Structure of SpoT reveals evolutionary tuning of catalysis via conformational constraint

Hedvig Tamman, Karin Ernits, Mohammad Roghanian, Andres Ainelo, Christina Julius, Anthony Perrier, Ariel Talavera, Hanna Ainelo, Rémy Dugauquier, Safia Zedek, Aurelien Thureau, Javier Pérez, Gipsi Lima-Mendez, Regis Hallez, Gemma Atkinson, Vasili Hauryliuk, Abel Garcia-Pino

Research output: Contribution to journalArticlepeer-review

64 Downloads (Pure)

Abstract

Stringent factors orchestrate bacterial cell reprogramming through increasing the level of the alarmones (p)ppGpp. In Beta- and Gammaproteobacteria, SpoT hydrolyzes (p)ppGpp to counteract the synthetase activity of RelA. However, structural information about how SpoT controls the levels of (p)ppGpp is missing. Here we present the crystal structure of the hydrolase-only SpoT from Acinetobacter baumannii and uncover the mechanism of intramolecular regulation of ‘long’-stringent factors. In contrast to ribosome-associated Rel/RelA that adopt an elongated structure, SpoT assumes a compact τ-shaped structure in which the regulatory domains wrap around a Core subdomain that controls the conformational state of the enzyme. The Core is key to the specialization of long RelA-SpoT homologs toward either synthesis or hydrolysis: the short and structured Core of SpoT stabilizes the τ-state priming the hydrolase domain for (p)ppGpp hydrolysis, whereas the longer, more dynamic Core domain of RelA destabilizes the τ-state priming the monofunctional RelA for efficient (p)ppGpp synthesis. [Figure not available: see fulltext.].

Original languageEnglish
Pages (from-to)334-345
Number of pages12
JournalNature Chemical Biology
Volume19
Issue number3
DOIs
Publication statusPublished - 5 Dec 2022

Funding

We are grateful to the Protein Expertise Platform at Ume\u00E5 University for constructing plasmids and acknowledge the use of beamtimes PROXIMA 1 and 2A and SWING at the SOLEIL synchrotron (Gif-sur-Yvette, France). This work was supported by the Fonds National de Recherche Scientifique (FNRS) (grant nos. FRFS-WELBIO CR-2017S-03, FNRS CDR J.0068.19, FNRS-EQP UN.025.19 and FNRS-PDR T.0066.18 to A.G.-P.); ERC (grant no. CoG DiStRes, no. 864311 to A.G.-P.) and Joint Programming Initiative on Antimicrobial Resistance, (JPIAMR) grant no. JPI-EC-AMR-R.8004.18 to A.G.-P.; the Program Actions de Recherche Concert\u00E9 2016-2021, Fonds d\u2019Encouragement \u00E0 la Recherche of ULB (A.G.-P.); Fonds Jean Brachet and the Fondation Van Buuren (A.G.-P.); Charg\u00E9 de Recherches fellowship from the FNRS grant no. CR/DM-392 (H.T.); the European Regional Development Fund through the Center of Excellence for Molecular Cell Technology (V.H.); project grant from the Knut and Alice Wallenberg Foundation (grant no. 2020-0037 to G.C.A.); Ragnar S\u00F6derberg foundation (V.H.); Swedish Research council (grant nos. 2019-01085 to G.C.A., 2017-03783 and 2021-01146 to V.H., and 2018-00956 to V.H. under the framework of Joint Programming Initiative on Antimicrobial Resistance, JPIAMR); the MIMS Excellence by Choice Postdoctoral Fellowship Programme grant no. 2018 (M.R.); the European Union\u2019s Horizon 2020 research and innovation program under the Marie Sk\u0142odowska-Curie grant no. 801505 (IF@ULB postdoctoral grant to A.A. and H.A.) and grant no. FRFS-WELBIO-CR-2019S-05 (R.H.). A.P. is an FRS\u2013FNRS Postdoctoral Researcher and R.H. is an FRS\u2013FNRS Research Associate.

FundersFunder number
European Resuscitation Council
FRS—FNRS
Protein Expertise Platform at Umeå University
Fondation Van Buuren
Ragnar Söderbergs stiftelse
European Regional Development Fund
Fonds Jean Brachet
Vetenskapsrådet2018, 2017-03783, 2018-00956, 2019-01085, 2021-01146
H2020 Marie Skłodowska-Curie ActionsFRFS-WELBIO-CR-2019S-05, 801505
Fonds National de Recherche ScientifiqueFNRS-PDR T.0066.18, FRFS-WELBIO CR-2017S-03, FNRS-EQP UN.025.19
Horizon 2020 Framework Programme864311
Joint Programming Initiative on Antimicrobial ResistanceCR/DM-392, JPI-EC-AMR-R.8004.18
Knut och Alice Wallenbergs Stiftelse2020-0037

    Fingerprint

    Dive into the research topics of 'Structure of SpoT reveals evolutionary tuning of catalysis via conformational constraint'. Together they form a unique fingerprint.

    Cite this