Analysis of mutations induced by replication of UV-damaged plasmid DNA in hela cell extracts

We have used an SV40-based shuttle vector, pZ189, to investigate the capacity of HeLa cell extracts to reproduce the in vivo process of mutation fixation. We showed previously that when UV-irradiated pZ189 is replicated in these extracts, bypass of UV photoproducts occurs, resulting in base substitution mutations in the supF gene of the vector. Here we report the DNA sequence characterization of a collection of 60 of these UV-induced mutants. Most of the mutations observed are single or tandem double base substitutions at dipyrimidine sites; of these, approximately 90% are G:C→A:T transitions. Mutations are observed predominantly at a few sites, in particular at positions 155 and 156 in the supF sequence. No dramatic differences in the mutation spectrum were observed when the orientation of the supF gene was reversed with respect to the SV40 origin of replication, suggesting that mutation fixation occurs similarly on both the leading and the lagging strands for DNA replication. Generally, the mutational hot spots observed in vitro are at the same sites as those observed when UV-irradiated pZ189 was passaged in human or monkey cells in culture. Thus, it appears that the replication and mutagenesis of UV-damaged templates in HeLa cell extracts accurately reflects these processes in the intact cell. © 1995 Wiley-Liss, Inc.     

Testing excision models for responses of mismatch-repair systems to UV photoproducts in DNA

Mismatch-repair (MMR) systems correct DNA replication errors and respond to a variety of DNA lesions. Previous observations that MMR antagonizes UV mutagenesis, and that the mismatch-recognition protein heterodimer MSH2*MSH6 (MutSalpha) selectively binds DNA containing "mismatched" photoproducts (T[CPD]T/AG, T[6-4]T/AG) but not "matched" photoproducts (T[CPD]T/AA, T[6-4]T/AA), suggested that mismatched photoproducts would provoke MMR excision similar to mismatched bases. Excision of incorrect nucleotides inserted opposite template photoproducts might then prevent UV-induced mutation. We tested T[CPD]T/AG DNA, in a sequence context in which it is bound substantially by hMutSalpha and in three other contexts, for stimulation of 3' MMR excision in mammalian nuclear extracts. T[CPD]T/AG was inactive in HeLa extracts, or in extracts deficient in the photoproduct-binding proteins DDB or XPC* hHR23B, arguing against interference from the nucleotide excision repair pathway. Prior incubation with hMutSalpha and MLH2.PMS2 (hMutLalpha) did not increase excision relative to homoduplex controls. T[6-4]T/AG also failed to provoke excision. T/G, C/A, and T/T substrates, even though bound by hMutSalpha no better than T[CPD]T/AG substrates, efficiently provoked excision. Even a substrate containing three T[CPD]T/AG photoproducts (in different contexts) did not significantly provoke excision. Thus, MMR may suppress UV mutagenesis by non-excisive mechanisms.     

A single (6-4) photoproduct inhibits plasmid DNA replication in xeroderma pigmentosum variant cell extracts

The human skin cancer-prone disease xeroderma pigmentosum variant (XPV) results from a mutation in the human RAD30 gene, which encodes the lesion bypass DNA polymerase eta. XPV cells are characterized by delayed completion of DNA replication and increased mutagenesis following UV-irradiation. Using extracts of an XPV lymphoblast cell line (GM2449C) that has a truncating mutation in the RAD30 gene, we investigated the effect of a (6-4) photoproduct and a cyclobutane pyrimidine dimer (CPD), at a unique -TT- site on either the leading or lagging strand, on plasmid DNA replication. Compared to normal cell extracts, XPV cell extracts have a reduced capacity to carry out complete replication of DNA containing either a (6-4) photoproduct or a CPD on the leading strand, whereas there is little difference between the two cell extracts in replication of DNA containing a lesion on the lagging strand. Inhibition of replication in the presence of a (6-4) photoproduct is attributed to arrest of nascent DNA strand synthesis at the lesion site; in XPV cell extracts, the proportion of arrested products is increased compared to that of normal cell extracts. These results are consistent with a requirement for functional DNA polymerase eta in the replication of a double-stranded plasmid containing either a (6-4) photoproduct or a CPD, on the leading but not the lagging strand.     

