Lignolytic-consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization

Biotechnology for Biofuels

Timothy D. H. Bugg¹  Geizecler Tomazetto²  Eduardo C. Moraes²  Juliana A. Aricetti²  Camila Caldana²  Gabriela F. Persinoti²  Douglas A. A. Paixão²  Livia B. Brenelli²  Gabriela C. Ematsu²  Neil Dixon³  Thabata M. Alvarez⁴  Fabio M. Squina⁵ 

[1] Department of Chemistry, University of Warwick;Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais;Manchester Institute of Biotechnology, School of Chemistry, University of Manchester;Master Program in Industrial Biotechnology, Universidade Positivo (UP);Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba;

关键词: Lignin;    Aromatic compound degradation;    Metagenome;    Vanillin;    Ferulic acid;   

DOI  :  10.1186/s13068-018-1073-4

来源: DOAJ

【 摘 要 】

Abstract Background Lignin is a heterogeneous polymer representing a renewable source of aromatic and phenolic bio-derived products for the chemical industry. However, the inherent structural complexity and recalcitrance of lignin makes its conversion into valuable chemicals a challenge. Natural microbial communities produce biocatalysts derived from a large number of microorganisms, including those considered unculturable, which operate synergistically to perform a variety of bioconversion processes. Thus, metagenomic approaches are a powerful tool to reveal novel optimized metabolic pathways for lignin conversion and valorization. Results The lignin-degrading consortium (LigMet) was obtained from a sugarcane plantation soil sample. The LigMet taxonomical analyses (based on 16S rRNA) indicated prevalence of Proteobacteria, Actinobacteria and Firmicutes members, including the Alcaligenaceae and Micrococcaceae families, which were enriched in the LigMet compared to sugarcane soil. Analysis of global DNA sequencing revealed around 240,000 gene models, and 65 draft bacterial genomes were predicted. Along with depicting several peroxidases, dye-decolorizing peroxidases, laccases, carbohydrate esterases, and lignocellulosic auxiliary (redox) activities, the major pathways related to aromatic degradation were identified, including benzoate (or methylbenzoate) degradation to catechol (or methylcatechol), catechol ortho-cleavage, catechol meta-cleavage, and phthalate degradation. A novel Paenarthrobacter strain harboring eight gene clusters related to aromatic degradation was isolated from LigMet and was able to grow on lignin as major carbon source. Furthermore, a recombinant pathway for vanillin production was designed based on novel gene sequences coding for a feruloyl-CoA synthetase and an enoyl-CoA hydratase/aldolase retrieved from the metagenomic data set. Conclusion The enrichment protocol described in the present study was successful for a microbial consortium establishment towards the lignin and aromatic metabolism, providing pathways and enzyme sets for synthetic biology engineering approaches. This work represents a pioneering study on lignin conversion and valorization strategies based on metagenomics, revealing several novel lignin conversion enzymes, aromatic-degrading bacterial genomes, and a novel bacterial strain of potential biotechnological interest. The validation of a biosynthetic route for vanillin synthesis confirmed the applicability of the targeted metagenome discovery approach for lignin valorization strategies.

【 授权许可】

Unknown