DNA replication in Escherichia coli 15T- growing at 20 degrees C

Escherichia coli 15T⁻ grows slowly in succinate or aspartate-M9 media. In both media, a gap in DNA replication is observed at 37 °C which is either not present at 20 °C or of very much shorter duration than at 37 °C. However, dichotomous replication is not observed in glucose M9 at 20 °C. The results suggest that initiation of replication in glucose is different from that in aspartate or succinate cultures.     

A 13C NMR study of [5,8-13C2]spermidine binding to tRNA and to Escherichia coli macromolecules

[5,8-13C2]Spermidine was prepared by synthesis, and its binding to macromolecular structures of Escherichia coli was studied. When added to E. coli cells, the two signals of [13C]spermidine (C-5, 47.8 ppm, and C-8, 39.6 ppm; JC-C = 5.8 Hz) were strongly broadened due to binding to macromolecules. When [13C]spermidine was added to E. coli tRNA, the C-5 resonance broadened to v1/2 = 4.7 Hz, whereas the C-8 resonance broadened to v1/2 = 2.7 Hz. tRNA-bound [13C]spermidine could be chased by [12C]spermidine or spermine, but not by putrescine or cadaverine. By using mixtures of [5-13C]- and [8-13C]spermidines (where 13C-13C coupling was avoided), it was possible to estimate a dissociation constant (Kd) of 3 x 10(-3) M using the C-5 v1/2obs values and a Kd of 2.10(-3) M using the C-8 v1/2obs values. The number of spermidine-binding sites (n) could also be estimated by fitting the bound spermidine molar fraction versus tRNA concentration. Values of n = 12 +/- 2 and 14 +/- 3 were obtained for C-5 and C-8, respectively. Measurements of line narrowing at increasing Mg2+ concentrations indicated that approximately 11 spermidines (of the 12-14 bound ones) could be displaced by the former, whereas 3 spermidines remain strongly bound to the tRNA backbone. Measurements of free and bound T1 allowed the determination of a correlation time of 10(-10)s for tRNA-bound spermidine.     

A comprehensive comparison of DNA replication past 2-deoxyribose and its tetrahydrofuran analog in Escherichia coli

Apurinic/apyrimidinic (AP) sites are alkali labile lesions that, when encountered during DNA replication, can block polymerases or potentially result in mutagenic events. Owing to the instability of 2-deoxyribose lesions (AP), a chemically stable tetrahydrofuran analog (F) is often used as a model of abasic sites. A comparison of the two lesions in Saccharomyces cerevisiae revealed that the model lesion and 2-deoxyribose have distinct in vivo effects. Comprehensive comparative analyses of F and AP have not been carried out in Escherichia coli. We conducted a side-by-side investigation of F and AP in E.coli to compare their biological effects and interactions with SOS polymerases. Both lesions were examined in SOS-induced and uninduced cells. Our studies reveal that in uninduced E.coli the effects of individual polymerases in the replication of plasmids containing F or AP are distinct. However, when cells are SOS-induced, the biological effects of F and AP are similar.     

Utilization of nitrogen from 15NH4Cl and [15N]alanine for urea synthesis in hepatocytes from fed and starved rats

Utilization of N from 15NH4Cl and [15N]alanine for urea synthesis in hepatocytes isolated from fed and 24 hr starved rats was investigated. In hepatocytes isolated from fed rats, 54 and 65% of the added [15N]ammonia was utilized for urea synthesis in the presence of 0.5 and 2.0 mM NH4Cl, respectively. This utilization of [15N]ammonia in hepatocytes from starved rats was 2-fold lower. The amount of urea synthetized from endogenous sources was, in the presence of 0.5 and 2.0 mM NH4Cl, about 44 and 60% higher than in the control conditions (without NH4Cl). The considerable amount of added ammonia (30-44%) was utilized in processes other than urea synthesis. Alanine markedly diminished the utilization of 15N from NH4Cl in hepatocytes from both fed and starved rats. In these conditions (NH4Cl present), alanine significantly increased the urea formation in hepatocytes from starved rats and failed to affect the urea production in hepatocytes from fed rats. On the basis of 15N determination, it was concluded that both NH4Cl and alanine caused an increase in the utilization of nitrogen from endogenous sources in rat hepatocytes. This conclusion is in contrast with the results based only on the changes in ammonia and urea concentrations.     

