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Interaction-based capture and identification of protein effectors of ppGpp, the master regulator of bacterial growth

ABSTRACT: The small nucleotide ppGpp is a conserved regulatory molecule in prokaryotes that tunes growth rate in response to nutrient availability. How ppGpp regulates growth remains poorly defined. In Escherichia coli, ppGpp directly binds RNA polymerase to modulate transcription, but it likely has other targets. Here, we develop a capture-compound mass spectrometry approach to identify more than 50 putative ppGpp targets that control many key cellular processes, including translation, polyamine synthesis, and nucleotide metabolism. We validate several proteins as bona fide ppGpp targets in vivo. In particular, we demonstrate that ppGpp inhibits the enzymes Gsk and PurF to block purine salvage and de novo synthesis, respectively. Our results indicate that downregulating ATP and GTP synthesis is a critical facet of growth control by ppGpp. Collectively, our results provide new insight into ppGpp-based growth control in E. coli and candidates for future exploration. The capture compounds developed will also enable identification of ppGpp targets in other species, including many pathogens.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Escherichia Coli

SUBMITTER: Amanda Del Rosario

LAB HEAD: Amanda Del Rosario

PROVIDER: PXD010402 | Pride | 2018-10-04

REPOSITORIES: Pride

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