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Extensive regulation of enzyme activity by phosphorylation in Escherichia coli

Protein serine/threonine/tyrosine (S/T/Y) phosphorylation is an essential and frequent post-translational modification in eukaryotes, but historically has been considered less prevalent in bacteria because fewer proteins were found to be phosphorylated and most proteins were modified to a lower degr...

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Autores principales: Schastnaya, Evgeniya, Raguz Nakic, Zrinka, Gruber, Christoph H., Doubleday, Peter Francis, Krishnan, Aarti, Johns, Nathan I., Park, Jimin, Wang, Harris H., Sauer, Uwe
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8463566/
https://www.ncbi.nlm.nih.gov/pubmed/34561442
http://dx.doi.org/10.1038/s41467-021-25988-4
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author Schastnaya, Evgeniya
Raguz Nakic, Zrinka
Gruber, Christoph H.
Doubleday, Peter Francis
Krishnan, Aarti
Johns, Nathan I.
Park, Jimin
Wang, Harris H.
Sauer, Uwe
author_facet Schastnaya, Evgeniya
Raguz Nakic, Zrinka
Gruber, Christoph H.
Doubleday, Peter Francis
Krishnan, Aarti
Johns, Nathan I.
Park, Jimin
Wang, Harris H.
Sauer, Uwe
author_sort Schastnaya, Evgeniya
collection PubMed
description Protein serine/threonine/tyrosine (S/T/Y) phosphorylation is an essential and frequent post-translational modification in eukaryotes, but historically has been considered less prevalent in bacteria because fewer proteins were found to be phosphorylated and most proteins were modified to a lower degree. Recent proteomics studies greatly expanded the phosphoproteome of Escherichia coli to more than 2000 phosphorylation sites (phosphosites), yet mechanisms of action were proposed for only six phosphosites and fitness effects were described for 38 phosphosites upon perturbation. By systematically characterizing functional relevance of S/T/Y phosphorylation in E. coli metabolism, we found 44 of the 52 mutated phosphosites to be functional based on growth phenotypes and intracellular metabolome profiles. By effectively doubling the number of known functional phosphosites, we provide evidence that protein phosphorylation is a major regulation process in bacterial metabolism. Combining in vitro and in vivo experiments, we demonstrate how single phosphosites modulate enzymatic activity and regulate metabolic fluxes in glycolysis, methylglyoxal bypass, acetate metabolism and the split between pentose phosphate and Entner-Doudoroff pathways through mechanisms that include shielding the substrate binding site, limiting structural dynamics, and disrupting interactions relevant for activity in vivo.
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spelling pubmed-84635662021-10-22 Extensive regulation of enzyme activity by phosphorylation in Escherichia coli Schastnaya, Evgeniya Raguz Nakic, Zrinka Gruber, Christoph H. Doubleday, Peter Francis Krishnan, Aarti Johns, Nathan I. Park, Jimin Wang, Harris H. Sauer, Uwe Nat Commun Article Protein serine/threonine/tyrosine (S/T/Y) phosphorylation is an essential and frequent post-translational modification in eukaryotes, but historically has been considered less prevalent in bacteria because fewer proteins were found to be phosphorylated and most proteins were modified to a lower degree. Recent proteomics studies greatly expanded the phosphoproteome of Escherichia coli to more than 2000 phosphorylation sites (phosphosites), yet mechanisms of action were proposed for only six phosphosites and fitness effects were described for 38 phosphosites upon perturbation. By systematically characterizing functional relevance of S/T/Y phosphorylation in E. coli metabolism, we found 44 of the 52 mutated phosphosites to be functional based on growth phenotypes and intracellular metabolome profiles. By effectively doubling the number of known functional phosphosites, we provide evidence that protein phosphorylation is a major regulation process in bacterial metabolism. Combining in vitro and in vivo experiments, we demonstrate how single phosphosites modulate enzymatic activity and regulate metabolic fluxes in glycolysis, methylglyoxal bypass, acetate metabolism and the split between pentose phosphate and Entner-Doudoroff pathways through mechanisms that include shielding the substrate binding site, limiting structural dynamics, and disrupting interactions relevant for activity in vivo. Nature Publishing Group UK 2021-09-24 /pmc/articles/PMC8463566/ /pubmed/34561442 http://dx.doi.org/10.1038/s41467-021-25988-4 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Schastnaya, Evgeniya
Raguz Nakic, Zrinka
Gruber, Christoph H.
Doubleday, Peter Francis
Krishnan, Aarti
Johns, Nathan I.
Park, Jimin
Wang, Harris H.
Sauer, Uwe
Extensive regulation of enzyme activity by phosphorylation in Escherichia coli
title Extensive regulation of enzyme activity by phosphorylation in Escherichia coli
title_full Extensive regulation of enzyme activity by phosphorylation in Escherichia coli
title_fullStr Extensive regulation of enzyme activity by phosphorylation in Escherichia coli
title_full_unstemmed Extensive regulation of enzyme activity by phosphorylation in Escherichia coli
title_short Extensive regulation of enzyme activity by phosphorylation in Escherichia coli
title_sort extensive regulation of enzyme activity by phosphorylation in escherichia coli
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8463566/
https://www.ncbi.nlm.nih.gov/pubmed/34561442
http://dx.doi.org/10.1038/s41467-021-25988-4
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