Aspartate transcarbamoylase genes of Pseudomonas putida: requirement for an inactive dihydroorotase for assembly into the dodecameric holoenzyme.

The nucleotide sequences of the genes encoding the enzyme aspartate transcarbamoylase (ATCase) from Pseudomonas putida have been determined. Our results confirm that the P. putida ATCase is a dodecameric protein composed of two types of polypeptide chains translated coordinately from overlapping genes. The P. putida ATCase does not possess dissociable regulatory and catalytic functions but instead apparently contains the regulatory nucleotide binding site within a unique N-terminal extension of the pyrB-encoded subunit. The first gene, pyrB, is 1,005 bp long and encodes the 334-amino-acid, 36.4-kDa catalytic subunit of the enzyme. The second gene is 1,275 bp long and encodes a 424-residue polypeptide which bears significant homology to dihydroorotase (DHOase) from other organisms. Despite the homology of the overlapping gene to known DHOases, this 44.2-kDa polypeptide is not considered to be the functional product of the pyrC gene in P. putida, as DHOase activity is distinct from the ATCase complex. Moreover, the 44.2-kDa polypeptide lacks specific histidyl residues thought to be critical for DHOase enzymatic function. The pyrC-like gene (henceforth designated pyrC') does not complement Escherichia coli pyrC auxotrophs, while the cloned pyrB gene does complement pyrB auxotrophs. The proposed function for the vestigial DHOase is to maintain ATCase activity by conserving the dodecameric assembly of the native enzyme. This unique assembly of six active pyrB polypeptides coupled with six inactive pyrC' polypeptides has not been seen previously for ATCase but is reminiscent of the fused trifunctional CAD enzyme of eukaryotes.

Unusual G + C content and codon usage in catIJF, a segment of the ben-cat supra-operonic cluster in the Acinetobacter calcoaceticus chromosome.

The nucleotide (nt) sequence of a 5.3-kb DNA segment containing the Gram- Acinetobacter calcoaceticus catBCIJFD operon is reported. This information completes determination of a 16-kb nt sequence containing the twelve ben and cat structural genes encoding enzymes required for catabolism of benzoate via the beta-ketoadipate pathway. Many of these genes can be traced to a common ancestry with genes from other organisms containing DNA with widely divergent G + C content. The A. calcoaceticus ben and cat genes are arranged in a supra-operonic cluster containing one known regulatory gene and three additional open reading frames (ORFs) that may have regulatory functions. Thirteen of the ben and cat genes, including the three ORFs with unknown function, are typical for A. calcoaceticus in that they possess a G + C content of 44.9 +/- 2.5%. Three exceptional A. calcoaceticus genes (catI, catJ and catF) possess G + C contents of 56.5 +/- 1.3%. These differences in G + C content are reflected in the distinctive patterns of codon usage shared by catI, catJ and catF. Thus, the catIJF region, known to exchange genetic information with the pcaIJF region in the same chromosome directing isofunctional proteins associated with the beta-ketoadipate pathway, has avoided the evolutionary forces that conferred characteristics G + C content upon the other ben and cat genes in A. calcoaceticus.

Regulatory sequences controlling short chain fatty acid metabolism in Escherichia coli.

Acetoacetate in Escherichia coli is metabolized via the combined enzymatic action of a CoA-transferase and a thiolase. Growth of E. coli on short chain fatty acids such as butyrate and valerate is also predicated upon the expression of these enzymes. The genes for these enzymes (atoDAB) are arranged in an operon and are coordinately transcribed in response to the inducer acetoacetate. A positive regulatory element, the product of the atoC gene, regulates expression of the operon. The atoC gene lies adjacent to the atoDAB operon and all the ato genes have been cloned as a single 6.2 kbp restriction fragment (kindly provided by Dr. Lauren Sallus Jenkins). We have isolated a series of mutant E. coli strains with altered regulatory properties that are either inducible by an alternate substrate, or that show constitutive expression of the atoDAB genes. The -10 and -35 regions upstream of the atoDAB operon poorly match consensus sequences. In addition, the transcriptional start is preceded by a catabolite activator protein binding site (CAP site), as well as a putative binding site for the atoC gene product as represented by a region of dyad symmetry.

Characterization of temperature-sensitive cytidine triphosphate synthase mutations in bacteria by high-performance liquid chromatography.

