Allosteric Regulation of Rhomboid Intramembrane Proteolysis

Overview

Journal EMBO J

Specialties Biotechnology
Molecular Biology

Date 2014 Jul 11

PMID 25009246

Citations 29

Authors

Elena Arutyunova

Pankaj Panwar

Pauline M Skiba

Nicola Gale

Michelle W Mak

M Joanne Lemieux

Affiliations

Soon will be listed here.

Abstract

Proteolysis within the lipid bilayer is poorly understood, in particular the regulation of substrate cleavage. Rhomboids are a family of ubiquitous intramembrane serine proteases that harbour a buried active site and are known to cleave transmembrane substrates with broad specificity. In vitro gel and Förster resonance energy transfer (FRET)-based kinetic assays were developed to analyse cleavage of the transmembrane substrate psTatA (TatA from Providencia stuartii). We demonstrate significant differences in catalytic efficiency (kcat/K0.5) values for transmembrane substrate psTatA (TatA from Providencia stuartii) cleavage for three rhomboids: AarA from P. stuartii, ecGlpG from Escherichia coli and hiGlpG from Haemophilus influenzae demonstrating that rhomboids specifically recognize this substrate. Furthermore, binding of psTatA occurs with positive cooperativity. Competitive binding studies reveal an exosite-mediated mode of substrate binding, indicating allostery plays a role in substrate catalysis. We reveal that exosite formation is dependent on the oligomeric state of rhomboids, and when dimers are dissociated, allosteric substrate activation is not observed. We present a novel mechanism for specific substrate cleavage involving several dynamic processes including positive cooperativity and homotropic allostery for this interesting class of intramembrane proteases.

Citing Articles

Evaluating the impact of the membrane thickness on the function of the intramembrane protease GlpG.

Engberg O, Mathath A, Dobel V, Frie C, Lemberg M, Chakraborty D Biophys J. 2024; 123(23):4067-4081.

PMID: 39488732 PMC: 11628809. DOI: 10.1016/j.bpj.2024.10.019.

Lipid environment modulates processivity and kinetics of a presenilin homolog acting on multiple substrates in vitro.

Wu Y, Thomas G, Thomsen M, Bahri S, Lieberman R J Biol Chem. 2024; 299(12):105401.

PMID: 38270390 PMC: 10679502. DOI: 10.1016/j.jbc.2023.105401.

Electrospray ionization of native membrane proteins proceeds a charge equilibration step.

Yen H, Abramsson M, Agasid M, Lama D, Gault J, Liko I RSC Adv. 2022; 12(16):9671-9680.

PMID: 35424940 PMC: 8972943. DOI: 10.1039/d2ra01282k.

Effect of Environmental Factors on the Catalytic Activity of Intramembrane Serine Protease.

Asadi M, Oanca G, Warshel A J Am Chem Soc. 2022; 144(3):1251-1257.

PMID: 35023734 PMC: 10349665. DOI: 10.1021/jacs.1c10494.

The iRhom homology domain is indispensable for ADAM17-mediated TNFα and EGF receptor ligand release.

Dusterhoft S, Kahveci-Turkoz S, Wozniak J, Seifert A, Kasparek P, Ohm H Cell Mol Life Sci. 2021; 78(11):5015-5040.

PMID: 33950315 PMC: 8233286. DOI: 10.1007/s00018-021-03845-3.

References

Mesak L, Mesak F, Dahl M . Expression of a novel gene, gluP, is essential for normal Bacillus subtilis cell division and contributes to glucose export. BMC Microbiol. 2004; 4:13. PMC: 408461. DOI: 10.1186/1471-2180-4-13. View

Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M . Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2006; 2:2006.0008. PMC: 1681482. DOI: 10.1038/msb4100050. View

Shelton C, Zhu L, Chau D, Yang L, Wang R, Djaballah H . Modulation of gamma-secretase specificity using small molecule allosteric inhibitors. Proc Natl Acad Sci U S A. 2009; 106(48):20228-33. PMC: 2787169. DOI: 10.1073/pnas.0910757106. View

Sekine S, Kanamaru Y, Koike M, Nishihara A, Okada M, Kinoshita H . Rhomboid protease PARL mediates the mitochondrial membrane potential loss-induced cleavage of PGAM5. J Biol Chem. 2012; 287(41):34635-45. PMC: 3464569. DOI: 10.1074/jbc.M112.357509. View

