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Rahlff J, Westmeijer G, Weissenbach J, Antson A, Holmfeldt K. Surface microlayer-mediated virome dissemination in the Central Arctic. MICROBIOME 2024; 12:218. [PMID: 39449105 PMCID: PMC11515562 DOI: 10.1186/s40168-024-01902-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 08/06/2024] [Indexed: 10/26/2024]
Abstract
BACKGROUND Aquatic viruses act as key players in shaping microbial communities. In polar environments, they face significant challenges such as limited host availability and harsh conditions. However, due to the restricted accessibility of these ecosystems, our understanding of viral diversity, abundance, adaptations, and host interactions remains limited. RESULTS To fill this knowledge gap, we studied viruses from atmosphere-close aquatic ecosystems in the Central Arctic and Northern Greenland. Aquatic samples for virus-host analysis were collected from ~60 cm depth and the submillimeter surface microlayer (SML) during the Synoptic Arctic Survey 2021 on icebreaker Oden in the Arctic summer. Water was sampled from a melt pond and open water before undergoing size-fractioned filtration, followed by genome-resolved metagenomic and cultivation investigations. The prokaryotic diversity in the melt pond was considerably lower compared to that of open water. The melt pond was dominated by a Flavobacterium sp. and Aquiluna sp., the latter having a relatively small genome size of 1.2 Mb and the metabolic potential to generate ATP using the phosphate acetyltransferase-acetate kinase pathway. Viral diversity on the host fraction (0.2-5 µm) of the melt pond was strikingly limited compared to that of open water. From the 1154 viral operational taxonomic units (vOTUs), of which two-thirds were predicted bacteriophages, 17.2% encoded for auxiliary metabolic genes (AMGs) with metabolic functions. Some AMGs like glycerol-3-phosphate cytidylyltransferase and ice-binding like proteins might serve to provide cryoprotection for the host. Prophages were often associated with SML genomes, and two active prophages of new viral genera from the Arctic SML strain Leeuwenhoekiella aequorea Arc30 were induced. We found evidence that vOTU abundance in the SML compared to that of ~60 cm depth was more positively correlated with the distribution of a vOTU across five different Arctic stations. CONCLUSIONS The results indicate that viruses employ elaborate strategies to endure in extreme, host-limited environments. Moreover, our observations suggest that the immediate air-sea interface serves as a platform for viral distribution in the Central Arctic. Video Abstract.
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Affiliation(s)
- Janina Rahlff
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.
- Aero-Aquatic Virus Research Group, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany.
| | - George Westmeijer
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Julia Weissenbach
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Alfred Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Karin Holmfeldt
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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2
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Kim E, Kwon GS, Choi S, Kim SY, Heo KY, Kim YS, Kim CY, Kim S, Jeong JC, Hwang J, Lee JH, Lee JH, Moh SH. Potential role of ice-binding protein in mitochondria-lipid and ATP mechanisms during freezing of plant callus. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108866. [PMID: 39002307 DOI: 10.1016/j.plaphy.2024.108866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/15/2024]
Abstract
Plant calli, a perpetually undifferentiated cell culture, have defects in maintaining their genetic fidelity during prolonged tissue culture. Cryopreservation using ice-binding proteins (IBP) is a potential solution. Despite a few studies on cryopreservation using IBPs in plant calli, detailed insights into the intracellular metabolism during freezing, thawing, and re-induction remain sparse. This study investigated and employed IBP from polar yeast Leucosporidium sp. (LeIBP) in the cryopreservation process across diverse taxa, including gymnosperms, monocots, dicots, and woody plants. Molecular-level analyses encompassing reactive oxygen species levels, mitochondrial function, and ATP and lipophilic compounds content were conducted. The results across nine plant species revealed the effects of LeIBP on callus competency post-thawing, along with enhanced survival rates, reactive oxygen species reduction, and restored metabolic activities to the level of those of fresh calli. Moreover, species-specific survival optimization with LeIBP treatments and morphological assessments revealed intriguing extracellular matrix structural changes post-cryopreservation, suggesting a morphological strategy for maintaining the original cellular states and paracrine signaling. This study pioneered the comprehensive application of LeIBP in plant callus cryopreservation, alleviating cellular stress and enhancing competence. Therefore, our findings provide new insights into the identification of optimal LeIBP concentrations, confirmation of genetic conformity post-thawing, and the intracellular metabolic mechanisms of cryopreservation advancements in plant research, thereby addressing the challenges associated with long-term preservation and reducing labor-intensive cultivation processes. This study urges a shift towards molecular-level assessments in cryopreservation protocols for plant calli, advocating a deeper understanding of callus re-induction mechanisms and genetic fidelity post-thawing.
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Affiliation(s)
- Euihyun Kim
- Plant cell Research Institute of BIO-FD&C Co. Ltd., Incheon, 21990, South Korea
| | - Gi-Sok Kwon
- Plant cell Research Institute of BIO-FD&C Co. Ltd., Incheon, 21990, South Korea
| | - Sunmee Choi
- Plant cell Research Institute of BIO-FD&C Co. Ltd., Incheon, 21990, South Korea
| | - Soo-Yun Kim
- Plant cell Research Institute of BIO-FD&C Co. Ltd., Incheon, 21990, South Korea
| | - Kyeong Yeon Heo
- Plant cell Research Institute of BIO-FD&C Co. Ltd., Incheon, 21990, South Korea
| | - Young Soon Kim
- Korea Research Institute of Bioscience and Biotechnology, South Korea
| | - Cha Young Kim
- Biological Resource Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Jeongeup, 56212, South Korea
| | - Soyoung Kim
- Biological Resource Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Jeongeup, 56212, South Korea; Department of Plant Biotechnology, College of Agriculture and Life Science, Chonnam National University, Gwangju, 61186, South Korea
| | - Jae Cheol Jeong
- Biological Resource Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Jeongeup, 56212, South Korea
| | - Jisub Hwang
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon, 21990, South Korea; Department of Polar Sciences, University of Science and Technology, Incheon, 21990, South Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon, 21990, South Korea; Department of Polar Sciences, University of Science and Technology, Incheon, 21990, South Korea
| | - Jeong Hun Lee
- Plant cell Research Institute of BIO-FD&C Co. Ltd., Incheon, 21990, South Korea
| | - Sang Hyun Moh
- Plant cell Research Institute of BIO-FD&C Co. Ltd., Incheon, 21990, South Korea.
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3
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Uko MP, Umana SI, Iwatt IJ, Udoekong NS, Mgbechidinma CL, Adie FU, Akan OD. Microbial ice-binding structures: A review of their applications. Int J Biol Macromol 2024; 275:133670. [PMID: 38971293 DOI: 10.1016/j.ijbiomac.2024.133670] [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: 03/12/2024] [Revised: 06/02/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024]
Abstract
Microorganisms' ice-binding structures (IBS) are macromolecules with potential commercial value in agriculture, food technology, material technology, cryobiology, and medicine. Microbial ice-structuring or microbial ice-binding particles, with their multi-applications, are simple to use, effective in low amounts, non-toxic, and environmentally friendly. Due to their source and composition diversities, microbial ice-binding structures are gaining attention because they are useable in various conditions. Some microorganisms also produce structures with dual ice-nucleating and anti-freezing properties. Structures that promote ice formation (ice nucleating particles- INPs) act as ice nuclei, lowering the energy barrier between supercooled liquid and ice, causing ice crystals to form. In contrast, anti-freeze particles (AFPs) prevent ice formation and recrystallization through several mechanisms, including disturbing the formation of string hydrogen bonds amongst water molecules, melting already formed ice crystals, and preventing crystal formation by binding to specific sites. Knowledge of the type and function of microbial ice-binding structures lends fundamental insight for possible scaling the production of cheap, functional, and advanced microbial structure-inspired mimics and by-products. This review focuses on microbial ice-binding structures and their potential uses in the food, medicinal, environmental, and agricultural sectors.
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Affiliation(s)
- Mfoniso Peter Uko
- Faculty of Biological Science, Akwa-Ibom State University, Akwa-Ibom State, Uyo 1167, Nigeria
| | - Senyene Idorenyin Umana
- Faculty of Biological Science, Akwa-Ibom State University, Akwa-Ibom State, Uyo 1167, Nigeria; Department of Microbiology, Faculty of Michael Okpara of Agriculture, Umudike, Nigeria
| | - Ifiok Joseph Iwatt
- Center for Wetlands and Wastes Management Studies, Faculty of Agriculture, University of Uyo, Uyo, Nigeria
| | | | - Chiamaka Linda Mgbechidinma
- School of Life Sciences, Centre for Cell and Development Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; Department of Microbiology, University of Ibadan, Ibadan 200243, Nigeria
| | - Francisca Upekiema Adie
- Department of Microbiology, Faculty of Biological Sciences, Cross River State University of Technology, Calabar, Nigeria
| | - Otobong Donald Akan
- Faculty of Biological Science, Akwa-Ibom State University, Akwa-Ibom State, Uyo 1167, Nigeria; College of Food Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha 410004, China.
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4
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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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5
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Ramasamy KP, Mahawar L, Rajasabapathy R, Rajeshwari K, Miceli C, Pucciarelli S. Comprehensive insights on environmental adaptation strategies in Antarctic bacteria and biotechnological applications of cold adapted molecules. Front Microbiol 2023; 14:1197797. [PMID: 37396361 PMCID: PMC10312091 DOI: 10.3389/fmicb.2023.1197797] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Abstract
Climate change and the induced environmental disturbances is one of the major threats that have a strong impact on bacterial communities in the Antarctic environment. To cope with the persistent extreme environment and inhospitable conditions, psychrophilic bacteria are thriving and displaying striking adaptive characteristics towards severe external factors including freezing temperature, sea ice, high radiation and salinity which indicates their potential in regulating climate change's environmental impacts. The review illustrates the different adaptation strategies of Antarctic microbes to changing climate factors at the structural, physiological and molecular level. Moreover, we discuss the recent developments in "omics" approaches to reveal polar "blackbox" of psychrophiles in order to gain a comprehensive picture of bacterial communities. The psychrophilic bacteria synthesize distinctive cold-adapted enzymes and molecules that have many more industrial applications than mesophilic ones in biotechnological industries. Hence, the review also emphasizes on the biotechnological potential of psychrophilic enzymes in different sectors and suggests the machine learning approach to study cold-adapted bacteria and engineering the industrially important enzymes for sustainable bioeconomy.
