Targeted mutation at cytosine-containing pyrimidine dimers: studies of Escherichia coli B/r with acetophenone and 313-nm light

Fume emissions from a low-cost 3-D printer with various filaments

3-D printing is an additive manufacturing process involving the injection of melted thermoplastic polymers, which are then laid down in layers to achieve a pre-designed shape. The heated deposition process raises concerns of potential aerosol and volatile organic compounds (VOC) emission and exposure. The decreasing cost of desktop 3-D printers has made the use of 3-D printers more acceptable in non-industrial workplaces lacking sufficient ventilation. Meanwhile, little is known about the characteristics of 3-D printing fume emission. The objective of this study was to characterize aerosols and VOC emissions generated from various filaments used with a low-cost 3-D printer in an environmental testing chamber. A pre-designed object was printed in 1.25 hours using eight types of filaments. A scanning mobility particle sizer and an aerodynamic particle sizer were employed to measure the particle size distribution in sub-half-micron fraction (<0.5 µm) and super-half-micron fraction (0.5-20 µm), respectively. VOC concentration was monitored real-time by a photoionization detector and sampled with a tri-sorbent thermal desorption tube, and analyzed by thermal desorption gas chromatography mass spectrometry (TD-GC/MS). Results showed high levels of fume particles emission rate (1.0 × 10⁷ to 1.2 × 10¹⁰ #/min) in the sub-half-micron range with mode sizes of 41-83 nm. Particle concentrations peaked during the heat-up and solid layer printing periods. Total VOC concentration in the chamber followed a first-order buildup, with predominant VOC species in the chamber were breakdown and reaction products of the filaments, such as styrene from ABS filaments. These findings and exposure scenario estimation suggest that although the VOC concentrations were much lower than occupational exposure limits, particles with size less than micron might be a concern for users of low-cost 3-D printers due to high respirablity, especially if used in settings without proper guidance and engineering control.

Photoreversal of UV-potentiated glutamine tRNA suppressor mutations in excision proficient Escherichia coli

UV-irradiated excision proficient Escherichia coli were exposed to light for photoenzymatic reversal (PR) of cyclobutane pyrimidine dimers (CPD) and assayed for reversion mutation (glutamine tRNA suppressor mutations) on semi-enriched medium or on the same medium containing acriflavine to inhibit excision repair. The initial mutation frequency without PR was relatively greater when assayed with acriflavine, and this difference increased as larger UV fluences were used. The PR kinetics were first order and about the same or slightly faster when cells were assayed with acriflavine (after 15, 30 or 45 J/m2, respectively). The results indicated mutation targeting by CPD in excision proficient cells. These results and conclusion contrast sharply with the original study of this type done several years ago. PR kinetics were considerably slower with assays containing acriflavine, sustaining the idea that PR causes repair of non-dimer targeting lesions by enhancing excision repair. To explain this contrast we devised a fluence-decrement rate for estimating the effectiveness of PR and measured PR-dependent excision repair (PER) as the difference in the fluence-decrement rate with excision proficient and deficient cells. PER was more evident when cells were prepared as in the original study but was still an insufficient factor. More importantly, the original study included a component of indirect photoreactivation or photoprotection (using unfiltered PR light) which accentuated the role of excision repair. Taking these factors into account, the original data also are consistent with the model that glutamine tRNA suppressor mutations produced by UV-mutagenesis in excision proficient E. coli result from targeting by CPD just as in excision defective cells. Thus, with regards to a common UV mutation assay, there does not appear to be two types of targeting lesion depending on excision proficiency.

Mutation frequency decline in Escherichia coli. II. Kinetics support the involvement of transcription-coupled excision repair

Mutation frequency decline (MFD) in Escherichia coli was examined to demonstrate repair of targeting photoproducts during the post-UV incubation required in this process. Repair of mutation-targeting cyclobutane pyrimidine dimers (T < > C) was demonstrated when a correlation was established between the mutation frequency normally associated with these lesions and the rate of mutation production at these lesions by spontaneous deamination of cytosines and photoreversal in ung-defective cells. An incubation producing a decline in mutation frequency, i.e., MFD, also produces lower rates of mutation increase via the deamination mechanism. Since the latter assay involves processes entirely within the post-UV incubation period, the lower rates are attributed to rapid transcription-coupled nucleotide excision repair (TCR) that reduces the number of relevant T < > C dimers during this period. Rediscovery of the neglected fact that MFD can be stimulated by post-UV incubation in buffer alone is part of the analysis. Results presented here and a variety of others are discussed to support a model of MFD as a particular example of TCR: effective repair of photoproducts in the transcribed DNA strand that target glutamine tRNA suppressor mutations occurs during the appropriate post-UV incubation and is responsible for MFD.

