Interrogating Plant-Microbe Interactions with Chemical Tools: Click Chemistry Reagents for Metabolic Labeling and Activity-Based Probes

Lin, Vivian

doi:10.3390/molecules26010243

Cited by 6 publications

(5 citation statements)

References 70 publications

(57 reference statements)

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“…Microbial virulence factors contribute to the establishment of a disease relationship between a microbe and a 'host' plant [29,30]. Methodical identification of these molecules in species across several microbial genera has advanced the understanding of phytochemicals, the chemicals involved in pathogen-pathogen and host-pathogen interactions [30][31][32][33].…”

Section: Introductionmentioning

confidence: 99%

Metabolomics Insights into Chemical Convergence in Xanthomonas perforans and Metabolic Changes Following Treatment with the Small Molecule Carvacrol

et al. 2021

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Microbes are natural chemical factories and their metabolome comprise diverse arrays of chemicals. The genus Xanthomonas comprises some of the most important plant pathogens causing devastating yield losses globally and previous studies suggested that species in the genus are untapped chemical minefields. In this study, we applied an untargeted metabolomics approach to study the metabolome of a globally spread important xanthomonad, X. perforans. The pathogen is difficult to manage, but recent studies suggest that the small molecule carvacrol was efficient in disease control. Bacterial strains were treated with carvacrol, and samples were taken at time intervals (1 and 6 h). An untreated control was also included. There were five replicates for each sample and samples were prepared for metabolomics profiling using the standard procedure. Metabolomics profiling was carried out using a thermo Q-Exactive orbitrap mass spectrometer with Dionex ultra high-performance liquid chromatography (UHPLC) and an autosampler. Annotation of significant metabolites using the Metabolomics Standards Initiative level 2 identified an array of novel metabolites that were previously not reported in Xanthomonas perforans. These metabolites include methoxybrassinin and cyclobrassinone, which are known metabolites of brassicas; sarmentosin, a metabolite of the Passiflora-heliconiine butterfly system; and monatin, a naturally occurring sweetener found in Sclerochiton ilicifolius. To our knowledge, this is the first report of these metabolites in a microbial system. Other significant metabolites previously identified in non-Xanthomonas systems but reported in this study include maculosin; piperidine; β-carboline alkaloids, such as harman and derivatives; and several important medically relevant metabolites, such as valsartan, metharbital, pirbuterol, and ozagrel. This finding is consistent with convergent evolution found in reported biological systems. Analyses of the effect of carvacrol in time-series and associated pathways suggest that carvacrol has a global effect on the metabolome of X. perforans, showing marked changes in metabolites that are critical in energy biosynthesis and degradation pathways, amino acid pathways, nucleic acid pathways, as well as the newly identified metabolites whose pathways are unknown. This study provides the first insight into the X. perforans metabolome and additionally lays a metabolomics-guided foundation for characterization of novel metabolites and pathways in xanthomonad systems.

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Section: Introductionmentioning

confidence: 99%

Metabolomics Insights into Chemical Convergence in Xanthomonas perforans and Metabolic Changes Following Treatment with the Small Molecule Carvacrol

et al. 2021

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“…Measurements of plant-microbe interactions are particularly difficult due to very high microbe heterogeneity, considerable variability in field samples, and poor correlation between laboratory model systems and field systems. [61] Thus far, ABPP has only yielded quantitative proteomic results when model systems are used with simulated microbial consortia, or curation of metagenomes for each sample analyzed. Despite these challenges, progress is being made.…”

Section: Abpp Of Plant-microbe Interactions and Soil Microbiomesmentioning

confidence: 99%

“…Additionally, chemical exposures or environmental factors, such as wetting, drought, or nutrient availability can dramatically alter plant‐microbe interactions. Measurements of plant‐microbe interactions are particularly difficult due to very high microbe heterogeneity, considerable variability in field samples, and poor correlation between laboratory model systems and field systems [61] . Thus far, ABPP has only yielded quantitative proteomic results when model systems are used with simulated microbial consortia, or curation of metagenomes for each sample analyzed.…”

Section: Abpp Of Environmental Microbiomesmentioning

confidence: 99%

“…However, the implications are massive for characterizing the biochemical mechanisms that support important phenotypes at microbiome through ecosystem scales. Success will open opportunities to better understand biogeochemical cycles, consequences of climate change, agricultural health and productivity, bioenergy production, environmental remediation, and provide new applied possibilities for synthetic biology and bioengineering [60–61] . Principal challenges include complex sample compositions, minimal genome annotation, and complex data processing and analysis [62] …”

Section: Introductionmentioning

confidence: 99%

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Activity‐Based Protein Profiling – Enabling Phenotyping of Host‐Associated and Environmental Microbiomes

Wright

Hudson

Garcia

2023

Israel Journal of Chemistry

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“…The flexibility imparted by using "click" tags in chemical probe designs make these an appealing strategy for multimodal analysis of probe-labeled protein targets in downstream steps of the workflow. 32,33 Due to their modular nature, chemical probes can be tailored for diverse applications and metabolites of interest.…”

Section: Introductionmentioning

confidence: 99%

Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders inAcinetobacter pittii

Kroll¹,

Fossen

Anderson

et al. 2023

Preprint

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Sorghum (Sorghum bicolor) is a major food and bioenergy grass species cultivated worldwide. To promote more robust and sustainable growth of this important crop, we need a deeper understanding of the plant-microbe interactions between sorghum and soil microbial communities that benefit plant host resiliency and enhance nutrient acquisition. The release of specific metabolites from plant roots, or root exudation, drives these plant-microbe interactions, but the molecular pathways by which root exudates shape the sorghum rhizosphere microbiome require further elucidation. To investigate these complex interkingdom interactions in the sorghum rhizosphere, we developed a photoaffinity probe based on sorgoleone, a hydrophobic secondary metabolite and allelochemical produced in sorghum seedling root exudates. Here, we apply a new synthetic sorgoleone diazirine alkyne photoaffinity probe (SoDA-PAL) to the identification of sorgoleone-binding proteins in Acinetobacter pittii SO1, a potential plant growth promoting microbe derived from Sorghum bicolor rhizosphere soil. Competitive photoaffinity labeling of A. pittii whole cell lysates with SoDA-PAL identified 137 statistically enriched proteins that were complementary to a previously identified gene cluster involved in sorgoleone catabolism. Proteins identified by SoDA-PAL included a select set of putative transporters, transcription regulators, and a subset of proteins with lipid and secondary metabolic activities. We confirm binding of SoDA-PAL to a putative hydrolase in the α/β fold family (OH685_09420) through structural bioinformatics and in-vitro recombinant protein analysis. This photoaffinity labeling approach using metabolite-based probes can be extended in the future to proteomic profiling of complex rhizosphere microbiomes to discover genes that can be leveraged to promote beneficial plant-microbe interactions.

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Interrogating Plant-Microbe Interactions with Chemical Tools: Click Chemistry Reagents for Metabolic Labeling and Activity-Based Probes

Cited by 6 publications

References 70 publications

Metabolomics Insights into Chemical Convergence in Xanthomonas perforans and Metabolic Changes Following Treatment with the Small Molecule Carvacrol

Metabolomics Insights into Chemical Convergence in Xanthomonas perforans and Metabolic Changes Following Treatment with the Small Molecule Carvacrol

Activity‐Based Protein Profiling – Enabling Phenotyping of Host‐Associated and Environmental Microbiomes

Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders inAcinetobacter pittii

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