Cloning of bacterial DNA replication genes in bacteriophage lambda

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.

The gamma subunit of DNA polymerase III holoenzyme of Escherichia coli is produced by ribosomal frameshifting

The tau and gamma subunits of DNA polymerase III holoenzyme are both products of the dnaX gene. Since tau and gamma are required as stoichiometric components of the replicative complex, a mechanism must exist for the cell to coordinate their synthesis and ensure that both subunits are present in an adequate quantity and ratio for assembly. We have proposed that gamma is produced by a translational frameshift event. In this report, we describe the use of dnaX-lacZ fusions in all three reading frames to demonstrate that gamma, the shorter product of dnaX, is generated by ribosomal frameshifting to the -1 reading frame of the mRNA within an oligo(A) sequence that is followed by a sequence predicted to form a stable secondary structure. Immediately after frameshifting a stop codon is encountered, leading to translational termination. Mutagenesis of the oligo(A) sequence abolishes frameshifting, and partial disruption of the predicted distal secondary structure severely impairs the efficiency. Comparison of the expression of lacZ fused to dnaX distal to the site of frameshifting in the -1 and 0 reading frames indicates that the efficiency of frameshifting is approximately 40%.

Acquisition of new metabolic capabilities: multicopy suppression by cloned transaminase genes in Escherichia coli K-12

The four general transaminases of Escherichia coli K-12 have overlapping, but discrete, substrate specificities and participate in the final step in the synthesis of at least seven different amino acids. Through the use of strains that have mutations in one or more transaminase genes and carry a different wild-type (wt) gene on a multicopy plasmid, it was possible to detect instances in which an amplified wt gene suppressed nonallelic mutations. In these cases, overproduction of the enzyme permitted a broader range of substrates to be used at physiologically significant levels, either because a low catalytic efficiency (in the case analyzed here) or a low affinity of the enzyme towards the substrate prevented its effective utilization under normal conditions. Consequently, by compensating for a low catalytic reaction rate, enzyme overproduction circumvents the original lesion and restores biosynthetic activity to the mutant strain. The suppression of a mutation in one gene by amplified copies of a different wt gene is termed 'multicopy suppression'. This phenomenon is useful for detecting poorly expressed genes, for detecting duplicate genes, for identifying secondary functions of the products of known genes, and for elucidating the metabolic role of the product of the suppressed gene.

The adjacent dnaZ and dnaX genes of Escherichia coli are contained within one continuous open reading frame

The dnaZ and dnaX loci of Escherichia coli have been genetically defined as separate genes, both of which are essential for DNA replication (1). The 2.1 kb region of DNA that complements mutations in both genes has a maximum coding capacity of approximately 80,000 daltons. Two protein products are produced from this region with molecular weights of 77,000 and 52,000 (2,3). We have sequenced a 2.7 kb fragment containing the dnaZ and dnaX genes and determined that it contains only one open reading frame of sufficient length to encode either of these proteins. This open reading frame may encode a protein of 71,147 daltons or of 68,451 daltons depending on which potential translational initiation codon is utilized. There are two transcriptional promoters preceding the gene as well as a ribosome binding site preceding the two potential initiation codons. Both the promoters and ribosome binding sites are predicted to be weak, perhaps contributing to the low expression of these genes.

DNA polymerase III holoenzyme of Escherichia coli: components and function of a true replicative complex

The DNA polymerase III holoenzyme is a complex, multisubunit enzyme that is responsible for the synthesis of most of the Escherichia coli chromosome. Through studies of the structure, function and regulation of this enzyme over the past decade, considerable progress has been made in the understanding of the features of a true replicative complex. The holoenzyme contains at least seven different subunits. Three of these, alpha, epsilon and theta, compose the catalytic core. Apparently alpha is the catalytic subunit and the product of the dnaE gene. Epsilon, encoded by dnaQ (mutD), is responsible for the proofreading 3'----5' activity of the polymerase. The function of the theta subunit remains to be established. The auxiliary subunits, beta, gamma and delta, encoded by dnaN, dnaZ and dnaX, respectively, are required for the functioning of the polymerase on natural chromosomes. All of the proteins participate in increasing the processivity of the polymerase and in the ATP-dependent formation of an initiation complex. Tau causes the polymerase to dimerize, perhaps forming a structure that can coordinate leading and lagging strand synthesis at the replication fork. This dimeric complex may be asymmetric with properties consistent with the distinct requirements for leading and lagging strand synthesis.

The dnaX gene encodes the DNA polymerase III holoenzyme tau subunit, precursor of the gamma subunit, the dnaZ gene product

The E. coli dnaX and dnaZ gene products, essential for E. coli DNA replication, serve in chain elongation. Both genes, located at 10.4 min and previously cloned into a lambda vector and a ColE1 plasmid, were subcloned into pBR322 (pMK212). The coding region for the dnaX and dnaZ genes was localized to a 2.2-kb segment by deletion analysis of pMK212. The products of dnaX and dnaZ genes were identified as 78 kd and 52 kd polypeptides, respectively, by using maxicells bearing deletion clones of pMK212. Peptide mapping after limited proteolysis showed that the dnaZ gene product (52 kd) is a part of the dnaX gene product (78 kd), thus accounting for the coding capacity of the 2.2 kb region for both the dnaX and dnaZ genes. The dnaX gene product appears to be the tau subunit of DNA polymerase III holoenzyme; the dnaZ gene product is confirmed as the gamma subunit of the holoenzyme.