Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulatingRhodococcus opacusPD630

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.

Cellular Analysis and Comparative Transcriptomics Reveal the Tolerance Mechanisms of Candida tropicalis Toward Phenol

“…However, the energy consumption, high cost, hazardous byproducts production, and poor efficiency of these methods limited their widespread applications (Banerjee and Ghoshal, 2011). The natural ability of microorganisms to degrade phenol, and a few biological treatments of phenol are explored and found to be more efficient than physicochemical methods (Jiang et al, 2005;Banerjee and Ghoshal, 2011;Yoneda et al, 2016). It is a challenge for the wide applications of biological methods that these compounds are toxic to microbial cells, can prolong the lag phase, and reduce the phenol degradation efficiency (Heipieper et al, 1991).…”

“…Although recent studies found that chromatin remodeling, efflux of toxic compounds, and aggregation of lipopolysaccharides on the outer cell membrane could increase the resistance of microorganisms to phenolic aldehydes derived from lignocellulose pretreatment Yi et al, 2015), a part of the above mechanisms might be associated with the aldehyde tolerance. Another study focused on R. opacus PD630 found that phenol tolerance mainly involved the import and degradation of extracellular phenol (Yoneda et al, 2016), but the understanding of the tolerance mechanisms, not degradation mechanisms, of strains to phenol is not very clear.…”

Lipid metabolism of phenol-tolerant Rhodococcus opacus strains for lignin bioconversion

“…Rhodococcus opacus PD630 (hereafter R. opacus) is an important microbial strain for bioproduction due to its inherently high aromatic tolerance and ability to consume many different aromatic compounds found in depolymerized lignin [19][20][21][22][23][24]. R. opacus is a Gram-positive actinomycete bacterium that can accumulate triacylglycerols (TAGs), a biodiesel precursor, up to ~ 78% of its cell dry weight when grown on sugars [25].…”

“…It also has a toxicity level that is similar to many other lignin-derived aromatic compounds [59]. In this work, phenol was chosen as a lignin depolymerization product model compound for studying changes in membrane composition that were hypothesized to be correlated with evolutionary changes that led to improved lignin depolymerization product (i.e., phenol) tolerance and utilization [20]. Increasing lignin depolymerization product tolerance in R. opacus could improve biorefinery economics by increasing product titers, yields, and productivities for lignin valorization via a hybrid conversion approach.…”

Comparative transcriptomics and cellular analysis reveal the tolerance mechanisms of Candida tropicalis towards phenol as the representative phenolic inhibitors from lignocellulosic hydrolysis

“…Since it includes both the aromatic group and phenolic hydroxyl group, phenol can effectively represent the phenolic inhibitors from lignocellulosic hydrolysis and can be used to explore the mechanisms of microorganisms' tolerance to these compounds. A previous study focused on the fermenting microorganism Rhodococcus opacus PD630 found that phenol tolerance mainly involved the import and degradation of extracellular phenol [24]. Since R.…”