Defining the architecture of the human TIM22 complex by chemical crosslinking.
Chromatography, Liquid
Cross-Linking Reagents
/ chemistry
HEK293 Cells
Humans
Membrane Transport Proteins
/ chemistry
Mitochondrial Membrane Transport Proteins
/ chemistry
Mitochondrial Membranes
/ metabolism
Mitochondrial Precursor Protein Import Complex Proteins
Mitochondrial Proteins
/ chemistry
Models, Molecular
Multienzyme Complexes
/ chemistry
Phosphotransferases (Alcohol Group Acceptor)
/ chemistry
Protein Conformation
Protein Subunits
/ chemistry
Protein Transport
Succinimides
/ chemistry
Tandem Mass Spectrometry
TIM22
carrier translocase
crosslinking-mass spectrometry
mitochondria
protein translocation
Journal
FEBS letters
ISSN: 1873-3468
Titre abrégé: FEBS Lett
Pays: England
ID NLM: 0155157
Informations de publication
Date de publication:
01 2021
01 2021
Historique:
received:
15
09
2020
revised:
19
10
2020
accepted:
25
10
2020
pubmed:
31
10
2020
medline:
16
7
2021
entrez:
30
10
2020
Statut:
ppublish
Résumé
The majority of mitochondrial proteins are nuclear encoded and imported into mitochondria as precursor proteins via dedicated translocases. The translocase of the inner membrane 22 (TIM22) is a multisubunit molecular machine specialized for the translocation of hydrophobic, multi-transmembrane-spanning proteins with internal targeting signals into the inner mitochondrial membrane. Here, we undertook a crosslinking-mass spectrometry (XL-MS) approach to determine the molecular arrangement of subunits of the human TIM22 complex. Crosslinking of the isolated TIM22 complex using the BS3 crosslinker resulted in the broad generation of crosslinks across the majority of TIM22 components, including the small TIM chaperone complex. The crosslinking data uncovered several unexpected features, opening new avenues for a deeper investigation into the steps required for TIM22-mediated translocation in humans.
Identifiants
pubmed: 33125709
doi: 10.1002/1873-3468.13978
doi:
Substances chimiques
Cross-Linking Reagents
0
Membrane Transport Proteins
0
Mitochondrial Membrane Transport Proteins
0
Mitochondrial Precursor Protein Import Complex Proteins
0
Mitochondrial Proteins
0
Multienzyme Complexes
0
Protein Subunits
0
Succinimides
0
TIM22 protein, human
0
TIMM29 protein, human
0
bis(sulfosuccinimidyl)suberate
E647932J7Z
AGK protein, human
EC 2.7.1.-
Phosphotransferases (Alcohol Group Acceptor)
EC 2.7.1.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
157-168Informations de copyright
© 2020 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.
Références
Gomkale R, Cruz-Zaragoza LD, Suppanz I, Guiard B, Montoya J, Callegari S, Pacheu-Grau D, Warscheid B and Rehling P (2020) Defining the substrate spectrum of the TIM22 complex identifies pyruvate carrier subunits as unconventional cargos. Curr Biol 30, 1119-1127.e5.
Rampelt H, Sucec I, Bersch B, Horten P, Perschil I, Martinou J-C, van der Laan M, Wiedemann N, Schanda P and Pfanner N (2020) The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biol 18, 2.
Horten P, Colina-Tenorio L and Rampelt H (2020) Biogenesis of mitochondrial metabolite carriers. Biomolecules 10, 1008.
Backes S, Hess S, Boos F, Woellhaf MW, Godel S, Jung M, Muhlhaus T and Herrmann JM (2018) Tom70 enhances mitochondrial preprotein import efficiency by binding to internal targeting sequences. J Cell Biol 217, 1369-1382.
Brix J, Dietmeier K and Pfanner N (1997) Differential recognition of preproteins by the purified cytosolic domains of the mitochondrial import receptors Tom20, Tom22, and Tom70. J Biol Chem 272, 20730-20735.
Brix J, Rudiger S, Bukau B, Schneider-Mergener J and Pfanner N (1999) Distribution of binding sequences for the mitochondrial import receptors Tom20, Tom22, and Tom70 in a presequence-carrying preprotein and a non-cleavable preprotein. J Biol Chem 274, 16522-16530.
