The alphaproteobacterium Sinorhizobium fredii NGR234 has an exceptionally wide host range, as it forms nitrogen-fixing nodules with more legumes than any other known microsymbiont. Within its 6.9-Mbp genome, it encodes two N-acyl-homoserinelactone synthase genes (i.e., traI and ngrI) involved in the biosynthesis of two distinct autoinducer I-type molecules. Here, we report on the construction of an NGR234-⌬traI and an NGR234-⌬ngrI mutant and their genome-wide transcriptome analysis. A high-resolution RNA sequencing (RNA-seq) analysis of early-stationary-phase cultures in the NGR234-⌬traI background suggested that up to 316 genes were differentially expressed in the NGR234-⌬traI mutant versus the parent strain. Similarly, in the background of NGR234-⌬ngrI 466 differentially regulated genes were identified. Accordingly, a common set of 186 genes was regulated by the TraI/R and NgrI/R regulon. Coregulated genes included 42 flagellar biosynthesis genes and 22 genes linked to exopolysaccharide (EPS) biosynthesis. Among the genes and open reading frames (ORFs) that were differentially regulated in NGR234-⌬traI were those linked to replication of the pNGR234a symbiotic plasmid and cytochrome c oxidases. Biotin and pyrroloquinoline quinone biosynthesis genes were differentially expressed in the NGR234-⌬ngrI mutant as well as the entire cluster of 21 genes linked to assembly of the NGR234 type III secretion system (T3SS-II). Further, we also discovered that genes responsible for rhizopine catabolism in NGR234 were strongly repressed in the presence of high levels of N-acyl-homoserine-lactones. Together with nodulation assays, the RNA-seq-based findings suggested that quorum sensing (QS)-dependent gene regulation appears to be of higher relevance during nonsymbiotic growth rather than for life within root nodules.

Here we announce the complete genome sequence of the symbiotic and nitrogen-fixing bacterium Sinorhizobium fredii USDA257. The genome shares a high degree of sequence similarity with the closely related broad-host-range strains S. fredii NGR234 and HH103. Most strikingly, the USDA257 genome encodes a wealth of secretory systems. Sinorhizobium fredii USDA257 is a Gram-negative soil bacterium that fixes nitrogen in symbiosis with legume plants. It was originally isolated from wild soybean cultivars (1) and has an extremely broad host range, comprising 79 legume plant genera (4). Only the closely related S. fredii NGR234 strain reveals a wider host range, being able to nodulate 112 plant genera (4). Both strains are the best-studied model organisms with respect to host range. The analysis of the recently published complete genome of S. fredii NGR234 and the genome of the broad-host-range strain S. fredii HH103 suggested that these three strains share a high degree of synteny in their genomes (3,5,6). The complete genome sequence of USDA257 therefore significantly increases our knowledge of molecular mechanisms involved in the determination of host range in the interaction of plants with microbes.

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