Computational Elucidation of Phylogenetic, Functional and Structural Features of Methioninase from Pseudomonas, Escherichia, Clostridium and Citrobacter Strains

BACKGROUND

L-Methioninase (EC 4.4.1.11; MGL) is a pyridoxal phosphate (PLP)-dependent enzyme that is produced by a variety of bacteria, fungi, and plants. L-methioninase, especially from Pseudomonas and Citrobacter sp., is considered as the efficient therapeutic enzyme, particularly in cancers such as glioblastomas, medulloblastoma, and neuroblastoma that are more sensitive to methionine starvation.

OBJECTIVE

The low stability is one of the main drawbacks of the enzyme; in this regard, in the current study, different features of the enzyme, including phylogenetic, functional, and structural from Pseudomonas, Escherichia, Clostridium, and Citrobacter strains were evaluated to find the best bacterial L-Methioninase.

METHODS

After the initial screening of L-Methioninase sequences from the above-mentioned bacterial strains, the three-dimensional structures of enzymes from Escherichia fergusonii, Pseudomonas fluorescens, and Clostridium homopropionicum were determined through homology modeling via GalaxyTBM server and refined by GalaxyRefine server.

RESULTS AND CONCLUSION

Afterwards, PROCHECK, verify 3D, and ERRAT servers were used for verification of the obtained models. Moreover, antigenicity, allergenicity, and physico-chemical analysis of enzymes were also carried out. In order to get insight into the interaction of the enzyme with other proteins, the STRING server was used. The secondary structure of the enzyme is mainly composed of random coils and alpha-helices. However, these outcomes should further be validated by wet-lab investigations.

A simple selection strategy for evolving highly efficient enzymes

Combining tunable transcription with an enzyme-degradation tag affords an effective means to reduce intracellular enzyme concentrations from high to very low levels. Such fine-tuned control allows selection pressure to be systematically increased in directed-evolution experiments. This facilitates identification of mutants with wild-type activity, as shown here for an engineered chorismate mutase. Numerous selection formats and cell-based screening methodologies may benefit from the large dynamic range afforded by this easily implemented strategy.

Construction of an Escherichia-Pseudomonas shuttle vector containing an aminoglycoside phosphotransferase gene and a lacZ'' Gene for alpha-complementation

A new 4.87 kb Escherichia-Pseudomonas shuttle vector has been constructed by inserting a 1.27 kb DNA fragment with a replication origin of a Pseudomonas plasmid pRO1614 into the 3.6 kb E. coli plasmid pBGS18. This vector, designated pJH1, contains an aminoglycoside phosphotransferase gene (aph) from Tn903, a lacZ'' gene for alpha-complementation and a versatile multiple cloning site possessing unique restriction sites for EcoRI, SacI, KpnI, SmaI, BamHI, XbaI, SalI, BspMI, PstI, SphI, and HindIII. When pJH1 was transformed into E. coli DH5alpha and into P. putida HK-6, it was episomally and stably maintained in both strains. In addition, the enhanced green fluorescent protein (EGFP) gene which was transcriptionally cloned into pJH1 rendered E. coli cells fluorescence when its transformants were illuminated at 488 nm.

Improving the pyrophosphate-inosine phosphotransferase activity of Escherichia blattae acid phosphatase by sequential site-directed mutagenesis

Escherichia blattae acid phosphatase/phosphotransferase (EB-AP/PTase) exhibits C-5'-position selective pyrophosphate-nucleoside phosphotransferase activity in addition to its intrinsic phosphatase. Improvement of its phosphotransferase activity was investigated by sequential site-directed mutagenesis. By comparing the primary structures of higher 5'-inosinic acid (5'-IMP) productivity and lower 5'-IMP productivity acid phosphatase/phosphotransferase, candidate residues of substitution were selected. Then a total of 11 amino acid substitutions were made with sequential substitutions. As the number of substituted amino acid residues increased, the 5'-IMP productivity of the mutant enzyme increased, and the activity of the 11 mutant phosphotransferases of EB-AP/PTase reached the same level as that of Morganella morganii AP/PTase. This result shows that Leu63, Ala65, Glu66, Asn69, Ser71, Asp116, Thr135, and Glu136, whose relevance was not directly established by structural analysis alone, also plays an important role in the phosphotransferase activity of EB-AP/PTase.

