1a). To reduce the number of sequences from the Rhodobacter genus, we only included one example of each group of sequences with a similarity value of 95% or more (see Table S1). When compared to a 16S-based
phylogeny (Fig. 1b), the RpoN-based tree shows no major changes in the branch distribution, suggesting an ancient origin of rpoN, at least within proteobacteria. Despite the low similarity level between the different copies of rpoN within the Rhodobacter group, all cluster together forming subgroups that correspond with their known or probable function and with their genomic context. This result supports the idea that the rpoN copies present in these strains are the result of several duplication events. Although a low number of sequences are FDA-approved Drug Library available, we tried to deduce the order in which the rpoN copies appeared. To do this, we looked at their distribution in the 16S rRNA gene-based tree (Fig. 1b). The presence of rpoN1 in all the strains Buparlisib manufacturer suggests that this may be the ancestral rpoN gene. If only duplication and deletion events are invoked, rpoN3 would be the first duplicated copy to appear,
because it is present in the early branching Rhodobacter sp. SW2. The R. capsulatus/blasticus group would have lost the rpoN3 gene after its separation from the R. sphaeroides clade and two new duplication events, first within the R. sphaeroides group and finally in the R. sphaeroides 2.4.1/17029 group, led to the appearance of rpoN2 and rpoN4, respectively. Alternatively, all the duplications may have occurred within the R. sphaeroides cAMP clade followed by HGT of rpoN3 to Rhodobacter sp. However, the distribution of the branches within the rpoN3 clade (Fig. 1a) resembles the 16S-based tree, indicating a linear inheritance of this gene. An interesting case is the phylogeny of RpoN1, where the R. capsulatus/blasticus group branches off from the rest of the species. This may be indicative of a different
selective pressure on the rpoN genes of these species, where a single copy of this gene is present. Our results allowed us to establish the genetic context of the rpoN genes sequenced in this work and to compare it with the genetic context of the rpoNs from fully sequenced genomes. As shown in Fig. 2, the rpoN gene from Rv. sulfidophilum is located downstream of the fixCX genes and upstream of a gene similar to hcpH/hpaI (potentially encoding a 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase), whereas in R. blasticus, the rpoN gene is flanked by fixCX and nifA, suggesting that the rpoN genes present in these bacteria are involved in nitrogen fixation. The genomic context of the rpoN1 and 2 genes identified in R. azotoformans is identical to that observed in R. sphaeroides 2.4.1., WS8, KD131, ATCC17029, and ATCC17025. In these bacteria, rpoN1 is flanked by nifW and a gene encoding a conserved hypothetical protein (DUF1810).