Comparative genomics reveals ‘novel’ Fur regulated sRNAs and coding genes in diverse proteobacteria

Ferric uptake regulator (Fur) is a transcriptional regulator controlling the expression of genes involved in iron homeostasis and plays an important role in pathogenesis. Fur-regulated sRNAs/CDSs were found to have upstream Fur Binding Sites (FBS). We have constructed a Positional Weight Matrix from 100 known FBS (19 nt) and tracked the ‘Orphan’ FBSs. Possible Fur regulated sRNAs and CDSs were identified by comparing their genomic locations with the ‘Orphan’ FBSs identified. Thirty-eight ‘novel’ and all known Fur regulated sRNAs in nine proteobacteria were identified. In addition, we identified high scoring FBSs in the promoter regions of the 304 CDSs and 68 of them were involved in siderophore biosynthesis, iron-transporters, two-component system, starch/sugar metabolism, sulphur/methane metabolism, etc. The present study shows that the Fur regulator controls the expression of genes involved in diverse metabolic activities and it is not limited to iron metabolism alone.

► Methodology for PWM construction from proteobacteria specific Fur Binding sites ► Training set was validated by retaining the known Fur regulated RyhB/NrrF sRNAs ► Fur regulon identified in nine bacteria with 38 ‘novel’ sRNAs and 304 CDSs ► Predicted Fur regulon compared with earlier reports ► 68/304 CDSs involve in many metabolic pathways and proved Fur as global regulator