The Escherichia coli ynfEFGHI operon encodes polypeptides which are paralogues of dimethyl sulfoxide reductase (DmsABC)

The ynfEFGHI operon is a paralogue of the Escherichia coli dmsABC operon. ynfE and ynfF are paralogues of dmsA. ynfG and ynfH are paralogues of dmsB and dmsC, respectively. YnfI (dmsD) has no dms paralogue. YnfE/F and YnfG could be detected by immunoblotting with anti-DmsAB antibodies when expressed under the control of a tac or dms promoter. Cells harbouring ynfFGH on a multicopy plasmid supported anaerobic growth with dimethyl sulfoxide (DMSO) as respiratory oxidant in a dmsABC deletion, suggesting that YnfFGH forms a heterotimeric enzyme complex similar to DmsABC. Exchange of DmsC by YnfH (DmsAB-YnfH) resulted in membrane localization, anaerobic growth on DMSO, and binding of 2-n-heptyl 4-hydroxyquinoline-N-oxide, indicating that YnfH was a competent anchor. YnfG can also replace DmsB as the electron transfer subunit and assembled [Fe-S] clusters as judged by electron paramagnetic resonance spectroscopy. YnfE and/or YnfF could not form a functional complex with DmsBC and expression of YnfE prevented the accumulation of YnfFGH.

An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA

The AUA codon-specific isoleucine tRNA (tRNA(Ile)) in eubacteria has the posttranscriptionally modified nucleoside lysidine (L) at the wobble position of the anticodon (position 34). This modification is a lysine-containing cytidine derivative that converts both the codon specificity of tRNA(Ile) from AUG to AUA and its amino acid specificity from methionine to isoleucine. We identified an essential gene (tilS; tRNA(Ile)-lysidine synthetase) that is responsible for lysidine formation in both Bacillus subtilis and Escherichia coli. The recombinant enzyme complexed specifically with tRNA(Ile) and synthesized L by utilizing ATP and lysine as substrates. The lysidine synthesis of this enzyme was shown to directly convert the amino acid specificity of tRNA(Ile) from methionine to isoleucine in vitro. Partial inactivation of tilS in vivo resulted in an AUA codon-dependent translational defect, which supports the notion that TilS is an RNA-modifying enzyme that plays a critical role in the accurate decoding of genetic information.

Identifying the methyltransferases for m(5)U747 and m(5)U1939 in 23S rRNA using MALDI mass spectrometry

There are three sites of m(5)U modification in Escherichia coli stable RNAs: one at the invariant tRNA position U54 and two in 23S rRNA at the phylogenetically conserved positions U747 and U1939. Each of these sites is modified by its own methyltransferase, and the tRNA methyltransferase, TrmA, is well-characterised. Two open reading frames, YbjF and YgcA, are approximately 30% identical to TrmA, and here we determine the functions of these candidate methyltransferases using MALDI mass spectrometry. A purified recombinant version of YgcA retains its activity and specificity, and methylates U1939 in an RNA transcript in vitro. We were unable to generate a recombinant version of YbjF that retained in vitro activity, so the function of this enzyme was defined in vivo by engineering a ybjF knockout strain. Comparison of the methylation patterns in 23S rRNAs from YbjF(+) and YbjF(-) strains showed that the latter differed only in the lack of the m(5)U747 modification. With this report, the functions of all the E.coli m(5)U RNA methyltransferases are identified, and a more appropriate designation for YbjF would be RumB (RNA uridine methyltransferases B), in line with the recent nomenclature change for YgcA (now RumA).

Molecular and biochemical characterization of a novel class A beta-lactamase (HER-1) from Escherichia hermannii

Escherichia hermannii showed a low level of resistance to amoxicillin and ticarcillin, reversed by clavulanate, and a moderate susceptibility to piperacillin but was susceptible to all cephalosporins. A bla gene was cloned and encoded a typical class A beta-lactamase (HER-1, pI 7.5), which shares 45, 44, 41, and 40% amino acid identity with other beta-lactamases, AER-1 from Aeromonas hydrophila, MAL-1/Cko-1 from Citrobacter koseri, and TEM-1 and LEN-1, respectively. No ampR gene was detected. Only penicillins were efficiently hydrolyzed, and no hydrolysis was observed for cefuroxime and broad-spectrum cephalosporins. Sequencing of the bla gene in 12 other strains showed 98 to 100% identity with bla(HER-1).

Cloning and sequencing of the beta-lactamase gene and surrounding DNA sequences of Citrobacter braakii, Citrobacter murliniae, Citrobacter werkmanii, Escherichia fergusonii and Enterobacter cancerogenus

To further identify the origins of plasmid-mediated cephalosporinases that are currently spreading worldwide, the chromosomal beta-lactamase genes of Citrobacter braakii, Citrobacter murliniae, Citrobacter werkmanii reference strains and of Escherichia fergusonii and Enterobacter cancerogenus clinical isolates were cloned and expressed into Escherichia coli and sequenced. These beta-lactamases had all a single pI value >8 and conferred a typical AmpC-type resistance pattern in E. coli recombinant strains. The cloned inserts obtained from genomic DNAs of each strain encoded Ambler class C beta-lactamases. The AmpC-type enzymes of C. murliniae, C. braakii and C. werkmanii shared 99%, 96% and 95% amino acid sequence identity, respectively, with chromosomal AmpC beta-lactamases from Citrobacter freundii. The AmpC-type enzyme of E. cancerogenus shared 85% amino acid sequence identity with the chromosomal AmpC beta-lactamase of Enterobacter cloacae OUDhyp and the AmpC-type enzyme of E. fergusonii shared 96% amino acid sequence identity with that of E. coli K12. The ampC genes, except for E. fergusonii, were associated with genes homologous to regulatory ampR genes of other chromosomal class C beta-lactamases that explain inducibility of beta-lactamase expression in these strains. This work provides further evidence of the molecular heterogeneity of class C beta-lactamases.

