Translesion DNA Synthesis

Abstract

All living organisms are continually exposed to agents that damage their DNA, which threatens the integrity of their genome. As a consequence, cells are equipped with a plethora of DNA repair enzymes to remove the damaged DNA. Unfortunately, situations nevertheless arise where lesions persist, and these lesions block the progression of the cell's replicase. Under these situations, cells are forced to choose between recombination-mediated "damage avoidance" pathways, or use a specialized DNA polymerase (pol) to traverse the blocking lesion. The latter process is referred to as Translesion DNA Synthesis (TLS). As inferred by its name, TLS not only results in bases being (mis)incorporated opposite DNA lesions, but also downstream of the replicase-blocking lesion, so as to ensure continued genome duplication and cell survival. Escherichia coli and Salmonella typhimurium possess five DNA polymerases, and while all have been shown to facilitate TLS under certain experimental conditions, it is clear that the LexA-regulated and damage-inducible pols II, IV and V perform the vast majority of TLS under physiological conditions. Pol V can traverse a wide range of DNA lesions and performs the bulk of mutagenic TLS, whereas pol II and pol IV appear to be more specialized TLS polymerases. KeywordsDNA polymerase II; DNA polymerase IV; DNA polymerase V; RecA, LexA, β-clamp; Y-family DNA polymerase; Mutagenesis; Replication Restart; Recombination; SOS response HISTORICAL OVERVIEWWe now know that TLS is largely facilitated by specialized DNA polymerases that can accommodate bulky adducts in their active sites. Such properties are usually associated with a dramatic decrease in replication fidelity and as a consequence, TLS is often error-prone, leading to an increase in cellular mutagenesis. Significant progress in understanding the FURTHER READINGFor additional recent reviews on TLS-related topics see references (6,76,101,122,167,173,179,180,203,214). HHS Public Access Author Manuscript Author ManuscriptAuthor ManuscriptAuthor Manuscript molecular mechanisms of TLS have been achieved in the past decade, following the successful purification and biochemical characterization of a number of TLS polymerases. However, prior to the characterization of the highly purified proteins, the pioneering studies on TLS were largely focused on its genetic endpoints, namely its mutagenic consequences. Indeed, the first hint that damage-induced mutagenesis is not a passive process came in the early '50s when Jean Weigle reported that mutagenesis of irradiated bacteriophage λ was significantly enhanced, if the host bacterium had also been irradiated (247). However, it was not until the pioneering studies of Evelyn Witkin working with bacteria that could be killed by UV irradiation, but not mutated, that the concept of damage inducible error-prone translesion DNA synthesis was born (249)(250)(251)253). These ideas were further expanded in 1970 by Miroslav Radman in a privately circulated letter in which he suggested that "SOS replication" ...

The SOS system: A complex and tightly regulated response to DNA damage

“…DNA Pol V, the second error‐prone polymerase is expressed at almost an undetectable level (Woodgate and Ennis, ). Participation of these accessory polymerases in E. coli chromosome replication and their effect on the fidelity of DNA replication and ability to copy damaged DNA was reviewed in (Walsh et al, ; Fijalkowska et al, ; Vaisman et al, ; Goodman et al, ; Jaszczur et al, ; Henrikus et al, ). Upon DNA damage the level of three TLS DNA polymerases, DNA polymerase II, DNA polymerase IV, and DNA polymerase V is elevated, as part of the E. coli inducible SOS response (Napolitano et al, ).…”

Translesion DNA Polymerases

“…E. coli Pol V has been the subject of intense study, but many orthologs are now known to exist in a wide range of prokaryotes and self-transmissible plasmids that they harbor (Vaisman et al 2012). Of particular interest are Pol V orthologs MucA′B and RumA′B found on the IncN R-plasmid R46/pKM101 (Perryand Walker 1982) and integrating conjugative element (ICE) R391 (Kulaeva et al 1995), respectively.…”

“…There are more than 60 different structures in the PDB database with individual “snapshots” of Dpo4 in the process of facilitating TLS (Vaisman et al 2012). What is evident is that the enzyme can perform a wide range of molecular gymnastics with either the template base or incoming nucleotide so as to allow TLS to occur.…”

Ribonucleotide discrimination by translesion synthesis DNA polymerases

“…Among the functionally-diverse A-family polymerases, are eukaryotic polymerases θ and ν that are involved in TLS and DNA repair pathways primarily related to processing the aberrant ends of strand breaks (Hogg et al , 2011; Rothwell and Waksman, 2005; Seki and Wood, 2008; Takata et al , 2006; Takata et al , 2010; Yamanaka et al , 2010). The B-family mainly comprised of high fidelity DNA polymerases involved in chromosomal replication, also contains bacterial (pol II) and eukaryotic (pol ζ); enzymes that play an important role in TLS (Fuchs and Fujii, 2007; Lange et al , 2011; Lawrence et al , 2000; Shcherbakova and Fijalkowska, 2006; Vaisman et al , 2012b). The X- and Y-families appear to consist of more functionally homogeneous polymerases which are all implicated in damaged DNA processing (Vaisman and Woodgate, 2017).…”