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Omar MN, Rahman RNZRA, Noor NDM, Latip W, Knight VF, Ali MSM. Exploring the Antarctic aminopeptidase P from Pseudomonas sp. strain AMS3 through structural analysis and molecular dynamics simulation. J Biomol Struct Dyn 2024:1-13. [PMID: 38555730 DOI: 10.1080/07391102.2024.2331093] [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: 11/30/2023] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
Aminopeptidase P (APPro) is a crucial metalloaminopeptidase involved in amino acid cleavage from peptide N-termini, playing essential roles as versatile biocatalysts with applications ranging from pharmaceuticals to industrial processes. Despite acknowledging its potential for catalysis in lower temperatures, detailed molecular basis and biotechnological implications in cold environments are yet to be explored. Therefore, this research aims to investigate the molecular mechanisms underlying the cold-adapted characteristics of APPro from Pseudomonas sp. strain AMS3 (AMS3-APPro) through a detailed analysis of its structure and dynamics. In this study, structure analysis and molecular dynamics (MD) simulation of a predicted model of AMS3-APPro has been performed at different temperatures to assess structural flexibility and thermostability across a temperature range of 0-60 °C over 100 ns. The MD simulation results revealed that the structure were able to remain stable at low temperatures. Increased temperatures present a potential threat to the overall stability of AMS3-APPro by disrupting the intricate hydrogen bond networks crucial for maintaining structural integrity, thereby increasing the likelihood of protein unfolding. While the metal binding site at the catalytic core exhibits resilience at higher temperatures, highlighting its local structural integrity, the overall enzyme structure undergoes fluctuations and potential denaturation. This extensive structural instability surpasses the localized stability observed at the metal binding site. Consequently, these assessments offer in-depth understanding of the cold-adapted characteristics of AMS3-APPro, highlighting its capability to uphold its native conformation and stability in low-temperature environments. In summary, this research provides valuable insights into the cold-adapted features of AMS3-APPro, suggesting its efficient operation in low thermal conditions, particularly relevant for potential biotechnological applications in cold environments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhamad Nadzmi Omar
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Wahhida Latip
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Victor Feizal Knight
- Research Centre for Chemical Defence, National Defence University of Malaysia, Kem Perdana Sungai Besi, Kuala Lumpur, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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Liu Y, Jia K, Chen H, Wang Z, Zhao W, Zhu L. Cold-adapted enzymes: mechanisms, engineering and biotechnological application. Bioprocess Biosyst Eng 2023; 46:1399-1410. [PMID: 37486422 DOI: 10.1007/s00449-023-02904-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/05/2023] [Indexed: 07/25/2023]
Abstract
Most cold-adapted enzymes display high catalytic activity at low temperatures (20-25 °C) and can still maintain more than 40-50% of their maximum activity at lower temperatures (0-10 °C) but are inactivated after a moderate increase in temperature. The activity of some cold-adapted enzymes increases significantly in the presence of high salt concentrations and metal ions. Interestingly, we also observed that some cold-adapted enzymes have a wide range of optimum temperatures, exhibiting not only maximum activity under low-temperature conditions but also the ability to maintain high enzyme activity under high-temperature conditions, which is a novel feature of cold-adapted enzymes. This unique property of cold-adapted enzymes is generally attractive for biotechnological and industrial applications because these enzymes can reduce energy consumption and the chance of microbial contamination, thereby lowering the production costs and maintaining the flavor, taste and quality of foods. How high catalytic activity is maintained at low temperatures remains unknown. The relationship between the structure of cold-adapted enzymes and their activity, flexibility and stability is complex, and thus far, a unified explanation has not been provided. Herein, we systematically review the sources, catalytic characteristics and cold adaptation of enzymes from four enzymes categories systematically and discuss how these properties may be exploited in biotechnology. A thorough understanding of the properties, catalytic mechanisms, and engineering of cold-adapted enzymes is critical for future biotechnological applications in the detergent industry and food and beverage industries.
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Affiliation(s)
- Yan Liu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Kaizhi Jia
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Hongyang Chen
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Zhulin Wang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Wei Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Liwen Zhu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China.
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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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Liu Y, Zhang N, Ma J, Zhou Y, Wei Q, Tian C, Fang Y, Zhong R, Chen G, Zhang S. Advances in cold-adapted enzymes derived from microorganisms. Front Microbiol 2023; 14:1152847. [PMID: 37180232 PMCID: PMC10169661 DOI: 10.3389/fmicb.2023.1152847] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
Cold-adapted enzymes, produced in cold-adapted organisms, are a class of enzyme with catalytic activity at low temperatures, high temperature sensitivity, and the ability to adapt to cold stimulation. These enzymes are largely derived from animals, plants, and microorganisms in polar areas, mountains, and the deep sea. With the rapid development of modern biotechnology, cold-adapted enzymes have been implemented in human and other animal food production, the protection and restoration of environments, and fundamental biological research, among other areas. Cold-adapted enzymes derived from microorganisms have attracted much attention because of their short production cycles, high yield, and simple separation and purification, compared with cold-adapted enzymes derived from plants and animals. In this review we discuss various types of cold-adapted enzyme from cold-adapted microorganisms, along with associated applications, catalytic mechanisms, and molecular modification methods, to establish foundation for the theoretical research and application of cold-adapted enzymes.
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Affiliation(s)
- Yehui Liu
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Na Zhang
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Jie Ma
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Yuqi Zhou
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Qiang Wei
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yi Fang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Rongzhen Zhong
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Guang Chen
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Sitong Zhang
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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Chen R, Liao YT, Gao TT, Zhang YM, Lu LH, Wang CH. Novel Salt-Tolerant Leucine Dehydrogenase from Marine Pseudoalteromonas rubra DSM 6842. Mol Biotechnol 2022; 64:1270-1278. [PMID: 35578070 DOI: 10.1007/s12033-022-00505-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/02/2022] [Indexed: 10/18/2022]
Abstract
This study reported the cloning, expression, and characterization of a new salt-tolerant leucine dehydrogenase (PrLeuDH) from Pseudoalteromonas rubra DSM 6842. A codon-optimized 1038 bp gene encoding PrLeuDH was successfully expressed on pET-22b( +) in E. coli BL21(DE3). The purified recombinant PrLeuDH showed a single band of about 38.7 kDa on SDS-PAGE. It exhibited the maximum activity at 40 °C and pH 10.5, while kept high activities in the range of 25-45 °C and pH 9.5-12. The Km value and turnover number kcat for leucine of PrLeuDH were 2.23 ± 0.12 mM and 35.39 ± 0.05 s-1, respectively, resulting in a catalytic efficiency kcat/Km of 15.87 s-1/mM. Importantly, PrLeuDH remained 92.1 ± 2.67% active in the presence of 4.0 M NaCl. The study provides the first in-depth understanding of LeuDH from marine Pseudoalteromonas rubra, meanwhile the unique properties of high activity at low temperature and high salt tolerance make it a promising biocatalyst for the synthesis of non-protein amino acids and α-ketoacids under special conditions in pharmaceutical industry.
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Affiliation(s)
- Rui Chen
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China
| | - Yu-Ting Liao
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China
| | - Tian-Tian Gao
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China
| | - Yan-Mei Zhang
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China
| | - Liang-Hua Lu
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China
| | - Cheng-Hua Wang
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China.
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Kumar A, Mukhia S, Kumar R. Industrial applications of cold-adapted enzymes: challenges, innovations and future perspective. 3 Biotech 2021; 11:426. [PMID: 34567931 DOI: 10.1007/s13205-021-02929-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Extreme cold environments are potential reservoirs of microorganisms producing unique and novel enzymes in response to environmental stress conditions. Such cold-adapted enzymes prove to be valuable tools in industrial biotechnology to meet the increasing demand for efficient biocatalysts. The inherent properties like high catalytic activity at low temperature, high specific activity and low activation energy make the cold-adapted enzymes well suited for application in various industries. The interest in this group of enzymes is expanding as they are the preferred alternatives to harsh chemical synthesis owing to their biodegradable and non-toxic nature. Irrespective of the multitude of applications, the use of cold-adapted enzymes at the industrial level is still limited. The current review presents the unique adaptive features and the role of cold-adapted enzymes in major industries like food, detergents, molecular biology and bioremediation. The review highlights the significance of omics technology i.e., metagenomics, metatranscriptomics and metaproteomics in enzyme bioprospection from extreme environments. It further points out the challenges in using cold-adapted enzymes at the industrial level and the innovations associated with novel enzyme prospection strategies. Documentations on cold-adapted enzymes and their applications are abundant; however, reports on the role of omics tools in exploring cold-adapted enzymes are still scarce. So, the review covers the aspect concerning the novel techniques for enzyme discovery from nature.
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Affiliation(s)
- Anil Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, Himachal Pradesh 176 061 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201 002 India
| | - Srijana Mukhia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, Himachal Pradesh 176 061 India
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, Himachal Pradesh 176 061 India
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A thermostable leucine dehydrogenase from Bacillus coagulansNL01: Expression, purification and characterization. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Enzymes from Marine Polar Regions and Their Biotechnological Applications. Mar Drugs 2019; 17:md17100544. [PMID: 31547548 PMCID: PMC6835263 DOI: 10.3390/md17100544] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
The microorganisms that evolved at low temperatures express cold-adapted enzymes endowed with unique catalytic properties in comparison to their mesophilic homologues, i.e., higher catalytic efficiency, improved flexibility, and lower thermal stability. Cold environments are therefore an attractive research area for the discovery of enzymes to be used for investigational and industrial applications in which such properties are desirable. In this work, we will review the literature on cold-adapted enzymes specifically focusing on those discovered in the bioprospecting of polar marine environments, so far largely neglected because of their limited accessibility. We will discuss their existing or proposed biotechnological applications within the framework of the more general applications of cold-adapted enzymes.
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