Thiouridine residues in tRNAs are responsible for a synergistic effect of UVA and UVB light in photoinactivation of Escherichia coli.

Since different wavelengths of light impact different cellular targets, microorganisms exposed to natural sunlight experience a combination of multiple stressors. In order to better understand the effects of sunlight on microorganisms we, therefore, need to understand how different wavelength act alone and in combination. Here, we describe a synergistic effect between UVA and UVB irradiation on viability of Escherichia coli bacteria. To investigate the basis of this synergistic effect we analysed mutant strains that were obtained through selection for increased resistance to combined UVA and UVB. By identifying and reconstructing genetic changes in the resistant strains we provide evidence that UVA-absorbing thiouridine residues in tRNAs are the key to the synergistic effect. Our study provides insights into how naturally occurring combinations of stressors can interact, and points to new ways for controlling microbial populations.

Combined exposure of ELF magnetic fields and x-rays increased mutant yields compared with x-rays alone in pTN89 plasmids.

We have examined mutations in the supF gene carried by pTN89 plasmids in Escherichia coli (E. coli) to examine the effects of extremely low frequency magnetic fields (ELFMFs) and/or X-rays to the plasmids. The plasmids were subjected to sham exposure or exposed to an ELFMF (5 mT), with or without X-ray irradiation (10 Gy). For the combined treatments, exposure to the ELFMF was immediately before or after X-ray irradiation. The mutant fractions were 0.94x10(-5 )for X-rays alone, 1.58x10(-5) for an ELFMF followed by X-rays, and 3.64x10(-5) for X-rays followed by an ELFMF. Increased mutant fraction was not detected following exposure to a magnetic field alone, or after sham exposure. The mutant fraction for X-rays followed by an ELFMF was significantly higher than those of other treatments. Sequence analysis of the supF mutant plasmids revealed that base substitutions were dominant on exposure to X-rays alone and X-rays plus an ELFMF. Several types of deletions were detected in only the combined treatments, but not with X-rays alone. We could not find any mutant colonies in sham irradiated and an ELFMF alone treatment, but exposure to ELFMFs immediately before or after X-ray irradiation may enhance the mutations. Our results indicate that an ELFMF increases mutation and alters the spectrum of mutations.

[Escherichia coli ribosomes as the model to test new photoactivated tRNA analogues, containing 6-thioguanosine]. / Ribosomy Escherichia coli kak model'dlia aprobattsii novykh fotoaffinnykh analogov tRNK, soderzhashchikh ostatki 6-tioguanozina.

Photoreactive derivatives of tRNAs, containing 6-thioguanosine or diazirine derivative of 5-methyleneaminouridine were compared as probes to modify Escherichia coli ribosomes. The derivatives of tRNA were synthesized by T7 transcription Proportion of the modified nucleotide analogues was optimised to obtain good yield, analogue incorporation and binding to the ribosome. Complexes of the tRNA analogues with the ribosomal P-site were irradiated with mild UV light. Cross-links were analysed by oligonucleotide-directed hydrolysis of rRNA by RNase H and reverse transcription. 6-thioguanosine was proved to be a perspective reagent for cross-linking studies of complex ribonucleoproteides.

Inhibition of sulfur incorporation to transfer RNA by ultraviolet-A radiation in Escherichia coli.

tRNA sulfurtransferase activity was assayed in Escherichia coli cell extracts obtained from bacterial suspensions exposed to a sub-lethal dose of ultraviolet-A radiation (fluence 148 kJ m(-2)) imparted at a low fluence rate (41 W m(-2)). We found that the irradiation reduced the enzymatic activity to one fourth of the control value, indicating that ultraviolet-A exposure inhibits the synthesis of 4-thiouridine, the most abundant thionucleoside in E. coli tRNA. Changes in the tRNA content of 4-thiouridine and its derived photoproduct 5-(4'-pyrimidin 2'-one) cytosine were studied in bacteria growing under ultraviolet-A irradiation. In these conditions the accumulation of photoproduct was limited, and the kinetics of this process was non-coincident with disappearance of 4-thiouridine. The results, which are compatible with the fact that ultraviolet-A induces an inhibition of the 4-thiouridine synthesis, suggest that the effect of radiation on tRNA modification is relevant to tRNA photo-inactivation in growing bacteria.

Transient reduction in the tRNA 4-thiouridine content induced by ultraviolet A during post-irradiation growth in Enterobacter cloacae.

