Novel (p)ppGpp Binding and Metabolizing Proteins of <italic toggle="yes">Escherichia coli</italic>

ABSTRACT The alarmone (p)ppGpp plays pivotal roles in basic bacterial stress responses by increasing tolerance of various nutritional limitations and chemical insults, including antibiotics. Despite intensive studies since (p)ppGpp was discovered over 4 decades ago, (p)ppGpp binding proteins have no...

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Autores principales: Yong Zhang, Eva Zborníková, Dominik Rejman, Kenn Gerdes
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Publicado: American Society for Microbiology 2018
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spelling oai:doaj.org-article:8bb57481ff8f456285196cee68d719132021-11-15T15:53:26ZNovel (p)ppGpp Binding and Metabolizing Proteins of <italic toggle="yes">Escherichia coli</italic>10.1128/mBio.02188-172150-7511https://doaj.org/article/8bb57481ff8f456285196cee68d719132018-05-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02188-17https://doaj.org/toc/2150-7511ABSTRACT The alarmone (p)ppGpp plays pivotal roles in basic bacterial stress responses by increasing tolerance of various nutritional limitations and chemical insults, including antibiotics. Despite intensive studies since (p)ppGpp was discovered over 4 decades ago, (p)ppGpp binding proteins have not been systematically identified in Escherichia coli. We applied DRaCALA (differential radial capillary action of ligand assay) to identify (p)ppGpp-protein interactions. We discovered 12 new (p)ppGpp targets in E. coli that, based on their physiological functions, could be classified into four major groups, involved in (i) purine nucleotide homeostasis (YgdH), (ii) ribosome biogenesis and translation (RsgA, Era, HflX, and LepA), (iii) maturation of dehydrogenases (HypB), and (iv) metabolism of (p)ppGpp (MutT, NudG, TrmE, NadR, PhoA, and UshA). We present a comprehensive and comparative biochemical and physiological characterization of these novel (p)ppGpp targets together with a comparative analysis of relevant, known (p)ppGpp binding proteins. Via this, primary targets of (p)ppGpp in E. coli are identified. The GTP salvage biosynthesis pathway and ribosome biogenesis and translation are confirmed as targets of (p)ppGpp that are highly conserved between E. coli and Firmicutes. In addition, an alternative (p)ppGpp degradative pathway, involving NudG and MutT, was uncovered. This report thus significantly expands the known cohort of (p)ppGpp targets in E. coli. IMPORTANCE Antibiotic resistance and tolerance exhibited by pathogenic bacteria have resulted in a global public health crisis. Remarkably, almost all bacterial pathogens require the alarmone (p)ppGpp to be virulent. Thus, (p)ppGpp not only induces tolerance of nutritional limitations and chemical insults, including antibiotics, but is also often required for induction of virulence genes. However, understanding of the molecular targets of (p)ppGpp and the mechanisms by which (p)ppGpp influences bacterial physiology is incomplete. In this study, a systematic approach was used to uncover novel targets of (p)ppGpp in E. coli, the best-studied model bacterium. Comprehensive comparative studies of the targets revealed conserved target pathways of (p)ppGpp in both Gram-positive and -negative bacteria and novel targets of (p)ppGpp, including an alternative degradative pathway of (p)ppGpp. Thus, our discoveries may help in understanding of how (p)ppGpp increases the stress resilience and multidrug tolerance not only of the model organism E. coli but also of the pathogenic organisms in which these targets are conserved.Yong ZhangEva ZborníkováDominik RejmanKenn GerdesAmerican Society for Microbiologyarticle(p)ppGppDRaCALAGTPaseNudixmultidrug tolerancepersistenceMicrobiologyQR1-502ENmBio, Vol 9, Iss 2 (2018)
institution DOAJ
collection DOAJ
language EN
topic (p)ppGpp
DRaCALA
GTPase
Nudix
