Experimental determination of organelle targeting-peptide cleavage sites using transient expression of green fluorescent protein translational fusions

Analytical Biochemistry

Volumn 434, Issue 1, 2013, Pages 44-51

  Candat, Adrien ^a   Poupart, Pauline ^b   Andrieu, Jean Pierre ^c   Chevrollier, Arnaud ^d   Reynier, Pascal ^d   Rogniaux, Hélène ^e   Avelange Macherel, Marie Hélène ^b   Macherel, David ^f  

^a Universite d'Angers   (France)

^b AGROCAMPUS OUEST   (France)

^c INSTITUT DE BIOLOGIE STRUCTURALE   (France)

^d UNIVERSITÉ D'ANGERS   (France)

^e INRA   (France)

^f UNIVERSITÉ D'ANGERS   (France)

Author keywords

Chloroplast; Edman; GFP; Import; Mass spectrometry; Mitochondria; N terminus; Plastid; Signal peptide; Targeting peptide; Transfection; Transit peptide

Indexed keywords

ANIMALS; CELL PROLIFERATION; FLUORESCENCE; MASS SPECTROMETRY; MITOCHONDRIA;

CHLOROPLAST; EDMAN; IMPORT; N TERMINUS; PLASTID; SIGNAL PEPTIDE; TARGETING PEPTIDES; TRANSFECTION; TRANSIT PEPTIDES;

PEPTIDES;

GREEN FLUORESCENT PROTEIN; HYBRID PROTEIN; PROTEIN PRECURSOR;

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; BIOINFORMATICS; CELL ORGANELLE; CELLULAR DISTRIBUTION; EMBRYO DEVELOPMENT; GENE EXPRESSION; GENE FUSION; MOLECULAR SIZE; MOLECULAR WEIGHT; NONHUMAN; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN PROCESSING; PROTEIN TARGETING; PROTOPLAST; QUALITY CONTROL; TRANSGENE; TRANSIENT EXPRESSION;

ANIMALIA;

EID: 84871415270     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2012.10.040     Document Type: Article

References (36)

