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.

The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions

“…palustris Bis A53 contains high-specialized enzymes capable of degrading complex aromatic compounds under anaerobic growth [ 2 ]. To exploit the growth precision of i DT1294 we evaluated 14 aromatic compounds (with two lignin precursors) commonly found in wastewater from chemical and food industries [ 7 , 72 ]. Based on the experimental growth conditions of the reference studies [ 7 , 72 ], the model was constraint using a single organic carbon source (i.e., aromatic substrate) for each experiment, ammonium and N 2 , and all minerals required for BOF optimization under anaerobic conditions in the light.…”

“…To exploit the growth precision of i DT1294 we evaluated 14 aromatic compounds (with two lignin precursors) commonly found in wastewater from chemical and food industries [ 7 , 72 ]. Based on the experimental growth conditions of the reference studies [ 7 , 72 ], the model was constraint using a single organic carbon source (i.e., aromatic substrate) for each experiment, ammonium and N 2 , and all minerals required for BOF optimization under anaerobic conditions in the light. The growth condition details employed for all experiments and simulations from the literature are summarized in S3 Material .…”

“…Pseudoreactions with unspecific intermediates or used to represent transformations with no known pathway were not included in the M-model to avoid inaccurate predictions. All pathways of aromatic compound utilization were curated based on experimental evidence from Harwood and Ma [ 7 , 72 ]. A detailed list of reactions, metabolites, and genes added to the model for these pathways is presented in S5 Material .…”

Thioredoxin Reductase-Type Ferredoxin: NADP+ Oxidoreductase of Rhodopseudomonas palustris: Potentiometric Characteristics and Reactions with Nonphysiological Oxidants

“…Due to the large differences in the structure between plant-type and TrxR-type FNRs, the main focus of this work was to disclose the possible differences and similarities in their redox properties. In addition to the mechanistic aspects of studies of the reactions of RpFNR with redox active xenobiotics, an important aspect is that R. palustris is a model microorganism of anaerobic metabolism of organic compounds [18] in which RpFNR may be involved.…”

“…On the other hand, RpFNR has low reactivity toward Fe 2 S 2 -type ferredoxin (RPA3956), whereas its reactivity toward Fe 4 S 4 -type Fds of R. palustris has not been reported[15].In order to extend the understanding of the redox properties of RpFNR, we investigated its reactions with nonphysiological electron acceptors with different structures and single-electron reduction potentials (E1 7 ). It is worth noting that R. palustris is capable of metabolizing aromatic compounds formed during plant degradation, which may involve FNR/Fd and cytochrome P-450-dependent redox systems[17,18]. Besides, some FNRs, such as the malaria parasite Plasmodium falciparum FNR, are a potential target for redox active drug candidates, quinones and nitroaromatic compounds[19,20].…”