Novel CaLB-like Lipase Found Using ProspectBIO, a Software for Genome-Based Bioprospection

Enzymes have been highly demanded in diverse applications such as in the food, pharmaceutical, and industrial fuel sectors. Thus, in silico bioprospecting emerges as an efficient strategy for discovering new enzyme candidates. A new program called ProspectBIO was developed for this purpose as it can...

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Published in:BioTech
Main Authors: Brêda, Gabriela C., Faria, Priscila E., Rodrigues, Yuri S., Pinheiro, Priscila B., Nucci, Maria Clara R., Ferrer, Pau, Freire, Denise M. G., Almeida, Rodrigo V., Mesquita, Rafael D.
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Language:English
Published: MDPI 2023
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Online Access:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9844320/
http://www.ncbi.nlm.nih.gov/pubmed/36648832
https://doi.org/10.3390/biotech12010006
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spelling ftpubmed:oai:pubmedcentral.nih.gov:9844320 2023-05-15T13:44:25+02:00 Novel CaLB-like Lipase Found Using ProspectBIO, a Software for Genome-Based Bioprospection Brêda, Gabriela C. Faria, Priscila E. Rodrigues, Yuri S. Pinheiro, Priscila B. Nucci, Maria Clara R. Ferrer, Pau Freire, Denise M. G. Almeida, Rodrigo V. Mesquita, Rafael D. 2023-01-06 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9844320/ http://www.ncbi.nlm.nih.gov/pubmed/36648832 https://doi.org/10.3390/biotech12010006 en eng MDPI http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9844320/ http://www.ncbi.nlm.nih.gov/pubmed/36648832 http://dx.doi.org/10.3390/biotech12010006 © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). CC-BY BioTech (Basel) Article Text 2023 ftpubmed https://doi.org/10.3390/biotech12010006 2023-01-22T02:02:54Z Enzymes have been highly demanded in diverse applications such as in the food, pharmaceutical, and industrial fuel sectors. Thus, in silico bioprospecting emerges as an efficient strategy for discovering new enzyme candidates. A new program called ProspectBIO was developed for this purpose as it can find non-annotated sequences by searching for homologs of a model enzyme directly in genomes. Here we describe the ProspectBIO software methodology and the experimental validation by prospecting for novel lipases by sequence homology to Candida antarctica lipase B (CaLB) and conserved motifs. As expected, we observed that the new bioprospecting software could find more sequences (1672) than a conventional similarity-based search in a protein database (733). Additionally, the absence of patent protection was introduced as a criterion resulting in the final selection of a putative lipase-encoding gene from Ustilago hordei (UhL). Expression of UhL in Pichia pastoris resulted in the production of an enzyme with activity towards a tributyrin substrate. The recombinant enzyme activity levels were 4-fold improved when lowering the temperature and increasing methanol concentrations during the induction phase in shake-flask cultures. Protein sequence alignment and structural modeling showed that the recombinant enzyme has high similarity and capability of adjustment to the structure of CaLB. However, amino acid substitutions identified in the active pocket entrance may be responsible for the differences in the substrate specificities of the two enzymes. Thus, the ProspectBIO software allowed the finding of a new promising lipase for biotechnological application without the need for laborious and expensive conventional bioprospecting experimental steps. Text Antarc* Antarctica PubMed Central (PMC) BioTech 12 1 6
institution Open Polar
collection PubMed Central (PMC)
op_collection_id ftpubmed
language English
topic Article
spellingShingle Article
Brêda, Gabriela C.
Faria, Priscila E.
Rodrigues, Yuri S.
Pinheiro, Priscila B.
Nucci, Maria Clara R.
Ferrer, Pau
Freire, Denise M. G.
Almeida, Rodrigo V.
Mesquita, Rafael D.
Novel CaLB-like Lipase Found Using ProspectBIO, a Software for Genome-Based Bioprospection
topic_facet Article
description Enzymes have been highly demanded in diverse applications such as in the food, pharmaceutical, and industrial fuel sectors. Thus, in silico bioprospecting emerges as an efficient strategy for discovering new enzyme candidates. A new program called ProspectBIO was developed for this purpose as it can find non-annotated sequences by searching for homologs of a model enzyme directly in genomes. Here we describe the ProspectBIO software methodology and the experimental validation by prospecting for novel lipases by sequence homology to Candida antarctica lipase B (CaLB) and conserved motifs. As expected, we observed that the new bioprospecting software could find more sequences (1672) than a conventional similarity-based search in a protein database (733). Additionally, the absence of patent protection was introduced as a criterion resulting in the final selection of a putative lipase-encoding gene from Ustilago hordei (UhL). Expression of UhL in Pichia pastoris resulted in the production of an enzyme with activity towards a tributyrin substrate. The recombinant enzyme activity levels were 4-fold improved when lowering the temperature and increasing methanol concentrations during the induction phase in shake-flask cultures. Protein sequence alignment and structural modeling showed that the recombinant enzyme has high similarity and capability of adjustment to the structure of CaLB. However, amino acid substitutions identified in the active pocket entrance may be responsible for the differences in the substrate specificities of the two enzymes. Thus, the ProspectBIO software allowed the finding of a new promising lipase for biotechnological application without the need for laborious and expensive conventional bioprospecting experimental steps.
format Text
author Brêda, Gabriela C.
Faria, Priscila E.
Rodrigues, Yuri S.
Pinheiro, Priscila B.
Nucci, Maria Clara R.
Ferrer, Pau
Freire, Denise M. G.
Almeida, Rodrigo V.
Mesquita, Rafael D.
author_facet Brêda, Gabriela C.
Faria, Priscila E.
Rodrigues, Yuri S.
Pinheiro, Priscila B.
Nucci, Maria Clara R.
Ferrer, Pau
Freire, Denise M. G.
Almeida, Rodrigo V.
Mesquita, Rafael D.
author_sort Brêda, Gabriela C.
title Novel CaLB-like Lipase Found Using ProspectBIO, a Software for Genome-Based Bioprospection
title_short Novel CaLB-like Lipase Found Using ProspectBIO, a Software for Genome-Based Bioprospection
title_full Novel CaLB-like Lipase Found Using ProspectBIO, a Software for Genome-Based Bioprospection
title_fullStr Novel CaLB-like Lipase Found Using ProspectBIO, a Software for Genome-Based Bioprospection
title_full_unstemmed Novel CaLB-like Lipase Found Using ProspectBIO, a Software for Genome-Based Bioprospection
title_sort novel calb-like lipase found using prospectbio, a software for genome-based bioprospection
publisher MDPI
publishDate 2023
url http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9844320/
http://www.ncbi.nlm.nih.gov/pubmed/36648832
https://doi.org/10.3390/biotech12010006
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http://www.ncbi.nlm.nih.gov/pubmed/36648832
http://dx.doi.org/10.3390/biotech12010006
op_rights © 2023 by the authors.
https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
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