Structural analysis of the ileR locus of Escherichia coli K12

Promoter interference in a bacteriophage lambda control region: effects of a range of interpromoter distances

The p(R) and p(RM) promoters of bacteriophage lambda direct transcription in divergent directions from start sites separated by 83 phosphodiester bonds. We had previously shown that the presence of an RNA polymerase at p(R) interfered with open complex formation at p(RM) and that this effect was alleviated by the deletion of 10 bp between the two promoters. Here we present a detailed characterization of the dependence of the interference on the interpromoter distance. It was found that the reduced interference between the two promoters is unique to the 10-bp deletion. The relief of interference was demonstrated to be due to the facilitation of a step subsequent to RNA polymerase binding to the p(RM) promoter. A model to explain these observations is proposed. A search of known Escherichia coli promoters identified three pairs of divergent promoters with similar separations to those investigated here.

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.

Mapping and disruption of the chpB locus in Escherichia coli

The chpB locus is a chromosomal homolog of the pem locus, which is responsible for stable maintenance of plasmid R100 within the host cells. Like pem, chpB codes for two genes, chpBK and chpBI, encoding a growth inhibitor and a suppressor for the killing action of the ChpBK protein, respectively. Here, we determined the precise location of the chpB locus, which is linked to ileR and ppa in the order ileR-chpB-ppa, at 95.7 min on the map of Escherichia coli. We then constructed mutants with an insertion of a (cat) fragment within chpBK or chpBI on the E. coli chromosome. These mutants grew normally, indicating that chpB is dispensable for cell growth.

chpA and chpB, Escherichia coli chromosomal homologs of the pem locus responsible for stable maintenance of plasmid R100

The pem locus is responsible for stable maintenance of plasmid R100 and consists of two genes, pemI and pemK. The pemK gene product is a growth inhibitor, while the pemI gene product is a suppressor of this inhibitory function. We found that the PemI amino acid sequence is homologous to two open reading frames from Escherichia coli called mazE and orf-83, which are located at 60 and 100 min on the chromosome, respectively. We cloned and sequenced these loci and found additional open reading frames, one downstream of each pemI homolog, both of which encode proteins homologous to PemK. The pem locus homolog at 60 min was named chpA and consists of two genes, chpAI and chpAK; the other, at 100 min, was named chpB and consists of two genes, chpBI and chpBK. The distal portion of chpBK was found to be adjacent to the ppa gene that encodes pyrophosphatase, whose map position had not been previously determined. We then demonstrated that the chpAK and chpBK genes encode growth inhibitors, while the chpAI and chpBI genes encode suppressors for the inhibitory function of the ChpAK and ChpBK proteins, respectively. These E. coli pem locus homologs may be involved in regulation of cell growth.

Maintenance of repression control of the ilvGMEDA operon in a temperature-sensitive leucyl-transfer RNA synthetase mutant of Escherichia coli K-12 at a restrictive temperature

The mechanism of L-leucine regulation of ilvGMEDA is thought to be by ribosome-mediated attenuation that is dependent upon the concentration of Leu-tRNA(Leu) which results from leucyl-tRNA synthetase (LeuRS) activity. The requirement for LeuRS activity in attenuation control was tested in an Escherichia coli K-12 strain containing a temperature-sensitive LeuRS and the ilvGMEDA operon with an active ilvGM. Growth of this strain at 30 degrees C followed by a shift to 37 degrees C to inactivate the LeuRS revealed that ilvGM expression decreased at the restrictive temperature whereas the downstream gene expression was slightly elevated. We suggest that ilvGM does not respond to a deattenuation signal, and that, possibly, a secondary repression/derepression mechanism exists.

Effects of the flrA regulatory locus on biosynthesis and excretion of amino acids in Escherichia coli B/r

We have partially characterized phenotypic effects of an unusual amino acid regulatory locus, flrA, in E. coli B/r that alters the expression of the ilv and leu operons [Kline, E.L (1972) J. Bacteriol. 110:1127-1134]. This study demonstrated that a primary effect of the flrA7 mutation in haploid strains was overproduction of valine. In diploid strains (FflrA+/flrA7) this mutation resulted in excretion of valine, isoleucine, leucine, aspartate, threonine, glutamate, histidine and lysine. Increased excretion of amino acids by mutant strains might be explained by a membrane alteration or by flrA encoding a positive regulatory factor that affects the ilv operon and has pleiotropic effects on other amino acid operons.

Specificity of attenuation control in the ilvGMEDA operon of Escherichia coli K-12

Three different approaches were used to examine the regulatory effects of the amino acids specified by the peptide-coding region of the leader transcript of the ilvGMEDA operon of Escherichia coli K-12. Gene expression was examined in strains carrying an ilvGMED'-lac operon fusion. In one approach, auxotrophic derivatives were starved of single amino acids for brief periods, and the burst of beta-galactosidase synthesis upon adding the missing amino acid was determined. Auxotrophic derivatives were also grown for brief periods with a limited supply of one amino acid (derepression experiments). Finally, prototrophic strains were grown in minimal medium supplemented with single and multiple supplements of the chosen amino acids. Although codons for arginine, serine, and proline are interspersed among the codons for the three branched-chain (regulatory) amino acids, they appeared to have no effect when added in excess to prototrophs or when supplied in restricted amounts to auxotrophs. Deletions removing the terminator stem from the leader removed all ilv-specific control, indicating that the attenuation mechanism is the sole mechanism for ilv-specific control.

Methionine biosynthesis in Enterobacteriaceae: biochemical, regulatory, and evolutionary aspects

The genes coding for the enzymes involved in methionine biosynthesis and regulation are scattered on the Escherichia coli chromosome. All of them have been cloned and most have been sequenced. From the information gathered, one can establish the existence (upstream of the structural genes coding for the biosynthetic genes and the regulatory gene) of "methionine boxes" consisting of two or more repeats of an octanucleotide sequence pattern. The comparison of these sequences allows the extraction of a consensus operator sequence. Mutations in these sequences lead to the constitutivity of the vicinal structural gene. The operator sequence is the target of a DNA-binding protein--the methionine aporepressor--which has been obtained in the pure state, for which S-adenosylmethionine acts as the corepressor. Mutations in the corresponding gene lead to the constitutive expression of all the methionine structural genes. The physicochemical properties of the methionine aporepressor are being investigated.

Molecular cloning of the wild-type phoM operon in Escherichia coli K-12

A metastable bacterial alkaline phosphatase (Bap) phenotype is seen in phoR mutants, which alternately express a Bap-constitutive or -negative phenotype. The alteration is affected by mutations in the phoM region near 0 min. By molecular cloning of the wild-type phoM operon onto a multicopy plasmid and recombining onto the plasmid the pho-510 mutation that abolishes variation, the phoM operon, rather than some nearby gene, was shown to control variation. Complementation tests indicated that the wild-type phoM allele is dominant to the pho-510 mutation when both are in single copy, but whichever allele is present in higher copy appears as dominant when multicopy plasmids are examined. The alternating phenotypic variation of BAP synthesis was not seen in phoR+ cells with multicopy wild-type phoM plasmids, thus showing that the variation is associated with phoM-dependent Bap expression. The alternation acted at the level of phoA transcription; it was also recA independent. BAP clonal variation is phenotypically similar to Salmonella phase variation, which is controlled by a DNA rearrangement. No evidence was found for a DNA change near the phoM operon that might be responsible for the variable Bap phenotype.