Mechanisms of transcription-repair coupling and mutation frequency decline

Mutation frequency decline is the rapid and irreversible decline in the suppressor mutation frequency of Escherichia coli cells if the cells are kept in nongrowth media immediately following the mutagenic treatment. The gene mfd, which is necessary for mutation frequency decline, encodes a protein of 130 kDa which couples transcription to excision repair by binding to RNA polymerase and to UvrA, which is the damage recognition subunit of the excision repair enzyme. Although current evidence suggests that transcription-repair coupling is the cause of the preferential repair of the transcribed strand of mRNA encoding genes as well as of suppressor tRNA genes, the decline occurs under stringent response conditions in which the tRNA genes are not efficiently transcribed. Thus, the mechanism of strand-specific repair is well understood, but some questions remain regarding the precise mechanism of mutation frequency decline.

The two-step model of UV mutagenesis reassessed: deamination of cytosine in cyclobutane dimers as the likely source of the mutations associated with photoreactivation

A large increase in the incidence of bacteriophage mutants is found after photoreactivation of UV-irradiated phage S13. The increase was seen only when the irradiated phage were stored before they were photoreactivated; the maximum mutation frequency was achieved after storage for 2 h at 4 degrees C or 30 min at 37 degrees C. The mutations can be attributed entirely to deamination of cytosine in cyclobutane dimers. Naked S13 DNA was stored for 2 h at 37 degrees C after being irradiated with wavelengths greater than or equal to 290 nm in the presence of 0.2% acetophenone, which sensitizes the formation of thymine-thymine but not cytosine-containing dimers; the specific mutation frequency was 7.2-fold lower compared to the frequency produced by irradiation in the absence of the photosensitizer, confirming that cytosine dimers are a major source of mutations. These results undermine the basis for the two-step model of UV mutagenesis in which a distinctly separate misincorporation step is supposed to precede the lesion bypass step; instead the results support a different two-step model, in which a deamination step precedes the bypass. The S13 capsid appears to completely inhibit the putative deamination reaction at about 75% of the dimer sites.

Inhibition of transient gene expression in Chinese hamster ovary cells by triplet-sensitized UV-B irradiation of transfected DNA

The biological effectiveness of thymine-thymine cyclobutane dimers specifically induced by photosensitized ultraviolet-B irradiation was analyzed by host-cell reactivation of triplet-sensitized, UV-B irradiated plasmid pRSV beta gal DNA transfected into normal and repair-deficient Chinese hamster ovary cells. For comparison, pRSV beta gal DNA was also UV-C irradiated and transfected into the same cell lines. Ultraviolet endonuclease-sensitive site induction was determined after UV-C irradiation or acetophenone-sensitized UV-B irradiation of plasmid pRSV beta gal DNA. These data were used to calculate the number of cyclobutane pyrimidine dimers required to inactivate expression of the lacZ reporter gene in each irradiation condition. Transfection with UV-C-irradiated plasmid DNA resulted in a significantly greater reduction of reporter gene expression than did transfection with acetophenone-sensitized UV-B-irradiated pRSV beta gal DNA at equivalent induction of enzyme-sensitive sites. Since only a fraction of the inhibition could be accounted for by noncyclobutane dimer photoproducts, these results suggest that cytosine-containing pyrimidine cyclobutane dimers may be more effective than thymine-thymine dimers in inhibiting transient gene expression as measured in such host-cell reactivation experiments in mammalian cells.

Specificity of mutation by UV light and delayed photoreversal in umuC-defective Escherichia coli K-12: a targeting intermediate at pyrimidine dimers

