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. 2024 Dec 7:45:e00869.
doi: 10.1016/j.btre.2024.e00869. eCollection 2025 Mar.

Prospective identification of extracellular triacylglycerol hydrolase with conserved amino acids in Amycolatopsis tolypomycina's high G+C genomic dataset

Supajit Sraphet  1 , Bagher Javadi  2
Affiliations

Prospective identification of extracellular triacylglycerol hydrolase with conserved amino acids in Amycolatopsis tolypomycina's high G+C genomic dataset

Supajit Sraphet et al. Biotechnol Rep (Amst). .

Abstract

Extracellular triacylglycerol hydrolases (ETH) play a critical role for microorganisms, acting as essential tools for lipid breakdown and survival in challenging environments. The pursuit of more effective ETH genes and enzymes through evolution holds significant potential for enhancing living conditions. This study employs a proteogenomic approach to identify high G+C ETH in a notable Gram-positive bacterium, Amycolatopsis tolypomycina. Utilizing knowledge from genome and machine learning algorithms, prospective ETH genes/enzymes were identified. Notably, the ETH structural conserved accessibility to solvent clearly indicated the specific sixteen residues (GLY50, PRO93, GLY141, ASP148, GLY151, ASP172, ALA176, GLY195, TYR196, SER197, GLN198, GLY199, GLY200, GLY225, PRO327, ASP336) with no frequency. By pinpointing key residues and understanding their role, this study sets the stage for enhancing ETH performance through computational proteogenomic and contributes to the broader field of enzyme engineering, facilitating the development of more efficient and versatile ETH enzymes tailored to specific industrial or environmental contexts.

Keywords: Amycolatopsis tolypomycina; Computational proteogenomics; Conserved-solvent accessibility; Enzyme stability; Structural biology analysis.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig 1
Fig. 1
Phylogenetic of A. tolypomycina extracellular triacylglycerol hydrolase and other bacteria.
Fig 2
Fig. 2
Hierarchical clustering of total solvent accessible surface area (SASA) (A), surface and nucleus SASA (B), conserved region-SASA (C), all features (D) of A. tolypomycina extracellular triacylglycerol hydrolase.
Fig 3
Fig. 3
The conserved residues with minimum SASA (zero) in the structure of A. tolypomycina Extracellular Triacylglycerol Hydrolase (I, II). The residues with maximum SASA in the structure of A. tolypomycina Extracellular Triacylglycerol Hydrolase (III). ETH1, ETH2, ETH3, ETH4 and ETH5 presented as (A), (B), (C), (D) and (E).
Fig 4
Fig. 4
Protein-protein interaction; SED48308.1: Extracellular Triacylglycerol Hydrolase, SEB32356.1: Lipase, SEB33493.1: Triacylglycerol esterase/lipase EstA, alpha/beta hydrolase fold, SEC27701.1: Long-chain acyl-CoA synthetase, SED50494.1: Long-chain acyl-CoA synthetase, SED61802.1: Site-specific DNA recombinase, SEC99939.1: S-formylglutathione hydrolase FrmB, SED48235.1: Uncharacterized protein, SEC46221.1: Regulatory protein, tetR family.
Fig 5
Fig. 5
Full genome presentations of A. tolypomycina sequence datasets (GenBank: FNSO01000004 (A), FNSO01000003 (B), FNSO01000002 (C), ETH highlighted with red asterisks.
See this image and copyright information in PMC

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