Inability of low thymine-requiring mutants of Escherichia coli lacking phosphodeoxyribomutase to be induced for deoxythymidine phosphorylase and deoxyriboaldolase

Screening of microbes, isolation, genetic manipulation, and physiological optimization of Brevibacterium helvolum to produce and excrete thymidine and deoxyuridine in high concentrations

Analogues of deoxypyrimidines are used in the treatment of a variety of human ailments. Azidothymidine, or AZT, is one such analogue used to treat AIDS. Thymidine is the precursor of AZT, and its cost contributes to the high price of AZT. Attempts are being made to isolate and genetically manipulate microbes that can produce and excrete this compound in high concentrations. To this end, 145 different microbial species from Zeneca and the American Type Culture Collection were screened. Moreover, soil samples were collected from 36 different sites in England, and microbes from these samples were isolated and screened. >From approximately 25,000 isolates screened as single colonies and from 4,000 in liquid cultures, a strain of Brevibacterium helvolum showed the most promising results. Pyrimidine metabolic pathways of this bacterium were worked out, the isolate was genetically manipulated, and physiological conditions were optimized to increase the production of thymidine and deoxyuridine. These mutants of B. helvolum are considered to be of commercial importance.

Genetic and biochemical characterization of Salmonella enterica serovar typhi deoxyribokinase

We identified in the genome of Salmonella enterica serovar Typhi the gene encoding deoxyribokinase, deoK. Two other genes, vicinal to deoK, were determined to encode the putative deoxyribose transporter (deoP) and a repressor protein (deoQ). This locus, located between the uhpA and ilvN genes, is absent in Escherichia coli. The deoK gene inserted on a plasmid provides a selectable marker in E. coli for growth on deoxyribose-containing medium. Deoxyribokinase is a 306-amino-acid protein which exhibits about 35% identity with ribokinase from serovar Typhi, S. enterica serovar Typhimurium, or E. coli. The catalytic properties of the recombinant deoxyribokinase overproduced in E. coli correspond to those previously described for the enzyme isolated from serovar Typhimurium. From a sequence comparison between serovar Typhi deoxyribokinase and E. coli ribokinase, whose crystal structure was recently solved, we deduced that a key residue differentiating ribose and deoxyribose is Met10, which in ribokinase is replaced by Asn14. Replacement by site-directed mutagenesis of Met10 with Asn decreased the V(max) of deoxyribokinase by a factor of 2.5 and increased the K(m) for deoxyribose by a factor of 70, compared to the parent enzyme.

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.

Regulation of thymidine metabolism in Escherichia coli K-12: studies on the inducer and the coordinateness of induction of the enzymes

A study was made of the regulation of three enzymes that act sequentially in the metabolism of thymidine in Escherichia coli K-12. Under a variety of conditions, two of the enzymes, thymidine phosphorylase and deoxyribose-5-phosphate aldolase, were found to be synthesized coordinately. However, the third enzyme, phosphodeoxyribomutase, was synthesized noncoordinately with the other two enzymes under the same conditions. In addition, the mutase could be fully induced, whereas basal levels of the phosphorylase and the aldolase were maintained. These findings indicate that two operons comprise the genes concerned with the reversible pathway leading from thymidine to acetaldehyde and glyceraldehyde-3-phosphate. In addition to thymidine, it was found that acetaldehyde was an external inducer of these enzymes. The results of induction experiments performed on wild-type cells and mutants defective in the mutase or the aldolase, with thymidine or acetaldehyde as exogenous inducers, strongly suggest that deoxyribose-5-phosphate is more proximal to the intracellular inducer than is thymidine, deoxyribose-1-phosphate, or acetaldehyde.

Regulation of thymidine metabolism in Escherichia coli K-12: evidence that at least two operons control the degradation of thymidine

In Escherichia coli K-12, the rise in activity of thymidine phosphorylase, phosphodeoxyribomutase, and deoxyribose-5-phosphate aldolase caused by exogenous thymidine is dependent on the synthesis of new enzyme protein. Phosphodeoxyribomutase is induced by the purine ribonucleosides adenosine and guanosine, whereas the other two enzymes are not. The mutase activity induced by thymidine and by the purine ribonucleosides has been shown to be the same enzyme by four different criteria. This independent induction of phosphodeoxyribomutase suggests that the gene for this enzyme is in an operon different from the one that may contain the genes for thymidine phosphorylase and deoxyribose-5-phosphate aldolase.