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Affiliation(s)
| | - Lovely Mahawar
- Department of Plant Physiology, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, Nitra, Slovakia
| | - Raju Rajasabapathy
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | | | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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6
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Du J, Zhang Y, Xin D, Xin Y, Zhang J. Antarcticirhabdus aurantiaca gen. nov., sp. nov., isolated from Antarctic gravel soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37068122 DOI: 10.1099/ijsem.0.005814] [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: 04/18/2023] Open
Abstract
Strain R10T was isolated from a gravel soil sample obtained from Deception Island, Antarctica. The isolate was a Gram-stain-negative, strictly aerobic, motile, short-rod-shaped bacterium, and its colonies were orange yellow in colour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R10T belonged to the family Aurantimonadaceae and shared highest sequence similarity with Jiella aquimaris LZB041T (96.3 % sequence similarity), Aurantimonas aggregata R14M6T (96.0 %) and Aureimonas frigidaquae JCM 14755T (96.0 %). Phylogenetic analysis showed that strain R10T affiliated with members of the family Aurantimonadaceae and represented an independent lineage. Growth occurred at 10-37 °C (optimum, 28-32 °C), up to 1.0 % (w/v) NaCl (optimum, 0 %) and pH 5.5-9.0 (optimum, pH 7.0). The major respiratory quinone of strain R10T was Q-10. Its major fatty acids were C18 : 1 ω7c and C16 : 0. The polar lipid profile of strain R10T comprised diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, two unknown phospholipids and two unknown aminophospholipids. The genome of strain R10T was 5.92 Mbp with a G+C content of 69.1 % based on total genome calculations. Average nucleotide identity (ANI) values between R10T and other related species of the family Aurantimonadaceae were found to be low (ANIm <87.0 %, ANIb <75.0 % and OrthoANIu <77.0 %). Furthermore, digital DNA-DNA hybridization (dDDH) and average amino acid identity (AAI) values between strain R10T and the closely related species ranged from 19.5-20.6% and from 60.6-64.0 %, respectively. Based on the results of our phylogenetic, phenotypic, genotypic and chemotaxonomic analyses, it is concluded that strain R10T represents a novel genus and species of the family Aurantimonadaceae, for which the name Antarcticirhabdus aurantiaca gen. nov., sp. nov. is proposed. The type strain is R10T (=KCTC 72466T=CGMCC 1.17155T).
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Affiliation(s)
- Jie Du
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Ying Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Di Xin
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Yuhua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jianli Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
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7
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Ferheen I, Ahmed Z, Alonazi WB, Pessina A, Ibrahim M, Pucciarelli S, Bokhari H. Diverse Repertoire and Relationship of Exopolysaccharide Genes in Cold-Adapted Acinetobacter sp. CUI-P1 Revealed by Comparative Genome Analysis. Microorganisms 2023; 11:microorganisms11040885. [PMID: 37110308 PMCID: PMC10143279 DOI: 10.3390/microorganisms11040885] [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: 02/21/2023] [Revised: 03/18/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
This study focused on the exploration of microbial communities inhabiting extreme cold environments, such as the Passu and Pisan glaciers of Pakistan, and their potential utilization in industrial applications. Among the 25 initially screened strains, five were found to be suitable candidates for exopolysaccharide (EPS) production, with strain CUI-P1 displaying the highest yield of 7230.5 mg/L compared to the other four strains. The purified EPS from CUI-P1 was tested for its ability to protect probiotic bacteria and E. coli expressing green fluorescence protein (HriGFP) against extreme cold temperatures, and it exhibited excellent cryoprotectant and emulsification activity, highlighting its potential use in the biotechnological industry. Furthermore, the genome of Acinetobacter sp., CUI-P1 comprised 199 contigs, with a genome size of 10,493,143bp and a G + C content of 42%, and showed 98.197% nucleotide identity to the type genome of Acinetobacter baumannii ATCC 17978. These findings offer promising avenues for the application of EPS as a cryoprotectant, an essential tool in modern biotechnology.
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Affiliation(s)
- Ifra Ferheen
- Department of Biosciences, COMSATS University Islamabad, Islamabad 44000, Pakistan
| | - Zaheer Ahmed
- Department of Nutritional Sciences and Environmental Design, Allama Iqbal Open University, Islamabad 44000, Pakistan
| | - Wadi B Alonazi
- Health Administration Department, College of Business Administration, King Saud University, Riyadh 11587, Saudi Arabia
| | - Alex Pessina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Muhammad Ibrahim
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal 55000, Pakistan
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy
| | - Habib Bokhari
- Department of Microbiology, Kohsar University Murree, Murree 47150, Pakistan
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8
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Dorrell RG, Kuo A, Füssy Z, Richardson EH, Salamov A, Zarevski N, Freyria NJ, Ibarbalz FM, Jenkins J, Pierella Karlusich JJ, Stecca Steindorff A, Edgar RE, Handley L, Lail K, Lipzen A, Lombard V, McFarlane J, Nef C, Novák Vanclová AM, Peng Y, Plott C, Potvin M, Vieira FRJ, Barry K, de Vargas C, Henrissat B, Pelletier E, Schmutz J, Wincker P, Dacks JB, Bowler C, Grigoriev IV, Lovejoy C. Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae. Life Sci Alliance 2023; 6:6/3/e202201833. [PMID: 36522135 PMCID: PMC9756366 DOI: 10.26508/lsa.202201833] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.
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Affiliation(s)
- Richard G Dorrell
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zoltan Füssy
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Elisabeth H Richardson
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikola Zarevski
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Nastasia J Freyria
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Federico M Ibarbalz
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Jerry Jenkins
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Juan Jose Pierella Karlusich
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Andrei Stecca Steindorff
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robyn E Edgar
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Lori Handley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kathleen Lail
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vincent Lombard
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - John McFarlane
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Charlotte Nef
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Anna Mg Novák Vanclová
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Yi Peng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Marianne Potvin
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Colomban de Vargas
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, Roscoff, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eric Pelletier
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Patrick Wincker
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Connie Lovejoy
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
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9
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Submilligram Level of Beetle Antifreeze Proteins Minimize Cold-Induced Cell Swelling and Promote Cell Survival. Biomolecules 2022; 12:biom12111584. [PMID: 36358934 PMCID: PMC9687565 DOI: 10.3390/biom12111584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 12/04/2022] Open
Abstract
Hypothermic (cold) preservation is a limiting factor for successful cell and tissue transplantation where cell swelling (edema) usually develops, impairing cell function. University of Wisconsin (UW) solution, a standard cold preservation solution, contains effective components to suppress hypothermia-induced cell swelling. Antifreeze proteins (AFPs) found in many cold-adapted organisms can prevent cold injury of the organisms. Here, the effects of a beetle AFP from Dendroides canadensis (DAFP-1) on pancreatic β-cells preservation were first investigated. As low as 500 µg/mL, DAFP-1 significantly minimized INS-1 cell swelling and subsequent cell death during 4 °C preservation in UW solution for up to three days. However, such significant cytoprotection was not observed by an AFP from Tenebrio molitor (TmAFP), a structural homologue to DAFP-1 but lacking arginine, at the same levels. The cytoprotective effect of DAFP-1 was further validated with the primary β-cells in the isolated rat pancreatic islets in UW solution. The submilligram level supplement of DAFP-1 to UW solution significantly increased the islet mass recovery after three days of cold preservation followed by rewarming. The protective effects of DAFP-1 in UW solution were discussed at a molecular level. The results indicate the potential of DAFP-1 to enhance cell survival during extended cold preservation.
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10
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John MS, Nagoth JA, Ramasamy KP, Mancini A, Giuli G, Miceli C, Pucciarelli S. Synthesis of Bioactive Silver Nanoparticles Using New Bacterial Strains from an Antarctic Consortium. Mar Drugs 2022; 20:md20090558. [PMID: 36135747 PMCID: PMC9505403 DOI: 10.3390/md20090558] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
In this study, we report on the synthesis of silver nanoparticles (AgNPs) achieved by using three bacterial strains Rhodococcus, Brevundimonas and Bacillus as reducing and capping agents, newly isolated from a consortium associated with the Antarctic marine ciliate Euplotes focardii. After incubation of these bacteria with a 1 mM solution of AgNO3 at 22 °C, AgNPs were synthesized within 24 h. Unlike Rhodococcus and Bacillus, the reduction of Ag+ from AgNO3 into Ag0 has never been reported for a Brevundimonas strain. The maximum absorbances of these AgNPs in the UV-Vis spectra were in the range of 404 nm and 406 nm. EDAX spectra showed strong signals from the Ag atom and medium signals from C, N and O due to capping protein emissions. TEM analysis showed that the NPs were spherical and rod-shaped, with sizes in the range of 20 to 50 nm, and they were clustered, even though not in contact with one another. Besides aggregation, all the AgNPs showed significant antimicrobial activity. This biosynthesis may play a dual role: detoxification of AgNO3 and pathogen protection against both the bacterium and ciliate. Biosynthetic AgNPs also represent a promising alternative to conventional antibiotics against common nosocomial pathogens.
