Copper ion altered association network among multi-genes and enzyme activity of laccase in Ganoderma lucidum
Author and article information
Abstract
Background: Laccases, copper-based polyphenol oxidases, played vital roles in lignin and humus degradation as well as fruiting body formation and stress response. Sixteen putative laccase genes (Lacc1-Lacc16) were reported in the genome of white-rot fungus Ganoderma lucidum. Members in this multi-gene family usually had close inter-relationships and may vary in the roles contributing to functions. Identifying the interactions among multiple genes and thus the conjoined consequence to an activity was essential for systematically unraveling the molecular mechanisms of laccase and improving laccase activity.
Methods: In this study, multivariate statistical analysis was applied to track the relationship between thetranscriptional level of laccase genes and the total enzymatic activities. We outlined and compared the interaction networks among the transcriptional levels of 16 laccase genes and associations with the total enzymatic activities with or without copper ion (Cu 2+ ).
Results: A multi-gene interaction network among the sixteen genes and laccase activity was constructed to figure out the changes induced by Cu 2+ . The interaction network showed that the enzyme activity was the result of interactions among genes, and these interactions might vary with the presence of Cu 2+ , subsequently leading to the alteration of enzyme activity. Some genes always kept relation with enzyme activity (positive or negative, Lacc13, Lacc10), some were irrelevant (Lacc1, Lacc6), while another some were inconsistent (Lacc3, Lacc8, Lacc14 and Lacc15).
Discussion: Network-based methods were applied to identify key functional genes and to outline associations among genes and phenotype in laccase multi-gene family. This is an exploratory strategy to describe the transcriptional complexity of laccase and its relevant responses to Cu 2+ stress. The identified key functional genes associated with laccase activity (e.g. Lacc10, Lacc13) and the associations among genes and activity will benefit for the regulation of enzyme activity.
Cite this as
2018. Copper ion altered association network among multi-genes and enzyme activity of laccase in Ganoderma lucidum. PeerJ Preprints 6:e26982v1 https://doi.org/10.7287/peerj.preprints.26982v1Author comment
This is a submission to PeerJ for review.
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Supplemental Information
Time course transcriptional profiles of putative laccase genes in G. lucidum
Distribution of putative cis-acting elements in the promoter region of gene Lacc1-Lacc16 upstream 2000 bp of the start codon
Raw data about the gene expression of laccase genes and the activity of laccase
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Xincong Kang analyzed the data, authored or reviewed drafts of the paper, approved the final draft.
Yuewen Chen performed the experiments, approved the final draft.
Sien Yan performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.
Luman Zeng analyzed the data, prepared figures and/or tables, approved the final draft.
Xuehui Liu contributed reagents/materials/analysis tools, prepared figures and/or tables, approved the final draft.
Yongquan Hu performed the experiments, approved the final draft.
Yunlin Wei authored or reviewed drafts of the paper, approved the final draft.
Xiuling Ji authored or reviewed drafts of the paper, approved the final draft.
Dongbo Liu conceived and designed the experiments, approved the final draft.
Data Deposition
The following information was supplied regarding data availability:
The raw measurements are provided in the supplementary Table S1,Fig. S1 and Fig. S2.
Funding
This work was supported by the National Natural Science Foundation of China (NSFC) (Grant No. 81773850). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
