title: Comparative genomics reveals 'novel' Fur regulated sRNAs and coding genes in diverse proteobacteria.
abstract: 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.
authors.affiliation: UGC-Networking Resource Centre in Biological Sciences, Madurai Kamaraj University, Madurai-625021, India. jsridhar@nrcbsmku.org
authors.forename: Jayavel
authors.initials: J
authors.lastname: Sridhar
authors.forename: Radhakrishnan
authors.initials: R
authors.lastname: Sabarinathan
authors.forename: Paramasamy
authors.initials: P
authors.lastname: Gunasekaran
authors.forename: Kanagaraj
authors.initials: K
authors.lastname: Sekar
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D001483:Base Sequence; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D053858:Metabolic Networks and Pathways / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics*; D020560:Proteobacteria / Q000235:genetics* / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000235:genetics*; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D012680:Sensitivity and Specificity; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D058727:RNA, Small Untranslated; D012097:Repressor Proteins; C068477:ferric uptake regulating proteins, bacterial