Chroococcidiopsis sp., Gloeocapsopsis pleurocapsoides, Gloeocapsa compacta, and Nostoc sp., as well as orange pigmented green microalgae from the Stephanospherinia clade. Single cell and filament sequencing coupled with 16S rRNA amplicon metagenomic profiling provided new insights into the phylogenetic and taxonomic diversity of the endolithic cyanobacteria. These organisms form differently pigmented zones within the gypsum. Our metagenomic profiling also showed differences in the taxonomic composition of endoliths in different gypsum varieties. Raman spectroscopy revealed that carotenoids were the most common pigments present in the samples. Other pigments such as gloeocapsin and scytonemin were also detected in the near-surface areas, suggesting that they play a significant role in the biology of endoliths in this environment. These pigments can be used as biomarkers for basic taxonomic identification, especially in case of cyanobacteria. The findings of this study provide new insights into the diversity and distribution of phototrophic microorganisms and their pigments in gypsum in Southern Sicily. Furthemore, this study highlights the complex nature of endolithic ecosystems and the effects of gypsum varieties on these communities, providing additional information on the general bioreceptivity of these environments.
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Affiliation(s)
- Kateřina Němečková
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
| | - Jan Mareš
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
- Center Algatech, Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czechia
| | - Lenka Procházková
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
| | - Adam Culka
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
| | - Filip Košek
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
| | - Jacek Wierzchos
- Department of Biochemistry and Microbial Ecology, Museo Nacional de Ciencias Naturales - Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Linda Nedbalová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
| | - Jan Dudák
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, Prague, Czechia
| | - Veronika Tymlová
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, Prague, Czechia
| | - Jan Žemlička
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, Prague, Czechia
| | - Andreja Kust
- Department of Earth and Planetary Science, University of Berkeley, Berkeley, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Jan Zima
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Eva Nováková
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Jan Jehlička
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
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Genetic and Structural Diversity of Prokaryotic Ice-Binding Proteins from the Central Arctic Ocean. Genes (Basel) 2023; 14:genes14020363. [PMID: 36833289 PMCID: PMC9957290 DOI: 10.3390/genes14020363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/01/2023] Open
Abstract
Ice-binding proteins (IBPs) are a group of ecologically and biotechnologically relevant enzymes produced by psychrophilic organisms. Although putative IBPs containing the domain of unknown function (DUF) 3494 have been identified in many taxa of polar microbes, our knowledge of their genetic and structural diversity in natural microbial communities is limited. Here, we used samples from sea ice and sea water collected in the central Arctic Ocean as part of the MOSAiC expedition for metagenome sequencing and the subsequent analyses of metagenome-assembled genomes (MAGs). By linking structurally diverse IBPs to particular environments and potential functions, we reveal that IBP sequences are enriched in interior ice, have diverse genomic contexts and cluster taxonomically. Their diverse protein structures may be a consequence of domain shuffling, leading to variable combinations of protein domains in IBPs and probably reflecting the functional versatility required to thrive in the extreme and variable environment of the central Arctic Ocean.
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Gilbertson R, Langan E, Mock T. Diatoms and Their Microbiomes in Complex and Changing Polar Oceans. Front Microbiol 2022; 13:786764. [PMID: 35401494 PMCID: PMC8991070 DOI: 10.3389/fmicb.2022.786764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/23/2022] [Indexed: 11/17/2022] Open
Abstract
Diatoms, a key group of polar marine microbes, support highly productive ocean ecosystems. Like all life on earth, diatoms do not live in isolation, and they are therefore under constant biotic and abiotic pressures which directly influence their evolution through natural selection. Despite their importance in polar ecosystems, polar diatoms are understudied compared to temperate species. The observed rapid change in the polar climate, especially warming, has created increased research interest to discover the underlying causes and potential consequences on single species to entire ecosystems. Next-Generation Sequencing (NGS) technologies have greatly expanded our knowledge by revealing the molecular underpinnings of physiological adaptations to polar environmental conditions. Their genomes, transcriptomes, and proteomes together with the first eukaryotic meta-omics data of surface ocean polar microbiomes reflect the environmental pressures through adaptive responses such as the expansion of protein families over time as a consequence of selection. Polar regions and their microbiomes are inherently connected to climate cycles and their feedback loops. An integrated understanding built on "omics" resources centered around diatoms as key primary producers will enable us to reveal unifying concepts of microbial co-evolution and adaptation in polar oceans. This knowledge, which aims to relate past environmental changes to specific adaptations, will be required to improve climate prediction models for polar ecosystems because it provides a unifying framework of how interacting and co-evolving biological communities might respond to future environmental change.
