Purification and properties of dipeptidase from Escherichia coli AJ005

Summary A Co²⁺-dependent dipeptidase from E. coli strain AJ005, a peptidase-deficient mutant, was purified with streptomycin sulfate, ammonium sulfate and DEAE-cellulose. The purified dipeptidase increased by about 106-fold in specific activity, with dilysine as a substrate. The dipeptidase cleaved dilysine to two lysines among the lysine homopolymers, the possibility remaining that it is active toward peptides other than dilysine, since it was investigated in the present study only for activity toward lysine homopolymers. Activity was inhibited 54% by 10^–3 M KCN and completely by 10^–3 M PCMB, EDTA and benzethonium chloride, but not at all by soybean trypsin inhibitors. 78% and 95% of its activity was lost with 30 minutes' treatment at 45°C and 50°C, respectively. The apparent Km value was 6.7 × 10^–4 M for dilysine. It is probable that the dipeptidase differs from dipeptidase DP.Abbreviations EDTA Ethylenediaminetetraacetate - PCMB pchloromercuribenzoate     

Purification of Peptidases of Aspergillus oryzae and Some Properties of the Purified Peptidases

The purification of Aspergillus oryzae peptidases was attempted by the fractional precipitation with acetone, ammonium sulphate, and by starch zone electrophoresis. We, thus, achieved a great success in the separation of dipeptidase free from aminopolypeptidase and proteinase as well as in the separation of aminopolypeptidase free from dipeptidase and proteinase.

The specific activity (C₀) of the former (leucylglycine hydrolysis) was 7000 and that of the latter (leucylglycylglycine hydrolysis) 22000.

The leucylglycine dipeptidase was remarkably activated by Zn⁺⁺, and Co⁺⁺. Some other enzyme properties were also found and are discussed.     

Mechanism of lysosome rupture by dipeptides

Low concentrations of some neutral dipeptides, such as L -Ala-L -Ala, rapidly disrupt rat liver lysosmes. The phenomenon has been attributed to an osmotic imbalance generated by the production of amino acids in the lysosme by lysosomal dipeptidase activity. This hypothesis is challenged by testing several pairs of dipeptides available in both D - and L -forms and a range of dipeptides whose susceptibility to lysosomal dipeptidase activity is known. A good correlation was found between the lytic ability of dipeptides and their capacity to cross the lysosome membrane and be hydrolysed by lysosomal dipeptidase. The osmotic-imbalance hypothesis is critically evaluated in the light of the results and of recent information concerning the carrier-mediated transport of amino acids and dipeptides across the lysosome membrane. It is concluded that intralysosomal generation of amino acids remains the most plausible explanation of the lytic activity of dipeptides, and that the dipeptide proter(s) in the lysosome membrane must have higher K_m than the amino acid porters.     

Catalytic triad heterogeneity in S51 peptidase family: Structural basis for functional variability

Peptidase E (PepE) is a nonclassical serine peptidase with a Ser-His-Glu catalytic triad. It is specific for dipeptides with an N-terminal aspartate residue (Asp-X dipeptidase activity). Its homolog from Listeria monocytogenes (PepElm) has a Ser-His-Asn “catalytic triad.” Based on sequence alignment we predicted that the PepE homolog from Deinococcus radiodurans (PepEdr) would have a Ser-His-Asp “catalytic triad.” We confirmed this by solving the crystal structure of PepEdr to 2.7 Å resolution. We show that PepElm and PepEdr lack the Asp-X dipeptidase activity. Our analyses suggest that absence of P1 pocket in the active site could be the main reason for this lack of typical activity. Sequence and structural data reveal that the PepE homologs can be divided into long and short PepEs based on presence or absence of a C-terminal tail which adopts a β-hairpin conformation in the canonical PepE from Salmonella enterica. A long PepE from Bacillus subtilis with Ser-His-Asp catalytic triad exhibits Asp-X dipeptidase activity. Whereas the three long PepEs enzymatically characterized till date have been found to possess the Asp-X dipeptidase activity, the three enzymatically characterized short PepEs lack this activity irrespective of the nature of their catalytic triads. This study illuminates the structural and functional heterogeneity in the S51 family and also provides structural basis for the functional variability among PepE homologs.     

