title: Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630.
abstract: Lignin-derived (e.g. phenolic) compounds can compromise the bioconversion of lignocellulosic biomass to fuels and chemicals due to their toxicity and recalcitrance. The lipid-accumulating bacterium Rhodococcus opacus PD630 has recently emerged as a promising microbial host for lignocellulose conversion to value-added products due to its natural ability to tolerate and utilize phenolics. To gain a better understanding of its phenolic tolerance and utilization mechanisms, we adaptively evolved R. opacus over 40 passages using phenol as its sole carbon source (up to 373% growth improvement over wild-type), and extensively characterized two strains from passages 33 and 40. The two adapted strains showed higher phenol consumption rates (∼20 mg/l/h) and ∼2-fold higher lipid production from phenol than the wild-type strain. Whole-genome sequencing and comparative transcriptomics identified highly-upregulated degradation pathways and putative transporters for phenol in both adapted strains, highlighting the important linkage between mechanisms of regulated phenol uptake, utilization, and evolved tolerance. Our study shows that the R. opacus mutants are likely to use their transporters to import phenol rather than export them, suggesting a new aromatic tolerance mechanism. The identified tolerance genes and pathways are promising candidates for future metabolic engineering in R. opacus for improved lignin conversion to lipid-based products.
authors.affiliation: Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Aki
authors.initials: A
authors.lastname: Yoneda
authors.affiliation: Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
authors.forename: William R
authors.initials: WR
authors.lastname: Henson
authors.affiliation: Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Nicholas K
authors.initials: NK
authors.lastname: Goldner
authors.affiliation: Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
authors.forename: Kun Joo
authors.initials: KJ
authors.lastname: Park
authors.affiliation: Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Forsberg
authors.affiliation: Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
authors.forename: Soo Ji
authors.initials: SJ
authors.lastname: Kim
authors.affiliation: Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Mitchell W
authors.initials: MW
authors.lastname: Pesesky
authors.affiliation: Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
authors.forename: Marcus
authors.initials: M
authors.lastname: Foston
authors.affiliation: Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA dantas@wustl.edu.
authors.forename: Gautam
authors.initials: G
authors.lastname: Dantas
authors.affiliation: Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA tsmoon@wustl.edu.
authors.forename: Tae Seok
authors.identifier: http://orcid.org/0000-0001-8373-9051
authors.initials: TS
authors.lastname: Moon
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001711:Biotransformation; D002244:Carbon / Q000378:metabolism; D002352:Carrier Proteins / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing; D050155:Lipogenesis / Q000235:genetics; D058977:Molecular Sequence Annotation; D010636:Phenols / Q000378:metabolism*; D012240:Rhodococcus / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D002352:Carrier Proteins; D010636:Phenols; D002244:Carbon
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