IscR regulon.
Expression of the Fe-S cluster biogenesis operons isc and suf in α-proteobacteria is repressed by the Fe-S cluster–containing transcription factor IscR [39] and the latter operon is also negatively regulated by Fur [51]. The suf gene loci in the Rhizobiales genomes are the predicted (and in the case of R. leguminosarum, validated) members of the RirA and Irr regulons. Unusually, these genomes lack an ortholog of the IscR repressor. However, the chromosomal clusters of suf genes in all other γ-proteobacteria, including obligate pathogenic Rickettsia, include an iscR homolog, allowing us to propose that the IscR-dependent mechanism of regulation is conserved in these species.
On the phylogenetic tree of the IscR subfamily there are two separate branches of α-proteobacterial IscR-like proteins (Figure 3B). The IscRα-I group is most similar to IscR proteins from γ-and β-proteobacteria, and the respective suf loci are preceded by a 19-bp palindromic motif that resembles the IscR-binding motif from α-proteobacteria [39] (Table S7; Figure 4E). The IscRα-II group, seen in four Sphingomonadales species and G. oxydans, is quite diverged from the IscRα-I group, and the predicted DNA recognition motif for the second group has only limited similarity to the IscRα-I motif (Figure 4E and 4F).