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Background   Frankia  sp. strains, the nitrogen-fixing facultative endosymbionts of actinorhizal plants, have long been proposed to secrete hydrolytic enzymes such as cellulases, pectinases, and proteases that may contribute to plant root penetration and formation of symbiotic root nodules. These or other secreted proteins might logically be involved in the as yet unknown molecular interactions between  Frankia  and their host plants. We compared the genome-based secretomes of three  Frankia  strains representing diverse host specificities. Signal peptide detection algorithms were used to predict the individual secretomes of each strain, and the set of secreted proteins shared among the strains, termed the core  Frankia  secretome. Proteins in the core secretome may be involved in the actinorhizal symbiosis.    Results  The  Frankia  genomes have conserved Sec (general secretory) and Tat (twin arginine translocase) secretion systems. The potential secretome of each  Frankia  strain comprised 4–5% of the total proteome, a lower percentage than that found in the genomes of other actinobacteria, legume endosymbionts, and plant pathogens. Hydrolytic enzymes made up only a small fraction of the total number of predicted secreted proteins in each strain. Surprisingly, polysaccharide-degrading enzymes were few in number, especially in strain CcI3, with more esterolytic, lipolytic and proteolytic enzymes having signal peptides. A total of 161 orthologous proteins belong to the core  Frankia  secretome. Of these, 52 also lack homologs in closely related actinobacteria, and are termed " Frankia- specific." The genes encoding these conserved secreted proteins are often clustered near secretion machinery genes.    Conclusion  The predicted secretomes of  Frankia  sp. are relatively small and include few hydrolases, which could reflect adaptation to a symbiotic lifestyle. There are no well-conserved secreted polysaccharide-degrading enzymes present in all three  Frankia  genomes, suggesting that plant cell wall polysaccharide degradation may not be crucial to root infection, or that this degradation varies among strains. We hypothesize that the relative lack of secreted polysaccharide-degrading enzymes in  Frankia  reflects a strategy used by these bacteria to avoid eliciting host defense responses. The esterases, lipases, and proteases found in the core  Frankia  secretome might facilitate hyphal penetration through the cell wall, release carbon sources, or modify chemical signals. The core secretome also includes extracellular solute-binding proteins and  Frankia -specific hypothetical proteins that may enable the actinorhizal symbiosis.

Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbionts