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PLoS One. 2015 May 28;10(5):e0127630. doi: 10.1371/journal.pone.0127630. eCollection 2015.

Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant.

Author information

1
Department of Ecology, Environment and Plant Sciences, Lilla Frescati, Stockholm University, 106 91, Stockholm, Sweden.
2
Department of Plant Sciences, University of California Davis, Davis, California, 95616, United States of America.
3
Department of Biology, Colorado State University, Pueblo, Colorado, 81001, United States of America.
4
Université Lyon 1, Université Lyon, CNRS, Ecologie Microbienne UMR5557, 69622, Villeurbanne Cedex, France.
5
Department of Biomedical Engineering, University of California Davis, Davis, California, 95616, United States of America; UC Davis Genome Center, University of California Davis, Davis, California, 95616, United States of America.
6
UC Davis Genome Center, University of California Davis, Davis, California, 95616, United States of America.
7
Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710, Reynosa, Tamaulipas, Mexico.
8
Genoscope, Évry, France.

Abstract

Frankia strains are nitrogen-fixing soil actinobacteria that can form root symbioses with actinorhizal plants. Phylogenetically, symbiotic frankiae can be divided into three clusters, and this division also corresponds to host specificity groups. The strains of cluster II which form symbioses with actinorhizal Rosales and Cucurbitales, thus displaying a broad host range, show suprisingly low genetic diversity and to date can not be cultured. The genome of the first representative of this cluster, Candidatus Frankia datiscae Dg1 (Dg1), a microsymbiont of Datisca glomerata, was recently sequenced. A phylogenetic analysis of 50 different housekeeping genes of Dg1 and three published Frankia genomes showed that cluster II is basal among the symbiotic Frankia clusters. Detailed analysis showed that nodules of D. glomerata, independent of the origin of the inoculum, contain several closely related cluster II Frankia operational taxonomic units. Actinorhizal plants and legumes both belong to the nitrogen-fixing plant clade, and bacterial signaling in both groups involves the common symbiotic pathway also used by arbuscular mycorrhizal fungi. However, so far, no molecules resembling rhizobial Nod factors could be isolated from Frankia cultures. Alone among Frankia genomes available to date, the genome of Dg1 contains the canonical nod genes nodA, nodB and nodC known from rhizobia, and these genes are arranged in two operons which are expressed in D. glomerata nodules. Furthermore, Frankia Dg1 nodC was able to partially complement a Rhizobium leguminosarum A34 nodC::Tn5 mutant. Phylogenetic analysis showed that Dg1 Nod proteins are positioned at the root of both α- and β-rhizobial NodABC proteins. NodA-like acyl transferases were found across the phylum Actinobacteria, but among Proteobacteria only in nodulators. Taken together, our evidence indicates an Actinobacterial origin of rhizobial Nod factors.

PMID:
26020781
PMCID:
PMC4447401
DOI:
10.1371/journal.pone.0127630
[Indexed for MEDLINE]
Free PMC Article

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