Nucleotide sequence of the promoter and amino-terminal encoding region of the Escherichia coli pepN gene

Over-expression, purification, and characterization of aminopeptidase N from Escherichia coli

The gene from Escherichia coli encoding aminopeptidase N (PepN) was subcloned into pET-26b, and PepN was over-expressed in BL21(DE3) E. coli and purified using Q-Sepharose chromatography. This protocol yielded over 17 mg of purified, recombinant PepN per liter of growth culture under optimum conditions. Gel filtration chromatography revealed that recombinant PepN exists as a monomer. MALDI-TOF mass spectra showed that the enzyme has a molecular mass of 98,750 Da, and steady-state kinetic studies revealed that as-isolated, recombinant PepN exhibits a k(cat) of 354 +/- 11s(-1) and a K(m) of 376 +/- 39 microM when using L-alanine-p-nitroanilide as the substrate. Metal analyses demonstrated that as-isolated, recombinant PepN binds 0.5 and <0.1 equivalents of iron and zinc, respectively. The addition of Zn(II) to recombinant PepN inhibits catalytic activity, while the addition of iron causes a slight decrease or no change in activity. Further metal binding studies revealed that recombinant PepN tightly binds 5 equivalents of iron and <0.1 equivalents of Zn(II). By using this over-expression and purification system, E. coli PepN can now be obtained in quantities necessary for structural characterization and possibly inhibitor design efforts.

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.

dcp gene of Escherichia coli: cloning, sequencing, transcript mapping, and characterization of the gene product

Dipeptidyl carboxypeptidase is a C-terminal exopeptidase of Escherichia coli. We have isolated the respective gene, dcp, from a low-copy-number plasmid library by its ability to complement a dcp mutation preventing the utilization of the unique substrate N-benzoyl-L-glycyl-L-histidyl-L-leucine. Sequence analysis of a 2.9-kb DNA fragment revealed an open reading frame of 2,043 nucleotides which was assigned to the dcp gene by N-terminal amino acid sequencing and electrophoretic molecular mass determination of the purified dcp product. Transcript mapping by primer extension and S1 protection experiments verified the physiological significance of potential initiation and termination signals for dcp transcription and allowed the identification of a single species of monocistronic dcp mRNA. The codon usage pattern and the effects of elevated gene copy number indicated a relatively low level of dcp expression. The predicted amino acid sequence of dipeptidyl carboxypeptidase, containing a potential zinc-binding site, is highly homologous (78.8%) to the corresponding enzyme from Salmonella typhimurium. It also displays significant homology to the products of the S. typhimurium opdA and the E. coli prlC genes and to some metalloproteases from rats and Saccharomyces cerevisiae. No potential export signals could be inferred from the amino acid sequence. Dipeptidyl carboxypeptidase was enriched 80-fold from crude extracts of E. coli and used to investigate some of its biochemical and biophysical properties.

Cloning and nucleotide sequence of the anaerobically regulated pepT gene of Salmonella typhimurium

The anaerobically regulated pepT gene of Salmonella typhimurium has been cloned in pBR328. Strains carrying the pepT plasmid, pJG17, overproduce peptidase T by approximately 70-fold. The nucleotide sequence of a 2.5-kb region including pepT has been determined. The sequence codes for a protein of 44,855 Da, consistent with a molecular weight of approximately 46,000 for peptidase T (as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration). The N-terminal amino acid sequence of peptidase T purified from a pJG17-containing strain matches that predicted by the nucleotide sequence. A plasmid carrying an anaerobically regulated pepT::lacZ transcriptional fusion contains only 165 bp 5' to the start of translation. This region contains a sequence highly homologous to that identified in Escherichia coli as the site of action of the FNR protein, a positive regulator of anaerobic gene expression. A region of the deduced amino acid sequence of peptidase T is similar to segments of Pseudomonas carboxypeptidase G2, the E. coli peptidase encoded by the iap gene, and E. coli peptidase D.

Molecular evolution and zinc ion binding motif of leukotriene A4 hydrolase

Leukotriene A4 (LTA4) hydrolase belongs to the aminopeptidase N family. In order to investigate the molecular evolution and physiological significance of LTA4 hydrolase, the enzymes belonging to the family were aligned and a phylogenetic tree was constructed. From the alignment, it was found that three residues involved in zinc binding and one residue of the active sites of aminopeptidases N were conserved in LTA4 hydrolase. In agreement with the observation, LTA4 hydrolase is a zinc protein as determined by atomic absorption spectroscopy.

Peptidase D gene (pepD) of Escherichia coli K-12: nucleotide sequence, transcript mapping, and comparison with other peptidase genes

The nucleotide sequence of a 2.3-kilobase-pair DNA fragment of Escherichia coli that contains the transcription signals and the coding region of the pepD gene specifying aminopeptidase D was determined. The location and extent of the open reading frame were verified by partial amino acid sequencing of the purified pepD product. By use of a promoter-screening vector, initiation signals for pepD transcription were located in the 5'-flanking region of the open reading frame. Analysis of pepD transcripts by S1 mapping, primer extension, and Northern (RNA) hybridization revealed two species of monocistronic mRNA with different 5' ends and a common 3' end. Calculation of the degree of codon usage bias in the coding region suggested that the efficiency of pepD translation is relatively low. As deduced from the predicted amino acid sequence, peptidase D is a slightly hydrophilic protein of 485 amino acid residues that contains no extended domains of marked hydrophobicity. Structural and functional features of the pepD gene are discussed and compared with other already sequenced peptidase genes of E. coli.