In vivo mutagenesis in the lungs of gpt-delta transgenic mice treated intratracheally with 1,6-dinitropyrene

1,6-Dinitropyrene (1,6-DNP) is a ubiquitous airborne pollutant found in diesel exhaust. In this study, mutagenesis was examined in the lungs of gpt-delta transgenic mice after intratracheal instillation of 0-0.1 mg 1,6-DNP. In addition, the 1,6-DNP-induced gpt mutation spectrum was compared with that of control mice. A single intratracheal injection of 0-0.05 mg 1,6-DNP resulted in significant dose-dependent increases in mutant frequency; the induced mutant frequency declined at the 0.1 mg dose. The average lung mutant frequencies at doses of 0.025, 0.05, and 0.1 mg 1,6-DNP were 2.9-, 4.1-, and 1.9-times higher than for control mice ((0.50+/-0.16)x10(-5)). The major mutations induced by 1,6-DNP included G:C-->A:T transitions, G:C-->T:A transversions, and 1-base deletions. Among the G:C-->A:T transitions isolated from 1,6-DNP-treated mice, five (at nucleotide positions 64, 110, 115, 116, and 418) were observed in four or more animals. These positions therefore are potential hotspots for 1,6-DNP mutation. The predominant frameshift mutations following 1,6-DNP treatment included single base pair deletions at G:C (9/13=69%). The results of this study indicate that 1,6-DNP is mutagenic for the lungs of mice.     

Cloning, Expression, and Partial Purification of Rep78: An Adeno-Associated Virus Replication Protein

Using the vaccinia virus/T7-RNA polymerase transient protein expression system, the AAV Rep78 protein was expressed in mammalian cells. Rep78 protein was found localized primarily to the nucleus of cells. Maximal steady-state protein levels were reached as early as 12 hr postinfection, with no discernable increase at later time points. The Rep78 protein has been partially purified from nuclear extracts of the expression system. We have successfully used the cloned, purified Rep78 protein to complement an uninfected HeLa cell extract in an in vitro AAV DNA replication assay. Rep78-containing fractions are sufficient to make an uninfected HeLa cell extract competent for AAV DNA replication.     

UV lesions located on the leading strand inhibit DNA replication but do not inhibit SV40 T-antigen helicase activity

DNA replication in eucaryotic cells involves a variety of proteins which synthesize the leading and lagging strands in an asymmetric coordinated manner. To analyse the effect of this asymmetry on the translesion synthesis of UV-induced lesions, we have incubated SV40 origin-containing plasmids with a unique site-specific cis,syn-cyclobutane dimer or a pyrimidine-pyrimidone (6-4) photoproduct on either the leading or lagging strand template with DNA replication-competent extracts made from human HeLa cells. Two dimensional agarose gel electrophoresis analyses revealed a strong blockage of fork progression only when the UV lesion is located on the leading strand template. Because DNA helicases are responsible for unwinding duplex DNA ahead of the fork and are then the first component to encounter any potential lesion, we tested the effect of these single photoproducts on the unwinding activity of the SV40 T antigen, the major helicase in our in vitro replication assay. We showed that the activity of the SV40 T-antigen helicase is not inhibited by UV-induced DNA lesions in double-stranded DNA substrate.     

Chromatid exchanges may be induced by damage in sites of transcriptional activity

A conditional expression system has allowed us to vary the expressionlevel of the xeroderma pigmentosum group A (XPA) photoproduct-specificDNA-binding protein in human cells and so control the responseof cells to damage by UV light. Using a form of XPA that containsa single missense mutation (R207G) enabled us to study a lowerrange of function than that obtained with the wild-type sequence.This form of XPA has been previously shown to stimulate pyrimidinedimer excision preferentially in actively transcribed genes.We found that UV resistance increased as a linear function ofXPA expression levels. Excision of (6–4) pyrimidine-pyrimidonephotoproducts in the whole genome increased to a maximum atabout the haploid level of XPA expression, but there was littlepyrimidine dimer excision from the whole genome. SCE frequencyinduced by UV light was high in cells with no XPA expressionand fell rapidly with increasing levels of XPA expression within0–50% of the haploid level of expression. No further reductionin SCE frequency was produced at the highest levels of XPA expression,when repair replication extended to the overall genome. We speculatethat a low level of repair, especially that occurring in activelytranscribed genes, may selectively eliminate photoproducts thatare particularly important in causing cell killing and SCEs. ³To whom correspondence should be addressed     

