A rhizobial non-coding RNA has an effect on symbiotic nodulation by regulating an ABC transporter

Rhizobium leguminosarum has been widely used as a model to study nodule biochemistry, its genomic sequence has been published. We screened the Rhizobium leguminosarum bv. viciae 3841 genome sequence using a bioinformatics analysis for discovering potential small non-coding RNAs. One of these identified non-coding RNAs, cis-encoded antisense RLS1, was found to affect the symbiotic nodulation and nitrogen fixation. The mature form of RLS1 was 258 nt of non-coding RNA, its disruption mutant strain (△RLS1) caused that the nodulation stages were delayed dramatically and the total number of nodules decreased, leading to a 25% reduction in the total amount of nitrogen fixed in the symbiotic system of Rhizobium- Pisum sativum, compared with wild-type strain. RLS1 targets an ABC transporter mRNA, bind to Hfq in vitro, and to be stable in the absence of Hfq. Further analysis showed that Hfq is not required for interactions between RLS1 and its target mRNAs. △RLS1 strain exhibited that its production of extracellular polysaccharide (EPS) was over three times higher than in wild-type strain. The findings suggest that RLS1 might affect nodulation by participating in the regulatory network for EPS accurate secretion, playing a pivotal role in the infection process and in root nodule formation.