«Promoter islands» of the E. coli genome as targets for sorption of the RNA processing enzymes

Abstract

In this work, a comparative analysis of proteins capable of interaction with the DNA fragments
taken from the promoter-enriched genomic regions of E. coli («promoter islands») and two regulatory
regions located upstream the dps, yjjM (lgoR) and yjjN (lgoD) genes was undertaken. Corresponding DNA
fragments were immobilised on streptavidin-coated magnetic beads and used for sorption of proteins from
cell lysate. After removal of the unbound polypeptides, proteins were eluted and used for electrophoretic
fractionation. As expected, several polypeptides showed specific affinity to each of studied promoter regions,
reflecting the features of their regulation. Surprisingly, two proteins with RNA processing potentiality
(RNAse Rnr and RNA-helicase SrmB) and the component of degradosome (RNA-helicase RhlB) were also
indentified in the complexes with “promoter islands”. The protein with electrophoretic mobility
corresponding to Rnr was also found in the other samples but with lower abundance. Suggesting the
possibility of continuous presence of processive RNase on the genome, this fact is also indicative of its
enhanced affinity to the promoter-enriched regions that can be mediated by the availability of key substrates
for this enzyme.