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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] [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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Zhu S, Jin Y, Yu J, Yang W, Lian J, Wei Z, Zhang D, Ding Y, Zhou X. Composition-antifreeze property relationships of gelatin and the corresponding mechanisms. Int J Biol Macromol 2024; 268:131941. [PMID: 38685545 DOI: 10.1016/j.ijbiomac.2024.131941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 04/08/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
The inherent functional fractions (gelation and ice-affinitive fractions) of gelatin enable it as a promising cryoprotectant alternative. However, the composition-antifreeze property relationships of gelatin remain to be investigated. In this study, the HW-PSG and LW-PSG fractions of gelatin from fish scales were obtained, according to the critical gelation conditions and ice-binding measurements, respectively. Thermal hysteresis (THA) value, associated with ice nucleation, of LW-PSG was higher than that of HW-PSG. Besides, the relatively low-sized ice crystals (210-550 μm2) indicated that HW-PSG showed strong ice recrystallization inhibition (IRI) ability, compared to other groups. These results suggested that LW-PSG inhibited ice nucleation, while HW-PSG displayed the strong IRI ability. Furthermore, the antifreeze mechanisms were clarified through IRI measurements and molecular dynamics simulation. The minimum size of ice crystals was found for HW-PSG gels with dense microstructure, suggesting the HW-PSG retarded the growth of ice crystals by restricting the migration and phase transformation of water molecules. The hydrogen bond interactions between the ice crystal surface and ASN1294 and PRO1433 residues of LW-PSG, and hydrophobic interactions contributed to inhibiting the nucleation of ice crystals. This study provided some references to further enhance antifreeze performance of gelatin by modulating fragment composition.
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Affiliation(s)
- Shichen Zhu
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China; Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, China; National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Yan Jin
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China; Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, China; National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
| | - Jiehang Yu
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China; Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, China; National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
| | - Wenting Yang
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China; Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, China; National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
| | - Jing Lian
- Comprehensive service center of market supervision and management of Rongcheng, Shandong, China
| | - Zhengpeng Wei
- Taixiang Group, Rongcheng Taixiang Food Products Co., Ltd., Ministry of Agriculture, Key Laboratory of Frozen Prepared Marine Foods Processing, Rongcheng 264300, China
| | - Dong Zhang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Yuting Ding
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China; Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, China; National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Xuxia Zhou
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China; Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, China; National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China.
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Sijin Z, Zhang L, Yin T, You J, Liu R, Wang L, Huang Q, Wang W, Ma H. Exploring the versatility of carbohydrates in surimi and surimi products: novel applications and future perspectives. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:1874-1883. [PMID: 37885307 DOI: 10.1002/jsfa.13081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/31/2023] [Accepted: 10/27/2023] [Indexed: 10/28/2023]
Abstract
Carbohydrate is one kind of the most important additives in the production of surimi and surimi products, mainly due to its wide range of sources and superior functionality. In recent years, new carbohydrates (oligosaccharides and polysaccharides) have been gradually applied in the production of surimi and surimi products which is mainly driven by consumer requirement on nutritional and the flavors or taste quality and producer requirement on extending the shelf life, like low calorie intake, dietary fiber enrichment, rich taste and improvement of antioxidant properties. Besides anti-freezing and improvement in gelling ability, novel functionalities have been explored such as fat substitution, improving flavor, antibacterial effect, antioxidant effect and improving three-dimensional printability. With an in-depth study of the mechanism of carbohydrate improving the qualities of surimi and surimi products, the application of carbohydrates in surimi would be more effective. Therefore, this review summarizes the new carbohydrates applied in the processing of surimi and surimi products, and their novel functionalities. Additionally, progress of the research on the mechanism of carbohydrate improving the qualities of surimi is also reviewed. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Zhang Sijin
- ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs; Key Laboratory of Aquaculture genetic and breeding and Healthy Aquaculture of Guangxi, Guangxi Academy of Fishery Sciences, Nanning, China
- Wuhan Business University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | | | - Tao Yin
- ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs; Key Laboratory of Aquaculture genetic and breeding and Healthy Aquaculture of Guangxi, Guangxi Academy of Fishery Sciences, Nanning, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- National R & D Branch Center for Conventional Freshwater Fish Processing, Wuhan, China
