DNA polymerase in SOS response

The SOS response is a cellular response to DNA damage and is named after the universal

distress call SOS – ‘save our ship’ or ‘save our souls.’ It leads to cell cycle arrest and DNA repair.
Upon DNA damage, the replicative DNA polymerase, pol III, is generally unable to copy
noncanonical or damaged DNA and so becomes uncoupled from DNA helicase. This leads to the
formation of a region of single-stranded DNA (ssDNA), on which the RecA protein polymerizes
which requires  ATP for the process, to form the RecA/ssDNA nucleoprotein filament(RecA*).
RecA has many roles in the DNA repair pathway i.e. homologous recombination.
Normally, the SOS response are respressed by a repressor lexA which is a dimeric protein
consisting of a DNA-binding domain and a protease domain and is bound to a regulatory
sequence known as ‘SOS box’.
SOS response is activated when RecA forms nucleoprotein filament around the ssDNA and
hence RecA activates. Activated RecA interacts with lexA repressor and self-cleavage from the
operator region of SOS gene occurs. As the level of active LexA decreases, the level of the
expression of the SOS genes, as well as that of the RecA gene, increases. There are many
genes associated with the SOS gene, depending upon the DNA damage the genes are induced.
Of them, first SOS response deployed is Nucleotide Excision Repair (NER).

In E. coli, uvr genes carry out NER followed by RecA. RuvAB and RecN are the coding genes for
homologous recombination. While polB and dinB encodes polymerase II and IV respectively. A
division inhibitor SulA is induced in order to slow down cell division so that it has sufficient time for
the repairs. Finally, if there are some damages that still requires repair, error-prone polymerase V
which is encoded by umuC and umuD genes is induced. It leads to mutation but it lets continuous
replication and cell survival.

Experiment:

 Classical techniques used for the study the SOS response involved treatments of bacterial
cultures by a DNA-damaging agent and then analysing it’s response. This was done by fusing
reporter genes an SOS promoter, or the direct quantification of LexA or RecA proteins by
immunoblotting. More recently, microarrays were used to measure the timing and the amplitude
of the induction in bacterial populations.

 PLoS Biology, Friedman and coworkers measured in single cells the level and kinetics of
activation of SOS promoters after UV-light treatment. To report promoter activity, the green
fluorescent protein (GFP) gene was placed under the control of the promoters of three different
SOS genes: recA, lexA, and umuCD. Unsurprisingly, when the signal in a cell population was
analyzed, the amount of GFP increased as a broad peak followed by a decrease as repair took
place and the SOS response was shut off. But surprisingly, in individual cells, one, two, or three
successive peaks of GFP expression were observed, depending on the UV dose. UV doses lower
than 10 showed one peak of GFP. This was centered at 20 to 25 minutes after irradiation for
the recA and the lexA promoter. Ten minutes later, as expected, the umuCD promoter was
induced. At UV doses of 20 joules or higher, two to three peaks of GFP expression were
observed, with the timing of the appearance of the first peak and its amplitude remaining
constant. This finding opens new possibilities for the control of the SOS response. It proposes
that in each cell, the SOS response is not simply turned on to an extent that depends on the level
of DNA damage and then turned off. Rather, it submits that the SOS promoters are induced to a
certain level sufficient to survive a certain dose of DNA-damaging agent, regardless of the initial
amount of DNA damage. If the level of DNA damage is too high for the cells to cope with in one
round of induction, a second round of induction or even a third round will follow.