Maintenance of Genome Integrity

The integrity of the genome, both in regard to sequence and to size, is essential for perpetuation of species. This integrity can be threatened in two ways. The first is by errors in DNA replication, as discussed earlier. A second inexorable process of DNA alteration occurs due to chemical reactions which can be either endogenous or induced by external agents, including environmental genotoxic compounds, drugs, and radiation. Contrary to an earlier belief that DNA is a rather inert chemical, it is, in fact, sensitive to certain chemical reactions, e.g., depurination (loss of purine bases) and deamination of C to U, which occurs at a low but significant rate in DNA. It has been estimated that several hundred to several thousand such lesions are generated in the genome of a human cell per day. Both of these changes could be mutagenic. Loss of purines leads to abasic sites in DNA, which could direct misincorporation of wrong bases during DNA replication. Conversion of C into U is definitely mutagenic, because the change of a GC to a GU pair will give rise to one GC pair and one AT pair after DNA replication because U, like T, pairs with A. Often, C in the mammalian genome is methylated at the C-5 position, as discussed elsewhere, and 5-methyl C is deaminated more readily than C. Its conversion to T induces the same GC→AT mutation and, unlike deamination of C→U, does not produce an “abnormal” base in the DNA. A variety of environmental chemicals and both ultraviolet light present in sunlight and ionizing radiation from radioactive sources and X-rays induce a plethora of DNA lesions which include both base damage and sugar damage and are accompanied by DNA strand breaks. Many of these lesions, in particular, strand breaks and bulky base adducts, are toxic to the cells by preventing both replication and transcription. Other types of base damage and adducts can be mutagenic because they will allow DNA replication to proceed, but will direct incorporation of improper bases in the progeny strand.

A. Prevention of Toxic and Mutagenic Effects of DNA Damage by Repair Processes
Multiple repair processes have evolved to restore genomic integrity in all organisms ranging from bacteria to mammals. Excision repair comprises one class in which the damaged part of a DNA strand is excised enzymatically from the duplexDNA, leaving a single-strand gap. The gap is then filled byDNApolymerases starting at the 3´-OHterminus by utilizing the undamaged complementary strand as the template, followed by ligation of the nascent segment to the 5´ phosphate terminus at the other end of the gap with DNA ligase. The excision repair process consists of three subgroups which are utilized for distinct types of damage, although there is some overlap in their activities. Base excision repair is more commonly used for small base adducts, and nucleotide excision repair is used for replication/transcription-blocking bulky adducts. Mismatch repair evolved primarily to remove DNA mispairs that are generated as errors of replication. Both nucleotide excision and mismatch repair deficiencies have been linked to tumorigenesis, which results from mutation mutation of critical oncogenes and/or tumor suppressor genes, thus causing uncontrolled cellular multiplication and prevention of cell death. Prevention of transcription of bulky adducts in active genes triggers nucleotide excision repair, at least in eukaryotes, in a process called “transcription coupled repair.” In fact, the repair complex has co-opted certain proteins of the transcription complex.

Although excision repair requires DNA synthesis, it is distinct from normal semi-conservative replication because it occurs throughout the cell cycle and may utilize nonreplicative DNA polymerases in both prokaryotes and eukaryotes. Pol II and Pol I in E.coli and DNA polymerase β have been identified as such repair polymerases. However, replicative polymerases can also be recruited in some cases, e.g., for mismatch repair synthesis.

Interestingly, during the last couple of years, a whole family of DNA polymerase have been identified and characterized in E. coli, yeast, and mammals (Table II). These enzymes are unique in their ability to bypass DNA base adducts which have lost the ability to base pair and thus are not utilized by standard DNA polymerases. It has been suggested that these replication bypass polymerases allow cell survival by allowing DNA replication even at the cost of introducing mutations.

B. Post-Replication Recombinational Repair
In contrast to the excision repair process in which the DNA damage is actually removed, both eukaryotic and prokaryotic cells have a novel mechanism of adapting to persistent, unrepaired damage by utilizing homologous recombination between the replicated progeny genomes. Recombination, the process of exchange between homologous DNA segments, involves unwinding of one duplex DNA and reciprocal strand exchange. When one strand in the parental DNA has a persistent lesion that prevents replication, a complete duplex is generated from the other, undamaged strand. The new strand subsequently acts as the template for the damaged region by strand exchange during replication of the damaged strand. Thus, recombination allows synthesis of the correct DNA sequence opposite the lesion.