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Box ICH, van der Burg KRL, Marshall KE. Analysis of Ice-Binding Protein Evolution. Methods Mol Biol 2024; 2730:219-229. [PMID: 37943462 DOI: 10.1007/978-1-0716-3503-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Discovering novel ice-binding proteins (IBPs) is important for understanding the evolution of IBPs but it is difficult to determine where resources should be directed in the search for novel IBPs. For this reason, we developed a simple bioinformatic approach for aiding in the determination of where to direct efforts in the search for IBPs. First, BLAST is used to obtain a candidate list of putative IBPs. Next, phylogenetic trees are constructed to map the candidate list of putative IBPs to determine if any patterns are forming. These candidate putative IBPs and their patterns are then assessed through the production of ancestral sequences and reverse BLAST searches, in addition to the use of IBP calculators, to determine which sequences should be cut to produce the final putative IBP list. Finally, we explain an avenue to investigate these putative IBPs further for the development of hypotheses on their evolution.
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Affiliation(s)
- Isaiah C H Box
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | | | - Katie E Marshall
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada.
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Dong X, Liu Z, Wei J, Zheng G, Li H, Wang Y, Tian H, Cui J, Wu Z, Cao X, Xu C. The BrAFP1 promoter drives gene-specific expression in leaves and stems of winter rapeseed (Brassica rapa L.) under cold induction. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 331:111669. [PMID: 36870371 DOI: 10.1016/j.plantsci.2023.111669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
BrAFP1(antifreeze protein in winter turnip rape) effectively limits recrystallization and growth of ice crystals. The BrAFP1 expression level determines whether the freezing-induced damage to winter turnip rape plants is avoided. This study analyzed the activity of the BrAFP1 promoters of several varieties at various cold tolerance levels. We cloned the BrAFP1 promoters from five winter rapeseed cultivars. The multiple sequence alignment revealed the presence of one inDel and eight single-nucleotide mutations (SNMs) in the promoters. One of these SNMs (base mutation from C to T) at the -836 site away from the transcription start site (TSS) enhanced the transcriptional activity of the promoter at low temperature. The promoter activity was specific in cotyledons and hypocotyls during the seedling stage and was referential in stems, leaves, and flowers but not the calyx. This consequently drove the downstream gene to be specifically expressed in leaves and stems, but not in roots at low temperature. The truncated fragment GUS staining assays revealed that the core region of the BrAFP1 promoter was included in the 98 bp fragment from the -933 to -836 site away from the TSS, which was necessary for transcriptional activity. The LTR element of the promoter significantly enhanced expression at low temperatures and suppressed expression at moderate temperatures. Moreover, the BrAFP1 5'-UTR intron bound the scarecrow-like transcription factor and enhanced expression at low temperature.
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Affiliation(s)
- Xiaoyun Dong
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zigang Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jiaping Wei
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Guoqiang Zheng
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Hui Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Ying Wang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Haiyan Tian
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Junmei Cui
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zefeng Wu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaodong Cao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Chunmei Xu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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Box ICH, Matthews BJ, Marshall KE. Molecular evidence of intertidal habitats selecting for repeated ice-binding protein evolution in invertebrates. J Exp Biol 2022; 225:274373. [PMID: 35258616 DOI: 10.1242/jeb.243409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/20/2021] [Indexed: 12/21/2022]
Abstract
Ice-binding proteins (IBPs) have evolved independently in multiple taxonomic groups to improve their survival at sub-zero temperatures. Intertidal invertebrates in temperate and polar regions frequently encounter sub-zero temperatures, yet there is little information on IBPs in these organisms. We hypothesized that there are far more IBPs than are currently known and that the occurrence of freezing in the intertidal zone selects for these proteins. We compiled a list of genome-sequenced invertebrates across multiple habitats and a list of known IBP sequences and used BLAST to identify a wide array of putative IBPs in those invertebrates. We found that the probability of an invertebrate species having an IBP was significantly greater in intertidal species than in those primarily found in open ocean or freshwater habitats. These intertidal IBPs had high sequence similarity to fish and tick antifreeze glycoproteins and fish type II antifreeze proteins. Previously established classifiers based on machine learning techniques further predicted ice-binding activity in the majority of our newly identified putative IBPs. We investigated the potential evolutionary origin of one putative IBP from the hard-shelled mussel Mytilus coruscus and suggest that it arose through gene duplication and neofunctionalization. We show that IBPs likely readily evolve in response to freezing risk and that there is an array of uncharacterized IBPs, and highlight the need for broader laboratory-based surveys of the diversity of ice-binding activity across diverse taxonomic and ecological groups.
