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Affinity-based capture and identification of protein effectors of the growth regulator ppGpp

The nucleotide ppGpp is a highly conserved regulatory molecule in prokaryotes that helps tune growth rate to nutrient availability. Despite decades of study, how ppGpp regulates growth remains poorly understood. Here, we develop and validate a capture-compound mass spectrometry approach that identif...

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Detalles Bibliográficos
Autores principales: Wang, Boyuan, Dai, Peng, Ding, David, Del Rosario, Amanda, Grant, Robert A., Pentelute, Bradley L., Laub, Michael T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366861/
https://www.ncbi.nlm.nih.gov/pubmed/30559427
http://dx.doi.org/10.1038/s41589-018-0183-4
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author Wang, Boyuan
Dai, Peng
Ding, David
Del Rosario, Amanda
Grant, Robert A.
Pentelute, Bradley L.
Laub, Michael T.
author_facet Wang, Boyuan
Dai, Peng
Ding, David
Del Rosario, Amanda
Grant, Robert A.
Pentelute, Bradley L.
Laub, Michael T.
author_sort Wang, Boyuan
collection PubMed
description The nucleotide ppGpp is a highly conserved regulatory molecule in prokaryotes that helps tune growth rate to nutrient availability. Despite decades of study, how ppGpp regulates growth remains poorly understood. Here, we develop and validate a capture-compound mass spectrometry approach that identifies >50 putative ppGpp targets in Escherichia coli. These targets control many key cellular processes and include 13 enzymes required for nucleotide synthesis. We demonstrate that ppGpp inhibits the de novo synthesis of all purine nucleotides by directly targeting the enzyme PurF. By solving a structure of PurF bound to ppGpp, we design a mutation that ablates ppGpp-based regulation, leading to a dysregulation of purine nucleotide synthesis following ppGpp accumulation. Collectively, our results provide new insights into ppGpp-based growth control and a nearly comprehensive set of targets for future exploration. The capture compounds developed will also now enable the rapid identification of ppGpp targets in any species, including pathogens.
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spelling pubmed-63668612019-06-17 Affinity-based capture and identification of protein effectors of the growth regulator ppGpp Wang, Boyuan Dai, Peng Ding, David Del Rosario, Amanda Grant, Robert A. Pentelute, Bradley L. Laub, Michael T. Nat Chem Biol Article The nucleotide ppGpp is a highly conserved regulatory molecule in prokaryotes that helps tune growth rate to nutrient availability. Despite decades of study, how ppGpp regulates growth remains poorly understood. Here, we develop and validate a capture-compound mass spectrometry approach that identifies >50 putative ppGpp targets in Escherichia coli. These targets control many key cellular processes and include 13 enzymes required for nucleotide synthesis. We demonstrate that ppGpp inhibits the de novo synthesis of all purine nucleotides by directly targeting the enzyme PurF. By solving a structure of PurF bound to ppGpp, we design a mutation that ablates ppGpp-based regulation, leading to a dysregulation of purine nucleotide synthesis following ppGpp accumulation. Collectively, our results provide new insights into ppGpp-based growth control and a nearly comprehensive set of targets for future exploration. The capture compounds developed will also now enable the rapid identification of ppGpp targets in any species, including pathogens. 2018-12-17 2019-02 /pmc/articles/PMC6366861/ /pubmed/30559427 http://dx.doi.org/10.1038/s41589-018-0183-4 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Wang, Boyuan
Dai, Peng
Ding, David
Del Rosario, Amanda
Grant, Robert A.
Pentelute, Bradley L.
Laub, Michael T.
Affinity-based capture and identification of protein effectors of the growth regulator ppGpp
title Affinity-based capture and identification of protein effectors of the growth regulator ppGpp
title_full Affinity-based capture and identification of protein effectors of the growth regulator ppGpp
title_fullStr Affinity-based capture and identification of protein effectors of the growth regulator ppGpp
title_full_unstemmed Affinity-based capture and identification of protein effectors of the growth regulator ppGpp
title_short Affinity-based capture and identification of protein effectors of the growth regulator ppGpp
title_sort affinity-based capture and identification of protein effectors of the growth regulator ppgpp
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366861/
https://www.ncbi.nlm.nih.gov/pubmed/30559427
http://dx.doi.org/10.1038/s41589-018-0183-4
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