J. Zuegge, S. Ralph, M. Schmuker, G.I. McFadden, G. Schneider
PATS identifies amino acid sequences that are potentially targeted to the apicoplast matrix of Plasmodium falciparum. Note that secondary analysis of candidate sequences is required for confirmation.
Targeting of proteins to the apicoplast of apicomplexan parasites requires a two part leader sequence . The first component is a canonical signal peptide that mediates entry of the protein into the endomembrane system. This component of leader can be predicted with several tools including hydrophobicity plots and the web analysis servers SIGNALP and PSORT. At this stage it is believed that a signal peptide is necessary for targeting to the apicoplast. The second component of the leader is a transit peptide, which has similar properties to the transit peptides directing proteins into plastids of plants and algae . The composition of the transit peptide in apicoplast targeted proteins is not well understood but it is basic.
The PATS neural network analysis makes predictions of the transit peptide component of the query sequence. The network has been trained with 84 Plasmodium falciparum proteins believed to be apicoplast targeted and 102 proteins thought not to be apicoplast targeted. If the protein you are analysing has an N-terminal signal peptide and is judged positive by PATS, then it is likely apicoplast targeted. As with any prediction software though there will be errors and researchers are encouraged to view predictions is indicative rather than definitive. PATS is specifically trained to recognise Plasmodium falciparum proteins containing transit peptides and may not work with Toxoplasma gondii transit peptides.
The PATS training data can be downloaded from here. The sequences are presented in the FASTA format. The sequences are not complete: Only the parts, that were relevant for training are included. The mature proteins are not in the data sets.
35 very likely apicoplast targeted proteins. Upper case letters indicate, that the amino adic is part of the signal peptide, whereas lower case letters indicate transit peptides.
49 further apicoplast targeted proteins with unknown length of the transit peptide. The SignalP predicted siganl peptides are in upper case.
102 non-apicoplast proteins.
If you are using PATS in your research, please cite:
Zuegge J, Ralph S, Schmuker M, McFadden GI, Schneider G (2001) Deciphering apicoplast targeting signals - feature extraction from nuclear-encoded precursors of Plasmodium falciparum apicoplast proteins. Gene 280; 19-26 Read abstract or full text at Science Direct
1. Waller RF, Keeling PJ, Donald RG, Striepen B, Handman E, Lang-Unnasch N, Cowman AF, Besra GS, Roos DS, McFadden GI (1998) Nuclear-encoded proteins target to the plastid in Toxoplasma gondii and Plasmodium falciparum. Proc Natl Acad Sci U S A 95; 12352-12357 Read abstract or full text at PNAS Online
2. Waller RF, Reed MB, Cowman AF, McFadden GI. (2000) Protein trafficking to the plastid of Plasmodium falciparum is via the secretory pathway. EMBO J 19; 1794-1802 Read abstract or full text at EMBO Journal Online