Multiparametric determination of genes and their point mutations for identification of beta-lactamases

More than half of all currently used antibiotics belong to the beta-lactam group, but their clinical effectiveness is severely limited by antibiotic resistance of microorganisms that are the causative agents of infectious diseases. Several mechanisms for the resistance of Enterobacteriaceae have been established, but the main one is the enzymatic hydrolysis of the antibiotic by specific enzymes called beta-lactamases. Beta-lactamases represent a large group of genetically and functionally different enzymes of which extended-spectrum beta-lactamases (ESBLs) pose the greatest threat. Due to the plasmid localization of the encoded genes, the distribution of these enzymes among the pathogens increases every year. Among ESBLs the most widespread and clinically relevant are class A ESBLs of TEM, SHV, and CTX-M types. TEM and SHV type ESBLs are derived from penicillinases TEM-1, TEM-2, and SHV-1 and are characterized by several single amino acid substitutions. The extended spectrum of substrate specificity for CTX-M beta-lactamases is also associated with the emergence of single mutations in the coding genes. The present review describes various molecular-biological methods used to identify determinants of antibiotic resistance. Particular attention is given to the method of hybridization analysis on microarrays, which allows simultaneous multiparametric determination of many genes and point mutations in them. A separate chapter deals with the use of hybridization analysis on microarrays for genotyping of the major clinically significant ESBLs. Specificity of mutation detection by means of hybridization analysis with different detection techniques is compared.

Recombinant Production of Horseradish Peroxidase Conjugates with Fab Antibodies in Pichia pastoris for Analytical Applications

Recombinant immunoconjugates of marker enzymes with antigens or antibodies present considerably more advantages than those obtained by conventional methods of chemical synthesis; i.e. they are homogeneous, have a strictly determined stoichiometry, and retain the functional activity of both a marker protein and an antigen/antibody. Based on the pPICZαB shuttle vector, we first managed to obtain a recombinant conjugate of key marker enzyme horseradish peroxidase (HRP) withFabfragments of antibodies against atrazine. The resulting genetic construction allows us to switch to any other antibody sequence, via the simple re-cloning of variable parts and an additional reporter enzyme. Conjugates were successfully produced in thePichia pastorismethylotrophic yeast expression system. The target activity of the conjugates (both enzymatic and antigen-binding) has been demonstrated by ELISA method.

Screening and purification for novel cytochrome b5 from uncultured environmental micro-organisms

AIMS

We describe a sequence-based PCR method suitable for the isolation of a novel soluble heme-binding domain of cytochrome b(5) (cyt b(5)) gene directly from metagenomic DNA is described.

METHODS AND RESULTS

Using the degenerate primer set, a cyt b(5) gene was isolated directly from metagenomic DNA. Based on the sequence-based PCR method, the similar conserved motif of cyt b(5) from Rhodopseudomonas palustris strain makes the novel target gene. The gene encoding cyt b(5) was cloned and expressed in Escherichia coli BL21 (DE3) using pET expression system. The expressed recombinant enzyme was purified by Ni-nitrilotriacetic acid affinity chromatography and characterized.

CONCLUSIONS

Sequence-based strategy is an effective method for application of the novel gene from metagenomic DNA.

SIGNIFICANCE AND IMPACT OF THE STUDY

Investigation of novel genes from metagenome, most of the micro-organism species are largely untapped, could represent an interesting and useful reservoir for biological processes.

Functional expression of Candida antarctica lipase B in the Escherichia coli cytoplasm—a screening system for a frequently used biocatalyst

In this paper, we report for the first time the functional expression of lipase B from the yeast Candida antarctica (CalB) in the Escherichia coli cytoplasm. The enzyme possessing three disulfide bonds was functionally expressed in the strain Origami B. Expression under the control of a lac promoter yielded 2 U mg(-1), whereas expression of a thioredoxin-CalB fusion protein yielded 17 U mg(-1). The native enzyme was most efficiently expressed under control of the cspA promoter (11 U mg(-1)). Coexpression of different chaperones led to a strong increase in active protein formation (up to 61 U mg(-1)). A codon-optimized synthetic variant of calb did not show significant effects on functional protein yield. Functional CalB expression was not only achieved in shake flasks but also in microtiter plate scale. Therefore, this CalB expression system is suitable for high-throughput applications, including the screening of large gene libraries as those derived from directed evolution experiments.

