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Proc Natl Acad Sci U S A. Jun 1989; 86(11): 4056–4060.
PMCID: PMC287387

Survey of amino-terminal proteolytic cleavage sites in mitochondrial precursor proteins: leader peptides cleaved by two matrix proteases share a three-amino acid motif.

Abstract

We have compiled sequences of precursor proteins for 50 mitochondrial proteins for which the mature amino terminus has been determined by amino acid sequence analysis. Included in this set are 8 precursors that have leader peptides that are cleaved in two places by mitochondrial matrix proteases. When these eight leader peptides are aligned and compared, a highly conserved three-amino acid motif is identified as being common to this class of leader peptides. This motif includes an arginine at position -10, a hydrophobic residue at position -8, and serine, threonine, or glycine at position -5 relative to the mature amino terminus. The initial cleavage of these peptides by matrix processing protease occurs within the motif, between residues at -9 and -8, such that arginine at position -10 is at position -2 relative to the cleaved bond. The rest of the motif is within the octapeptide removed by subsequent cleavage catalyzed by intermediate-specific protease. An additional 14 leader peptides in this collection (all of those that contain an arginine at -10) conform to this motif. Assuming that these 14 precursors are matured in two steps, we compared the internal cleavage sites at position -8 with the ends of the other 30 leader peptides in the collection. We find that 74% of matrix processing protease cleavage sites follow an arginine at position -2 relative to cleavage.

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  • von Heijne G. Mitochondrial targeting sequences may form amphiphilic helices. EMBO J. 1986 Jun;5(6):1335–1342. [PMC free article] [PubMed]
  • Baker A, Schatz G. Sequences from a prokaryotic genome or the mouse dihydrofolate reductase gene can restore the import of a truncated precursor protein into yeast mitochondria. Proc Natl Acad Sci U S A. 1987 May;84(10):3117–3121. [PMC free article] [PubMed]
  • Roise D, Theiler F, Horvath SJ, Tomich JM, Richards JH, Allison DS, Schatz G. Amphiphilicity is essential for mitochondrial presequence function. EMBO J. 1988 Mar;7(3):649–653. [PMC free article] [PubMed]
  • Miura S, Amaya Y, Mori M. A metalloprotease involved in the processing of mitochondrial precursor proteins. Biochem Biophys Res Commun. 1986 Feb 13;134(3):1151–1159. [PubMed]
  • Kalousek F, Hendrick JP, Rosenberg LE. Two mitochondrial matrix proteases act sequentially in the processing of mammalian matrix enzymes. Proc Natl Acad Sci U S A. 1988 Oct;85(20):7536–7540. [PMC free article] [PubMed]
  • Hurt EC, Allison DS, Müller U, Schatz G. Amino-terminal deletions in the presequence of an imported mitochondrial protein block the targeting function and proteolytic cleavage of the presequence at the carboxy terminus. J Biol Chem. 1987 Jan 25;262(3):1420–1424. [PubMed]
  • Kraus JP, Novotný J, Kalousek F, Swaroop M, Rosenberg LE. Different structures in the amino-terminal domain of the ornithine transcarbamylase leader peptide are involved in mitochondrial import and carboxyl-terminal cleavage. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8905–8909. [PMC free article] [PubMed]
  • Vassarotti A, Chen WJ, Smagula C, Douglas MG. Sequences distal to the mitochondrial targeting sequences are necessary for the maturation of the F1-ATPase beta-subunit precursor in mitochondria. J Biol Chem. 1987 Jan 5;262(1):411–418. [PubMed]
