Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid

Background: The genome DNA of Escherichia coli is folded into the nucleosom e-like structure, often called a nucleoid, by the binding of several DNA-bi nding proteins. We previously determined the specificity and affinity of DN A-binding for 12 species of the E. coli DNA-binding protein, and their intr acellular concentrations at various growth phases. The intracellular locali zation of these proteins in E. coli could be predicted from these data, but no attempt;has been made thus far to directly observe the intracellular di stribution of the DNA-binding proteins. Results: The intracellular localization in Escherichia coli of 10 species o f the nucleoid-associated protein, three components of the transcription ap paratus, and three components of the translation machinery was investigated by indirect immune-fluorescence microscopy. The DNA-binding proteins could be classified into two groups. The group-I proteins, including the major n ucleoid-structural proteins, H-NS, HU, IHF, StpA and Dps, are distributed u niformly within the entire nucleoid. In contrast, the group-II proteins, wh ich are presumed to possess regulatory activities of DNA functions accumula te at specific loci within the nucleoid, forming 2 (SeqA), 3-4 (CbpA and Cb pB) and 6-10 (Fis and IciA) immune-stained dots. Each immunostained dot may represent either the association of a hundred to one thousand molecules of each DNA-binding protein at a specific locus of the genome DNA or the asse mbly of protein-associated DNA segments from different domains of the folde d genome. Both the RNA polymerase core enzyme and the sigma(70) subunit are mainly associated with the nucleoid, but the anti-sigma(70) factor (Rsd) a ppears to be accumulated at the boundary between the nucleoid and the cytos ol in the stationary-phase cells. Here we show that the majority of Hfq is present in cytoplasm together with ribosomal proteins L7/L12 and RME. Conclusion: The DNA-binding proteins of E. coli could be classified into tw o groups. One group proteins was distributed uniformly within the nucleoid, but the other group of proteins showed an irregular distribution, forming immune-stained spots or clumps.