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Affiliation(s)
- Maria Sindhura John
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joseph Amruthraj Nagoth
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy
| | - Kesava Priyan Ramasamy
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy
| | - Alessio Mancini
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy
| | - Gabriele Giuli
- School of Sciences and Technology, University of Camerino, 62032 Camerino, Italy
| | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy
- Correspondence:
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11
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Tran-Guzman A, Moradian R, Walker C, Cui H, Corpuz M, Gonzalez I, Nguyen C, Meza P, Wen X, Culty M. Toxicity Profiles and Protective Effects of Antifreeze Proteins From Insect in Mammalian Models. Toxicol Lett 2022; 368:9-23. [PMID: 35901986 PMCID: PMC10174066 DOI: 10.1016/j.toxlet.2022.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/24/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022]
Abstract
Antifreeze proteins (AFPs), found in many cold-adapted organisms, can protect them from cold and freezing damages and have thus been considered as additional protectants in current cold tissue preservation solutions that generally include electrolytes, osmotic agents, colloids and antioxidants, to reduce the loss of tissue viability associated with cold-preservation. Due to the lack of toxicity profile studies on AFPs, their inclusion in cold preservation solutions has been a trial-and-error process limiting the development of AFPs' application in cold preservation. To assess the feasibility of translating the technology of AFPs for mammalian cell cold or cryopreservation, we determined the toxicity profile of two highly active beetle AFPs, DAFP1 and TmAFP, from Dendroides canadensis and Tenebrio molitor in this study. Toxicity was examined on a panel of representative mammalian cell lines including testicular spermatogonial stem cells and Leydig cells, macrophages, and hepatocytes. Treatments with DAFP1 and TmAFP at up to 500μg/mL for 48 and 72hours were safe in three of the cell lines, except for a 20% decrease in spermatogonia treated with TmAFP. However, both AFPs at 500μg/mL or below reduced hepatocyte viability by 20 to 40% at 48 and 72h. At 1000μg/mL, DAFP1 and TmAFP reduced viability in most cell lines. While spermatogonia and Leydig cell functions were not affected by 1000μg/mL DAFP1, this treatment induced inflammatory responses in macrophages. Adding 1000μg/ml DAFP1 to rat kidneys stored at 4°C for 48hours protected the tissues from cold-related damage, based on tissue morphology and gene and protein expression of two markers of kidney function. However, DAFP1 and TmAFP did not prevent the adverse effects of cold on kidneys over 72hours. Overall, DAFP1 is less toxic at high dose than TmAFP, and has potential for use in tissue preservation at doses up to 500μg/mL. However, careful consideration must be taken due to the proinflammatory potential of DAFP1 on macrophages at higher doses and the heighten susceptibility of hepatocytes to both AFPs.
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Affiliation(s)
- A Tran-Guzman
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - R Moradian
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - C Walker
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - H Cui
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - M Corpuz
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - I Gonzalez
- Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles, CA, USA
| | - C Nguyen
- Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles, CA, USA
| | - P Meza
- Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles, CA, USA
| | - X Wen
- Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles, CA, USA
| | - M Culty
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.
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12
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Freyria NJ, Kuo A, Chovatia M, Johnson J, Lipzen A, Barry KW, Grigoriev IV, Lovejoy C. Salinity tolerance mechanisms of an Arctic Pelagophyte using comparative transcriptomic and gene expression analysis. Commun Biol 2022; 5:500. [PMID: 35614207 PMCID: PMC9133084 DOI: 10.1038/s42003-022-03461-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 05/09/2022] [Indexed: 11/09/2022] Open
Abstract
Little is known at the transcriptional level about microbial eukaryotic adaptations to short-term salinity change. Arctic microalgae are exposed to low salinity due to sea-ice melt and higher salinity with brine channel formation during freeze-up. Here, we investigate the transcriptional response of an ice-associated microalgae over salinities from 45 to 8. Our results show a bracketed response of differential gene expression when the cultures were exposed to progressively decreasing salinity. Key genes associated with salinity changes were involved in specific metabolic pathways, transcription factors and regulators, protein kinases, carbohydrate active enzymes, and inorganic ion transporters. The pelagophyte seemed to use a strategy involving overexpression of Na+-H+ antiporters and Na+ -Pi symporters as salinity decreases, but the K+ channel complex at higher salinities. Specific adaptation to cold saline arctic conditions was seen with differential expression of several antifreeze proteins, an ice-binding protein and an acyl-esterase involved in cold adaptation.
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Affiliation(s)
- Nastasia J Freyria
- Département de biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada.
- Québec Océan, Département de biologie, Université Laval, Québec, Canada.
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mansi Chovatia
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie W Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Connie Lovejoy
- Département de biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada.
- Québec Océan, Département de biologie, Université Laval, Québec, Canada.
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13
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Ekpo MD, Xie J, Hu Y, Liu X, Liu F, Xiang J, Zhao R, Wang B, Tan S. Antifreeze Proteins: Novel Applications and Navigation towards Their Clinical Application in Cryobanking. Int J Mol Sci 2022; 23:2639. [PMID: 35269780 PMCID: PMC8910022 DOI: 10.3390/ijms23052639] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/16/2022] [Accepted: 02/25/2022] [Indexed: 12/04/2022] Open
Abstract
Antifreeze proteins (AFPs) or thermal hysteresis (TH) proteins are biomolecular gifts of nature to sustain life in extremely cold environments. This family of peptides, glycopeptides and proteins produced by diverse organisms including bacteria, yeast, insects and fish act by non-colligatively depressing the freezing temperature of the water below its melting point in a process termed thermal hysteresis which is then responsible for ice crystal equilibrium and inhibition of ice recrystallisation; the major cause of cell dehydration, membrane rupture and subsequent cryodamage. Scientists on the other hand have been exploring various substances as cryoprotectants. Some of the cryoprotectants in use include trehalose, dimethyl sulfoxide (DMSO), ethylene glycol (EG), sucrose, propylene glycol (PG) and glycerol but their extensive application is limited mostly by toxicity, thus fueling the quest for better cryoprotectants. Hence, extracting or synthesizing antifreeze protein and testing their cryoprotective activity has become a popular topic among researchers. Research concerning AFPs encompasses lots of effort ranging from understanding their sources and mechanism of action, extraction and purification/synthesis to structural elucidation with the aim of achieving better outcomes in cryopreservation. This review explores the potential clinical application of AFPs in the cryopreservation of different cells, tissues and organs. Here, we discuss novel approaches, identify research gaps and propose future research directions in the application of AFPs based on recent studies with the aim of achieving successful clinical and commercial use of AFPs in the future.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Songwen Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (M.D.E.); (J.X.); (Y.H.); (X.L.); (F.L.); (J.X.); (R.Z.); (B.W.)
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14
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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.
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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.
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15
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Shen L, Zhang S, Chen G. Regulated strategies of cold-adapted microorganisms in response to cold: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:68006-68024. [PMID: 34648167 DOI: 10.1007/s11356-021-16843-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
There are a large number of active cold-adapted microorganisms in the perennial cold environment. Due to their high-efficiency and energy-saving catalytic properties, cold-adapted microorganisms have become valuable natural resources with potential in various biological fields. In this study, a series of cold response strategies for microorganisms were summarized. This mainly involves the regulation of cell membrane fluidity, synthesis of cold adaptation proteins, regulators and metabolic changes, energy supply, and reactive oxygen species. Also, the potential of biocatalysts produced by cold-adapted microorganisms including cold-active enzymes, ice-binding proteins, polyhydroxyalkanoates, and surfactants was introduced, which provided a guidance for expanding its application values. Overall, new insights were obtained on response strategies of microorganisms to cold environments in this review. This will deepen the understanding of the cold tolerance mechanism of cold-adapted microorganisms, thus promoting the establishment and application of low-temperature biotechnology.
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Affiliation(s)
- Lijun Shen
- College of Life Sciences, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China
| | - Sitong Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun, China.
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China.
| | - Guang Chen
- College of Life Sciences, Jilin Agricultural University, Changchun, China.
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China.
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16
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Baskaran A, Kaari M, Venugopal G, Manikkam R, Joseph J, Bhaskar PV. Anti freeze proteins (Afp): Properties, sources and applications - A review. Int J Biol Macromol 2021; 189:292-305. [PMID: 34419548 DOI: 10.1016/j.ijbiomac.2021.08.105] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022]
Abstract
Extreme cold marine and freshwater temperatures (below 4 °C) induce massive deterioration to the cell membranes of organisms resulting in the formation of ice crystals, consequently causing organelle damage or cell death. One of the adaptive mechanisms organisms have evolved to thrive in cold environments is the production of antifreeze proteins with the functional capabilities to withstand frigid temperatures. Antifreeze proteins are extensively identified in different cold-tolerant species and they facilitate the persistence of cold-adapted organisms by decreasing the freezing point of their body fluids. Various structurally diverse types of antifreeze proteins detected possess the ability to modify ice crystal growth by thermal hysteresis and ice recrystallization inhibition. The unique properties of antifreeze proteins have made them a promising resource in industry, biomedicine, food storage and cryobiology. This review collates the findings of the various studies carried out in the past and the recent developments observed in the properties, functional mechanisms, classification, distinct sources and the ever-increasing applications of antifreeze proteins. This review also summarizes the possibilities of the way forward to identify new avenues of research on anti-freeze proteins.
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Affiliation(s)
- Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Gopikrishnan Venugopal
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India.
| | - Jerrine Joseph
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Parli V Bhaskar
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama 403804, Goa, India
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17
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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: 6] [Impact Index Per Article: 2.0] [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.