Enhancement of nucleoside phosphorylation activity in an acid phosphatase

Escherichia blattae non-specific acid phosphatase (EB-NSAP) possesses a pyrophosphate-nucleoside phosphotransferase activity, which is C-5'-position selective. Current mutational and structural data were used to generate a mutant EB-NSAP for a potential industrial application as an effective and economical protein catalyst in synthesizing nucleotides from nucleosides. First, Gly74 and Ile153 were replaced by Asp and Thr, respectively, since the corresponding replacements in the homologous enzyme from Morganella morganii reduced the K(m) value for inosine and thus increased the productivity of 5'-IMP. We determined the crystal structure of G74D/I153T, which has a reduced K(m) value for inosine, as expected. The tertiary structure of G74D/I153T was virtually identical to that of the wild-type. In addition, neither of the introduced side chains of Asp74 and Thr153 is directly involved in the interaction with inosine in a hypothetical binding mode of inosine to EB-NSAP, although both residues are situated near a potential inosine-binding site. These findings suggested that a slight structural change caused by an amino acid replacement around the potential inosine-binding site could significantly reduce the K(m) value. Prompted by this hypothesis, we designed several mutations and introduced them to G74D/I153T, to decrease the K(m) value further. This strategy produced a S72F/G74D/I153T mutant with a 5.4-fold lower K(m) value and a 2.7-fold higher V(max) value as compared to the wild-type EB-NSAP.

Shigella apyrase--a novel variant of bacterial acid phosphatases?

A virulence-associated ATP diphosphohydrolase activity in the periplasm of Shigella, identified as apyrase, was found to be markedly similar to bacterial non-specific acid phosphatases in primary structure. When the Shigella apyrase sequence was threaded in to the recently published 3D structure of the highly similar (73%) Escherichia blattae acid phosphatase it was found to have a highly overlapping 3D structure. Our analysis, which included assays for phosphatase, haloperoxidase and catalase activities, led us to hypothesize that Shigella apyrase might belong to a new class of pyrophosphatase originating as one more variant in the family of bacterial non-specific acid phosphatases. It revealed interesting structure-function relationships and probable roles relevant to pathogenesis.

X-ray structures of a novel acid phosphatase from Escherichia blattae and its complex with the transition-state analog molybdate

The structure of Escherichia blattae non-specific acid phosphatase (EB-NSAP) has been determined at 1.9 A resolution with a bound sulfate marking the phosphate-binding site. The enzyme is a 150 kDa homohexamer. EB-NSAP shares a conserved sequence motif not only with several lipid phosphatases and the mammalian glucose-6-phosphatases, but also with the vanadium-containing chloroperoxidase (CPO) of Curvularia inaequalis. Comparison of the crystal structures of EB-NSAP and CPO reveals striking similarity in the active site structures. In addition, the topology of the EB-NSAP core shows considerable similarity to the fold of the active site containing part of the monomeric 67 kDa CPO, despite the lack of further sequence identity. These two enzymes are apparently related by divergent evolution. We have also determined the crystal structure of EB-NSAP complexed with the transition-state analog molybdate. Structural comparison of the native enzyme and the enzyme-molybdate complex reveals that the side-chain of His150, a putative catalytic residue, moves toward the molybdate so that it forms a hydrogen bond with the metal oxyanion when the molybdenum forms a covalent bond with NE2 of His189.

Direct localization of a beta-subunit domain on the three-dimensional structure of Escherichia coli RNA polymerase

To identify the location of a domain of the beta-subunit of Escherichia coli RNA polymerase (RNAP) on the three-dimensional structure, we developed a method to tag a nonessential surface of the multisubunit enzyme with a protein density easily detectable by electron microscopy and image processing. Four repeats of the IgG-binding domain of Staphylococcus aureus protein A were inserted at position 998 of the E. coli RNAP beta-subunit. The mutant RNAP supported E. coli growth and showed no apparent functional defects in vitro. The structure of the mutant RNAP was determined by cryoelectron microscopy and image processing of frozen-hydrated helical crystals. Comparison of the mutant RNAP structure with the previously determined wild-type RNAP structure by Fourier difference analysis at 20-A resolution directly revealed the location of the inserted protein domain, thereby locating the region around position 998 of the beta-subunit within the RNAP three-dimensional structure and refining a model for the subunit locations within the enzyme.

