Molecular and Structural Insights into An asymmetric Proteolytic Complex (ClpP1P2) from Mycobacterium Smegmatis

Overview

Journal Sci Rep

Specialty Science

Date 2019 Dec 4

PMID 31792243

Citations 10

Authors

Jyotsna Nagpal

Jason J Paxman

Jessica E Zammit

Adam A. Thomas

Kaye N Truscott

Begona Heras

David A Dougan

Affiliations

Soon will be listed here.

Abstract

The ClpP protease is found in all kingdoms of life, from bacteria to humans. In general, this protease forms a homo-oligomeric complex composed of 14 identical subunits, which associates with its cognate ATPase in a symmetrical manner. Here we show that, in contrast to this general architecture, the Clp protease from Mycobacterium smegmatis (Msm) forms an asymmetric hetero-oligomeric complex ClpP1P2, which only associates with its cognate ATPase through the ClpP2 ring. Our structural and functional characterisation of this complex demonstrates that asymmetric docking of the ATPase component is controlled by both the composition of the ClpP1 hydrophobic pocket (Hp) and the presence of a unique C-terminal extension in ClpP1 that guards this Hp. Our structural analysis of ClpP1 also revealed openings in the side-walls of the inactive tetradecamer, which may represent sites for product egress.

Citing Articles

Cryo-EM structures of human ClpXP reveal mechanisms of assembly and proteolytic activation.

Chen W, Yang J, Lander G bioRxiv. 2024; .

PMID: 39605471 PMC: 11601447. DOI: 10.1101/2024.11.12.623337.

Molecular Characterization of the ClpC AAA+ ATPase in the Biology of Chlamydia trachomatis.

Pan S, Jensen A, Wood N, Henrichfreise B, Brotz-Oesterhelt H, Fisher D mBio. 2023; 14(2):e0007523.

PMID: 36975997 PMC: 10128030. DOI: 10.1128/mbio.00075-23.

Cellular functions of the ClpP protease impacting bacterial virulence.

Aljghami M, Barghash M, Majaesic E, Bhandari V, Houry W Front Mol Biosci. 2022; 9:1054408.

PMID: 36533084 PMC: 9753991. DOI: 10.3389/fmolb.2022.1054408.

Antibiotic Acyldepsipeptides Stimulate the Clp-ATPase/ClpP Complex for Accelerated Proteolysis.

Reinhardt L, Thomy D, Lakemeyer M, Westermann L, Ortega J, Sieber S mBio. 2022; 13(6):e0141322.

PMID: 36286522 PMC: 9765437. DOI: 10.1128/mbio.01413-22.

Identification of Arginine Phosphorylation in Mycolicibacterium smegmatis.

Ogbonna E, Anderson H, Schmitz K Microbiol Spectr. 2022; 10(5):e0204222.

PMID: 36214676 PMC: 9604228. DOI: 10.1128/spectrum.02042-22.

References

Gur E, Ottofueling R, Dougan D . Machines of destruction - AAA+ proteases and the adaptors that control them. Subcell Biochem. 2013; 66:3-33. DOI: 10.1007/978-94-007-5940-4_1. View

Wood N, Chung K, Blocker A, Rodrigues de Almeida N, Conda-Sheridan M, Fisher D . Initial Characterization of the Two ClpP Paralogs of Suggests Unique Functionality for Each. J Bacteriol. 2018; 201(2). PMC: 6304667. DOI: 10.1128/JB.00635-18. View

Muller A, Weber-Ban E . The Bacterial Proteasome at the Core of Diverse Degradation Pathways. Front Mol Biosci. 2019; 6:23. PMC: 6466877. DOI: 10.3389/fmolb.2019.00023. View

Leodolter J, Warweg J, Weber-Ban E . The Mycobacterium tuberculosis ClpP1P2 Protease Interacts Asymmetrically with Its ATPase Partners ClpX and ClpC1. PLoS One. 2015; 10(5):e0125345. PMC: 4416901. DOI: 10.1371/journal.pone.0125345. View

Schmitz K, Sauer R . Substrate delivery by the AAA+ ClpX and ClpC1 unfoldases activates the mycobacterial ClpP1P2 peptidase. Mol Microbiol. 2014; 93(4):617-28. PMC: 4131744. DOI: 10.1111/mmi.12694. View