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18
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Adiram-Filiba N, Ohaion E, Verner G, Schremer A, Nadav-Tsubery M, Lublin-Tennenbaum T, Keinan-Adamsky K, Lucci M, Luchinat C, Ravera E, Goobes G. Structure and Dynamics Perturbations in Ubiquitin Adsorbed or Entrapped in Silica Materials Are Related to Disparate Surface Chemistries Resolved by Solid-State NMR Spectroscopy. Biomacromolecules 2021; 22:3718-3730. [PMID: 34333966 DOI: 10.1021/acs.biomac.1c00495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein immobilization on material surfaces is emerging as a powerful tool in the design of devices and active materials for biomedical and pharmaceutical applications as well as for catalysis. Preservation of the protein's biological functionality is crucial to the design process and is dependent on the ability to maintain its structural and dynamical integrity while removed from the natural surroundings. The scientific techniques to validate the structure of immobilized proteins are scarce and usually provide limited information as a result of poor resolution. In this work, we benchmarked the ability of standard solid-state NMR techniques to resolve the effects of binding to dissimilar silica materials on a model protein. In particular, the interactions between ubiquitin and the surfaces of MCM41, SBA15, and silica formed in situ were tested for their influence on the structure and dynamics of the protein. It is shown that the protein's globular fold in the free state is only slightly perturbed in the three silica materials. Local motions on a residue level that are quenched by immobilization or, conversely, that arise from the process are also detailed. NMR measurements show that these perturbations are unique to each silica material and can serve as reporters of the characteristic surface chemistry.
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Affiliation(s)
| | - Eli Ohaion
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Gilit Verner
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Avital Schremer
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | | | | | | | - Massimo Lucci
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Gil Goobes
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
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19
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Khan NMMU, Arai T, Tsuda S, Kondo H. Characterization of microbial antifreeze protein with intermediate activity suggests that a bound-water network is essential for hyperactivity. Sci Rep 2021; 11:5971. [PMID: 33727595 PMCID: PMC7966756 DOI: 10.1038/s41598-021-85559-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/03/2021] [Indexed: 12/27/2022] Open
Abstract
Antifreeze proteins (AFPs) inhibit ice growth by adsorbing onto specific ice planes. Microbial AFPs show diverse antifreeze activity and ice plane specificity, while sharing a common molecular scaffold. To probe the molecular mechanisms responsible for AFP activity, we here characterized the antifreeze activity and crystal structure of TisAFP7 from the snow mold fungus Typhula ishikariensis. TisAFP7 exhibited intermediate activity, with the ability to bind the basal plane, compared with a hyperactive isoform TisAFP8 and a moderately active isoform TisAFP6. Analysis of the TisAFP7 crystal structure revealed a bound-water network arranged in a zigzag pattern on the surface of the protein's ice-binding site (IBS). While the three AFP isoforms shared the water network pattern, the network on TisAFP7 IBS was not extensive, which was likely related to its intermediate activity. Analysis of the TisAFP7 crystal structure also revealed the presence of additional water molecules that form a ring-like network surrounding the hydrophobic side chain of a crucial IBS phenylalanine, which might be responsible for the increased adsorption of AFP molecule onto the basal plane. Based on these observations, we propose that the extended water network and hydrophobic hydration at IBS together determine the TisAFP activity.
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Affiliation(s)
- N M-Mofiz Uddin Khan
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.,Department of Chemistry, Dhaka University of Engineering and Technology, Gazipur Gazipur, 1700, Bangladesh
| | - Tatsuya Arai
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Sakae Tsuda
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1, Tsukisamu-Higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.,OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8563, Japan
| | - Hidemasa Kondo
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan. .,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1, Tsukisamu-Higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
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20
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Gruneberg AK, Graham LA, Eves R, Agrawal P, Oleschuk RD, Davies PL. Ice recrystallization inhibition activity varies with ice-binding protein type and does not correlate with thermal hysteresis. Cryobiology 2021; 99:28-39. [PMID: 33529683 DOI: 10.1016/j.cryobiol.2021.01.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/07/2021] [Accepted: 01/23/2021] [Indexed: 01/06/2023]
Abstract
Ice-binding proteins (IBPs) inhibit the growth of ice through surface adsorption. In some freeze-resistant fishes and insects, circulating IBPs serve as antifreeze proteins to stop ice growth by lowering the freezing point. Plants are less able to avoid freezing and some use IBPs to minimize the damage caused in the frozen state by ice recrystallization, which is the growth of large ice grains at the expense of small ones. Here we have accurately and reproducibly measured the ice recrystallization inhibition (IRI) activity of over a dozen naturally occurring IBPs from fishes, insects, plants, and microorganisms using a modified 'splat' method on serial dilutions of IBPs whose concentrations were determined by amino acid analysis. The endpoint of IRI, which was scored as the lowest protein concentration at which no recrystallization was observed, varied for the different IBPs over two orders of magnitude from 1000 nM to 5 nM. Moreover, there was no apparent correlation between their IRI levels and reported antifreeze activities. IBPs from insects and fishes had similar IRI activity, even though the insect IBPs are typically 10x more active in freezing point depression. Plant IBPs had weak antifreeze activity but were more effective at IRI. Bacterial IBPs involved in ice adhesion showed both strong freezing point depression and IRI. Two trends did emerge, including that basal plane binding IBPs correlated with stronger IRI activity and larger IBPs had higher IRI activity.
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Affiliation(s)
- Audrey K Gruneberg
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada
| | - Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada
| | - Robert Eves
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada
| | - Prashant Agrawal
- Department of Chemistry, Queen's University. 90 Bader Lane, Kingston, Ontario, K7L2S8, Canada
| | - Richard D Oleschuk
- Department of Chemistry, Queen's University. 90 Bader Lane, Kingston, Ontario, K7L2S8, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University. 18 Stuart Street, Kingston, Ontario, K7L3N6, Canada.
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21
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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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22
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Orlando M, Pucciarelli S, Lotti M. Endolysins from Antarctic Pseudomonas Display Lysozyme Activity at Low Temperature. Mar Drugs 2020; 18:E579. [PMID: 33233712 PMCID: PMC7699920 DOI: 10.3390/md18110579] [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: 10/26/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/18/2022] Open
Abstract
Organisms specialized to thrive in cold environments (so-called psychrophiles) produce enzymes with the remarkable ability to catalyze chemical reactions at low temperature. Cold activity relies on adaptive changes in the proteins' sequence and structural organization that result in high conformational flexibility. As a consequence of flexibility, several such enzymes are inherently heat sensitive. Cold-active enzymes are of interest for application in a number of bioprocesses, where cold activity coupled with easy thermal inactivation can be of advantage. We describe the biochemical and functional properties of two glycosyl hydrolases (named LYS177 and LYS188) of family 19 (GH19), identified in the genome of an Antarctic marine Pseudomonas. Molecular evolutionary analysis placed them in a group of characterized GH19 endolysins active on lysozyme substrates, such as peptidoglycan. Enzyme activity peaks at about 25-35 °C and 40% residual activity is retained at 5 °C. LYS177 and LYS188 are thermolabile, with Tm of 52 and 45 °C and half-lives of 48 and 12 h at 37 °C, respectively. Bioinformatics analyses suggest that low heat stability may be associated to temperature-driven increases in local flexibility occurring mainly in a specific region of the polypeptide that is predicted to contain hot spots for aggregation.
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Affiliation(s)
- Marco Orlando
- Department of Biotechnology and Biosciences, State University of Milano Bicocca, 20126 Milano, Italy;
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy;
| | - Marina Lotti
- Department of Biotechnology and Biosciences, State University of Milano Bicocca, 20126 Milano, Italy;
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23
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Characterization of Ice-Binding Proteins from Sea-Ice Microalgae. Methods Mol Biol 2020. [PMID: 32607989 DOI: 10.1007/978-1-0716-0660-5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Several species of polar microalgae are able to live and thrive in the extreme environment found within sea ice, where ice crystals may reduce the organisms' living space and cause mechanical damage to the cells. Among the strategies adopted by these organisms to cope with the harsh conditions in their environment, ice-binding proteins (IBPs) seem to play a key role and possibly contribute to the success of microalgae in sea ice. Indeed, IBPs from microalgae predominantly belong to the so-called "DUF 3494-IBP" family, which today represents the most widespread IBP family. Since IBPs have the ability to control ice crystal growth, their mechanism of function is of interest for many potential applications. Here, we describe methods for a classical determination of the IBP activity (thermal hysteresis, recrystallization inhibition) and further methods for protein activity characterization (ice pitting assay, determination of the nucleating temperature).
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24
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Vallesi A, Pucciarelli S, Buonanno F, Fontana A, Mangiagalli M. Bioactive molecules from protists: Perspectives in biotechnology. Eur J Protistol 2020; 75:125720. [PMID: 32569992 DOI: 10.1016/j.ejop.2020.125720] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/11/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022]
Abstract
For hundreds of years, mankind has benefited from the natural metabolic processes of microorganisms to obtain basic products such as fermented foods and alcoholic beverages. More recently, microorganisms have been exploited for the production of antibiotics, vitamins and enzymes to be used in medicine and chemical industries. Additionally, several modern drugs, including those for cancer therapy, are natural products or their derivatives. Protists are a still underexplored source of natural products potentially of interest for biotechnological and biomedical applications. This paper focuses on some examples of bioactive molecules from protists and associated bacteria and their possible use in biotechnology.
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Affiliation(s)
- Adriana Vallesi
- School of Biosciences and Veterinary Medicine, Università degli Studi di Camerino, Camerino (MC), Italy.
