Comparative analysis of the structural and functional features of endoglucanases with different temperature optima
https://doi.org/10.21285/achb.946
EDN: SRPVFQ
Abstract
Cellulases whose temperature optimum is shifted to extremely high or low values are of particular interest since they allow for greater flexibility in controlling the technological conditions of their industrial use. Nevertheless, the mechanisms that explain enzymatic adaptations to limiting temperatures are not fully established. The study was aimed at using bioinformatics methods to examine how the structure of microbial endoglucanases depends on two factors: the belonging of producers to different taxonomic groups of higher rank (bacteria, fungi, and archaea) and the temperature optimum of their habitat (psychro-, meso-, and thermophiles). Enzymes retrieved from Uniprot and GenBank were analyzed via pairwise and multiple sequence alignment, pairwise structural alignment, and comparison of amino acid profiles. It is shown that the sequences cluster according to the systematics of producers and do not contain patterns associated with adaptations to temperature conditions. However, the amino acid profile of proteins depends also on the temperature conditions of the microbial habitat: the frequencies of some amino acids (E, I, Y, D, and Q) differ significantly in enzymes with different temperature optima. The study also identified a set of enzymes with low sequence identity but high similarity of 3D structures. This set includes enzymes from related taxa but with different temperature optima, as well as endoglucanases from microorganisms that are systematically distant while living under similar temperature conditions. Among other things, the possible mechanisms of the observed differences between the identity scores of different structural levels of protein are discussed.
About the Authors
O. S. Petukhova
Irkutsk State University
Russian Federation
Russian Federation
Olga S. Petukhova, Postgraduate Student
1, Karl Marx St., Irkutsk, 664033
A. A. Pristavka
Irkutsk State University
Russian Federation
Russian Federation
Aleksei A. Pristavka, Cand. Sci. (Biology), Associate Professor, Associate Professor
1, Karl Marx St., Irkutsk, 664033
E. A. Pristavka
Institute of Solar-Terrestrial Physics SB RAS
Russian Federation
Russian Federation
Egor A. Pristavka, Software Engineer
126a, Lermontov St., Irkutsk, 664033
D. E. Gavrikov
Irkutsk State University
Russian Federation
Russian Federation
Dmitrii E. Gavrikov, Cand. Sci. (Biology), Associate Professor, Associate Professor
1, Karl Marx St., Irkutsk, 664033
V. P. Salovarova
Irkutsk State University
Russian Federation
Russian Federation
Valentina P. Salovarova, Dr. Sci. (Biology), Professor, Department Chair
1, Karl Marx St., Irkutsk, 664033
References
1. Klyosov A.A., Grigorash S.Yu. Enzymatic hydrolysis of cellulose. Regulatory effect of the non-soluble substrate on the effectiveness of the enzymatic reaction. Biokhimiya. 1982;47(3):409-418. (In Russian).
2. Singhania R.R., Adsul M., Pandey A., Patel A.K. Cellulases. In: Pandey A., Negi S., Soccol C.R. (eds). Current developments in biotechnology and bioengineering. Elsevier; 2017, p. 73-101. DOI: 10.1016/B978-0-444-63662-1.00004-X.
3. Ahmed A., Bibi A. Fungal cellulase; production and applications: minireview. LIFE: International Journal of Health and Life-Sciences. 2018:4(1):19-36. DOI: 10.20319/lijhls.2018.41.1936.
4. Magrey A., Sahay S., Gothalwal R. Cellulases for biofuel: a review. International Journal of Recent Trends in Science and Technology. 2018;17-25. Available from: https://www.statperson.com/Journal/ScienceAndTechnology/Article/SpecialIssue/ACAEE_4.pdf [Accessed 17th June 2024].
5. Srivastava N., Srivastava M., Mishra P.K., Gupta V.K., Molina G., Rodriguez-Couto S., et al. Applications of fungal cellulases in biofuel production: advances and limitations. Renewable and Sustainable Energy Reviews. 2018;82:2379- 2386. DOI: 10.1016/j.rser.2017.08.074.
6. Chang W.H., Lai A.G. Mixed evolutionary origins of endogenous biomass-depolymerizing enzymes in animals. BMC Genomics. 2018;19:483. DOI: 10.1186/s12864-018-4861-0.
