When damage to DNA is sensed, the SOS signal induces over 20 unlinked genes. These genes cope with the DNA damage by remairing the damaged DNA, allowing DNA replication to proceed past the damaged site (translesion synthesis), and stalling cell division to allow time for DNA repair. Normally, the SOS response system is suppressed by down regulating the SOS genes. This process is governed by a master repressor protein called LexA.
Damage to DNA is dected when DNA polymerase encounters a lesion during DNA replication. This causes replication to stop, which leaves a tract of single stranded DNA exposed without being replicated. Since ssDNA is prone to attack, the cell covers the exposed DNA with a protein termed RecA, which starts binding at the 3’ end. The RecA-DNA complex causes LexA to bind and cleave. After enough LexA is broken, the repair genes are expressed. SOS genes have LexA boxes at their promoters. The LexA boxes have slight differences in sequence, and therefore slight differences in their affinity for LexA. Genes with weak affinity for LexA get expressed earlier than genes with strong affinity for LexA, thereby allowing a cascade of gene expression based on the amount of LexA present (which is directly tied to the amount of RecA-DNA complex, which is directly caused by the amount of single strand DNA exposed, which is a measure of the DNA damage).
Some of the earliest genes expressed in response to damage are the uvr genes, which encode for nucleotide excision repair (NER). These proteins detect damage on a single strand of DNA, and excise the damaged area, along with bases on either side of the damage. The gap is filled in by DNA polymerases, which leave the DNA intact and replication can continue. Most lesions are fixed in this manner.
If NER is insufficient to repair the damage, then RecA carries out recombination. The RecA-DNA complex formed at the first sign of damage catalyses the pairing of ssDNA with duplex DNA, one strand of which is homologous to the ssDNA. Once the homologous tract is found, RecA will facilitate strand exchange.
If even recombination doesn’t work, the umuDC operon is expressed, which restarts replication at the stalled fork by employing mutagenesis. PolV, a special DNA polymerase, is encoded by the umuDC operon, and it inaccurately replicates DNA over the lesion. It may introduce incorrect nucleotides, and with them mutations. PolV is formed when the UmuD protein is cleaved by RecA, and associates with UmuC, thus forming PolV. After PolV places a few nucleotides, it is replaced by the accurage PolIII DNA polymerase, and replication continues as normal until another lesion is encountered.
The whole process of DNA repair must happen before a cell divides, and therefore cell division is delayed by the SOS protein SulA. This inhibits the function of proteins involved in cell division, including FtsZ (the septation protein). Once DNA is repaired, Lon protease can use SulA as a substrate, breaking down SulA and allowing the cell to septate as normal.
After DNA repair is accomplished, LexA concentration must be restored to shut off the SOS network. This is done by a number of proteins, one of which is called DinI. DinI structure resembles DNA, and this allows DinI to interact with the RecA filiment. This interaction inhibits both the recombinase and protease activity of RecA. Once RecA is inhibited, it no longer breaks down LexA, which begins to build up in the cell again, and once again works as a master repressor. There are other proteins involved in the shut off of the SOS network (such as RecX) but many of these have not been well studied.