Kinetic modeling of anaerobic degradation of plant-derived aromatic mixtures by Rhodopseudomonas palustris

Abstract

Rhodopseudomonas palustris is a model microorganism for studying the anaerobic metabolism of aromatic compounds. While it is well documented which aromatics can serve as sole organic carbon sources, co-metabolism of other aromatics is poorly understood. This study used kinetic modeling to analyze the simultaneous degradation of aromatic compounds present in corn stover hydrolysates and model the co-metabolism of aromatics not known to support growth of R. palustris as sole organic substrates. The simulation predicted that p-coumaroyl amide and feruloyl amide were hydrolyzed to p-coumaric acid and ferulic acid, respectively, and further transformed via p-coumaroyl-CoA and feruloyl-CoA. The modeling also suggested that metabolism of p-hydroxyphenyl aromatics was slowed by substrate inhibition, whereas the transformation of guaiacyl aromatics was inhibited by their p-hydroxyphenyl counterparts. It also predicted that substrate channeling may occur during degradation of p-coumaroyl-CoA and feruloyl-CoA, resulting in no detectable accumulation of p-hydroxybenzaldehyde and vanillin, during the transformation of these CoA ligated compounds to p-hydroxybenzoic acid and vanillic acid, respectively. While the simulation correctly represented the known transformation of p-hydroxybenzoic acid via the benzoyl-CoA pathway, it also suggested co-metabolism of vanillic acid and syringic acid, which are known not to serve as photoheterotrophic growth substrate for R. palustris.

Keywords: Anaerobic degradation; Co-metabolism; Kinetic modeling; Plant-derived aromatics; Rhodopseudomonas palustris; Substrate inhibition.

Fig. 1

Proposed degradation pathways for plant-derived aromatic compounds detected in the experiment of Austin et al. (2015). Solid arrows indicated reactions that are experimentally demonstrated in R. palustris. Dashed arrows indicated hypothetical reactions of this study. Compounds colored in blue (p-coumaroyl-CoA and feruloyl-CoA) represent intermediates not measured

Fig. 2

Kinetic modeling of a p-hydroxyphenyl, b guaiacyl, and c syringyl aromatics with alternative models exploring factors that may influence their transformation rates. For p-hydroxyphenyl and guaiacyl aromatics, Case 1 and 2: no inhibition effects; Case 3: H type aromatics inhibit degradation of structurally similar G type aromatics; Case 4: substrate inhibition of both H and G type aromatics; Case 5: substrate inhibition of H type aromatics, and H type aromatics inhibit degradation of structurally similar G type aromatics. Case 1: no substrate channeling; Case 2–5: substrate channeling in degradation of p-coumaroyl-CoA and feruloyl-CoA. Degradation rate (k), inhibition factor (k_i) and inhibitory substrate (S_i) of each reaction are shown in Table S1

Fig. 3

Comparison of experimental and modeling results for a protocatechuic acid production from vanillic acid assuming first order rates of protocatechuic production and consumption, and b benzoic acid consumption assuming first order degradation rate. The units of the estimated first order rates are l mg⁻¹ h⁻¹