The ROK kinase N-acetylglucosamine kinase uses a sequential random enzyme mechanism with successive conformational changes upon each substrate binding.

N-acetyl-d-glucosamine (GlcNAc) is a major component of bacterial cell walls. Many organisms recycle GlcNAc from the cell wall or metabolize environmental GlcNAc. The first step in GlcNAc metabolism is phosphorylation to GlcNAc-6-phosphate. In bacteria, the ROK family kinase N-acetylglucosamine kinase (NagK) performs this activity. Although ROK kinases have been studied extensively, no ternary complex showing the two substrates has yet been observed. Here, we solved the structure of NagK from the human pathogen Plesiomonas shigelloides in complex with GlcNAc and the ATP analog AMP-PNP. Surprisingly, PsNagK showed distinct conformational changes associated with the binding of each substrate. Consistent with this, the enzyme showed a sequential random enzyme mechanism. This indicates that the enzyme acts as a coordinated unit responding to each interaction. Our molecular dynamics modeling of catalytic ion binding confirmed the location of the essential catalytic metal. Additionally, site-directed mutagenesis confirmed the catalytic base and that the metal-coordinating residue is essential. Together, this study provides the most comprehensive insight into the activity of a ROK kinase.

High-level extracellular production and immobilisation of methyl parathion hydrolase from Plesiomonas sp. M6 expressed in Pichia pastoris.

Methyl parathion hydrolase (MPH) hydrolyses methyl parathion efficiently and specifically. Herein, we produced MPH from Plesiomonas sp. M6 using a Pichia pastoris multi-copy expression system. The original signal peptide sequence of the target gene was removed, and a modified coding sequence was synthesised. Multi-copy expression plasmids containing MPH were constructed using pHBM905BDM, and used to generate recombinant strains containing 1, 2, 3 or 4 copies of the MPH gene. The results showed that a higher target gene copy number increased the production of recombinant MPH (MPH-R), as anticipated. The expression level of the recombinant strain containing four copies of the MPH gene was increased to 1.9 U/ml using 500 ml shake flasks, and the specific activity was 15.8 U/mg. High-density fermentation further increased the target protein yield to 18.4 U/ml. Several metal ions were tested as additives, and Ni2+, Co2+ and Mg2+ at a concentration of 1 mM enhanced MPH-R activity by 196%, 201% and 154%, respectively. Enzyme immobilisation was then applied to overcome the difficulties in recovery, recycling and long-term stability associated with the free enzyme. Immobilised MPH-R exhibited significantly enhanced thermal and long-term stability, as well as broad pH adaptability. In the presence of inhibitors and chelating agents such as sodium dodecyl sulphate (SDS), immobilised MPH-R displayed 2-fold higher activity than free MPH-R, demonstrating its potential for industrial application.

Entrapment of methyl parathion hydrolase in cross-linked poly(γ-glutamic acid)/gelatin hydrogel.

Methyl parathion hydrolase (MPH) is an important enzyme in hydrolyzing toxic organophosphorus (OP) compounds. However, MPH is easily deactivated when subjected to extreme environmental conditions and is difficult to recover from the reaction system for reuse, thereby limiting its practical application. To address these shortcomings, we examined the entrapment of MPH in an environment-friendly, biocompatible and biodegradable cross-linked poly(γ-glutamic acid)/gelatin hydrogel. The cross-linked poly(γ-glutamic acid)/gelatin hydrogels were prepared with different gelatin/poly(γ-glutamic acid) mass ratios using water-soluble carbodiimide as the cross-linking agent. The MPH-entrapped cross-linked poly(γ-glutamic acid)/gelatin hydrogel (CPE-MPH) not only possessed improved thermostability, pH stability, and reusability but also exhibited enhanced efficiency in hydrolyzing OP compounds. Furthermore, CPE-MPH possesses high water-absorbing and water-retaining capabilities. We believe that the cross-linked poly(γ-glutamic acid)/gelatin hydrogels are an attractive carrier for the entrapment of diverse enzymes, affording a new approach for enzyme entrapment.

Altered architecture of substrate binding region defines the unique specificity of UDP-GalNAc 4-epimerases.

