Isolation and characterization of the dut gene of Escherichia coli. II. Restriction enzyme mapping and analysis of polypeptide products

dUTPase from Escherichia coli; high-level expression and one-step purification

The dut gene, which encodes Escherichia coli deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase), has been recloned to increase overexpression of the enzyme and to enable simplification of the purification protocol into a one-step procedure. The gene was cloned into the vector pET-3a and expressed in E. coli BL21(DE3) pLysS under the control of a bacteriophage T7 promotor. Induction results in production of dUTPase corresponding to 60% of the extracted protein. Phosphocellulose chromatography at low pH was utilised for one-step purification, resulting in a homogenous preparation of the recombinant protein with a highly specific activity. The yield of purified enzyme is 500 mg per litre of bacterial culture, a significant increase compared to previously employed methods.

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 gene encoding cAMP receptor protein is required for competence development in Haemophilus influenzae Rd

The Haemophilus influenzae Rd strain JG87 contains a single mini-Tn10kan insertion that causes a deficiency in the development of competence for genetic transformation. The DNA fragment containing this insertion mutation, as well as the wild-type locus, was cloned, mapped, and sequenced. The sequence contained an open reading frame for a protein of 224 amino acids with a predicted Mr of 25,152. The deduced protein sequence showed strong similarity to the Escherichia coli cAMP receptor protein. The E. coli crp gene cloned on a multicopy plasmid was shown to fully complement the competence-deficient phenotype of the mutant strain; thus, the H. influenzae gene was named crp. These results suggest that H. influenzae cAMP-cAMP receptor protein complex functions to regulate one or more promoters essential for the development of competence in H. influenzae Rd. Features of a gene upstream of H. influenzae crp that is homologous to the E. coli ttk gene are also described.

Lethality of a dut (deoxyuridine triphosphatase) mutation in Escherichia coli

A chloramphenicol resistance gene was cloned into a plasmid-borne dut gene, producing an insertion mutation that was then transferred to the chromosome by allelic exchange. The mutation could not be acquired by haploid strains through substitutive recombination, even when two flanking markers were simultaneously transduced. The insertion was easily transferred, via generalized transduction, into the chromosomal dut region of strains harboring a lambda dut + transducing phage; however, the resulting dut mutant/lambda dut + merodiploid could not then be cured of the prophage. This apparent lethality of the mutation could not be explained by effects on adjacent genes; the dfp gene retained complementing activity, and a ttk insertion mutant was viable. The dut gene product, deoxyuridine triphosphatase, is known to reduce incorporation of uracil into DNA and to be required in the de novo synthesis of thymidylate. Therefore, an attempt was made to determine whether the dut insertion would be tolerated in strains carrying the following compensatory mutations: dcd (dCTP deaminase) and cdd (deoxycytidine deaminase), which should reduce dUTP formation; ung (uracil-DNA glycosylase), which should reduce fatally excessive excision repair; deoA (thymidine phosphorylase), which should enhance the utilization of exogenous thymidine; and sulA, which should reduce the lethal side effects of SOS regulon induction. These mutations, either alone or in various combinations, did not permit the survival of a haploid dut insertion mutant, suggesting that the dut gene product might have an essential function apart from its deoxyuridine triphosphatase activity.

dfp Gene of Escherichia coli K-12, a locus affecting DNA synthesis, codes for a flavoprotein

The cloned dfp gene complements dna-707 (now designated dfp-707), a temperature-sensitive conditionally lethal mutation that results in a slow cessation of DNA synthesis while protein synthesis is maintained. In vitro and in vivo experiments failed to demonstrate a specific defect in the initiation of DNA replication, and turn-off of DNA synthesis at high temperature was slower than that of a typical initiation (dnaA) mutant. The gene was localized, and its product was identified through the construction and analysis of deletion and insertion mutants of dfp-containing plasmids. dfp is located between the rpmB and dut genes at 81 min on the linkage map of Escherichia coli K-12. It is transcribed clockwise, independently of dut. The ability of a plasmid to complement a chromosomal dfp-707 mutation was correlated with its ability to produce a 45-kilodalton polypeptide. The purified protein contained 1 mol of flavin mononucleotide per mol of polypeptide.

Nucleotide sequence of the Escherichia coli pyrE gene and of the DNA in front of the protein-coding region

Orotate phosphoribosyltransferase (EC 2.4.2.10) was purified to electrophoretic homogeneity from a strain of Escherichia coli containing the pyrE gene cloned on a multicopy plasmid. The relative molecular masses (Mr) of the native enzyme and its subunit were estimated by means of gel filtration and electrophoresis in the presence of dodecyl sulfate. The amino acid sequences at the N and C termini, as well as the amino acid composition, were determined. The nucleotide sequence of the structural pyrE gene, including 394 nucleotide residues preceding the beginning of the coding frame, was also established. From the results the following conclusions may be drawn. Orotate phosphoribosyltransferase is a dimeric protein with subunits of Mr 23 326 consisting of 211 amino acid residues. The pyrE gene is transcribed in a counter-clock wise direction from the E. coli chromosome as an mRNA with a considerable leader segment in front of the protein-coding region. This leader contains a structure with features characteristic for a (translated?) rho-independent transcriptional terminator, which is preceded by a cluster of uridylate residues. This indicates that the frequency of pyrE transcription is regulated by an RNA polymerase (UTP) modulated attenuation.

Isolation and characterization of the dut gene of Escherichia coli. I. Cloning in thermoinducible plasmids

We have constructed thermoinducible plasmids carrying the gene (dut) for the enzyme deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase, EC 3.6.1.23) from Escherichia coli. A 9.4-kb BamHI restriction enzyme fragment carrying the dut gene was inserted into the runaway-replication plasmid pKN402A (Uhlin et al., Gene 6 (1979) 91-106). Strains carrying such plasmids increased their dUTPase activity considerably. In minimal medium a 200-fold increase was demonstrated. A smaller (1.5-kb) SacI-BamHI fragment from the dut region was also cloned into pKN402A. The dUTPase production in dut mutant strains carrying this plasmid (pKK141) was only at about wild-type level after temperature shift. To test the hypothesis that the SacI cleavage used affects a control region for the dut gene, we recloned the dut fragment by transferring it from pKK141 into pHUB2 (Bernard et al., Gene 5 (1979) 59-76), a plasmid carrying the phage lambda pL promoter. A 3.6-kb EcoRI-BamHI fragment from pKK141, including the 1.5-kb SacI-BamHI segment from the dut region, was inserted downstream from the pL promoter. When this plasmid was present in a strain containing a thermosensitive lambda repressor gene, thermoinduction of dUTPase was negligible, apparently due to the presence of some termination signals between pL and dut. Therefore, we removed a 1.9-kb EcoRI-SacI fragment from the region between pL and the dut gene and replaced it with a 0.22-kb EcoRI-SacI fragment, obtained from the b2 region of lambda. Strains carrying such a shortened dut-pHUB2 derivative and a temperature-sensitive lambda repressor overproduced dUTPase very dramatically after heat induction. The final level reached was 300-400 times the wild-type level, corresponding to 10% of the total soluble protein. The information obtained, together with analysis of plasmid-directed polypeptide products described by Lundberg et al. (Gene 22 (1983) 127-131) shows that the SacI site is indeed on the promoter-proximal side of the dut gene.