Identification of a trans-acting regulatory factor involved in the control of the pyrimidine pathway in E. coli

Regulation of Escherichia coli pyrC by the purine regulon repressor protein

The purine regulon repressor, PurR, was identified as a component of the Escherichia coli regulatory system for pyrC, the gene that encodes dihydroorotase, an enzyme in de novo pyrimidine nucleotide synthesis. PurR binds to a pyrC control site that resembles a pur regulon operator and represses expression by twofold. Mutations that increase binding of PurR to the control site in vitro concomitantly increase in vivo regulation. There are completely independent mechanisms for regulation of pyrC by purine and pyrimidine nucleotides. Cross pathway regulation of pyrC by PurR may provide one mechanism to coordinate synthesis of purine and pyrimidine nucleotides.

Molecular and mutational analysis of three genes preceding pyrE on the Escherichia coli chromosome

The nucleotide sequence of two kilobase pairs (kb) 5' to the orfE-pyrE operon has been determined. The sequence revealed two open reading frames, orfX and orfY, consisting of 286 and 274 codons, respectively, and having a transcriptional orientation opposite that of the orfE-pyrE operon. Analysis of transcription initiations showed that the promoters of orfE and orfX constitute a pair of divergent promoters with overlapping -35 regions and that orfY is transcribed from an independent promoter. Translational analysis indicated that the orfs are expressed in Escherichia coli. The orfE, orfX, and orfY genes were inactivated on the bacterial chromosome by deletion-insertion mutagenesis using a kanamycin resistance cassette. The mutants were all viable. However, the orfE deletion caused a dramatic reduction in the level of pyrE expression and a partial pyrimidine requirement, because this mutation prevented transcription of pyrE. the orfE protein seemed without significance for pyr-gene expression in E. coli, and the mutations in orfX and orfY were without detectable phenotypes.

carP, a novel gene regulating the transcription of the carbamoylphosphate synthetase operon of Escherichia coli

The carAB operon, encoding carbamoylphosphate synthetase (CPSase; EC 6.3.5.5) is transcribed from two tandem promoters. The upstream promoter (P1) is controlled by pyrimidines and the downstream promoter (P2) is controlled by arginine. We have isolated a new type of constitutive mutation (carP) that specifically affects the control of the pyrimidine-sensitive promoter but does not appear to influence other genes of the pyrimidine pathway. The carP mutation acts in trans and is dominant, which suggests that the carP product is an activator of car transcription. The downstream promoter P2, which is repressed by arginine, overlaps two operator modules characteristic of the arginine regulon. We have isolated two operator-constitutive mutations that specifically affect P2; both map in the upstream ARG box at a strongly conserved position.

Nucleotide sequence of the structural gene for dihydroorotase of Escherichia coli K12

The nucleotide sequence of the dihydroorotase structural gene, pyrC, of Escherichia coli K12 has been determined. The DNA sequence predicts a polypeptide chain of 347 amino acid residues corresponding in size and composition to the previously purified dihydroorotase subunit. Nuclease S1 mapping indicated that transcription of pyrC is initiated around 40 base pairs upstream from the translational start. The transcriptional leader region contains a region of dyad symmetry, which allows a stable hairpin to be formed. This sequence may have regulatory functions since similar structures are found in other pyr genes. The nucleotide sequence also contains a 186-codon open reading frame in front of pyrC. Nuclease Bal31-deletion derivatives of pyrC plasmids indicate that this gene does not affect the expression of pyrC. The predicted polypeptide chain shows a putative signal sequence. Downstream from the structural gene a sequence similar to a rho-independent transcriptional terminator is found. This unknown gene may thus encode a membrane protein of unknown function.

Toxicity of the pyrimidine biosynthetic pathway intermediate carbamyl aspartate in Salmonella typhimurium