Sollner T, Pfaller R, Griffiths G, Pfanner N and Neupert W (1990) A mitochondrial import receptor for the ADP/ATP carrier. Cell 62, 107-115.
Steger HF, Söllner T, Kiebler M, Dietmeier KA, Pfaller R, Trülzsch KS, Tropschug M, Neupert W and Pfanner N (1990) Import of ADP/ATP carrier into mitochondria: two receptors act in parallel. J Cell Biol 111, 2353-2363.
Weinhäupl K, Lindau C, Hessel A, Wang Y, Schütze C, Jores T, Melchionda L, Schönfisch B, Kalbacher H, Bersch B et al. (2018) Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. Cell 175, 1365-1379.e25.
Endres M, Neupert W and Brunner M (1999) Transport of the ADP/ATP carrier of mitochondria from the TOM complex to the TIM22.54 complex. EMBO J 18, 3214-3221.
Koehler CM, Jarosch E, Tokatlidis K, Schmid K, Schweyen RJ and Schatz G (1998) Import of mitochondrial carriers mediated by essential proteins of the intermembrane space. Science 279, 369-373.
Rehling P, Model K, Brandner K, Kovermann P, Sickmann A, Meyer HE, Kühlbrandt W, Wagner R, Truscott KN and Pfanner N (2003) Protein insertion into the mitochondrial inner membrane by a twin-pore translocase. Science 299, 1747-1751.
Kovermann P, Truscott KN, Guiard B, Rehling P, Sepuri NB, Müller H, Jensen RE, Wagner R and Pfanner N (2002) Tim22, the essential core of the mitochondrial protein insertion complex, forms a voltage-activated and signal-gated channel. Mol Cell 9, 363-373.
Sirrenberg C, Bauer MF, Guiard B, Neupert W and Brunner M (1996) Import of carrier proteins into the mitochondrial inner membrane mediated by Tim22. Nature 384, 582-585.
Gebert N, Gebert M, Oeljeklaus S, von der Malsburg K, Stroud DA, Kulawiak B, Wirth C, Zahedi RP, Dolezal P, Wiese S et al. (2011) Dual function of Sdh3 in the respiratory chain and TIM22 protein translocase of the mitochondrial inner membrane. Mol Cell 44, 811-818.
Hwang DK, Claypool SM, Leuenberger D, Tienson HL and Koehler CM (2007) Tim54p connects inner membrane assembly and proteolytic pathways in the mitochondrion. J Cell Biol 178, 1161-1175.
Koehler CM, Murphy MP, Bally NA, Leuenberger D, Oppliger W, Dolfini L, Junne T, Schatz G and Or E (2000) Tim18p, a new subunit of the TIM22 complex that mediates insertion of imported proteins into the yeast mitochondrial inner membrane. Mol Cell Biol 20, 1187-1193.
Kerscher O, Sepuri NB and Jensen RE (2000) Tim18p is a new component of the Tim54p-Tim22p translocon in the mitochondrial inner membrane. Mol Biol Cell 11, 103-116.
Kerscher O, Holder J, Srinivasan M, Leung RS and Jensen RE (1997) The Tim54p-Tim22p complex mediates insertion of proteins into the mitochondrial inner membrane. J Cell Biol 139, 1663-1675.
Callegari S, Richter F, Chojnacka K, Jans DC, Lorenzi I, Pacheu-Grau D, Jakobs S, Lenz C, Urlaub H, Dudek J et al. (2016) TIM29 is a subunit of the human carrier translocase required for protein transport. FEBS Lett 590, 4147-4158.
Kang Y, Baker MJ, Liem M, Louber J, McKenzie M, Atukorala I, Ang C-S, Keerthikumar S, Mathivanan S and Stojanovski D (2016) Tim29 is a novel subunit of the human TIM22 translocase and is involved in complex assembly and stability. Elife 5, e17463.
Kang Y, Stroud DA, Baker MJ, De Souza DP, Frazier AE, Liem M, Tull D, Mathivanan S, McConville MJ, Thorburn DR et al. (2017) Sengers syndrome-associated mitochondrial acylglycerol kinase is a subunit of the human TIM22 protein import complex. Mol Cell 67, 457-470.e5.
