Prediction of dual protein targeting to plant organelles.
* Dual targeting of proteins to more than one subcellular localization has been found in animals, in fungi and in plants. In the latter, ambiguous N-terminal targeting signals have been described that result in the protein being located in both mitochondria and plastids. We have developed ambiguous targeting predictor (ATP), a machine-learning implementation that classifies such ambiguous targeting signals. * Ambiguous targeting predictor is based on a support vector machine implementation that makes use of 12 different amino acid features. Prediction results were validated using fluorescent protein fusion. * Both in silico and in vivo evaluations demonstrate that ambiguous targeting predictor is useful for predicting dual targeting to mitochondria and plastids. Proteins that are targeted to both organelles by tandemly arrayed signals (so-called twin targeting) can be predicted by both ambiguous targeting predictor and a combination of single targeting prediction tools. Comparison of ambiguous targeting predictor with previous experimental approaches, as well as in silico approaches, shows good congruence. * Based on the prediction results, land plant genomes are expected to encode, on average, > 400 proteins that are located in mitochondria and plastids. Ambiguous targeting predictor is helpful for functional genome annotation and can be used as a tool to further our understanding about dual protein targeting and its evolution.
Plant Biotechnology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany.
Jan
J
Mitschke
Plant Biotechnology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany.
Janina
J
Fuss
Center for Bioinformatics Tübingen, University of Tübingen, Sand 14, D-72076 Tübingen, Germany.
Torsten
T
Blum
Center for Bioinformatics Tübingen, University of Tübingen, Sand 14, D-72076 Tübingen, Germany.
Annette
A
Höglund
Plant Biotechnology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany.|FRISYS, Faculty of Biology, University of Freiburg, Hauptstr. 1, D-79104 Freiburg, Germany.
Ralf
R
Reski
Center for Bioinformatics Tübingen, University of Tübingen, Sand 14, D-72076 Tübingen, Germany.
Oliver
O
Kohlbacher
FRISYS, Faculty of Biology, University of Freiburg, Hauptstr. 1, D-79104 Freiburg, Germany.
Stefan A
SA
Rensing
D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D019068:Bryopsida / Q000378:metabolism; D002736:Chloroplasts / Q000378:metabolism*; D003198:Computer Simulation; D018745:Genome, Plant; D049452:Green Fluorescent Proteins; D008928:Mitochondria / Q000378:metabolism*; D010940:Plant Proteins / Q000378:metabolism*; D010944:Plants / Q000235:genetics / Q000378:metabolism*; D012372:ROC Curve; D015398:Signal Transduction
D010940:Plant Proteins; D049452:Green Fluorescent Proteins