Host components required for the replication of the resistance plasmid R124 and a copy mutant derivative

The replication of R124, and a copy mutant derivative of it, was measured with respect to dependence on the host DnaA, DnaB, DnaC, DnaE, DnaG, and Po1A gene products. Both plasmids replicated under conditions where the DnaA gene product was inactivated or where the polymerising activity of the PolA gene product was reduced. In contrast, neither plasmid replicated to any appreciable extent, if the DnaB, DnaC, DnaE or DnaG gene products were inactivated. R124 integratively suppressed the lesion of the dnaA mutant but the copy mutant derivative had only a very weak suppressing effect. Neither plasmid suppressed the lesions of any of the other dna mutants.     

Construction of transposition insertion libraries and specific gene inactivation in the pathogen Lactococcus garvieae

This paper reports the development of genetic tools in Lactococcus garvieae, an important Gram-positive bacterial pathogen affecting both fish and mammals. The vector pGKV210, a broad host range vector, was introduced by electroporation into L. garvieae UNIUD074. The maximal frequency obtained was 3.2 x 10(5) transformants/mug of DNA. Moreover, this effect is highly reproducible and appears to be constant, since all L. garvieae strains tested were transformed. Once the optimal transformation procedure was established, it was used to generate isogenic and transposition mutants. Insertional mutagenesis of the L. garvieae SA9H10L gene, similar to a Streptococcus pyogenes gene encoding the M protein (emm64), was carried out using the conditional replication plasmid pORI19. Transposition mutagenesis using the streptococcal temperature-sensitive suicide vector pTV408 to deliver Tn917 into the chromosome of L. garvieae was also achieved at a frequency of ca. 10(-4). Transposon flanking DNA sequences were obtained by plasmid rescue in Escherichia coli and their sequencing analysis demonstrated that the transposon was inserted at different chromosomal loci. Tn917 also made it possible to select a mutant in the operon involved in mannitol fermentation in this microorganism. The results obtained in the present study lay the foundation for future research on the virulence mechanisms of L. garvieae.     

Rolling circle replication of human papillomavirus type 16 DNA in epithelial cell extracts

Replication of human papillomavirus (HPV) genomes requires an origin of replication and two viral proteins: the DNA helicase E1 and the auxiliary factor E2. To dissect the profile of HPV replication in the epithelium, we analyzed replication of an HPV16 origin-containing plasmid in human epithelial cell extracts supplemented with purified E1 and E2. We found that in addition to well-defined circular replication products, high-molecular-weight DNA was synthesized in a manner that depended on the origin, E1 and E2. The high-molecular-weight DNA was converted to a unit-length linear DNA by treatment with restriction enzymes that cleave the plasmid once, implying that a concatemeric DNA was generated by rolling circle replication. Nicking or relaxing the template plasmid enhanced the level of HPV rolling circle replication. In contrast, the addition of an extract from non-epithelial cells diminished the generation of the rolling circle replication product in the epithelial cell extract, indicating factors that counteract HPV rolling circle replication. These results suggest a rolling circle replication mechanism for the HPV genome in cervical epithelial cells, which may have physiological implications for generation of the tandem-repeated HPV genomes occasionally found integrated into the chromosome of cervical cancer cells.     

In vitro encapsidation of plasmid DNA into human adenovirus empty capsids

Plasmid DNA, added to extracts of human adenovirus type 3-infected HeLa cells, binds to empty viral capsids and can be purified using cesium density gradient centrifugation. The fraction of DNA bound depends on the amount of DNA added to the extract, and the capsid partially protects the bound DNA from digestion by DNase I. This capsid binding of plasmid DNA does not require the presence of the adenovirus DNA packaging sequence. However, the presence of the adenovirus packaging sequence in the plasmid results in better protection of the bound plasmid molecule from cellular nucleases.     