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Affiliation(s)
- Reuben Gilbertson
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Emma Langan
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- The Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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Hauptmann A, Hoelzl G, Loerting T. Optical cryomicroscopy and differential scanning calorimetry of buffer solutions containing cryoprotectants. Eur J Pharm Biopharm 2021; 163:127-140. [PMID: 33813056 DOI: 10.1016/j.ejpb.2021.03.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/21/2021] [Accepted: 03/27/2021] [Indexed: 12/12/2022]
Abstract
In the pharmaceutical industry, cryoprotectants are added to buffer formulations to protect the active pharmaceutical ingredient from freeze- and thaw damage. We investigated the freezing and thawing of aqueous sodium citrate buffer with various cryoprotectants, specifically amino acids (cysteine, histidine, arginine, proline and lysine), disaccharides (trehalose and sucrose), polyhydric alcohols (glycerol and mannitol) and surfactants (polysorbate 20 and polysorbate 80). Hereby, we employed optical cryomicroscopy in combination with differential scanning calorimetry in the temperature range to -80 °C. The effect of cryoprotectants on the morphology of the ice crystals, the glass transition temperature and the initial melting temperature is presented. Some of the cryoprotectants have a significant impact on ice crystal size. Disaccharides restrict ice crystal growth, whereas surfactants and glycerol allow ice crystals to increase in size. Cysteine and mannitol cause dehydration after thawing. Either one or two glass transition temperatures were detected, where arginine, surfactants, glycerol, proline and lysine suppress the second, implying a uniform freeze-concentrated solution. The initial melting temperature of pure buffer solution can be shifted up by adding mannitol, both disaccharides and both surfactants; but down by glycerol, proline and lysine.
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Affiliation(s)
- Astrid Hauptmann
- Sandoz GmbH, Biochemiestrasse 10, 6336 Langkampfen, Austria; Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria.
| | - Georg Hoelzl
- Sandoz GmbH, Biochemiestrasse 10, 6336 Langkampfen, Austria.
| | - Thomas Loerting
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria.
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Ice-Binding Proteins Associated with an Antarctic Cyanobacterium, Nostoc sp. HG1. Appl Environ Microbiol 2021; 87:AEM.02499-20. [PMID: 33158891 PMCID: PMC7783341 DOI: 10.1128/aem.02499-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Ice-binding proteins (IBPs) have been identified in numerous polar algae and bacteria, but so far not in any cyanobacteria, despite the abundance of cyanobacteria in polar regions. We previously reported strong IBP activity associated with an Antarctic Nostoc species. In this study, to identify the proteins responsible, as well as elucidate their origin, we sequenced the DNA of an environmental sample of this species, designated Nostoc sp. HG1, and its bacterial community and attempted to identify IBPs by looking for known IBPs in the metagenome and by looking for novel IBPs by tandem mass spectrometry (MS/MS) proteomics analyses of ice affinity-purified proteins. The metagenome contained over 116 DUF3494-type IBP genes, the most common type of IBP identified so far. One of the IBPs could be confidently assigned to Nostoc, while the others could be attributed to diverse bacteria, which, surprisingly, accounted for the great majority of the metagenome. Recombinant Nostoc IBPs (nIBPs) had strong ice-structuring activities, and their circular dichroism spectra were consistent with the secondary structure of a DUF3494-type IBP. nIBP is unusual in that it is the only IBP identified so far to have a PEP (amino acid motif) C-terminal signal, a signal that has been associated with anchoring to the outer cell membrane. These results suggest that the observed IBP activity of Nostoc sp. HG1 was due to a combination of endogenous and exogenous IBPs. Amino acid and nucleotide sequence analyses of nIBP raise the possibility that it was acquired from a planctomycete.IMPORTANCE The horizontal transfer of genes encoding ice-binding proteins (IBPs), proteins that confer freeze-thaw tolerance, has allowed many microorganisms to expand their ranges into polar regions. One group of microorganisms for which nothing is known about its IBPs is cyanobacteria. In this study, we identified a cyanobacterial IBP and showed that it was likely acquired from another bacterium, probably a planctomycete. We also showed that a consortium of IBP-producing bacteria living with the Nostoc contribute to its IBP activity.