Vukotic M, Nolte H, Konig T, Saita S, Ananjew M, Kruger M, Tatsuta T and Langer T (2017) Acylglycerol kinase mutated in Sengers syndrome is a subunit of the TIM22 protein translocase in mitochondria. Mol Cell 67, 471-483.e7.
Wrobel L, Sokol AM, Chojnacka M and Chacinska A (2016) The presence of disulfide bonds reveals an evolutionarily conserved mechanism involved in mitochondrial protein translocase assembly. Sci Rep 6, 27484.
Bauer MF, Rothbauer U, Muhlenbein N, Smith RJ, Gerbitz K, Neupert W, Brunner M and Hofmann S (1999) The mitochondrial TIM22 preprotein translocase is highly conserved throughout the eukaryotic kingdom. FEBS Lett 464, 41-47.
Paschen SA, Rothbauer U, Kaldi K, Bauer MF, Neupert W and Brunner M (2000) The role of the TIM8-13 complex in the import of Tim23 into mitochondria. EMBO J 19, 6392-6400.
Curran SP, Leuenberger D, Schmidt E and Koehler CM (2002) The role of the Tim8p-Tim13p complex in a conserved import pathway for mitochondrial polytopic inner membrane proteins. J Cell Biol 158, 1017-1027.
Adam A, Endres M, Sirrenberg C, Lottspeich F, Neupert W and Brunner M (1999) Tim9, a new component of the TIM22.54 translocase in mitochondria. EMBO J 18, 313-319.
Wagner K, Gebert N, Guiard B, Brandner K, Truscott KN, Wiedemann N, Pfanner N and Rehling P (2008) The assembly pathway of the mitochondrial carrier translocase involves four preprotein translocases. Mol Cell Biol 28, 4251-4260.
Kang Y, Anderson AJ, Jackson TD, Palmer CS, De Souza DP, Fujihara KM, Stait T, Frazier AE, Clemons NJ, Tull D et al. (2019) Function of hTim8a in complex IV assembly in neuronal cells provides insight into pathomechanism underlying Mohr-Tranebjaerg syndrome. Elife 8, e48828.
Muhlenbein N, Hofmann S, Rothbauer U and Bauer MF (2004) Organization and function of the small Tim complexes acting along the import pathway of metabolite carriers into mammalian mitochondria. J Biol Chem 279, 13540-13546.
Webb CT, Gorman MA, Lazarou M, Ryan MT and Gulbis JM (2006) Crystal structure of the mitochondrial chaperone TIM9.10 reveals a six-bladed alpha-propeller. Mol Cell 21, 123-133.
Pacheu-Grau D, Callegari S, Emperador S, Thompson K, Aich A, Topol SE, Spencer EG, McFarland R, Ruiz-Pesini E, Torkamani A et al. (2018) Mutations of the mitochondrial carrier translocase channel subunit TIM22 cause early-onset mitochondrial myopathy. Hum Mol Genet 27, 4135-4144.
Calvo SE, Compton AG, Hershman SG, Lim SC, Lieber DS, Tucker EJ, Laskowski A, Garone C, Liu S, Jaffe DB et al. (2012) Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. Sci Transl Med 4, 118ra10.
Siriwardena K, MacKay N, Levandovskiy V, Blaser S, Raiman J, Kantor PF, Ackerley C, Robinson BH, Schulze A and Cameron JM (2013) Mitochondrial citrate synthase crystals: novel finding in Sengers syndrome caused by acylglycerol kinase (AGK) mutations. Mol Genet Metab 108, 40-50.
Haghighi A, Haack TB, Atiq M, Mottaghi H, Haghighi-Kakhki H, Bashir RA, Ahting U, Feichtinger RG, Mayr JA, Rötig A et al. (2014) Sengers syndrome: six novel AGK mutations in seven new families and review of the phenotypic and mutational spectrum of 29 patients. Orphanet J Rare Dis 9, 119.
Mayr JA, Haack TB, Graf E, Zimmermann FA, Wieland T, Haberberger B, Superti-Furga A, Kirschner J, Steinmann B, Baumgartner MR et al. (2012) Lack of the mitochondrial protein acylglycerol kinase causes Sengers syndrome. Am J Hum Genet 90, 314-320.