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, Università degli Studi di Camerino, Camerino (MC), Italy.
| | - Federico Buonanno
- Laboratory of Protistology and Biology Education, Department of E.C.H.T. Università degli Studi di Macerata, Macerata, Italy
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, CNR-Institute of Biomolecular Chemistry, Pozzuoli, Napoli, Italy
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
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25
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Fayter A, Huband S, Gibson MI. X-ray diffraction to probe the kinetics of ice recrystallization inhibition. Analyst 2020; 145:3666-3677. [PMID: 32266881 DOI: 10.1039/c9an02141h] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Understanding the nucleation and growth of ice is crucial in fields ranging from infrastructure maintenance, to the environment, and to preserving biologics in the cold chain. Ice binding and antifreeze proteins are potent ice recrystallization inhibitors (IRI), and synthetic materials that mimic this function have emerged, which may find use in biotechnology. To evaluate IRI activity, optical microscopy tools are typically used to monitor ice grain size either by end-point measurements or as a function of time. However, these methods provide 2-dimensional information and image analysis is required to extract the data. Here we explore using wide angle X-ray scattering (WAXS/X-ray powder diffraction (XRD)) to interrogate 100's of ice crystals in 3-dimensions as a function of time. Due to the random organization of the ice crystals in the frozen sample, the number of orientations measured by XRD is proportional to the number of ice crystals, which can be measured as a function of time. This method was used to evaluate the activity for a panel of known IRI active compounds, and shows strong agreement with results obtained from cryo-microscopy, as well as being advantageous in that time-dependent ice growth is easily extracted. Diffraction analysis also confirmed, by comparing the obtained diffraction patterns of both ice binding and non-binding additives, that the observed hexagonal ice diffraction patterns obtained cannot be used to determine which crystal faces are being bound. This method may help in the discovery of new IRI active materials as well as enabling kinetic analysis of ice growth.
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Affiliation(s)
- Alice Fayter
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, UK.
| | - Steven Huband
- Department of Physics, University of Warwick, Gibbet Hill Road, CV4 7AL, UK
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, UK. and Warwick Medical School, University of Warwick, Gibbet Hill Road, CV4 7AL, UK
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26
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Mangiagalli M, Brocca S, Orlando M, Lotti M. The “cold revolution”. Present and future applications of cold-active enzymes and ice-binding proteins. N Biotechnol 2020; 55:5-11. [DOI: 10.1016/j.nbt.2019.09.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 09/06/2019] [Accepted: 09/16/2019] [Indexed: 11/24/2022]
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27
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Surís-Valls R, Voets IK. Peptidic Antifreeze Materials: Prospects and Challenges. Int J Mol Sci 2019; 20:E5149. [PMID: 31627404 PMCID: PMC6834126 DOI: 10.3390/ijms20205149] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 12/28/2022] Open
Abstract
Necessitated by the subzero temperatures and seasonal exposure to ice, various organisms have developed a remarkably effective means to survive the harsh climate of their natural habitats. Their ice-binding (glyco)proteins keep the nucleation and growth of ice crystals in check by recognizing and binding to specific ice crystal faces, which arrests further ice growth and inhibits ice recrystallization (IRI). Inspired by the success of this adaptive strategy, various approaches have been proposed over the past decades to engineer materials that harness these cryoprotective features. In this review we discuss the prospects and challenges associated with these advances focusing in particular on peptidic antifreeze materials both identical and akin to natural ice-binding proteins (IBPs). We address the latest advances in their design, synthesis, characterization and application in preservation of biologics and foods. Particular attention is devoted to insights in structure-activity relations culminating in the synthesis of de novo peptide analogues. These are sequences that resemble but are not identical to naturally occurring IBPs. We also draw attention to impactful developments in solid-phase peptide synthesis and 'greener' synthesis routes, which may aid to overcome one of the major bottlenecks in the translation of this technology: unavailability of large quantities of low-cost antifreeze materials with excellent IRI activity at (sub)micromolar concentrations.
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Affiliation(s)
- Romà Surís-Valls
- Laboratory of Self-Organizing Soft Matter, Laboratory of Macro-Organic Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, The Netherlands.
| | - Ilja K Voets
- Laboratory of Self-Organizing Soft Matter, Laboratory of Macro-Organic Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, The Netherlands.
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28
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Xue B, Zhao L, Qin X, Qin M, Lai J, Huang W, Lei H, Wang J, Wang W, Li Y, Cao Y. Bioinspired Ice Growth Inhibitors Based on Self-Assembling Peptides. ACS Macro Lett 2019; 8:1383-1390. [PMID: 35651174 DOI: 10.1021/acsmacrolett.9b00610] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antifreeze proteins (AFPs) are widely found in organisms living in subzero environments. Their strong ability to inhibit ice growth and recrystallization have inspired considerable bioinspired efforts to engineer artificial ice growth inhibitors for cryopreservation. However, it remains challenging to engineer biocompatible and cost-effective synthetic ice growth inhibitors to meet the increasing needs of cryoprotectants in biomedical research and industry. Here we report the design of artificial ice growth inhibitors based on self-assembling peptides. We demonstrate the importance of threonine residues as well as their spatial arrangement for effective ice binding. The engineered self-assembling ice growth inhibiting peptides show moderate ice inhibiting activity including suppression of ice growth rates and retardation of recrystallization of ice crystals. The applications of these peptides in cryopreservation of enzymes and cells were also demonstrated.
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Affiliation(s)
- Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Lishan Zhao
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Xuehua Qin
- College of Life Sciences and Health, Northeastern University, Shenyang 110169, People’s Republic of China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Jiancheng Lai
- State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Wenmao Huang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Hai Lei
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Jianjun Wang
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Ying Li
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, People’s Republic of China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing 210093, People’s Republic of China
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29
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A beetle antifreeze protein protects lactate dehydrogenase under freeze-thawing. Int J Biol Macromol 2019; 136:1153-1160. [DOI: 10.1016/j.ijbiomac.2019.06.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/06/2019] [Accepted: 06/11/2019] [Indexed: 12/19/2022]
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30
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Le Tri D, Childers CL, Adam MK, Ben RN, Storey KB, Biggar KK. Characterization of ice recrystallization inhibition activity in the novel freeze-responsive protein Fr10 from freeze-tolerant wood frogs, Rana sylvatica. J Therm Biol 2019; 84:426-430. [DOI: 10.1016/j.jtherbio.2019.07.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 07/09/2019] [Accepted: 07/27/2019] [Indexed: 11/26/2022]
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31
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Kaleda A, Haleva L, Sarusi G, Pinsky T, Mangiagalli M, Bar Dolev M, Lotti M, Nardini M, Braslavsky I. Saturn-Shaped Ice Burst Pattern and Fast Basal Binding of an Ice-Binding Protein from an Antarctic Bacterial Consortium. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:7337-7346. [PMID: 30198719 DOI: 10.1021/acs.langmuir.8b01914] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ice-binding proteins (IBPs) bind to ice crystals and control their growth, enabling host organisms to adapt to subzero temperatures. By binding to ice, IBPs can affect the shape and recrystallization of ice crystals. The shapes of ice crystals produced by IBPs vary and are partially due to which ice planes the IBPs are bound to. Previously, we have described a bacterial IBP found in the metagenome of the symbionts of Euplotes focardii ( EfcIBP). EfcIBP shows remarkable ice recrystallization inhibition activity. As recrystallization inhibition of IBPs and other materials are important to the cryopreservation of cells and tissues, we speculate that the EfcIBP can play a future role as an ice recrystallization inhibitor in cryopreservation applications. Here we show that EfcIBP results in a Saturn-shaped ice burst pattern, which may be due to the unique ice-plane affinity of the protein that we elucidated using the fluorescent-based ice-plane affinity analysis. EfcIBP binds to ice at a speed similar to that of other moderate IBPs (5 ± 2 mM-1 s-1); however, it is unique in that it binds to the basal and previously unobserved pyramidal near-basal planes, while other moderate IBPs typically bind to the prism and pyramidal planes and not basal or near-basal planes. These insights into EfcIBP allow a better understanding of the recrystallization inhibition for this unique protein.
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Affiliation(s)
- Aleksei Kaleda
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment , The Hebrew University of Jerusalem , Rehovot 7610001 , Israel
- Department of Chemistry and Biotechnology, School of Science , Tallinn University of Technology , Ehitajate tee 5 , 19086 Tallinn , Estonia
| | - Lotem Haleva
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment , The Hebrew University of Jerusalem , Rehovot 7610001 , Israel
| | - Guy Sarusi
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment , The Hebrew University of Jerusalem , Rehovot 7610001 , Israel
| | - Tova Pinsky
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment , The Hebrew University of Jerusalem , Rehovot 7610001 , Israel
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Maya Bar Dolev
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment , The Hebrew University of Jerusalem , Rehovot 7610001 , Israel
| | - Marina Lotti
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Marco Nardini
- Department of Biosciences , University of Milano , Via Celoria 26 , 20133 Milan , Italy
| | - Ido Braslavsky
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment , The Hebrew University of Jerusalem , Rehovot 7610001 , Israel
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32
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Bartels-Rausch T, Montagnat M. The physics and chemistry of ice. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2019; 377:20190138. [PMID: 30982453 PMCID: PMC6501922 DOI: 10.1098/rsta.2019.0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/13/2019] [Indexed: 06/09/2023]
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33
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Liu Q, Liu HC, Zhou YG, Xin YH. Microevolution and Adaptive Strategy of Psychrophilic Species Flavobacterium bomense sp. nov. Isolated From Glaciers. Front Microbiol 2019; 10:1069. [PMID: 31178833 PMCID: PMC6538692 DOI: 10.3389/fmicb.2019.01069] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Numerous mountain glaciers located on the Tibetan Plateau are inhabited by abundant microorganisms. The microorganisms on the glacier surface are exposed to the cold, barren, and high-ultraviolet radiation environments. Although the microbial community composition on glaciers has been revealed by high-throughput sequencing, little is known about the microevolution and adaptive strategy of certain bacterial populations. In this study, we used a polyphasic approach to determine the taxonomic status of 11 psychrophilic Flavobacterium strains isolated from glaciers on the Tibetan Plateau and performed a comparative genomic analysis. The phylogenetic tree based on the concatenated single-copy gene sequences showed the 11 strains clustered together, forming a distinct and novel clade in the genus Flavobacterium. The average nucleotide identity (ANI) values among these strains were higher than 96%. However, the values much lower than 90% between them and related species indicated that they represent a novel species and the name Flavobacterium bomense sp. nov. is proposed. The core and accessory genomes of strains in this new Flavobacterium species showed diverse distinct patterns of gene content and metabolism pathway. In order to infer the driving evolutionary forces of the core genomes, homologous recombination was found to contribute twice as much to nucleotide substitutions as mutations. A series of genes encoding proteins with known or predicted roles in cold adaptation were found in their genomes, for example, cold-shock protein, proteorhodopsin, osmoprotection, and membrane-related proteins. A comparative analysis of the group with optimal growth temperature (OGT) ≤ 20°C and the group with OGT > 20°C of the 32 Flavobacterium type strains and 11 new strains revealed multiple amino acid substitutions, including the decrease of the proline and glutamine content and the increase of the methionine and isoleucine content in the group with OGT ≤ 20°C, which may contribute to increased protein flexibility at low temperatures. Thus, this study discovered a novel Flavobacterium species in glaciers, which has high intraspecific diversity and multiple adaptation mechanisms that enable them to cope and thrive in extreme habitats.