UDP-hexose 4-epimerases play a pivotal role in lipopolysaccharide (LPS) biosynthesis and Leloir pathway. These epimerases are classified into three groups based on whether they recognize nonacetylated UDP-hexoses (Group 1), both N-acetylated and nonacetylated UDP-hexoses (Group 2) or only N-acetylated UDP-hexoses (Group 3). Although the catalysis has been investigated extensively, yet a definitive model rationalizing the substrate specificity of all the three groups on a common platform is largely lacking. In this work, we present the crystal structure of WbgU, a novel UDP-hexose 4-epimerase that belongs to the Group 3. WbgU is involved in biosynthetic pathway of the unusual glycan 2-deoxy-L-altruronic acid that is found in the LPS of the pathogen Pleisomonas shigelloides. A model that defines its substrate specificity is proposed on the basis of the active site architecture. Representatives from all the three groups are then compared to rationalize their substrate specificity. This investigation reveals that the Group 3 active site architecture is markedly different from the "conserved scaffold" of the Group 1 and the Group 2 epimerases and highlights the interactions potentially responsible for the origin of specificity of the Group 3 epimerases toward N-acetylated hexoses. This study provides a platform for further engineering of the UDP-hexose 4-epimerases, leads to a deeper understanding of the LPS biosynthesis and carbohydrate recognition by proteins. It may also have implications in development of novel antibiotics and more economic synthesis of UDP-GalNAc and downstream products such as carbohydrate based vaccines.

Expression of methyl parathion hydrolase in Pichia pastoris.

In the Pichia pastoris expression system, increasing the copy number of the expression cassette often has the effect of increasing the amount of protein expressed. To improve the expression level of methyl parathion hydrolase (MPH), we constructed two integration vectors with four and eight direct repeats of the expression cassette using an in vitro multimerization approach. After two successive integrations, at least 12 copies of the MPH expression cassette were integrated into the P. pastoris chromosome. Under shake-flask conditions, over 55 mg active MPH/l was secreted into the medium by the multicopy clones. The extracellular enzyme activity was about 10-fold higher for the multicopy clones than for clones containing a single copy of the gene. Further investigations revealed that the multicopy MPH expression cassette could remain stably integrated and functional over five generations. Note that the expression vector pRF constructed in our study can be not only used to construct multiple copies of the expression cassette in vitro, but also integrated into the P. pastoris genome without introducing any antibiotic resistance gene, which is desirable for production of biotherapeutic proteins.

Export of methyl parathion hydrolase to the periplasm by the twin-arginine translocation pathway in Escherichia coli.

The uptake of organophosphates (OPs) is a rate-limiting factor in whole-cell biocatalysis systems. Here, we report the periplasmic secretion of methyl parathion hydrolase (MPH) by employing the twin-arginine translocation (Tat) pathway in Escherichia coli. The twin-arginine signal peptide of trimethylamine N-oxide reductase (TorA) from E. coli was used for exporting MPH to the periplasm of E. coli, alleviating the substrate uptake limitation. A periplasmic expression vector, pUTM18, coding for TorA-MPH was constructed, and the periplasmic secretion and functionality of MPH were demonstrated by cell fractionation, immunoblotting, and enzyme activity assays. The strain expressing periplasmic MPH showed 3-fold higher whole-cell activity than the control strain expressing cytoplasmic MPH. Suspended cultures also exhibited good stability, retaining almost 100% activity over a period of 2 weeks. Owing to their high activity and superior stability, these "live biocatalysts" are ideal for large-scale detoxification of OPs.

The key role of chlorocatechol 1,2-dioxygenase in phytoremoval and degradation of catechol by transgenic Arabidopsis.

Transgenic exploitation of bacterial degradative genes in plants has been considered a favorable strategy for degrading organic pollutants in the environment. The aromatic ring characteristic of these pollutants is mainly responsible for their recalcitrance to degradation. In this study, a Plesiomonas-derived chlorocatechol 1,2-dioxygenase (TfdC) gene (tfdC), capable of cleaving the aromatic ring, was introduced into Arabidopsis (Arabidopsis thaliana). Morphology and growth of transgenic plants are indistinguishable from those of wild-type plants. In contrast, they show significantly enhanced tolerances to catechol. Transgenic plants also exhibit strikingly higher capabilities of removing catechol from their media and high efficiencies of converting catechol to cis,cis-muconic acid. As far-less-than-calculated amounts of cis,cis-muconic acid were accumulated within the transgenic plants, existence of endogenous TfdD- and TfdE-like activities was postulated and, subsequently, putative orthologs of bacterial tfdD and tfdE were detected in Arabidopsis. However, no TfdC activity and no putative orthologs of either tfdC or tfdF were identified. This work indicates that the TfdC activity, conferred by tfdC in transgenic Arabidopsis, is a key requirement for phytoremoval and degradation of catechol, and also suggests that microbial degradative genes may be transgenically exploited in plants for bioremediation of aromatic pollutants in the environment.

