Human DNA polymerase beta initiates DNA synthesis during long-patch repair of reduced AP sites in DNA.

Simple base damages are repaired through a short-patch base excision pathway where a single damaged nucleotide is removed and replaced. DNA polymerase beta (Pol beta) is responsible for the repair synthesis in this pathway and also removes a 5'-sugar phosphate residue by catalyzing a beta-elimination reaction. How ever, some DNA lesions that render deoxyribose resistant to beta-elimination are removed through a long-patch repair pathway that involves strand displacement synthesis and removal of the generated flap by specific endonuclease. Three human DNA polymerases (Pol beta, Pol delta and Pol epsilon) have been proposed to play a role in this pathway, however the identity of the polymerase involved and the polymerase selection mechanism are not clear. In repair reactions catalyzed by cell extracts we have used a substrate containing a reduced apurinic/apyrimidinic (AP) site resistant to beta-elimination and inhibitors that selectively affect different DNA polymerases. Using this approach we find that in human cell extracts Pol beta is the major DNA polymerase incorporating the first nucleotide during repair of reduced AP sites, thus initiating long-patch base excision repair synthesis.

DNA synthesis and dRPase activities of polymerase beta are both essential for single-nucleotide patch base excision repair in mammalian cell extracts.

In mammalian cells the majority of altered bases in DNA are processed through a single-nucleotide patch base excision repair mechanism. Base excision repair is initiated by a DNA glycosylase that removes a damaged base and generates an abasic site (AP site). This AP site is further processed by an AP endonuclease activity that incises the phosphodiester bond adjacent to the AP site and generates a strand break containing 3'-OH and 5'-sugar phosphate ends. In mammalian cells, the 5'-sugar phosphate is removed by the AP lyase activity of DNA polymerase beta (Pol beta). The same enzyme also fills the gap, and the DNA ends are finally rejoined by DNA ligase. We measured repair of oligonucleotide substrates containing a single AP site in cell extracts prepared from normal and Pol beta-null mouse cells and show that the reduced repair in Pol beta-null extracts can be complemented by addition of purified Pol beta. Using this complementation assay, we demonstrate that mutated Pol beta without dRPase activity is able to stimulate long patch BER. Mutant Pol beta deficient in DNA synthesis, but with normal dRPase activity, does not stimulate repair in Pol beta-null cells. However, under conditions where we measure base excision repair accomplished exclusively through a single-nucleotide patch BER, neither dRPase nor DNA synthesis mutants of Pol beta alone, or the two together, were able to complement the repair defect. These data suggest that the dRPase and DNA synthesis activities of Pol beta are coupled and that both of these Pol beta functions are essential during short patch BER and cannot be efficiently substituted by other cellular enzymes.

Hydrogen peroxide induced mutations at the HPRT locus in primary human T-lymphocytes.

Reactive oxygen species (ROS) produced by intracellular metabolism are believed to contribute to spontaneous mutagenesis in somatic cells. Hydrogen peroxide (H(2)O(2)) has been shown to induce a variety of genetic alterations, probably by the generation of hydroxyl radicals via the Fenton reaction. The kinds of DNA sequence alterations caused by H(2)O(2) in prokaryotic cells have been studied extensively, whereas relatively little is known about the mutational spectrum induced by H(2)O(2) in mammalian genes. We have used the T-cell cloning assay to study the ability of H(2)O(2) to induce mutations at the hypoxanthine guanine phosphoribosyltransferase (HPRT) locus in primary human lymphocytes. Treatment of cells for 1 h with 0.34-1.35 mM of H(2)O(2) caused a dose dependent decrease of cell survival and increase of the HPRT mutant frequency (MF). After 8 days of expression time, the highest dose of H(2)O(2) caused a 5-fold increase of MF compared to the untreated control cells. Mutant clones were collected and the genomic rearrangements at the T-cell receptor (TCR) gamma-locus were studied to identify independent mutations. RT-PCR and DNA sequencing was used to identify mutations in the HPRT coding region. Due to a relatively high frequency of sibling clones, only six independent mutations were obtained among the controls, and 20 among the H(2)O(2) treated cells. In both sets, single base pair substitutions were the most common type of mutation (5/6 and 13/20, respectively), with a predominance of transitions at GC base pairs, which is also the most common type of HPRT mutation in T-cells in vivo. Among the single base pair substitutions, five were new mutations not previously reported in the human HPRT mutation database. Overall, the kinds of mutation occurring in T-cells in vivo and H(2)O(2) treated cells were similar, albeit the number of mutants was too small to allow a meaningful statistical comparison. These results demonstrate that H(2)O(2) is mutagenic to primary human T-lymphocytes in vitro and induces mutations of the same kind that is observed in the background spectrum of HPRT mutation in T-cells in vivo.