7. Thapa S., Mishra J., Arora N., Mishra P., Li H., O′Hair J., et al. Microbial cellulolytic enzymes: diversity and biotechnology with reference to lignocellulosic biomass degradation. Reviews in Environmental Science and Bio/Technology. 2020;19:621-648. DOI: 10.1007/s11157-020-09536-y.
8. Ajeje S.B., Hu Y., Song G., Peter S.B., Afful R.G., Sun F., et al. Thermostable cellulases / xylanases from thermophilic and hyperthermophilic microorganisms: current perspective. Frontiers in Bioengineering and Biotechnology. 2021;9:794304. DOI: 10.3389/fbioe.2021.794304.
9. Akram F., ul Haq I., Aqeel A., Ahmed Z., Shah F.I. Thermostable cellulases: structure, catalytic mechanisms, directed evolution and industrial implementations. Renewable and Sustainable Energy Reviews. 2021;151:111597. DOI: 10.1016/j.rser.2021.111597.
10. Akram F., ul Haq I., Imran W., Mukhtar H. Insight perspectives of thermostable endoglucanases for bioethanol production: a review. Renewable Energy. 2018;122:225- 238. DOI: 10.1016/j.renene.2018.01.095.
11. Cai L.N., Xu S.N., Lu T., Lin D.Q., Yao S.J. Salt-tolerant and thermostable mechanisms of an endoglucanase from marine Aspergillus niger. Bioresources and Bioprocessing. 2022;9:44. DOI: 10.1186/s40643-022-00533-3.
12. Kasana R.C., Gulati A. Cellulases from psychrophilic microorganisms: a review. Journal of Basic Microbiology. 2011;51(6):572-579. DOI: 10.1002/jobm.201000385.
13. Chavan S., Shete A., Mirza Y., Dharne M.S. Investigation of cold-active and mesophilic cellulases: opportunities awaited. Biomass Conversion and Biorefinery. 2023;13:8829-8852. DOI: 10.1007/s13399-021-02047-y.
14. Gupta S.K., Kataki S., Chatterjee S., Prasad R.K., Datta S., Vairale M.G., et al. Cold adaptation in bacteria with special focus on cellulase production and its potential application. Journal of Cleaner Production. 2020;258:120351. DOI: 10.1016/j.jclepro.2020.120351.
15. Yunus G., Kuddus M. Cold-active microbial cellulase: novel approach to understand mechanism and its applications in food and beverages industry. Journal of Microbiology, Biotechnology and Food Sciences. 2021;10(4):524-530. DOI: 10.15414/jmbfs.2021.10.4.524-530.
16. Yusof N.A., Hashim N.H.F., Bharudin I. Cold adaptation strategies and the potential of psychrophilic enzymes from the Antarctic yeast, Glaciozyma antarctica PI12. Journal of Fungi. 2021;7(7):528. DOI: 10.3390/jof7070528.
17. Öten A.M., Atak E., Karaca B.T., Fırtına S., Kutlu A. Discussing the roles of proline and glycine from the perspective of cold adaptation in lipases and cellulases. Biocatalysis and Biotransformation. 2023;41(4):243-260. DOI: 10.1080/10242422.2022.2124111.
18. Waterhouse A., Bertoni M., Bienert S., Studer G., Tauriello G., Gumienny R., et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Research. 2018;46(W1):W296-W303. DOI: 10.1093/nar/gky427.
19. Tamura K., Stecher G., Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution. 2021;38(7):3022-3027. DOI: 10.1093/molbev/msab120.
20. Farias S.T., Bonato M.C.M. Preferred amino acids and thermostability. Genetics and Molecular Research. 2003;2(4):383-393.
Review
For citations:
Petukhova O.S., Pristavka A.A., Pristavka E.A., Gavrikov D.E., Salovarova V.P. Comparative analysis of the structural and functional features of endoglucanases with different temperature optima. Proceedings of Universities. Applied Chemistry and Biotechnology. 2024;14(4):596-604. (In Russ.) https://doi.org/10.21285/achb.946. EDN: SRPVFQ
Views:
100
Email this article 