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PreprintCited by 5Microbial Natural Products and BiosynthesisPlant biochemistry and biosynthesisEnzyme Catalysis and Immobilization

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Discovery and heterologous expression of functional 4-O-dimethylallyl-L-tyrosine synthases from lichen-forming fungi

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Iacovelli, Riccardo, He, Siqi, Sokolova, Nika, Lokhorst, Iris, Borg, Maikel, Fodran, Peter, Haslinger, Kristina·2024·Journal of Natural Products
DOI 10.1101/2024.03.23.586307PMC PMC11443524

Preprint — published as 10.1021/acs.jnatprod.4c00619 · Paper page

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Abstract

Fungal DMATS-type aromatic prenyltransferases are a family of biosynthetic enzymes that catalyze the prenylation of a range of aromatic substrates during the biosynthesis of bioactive indole alkaloids, diketopiperazines, and meroterpenoids. Together with their broad substrate scope and soluble nature, this makes DMATS-type prenyltransferases particularly adept for applications in biocatalysis, for example to derivatize aromatic drug leads and improve their bioactivity. Here, we investigated four putative DMATS-type prenyltransferases from lichen-forming fungi, an underexplored group of organisms that produce more than 1,000 unique metabolites. We were able to successfully express two functional lichen prenyltransferases in the heterologous host A. oryzae , which allowed us to identify them as 4-O-dimethylallyltyrosine synthases. Our extensive bioinformatic analysis shows that related lichen prenyltransferases are likely not active on indoles but rather on aromatic polyketides and phenylpropanoids, common metabolites in these organisms. Overall, our work not only provides new insights into fungal DMATS-type prenyltransferases at the family level, but it also enables future efforts aimed at identifying new candidates for biocatalytic transformations of aromatic compounds.