[An additional dehydrogenase or oxidation-reduction test in the classification of enterobacteria]

The dehydrogenase (DHG) or oxidation-reduction test is proposed for use together with the determination of such enzymes as hydrolases, cytochrome oxidase, dehydrocarboxylase, urease, etc. 200 Citrobacter freundii cultures and 76 strains of enteropathogenic Escherichia (EPE) were studied with the determination of their DHG activity in semiliquid mannitol and in Kligler's medium. The study revealed that this test, characterized by the reduction of the indicator, similarly to that in salmonellae and shigellae, was constantly negative in semiliquid mannitol in C. freundii and in 97.3% of cases in EPE. In 17.5% of C. freundii lactose-positive cultures the DHG test in Kligler's medium was positive, which made it possible to regard them as a separate biovar. Taking into account the results of this investigation, the subdivision of C. freundii into 3 biovars is proposed.

Escherichia hermannii: susceptibility pattern to beta-lactams and production of beta-lactamase

The susceptibility pattern of Escherichia hermannii, although closely related to Escherichia coli according to its biochemical patterns, was clearly distinguishable by its susceptibility to beta-lactams by both diffusion and dilution methods from E. coli penicillinase producing or non-producing strains, Citrobacter diversus, Klebsiella pneumoniae, and Klebsiella oxytoca. Beta-lactamase clavulanate-sensitive activity was localized with various isoelectric points from 7.0 to 8.5. No cross hybridization with DNA intragenic probes (blaTEM, blaSHV, blaCARB and blaOXY) was observed by dot blot procedure.

Cloning and expression of a Pseudomonas 3 alpha-hydroxysteroid dehydrogenase-encoding gene in Escherichia coli

A bacterial strain, B-0831, which produced 3 alpha-hydroxysteroid dehydrogenase (3 alpha HSD) was isolated and identified as belonging to the genus, Pseudomonas. Molecular weights of the purified 3 alpha HSD, determined by SDS-PAGE and by chromatography on Sephacryl S-200, were about 25 and 50 kDa, respectively. A genomic library of Pseudomonas sp. B-0831, prepared in the plasmid vector pACYC184, was screened with probes based on the amino acid (aa) sequence of the protein to obtain the plasmid, p3 alpha HSD1, identified by hybridization with the probes, that contained a 2.4-kb insert from Pseudomonas DNA. When the 1.4-kb SphI fragment of p3 alpha HSD1 was inserted into the vector, pUC118, and introduced into Escherichia coli DH1 under the control of lacZ promoter in the vector, the transformants produced 200-fold more 3 alpha HSD intracellularly than Pseudomonas sp. B-0831. Sequence analysis of the 3 alpha HSD gene revealed that an ORF encoding 3 alpha HSD consists of 254 aa, with a calculated M(r) of 25,761, suggesting that the enzyme consists of homodimer subunits.

Assay for beta-glucuronidase in species of the genus Escherichia and its applications for drinking-water analysis

Recently, Escherichia species other than Escherichia coli have been isolated from potable water. Environmental isolates as well as clinical isolates of E. adecarboxylata, E. blattae, E. fergusonii, E. hermannii, and E. vulneris were assayed for the enzyme beta-glucuronidase by using EC MUG medium and the Colilert system. None of the isolates were positive for the enzyme by either method.

The linear tetrasaccharide, Gal beta 1-4GlcNAc beta 1-6Gal beta 1-4GlcNAc, isolated from radiolabeled teratocarcinoma poly-N-acetyllactosaminoglycan resists the action of E. freundii endo-beta-galactosidase

A novel linear tetrasaccharide, Gal beta 1-4GlcNAc beta 1-6Gal beta 1-4GlcNAc, was isolated from partial acid hydrolysates of metabolically labeled poly-N-acetyllactosaminoglycans of murine teratocarcinoma cells. It was characterized by exo-glycosidase sequencing and by mild acid hydrolysis followed by identification of all partial cleavage products. The tetrasaccharide, and likewise labelled GlcNAc beta 1-6Gal beta 1-4GlcNAc, resisted the action of endo-beta-galactosidase (EC 3.2.1.103) from E. freundii at a concentration of 125 mU/ml, while the isomeric, radioactive teratocarcinoma saccharides Gal beta 1-4GlcNAc beta 1-3Gal beta 1-4GlcNAc and GlcNAc beta 1-3Gal beta 1-4GlcNAc were cleaved in the expected manner.

Immunological relationship among glyceraldehyde-3-phosphate dehydrogenases in the genera Enterobacter and Escherichia

The comparative immunological study of glyceraldehyde-3-phosphate dehydrogenase (G-3-PDH) among Enterobacteriaceae carried out with an anti-Enterobacter cloacae G-3-PDH serum pointed out the large heterogeneity of the genera Enterobacter and Escherichia. The use of two-dimensional maps integrating our new data and previously acquired quantitative data confirmed these results.

Effect of detergents on aspartate ammonia-lyase activity in Escherichia alcalescens

The effect of twelve detergents on aspartate ammonia-lyase activity of Escherichia alcalescens used for the production of L-aspartic acid was tested. Best permeabilization was found with Triton X-100, Slovafol 910 and Corona, a mixed commercial preparation. In contrast to Triton X-100 and Slovafol 910, a much narrower range of suitable concentrations was observed with Corona.

