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PROMIS, global analysis of PROtein-Metabolite Interactions using Size separation in Arabidopsis thaliana

ABSTRACT: Herein, we describe a method, dubbed PROMIS that allows simultaneous, global analysis of endogenous protein–small-molecule and protein-protein complexes. To this end a cell-free native lysate was subjected to size-exclusion chromatography followed by quantitative metabolomic and proteomic analysis. Applying this approach to an extract from Arabidopsis thaliana cell cultures, we could retrieve known protein-protein (PPI) and protein–metabolite (PMI) interactions, validating our strategy.

OTHER RELATED OMICS DATASETS IN: MTBLS94

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell, Cell Culture

SUBMITTER: Michal Gorka

LAB HEAD: Aleksandra Skirycz

PROVIDER: PXD009714 | Pride | 2018-06-06

REPOSITORIES: Pride

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PROMIS, global analysis of PROtein-metabolite interactions using size separation in Arabidopsis thaliana.

Veyel Daniel D Sokolowska Ewelina M EM Moreno Juan C JC Kierszniowska Sylwia S Cichon Justyna J Wojciechowska Izabela I Luzarowski Marcin M Kosmacz Monika M Szlachetko Jagoda J Gorka Michal M Méret Michaël M Graf Alexander A Meyer Etienne H EH Willmitzer Lothar L Skirycz Aleksandra A

The Journal of biological chemistry 20180531 32

Small molecules not only represent cellular building blocks and metabolic intermediates, but also regulatory ligands and signaling molecules that interact with proteins. Although these interactions affect cellular metabolism, growth, and development, they have been largely understudied. Herein, we describe a method, which we named PROtein-Metabolite Interactions using Size separation (PROMIS), that allows simultaneous, global analysis of endogenous protein-small molec ...[more]

PMID: 29853640

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Dynamic maps of protein-protein-metabolite complexes of Arabidopsis Thaliana seedlings

Project description:The project aimed to create dynamic maps of protein-protein-metabolite complexes of Arabidopsis thaliana seedlings using PROMIS (PROtein–Metabolite Interactions using Size separation). The approach involves using size exclusion chromatography (SEC) to separate complexes, followed by LC-MS-based proteomics and metabolomics analysis of the obtained fractions. Co-elution is used to reconstruct the protein-metabolite interactions (PMIs) networks. PROMIS strongly progresses understanding protein-small molecule interactions due to its non-targeted manner, cell-wide scale, and generic nature, making it suitable across biological systems. Combining PROMIS with mashing learning approach SLIMP “supervised learning of metabolite-protein interactions from multiple co-fractionation mass spectrometry datasets” allows computing a global map of metabolite-protein interactions in vivo.

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