The influence of previous exposure to ultraviolet-A radiation (UVA) was studied on the susceptibility of Enterobacter cloacae to undergo the growth delay effect. Comparison of growth curves corresponding to irradiated and control cells showed that a previous treatment with UVA almost abolished the growth delay effect. UV absorption spectra of tRNA, and reverse phase HPLC analysis of hydrolysed tRNA, demonstrated a low content of 4-thiouridine in E. cloacae cells grown after UVA exposure at low doses. Since 4-thiouridine is the UVA target responsible for initiation of growth delay, this observation explained the influence of previous exposure to UVA on the susceptibility of this organism to undergo growth delay. A similar but weaker alteration was found when Escherichia coli was assayed. The results suggest that, in addition to cross-linking with cytidine residues, the content of 4-thiouridine in tRNA may be modified by UVA by an unknown mechanism.

Three-dimensional folding of the tRNA-like domain of Escherichia coli tmRNA.

UV irradiation of Escherichia coli tmRNA both on and off the ribosome induced covalent cross-links between its 3'- and its 5'-terminal segments. Cross-linking was unaffected in a molecule that lacked the tag-peptide codon region and pseudoknots 2, 3, and 4. Intact and truncated cross-linked tmRNAs were aminoacylated as efficiently as the respective nonirradiated molecules, suggesting that the added UV-induced bonds did not disturb tmRNA conformation. Using RNase H digestion followed by primer extension with reverse transcriptase, two cross-linked sites were identified within the tRNA-like region of tmRNA. The first was formed between nucleotides U9/U10 near the 5' end and nucleotides C346/U347 in the T loop. The second cross-link involved residues at positions 25-28 and 326-329 within helix 2a. Together with comparative sequence analysis, these findings yielded a three-dimensional model of the tRNA-like domain of E. coli tmRNA. Despite significant reduction of the D domain and the proximity of U9/U10 and C346/U347, the model closely resembles the L-shaped structure of canonical tRNA.

Oligonucleotide-conjugated thiazole orange probes as "light-up" probes for messenger ribonucleic acid molecules in living cells.

"Light-up" probes, icosa-alpha-thymidylate-thiazole orange conjugates, for the in situ time-resolved detection of messenger ribonucleic acid (mRNA) in living cells are evaluated. Upon annealing with polyA in aqueous solutions, the icosa-alpha-thymidylate-thiazole orange conjugates were shown to be up to 15 times more fluorescent. Microinjection of these probes into adherent fibroblasts resulted in high yields of hybridization and fluorescent signals. Incubation of cells in the presence of these probes resulted in facile internalization of the probe and similar painting of the messenger RNA in the nuclear and cytosolic regions.

Effects of photoreactivation of cyclobutane pyrimidine dimers and pyrimidine (6-4) pyrimidone photoproducts on ultraviolet mutagenesis in SOS-induced repair-deficient Escherichia coli.

Using purified photolyases for pyrimidine (6-4) pyrimidone photoproducts [(6-4)PP] and cyclobutane pyrimidine dimers (CPD), the effects of photoreactivation on mutagenesis were examined in the supF gene on a plasmid transfected into repair-deficient SOS-induced Escherichia coli host cells. More than 95% of CPD and (6-4)PP were removed from plasmid DNA by treatment with CPD photolyase and (6-4)photolyase, respectively. In each photolyase treatment, base substitutions at dipyrimidine sequences were predominantly observed. Of the single base substitutions observed after CPD photoreactivation, 83% were A:T-->G:C transitions at 5'-TT-3' sites. After (6-4)photolyase treatment, 81% were G:C-->A:T transitions at 5'-CC-3' and 5'-TC-3' sequences. Thus, the major mutagenic photoproducts of single-base substitutions were CPD at 5'-CC-3' or 5'-TC-3' sites and (6-4)PP at 5'-TT-3' sites. Tandem double mutations occurred mainly at 5'-CC-3' sites and were CPD-photoreactivated, suggesting that CPD at 5'-CC-3' was responsible for tandem double mutations. After photoreactivation of both CPD and (6-4)PP, single-base substitutions were primarily G:C-->A:T transitions at 5'-CC-3' or 5'-TC-3' sites and A:T-->G:C transitions at 5'-TT-3' sites, and secondarily G:C-->T:A transversions at 5'-CC-3' sites, G:C-->C:G transversions at 5'-CC-3' sites and A:T-->T:A transversions at 5'-TT-3' sites, which were essentially the same as those observed after photoreactivation of CPD alone, (6-4)PP alone and without photoreactivation. Thus, these transversions were not derived from unknown UV adducts but from incompletely repaired CPD and (6-4)PP.

Organization of the 16S rRNA around its 5' terminus determined by photochemical crosslinking in the 30S ribosomal subunit.

