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Trends Microbiol. 2009 Apr;17(4):139-45. doi: 10.1016/j.tim.2009.01.004. Epub 2009 Mar 18.

Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue.

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INRA (Institut National de la Recherche Agronomique), UR454 Microbiologie, Centre de Recherche Clermont-Ferrand, F-63122 Saint-Genès Champanelle, France.


Extracellular proteins are a subject of intense interest because of their essential roles in bacterial lifestyles. However, several terms related to secretion are used confusingly in the literature, and this is a topical issue in genomics and proteomics. Defining a secreted protein as actively translocated via a secretion system, here, we put into perspective that homologous translocation systems can result in radically different subcellular localizations of a secreted protein. We propose using standardized nomenclature for secretion systems from type I to type VIII for Gram-negative bacteria only, whereas the terms 'Sec' (secretion), 'Tat' (twin-arginine translocation), 'FEA' (flagella export apparatus), 'FPE' (fimbrilin-protein exporter), 'holin' (hole forming) and 'Wss' (WXG100 secretion system) should be applied to translocation systems across the cytoplasmic membrane of both Gram-positive and Gram-negative bacteria. Finally, we discuss why the term 'exoproteome' should be favoured over 'secretome' when describing the subset of proteins present in the extracellular milieu.

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