DNA Glycosylases in the Base Excision Repair of DNA
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DESCRIPTIONUNIGEN Center for Molecular Biology Norway 1997Authors: Hans E. KROKAN, Rune STANDAL and Geir SLUPPHAUG
Biochem. J. (1997) 325, 116 (Printed in Great Britain) 1
REVIEW ARTICLEDNA glycosylases in the base excision repair of DNAHans E. KROKAN*, Rune STANDAL and Geir SLUPPHAUGUNIGEN Center for Molecular Biology, The Medical Faculty, Norwegian University of Science and Technology, N-7005 Trondheim, Norway
A wide range of cytotoxic and mutagenic DNA bases areremoved by dierent DNA glycosylases, which initiate the baseexcision repair pathway. DNA glycosylases cleave the N-glycosylic bond between the target base and deoxyribose, thusreleasing a free base and leaving an apurinic}apyrimidinic (AP)site. In addition, several DNA glycosylases are bifunctional,since they also display a lyase activity that cleaves the phospho-diester backbone 3 to the AP site generated by the glycosylaseactivity. Structural data and sequence comparisons have identi-fied common features among many of the DNA glycosylases.Their active sites have a structure that can only bind extrahelicaltarget bases, as observed in the crystal structure of human uracil-DNA glycosylase in a complex with double-stranded DNA.Nucleotide flipping is apparently actively facilitated by theenzyme. With bacteriophage T4 endonuclease V, a pyrimidine-
INTRODUCTIONThe structural integrity of DNA is continuously challenged by anumber of exogenous and endogenous agents, as well as by somecellular processes . To counteract these threats, cells haveseveral defence mechanisms that act at dierent levels to preventor repair damage or to eliminate damaged cells. DNA damagecauses a temporary arrest of cell-cycle progression, allowingDNA repair to take place prior to replication. DNA repair isthus only one of several processes that co-operate to maintain theintegrity of the genome (Figure 1). A large number of factors co-ordinate the complex interplay between dierent cellularprocesses.Damaged bases may be cytotoxic, miscoding or both.
Mutations resulting from miscoding are thought to be a majormechanism by which DNA-reactive agents cause diseases such ascancer. In the simplest type of DNA repair, the damaged base isrepaired directly, e.g. dealkylated, by a one-step mechanism,rather than being excised and replaced by the correct one.However, most lesions in DNA are repaired by the much morecomplex recombination repair or excision repair systems. Thelatter include nucleotide excision repair (NER), mismatch repairand base excision repair (BER). NER is the most complicated ofthe excision repair systems, and involves the products of about30 genes. The system acts upon a wide range of alterations thatresult in large local distortions in DNA. The damage is removedas part of an oligonucleotide, and new DNA is synthesized usingthe intact strand as a template. Mismatch repair refers to therepair of mispaired bases in DNA, and may occur by severalbiochemical pathways, including NER and BER.
Abbreviations used: AP site, apurinic/apyrimidinic site ; BER, base excision repair ; dRpase, deoxyribophosphodiesterase ; dsDNA, double-strandedDNA; EndoIII (etc.), endonuclease III (etc.) ; fapy, 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine; Fpg, formamidopyrimidine-DNA glycosylase ;GPD motif, Pro/Gly-rich stretch with a conserved Asp residue C-terminal to it ; HhH, helixhairpinhelix ; hmUra, 5-hydroxymethyluracil ; 3-meA (etc.),3-methyladenine (etc.) ; MGMT, O6-alkylguanine-DNA alkyltransferase ; MPG, 3-meA-DNA glycosylase (in plants and mammals) ; NER, nucleotideexcision repair ; 8-oxoG, 7,8-dihydro-8-oxoguanine; RPA, replication protein A; T4endoV, bacteriophage T4 endonuclease V; TDG, thymine-DNAglycosylase ; UDG, uracil-DNA glycosylase ; XRCC1, X-ray cross-complementation protein 1.
* To whom correspondence should be addressed.
dimer glycosylase, the enzyme gains access to the target base byflipping out an adenine opposite to the dimer. A conservedhelixhairpinhelix motif and an invariant Asp residue are foundin the active sites of more than 20 monofunctional and bi-functional DNA glycosylases. In bifunctional DNA glycosylases,the conserved Asp is thought to deprotonate a conserved Lys,forming an amine nucleophile. The nucleophile forms a covalentintermediate (Schi base) with the deoxyribose anomeric carbonand expels the base. Deoxyribose subsequently undergoes severaltransformations, resulting in strand cleavage and regeneration ofthe free enzyme. The catalytic mechanism of monofunctionalglycosylases does not involve covalent intermediates. Instead theconserved Asp residue may activate a water molecule which actsas the attacking nucleophile.