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Gálvez FE, Saldarriaga-Córdoba M, Huovinen P, Silva AX, Gómez I. Revealing the Characteristics of the Antarctic Snow Alga Chlorominima collina gen. et sp. nov. Through Taxonomy, Physiology, and Transcriptomics. FRONTIERS IN PLANT SCIENCE 2021; 12:662298. [PMID: 34163502 PMCID: PMC8215615 DOI: 10.3389/fpls.2021.662298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/10/2021] [Indexed: 05/13/2023]
Abstract
Snow algae play crucial roles in cold ecosystems, however, many aspects related to their biology, adaptations and especially their diversity are not well known. To improve the identification of snow algae from colored snow, in the present study we used a polyphasic approach to describe a new Antarctic genus, Chlorominima with the species type Chlorominima collina. This new taxon was isolated of colored snow collected from the Collins Glacier (King George Island) in the Maritime Antarctic region. Microscopy revealed biflagellated ellipsoidal cells with a rounded posterior end, a C-shaped parietal chloroplast without a pyrenoid, eyespot, and discrete papillae. Several of these characteristics are typical of the genus Chloromonas, but the new isolate differs from the described species of this genus by the unusual small size of the cells, the presence of several vacuoles, the position of the nucleus and the shape of the chloroplast. Molecular analyzes confirm that the isolated alga does not belong to Chloromonas and therefore forms an independent lineage, which is closely related to other unidentified Antarctic and Arctic strains, forming a polar subclade in the Stephanosphaerinia phylogroup within the Chlamydomonadales. Secondary structure comparisons of the ITS2 rDNA marker support the idea that new strain is a distinct taxon within of Caudivolvoxa. Physiological experiments revealed psychrophilic characteristics, which are typical of true snow algae. This status was confirmed by the partial transcriptome obtained at 2°C, in which various cold-responsive and cryoprotective genes were identified. This study explores the systematics, cold acclimatization strategies and their implications for the Antarctic snow flora.
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Affiliation(s)
- Francisca E. Gálvez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
- *Correspondence: Francisca E. Gálvez,
| | - Mónica Saldarriaga-Córdoba
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Pirjo Huovinen
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
| | - Andrea X. Silva
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- AUSTRAL-omics, Vicerrectoría de Investigación, Desarrollo y Creación Artística, Universidad Austral de Chile, Valdivia, Chile
| | - Iván Gómez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
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Hoham RW, Remias D. Snow and Glacial Algae: A Review 1. JOURNAL OF PHYCOLOGY 2020; 56:264-282. [PMID: 31825096 PMCID: PMC7232433 DOI: 10.1111/jpy.12952] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/20/2019] [Indexed: 05/03/2023]
Abstract
Snow or glacial algae are found on all continents, and most species are in the Chlamydomonadales (Chlorophyta) and Zygnematales (Streptophyta). Other algal groups include euglenoids, cryptomonads, chrysophytes, dinoflagellates, and cyanobacteria. They may live under extreme conditions of temperatures near 0°C, high irradiance levels in open exposures, low irradiance levels under tree canopies or deep in snow, acidic pH, low conductivity, and desiccation after snow melt. These primary producers may color snow green, golden-brown, red, pink, orange, or purple-grey, and they are part of communities that include other eukaryotes, bacteria, archaea, viruses, and fungi. They are an important component of the global biosphere and carbon and water cycles. Life cycles in the Chlamydomonas-Chloromonas-Chlainomonas complex include migration of flagellates in liquid water and formation of resistant cysts, many of which were identified previously as other algae. Species differentiation has been updated through the use of metagenomics, lipidomics, high-throughput sequencing (HTS), multi-gene analysis, and ITS. Secondary metabolites (astaxanthin in snow algae and purpurogallin in glacial algae) protect chloroplasts and nuclei from damaging PAR and UV, and ice binding proteins (IBPs) and polyunsaturated fatty acids (PUFAs) reduce cell damage in subfreezing temperatures. Molecular phylogenies reveal that snow algae in the Chlamydomonas-Chloromonas complex have invaded the snow habitat at least twice, and some species are polyphyletic. Snow and glacial algae reduce albedo, accelerate the melt of snowpacks and glaciers, and are used to monitor climate change. Selected strains of these algae have potential for producing food or fuel products.