Stereochemistry and mechanism of reactions catalyzed by tyrosine phenol-lyase from Escherichia intermedia

Stereochemical studies on tyrosine phenol-lyase from Escherichia intermedia have shown that the alpha, beta-elimination reactions of L-serine and D- and L-tyrosine proceed with retention of configuration at C-beta. Stereospecifically beta-tritiated L-serine is slowly racemized at C-beta. Deuterium from the alpha-position of L-tyrosine is partially transferred to C-4 of the phenol formed when the alpha, beta-elimination reaction is carried out in H2O, although no transfer of alpha-1H in 2H2O was seen. The result favors tautomerization of the p-hydroxyphenyl to a cyclohexadienonyl moiety prior to carbon-carbon bond cleavage. In the conversion of L- to D-alanine catalyzed by tyrosine phenol-lyase, some alpha-hydrogen recycling is observed, pointing to a single-base racemization mechanism. Attempts to demonstrate cofactor motion during racemization by NaBH4 reduction of [3H]PLP-enzyme: D- and L-alanine complexes failed, but showed that, as in other PLP enzymes, the holoenzyme is reduced preferentially from the Re face with respect to C-4' of PLP and enzyme-substrate complexes preferentially from the Si face.

Substrate specificity of endo-beta-galactosidases from Flavobacterium keratolyticus and Escherichia freundii is different from that of Pseudomonas sp

The substrate specificity of endo-beta-galactosidase of Pseudomonas sp. was found to differ from that of Flavobacterium keratolyticus or Escherichia freundii, based on the following experimental results. The endo-beta-galactosidases from these three bacteria released 6-O-sulfo-GlcNAc beta 1-3Gal as one of the major products from keratan sulfates from different sources. In addition to the sulfated disaccharide, Flavobacterium and Escherichia enzymes produced GlcNAc beta 1-3Gal, which is also an integral repeating unit of keratan sulfate, whereas the Pseudomonas enzyme did not release any non-sulfated disaccharide. Tetrasaccharides were prepared from the teleost skin keratan sulfate by digestion with Pseudomonas enzyme followed by gel filtration on Sephadex G-50 chromatography. A part of the tetrasaccharide fraction was hydrolyzed by Flavobacterium enzyme to produce 6-O-sulfo-GlcNAc beta 1-3Gal and GlcNAc beta 1-3Gal, whereas the fraction was completely resistant to retreatment with the Pseudomonas enzyme. Endo-beta-galactosidases from F. keratolyticus and E. freundii hydrolyzed the internal beta-1,4-galactosyl linkage of various neolacto-type glycosphingolipids to produce glucosylceramides. However, these glycosphingolipids were completely resistant to the Pseudomonas enzyme. These findings clearly show that the sulfation on the N-acetylglucosamine adjacent to galactose in the lactosaminoglycans is essential for expression of the Pseudomonas enzyme, but not for that of the Flavobacterium or Escherichia enzyme.

[Characterization of Escherichia hermannii by electrophoresis of esterases, acid phosphatase and glutamate and malate dehydrogenases]

Esterases, acid phosphatase and glutamate and malate dehydrogenases of 11 strains of Escherichia hermannii were analysed by horizontal electrophoresis in polyacrylamide agarose gel. Seven esterase bands were defined by their range of activity on synthetic substrates and their sensitivity or resistance to di-isopropyl fluorophosphate. These bands were different in activity and in mobility from those produced by E. coli strains. On the basis of variations in mobility of glutamate and malate dehydrogenases and in the number and mobility of esterases, the strains were divided into 3 zymotypes.

Endo-beta-D-galactosidases of Bacteroides fragilis and Escherichia freundii hydrolyze linear but not branched oligosaccharide domains of glycolipids of the neolacto series

The specificities of the endo-beta-galactosidases of Bacteroides fragilis and Escherichia freundii towards linear and branched oligosaccharides of the lacto-N-glycosyl series were investigated using as substrates glycolipids containing (a) linear neolactotetra - or hexaosyl sequences, (b) branched biantennary neolactooctaosyl sequences, and (c) triantennary neolactononaor dodecaglycosyl sequences. Glycolipid and oligosaccharide hydrolysis products were identified by tlc and/or paper chromatography. The rate of hydrolysis was assessed in time course experiments in which the oligosaccharides released were quantified as 3H-labeled alditols. The salient observations were as follows. (i) With the substrates thus far tested in the present and a previous study ( Scudder , P., Uemura , K., Dolby , J., Fukuda, M.N., and Feizi , T. (1983) Biochem. J. 213, 485-494), the endo-beta-galactosidases from B. fragilis and E. freudii have indistinguishable specificities. (ii) The beta-galactosidic linkage of the branch point sequence (Formula: see text) is completely resistant to hydrolysis by these enzymes, although the unbranched sequence GlcNAc beta 1-3Gal beta 1-4GlcNAc/Glc is readily cleaved. (iii) At an optimal concentration of detergent, the endo-beta-galactosidase susceptibility of the GlcNAc beta 1-3Gal beta 1-4Glc sequence near the ceramide moiety of branched glycolipids is similar to that of the corresponding sequence in linear glycolipids.