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Affiliation(s)
- Qing Liu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yu-Hua Xin
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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34
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Robles V, Valcarce DG, Riesco MF. The Use of Antifreeze Proteins in the Cryopreservation of Gametes and Embryos. Biomolecules 2019; 9:E181. [PMID: 31075977 PMCID: PMC6571776 DOI: 10.3390/biom9050181] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 01/09/2023] Open
Abstract
The cryopreservation of gametes and embryos is a technique widely used in reproductive biology. This technology helps in the reproductive management of domesticated animals, and it is an important tool for gene banking and for human-assisted reproductive technologies. Antifreeze proteins are naturally present in several organisms exposed to subzero temperatures. The ability for these proteins to inhibit ice recrystallization together with their ability to interact with biological membranes makes them interesting molecules to be used in cryopreservation protocols. This mini-review provides a general overview about the use of antifreeze proteins to improve the short and long term storage of gametes and embryos.
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Affiliation(s)
- Vanesa Robles
- Spanish Institute of Oceanography (IEO), Santander, 39012, Spain.
- MODCELL GROUP, Department of Molecular Biology, Universidad de León, 24071 León, Spain.
| | - David G Valcarce
- Spanish Institute of Oceanography (IEO), Santander, 39012, Spain.
| | - Marta F Riesco
- Spanish Institute of Oceanography (IEO), Santander, 39012, Spain.
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35
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Parrilli E, Tedesco P, Fondi M, Tutino ML, Lo Giudice A, de Pascale D, Fani R. The art of adapting to extreme environments: The model system Pseudoalteromonas. Phys Life Rev 2019; 36:137-161. [PMID: 31072789 DOI: 10.1016/j.plrev.2019.04.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/02/2019] [Indexed: 01/10/2023]
Abstract
Extremophilic microbes have adapted to thrive in ecological niches characterized by harsh chemical/physical conditions such as, for example, very low/high temperature. Living organisms inhabiting these environments have developed peculiar mechanisms to cope with extreme conditions, in such a way that they mark the chemical-physical boundaries of life on Earth. Studying such mechanisms is stimulating from a basic research viewpoint and because of biotechnological applications. Pseudoalteromonas species are a group of marine gamma-proteobacteria frequently isolated from a range of extreme environments, including cold habitats and deep-sea sediments. Since deep-sea floors constitute almost 60% of the Earth's surface and cold temperatures represent the most common of the extreme conditions, the genus Pseudoalteromonas can be considered one of the most important model systems for studying microbial adaptation. Particularly, among all Pseudoalteromonas representatives, P. haloplanktis TAC125 has recently gained a central role. This bacterium was isolated from seawater sampled along the Antarctic ice-shell and is considered one of the model organisms of cold-adapted bacteria. It is capable of thriving in a wide temperature range and it has been suggested as an alternative host for the soluble overproduction of heterologous proteins, given its ability to rapidly multiply at low temperatures. In this review, we will present an overview of the recent advances in the characterization of Pseudoalteromonas strains and, more importantly, in the understanding of their evolutionary and chemical-physical strategies to face such a broad array of extreme conditions. A particular attention will be given to systems-biology approaches in the study of the above-mentioned topics, as genome-scale datasets (e.g. genomics, proteomics, phenomics) are beginning to expand for this group of organisms. In this context, a specific section dedicated to P. haloplanktis TAC125 will be presented to address the recent efforts in the elucidation of the metabolic rewiring of the organisms in its natural environment (Antarctica).
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Affiliation(s)
- Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario M. S. Angelo, Via Cintia, 80126 Napoli, Italy
| | - Pietro Tedesco
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Marco Fondi
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, ViaMadonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario M. S. Angelo, Via Cintia, 80126 Napoli, Italy
| | | | - Donatella de Pascale
- Institute of Protein Biochemistry, CNR, Napoli, Italy, Stazione Zoologica "Anthon Dorn", Villa Comunale, I-80121 Napoli, Italy
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, ViaMadonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy.
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36
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El Assal R, Abou‐Elkacem L, Tocchio A, Pasley S, Matosevic S, Kaplan DL, Zylberberg C, Demirci U. Bioinspired Preservation of Natural Killer Cells for Cancer Immunotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1802045. [PMID: 30937270 PMCID: PMC6425501 DOI: 10.1002/advs.201802045] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Indexed: 05/11/2023]
Abstract
The ability to cryopreserve natural killer (NK) cells has a significant potential in modern cancer immunotherapy. Current cryopreservation protocols cause deterioration in NK cell viability and functionality. This work reports the preservation of human cytokine-activated NK cell viability and function following cryopreservation using a cocktail of biocompatible bioinspired cryoprotectants (i.e., dextran and carboxylated ε-poly-L-lysine). Results demonstrate that the recovered NK cells after cryopreservation and rewarming maintain their viability immediately after thawing at a comparable level to control (dimethyl sulfoxide-based cryopreservation). Although, their viability drops in the first day in culture compared to controls, the cells grow back to a comparable level to controls after 1 week in culture. In addition, the anti-tumor functional activity of recovered NK cells demonstrates higher cytotoxic potency against leukemia cells compared to control. This approach presents a new direction for NK cell preservation, focusing on function and potentially enabling storage and distribution for cancer immunotherapy.
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Affiliation(s)
- Rami El Assal
- Bio‐Acoustic‐MEMS in Medicine (BAMM) LaboratoriesCanary Center at Stanford for Cancer Early DetectionDepartment of RadiologyStanford University School of MedicinePalo AltoCA94304USA
| | - Lotfi Abou‐Elkacem
- Molecular Imaging Program at Stanford (MIPS)Department of RadiologyStanford University School of MedicinePalo AltoCA94304USA
| | - Alessandro Tocchio
- Bio‐Acoustic‐MEMS in Medicine (BAMM) LaboratoriesCanary Center at Stanford for Cancer Early DetectionDepartment of RadiologyStanford University School of MedicinePalo AltoCA94304USA
| | | | - Sandro Matosevic
- Department of Industrial and Physical PharmacyCollege of PharmacyPurdue UniversityWest LafayetteIN47907USA
| | - David L. Kaplan
- Department of Biomedical EngineeringTufts University School of EngineeringMedfordMA02155USA
| | | | - Utkan Demirci
- Bio‐Acoustic‐MEMS in Medicine (BAMM) LaboratoriesCanary Center at Stanford for Cancer Early DetectionDepartment of RadiologyStanford University School of MedicinePalo AltoCA94304USA
- Department of Electrical Engineering (by courtesy)Stanford University School of EngineeringPalo AltoCA94304USA
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37
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Eickhoff L, Dreischmeier K, Zipori A, Sirotinskaya V, Adar C, Reicher N, Braslavsky I, Rudich Y, Koop T. Contrasting Behavior of Antifreeze Proteins: Ice Growth Inhibitors and Ice Nucleation Promoters. J Phys Chem Lett 2019; 10:966-972. [PMID: 30742446 DOI: 10.1021/acs.jpclett.8b03719] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Several types of natural molecules interact specifically with ice crystals. Small antifreeze proteins (AFPs) adsorb to particular facets of ice crystals, thus inhibiting their growth, whereas larger ice-nucleating proteins (INPs) can trigger the formation of new ice crystals at temperatures much higher than the homogeneous ice nucleation temperature of pure water. It has been proposed that both types of proteins interact similarly with ice and that, in principle, they may be able to exhibit both functions. Here we investigated two naturally occurring antifreeze proteins, one from fish, type-III AFP, and one from beetles, TmAFP. We show that in addition to ice growth inhibition, both can also trigger ice nucleation above the homogeneous freezing temperature, providing unambiguous experimental proof for their contrasting behavior. Our analysis suggests that the predominant difference between AFPs and INPs is their molecular size, which is a very good predictor of their ice nucleation temperature.