Cytidine triphosphate (CTP) synthase catalyzes the last step in pyrimidine ribonucleotide synthesis, namely the formation of CTP from UTP, ATP, and glutamine. Mutants devoid of CTP synthase activity require cytidine for growth and have been designated pyrG in an obligate cdd background. Using a ts mutation blocked in the conversion of UTP to CTP at 43 degrees C, it was demonstrated that the conversion occurs by growing cells at 33 degrees C or below where UTP and CTP pools are normal. Growth at 43 degrees C shuts off the enzyme, while UTP accumulates and CTP is decreased significantly. By now feeding exogenous cytidine the CTP pool can be restored to the level found at the permissive temperature. Intracellular nucleoside triphosphates (CTP and UTP) were separated on a Partisil SAX10 cartridge, using a linear gradient of low buffer (7 mM ammonium dihydrogenphosphate, pH 3.8) to high buffer (250 mM ammonium dihydrogenphosphate, pH 4.5 with 500 mM potassium chloride). Nucleoside triphosphates were also separated after enzymatic conversion of UTP to CTP in solution by cell extracts using ion-pair reversed-phase chromatography on a C18 cartridge eluted with a mixture of 95% buffer A (25 mM ammonium dihydrogenphosphate with 1 mM tetrabutylammonium phosphate, pH 7.0) and 5% buffer B (15% aqueous acetonitrile). Using the two different separation techniques, it was possible to monitor the level of UTP and CTP inside cells as well as the enzymatic conversion of UTP to CTP by the enzyme CTP synthase.

Natural transformation in Acinetobacter calcoaceticus.

Acinetobacter calcoaceticus is a metabolically versatile microorganism that is naturally competent for DNA uptake and incorporation. We have exploited the natural state of competency for studies involving the cloning, organization and expression of genes encoding catabolic enzymes. A. calcoaceticus is able to take up, at high efficiency, genetically engineered DNA, incorporate the DNA and stably maintain and express the DNA. Sequence analysis of cloned A. calcoaceticus DNA reveals a great deal of internal repetition and secondary structure, but no specific sequences associated with uptake appear to be present. Uptake and transformation occurs in solid and liquid medium, at a wide range of DNA concentrations and with little restriction barrier to the source of the transforming DNA.

Cloning and expression of Acinetobacter calcoaceticus catBCDE genes in Pseudomonas putida and Escherichia coli.

This report describes the isolation and preliminary characterization of a 5.0-kilobase-pair (kbp) EcoRI DNA restriction fragment carrying the catBCDE genes from Acinetobacter calcoaceticus. The respective genes encode enzymes that catalyze four consecutive reactions in the catechol branch of the beta-ketoadipate pathway: catB, muconate lactonizing enzyme (EC 5.5.1.1); catC, muconolactone isomerase (EC 5.3.3.4); catD, beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24); and catE, beta-ketoadipate succinyl-coenzyme A transferase (EC 2.8.3.6). In A. calcoaceticus, pcaDE genes encode products with the same enzyme activities as those encoded by the respective catDE genes. In Pseudomonas putida, the requirements for both catDE and pcaDE genes are met by a single set of genes, designated pcaDE. A P. putida mutant with a dysfunctional pcaE gene was used to select a recombinant pKT230 plasmid carrying the 5.0-kbp EcoRI restriction fragment containing the A. calcoaceticus catE structural gene. The recombinant plasmid, pAN1, complemented P. putida mutants with lesions in catB, catC, pcaD, and pcaE genes; the complemented activities were expressed constitutively in the recombinant P. putida strains. After introduction into Escherichia coli, the pAN1 plasmid expressed the activities constitutively but at much lower levels that those found in the P. putida transformants or in fully induced cultures of A. calcoaceticus or P. putida. When placed under the control of a lac promoter on a recombinant pUC13 plasmid in E. coli, the A. calcoaceticus restriction fragment expressed catBCDE activities at levels severalfold higher than those found in fully induced cultures of A. calcoaceticus. Thus there is no translational barrier to expression of the A. calcoaceticus genes at high levels in E. coli. The genetic origin of the cloned catBCDE genes was demonstrated by the fact that the 5.0-kbp EcoRI restriction fragment hybridized with a corresponding fragment from wild-type A. calcoaceticus DNA. This fragment was missing in DNA from an A. calcoaceticus mutant in which the cat genes had been removed by deletion. The properties of the cloned fragment demonstrate physical linkage of the catBCDE genes and suggest that they are coordinately transcribed.

A Salmonella typhimurium strain defective in uracil catabolism and beta-alanine synthesis.

A selection procedure for uracil catabolism mutant strains involving indicator dye plates was developed. Using this method, a strain defective in uracil catabolism has been isolated in Salmonella typhimurium that was temperature-sensitive at 42 degrees C where it required low concentrations of N-carbamoyl-beta-alanine, beta-alanine or pantothenic acid for growth. An extract of the mutant strain degraded uracil at 37 degrees C at a significantly diminished rate compared to that observed for the wild-type strain under the same growth conditions. The conversion of dihydrouracil to N-carbamoyl-beta-alanine was blocked at all temperatures examined in the mutant strain. By means of genetic analysis, the mutant strain was determined to be defective at two genetic loci. Transduction studies with bacteriophage P22 indicated that the panD gene is mutated in this strain, accounting for its beta-alanine requirement. Episomal transfers between Escherichia coli and the mutant strain provided evidence that the defect in uracil catabolism was located in another region of the S. typhimurium chromosome.

Properties of hybrid aspartate transcarbamoylase formed with native subunits from divergent bacteria.

