DNA in Bacteria (With Diagram)

In this article we will discuss about the organisation of DNA in bacteria.

The DNA of bacteria, e.g. E. coli, is a covalently closed circular molecule. It forms the bacterial chromosome, though this chromosome is much simpler in structure and in level of organization than the eukaryotic chromosomes of plants and animals. Also, each bacterial cell normally has a single chromosome containing a single circular DNA molecule.

In E.coli, the DNA molecule is 1,300 μm long when fully stretched containing some 4,700 x 10³ base-pairs which encode about 4,000 genes. In order to pack this long DNA molecule into a cell measuring only about 1 μm x 3 μm, the molecule has to be highly folded and supercoiled.

The prokaryotic chromosome — which is also called a nucleoid — consists of a number of loops which are held together by several proteins. For example, E. coli nucleoid has 45 (40-50) loops which radiate from a central protein core. Each loop is supercoiled (Fig. 9.8A). The supercoiled state of the loops of DNA can be removed by treatment with DNase which causes a single-stranded break (nick).

A single nick results in the uncoiling of a single loop without affecting the supercoiling of other loops (Fig. 9.8B). This shows that each loop is isolated from the other, although the ds-DNA molecule runs through all the loops. The association with proteins in the nucleoid core prevents unwinding of other loops. The E. coli chromosome needs some 45 nicks to remove all the supercoiled loops, thereby producing a closed circular ring.

A circular DNA molecule without any supercoiling is said to be in a relaxed state. In this state, the standard right-handed DNA-double helix contains about 10 nucleotide pairs per turn of the helix. If now one of the two strands is nicked and rotated through 360° to unwind one complete turn of the helix and the cut-ends are resealed, the circular DNA molecule may respond in either of the two following ways—It may produce a region of unpaired bases, called a bubble; or, alternatively it may twist in a direction opposite to that of unwinding to produce a negatively supercoiled circular DNA molecule.

The three states of circular DNA — relaxed, with bubble and negatively supercoiled — are diagrammatically shown in Fig. 9.9:

Negative supercoiling of ds-DNA is produced by a class of enzymes known as topoisomerases. The single stranded nick is generated by topoisomerase I producing a break or gap in the phosphodiester bond of the DNA strand. The intact complementary strand is passed through the gap and the nick is then resealed. Another class of topoisomerases, topoisomerase II, is also known as DNA- gyrase.

These enzymes induce double-stranded break in the phosphodiester bonds of both strands. This class of enzymes plays a vital role in DNA replication. By inducing breaks in both strands, the enzyme helps to pass an intact double-stranded DNA molecule or a part to pass through another.

Thus, when a circular DNA molecule replicates, the two daughter molecules may be interlocked like two rings of a chain. DNA gyrase can separate the two molecules by inducing a double-cut in one and allowing the other to pass through the gap which is then resealed.

DNA gyrase has a more important function in normal DNA replication. With the advancement of the replication fork a positive supercoiling develops in the un-replicated portion of the ds-DNA helix. To compensate the tension, DNA gyrase introduces negative supercoiling by nicking.