  • Sztul ES, Hendrick JP, Kraus JP, Wall D, Kalousek F, Rosenberg LE. Import of rat ornithine transcarbamylase precursor into mitochondria: two-step processing of the leader peptide. J Cell Biol. 1987 Dec;105(6 Pt 1):2631–2639. [PMC free article] [PubMed]
  • Sztul ES, Chu TW, Strauss AW, Rosenberg LE. Import of the malate dehydrogenase precursor by mitochondria. Cleavage within leader peptide by matrix protease leads to formation of intermediate-sized form. J Biol Chem. 1988 Aug 25;263(24):12085–12091. [PubMed]
  • Schmidt B, Wachter E, Sebald W, Neupert W. Processing peptidase of Neurospora mitochondria. Two-step cleavage of imported ATPase subunit 9. Eur J Biochem. 1984 Nov 2;144(3):581–588. [PubMed]
  • Rosenberg LE, Kalousek F, Orsulak MD. Biogenesis of ornithine transcarbamylase in spfash mutant mice: two cytoplasmic precursors, one mitochondrial enzyme. Science. 1983 Oct 28;222(4622):426–428. [PubMed]
  • Hartl FU, Schmidt B, Wachter E, Weiss H, Neupert W. Transport into mitochondria and intramitochondrial sorting of the Fe/S protein of ubiquinol-cytochrome c reductase. Cell. 1986 Dec 26;47(6):939–951. [PubMed]
  • Hurt EC, Pesold-Hurt B, Suda K, Oppliger W, Schatz G. The first twelve amino acids (less than half of the pre-sequence) of an imported mitochondrial protein can direct mouse cytosolic dihydrofolate reductase into the yeast mitochondrial matrix. EMBO J. 1985 Aug;4(8):2061–2068. [PMC free article] [PubMed]
  • Tropschug M, Nicholson DW, Hartl FU, Köhler H, Pfanner N, Wachter E, Neupert W. Cyclosporin A-binding protein (cyclophilin) of Neurospora crassa. One gene codes for both the cytosolic and mitochondrial forms. J Biol Chem. 1988 Oct 5;263(28):14433–14440. [PubMed]
  • Horwich AL, Fenton WA, Williams KR, Kalousek F, Kraus JP, Doolittle RF, Konigsberg W, Rosenberg LE. Structure and expression of a complementary DNA for the nuclear coded precursor of human mitochondrial ornithine transcarbamylase. Science. 1984 Jun 8;224(4653):1068–1074. [PubMed]
  • Veres G, Gibbs RA, Scherer SE, Caskey CT. The molecular basis of the sparse fur mouse mutation. Science. 1987 Jul 24;237(4813):415–417. [PubMed]
  • Kraus JP, Hodges PE, Williamson CL, Horwich AL, Kalousek F, Williams KR, Rosenberg LE. A cDNA clone for the precursor of rat mitochondrial ornithine transcarbamylase: comparison of rat and human leader sequences and conservation of catalytic sites. Nucleic Acids Res. 1985 Feb 11;13(3):943–952. [PMC free article] [PubMed]
  • Joh T, Takeshima H, Tsuzuki T, Shimada K, Tanase S, Morino Y. Cloning and sequence analysis of cDNAs encoding mammalian mitochondrial malate dehydrogenase. Biochemistry. 1987 May 5;26(9):2515–2520. [PubMed]
  • Grant PM, Tellam J, May VL, Strauss AW. Isolation and nucleotide sequence of a cDNA clone encoding rat mitochondrial malate dehydrogenase. Nucleic Acids Res. 1986 Aug 11;14(15):6053–6066. [PMC free article] [PubMed]
  • Harnisch U, Weiss H, Sebald W. The primary structure of the iron-sulfur subunit of ubiquinol-cytochrome c reductase from Neurospora, determined by cDNA and gene sequencing. Eur J Biochem. 1985 May 15;149(1):95–99. [PubMed]
  • Tropschug M, Nicholson DW, Hartl FU, Köhler H, Pfanner N, Wachter E, Neupert W. Cyclosporin A-binding protein (cyclophilin) of Neurospora crassa. One gene codes for both the cytosolic and mitochondrial forms. J Biol Chem. 1988 Oct 5;263(28):14433–14440. [PubMed]
  • Maarse AC, Van Loon AP, Riezman H, Gregor I, Schatz G, Grivell LA. Subunit IV of yeast cytochrome c oxidase: cloning and nucleotide sequencing of the gene and partial amino acid sequencing of the mature protein. EMBO J. 1984 Dec 1;3(12):2831–2837. [PMC free article] [PubMed]
