These authors contributed equally to this work.
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Prediction of dual protein targeting to plant organelles
Article first published online: 7 APR 2009
DOI: 10.1111/j.1469-8137.2009.02832.x
© The Authors (2009). Journal compilation © New Phytologist (2009)
Additional Information
How to Cite
Mitschke, J., Fuss, J., Blum, T., Höglund, A., Reski, R., Kohlbacher, O. and Rensing, S. A. (2009), Prediction of dual protein targeting to plant organelles. New Phytologist, 183: 224–236. doi: 10.1111/j.1469-8137.2009.02832.x
Publication History
- Issue published online: 3 JUN 2009
- Article first published online: 7 APR 2009
- Received: 27 November 2008Accepted: 15 February 2009
Keywords:
- ambiguous targeting;
- chloroplast;
- genome annotation;
- intracellular sorting;
- mitochondrion
Summary
- • 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.