Validation of the human T-lymphocyte cloning assay--ring test report from the EU concerted action on HPRT mutation (EUCAHM).

The T-cell cloning assay, which enables the enumeration and molecular analysis of 6-thioguanine resistant (HPRT-negative) mutant T-cells, has been extensively used for studying human somatic gene mutation in vivo. However, large inter-laboratory variations in the HPRT mutant frequency (MF) call for further investigation of inter-laboratory differences in the experimental methodology, and development of an optimal but easy uniform cloning protocol. As part of the EU Concerted Action on HPRT Mutation (EUCAHM), we have carried out two Ring tests for the T-cell cloning assay. For each test, duplicate and coded samples from three buffy coats were distributed to five laboratories for determination of MF using six different protocols. The results indicated a good agreement between split samples within each laboratory. However, both the cloning efficiencies (CEs) and MFs measured for the same blood donors showed substantial inter-laboratory variations. Also, different medium compositions used in one and the same laboratory resulted in a remarkable difference in the level of MF. A uniform operating protocol (UOP) was proposed and compared with the traditional protocols in the second Ring test. The UOP (preincubation) increased the CE in laboratories traditionally using preincubation, but decreased the CE in laboratories traditionally using priming. Adjusted for donor, use of different protocols contributed significantly to the overall variation in lnCE (P = 0.0004) and lnMF (P = 0.03), but there was no significant laboratory effect on the lnCE (P = 0.38) or lnMF (P = 0.14) produced by the UOP alone. Finally, a simplified version of the UOP using the serum-free medium X-Vivo 10 and PMA was tested in one laboratory, and found to produce a considerable increase in CE. This modified UOP needs to be further evaluated in order to be used for future databases on HPRT MFs in various populations.

Influence of smoking and donor age on the spectrum of in vivo mutation at the HPRT-locus in T lymphocytes of healthy adults.

Types and frequencies of in vivo mutation in the hypoxanthine-guanine phosphoribosyl-transferase (HPRT) gene was studied in 142 T cell mutants from 78 healthy nonsmoking and smoking adults with a mean of 65 years. The HPRT mutant frequency in the nonsmokers was 18.7 +/- 12.0 x 10(-6), and in the smokers 26.6 +/- 18.5 x 10(-6) (mean +/- S.D., P < 0.01). Among 107 single base pair substitutions (SBS) in the coding region of the HPRT gene, one new mutable site, one novel nonsense mutation and three not previously reported SBS were identified. Transitions accounted for 59% of the SBS and transversions for 41%. GC > AT transitions were the predominant type of mutation, with 50% of all SBS. The mutations showed a nonrandom distribution along the coding sequence, with three significant hotspots at positions 143, 197 and 617 (13, 14 and 7 mutations, respectively). There was no difference between smokers and nonsmokers with regard to the distribution of mutations at these hotspot positions. However, 85% of the mutations at GC base pairs and 88% of the mutations at AT base pairs in smokers occurred at sites with guanine or thymine, respectively, in the nontranscribed DNA strand. Moreover, smokers had a higher frequency of transversions and lower frequency of transitions than nonsmokers did. Particularly, GC > TA transversions were increased in smokers (11%) compared to nonsmokers (2%), which suggests that tobacco-smoke induced adducts at guanine bases in the nontranscribed DNA strand contributes to the increase of HPRT mutation in smokers. Overall, these results were very similar to the mutational spectra in two younger study populations reported previously [K.J. Burkhart-Schultz, C.L. Thompson, I.M. Jones, Spectrum of somatic mutation at the hypoxanthine phosphoribosyltransferase (HPRT) gene of healthy people, Carcinogenesis 17 (1996) 1871-1883; A. Podlutsky, A.-M. Osterholm, S.-M. Hou, A. Hofmaier, B. Lambert, Spectrum of point mutations in the coding region of the hypoxanthine-guanine phosphoribosyltransferase, Carcinogenesis 19 (1998) 557-566]. With the possible exception of an increase of mutations at hotspot position 143, and a decrease of 5-methylcytosine deamination mediated transitions at CpG-sites in the older individuals, there were no differences between the mutational spectra of old and young adults. In conclusion, both smoking and ageing seem to have minor influences on the spectrum of HPRT mutation in T cells.

