Characterization of the preprotein and amino acid transporter gene family in Arabidopsis

Plant Physiology

Volumn 143, Issue 1, 2007, Pages 199-212

  Murcha, Monika W ^a   Elhafez, Dina ^a   Lister, Ryan ^a   Tonti Filippini, Julian ^a   Baumgartner, Manuela ^b   Philippar, Katrin ^b   Carrie, Chris ^a   Mokranjac, Dejana ^b   Soll, Jürgen ^b   Whelan, James ^a  

^a UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^b UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BIOASSAY; CROPS; GENETIC ENGINEERING; MICROORGANISMS; PLANTS (BOTANY);

ARABIDOPSIS THALIANA; EUKARYOTIC ORGANISMS; ORYZA SATIVA; PREPROTEIN;

PROTEINS;

CELLS; GENES; MITOCHONDRIA; PLANTS; PROTEINS; TISSUE CULTURE;

ARABIDOPSIS; ARABIDOPSIS THALIANA; DICOTYLEDONEAE; EUKARYOTA; ORYZA SATIVA; SACCHAROMYCES CEREVISIAE;

EID: 33846391338     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.106.090688     Document Type: Article

References (76)

1. Ahting U, Thieffry M, Engelhardt H, Hegerl R, Neupert W, Nussberger S (2001) Tom40, the pore-forming component of the protein-conducting TOM channel in the outer membrane of mitochondria. J Cell Biol 153: 1151-1160
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402
3. Anderson S, Smith SM (1986) Synthesis of the small subunit of ribulose bisphosphate carboxylase from genes cloned into plasmids containing the SP6 promoter. Biochem J 240: 709-715
4. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
5. Aronsson H, Jarvis P (2002) A simple method for isolating import-competent Arabidopsis chloroplasts. FEBS Lett 529: 215-220
6. Bathgate B, Baker A, Leaver CJ (1989) Two genes encode the adenine nucleotide translocator of maize mitochondria: isolation, characterisation and expression of the structural genes. Eur J Biochem 183: 303-310
7. Bauer MF, Hofmann S, Neupert W, Brunner M (2000) Protein translocation into mitochondria: the role of T1M complexes. Trends Cell Biol 10: 25-31
8. Beardslee TA, Roy-Chowdhury S, Jaiswal P, Buhot L, Lerbs-Mache S, Stern DB, Allison LA (2002) A nucleus-encoded maize protein with sigma factor activity accumulates in mitochondria and chloroplasts. Plant J 31: 199-209
9. Bedard J, Jarvis P (2005) Recognition and envelope rranslocation of chloroplast preproteins. J Exp Bot 56: 2287-2320
10. Bhushan S, Lefebvre B, Stahl A, Wright SJ, Bruce BD, Boutry M, Glaser E (2003) Dual targeting and function of a protease in mitochondria and chloroplasts. EMBO Rep 4: 1073-1078
11. Brugiere S, Kowalski S, Ferro M, Seigneurin-Berny D, Miras S, Salvi D, Ravanel S, d'Herin P, Garin J, Bourguignon J, et al (2004) The hydrophobic proteome of mitochondrial membranes from Arabidopsis cell suspensions. Phytochernistry 65: 1693-1707
12. Carrie C, Murcha MW, Millar AH, Smith SM, Whelan J (2007) Nine 3-ketoacyl-CoA thiolases (KATs) and acetoacetyl-CoA thiolases (ACATs) encoded by five genes in Arabidopsis thaliana are targeted either to peroxisomes or cytosol but not to mitochondria. Plant Mol Biol (in press)
13. Carroll J, Shannon RJ, Fearnley IM, Walker JE, Hirst J (2002) Definition of the nuclear encoded protein composition of bovine heart mitochondrial complex I: identification of two new subunits. J Biol Chern 277: 50311-50317
14. Chacinska A, Lind M, Frazier AE, Dudek J, Meisinger C, Geissler A, Sickmann A, Meyer HE, Truscott KN, Guiard B, et al (2005) Mitochondrial presequence translocase: switching between TOM tethering and motor recruitment involves Tim21 and Tim17. Cell 120: 817-829