  • Koike K, Ohta S, Urata Y, Kagawa Y, Koike M. Cloning and sequencing of cDNAs encoding alpha and beta subunits of human pyruvate dehydrogenase. Proc Natl Acad Sci U S A. 1988 Jan;85(1):41–45. [PMC free article] [PubMed]
  • Browning KS, Uhlinger DJ, Reed LJ. Nucleotide sequence for yeast dihydrolipoamide dehydrogenase. Proc Natl Acad Sci U S A. 1988 Mar;85(6):1831–1834. [PMC free article] [PubMed]
  • Mueckler MM, Pitot HC. Sequence of the precursor to rat ornithine aminotransferase deduced from a cDNA clone. J Biol Chem. 1985 Oct 25;260(24):12993–12997. [PubMed]
  • Inana G, Totsuka S, Redmond M, Dougherty T, Nagle J, Shiono T, Ohura T, Kominami E, Katunuma N. Molecular cloning of human ornithine aminotransferase mRNA. Proc Natl Acad Sci U S A. 1986 Mar;83(5):1203–1207. [PMC free article] [PubMed]
  • Lomax MI, Bachman NJ, Nasoff MS, Caruthers MH, Grossman LI. Isolation and characterization of a cDNA clone for bovine cytochrome c oxidase subunit IV. Proc Natl Acad Sci U S A. 1984 Oct;81(20):6295–6299. [PMC free article] [PubMed]
  • Zeviani M, Nakagawa M, Herbert J, Lomax MI, Grossman LI, Sherbany AA, Miranda AF, DiMauro S, Schon EA. Isolation of a cDNA clone encoding subunit IV of human cytochrome c oxidase. Gene. 1987;55(2-3):205–217. [PubMed]
  • Breen GA. Bovine liver cDNA clones encoding a precursor of the alpha-subunit of the mitochondrial ATP synthase complex. Biochem Biophys Res Commun. 1988 Apr 15;152(1):264–269. [PubMed]
  • Bawden MJ, Borthwick IA, Healy HM, Morris CP, May BK, Elliott WH. Sequence of human 5-aminolevulinate synthase cDNA. Nucleic Acids Res. 1987 Oct 26;15(20):8563–8563. [PMC free article] [PubMed]
  • Srivastava G, Borthwick IA, Maguire DJ, Elferink CJ, Bawden MJ, Mercer JF, May BK. Regulation of 5-aminolevulinate synthase mRNA in different rat tissues. J Biol Chem. 1988 Apr 15;263(11):5202–5209. [PubMed]
  • Borthwick IA, Srivastava G, Day AR, Pirola BA, Snoswell MA, May BK, Elliott WH. Complete nucleotide sequence of hepatic 5-aminolaevulinate synthase precursor. Eur J Biochem. 1985 Aug 1;150(3):481–484. [PubMed]
  • Okamura T, John ME, Zuber MX, Simpson ER, Waterman MR. Molecular cloning and amino acid sequence of the precursor form of bovine adrenodoxin: evidence for a previously unidentified COOH-terminal peptide. Proc Natl Acad Sci U S A. 1985 Sep;82(17):5705–5709. [PMC free article] [PubMed]
  • Picado-Leonard J, Voutilainen R, Kao LC, Chung BC, Strauss JF, 3rd, Miller WL. Human adrenodoxin: cloning of three cDNAs and cycloheximide enhancement in JEG-3 cells. J Biol Chem. 1988 Mar 5;263(7):3240–3244. [PubMed]
  • Gay NJ, Walker JE. Two genes encoding the bovine mitochondrial ATP synthase proteolipid specify precursors with different import sequences and are expressed in a tissue-specific manner. EMBO J. 1985 Dec 16;4(13A):3519–3524. [PMC free article] [PubMed]
  • Simmaco M, John RA, Barra D, Bossa F. The primary structure of ornithine aminotransferase. Identification of active-site sequence and site of post-translational proteolysis. FEBS Lett. 1986 Apr 7;199(1):39–42. [PubMed]
  • Obaru K, Nomiyama H, Shimada K, Nagashima F, Morino Y. Cloning and sequence analysis of mRNA for mouse aspartate aminotransferase isoenzymes. J Biol Chem. 1986 Dec 25;261(36):16976–16983. [PubMed]
  • Joh T, Nomiyama H, Maeda S, Shimada K, Morino Y. Cloning and sequence analysis of a cDNA encoding porcine mitochondrial aspartate aminotransferase precursor. Proc Natl Acad Sci U S A. 1985 Sep;82(18):6065–6069. [PMC free article] [PubMed]
