Non-classical protein secretion in bacteria

Abstract

Background: We present an overview of bacterial non-classical secretion and a prediction method for identification of proteins following signal peptide independent secretion pathways. We have compiled a list of proteins found extracellularly despite the absence of a signal peptide. Some of these proteins also have known roles in the cytoplasm, which means they could be so-called "moon-lightning" proteins having more than one function.

Results: A thorough literature search was conducted to compile a list of currently known bacterial non-classically secreted proteins. Pattern finding methods were applied to the sequences in order to identify putative signal sequences or motifs responsible for their secretion. We have found no signal or motif characteristic to any majority of the proteins in the compiled list of non-classically secreted proteins, and conclude that these proteins, indeed, seem to be secreted in a novel fashion. However, we also show that the apparently non-classically secreted proteins are still distinguished from cellular proteins by properties such as amino acid composition, secondary structure and disordered regions. Specifically, prediction of disorder reveals that bacterial secretory proteins are more structurally disordered than their cytoplasmic counterparts. Finally, artificial neural networks were used to construct protein feature based methods for identification of non-classically secreted proteins in both Gram-positive and Gram-negative bacteria.

Conclusion: We present a publicly available prediction method capable of discriminating between this group of proteins and other proteins, thus allowing for the identification of novel non-classically secreted proteins. We suggest candidates for non-classically secreted proteins in Escherichia coli and Bacillus subtilis. The prediction method is available online.

Figure 1

Bacterial secreted proteins are more disordered in structure than cytoplasmic proteins. The predicted number of coils (average per residue) by DisEMBL is higher for secreted proteins than for cytoplasmic ones. The tendency also holds for the two other measures of disorder predicted by DisEMBL (not shown).

Figure 2

Prediction on different proteins in different organisms. Four proteins from five bacterial species. Scores above 0.5 indicate predicted secretion of that particular protein. For details, please refer to the text.

Figure 3

Putative non-classical secretory proteins. The top 100 scoring proteins are grouped based on annotation. Several groups have obvious relations to extracellular functions. For proteins with no annotation (grouped in 'Unknown'), our prediction method suggests an extracellular role. Proteins grouped in 'Other' may have an extracellular function, although this is not apparent in the current annotation.