Abstract
Hyaluronidases are a group of glycosidases enzymes, which are widely produced by different organisms. To find a bacterial source of hyaluronidases with promising industrial characteristics, different species of Bacillus were analyzed according to their various physiochemical properties, multiple sequence alignment, phylogenetic tree construction, homology search for motifs, and structural and functional properties via various computational approaches. The evaluation showed that the hyaluronidase of B. selenitireducens with the highest molecular mass, a high level of thermostability and solubility, and the phylogenetic relationship to hyaluronidas derivative from S. aureus can be considered as a potential candidate for biotechnological applications. Generally, the present study provides a detailed overview of functional, and structural characteristics as well as phylogenetic relation of Bacillus hyaluronidases, which could be helpful for future investigations in order to find the best bacterial hyaluronidase.
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Abbreviations
- CDD:
-
Conserved Domain Database
- HAase:
-
Hyaluronate lyase
- MD:
-
Molecular Dynamics
- BTH:
-
Bovine testicular hyaluronidase
- pI:
-
Isoelectric point
- PSIPRED:
-
PSIblast based secondary structure prediction
- CFSSP:
-
Chou and Fasman secondary structure prediction
- PSI-BLAST:
-
Position Specific Iterated - BLAST
- 3D:
-
Three-dimensional
- Mw:
-
Molecular weight
- EC:
-
Extinction coefficient
- GRAVY:
-
Grand average of hydropathicity
- MSA:
-
Multiple sequence alignment
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This work was supported by grant from Gerash University of Medical Sciences, Gerash, Iran (Grant NO. 98000047). Compliance with Ethical Standards.
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Fig. S1
The 3D- structures of hyaluronate lyase from different Bacillus species predicted by Galaxy TBM server. Five models have been predicted for hyaluronidase protein of every Bacillus sp.; left to right: 1–5. The models of B. cereus, Bacillus sp. OK48, Bacillus sp. LF1, B. niacini, B. selenitireducens have been depicted vertically A to E, respectively. (JPG 9000 kb)
Fig. S2
ProSA-web z-score plot. The z-score indicates overall model quality. The plot contains the z-score of all typically found for native proteins of similar size from different sources (X-ray, NMR). The z-score value of the selected hyaluronate lyase protein has been shown with (.) in the plots. The Five z-score plots have been depicted for five predicted models of hyaluronidase protein of every Bacillus sp.; left to right: 1–5. The z-score plots of B. cereus, Bacillus sp. OK48, Bacillus sp. LF1, B. niacini, B. selenitireducens have been depicted vertically A to E, respectively. (JPG 6829 kb)
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Karimi, Z., Abed, L., Abdollahi, A. et al. Computational analysis of phylogenetic, functional and structural features of Bacillus hyaluronate lyases. Biologia 76, 381–393 (2021). https://doi.org/10.2478/s11756-020-00580-1
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DOI: https://doi.org/10.2478/s11756-020-00580-1