Base excision repair (BER) is initiated by a DNA glycosylase and is completed by alternative routes, one of which requires proliferating cell nuclear antigen (PCNA) and other proteins also involved in DNA replication. We report that the major nuclear uracil-DNA glycosylase (UNG2) increases in S phase, during which it co-localizes with incorporated BrdUrd in replication foci. Uracil is rapidly removed from replicatively incorporated dUMP residues in isolated nuclei. Neutralizing antibodies to UNG2 inhibit this removal, indicating that UNG2 is the major uracil-DNA glycosylase responsible. PCNA and replication protein A (RPA) co-localize with UNG2 in replication foci, and a direct molecular interaction of UNG2 with PCNA (one binding site) and RPA (two binding sites) was demonstrated using two-hybrid assays, a peptide SPOT assay and enzyme-linked immunosorbent assays. These results demonstrate rapid post-replicative removal of incorporated uracil by UNG2 and indicate the formation of a BER complex that contains UNG2, RPA and PCNA close to the replication fork.

A distinct nuclear form of human uracil-DNA glycosylase [UNG2, open reading frame (ORF) 313 amino acid residues] from the UNG gene has been identified. UNG2 differs from the previously known form (UNG1, ORF 304 amino acid residues) in the 44 amino acids of the N-terminal sequence, which is not necessary for catalytic activity. The rest of the sequence and the catalytic domain, altogether 269 amino acids, are identical. The alternative N-terminal sequence in UNG2 arises by splicing of a previously unrecognized exon (exon 1A) into a consensus splice site after codon 35 in exon 1B (previously designated exon 1). The UNG1 sequence starts at codon 1 in exon 1B and thus has 35 amino acids not present in UNG2. Coupled transcription/translation in rabbit reticulocyte lysates demonstrated that both proteins are catalytically active. Similar forms of UNG1 and UNG2 are expressed in mouse which has an identical organization of the homologous gene. Constructs that express fusion products of UNG1 or UNG2 and green fluorescent protein (EGFP) were used to study the significance of the N-terminal sequences in UNG1 and UNG2 for subcellular targeting. After transient transfection of HeLa cells, the pUNG1-EGFP-N1 product colocalizes with mitochondria, whereas the pUNG2-EGFP-N1 product is targeted exclusively to nuclei.

Uracil-DNA glycosylase releases free uracil from DNA and initiates base excision repair for removal of this potentially mutagenic DNA lesion. Using the yeast twohybrid system, human uracil-DNA glycosylase encoded by the UNG gene (UNG) was found to interact with the C-terminal part of the 34-kDa subunit of replication protein A (RPA2). No interaction with RPA4 (a homolog of RPA2), RPA1, or RPA3 was observed. A sandwich enzyme-linked immunosorbent assay with trimeric RPA and the two-hybrid system both demonstrated that the interaction depends on a region in UNG localized between amino acids 28 and 79 in the open reading frame. In this part of UNG a 23-amino acid sequence has a significant homology to the RPA2-binding region of XPA, a protein involved in damage recognition in nucleotide excision repair. Trimeric RPA did not enhance the activity of UNG in vitro on single-or double-stranded DNA. A part of the N-terminal region of UNG corresponding in size to the complete presequence was efficiently removed by proteinase K, leaving the proteinase K-resistant compact catalytic domain intact and fully active. These results indicate that the N-terminal part constitutes a separate structural domain required for RPA binding and suggest a possible function for RPA in base excision repair. Uracil-DNA glycosylase (UDG)1 is the first enzyme in base excision repair for removal of uracil from DNA and its main function is probably to remove mutagenic uracil residues resulting from deamination of cytosine in DNA (1). The subsequent steps in the base excision repair pathway include, as the minimal enzymatic requirement in vitro, an apurinic/apyrimidinic endonuclease, a deoxyribophosphodiesterase activity (which may be contributed by DNA polymerase ␤), DNA polymerase ␤, and a DNA ligase (2). In analogy to the complexity of the nucleotide excision repair pathway, base excision repair is likely to be more complex in vivo. This is in fact supported by the finding of an alternative, short patch pathway, requiring proliferating cell nuclear antigen and DNA polymerase ␦ (3, 4). A catalytically fully active form of human UDG has been expressed in Escherichia coli (5) and structure-function relationships determined by site-directed mutagenesis and x-ray crystallography (6). These studies identified this form of human UDG as a one domain structure with a positively charged DNA-binding groove. UDGs are relatively small monomeric enzymes that, at least in vitro, do not require cofactors. However, UDG is preferentially associated with replicating SV40 minichromosomes, indicating a possible interaction with components of the replication machinery (7). The gene encoding the major human UDG, UNG, is transcribed predominantly late in the G 1 -phase, resulting in a 2-3-fold increase in UDG activity early in the S-phase (8). The cell cycle regulation is consistent with the presence of several putative regulatory elements detected in the UNG gene (9), including a putative element for binding of replication protein A (RPA) (10) reported previously in D...