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Affiliation(s)
- Ronald W. Hoham
- Department of BiologyColgate UniversityHamiltonNew York13346USA
| | - Daniel Remias
- School of EngineeringUniversity of Applied Sciences Upper AustriaWels4600Austria
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Cho SM, Kim S, Cho H, Lee H, Lee JH, Lee H, Park H, Kang S, Choi HG, Lee J. Type II Ice-Binding Proteins Isolated from an Arctic Microalga Are Similar to Adhesin-Like Proteins and Increase Freezing Tolerance in Transgenic Plants. PLANT & CELL PHYSIOLOGY 2019; 60:2744-2757. [PMID: 31418793 DOI: 10.1093/pcp/pcz162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 08/11/2019] [Indexed: 06/10/2023]
Abstract
Microalgal ice-binding proteins (IBPs) in the polar region are poorly understood at the genome-wide level, although they are important for cold adaptation. Through the transcriptome study with the Arctic green alga Chloromonas sp. KNF0032, we identified six Chloromonas IBP genes (CmIBPs), homologous with the previously reported IBPs from Antarctic snow alga CCMP681 and Antarctic Chloromonas sp. They were organized with multiple exon/intron structures and low-temperature-responsive cis-elements in their promoters and abundantly expressed at low temperature. The biological functions of three representative CmIBPs (CmIBP1, CmIBP2 and CmIBP3) were tested using in vitro analysis and transgenic plant system. CmIBP1 had the most effective ice recrystallization inhibition (IRI) activities in both in vitro and transgenic plants, and CmIBP2 and CmIBP3 had followed. All transgenic plants grown under nonacclimated condition were freezing tolerant, and especially 35S::CmIBP1 plants were most effective. After cold acclimation, only 35S::CmIBP2 plants showed slightly increased freezing tolerance. Structurally, the CmIBPs were predicted to have β-solenoid forms with parallel β-sheets and repeated TXT motifs. The repeated TXT structure of CmIBPs appears similar to the AidA domain-containing adhesin-like proteins from methanogens. We have shown that the AidA domain has IRI activity as CmIBPs and phylogenetic analysis also supported that the AidA domains are monophyletic with ice-binding domain of CmIBPs, and these results suggest that CmIBPs are a type of modified adhesins.