De novo synthesis and hormonal regulation of a dipeptidase in Cucurbita maxima

The following evidence was obtained for the de novo synthesis of dipeptidase in squash (Cucurbita maxima Duch. var. Hubbard) cotyledons during germination: (i) the amount of [¹⁴C]leucine incorporated into the dipeptidase was greater than that found in other proteins; (ii) the enzyme coincided with a peak of radioactivity in DEAE column chromatography; and (iii) the specific radioactivity of the enzyme increased with purification. There was also a positive correlation between the rate of [¹⁴C]leucine incorporation into dipeptidase and the rate of dipeptidase development. Four plant growth regulators, gibberellic acid (GA) benzyladenine (BA), indol-3-acetic acid (IAA), and abscisic acid (ABA) were examined for their effect on the development of dipeptidase activity at 5 × 10^?6 and 5 × 10^?5 M. None of these regulators affected the activity of the isolated dipeptidase per se. In intact see ds, BA and IAA inhibited the development of dipeptidase activity at the higher concentration, ABA reduced the activity at both concentrations; however, GA enhanced its development at the higher concentration. In distal-half cotyledons, BA and GA stimulated enzyme development but they showed no synergistic effect. IAA suppressed the development of enzyme activity at the higher concentration and ABA inhibited development at both levels.     

Binding mode analysis between membrane dipeptidase and its substrates

Membrane dipeptidase (MDP) is a membrane-bound glycoprotein involved in the hydrolysis of dipeptides, showing specific activity for dipeptides. Recent study showed that membrane dipeptidase was the receptor for a lung-targeting peptide identified by in vivo phage display and the crystal structure of the cilastatin-liganded human renal dipeptidase was determined. We performed a pharmacophore-based virtual screening and molecular docking in order to characterize MDP binding interactions with its substrates. A ligand-based pharmacophore model represented only a slight enrichment because of a lacked variety and centralization of ligand features. Molecular docking study was used to incorporate ligand conformational changes in the binding sites and the performance was much better than pharmacophore model; only 10% of compound library needed to be screened in order to detect all included active compounds. In addition, we found that one of the crystallographically observed water molecules plays an important role in the binding modes between MDP and its substrate.     

Cloning of peptidase genes from Lactobacillus helveticus CNRZ 32

Lactic acid bacteria express a complex proteolytic enzyme system that is capable of hydrolyzing casein to amino acids. We have begun to examine the number and specificity of exopeptidases from Lactobacillus helveticus CNRZ 32. A genomic library of L. helveticus CNRZ 32 DNA fragments from a Sau3A partial digestion was constructed in Escherichia coli DH5 utilizing pJDC9. This library was screened for the presence of aminopeptidase, X-prolyl dipeptidyl aminopeptidase (X-PDAP), and dipeptidase activities by two methods. The first screening identified an aminopeptidase II (APII) and X-PDAP. The X-PDAP was determined to be present on four independent DNA inserts ranging in size from 3.5 to 7.7 kilobase pairs (kbp). EcoRI/EcoRV digests of these plasmids suggested that all inserts had 1.0 and 1.8 kbp fragments in common. The gene for APII was determined to be present on three independent DNA inserts ranging in size from 8.2 to 11.3 kbp. EcoRI digestion of these plasmids indicated that 1.2 and 1.8 kbp fragments were in common. The second screening identified an additional aminopeptidase (API), a di/tripeptidase (DTP) with prolinase activity, a broad-specificity dipeptidase (DPI), and a narrow-specificity dipeptidase (DPII). The insert size of clones expressing API, DTP, DPI, DPII were 4.8, 9.5, 5.8, and 6.3 kbp, respectively. Histochemical staining of native polyacrylamide gels from recombinant E. coli cultures demonstrated that the cloned peptidase co-migrated with native L. helveticus CNRZ 32 enzymes. Correspondence to: J. L. Steele     

