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Protein Engineering, Vol. 14, No. 1, 17-25, January 2001
© 2001 Oxford University Press

Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes

Birgit Eisenhaber1,2,3, Peer Bork1,4 and Frank Eisenhaber2

1 Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Straße 10, D-13122 Berlin-Buch, Germany, 2 Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria and 4 European Molecular Biology Laboratory, Meyerhofstrasse1, Postfach 10.2209, D-69012 Heidelberg, Germany

To investigate the occurrence of glycosylphosphatidylinositol (GPI) lipid anchor modification in various taxonomic ranges, potential substrate proteins have been searched for in completely sequenced genomes. We applied the big-{pi} predictor for the recognition of propeptide cleavage and anchor attachment sites with a new, generalized analytical form of the extreme-value distribution for evaluating false-positive prediction rates. (i) We find that GPI modification is present among lower and higher Eukaryota (~0.5% of all proteins) but it seems absent in all eubacterial and three archaeobacterial species studied. Four other archaean genomes appear to encode such a fraction of substrate proteins (in the range of eukaryots) that they cannot be explained as false-positive predictions. This result supports the possible existence of GPI anchor modification in an archaean subgroup. (ii) The frequency of GPI-modified proteins on various chromosomes of a given eukaryotic species is different. (iii) Lists of potentially GPI-modified proteins in complete genomes with their predicted cleavage sites are available at http://mendel.imp.univie.ac.at/gpi/gpi_genomes.html. (iv) Orthologues of known transamidase subunits have been found only for Eukarya. Inconsistencies in domain structure among homologues some of which may indicate sequencing errors are described. We present a refined model of the transamidase complex.


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