On the structure of the deo operon of Escherichia coli

Purine nucleoside phosphorylase: its use in a spectroscopic assay for inorganic phosphate and for removing inorganic phosphate with the aid of phosphodeoxyribomutase

The kinetics of the phosphorolysis of 7-methylated guanosine analogues catalyzed by purine nucleoside phosphorylase has been analyzed to understand the use of this system as a "Pi mop" to remove Pi from solutions and as a spectroscopic assay for Pi at micromolar concentrations. An expression system was developed for the phosphorylase from Escherichia coli: this protein (subunit molecular mass 26 kDa) and one from a commercial source (29 kDa) were used in this study. Rates of >50 s-1 were obtained for the phosphorolysis at 30 degrees C, so that when the phosphorylase is coupled to the phosphatase being studied, rates of Pi release from the phosphatase can be measured close to this rate. The kinetic mechanism appears to obey the Michaelis-Menten model in the steady state with the bond cleavage rate limiting. Slow hydrolysis of ribose-1-phosphate to Pi catalyzed by the phosphorylase limits the efficiency of the Pi mop. To overcome this, phosphodeoxyribomutase was used to catalyze the conversion of ribose-1-phosphate to ribose-5-phosphate, enabling the Pi mop to remove large amounts of Pi quantitatively. Acyclovir diphosphate provides a simple method to switch off the Pi mop as it is a tight inhibitor (Kd 12 nM) of purine nucleoside phosphorylase.

Construction of chromosomally encoded secreted hemolysin fusion proteins by use of mini-TnhlyAs transposon

We used the minitransposon TnhlyAs [Gentschev, I., Maier, G., Kranig, A. and Goebel, W. (1996) Mol. Gen. Genet. 252, 266-274] for random insertion of the secretion signal (HlyAs) of Escherichia coli hemolysin (HlyA) into chromosomal genes. Four mini-TnhlyAs derivatives bearing the gltA (citrate synthase), deoC (2 deoxyribose-5 phosphate aldolase), tig (trigger factor) genes and an unknown ORF fused to hlyAs were identified and characterized. Our data suggest that TnhlyAs-generated hemolysin fusion proteins are secreted efficiently by the HlyB/HlyD/TolC hemolysin secretion machinery and that this can be useful for studies of gene expression or function.

Studies on deo operon regulation in Escherichia coli: cloning and expression of the deoR structural gene

Recombinant plasmid pBR322 derivatives containing the Escherichia coli deoR structural gene (coding for one repressor of the deo operon) and a mutant allele of the cmlA gene (chromosomally encoded chloramphenicol resistance) have been constructed and the positions of these genes on a 6.3-kb EcoRI fragment have been determined. Transformation of an E. coli deoR single mutant with any of the deoR+ plasmids resulted in complementation of the chromosomal deoR mutation. More importantly, however, transformation of a deoR cytR double mutant with the deoR+ plasmids also resulted in complete repression of Deo enzyme synthesis. Based on these data, we conclude that transcription of the deo operon initiating from both the cAMP/CRP-independent promoter-operator site, PO1, and the cAMP/CRP-dependent promoter-operator site, PO2, is negatively controlled by the deoR-encoded repressor, whereas the cytR-encoded repressor regulates deo operon expression only from the cAMP/CRP-dependent promoter-operator site, PO2.

Isolation and characterization of the dut gene of Escherichia coli. I. Cloning in thermoinducible plasmids

We have constructed thermoinducible plasmids carrying the gene (dut) for the enzyme deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase, EC 3.6.1.23) from Escherichia coli. A 9.4-kb BamHI restriction enzyme fragment carrying the dut gene was inserted into the runaway-replication plasmid pKN402A (Uhlin et al., Gene 6 (1979) 91-106). Strains carrying such plasmids increased their dUTPase activity considerably. In minimal medium a 200-fold increase was demonstrated. A smaller (1.5-kb) SacI-BamHI fragment from the dut region was also cloned into pKN402A. The dUTPase production in dut mutant strains carrying this plasmid (pKK141) was only at about wild-type level after temperature shift. To test the hypothesis that the SacI cleavage used affects a control region for the dut gene, we recloned the dut fragment by transferring it from pKK141 into pHUB2 (Bernard et al., Gene 5 (1979) 59-76), a plasmid carrying the phage lambda pL promoter. A 3.6-kb EcoRI-BamHI fragment from pKK141, including the 1.5-kb SacI-BamHI segment from the dut region, was inserted downstream from the pL promoter. When this plasmid was present in a strain containing a thermosensitive lambda repressor gene, thermoinduction of dUTPase was negligible, apparently due to the presence of some termination signals between pL and dut. Therefore, we removed a 1.9-kb EcoRI-SacI fragment from the region between pL and the dut gene and replaced it with a 0.22-kb EcoRI-SacI fragment, obtained from the b2 region of lambda. Strains carrying such a shortened dut-pHUB2 derivative and a temperature-sensitive lambda repressor overproduced dUTPase very dramatically after heat induction. The final level reached was 300-400 times the wild-type level, corresponding to 10% of the total soluble protein. The information obtained, together with analysis of plasmid-directed polypeptide products described by Lundberg et al. (Gene 22 (1983) 127-131) shows that the SacI site is indeed on the promoter-proximal side of the dut gene.

