A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630

Carr, Rhiannon; Campbell, Tayte; Shang, Zeyu; Henson, William R.; Czajka, Jeffrey J.; Martín, Héctor García; Zhang, Fuzhong; Foston, Marcus; Dantas, Gautam; Moon, Tae Seok; Tang, Yinjie J.

doi:10.1016/j.ymben.2019.06.013

Cited by 39 publications

(31 citation statements)

References 51 publications

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Section: Catabolism Of Different Carbon Sources and Lipogenesis Pathways Are Coupled In Oleaginous Rhodococcimentioning

confidence: 99%

“…Roell et al reported the ability of R. opacus PD630 to use phenol, a lignin depolymerization model product, as a carbon source for growth and TAG biosynthesis [ 76 ]. This strain produced TAG from phenol with less unsaturated fatty acids and approximately 20% of branched chain C 18 (BCFAs) [ 76 , 77 ]. The internal branches observed enhance cold-flow properties of a potential biodiesel, in comparison with those offered by terminal branches [ 78 ].…”

Section: Catabolism Of Different Carbon Sources and Lipogenesis Pathways Are Coupled In Oleaginous Rhodococcimentioning

confidence: 99%

“…The internal branches observed enhance cold-flow properties of a potential biodiesel, in comparison with those offered by terminal branches [ 78 ]. Using 13 C-pathway tracing analyses, the authors demonstrated that phenol was metabolized mainly through the ortho-cleavage pathway, with TCA cycle and gluconeogenesis as key metabolic processes during growth on phenol and with NADPH generation mainly via NADPH-dependent isocitrate dehydrogenase [ 76 ]. Catabolite repression by other carbon substrates, such as glucose and acetate, was absent in R. opacus PD630, although benzoate inhibited phenol utilization.…”

Section: Catabolism Of Different Carbon Sources and Lipogenesis Pathways Are Coupled In Oleaginous Rhodococcimentioning

confidence: 99%

“…Catabolite repression by other carbon substrates, such as glucose and acetate, was absent in R. opacus PD630, although benzoate inhibited phenol utilization. The authors suggested that the strong carbon fluxes through the TCA cycle in phenol-fed R. opacus make this host ideal for producing chemicals derived from TCA cycle intermediates, such as acetyl-CoA, which is the main precursor for lipogenesis [ 76 ]. In contrast, R. opacus was not a good model for the production of chemicals derived from sugar phosphates during growth on phenol since its carbon fluxes through gluconeogenesis are small [ 76 ].…”

Section: Catabolism Of Different Carbon Sources and Lipogenesis Pathways Are Coupled In Oleaginous Rhodococcimentioning

confidence: 99%

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Rhodococcus as Biofactories for Microbial Oil Production

et al. 2021

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Bacteria belonging to the Rhodococcus genus are frequent components of microbial communities in diverse natural environments. Some rhodococcal species exhibit the outstanding ability to produce significant amounts of triacylglycerols (TAG) (>20% of cellular dry weight) in the presence of an excess of the carbon source and limitation of the nitrogen source. For this reason, they can be considered as oleaginous microorganisms. As occurs as well in eukaryotic single-cell oil (SCO) producers, these bacteria possess specific physiological properties and molecular mechanisms that differentiate them from other microorganisms unable to synthesize TAG. In this review, we summarized several of the well-characterized molecular mechanisms that enable oleaginous rhodococci to produce significant amounts of SCO. Furthermore, we highlighted the ability of these microorganisms to degrade a wide range of carbon sources coupled to lipogenesis. The qualitative and quantitative oil production by rhodococci from diverse industrial wastes has also been included. Finally, we summarized the genetic and metabolic approaches applied to oleaginous rhodococci to improve SCO production. This review provides a comprehensive and integrating vision on the potential of oleaginous rhodococci to be considered as microbial biofactories for microbial oil production.

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Section: Catabolism Of Different Carbon Sources and Lipogenesis Pathways Are Coupled In Oleaginous Rhodococcimentioning

confidence: 99%

Section: Catabolism Of Different Carbon Sources and Lipogenesis Pathways Are Coupled In Oleaginous Rhodococcimentioning

confidence: 99%

Section: Catabolism Of Different Carbon Sources and Lipogenesis Pathways Are Coupled In Oleaginous Rhodococcimentioning

confidence: 99%

Section: Catabolism Of Different Carbon Sources and Lipogenesis Pathways Are Coupled In Oleaginous Rhodococcimentioning

confidence: 99%

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Rhodococcus as Biofactories for Microbial Oil Production

et al. 2021

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“…An additional metabolomic study elucidated the biodegradation pathway of a lignin-derived aromatic compound, i.e., phenol, via quantitative flux balance analysis (FBA). In the presence of phenol, PD630 metabolic network showed strong metabolic fluxes through the TCA cycle, making this strain an ideal host for the production of metabolic intermediates such as acetyl-CoA and α-ketoglutarate for TAG production from lignocellulosic biomass (Roell et al 2019).…”

Section: Adaptive Laboratory Evolutionmentioning

confidence: 99%

Systems biology and metabolic engineering of Rhodococcus for bioconversion and biosynthesis processes

2021

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Rhodococcus spp. strains are widespread in diverse natural and anthropized environments thanks to their high metabolic versatility, biodegradation activities, and unique adaptation capacities to several stress conditions such as the presence of toxic compounds and environmental fluctuations. Additionally, the capability of Rhodococcus spp. strains to produce high value-added products has received considerable attention, mostly in relation to lipid accumulation. In relation with this, several works carried out omic studies and genome comparative analyses to investigate the genetic and genomic basis of these anabolic capacities, frequently in association with the bioconversion of renewable resources and low-cost substrates into triacylglycerols. This review is focused on these omic analyses and the genetic and metabolic approaches used to improve the biosynthetic and bioconversion performance of Rhodococcus. In particular, this review summarizes the works that applied heterologous expression of specific genes and adaptive laboratory evolution approaches to manipulate anabolic performance. Furthermore, recent molecular toolkits for targeted genome editing as well as genome-based metabolic models are described here as novel and promising strategies for genome-scaled rational design of Rhodococcus cells for efficient biosynthetic processes application.

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Comparative genomics reveals response of Rhodococcus pyridinivorans B403 to phenol after evolution

Peng

Liu

et al. 2022

Appl Microbiol Biotechnol

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A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630

Cited by 39 publications

References 51 publications

Rhodococcus as Biofactories for Microbial Oil Production

Rhodococcus as Biofactories for Microbial Oil Production

Systems biology and metabolic engineering of Rhodococcus for bioconversion and biosynthesis processes

Comparative genomics reveals response of Rhodococcus pyridinivorans B403 to phenol after evolution

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