Significant Natural Product Biosynthetic Potential of Actinorhizal Symbionts of the Genus Frankia, as Revealed by Comparative Genomic and Proteomic Analyses

Abstract

Bacteria of the genus Frankia are mycelium-forming actinomycetes that are found as nitrogen-fixing facultative symbionts of actinorhizal plants. Although soil-dwelling actinomycetes are well-known producers of bioactive compounds, the genus Frankia has largely gone uninvestigated for this potential. Bioinformatic analysis of the genome sequences of Frankia strains ACN14a, CcI3, and EAN1pec revealed an unexpected number of secondary metabolic biosynthesis gene clusters. Our analysis led to the identification of at least 65 biosynthetic gene clusters, the vast majority of which appear to be unique and for which products have not been observed or characterized. More than 25 secondary metabolite structures or structure fragments were predicted, and these are expected to include cyclic peptides, siderophores, pigments, signaling molecules, and specialized lipids. Outside the hopanoid gene locus, no cluster could be convincingly demonstrated to be responsible for the few secondary metabolites previously isolated from other Frankia strains. Few clusters were shared among the three species, demonstrating species-specific biosynthetic diversity. Proteomic analysis of Frankia sp. strains CcI3 and EAN1pec showed that significant and diverse secondary metabolic activity was expressed in laboratory cultures. In addition, several prominent signals in the mass range of peptide natural products were observed in Frankia sp. CcI3 by intact-cell matrix-assisted laser desorption-ionization mass spectrometry (MALDI-MS). This work supports the value of bioinformatic investigation in natural products biosynthesis using genomic information and presents a clear roadmap for natural products discovery in the Frankia genus.

Antibiotics from neglected bacterial sources

“…With the completion of many bacterial genome sequences, it has become evident that many more bacteria than previously thought have the ability to produce secondary metabolites (Donadio et al, 2007;Letzel et al, 2012;Udwary et al, 2011). Furthermore, even well-studied producer organisms have been shown to have more genes for secondary metabolite production than there are currently described natural products.…”

Mining for Microbial Gems: Integrating Proteomics in the Postgenomic Natural Product Discovery Pipeline

“…Some of these were smaller than 200 kDa and contained no domains that could be detected using molecular probes. This approach was applied successfully to analyze the NP‐producing potential of nitrogen‐fixing Frankia species …”

The Beat

“…A new study shows these bacteria have the genetic capacity to produce products such as antibiotics, herbicides, and anticancer agents 7 . Researchers used bioinformatic analysis of three strains of Frankia to identify dozens of biosynthetic gene clusters—that is, genes used by Frankia to manufacture the compounds it needs to survive and thrive.…”