The organization of the 5' terminus region in the 16S rRNA was investigated using a series of RNA constructs in which the 5' terminus was extended by 5 nt or was shortened to give RNA molecules that started at positions -5, +1, +5, +8, +14, or +21. The structural and functional effects of the 5' extension/truncations were determined after the RNAs were reconstituted. 30S subunits containing 16S rRNA with 5' termini at -5, +1, +5, +8 and +14 had similar structures (judged by UV-induced crosslinking) and exhibited a gradual reduction in tRNA binding activity compared to that seen with 30S subunits reconstituted with native 16S rRNA. To create the 5' terminal site-specific photocrosslinking agent, the reagent azidophenacylbromide (APAB) was attached to the 5' terminus of 16S rRNA through a guanosine monophosphorothioate and the APA-16S rRNAs were reconstituted. Crosslinking carried out with the APA revealed sites in six regions around positions 300-340, 560, 900, 1080, the 16S rRNA decoding region, and at 1330. Differences in the pattern and efficiency of crosslinking for the different constructs allow distance estimates for the crosslinked sites from nucleotide G9. These measurements provide constraints for the arrangement of the RNA elements in the 30S subunit. Similar experiments carried out in the 70S ribosome resulted in a five- to tenfold lower frequency of crosslinking. This is most likely due to a repositioning of the 5' terminus upon subunit association.

Characterization of U6 snRNA-protein interactions.

Through a combination of in vitro snRNP reconstitution, photocross-linking and immunoprecipitation techniques, we have investigated the interaction of proteins with the spliceosomal U6 snRNA in U6 snRNPs, U4/U6 di-snRNPs and U4/U6.U5 tri-snRNPs. Of the seven Lsm (Sm-like) proteins that associate specifically with this spliceosomal snRNA, three were shown to contact the RNA directly, and to maintain contact as the U6 RNA is incorporated into tri-snRNPs. In tri-snRNPs, the U5 snRNP protein Prp8 contacts position 54 of U6, which is in the conserved region that contributes to the formation of the catalytic core of the spliceosome. Other tri-snRNP-specific contacts were also detected, indicating the dynamic nature of protein interactions with this important snRNA. The uridine-rich extreme 3' end of U6 RNA was shown to be essential but not sufficient for the association of the Lsm proteins. Interestingly, the Lsm proteins associate efficiently with the 3' half of U6, which contains the 3' stem-loop and uridine-rich 3' end, suggesting that the Lsm and Sm proteins may recognize similar features in RNAs.

Specificity of mutations induced by riboflavin mediated photosensitization in the supF gene of Escherichia coli.

Riboflavin-mediated photosensitization has been shown to produce 8-hydroxyguanine (oh8Gua) in DNA. We investigated the specificity of mutation of photosensitized supF gene induced in Escherichia coli. The oh8Gua repair deficient E. coli mutant mutM and mutY were transformed with plasmid pUB3 carrying the supF gene irradiated with white light in the presence of riboflavin. Under these conditions, riboflavin photosensitization increased the amounts of oh8Gua in pUB3 DNA. Three types of a single base substitution occurring at G:C pairs were detected in both wild-type and mutM mutant strains. Almost all base substitutions were transversions to T:A or C:G pairs occurring at a similar extent in both wild-type and mutM strains. Mutations derived from mutY strain transformed with photosensitized DNA were only G:C to T:A transversions. These G:C to T:A transversions observed in the mutY strain were suggested to be the result of mispairing of oh8Gua with adenine. Riboflavin-mediated photosensitization may also produce lesions on DNA causing G:C to C:G changes by unknown mechanisms.

Mutation induction and mutation frequency decline in halogen light-irradiated Escherichia coli K-12 AB1157 strains.

The effects of halogen light irradiation on reversion of argE3-->Arg+ in E. coli K12 strain AB1157 and its mfd- mutant, and on mutation frequency decline (MFD) after transiently incubating irradiated bacteria under non-growing conditions were studied. The induction of mutations, the mutational specificity, and the MFD effect had the same characteristic features as those seen in E. coli B strains after irradiation with 254 nm UV light. MFD which is due to repair of premutagenic lesion in the transcribed strand of glnU gene and prevents mutations leading to supB formation, was not observed in halogen light-induced mutations in the mfd-1 strain. Overproduction of UmuD'C proteins led to a large increase in mutation frequency, which was much greater in mfd- than in mfd+ strains. In bacteria irradiated with halogen light and incubated immediately in a rich medium to express mutations, the formation of supB predominated strongly over that of supE(ochre) in mfd- cells but was at a similar level in mfd+ cells. Introduction of zcf117::Tn10 to AB1157 strain makes cells more sensitive to halogen light irradiation, whereas introduction of mfd-1 does not.

Interactions of transfer RNA pseudouridine synthases with RNAs substituted with fluorouracil.