Isolation and characterization of an endo-beta-galactosidase from Bacteroides fragilis

Six strains of Bacteroides fragilis were examined and all found to produce endo-beta-galactosidase, an enzyme that hydrolyses internal beta-galactosidic linkages of oligosaccharides belonging to the poly-N-acetyl-lactosamine series, with the common structure GlcNAc beta 1 leads to 3Gal beta 1 leads to 4GlcNAc/Glc. The enzyme was produced without the addition of an inducer such as keratan sulphate. It was purified 7000-fold from the culture supernatant and obtained with a yield 4-10-fold greater than from sources described previously. The specificity of the enzyme towards bovine corneal keratan sulphate, milk oligosaccharides and the glycolipids lacto-N-neotetraosylceramide and lacto-N-tetraosylceramide closely resembled that of the endo-beta-galactosidase isolated from Escherichia freundii. A novel observation was that both enzymes hydrolysed the type 2 sequence, Gal beta 1 leads to 4GlcNAc beta 1 leads to 3Gal beta 1 leads to 4Glc, at about twice the rate of the type 1 isomer, Gal beta 1 leads to 3GlcNAc beta 1 leads to 3Gal beta 1 leads to 4Glc. Because of the ease of purification of the enzyme and high yield in the absence of contaminating glycosidases and proteinases, Bacteroides fragilis is a valuable source of endo-beta-galactosidase for the structural analysis of carbohydrate chains.

Molecular cloning of genes for cellobiose utilization and their expression in Escherichia coli

The genes for cellobiose utilization in Escherichia adecarboxylata were cloned by using recombinant deoxyribonucleic acid techniques and transferred to Escherichia coli. Preliminary analysis of the beta-glucosidase activity expressed in these host cells indicated that the enzyme is membrane bound and required magnesium ions, phosphate ions, and heat-stable, non-dialyzable factors from the bacterial cytoplasm.

Purification and characterization of endo-beta-galactosidase from Escherichia freundii induced by hog gastric mucin

A new procedure for inducing and purifying endo-beta-galactosidase from Escherichia freundii was described. The enzyme was found to be induced with high efficiency in culture medium containing Smith-degraded hog gastric mucin, which was prepared from a commercially available starting material. Endo-beta-galactosidase was then purified by ammonium sulfate fractionation, DEAE-Sephadex chromatography, and affinity chromatography on Sepharose conjugated with the Smith-degraded mucin. The enzyme thus purified by only three steps showed no other glycosidase or protease activities and had higher specific activity compared to the previous method. This new method has a great advantage since the gastric mucin is abundantly available and the efficiency of enzyme production was high without significant induction of exoglycosidase. The hydrolysis of oligosaccharides, glycosphingolipid, and keratansulfate was studied by using this newly purified enzyme. Kinetic data indicate that hydrolyzability of these substrates is largely affected by substrate concentration, enzyme concentration and the structure of substrates. Based on these results, the specificity of E. freundii endo-beta-galactosidase was discussed.

Isolation and characterization of an endo-beta-galactosidase from a new strain of Escherichia freundii

A new strain of Escherichia freundii was isolated from human feces. Compared with the previous strain (Kitamikado, M., and Ueno, R. (1970) Bull. Jpn. Soc. Sci. Fish. 36, 1175-1180), this strain releases comparable levels of endo-beta-galactosidase with lower levels of exoglycosidases in the culture medium containing 0.3% of keratan sulfate. Endo-beta-galactosidase was purified by an improved purification procedure involving Amicon H1P10 hollow fiber filtration, QAE-Sephadex A-50, and CM-Sephadex C-50 chromatographies. The purified enzyme is completely free from proteases and exoglycosidases. The general properties of this enzyme are: molecular weight, 28,000; optimal pH, 5.5 TO 5.8; PI, pH 8.0. This enzyme hydrolyzed keratan sulfates isolated from different sources to produce 6-O-sulfo-GlcNAc beta1 leads to 3Gal as the major product. In addition, the specificity of this enzyme toward various glycoconjugates was also studied.

[Isolation, purification and some properties of tyrosine-phenol-lyase from Citrobacter freundii cells]

A new procedure for isolation of tyrosine-phenol-lyase from the cells of C. freundii strain 62 allowing to obtain a highly purified enzyme with a high yield at a reduced time expenditure has been developed. The procedure described differs from the well-known method for isolation of the enzyme from the cells of Escherichia intermedia and Erwinia herbicola. Some properties of the enzyme from C. freundii 62, e.g. stability, dependence of the enzyme activity on some mono- and bivalent cations and pH- and temperature dependences of the enzyme have been studied. It was shown that the enzyme is activated by NH4+, K+, Na+ and is inhibited by Ca2+, Cu2+ and Mg2+. The enzyme loses up to 50% of its activity upon storage in glycerol with 2-mercaptoethanol during 1,5 months at -18 degrees.