Cleavage of di- and tripeptides by Prevotella ruminicola

The final step in the conversion of protein to amino acids by the common Gram-negative rumen bacterium, Prevotella (formerly Bacteroides) ruminicola , is the cleavage of di- and tripeptides. Dipeptidase and tripeptidase activities were predominantly cytoplasmic, and toluene treatment increased the rate of Ala₂ and Ala₃ hydrolysis by whole cells, suggesting that transport limited the rate of hydrolysis of extracellular di- and tripeptides. The hydrolysis of Ala₂ and Ala₃ by whole cells was not affected by protonophores, ionophores or dicyclohexylcarbodiimide, but Ala₂ hydrolysis by EDTA-treated cells was inhibited by the Ca²⁺/H⁺ ionophore, tetronasin. Ala₃ hydrolysis was not affected by protonophores or ionophores in EDTA-treated cells. The dipeptidase of strain M384 was inhibited > 99% by 1,10-phenanthroline and 39% by EDTA but not other protease inhibitors, consistent with the enzyme being a metalloprotease. Tripeptidase was insensitive to protease inhibitors, except for a 33% inhibition by EDTA. Cleavage of tripeptides occurred at the bond adjacent to the N-terminal amino acid. Distinct di-, tri- and oligopeptidase peaks were obtained by anion-exchange liquid chromatography of disrupted cells. Banding patterns on native PAGE using activity staining also indicated that P. ruminicola M384 had separate single dipeptidase and tripeptidase enzymes which hydrolysed a range of peptides. The dipeptidase of strain M384 was different from other strains of P. ruminicola: strains GA33 and B₁4 had activities which ran at the same R_f; strain GA33 had another band of lower activity; strain 23 had two bands different from those of the other strains. The tripeptidases ran at the same R_f for the different strains. Dipeptidase activity of all strains was inhibited by 1,10-phenanthroline on gels. Gel permeation chromatography indicated that the M_r of the dipeptidases from strains M384 and B₁4 were 115 000 and 114 500 respectively, and 112 500 and 121 500 for the corresponding tripeptidases. Thus the metabolism of small peptides by P. ruminicola involves separate permeases and intracellular peptidases for di- and tripeptides.     

Role of Divalent Metal Ions on Activity and Stability of Thermostable Dipeptidase from Bacillus stearothermophilus

Thermostable dipeptidase from Bacillus stearothermophilus, a typical metalloenzyme containing 1.0g atom of Zn per mole of subunit of the dimeric enzyme was markedly activated by exogenous divalent metal ions such as Mn²⁺, Co²⁺, and Cd²⁺ . In contrast, several others including Ba²⁺, Hg²⁺, and Cu²⁺ considerably inhibited the enzyme, even the inherent metal, Zn²⁺, being slightly inhibitory. To study the metal-binding properties of this dipeptidase, the enzyme was completely resolved to the inactive, Zn-free apoenzyme by treatment with EDTA in the presence of guanidine hydrochloride in a weakly acidic buffer. The apoenzyme was readily reconstituted by incubation with either Zn²⁺, Mn²⁺, or Co²⁺, restoring the catalytic activity. The Mn-reconstituted enzyme had nearly twice the activity of the original Zn-enzyme. Combined with kinetic analyses of reconstitution of the apoenzyme with metal ions, these results show that the enzyme has two non-identical metal-binding sites, each with a different property. Furthermore, substitution of Mn²⁺ or Co²⁺ for Zn²⁺ considerably lowered the thermostability of the enzyme without affecting the overall conformation of the enzyme protein, suggesting that the prosthetic Zn is playing dual roles in conformational stability and catalysis of the thermostable dipeptidase.     

