Computationally Prospecting Potential Pathways from Lignin Monomers and Dimers toward Aromatic Compounds

The heterogeneity of the aromatic products originating from lignin catalytic depolymerization remains one of the major challenges associated with lignin valorization. Microbes have evolved catabolic pathways that can funnel heterogeneous intermediates to a few central aromatic products. These aromatic compounds can subsequently undergo intra- or extradiol ring opening to produce value-added chemicals. However, such funneling pathways are only partially characterized for a few organisms such as Sphingobium sp. SYK-6 and Pseudomonas putida KT2440. Herein, we apply the de novo pathway design tool (novoStoic) to computationally prospect possible ways of funneling lignin-derived mono- and biaryls. novoStoic employs reaction rules between molecular moieties to hypothesize de novo conversions by flagging known enzymes that carry out the same biotransformation on the most similar substrate. Both reaction rules and known reactions are then deployed by novoStoic to identify a mass-balanced biochemical network that converts a source to a target metabolite while minimizing the number of de novo steps. We demonstrate the application of novoStoic for (i) designing alternative pathways of funneling S, G, and H lignin monomers, and (ii) exploring cleavage pathways of β-1 and β-β dimers. By exploring the uncharted chemical space afforded by enzyme promiscuity, novoStoic can help predict previously unknown native pathways leveraging enzyme promiscuity and propose new carbon/energy efficient lignin funneling pathways with few heterologous enzymes.

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Work Title Computationally Prospecting Potential Pathways from Lignin Monomers and Dimers toward Aromatic Compounds
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Open Access
Creators
  1. Lin Wang
  2. Costas D. Maranas
Keyword
  1. lignin valorization
  2. funneling pathway
  3. de novo pathway design
  4. pseudomonas patida KT2440
  5. enzyme promiscuity
License In Copyright (Rights Reserved)
Work Type Article
Publisher
  1. ACS Synthetic Biology
Publication Date April 20, 2021
Publisher Identifier (DOI)
  1. https://doi.org/10.1021/acssynbio.0c00598
Deposited August 12, 2024

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  • Created
  • Added acssynbio.0c00598.pdf
  • Added Creator Lin Wang
  • Added Creator Costas D. Maranas
  • Published
  • Updated
  • Updated Keyword, Publication Date Show Changes
    Keyword
    • lignin valorization, funneling pathway, de novo pathway design, pseudomonas patida KT2440, enzyme promiscuity
    Publication Date
    • 2021-05-21
    • 2021-04-20