Abstract
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.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Adler-Nissen J (2007) Limited enzymic degradation of proteins: A new approach in the industrial application of hydrolases. J Chem Technol Biotechnol 32:138–156. https://doi.org/10.1002/jctb.5030320118
Andrew EB (2012) Needleman-wunsch algorithm. GitHub repository. https://github.com/aebruno/needleman-wunsch. Accessed 05 Jan 2021
Anne M, Thierry L, Elisabeth C et al (2020) The UniProt Consortium, Enzyme annotation in UniProtKB using Rhea. Bioinformatics 36:1896–1901. https://doi.org/10.1093/bioinformatics/btz817
Aziz RK, Bartels D, Best A et al (2008) The RAST Server: Rapid annotations using subsystems technology. BMC Genom 9:1–15. https://doi.org/10.1186/1471-2164-9-75
Berman HM, Battistuz T, Bhat TN et al (2002) The protein data bank. Acta Crystallogr Sect D Biol Crystallogr 58:899–907. https://doi.org/10.1107/S0907444902003451
Busto E, Gotor-Fernández V, Gotor V (2010) Hydrolases: Catalytically promiscuous enzymes for non-conventional reactions in organic synthesis. Chem Soc Rev 39:4504–4523. https://doi.org/10.1039/C003811C
Casanueva A, Tuffin M, Cary C, Cowan DA (2010) Molecular adaptations to psychrophily: The impact of “omic” technologies. Trends Microbiol 18:374–381. https://doi.org/10.1016/j.tim.2010.05.002
Celik Y, Drori R, Pertaya-Braun N et al (2013) Microfluidic experiments reveal that antifreeze proteins bound to ice crystals suffice to prevent their growth. Proc Natl Acad Sci USA 110:1309–1314. https://doi.org/10.1073/pnas.1213603110
Coker JA (2019) Recent advances in understanding extremophiles. F1000research. https://doi.org/10.12688/f1000research.20765.1
Collins T, Margesin R (2019) Psychrophilic lifestyles: mechanisms of adaptation and biotechnological tools. Appl Microbiol Biotechnol 103:2857–2871. https://doi.org/10.1007/s00253-019-09659-5
Dumorné K, Córdova DC, Astorga-Eló M, Renganathan P (2017) Extremozymes: A potential source for industrial applications. J Microbiol Biotechnol 27:649–659. https://doi.org/10.4014/jmb.1611.11006
Elleuche S, Schröder C, Sahm K, Antranikian G (2014) Extremozymes-biocatalysts with unique properties from extremophilic microorganisms. Curr Opin Biotechnol 29:116–123. https://doi.org/10.1016/j.copbio.2014.04.003
Faheem K (2021) Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati http://www.exprotdb.com/. Accessed 5 Jan 2021
Hait S, Mallik S, Basu S, Kundu S (2020) Finding the generalized molecular principles of protein thermal stability. Proteins Struct Funct Bioinforma 88:788–808. https://doi.org/10.1002/prot.25866
Jamroze A, Perugino G, Valenti A et al (2014) The reverse gyrase from Pyrobaculum calidifontis, a novel extremely Thermophilic DNA Topoisomerase endowed with DNA unwinding and Annealing activities. J Biol Chem 289:3231–3243. https://doi.org/10.1074/jbc.M113.517649
Kans J (2010–) Entrez direct: E-utilities on the Unix Command Line. 2013 Apr 23 [Updated 2021 Apr 29]. In: Entrez programming utilities help [Internet]. National Center for Biotechnology Information (US), Bethesda (MD). https://www.ncbi.nlm.nih.gov/books/NBK179288/
Kanz C, Aldebert P, Althorpe N et al (2005) The EMBL nucleotide sequence database. Nucleic Acids Res 33:29–33. https://doi.org/10.1093/nar/25.1.7
Keegan KP, Glass EM, Meyer F (2016) MG-RAST, a metagenomics service for analysis of microbial community structure and function. Methods Mol Biol 1399:207–233. https://doi.org/10.1007/8623_2015_119
Korendovych IV (2018) Rational and semirational protein design. Methods Mol Biol 1685:15–23. https://doi.org/10.1007/978-1-4939-7366-8_2
Krüger A, Schäfers C, Schröder C, Antranikian G (2018) Towards a sustainable biobased industry – Highlighting the impact of extremophiles. N Biotechnol 40:144–153. https://doi.org/10.1016/j.nbt.2017.05.002
Liao J, Warmuth MK, Govindarajan, et al (2007) Engineering proteinase K using machine learning and synthetic genes. BMC Biotechnol 7:1–19. https://doi.org/10.1186/1472-6750-7-16