Cloning, recombinant expression and biochemical characterisation of novel esterases from Bacillus sp. associated with the marine sponge Aplysina aerophoba

Two novel esterases (EstB1 and EstB2) were isolated from a genomic library of Bacillus sp. associated with the marine sponge Aplysina aerophoba. EstB1 shows low identity (26-44%) with the published hydrolases of the genus Bacillus, whereas EstB2 shows high identity (73-74%) with the carboxylesterases from B. cereus and B. anthracis. Both esterases were efficiently expressed in Escherichia coli under the control of T7 promoter using the vector pET-22b(+). Recombinant EstB1 was purified in a single step to electrophoretic homogeneity by IMAC. A method for the refolding of inclusion bodies formed by the recombinant EstB2 was established to obtain active enzyme. Substrate specificity of the two enzymes towards p-nitrophenyl and methyl esters and the respective kinetic parameters K(m) and V(max) were determined. The temperature optima of EstB1 and EstB2 were determined to be in the range of 30-50 degrees C and 20-35 degrees C, respectively. The pH optima were found to be in the range of 6.5-7.5 and 6.5-8.0, respectively. Both enzymes showed the highest stability in up to 50% (v/v) DMSO followed by methanol, ethanol and 2-propanol. The influence of high NaCl and KCl concentrations was tested. The inhibition effect of 10-50 mM Zn(2+) and 50 mM Mg(2+) and Ca(2+) ions was observed for both esterases. One to five millimolar PMSF deactivated the enzymes, whereas beta-mercaptoethanol, DTT and EDTA had no effect on the enzymes activity.

Cloning, expression and characterisation of CYP102A2, a self-sufficient P450 monooxygenase from Bacillus subtilis

The gene encoding CYP102A2, a novel P450 monooxygenase from Bacillus subtilis, was cloned and expressed in Escherichia coli. The recombinant enzyme formed was purified by immobilised metal chelate affinity chromatography (IMAC) and characterised. CYP102A2 is a 119-kDa self-sufficient monooxygenase, consisting of an FMN/FAD-containing reductase domain and a heme domain. The deduced amino acid sequence of CYP102A2 exhibits a high level of identity with the amino acid sequences of CYP102A1 from B. megaterium (59%) and CYP102A3 from B. subtilis (60%). In reduced, CO-bound form, the enzyme shows a typical Soret band at 449 nm. It catalyses the oxidation of even- and odd-chain saturated and unsaturated fatty acids. In all reactions investigated, the products were the respective omega-3, omega-2 and omega-1 hydroxylated fatty acids. Activity was highest towards oleic acid (K(M)=17.36+/-1.4 microM, k(cat)=2,244+/-72 min(-1)) and linoleic acid (K(M)=12.25+/-1.8 microM, k(cat)=1,950+/-84 min(-1)). Comparison of a CYP102A2 homology model with the CYP102A1 crystal structure revealed significant differences in the substrate access channels, which might explain the differences in the catalytic properties of these two enzymes.

CYP175A1 from Thermus thermophilus HB27, the first �-carotene hydroxylase of the P450 superfamily

The biological function of thermostable P450 monooxygenase CYP175A1 from Thermus thermophilus HB27 was studied by functional complementation in Escherichia coli. The gene product of CYP175A1 added hydroxyl groups to both beta rings of beta-carotene to form zeaxanthin (beta,beta-carotene-3,3'-diol) in E. coli, which produces beta-carotene due to the Erwinia uredovora carotenoid biosynthesis genes. In addition, spectroscopic methods revealed that E. coli carrying CYP175A1 and the cDNA of the Haematococcus pluvialis carotene ketolase was able to synthesise hydroxyechinenone. The predicted amino acid sequence of the enzyme from T. thermophilus does not show substantial similarity with other known beta-carotene hydroxylases, but 41% with the cytochrome P450 monooxygenase from Bacillus megaterium (CYP102A1, P450 BM3). It is concluded that CYP175 A1 represents a new type of beta-carotene hydroxylase of the P450 superfamily.

DNA isolation from soil samples for cloning in different hosts

Many protocols to extract DNA directly from soil samples have been developed in recent years. We employed two extraction methods which differed in the method of lysis and compared these methods with respect to yield, purity and degree of shearing. The main focus was on the specific isolation of DNA from different microorganisms, especially DNA from actinomycetes, as these cells are very difficult to lyse, in contrast to non-actinomycetes. Thus, we used both methods to isolate DNA from Pseudomonas, Arthrobacter and Rhodococcus and from soil spiked with the respective microorganisms. Both methods rendered high DNA yields with a low degree of shearing, but differed in the type of cells that were lysed. By one protocol (utilizing enzymatic lysis) only DNA from the Gram-negative Pseudomonas strain could be obtained whereas, by the other protocol (utilizing mechanical lysis), all microorganisms that were used could be lysed and DNA extracted from them. Using a combination of both protocols, DNA from those organisms could be obtained selectively. Furthermore, one of the protocols was modified, resulting in higher DNA yield and purity.