  • Jaussi R, Cotton B, Juretić N, Christen P, Schümperli D. The primary structure of the precursor of chicken mitochondrial aspartate aminotransferase. Cloning and sequence analysis of cDNA. J Biol Chem. 1985 Dec 25;260(30):16060–16063. [PubMed]
  • Jansen R, Kalousek F, Fenton WA, Rosenberg LE, Ledley FD. Cloning of full-length methylmalonyl-CoA mutase from a cDNA library using the polymerase chain reaction. Genomics. 1989 Feb;4(2):198–205. [PubMed]
  • Kraus JP, Matsubara Y, Barton D, Yang-Feng TL, Glassberg R, Ito M, Ikeda Y, Mole J, Francke U, Tanaka K. Isolation of cDNA clones coding for rat isovaleryl-CoA dehydrogenase and assignment of the gene to human chromosome 15. Genomics. 1987 Nov;1(3):264–269. [PubMed]
  • Dahl HH, Hunt SM, Hutchison WM, Brown GK. The human pyruvate dehydrogenase complex. Isolation of cDNA clones for the E1 alpha subunit, sequence analysis, and characterization of the mRNA. J Biol Chem. 1987 May 25;262(15):7398–7403. [PubMed]
  • Koerner TJ, Hill J, Tzagoloff A. Cloning and characterization of the yeast nuclear gene for subunit 5 of cytochrome oxidase. J Biol Chem. 1985 Aug 15;260(17):9513–9515. [PubMed]
  • Patterson TE, Poyton RO. COX8, the structural gene for yeast cytochrome c oxidase subunit VIII. DNA sequence and gene disruption indicate that subunit VIII is required for maximal levels of cellular respiration and is derived from a precursor which is extended at both its NH2 and COOH termini. J Biol Chem. 1986 Dec 25;261(36):17192–17197. [PubMed]
  • Henning WD, Upton C, McFadden G, Majumdar R, Bridger WA. Cloning and sequencing of the cytoplasmic precursor to the alpha subunit of rat liver mitochondrial succinyl-CoA synthetase. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1432–1436. [PMC free article] [PubMed]
  • Velours J, Durrens P, Aigle M, Guérin B. ATP4, the structural gene for yeast F0F1 ATPase subunit 4. Eur J Biochem. 1988 Jan 4;170(3):637–642. [PubMed]
  • Takeda M, Chen WJ, Saltzgaber J, Douglas MG. Nuclear genes encoding the yeast mitochondrial ATPase complex. Analysis of ATP1 coding the F1-ATPase alpha-subunit and its assembly. J Biol Chem. 1986 Nov 15;261(32):15126–15133. [PubMed]
  • Viebrock A, Perz A, Sebald W. The imported preprotein of the proteolipid subunit of the mitochondrial ATP synthase from Neurospora crassa. Molecular cloning and sequencing of the mRNA. EMBO J. 1982;1(5):565–571. [PMC free article] [PubMed]
  • Nyunoya H, Broglie KE, Widgren EE, Lusty CJ. Characterization and derivation of the gene coding for mitochondrial carbamyl phosphate synthetase I of rat. J Biol Chem. 1985 Aug 5;260(16):9346–9356. [PubMed]
  • Matsubara Y, Kraus JP, Ozasa H, Glassberg R, Finocchiaro G, Ikeda Y, Mole J, Rosenberg LE, Tanaka K. Molecular cloning and nucleotide sequence of cDNA encoding the entire precursor of rat liver medium chain acyl coenzyme A dehydrogenase. J Biol Chem. 1987 Jul 25;262(21):10104–10108. [PubMed]
  • Kelly DP, Kim JJ, Billadello JJ, Hainline BE, Chu TW, Strauss AW. Nucleotide sequence of medium-chain acyl-CoA dehydrogenase mRNA and its expression in enzyme-deficient human tissue. Proc Natl Acad Sci U S A. 1987 Jun;84(12):4068–4072. [PMC free article] [PubMed]
  • Evans CT, Owens DD, Sumegi B, Kispal G, Srere PA. Isolation, nucleotide sequence, and expression of a cDNA encoding pig citrate synthase. Biochemistry. 1988 Jun 28;27(13):4680–4686. [PubMed]
  • Nonaka Y, Murakami H, Yabusaki Y, Kuramitsu S, Kagamiyama H, Yamano T, Okamoto M. Molecular cloning and sequence analysis of full-length cDNA for mRNA of adrenodoxin oxidoreductase from bovine adrenal cortex. Biochem Biophys Res Commun. 1987 Jun 30;145(3):1239–1247. [PubMed]