As the name implies, the initial step in BER is the removal ofa base rather than a nucleotide. This step is carried out by DNAglycosylases, which are the focus of the present review. Ingeneral, the damaged or mismatched base recognized by a DNAglycosylase does not cause major helix distortions, although thedamage may be caused by a variety of agents and processes, suchas spontaneous deamination of bases, radiation, oxidative stress,alkylating agents or replication errors. BER is quantitativelyprobably the most important mechanism of DNA repair, yet nodisease has so far been clearly related to deficiencies in thispathway. Most DNA glycosylases remove several structurallydierent damaged bases, while a few have very narrow substratespecificities. The information on enzymes involved in BER hasflourished in the last few years. This is particularly true for someof the DNA glycosylases, which are now among the bestunderstood enzymes involved in nucleic acid metabolism. Thesestudies have also contributed new concepts about the interactionsbetween proteins and DNA in general.
DNA N-GLYCOSYLASES AND THE BER PATHWAY
DNA N-glycosylases hydrolyse the N-glycosylic bond betweenthe target base and deoxyribose, thus releasing a free base andleaving an apurinic}apyrimidinic (AP) site in DNA . Such APsites are cytotoxic and mutagenic, and must be further processed. Some DNA glycosylases also have an associated AP lyaseactivity that cleaves the phosphodiester bond 3 to the AP site (b-lyase). DNA glycosylases are relatively small monomeric proteinsthat do not require cofactors for their activity, and they are
2 H. E. Krokan, R. Standal and G. Slupphaug
Spontaneousda m age
D N A da m age
D N Areplication
Residualda m age
D N Areplication
RestoredD N A
Irreparableda m age
BER, N ER,reco m bination ,
mism atch repair,direct reversal
Figure 1 Cellular mechanisms contributing to the maintenance of thegenome
therefore excellent models for studying interactions betweendamaged DNA and proteins. In Figure 2, typical base lesionsand DNA glycosylases involved in their removal are shown.In itro reconstitution of the BER pathway with cell-free
extracts or purified components has been carried out usinguracil-DNA glycosylase (UDG)  or mismatch-specificthymine-DNA glycosylase (TDG)  as the initiating enzyme.These studies have established the minimal enzymic requirementsfor the repair of the resulting AP sites, and indicate that therepair may proceed via two alternative pathways (Figure 3). Inthe first of these, a 5-AP endonuclease  and a deoxyribo-phosphodiesterase (dRpase) create a single nucleotide gap, whichin eukaryotic cells is filled in by DNA polymerase b and DNAligase III . This route may also be initiated by bifunctionalDNA glycosylases, in which the gap may be created by successiveb- and d-eliminations [10,11]. A role for the presumably non-catalytic XRCC1 (X-ray cross-complementation protein 1) inBERwas recently also established. This protein interacts throughits N-terminal half with DNA polymerase b, whereas theC-terminal region interacts with DNA ligase III [9,12]. DNAstrand displacement and excessive gap-filling were observed incell-free extracts lacking XRCC1, indicating that XRCC1 mightserve as a scaold protein during BER. Moreover, human UDGwas recently found to interact with both the 34 kDa subunit andthe trimeric form of replication protein A (RPA) . In thealternative BER pathway, a short patch containing the abasicsite is excised and replaced by normal nucleotides [14,15]. Ineukaryotes this nucleotide patch is apparently displaced bypolymerase d or e, and the resulting overhang is removed bythe flap-endonuclease FEN-1 in a process involving PCNA(proliferating cell nuclear antigen) .In Escherichia coli, the AP-endonucleolytic step is catalysed by
endonuclease IV (EndoIV), which is damage-inducible, or byexonuclease III, which is constitutively expressed . Exonuclease
III was originally characterized as an exonuclease, but was latershown to be a multifunctional enzyme which probably functionsprimarily as a 5 AP-endonuclease . The dRpase activity is aproperty of the recJ gene product . At least one E. coli DNAglycosylase, the formamidopyrimidine-DNA glycosylase (Fpg)protein, may also create a DNA gap alone. Fpg releases bothsome purine bases with damaged imidazole rings and a deoxy-ribose derivative, leaving a gap bordered by 5- and 3-phosphorylgroups . Further processing requires a 3-phosphatase, prob-ably contributed by EndoIV [18,19], to produce a primer forDNA polymerase. If an AP site has already been incised by anAP-endonuclease 5-terminal to the deoxyribose, Fpg alsopromotes release of deoxyribophosphate [10,11]. A reporteddRpase activity associated with E. coli exonuclease I  has notbeen reproduced by others . Studies with double mutantsdeficient in RecJ and Fpg have indicated that the dRpaseactivities of these enzymes are not essential for BER, indicatingthe presence of a back-up function so far not identified . Thegaps resulting from dRpase activities are filled by DNA poly-merase I and th