Prospective Identification of Extracellular Triacylglycerol Hydrolase with Conserved Amino Acids in 's High G+C Genomic Dataset

Overview

Journal Biotechnol Rep (Amst)

Specialty Biotechnology

Date 2025 Jan 6

PMID 39758972

Authors

Supajit Sraphet

Bagher Javadi

Affiliations

Soon will be listed here.

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, . 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.

References

Lassalle F, Perian S, Bataillon T, Nesme X, Duret L, Daubin V . GC-Content evolution in bacterial genomes: the biased gene conversion hypothesis expands. PLoS Genet. 2015; 11(2):e1004941. PMC: 4450053. DOI: 10.1371/journal.pgen.1004941. View

Sraphet S, Javadi B . Computational characterizations of GDP-mannose 4,6-dehydratase (NoeL) Rhizobial proteins. Curr Genet. 2021; 67(5):769-784. DOI: 10.1007/s00294-021-01184-1. View

Dietel A, Merker H, Kaltenpoth M, Kost C . Selective advantages favour high genomic AT-contents in intracellular elements. PLoS Genet. 2019; 15(4):e1007778. PMC: 6519830. DOI: 10.1371/journal.pgen.1007778. View

van Tilbeurgh H, Egloff M, Martinez C, Rugani N, Verger R, Cambillau C . Interfacial activation of the lipase-procolipase complex by mixed micelles revealed by X-ray crystallography. Nature. 1993; 362(6423):814-20. DOI: 10.1038/362814a0. View

Derewenda Z, Derewenda U, Dodson G . The crystal and molecular structure of the Rhizomucor miehei triacylglyceride lipase at 1.9 A resolution. J Mol Biol. 1992; 227(3):818-39. DOI: 10.1016/0022-2836(92)90225-9. View

Hildebrand F, Meyer A, Eyre-Walker A . Evidence of selection upon genomic GC-content in bacteria. PLoS Genet. 2010; 6(9):e1001107. PMC: 2936529. DOI: 10.1371/journal.pgen.1001107. View

Corpet F . Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 1988; 16(22):10881-90. PMC: 338945. DOI: 10.1093/nar/16.22.10881. View

Kumar S, Stecher G, Li M, Knyaz C, Tamura K . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35(6):1547-1549. PMC: 5967553. DOI: 10.1093/molbev/msy096. View

Yu C, Chen Y, Lu C, Hwang J . Prediction of protein subcellular localization. Proteins. 2006; 64(3):643-51. DOI: 10.1002/prot.21018. View

10.

Tang W, Lan D, Zhao Z, Li S, Li X, Wang Y . A Thermostable Monoacylglycerol Lipase from Marine sp. 12AMOR1: Biochemical Characterization and Mutagenesis Study. Int J Mol Sci. 2019; 20(3). PMC: 6386982. DOI: 10.3390/ijms20030780. View

11.

Veit-Acosta M, de Azevedo Junior W . Computational Prediction of Binding Affinity for CDK2-ligand Complexes. A Protein Target for Cancer Drug Discovery. Curr Med Chem. 2021; 29(14):2438-2455. DOI: 10.2174/0929867328666210806105810. View

12.

Muller J, Sowa M, Fredrich B, Brundiek H, Bornscheuer U . Enhancing the Acyltransferase Activity of Candida antarctica Lipase A by Rational Design. Chembiochem. 2015; 16(12):1791-6. DOI: 10.1002/cbic.201500187. View

13.

Paraje M, Correa S, Renna M, Theumer M, Sotomayor C . Candida albicans-secreted lipase induces injury and steatosis in immune and parenchymal cells. Can J Microbiol. 2008; 54(8):647-59. DOI: 10.1139/w08-048. View

14.

Verma M, Kaur J, Kumar M, Kumari K, Saxena A, Anand S . Whole genome sequence of the rifamycin B-producing strain Amycolatopsis mediterranei S699. J Bacteriol. 2011; 193(19):5562-3. PMC: 3187414. DOI: 10.1128/JB.05819-11. View

15.

Kogay R, Wolf Y, Koonin E, Zhaxybayeva O . Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents. mBio. 2020; 11(4). PMC: 7360931. DOI: 10.1128/mBio.01206-20. View

16.

Padhi S, Fujii R, Legatt G, Fossum S, Berchtold R, Kazlauskas R . Switching from an esterase to a hydroxynitrile lyase mechanism requires only two amino acid substitutions. Chem Biol. 2010; 17(8):863-71. DOI: 10.1016/j.chembiol.2010.06.013. View

17.

Chahinian H, Sarda L . Distinction between esterases and lipases: comparative biochemical properties of sequence-related carboxylesterases. Protein Pept Lett. 2009; 16(10):1149-61. DOI: 10.2174/092986609789071333. View

18.

Weissman J, Fagan W, Johnson P . Linking high GC content to the repair of double strand breaks in prokaryotic genomes. PLoS Genet. 2019; 15(11):e1008493. PMC: 6867656. DOI: 10.1371/journal.pgen.1008493. View

19.

Pettersen E, Goddard T, Huang C, Couch G, Greenblatt D, Meng E . UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004; 25(13):1605-12. DOI: 10.1002/jcc.20084. View

20.

Kumari R, Singh P, Lal R . Genetics and Genomics of the Genus Amycolatopsis. Indian J Microbiol. 2016; 56(3):233-46. PMC: 4920768. DOI: 10.1007/s12088-016-0590-8. View