  • Pons G, Raefsky-Estrin C, Carothers DJ, Pepin RA, Javed AA, Jesse BW, Ganapathi MK, Samols D, Patel MS. Cloning and cDNA sequence of the dihydrolipoamide dehydrogenase component human alpha-ketoacid dehydrogenase complexes. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1422–1426. [PMC free article] [PubMed]
  • Zeviani M, Sakoda S, Sherbany AA, Nakase H, Rizzuto R, Samitt CE, DiMauro S, Schon EA. Sequence of cDNAs encoding subunit Vb of human and bovine cytochrome c oxidase. Gene. 1988 May 15;65(1):1–11. [PubMed]
  • Rizzuto R, Nakase H, Zeviani M, DiMauro S, Schon EA. Subunit Va of human and bovine cytochrome c oxidase is highly conserved. Gene. 1988 Sep 30;69(2):245–256. [PubMed]
  • Wright RM, Ko C, Cumsky MG, Poyton RO. Isolation and sequence of the structural gene for cytochrome c oxidase subunit VI from Saccharomyces cerevisiae. J Biol Chem. 1984 Dec 25;259(24):15401–15407. [PubMed]
  • Morohashi K, Fujii-Kuriyama Y, Okada Y, Sogawa K, Hirose T, Inayama S, Omura T. Molecular cloning and nucleotide sequence of cDNA for mRNA of mitochondrial cytochrome P-450(SCC) of bovine adrenal cortex. Proc Natl Acad Sci U S A. 1984 Aug;81(15):4647–4651. [PMC free article] [PubMed]
  • Runswick MJ, Powell SJ, Nyren P, Walker JE. Sequence of the bovine mitochondrial phosphate carrier protein: structural relationship to ADP/ATP translocase and the brown fat mitochondria uncoupling protein. EMBO J. 1987 May;6(5):1367–1373. [PMC free article] [PubMed]
  • Ohta S, Kagawa Y. Human F1-ATPase: molecular cloning of cDNA for the beta subunit. J Biochem. 1986 Jan;99(1):135–141. [PubMed]
  • Hu CW, Lau KS, Griffin TA, Chuang JL, Fisher CW, Cox RP, Chuang DT. Isolation and sequencing of a cDNA encoding the decarboxylase (E1)alpha precursor of bovine branched-chain alpha-keto acid dehydrogenase complex. Expression of E1 alpha mRNA and subunit in maple-syrup-urine-disease and 3T3-L1 cells. J Biol Chem. 1988 Jun 25;263(18):9007–9014. [PubMed]
  • Zhang B, Kuntz MJ, Goodwin GW, Harris RA, Crabb DW. Molecular cloning of a cDNA for the E1 alpha subunit of rat liver branched chain alpha-ketoacid dehydrogenase. J Biol Chem. 1987 Nov 5;262(31):15220–15224. [PubMed]
  • Bilofsky HS, Burks C. The GenBank genetic sequence data bank. Nucleic Acids Res. 1988 Mar 11;16(5):1861–1863. [PMC free article] [PubMed]
  • Hawlitschek G, Schneider H, Schmidt B, Tropschug M, Hartl FU, Neupert W. Mitochondrial protein import: identification of processing peptidase and of PEP, a processing enhancing protein. Cell. 1988 Jun 3;53(5):795–806. [PubMed]
  • Matocha MF, Waterman MR. Discriminatory processing of the precursor forms of cytochrome P-450scc and adrenodoxin by adrenocortical and heart mitochondria. J Biol Chem. 1984 Jul 10;259(13):8672–8678. [PubMed]
  • Horwich AL, Kalousek F, Fenton WA, Pollock RA, Rosenberg LE. Targeting of pre-ornithine transcarbamylase to mitochondria: definition of critical regions and residues in the leader peptide. Cell. 1986 Feb 14;44(3):451–459. [PubMed]
  • Chu TW, Grant PM, Strauss AW. The role of arginine residues in the rat mitochondrial malate dehydrogenase transit peptide. J Biol Chem. 1987 Sep 15;262(26):12806–12811. [PubMed]
  • Nguyen M, Argan C, Sheffield WP, Bell AW, Shields D, Shore GC. A signal sequence domain essential for processing, but not import, of mitochondrial pre-ornithine carbamyl transferase. J Cell Biol. 1987 May;104(5):1193–1198. [PMC free article] [PubMed]

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