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.

doi:10.1038/s41589-018-0183-4

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

Journal Article · Mon Dec 17 00:00:00 EST 2018 · Nature Chemical Biology

DOI:https://doi.org/10.1038/s41589-018-0183-4· OSTI ID:1569903

Wang, Boyuan ^[1];

^[1]; Ding, David ^[1]; Del Rosario, Amanda ^[2]; Grant, Robert A. ^[1]; Pentelute, Bradley L. ^[3];

^[4]

Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Koch Inst. for Cancer Research
Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Koch Inst. for Cancer Research; Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Center for Environmental Health Sciences; Broad Inst. of Harvard and MIT, Cambridge, MA (United States)
Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Howard Hughes Medical Inst.

The nucleotide ppGpp is a highly conserved regulatory molecule in bacteria that helps tune growth rate to nutrient availability. Despite decades of study, how ppGpp regulates growth remains poorly understood. Here, we developed and validated a capture-compound mass spectrometry approach that identified >50 putative ppGpp targets in Escherichia coli. These targets control many key cellular processes and include 13 enzymes required for nucleotide synthesis. We demonstrated 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 designed a mutation that ablates ppGpp-based regulation, leading to 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. Furthermore, the capture compounds developed should also enable the rapid identification of ppGpp targets in any species, including pathogens.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE; National Science Foundation (NSF); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-06CH11357; NSF-0070319; R01GM082899

OSTI ID:: 1569903

Journal Information:: Nature Chemical Biology, Vol. 15, Issue 2; ISSN 1552-4450

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 104 works

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How the initiating ribosome copes with ppGpp to translate mRNAs Vinogradova, Daria S.; Zegarra, Victor; Maksimova, Elena PLOS Biology, Vol. 18, Issue 1 https://doi.org/10.1371/journal.pbio.3000593	journal	January 2020
Characterization of Autoinducer-3 Structure and Biosynthesis in E. coli Kim, Chung Sub; Gatsios, Alexandra; Cuesta, Santiago ACS Central Science, Vol. 6, Issue 2 https://doi.org/10.1021/acscentsci.9b01076	journal	January 2020
Evolution of (p)ppGpp-HPRT regulation through diversification of an allosteric oligomeric interaction Anderson, Brent W.; Liu, Kuanqing; Wolak, Christine eLife, Vol. 8 https://doi.org/10.7554/elife.47534	journal	September 2019
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