Distribution,properties, and functions of midgut carboxypeptidases and dipeptidases from Musca domestica larvae

Dipeptidase and carboxypeptidase A activities were determined in cells and luminal contents of the fore-, mid-, and hind-midgut of Musca domestica larvae. Dipeptidase activity was found mainly in hind-midgut cells, whereas carboxy-peptidase activity was recovered in major amounts in both cells and in luminal contents of hind-midguts. The subcellular distribution of dipeptidase and part of the carboxypeptidase A activities is similar to that of a plasma membrane enzyme marker (aminopeptidase), suggesting that these activities are bound to the microvillar membranes. Soluble carboxypeptidase A seems to occur both bound to secretory vesicles and trapped in the cell glycocalyx. Based on density-gradient ultracentrifugation and thermal inactivation, there seems to be only one molecular species of each of the following enzymes (soluble in water or solubilized in Triton X-100): membrane-bound dipeptidase (pH optimum 8.0; Km 3.7 mM GlyLeu, M_r 111,000), soluble carboxypeptidase (pH optimum 8.0; Km 1.22 mM N-carbobenzoxy-glycyl-L-phenylalanine (ZGlyPhe), M_r45,000) and membrane-bound carboxypeptidase (pH optimum 7.5, Km 2.3 mM ZGlyPhe, M_r58,000). The results suggest that protein digestion is accomplished sequentially by luminal trypsin and luminal carboxypeptidase, by membrane-bound carboxypeptidase and aminopeptidase, and finally by membrane-bound dipeptidase.     

Studies on Peptidases of Aspergillus oryzae

The homogeneity of Aspergillus dipeptidase prepared according to the standard method established by us was ascertained by ultracentrifugation and some characteristic properties of the enzyme was further investigated.

Hydrolysis of various dipeptides by the purified dipetidase was tested in the presence of divalent metal ions such as Co⁺⁺ or Zn⁺⁺, and the characteristics of greatest interest may be enumerated as follows:

1. The homogeneous dipeptidase requires Zn⁺⁺ for activation in the case of the hydrolysis of leucylglycine, leucylalanine leucylleucine, etc.

2. The homogeneous dipeptidase requires Co⁺⁺ for activation in the case of the hydrolysis of glycylleucine, glycylleucine, glycylglycine, glycylphenylalanine, etc.

3. In the case of the hydrolysis of alanylglycine, alanylleucine, valylglycine, etc., this enzyme does not require any metal ions.

     

Studies on Peptidases of Aspergillus oryzae

Screening experiments for dipeptidase and aminopolypeptidase from 40 strains of molds were conducted using Leu-Gly, Gly-Leu, Ala-Gly and Gly-Gly-Leu as substrates.

The strains of Aspergillus oryzae RO-0129 A-2, IAM-2600 and IAM-2616 showed strong activities of both dipeptidase and aminopolypeptidase.

Further, optimal conditions for making culture as well as those for the extractions of the peptidases from the mycerial mats were investigated.     

Dipeptidase development in cotyledons of Cucurbita maxima during germination

The dipeptidase activity of an unpurified soluble extract of the cotyledons of Cucurbita maxima Duch. var. Hubbard remained unchanged during the first 2 days of germination and then increased at a rapid rate during the next 3 days. The dipeptidase activity of two of three lots of seeds required the presence of the embryo axis for maximal dipeptidase activity, whereas the third lot was uninfluenced by the embryo axis. This discrepancy was possibly due to genetic differences. In those seeds which required the presence of the embryo axis for maximal dipeptidase activity, the cytokinin benzyladenine could replace the embryonic axis. When the protein synthesis inhibitor cycloheximide was added to the seeds at the beginning of germination, it inhibited dipeptidase activity of the cotyledons from 26 to 55 per cent, depending of the basis of calculation, at 5 days. When the cycloheximide was added to 3-day-old seedling the inhibition of dipeptidase activity in the cotyledons was almost immediate. The relative hydrolysis of -leucylglycine and glycylglycine were compared after temperature inactivation and purification; the results showed that more than one enzyme was responsible for the dipeptidase activity. The presence of a dialysable dipeptidase inhibitor(s) was demonstrated. Relatively high dipeptidase activity was also found in the roots and shoots.     