Spectrum of point mutations in the coding region of the hypoxanthine-guanine phosphoribosyltransferase (hprt) gene in human T-lymphocytes in vivo.

The hypoxanthine-guanine phosphoribosyl transferase (hprt) locus in 6-thioguanine (TG) resistant T-lymphocytes is a useful target for the study of somatic in vivo mutagenesis, since it provides information about a broad spectrum of mutation. Mutations in the hprt coding region were studied in 124 TG-resistant T-cell clones from 38 healthy, non-smoking male donors from a previously studied population of bus maintenance workers, fine-mechanics and laboratory personnel. Their mean age was 43 years (range 23-64) and their hprt mutant frequency was 9.3 +/- 5.2 x 10(-6) (mean +/- SD, range 1.4-22.6 x 10(-6)). Sequence analysis of hprt cDNA identified 115 unique mutations; 76% were simple base substitutions, 10% were +/-1 bp frameshifts, and 10% were small deletions within exons (3-52 bp). In addition, two tandem base substitutions and one complex mutation were observed. Simple base substitutions were observed at 55 (20%) of 281 sites known to be mutable in the hprt coding sequence. The distribution of these mutations was significantly different than would be expected based upon a Poisson distribution (P < 0.0001), suggesting the existence of 'hotspots'. All of the 87 simple base substitutions occurred at known mutable sites, but eight were substitutions of a kind that have not previously been reported at these sites. The most frequently mutated sites were cDNA positions 197 and 146, with six and five independent mutations respectively. Four mutations were observed at position 131, and three each at positions 143, 208, 508 and 617. Transitions (52%) were slightly more frequent than tranversions (48%), and mutations at GC base pairs (56%) more common than mutations at AT base pairs (44%). GC > AT was the most common type of base pair substitution (37%). The majority of the mutations at GC base pairs (78%) occurred at sites with G in the non-transcribed strand. All but one of eight mutations at CpG-sites were of the kind expected from deamination of methylated cytosine. Deletion of a single base pair (-1 frameshift) was three times more frequent than insertion of a single bp (+1 frameshift). Almost half (6/13) of the small (3-52 bp) deletions within the coding sequence clustered in the 5' end of exon 2. Short repeats and other sequence motifs that have been associated with replication error were found in the flanking regions of most of the frameshifts and small deletions. However, several differences in the local sequence context between +/-1 frameshift and deletion mutations were also noticed. The present results identify positions 197, 146 and possibly 131 as hotspots for base substitution mutations, and confirm previously reported hotspots at positions 197, 508 and 617. In addition, the earlier notion of a deletion hotspot in the 5'end of exon 2 was confirmed. The observations of these mutational cluster regions in different human populations suggest that they are due to endogeneous mechanisms of mutagenesis, or to ubiquitous environmental influences. The emerging background spectrum of somatic in vivo mutation in the human hprt gene provides a useful basis for comparisons with radiation or chemically induced mutational spectra, as well as with gene mutations in human tumors.

Molecular analysis of styrene oxide-induced hprt mutation in human T-lymphocytes.

Styrene-7,8-oxide (SO), the mutagenic in vivo metabolite of the widely used chemical monomer styrene, has been classified as a probable human carcinogen (IARC, 1994). We examined mutations in the hypoxanthine-guanine phosphoribosyl transferase (hprt) gene of primary human T-lymphocytes exposed to 0.2 mM SO for 6 days in vitro. PCR amplification and direct DNA sequencing were used to identify 55 SO-induced mutations from two experiments in which the mutation frequencies increased 3.6 and 4.8 times respectively, and 44 control mutations from untreated T-cell cultures. Base substitutions were the dominating type of mutation in both groups, with 35 and 23 independent changes, of which nine and six respectively, have not previously been described in human T-cells. Frameshift mutations (+/-1 bp) and small deletions (2-200 bp) were less frequent and splicing mutations more frequent among the SO-induced than among the control mutations. In SO-treated mutants, base substitutions in the coding region occurred at 15 sites, nine of which were AT bp, and in the splice donor and acceptor regions six of 10 mutated sites were AT bp. Altogether six independent mutations were found at site 539 in cells from the two SO experiments (four GC > AT and two GC > TA). In the control cultures, base substitutions in the coding and splicing regions were identified at 20 sites, eight of which were AT bp. In published data on hprt mutation in untreated T-cells in vivo and in vitro, 31 of 88 base substitutions have been reported to occur at AT bp. These results indicate that SO-induced mutations at the hprt locus in human T-lymphocytes are predominantly base substitutions, and suggest that in addition to DNA adducts at guanine bases, adducts at A and/or T bases also deserve attention with regard to the mutagenesis of SO.

