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

doi:10.1038/s41589-022-01198-x

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

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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 language	English
Pages (from-to)	334-345
Number of pages	12
Journal	Nature Chemical Biology
Volume	19
Issue number	3
DOIs	https://doi.org/10.1038/s41589-022-01198-x
Publication status	Published - 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.

Funders	Funder 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
Vetenskapsrådet	2018, 2017-03783, 2018-00956, 2019-01085, 2021-01146
H2020 Marie Skłodowska-Curie Actions	FRFS-WELBIO-CR-2019S-05, 801505
Fonds National de Recherche Scientifique	FNRS-PDR T.0066.18, FRFS-WELBIO CR-2017S-03, FNRS-EQP UN.025.19
Horizon 2020 Framework Programme	864311
Joint Programming Initiative on Antimicrobial Resistance	CR/DM-392, JPI-EC-AMR-R.8004.18
Knut och Alice Wallenbergs Stiftelse	2020-0037

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Tamman et al., 2022_Nat_Chem_BiolFinal published version, 4.47 MBLicence: CC BY

Cite this

Tamman, H., Ernits, K., Roghanian, M., Ainelo, A., Julius, C., Perrier, A., Talavera, A., Ainelo, H., Dugauquier, R., Zedek, S., Thureau, A., Pérez, J., Lima-Mendez, G., Hallez, R., Atkinson, G., Hauryliuk, V., & Garcia-Pino, A. (2022). Structure of SpoT reveals evolutionary tuning of catalysis via conformational constraint. Nature Chemical Biology, 19(3), 334-345. https://doi.org/10.1038/s41589-022-01198-x

@article{d9a19a792a9245a2942bf883e76a3f76,

title = "Structure of SpoT reveals evolutionary tuning of catalysis via conformational constraint",

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 {\textquoteleft}long{\textquoteright}-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.].",

author = "Hedvig Tamman and Karin Ernits and Mohammad Roghanian and Andres Ainelo and Christina Julius and Anthony Perrier and Ariel Talavera and Hanna Ainelo and R{\'e}my Dugauquier and Safia Zedek and Aurelien Thureau and Javier P{\'e}rez and Gipsi Lima-Mendez and Regis Hallez and Gemma Atkinson and Vasili Hauryliuk and Abel Garcia-Pino",

note = "Funding Information: We are grateful to the Protein Expertise Platform at Ume{\aa} 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{\'e} 2016-2021, Fonds d{\textquoteright}Encouragement {\`a} la Recherche of ULB (A.G.-P.); Fonds Jean Brachet and the Fondation Van Buuren (A.G.-P.); Charg{\'e} 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{\"o}derberg 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{\textquoteright}s Horizon 2020 research and innovation program under the Marie Sk{\l}odowska-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–FNRS Postdoctoral Researcher and R.H. is an FRS–FNRS Research Associate. Funding Information: We are grateful to the Protein Expertise Platform at Ume{\aa} 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{\'e} 2016-2021, Fonds d{\textquoteright}Encouragement {\`a} la Recherche of ULB (A.G.-P.); Fonds Jean Brachet and the Fondation Van Buuren (A.G.-P.); Charg{\'e} 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{\"o}derberg 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{\textquoteright}s Horizon 2020 research and innovation program under the Marie Sk{\l}odowska-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–FNRS Postdoctoral Researcher and R.H. is an FRS–FNRS Research Associate. Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = dec,

day = "5",

doi = "10.1038/s41589-022-01198-x",

language = "English",

volume = "19",

pages = "334--345",

journal = "Nature Chemical Biology",

issn = "1552-4450",

publisher = "Nature Research",

number = "3",

}

Tamman, H, Ernits, K, Roghanian, M, Ainelo, A, Julius, C, Perrier, A, Talavera, A, Ainelo, H, Dugauquier, R, Zedek, S, Thureau, A, Pérez, J, Lima-Mendez, G , Hallez, R, Atkinson, G, Hauryliuk, V & Garcia-Pino, A 2022, 'Structure of SpoT reveals evolutionary tuning of catalysis via conformational constraint', Nature Chemical Biology, vol. 19, no. 3, pp. 334-345. https://doi.org/10.1038/s41589-022-01198-x

TY - JOUR

T1 - Structure of SpoT reveals evolutionary tuning of catalysis via conformational constraint

AU - Tamman, Hedvig

AU - Ernits, Karin

AU - Roghanian, Mohammad

AU - Ainelo, Andres

AU - Julius, Christina

AU - Perrier, Anthony

AU - Talavera, Ariel

AU - Ainelo, Hanna

AU - Dugauquier, Rémy

AU - Zedek, Safia

AU - Thureau, Aurelien

AU - Pérez, Javier

AU - Lima-Mendez, Gipsi

AU - Hallez, Regis

AU - Atkinson, Gemma

AU - Hauryliuk, Vasili

AU - Garcia-Pino, Abel

N1 - Funding Information: We are grateful to the Protein Expertise Platform at Umeå 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 Concerté 2016-2021, Fonds d’Encouragement à la Recherche of ULB (A.G.-P.); Fonds Jean Brachet and the Fondation Van Buuren (A.G.-P.); Chargé 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 Söderberg 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’s Horizon 2020 research and innovation program under the Marie Skłodowska-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–FNRS Postdoctoral Researcher and R.H. is an FRS–FNRS Research Associate. Funding Information: We are grateful to the Protein Expertise Platform at Umeå 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 Concerté 2016-2021, Fonds d’Encouragement à la Recherche of ULB (A.G.-P.); Fonds Jean Brachet and the Fondation Van Buuren (A.G.-P.); Chargé 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 Söderberg 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’s Horizon 2020 research and innovation program under the Marie Skłodowska-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–FNRS Postdoctoral Researcher and R.H. is an FRS–FNRS Research Associate. Publisher Copyright: © 2022, The Author(s).

PY - 2022/12/5

Y1 - 2022/12/5

N2 - 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.].

AB - 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.].

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U2 - 10.1038/s41589-022-01198-x

DO - 10.1038/s41589-022-01198-x

M3 - Article

SN - 1552-4450

VL - 19

SP - 334

EP - 345

JO - Nature Chemical Biology

JF - Nature Chemical Biology

IS - 3

ER -

Structure of SpoT reveals evolutionary tuning of catalysis via conformational constraint

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