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Affiliation(s)
- Lukas Eickhoff
- Bielefeld University , Faculty of Chemistry , D-33615 Bielefeld , Germany
| | | | - Assaf Zipori
- The Weizmann Institute of Science , Department of Earth and Planetary Sciences , Rehovot 7610001 , Israel
| | - Vera Sirotinskaya
- The Hebrew University of Jerusalem , Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science and Nutrition , Rehovot 7610001 , Israel
| | - Chen Adar
- The Hebrew University of Jerusalem , Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science and Nutrition , Rehovot 7610001 , Israel
| | - Naama Reicher
- The Weizmann Institute of Science , Department of Earth and Planetary Sciences , Rehovot 7610001 , Israel
| | - Ido Braslavsky
- The Hebrew University of Jerusalem , Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science and Nutrition , Rehovot 7610001 , Israel
| | - Yinon Rudich
- The Weizmann Institute of Science , Department of Earth and Planetary Sciences , Rehovot 7610001 , Israel
| | - Thomas Koop
- Bielefeld University , Faculty of Chemistry , D-33615 Bielefeld , Germany
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38
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Vance TDR, Bayer-Giraldi M, Davies PL, Mangiagalli M. Ice-binding proteins and the 'domain of unknown function' 3494 family. FEBS J 2019; 286:855-873. [PMID: 30680879 DOI: 10.1111/febs.14764] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/03/2019] [Accepted: 01/22/2019] [Indexed: 02/03/2023]
Abstract
Ice-binding proteins (IBPs) control the growth and shape of ice crystals to cope with subzero temperatures in psychrophilic and freeze-tolerant organisms. Recently, numerous proteins containing the domain of unknown function (DUF) 3494 were found to bind ice crystals and, hence, are classified as IBPs. DUF3494 IBPs constitute today the most widespread of the known IBP families. They can be found in different organisms including bacteria, yeasts and microalgae, supporting the hypothesis of horizontal transfer of its gene. Although the 3D structure is always a discontinuous β-solenoid with a triangular cross-section and an adjacent alpha-helix, DUF3494 IBPs present very diverse activities in terms of the magnitude of their thermal hysteresis and inhibition of ice recrystallization. The proteins are secreted into the environments around the host cells or are anchored on their cell membranes. This review covers several aspects of this new class of IBPs, which promise to leave their mark on several research fields including structural biology, protein biochemistry and cryobiology.
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Affiliation(s)
- Tyler D R Vance
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Maddalena Bayer-Giraldi
- Department of Glaciology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
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39
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Kondo H, Mochizuki K, Bayer-Giraldi M. Multiple binding modes of a moderate ice-binding protein from a polar microalga. Phys Chem Chem Phys 2018; 20:25295-25303. [PMID: 30255887 DOI: 10.1039/c8cp04727h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ice-binding proteins (IBPs) produced by cold-tolerant organisms interact with ice and strongly control crystal growth. The molecular basis for the different magnitudes of activity displayed by various IBPs (moderate and hyperactive) has not yet been clarified. Previous studies questioned whether the moderate activity of some IBPs relies on their weaker binding modus to the ice surface, compared to hyperactive IBPs, rather than relying on binding only to selected faces of the ice crystal. We present the structure of one moderate IBP from the sea-ice diatom Fragilariopsis cylindrus (fcIBP) as determined by X-ray crystallography and investigate the protein's binding modes to the growing ice-water interface using molecular dynamics simulations. The structure of fcIBP is the IBP-1 fold, defined by a discontinuous β-solenoid delimitated by three faces (A, B and C-faces) and braced by an α-helix. The fcIBP structure shows capping loops on both N- and C-terminal parts of the solenoid. We show that the protein adsorbs on both the prism and the basal faces of ice crystals, confirming experimental results. The fcIBP binds irreversibly to the prism face using the loop between the B and the C-faces, involving also the B-face in water immobilization despite its irregular structure. The α-helix attaches the protein to the basal face with a partly reversible modus. Our results suggest that fcIBP has a looser attachment to ice and that this weaker binding modus is the basis to explain the moderate activity of fcIBP.
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Affiliation(s)
- Hidemasa Kondo
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
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40
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Lotti M, Brocca S, Mangiagalli M, Pischedda A, Orlando M, Maione S, De Pascale D, Pucciarelli S, Nardini M, Braslavsky I. Enzymes and ice binding proteins from Antarctic organisms. N Biotechnol 2018. [DOI: 10.1016/j.nbt.2018.05.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Hasan M, Fayter AER, Gibson MI. Ice Recrystallization Inhibiting Polymers Enable Glycerol-Free Cryopreservation of Microorganisms. Biomacromolecules 2018; 19:3371-3376. [PMID: 29932648 PMCID: PMC6588267 DOI: 10.1021/acs.biomac.8b00660] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/20/2018] [Indexed: 02/08/2023]
Abstract
All modern molecular biology and microbiology is underpinned by not only the tools to handle and manipulate microorganisms but also those to store, bank, and transport them. Glycerol is the current gold-standard cryoprotectant, but it is intrinsically toxic to most microorganisms: only a fraction of cells survive freezing and the presence of glycerol can impact downstream applications and assays. Extremophile organisms survive repeated freeze/thaw cycles by producing antifreeze proteins which are potent ice recrystallization inhibitors. Here we introduce a new concept for the storage/transport of microorganisms by using ice recrystallization inhibiting poly(vinyl alcohol) in tandem with poly(ethylene glycol). This cryopreserving formulation is shown to result in a 4-fold increase in E. coli yield post-thaw, compared to glycerol, utilizing lower concentrations, and successful cryopreservation shown as low as 1.1 wt % of additive. The mechanism of protection is demonstrated to be linked not only to inhibiting ice recrystallization (by comparison to a recombinant antifreeze protein) but also to the significantly lower toxicity of the polymers compared to glycerol. Optimized formulations are presented and shown to be broadly applicable to the cryopreservation of a panel of Gram-negative, Gram-positive, and mycobacteria strains. This represents a step-change in how microorganisms will be stored by the design of new macromolecular ice growth inhibitors; it should enable a transition from traditional solvent-based to macromolecular microbiology storage methods.
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Affiliation(s)
- Muhammad Hasan
- Department
of Chemistry and Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - Alice E. R. Fayter
- Department
of Chemistry and Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - Matthew I. Gibson
- Department
of Chemistry and Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
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42
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Growth suppression of ice crystal basal face in the presence of a moderate ice-binding protein does not confer hyperactivity. Proc Natl Acad Sci U S A 2018; 115:7479-7484. [PMID: 29967176 DOI: 10.1073/pnas.1807461115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ice-binding proteins (IBPs) affect ice crystal growth by attaching to crystal faces. We present the effects on the growth of an ice single crystal caused by an ice-binding protein from the sea ice microalga Fragilariopsis cylindrus (fcIBP) that is characterized by the widespread domain of unknown function 3494 (DUF3494) and known to cause a moderate freezing point depression (below 1 °C). By the application of interferometry, bright-field microscopy, and fluorescence microscopy, we observed that the fcIBP attaches to the basal faces of ice crystals, thereby inhibiting their growth in the c direction and resulting in an increase in the effective supercooling with increasing fcIBP concentration. In addition, we observed that the fcIBP attaches to prism faces and inhibits their growth. In the event that the effective supercooling is small and crystals are faceted, this process causes an emergence of prism faces and suppresses crystal growth in the a direction. When the effective supercooling is large and ice crystals have developed into a dendritic shape, the suppression of prism face growth results in thinner dendrite branches, and growth in the a direction is accelerated due to enhanced latent heat dissipation. Our observations clearly indicate that the fcIBP occupies a separate position in the classification of IBPs due to the fact that it suppresses the growth of basal faces, despite its moderate freezing point depression.
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43
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Ma R, Huang H, Bai Y, Luo H, Fan Y, Yao B. Insight into the cold adaptation and hemicellulose utilization of Cladosporium neopsychrotolerans from genome analysis and biochemical characterization. Sci Rep 2018; 8:6075. [PMID: 29666397 PMCID: PMC5904165 DOI: 10.1038/s41598-018-24443-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/20/2018] [Indexed: 11/30/2022] Open
Abstract
The occurrence of Cladosporium in cold ecosystems has been evidenced long before, and most of the knowledge about nutrient utilization of this genus is sporadic. An alpine soil isolate C. neopsychrotolerans SL-16, showing great cold tolerance and significant lignocellulose-degrading capability, was sequenced to form a 35.9 Mb genome that contains 13,456 predicted genes. Functional annotation on predicted genes revealed a wide array of proteins involved in the transport and metabolism of carbohydrate, protein and lipid. Large numbers of transmembrane proteins (967) and CAZymes (571) were identified, and those related to hemicellulose degradation was the most abundant. To undermine the hemicellulose (xyaln as the main component) utilization mechanism of SL-16, the mRNA levels of 23 xylanolytic enzymes were quantified, and representatives of three glycoside hydrolase families were functionally characterized. The enzymes showed similar neutral, cold active and thermolabile properties and synergistic action on xylan degradation (the synergy degree up to 15.32). Kinetic analysis and sequence and structure comparison with mesophilic and thermophilic homologues indicated that these cold-active enzymes employed different cold adaptation strategies to function well in cold environment. These similar and complementary advantages in cold adaptation and catalysis might explain the high efficiency of lignocellulose conversion observed in SL-16 under low temperatures.