15. Chew O, Lister R, Qbadou S, Heazlewood JL, Soil J, Schleiff E, Millar AH, Whelan J (2004) A plant outer mitochondrial membrane protein with high amino acid sequence identity to a chloroplast protein import receptor. FEBS Lett 557: 109-114
16. Chew O, Rudhe C, Glaser E, Whelan J (2003a) Characterization of the targeting signal of dual-targeted pea glutathione reductase. Plant Mol Biol 53: 341-356
17. Chew O, Whelan J (2004) Just read the message: a model for sorting of proteins between mitochondria and chloroplasts. Trends Plant Sci 9: 318-319
18. Chew O, Whelan J, Millar AH (2003b) Molecular definition of the ascorbate-glutathione cycle in Arabidopsis mitochondria reveals dual targeting of antioxidant defenses in plants. J Biol Chem 278: 46869-46877
19. Christensen AC, Lyznik A, Mohammed S, Elowsky CG, Elo A, Yule R, Mackenzie SA (2005) Dual-domain, dual-targeting organellar protein presequences in Arabidopsis can use non-AUG start codons. Plant Cell 17: 2805-2816
20. Cleary SP, Tan FC, Nakrieko KA, Thompson SJ, Mullineaux PM, Creissen GP, von Stedingk E, Glaser E, Smith AG, Robinson C (2002) Isolated plant mitochondria import chloroplast precursor proteins in vitro with the same efficiency as chloroplasts. J Biol Chem 277: 5562-5569
21. Clifton R, Lister R, Parker KL, Sappl P, Elhafez D, Millar AH, Day DA, Whelan J (2005) Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana. Plant Mol Biol 58: 193-212
22. Cserzo M, Wallin E, Simon I, von Heijne G, Elofsson A (1997) Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Eng 10: 673-676
23. Drea SC, Lao NT, Wolfe KH, Kavanagh TA (2006) Gene duplication, exon gain and neofunctionalization of OEP16-related genes in land plants. Plant J 46: 723-735
24. Duchene AM, Giritch A, Hoffmann B, Cognat V, Lancelin D, Peeters NM, Zaepfel M, Marechal-Drouard L, Small ID (2005) Dual targeting is the rule for organellar aminoacyl-tRNA synthetases in Arabidopsis thaliana. Proc Natl Acad Sci USA 102: 16484-16489
25. Ferro M, Salvi D, Brugiere S, Miras S, Kowalski S, Louwagie M, Garin J, Joyard J, Rolland N (2003) Proteomics of the chloroplast envelope membranes from Arabidopsis thaliana. Mol Cell Proteomics 2: 325-345
26. Froehlich JE, Wilkerson CG, Ray WK, McAndrew RS, Osteryoung KW, Gage DA, Phinney BS (2003) Proteomic study of Arabidopsis thaliana chloroplastic envelope membrane utilizing alternatives to traditional two-dimensional electrophoresis. J Proteome Res 2: 413-425
27. Gietz D, St Jean A, Woods RA, Schiestl RH (1992) Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res 20: 1425
28. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286: 531-537
29. Heazlewood JL, Tonti-Filippini JS, Gout AM, Day DA, Whelan J, Millar AH (2004) Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins. Plant Cell 16: 241-256
30. Heazlewood JL, Tonti-Filippini J, Verboom RE, Millar AH (2005) Combining experimental and predicted datasets for determination of the subcellular location of proteins in Aiabidopsis. Plant Physiol 139: 598-609
31. Heins L, Schmitz UK (1996) A receptor for protein import into potato mitochondria. Plant J 9: 829-839
32. Hinnah SC, Wagner R, Sveshnikova N, Harrer R, Soll J (2002) The chloroplast protein import channel Toc75: pore properties and interaction with transit peptides. Biophys J 83: 899-911
33. Jansch L, Kruft V, Schmitz UK, Braun HP (1998) Unique composition of the preprotein translocase of the outer mitochondrial membrane from plants. J Biol Chem 273: 17251-17257
34. Kruft V, Eubel H, Jansch L, Werhahn W, Braun HP (2001) Proteomic approach to identify novel mitochondrial proteins in Arabidopsis. Plant Physiol 127: 1694-1710
