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Advances in genomics have profoundly influenced drug discovery by increasing both the speed and accuracy of pharmaceutical development. Pharmacogenomics, which examines how genetic variation influences drug response, facilitates the identification of novel therapeutic targets and enables patient stratification for personalized treatment. These strategies contribute to improved drug efficacy, minimized adverse effects, and more efficient clinical trial design.Mapping genetic differences...

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Defining Substrate Specificities for Lipase and Phospholipase Candidates
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Novel CaLB-like Lipase Found Using ProspectBIO, a Software for Genome-Based Bioprospection.

Gabriela C Brêda1, Priscila E Faria1, Yuri S Rodrigues1

  • 1Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos 149, Rio de Janeiro 21941-909, Brazil.

Biotech (Basel (Switzerland))
|January 17, 2023
PubMed
Summary

A new software, ProspectBIO, efficiently discovers novel enzymes like lipases by searching genomes for enzyme homologs. This method found more candidates than traditional searches, leading to a new lipase from Ustilago hordei with improved activity for biotechnological applications.

Keywords:
CaLBbioprospectionfunctional characterizationprotein

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Area of Science:

  • Biotechnology
  • Bioinformatics
  • Enzyme Engineering

Background:

  • Enzymes are crucial in food, pharmaceutical, and industrial fuel sectors.
  • In silico bioprospecting offers an efficient strategy for discovering new enzyme candidates.
  • Limitations exist in conventional similarity-based searches for novel enzymes.

Purpose of the Study:

  • To introduce and validate the ProspectBIO software for in silico enzyme discovery.
  • To identify novel lipase candidates using sequence homology and conserved motifs.
  • To experimentally validate a newly discovered lipase for biotechnological applications.

Main Methods:

  • Development of ProspectBIO software for non-annotated sequence identification via genome-based homolog searching.
  • Prospecting for lipases using sequence homology to *Candida antarctica* lipase B (CaLB) and conserved motifs.
  • Experimental validation including gene expression in *Pichia pastoris*, enzyme activity assays, and structural analysis.

Main Results:

  • ProspectBIO identified 1672 lipase sequences, significantly more than the 733 found by conventional database searches.
  • A novel lipase gene from *Ustilago hordei* (UhL) was selected based on homology and lack of patent protection.
  • Recombinant UhL exhibited tributyrin hydrolysis activity, with activity enhanced 4-fold under optimized induction conditions.
  • Structural analysis revealed high similarity to CaLB but with distinct active pocket entrance features, suggesting altered substrate specificity.

Conclusions:

  • ProspectBIO is an effective tool for discovering novel enzyme candidates, including lipases, from genomic data.
  • The identified *Ustilago hordei* lipase (UhL) shows promise for biotechnological applications.
  • Optimized expression and structural insights provide a foundation for further enzyme engineering and application development.