Proteome Analysis Reveals a Significant Host-Specific Response in Rhizobium leguminosarum bv. viciae Endosymbiotic Cells

The Rhizobium-legume symbiosis is a beneficial interaction in which the bacterium converts atmospheric nitrogen into ammonia and delivers it to the plant in exchange for carbon compounds. This symbiosis implies the adaptation of bacteria to live inside host plant cells. In this work, we apply RP-LC-MS/MS and isobaric tags as relative and absolute quantitation techniques to study the proteomic profile of endosymbiotic cells (bacteroids) induced by Rhizobium leguminosarum bv viciae strain UPM791 in legume nodules. Nitrogenase subunits, tricarboxylic acid cycle enzymes, and stress–response proteins are among the most abundant from over 1000 rhizobial proteins identified in pea (Pisum sativum) bacteroids. Comparative analysis of bacteroids induced in pea and in lentil (Lens culinaris) nodules revealed the existence of a significant host-specific differential response affecting dozens of bacterial proteins, including stress-related proteins, transcriptional regulators, and proteins involved in the carbon and nitrogen metabolisms. A mutant affected in one of these proteins, homologous to a GntR-like transcriptional regulator, showed a symbiotic performance significantly impaired in symbiosis with pea but not with lentil plants. Analysis of the proteomes of bacteroids isolated from both hosts also revealed the presence of different sets of plant-derived nodule-specific cysteine-rich peptides, indicating that the endosymbiotic bacteria find a host-specific cocktail of chemical stressors inside the nodule. By studying variations of the bacterial response to different plant cell environments, we will be able to identify specific limitations imposed by the host that might give us clues for the improvement of rhizobial performance. [Display omitted] •LC-MS/MS proteome of Rhizobium bacteroids in pea and lentil nodules.•Legume host affects the presence of multiple rhizobial proteins in nodule bacteroids.•A pea-specific GntR-like regulator contributes to symbiosis in pea nodules.•Different profiles of plant-derived NCR peptides in pea and lentil bacteroids. Comparison of proteomes from nodule bacteroids produced by a single Rhizobium leguminosarum strain in two different hosts (pea and lentil) reveals the existence of dozens of host-specific rhizobial proteins in the endosymbiotic cells, thus suggesting the requirement of rhizobia to adapt to different cellular environments. Host-specific sets of plant-derived nodule-specific cysteine-rich peptides were also found in the