35. Lee MN, Whelan J (2004) Identification of signals required for import of the soybean F(A)d subunit of ATP synthase into mitochondria. Plant Mol Biol 54: 193-203
36. Linke D, Frank J, Pope MS, Soll J, Ilkavets I, Fromme P, Burstein EA, Reshetnyak YK, Emelyanenko VI (2004) Folding kinetics and structure of OEP16. Biophys J 86: 1479-1487
37. Lister R, Chew O, Lee MN, Heazlewood JL, Clifton R, Parker KL, Millar AH, Whelan J (2004) A transcriptomic and proteomic characterization of the Arabidopsis mitochondrial protein import apparatus and its response to mitochondrial dysfunction. Plant Physiol 134: 777-789
38. Lister R, Hulett JM, Lithgow T, Whelan J (2005) Protein import into mitochondria: origins and functions today (review). Mol Membr Biol 22: 87-100
39. Marmagne A, Rouet MA, Ferro M, Rolland N, Alcon C, Joyard J, Garin J, Barbier-Brygoo H, Ephritikhine G (2004) Identification of new intrinsic proteins in Arabidopsis plasma membrane proteome. Mol Cell Proteomics 3: 675-691
40. Martin W, Herrmann RG (1998) Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiol 118: 9-17
41. Millar AH, Heazlewood JL, Kristensen BK, Braun HP, Moller IM (2005) The plant mitochondrial proteome. Trends Plant Sci 10: 36-43
42. Murcha MW, Elhafez D, Millar AH, Whelan J (2005) The C-terminal region of TIM17 links the outer and inner mitochondrial membranes in Arabidopsis and is essential for protein import. J Biol Chem 280: 16476-16483
43. Murcha MW, Lister R, Ho AY, Whelan J (2003) Identification, expression, and import of components 17 and 23 of the inner mitochondrial membrane translocase from Arabidopsis. Plant Physiol 131: 1737-1747
44. Nehls U, Hemmer S, Rohlen DA, Van der Pas JC, Preis D, Sackmann U, Weiss H (1991) cDNA and genomic DNA sequence of the 21.3 kDa subunit of NADH:ubiquinone reductase (complex I) from Neurospora crassa. Biochim Biophys Acta 1088: 325-326
45. Neupert W (1997) Protein import into mitochondria. Annu Rev Biochem 66: 863-917
46. Peeters N, Small I (2001) Dual targeting to mitochondria and chloroplasts. Biochim Biophys Acta 1541: 54-63
47. Pfanner N, Geissler A (2001) Versatility of the mitochondrial protein import machinery. Nat Rev Mol Cell Biol 2: 339-349
48. Pohlmeyer K, Soll J, Steinkamp T, Hinnah S, Wagner R (1997) Isolation and characterization of an amino acid-selective channel protein present in the chloroplastic outer envelope membrane. Proc Natl Acad Sci USA 94: 9504-9509
49. Pracharoenwattana I, Cornah JE, Smith SM (2005) Arabidopsis peroxisomal citrate synthase is required for fatty acid respiration and seed germination. Plant Cell 17: 2037-2048
50. Rassow J, Dekker PJ, van Wilpe S, Meijer M, Soll J (1999) The preprotein translocase of the mitochondrial inner membrane: function and evolution. J Mol Biol 286: 105-120
51. Rehling P, Brandner K, Pfanner N (2004) Mitochondrial import and the twin-pore translocase. Nat Rev Mol Cell Biol 5: 519-530
52. Rehling P, Wiedemann N, Pfanner N, Truscott KN (2001) The mitochondrial import machinery for preproteins. Crit Rev Biochem Mol Biol 36: 291-336
53. Reinbothe S, Pollmann S, Springer A, James RJ, Tichtinsky G, Reinbothe C (2005) A role of Toc33 in the protochlorophyllide-dependent plastid import pathway of NADPH:protochlorophyllide oxidoreductase (POR) A. Plant J 42: 1-12
54. Reinbothe S, Quigley F, Gray J, Schemenewitz A, Reinbothe C (2004a) Identification of plastid envelope proteins required for import of protochlorophyllide oxidoreductase A into the chloroplast of barley. Proc Natl Acad Sci USA 101: 2197-2202
