Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis
Open accessAbstract
An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using 13 C-labeled sugars and [ 15 N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals.
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Lignocellulosic-derived inhibitors such as acetate, furfural, and phenolics can impair microbial metabolism.
“While the pretreatment process releases fermentable sugars like glucose and xylose, it also generates lignocellulosic-derived inhibitors, such as acetate, furfural, and phenolics, that can impair microbial metabolism (47).”
From Physiological and metabolic responses of <i>Zymomonas mobilis</i> to lignocellulosic hydrolysate (2025) · cites this paper as [47]
The Introduction states that pretreatment releases fermentable sugars and generates compounds detrimental to microbial fermentation; it specifically identifies furfural and phenolic inhibitors. It does not identify acetate as one of those pretreatment-derived inhibitors in the paper’s discussion, so that example is not supported by the cited text. (LLM, conf=0.85)
Experimental — accuracy not yet measuredThe pretreatment process generates lignocellulosic-derived inhibitors, such as acetate, furfural, and phenolics.
“While the pretreatment process releases fermentable sugars like glucose and xylose, it also generates lignocellulosic-derived inhibitors, such as acetate, furfural, and phenolics, that can impair microbial metabolism (47).”
From Physiological and metabolic responses of <i>Zymomonas mobilis</i> to lignocellulosic hydrolysate (2025) · cites this paper as [47]
The Introduction says biomass pretreatment generates compounds detrimental to microbial fermentation and identifies furfural from acid pretreatment and phenolic inhibitors from ammonia-based pretreatment. It does not identify acetate as a pretreatment-generated inhibitor; acetate or acetic acid appears in reference titles, not in a passage making that point. (LLM, conf=0.85)
Experimental — accuracy not yet measuredThe pretreatment process releases fermentable sugars like glucose and xylose.
“While the pretreatment process releases fermentable sugars like glucose and xylose, it also generates lignocellulosic-derived inhibitors, such as acetate, furfural, and phenolics, that can impair microbial metabolism (47).”
From Physiological and metabolic responses of <i>Zymomonas mobilis</i> to lignocellulosic hydrolysate (2025) · cites this paper as [47]
The Introduction says biomass pretreatment processes, coupled with enzymatic hydrolysis, transform sugar polymers into fermentable monosaccharides such as glucose and xylose. It supports the sugars named in the claim, but does not attribute their release to pretreatment alone. (LLM, conf=0.82)
Experimental — accuracy not yet measured
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Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption
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Self-citationPhysiological and metabolic responses of <i>Zymomonas mobilis</i> to lignocellulosic hydrolysate
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“While the pretreatment process releases fermentable sugars like glucose and xylose, it also generates lignocellulosic-derived inhibitors, such as acetate, furfural, and phenolics, that can impair microbial metabolism (47).”
Self-citation
- Authors
- Pisithkul, T., Jacobson, T. B., O'Brien, T. J., Stevenson, D. M., & Amador-Noguez, D.
- Affiliations
- University of Wisconsin–Madison (US)
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Venue
- Applied and Environmental Microbiology
- Publisher
- American Society for Microbiology
- Published
- 2015-09
- Volume
- 81
- Issue
- 17
- Pages
- 5761-5772
- ISSN
- 0099-2240 (ISSN-L)
- 1098-5336
- PMC
- PMC4551265
- OpenAlex
- W2119674204
- Cited by
- 39
- References
- 50
- Citations by year
- 2026: 4 · 2025: 4 · 2024: 4 · 2023: 1 · 2022: 2 · 2021: 2 · 2020: 1 · 2019: 7 · 2018: 4 · 2017: 6 · 2016: 4
- FWCI
- 2.02
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Applied and Environmental Microbiology (publishedVersion, cc-by-nc-sa)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-sa)
- PubMed Central (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- U.S. Department of Energy (DEFC0207ER64494)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Molecular Research
- Physical Sciences › Engineering › Biomedical Engineering › Biofuel production and bioconversion
- Keywords
- phenolic amides, lignocellulose-derived inhibitors, purine biosynthesis, pyrimidine synthesis, 5-phosphoribosyl-1-pyrophosphate, glutamine amidotransferase, purF, competitive inhibition, nucleotide salvage pathway, nucleoside supplementation, Escherichia coli, biofuel production, isotope tracers
- MeSH terms
- Amides, Amidophosphoribosyltransferase, Enzyme Inhibitors, Escherichia coli, Purines, Pyrimidines, Phenol, Escherichia coli Proteins, Biosynthetic Pathways
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