Influence of the rho-15 temperature-sensitive (ts) mutation on the expression of the deo-operon in Escherichia coli

In the rho-15 temperature-sensitive (ts) mutant deo-operon enzymes show no sensitivity to catabolite repression and are not derepressed under the influence of a constitutive regulatory mutation, cytR. These data suggest that intact Rho-protein along with CRP protein is necessary for a catabolite sensitive deo-operon promoter cytP to work. In addition, there are data suggesting that Rho-factor and CRP-protein interact with each other in regulation of the deo-operon. Thus, in studies of the effect of the rho-15 (ts) and crp mutations, maximum deo-enzyme levels have been found in the double rho-15 (ts) crp mutant, and therefore intact Rho-protein in the crp genome or intact CRP-protein on the rho-15 (ts) background seems to be an obstacle for the deoP promoter in the deo-operon. In rho-15 (ts) a relative increase has been observed in the enzyme activity for a distal purine nucleoside phosphorylase gene with respect to a proximal thymidine phosphorylase gene. However in crp, the rho-15 (ts) mutation has no effect on the polarity gradient, that is on the background of impaired CRP protein Rho-factor does not seem to work as a transcription terminator within the operon.

The primary structure of Escherichia coli K12 2-deoxyribose 5-phosphate aldolase. Nucleotide sequence of the deoC gene and the amino acid sequence of the enzyme

The sequence of the deoC gene of Escherichia coli K12 and the amino acid sequence of the corresponding protein, deoxyriboaldolase, has been established. The protein consists of 259 amino acids with a molecular weight of 27 737. The purified enzyme may exist both as a monomer and as a dimer. On the basis of amino acid composition, molecular weight and catalytic properties, the enzymes from E. coli and Salmonella typhimurium seem to be almost similar. They belong to the class I aldolases, which form Schiff base intermediates. Using data for the S. typhimurium enzyme, the lysine residue involved in the active site in the E. coli enzyme was tentatively identified.

The cloning of the Escherichia coli K-12 deoxyribonucleoside operon

A 6.1-kb EcoRI DNA fragment containing the four structural genes (deoC, deoA, deoB, deoD) of the deoxyribonucleoside operon has been cloned into the plasmid pMFS53. By use of a unique, asymmetrically positioned HindIII site on the 6.1 kb insert, plasmids containing the deoC,deoA genes (pMFS50) or the deoB,deoD genes (pMFS55) have been constructed. Enzyme assays performed on extracts prepared from clones harboring pMFS53, pMFS50 or pMFS55 revealed that each clone possessed amplified deo enzyme levels and that the spectrum of enzyme amplification corresponded to the genetic composition of the plasmids carried by each clone. A plasmid (pMFS50l) having functional deoA, deoB and deoD genes but devoid of the deo regulatory region and a portion of the deoC structural gene has been isolated following treatment of BamHI cleaved pMFS53 and BAL31 nuclease. Comparison of the deo enzyme levels for clones harboring pMFS53 and pMFS501 suggest that plasmid pMFS53 possesses a functional deo regulatory region in addition to the four structural genes of the operon.

Regulation of the synthesis of nucleoside catabolic enzymes in Escherichia coli: further analysis of a deo Oc mutant strain

Four genes, deoA, deoB, deoC, and deoD, involved in the synthesis of nucleoside and deoxynucleoside catabolic enzymes, are located contiguously in the order C-A-B-D on the linkage map of E. coli. They constitute two overlapping operons, one transcribing all the four genes and the other deoB and deoD. To the left of deoC are located two promoter-operator regions in the order deoPO-cytPO. They are involved in controlling the expression of the tetracistronic mRNA. For efficient binding of RNA polymerase at the cytPO site the cAMP+CRP complex is required, whereas binding of RNA polymerase at the deoPO site is independent of this complex. Evidence is available for the existence of yet another controlling site, PO-3, located between deoA and deoB; this controls the expression of deoB and deoD. Both the operons are transcribed in a clockwise direction. An operator constitutive (Oc) type mutant affecting the synthesis of all four deo enzymes has been analysed. Because of this mutation the strain has become insensitive to catabolite repression. The results confirm the order of the gene in the controlling region to be deoPO-cytPO and the mutation, previously analysed as a deletion, appears to have deleted cytPO deoC region of the chromosome.