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Affiliation(s)
- Sung Mi Cho
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Sanghee Kim
- Division of Polar Life Sciences, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Hojin Cho
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Polar Science, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Hyoungseok Lee
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Polar Science, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Polar Science, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Horim Lee
- Department of Biotechnology, Duksung Women's University, Seoul 01369, Republic of Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Polar Science, University of Science and Technology, Daejeon 34113, Republic of Korea
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Seunghyun Kang
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Han-Gu Choi
- Division of Polar Life Sciences, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Jungeun Lee
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Polar Science, University of Science and Technology, Daejeon 34113, Republic of Korea
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10
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Raymond JA, Remias D. Ice-Binding Proteins in a Chrysophycean Snow Alga: Acquisition of an Essential Gene by Horizontal Gene Transfer. Front Microbiol 2019; 10:2697. [PMID: 31849866 PMCID: PMC6892780 DOI: 10.3389/fmicb.2019.02697] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/06/2019] [Indexed: 01/08/2023] Open
Abstract
All ice-associated algae examined so far have genes for ice-binding proteins (IBPs), which suggest that these proteins are essential for survival in icy habitats. The most common type of IBP, type 1 IBPs (also referred to as DUF3494 IBPs), is also found in ice-associated bacteria and fungi. Previous studies have suggested that algal IBP genes were acquired by horizontal transfer from other microorganisms (probably bacteria). However, it remains unclear whether this is also the case for algae distantly related to the ones examined so far and whether microorganisms other than bacteria could be the donors. Furthermore, there is only limited evidence that these proteins are expressed at low temperature. Here, we show that Kremastochrysopsis austriaca (Chrysophyceae), an Austrian snow alga that is not closely related to any of the ice-associated algae examined so far, also produces IBPs, although their activity was weak. Sequencing the algal genome and the transcriptomes of cells grown at 1 and 15°C revealed three isoforms of a type 1 IBP. In agreement with their putative function, the three isoforms were strongly upregulated by one to two orders of magnitude at 1°C compared to 15°C. In a phylogenetic tree, the K. austriaca IBPs were distant from other algal IBPs, with the closest matches being bacterial proteins. These results suggest that the K. austriaca IBPs were derived from a gene that was acquired from a bacterium unrelated to other IBP donor bacteria and confirm by their presence in yet another alga the essential role of algal IBPs.
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Affiliation(s)
- James A Raymond
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, United States
| | - Daniel Remias
- School of Engineering, University of Applied Sciences Upper Austria, Wels, Austria
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Kim M, Gwak Y, Jung W, Jin E. Identification and Characterization of an Isoform Antifreeze Protein from the Antarctic Marine Diatom, Chaetoceros neogracile and Suggestion of the Core Region. Mar Drugs 2017; 15:md15100318. [PMID: 29057803 PMCID: PMC5666426 DOI: 10.3390/md15100318] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/13/2017] [Accepted: 10/16/2017] [Indexed: 11/16/2022] Open
Abstract
Antifreeze proteins (AFPs) protecting the cells against freezing are produced in response to extremely low temperatures in diverse psychrophilic organisms, and they are encoded by multiple gene families. The AFP of Antarctic marine diatom Chaetoceros neogracile is reported in our previous research, but like other microalgae, was considered to probably have additional genes coding AFPs. In this paper, we reported the cloning and characterization of additional AFP gene from C. neogracile (Cn-isoAFP). Cn-isoAFP protein is 74.6% identical to the previously reported Cn-AFP. The promoter sequence of Cn-isoAFP contains environmental stress responsive elements for cold, thermal, and high light conditions. Cn-isoAFP transcription levels increased dramatically when cells were exposed to freezing (−20 °C), thermal (10 °C), or high light (600 μmol photon m−2 s−1) stresses. The thermal hysteresis (TH) activity of recombinant Cn-isoAFP was 0.8 °C at a protein concentration of 5 mg/mL. Results from homology modeling and TH activity analysis of site-directed mutant proteins elucidated AFP mechanism to be a result of flatness of B-face maintained via hydrophobic interactions.
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Affiliation(s)
- Minjae Kim
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133-791, Korea.
| | - Yunho Gwak
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133-791, Korea.
| | - Woongsic Jung
- Division of Polar Life Science, Korea Polar Research Institute, KIOST, Incheon 406-840, Korea.
| | - EonSeon Jin
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133-791, Korea.