1. P.F. Teixeira, and E. Glaser Processing peptidases in mitochondria and chloroplasts Biochim. Biophys. Acta 2012 10.1016/j.bbamcr.2012.03.012
2. A. Varshavsky The N-end rule: functions, mysteries, uses Proc. Natl. Acad. Sci. U.S.A. 93 1996 12142 12149
3. D.A. Dougan, K.N. Truscott, and K. Zeth The bacterial N-end rule pathway: expect the unexpected Mol. Microbiol. 76 2010 545 558
4. M.F. Hoylaerts, L. Ding, S. Narisawa, S. Van Kerckhoven, and J.L. Millan Mammalian alkaline phosphatase catalysis requires active site structure stabilization via the N-terminal amino acid microenvironment Biochemistry 45 2006 9756 9766
5. K.C. Chou, and H.B. Shen Recent progress in protein subcellular location prediction Anal. Biochem. 370 2007 1 16
6. X. Wang, and G.Z. Li A multi-label predictor for identifying the subcellular locations of singleplex and multiplex eukaryotic proteins PLoS One 7 2012 e36317
7. A.H. Millar, C. Carrie, B. Pogson, and J. Whelan Exploring the function-location nexus: using multiple lines of evidence in defining the subcellular location of plant proteins Plant Cell 21 2009 1625 1631
8. O. Emanuelsson, S. Brunak, G. von Heijne, and H. Nielsen Locating proteins in the cell using TargetP, SignalP and related tools Nat. Protoc. 2 2007 953 971
9. F. Rebeille, C. Alban, J. Bourguignon, S. Ravanel, and R. Douce The role of plant mitochondria in the biosynthesis of coenzymes Photosynth. Res. 92 2007 149 162
10. J. Bardel, M. Louwagie, M. Jaquinod, A. Jourdain, S. Luche, T. Rabilloud, D. Macherel, J. Garin, and J. Bourguignon A survey of the plant mitochondrial proteome in relation to development Proteomics 2 2002 880 898
11. D. Wellner, C. Panneerselvam, and B.L. Horecker Sequencing of peptides and proteins with blocked N-terminal amino-acids - N-acetylserine or N-acetylthreonine Proc. Natl. Acad. Sci. U.S.A. 87 1990 1947 1949
12. W.J. Henzel, J. Tropea, and D. Dupont Protein identification using 20-minute Edman cycles and sequence mixture analysis Anal. Biochem. 267 1999 148 160
13. B. Zybailov, H. Rutschow, G. Friso, A. Rudella, O. Emanuelsson, Q. Sun, and K.J. van Wijk Sorting signals, N-terminal modifications and abundance of the chloroplast proteome PLoS One 3 2008 e1994
14. S. Huang, N.L. Taylor, J. Whelan, and A.H. Millar Refining the definition of plant mitochondrial presequences through analysis of sorting signals, N-terminal modifications, and cleavage motifs Plant Physiol. 150 2009 1272 1285
15. S.P. Cleary, F.C. Tan, K.A. Nakrieko, S.J. Thompson, P.M. Mullineaux, G.P. Creissen, E. von Stedingk, E. Glaser, A.G. Smith, and C. Robinson Isolated plant mitochondria import chloroplast precursor proteins in vitro with the same efficiency as chloroplasts J. Biol. Chem. 277 2002 5562 5569
16. D.W. Lee, J.K. Kim, S. Lee, S. Choi, S. Kim, and I. Hwang Arabidopsis nuclear-encoded plastid transit peptides contain multiple sequence subgroups with distinctive chloroplast-targeting sequence motifs Plant Cell 20 2008 1603 1622
17. M. Karimi, D. Inzq, and A. Depicker GATEWAY™ vectors for Agrobacterium-mediated plant transformation Trends Plant Sci. 7 2002 193 195
18. S.D. Yoo, Y.H. Cho, and J. Sheen Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis Nat. Protoc. 2 2007 1565 1572
19. E. Chatelain, M. Hundertmark, O. Leprince, S. le Gall, P. Satour, S.P. Deligny-Penninck, H. Rogniaux, and J. Buitink Temporal profiling of the heat stable proteome during the late maturation of Medicago truncatula seeds identifies a restricted subset of late embryogenesis abundant proteins associated with longevity Plant Cell Environ. 35 2012 1440 1455
20. P. Horton, K.J. Park, T. Obayashi, N. Fujita, H. Harada, C.J. Adams-Collier, and K. Nakai WoLF PSORT: protein localization predictor Nucleic Acids Res. 35 2007 W585 W587
21. O. Emanuelsson, H. Nielsen, and G. von Heijne ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites Protein Sci. 8 1999 978 984
22. M.G. Claros, and P. Vincens Computational method to predict mitochondrially imported proteins and their targeting sequences Eur. J. Biochem. 241 1996 779 786
23. T.N. Petersen, S. Brunak, G. von Heinje, and H. Nielsen SignalP 4.0: discriminating signal peptides from transmembrane regions Nat. Methods 8 2011 785 786
24. M. Hundertmark, and D. Hincha LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana BMC Genomics 9 2008 118
25. E. Jaspard, D. Macherel, and G. Hunault Computational and statistical analyses of amino acid usage and physico-chemical properties of the twelve late embryogenesis abundant protein classes PLoS One 7 2012 e36968
26. L. Ho, I.D. Wexler, T.C. Liu, T.J. Thekkumkara, and M.S. Patel Characterization of cDNAs encoding human pyruvate dehydrogenase alpha subunit Proc. Natl. Acad. Sci. U.S.A. 86 1989 5330 5334
27. D.C. Logan, and C.J. Leaver Mitochondria-targeted GFP highlights the heterogeneity of mitochondrial shape, size and movement within living plant cells J. Exp. Bot. 51 2000 865 871
28. A. Matagne, B. Joris, and J.M. Frere Anomalous behaviour of a protein during SDS/PAGE corrected by chemical modification of carboxylic groups Biochem. J. 280 1991 553 556
29. S.M. Gomez, K.Y. Bil', R. Aguilera, J.N. Nishio, K.F. Faull, and J.P. Whitelegge Transit peptide cleavage sites of integral thylakoid membrane proteins Mol. Cell. Proteomics 2 2003 1068 1085
30. M. Schubert, U.A. Petersson, B.J. Haas, C. Funk, W.P. Schroder, and T. Kieselbach Proteome map of the chloroplast lumen of Arabidopsis thaliana J. Biol. Chem. 277 2002 8354 8365
31. Q. Sun, O. Emanuelsson, and K.J. van Wijk Analysis of curated and predicted plastid subproteomes of Arabidopsis: subcellular compartmentalization leads to distinctive proteome properties Plant Physiol. 135 2004 723 734
32. Y. Henry, M. Bedhomme, and G. Blanc History, protohistory and prehistory of the Arabidopsis thaliana chromosome complement Trends Plant Sci. 11 2006 267 273
33. O. Carugo Detailed estimation of bioinformatics prediction reliability through the fragmented prediction performance plots BMC Bioinformatics 8 2007 380
34. D. Suckau, and D. Cornett Protein sequencing by ISD and PSD MALDI-TOF MS Analusis 26 1998 18 21
35. J. Hardouin Protein sequence information by matrix-assisted laser desorption/ionization in-source decay mass spectrometry Mass Spectrom. Rev. 26 2007 672 682
36. D.M. Chudakov, M.V. Matz, S. Lukyanov, and K.A. Lukyanov Fluorescent proteins and their applications in imaging living cells and tissues Physiol. Rev. 90 2010 1103 1163