Identification of a Degradation Signal Sequence Within Substrates of the Mitochondrial I-AAA Protease

Overview

Journal J Mol Biol

Publisher Elsevier

Specialties Microbiology
Molecular Biology

Date 2017 Feb 20

PMID 28214511

Citations 15

Authors

Anthony J Rampello

Steven E Glynn

Affiliations

Soon will be listed here.

Abstract

The i-AAA protease is a component of the mitochondrial quality control machinery that regulates respiration, mitochondrial dynamics, and protein import. The protease is required to select specific substrates for degradation from among the diverse complement of proteins present in mitochondria, yet the rules that govern this selection are unclear. Here, we reconstruct the yeast i-AAA protease, Yme1p, to examine the in vitro degradation of two intermembrane space chaperone subunits, Tim9 and Tim10. Yme1p degrades Tim10 more rapidly than Tim9 despite high sequence and structural similarity, and loss of Tim10 is accelerated by the disruption of conserved disulfide bonds within the substrate. An unstructured N-terminal region of Tim10 is necessary and sufficient to target the substrate to the protease through recognition of a short phenylalanine-rich motif, and the presence of similar motifs in other small Tim proteins predicts robust degradation by the protease. Together, these results identify the first specific degron sequence within a native i-AAA protease substrate.

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References

Donzeau M, Kaldi K, Adam A, Paschen S, Wanner G, Guiard B . Tim23 links the inner and outer mitochondrial membranes. Cell. 2000; 101(4):401-12. DOI: 10.1016/s0092-8674(00)80850-8. View

Bolender N, Sickmann A, Wagner R, Meisinger C, Pfanner N . Multiple pathways for sorting mitochondrial precursor proteins. EMBO Rep. 2008; 9(1):42-9. PMC: 2246611. DOI: 10.1038/sj.embor.7401126. View

Calvo S, Clauser K, Mootha V . MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. Nucleic Acids Res. 2015; 44(D1):D1251-7. PMC: 4702768. DOI: 10.1093/nar/gkv1003. View

Flynn J, Levchenko I, Seidel M, Wickner S, Sauer R, Baker T . Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis. Proc Natl Acad Sci U S A. 2001; 98(19):10584-9. PMC: 58509. DOI: 10.1073/pnas.191375298. View

Sickmann A, Reinders J, Wagner Y, Joppich C, Zahedi R, Meyer H . The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci U S A. 2003; 100(23):13207-12. PMC: 263752. DOI: 10.1073/pnas.2135385100. View

Gentle I, Perry A, Alcock F, Likic V, Dolezal P, Ng E . Conserved motifs reveal details of ancestry and structure in the small TIM chaperones of the mitochondrial intermembrane space. Mol Biol Evol. 2007; 24(5):1149-60. DOI: 10.1093/molbev/msm031. View

Popov-celeketic D, Mapa K, Neupert W, Mokranjac D . Active remodelling of the TIM23 complex during translocation of preproteins into mitochondria. EMBO J. 2008; 27(10):1469-80. PMC: 2396396. DOI: 10.1038/emboj.2008.79. View

Gonzalez M, Frank E, Levine A, Woodgate R . Lon-mediated proteolysis of the Escherichia coli UmuD mutagenesis protein: in vitro degradation and identification of residues required for proteolysis. Genes Dev. 1998; 12(24):3889-99. PMC: 317269. DOI: 10.1101/gad.12.24.3889. View

Gur E, Vishkautzan M, Sauer R . Protein unfolding and degradation by the AAA+ Lon protease. Protein Sci. 2011; 21(2):268-78. PMC: 3324771. DOI: 10.1002/pro.2013. View

10.

Leonhard K, Guiard B, Pellecchia G, Tzagoloff A, Neupert W, Langer T . Membrane protein degradation by AAA proteases in mitochondria: extraction of substrates from either membrane surface. Mol Cell. 2000; 5(4):629-38. DOI: 10.1016/s1097-2765(00)80242-7. View

11.

Sauer R, Baker T . AAA+ proteases: ATP-fueled machines of protein destruction. Annu Rev Biochem. 2011; 80:587-612. DOI: 10.1146/annurev-biochem-060408-172623. View

12.

Lin M, Beal M . Mitochondrial dysfunction and oxidative stress in neurodegenerative diseases. Nature. 2006; 443(7113):787-95. DOI: 10.1038/nature05292. View

13.

Shi H, Rampello A, Glynn S . Engineered AAA+ proteases reveal principles of proteolysis at the mitochondrial inner membrane. Nat Commun. 2016; 7:13301. PMC: 5095350. DOI: 10.1038/ncomms13301. View

14.

Spiller M, Guo L, Wang Q, Tran P, Lu H . Mitochondrial Tim9 protects Tim10 from degradation by the protease Yme1. Biosci Rep. 2015; 35(3). PMC: 4438305. DOI: 10.1042/BSR20150038. View

15.

Tatsuta T, Langer T . AAA proteases in mitochondria: diverse functions of membrane-bound proteolytic machines. Res Microbiol. 2009; 160(9):711-7. DOI: 10.1016/j.resmic.2009.09.005. View

16.

Koehler C . The small Tim proteins and the twin Cx3C motif. Trends Biochem Sci. 2004; 29(1):1-4. DOI: 10.1016/j.tibs.2003.11.003. View

17.

Schneider C, Rasband W, Eliceiri K . NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012; 9(7):671-5. PMC: 5554542. DOI: 10.1038/nmeth.2089. View

18.

Stinson B, Nager A, Glynn S, Schmitz K, Baker T, Sauer R . Nucleotide binding and conformational switching in the hexameric ring of a AAA+ machine. Cell. 2013; 153(3):628-39. PMC: 3674332. DOI: 10.1016/j.cell.2013.03.029. View

19.

Goemans C, Boya P, Skirrow C, Tolkovsky A . Intra-mitochondrial degradation of Tim23 curtails the survival of cells rescued from apoptosis by caspase inhibitors. Cell Death Differ. 2008; 15(3):545-54. DOI: 10.1038/sj.cdd.4402290. View

20.

Bailey T, Boden M, Buske F, Frith M, Grant C, Clementi L . MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009; 37(Web Server issue):W202-8. PMC: 2703892. DOI: 10.1093/nar/gkp335. View