Kang S, Maurizi M, Thompson M, Mueser T, Ahvazi B . Crystallography and mutagenesis point to an essential role for the N-terminus of human mitochondrial ClpP. J Struct Biol. 2004; 148(3):338-52. DOI: 10.1016/j.jsb.2004.07.004. View

Delley C, Laederach J, Ziemski M, Bolten M, Boehringer D, Weber-Ban E . Bacterial proteasome activator bpa (rv3780) is a novel ring-shaped interactor of the mycobacterial proteasome. PLoS One. 2014; 9(12):e114348. PMC: 4254994. DOI: 10.1371/journal.pone.0114348. View

Dahmen M, Vielberg M, Groll M, Sieber S . Structure and mechanism of the caseinolytic protease ClpP1/2 heterocomplex from Listeria monocytogenes. Angew Chem Int Ed Engl. 2015; 54(12):3598-602. DOI: 10.1002/anie.201409325. View

Wang J, Hartling J, Flanagan J . The structure of ClpP at 2.3 A resolution suggests a model for ATP-dependent proteolysis. Cell. 1997; 91(4):447-56. DOI: 10.1016/s0092-8674(00)80431-6. View

10.

Striebel F, Kress W, Weber-Ban E . Controlled destruction: AAA+ ATPases in protein degradation from bacteria to eukaryotes. Curr Opin Struct Biol. 2009; 19(2):209-17. DOI: 10.1016/j.sbi.2009.02.006. View

11.

Li D, Chung Y, Gloyd M, Joseph E, Ghirlando R, Wright G . Acyldepsipeptide antibiotics induce the formation of a structured axial channel in ClpP: A model for the ClpX/ClpA-bound state of ClpP. Chem Biol. 2010; 17(9):959-69. PMC: 2955292. DOI: 10.1016/j.chembiol.2010.07.008. View

12.

Akopian T, Kandror O, Raju R, Unnikrishnan M, Rubin E, Goldberg A . The active ClpP protease from M. tuberculosis is a complex composed of a heptameric ClpP1 and a ClpP2 ring. EMBO J. 2012; 31(6):1529-41. PMC: 3321190. DOI: 10.1038/emboj.2012.5. View

13.

Brodie E, Zhan H, Saiyed T, Truscott K, Dougan D . Perrault syndrome type 3 caused by diverse molecular defects in CLPP. Sci Rep. 2018; 8(1):12862. PMC: 6110781. DOI: 10.1038/s41598-018-30311-1. View

14.

Elsholz A, Birk M, Charpentier E, Turgay K . Functional Diversity of AAA+ Protease Complexes in . Front Mol Biosci. 2017; 4:44. PMC: 5506225. DOI: 10.3389/fmolb.2017.00044. View

15.

Painter J, Merritt E . Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr D Biol Crystallogr. 2006; 62(Pt 4):439-50. DOI: 10.1107/S0907444906005270. View

16.

Liu K, Ologbenla A, Houry W . Dynamics of the ClpP serine protease: a model for self-compartmentalized proteases. Crit Rev Biochem Mol Biol. 2014; 49(5):400-12. DOI: 10.3109/10409238.2014.925421. View

17.

Lavey N, Shadid T, Ballard J, Duerfeldt A . Clostridium difficile ClpP Homologues are Capable of Uncoupled Activity and Exhibit Different Levels of Susceptibility to Acyldepsipeptide Modulation. ACS Infect Dis. 2018; 5(1):79-89. PMC: 6497155. DOI: 10.1021/acsinfecdis.8b00199. View

18.

Kim Y, Levchenko I, Fraczkowska K, Woodruff R, Sauer R, Baker T . Molecular determinants of complex formation between Clp/Hsp100 ATPases and the ClpP peptidase. Nat Struct Biol. 2001; 8(3):230-3. DOI: 10.1038/84967. View

19.

Martin A, Baker T, Sauer R . Distinct static and dynamic interactions control ATPase-peptidase communication in a AAA+ protease. Mol Cell. 2007; 27(1):41-52. PMC: 2074893. DOI: 10.1016/j.molcel.2007.05.024. View

20.

Dougan D, Reid B, Horwich A, Bukau B . ClpS, a substrate modulator of the ClpAP machine. Mol Cell. 2002; 9(3):673-83. DOI: 10.1016/s1097-2765(02)00485-9. View