| | - Juan You
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- National R & D Branch Center for Conventional Freshwater Fish Processing, Wuhan, China
| | - Ru Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- National R & D Branch Center for Conventional Freshwater Fish Processing, Wuhan, China
| | - Lan Wang
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs, Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, China
- Agro-Product Processing Research Sub-Center of Hubei Innovation Center of Agriculture Science and Technology, Wuhan, China
| | - Qilin Huang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- National R & D Branch Center for Conventional Freshwater Fish Processing, Wuhan, China
| | - Weisheng Wang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, China
| | - Huawei Ma
- ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs; Key Laboratory of Aquaculture genetic and breeding and Healthy Aquaculture of Guangxi, Guangxi Academy of Fishery Sciences, Nanning, China
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Hannon Bozorgmehr J. Four classic "de novo" genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences. Mol Genet Genomics 2024; 299:6. [PMID: 38315248 DOI: 10.1007/s00438-023-02090-6] [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: 05/27/2023] [Accepted: 10/15/2023] [Indexed: 02/07/2024]
Abstract
Despite being previously regarded as extremely unlikely, the idea that entirely novel protein-coding genes can emerge from non-coding sequences has gradually become accepted over the past two decades. Examples of "de novo origination", resulting in lineage-specific "orphan" genes, lacking coding orthologs, are now produced every year. However, many are likely cases of duplicates that are difficult to recognize. Here, I re-examine the claims and show that four very well-known examples of genes alleged to have emerged completely "from scratch"- FLJ33706 in humans, Goddard in fruit flies, BSC4 in baker's yeast and AFGP2 in codfish-may have plausible evolutionary ancestors in pre-existing genes. The first two are likely highly diverged retrogenes coding for regulatory proteins that have been misidentified as orphans. The antifreeze glycoprotein, moreover, may not have evolved from repetitive non-genic sequences but, as in several other related cases, from an apolipoprotein that could have become pseudogenized before later being reactivated. These findings detract from various claims made about de novo gene birth and show there has been a tendency not to invest the necessary effort in searching for homologs outside of a very limited syntenic or phylostratigraphic methodology. A robust approach is used for improving detection that draws upon similarities, not just in terms of statistical sequence analysis, but also relating to biochemistry and function, to obviate notable failures to identify homologs.
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Diao Y, Hao T, Liu X, Yang H. Advances in single ice crystal shaping materials: From nature to synthesis and applications in cryopreservation. Acta Biomater 2024; 174:49-68. [PMID: 38040076 DOI: 10.1016/j.actbio.2023.11.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/23/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
Antifreeze (glyco) proteins [AF(G)Ps], which are widely present in various extreme microorganisms, can control the formation and growth of ice crystals. Given the significance of cryogenic technology in biomedicine, climate science, electronic energy, and other fields of research, scientists are quite interested in the development and synthesis high-efficiency bionic antifreeze protein materials, particularly to reproduce their dynamic ice shaping (DIS) characteristics. Single ice crystal shaping materials, a promising class of ice-controlling materials, can alter the morphology and growth rate of ice crystals at low temperatures. This review aims to highlight the development of single ice crystal shaping materials and provide a brief comparison between a series of natural and bionic synthetic materials with DIS ability, which include AF(G)Ps, polymers, salts, and nanomaterials. Additionally, we summarize their applications in cryopreservation. Finally, this paper presents the current challenges and prospects encountered in developing high-efficiency and practical single ice crystal shaping materials. STATEMENT OF SIGNIFICANCE: The formation and growth of ice crystals hold a significant importance to an incredibly broad range of fields. Therefore, the design and fabrication of the single ice crystal shaping materials have gained the increasing popularity due to its key role in dynamic ice shaping (DIS) characteristics. Especially, single ice crystal shaping materials are considered one of the most promising candidates as ice inhibitors, presenting tremendous prospects for enhancing cryopreservation. In this work, we focus on the molecular characteristics, structure-function relationships, and DIS mechanisms of typical natural and biomimetic synthetic materials. This review may provide inspiration for the design and preparation of single ice crystal shaping materials and give guidance for the development of effective cryopreservation agent.
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Affiliation(s)
- Yunhe Diao
- School of Materials Science and Engineering, Zhengzhou University, 450001 Zhengzhou, Henan, China
| | - Tongtong Hao
- School of Materials Science and Engineering, Beijing Institute of Technology, 100081 Beijing, China
| | - Xuying Liu
- School of Materials Science and Engineering, Zhengzhou University, 450001 Zhengzhou, Henan, China
| | - Huige Yang
- School of Materials Science and Engineering, Zhengzhou University, 450001 Zhengzhou, Henan, China..
