Purification and properties of the membrane-bound CDP-diglyceride synthetase from Escherichia coli

The enzyme CDP-diglyceride synthetase (CTP: phosphatidate cytidylyltransferase; EC 2.7.7.41) has been purified to 90% homogeneity from Escherichia coli cells that overproduce the enzyme 50-fold through the use of recombinant DNA technology. The purification required the use of different detergents at each step, illustrating the refractory hydrophobic nature of this protein. Apparent physical effects of EDTA on the enzyme were also utilized in the purification. The enzyme has an apparent minimum subunit mass of 27,000 daltons, as estimated by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The amino acid composition of the protein was determined, and it correlates well with the theoretical protein product of the cds gene, the sequence of which is reported in the accompanying paper (Icho, T., Sparrow, C. P., and Raetz, C. R. H. (1985) J. Biol. Chem. 260, 12078-12083). The pure enzyme displays surface dilution kinetics when assayed in the presence of Triton X-100. As previously suggested on the basis of studies using partially purified preparations, the enzyme mechanism is sequential, and computer-calculated kinetic constants are reported herein. The substrate specificity of the enzyme is also investigated. This is the first time this enzyme has been purified to homogeneity from any source, despite the fact that it is essential for phospholipid biosynthesis in all organisms.     

Formation of Membrane-bound CDP-diglyceride from Membrane-bound Phosphatidic Acid in Escherichia coli

The title compounds were synthesized from starting materials of microbial origin by employing a Wittig reaction as the key step.     

Molecular cloning and sequencing of the gene for CDP-diglyceride hydrolase of Escherichia coli

Previous work from this laboratory had demonstrated that CDP-diglyceride hydrolase of Escherichia coli is encoded by the cdh gene that maps near minute 88 (Bulawa, C. E., and Raetz, C. R. H. (1984) J. Biol. Chem. 259, 11257-11264). We now report the construction of hybrid plasmids and the sequencing of a 1,243-base pair insert carrying cdh. The further construction of BAL31 deletions of this insert, in conjunction with maxicell experiments and in vitro enzyme assay, has led to the identification of a 756-base pair coding sequence for the cdh polypeptide. The molecular weight of the primary translation product deduced from the DNA sequence of the cdh gene is 28,450, in agreement with maxicell experiments. Parallel purification of the enzyme from extracts of wild-type and overproducing strains confirms the presence of a 27-kDa polypeptide in the overproducer, as judged by polyacrylamide gel electrophoresis of the most purified fractions. Inspection of the DNA sequence reveals a very hydrophobic N-terminal domain that may be either a signal peptide or a special region, anchoring the hydrolase to the membrane. In contrast to the CDP-diglyceride synthetase, the overall amino acid composition of the CDP-diglyceride hydrolase is not extraordinarily hydrophobic. Although both CDP-diglyceride synthetase and CDP-diglyceride hydrolase can transfer the CMP moiety of CDP-diglyceride to a suitable acceptor, the primary structures and mechanisms of action of these two enzymes are very different.     

Molecular cloning and sequencing of the gene for CDP-diglyceride synthetase of Escherichia coli

The cds gene of Escherichia coli codes for the enzyme CDP-diglyceride synthetase. We now report the construction of plasmids which carry cds. Using these plasmids, we have sequenced 1274 base pairs of DNA, including a 750-base pair open reading frame which is the coding region of the cds gene. This DNA sequence allows the deduction of the primary peptide sequence for CDP-diglyceride synthetase. The protein is very hydrophobic, and, assuming no processing or modification, has a molecular weight of 27,570. Furthermore, there is a second open reading frame immediately after cds, implying that cds may be part of an operon. We have also constructed a runaway replication cds-plasmid that directs approximately 50-fold overproduction of CDP-diglyceride synthetase. This overproduction has been utilized in the purification of the enzyme to homogeneity, as described in the accompanying paper (Sparrow, C.P., and Raetz, C.R.H., J. Biol. Chem. 260, 12084-12091). Finally, the molecular cloning work reported herein allows the exact placement of the cds gene on the E. coli genetic map.     

Non-covalently bound adenine nucleotides in adenosine triphosphatase of Escherichia coli.

The term, xeroderma pigmentosum variants designates patients who suffer from the clinical manifestations of the disease, but whose cells have normal rates of excision repair of UV-induced lesions in DNA. In contrast to normal human fibroblasts, if cells from such variants are maintained in medium containing caffeine from immediately following exposure to UV until the survivors have undergone three doublings, the cytotoxic and mutagenic effect of UV light is dramatically increased. In the presence of 0.7mM caffeine, the slope of the UV survival curve increases $\text{ca.}$ 3-fold. Similarly, the slope of the curve describing the frequency of mutations to azaguanine resistance induced by UV as a function of dose is $\text{ca.}$ 3-fold steeper.     

