Research Article: Osmotic stress activates nif and fix genes and induces the Rhizobium tropici CIAT 899 Nod factor production via NodD2 by up-regulation of the nodA2 operon and the nodA3 gene

Date Published: March 27, 2019

Publisher: Public Library of Science

Author(s): Pablo del Cerro, Manuel Megías, Francisco Javier López-Baena, Antonio Gil-Serrano, Francisco Pérez-Montaño, Francisco Javier Ollero, Marie-Joelle Virolle.


The symbiosis between rhizobia and legumes is characterized by a complex molecular dialogue in which the bacterial NodD protein plays a major role due to its capacity to activate the expression of the nodulation genes in the presence of appropiate flavonoids. These genes are involved in the synthesis of molecules, the nodulation factors (NF), responsible for launching the nodulation process. Rhizobium tropici CIAT 899, a rhizobial strain that nodulates Phaseolus vulgaris, is characterized by its tolerance to multiple environmental stresses such as high temperatures, acidity or elevated osmolarity. This strain produces nodulation factors under saline stress and the same set of CIAT 899 nodulation genes activated by inducing flavonoids are also up-regulated in a process controlled by the NodD2 protein. In this paper, we have studied the effect of osmotic stress (high mannitol concentrations) on the R. tropici CIAT 899 transcriptomic response. In the same manner as with saline stress, the osmotic stress mediated NF production and export was controlled directly by NodD2. In contrast to previous reports, the nodA2FE operon and the nodA3 and nodD1 genes were up-regulated with mannitol, which correlated with an increase in the production of biologically active NF. Interestingly, in these conditions, this regulatory protein controlled not only the expression of nodulation genes but also the expression of other genes involved in protein folding and synthesis, motility, synthesis of polysaccharides and, surprinsingly, nitrogen fixation. Moreover, the non-metabolizable sugar dulcitol was also able to induce the NF production and the activation of nod genes in CIAT 899.

Partial Text

Legume plants can establish a symbiotic interaction with a group of soil bacteria, known as rhizobia, that fix atmospheric nitrogen in specialized root organs called nodules. This process requires a complex and evolved molecular dialogue between both organisms, which is initiated by the exudation of plant flavonoids [1]. These molecules are recognized by the NodD protein, a bacterial transcriptional regulator that binds to specific promoter sequences denominated nod boxes (NB), activating the expression of the nodulation (nod) genes. Proteins encoded by these genes are responsible for the synthesis and export of specific rhizobial lipochitooligosaccharides, also called Nod factors (NF) [2,3], whose recognition by the host plant triggers both rhizobial infection and initiation of nodule organogenesis [4]. Interestingly, in Rhizobium tropici CIAT 899 (hereafter CIAT 899), a broad host-range strain microsymbiont of Phaseolus vulgaris (common bean), the synthesis and export of NF is not only triggered by inducing flavonoids but also by acidity or high concentrations of salt [5–7]. The analysis of the CIAT 899 genome indicates that this bacterium harbours in the symbiotic plasmid three different nodA genes and five different nodD genes, which are responsible for the CIAT 899 capacity to produce a large variety of NF under different environmental conditions [8–11].

The osmolarity of the environment is one of the physical parameters that determines the capacity of organisms to proliferate in different habitats [38]. Our RNA-seq analysis revealed different genomic traits related to osmotic-stress tolerance in R. tropici CIAT 899 (Figs 1 and 2). Similar patterns of transcriptomic responses have been previously described for other bacteria in response to different abiotic-stresses. Common DEG encode proteins involved in the correct folding of proteins, chemotaxis, accumulation of organic osmolytes like glycerol, production of cyclic β-(1, 2)-glucans, transcription and translation or in the generation of energy (S2 File) [14,39–43].




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