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

Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein

The gua promoter (guaP) of Escherichia coli resembles those for ribosomal RNA (rrn) operons and lies in a close back-to-back arrangement with the promoter for xseA (xseP). Transcription from guaP is subject to stringent control and growth-rate-dependent regulation, and to repression by DnaA and PurR. In addition, transcription from guaP is regulated by the cyclic AMP receptor protein (CRP). Plasmid-borne promoter fusions to the receptor gene for chloramphenicol acetyl transferase were used to assess the role of CRP in controlling transcription from guaP and xseP following a downshift of cultures from rich into minimal medium. CRP is required to activate guaBA transcription and repress xseA transcription following downshift. Bandshift assays with a DNA fragment carrying the divergent promoters revealed specific binding of CRP. We propose that CRP, binding to a near-consensus site centred at -117.5, activates transcription from guaP and obstructs transcription from the xseA promoter.

Inosine-5'-monophosphate dehydrogenase: regulation of expression and role in cellular proliferation and T lymphocyte activation

Guanine nucleotide synthesis is essential for the maintenance of normal cell growth and function, as well as for cellular transformation and immune responses. The expression of two genes encoding human inosine-5'-monophosphate dehyrogenase (IMPDH) type I and type II results in the translation of catalytically indistinguishable enzymes that control the rate-limiting step in the de novo synthesis of guanine nucleotides. Cellular IMPDH activity is increased more than 10-fold in activated peripheral blood T lymphocytes and is attributable to the increased expression of both the type I and type II enzymes. In contrast, abrogation of cellular IMPDH activity by selective inhibitors prevents T lymphocyte activation and establishes a requirement for elevated IMPDH activity in T lymphocytic responses. In order to assess the molecular mechanisms governing the expression of the IMPDH type I and type II genes in resting and activated peripheral blood T lymphocytes, we have cloned the human IMPDH type I and type II genes and characterized their genomic organization and their respective 5'-flanking regions. Both genes contain 14 highly conserved exons that vary in size from 49 to 207 base pairs. However, the intron structures are completely divergent, resulting in disparities in gene length (18 kilobases for type I and 5.8 kilobases for type II). In addition, the 5'-regulatory sequences are highly divergent; expression of the IMPDH type I gene is controlled by three distinct promoters in a tissue specific manner while the type II gene is regulated by a single promoter and closely flanked in the 5' region by a gene of unknown function. The conservation of the IMPDH type I and type II coding sequence in the presence of highly divergent 5'-regulatory sequences points to a multifactorial control of enzyme expression and suggests that tissue-specific and/or developmentally specific regulation of expression may be important. Delineation of these regulatory mechanisms will aid in the elucidation of the signaling events that ultimately lead to the synthesis of guanine nucleotides required for cellular entry into S phase and the initiation of DNA replication.

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.

Specific binding of DnaA protein to a DnaA box in the guaB gene of Escherichia coli K12

Expression of the guaBA operon of Escherichia coli is regulated by the DNA replication-initiating protein, DnaA. Two DnaA boxes, which are potential binding sites for DnaA, are present in the gua operon. One box (with 8/9 match to the DnaA box consensus sequence) is at the gua promoter; the other box, which has a consensus sequence, is on the non-transcribed strand within the guaB coding region approximately 200 bp downstream of the initiation codon. The binding in vitro of purified DnaA protein to these boxes was investigated by filter retention and gel retardation analysis, and by deoxyribonuclease I footprinting, using restriction fragments of gua operon DNA. DnaA protein was shown to bind specifically only to the fragment carrying the consensus sequence DnaA box, and to protect this box from deoxyribonuclease I. Transcription termination resulting from the binding of DnaA to this box within the guaB gene explains repression by DnaA of the gua operon in vivo.

Gene amplification and dual point mutations of mouse IMP dehydrogenase associated with cellular resistance to mycophenolic acid

Mouse neuroblastoma cells (NB) selected for 10,000-fold increased resistance to mycophenolic acid (NB-Myco) showed a 200-500-fold increase in IMP dehydrogenase protein, and the enzyme (IMP: NAD+ oxidoreductase, EC 1.1.1.205) also exhibited a 2400-fold increased ki for mycophenolic acid and reduced catalytic efficiency (Hodges, S.D., Fung, E., McKay, D.J., Renaux, B.S., and Snyder, F.F. (1989) J. Biol. Chem. 264, 18137-18141). The molecular basis of these changes is the subject of the present study. The nucleotide sequence of IMP dehydrogenase cDNA from NB-Myco cells revealed four nucleotide changes. One of these changes did not result in a codon change, and a second one corresponding to methionine-483 was present in the parental NB mouse line. The remaining two nucleotide substitutions and deduced residue changes are: the C to T transition at base 998 relative to initiation of translation, altering threonine-333 to isoleucine; and the C to A transversion at base 1052, altering serine-351 to tyrosine. Evidence was also obtained for IMP dehydrogenase having undergone gene amplification. IMP dehydrogenase mRNA levels were 500-fold increased in NB-Myco cells as compared to parental NB cells. DNA dot blot analysis showed a 25-fold increase in IMP dehydrogenase gene copy number and restriction enzyme analysis revealed similar gene structure for NB and NB-myco cells.

