Purification and Properties of Dipeptidase M from Escherichia coli B

The structure and the characteristic DNA binding property of the C-terminal domain of the RNA polymerase alpha subunit from Thermus thermophilus

The C-terminal domain of the alpha subunit of the RNA polymerase (alphaCTD) from Escherichia coli (Ec) regulates transcription by interacting with many kinds of proteins and promoter upstream (UP) elements consisting of AT-rich sequences. However, it is unclear how this system is common in all eubacteria. We investigate the structure and properties of alphaCTD from an extremely thermophilic eubacterium, Thermus thermophilus (Tt). The solution structure of Tt alphaCTD (85 amino acids) was determined by NMR, and the interaction between Tt alphaCTD and DNA with different sequences was investigated by means of chemical shift perturbation experiments. The tertiary structure of Tt alphaCTD is almost identical with that of Ec alphaCTD despite 32% sequence homology. However, Tt alphaCTD interacts with the upstream region sequence of the promoter in the Tt 16 S ribosomal protein operon rather than the Ec UP element DNA. The upstream region sequence of Tt is composed of 25 base pairs with 40% AT, unlike the Ec UP element with 80% AT. The DNA binding site in Tt alphaCTD is located on the surface composed of helix 4 and the loop preceding helix 4. The electric charges on this surface are not remarkably localized like those of Ec alphaCTD.

Bacterial aminopeptidases: properties and functions

Aminopeptidases are exopeptidases that selectively release N-terminal amino acid residues from polypeptides and proteins. Bacteria display several aminopeptidasic activities which may be localised in the cytoplasm, on membranes, associated with the cell envelope or secreted into the extracellular media. Studies on the bacterial aminopeptide system have been carried out over the past three decades and are significant in fundamental and biotechnological domains. At present, about one hundred bacterial aminopeptidases have been purified and biochemically studied. About forty genes encoding aminopeptidases have also been cloned and characterised. Recently, the three-dimensional structure of two aminopeptidases, the methionine aminopeptidase from Escherichia coli and the leucine aminopeptidase from Aeromonas proteolytica, have been elucidated by crystallographic studies. Most of the quoted studies demonstrate that bacterial aminopeptidases generally show Michaelis-Menten kinetics and can be placed into either of two categories based on their substrate specificity: broad or narrow. These enzymes can also be classified by another criterium based on their catalytic mechanism: metallo-, cysteine- and serine-aminopeptidases, the former type being predominant in bacteria. Aminopeptidases play a role in several important physiological processes. It is noteworthy that some of them take part in the catabolism of exogenously supplied peptides and are necessary for the final steps of protein turnover. In addition, they are involved in some specific functions, such as the cleavage of N-terminal methionine from newly synthesised peptide chains (methionine aminopeptidases), the stabilisation of multicopy ColE1 based plasmids (aminopeptidase A) and the pyroglutamyl aminopeptidase (Pcp) present in many bacteria and responsible for the cleavage of the N-terminal pyroglutamate.

Purification and characterization of an aminopeptidase from Streptococcus mitis ATCC 903

An aminopeptidase isolated from the cytoplasmic fraction of a cell extract of Streptococcus mitis ATCC 903 was purified 330-fold by ion-exchange chromatography, gel filtration, and hydroxyapatite chromatography. The partially purified enzyme had a broad substrate specificity. Twelve aminoacyl-beta-naphthylamide substrates were hydrolyzed and also several di-, tri-, tetra-, and pentapeptides and bradykinin. The enzyme hydrolyzed arginine-beta-naphthylamide at the highest rate. Optimal conditions for activity were at pH 7.0-7.2 and at 37-40 degrees C. The molecular weight of the enzyme was estimated to be 93,000. The enzyme was activated by Co2+ ions. Hg2+ inhibited the activity completely. SDS, EDTA, urea, and pCMB also inhibited activity. Inhibition by EDTA could be completely reversed by dialysis and addition of Co2+ ions. Reducing agents, sodium fluoride, and PMSF had no effect on the activity of the enzyme. The isoelectric point of the enzyme was at pH 4.3. High substrate concentrations inhibited activity. Substrate inhibition increased in the presence of high concentrations of Co2+ ions.