Growth of Salmonella typhimurium pyrC or pyrD auxotrophs was severely inhibited in media that caused derepressed pyr gene expression. No such inhibition was observed with derepressed pyrA and pyrB auxotrophs. Growth inhibition was not due to the depletion of essential pyrimidine biosynthetic pathway intermediates or substrates. This result and the pattern of inhibition indicated that the accumulation of the pyrimidine biosynthetic pathway intermediate carbamyl aspartate was toxic. This intermediate is synthesized by the sequential action of the first two enzymes of the pathway encoded by pyrA and pyrB and is a substrate for the pyrC gene product. It should accumulate to high levels in pyrC or pyrD mutants when expression of the pyrA and pyrB genes is elevated. The introduction of either a pyrA or pyrB mutation into a pyrC strain eliminated the observed growth inhibition. Additionally, a direct correlation was shown between the severity of growth inhibition of a pyrC auxotroph and the levels of the enzymes that synthesize carbamyl aspartate. The mechanism of carbamyl aspartate toxicity was not identified, but many potential sites of growth inhibition were excluded. Carbamyl aspartate toxicity was shown to be useful as a phenotypic trait for classifying pyrimidine auxotrophs and may also be useful for positive selection of pyrA or pyrB mutants. Finally, we discuss ways of overcoming growth inhibition of pyrC and pyrD mutants under derepressing conditions.

Cloning and characterization of the pyrE gene and of PyrE::Mud1 (Ap lac) fusions from Salmonella typhimurium

A lambda-specialized transducing phage carrying the pyrE gene from Salmonella typhimurium LT2 was constructed and used as the source of DNA for subcloning the pyrE gene into pBR322. The pyrE gene product was identified as a 23-kDa polypeptide using a minicell system for analysis of plasmid-encoded proteins. Studies utilizing a promoter-cloning vehicle provided evidence for the existence of two promoter regions, one located close to the start of the structural gene and the other positioned more than 300 base pairs upstream. Transcription from the more distal promotor was the only situation in which significant regulation by pyrimidines was observed. Additional studies served to localize sites involved in the regulation of pyrE expression and led to the inference that regulation does not occur at the level of initiation of transcription. A procedure was developed for the construction of plasmids through recombination in vivo, whereby pyrE::Mud1 (Ap lac) fusions were transferred to a recipient pyrE+ plasmid by bacteriophage P22-mediated transduction. This enabled the identification of the integration sites of Mud within pyrE and also verified the deduced orientation of the pyrE gene in the parental plasmid. The nucleotide sequence of the 5' end of the pyrE gene was determined, including 150 nucleotide residues encoding the first 50 N-terminal amino acids of orotate phosphoribosyltransferase, and 400 nucleotides upstream from the start of the coding region. The leader region contains sequences characteristic of a rho-independent transcriptional terminator preceded by a cluster of thymidylate residues. In addition, the leader RNA contains an open reading frame with a UGA stop codon immediately preceding the putative transcriptional terminator. The nucleotide sequence suggests that pyrE expression is regulated by modulated attenuation, as has been proposed to be the case for both pyrB and pyrE expression in Escherichia coli.

Studies on the structure and expression of Escherichia coli pyrC, pyrD, and pyrF using the cloned genes

The Escherichia coli pyrC, pyrD and pyrF genes were cloned on multicopy plasmids derived from pBR322 and analysed by means of restriction endonucleases. It was found that the pyrC gene is destroyed by cutting with the restriction endonuclease BamHI, that the entire pyrD gene can be isolated on a 1300-base pairs DNA fragment generated by EcoRI cleavage and that cutting with EcoRI removes the promotor and probably also the translational start site from the pyrF gene. More details on the restriction maps are presented. Further, it was found that the presence of a pyr gene in multiple copies on a plasmid does not significantly interfere with the activity of the chromosomal pyr genes. Using the 'minicell' technique, the polypeptides encoded by the three cloned pyr genes were identified. The relative molecular masses for the pyrC-encoded and pyrD-encoded polypeptides are 38 000-40 000 and 36 000-38 000, respectively. Thus in their native form, dihydroorotase and dihydroorotate oxidase appear to be dimeric proteins. The 'minicell' experiments positively identified a protein chain of Mr 23 000-24 000 as being a subunit of OMP decarboxylase encoded by pyrF. Moreover, the coding frame for this polypeptide seems to be expressed as the first gene in the operon with the coding frame for another protein chain of Mr 13 000-14 000. Since, however, the native OMP decarboxylase during sedimentation and gel filtration behaves as a protein of Mr 45 000 +/- 4000, this latter polypeptide (Mr 13 000-14 000) is hardly a component of the enzyme. Pyr-lac+ operon fusions were constructed by the Mu d1 procedure. By integrating an F'lac episome into the lac part of the fusions and determining the direction of chromosomal transfer from the resultant Hfr strains, the direction of pyrC transcription was found to be counter-clockwise, while pyrD and pyrF were found to be transcribed in a clockwise direction.