Bacterial DNA Replication

Bacterial DNA replication begins at a specific 245 base pair DNA sequence called OriC. The DNAA protein, which increases in concentration as the cell prepares for division, binds to specific 9 base pair repeats at OriC. This binding distorts the DNA, leading to the opening of adjacent 13 base pair repeats.

The opening in the DNA at OriC allows protein complexes, each consisting of DNA helicase (DNA B) and DNA helicase loader (DNA C), to enter the replication bubble and bind to the single-stranded DNA. The loaders open the helicase protein rings and place them around the DNA, then are released. The helicases use ATP hydrolysis to unwind the DNA helix at the two replication forks.

Each DNA helicase recruits DNA primase, which synthesizes an RNA primer on the DNA template. This RNA primer provides a 3'-hydroxyl group, essential for DNA polymerase to add new DNA nucleotides. DNA polymerase III, the main replication polymerase in E. coli, is then brought to the replication forks by clamp loaders, which also carry and place sliding clamps onto the DNA. The sliding clamp holds DNA polymerase III in position to synthesize new DNA.

DNA synthesis occurs in the 5' to 3' direction. The leading strand is synthesized continuously towards the replication fork. In contrast, due to the anti-parallel nature of the template strands, the lagging strand is built discontinuously in short fragments called Okazaki fragments. Single-strand DNA binding proteins coat and protect exposed single-stranded DNA regions, though they are omitted for simplicity in further explanations.

As DNA replication continues, DNA polymerase on the lagging strand disengages when it meets the 5' end of the next primer. After helicase moves about 1,000 bases, a new RNA primer is synthesized, and a new sliding clamp and DNA polymerase are added to begin synthesis on a new Okazaki fragment. This cycle repeats along the template.

The lagging strand consists of Okazaki fragments with RNA segments. An enzyme called RNAse H cleaves the RNA primers. DNA polymerase I then uses the 3'-OH group of the adjacent Okazaki fragment to fill in the gaps with DNA nucleotides. Finally, DNA ligase closes the remaining nicks, creating a continuous DNA molecule.

Through these coordinated steps, an E. coli chromosome is replicated simultaneously at two replication forks, proceeding around the entire circular molecule to produce two complete DNA copies.