Molecular cloning and characterisation of the gua regulatory region of Escherichia coli K12

The dynamic determinants of reaction specificity in the IMPDH/GMPR family of (β/α)(8) barrel enzymes

The inosine monophosphate dehydrogenase (IMPDH)/guanosine monophosphate reductase (GMPR) family of (β/α)(8) enzymes presents an excellent opportunity to investigate how subtle changes in enzyme structure change reaction specificity. IMPDH and GMPR bind the same ligands with similar affinities and share a common set of catalytic residues. Both enzymes catalyze a hydride transfer reaction involving a nicotinamide cofactor hydride, and both reactions proceed via the same covalent intermediate. In the case of IMPDH, this intermediate reacts with water, while in GMPR it reacts with ammonia. In both cases, the two chemical transformations are separated by a conformational change. In IMPDH, the conformational change involves a mobile protein flap while in GMPR, the cofactor moves. Thus reaction specificity is controlled by differences in dynamics, which in turn are controlled by residues outside the active site. These findings have some intriguing implications for the evolution of the IMPDH/GMPR family.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Regulation of the gua operon of Escherichia coli by the DnaA protein

The guaBA operon determines production of the two enzymes required to convert hypoxanthine to guanine at the nucleotide level during guanine nucleotide biosynthesis. Two DnaA boxes, binding sites for the DNA replication-initiating DnaA protein, are present in the gua operon, one at the gua promoter (guaP) and the other within the guaB coding sequence. Regulation of the guaBA operon by DnaA protein was studied using strains carrying chromosomal gua-lacZ fusions. In these strains beta-galactosidase acts as a reporter enzyme for transcription initiated at guaP. When the intracellular levels of DnaA were increased (by induction of a multicopy plasmid carrying the dnaA gene fused to the tac promoter) transcription from the gua promoter was repressed. Reducing the intracellular level of DnaA, either by sequestration with an oriC plasmid or by placing a temperature-sensitive dnaA mutant at the restrictive temperature, resulted in increased transcription from guaP. Thus the transcriptional activity of the gua operon is coupled, through the DnaA protein, to the DNA replication cycle. Repression of guaP by DnaA was dependent on the presence of both boxes in the gua-lacZ fusion; constructs containing only the box at guaP were unaffected by DnaA.

Secondary attachment site for bacteriophage lambda in the guaB gene of Escherichia coli

lambda gua transducing bacteriophages were used to identify and sequence the secondary attachment site for lambda in the guaB gene of Escherichia coli. The sequence matched the primary core sequence at nine positions, and a putative integrase binding-site overlapped the left core-arm junction. Recombinational crossover occurred between nucleotides -3 and +2 of the core region.

Nucleotide sequence of the guaB locus encoding IMP dehydrogenase of Escherichia coli K12

IMP dehydrogenase, the product of the guaB locus in Escherichia coli K12, catalyzes the synthesis of XMP by the NAD+ dependent oxidation of IMP. The guaB locus has been subcloned from the Clarke and Carbon plasmid pLC34-10. The sequence of the guaB structural gene and surrounding DNA was determined by the dideoxy chain termination method of Sanger. The 1.533 kb guaB gene encodes an IMP dehydrogenase subunit of molecular weight 54,512. S1 nuclease mapping placed the site of guaBA mRNA initiation approximately 188 bp from the start of the guaB structural gene. The -10 and -35 regions that define the guaBA promoter were located upstream of the start of the guaBA transcription initiation site. The control region of approximately 188 bp does not show any obvious potential for secondary structure. A secondary lambda att site has been identified 42 bp distal to the guaB start codon.

Nucleotide sequence and organisation of the gua promoter region of Escherichia coli

Overlapping restriction fragments of DNA carrying the gua promoter region of Escherichia coli have been cloned using promoter-probe plasmids. Antibiotic resistance conferred by the constructed plasmids is repressed by guanine and enhanced by adenine, two features characteristic of expression of the gua operon. The nucleotide sequence of these fragments reveals the gua promoter 43 bp upstream of the translational start codon for inosine 5'-monophosphate (IMP) dehydrogenase. The promoter is preceded by an A + T-rich region and several potential polymerase secondary binding sites, and is immediately followed by a G + C-rich discriminator, suggesting that the gua operon may be under stringent control. A sequence with twofold symmetry overlaps both promoter and discriminator and is therefore located where repressor binding could interfere with transcription initiation. A stem and loop can be formed from the leader mRNA, thus sequestering the ribosome-binding site.