Insertion of bacteriophage lambda into the deo operon of Escherichia coli K-12 and isolation of plaque-forming lambdadeo+ transducing bacteriophages

A procedure has been devised to isolate plaque-forming lambda cI857S7 transducing bacteriophage which carry the internal promoter, P3, of the deo operon of Escherichia coli and the deoB and deoD genes, while lacking the deoP and cytP promoters of the same operon, in order to study, specifically, regulation at the P3 site. This has been accomplished by selecting for the insertion of bacteriophage lambda into the deoA gene in a strain deleted for the normal lambda attachment site (delta att lambda) and isolating from this lysogen lambda spi- and lambda EDTAr phage. Among these, lambda pdeoB+D+ phage were identified by their transducing abilities. From in vivo enzyme induction experiments performed on a delta deo strain lysogenized with such phage, they were shown to carry the P3 promoter while lacking the deoP and cytP promoters. A lambdapdeo B+D+ phage phage was used to lysogenize a deo+ delta att lambda strain, integration of lambda occurring within the region of homology, and, from a heat-induced lysate of this strain, a plaque-forming lambda+ phage carrying the complete deo operon was obtained. Phage lambda was also inserted into the deoB and deoD genes and into the tdk gene. By isolating lambdaspi- and lambdaEDTAr phage from the deo::(lambda) mutants and determining which bacterial genes they carried and whether they retained the int gene of lambda, it was found that lambda had inserted into deoD with the same orientation as lambda inserted into attlambda, whereas lambda inserted into deoA and deoB had the opposite orientation. Deletions extending from the site of lambda insertion into the bacterial chromosome were isolated by selecting for heat-resistant revertants. These confirmed the order of markers to be deo-serB-trpR-thr and also placed a locus, msp, determining sensitivity or resistance of male strains to male-specific phages, between trpR and thr. For some reason unknown, but which may be related to the orientation of the lambda prophages, short deletions rendering the bacterium Ser- Thr+ were of much lower frequency from the deoD::(lambda) lysogen than from the other two lysogens. From an examination of the residual deoD enzyme levels in deoB::(lambda) mutants, it was deduced that there may be two promoter sites within the deoB::(lambda) mutants, it was deduced that there may be two promoter sites within the deoB gene, transcription from one of these being sufficient to account for the noncoordinate nature of the induction of deoB and deoD gene products.

A ribosomal RNA gene, rrnC, of Escherichia coli, mapped by specialized transducing lambdadilv and lambda drbs phages

Specialized transducing phages carrying segments of the Escherichia coli chromosome from the rbs-ilv region including rrn genes have been isolated. These phages carry rrn transcription units coding for 16S and 23S rRNA with the direction of transcription clockwise towards the ilv operon. While one of the phages (lambdad279rbs) appears to carry the genuine rrn gene, denoted rrnC, located between rbs and ilv at 82 min on the E. coli chromosome another one isolated as an ilv transducing phage, lambda5ilv, carries a hybrid rrn gene, denoted rrnX, which has originated from a recombinational cross-over between the rrnC and one of the other rrn genes.

Reduced expression of a distal gene of the prn gene cluster in deletion mutants of Aspergillus nidulans: genetic evidence for a dicistronic messenger in an eukaryote

The prn gene cluster involved in L-proline catabolism in Aspergillus nidulans, has the gene order prnA-prnD-regulatory region-prnB-prnC. prnB, prnD, and prnC specify proline permease, proline oxidase, and delta1-pyrroline-5-carboxylate (P5C) dehydrogenase, respectively. prnA is probably a positive regulatory gene whose product is necessary for expression of the prn activities. Proline induces proline permease and P5C dehydrogenase in prnD- mutants which lack proline oxidase, showing that proline does not have to be converted to P5C to act as inducer. Deletion mutations extending from within prnD to within prnB result in considerably reduced expression of prnC, whereas a prnD- prnB- double mutant shows normal prnC expression. This strongly suggests that the deletion mutations eliminate a promotor/initiator site for transcription of a dicistronic messenger for prnB and prnC. The fact that the deletions do not eliminate prnC expression altogether indicates that at least one other species of prnC transcript (monocistronic, tricistronic, or tetracistronic) can be made.

Regulation of the deo operon in Escherichia coli: the double negative control of the deo operon by the cytR and deoR repressors in a DNA directed in vitro system

The synthesis of the four enzymes of the deo operon in Escherichia coli is known from in vivo experiments to be subject to a double negative control, exerted by the products of the cytR and deoR genes. A DNA-directed in vitro protein synthesizing system makes the deo enzymes (exemplified by thymidine phosphorylase) in agreement with in vivo results. Enzyme synthesis is stimulated by cyclic AMP and repressed by the cytR and deoR gene products. Repression by the cytR repressor is reversed by cytidine or adenosine in the presence of cyclic AMP, while repression by the deoR repressor is reversed by deoxyribose-5-phosphate. Assays for the presence of the cytR and deoR repressors were established by use of S-30 extracts prepared from the regulatory mutants. Dissociation constants for repressor-operator binding as well as for repressor-inducer interactions have been estimated from the results.