DNA Replication, Repair, and Mutagenesis in Eukaryotic a

Child Health And Human Development

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Abstract

Lesions in DNA often pose considerable impediments to genome duplication. To overcome this block to DNA replication, cells utilize specialized accessory factors that allow synthesis of nascent DNA chains opposite the blocking lesion. Recent studies suggest that many of the key participants in translesion DNA synthesis belong to a large family of structurally related DNA polymerases that are found in prokaryotes, archaea and eukaryotes. Phylogenetic analysis of these polymerases suggest that they can be broadly subdivided into four groups typified by Escherichia coli UmuC, E. coli DinB, Saccharomyces cerevisiae Rev1 and the S. cerevisiae Rad30 protein that collectively have recently been named the Y-family of DNA polymerases. In the past year, the laboratory has focussed on mechanisms of translesion replication in all three kingdoms of life: bacteria, archaea and eukaryotic cells. In E. coli, this process only occurs when UmuC physically interacts with UmuD' to form UmuD'2C, (polV). Because polV is a low-fidelity enzyme, its activities within the cell are strictly controlled. For example, the enzyme is greatly stimulated by interactions with the RecA protein. RecA normally binds to regions of single stranded DNA and generally blocks genome duplication by replicative enzymes. However, studies revealed that polV acts as a locomotive "cowcatcher", effectively removing RecA from the single-stranded DNA while concomitantly facilitating translesion DNA synthesis. Scientist within the lab have recently identified and cloned a DinB homolog from the archaeon Sulfolobus solfataricus P2, called DNA polymerase IV (Dpo4). Characterization of the enzyme reveals that the protein possesses many biochemical properties similar to other DinB polymerases, However, in contrast to DinB polymerases which are unable to bypass a thymine-thymine cyclobutane dimer, Dpo4 bypasses the lesion efficiently. In this regard, the enzyme is more akin to the distantly related eukaryotic DNA polymerase eta (Rad30 protein). S. solfataricus Dpo4 has been overproduced, purified and its structure has recently been solved by X-ray crystallography. Like all DNA polymerases characterized to date, the enzyme possesses a topology similar to a right hand with domains that resemble "fingers", a "palm" and a "thumb". Dpo4 also possesses a unique domain called the "little finger" that helps the enzyme bind to DNA. Interestingly, the active site of the enzyme is large enough to accommodate two bases at one time, thus potentially explaining its ability to bypass thymine-thymine dimers. Studies with human DNA polymerase iota, which was recently discovered by scientist in the section, revealed that in addition to exhibiting a remarkable template-dependent misincorporation spectrum in vitro, the enzyme also possesses deoxyribose lyase activity and probably participates in a specialized form of base excision repair. A hallmark of pol iota is its ability to misinsert guanine opposite thymine at least three fold better than the "correct" base adenine. Recent studies suggest that the enzyme also exhibits a similar spectrum opposite Uracil and its derivatives. In living cells, Uracil frequently arises from the spontaneous deamination of cytosine residues. This results in an increase in spontaneous mutagenesis as the uracil base pairs with thymine, not guanine as it would if the base were cytosine, Thus, the ability of pol iota to misinsert guanosine opposite uracils (which were once cytosines), provides a potential mechanism for cells to reduce the extent of spontaneous mutagenesis caused by deamination of cytosine.