Characterization of a Bifidobacterium longum BORI Dipeptidase Belonging to the U34 Family

A dipeptidase was purified from a cell extract of Bifidobacterium longum BORI by ammonium sulfate precipitation and chromatography on DEAE-cellulose and Q-Sepharose columns. The purified dipeptidase had a molecular mass of about 49 kDa and was optimally active at pH 8.0 and 50°C. The enzyme was a strict dipeptidase, being capable of hydrolyzing a range of dipeptides but not tri- and tetrapeptides, p-nitroanilide derivatives of amino acids, or N- or C-terminus-blocked dipeptides. A search of the amino acid sequence of an internal tryptic fragment against protein sequences deduced from the total genome sequence of B. longum NCC2705 revealed that it was identical to an internal sequence of the dipeptidase gene (pepD), which comprised 1,602 nucleotides encoding 533 amino acids with a molecular mass of 60 kDa, and thereby differed considerably from the 49-kDa mass of the purified dipeptidase. To understand this discrepancy, pepD was cloned into an Escherichia coli expression vector (pBAD-TOPO derivative) to generate the recombinant plasmids pBAD-pepD and pBAD-pepD-His (note that His in the plasmid designation stands for a polyhistidine coding region). Both plasmids were successfully expressed in E. coli, and the recombinant protein PepD-His was purified using nickel-chelating affinity chromatography and reconfirmed by internal amino acid sequencing. The PepD sequence was highly homologous to those of the U34 family of peptidases, suggesting that the B. longum BORI dipeptidase is a type of cysteine-type N-terminal nucleophile hydrolase and has a β-hairpin motif similar to that of penicillin V acylase, which is activated by autoproteolytic processing.     

Biochemical and Biophysical Characterization of an Unexpected Bacteriolytic Activity of VanX,a Member of the Vancomycin-resistance vanA Gene Cluster

VanX is a d-alanyl-d-alanine (d-Ala–d-Ala) dipeptidase encoded in the vancomycin-resistance vanA gene cluster. Here we report that strong bacteriolysis occurred when isolated VanX was expressed in Escherichia coli at temperatures lower than 30 °C, which was unexpected because the vanA operon confers vancomycin resistance by protecting the cell wall. Therefore, we monitored cell lysis by measuring sample turbidity with absorbance at 590 nm and VanX expression using SDS-PAGE. No cell lysis was observed when VanX was expressed, even in large quantities, in the cell inclusion bodies at 37 °C, suggesting that a natively folded VanX is required for lysis. In addition, VanX mutants with suppressed dipeptidase activity did not lyse E. coli cells, confirming that bacteriolysis originated from the dipeptidase activity of VanX. We also observed shape changes in E. coli cells undergoing VanX-mediated lysis with optical microscopy and classified these changes into three classes: bursting, deformation, and leaking fluid. Optical microscopic image analysis fully corroborated our interpretation of the turbidity changes in the samples. From a practical perspective, the finding that VanX expressed in isolation induces cell lysis suggests that inhibitors of VanA and VanH that act downstream from VanX could provide a new class of therapeutic chemicals against bacteria expressing the vancomycin-resistance gene cluster.     

Hydrolysis of the brain dipeptide N-acetyl-L-aspartyl-L-glutamate. Identification and characterization of a novel N-acetylated alpha-linked acidic dipeptidase activity from rat brain

High performance liquid chromatography studies documented the presence of an enzyme activity, N-acetylated alpha-linked acidic dipeptidase (NAALA dipeptidase), in rat brain membranes that cleaves the endogenous brain dipeptide, N-acetyl-L-aspartyl-L-glutamate to N-acetyl-aspartate and glutamate. With ion exchange chromatography, which quantitatively separated [3,4-3H]glutamate from N-acetyl-L-aspartyl-L-[3,4-3H]glutamate, we found that NAALA dipeptidase activity was essentially restricted to nervous tissue and kidney. We characterized NAALA dipeptidase activity in lysed synaptosomal membranes obtained from rat forebrain. Membrane-bound NAALA dipeptidase activity was optimal between pH 6.0 and 7.4 at 37 degrees C. Eadie-Hofstee analysis of kinetic data revealed a rather high apparent affinity for N-acetyl-L-aspartyl-L-glutamate with a Km = 540 nM and a Vmax = 180 nM/mg of protein/min. While NAALA dipeptidase showed a requirement for monovalent anions such as Cl-, the polyvalent anions phosphate and sulfate inhibited enzyme activity 50% at 100 microM and 1 mM, respectively. The divalent metal ion chelators EGTA, EDTA, and o-phenanthroline completely abolished activity, which was partially restored by manganese. Treatment of membranes with 1 mM dithiothreitol abolished NAALA dipeptidase activity. NAALA dipeptidase activity was also sensitive to the aminopeptidase inhibitors bestatin and puromycin, although not to the selective aminopeptidase A inhibitor amastatin. Structure-activity relationships inferred from inhibitor studies suggest that this enzyme shows specificity for N-acetylated alpha-linked acidic dipeptides. NAALA dipeptidase was also potently inhibited by the excitatory amino acid agonist L-quisqualate. Comparison of the properties of NAALA dipeptidase to those of previously characterized enzymes suggests that this is a novel peptidase which may be involved in the synaptic degradation of N-acetyl-L-aspartyl-L-glutamate.     

