Control of RNA Structure by CspA Proteins in Rhizobia
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Rhizobia are soil bacteria that can associate with some legumes and participate in symbiotic nitrogen fixation. Bacterial CspA family members are small, single stranded nucleic acid binding proteins conserved throughout all domains of life. Here, the role of CspA family proteins in the symbiotic development of Sinorhizobium meliloti with Medicago sativa (alfalfa) is investigated. Expression and genetic deletion strain analysis revealed that CspA family proteins are differentially expressed in symbiosis and contribute to symbiotic effectiveness. RNAseq analysis of native co-immunoprecipitated RNAs identified a novel interaction between several CspA family proteins and the αR14 family of small non-coding RNA (sRNAs). Whole transcriptome analysis defined transcriptional defects associated with loss of CspA function. The development of a new in vitro RNA binding assay using broccoli, a Green Fluorescent Protein (GFP) RNA mimic, is described as well as its use in defining binding specificity of CspA family proteins with synthetic and native αR14 family sRNA structures. This work concludes that CspA family proteins interact with and influence the stability of specific RNA structures and these interactions control RNA regulated processes important for symbiotic development.