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12
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Raymond JA, Morgan-Kiss R. Multiple ice-binding proteins of probable prokaryotic origin in an Antarctic lake alga, Chlamydomonas sp. ICE-MDV (Chlorophyceae). JOURNAL OF PHYCOLOGY 2017; 53:848-854. [PMID: 28543018 PMCID: PMC5546997 DOI: 10.1111/jpy.12550] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/27/2017] [Indexed: 05/14/2023]
Abstract
Ice-associated algae produce ice-binding proteins (IBPs) to prevent freezing damage. The IBPs of the three chlorophytes that have been examined so far share little similarity across species, making it likely that they were acquired by horizontal gene transfer (HGT). To clarify the importance and source of IBPs in chlorophytes, we sequenced the IBP genes of another Antarctic chlorophyte, Chlamydomonas sp. ICE-MDV (Chlamy-ICE). Genomic DNA and total RNA were sequenced and screened for known ice-associated genes. Chlamy-ICE has as many as 50 IBP isoforms, indicating that they have an important role in survival. The IBPs are of the DUF3494 type and have similar exon structures. The DUF3494 sequences are much more closely related to prokaryotic sequences than they are to sequences in other chlorophytes, and the chlorophyte IBP and ribosomal 18S phylogenies are dissimilar. The multiple IBP isoforms found in Chlamy-ICE and other algae may allow the algae to adapt to a greater variety of ice conditions than prokaryotes, which typically have a single IBP gene. The predicted structure of the DUF3494 domain has an ice-binding face with an orderly array of hydrophilic side chains. The results indicate that Chlamy-ICE acquired its IBP genes by HGT in a single event. The acquisitions of IBP genes by this and other species of Antarctic algae by HGT appear to be key evolutionary events that allowed algae to extend their ranges into polar environments.
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Affiliation(s)
- James A. Raymond
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada 89154 USA
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Kim HJ, Lee JH, Hur YB, Lee CW, Park SH, Koo BW. Marine Antifreeze Proteins: Structure, Function, and Application to Cryopreservation as a Potential Cryoprotectant. Mar Drugs 2017; 15:md15020027. [PMID: 28134801 PMCID: PMC5334608 DOI: 10.3390/md15020027] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [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.
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Affiliation(s)
- Hak Jun Kim
- Department of Chemistry, Pukyong National University, Busan 48513, Korea.
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Young Baek Hur
- Tidal Flat Research Institute, National Fisheries Research and Development Institute, Gunsan, Jeonbuk 54014, Korea.
| | - Chang Woo Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Sun-Ha Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
| | - Bon-Won Koo
- Department of Chemistry, Pukyong National University, Busan 48513, Korea.
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14
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Bredow M, Walker VK. Ice-Binding Proteins in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:2153. [PMID: 29312400 PMCID: PMC5744647 DOI: 10.3389/fpls.2017.02153] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 12/05/2017] [Indexed: 05/04/2023]
Abstract
Sub-zero temperatures put plants at risk of damage associated with the formation of ice crystals in the apoplast. Some freeze-tolerant plants mitigate this risk by expressing ice-binding proteins (IBPs), that adsorb to ice crystals and modify their growth. IBPs are found across several biological kingdoms, with their ice-binding activity and function uniquely suited to the lifestyle they have evolved to protect, be it in fishes, insects or plants. While IBPs from freeze-avoidant species significantly depress the freezing point, plant IBPs typically have a reduced ability to lower the freezing temperature. Nevertheless, they have a superior ability to inhibit the recrystallization of formed ice. This latter activity prevents ice crystals from growing larger at temperatures close to melting. Attempts to engineer frost-hardy plants by the controlled transfer of IBPs from freeze-avoiding fish and insects have been largely unsuccessful. In contrast, the expression of recombinant IBP sequences from freeze-tolerant plants significantly reduced electrolyte leakage and enhanced freezing survival in freeze-sensitive plants. These promising results have spurred additional investigations into plant IBP localization and post-translational modifications, as well as a re-evaluation of IBPs as part of the anti-stress and anti-pathogen axis of freeze-tolerant plants. Here we present an overview of plant freezing stress and adaptation mechanisms and discuss the potential utility of IBPs for the generation of freeze-tolerant crops.
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Affiliation(s)
- Melissa Bredow
- Department of Biology, Queen’s University, Kingston, ON, Canada
- *Correspondence: Melissa Bredow,
| | - Virginia K. Walker
- Department of Biomedical and Molecular Sciences, and School of Environmental Studies, Queen’s University, Kingston, ON, Canada
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