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

The Journal of Biological Chemistry
Daniel VeyelAleksandra Skirycz

Abstract

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 molecule and of protein-protein complexes. To this end, a cell-free native lysate from Arabidopsis thaliana cell cultures was fractionated by size-exclusion chromatography, followed by quantitative metabolomic and proteomic analyses. Proteins and small molecules showing similar elution behavior, across protein-containing fractions, constituted putative interactors. Applying PROMIS to an A. thaliana extract, we ascertained known protein-protein (PPIs) and protein-metabolite (PMIs) interactions and reproduced binding between small-molecule protease inhibitors and their respective proteases. More importantly, we present examples of two experimental strategies that exploit the PROMIS dataset to identify novel PMIs. By looking for similar elution behavior of metabolites and ...Continue Reading

References

May 9, 2000·The Journal of Biological Chemistry·N TanahashiK Tanaka
Jun 19, 2001·Medicinal Research Reviews·J MyungC M Crews
Dec 17, 2003·The Plant Journal : for Cell and Molecular Biology·Harald H OttenhofAlison G Smith
Jun 6, 2009·Annual Review of Biochemistry·Daniel Finley
Dec 10, 2009·Proceedings of the National Academy of Sciences of the United States of America·Brett LomenickJing Huang
Jan 22, 2010·Phytochemistry·Sutton Mooney, Hanjo Hellmann
Jan 25, 2011·Journal of Proteome Research·Jürgen CoxMatthias Mann
Mar 23, 2011·PloS One·Stephan KruegerDirk Steinhauser
Aug 5, 2011·Assay and Drug Development Technologies·Moran Jerabek-WillemsenStefan Duhr
Jul 4, 2012·Methods : a Companion to Methods in Enzymology·Grace Xiaolu YangMichael Snyder
Aug 7, 2012·Nature Methods·Anders R KristensenLeonard J Foster
Feb 12, 2013·Nature Methods·Jonathan J HulceBenjamin F Cravatt
Aug 15, 2014·The Plant Journal : for Cell and Molecular Biology·Dorothea Tholl, Asaph Aharoni
Oct 9, 2014·The Plant Cell·Uma K AryalDaniel B Szymanski
Nov 18, 2014·Biochemical Society Transactions·Brian Henderson, Andrew C R Martin
Sep 22, 2015·Nature Methods·Kilian V M HuberGiulio Superti-Furga
Nov 3, 2015·Nature Methods·Friedrich B M ReinhardGerard Drewes
Nov 22, 2015·Nucleic Acids Research·Damian SzklarczykMichael Kuhn
Sep 30, 2016·Nucleic Acids Research·Juan Antonio VizcaínoHenning Hermjakob
Dec 3, 2016·Nucleic Acids Research·Cornelia M HooperA Harvey Millar
Jun 7, 2017·Journal of Experimental Botany·Marcin LuzarowskiAleksandra Skirycz
Apr 6, 2018·Plant Physiology·Monika KosmaczAleksandra Skirycz

❮ Previous
Next ❯

Citations

Sep 25, 2019·The Biochemical Journal·Bruno E RojasAlberto A Iglesias
Nov 22, 2019·Current Protocols in Plant Biology·Ewelina M SokolowskaAleksandra Skirycz
Sep 25, 2019·Research : a Science Partner Journal·Alisdair R FernieLee J Sweetlove
May 16, 2019·Journal of Experimental Botany·Marcin Luzarowski, Aleksandra Skirycz
Aug 21, 2020·Cell Death & Disease·Caitlyn B BrashearsJason M Held
Mar 1, 2019·Nature Reviews. Molecular Cell Biology·Markus M RinschenGary Siuzdak
Apr 25, 2019·Journal of Experimental & Clinical Cancer Research : CR·Yuanliang YanZhijie Xu
Dec 29, 2020·Journal of Plant Physiology·Federico ScossaAlisdair R Fernie
Jan 23, 2021·Trends in Plant Science·Jhon Venegas-MolinaAlain Goossens
May 14, 2021·Patterns·Mohammad Amin OmidbakhshfardAleksandra Skirycz
Jun 23, 2021·The EMBO Journal·Juan C MorenoAleksandra Skirycz
Jun 18, 2021·Computational and Structural Biotechnology Journal·Zahra Razaghi-MoghadamZoran Nikoloski

❮ Previous
Next ❯

Datasets Mentioned

BETA
MTBLS94

Methods Mentioned

BETA
size-filtration
size-exclusion chromatography
microscale thermophoresis
affinity purification
transgenic
thermal shift

Software Mentioned

Excel
DARTS
MetaboLights
AP
Prometheus
Andromeda
MO Affinity Analysis
MST
MaxQuant
MetaSysX

Related Concepts

Related Feeds

ASBMB Publications

The American Society for Biochemistry and Molecular Biology (ASBMB) includes the Journal of Biological Chemistry, Molecular & Cellular Proteomics, and the Journal of Lipid Research. Discover the latest research from ASBMB here.