55. Reinbothe S, Quigley F, Springer A, Schemenewitz A, Reinbothe C (2004b) The outer plastid envelope protein Oep16: role as precursor translocase in import of protochlorophyllide oxidoreductase A. Proc Natl Acad Sci USA 101: 2203-2208
56. Rudhe C, Chew O, Whelan J, Glaser E (2002) A novel in vitro system for simultaneous import of precursor proteins into mitochondria and chloroplasrs. Plant J 30: 213-220
57. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual, Ed 2. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
58. Schwacke R, Schneider A, van der Graaff E, Fischer K, Catoni E, Desimone M, Frommer WB, Flugge UI, Kunze R (2003) ARAMEMNON, a novel database for Arabidopsis integral membrane proteins. Plant Physiol 131: 16-26
59. Siedow JN, Day DA (2002) Respiration and photosynthesis. In B Buchanan, W Gruissem, RL Jones, eds, Biochemistry and Molecular Biology of Plants. John Wiley and Sons, New York, pp 676-728
60. Sirrenberg C, Bauer MF, Guiard B, Neupert W, Brunner M (1996) Import of carrier proteins into the mitochondrial inner membrane mediated by Tim22. Nature 384: 582-585
61. Soll J, Schleiff E (2004) Protein import into chloroplasts. Nat Rev Mol Cell Biol 5: 198-208
62. Stahl A, Nilsson S, Lundberg P, Bhushan S, Biverstahl H, Moberg P, Morisset M, Vener A, Maler L, Langel U, et al (2005) Two novel targeting peptide degrading proteases, PrePs, in mitochondria and chloroplasts, so similar and still different. J Mol Biol 349: 847-860
63. Stojanovski D, Johnston AJ, Streimann I, Hoogenraad NJ, Ryan MT (2003) Import of nuclear-encoded proteins into mitochondria. Exp Physiol 88: 57-64
64. Swofford DL (2002) PAUP: Phylogenetic Analysis Using Parsimony Version 4.0 b10. Sinauer Associates, Sunderland, MA
65. Szponarski W, Sommerer N, Boyer JC, Rossignol M, Gibrat R (2004) Large-scale characterization of integral proteins from Arabidopsis vacuolar membrane by two-dimensional liquid chromatography. Proteomics 4: 397-406
66. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 96: 2907-2912
67. Tanudji M, Sjoling S, Glaser E, Whelan J (1999) Signals required for the import and processing of the alternative oxidase into mitochondria. J Biol Chem 274: 1286-1293
68. Thirkettle-Watts D, McCabe TC, Clifton R, Moore C, Finnegan PM, Day DA, Whelan J (2003) Analysis of the alternative oxidase promoters from soybean. Plant Physiol 133: 1158-1169
69. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882
70. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680
71. Truscott KN, Brandner K, Pfanner N (2003) Mechanisms of protein import into mitochondria. Curr Biol 13: R326-R337
72. Truscott KN, Wiedemann N, Rehling P, Muller H, Meisinger C, Pfanner N, Guiard B (2002) Mitochondrial import of the ADP/ATP carrier: the essential TIM complex of the intermembrane space is required for precursor release from the TOM complex. Mol Cell Biol 22: 7780-7789
73. Tsukamoto T, Hata S, Yokota S, Miura S, Fujiki Y, Hijikata M, Miyazawa S, Hashimoto T, Osumi T (1994) Characterization of the signal peptide at the amino terminus of the rat peroxisomal 3-ketoacyl-CoA thiolase precursor. J Biol Chem 269: 6001-6010
74. van Wijk KJ (2004) Plastid proteomics. Plant Physiol Biochem 42: 963-977
75. Vernet T, Dignard D, Thomas DY (1987) A family of yeast expression vectors containing the phage f1 intergenic region. Gene 52: 225-233
76. Winning BM, Sarah CJ, Purdue PE, Day CD, Leaver CJ (1992) The adenine nucleotide translocator of higher plants is synthesized as a large precursor that is processed upon import into mitochondria. Plant J 2: 763-773