Mapping of insertion mutations in gnd of Escherichia coli with deletions defining the ends of the gene

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.

Superoxide accelerates DNA damage by elevating free-iron levels

Superoxide promotes hydroxyl-radical formation and consequent DNA damage in cells of all types. The long-standing hypothesis that it primarily does so by delivering electrons to adventitious iron on DNA was refuted by recent studies in Escherichia coli. Alternative proposals have suggested that superoxide may accelerate oxidative DNA damage by leaching iron from storage proteins or enzymic [4Fe-4S] clusters. The released iron might then deposit on the surface of the DNA, where it could catalyze the formation of DNA oxidants using other electron donors. The latter model is affirmed by the experiments described here. Whole-cell electron paramagnetic resonance demonstrated that the level of loose iron in superoxide-stressed cells greatly exceeds that of unstressed cells. Bacterial iron storage proteins were not the major source for free iron, since superoxide also increased iron levels in mutants lacking these iron storage proteins. However, overproduction of an enzyme containing a labile [4Fe-4S] cluster dramatically increased the free iron content of cells when they were growing in air. The rates of spontaneous mutagenesis and DNA damage from exogenous H2O2 increased commensurately. It is striking that both growth defects and DNA damage caused by superoxide ensue from its ability to damage a subset of iron-sulfur clusters.

DNA sequence of the Escherichia coli gene, gnd, for 6-phosphogluconate dehydrogenase

Expression of gnd of Escherichia coli, which encodes 6-phosphogluconate dehydrogenase, an enzyme of the hexose monophosphate shunt, is subject to growth rate-dependent regulation and is gene dosage-dependent: the level of the enzyme increases in direct proportion to the cellular growth rate at both low and high gene copy numbers. We have determined the nucleotide sequence of gnd and flanking control regions, the 5'-end of in vivo gnd mRNA, and the start codon of the structural gene. Analysis of the sequence indicated that: (i) the gnd promoter is typical of other E. coli promoters and the structural gene is followed by a rho-independent transcription termination signal; (ii) the 56-nucleotide leader of gnd mRNA does not contain a rho-independent transcription termination signal, so growth rate-dependent regulation of 6-phosphogluconate dehydrogenase level is not carried out by an attenuation mechanism analogous to the one that controls expression of the E. coli ampC gene; (iii) the codon composition of the structural gene resembles that of other highly expressed E. coli genes and thus is not responsible for the regulation either; (iv) the structural gene is preceded at an optimal distance by a strong Shine-Dalgarno (SD) sequence, AGGAG ; (v) the leader region of the mRNA contains regions of dyad symmetry that have the potential to sequester the SD sequence and the start codon. This latter feature of the gene suggests that growth rate-dependent regulation may involve regulation of translation initiation frequency.

Growth rate-dependent regulation of 6-phosphogluconate dehydrogenase level in Escherichia coli K-12: beta-galactosidase expression in gnd-lac operon fusion strains

The level of 6-phosphogluconate dehydrogenase is positively correlated with the cellular growth rate. To determine whether growth rate-dependent regulation of expression of gnd, which encodes this enzyme, is carried out by a transcriptional mechanism, the structural genes of the lactose operon were fused to and brought under the control of the gnd promoter through the use of phage Mu d1(Apr lac). Four independent gnd::Mu d1(Apr lac) operon fusion strains were isolated. After the Mu d1 prophage was replaced with lambda p1(209), Lac+ specialized transducing phages carrying the gnd-lac fusions were prepared. These phages were used to demonstrate that the lac genes were fused to the gnd promoter by crossing them with gnd promoter deletion mutants and with polar phage Mu cts-induced gnd mutants. A genetic map of the fusion joints was deduced. The level of beta-galactosidase in each fusion strain was the same in cells growing on acetate as in cells growing on glucose (with specific growth rate constants of 0.1 and 0.55 h-1, respectively) and was unaffected by the presence of a gnd+ gene in trans. Our results suggest that a post-transcriptional mechanism mediates growth rate-dependent regulation of gnd and that this regulation is not autogenous. Models for regulation are discussed with respect to these results and the physiology and DNA sequence of gnd.

Molecular cloning, correlation of genetic and restriction maps, and determination of the direction of transcription of gnd of Escherichia coli

Expression of the gene gnd of Escherichia coli, which encodes 6-phosphogluconate dehydrogenase, is regulated by growth rate. Using deoxyribonucleic acid from the specialized transducing phage lambda h80 dgnd his as the source of gnd, we cloned restriction fragments carrying the complete gene and portions of it on the plasmid vector pBR322. A hybrid plasmid carrying a 3.7-megadalton HindIII restriction fragment from the phage was prepared and found to be gnd+. Through restriction mapping of this fragment and subcloning segments of it, we prepared a gnd+ hybrid plasmid which carried only 1.85 megadaltons of E. coli deoxyribonucleic acid. A cleavage site for the restriction endonuclease PstI was located on the genetic map of gnd by cloning adjacent EcoRI-PstI restriction fragments and crossing the resulting hybrid plasmids with previously mapped gnd deletion and bacteriophage Mu insertion mutants. A maxicell experiment was used to determine the direction of transcription of gnd, to identify which EcoRI-PstI fragment contains the gnd promote, and to localize th beginning of the structural gene to a region about 850 +/- 150 base pairs from the PstI cleavage site. A fine-structure restriction map surrounding the PstI cleavage site was prepared for endonucleases KpnI, HincII, HaeIII, HpaII, and TaqI.