The aspartate transcarbamoylases (ATCase) from Serratia marcescens and Escherichia coli exhibit unique regulatory and kinetic properties and were dissociated into their constituent regulatory and catalytic subunits. A hybrid ATCase holoenzyme was formed with catalytic subunits from S. marcescens and regulatory subunits from E. coli as demonstrated by the molecular weight, the recovery of cooperative, homotropic response to the substrate aspartate, and the re-establishment of heterotropic responses to the allosteric effectors ATP and CTP. This hybrid is of interest since ATCase from E. coli is inhibited by CTP and activated by ATP while ATCase from S. marcescens is activated by both nucleotides. The activity of the catalytic subunits was reduced upon formation of the catalytic subunits was reduced upon formation of the hybrid ATCase enzyme which exhibited an exaggerated requirement for aspartate; the [S]0.5 was 100-125 mM aspartate compared to 5 mM for the E. coli holoenzyme and 20 mM for the native ATCase from S. marcescens. Still, the heterotropic response to effectors was communicated efficiently through the various protein:protein domains of bonding in ATCase as 1 mM ATP activated the hybrid ATCase while 1 mM CTP inhibited the enzyme. ATP did not influence the pH profile of the hybrid enzyme but increasing concentrations of the substrate aspartate shifted the pH optimum from pH 6 to pH 6.8. These data support the view that homotropic and heterotropic responses in ATCase can be altered separately. Since the hybrid ATCase was formed with native, unmodified regulatory and catalytic subunits, the r:r and c:c domains in the hybrid holoenzyme remained fundamentally unaltered. Therefore, it appears that the r:c domains provide the primary communication for changes in quaternary structure that define the allosteric and enzymatic properties of the holoenzyme.

Assembly of the aspartate transcarbamoylase holoenzyme from transcriptionally independent catalytic and regulatory cistrons.

The cistrons encoding the regulatory and catalytic polypeptides of aspartate transcarbamoylase (EC 2.1.3.2) from Escherichia coli K-12 have been cloned separately on plasmids from different incompatability groups. The catalytic cistron (pyrB) was carried by pACYC184 and expressed from its own promoter, whereas the regulatory cistron was expressed from the lac po of pBH20. The catalytic polypeptide chains assembled into enzymatically active trimers (c3) in vivo when expressed in the absence of regulatory subunits. Similarly, the regulatory polypeptide chains assembled into regulatory dimers (r2) in vivo in the absence of catalytic subunits. When cellular extracts containing regulatory dimers and catalytic trimers synthesized in separate cells were combined in vitro, partial spontaneous holoenzyme assembly occurred. When pyrB and pyrI were expressed from transcriptionally independent cistrons in the same cell, all detectable catalytic polypeptides were incorporated into the functional aspartate transcarbamoylase holoenzyme, 2(c3):3(r2). Thus, it is clear that the in vivo assembly of ATCase holoenzyme is a direct, spontaneous process involving the association of preformed regulatory subunits (r2) and catalytic subunits (c3). This procedure provides a general method for the construction of hybrid aspartate transcarbamoylase in vivo and may be applicable to other oligomeric enzymes constructed from different polypeptides.

New assay for enzymatic phosphate release: application to aspartate transcarbamylase and other enzymes.

The colorimetric method for phosphate determination described in the preceding paper is adapted for the assay of orthophosphate liberated in the aspartate transcarbamylase reaction. The method provides for simple, accurate, and sensitive measurement of enzyme activity. The assay uses ammonium molybdate and zinc acetate to form a colored complex with the enzymatically released phosphate; mild conditions which minimize the nonenzymatic background degradation of the substrate, carbamoyl phosphate, are used. Since the assay procedure is relatively rapid, it is especially attractive in situations where results are desired immediately. The method can be used for the assay of any enzyme which releases inorganic phosphate, even in the presence of labile organophosphate compounds.

Purification and some properties of cytosine deaminase from Salmonella typhimurium.

Cytosine deaminase (EC 3.5.4.1) from Salmonella typhimurium has been purified 419-fold to apparent homogeneity. SDS polyacrylamide gel electrophoresis indicated that the final cytosine deaminase preparation was homogeneous. The molecular weight of cytosine deaminase was determined to be approx. 230000 containing four identical subunits with each subunit having a molecular weight 54000. Cytosine was deaminase has a pH optimum of 7.30 to 7.50 and a temperature optimum of 45 to 50 degrees C. Cytosine was deaminated specifically; 5-fluorocytosine was deaminated to a lesser extent. The Km and V values for cytosine were 0.74 mM and 47.16 mumole/min, respectively. As effectors of enzyme activity, PPi stimulated the deamination while metal ions and orotidine monophosphate inhibited it. The physical characteristics of cytosine deaminase lend credence to its proposed salvage role in pyrimidine metabolism as indicated previously by physiological studies (West, T.P. and O'Donovan, G.A., J. Bacteriol. (1982) 149, 1171-1174).