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Predicting Protein Secretion in an Archaeal Genome: The Signal Peptides of Methanococcus jannaschii

Henrik Nielsen, Soren Brunak and Gunnar von Heijne

Secretory signal peptides from eukaryotes and bacteria are well described, but very few experimentally verified examples are known from the third domain of life --- the Archaea. We have used SignalP, a neural network method for prediction of signal peptides, to analyze the genome of Methanococcus jannaschii, the first Archaeon to be completely sequenced. SignalP provides different predictions for sequences from eukaryotes, Gram-positive bacteria, and Gram-negative bacteria. By employing a consensus of the eukaryotic and bacterial SignalP predictions, we have assembled a set of 32 putative M. jannaschii signal peptides. Analysis of this set suggests that archaeal signal peptides have a eukaryotic-looking cleavage site, a bacterial-looking charge distribution, and a unique composition of the hydrophobic region.

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