Pyrimidine-rich region mutations compensate for a stem-loop V lesion in the 5' noncoding region of poliovirus genomic RNA

Five revertants of a linker-scanning mutation adjacent to the stem-loop V attenuation determinant (X472) in the 5' noncoding region of poliovirus RNA were independently isolated from neuroblastoma cells and contained RNAs with seven nucleotide changes in the pyrimidine-rich region. Generation of the identical rare second-site mutations suggests the existence of a replicase-dependent mutagenesis mechanism during poliovirus replication. Enzymatic structure probing of the mutated pyrimidine-rich domain identified secondary structure changes between stem-loops V and VI. A consensus secondary structure model is presented for wild-type stem-loops V and VI and the pyrimidine-rich region located in the 5' noncoding region of poliovirus RNA. A pyrimidine-rich region mutant (X472-R4N) produced large plaques in neuroblastoma cells and small plaques in HeLa cells, but the plaque size differences were not due to cell-type differences in viral translation or RNA replication. Release of X472-R4N from HeLa cells was 10-fold lower than release from neuroblastoma cells, which may explain the small plaque phenotype of X472-R4N in HeLa cells. Wild-type poliovirus was also released more efficiently from neuroblastoma cells (approximately 4-fold increase compared with release from HeLa cells), indicating that poliovirus neurotropism may be influenced by the cell-type efficiency of virus release. Thermal treatment increased the levels of infectious X472-R4N virions but not wild-type virus particles; thus RNA sequence and structural changes in the mutated 5' noncoding region of X472-R4N may have altered RNA-protein interactions necessary for virus infectivity.     

A rapid method to monitor repair and mis-repair of DNA double-strand breaks by using cell extracts of the yeast Saccharomyces cerevisiae

We present a rapid in vitro method to scan the repair of DNA double-strand breaks (DSBs). A DSB was introduced at the EcoRI site within the lacZ gene of the plasmid pUC18 and the plasmid was exposed to cellular extracts from a wild-type repair-competent (RAD) and a mutant (rad52Δ) strain of the yeast Saccharomyces cerevisiae. The fidelity of rejoining was determined by the expression of the lacZ gene after bacterial transformation with the treated plasmid. A cellular extract from the yeast S. cerevisiae was found to be capable of rejoining DNA DSBs. Breaks at the EcoRI site were rejoined by extracts from both wild-type and mutant strains to form circular plasmids with almost equal efficiency. However, the fidelity of rejoining was lower for the rad52Δ extract than for normal wild-type. Received: 2 September /2 November 1997     

Characteristics of a persistent respiratory syncytial virus infection in HeLa cells

Persistent infection with respiratory syncytial (RS) virus has been established in HeLa cells. The persistently infected cell line (HeLa_RS) continues to produce virus (RSpi) at low levels after 230 passages during 3 years. The cells are morphologically similar to the parental HeLa cell line, and susceptible to vesicular stomatitis virus, but resist superinfection with standard RS virus (RS_wt). The block in RS_wt replication is not at attachment. Although infectious center and immunofluorescence assays suggested that only 5 to 30% of the cells in the culture were infected, 30 of 32 clones isolated from HeLa_RS contained some cells with virus antigen and 23 of those clones produced virus. All the clones, including the 2 that appeared not to be infected, were more resistant to RS_wt than HeLa. The clones that produced virus were significantly more resistant than the others. RS_pi is a small-plaque mutant, but not a temperature-sensitive mutant, of RS_wt. Although prior infection of HeLa with RS_pi interferes with RS_wt replication, the interference appears not to be caused by defective interfering particles, but by RS_pi virions. RS_pi initiates a persistent infection in HeLa only after a cytolytic phase similar to that which preceded the establishment of HeLa_RS.     