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Figures

Figure 1 LC-MS-based detection of two new peaks in the extracts of DMATS expression strains. (a) Extracted ion chromatograms of fungal extracts for m/z 250 (1) and m/z 292 (2) (±0.2 Da). (b) Peak areas (log10 scale) of 1 and 2 in fungal extracts. The minimum value for the y axis is equal to a signal intensity of 1 × 104, which corresponds to baseline levels. The values were normalized for the internal standard caffeine. Bars represent mean ± SD (n = 4). Only one control trace is shown.
Figure 1 LC-MS-based detection of two new peaks in the extracts of DMATS expression strains. (a) Extracted ion chromatograms of fungal extracts for m/z 250 (1) and m/z 292 (2) (±0.2 Da). (b) Peak areas (log10 scale) of 1 and 2 in fungal extracts. The minimum value for the y axis is equal to a signal intensity of 1 × 104, which corresponds to baseline levels. The values were normalized for the internal standard caffeine. Bars represent mean ± SD (n = 4). Only one control trace is shown.CC BY · PubMed Central
Figure 2 Structural characterization of compounds 1 and 2. (a) Total ion chromatograms of total culture extract from Ri DMATS expression strain and enriched fraction containing compounds 1 and 2 obtained via semipreparative HPLC. Retention times are different compared to Figure 1 because a shorter analysis method was used here. (b) Chemical shifts of aromatic protons from the 1H NMR spectrum (600 MHz) of the enriched fraction (Figure S3), assigned based on 1H NMR spectra of reference compounds (Figures S6 and S8). The 4 major doublets indicate that the aromatic rings of 1 and 2 are free of substitutions, consistent with prenylation occurring on the 4-OH group of the substrates. The chemical shift of the prenyl proton is also observed.
Figure 2 Structural characterization of compounds 1 and 2. (a) Total ion chromatograms of total culture extract from Ri DMATS expression strain and enriched fraction containing compounds 1 and 2 obtained via semipreparative HPLC. Retention times are different compared to Figure 1 because a shorter analysis method was used here. (b) Chemical shifts of aromatic protons from the 1H NMR spectrum (600 MHz) of the enriched fraction (Figure S3), assigned based on 1H NMR spectra of reference compounds (Figures S6 and S8). The 4 major doublets indicate that the aromatic rings of 1 and 2 are free of substitutions, consistent with prenylation occurring on the 4-OH group of the substrates. The chemical shift of the prenyl proton is also observed.CC BY · PubMed Central
Figure 3 SSN of fungal DMATS-type PTs. The organic layout from yFiles was applied. Edge selection cutoff: sequence ID% > 34.2. The different clusters are colored based on the default color scheme of EFI-EST. Lichen enzymes are colored in black with green borders, regardless of their location within the network. The 4 enzymes subject of this work are highlighted in pink boxes and with underlined labels. Enzymes with known substrate specificity and type of reaction catalyzed (indicated in red) are circled in black and labeled (organism + enzyme name). For visualization purposes, dashed lines encircle groups of enzymes that catalyze the same type of reaction, although it should be stated that this notation only refers to characterized enzymes labeled in black. *Enzymes from the same species but different strains. **For simplicity, no annotation on substrate specificity/reaction was included for At AtaPT because of its broad donor (DMAPP, GPP, FPP) and acceptor (peptides, flavonoids, aromatics) substrate scope.39
Figure 3 SSN of fungal DMATS-type PTs. The organic layout from yFiles was applied. Edge selection cutoff: sequence ID% > 34.2. The different clusters are colored based on the default color scheme of EFI-EST. Lichen enzymes are colored in black with green borders, regardless of their location within the network. The 4 enzymes subject of this work are highlighted in pink boxes and with underlined labels. Enzymes with known substrate specificity and type of reaction catalyzed (indicated in red) are circled in black and labeled (organism + enzyme name). For visualization purposes, dashed lines encircle groups of enzymes that catalyze the same type of reaction, although it should be stated that this notation only refers to characterized enzymes labeled in black. *Enzymes from the same species but different strains. **For simplicity, no annotation on substrate specificity/reaction was included for At AtaPT because of its broad donor (DMAPP, GPP, FPP) and acceptor (peptides, flavonoids, aromatics) substrate scope.39CC BY · PubMed Central
Figure 4 Comparison of Ri DMATS and As DMATS models with the crystal structure of Af FgaPT2 (PDB ID: 3I4X). (a) Superimposition of the structures shows that the overall ABBA fold and the central β-barrel where the tyrosine shield and active site are located are well conserved in the lichen DMATS. Two additional α-helices can be observed at the N-terminus of Ri DMATS, though these are predicted with low confidence (Figure S15). In the corresponding region, As DMATS is instead missing the N-terminal α-helix present in FgaPT2, and an additional, large, unstructured loop is predicted at its C-terminus (also with low confidence, Figure S15). (b) Active site comparison of Ri DMATS and Af FgaPT2. All amino acids within a 5 Å radius from the substrates are displayed as sticks colored by element: oxygen, red; nitrogen, dark blue; sulfur, light yellow; phosphate, orange; carbon, as indicated in the legend. The binding pockets show a similar architecture and substrate positioning. Key catalytic residues in FgaPT2 and corresponding residues in Ri DMATS are underlined. The structures were visualized using UCSF Chimera and aligned with the Matchmaker tool.
Figure 4 Comparison of Ri DMATS and As DMATS models with the crystal structure of Af FgaPT2 (PDB ID: 3I4X). (a) Superimposition of the structures shows that the overall ABBA fold and the central β-barrel where the tyrosine shield and active site are located are well conserved in the lichen DMATS. Two additional α-helices can be observed at the N-terminus of Ri DMATS, though these are predicted with low confidence (Figure S15). In the corresponding region, As DMATS is instead missing the N-terminal α-helix present in FgaPT2, and an additional, large, unstructured loop is predicted at its C-terminus (also with low confidence, Figure S15). (b) Active site comparison of Ri DMATS and Af FgaPT2. All amino acids within a 5 Å radius from the substrates are displayed as sticks colored by element: oxygen, red; nitrogen, dark blue; sulfur, light yellow; phosphate, orange; carbon, as indicated in the legend. The binding pockets show a similar architecture and substrate positioning. Key catalytic residues in FgaPT2 and corresponding residues in Ri DMATS are underlined. The structures were visualized using UCSF Chimera and aligned with the Matchmaker tool.CC BY · PubMed Central

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Citations

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Metadata

Authors
Iacovelli, R., He, S., Sokolova, N., Lokhorst, I., Borg, M., Fodran, P., & Haslinger, K.
Affiliations
University of Groningen (NL)
Corresponding author
Haslinger, Kristina
ORCID
Venue
Journal of Natural Products
Publisher
openRxiv
Published
2024-03-25
Volume
87
Issue
9
Pages
2243-2254
ISSN
0163-3864 (ISSN-L)
DOI
10.1101/2024.03.23.586307
PMC
PMC11443524
OpenAlex
W4402405433
Cited by
5
References
1
Citations by year
2026: 1 · 2025: 3 · 2024: 1
FWCI
1.42
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Journal of Natural Products (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, cc-by)
  • University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by-nc)
Funders
  • Rijksuniversiteit Groningen
  • China Scholarship Council (201806300121)
  • Teknologian Tutkimuskeskus VTT
Topics
  • Life Sciences › Immunology and Microbiology › Applied Microbiology and Biotechnology › Microbial Natural Products and Biosynthesis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Plant biochemistry and biosynthesis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Enzyme Catalysis and Immobilization
Keywords
aromatic prenyltransferase, lichen-forming fungi, heterologous expression, Aspergillus oryzae, biocatalysis, aromatic polyketides, phenylpropanoids, lichen metabolites
MeSH terms
Aspergillus oryzae, Dimethylallyltranstransferase, Lichens, Molecular Structure, Prenylation

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