Liu Y, Song Y, Madahar V, Liao J . Quantitative Förster resonance energy transfer analysis for kinetic determinations of SUMO-specific protease. Anal Biochem. 2012; 422(1):14-21. DOI: 10.1016/j.ab.2011.12.019. View

Wu Z, Yan N, Feng L, Oberstein A, Yan H, Baker R . Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry. Nat Struct Mol Biol. 2006; 13(12):1084-91. DOI: 10.1038/nsmb1179. View

Lemberg M, Freeman M . Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases. Genome Res. 2007; 17(11):1634-46. PMC: 2045146. DOI: 10.1101/gr.6425307. View

Strisovsky K, Sharpe H, Freeman M . Sequence-specific intramembrane proteolysis: identification of a recognition motif in rhomboid substrates. Mol Cell. 2010; 36(6):1048-59. PMC: 2941825. DOI: 10.1016/j.molcel.2009.11.006. View

Urban S, Lee J, Freeman M . Drosophila rhomboid-1 defines a family of putative intramembrane serine proteases. Cell. 2001; 107(2):173-82. DOI: 10.1016/s0092-8674(01)00525-6. View

10.

Johnson D, Li W, Adams T, Huntington J . Antithrombin-S195A factor Xa-heparin structure reveals the allosteric mechanism of antithrombin activation. EMBO J. 2006; 25(9):2029-37. PMC: 1456925. DOI: 10.1038/sj.emboj.7601089. View

11.

Nguyen A, Daugherty P . Evolutionary optimization of fluorescent proteins for intracellular FRET. Nat Biotechnol. 2005; 23(3):355-60. DOI: 10.1038/nbt1066. View

12.

Craik C, Roczniak S, Largman C, Rutter W . The catalytic role of the active site aspartic acid in serine proteases. Science. 1987; 237(4817):909-13. DOI: 10.1126/science.3303334. View

13.

Brooks C, Lazareno-Saez C, Lamoureux J, Mak M, Lemieux M . Insights into substrate gating in H. influenzae rhomboid. J Mol Biol. 2011; 407(5):687-97. DOI: 10.1016/j.jmb.2011.01.046. View

14.

Wang Y, Zhang Y, Ha Y . Crystal structure of a rhomboid family intramembrane protease. Nature. 2006; 444(7116):179-80. DOI: 10.1038/nature05255. View

15.

Edbauer D, Winkler E, Regula J, Pesold B, Steiner H, Haass C . Reconstitution of gamma-secretase activity. Nat Cell Biol. 2003; 5(5):486-8. DOI: 10.1038/ncb960. View

16.

Chavez-Gutierrez L, Tolia A, Maes E, Li T, Wong P, De Strooper B . Glu(332) in the Nicastrin ectodomain is essential for gamma-secretase complex maturation but not for its activity. J Biol Chem. 2008; 283(29):20096-105. DOI: 10.1074/jbc.M803040200. View

17.

Rodriguez F, Rouse S, Tait C, Harmer J, De Riso A, Timmel C . Structural model for the protein-translocating element of the twin-arginine transport system. Proc Natl Acad Sci U S A. 2013; 110(12):E1092-101. PMC: 3607022. DOI: 10.1073/pnas.1219486110. View

18.

Chan E, McQuibban G . The mitochondrial rhomboid protease: its rise from obscurity to the pinnacle of disease-relevant genes. Biochim Biophys Acta. 2013; 1828(12):2916-25. DOI: 10.1016/j.bbamem.2013.05.012. View

19.

Stevenson L, Strisovsky K, Clemmer K, Bhatt S, Freeman M, Rather P . Rhomboid protease AarA mediates quorum-sensing in Providencia stuartii by activating TatA of the twin-arginine translocase. Proc Natl Acad Sci U S A. 2007; 104(3):1003-8. PMC: 1783354. DOI: 10.1073/pnas.0608140104. View

20.

Li X, Dang S, Yan C, Gong X, Wang J, Shi Y . Structure of a presenilin family intramembrane aspartate protease. Nature. 2012; 493(7430):56-61. DOI: 10.1038/nature11801. View