Nuclear (UNG2) and mitochondrial (UNG1) forms of human uracil-DNA glycosylase are both encoded by the UNG gene but have different N-terminal sequences. We have expressed fusion constructs of truncated or site-mutated UNG cDNAs and green fluorescent protein cDNA and studied subcellular sorting. The unique 44 N-terminal amino acids in UNG2 are required, but not sufficient, for complete sorting to nuclei. In this part the motif R17K18R19is essential for sorting. The complete nuclear localization signal (NLS) in addition requires residues common to UNG2 and UNG1 within the 151 N-terminal residues. Replacement of certain basic residues within this region changed the pattern of subnuclear distribution of UNG2. The 35 unique N-terminal residues in UNG1 constitute a strong and complete mitochondrial localization signal (MLS) which when placed at the N-terminus of UNG2 overrides the NLS. Residues 11-28 in UNG1 have the potential of forming an amphiphilic helix typical of MLSs and residues 1-28 are essential and sufficient for mitochondrial import. These results demonstrate that UNG1 contains a classical and very strong MLS, whereas UNG2 contains an unusually long and complex NLS, as well as subnuclear targeting signals in the region common to UNG2 and UNG1.

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Quantitative analysis in confocal microscopy meets with several problems such as fading of the fluorophore during scanning and attenuation of the fluorescence in thick tissue specimens. The present study reports a quantitative investigation of the enzyme uracil-DNA glycosylase (UDG), which removes uracils from DNA. For this study we developed a fading correction algorithm which takes into account both the number of prior scans in the specimen, and the differences in fading through the specimen from each prior scan, presumably due to differences in laser intensity at various axial distances from the focus position. On this point, our findings are in contrast with results reported in other well known papers, and indicate different fading at various distances from the laser focus position. The correction procedure can and should be established for the same specimen, but on a different part of the specimen from that used in the actual biological study. Calibration can thus be done on an unknown or inhomogenous object. For a series of confocal xy-scans through the immunostained cells, a corrected summation image representing total FITC-fluorescence related to UDG was obtained. Both noise removal and fading corrections were performed on each image in the series before the summation image was made. Estimates of total amounts of UDG localized in the cells and nuclei, respectively, could then be obtained. Measurement of the total cellular UDG-content by flow cytometry was also performed in order to make a comparison of the two methods for quantitative analysis. For both methods a range of approximately 4.5 was obtained between total UDG-content of cells at the 5 and 95 percentage points.

Quantitative analysis in confocal microscopy meets with several problems such as fading of the fluorophore during scanning and attenuation of the fluorescence in thick tissue specimens. The present study reports a quantitative investigation of the enzyme uracil‐DNA glycosylase (UDG), which removes uracils from DNA. For this study we developed a fading correction algorithm which takes into account both the number of prior scans in the specimen, and the differences in fading through the specimen from each prior scan, presumably due to differences in laser intensity at various axial distances from the focus position. On this point, our findings are in contrast with results reported in other well known papers, and indicate different fading at various distances from the laser focus position. The correction procedure can and should be established for the same specimen, but on a different part of the specimen from that used in the actual biological study. Calibration can thus be done on an unknown or inhomogenous object. For a series of confocal xy‐scans through the immunostained cells, a corrected summation image representing total FITC‐fluorescence related to UDG was obtained. Both noise removal and fading corrections were performed on each image in the series before the summation image was made. Estimates of total amounts of UDG localized in the cells and nuclei, respectively, could then be obtained. Measurement of the total cellular UDG‐content by flow cytometry was also performed in order to make a comparison of the two methods for quantitative analysis. For both methods a range of approximately 4.5 was obtained between total UDG‐content of cells at the 5 and 95 percentage points. © 1996 Wiley‐Liss, Inc.

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