Bioinformatics prediction discovers new CoAttSS protein substrates in Bacteroidetes

Proteomic analyses revealed a group of surface associated proteins in the Gram-negative oral pathogens Porphyromonas gingivalis and Tannerella forsythia that are post-translationally modified and have a highly conserved C-Terminal Domain (CTD). As these bacteria lack components of the seven known bacterial secretion systems, we and other groups are proposing that they are translocated by a novel secretion system, the Combined Attachment Secretion system (CoAttSS). Mutagenesis studies have suggested that the CTD region of the CoAttSS protein substrates contains signal sequences that are recognised by the CoAttSS. Objectives: This project aims to define the CTD and the motifs it contains, find all the members of the CoAttSS protein substrates family, and identify bacteria containing CoAttSS protein substrates and components of the Combined Attachment Secretion System using Bioinformatics approaches. Methods: Experimentally identified CoAttSS protein substrates sequences were analysed using motif discovery methods to characterise the CTD motif. After characterization, the motif sequences were profiled using Hidden Markov Model (HMM) methodology which were able to compress all the information of the known CoAttSS protein substrates into a HMM profile. Using this profile, database searching was done against major protein sequence databases. Results: The CTDs of the CoAttSS Protein Substrates are approximately 60 amino acids in length and contain a motif of approximately 42 amino acids in length. The CTD motif consists of three smaller motifs with variable gaps between these motifs. The lengths of these motifs are approximately 13 amino acids for Motif 1, 11 amino acids for Motif 2 and 7 amino acids for Motif 3. 396 candidate CoAttSS Protein Substrates were found in 17 other species of bacteria apart from P. gingivalis and T. forsythia, all of which are members of the Bacteroidetes phylum. Conclusions: This information may provide targets for new specific treatments and preventive regimes for chronic periodontitis.