Qualitative metabolomics-based characterization of a phenolic UDP-xylosyltransferase with a broad substrate spectrum from
            <i>Lentinus brumalis</i>

Jeong, Eunah; Kim, Wonyong; Son, Seungju; Yang, Si; Gwon, Dasom; Hong, Jihee; Cho, Yoonhee; Jang, Chang-Young; Steinegger, Martin; Lim, Young Woon; Kang, Kyo Bin

doi:10.1073/pnas.2301007120

Cited by 3 publications

(2 citation statements)

References 88 publications

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“…To investigate the mechanism behind these chemical transformations, one could take the purified known compounds and systematically treat them with relevant fungal species, or acidified solutions, and with the aid of GNPS clustering determine if the conversion is enzymatic or non-enzymatic. A recent study by Kang et al systematically investigated the potential biotransformations of phytochemicals by a panel of fungi using GNPS ( 82 ).…”

Section: Discussionmentioning

confidence: 99%

Unveiling the fungal diversity and associated secondary metabolism on black apples

Cowled,

Phippen,

Kromphardt

et al. 2024

Appl Environ Microbiol

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Black apples are the result of late-stage microbial decomposition after falling to the ground. This phenomenon is highly comparable from year to year, with the filamentous fungus Monilinia fructigena most commonly being the first invader, followed by Penicillium expansum . Motivated by the fact that only little chemistry has been reported from apple microbiomes, we set out to investigate the chemical diversity and potential ecological roles of secondary metabolites (SMs) in a total of 38 black apples. Metabolomics analyses were conducted on either whole apples or small excisions of fungal biomass derived from black apples. Annotation of fungal SMs in black apple extracts was aided by the cultivation of 15 recently isolated fungal strains on 9 different substrates in a One Strain Many Compounds (OSMAC) approach, leading to the identification of 3,319 unique chemical features. Only 6.4% were attributable to known compounds based on analysis of high-performance liquid chromatography–high-resolution mass spectrometry (HPLC–HRMS/MS) data using spectral library matching tools. Of the 1,606 features detected in the black apple extracts, 32% could be assigned as fungal-derived, due to their presence in the OSMAC-based training data set. Notably, the detection of several antifungal compounds indicates the importance of such compounds for the invasion of and control of other microbial competitors on apples. In conclusion, the diversity and abundance of microbial SMs on black apples were found to be much higher than that typically observed for other environmental microbiomes. Detection of SMs known to be produced by the six fungal species tested also highlights a succession of fungal growth following the initial invader M. fructigena . IMPORTANCE Microbial secondary metabolites constitute a significant reservoir of biologically potent and clinically valuable chemical scaffolds. However, their usefulness is hampered by rapidly developing resistance, resulting in reduced profitability of such research endeavors. Hence, the ecological role of such microbial secondary metabolites must be considered to understand how best to utilize such compounds as chemotherapeutics. Here, we explore an under-investigated environmental microbiome in the case of black apples; a veritable “low-hanging fruit,” with relatively high abundances and diversity of microbially produced secondary metabolites. Using both a targeted and untargeted metabolomics approach, the interplay between metabolites, other microbes, and the apple host itself was investigated. This study highlights the surprisingly low incidence of known secondary metabolites in such a system, highlighting the need to study the functionality of secondary metabolites in microbial interactions and complex microbiomes.

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Section: Discussionmentioning

confidence: 99%

Unveiling the fungal diversity and associated secondary metabolism on black apples

Cowled,

Phippen,

Kromphardt

et al. 2024

Appl Environ Microbiol

View full text Add to dashboard Cite

show abstract

“…A recent study by Kang, K. B and coworkers systematically investigated the potential biotransformations of phytochemicals by a panel of fungi using GNPS. (80)…”

Section: Discussionmentioning

confidence: 99%

Unveiling the Microbial Diversity and Associated Secondary Metabolism on Black Apples

