Transcriptome profiling of a Rhizobium leguminosarum bv. trifolii rosR mutant reveals the role of the transcriptional regulator RosR in motility, synthesis of cell-surface components, and other cellular processes.

Kamila Rachwał,Monika Janczarek,Ewa Matczyńska

doi:10.1186/s12864-015-2332-4

Abstract

BackgroundRhizobium leguminosarum bv. trifolii is a soil bacterium capable of establishing a symbiotic relationship with red clover (Trifolium pratense). The presence of surface polysaccharides and other extracellular components as well as motility and competitiveness are essential traits for both adaptation of this bacterium to changing environmental conditions and successful infection of host plant roots. The R. leguminosarum bv. trifolii rosR gene encodes a protein belonging to the family of Ros/MucR transcriptional regulators, which contain a Cys2His2-type zinc-finger motif and are involved in the regulation of exopolysaccharide synthesis in several rhizobial species. Previously, it was established that a mutation in the rosR gene significantly decreased exopolysaccharide synthesis, increased bacterial sensitivity to some stress factors, and negatively affected infection of clover roots.ResultsRNA-Seq analysis performed for the R. leguminosarum bv. trifolii wild-type strain Rt24.2 and its derivative Rt2472 carrying a rosR mutation identified a large number of genes which were differentially expressed in these two backgrounds. A considerable majority of these genes were up-regulated in the mutant (63.22 %), indicating that RosR functions mainly as a repressor. Transcriptome profiling of the rosR mutant revealed a role of this regulator in several cellular processes, including the synthesis of cell-surface components and polysaccharides, motility, and bacterial metabolism. Moreover, it was established that the Rt2472 strain was characterized by a longer generation time and showed an increased aggregation ability, but was impaired in motility as a result of considerably reduced flagellation of its cells.ConclusionsThe comparative transcriptome analysis of R. leguminosarum bv. trifolii wild-type Rt24.2 and the Rt2472 mutant identified a set of genes belonging to the RosR regulon and confirmed the important role of RosR in the regulatory network. The data obtained in this study indicate that this protein affects several cellular processes and plays an important role in bacterial adaptation to environmental conditions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2332-4) contains supplementary material, which is available to authorized users.

Highlights

Rhizobium leguminosarum bv. trifolii is a soil bacterium capable of establishing a symbiotic relationship with red clover (Trifolium pratense)
RNA-Seq analysis of the wild-type strain Rt24.2 and its derivative rosR mutant Rt2472 Our previous studies of R. leguminosarum bv. trifolii rosR had suggested that this gene could play a global regulatory role in the functioning of rhizobial cells
The sequence of Rt24.2 was compared with genomes of closely related rhizobial strains

Summary

Introduction

Rhizobium leguminosarum bv. trifolii is a soil bacterium capable of establishing a symbiotic relationship with red clover (Trifolium pratense). Rhizobia are a unique group of bacteria which can either exist as free-living organisms in soil or establish a nitrogen-fixing symbiosis with legumes [1, 2] This type of plant–microbe interaction is essential for the functioning of the biosphere, since it provides nutrients to plants and increases soil fertility and field crops. Before rhizobia can find a compatible host plant, they often must survive long periods of time as free-living bacteria in the soil In such periods, rhizobial cells are exposed to the action of environmental factors such as nutrient limitation, pH, salinity, drought, temperature variation, heavy metals, and oxidative stress [3,4,5,6,7,8,9]. NP, cellulose fibrils, and LPS are required for attachment to and biofilm formation on soil particles and plant roots, as well as successful infection of the host plant and adaptation to the conditions prevailing inside the nodule, a specific organ formed on legume roots [13,14,15,16,17]

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