A similar defect in UV-induced mutagenesis conferred by the rad6 and rad18 mutations of Saccharomyces cerevisiae

The single rad6 and rad18 yeast mutants share a number of physiological and biochemical properties related to DNA repair, suggesting that they affect closely related steps. However, it has been reported that UV-induced mutagenesis is considerably more depressed in rad6 than it is in rad18 cells. In an attempt to better understand the role of these genes, a genetic system believed to differentiate between targeted and untargeted events was used. The data are interpreted to mean that both mutations prevent the occurrence of targeted events, as if they prevent error-prone replication in front of pyrimidine dimers. The number of non-targeted mutants per survivor in each mutant was increased by UV irradiation. This may correspond to a stimulation of the error-prone replication.     

HBc二聚体组装核衣壳相关功能域突变对HBV复制的影响

目的 探讨乙型肝炎病毒核心蛋白(hepatitis B virus core protein,HBc)二聚体组装相关功能域突变对核心颗粒组装及HBV复制的影响.方法 基于HBc空间结构,PCR定点诱变二聚体组装核衣壳相关功能域重要氨基酸位点,以pcDNA3.1为载体构建4个突变体表达质粒pHBc14-18M、pHBc120-135M、pHBc23-39M和pHBc122-139M.将突变质粒与HBc缺失的含1.2拷贝HBV基因质粒pHBV1.2-core-共转染HepG2细胞,通过Northern blot检测HBV前基因组(pgRNA),Southern blot检测复制中间体,非变性琼脂糖凝胶电泳(native agarose gel electrophoresis)及Western blot检测细胞核心颗粒观察突变质粒自身形成核衣壳情况.将突变质粒与含有1.2拷贝HBV基因质粒pHBV1.2共转染HepG2细胞观测突变质粒对野生型HBc组装及HBV复制的影响.结果 突变质粒与pHBV1.2-core-质粒共转染HepG2细胞,pHBc14-18M、pHBc120-135M和pHBc122-139M突变能够组成核衣壳样结构.pHBc23-39M不能形成核衣壳样结构.Northern blot结果显示所有突变质粒组均未见pgRNA条带,Southern blot检测复制中间体也未见条带.将突变质粒与pHBV1.2共转染HepG2细胞,pHBc14-18M、pHBc120-135M和pHBc122-139M组HBV复制中间体及上清中病毒颗粒明显减少,而pHBc23-39M组无减少.结论 HBc23-39位氨基酸突变可阻止二聚体多聚化,不能形成核衣壳样结构,且不能与野生HBc二聚体相互作用.HBc14-18、120-135、122-139区域的氨基酸突变,能够形成核衣壳样结构但不支持HBV DNA复制,并且能与野生HBc二聚体相互作用,形成杂合体,干扰野生型HBV DNA的复制.     

Posttreatment with sodium arsenite alters the mutational spectrum induced by ultraviolet light irradiation in Chinese hamster ovary cells.

Arsenic, a potent carcinogen, fails to induce gene mutations in mammalian cells. However, posttreatment of ultraviolet light (UV) irradiated cells with sodium arsenite synergistically enhances the mutation frequency on the hypoxanthine (guanine) phosphoribosyltransferase locus. To investigate the molecular mechanism of the comutagenic effects of sodium arsenite, we characterized the alterations of nucleotide sequences in 30 UV-induced and 39 sodium arsenite enhanced hprt mutants from Chinese hamster ovary K1 cells by direct sequencing of mRNA-PCR amplified cDNA. The majority of sequence alterations derived from UV irradiation (80%) and from sodium arsenite posttreatment (70%) were single base substitutions. UV irradiation induced all types of base substitutions. Among them, 57% were transversions. The frequency of transversions increased to 70% in sodium arsenite enhanced mutants. While base substitutions observed in UV-induced mutants were evenly distributed along with the whole coding region, exons 3 and 8 were most frequently mutated in sodium arsenite enhanced mutants. Sodium arsenite posttreatment did not alter the strand bias for mutation induction, i.e., 73% and 78%, of the mutations were located on the non-transcribed strand in UV-induced and sodium arsenite enhanced mutants, respectively. In contrast to UV-induced mutations, bases at the 5' position of TT and the 3' position of CT sequences were the most frequent mutation sites observed in sodium arsenite enhanced mutants. We hypothesize that sodium arsenite may interfere with the process of mutation fixation of TT and CT dimers during DNA replication.