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Functional genomic analysis of bacterial lignin degraders: diversity in mechanisms of lignin oxidation and metabolism

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Abstract

Although several bacterial lignin-oxidising enzymes have been discovered in recent years, it is not yet clear whether different lignin-degrading bacteria use similar mechanisms for lignin oxidation and degradation of lignin fragments. Genome sequences of 13 bacterial lignin-oxidising bacteria, including new genome sequences for Microbacterium phyllosphaerae and Agrobacterium sp., were analysed for the presence of lignin-oxidising enzymes and aromatic degradation gene clusters that could be used to metabolise the products of lignin degradation. Ten bacterial genomes contain DyP-type peroxidases, and ten bacterial strains contain putative multi-copper oxidases (MCOs), both known to have activity for lignin oxidation. Only one strain lacks both MCOs and DyP-type peroxidase genes. Eleven bacterial genomes contain aromatic degradation gene clusters, of which ten contain the central β-ketoadipate pathway, with variable numbers and types of degradation clusters for other aromatic substrates. Hence, there appear to be diverse metabolic strategies used for lignin oxidation in bacteria, while the β-ketoadipate pathway appears to be the most common route for aromatic metabolism in lignin-degrading bacteria.

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Acknowledgements

This work was supported by research grants from BBSRC (research grant BB/P01738X/1) and FAPESP (research grant 2015/50590-4), and a PhD studentship (to RSGT) funded by Secretaria de Educacion Superior, Ciencia, Tecnologia e Innovacion (SENESCYT), Ecuador. We thank Brazilian Biorenewable National Laboratory LNBR NGS Sequencing Facility for generating the DNA sequencing of Agrobacterium sp. strain.

Funding

This study was funded by research grants from BBSRC (research grant BB/P01738X/1) and FAPESP (research grant 2015/50590-4), and a PhD studentship (to RSGT) funded by Secretaria de Educacion Superior, Ciencia, Tecnologia e Innovacion (SENESCYT), Ecuador.

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  1. Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK

    Rommel Santiago Granja-Travez & Timothy D. H. Bugg

  2. Facultad de Ciencias de la Ingeniería e Industrias, Universidad UTE, Quito, Ecuador

    Rommel Santiago Granja-Travez

  3. Laboratório Nacional de Biorrenováveis (LNBR/CNPEM), Campinas, Brazil

    Gabriela Felix Persinoti

  4. Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil

    Fabio M. Squina

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  1. Rommel Santiago Granja-Travez
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  2. Gabriela Felix Persinoti
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  4. Timothy D. H. Bugg
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Granja-Travez, R.S., Persinoti, G.F., Squina, F.M. et al. Functional genomic analysis of bacterial lignin degraders: diversity in mechanisms of lignin oxidation and metabolism. Appl Microbiol Biotechnol 104, 3305–3320 (2020). https://doi.org/10.1007/s00253-019-10318-y

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