Tk polyagglutination produced in vitro by an endo-beta-galactosidase

After treatment with the culture supernatant of Bacteroides fragilis or with an endo-beta-galactosidase from Escherichia freundii, the human red blood cells are Tk-activated, i.e. agglutinable by BS II lectin and their blood group I and i activities are reduced. These results suggest that B. fragilis produces an endo-beta-galactosidase activity and that the main antigenic determinant of Tk polyagglutinable red cells is a terminal N-acetyl-glucosamine residue.

Consequence of cerulenin-released beta-lactamase in clinical coliforms

Periplasmic beta-lactamase of certain clinical coliforms was released, without affecting cell viability, by perturbation of the outer membrane utilizing the fatty acid-mimicking antibiotic cerulenin. Release of such compartmentalized beta-lactamase, at high population density, seems to provide an extra margin of resistance to the organisms against cephaloridine.

Endo-beta-galactosidase of Escherichia freundii. Purification and endoglycosidic action on keratan sulfates, oligosaccharides, and blood group active glycoprotein

Endo-beta-galactosidase was purified 4400-fold from a culture filtrate of Escherichia freundii with 45% recovery. The enzyme preparation was practically free of exoglycosidases, sulfatase, and proteases. This enzyme hydrolyzed several keratan sulfates, endoglycosidically releasing oligosaccharides of various molecular sizes. Among the digestion products of the corneal keratan sulfate, the structure of a disaccharride and a tetrasaccharride were shown to be 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucosyl-(1 leads to 3)-D-galactose and 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucosyl-(1 leads to 3)-6-O-sulfo-beta-D-galactosyl-(1 leads to 4)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucosyl-(1 leads to 3)-D-galactose, respectively. These oligosaccharide structures indicate that this enzyme specifically hydrolyzes the galactosidic bonds in which nonsulfated galactose residues participate. The enzyme could also hydrolyze a small oligosaccharide such as lacto-N-neotetraitol as follows: Gal(beta 1 leads to 4)GlcNAc(beta 1 leads to 3)Gal(beta 1 leads to 4) sorbitol leads to Gal(beta 1 leads to 4)GlcNAc(beta 1 leads to 3)Gal + sorbitol AB active blood group substance could be hydrolyzed by this enzyme only after Smith degradation. After enzymatic digestion small oligosaccharides and resistant macromolecules were produced. These findings indicate that the enzyme should be useful in studying the precise structures of keratan sulfates, related glycoproteins, and oligosaccharides.

Rapid diagnosis of Enterobacteriaceae. I. Detection of bacterial glycosidases

The paper describes a number of tests for the rapid detection of glycosidases including alpha-glucosidase, beta-glucosidase, beta-glucuronidase, beta-xylosidase and alpha-fucosidase. The methods use heavy suspensions of viable but non-multiplying bacteria in a buffered solution of a chromogenic substrate. The results of the tests are readable within 4 h. The application of these tests to a collection of 633 strains of Enterobacteriaceae and Vibrionaceae demonstrates that some of the tests may be valuable additions to the present tests available for the identification of bacteria belonging to these families. beta-glucuronidase activity was observed only in strains of the Escherichia-Shigella group. 97 per cent of the Escherichia strains possessed beta-glucuronidase activity. beta-xylosidase activity was almost completely restricted to strains of the Klebsiella-Enterobacter group in addition to Yersinia strains. None of the strains possessed alpha-fucosidase activity.

[Physical and chemical properties of tryptophenases of five species of Enterobacteriaceae]

The molecular weight, sedimentation coefficient, and amino acids composition were determined on five tryptophanases (TPases) from Escherichia coli B and E. aurescens, Shigella alkalescens, and Proteus vulgaris and P. morganii. These TPases have identical sedimentation profile and coefficient (9.6 S), and the same molecular weight (220 000). Each enzyme is constituted of four identical subunits having a molecular weight of 55 000. The amino acids composition of these TPases is very similar, with the exception of P. morganii and P. vulgaris TPases which present significative variations in basic amino acids and tryptophan content. The species differentiation of the coli group cannot be made on their TPase characteristics only, contrary to P. morganii and P. vulgaris which can be differentiated between them and from the coli group.