Manganese: its acquisition by and function in the lactic acid bacteria

The transition metal manganese is considered to be a minor micronutrient in both pro- and eukaryotes, usually being required from the environment at subnanomolar levels. Until recently, Mn was only known to function in cells as a cofactor for a few enzymatic reactions. A notable exception has been reported in many lactic acid bacterial species which require micromolar medium Mn levels for growth and contain up to 35 mM Mn. These high Mn concentrations are accompanied by the near or complete absence of intracellular iron and superoxide dismutase (SOD). Lacking hemes, Lactobacillus plantarum and related species contain a unique Mn-cofactored catalase as well as millimolar Mn(II) in a nonenzymic complex performing the function of the micromolar superoxide dismutase found in most other aerotolerant cells. The high Mn(II) levels are accumulated via an efficient active transport system and are stored intracellularly in a high molecular weight complex. Study of Lactobacillus plantarum has provided an interesting example of the substitution of Mn for Fe in several of the biological roles of Fe, an alternative mechanism of aerotolerance, and a better understanding of the unique biochemistry of the lactic acid bacteria.

The initiation of fetal hemoglobin biosynthesis

Biosynthesis of the alpha and beta chains of rabbit and human adult hemoglobin is initiated with a methionyl residue, which is removed during elongation of the peptide chain. To study the initiation of biosynthesis of the delta chain of human fetal hemoglobin, fresh placental blood was used for labeling experiments with radioactive amino acids. Labeled nascent peptide chains were purified from the polysomal fraction of placental blood reticulocytes. The number of amino acid residues in nascent gamma chain at the time of removal of its N-terminal methionine was estimated to be 40--60 from the relative yields of labeled tryptic peptides.

Peptidase-deficient mutants of Escherichia coli

Mutant derivatives of Escherichia coli K-12 deficient in several peptidases have been obtained. Mutants lacking a naphthylamidase, peptidase N, were isolated by screening for colonies unable to hydrolyze L-alanine beta-naphthylamide. Other mutants were isolated using positive selections for resistance to valine peptides. Mutants lacking peptidase A, a broad-specificity aminopeptidase, were obtained by selection for resistance to L-valyl-L-leucine amide. Mutants lacking a dipeptidase, peptidase D, were isolated from a pepN pepA strain by selection for resistance to L-valyl-glycine. Starting with a pepN pepA pepD strain, selection for resistance to L-valyl-glycyl-glycine or several other valine peptides produced mutants deficient in another aminopeptidase, peptidase B. Mutants resistant to L-valyl-L-proline lack peptidase Q, an activity capable of rapid hydrolysis of X-proline dipeptides. Using these selection procedures, a strain (CM89) lacking five different peptidases has been isolated. Although still sensitive to valine, this strain is resistant to a variety of valine di- and tripeptides. The ability of this strain to use peptides as sources of amino acids is much more restricted than that of wild-type E. coli strains. Strains containing only one of the five peptidases missing in CM89 have been constructed by transduction. The peptide utilization profiles of these strains show that each of the five peptidases can function during growth in the catabolism of peptides.

Purification and properties of a new aminopeptidase from Escherichia COLI K12

An aminopeptidase (EC 3.4.11.-) capmable of hydrolyzing L-alanyl-beta-naphthyl-amide and certain other aminoacyl beta-naphthylamides was purified to homogeneity from extracts of Exherichia coli K-12. The enzyme, designated aminopeptidase II, is a monomeric protein of mol. wt. 100 000. It exhibits a broad pH optimum in the range pH 7.0--9.0. Although Zn2+, Fe3+ and Cr3+ are strong inhibitors of enzyme activity, a metal requirement for catalysis could not be firmly established. Neither sulfhydryl reagents nor serine protease inhibitors affected enzyme activity.