Regulation of thymidine metabolism in Escherichia coli K-12: optimal conditions for the assay of 1,5-phosphodeoxyribomutase in ultrasonic extracts

Assay conditions have been established which allow maximum expression of phosphodeoxyribomutase activity in ultrasonic extracts of Escherichia coli K-12. The enzyme requires 2-mercaptoethanol, manganous ions, and glucose 1,6-diphosphate for optimal activity. When cells are grown in minimal medium with glycerol as the carbon source and supplemented with 10(-3)m thymidine, phosphodeoxyribomutase is induced three- to four-fold. Cell pellets may be frozen for 24 hr before sonic disruption without loss of enzyme activity. The assay is highly reproducible.

Genetic regulation of ribonucleoside and deoxyribonucleoside catabolism in Salmonella typhimurium

Four enzymes involved in ribonucleoside and deoxyribonucleoside catabolism (deoxyribose-5-P aldolase, thymidine phosphorylase, phosphodeoxyribomutase, and purine nucleoside phosphorylase) are coded for by four closely linked structural genes on the Salmonella chromosome. The genetic order of these genes is (deoC-deoA-deoB-deoD)-serB-thr. Studies on polarity mutants and induction patterns indicate that the deoB and deoD genes may constitute a single operon and that the deoC and deoA genes may constitute a second closely linked operon.

Specificity and efficiency of thymidine incorporation in Escherichia coli lacking thymidine phosphorylase

A mutant of Escherichia coli lacking the catabolic enzyme thymidine phosphorylase readily incorporates exogenous thymidine into deoxyribonucleic acid (DNA) even when provided at concentrations as low as 0.2 mug/ml. Incorporation by this prototrophic strain occurs specifically into DNA, since, with radioactively labeled thymidine, (i) more than 98% is incorporated into alkali-stable material, (ii) at least 90% is recovered as thymine after brief formic acid hydrolysis, and (iii) at least 90% is incorporated into material with the buoyant density of DNA. During growth in medium containing thymidine, the bacteria obtain approximately half of their DNA thymines from the exogenous thymidine and half from endogenous synthesis. The thymines and cytosines of DNA can be simultaneously and specifically labeled by thymidine-2-(14)C and uridine-5-(3)H, respectively. The mutant, which does not degrade thymidine, retains the ability to degrade the thymidine analogue 5-bromodeoxyuridine.

2-Deoxyribose gene-enzyme complex in Salmonella typhimurium: regulation of phosphodeoxyribomutase

Phosphodeoxyribomutase, the enzyme which catalyzes the interconversion of 2-deoxyribose-1-phosphate to 2-deoxyribose-5-phosphate, has been partially purified from Salmonella typhimurium. The enzyme had an absolute requirement for manganese ion and was stimulated by glucose-1, 6-diphosphate. Phosphodeoxyribomutase was induced by deoxyribose-5-phosphate and was coordinately regulated with the enzymes thymidine phosphorylase and deoxyribose-5-phosphate aldolase, type II. Mutants deficient in these three enzymes were isolated and mapped close to the threonine locus in S. typhimurium. The three enzymes thymidine phosphorylase, deoxyribose-5-phosphate aldolase, type II, and phosphodeoxyribomutase are controlled by a series of linked genes and appear to constitute an operon.

Characteristics of the deo operon: role in thymine utilization and sensitivity to deoxyribonucleosides

Inability to grow on deoxyribonucleosides as the sole carbon source is characteristic of deo mutants of Escherichia coli. Growth of deoC mutants, which lack deoxyribose 5-phosphate aldolase, is reversibly inhibited by deoxyribonucleosides through inhibition of respiration. By contrast, deoB mutants are not sensitive to deoxyribonucleosides, and deoxyribose 5-phosphate aldolase and thymidine phosphorylase are present at normal levels but are not inducible by thymidine. Organisms with the genotype deoB(-)thy(-) or deoC(-)thy(-) are able to grow on low levels of thymine, whereas deoB(+)thy(-) or deoC(+)thy(-) strains require high levels of thymine for growth. The deoB and deoC mutations are transducible with and map on the counterclockwise side of the threonine marker. They are closely linked to deoA, a gene determining thymidine phosphorylase. Merodiploids heterozygous for either the deoB or deoC genes are resistant to deoxyribonucleosides and, in combination with the thy mutation, require high levels of thymine for growth. Cultures of thy(+)deoC(-) mutants are inhibited by thymidine until this compound has been completely degraded and excreted as deoxyribose and thymine, whereupon growth promptly resumes at a normal rate. The inhibition of respiration in deoC strains and the induction of thymidine phosphorylase and deoxyribose 5-phosphate aldolase in the wild-type organism are considered to result from the accumulation of deoxyribose 5-phosphate.