We have previously purified and characterized two different S. cerevisiae enzymes that produce pseudouridine specifically in nucleotide positions 13 and 55, respectively, in their tRNA substrates. The interactions of these enzymes with fluorinated tRNAs have now been studied. Such RNAs were produced by in vitro transcription using as templates synthetic genes that encode variants of a yeast glycine tRNA. RNAs substituted with fluorouracil were found to markedly inhibit pseudouridine synthase activity and the inhibitory effect of a tRNA was to a large extent dependent on the presence of fluorouracil in the nucleotide position where normally pseudouridylation occurs. Pseudouridine synthases were shown to form highly stable, non-covalent complexes with fluorinated tRNAs and we demonstrate that this interaction may be used to further characterize and purify these enzymes. The use of 5-fluorouracil as a cancer therapeutic agent is discussed in relation to our results.

Partial tRNA deacylation specifically triggers Escherichia coli cell volume reduction.

Limitation of Escherichia coli cell growth rate either by means of continuous 366 nm illumination, which is known to decrease the in vivo acylation level of some tRNA species, or by means of specific inhibitors of tRNA acylation allows the division rate to remain unchanged for a few generations, resulting in cell volume reduction. In contrast the cell volume remains stable or increases after treatment with inhibitors of DNA replication and transcription, or with drugs acting at any other step of protein synthesis. The conclusion that limiting acylation of some tRNA species is the triggering event is confirmed by the use of thermosensitive mutants of aminoacyl-tRNA synthetases or of tRNA (the divE strain mutated in the tRNA1Ser gene). Other cellular responses modulate the expression of cell volume reduction. The relA+ stringent response helps expression of the effect but does not appear to be strictly required. However, cell volume reduction may be masked under conditions triggering the SOS response. The data suggest that tRNA acylation is one of the major steps where cells sense change in their nutrient environment.

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.

Conservation of RNA sequence and cross-linking ability in ribosomes from a higher eukaryote: photochemical cross-linking of the anticodon of P site bound tRNA to the penultimate cytidine of the UACACACG sequence in Artemia salina 18S rRNA.

The complex of Artemia salina ribosomes and Escherichia coli acetylvalyl-tRNA could be cross-linked by irradiation with near-UV light. Cross-linking required the presence of the codon GUU, GUA being ineffective. The acetylvalyl group could be released from the cross-linked tRNA by treatment with puromycin, demonstrating that cross-linking had occurred at the P site. This was true both for pGUU- and also for poly(U2,G)-dependent cross-linking. All of the cross-linking was to the 18S rRNA of the small ribosomal subunit. Photolysis of the cross-link at 254 nm occurred with the same kinetics as that for the known cyclobutane dimer between this tRNA and Escherichia coli 16S rRNA. T1 RNase digestion of the cross-linked tRNA yielded an oligonucleotide larger in molecular weight than any from un-cross-linked rRNA or tRNA or from a prephotolyzed complex. Extended electrophoresis showed this material to consist of two oligomers of similar mobility, a faster one-third component and a slower two-thirds component. Each oligomer yielded two components on 254-nm photolysis. The slower band from each was the tRNA T1 oligomer CACCUCCCUVACAAGp, which includes the anticodon. The faster band was the rRNA 9-mer UACACACCGp and its derivative UACACACUG. Unexpectedly, the dephosphorylated and slower moving 9-mer was derived from the faster moving dimer. Deamination of the penultimate C to U is probably due to cyclobutane dimer formation and was evidence for that nucleotide being the site of cross-linking. Direct confirmation of the cross-linking site was obtained by "Z"-gel analysis [Ehresmann, C., & Ofengand, J. (1984) Biochemistry 23, 438-445].(ABSTRACT TRUNCATED AT 250 WORDS)

Mutagenesis and growth delay induced in Escherichia coli by near-ultraviolet radiations.

The literature relating to genetic changes induced in Escherichia coli by near-ultraviolet radiations is reviewed and summarized: i) these radiations are much less mutagenic than would be expected from the known level of DNA damage, ii) pre-illumination with near-UV light antagonizes the mutagenic effect of UV (254 nm) light. In agreement with these findings, the SOS functions are not induced by near-UV radiations. Furthermore prior exposure of cells to near-UV light inhibits the subsequent 254 nm induction of the SOS response. Among the several hypothesis considered to explain these observations, one can be clearly favoured. Near-UV light triggers, at sublethal fluences, the growth delay effect. The target molecules, tRNAs, are photocrosslinked and some tRNA species become poor substrates in the acylation reaction. In vivo these tRNA molecules accumulate on the uncharged form, leading to a transient cessation of protein synthesis. The SOS response is inducible and as such requires protein synthesis. We therefore propose that near-ultraviolet radiations have a dual effect: i) they induce, mostly indirectly, DNA lesions which are potentially able to trigger the SOS response, ii) they prevent the expression of the SOS functions through the transient inhibition of protein synthesis (growth delay).