Anaerobiosis-induced novel nucleoid protein of Escherichia coli: Architectural role in genome DNA compaction

A systematic search has been performed for DNA-binding sequences recognized by YgiP, an uncharacterized transcription factor of Escherichia coli, using the newly developed Genomic SELEX. By SELEX-clos procedure, a total of 333 sequences have been isolated from a total of 126 loci of the E. coli genome while more than 703 YgiP-binding loci have been identified after the genome-wide profiling by SELEX-chip procedure. Gel mobility shift assay indicated the presence of multiple YgiP-binding sites along each SELEX DNA fragment while DNase-I foot-printing assay indicated protection of short-specific sequences by YgiP, together suggesting YgiP as a nucleoid protein with broad specificity of DNA binding. Atomic force microscope (AFM) observation indicated that at low concentrations, YgiP binds to various sites in non-specific manner, but at high concentrations, YgiP covers the entire DNA surface. The intracellular level of YgiP was found to be very low in steady-state of cell growth under aerobic conditions, but increased more than 100-fold to the level as high as those of HU and IHF under hypoxic or anaerobic culture conditions. An E. coli mutant lacking ygiP showed abnormal growth under anaerobic conditions. Taken together we conclude that YgiP is a novel nucleoid protein of E. coli under the anaerobic conditions, and thus propose to rename YgiP to Dan (DNA-binding protein under anaerobic conditions).