Genetic control of dipeptidase in the Triticeae

Summary Isoelectric focusing has been employed to elucidate the genetic control of a series of dipeptidase isozymes in wheat and its relatives. The phenotype of wheat shows four bands, three of which are shown by aneuploid analysis to be controlled by the loci Dip-A1, Dip-B1 and Dip-D1 on chromosome arms 6AL, 6BL and 6DL, respectively. Varietal polymorphism for Dip-A1 and Dip-B1 was observed. Different homoeoloci were found in barley, Haynaldia villosa and Agropyron junceum.     

Rat brain N-acetylated alpha-linked acidic dipeptidase activity. Purification and immunologic characterization

N-Acetylated alpha-linked acidic dipeptidase (NAALA dipeptidase) is a membrane-bound metallopeptidase that cleaves glutamate from the endogenous neuropeptide N-acetyl-L-aspartyl-L-glutamate. In this report, we have solubilized NAALA dipeptidase activity from synaptosomal membranes with Triton X-100 and purified it to apparent homogeneity by sequential column chromatography on DEAE-Sepharose, CM-Sepharose, and lentil lectin-Sepharose. This procedure resulted in a 720-fold purification with 1.6% yield. The purified ezyme migrated as a single silver-stained band on a sodium dodecyl sulfate gel with an apparent molecular weight of 94 kDa. Using an enzymatic stain to visualize NAALA dipeptidase activity within a gel matrix, we have confirmed that the 94-kDa band is, indeed, NAALA dipeptidase. The purified enzyme was characterized and found to be pharmacologically similar to NAALA dipeptidase activity described previously in synaptosomal membrane extracts. Using the purified NAALA dipeptidase as antigen, we have raised specific and high titer polyclonal antibodies in guinea pig. Immunocytochemical studies show intense NAALA dipeptidase immunoreactivity in the cerebellar and renal cortices.     

Distribution of dipeptidase activity between lysosomes and soluble fraction of rat liver.

Dipeptidase activity toward Arg-Phe, Arg-Gly, and Trp-Leu exhibited bimodal distribution in the lysosomal and soluble fractions of rat liver. The majority (50-70 percent) of the dipeptidase activity was present in the soluble fraction. Some evidence for a plasma membrane dipeptidase, which hydrolyzes Trp-Leu but not Arg-Phe or Arg-Gly, also was found. The lysosomal dipeptidase activity had a pH optimum of 6.0-7.0, and was activated by sulfhydryl reagents. Lysosomal localization for some of the dipeptidase activity was established with Triton WR-1339 fractionation and latency experiments.     

Biochemical Studies on “Bakanae” Fungus. Part XXXVI The Physiological Action of Gibberellin. VIII

The seventh leaf-sheaths of rice plants grown in solution and treated with gibberellin were analyzed to examine their changes in the activities of various enzymes during period of growth, in comparison with that of the control plants. Phosphatase, alkalipyrophosphatase, acetylesterase, maltase, β-glucosidase, α-galactosidase, β-galactosidase, amylase, urease, dipeptidase, ascorbic acid oxidase, and catalase activities were decreased in extracts of sheaths on a fresh weight basis by treatment with gibberellin. Activities of peroxidase and invertase were markedly increased.