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Genome-wide study of Cerrena unicolor 87613 laccase gene family and their mode prediction in association with substrate oxidation

BACKGROUND: Laccases are green biocatalysts with wide industrial applications. The study of efficient and specific laccase producers remains a priority. Cerrena species have been shown to be promising basidiomycete candidates for laccase production. Although two sets of Cerrena genome data have been...

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Autores principales: Zhang, Long-Bin, Yang, Wu-Wei-Jie, Qiu, Ting-Ting
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10466755/
https://www.ncbi.nlm.nih.gov/pubmed/37649000
http://dx.doi.org/10.1186/s12864-023-09606-9
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author Zhang, Long-Bin
Yang, Wu-Wei-Jie
Qiu, Ting-Ting
author_facet Zhang, Long-Bin
Yang, Wu-Wei-Jie
Qiu, Ting-Ting
author_sort Zhang, Long-Bin
collection PubMed
description BACKGROUND: Laccases are green biocatalysts with wide industrial applications. The study of efficient and specific laccase producers remains a priority. Cerrena species have been shown to be promising basidiomycete candidates for laccase production. Although two sets of Cerrena genome data have been publicly published, no comprehensive bioinformatics study of laccase gene family in C. unicolor has been reported, particularly concerning the analysis of their three-dimensional (3D) structures and molecular docking to substrates, like ABTS and aflatoxin B(1) (AFB(1)). RESULTS: In this study, we conducted a comprehensive genome-wide analysis of laccase gene family in C. unicolor 87613. We identified eighteen laccase genes (CuLacs) and classified them into three clades using phylogenetic analysis. We characterized these laccases, including their location in contig 5,6,9,12,15,19,26,27, gene structures of different exon-intron arrangements, molecular weight ranging from 47.89 to 141.41 kDa, acidic pI value, 5–15 conserved protein motifs, signaling peptide of extracellular secretion (harbored by 13 CuLacs) and others. In addition, the analysis of cis-acting element in laccase promoters indicated that the transcription response of CuLac gene family was regulatable and complex under different environmental cues. Furthermore, analysis of transcription pattern revealed that CuLac8, 12 and CuLac2, 13 were the predominant laccases in response to copper ions or oxidative stress, respectively. Finally, we focused on the 3D structure analysis of CuLac proteins. Seven laccases with extra transmembrane domains or special sequences were particularly interesting. Predicted structures of each CuLac protein with or without these extra sequences showed altered interacting amino acid residues and binding sites, leading to varied affinities to both ABTS and AFB(1). As far as we know, it is the first time to discuss the influence of the extra sequence on laccase’s affinity to substrates. CONCLUSIONS: Our findings provide robust genetic data for a better understanding of the laccase gene family in C. unicolor 87613, and create a foundation for the molecular redesign of CuLac proteins to enhance their industrial applications. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09606-9.
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spelling pubmed-104667552023-08-31 Genome-wide study of Cerrena unicolor 87613 laccase gene family and their mode prediction in association with substrate oxidation Zhang, Long-Bin Yang, Wu-Wei-Jie Qiu, Ting-Ting BMC Genomics Research BACKGROUND: Laccases are green biocatalysts with wide industrial applications. The study of efficient and specific laccase producers remains a priority. Cerrena species have been shown to be promising basidiomycete candidates for laccase production. Although two sets of Cerrena genome data have been publicly published, no comprehensive bioinformatics study of laccase gene family in C. unicolor has been reported, particularly concerning the analysis of their three-dimensional (3D) structures and molecular docking to substrates, like ABTS and aflatoxin B(1) (AFB(1)). RESULTS: In this study, we conducted a comprehensive genome-wide analysis of laccase gene family in C. unicolor 87613. We identified eighteen laccase genes (CuLacs) and classified them into three clades using phylogenetic analysis. We characterized these laccases, including their location in contig 5,6,9,12,15,19,26,27, gene structures of different exon-intron arrangements, molecular weight ranging from 47.89 to 141.41 kDa, acidic pI value, 5–15 conserved protein motifs, signaling peptide of extracellular secretion (harbored by 13 CuLacs) and others. In addition, the analysis of cis-acting element in laccase promoters indicated that the transcription response of CuLac gene family was regulatable and complex under different environmental cues. Furthermore, analysis of transcription pattern revealed that CuLac8, 12 and CuLac2, 13 were the predominant laccases in response to copper ions or oxidative stress, respectively. Finally, we focused on the 3D structure analysis of CuLac proteins. Seven laccases with extra transmembrane domains or special sequences were particularly interesting. Predicted structures of each CuLac protein with or without these extra sequences showed altered interacting amino acid residues and binding sites, leading to varied affinities to both ABTS and AFB(1). As far as we know, it is the first time to discuss the influence of the extra sequence on laccase’s affinity to substrates. CONCLUSIONS: Our findings provide robust genetic data for a better understanding of the laccase gene family in C. unicolor 87613, and create a foundation for the molecular redesign of CuLac proteins to enhance their industrial applications. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09606-9. BioMed Central 2023-08-30 /pmc/articles/PMC10466755/ /pubmed/37649000 http://dx.doi.org/10.1186/s12864-023-09606-9 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Zhang, Long-Bin
Yang, Wu-Wei-Jie
Qiu, Ting-Ting
Genome-wide study of Cerrena unicolor 87613 laccase gene family and their mode prediction in association with substrate oxidation
title Genome-wide study of Cerrena unicolor 87613 laccase gene family and their mode prediction in association with substrate oxidation
title_full Genome-wide study of Cerrena unicolor 87613 laccase gene family and their mode prediction in association with substrate oxidation
title_fullStr Genome-wide study of Cerrena unicolor 87613 laccase gene family and their mode prediction in association with substrate oxidation
title_full_unstemmed Genome-wide study of Cerrena unicolor 87613 laccase gene family and their mode prediction in association with substrate oxidation
title_short Genome-wide study of Cerrena unicolor 87613 laccase gene family and their mode prediction in association with substrate oxidation
title_sort genome-wide study of cerrena unicolor 87613 laccase gene family and their mode prediction in association with substrate oxidation
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10466755/
https://www.ncbi.nlm.nih.gov/pubmed/37649000
http://dx.doi.org/10.1186/s12864-023-09606-9
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