Cowled,

Phippen,

Kromphardt

et al. 2023

Preprint

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Black apples are the late-stage microbial decomposition of apples after having fallen to the ground. This phenomenon is highly comparable from year to year, with the filamentous fungusMonilinia fructigenamost commonly being the first invader, followed byPenicillium expansum. Motivated by the fact that only little chemistry has been reported from apple microbiomes, we set out to investigate the chemical diversity and potential ecological roles of secondary metabolites (SMs) in a total of 38 black apples. Metabolomics analyses were conducted on either whole apples or small excisions of fungal biomass derived from black apples. Annotation of fungal SMs in black apple extracts was aided by cultivation of 15 recently isolated fungal strains on 9 different substrates in an OSMAC approach, leading to identification of 3319 unique chemical features. Only 6.8% were attributable to known compounds based on analysis of HPLC-HRMS/MS data using spectral library matching tools. Of the 1606 features detected in the black apple extracts, 32% could be assigned as fungal-derived, due to their presence in the OSMAC-based training dataset. Notably, the detection of several antifungal compounds clearly indicates the importance of such compounds for invasion of and control of other microbial competitors on apples. In conclusion, the diversity and abundance of microbial SMs on black apples was found to be much higher than that typically observed for other environmental microbiomes. Detection of SMs known to be produced by the six fungal species tested also highlights a succession of fungal growth following the initial invaderM. fructigena.ImportanceMicrobial secondary metabolites constitute a significant reservoir of biologically potent and clinically valuable chemical scaffolds. However, their usefulness is hampered by rapidly developing resistance, resulting in reduced profitability of such research endeavours. Hence, it is vital that the ecological role of such microbial secondary metabolites be considered to understand how best to utilise such compounds as chemotherapeutics. Here, we explore an under-investigated environmental microbiome in the case of black apples; a veritable “low-hanging fruit”, with relatively high abundances and diversity of microbially produced secondary metabolites. Using both a targeted and untargeted metabolomics approach, the interplay between metabolites, other microbes and the apple host itself was investigated. This study highlights the surprisingly low incidence of known secondary metabolites in such a system, highlighting the need to study the functionality of secondary metabolites in microbial interactions and complex microbiomes.

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Qualitative metabolomics-based characterization of a phenolic UDP-xylosyltransferase with a broad substrate spectrum from Lentinus brumalis

Jeong

Kim

Son

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Wood-decaying fungi are the major decomposers of plant litter. Heavy sequencing efforts on genomes of wood-decaying fungi have recently been made due to the interest in their lignocellulolytic enzymes; however, most parts of their proteomes remain uncharted. We hypothesized that wood-decaying fungi would possess promiscuous enzymes for detoxifying antifungal phytochemicals remaining in the dead plant bodies, which can be useful biocatalysts. We designed a computational mass spectrometry–based untargeted metabolomics pipeline for the phenotyping of biotransformation and applied it to 264 fungal cultures supplemented with antifungal plant phenolics. The analysis identified the occurrence of diverse reactivities by the tested fungal species. Among those, we focused on O -xylosylation of multiple phenolics by one of the species tested, Lentinus brumalis . By integrating the metabolic phenotyping results with publicly available genome sequences and transcriptome analysis, a UDP-glycosyltransferase designated UGT66A1 was identified and validated as an enzyme catalyzing O -xylosylation with broad substrate specificity. We anticipate that our analytical workflow will accelerate the further characterization of fungal enzymes as promising biocatalysts.

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Qualitative metabolomics-based characterization of a phenolic UDP-xylosyltransferase with a broad substrate spectrum from Lentinus brumalis

Cited by 3 publications

References 88 publications

Unveiling the fungal diversity and associated secondary metabolism on black apples

Unveiling the fungal diversity and associated secondary metabolism on black apples

Unveiling the Microbial Diversity and Associated Secondary Metabolism on Black Apples

Qualitative metabolomics-based characterization of a phenolic UDP-xylosyltransferase with a broad substrate spectrum from Lentinus brumalis

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