A Combined Omics Approach to Elucidate the Molecular Interplay behind a Beneficial Arabidopsis-Caulobacter...

Plants rely on complex signaling networks to interact with beneficial plant growth-promoting rhizobacteria (PGPR). Among these microbes, Caulobacter RHG1 is recognized by Arabidopsis thaliana roots via specific receptor-like kinases (RLKs), but the molecular mechanisms underlying the plant growth-promotion effect remain largely unknown. To investigate these mechanisms, we used an integrative approach combining proteomics and phosphoproteomics. Our phosphoproteome analysis revealed that RHG1 triggers a range of signaling events, involving two RLKs (LysM RLK1-INTERACTING KINASE 1 [LIK1] and an uncharacterized RLK, AT5G49770). Notably, via the proteome analysis, we revealed that upon RHG1 treatment, defense proteins are downregulated early. Later on, developmental processes, such as ribosome biogenesis and maturation, might lead to enhanced cell division and/or activity to promote growth. Our findings suggest that RHG1 triggered phosphorylation-based signaling pathways, resulting in the timely modulation of defense and developmental processes, which eventually lead to plant growth promotion. Our data, combined with that of previous reports, suggest that RHG1 activates a broad network of regulatory mechanisms that extend beyond a single pathway. Understanding the mechanisms behind such beneficial plant-microbe interactions can pave the way for more effective commercialization of PGPR-based agricultural products.