Hydrolysis of oxidized nucleotides by the Escherichia coli Orf135 protein.

To examine the possibility that the Orf135 protein of Escherichia coli functions as a hydrolyzing enzyme for a damaged DNA precursor (deoxyribonucleoside 5'-triphosphate), we purified the recombinant Orf135 protein and incubated it with oxidized deoxynucleotides. Of the nucleotides tested, 2-hydroxydeoxyadenosine 5'-triphosphate, and somewhat less efficiently, 8-hydroxydeoxyguanosine 5'-triphosphate, were hydrolyzed by this protein. These damaged deoxynucleotides elicit transversion mutations in E. coli (Inoue, M., Kamiya, H., Fujikawa, K., Ootsuyama, Y., Murata-Kamiya, N., Osaki, T., Yasumoto, K., Kasai, H. (1998) J. Biol. Chem. 273, 11069-11074). These results suggest that this protein may be involved in the prevention of mutations induced by these oxidized deoxynucleotides.     

pH-sensitive CDP-diglyceride synthetase mutants of Escherichia coli: phenotypic suppression by mutations at a second site.

In Escherichia coli, mutations which lower the level of CDP-diglyceride synthetase are designated cds and map at min 4. The cds-8 mutation resulted in strikingly defective enzyme activity and also rendered cells pH sensitive for growth. Both the inhibition of growth and the massive accumulation of phosphatidic acid which occur in a cds-8 mutant at pH 8 were suppressed by mutations at a second locus, designated cdsS, which mapped between argG and gltB near min 68. The cdsS3 mutation by itself did not affect CDP-diglyceride synthetase activity in wild-type cells, but it caused a twofold stimulation of the residual activity present in strains harboring cds-8. Both the insensitivity to pH and the twofold stimulation of residual activity were lost by introduction of an F' strain carrying cdsS+ into a recA1 cds-8 cdsS3 host. When a culture of a cds-8 cdsS+ strain was shifted to pH 8, the residual specific activity of synthetase dropped by 75% within 100 min. In a cds-8 cdsS3 double mutant under the same conditions, the activity declined appreciably less, about to the level found in the cds-8 cdsS+ strain under permissive conditions (pH 6). Thus, it appears that mutations in the cdsS gene suppress the pH sensitivity of cds mutants by inhibiting the decay of residual CDP-diglyceride synthetase activity at the nonpermissive pH. The cdsS locus appears to be distinct from any known nonsense or missense suppressor.     

Role of recBC nuclease in Escherichia coli transformation.

In Escherichia coli transformation with linear donor deoxyribonucleic acid, the recBC pathway is functional, but genetic analysis shows that the recBC nuclease is deleterious to linear deoxyribonucleic acid.     

Transport-defective Escherichia coli ecf mutant permeable to protons and nucleotides.

This paper describes a third type of transport-defective ecf mutant of Escherichia coli which is altered in membrane proton permeability. Mutants of this class also excrete ATP and other nucleotides and form filament-like cells. This lesion requires cell growth at the nonpermissive temperature.     

Quantitative extraction and estimation of intracellular nicotinamide nucleotides of Escherichia coli.

The conditions of extraction of nicotinamide nucleotides from Escherichia coli were systematically investigated. The optimum pH for NAD⁺ and NADP⁺ appeared to be around 1.5 while that for NADH and NADPH was around 12.5. Seven minutes at 60°C was chosen for the extraction of all four nucleotides. Addition of CuCl to the alkaline extract improved considerably the recovery of the reduced forms. Two sensitive (10–100 pmol) assay methods for nicotinamide nucleotides were compared. A spectrophotometric cycling method based on the measurement of reduced thiazolyl blue formation appeared to be more sensitive and more reproducible and gave better recovery than a fluorometric cycling method used earlier in bacterial studies.     

Massive accumulation of phosphatidic acid in conditionally lethal CDP-diglyceride synthetase mutants and cytidine auxotrophs of Escherichia coli

