Wild nodules can be broken: proteomics of Frankia in field-collected root nodules

Abstract

With the genomes of three Frankia strains available, high-throughput proteomics methods can be used to reveal the set of proteins expressed by these bacteria in symbiosis with plants. A question we address is the degree to which the known genomes can be used to study proteomes of uncharacterized frankiae growing in field-collected root nodules. To this end, we have characterized the symbiotic proteomes of Frankia from three plant species, Alnus incana subsp. rugosa, Ceanothus americanus, and Elaeagnus angustifolia. Root nodule proteins were identified using two-dimensional liquid chromatography coupled to tandem mass spectrometry (LC MS/MS) of trypsin-digested protein samples. We identified 1300 Frankia proteins in A. incana nodules using the Frankia alni ACN14a genome and 1100 proteins from E. angustifolia nodules using the EAN1pec genome. In addition, over 100 proteins were identified from C. americanus nodules using a more limited one dimensional LC MS/MS analysis. Many of the most abundant proteins identified are involved in energy and nitrogen metabolism. The enzyme nitrogenase and the nitrogenase iron protein were among the most abundant proteins, reflecting the major process occurring in symbiosis. Several hundred plant proteins were also identified. We highlight the power of proteomics to uncover the physiology of symbiotic Frankia in the environment using heterologous genome information.

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

“…CcI3, of which three (FC03, FC12, and FC19) contained two or more protein hits with two peptide identifications per protein. Furthermore, other transcriptome and proteome studies show expression of some of these biosynthetic clusters (1,3,5,33,34,44). These data together indicate that Frankia has both the genetic capacity and the biosynthetic capacity to produce secondary metabolites.…”

“…43 Mb for the narrow-host-range Frankia strain CcI3 to 7.50 Mb for the medium-host-range Frankia strain ACN14a (ACN) to 8.98 Mb for the broad-host-range Frankia strain EAN1pec (EAN). Since the elucidation of these Frankia genomes, bioinformatic approaches have illuminated codon usage patterns (47), predicted secretosome profiles (35), and led to genomeguided studies on the Frankia transcriptome (3,44) and proteome (1,5,33,34). Genome mining also provides an opportunity to identify important physiology and metabolic functions, including secondary metabolism.…”

Postgenomic Analyses Reveal Development of Infectious Anaplasma phagocytophilum during Transmission from Ticks to Mice

“…We used the genome of A. phagocytophilum strain HZ as a reference genome to identify peptides and transcripts from our salivary gland isolate, collected in Connecticut and infectious to both mice and humans (see Materials and Methods). Reference genomes are very useful for unsequenced strains, as previously shown for other host-associated bacteria (26). By direct sampling of tick salivary glands, our analysis complements culture-based studies and identifies additional proteins that may be particularly important for survival during transmission to mammalian hosts.…”

Life in soil by the actinorhizal root nodule endophyte Frankia. A review

“…Hopefully this will facilitate finding the requirements for in vitro growth in those cases where isolation of Frankia from nodules so far has failed. In order to understand the potential of Frankia to synthesize and respond to plant signals related to the interaction and recognition with the host root, Frankia genomes are also subject to proteomics experiments, i.e., to search for genes that are differentially expressed in nodules or in the presence of root exudates, in order to investigate the communication system and the genetic basis of molecular interactions in actinorhizal symbioses Bagnarol et al 2007;Mastronunzio and Benson 2010).…”