Mismatch Repair Pathway in Prokaryotes
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Mismatch Repair Pathway in Prokaryotes
The integrity of genetic information depends on the fidelity of DNA replication and on the efficiency of several different DNA repair processes. Among many types of DNA repair, the general MMR (DNA Mismatch Repair) pathway is responsible for correcting base substitution mismatches which is generated during DNA replication in organisms from bacteria to mammals. The MMR system improves the fidelity of DNA synthesis by 100-1000 fold. The MMR also corrects IDLs (Insertion-Deletion Loops) which may occur during replication and recombination of DNA. MMR also able to correct DNA damages caused by internal or external sources. Inactivation or deterioration of this pathway has been linked to a variety of cancers, most notably Hereditary Non-Polyposis Colorectal Cancer. MMR can be permanent or may occur transiently when MMR proteins become limiting during periods of rapid, inaccurate replication or when cells are stressed in a stationary phase. MMR proteins participate in a wide variety of DNA transactions, such that their inactivation can have profound biological consequences on microbes, microbial populations and multicellular organisms(Ref. 1 & 2).

The Escheria coli MMR recognizes and repairs base mispairings and unpaired bases. The MMR system is composed of several proteins that act sequentially in the repair cascade. MutS, MutL and MutH are the three essential proteins for initiation of methyl-directed DNA mismatch repair to correct mistakes made during DNA replication in Escheria coli . The DNA template is methylated at d(GATC) sequences by the DAM methylase, but a newly synthesized strand is not methylated until it is modifed by the methylase. The MutS protein recognizes the lesion, and initiates the assembly of a repair complex containing all three proteins. The MutS protein binds the second protein, MutL which then activate the endonuclease MutH, which nicks the newly synthesized DNA strand at hemimethylated d(GATC) sites. The MutS proteins appear to behave as molecular switches that use nucleotide binding to alternate between distinct active states. The DNA-bound MutS protein binds ATP and in association with dimeric MutL forms Alpha-looped structures with concomitant hydrolysis of ATP. ADP stabilizes DNA binding and ATP increases dissociation (Ref. 3 & 4). ATP binding induces a state in which MutS slides away from the mismatch to allow new molecules to bind the mismatch. This increases the local concentration and triggers the repair process. This ATP binding is also used to aid in discrimination between homoduplex and heteroduplex DNA and in triggering the binding of MutL. The MutS-MutL complex does not move away from the mismatch but directs the subsequent steps of the repair cascade while tethered to the DNA (Ref. 2, 5, 6 & 7). But excision of the region containing the mismatch and subsequent resynthesis restores the correct nucleotide sequence. The DamMT (Dam Methyltransferase) and MutH proteins have hemimethylated d(GATC) sequences as a common substrate. Overproduction of DamMT prevents the action of MutH but the reverse is not true (Ref 8 & 9). Whereas MutH is a 28 kDa endonuclease which is inactive until activated by MutS and MutL associated with a mismatched base pairs. The endonuclease activity of MutH is dependent on Mg2+. Both MutH and Sau3AI,recognize the sequence d(GATC) and cleave 5’ to the G. However, MutH cleaves only the unmethylated strand of hemimethylated d(GATC) sequence while Sau3AI makes a double strand break regardless of its methylation state. These actions result in the formation of DSBs, which require recombination to restore genomic integrity, as mutations in genes encoding recombination proteins in combination with dam results in a lethal phenotype. These DSBs (Double-Strand Breaks) are produced by cisplatin, methylating agents and oxidative damage and this need to be repaired by homologous recombination. Inhibition of recombination at drug-induced lesions in a dam mutant exposed to these agents, therefore, is expected to be lethal and for cisplatin lesions, MutS blocks the action of RecA protein during the initiation of recombination repair. The resulting nick, which can be either 3 or 5 to the mismatch, is the entry point for MutL-dependent loading of DNA helicase II and binding of single-strand DNA-binding protein. Working together, these proteins generate ssDNA (Single-Stranded DNA). ssDNA that is digested by either 3 or 5 exonucleases, depending on the location of the nick relative to the mismatch. This excision removes the error and allows highly accurate DNA polymerase III to correctly resynthesize the strand. DNA ligase seals the nick to complete MMR (Ref. 2, 10 & 11).

Mutations in MMR genes can inactivate MMR and thus strongly elevate spontaneous mutation rates, especially addition and deletion mutations in short, repetitive (Microsatellite) sequences. These MMR gene mutations also predispose humans and mice to tissue-specific cancers. In addition to inactivation via gene mutation, MMR activity can also be modulated by changes in expression of MMR genes . Overall this pathway reveals the close relationship between the Escheria coli MMR proteins and the DNA polymerase III subunits and the ATP modulation of these interactions. The interaction network formulated based on established information and the new findings provide strong evidence to support the notion that DNA replication and MMR are highly associated with each other (Ref.10 & 12).