Genomic Insights Into Plant-Growth-Promoting Potentialities of the Genus Frankia

Abstract

This study was designed to determine the plant growth promoting (PGP) potential of members of the genus <i>Frankia</i>. To this end, the genomes of 21 representative strains were examined for genes associated directly or indirectly with plant growth. All of the <i>Frankia</i> genomes contained genes that encoded for products associated with the biosynthesis of auxins [indole-3-glycerol phosphate synthases, anthranilate phosphoribosyltransferases (<i>trp</i>D), anthranilate synthases, and aminases (<i>trp</i>A and B)], cytokinins (11 well-conserved genes within the predicted biosynthetic gene cluster), siderophores, and nitrogenases (<i>nif</i> operon except for atypical <i>Frankia</i>) as well as genes that modulate the effects of biotic and abiotic environmental stress (e.g., alkyl hydroperoxide reductases, aquaporin Z, heat shock proteins). In contrast, other genes were associated with strains assigned to one or more of four host-specific clusters. The genes encoding for phosphate solubilization (e.g., low-affinity inorganic phosphate transporters) and lytic enzymes (e.g., cellulases) were found in <i>Frankia</i> cluster 1 genomes, while other genes were found only in cluster 3 genomes (e.g., alkaline phosphatases, extracellular endoglucanases, pectate lyases) or cluster 4 and subcluster 1c genomes (e.g., NAD(P) transhydrogenase genes). Genes encoding for chitinases were found only in the genomes of the type strains of <i>Frankia casuarinae</i>, <i>F. inefficax</i>, <i>F. irregularis</i>, and <i>F. saprophytica</i>. In short, these <i>in silico</i> genome analyses provide an insight into the PGP abilities of <i>Frankia</i> strains of known taxonomic provenance. This is the first study designed to establish the underlying genetic basis of cytokinin production in <i>Frankia</i> strains. Also, the discovery of additional genes in the biosynthetic gene cluster involved in cytokinin production opens up the prospect that <i>Frankia</i> may have novel molecular mechanisms for cytokinin biosynthesis.