Biocatalysts provide many advantages over the traditional chemically assisted processes prevalent in industries. Consequently, the search for novel enzymes has increased over the years with a renewed interest in thermophilic and psychrophilic bacterial species. Enzymes or extremozymes extracted from such species have exhibited an affinity to extreme temperatures which is a prerequisite for many industrial applications. However, utilisation of these enzymes faces a major bottleneck. The distribution of sequence data associated with thermophiles and psychrophiles is overwhelming, spanning various databases and scientific literature. Based on more than 100 publications and genomes from over 300 thermophilic and psychrophilic bacterial species, we have constructed the database IND-Enzymes (indenzymes.srmist.edu.in). This database consists of over 20,120 nucleotide and protein sequences belonging to the hydrolytic enzyme class lipase, protease, esterase and amylase. Users can access over 100 published enzymes, 200 PDB structural data. Enzymes derived from genomes can be directly downloaded and users can also access the entire annotation data derived from species individually. Along with an alignment tool and python based pipelines, IND-Enzymes serves as the largest sequence repository for hydrolytic enzymes from thermophilic and psychrophilic bacterial species. This database showcases resources that are essential for protein engineering of hot-cold stable enzymes.
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http://dx.doi.org/10.1007/s00792-021-01231-2 | DOI Listing |
Comput Biol Med
December 2024
College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, China; Country Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu, 610106, China.
Thermophilic proteins, mesophiles proteins and psychrophilic proteins have wide industrial applications, as enzymes with different optimal temperatures are often needed for different purposes. Convenient methods are needed to determine the optimal temperatures for proteins; however, laboratory methods for this purpose are time-consuming and laborious, and existing machine learning methods can only perform binary classification of thermophilic and non-thermophilic proteins, or psychrophilic and non-psychrophilic proteins. Here, we developed a deep learning model, PSTP-BERT, based on protein sequences that can directly perform Three classes identification of thermophilic, mesophilic, and psychrophilic proteins.
View Article and Find Full Text PDFFront Microbiol
November 2024
Research Center of Molecular Diagnostics and Sequencing, Research Institute of Tsinghua University in Shenzhen, Shenzhen, China.
Curr Res Microb Sci
November 2024
Department of Microbiology, School of Life Sciences, Sikkim University, Tadong, Gangtok, Sikkim 737102, India.
Geothermal habitats present a unique opportunity to study microbial adaptation to varying temperature conditions. In such environments, distinct temperature gradients foster diverse microbial communities, each adapted to its optimal niche. However, the complex dynamics of bacterial populations in across these gradients high-altitude hot springs remain largely unexplored.
View Article and Find Full Text PDFMar Drugs
November 2024
School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy.
In the present review, we summarize genome mining of genomic data obtained from the psychrophilic Antarctic marine ciliate and its evolutionary-close mesophilic cosmopolitan counterpart . This analysis highlights adaptation strategies that are unique to the Antarctic ciliate, including antioxidant gene duplication and distinctive substitutions that may play roles in increased drug binding affinity and enzyme reaction rate in cold environments. Enzymes from psychrophiles are usually characterized by high activities and reaction rates at low temperatures compared with their counterparts from mesophiles and thermophiles.
View Article and Find Full Text PDFJ Mol Evol
December 2024
Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Malaysia.
Cold-active enzymes have recently gained popularity because of their high activity at lower temperatures than their mesophilic and thermophilic counterparts, enabling them to withstand harsh reaction conditions and enhance industrial processes. Cold-active lipases are enzymes produced by psychrophiles that live and thrive in extremely cold conditions. Cold-active lipase applications are now growing in the detergency, synthesis of fine chemicals, food processing, bioremediation, and pharmaceutical industries.
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