Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630

Yoneda, Aki; Henson, William R.; Goldner, Nicholas K.; Park, Kun Joo; Forsberg, Kevin J.; Kim, Soo Ji; Pesesky, Mitchell W.; Foston, Marcus; Dantas, Gautam; Moon, Tae Seok

doi:10.1093/nar/gkw055

Title: Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630

Journal Article · Tue Feb 02 00:00:00 EST 2016 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkw055· OSTI ID:1255221

Yoneda, Aki ^[1]; Henson, William R. ^[2]; Goldner, Nicholas K. ^[1]; Park, Kun Joo ^[2]; Forsberg, Kevin J. ^[1]; Kim, Soo Ji ^[2]; Pesesky, Mitchell W. ^[1]; Foston, Marcus ^[2]; Dantas, Gautam ^[3];

^[2]

Washington Univ., St. Louis, MO (United States). St. Louis School of Medicine
Washington Univ., St. Louis, MO (United States)
Washington Univ., St. Louis, MO (United States). St. Louis School of Medicine; Washington Univ., St. Louis, MO (United States)

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.

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Research Organization:: Washington Univ., St. Louis, MO (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0012705

OSTI ID:: 1255221

Journal Information:: Nucleic Acids Research, Vol. 44, Issue 5; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 72 works

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Engineering levoglucosan metabolic pathway in Rhodococcus jostii RHA1 for lipid production Xiong, Xiaochao; Lian, Jieni; Yu, Xiaochen Journal of Industrial Microbiology & Biotechnology, Vol. 43, Issue 11 https://doi.org/10.1007/s10295-016-1832-9	journal	August 2016
A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion Mallinson, Sam J. B.; Machovina, Melodie M.; Silveira, Rodrigo L. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04878-2	journal	June 2018
Urinary tract colonization is enhanced by a plasmid that regulates uropathogenic Acinetobacter baumannii chromosomal genes Di Venanzio, Gisela; Flores-Mireles, Ana L.; Calix, Juan J. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-10706-y	journal	June 2019
Characterization of a Novel Tectivirus Phage Toil and Its Potential as an Agent for Biolipid Extraction Gill, Jason J.; Wang, Baixin; Sestak, Emily Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-19455-2	journal	January 2018
Selection of stable reference genes for RT-qPCR in Rhodococcus opacus PD630 DeLorenzo, Drew M.; Moon, Tae Seok Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-24486-w	journal	April 2018
Passive membrane transport of lignin-related compounds Vermaas, Josh V.; Dixon, Richard A.; Chen, Fang Proceedings of the National Academy of Sciences, Vol. 116, Issue 46 https://doi.org/10.1073/pnas.1904643116	journal	October 2019
Mechanism of High-Level Daptomycin Resistance in Corynebacterium striatum Goldner, Nicholas K.; Bulow, Christopher; Cho, Kevin mSphere, Vol. 3, Issue 4 https://doi.org/10.1128/mspheredirect.00371-18	journal	August 2018
Metabolism of aromatics by Trichosporon oleaginosus while remaining oleaginous Yaguchi, Allison; Robinson, Alana; Mihealsick, Erin Microbial Cell Factories, Vol. 16, Issue 1 https://doi.org/10.1186/s12934-017-0820-8	journal	November 2017
Microalgae for the production of lipid and carotenoids: a review with focus on stress regulation and adaptation Sun, Xiao-Man; Ren, Lu-Jing; Zhao, Quan-Yu Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1275-9	journal	October 2018
Lipid metabolism of phenol-tolerant Rhodococcus opacus strains for lignin bioconversion Henson, William R.; Hsu, Fong-Fu; Dantas, Gautam Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1337-z	journal	December 2018
Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high-value compounds Anthony, Winston E.; Carr, Rhiannon R.; DeLorenzo, Drew M. Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1535-3	journal	August 2019
Genome Sequencing and Comparative Transcriptomics Provide a Holistic View of 4-Nitrophenol Degradation and Concurrent Fatty Acid Catabolism by Rhodococcus sp. Strain BUPNP1 Sengupta, Kriti; Swain, Martin T.; Livingstone, Paul G. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.03209	journal	January 2019
A new Rhodococcus aetherivorans strain isolated from lubricant-contaminated soil as a prospective phenol-biodegrading agent Nogina, Taisiya; Fomina, Marina; Dumanskaya, Tatiana Applied Microbiology and Biotechnology, Vol. 104, Issue 8 https://doi.org/10.1007/s00253-020-10385-6	journal	February 2020
Development of Chemical and Metabolite Sensors for Rhodococcus opacus PD630 DeLorenzo, Drew M.; Henson, William R.; Moon, Tae Seok ACS Synthetic Biology, Vol. 6, Issue 10 https://doi.org/10.1021/acssynbio.7b00192	journal	June 2017
Re: Urinary Tract Colonization is Enhanced by a Plasmid that Regulates Uropathogenic Acinetobacter baumannii Chromosomal Genes Atala, Anthony Journal of Urology, Vol. 202, Issue 6 https://doi.org/10.1097/ju.0000000000000543	journal	December 2019

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