User talk:Sri1989vathsan/SOS Response

The SOS system is a global gene regulatory system implemented by bacteria, in response to situations where the DNA damage (for example formation of thiamine diamers by UV) exceeds beyond the normal repairing capability of the cell. About 30 genes are involved in the above mentioned process, which are expressed at an increased rate during the response. These genes are termed as SOS genes and are collectively called as SOS regulon.

There are two major regulatory genes for the SOS pathway - LexA repressor - which inhibits the expression of SOS genes during normal cell growth and RecA protein which is activated by the damage causing signal. RecA helps in the self-cleavage of LexA dimer (thus inactivating it) leading to the expression of the SOS genes. These SOS genes act as a "last ditch" effort to allow DNA replication (and thus survival of the cell itself) to proceed. It is a bypass system which allows replication of DNA even across its damaged sections, by compensating the fidelity of replication. It is an error prone mechanism which results in intact DNA strands but often with incorrect bases. The process is not very well understood but it is believed that there occurs a relaxation in the editing system of the DNA polymerase thus allowing it to proceed across the dimer inspite of there being a distorion in the helix. It is the major cause of mutagenesis by UV and many other chemical mutagens in bacteria.

Role of RecA in SOS repair
A combination of invivo and invitro studies have showed that the activation of the RecA - ssDNA (the short segment formed due to dimerization of thiamine or the ssDNA formed due to stalling of DNA polymerase) by ATP results in most of its activities. The active form of RecA(RecA*) had been found to help in the self-cleavage of cI repressor during the shift from lysogenic to lytic phase. It was found that RecA* causes a conformational change in the structure of the repressor, thereby bringing the protease active site(present in the cI repressor) close to the repressor protein, resulting in the autoproteolysis of the cI repressor. Similar to this are the effects of RecA* towards proteins involved in the SOS pathway.

RecA* has several functions in SOS repair. It directly inhibits the proof-reading mechanism of DNA polymerase III. First, it tightly binds to the region of distortion caused due to formation of a pyrimidine dimer. Then when DNA polymerase III comes to that particular point, RecA interacts with the proof-reading subunit of  DNA polymerase III - inhibiting its effect and allowing the polymerase to move past this point. UmuDC are genes whose products are required for error-prone DNA repair in bacteria. It has been observed that even though these set of genes are inactive in many of the bacteria, there do exist functional homologs of the same in several plasmids. RecA helps in the proteolytics cleavage of umuD producing an active C-terminal fragment. This fragment forms a complex with umuC which then in the presence of RecA help the DNA polymerase to move past the stalling point.

Mechanism
In a normal, healthy cell, the SOS genes are tightly regulated by the inhibitory effect of the LexA protein. The LexA protein a small (22kD)) that is relatively stable in untreated cells. It has a latent protease activity that is activated by RecA. It exists as a dimer which binds to a 20 basepair consensus sequence with 8 absolutely conserved positions (known as SOS box) in the operator region of the SOS genes. Like other operators, the SOS boxes overlap with the respective promoters. The repression of the genes depends on the affinity of the LexA to the SOS box which in turn depends on the sequence. When there is DNA damage, RecA protein is activated and it helps in the proteolytic cleavage of LexA repressor (which represses RecA - thus resulting in an amplified effect). The repressor thus decreases in concentration and thus its action of inhibition on SOS genes is suppressed. The level of decrease in repression depends on the affinity of LexA for the SOS box. Thus genes having a weaker SOS box (like lexA, recA, uvrA, uvrB, and uvrD) would be activated first compared to that having a higher affinity for LexA. These proteins activate the Nucleotide excision repair (NER) mechanism, which aims at fixing the DNA damage without commitment to a full-fledged SOS response. If the damage is not repaired by the NER mechanism, the concentration of lexA would decrease further as a result activating the genes with stronger SOS box(sulA, umuD, umuC). SulA stops cell division by binding to the protein FtsZ which causes filamentation and the induction of umuDC pathway.

Discovery
The discovery of the SOS response system evolved from studies on the effect of UV irradiation on Escherichia coli and consideration of seemingly unconnected data. It was observed that reactivation and mutagenesis of UV-irradiated phage l were increased when the phage infected an E. coli host that had been previously irradiated. It was also observed that UV-irradition shifted the lambda-infected cells from lysogenic to lytic development, caused filamentation of cells and also mutations in bacteria. This led Miroslaw Radman to propose under stress bacteria are able to produce protein - which are otherwise under repressed state - which allow the repair of DNA and reactivation of DNA synthesis.

Family
The importance of RecA is evidenced by the presence of more than 60 different but highly conserved homologs that have been characterized in a wide variety of bacteria and archae. The most famous eukaryotic homolg of RecA is Rad51 - a human gene which assists in the damage of DNA double strand breaks. Several homologs of RecA have recently been identified in S. cerevisiae like Rad51p, Rad55p, Rad57p, Dmc1p. The Rad51p gene shows not only structural homology to RecA gene in bacteria but is also conserved from yeast to humans. Other identified RecA-like genes in mammals are Rad51L1/B, Rad51L2/C, Rad51L3/D, XRCC2, XRCC3, and DMC1/Lim15. All of these proteins, with the exception of meiosis-specific DMC1, are essential for development in mammals.

LexA has several homologs like dinR in Bacillus subtillus and several other genes in Pseudomonas aeruginosa, Pseudomonas putida, and Aeromonas hydrophila. Not only this, sequences identical to LexA binding sites have also been identified in various prokaryotes. Various structural studies have shown that lexA belongs to the catabolite repressor protein (CAP) -like binding superfamily.