Simultaneous acquisition of [13C,15N]- and [15N,15N]-separated 4D gradient-enhanced NOESY spectra in proteins

Summary The simultaneous acquisition of a 4D gradient-enhanced and sensitivity-enhanced [¹³C,¹⁵N]/[¹⁵N,¹⁵N]-separated NOESY is presented for the 74-residue [¹³C,¹⁵N]-labeled N-terminal SH3 domain of mGrb2 complexed with a peptide gragment from mSOS-2 in 90% H₂O. The method readily accommodates different ¹³C and ¹⁵N spectral widths, but requires that the same number of increments be collected for both ¹³C and ¹⁵N in the simultaneous dimension (F₂). For purposes of display and analysis, the two 4D spectra can be deconvolved during the processing stage by the appropriate linear combination of separately stored FIDs. Compared to collecting each of these two 4D data sets separately, the presented method is a factor (2)^1/2 more efficient in sensitivity per unit acquisition time. The interleaved nature of this method may also lead to improved peak registration between the two 4D spectra.     

Similar binding of the carcinostatic drugs cis-[Pt(NH3)2Cl2] and [Ru(NH3)5Cl] Cl2 to tRNAphe and a comparison with the binding of the inactive trans-[Pt(NH3)2Cl2] complex - reluctance in binding to Watson-Crick base pairs within double helix.

A comparative study of the binding of square planar cis- and trans-[Pt(NH3)2Cl2] complexes and the octahedral [Ru(NH3)5(H2O)]3+ complex to tRNAphe from yeast was carried out by X-ray crystallography. Both of the carcinostatic compounds, cis-[Pt(NH3)2Cl2] and [Ru(NH3)5(H2O)]3+ show similarities in their mode of binding to tRNA. These complexes bind specifically to the N(7) positions of guanines G15 and G18 in the dihydrouridine loop. [Ru(NH3)5(H2O)]3+ has an additional binding site at N(7) of residue G1 after extensive soaking times (58 days). A noncovalent binding site for ruthenium is also observed in the deep groove of the acceptor stem helix with shorter (25 days) soaking time. The major binding site for the inactive trans-[Pt(NH3)Cl2] complex is at the N(1) position of residue A73, with minor trans-Pt binding sites at the N(7) positions of residues Gm34, G18 and G43. The similarities in the binding modes of cis-[Pt(NH3)2Cl2] and [Ru(NH3)5(H2O)]3+ are expected to be related to their carcinostatic properties.     

The effect of trans-[Rh(4-ethylpyridine)4Cl2]Cl x 2H2O on nucleic acid and protein syntheses in Escherichia coli

The effect of the transition metal compound trans-[Rh(4-ethylpyridine)4Cl2]Cl x 2H2O on the syntheses of DNA, RNA, and protein has been investigated for an auxotrophic bacterial strain, Escherichia coli JS-1, incapable of thymidine, uridine, and histidine syntheses. At low concentration (7.4 x 10(-6) M), this rhodium complex interferes with normal cell division and induces the formation of filaments comparable to those observed in the presence of the cis-(NH3)2PtClx antitumour agents. Once the suppressed growth rate of the filamenting cells has been taken into account, the rhodium compound is found not to alter macromolecular synthesis. Again this is consistent with similar observations made for the platinum compounds.     

Mutation by [5-3H]cytosine decay in DNA of Escherichia coli lacking uracil-DNA glycosylase activity

The mutagenic local effect of tritium decay at the 5 position of cytosine in DNA of Escherichia coli was determined in wild-type and in ung strains defective in uracil-DNA glycosylase. In the absence of this in vivo activity any genetic consequences of uracil residues formed in DNA should be enhanced. However, the mutation frequency response was no greater in the mutant strain than in the wild type. This finding is inconsistent with the earlier suggestion that efficient production of C to T transitions by the local effect of [5-3H]cytosine decay results from the formation of uracil in cellular DNA. Some other intermediate should be considered, one that is not a substrate for uracil-DNA glycosylase.     

A 13C-NMR study on the influxes into the tricarboxylic acid cycle of a renal epithelial cell line, LLC-PK1/Cl4: the metabolism of [2-13C]glycine, L-[3-13C]alanine and L-[3-13C]aspartic acid in renal epithelial cells

Perchloric acid extracts of LLC-PK1/Cl4 cells, a renal epithelial cell line, incubated with either [2-13C]glycine L-[3-13C]alanine, or D,L-[3-13C]aspartic acid were investigated by 13C-NMR spectroscopy. All amino acids, except labelled glycine, gave rise to glycolytic products and tricarboxylic acid cycle (TCA) intermediates. For the first time we also observed activity of gamma-glutamyltransferase activity and glutathione synthetase activity in LLC-PK1 cells, as is evident from enrichment of reduced glutathione. Time courses showed that only 6% of the labelled glycine was utilized in 30 min, whereas 31% of L-alanine and 60% of L-aspartic acid was utilized during the same period. 13C-NMR was also shown to be a useful tool for the determination of amino acid uptake in LLC-PK1 cells. These uptake experiments indicated that glycine, alanine and aspartic acid are transported into Cl4 cells via a sodium-dependent process. From the relative enrichment of the glutamate carbons, we calculated the activity of pyruvate dehydrogenase to be about 61% when labelled L-alanine was the only carbon source for LLC-PK1/Cl4 cells. Experiments with labelled D,L-aspartic, however, showed that about 40% of C-3-enriched oxaloacetate (arising from a de-amination of aspartic acid) reached the pyruvate pool.     