Expression, purification, and characterization of a novel methyl parathion hydrolase.

The mpd gene coding for a novel methyl parathion hydrolase (MPH) was previously reported and its putative open reading frame was also identified. To further confirm its coding region, the intact region encoding MPH was obtained by PCR and expressed in Escherichia coli as a hexa-His C-terminal fusion protein. The fusion protein was purified to homogeneity by metal-affinity chromatography. The enzyme activity and zymogram assay showed that the fusion protein was functional in degrading methyl parathion. The amino terminal sequencing of the purified recombinant MPH indicated that a signal peptide of the first 35 amino acids was cleaved from its precursor to form active MPH. A rat polyclonal antiserum was raised against the purified mature fusion protein. The results of Western blot and zymogram demonstrated that mature MPH in native Plesiomonas sp. strain M6 was also processed from its precursor by cleavage of a putative signal peptide at the amino terminus. The production of active MPH in E. coli was greatly improved after the coding region for the signal peptide was deleted. HPLC gel filtration of the purified mature recombinant MPH revealed that the MPH was a monomer.

Effect of inoculum density on susceptibility of Plesiomonas shigelloides to cephalosporins.

OBJECTIVES: Resistance of Plesiomonas shigelloides to cephalosporins at higher cell densities has been reported. We investigated whether these inoculum effects are due to the production of beta-lactamases. METHODS: beta-Lactamase production of five P. shigelloides strains was characterized by activity tests, SDS-PAGE and isoelectric focusing. For all strains, MIC values of different cephalosporins were determined by microdilution methodology using inocula of 1 x 10(5) cfu/mL and 1 x 10(6) cfu/mL. Subsequently, the morphology of cells was determined by light microscopy. For one isolate, kill kinetics of cefpodoxime were determined using batch cultures with the lower and higher inocula. RESULTS: Four of five P. shigelloides strains were shown to be beta-lactamase-positive, producing different amounts of constitutively expressed non-inducible enzymes. Inoculum effects for cephalosporin susceptibility were observed for all strains. Examination of cells revealed a very strong filamentation, with filament sizes ranging from 100 microm up to 2 mm. The kill kinetics with cefpodoxime showed similar killing capacities of the antibiotic at both inoculum sizes. CONCLUSIONS: The reported resistance of P. shigelloides to cephalosporins at higher cell densities is not due to an inoculum-dependent regulation of beta-lactamases, but can be explained by the formation of extensive filaments.

The effect of disinfectants on Plesiomonas shigelloides.

The effects of ten commercially available disinfectants on virulence associated properties of Plesiomonas shigelloides were tested. All the disinfectants tested contained quaternary ammonium salts. The majority of the disinfectants when used at subinhibitory concentrations increased surface hydrophobicity as evaluated by bacterial adherence to xylene and decreased bacterial motility in a concentration dependent manner. Disinfectants did not significantly affect lipase activity. However, more than half of the antimicrobials tested increased the resistance of bacteria to hydrogen peroxide. The disinfectants, in a similar manner to antibiotics at concentrations below MIC, interfered with potential virulence factors of Plesiomonas shigelloides.

New UDP-GlcNAc C4 epimerase involved in the biosynthesis of 2-acetamino-2-deoxy-L-altruronic acid in the O-antigen repeating units of Plesiomonas shigelloides O17.

Plesiomonas shigelloides is a ubiquitous waterborne pathogen responsible for diseases such as diarrhea and bacillary dysentery, commonly afflicting infants and children. This bacterium is endowed with an O-antigen gene cluster consisting of 10 consecutive reading frames. One of these, designated wbgU (orf3), has been overexpressed and biochemically characterized to show that it encodes a uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) C4 epimerase, only the second microbial enzyme characterized to have this activity. Epimerization is an equilibrium reaction resulting in a 70:30 ratio of UDP-GlcNAc to uridine diphosphate-N-acetylgalactosamine (UDP-GalNAc), irrespective of the initial substrate. The K(m) values for UDP-GalNAc and UDP-GlcNAc are 131 microM and 137 microM, respectively. WbgU is also capable of converting nonacetylated derivatives but with much lower efficiency. It contains a tightly bound nicotinamide adenine dinucleotide [NAD(H)] molecule and requires no other cofactors for activity. We propose here that this enzyme catalyzes the first of the three transformations in the biosynthetic pathway of 2-acetamino-2-deoxy-L-altruronic acid, an unusual sugar present in the O-specific side chains of lipopolysaccharide of P. shigelloides O17 and its close relative Escherichia coli Sonnei.

beta-lactamase expression in Plesiomonas shigelloides.