Littlechild JA (2017) Improving the ‘tool box’ for robust industrial enzymes. J Ind Microbiol Biotechnol 44:711–720. https://doi.org/10.1007/s10295-017-1920-5
Loukas A, Kappas I, Abatzopoulos TJ (2018) HaloDom: A new database of halophiles across all life domains. J Biol Res 25:1–8. https://doi.org/10.1186/s40709-017-0072-0
Lutz S (2011) Beyond directed evolution—semi-rational protein engineering and design. Curr Opin Biotechnol 21:734–743. https://doi.org/10.1016/j.copbio.2010.08.011
McKinney W, et al (2010) Data structures for statistical computing in python. In: Proceedings of the 9th python in science conference, vol 445. pp 51–56. https://doi.org/10.25080/Majora-92bf1922-00a
Oren A (2004) Prokaryote diversity and taxonomy: Current status and future challenges. Philos Trans R Soc B Biol Sci 359:623–638. https://doi.org/10.1098/rstb.2003.1458
Pleissner D, Kümmerer K (2020) Green chemistry and its contribution to industrial biotechnology. Adv Biochem Eng Biotechnol 173:281–298. https://doi.org/10.1007/10_2018_73
Rampelotto PH (2013) Extremophiles and extreme environments. Life 3:482–485. https://doi.org/10.3390/life3030482
Reimer LC, Vetcininova A, Carbasse JS et al (2019) BacDive in 2019: Bacterial phenotypic data for High-throughput biodiversity analysis. Nucleic Acids Res 47:D631–D636. https://doi.org/10.1093/nar/gky879
Rigoldi F, Donini S, Redaelli A, Parisini E, Gautieri A (2018) Review: Engineering of thermostable enzymes for industrial applications. APL Bioeng 2:011501. https://doi.org/10.1063/1.4997367
Salwan R, Sharma V (2019) Trends in extracellular serine proteases of bacteria as detergent bioadditive: alternate and environmental friendly tool for detergent industry. Arch Microbiol 201:863–877. https://doi.org/10.1007/s00203-019-01662-8
Sang P, Liu SQ, Yang LQ (2020) New insight into mechanisms of protein adaptation to high temperatures: A comparative molecular dynamics simulation study of thermophilic and mesophilic subtilisin-like serine proteases. Int J Mol Sci 21:3128. https://doi.org/10.3390/ijms21093128
Sarmiento F, Peralta R, Blamey JM (2015) Cold and hot extremozymes: Industrial relevance and current trends. Front Bioeng Biotechnol 3:148. https://doi.org/10.3389/fbioe.2015.00148
Sharma N, Farooqi MS, Chaturvedi KK et al (2014) The halophile protein database. Database 2014:1–9. https://doi.org/10.1093/database/bau114
Siliakus MF, van der Oost J, Kengen SWM (2017) Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure. Extremophiles 21:651–670. https://doi.org/10.1007/s00792-017-0939-x
Tatusova T, DiCuccio M, Badretdin A et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569
Acknowledgement
Authors like to thank the Office of Information Technology and Knowledge Management (ITKM) SRM-IST, for hosting our database on the institute server. We also acknowledge the ITKM support team for their assistance with database related queries and the Dept. of Biotechnology for allotting the necessary permissions and resources.
Funding
No funding was received in support of this work.
Author information
Authors and Affiliations
Contributions
Jithin S. Sunny: Data curation, Formal analysis, Software, Resources, Data curation, Writing—Original Draft. Khairun Nisha: Data curation. Anuradha Natarajan: Data curation. Lilly M. Saleena: Project administration, Conceptualization, Writing—Review & Editing.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflicting financial interests.
Additional information
Communicated by I. Cann.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Sunny, J.S., Nisha, K., Natarajan, A. et al. IND-enzymes: a repository for hydrolytic enzymes derived from thermophilic and psychrophilic bacterial species with potential industrial usage. Extremophiles 25, 319–325 (2021). https://doi.org/10.1007/s00792-021-01231-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00792-021-01231-2