[Differentiation of tryptophanases of five species of Enterobacteriaceae by sulfhydryl groups]

We have studied the sulfhydryl groups (-SH) on the tryptophanases (TPases) from Escherichia coli B. and E. aurescens, Shigella alkalescens, and Proteus vulgaris and P. morganii. The coli group and the P. morganii apo TPases have 20 -SH groups per mole of enzyme, where as P. vulgaris apoTPase has 16. In coli group TPases, there are 16 -SH groups on the mole surface and they are all implicated in the activity and the enzyme-substrate bond. Proteus morganii TPase has 8 surface -SH groups, 4 of which are implicated in the activity; the remaining 12 -SH groups are located inside the mole and take part in the activity and the enzyme-substrate bond. Proteus vulgaris TPase has 4 surface -SH groups which are constructive of the enzyme structure, whereas the 12 remaining -SH groups are located inside the mole and take part in the activity and the enzyme-substrate bond. It is concluded that Proteus TPases are molecules which have inverted quaternary structure in comparison to those of the coli group. The studied TPases have four subunits, each of them is constituted of one polypeptidic chain having a molecular weight of 55,000.

[The effect of pyridoxal phosphate on the tryptophanases of five species of Enterobacteriaceae]

Escherichia coli B and E. aurescens, Shigella alkalescens, and Proteus vulgaris et P. morganii tryptophanases (TPases) were studied for the spectral forms of the enzyme. The pH effect on the absorption spectrum and on the enzyme specific activity revealed that the coli group TPases are identical with but differ from Proteus TPases which differ themselves. The coli group TPases attach 4 mol of pyridoxal phosphate (PLP)/mol of enzyme, independently of the pH in the presence of K(plus) ions, and 9 mol of PLP/mol of enzyme must be reduced to achieve complete inactivation. The Proteus TPases attach 4 mol of PLP/mol of enzyme at PH 6.8, and 3 mol of PLP/mol of enzyme at pH 7.8 in K(plus) buffer. In P. morganii, 7 mol of PLP/mol of enzyme must be reduced to inactivate the enzyme, whereas P. vulgaris TPase cannot be completely inactivated by this method. These five TPases attach only 3 mol of PLP/mol of enzyme in a Na(plus) buffer, independently of the pH.

Tryptophanase of fecal flora as a possible factor in the etiology of colon cancer

Twenty-three strains of intestinal anaerobes obtained from two laboratories were examined for indole production from tryptophan. Among the 23 isolates tested, three of Bacteroides fragilis thetaiotaomicron and one Citrobacter sp. were indole positive. The tryptophanase of the indole-positive strains of intestinal anaerobes was inducible by tryptophan and was susceptible to glucose repression. The products of tryptophanase activity were formed in stoichiometric amounts by dialyzed, freshly prepared extracts. The tryptophan concentration and tryptophanase activity in feces from rats on an all-meat diet were significantly higher than those in feces from rats on a normal diet. The results indicated that the higher tryptophanase activity in the feces of rats fed an all-meat diet is due to the inducibility of this enzyme by tryptophan and is not due to any inhibitor in the feces of rats on a normal diet. The results also suggested that a population with a diet rich in meat has a greater chance for exposure to possible carcinogens such as indole and other tryptophan metabolites. This agrees with the hypothesis, based on epidemiologic data, that a high intake of meat may be related to the development of colon cancer in man.

Comparative studies on the properties of tryptophanase and tyrosine phenol-lyase immobilized directly on Sepharose or by use of Sepharose-bound pyridoxal 5'-phosphate

Tryptophanase from Escherichia coli B/qt 7-A and tyrosine phenol-lyase (beta-tyrosinase) from Escherichia intermedia were immobilized on Sepharose 4B by several direct coupling reactions or through pyridoxal 5'-phosphate previously bound to Sepharose. The most active preparation of immobilized tryptophanase was obtained by coupling tetrameric apoenzyme to pyridoxal-P bound on Sepharose at the 6-position through a diazo linkage. This immobilization procedure involves the formation to Schiff base linkage between 4-formyl group of Sepharose-bound pyridoxal-P and the epsilon-amino group of the lysine residue at the active center of one subunit of tetrameric apo-tryptophanase, followed by the fixation of the Schiff base linkage by reduction with NaBH4. In the case of beta-tyrosinase having two catalytic centers, however, this method was not so suitable as the case of tryptophanase. Direct coupling of the apoenzyme to CNBr-activated Sepharose or to a bromoacetyl derivative of Sepharose gave better results. In each case, the affinity for substrate or coenzyme was scarcely influenced by the immobilization. When used repeatedly in a batch system or continuously in a flow system in the absence of added pyridoxal-P, immobilized holo-tryptophanase of holo-beta-tyrosinase gradually lost its original activity; however, supplement of pyridoxal-P to the reaction system restored its initial activity. From the kinetic analyses of these phenomena, the rate constants of coenzyme dissociation from immobilized tryptophanase and beta-tyrosinase were calculated. Upon immobilization, the pH optima of both enzymes shifted 0.5 to 1.0 pH unit to the alkaline side. Both immobilized enzymes showed higher thermal stability and resistance to a denaturing agent such as guinidine-HCl than their free counterpart. Furthermore, the reactivity of sulfhydryl group of beta-tyrosinase, in connection with its coenzyme-binding property, was conveniently studied by use of the immobilized enzyme.