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Affiliation(s)
- Isaiah C H Box
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, CanadaV6T 1Z4
| | - Benjamin J Matthews
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, CanadaV6T 1Z4
| | - Katie E Marshall
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, CanadaV6T 1Z4
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Dong X, Liu Z, Mi W, Xu C, Xu M, Zhou Y, Zhen G, Cao X, Fang X, Mi C. Overexpression of BrAFP1 gene from winter rapeseed (Brassica rapa) confers cold tolerance in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 155:338-345. [PMID: 32798902 DOI: 10.1016/j.plaphy.2020.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Antifreeze proteins (AFPs) can bind to ice crystals and restrain the formation of larger crystals, a strategy vital to the survival of plants in freezing environments. The BrAFP1 from winter rapeseed cultivars 'Longyou 7' with high cold tolerance was cloned and overexpressed in Arabidopsis. BrAFP1 was localized in the cytoplasm and nucleus. Under cold stress, SOD activity and free proline content were higher, MDA content and relative conductivity were lower in transgenic lines than those in wide-type Arabidopsis. Frostbite of transgenic plants was minimized, whereas frostbite of the Arabidopsis afp1 mutant was severe. Transition of the amino acid at position 17 of BrAFP1 was related to the increased winter survival of the rapeseed cultivar. Cultivars with higher survival rates had a predilection for tyrosine, not tryptophan, at the 17th site in the amino sequence of BrAFP1. Transcription of BrAFP1 was induced more rapidly, and the expression of the gene was also higher, in Longyou 7 than that in Tianyou 4 under cold stress. Overall, the high expression of BrAPF1 confers more cold-tolerance in Longyou 7.
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Affiliation(s)
- Xiaoyun Dong
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zigang Liu
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Wenbo Mi
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Chunmei Xu
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Minxia Xu
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ya Zhou
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Guoqiang Zhen
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiaodong Cao
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xinlin Fang
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Chao Mi
- Gansu Provincial Key Laboratory of AridLand Crop Sciences, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
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Extraction of antifreeze proteins from cold acclimated leaves of Drimys angustifolia and their application to star fruit (Averrhoa carambola) freezing. Food Chem 2019; 289:65-73. [DOI: 10.1016/j.foodchem.2019.03.055] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 03/07/2019] [Accepted: 03/11/2019] [Indexed: 12/14/2022]
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Baalsrud HT, Tørresen OK, Solbakken MH, Salzburger W, Hanel R, Jakobsen KS, Jentoft S. De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data. Mol Biol Evol 2018; 35:593-606. [PMID: 29216381 PMCID: PMC5850335 DOI: 10.1093/molbev/msx311] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
New genes can arise through duplication of a pre-existing gene or de novo from non-coding DNA, providing raw material for evolution of new functions in response to a changing environment. A prime example is the independent evolution of antifreeze glycoprotein genes (afgps) in the Arctic codfishes and Antarctic notothenioids to prevent freezing. However, the highly repetitive nature of these genes complicates studies of their organization. In notothenioids, afgps evolved from an extant gene, yet the evolutionary origin of afgps in codfishes is unknown. Here, we demonstrate that afgps in codfishes have evolved de novo from non-coding DNA 13-18 Ma, coinciding with the cooling of the Northern Hemisphere. Using whole-genome sequence data from several codfishes and notothenioids, we find higher copy number of afgp in species exposed to more severe freezing suggesting a gene dosage effect. Notably, antifreeze function is lost in one lineage of codfishes analogous to the afgp losses in non-Antarctic notothenioids. This indicates that selection can eliminate the antifreeze function when freezing is no longer imminent. In addition, we show that evolution of afgp-assisting antifreeze potentiating protein genes (afpps) in notothenioids coincides with origin and lineage-specific losses of afgp. The origin of afgps in codfishes is one of the first examples of an essential gene born from non-coding DNA in a non-model species. Our study underlines the power of comparative genomics to uncover past molecular signatures of genome evolution, and further highlights the impact of de novo gene origin in response to a changing selection regime.
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Affiliation(s)
- Helle Tessand Baalsrud
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Ole Kristian Tørresen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Monica Hongrø Solbakken
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Walter Salzburger
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Reinhold Hanel
- Institute of Fisheries Ecology, Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Hamburg, Germany
| | - Kjetill S Jakobsen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
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Provesi JG, Valentim Neto PA, Arisi ACM, Amante ER. Antifreeze proteins in naturally cold acclimated leaves of Drimys angustifolia, Senecio icoglossus, and Eucalyptus ssp. BRAZILIAN JOURNAL OF FOOD TECHNOLOGY 2016. [DOI: 10.1590/1981-6723.11016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Summary Antifreeze proteins (AFPs) present in plants may inhibit ice recrystallization even at low concentrations, and show potential application to many frozen foods. This study evaluated the presence of antifreeze proteins in naturally cold acclimated and non-acclimated leaves of Drimys angustifolia, Senecio icoglossus and Eucalyptus ssp. No proteins were detected in apoplastic extracts of Eucalyptus ssp. Extracts of cold acclimated and non-acclimated S. icoglossus showed protein concentrations of 42.89 and 17.76 µg mL-1, both with bands between 25 and 37 kDa in the SDS-PAGE. However, they did not inhibit recrystallization. The extract of cold acclimated D. angustifolia contained a protein concentration of 95.17 µg mL-1, almost five times higher than the extract of non-acclimated D. angustifolia. In the extract of cold acclimated D. angustifolia, there was presence of ice recrystallization inhibitors. This extract showed a protein band just below 37 kDa and another more intense band between 20 and 25 kDa. It is the first time that the presence of antifreeze proteins in this species is being described.
