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. 1999 May;8(5):978–984. doi: 10.1110/ps.8.5.978

ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites.

O Emanuelsson 1, H Nielsen 1, G von Heijne 1
PMCID: PMC2144330  PMID: 10338008

Abstract

We present a neural network based method (ChloroP) for identifying chloroplast transit peptides and their cleavage sites. Using cross-validation, 88% of the sequences in our homology reduced training set were correctly classified as transit peptides or nontransit peptides. This performance level is well above that of the publicly available chloroplast localization predictor PSORT. Cleavage sites are predicted using a scoring matrix derived by an automatic motif-finding algorithm. Approximately 60% of the known cleavage sites in our sequence collection were predicted to within +/-2 residues from the cleavage sites given in SWISS-PROT. An analysis of 715 Arabidopsis thaliana sequences from SWISS-PROT suggests that the ChloroP method should be useful for the identification of putative transit peptides in genome-wide sequence data. The ChloroP predictor is available as a web-server at http://www.cbs.dtu.dk/services/ChloroP/.

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Selected References

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  1. Akashi K., Grandjean O., Small I. Potential dual targeting of an Arabidopsis archaebacterial-like histidyl-tRNA synthetase to mitochondria and chloroplasts. FEBS Lett. 1998 Jul 10;431(1):39–44. doi: 10.1016/s0014-5793(98)00717-0. [DOI] [PubMed] [Google Scholar]
  2. Altschul S. F., Boguski M. S., Gish W., Wootton J. C. Issues in searching molecular sequence databases. Nat Genet. 1994 Feb;6(2):119–129. doi: 10.1038/ng0294-119. [DOI] [PubMed] [Google Scholar]
  3. Bailey T. L., Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol. 1994;2:28–36. [PubMed] [Google Scholar]
  4. Bairoch A., Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res. 1998 Jan 1;26(1):38–42. doi: 10.1093/nar/26.1.38. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Brunak S., Engelbrecht J., Knudsen S. Prediction of human mRNA donor and acceptor sites from the DNA sequence. J Mol Biol. 1991 Jul 5;220(1):49–65. doi: 10.1016/0022-2836(91)90380-o. [DOI] [PubMed] [Google Scholar]
  6. Chow K. S., Singh D. P., Roper J. M., Smith A. G. A single precursor protein for ferrochelatase-I from Arabidopsis is imported in vitro into both chloroplasts and mitochondria. J Biol Chem. 1997 Oct 31;272(44):27565–27571. doi: 10.1074/jbc.272.44.27565. [DOI] [PubMed] [Google Scholar]
  7. Creissen G., Reynolds H., Xue Y., Mullineaux P. Simultaneous targeting of pea glutathione reductase and of a bacterial fusion protein to chloroplasts and mitochondria in transgenic tobacco. Plant J. 1995 Aug;8(2):167–175. doi: 10.1046/j.1365-313x.1995.08020167.x. [DOI] [PubMed] [Google Scholar]
  8. Gavel Y., von Heijne G. A conserved cleavage-site motif in chloroplast transit peptides. FEBS Lett. 1990 Feb 26;261(2):455–458. doi: 10.1016/0014-5793(90)80614-o. [DOI] [PubMed] [Google Scholar]
  9. Hobohm U., Scharf M., Schneider R., Sander C. Selection of representative protein data sets. Protein Sci. 1992 Mar;1(3):409–417. doi: 10.1002/pro.5560010313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Karlin S., Altschul S. F. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci U S A. 1990 Mar;87(6):2264–2268. doi: 10.1073/pnas.87.6.2264. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Matthews B. W. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta. 1975 Oct 20;405(2):442–451. doi: 10.1016/0005-2795(75)90109-9. [DOI] [PubMed] [Google Scholar]
  12. Menand B., Maréchal-Drouard L., Sakamoto W., Dietrich A., Wintz H. A single gene of chloroplast origin codes for mitochondrial and chloroplastic methionyl-tRNA synthetase in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):11014–11019. doi: 10.1073/pnas.95.18.11014. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Nakai K., Kanehisa M. A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics. 1992 Dec;14(4):897–911. doi: 10.1016/S0888-7543(05)80111-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Nielsen H., Engelbrecht J., Brunak S., von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 1997 Jan;10(1):1–6. doi: 10.1093/protein/10.1.1. [DOI] [PubMed] [Google Scholar]
  15. Pedersen A. G., Nielsen H. Neural network prediction of translation initiation sites in eukaryotes: perspectives for EST and genome analysis. Proc Int Conf Intell Syst Mol Biol. 1997;5:226–233. [PubMed] [Google Scholar]
  16. Qian N., Sejnowski T. J. Predicting the secondary structure of globular proteins using neural network models. J Mol Biol. 1988 Aug 20;202(4):865–884. doi: 10.1016/0022-2836(88)90564-5. [DOI] [PubMed] [Google Scholar]
  17. Richter S., Lamppa G. K. A chloroplast processing enzyme functions as the general stromal processing peptidase. Proc Natl Acad Sci U S A. 1998 Jun 23;95(13):7463–7468. doi: 10.1073/pnas.95.13.7463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Robinson C., Ellis R. J. Transport of proteins into chloroplasts. Partial purification of a chloroplast protease involved in the processing of important precursor polypeptides. Eur J Biochem. 1984 Jul 16;142(2):337–342. doi: 10.1111/j.1432-1033.1984.tb08291.x. [DOI] [PubMed] [Google Scholar]
  19. Robinson C., Hynds P. J., Robinson D., Mant A. Multiple pathways for the targeting of thylakoid proteins in chloroplasts. Plant Mol Biol. 1998 Sep;38(1-2):209–221. [PubMed] [Google Scholar]
  20. Schneider G., Sjöling S., Wallin E., Wrede P., Glaser E., von Heijne G. Feature-extraction from endopeptidase cleavage sites in mitochondrial targeting peptides. Proteins. 1998 Jan;30(1):49–60. [PubMed] [Google Scholar]
  21. Schneider T. D., Stephens R. M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990 Oct 25;18(20):6097–6100. doi: 10.1093/nar/18.20.6097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Soll J., Tien R. Protein translocation into and across the chloroplastic envelope membranes. Plant Mol Biol. 1998 Sep;38(1-2):191–207. [PubMed] [Google Scholar]
  23. von Heijne G., Steppuhn J., Herrmann R. G. Domain structure of mitochondrial and chloroplast targeting peptides. Eur J Biochem. 1989 Apr 1;180(3):535–545. doi: 10.1111/j.1432-1033.1989.tb14679.x. [DOI] [PubMed] [Google Scholar]
  24. von Heijne G. The signal peptide. J Membr Biol. 1990 May;115(3):195–201. doi: 10.1007/BF01868635. [DOI] [PubMed] [Google Scholar]

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