Sequence analysis of deletion mutations at the HPRT locus of human T-lymphocytes: association of a palindromic structure with a breakpoint cluster in exon 2.

To study the structure and mechanism of deletion mutation in human somatic cells in vivo, we have identified and sequenced the breakpoints of 16 independent deletions at the hypoxanthine-guanine phosphoribosyl transferase (HPRT) locus in human T-lymphocytes. Seven deletions were found in exon 2, three in each of exon 3 and 6, and one in each of intron 3, exon 8 and exon 9. Most of the deletions seemed to result from non-homologous recombination, possibly by a slippage-misalignment mechanism between short repeat sequences. Putative secondary DNA structures, possibly acting as intermediates in the deletion formation, were identified in several mutants. Six of the seven exon 2 deletions had a breakpoint within a 12 bp region (in the 5' end of exon 2) which contains a 9 nucleotide palindrome (AACCAGGTT) and is preceded by a TGA direct repeat tract. One of the mutants had two deletions in tandem, separated by the palindrome. Another mutant, in which 23 bp containing the palindromic sequence was deleted, had an additional base (C) inserted between the breakpoints forming a direct repeat (gACGAC) in the deletion junction. Taken together with previously reported deletion mutations at the HPRT locus, these results suggest that the deletion cluster in the 5' part of HPRT exon 2 in T-cells in vivo is promoted by the 9 nucleotide palindrome sequence and the TGA repeat tract. The former may act as a stabilizer in a putative intermediate structure, and the latter may induce slippage and misalignment during replication.

Reduced proliferation rate of hypoxanthine-phosphoribosyl transferase mutant human T-lymphocytes in vitro.

The clonal hprt mutation assay in human T-cell is based on the assumption that wild-type cells and hypoxanthine-phosphoribosyl transferase (hprt) mutant cells survive and proliferate at the same rate during the expression phase which is required for the expression of in vitro-induced mutants. We have tested this assumption in a study of mutant frequency (MF) and proliferation rate at different time points during in vitro expansion of human T-cells in non-selective medium. Peripheral blood lymphocytes from 11 individuals were studied using standard cloning procedures to determine the cloning efficiency (CE) and the hprt MF by 6-thioguanine (TG) selection. Another cell portion from each individual was allowed to proliferate in bulk culture for 8 days in vitro, before measuring CE and MF as above. In the directly plated cell population the CE was 45% and the MF 18.7 +/- 15.3 x 10(-6) (mean +/- S.D.), whereas the in vitro expanded cell population showed a CE of 38% and a significantly reduced MF of 8.3 +/- 6.9 x 10(-6) (P = 0.0033). Thus, the mean MF was 56% lower in the in vitro expanded than in the directly plated cell population. The experiment was repeated in another group of ten individuals with essentially the same result. In a third experiment, freshly prepared cells from two donors were allowed to grow for up to 15 days in bulk culture in vitro. Cell growth, CE, and MF were determined every third day. The MF decreased gradually, and at day 12-15 it was only 25% of the initial value. The total number of clonable cells increased 13-fold during the 15 days of in vitro expansion, while the mutant, TG-resistant cell population increased only 3-fold. These results suggest that human hprt mutant T-lymphocytes have a reduced proliferation rate compared to wild-type cells during in vitro proliferation. Thus, measurements of chemical and radiation induced MF with the T-cell clonal assay may underestimate the true MF by a factor of 2 or more.

Ultrastructural analysis of organization of roots obtained from cell cultures at clinostating and under microgravity.

Data are presented of a comparative analysis on rhizogenesis in the Arabidopsis thaliana tissue culture growing in a solid nutrient medium under stationary conditions, clinostatic conditions and microgravity. Tissue samples weighing 100 mg. were set in the Petri dishes and placed in a horizontal slow clinostat /2 revs/min/. After 14 days of growth they were analyzed. On clinostating the number of roots formed from the callus cells was approximately one half the control. The formed root cap manifested no essential differences, in comparison with the stationary control, in the number of layers and cell sizes in its layers. In callusogenic roots, formed from clinostated cells, differentiation including root cap cells, proceeds without noticeable deviations from the norm. At the same time, gravireceptor cells do not function under these conditions. This is clearly displayed at a structural level in the location of amyloplasts-statoliths throughout the cytoplasm. The callus cell cultures experienced microgravity for 8 days. The number of formed roots under the influence of this factor was 36% relative to the stationary control. Root cap formation was abnormal. Gravireceptor cells did not formed under microgravity.