DNA supercoiling and protein binding in the E. coli chromosome
As discussed earlier, the DNA of the E. coli chromosome is highly negatively supercoiled due to the action of the DNA gyrase enzyme (Section 3.2). This negative supercoiling serves to assist in compaction of the DNA, with the repulsive forces of the sugar-phosphate backbones being counteracted by polyamines. Many of the proteins that are major components of the chromosome play roles in both its packaging and in the metabolic processes that take place on the DNA. These proteins are often called the ‘histone-like’ proteins, not because of any sequence similarity to the eukaryotic histone proteins, but because, like the histones, they are small, basic (and therefore positively charged) DNA-binding proteins. Three such proteins, called HU, H-NS and IHF, are shown in Figure 26. We will describe briefly their roles in DNA packaging in E. coli.
The HU, H-NS and IHF proteins all function as dimers. The HU and H-NS proteins both interact with chromosomal DNA non-specifically and serve to stabilise negative supercoils in the DNA. Whilst they do not bind DNA in a sequence-specific manner, both these proteins show some preference for binding DNA that has a ‘bendable’ structure. The HU protein is one of the most common proteins on the E. coli chromosome and it plays a central role in stabilising the compacted chromosome structure. An E. coli contains approximately 20 000 molecules of the H-NS protein, which binds approximately once every 300–400 bp along the chromosome. HU and H-NS help compact the DNA strand, but each also plays supporting roles in replication and transcription by establishing or maintaining appropriate structural and torsional environments for these processes.
The IHF dimer binds DNA such that two central helices cross at the core of the structure, as shown in Figure 26b. Note how the two separate subunits cross over and two ‘fingers’ extend around the DNA strand into the minor groove. Binding of IHF induces almost a 180° bend in the DNA over a 40 bp region – one of the largest DNA bends induced by any DNA binding protein identified to date. Rather like TBP, IHF utilises two hydrophobic residues (in this case, prolines), which are located on the tips of these fingers, to intercalate between bases. In forming hydrophobic bonds with the bases, the proline residues disrupt the base stacking of the DNA. Numerous positively charged residues that contribute to the bending process lie along the body of the protein. Bends in DNA such as those introduced by HU, H-NS and IHF assist in chromosome compaction.