Roesch K, Curran SP, Tranebjaerg L and Koehler CM (2002) Human deafness dystonia syndrome is caused by a defect in assembly of the DDP1/TIMM8a-TIMM13 complex. Hum Mol Genet 11, 477-486.
Jin H, May M, Tranebjaerg L, Kendall E, Fontán G, Jackson J, Subramony Sh, Arena F, Lubs H, Smith S et al. (1996) A novel X-linked gene, DDP, shows mutations in families with deafness (DFN-1), dystonia, mental deficiency and blindness. Nat Genet 14, 177-180.
Callegari S, Müller T, Schulz C, Lenz C, Jans DC, Wissel M, Opazo F, Rizzoli SO, Jakobs S, Urlaub H et al. (2019) A MICOS-TIM22 association promotes carrier import into human mitochondria. J Mol Biol 431, 2835-2851.
Mohanraj K, Wasilewski M, Benincá C, Cysewski D, Poznanski J, Sakowska P, Bugajska Z, Deckers M, Dennerlein S, Fernandez-Vizarra E et al. (2019) Inhibition of proteasome rescues a pathogenic variant of respiratory chain assembly factor COA7. EMBO Mol Med 11, e9561.
Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM and Krijgsveld J (2014) Ultrasensitive proteome analysis using paramagnetic bead technology. Mol Syst Biol 10, 757.
Moggridge S, Sorensen PH, Morin GB and Hughes CS (2018) Extending the compatibility of the SP3 paramagnetic bead processing approach for proteomics. J Proteome Res 17, 1730-1740.
Leitner A, Reischl R, Walzthoeni T, Herzog F, Bohn S, Forster F and Aebersold R (2012) Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography. Mol Cell Proteomics 11, M111.014126.
Chen Z-L, Meng J-M, Cao Y, Yin J-L, Fang R-Q, Fan S-B, Liu C, Zeng W-F, Ding Y-H, Tan D et al. (2019) A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides. Nat Commun 10, 3404.
Cox J and Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26, 1367-1372.
Combe CW, Fischer L and Rappsilber J (2015) xiNET: cross-link network maps with residue resolution. Mol Cell Proteomics 14, 1137-1147.
Emsley P, Lohkamp B, Scott WG and Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66, 486-501.
Nivon LG, Moretti R and Baker D (2013) A Pareto-optimal refinement method for protein design scaffolds. PLoS One 8, e59004.
Shiota T, Imai K, Qiu J, Hewitt Vl, Tan K, Shen H-h, Sakiyama N, Fukasawa Y, Hayat S, Kamiya M et al. (2015) Molecular architecture of the active mitochondrial protein gate. Science 349, 1544-1548.
Spahr H, Rozanska A, Li X, Atanassov I, Lightowlers RN, Chrzanowska-Lightowlers ZM, Rackham O and Larsson NG (2016) SLIRP stabilizes LRPPRC via an RRM-PPR protein interface. Nucleic Acids Res 44, 6868-6882.
Sasarman F, Brunel-Guitton C, Antonicka H, Wai T, Shoubridge EA and LSFC Consortium (2010) LRPPRC and SLIRP interact in a ribonucleoprotein complex that regulates posttranscriptional gene expression in mitochondria. Mol Biol Cell 21, 1315-1323.
Linden A, Deckers M, Parfentev I, Pflanz R, Homberg B, Neumann P, Ficner R, Rehling P and Urlaub H (2020) A cross-linking mass spectrometry approach defines protein interactions in yeast mitochondria. Mol Cell Proteomics 19, 1161-1178.
Kumar A, Matta SK and D'Silva P (2020) Conserved regions of budding yeast Tim22 have a role in structural organization of the carrier translocase. J Cell Sci 133.
Baker MJ, Webb CT, Stroud DA, Palmer CS, Frazier AE, Guiard B, Chacinska A, Gulbis JM and Ryan MT (2009) Structural and functional requirements for activity of the Tim9-Tim10 complex in mitochondrial protein import. Mol Biol Cell 20, 769-779.
Qi L, Wang Q, Guan Z, Wu Y, Shen C, Hong S, Cao J, Zhang X, Yan C and Yin P (2020) Cryo-EM structure of the human mitochondrial translocase TIM22 complex. Cell Res. https://doi.org/10.1038/s41422-020-00400-w. [Epub ahead of print].