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Salicari L, Baiesi M, Orlandini E, Trovato A. Folding kinetics of an entangled protein. PLoS Comput Biol 2023; 19:e1011107. [PMID: 37956216 PMCID: PMC10681328 DOI: 10.1371/journal.pcbi.1011107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 11/27/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
The possibility of the protein backbone adopting lasso-like entangled motifs has attracted increasing attention. After discovering the surprising abundance of natively entangled protein domain structures, it was shown that misfolded entangled subpopulations might become thermosensitive or escape the homeostasis network just after translation. To investigate the role of entanglement in shaping folding kinetics, we introduce a novel indicator and analyze simulations of a coarse-grained, structure-based model for two small single-domain proteins. The model recapitulates the well-known two-state folding mechanism of a non-entangled SH3 domain. However, despite its small size, a natively entangled antifreeze RD1 protein displays a rich refolding behavior, populating two distinct kinetic intermediates: a short-lived, entangled, near-unfolded state and a longer-lived, non-entangled, near-native state. The former directs refolding along a fast pathway, whereas the latter is a kinetic trap, consistently with known experimental evidence of two different characteristic times. Upon trapping, the natively entangled loop folds without being threaded by the N-terminal residues. After trapping, the native entangled structure emerges by either backtracking to the unfolded state or threading through the already formed but not yet entangled loop. Along the fast pathway, trapping does not occur because the native contacts at the closure of the lasso-like loop fold after those involved in the N-terminal thread, confirming previous predictions. Despite this, entanglement may appear already in unfolded configurations. Remarkably, a longer-lived, near-native intermediate, with non-native entanglement properties, recalls what was observed in cotranslational folding.
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Affiliation(s)
- Leonardo Salicari
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
| | - Marco Baiesi
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
| | - Enzo Orlandini
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
| | - Antonio Trovato
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
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El-Sayed AFM, Khaled AA, Hamdan AM, Makled SO, Hafez EE, Saleh AA. The role of antifreeze genes in the tolerance of cold stress in the Nile tilapia (Oreochromis niloticus). BMC Genomics 2023; 24:476. [PMID: 37612592 PMCID: PMC10464439 DOI: 10.1186/s12864-023-09569-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Tilapia is one of the most essential farmed fishes in the world. It is a tropical and subtropical freshwater fish well adapted to warm water but sensitive to cold weather. Extreme cold weather could cause severe stress and mass mortalities in tilapia. The present study was carried out to investigate the effects of cold stress on the up-regulation of antifreeze protein (AFP) genes in Nile tilapia (Oreochromis niloticus). Two treatment groups of fish were investigated (5 replicates of 15 fish for each group in fibreglass tanks/70 L each): 1) a control group; the fish were acclimated to lab conditions for two weeks and the water temperature was maintained at 25 °C during the whole experimental period with feeding on a commercial diet (30% crude protein). 2) Cold stress group; the same conditions as the control group except for the temperature. Initially, the temperature was decreased by one degree every 12 h. The fish started showing death symptoms when the water temperature reached 6-8 °C. In this stage the tissue (muscle) samples were taken from both groups. The immune response of fish exposed to cold stress was detected and characterized using Differential Display-PCR (DD-PCR). RESULTS The results indicated that nine different up-regulation genes were detected in the cold-stressed fish compared to the control group. These genes are Integrin-alpha-2 (ITGA-2), Gap junction gamma-1 protein-like (GJC1), WD repeat-containing protein 59 isoform X2 (WDRP59), NUAK family SNF1-like kinase, G-protein coupled receptor-176 (GPR-176), Actin cytoskeleton-regulatory complex protein pan1-like (PAN-1), Whirlin protein (WHRN), Suppressor of tumorigenicity 7 protein isoform X2 (ST7P) and ATP-binding cassette sub-family A member 1-like isoform X2 (ABCA1). The antifreeze gene type-II amplification using a specific PCR product of 600 bp, followed by cloning and sequencing analysis revealed that the identified gene is antifreeze type-II, with similarity ranging from 70 to 95%. The in-vitro transcribed gene induced an antifreeze protein with a molecular size of 22 kDa. The antifreeze gene, ITGA-2 and the WD repeat protein belong to the lectin family (sugar-protein). CONCLUSIONS In conclusion, under cold stress, Nile tilapia express many defence genes, an antifreeze gene consisting of one open reading frame of approximately 0.6 kbp.
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Affiliation(s)
| | - Asmaa A Khaled
- Animal and Fish Production Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria City, 21531, Egypt
| | - Amira M Hamdan
- Oceanography Department, Faculty of Science, Alexandria University, Alexandria City, Egypt
| | - Sara O Makled
- Oceanography Department, Faculty of Science, Alexandria University, Alexandria City, Egypt
| | - Elsayed E Hafez
- Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications, New Borg El Arab, Alexandria City, 21934, Egypt
| | - Ahmed A Saleh
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria City, 11865, Egypt.
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