Prototrophic mutants produced by UV light in Escherichia coli K-12 strains with argE3(Oc) and hisG4(Oc) defects are distinguished as backmutations and specific nonsense suppressor mutations. In strains carrying a umuC defect, mutants are not produced unless irradiated cells are incubated and then exposed to photoreversing light (delayed photoreversal mutagenesis). The mutants thus produced are found to be specifically suppressor mutations and not backmutations. The suppressor mutations are primarily glutamine tRNA ochre suppressor mutations, which have been attributed previously to mutation targeted at T = C pyrimidine dimers. In a lexA51 recA441 strain, where the SOS mutagenesis functions are constitutive, targeting at dimers is confirmed by demonstrating that the induction of glutamine tRNA suppressor mutations is susceptible to photoreversal. In the same strain induction of backmutations is not susceptible to photoreversal. Thus delayed photoreversal mutagenesis produces suppressor mutations that can be targeted at pyrimidine dimers and does not produce backmutations that are not targeted at pyrimidine dimers. This correlation supports the idea that delayed photoreversal mutagenesis in umuC defective cells reflects a mutation process arrested at a targeting pyrimidine dimer photoproduct, which is the immediate cause of both the alteration in DNA sequence and the obstruction (unless repaired) to mutation fixation and ultimate expression.

Mutation probe of gene structure in E. coli: suppressor mutations in the seven-tRNA operon

Cells defective in uracil-DNA glycosylase (ung::Tn10) were used in two ways to reveal differences in select point mutations (GC to AT transitions) within the seven-tRNA operon of E. coli. The mutations were indicated as de novo or converted glutamine tRNA suppressor mutations in the genes glnU and/or glnV: the kinetics of photoenzymatic monomerization of pyrimidine dimers quantitated by ung-dependent UV mutagenesis indicated more rapid repair of dimers at sites for converted suppressor mutation than of dimers at sites for de novo suppressor mutation, and spontaneous deamination of cytosine was considerably more frequent at sites for converted suppressor mutation than at sites for de novo suppressor mutation. To explain these results we suggest the physical structure of the DNA in vivo is different at different sites in the seven-tRNA operon. The non-transcribed strand including specifically the anticodon region of the site for converted suppressor mutation may frequently be looped out in a single strand so that a T = C dimer is more accessible to DNA photolyase or a free cytosine residue of non-irradiated DNA is in an aqueous environment conducive to deamination. In addition, we analysed the spontaneous de novo suppressor mutation data to determine an estimate for the in vivo rate of cytosine deamination in double strand DNA of 3.2 X 10(-13)/sec.

The C-C (6-4) UV photoproduct is mutagenic in Escherichia coli

Mutation induced by ultraviolet light is predominantly targeted by UV photoproducts. Two primary candidates for the premutagenic lesion are the cyclobutane pyrimidine dimer and the less frequent (by a factor of 10) pyrimidine-pyrimidone (6-4) photoproduct. Methylation of the 3'-cytosine in the sequence 5' CCAGG 3' reduces the yield of (6-4) lesions, but not of cyclobutane dimers, at these sites. By taking advantage of mutants deficient in cytosine methylation, we show here that at the three sites in the lacI gene of Escherichia coli having this sequence, the specific increase in the formation of the (6-4) photoproducts is accompanied by a concomitant increase in mutation. At each site, a G X C to A X T transition results in an amber mutation. In the unmethylated state, these sites become among the most frequent nonsense mutations recovered. We conclude that the (6-4) photoproduct constitutes a major premutagenic lesion in E. coli.

Thermal resistance of UV-mutagenesis to photoreactivation in E. coli B/r uvrA ung: estimate of activation energy and further analysis

Ultraviolet light (UV) induced mutations in the glnU and glnVa tRNA genes in Escherichia coli are thought to be targeted by UV photoproducts. In a previous study with a uracil-DNA glycosylase deficient strain, UV-induced glnU0 and glnV0 tRNA suppressor mutations became resistant to photoreactivation (PR) following thermal treatment. It was proposed that deamination of cytosine in the cytosine-containing cyclobutyl dimers at the sites of these suppressor mutations produced uracil residues in sequence upon PR. In the absence of glycosylase, the C----U conversion yielded the requisite G:C----A:T transitions. In the present study, this thermal resistance of UV-mutagenesis to PR is characterized. It is dependent on the initial UV-fluence and temperature of holding but not on the UmuC+ gene product. The data obtained yield an estimate of an activation energy of 17 +/- 3 kcal/mol for the deamination of cytosines contained in dimers. This compares to 29 kcal/mol for unaffected cytosines in DNA. In addition, an estimate of the probability of cyclobutyl dimer formation at the target sites for glnU0 and glnV0 suppressor mutations indicate that these lesions can not entirely account for the mutation frequencies recovered in the absence of PR. This is interpreted as an indication that, in addition to thymine-cytosine cyclobutyl dimers, other UV-induced lesions, possibly Thy(6-4)Cyt photoproducts, may also target glnU0 and glnV0 suppressor mutations.