A catenated DNA molecule as an intermediate in the replication of the resistance transfer factor R6K in Escherichia coli

Pulse-labeling of an $\text{Escherichia coli}$ strain harboring the resistance transfer factor R6K results in a transient increase in labeled catenated R6K DNA molecules. After a chase the level of labeled catenated DNA molecules is greatly reduced concomitant with a marked increase in labeling of the supercoiled DNA form of R6K. The data presented support a role for the catenated DNA molecule as an intermediate in the replication of the plasmid R6K.     

A new substrate cycle in plants. Evidence for a high glucose-phosphate-to-glucose turnover from in vivo steady-state and pulse-labeling experiments with [13C]glucose and [14C]glucose

Substrate (futile) cycling involving carbohydrate turnover has been widely reported in plant tissues, although its extent, mechanisms, and functions are not well known. In this study, two complementary approaches, short and steady-state labeling experiments, were used to analyze glucose metabolism in maize (Zea mays) root tips. Unidirectional rates of synthesis for storage compounds (starch, Suc, and cell wall polysaccharides) were determined by short labeling experiments using [U-14C]glucose and compared with net synthesis fluxes to determine the rate of glucose production from these storage compounds. Steady-state labeling with [1-(13)C]glucose and [U-13C]glucose showed that the redistribution of label between carbon C-1 and C-6 in glucose is close to that in cytosolic hexose-P. These results indicate a high resynthesis flux of glucose from hexose-P that is not accounted for by glucose recycling from storage compounds, thus suggesting the occurrence of a direct glucose-P-to-glucose conversion. An enzyme assay confirmed the presence of substantial glucose-6-phosphatase activity in maize root tips. This new glucose-P-to-glucose cycle was shown to consume around 40% of the ATP generated in the cell, whereas Suc cycling consumes at most 3% to 6% of the ATP produced. The rate of glucose-P cycling differs by a factor of 3 between a maize W22 line and the hybrid maize cv Dea, and is significantly decreased by a carbohydrate starvation pretreatment.     

Mechanism of irreversible inactivation of phenylalanine-4- and tryptophan-5-hydroxylases by [4-36Cl, 2-14C]p-chlorophenylalanine: A revision

Intraperitoneal injection of [4-³⁶Cl, 2-¹⁴C]p-chlorophenylalanine (pCPA) (300 mg/kg) in rats revealed absence of chlorine in pure hepatic phenylalanine hydroxyase, while the carbon label appeared as 1–4 moles/mole of [¹⁴C]tyrosine in the inactivated phenylalanine and cerebral tryptophan-5-hydroxylase. Crystalline muscle aldolase and tyrosine hydroxylase also revealed the presence of [2-¹⁴C]tyrosine from [2-¹⁴C]pCPA without inactivating these enzymes. Injection of L-[(U)-¹⁴C] tyrosine led to its incorporation into the above enzymes, but to a different degree without altering the enzyme activity. Repeated injections ofp-chlorophenylacetic acid had no effect on phenylalanine or tryptophan-hydroxylase. Administration of pCPA did not change the levels of cerebral biopterins. Reexamination of the effect of cycloheximide on reversing enzymic inactivation by pCPA failed to confirm our earlier observation.     

A stable isotope dilution assay for disopyramide and its [13C, 15N]labelled analogue in biological fluids

The mass spectra of disopyramide phosphate and two stable isotopically labelled analogues have been obtained using electron impact and chemical ionization. The low isotopic purity of [13C, 15N)disopyramide phosphate was shown to be due to the low isotopic purity of the 15N label. A stable isotope dilution assay for disopyramide and [13C, 15N]disopyramide in biological fluids has been developed using [2H14]disopyramide phosphate as the internal standard. This assay will be used to analyse samples obtained after the co-administration of disopyramide phosphate intravenously and [13C, 15N]disopyramide phosphate orally to several animal species.     

A method for the determination of glucose-6-phosphatase activity in rat liver with [U-14C]glucose 6-phosphate as substrate.

A method is described for measuring the activity of glucose-6-phosphatase (EC 3.1.3.9) in rat liver. [U-¹⁴C]Glucose 6-phosphate, as substrate, is converted by the enzyme to [¹⁴C]glucose and inorganic phosphate. The addition of ZnSO₄ and Ba(OH)₂ at the end of the reaction precipitates phosphate and the unreacted [¹⁴C]glucose 6-phosphate, whereas [¹⁴C]glucose is not precipitated. After centrifugation, the amount of [¹⁴C]glucose formed is determined in a liquid scintillation counter.