Probing the active site of human IMP dehydrogenase using halogenated purine riboside 5'-monophosphates and covalent modification reagents

Active-site amino acid residues of human type II inosine 5'-monophosphate dehydrogenase (IMPDH) were investigated using the covalent modification reagents 6-chloroinosine 5'-monophosphate (6-Cl-IMP) and iodoacetamide. IMPDH was incubated with these reagents in the presence and absence of IMP, NAD, and NADH, and the activity of the enzyme for IMP dehydrogenation or 2-Cl-IMP dehalogenation was followed. IMPDH activity was rapidly lost when the enzyme was incubated with the IMP analog, 6-Cl-IMP, or with iodoacetamide. The enzyme was protected against inactivation in the presence of the substrate IMP. It was not protected against inactivation by NAD alone. Saturating concentrations of IMP and NADH reduced the inactivation rate by about the same amount as with IMP alone. IMPDH samples labeled with 6-Cl-IMP and an unlabeled control were alkylated with iodoacetamide, digested with trypsin, and analyzed by HPLC-mass spectrometry (HPLC-MS). All eight cysteines of human type II IMPDH were found to exist as free sulfhydryls on the active, unlabeled form of the enzyme. At an enzyme/inactivator ratio of 1:4, only one cysteine residue, Cys-331, was found to be covalently modified by 6-Cl-IMP. From the results of the substrate protection experiments and HPLC-MS data, it is concluded that 6-Cl-IMP binds in the IMP binding site of IMPDH and reacts covalently with Cys-331 to form a purine riboside 5'-monophosphate-enzyme adduct.

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.

Isolation and sequence of a cDNA encoding mouse IMP dehydrogenase

Inosinic acid (IMP) dehydrogenase (IMPD) catalyzes the conversion of IMP to XMP as the first committed step in GMP biosynthesis de novo. We have isolated a cDNA containing the complete coding region of mouse IMPD by its ability to complement a bacterial mutant lacking IMPD activity. Two independent cDNA clones were isolated by complementation, of which the longest was 1.7 kb in length. Northern analyses, using the IMPD cDNA as a probe, indicated that mature IMPD mRNA was a single species approx. 2.0 kb in size. Mouse IMPD is almost identical to Chinese hamster and human IMPDs and is highly conserved between Escherichia coli and mouse, with a direct amino acid (aa) identity of 39%, which increases to 60% if conserved aa are considered. The leader region of our longest cDNA clone is G + C-rich and contains two tandem copies of a G + C-rich direct repeat.

Identification of hypoxanthine and guanine as the co-repressors for the purine regulon genes of Escherichia coli

Addition of purine compounds to the growth medium of Escherichia coli and Salmonella typhimurium causes repressed synthesis of the purine biosynthetic enzymes. The repression is mediated through a regulatory protein, PurR. To identify the co-repressor(s) of PurR, two approaches were used: (i) mutations were introduced into purine salvage genes and the effects of different purines on pur gene expression were determined; (ii) purine compounds which dictate the binding of the PurR protein to its operator DNA were resolved by gel retardation. Both the in vivo and the in vitro data indicated that guanine and hypoxanthine are co-repressors. The toxic purine analogues 6-mercaptopurine and 6-thioguanine also activated the binding of PurR to its operator DNA.

Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli

The purR gene encodes a repressor (PurR) controlling the synthesis of the enzymes of purine biosynthesis. The subunit of PurR was identified as a 38-kDa polypeptide by SDS/polyacrylamide gel electrophoresis. Analysis of a purR-lacZ transcriptional fusion indicated that purR expression is autoregulated. This was confirmed by gel retardation and DNaseI footprinting experiments, where two PurR-binding sites were identified in the transcribed part of purR. Introduction of a purR mutation in wild-type and pur-lac fusion strains was found to abolish purine repression of all genes of the purine biosynthetic pathway except for purA.

Nucleotide sequence analysis of the purEK operon encoding 5'-phosphoribosyl-5-aminoimidazole carboxylase of Escherichia coli K-12

5'-Phosphoribosyl-5-aminoimidazole (AIR) carboxylase (EC 4.1.1.21) catalyzes step 6, the carboxylation of AIR to 5'-phosphoribosyl-5-aminoimidazole-4-carboxylic acid, in the de novo biosynthesis of purine nucleotides. As deduced from the DNA sequence of restriction fragments encoding AIR carboxylase and supported by maxicell analyses, AIR carboxylase was found to be composed of two nonidentical subunits. In agreement with established complementation data, the catalytic subunit (deduced Mr, 17,782) was encoded by the purE gene, while the CO2-binding subunit (deduced Mr, 39,385) was encoded by the purK gene. These two genes formed an operon in which the termination codon of the purE gene overlapped the initiation codon of the purK gene. The 5' end of the purEK mRNA was determined by mung bean nuclease mapping and was located 41 nucleotides upstream of the proposed initiation codon. The purEK operon is regulated by the purR gene product, and a purR regulatory-protein-binding site related to the sequences found in other pur loci was identified in the purEK operon control region.

Nucleotide sequence of the gene encoding the GMP reductase of Escherichia coli K12

(1) The nucleotide sequence of a 1991 bp segment of DNA that expresses the GMP reductase (guaC) gene of Escherichia coli K12 was determined. (2) This gene comprises 1038 bp, 346 codons (including the initiation codon but excluding the termination codon), and it encodes a polypeptide of Mr 37,437 which is in good agreement with previous maxicell studies. (3) The sequence contains a putative promoter 102 bp upstream of the translational start codon, and this is immediately followed by a (G + C)-rich discriminator sequence suggesting that guaC expression may be under stringent control (4) The GMP reductase exhibits a high degree of sequence identity (34%) with IMP dehydrogenase (the guaB gene product) indicative of a close evolutionary relationship between the salvage pathway and the biosynthetic enzymes, GMP reductase and IMP dehydrogenase, respectively. (5) A single conserved cysteine residue, possibly involved in IMP binding to IMP dehydrogenase, was located within a region that possesses some of the features of a nucleotide binding site. (6) The IMP dehydrogenase polypeptide contains an internal segment of 123 amino acid residues that has no counterpart in GMP reductase and may represent an independent folding domain flanked by (alanine + glycine)-rich interdomain linkers.

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.