multidrug tolerance
persistence
Microbiology
QR1-502
spellingShingle (p)ppGpp
DRaCALA
GTPase
Nudix
multidrug tolerance
persistence
Microbiology
QR1-502
Yong Zhang
Eva Zborníková
Dominik Rejman
Kenn Gerdes
Novel (p)ppGpp Binding and Metabolizing Proteins of <italic toggle="yes">Escherichia coli</italic>
description ABSTRACT The alarmone (p)ppGpp plays pivotal roles in basic bacterial stress responses by increasing tolerance of various nutritional limitations and chemical insults, including antibiotics. Despite intensive studies since (p)ppGpp was discovered over 4 decades ago, (p)ppGpp binding proteins have not been systematically identified in Escherichia coli. We applied DRaCALA (differential radial capillary action of ligand assay) to identify (p)ppGpp-protein interactions. We discovered 12 new (p)ppGpp targets in E. coli that, based on their physiological functions, could be classified into four major groups, involved in (i) purine nucleotide homeostasis (YgdH), (ii) ribosome biogenesis and translation (RsgA, Era, HflX, and LepA), (iii) maturation of dehydrogenases (HypB), and (iv) metabolism of (p)ppGpp (MutT, NudG, TrmE, NadR, PhoA, and UshA). We present a comprehensive and comparative biochemical and physiological characterization of these novel (p)ppGpp targets together with a comparative analysis of relevant, known (p)ppGpp binding proteins. Via this, primary targets of (p)ppGpp in E. coli are identified. The GTP salvage biosynthesis pathway and ribosome biogenesis and translation are confirmed as targets of (p)ppGpp that are highly conserved between E. coli and Firmicutes. In addition, an alternative (p)ppGpp degradative pathway, involving NudG and MutT, was uncovered. This report thus significantly expands the known cohort of (p)ppGpp targets in E. coli. IMPORTANCE Antibiotic resistance and tolerance exhibited by pathogenic bacteria have resulted in a global public health crisis. Remarkably, almost all bacterial pathogens require the alarmone (p)ppGpp to be virulent. Thus, (p)ppGpp not only induces tolerance of nutritional limitations and chemical insults, including antibiotics, but is also often required for induction of virulence genes. However, understanding of the molecular targets of (p)ppGpp and the mechanisms by which (p)ppGpp influences bacterial physiology is incomplete. In this study, a systematic approach was used to uncover novel targets of (p)ppGpp in E. coli, the best-studied model bacterium. Comprehensive comparative studies of the targets revealed conserved target pathways of (p)ppGpp in both Gram-positive and -negative bacteria and novel targets of (p)ppGpp, including an alternative degradative pathway of (p)ppGpp. Thus, our discoveries may help in understanding of how (p)ppGpp increases the stress resilience and multidrug tolerance not only of the model organism E. coli but also of the pathogenic organisms in which these targets are conserved.
format article
author Yong Zhang
Eva Zborníková
Dominik Rejman
Kenn Gerdes
author_facet Yong Zhang
Eva Zborníková
Dominik Rejman
Kenn Gerdes
author_sort Yong Zhang
title Novel (p)ppGpp Binding and Metabolizing Proteins of <italic toggle="yes">Escherichia coli</italic>
title_short Novel (p)ppGpp Binding and Metabolizing Proteins of <italic toggle="yes">Escherichia coli</italic>
title_full Novel (p)ppGpp Binding and Metabolizing Proteins of <italic toggle="yes">Escherichia coli</italic>
title_fullStr Novel (p)ppGpp Binding and Metabolizing Proteins of <italic toggle="yes">Escherichia coli</italic>
title_full_unstemmed Novel (p)ppGpp Binding and Metabolizing Proteins of <italic toggle="yes">Escherichia coli</italic>
title_sort novel (p)ppgpp binding and metabolizing proteins of <italic toggle="yes">escherichia coli</italic>
publisher American Society for Microbiology
publishDate 2018
url https://doaj.org/article/8bb57481ff8f456285196cee68d71913
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