Evidence for an aminoendopeptidase localized near the cell surface of Escherichia coli. Regulation of synthesis by inorganic phosphate

An enzyme capable of hydrolyzing the substrate L-alanine p-nitroanilide has been found in the various Escherichia coli strains tested. This enzyme has been called aminoendopeptidase since it shows both activities (see accompanying paper). It is released from the cells by osmotic shock and by lysozyme -- EDTA spheroplasting treatment, and 50% of the total activity is directly detectable with suspensions of intact cells. However, the release by osmotic shock or spheroplasting is not as efficient as it is for alkaline phosphatase. This periplasmic aminoendopeptidase is constitutively produced but the differential rate of synthesis is increased 4-fold when the cell growth is limited by Pi. The occurrence of this 'derepression' is simultaneous with that of alkaline phosphatase. Increasing the concentration of inorganic phosphate in the medium has no effect on the constitutive aminoendopeptidase synthesis. The effect of phosphate starvation is specific since starvation for neither nitrogen nor carbon and energy source are effective in derepressing aminoendopeptidase.

Purification and properties of a periplasmic aminoendopeptidase from Escherichia coli

A periplasmic aminoendopeptidase from Escherichia coli has been purified to hemogeneity. It is a monomer of molecular weight 45000 and containing one -- SH group that is necessary for catalytic activity. The study of its substrate specificity indicated that the enzyme has both aminopeptidase and endopeptidase activity. The pH optimum for L-alanine p-nitroanilide hydrolysis is between 7 and 7.5 and that for 125I-labeled casein proteolysis between 7.3 and 7.6. The activation energy for the hydrolysis of L-anine p-nitroanilide was calculated to be 5.3 kcal X mol-1 (22.2 kJ X mol-1).

Properties of a cytoplasmic proteolytic enzyme from Escherichia coli

A cytoplasmic protease was partially purified from Escherichia coli; its sedimentation coefficient was found to be 5.3 S. This enzyme (which we call protease A) is not a serine protease and cysteine is not required for its activity; it is only active in the presence of divalent ions which are strongly bound to it. After inactivation of protease A by incubation at 50 degrees C in the presence of 1 mM EDTA, the enzyme is reactived by Mg2+, Mn2+ or Ca2+. We have tried most of the usual esters as substrates and found that none was hydrolyzed by the enzyme which induces a highly restricted specificity.

Peptidase mutants of Salmonella typhimurium

Six peptidase activities have been distinguished electrophoretically in cell extracts of Salmonella typhimurium with the aid of a histochemical stain. The activities can also be partially separated by chromatography on diethylaminoethyl-cellulose. These peptidases show overlapping substrate specificities. Mutants (pepN) of the parent strain leu-485 lacking one of these enzymes (peptidase N) were obtained by screening for colonies that do not hydrolyze the chromogenic substrate l-alanyl-beta-naphthylamide. The absence of this broad-specificity peptidase in leu-485 pepN(-) mutants allowed the selection of mutants unable to use l-leucyl-l-alaninamide as a leucine source. These mutants (leu-485 pepN(-)pepA(-)) lack a broad-specificity peptidase (peptidase A) similar to aminopeptidase I previously described in Escherichia coli. Mutants (pepD) lacking a dipeptidase (peptidase D) have been isolated from a leu-485 pepN(-)pepA(-) parent by penicillin selection for mutants unable to use l-leucyl-l-glycine as a leucine source. Mutants (pepB) lacking a fourth peptidase (peptidase B) have been isolated from a leu-485 pepN(-)pepA(-)pepD(-) strain by penicillin selection for failure to utilize l-leucyl-l-leucine as a source of leucine. Single recombinants were obtained by transduction for each of the peptidases missing in a leu-485 pepN(-)pepA(-)pepD(-)pepB(-) strain. The growth response of these recombinants to leucine peptides shows that all of these peptidases can function in the catabolism of peptides and that they display overlapping substrate specificities in vivo.

Physiological roles of pneumococcal peptidases

A methionyl-specific dipeptidase from Streptococcus pneumoniae has been described. This enzyme and the pneumococcal tripeptidase have been shown to be intracellular, soluble, and constitutive. In addition to their function in cleavage of peptide nutrients, these peptidases may play a role in protein synthesis and turnover.