Linkage map of Escherichia coli K-12, edition 8

The linkage map of Escherichia coli K-12 depicts the arrangement of genes on the circular chromosome of this organism. The basic units of the map are minutes, determined by the time-of-entry of markers from Hfr into F- strains in interrupted-conjugation experiments. The time-of-entry distances have been refined over the years by determination of the frequency of cotransduction of loci in transduction experiments utilizing bacteriophage P1, which transduces segments of DNA approximately 2 min in length. In recent years, the relative positions of many genes have been determined even more precisely by physical techniques, including the mapping of restriction fragments and the sequencing of many small regions of the chromosome. On the whole, the agreement between results obtained by genetic and physical methods has been remarkably good considering the different levels of accuracy to be expected of the methods used. There are now few regions of the map whose length is still in some doubt. In some regions, genetic experiments utilizing different mutant strains give different map distances. In other regions, the genetic markers available have not been close enough to give accurate cotransduction data. The chromosome is now known to contain several inserted elements apparently derived from lambdoid phages and other sources. The nature of the region in which the termination of replication of the chromosome occurs is now known to be much more complex than the picture given in the previous map. The present map is based upon the published literature through June of 1988. There are now 1,403 loci placed on the linkage group, which may represent between one-third and one-half of the genes in this organism.

Molecular cloning of the murine BP-1/6C3 antigen: a member of the zinc-dependent metallopeptidase family

The BP-1/6C3 antigen is a phosphorylated cell surface glycoprotein that can be identified by monoclonal antibodies on mouse pre-B cells, immature B cells, and certain stromal cell lines from bone marrow. Expression of this antigen is increased in stromal-dependent pre-B cell lines and retrovirally transformed pre-B cells. Expression of the BP-1/6C3 antigen thus correlates with proliferation and transformation of immature B-lineage cells. In this study, we report the isolation and characterization of cDNAs encoding the BP-1/6C3 antigen. Northern blot analysis revealed a major 4.1-kilobase mRNA in all BP-1/6C3+ mouse pre-B lines and in a human pre-B cell line. BP-1/6C3 mRNA was either absent or truncated in BP-1/6C3- cell lines. The cDNA sequence predicts a type II integral membrane protein of 945 amino acids with an intracytoplasmic amino terminus of only 17 amino acids and a typical zinc-binding motif in its extracellular domain. BP-1/6C3 has significant homology to aminopeptidase N and is the second member of the zinc-dependent metallopeptidase gene family to be found on the surface of early B-lineage cells.

Deletion analysis of the promoter region of the Escherichia coli pepN gene, a gene subject in vivo to multiple global controls

The pepN gene codes for aminopeptidase N whose expression is regulated at the transcriptional level by anaerobiosis and phosphate starvation. To define and characterize the functional region of the pepN promoter (pepNp), various promoter fragments were fused to the malPQ operon of Escherichia coli and transferred to the chromosome. The expression of the single copy operon fusion was measured by assaying the amylomaltase activity. Sequences upstream from the canonical promoter elements, located 110 to 60 bp preceding the transcription start site, are important for promoter functioning. This region plays a role in the expression of the two divergent promoters pepNp and pncBp. The regulation of pepNp under phosphate starvation was conserved in the various constructs in which pepNp is functional. However, no particular sequence specific for phosphate regulation was detected. In addition, the regulation of pncBp by Pi starvation was demonstrated.

Mutation that affects pepN translation initiation in Escherichia coli

Mutants altered in their expression of the hybrid pepN-lacZ gene have been selected for resistance to p-nitrophenyl-beta-D-thiogalactopyranoside (a bacteriostatic compound that enters the cells via lac permease). A unique mutation decreasing the level of pepN expression to 9% of that of the wild type has been studied in detail. This mutation controls in cis the expression of the pepN gene. The pepN region from a pepN-lacZ gene fusion has been cloned and sequenced. Comparison of the mutant and wild type sequences indicates that the mutation lies between the Shine-Dalgarno sequence (AGGT) and the initiation codon (AUG). This mutation is a T----C transition which might allow the formation of a stable secondary structure in the region of translation initiation thus decreasing the level of pepN expression.

The nucleotide sequence of the pepN gene and its over-expression in Escherichia coli

The complete nucleotide sequence has been determined for the pepN gene of Escherichia coli K-12. The product of this gene, peptidase N, is apparently 870 amino acids in length. The coding sequence is followed by a tandem pair of stop codons and then a sequence capable of forming a stem-and-loop structure in the pepN mRNA. In the process of subcloning the pepN gene we constructed a plasmid which causes peptidase N to be produced at a level of 50% of total protein. The peptidase is fully active and completely soluble and these overproducing cells appear otherwise normal.