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PROVESI JG, AMANTE ER. Revisão: Proteínas anticongelantes – uma tecnologia emergente para o congelamento de alimentos. BRAZILIAN JOURNAL OF FOOD TECHNOLOGY 2015. [DOI: 10.1590/1981-6723.7714] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Um dos métodos mais tradicionais na conservação de alimentos, o congelamento também pode alterar de forma significativa as características do produto. Grandes cristais de gelo provocam alteração na textura e/ou danos a membranas e componentes celulares. As técnicas de congelamento rápido formam cristais de gelo menores do que o processo lento, porém as flutuações de temperatura durante a distribuição e transporte podem promover o crescimento dos cristais. Esse processo é conhecido como recristalização e é uma barreira na utilização do congelamento como método de conservação em muitos casos. O uso de crioprotetores tradicionais, como a sacarose, é uma alternativa limitada, uma vez que concentrações elevadas são requeridas. Na década de 1970, foi descrita em peixes de águas frias uma classe de proteínas que, em baixa concentração, pode interagir e influenciar o crescimento do cristal de gelo. Elas foram chamadas de proteínas anticongelantes (PACs), sendo encontradas também em plantas, animais e micro-organismos ambientados a baixas temperaturas. Essas proteínas podem intervir no processo de formação do núcleo inicial do gelo, reduzir o ponto de congelamento da água, ou, ainda, inibir a recristalização, principalmente para PACs de vegetais. Há diversos trabalhos publicados e algumas patentes registradas para o uso de PACs em diversos alimentos, como lácteos, carnes, massas, frutas e hortaliças, conservando de melhor forma as características originais do alimento. Atualmente, o custo ainda é uma barreira para utilização comercial das PACs. Contudo, a descoberta de novas fontes pode reduzir seu custo e tornar essas proteínas uma ferramenta efetiva na manutenção da textura de alimentos congelados. Baseada em trabalhos que avaliaram aspectos químicos das PACs e exemplos de sua aplicação, esta revisão tem como objetivo principal apresentar as características gerais das PACs e discutir sobre sua utilização.
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Deng LQ, Yu HQ, Liu YP, Jiao PP, Zhou SF, Zhang SZ, Li WC, Fu FL. Heterologous expression of antifreeze protein gene AnAFP from Ammopiptanthus nanus enhances cold tolerance in Escherichia coli and tobacco. Gene 2014; 539:132-40. [PMID: 24502990 DOI: 10.1016/j.gene.2014.01.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 01/02/2014] [Accepted: 01/03/2014] [Indexed: 11/23/2022]
Abstract
Antifreeze proteins are a class of polypeptides produced by certain animals, plants, fungi and bacteria that permit their survival under the subzero environments. Ammopiptanthus nanus is the unique evergreen broadleaf bush endemic to the Mid-Asia deserts. It survives at the west edge of the Tarim Basin from the disappearance of the ancient Mediterranean in the Tertiary Period. Its distribution region is characterized by the arid climate and extreme temperatures, where the extreme temperatures range from -30 °C to 40 °C. In the present study, the antifreeze protein gene AnAFP of A. nanus was used to transform Escherichia coli and tobacco, after bioinformatics analysis for its possible function. The transformed E. coli strain expressed the heterologous AnAFP gene under the induction of isopropyl β-D-thiogalactopyranoside, and demonstrated significant enhancement of cold tolerance. The transformed tobacco lines expressed the heterologous AnAFP gene in response to cold stress, and showed a less change of relative electrical conductivity under cold stress, and a less wilting phenotype after 16 h of -3 °C cold stress and thawing for 1h than the untransformed wild-type plants. All these results imply the potential value of the AnAFP gene to be used in genetic modification of commercially important crops for improvement of cold tolerance.
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Affiliation(s)
- Long-Qun Deng
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Hao-Qiang Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Yan-Ping Liu
- Faculty of Plant Science, Tarim University, Alar, Xinjiang 843300, PR China
| | - Pei-Pei Jiao
- Faculty of Plant Science, Tarim University, Alar, Xinjiang 843300, PR China
| | - Shu-Feng Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Su-Zhi Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Wan-Chen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China.
| | - Feng-Ling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China.
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