| Abstract |
More than one third of the total proteome of all organisms is secreted from the cytoplasm through protein channels. The existence of signal peptides which are an amino acid extension at the amino terminal of secretory proteins, is known for over 30 years. (Halegoua, et al. 1977; Inouye, et al. 1977; Sekizawa, et al. 1977). Most of the bacterial proteome is getting secreted or inserted in the inner membrane through SecYEG channel. The role of signal peptides is protein targeting to the channel. Recently it was proven by experiments that the mature region of the secretory proteins contributes also to targeting of the proteins (Gouridis, et al. 2009). Experiments that are in progress in economou laboratory suggest that the secretion is determined by the combination of the mature domain and the signal peptide. The contribution of the mature domain in the secretion process casts a new parameter in understanding completely the secretion mechanism. Many bioinformatic tools have been developed through years in order to predict the existence of signal peptides and the subcellular location of the proteins (Bendtsen, et al. 2005; Emanuelsson, et al. 2007; Gardy, et al. 2005; Gardy, et al. 2003; Juncker, et al. 2003). None of these prediction tools takes into account the contribution of the mature domain.
We present an analysis of the secretory proteins of the Gram negative bacterium E. coli Secretome of E. coli was defined though an analysis of the whole proteome subcellular location that we performed. Through this analysis a new categorization of the proteins emerged where new categories were defined and enriched.
A conservation analysis of the mature domain indicates that there are conserved features in the early mature domain, more specifically negatively charge residues in the first 2 positions.
Then secreted proteins were separated from cytoplasmic ones though machine learning methods (Statnikov, et al. 2004; Statnikov, et al. 2005). The separation of the mature domain of secreted
proteins from cytoplasmic proteins proved that the mature domain has unique and discernable primary amino acid sequene. The most important features are on the first 20 to 40 amino acids of
amino acid sequence, some preferred and others disfavored in the early mature region. A comparison with other similar tools (SignalP HMM, SignalP Neural Networks και LipoP) and a validation through experimental data renders our separation models best in performance.
Finally we performed an in silico experiment were we combined all signal peptides with mature domains and cytoplasmic proteins. What this experiment suggests is in agreement with
experimental indications that the combination of signal peptide and mature domain determines the secretion efficiency.
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Ανάλυση σηματοδοτικών αλληλουχιών σε εκκρινόμενες πρωτείνες
