Metagenomic investigation of bacterial laccases in a straw-amended soil
Background Bacterial laccases play a crucial role in the degradation of lignin and the turnover of soil organic matter. Their advantageous properties make them highly suitable for a wide range of industrial applications. However, the limited identification of these potential enzymes has impeded thei...
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PeerJ Inc.
2025-04-01
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| author | Dali Yu Ying Liu Hongying Cai Wanqiu Huang Huijun Wu Peilong Yang |
| author_facet | Dali Yu Ying Liu Hongying Cai Wanqiu Huang Huijun Wu Peilong Yang |
| author_sort | Dali Yu |
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| description | Background Bacterial laccases play a crucial role in the degradation of lignin and the turnover of soil organic matter. Their advantageous properties make them highly suitable for a wide range of industrial applications. However, the limited identification of these potential enzymes has impeded their full utilization. The straw-amended soil provides materials for the development of bacterial laccases. Methods Metagenomic sequencing of a straw-amended soil was conducted to explore novel bacterial laccases. The putative bacterial laccases were then screened using profile hidden Markov models for further analysis. The most abundant gene, lacS1, was heterologously expressed in Escherichia coli and the recombinant laccase was purified for enzymatic characterization. Results A total of 322 putative bacterial laccases were identified in the straw-amended soil. Among them, 45 sequences had less than 30% identity to any entries in the Carbohydrate-Active Enzyme database and only 4.66% were more than 75% similar to proteins in the NCBI environmental database, exhibiting their novelty. These enzymes were found across various bacterial orders, demonstrating substantial diversity. Phylogenetic analysis revealed a number of the bacterial laccase sequences clustered with homologs characterized by favorable enzymatic properties. Five full-length representative bacterial laccase genes were obtained by modified thermal asymmetric interlaced PCR. The laccase activity of lacS1 was validated. It was a mesophilic enzyme with alkaline stability and halotolerance, indicating its promise for industrial applications. Implications These findings highlight novel bacterial laccase resources with potential for industrial applications and enzyme engineering. |
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| language | English |
| publishDate | 2025-04-01 |
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| spelling | doaj-art-ff6bb2e8eda34a51a48bcadf9daac0952025-08-20T01:48:28ZengPeerJ Inc.PeerJ2167-83592025-04-0113e1932710.7717/peerj.19327Metagenomic investigation of bacterial laccases in a straw-amended soilDali Yu0Ying Liu1Hongying Cai2Wanqiu Huang3Huijun Wu4Peilong Yang5Qilu Normal University, Jinan, Shandong, ChinaQilu Normal University, Jinan, Shandong, ChinaKey Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, National Engineering Research Center of Biological Feed, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, ChinaKey Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, National Engineering Research Center of Biological Feed, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, ChinaKey Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, National Engineering Research Center of Biological Feed, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, ChinaBackground Bacterial laccases play a crucial role in the degradation of lignin and the turnover of soil organic matter. Their advantageous properties make them highly suitable for a wide range of industrial applications. However, the limited identification of these potential enzymes has impeded their full utilization. The straw-amended soil provides materials for the development of bacterial laccases. Methods Metagenomic sequencing of a straw-amended soil was conducted to explore novel bacterial laccases. The putative bacterial laccases were then screened using profile hidden Markov models for further analysis. The most abundant gene, lacS1, was heterologously expressed in Escherichia coli and the recombinant laccase was purified for enzymatic characterization. Results A total of 322 putative bacterial laccases were identified in the straw-amended soil. Among them, 45 sequences had less than 30% identity to any entries in the Carbohydrate-Active Enzyme database and only 4.66% were more than 75% similar to proteins in the NCBI environmental database, exhibiting their novelty. These enzymes were found across various bacterial orders, demonstrating substantial diversity. Phylogenetic analysis revealed a number of the bacterial laccase sequences clustered with homologs characterized by favorable enzymatic properties. Five full-length representative bacterial laccase genes were obtained by modified thermal asymmetric interlaced PCR. The laccase activity of lacS1 was validated. It was a mesophilic enzyme with alkaline stability and halotolerance, indicating its promise for industrial applications. Implications These findings highlight novel bacterial laccase resources with potential for industrial applications and enzyme engineering.https://peerj.com/articles/19327.pdfBacterial laccaseMetagenomicsStraw-amended soilProfile hidden Markov models |
| spellingShingle | Dali Yu Ying Liu Hongying Cai Wanqiu Huang Huijun Wu Peilong Yang Metagenomic investigation of bacterial laccases in a straw-amended soil PeerJ Bacterial laccase Metagenomics Straw-amended soil Profile hidden Markov models |
| title | Metagenomic investigation of bacterial laccases in a straw-amended soil |
| title_full | Metagenomic investigation of bacterial laccases in a straw-amended soil |
| title_fullStr | Metagenomic investigation of bacterial laccases in a straw-amended soil |
| title_full_unstemmed | Metagenomic investigation of bacterial laccases in a straw-amended soil |
| title_short | Metagenomic investigation of bacterial laccases in a straw-amended soil |
| title_sort | metagenomic investigation of bacterial laccases in a straw amended soil |
| topic | Bacterial laccase Metagenomics Straw-amended soil Profile hidden Markov models |
| url | https://peerj.com/articles/19327.pdf |
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