Escherichia coli mutants partially defective in CTP: phosphatidic acid cytidylyltransferase (CDP-diglyceride synthetase) are more resistant to the antibiotic erythromycin than are isogenic wild type strains. When 100 micrograms/ml erythromycin is added to nutrient agar plates, it is possible to obtain a 30-fold enrichment for cds mutants from a mutagen-treated stock, as judged by colony autoradiography (Ganong, B. R., Leonard, J. M., and Raetz, C. R. H. (1980) J. Biol. Chem. 255, 1623-1629). Using this approach, we have isolated 38 new cds mutants, nine of which are unable to grow at a culture pH greater than 8. A typical conditionally lethal mutant like GN80 contains a 3 to 5% phosphatidic acid below pH 7. Above pH 8, GN80 accumulates phosphatidic acid to about 30% of the total membrane lipid, while the de novo syntheses of phosphatidylethanolamine and phosphatidylglycerol are abruptly inhibited by over 10-fold. GN80 loses viability after 60 min at pH 8.5, and the liponucleotide pool of GN80 is about one-seventh that of an isogenic wild type, GN85, under these conditions. The pH optimum of the residual CDP-diglyceride synthetase present in extracts of GN80 is 0.5 pH units lower than normal. Twenty-one of 26 spontaneous pH-resistant revertants of GN80 concomitantly regain parental levels of the enzyme. Our results constitute definitive physiological proof that CDP-diglyceride is an obligatory precursor for over 90% of the phosphatidylethanolamine and phosphatidylglycerol in E. coli. Independent evidence for this is provided by the observation that cytidine auxotrophs, which are defective in the conversion of UTP to CTP, also accumulate very high levels of phosphatidic acid after 1 h of cytidine starvation.     

Gene conversion in Escherichia coli. Resolution of heteroallelic mismatched nucleotides by co-repair

We have constructed heteroduplex plasmid DNA that is similar in structure to the heteroduplex DNA expected to be produced during genetic recombination of plasmids, and studied its repair after transformation into different Escherichia coli strains. The heteroduplex DNA was constructed using two different parental plasmids, each of which contained a different ten-nucleotide insertion mutation. The effect of different defined states of dam-methylation on repair was also examined. We found that heteroduplex DNA repair occurred prior to the replication of the substrate DNA 60 to 80% of the time, regardless of the state of DNA methylation. Most excision/synthesis tracts covered two markers separated by 1243 base-pairs, and this process has been termed co-repair. The most efficient co-repair pathway was the Dam-instructed repair pathway that required the mutH, mutL, mutS and uvrD gene products and preferentially used the methylated strand as the template for DNA synthesis. If there was no methylation asymmetry, mismatch nucleotide repair occurred with a similar frequency; however, no strand bias was observed. Co-repair of symmetrically methylated heteroduplex DNA required the mutS and uvrD gene products, while repair of unmethylated heteroduplex DNA also required the mutL and mutH gene products.     

Role of mismatch repair in the Escherichia coli UVM response.

Mutagenesis at 3,N4-ethenocytosine (epsilonC), a nonpairing mutagenic lesion, is significantly enhanced in Escherichia coli cells pretreated with UV, alkylating agents, or H2O2. This effect, termed UVM (for UV modulation of mutagenesis), is distinct from known DNA damage-inducible responses, such as the SOS response, the adaptive response to alkylating agents, or the oxyR-mediated response to oxidative agents. Here, we have addressed the hypothesis that UVM results from transient depletion of a mismatch repair activity that normally acts to reduce mutagenesis. To test whether the loss of mismatch repair activities results in the predicted constitutive UVM phenotype, E. coli cells defective for methyl-directed mismatch repair, for very-short-patch repair, or for the N-glycosylase activities MutY and MutM were treated with the UVM-inducing agent 1-methyl-3-nitro-1-nitrosoguanidine, with subsequent transfection of M13 viral single-stranded DNA bearing a site-specific epsilonC lesion. Survival of the M13 DNA was measured as transfection efficiency, and mutation fixation at the lesion was characterized by multiplex sequencing technology. The results showed normal UVM induction patterns in all the repair-defective strains tested. In addition, normal UVM induction was observed in cells overexpressing MutH, MutL, or MutS. All strains displayed UVM reactivation, the term used to describe the increased survival of epsilonC-containing DNA in UVM-induced cells. Taken together, these results indicate that the UVM response is independent of known mismatch repair systems in E. coli and may thus represent a previously unrecognized misrepair or misreplication pathway.     

Role of gene fadR in Escherichia coli acetate metabolism.

Mutants of Escherichia coli K-12 constitutive for fatty acid degradation (fadR) showed an increased rate of utilization of exogenous acetate. Acetate transport, oxidation, and incorporation into macromolecules was approximately fivefold greater in fadR mutants than fadR+ strains during growth on succinate as a carbon source. This effect was due to the elevated levels of glyoxylate shunt enzymes in fadR mutants, since (i) similar results were seen with mutants constitutive for the glyoxylate shunt enzymes (iclR), (ii) induction of the glyoxylate shunt in fadR+ strains by growth on acetate or oleate increased the rate of acetate utilization to levels comparable to those in fadR mutants, and (iii) fadR and fadR+ derivatives of mutants defective for the glyoxylate shunt enzymes showed equivalent rates of acetate utilization under these conditions. These results suggest that the operation of the glyoxylate shunt may play a significant role in the utilization of exogenous acetate by fadR mutants.