We have examined the production of beta-lactamases by 11 clinical and nine environmental isolates of Plesiomonas shigelloides from Czechoslovakia, the Czech Republic and Cuba. Ten isolates (50%) expressed detectable amounts of a chromosomally encoded, non-inducible beta-lactamase, though all isolates showed a broadly similar resistance profile: low-level resistance to ampicillin and higher-level resistance to carbenicillin. All strains were susceptible to cephalosporins and meropenem. Three clinical isolates expressed a beta-lactamase similar to a class 2c carbenicillinase, with a pI of 5.2 and three expressed an enzyme similar to a class 2d oxacillinase, with a pI of 5.3. The environmental isolates produced a variety of penicillinases, indicating that there is a reservoir of heterogeneous beta-lactamase genes in this species.

[Cloning of a new catechol 1,2-dioxygenase gene (tfd C) from Plesiomonas and its expression in the E. coli].

A new catechol-1,2-dioxygenase gene (tfd C) was cloned from the Plesiomonas using the PCR method. Primers were designed according to the reported sequence of Catechol-1,2-dioxygenase (C120) gene from Alcaligenes eutroplus. The amplified fragment contained a 765 bp open reading frame (ORF), encoding a protein of 255 amino acids. The new tfd C gene shared a high homology with the one cloned from Alcaligenes eutroplus, showing only one base difference at 693 site (C-->A) and consequently one amino acid difference at 228 site (P-->T). The ORF was cloned to the plasmid pBluescriptII KS, which was transferred to E. coli JM109 and a positive clone, pBt2G, was then selected. A significant activity of C120 was detected in the positive clone. When the ORF was cloned to the plasmid pET-30a, which was transferred to E. coli BL21(DE3) plysS, the expected 33 kD protein was detected from a positive clone, pET30A, by SDS-PAGE. The C120 is a key enzyme in degrading aromatic pollutants in the environment. In order to use plants to degrade aromatic pollutants, the gene will be introduced into the turfgrass. To express the gene properly in plants, its translation initiation codon was modified from GTG to ATG. A similar activity of C120 was obtained following the modification.

Hemolytic and elastolytic activities influenced by iron in Plesiomonas shigelloides.

The aim of this study was to determine the presence of hemolytic and elastolytic enzymes in several strains of Plesiomonas shigelloides in relation to the availability of iron in culture media. Hemolytic activity and elastolytic activity were detected in strains of P. shigelloides and were enhanced when the strains were grown in an iron-depleted medium and lost after thermal treatment at 100 degrees C for 10 min. Also, elastolytic activity was inactivated by phenylmethyl sulfonyl fluoride, an inhibitor of serine proteases. Hemolytic activity was detected extracellularly in cell-free supernatants, whereas elastin degradation activity was cell associated. Both activities may be related to the virulence of P. shigelloides.

Isolation and characterization of restriction endonuclease in Plesiomonas shigelloides and Aeromonas species.

Five restriction endonucleases (ENases) and one ENase were found in a screen of 196 strains of Plesiomonas shigelloides and 147 strains of Aeromonas species. Plesiomonas and Aeromonas species are classified as Vibrionaceae, identified as food-poisoning bacteria, are closely genetically related to each other, and their ENases producing abilities have not bee reported. ENases were detected at relatively low frequencies in these species as compared to those in other species, such as Salmonella species and Vibrio parahaemolyticus. All Enases were shown to be isoschizomers of already known ENases. One of the Plesiomonas ENases, designated PshBI, recognizing the sequence 5'-AT/TAAT-3' should be useful, since PshBI ENase is produced at a high yield of 7000 units/g of wet cells. The specificities of other ENases are also described in this paper.

Production of extracellular proteases and amylases by some acidophilic and alkalophilic bacteria.

Twelve bacteria were isolated from two effluent sources of Shaw-Wallace Gelatins, Jabalpur. Six bacteria from dicalcium phosphate plant effluent (pH-5) and six from main drain of the factory (pH-10) were isolated. Two facultatively acidophilic and two facultatively alkalophilic bacteria were selected and tentatively identified as Plesiomonas shigelloides, Aeromonas hydrophilla, Klebsiella pneumoniae and Staphylococcus saprophyticus respectively. Acidic amylases were produced in higher amounts on 4th day of incubation by Plesiomonas shigelloides and on 6th day by Aeromonas hydrophilla. Alkaline amylases were produced in higher amounts on 4th day of incubation by Klebsiella pneumoniae and on 8th day by Staphylococcus saprophyticus in vitro.