PT  - JOURNAL ARTICLE
AU  - Sophie S Abby
AU  - Jean Cury
AU  - Julien Guglielmini
AU  - Bertrand Néron
AU  - Marie Touchon
AU  - Eduardo PC Rocha
TI  - Identification of protein secretion systems in bacterial genomes
AID  - 10.1101/031039
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 031039
4099  - http://biorxiv.org/content/early/2015/11/09/031039.short
4100  - http://biorxiv.org/content/early/2015/11/09/031039.full
AB  - Bacteria with two cell membranes (diderms) have evolved complex systems for protein secretion. These systems were extensively studied in some model bacteria, but the characterisation of their diversity has lagged behind due to lack of standard annotation tools. We built models for accurate identification of protein secretion systems and related appendages in bacteria with LPS-containing outer membranes. They can be used with MacSyFinder (standalone program) or online (http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::txsscan). They include protein profiles and information on the system’s composition and genetic organisation. They can be used to search for T1SS-T6SS, T9SS, and accessorily for flagella, Type IV and Tad pili. We identified ~10,000 systems in bacterial genomes, where T1SS and T5SS were by far the most abundant and widespread. The recently described T6SSiii and T9SS were restricted to Bacteroidetes, and T6SSii to Francisella. T2SS, T3SS, and T4SS were frequently encoded in single-copy in one locus, whereas most T1SS were encoded in two loci. The secretion systems of diderm Firmicutes were similar to those found in other diderms. Novel systems may remain to be discovered, since some clades of environmental bacteria lacked all known protein secretion systems. Our models can be fully customized, which should facilitate the identification of novel systems.Introduction