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Affiliation(s)
- Rui Ma
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Biotechnology Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunliu Fan
- Biotechnology Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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44
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Mangiagalli M, Sarusi G, Kaleda A, Bar Dolev M, Nardone V, Vena VF, Braslavsky I, Lotti M, Nardini M. Structure of a bacterial ice binding protein with two faces of interaction with ice. FEBS J 2018. [PMID: 29533528 DOI: 10.1111/febs.14434] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ice-binding proteins (IBPs) contribute to the survival of many living beings at subzero temperature by controlling the formation and growth of ice crystals. This work investigates the structural basis of the ice-binding properties of EfcIBP, obtained from Antarctic bacteria. EfcIBP is endowed with a unique combination of thermal hysteresis and ice recrystallization inhibition activity. The three-dimensional structure, solved at 0.84 Å resolution, shows that EfcIBP belongs to the IBP-1 fold family, and is organized in a right-handed β-solenoid with a triangular cross-section that forms three protein surfaces, named A, B, and C faces. However, EfcIBP diverges from other IBP-1 fold proteins in relevant structural features including the lack of a 'capping' region on top of the β-solenoid, and in the sequence and organization of the regions exposed to ice that, in EfcIBP, reveal the presence of threonine-rich ice-binding motifs. Docking experiments and site-directed mutagenesis pinpoint that EfcIBP binds ice crystals not only via its B face, as common to other IBPs, but also via ice-binding sites on the C face. DATABASE Coordinates and structure factors have been deposited in the Protein Data Bank under accession number 6EIO.
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Affiliation(s)
- Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Guy Sarusi
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Aleksei Kaleda
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.,Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Estonia
| | - Maya Bar Dolev
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | | | - Ido Braslavsky
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Italy
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45
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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]
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46
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Vance TDR, Graham LA, Davies PL. An ice-binding and tandem beta-sandwich domain-containing protein in Shewanella frigidimarina is a potential new type of ice adhesin. FEBS J 2018; 285:1511-1527. [PMID: 29498209 DOI: 10.1111/febs.14424] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/16/2018] [Accepted: 02/23/2018] [Indexed: 11/29/2022]
Abstract
Out of the dozen different ice-binding protein (IBP) structures known, the DUF3494 domain is the most widespread, having been passed many times between prokaryotic and eukaryotic microorganisms by horizontal gene transfer. This ~25-kDa β-solenoid domain with an adjacent parallel α-helix is most commonly associated with an N-terminal secretory signal peptide. However, examples of the DUF3494 domain preceded by tandem Bacterial Immunoglobulin-like (BIg) domains are sometimes found, though uncharacterized. Here, we present one such protein (SfIBP_1) from the Antarctic bacterium Shewanella frigidimarina. We have confirmed and characterized the ice-binding activity of its ice-binding domain using thermal hysteresis measurements, fluorescent ice plane affinity analysis, and ice recrystallization inhibition assays. X-ray crystallography was used to solve the structure of the SfIBP_1 ice-binding domain, to further characterize its ice-binding surface and unique method of stabilizing or 'capping' the ends of the solenoid structure. The latter is formed from the interaction of two loops mediated by a combination of tandem prolines and electrostatic interactions. Furthermore, given their domain architecture and membrane association, we propose that these BIg-containing DUF3494 IBPs serve as ice-binding adhesion proteins that are capable of adsorbing their host bacterium onto ice. DATABASE Submitted new structure to the Protein Data Bank (PDB: 6BG8).
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Affiliation(s)
- Tyler D R Vance
- Department of Biomedical and Molecular Science, Queen's University, Kingston, Canada
| | - Laurie A Graham
- Department of Biomedical and Molecular Science, Queen's University, Kingston, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Science, Queen's University, Kingston, Canada
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47
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Kryshtafovych A, Albrecht R, Baslé A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T. Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins 2018; 86 Suppl 1:27-50. [PMID: 28960539 PMCID: PMC5820184 DOI: 10.1002/prot.25392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/19/2017] [Accepted: 09/25/2017] [Indexed: 12/27/2022]
Abstract
The functional and biological significance of the selected CASP12 targets are described by the authors of the structures. The crystallographers discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP12 experiment.
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Affiliation(s)
- Andriy Kryshtafovych
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California, 95616
| | - Reinhard Albrecht
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Pedro Bule
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Portugal, Lisboa
| | - Alessandro T Caputo
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
| | - Ana Luisa Carvalho
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Cien⁁cias e Tecnologia, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Kinlin L Chao
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, 20850
| | - Ron Diskin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Krzysztof Fidelis
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California, 95616
| | - Carlos M G A Fontes
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Portugal, Lisboa
| | - Folmer Fredslund
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Celia W Goulding
- Department of Molecular Biology and Biochemistry/Pharmaceutical Sciences, University of California Irvine, Irvine, California, 92697
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology/Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California, 93106
| | - Osnat Herzberg
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, 20850
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742
| | - Johan C Hill
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
| | - Andrzej Joachimiak
- Argonne National Laboratory, Midwest Center for Structural Genomics/Structural Biology Center, Biosciences Division, Argonne, Illinois, 60439
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637
| | - Gert-Wieland Kohring
- Microbiology, Saarland University, Campus Building A1.5, Saarbrücken, Saarland, D-66123, Germany
| | - Roman I Koning
- Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University, 2333, CC Leiden, The Netherlands
- Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, 20126, Italy
| | - Karolina Michalska
- Argonne National Laboratory, Midwest Center for Structural Genomics/Structural Biology Center, Biosciences Division, Argonne, Illinois, 60439
| | - John Moult
- Department of Cell Biology and Molecular genetics, University of Maryland, 9600 Gudelsky Drive, Institute for Bioscience and Biotechnology Research, Rockville, Maryland, 20850
| | - Shabir Najmudin
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Portugal, Lisboa
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano, 20133, Italy
| | - Valentina Nardone
- Department of Biosciences, University of Milano, Milano, 20133, Italy
| | - Didier Ndeh
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Thanh-Hong Nguyen
- Department of Macromolecular Structures, Centro Nacional de Biotecnologia (CSIC), calle Darwin 3, Madrid, 28049, Spain
| | - Guido Pintacuda
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Villeurbanne, 69100, France
| | - Sandra Postel
- University of Maryland School of Medicine, Institute of Human Virology, Baltimore, Maryland, 21201
| | - Mark J van Raaij
- Department of Macromolecular Structures, Centro Nacional de Biotecnologia (CSIC), calle Darwin 3, Madrid, 28049, Spain
| | - Pietro Roversi
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, University Road, Leicester, LE1 7RN, UK
| | - Amir Shimon
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Abhimanyu K Singh
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, United Kingdom
| | - Eric J Sundberg
- Department of Medicine and Department of Microbiology and Immunology, University of Maryland School of Medicine, Institute of Human Virology, Baltimore, Maryland, 21201
| | - Kaspars Tars
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
- Faculty of Biology, Department of Molecular Biology, University of Latvia, Jelgavas 1, Riga, LV-1004, Latvia
| | - Nicole Zitzmann
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
| | - Torsten Schwede
- Biozentrum/SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50, Basel, 4056, Switzerland
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Effect of Marine-Derived Ice-Binding Proteins on the Cryopreservation of Marine Microalgae. Mar Drugs 2017; 15:md15120372. [PMID: 29194380 PMCID: PMC5742832 DOI: 10.3390/md15120372] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/17/2017] [Accepted: 11/23/2017] [Indexed: 11/17/2022] Open
Abstract
Ice-binding protein (IBPs) protect cells from cryo-injury during cryopreservation by inhibiting ice recrystallization (IR), which is a main cause of cell death. In the present study, we employed two IBPs, one, designated LeIBP from Arctic yeast, and the other, designated FfIBP from Antarctic sea ice bacterium, in the cryopreservation of three economically valuable marine microalgae, Isochrysis galbana, Pavlova viridis, and Chlamydomonas coccoides. Both of the IBPs showed IR inhibition in f/2 medium containing 10% DMSO, indicating that they retain their function in freezing media. Microalgal cells were frozen in 10% DMSO with or without IBP. Post-thaw viability exhibited that the supplementation of IBPs increased the viability of all cryopreserved cells. LeIBP was effective in P. viridis and C. coccoides, while FfIBP was in I. galbana. The cryopreservative effect was more drastic with P. viridis when 0.05 mg/mL LeIBP was used. These results clearly demonstrate that IBPs could improve the viability of cryopreserved microalgal cells.
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Adiram-Filiba N, Schremer A, Ohaion E, Nadav-Tsubery M, Lublin-Tennenbaum T, Keinan-Adamsky K, Goobes G. Ubiquitin immobilized on mesoporous MCM41 silica surfaces - Analysis by solid-state NMR with biophysical and surface characterization. Biointerphases 2017; 12:02D414. [PMID: 28565916 PMCID: PMC5451314 DOI: 10.1116/1.4983273] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 12/16/2022] Open
Abstract
Deriving the conformation of adsorbed proteins is important in the assessment of their functional activity when immobilized. This has particularly important bearings on the design of contemporary and new encapsulated enzyme-based drugs, biosensors, and other bioanalytical devices. Solid-state nuclear magnetic resonance (NMR) measurements can expand our molecular view of proteins in this state and of the molecular interactions governing protein immobilization on popular biocompatible surfaces such as silica. Here, the authors study the immobilization of ubiquitin on the mesoporous silica MCM41 by NMR and other techniques. Protein molecules are shown to bind efficiently at pH 5 through electrostatic interactions to individual MCM41 particles, causing their agglutination. The strong attraction of ubiquitin to MCM41 surface is given molecular context through evidence of proximity of basic, carbonyl and polar groups on the protein to groups on the silica surface using NMR measurements. The immobilized protein exhibits broad peaks in two-dimensional 13C dipolar-assisted rotational resonance spectra, an indication of structural multiplicity. At the same time, cross-peaks related to Tyr and Phe sidechains are missing due to motional averaging. Overall, the favorable adsorption of ubiquitin to MCM41 is accompanied by conformational heterogeneity and by a major loss of motional degrees of freedom as inferred from the marked entropy decrease. Nevertheless, local motions of the aromatic rings are retained in the immobilized state.
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Affiliation(s)
| | - Avital Schremer
- Department of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Eli Ohaion
- Department of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
| | | | | | | | - Gil Goobes
- Department of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
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50
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Corrigendum. FEBS J 2017; 284:831. [DOI: 10.1111/febs.14037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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