Microbial P450 enzymes in biotechnology

Oxidations are key reactions in chemical syntheses. Biooxidations using fermentation processes have already conquered some niches in industrial oxidation processes since they allow the introduction of oxygen into non-activated carbon atoms in a sterically and optically selective manner that is difficult or impossible to achieve by synthetic organic chemistry. Biooxidation using isolated enzymes is limited to oxidases and dehydrogenases. Surprisingly, cytochrome P450 monooxygenases have scarcely been studied for use in biooxidations, although they are one of the largest known superfamilies of enzyme proteins. Their gene sequences have been identified in various organisms such as humans, bacteria, algae, fungi, and plants. The reactions catalyzed by P450s are quite diverse and range from biosynthetic pathways (e.g. those of animal hormones and secondary plant metabolites) to the activation or biodegradation of hydrophobic xenobiotic compounds (e.g. those of various drugs in the liver of higher animals). From a practical point of view, the great potential of P450s is limited by their functional complexity, low activity, and limited stability. In addition, P450-catalyzed reactions require a constant supply of NAD(P)H which makes continuous cell-free processes very expensive. Quite recently, several groups have started to investigate cost-efficient ways that could allow the continuous supply of electrons to the heme iron. These include, for example, the use of electron mediators, direct electron supply from electrodes, and enzymatic approaches. In addition, methods of protein design and directed evolution have been applied in an attempt to enhance the activity of the enzymes and improve their selectivity. The promising application of bacterial P450s as catalyzing agents in biocatalytic reactions and recent progress made in this field are both covered in this review.

A long insertion reverts the functional effect of a substitution in acetylcholinesterase

Proteins are thought to undertake single substitutions, deletions and insertions to explore the fitness landscape. Nevertheless, the ways in which these different kind of mutations act together to alter a protein phenotype remain poorly described. We introduced incrementally the single substitution W290A and a 26 amino acid long insertion at the 297 location in the Nippostrongylus brasiliensis acetylcholinesterase B sequence and analysed in vitro the induced changes in the hydrolysis rate of three hemi-substrates: pirimicarb, paraoxon methyl and omethoate. The substitution decreased the hydrolysis rate of the three hemi-substrates. The insertion did not influence this kinetic alteration induced by the substitution for the former hemi-substrate, but reverted it for the two others. These results show that two different kinds of mutations can interact together to influence the direction of a protein's adaptative walk on the fitness landscape.

Identification of factors impeding the production of a single-chain antibody fragment in Escherichia coliby comparing in vivo and in vitro expression

The atrazine-specific single-chain variable antibody fragments (scFv) K411B was produced by expression in either the cytoplasm or the periplasm of Escherichia coli BL21(DE3). For periplasmic production, the pelB leader was N-terminally fused to scFv, whereas the unfused variant resulted in cytoplasmic expression. The extent of protein accumulation differed significantly. Expression of scFv with leader was 2.3 times higher than that of the protein without leader. This was further investigated by generating the respective translation profiles using coupled in vitro transcription/translation assays, the results of which were in agreement. This comparative approach was also applied to functionality: Periplasmic expression and in vitro expression resulted in only 10% correctly folded scFv, indicating that the oxidizing environment of the periplasm did not increase proper folding. Thus, the data obtained in vitro confirmed the findings observed in vivo and suggested that the discrepancy in expression levels was due to different translation efficiencies. However, the in vivo production of scFv with enhanced green fluorescent protein (EGFP) fused C-terminally (scFv-EGFP) was only successful in the cytoplasm, although in vitro the expression with and without the leader rendered the same production profile as for scFv. This indicated that neither the translation efficiency nor the solubility but other factors impeded periplasmic expression of the fusion protein.

Bioavailable nitrate detection in water by an immobilized luminescent cyanobacterial reporter strain

Cyanobacteria are a major group of photosynthetic bacteria that can accumulate in surface water as so-called "blooms" in response to environmental factors such as temperature, light and certain nutrients such as N, P, and Fe. Some species of cyanobacteria produce toxins, causing a considerable danger for human and livestock health. As a consequence, monitoring of bloom formation and toxin production of drinking water supplies has become a major concern. To enable prediction and monitoring of cyanobacterial blooms, tools to detect nutrient bioavailability in water would be advantageous. A whole-cell biosensor was developed for monitoring nitrate (NO(3-)) bioavailability in aquatic ecosystems using the recombinant bioluminescent cyanobacterial strain Synechocystis PCC 6803 harboring an insertion of a luxAB-kmr fusion with nblA1 in its chromosomal DNA, leading to PnblA::luxAB-kmr. This reporter strain was designated N1LuxKm. Cells were immobilized in microtiter plates and showed a dose-dependent response to nitrate deprivation. The resultant CyanoSensor could detect nitrate in the 4-100 micro M concentration range after a sample incubation time of 10 h under continuous illumination (50 micro E m(-2) s(-1)). The optimal temperature for sensor operation was 29 degrees C and the immobilized biosensor could be stored at 4 degrees C in dark for about 1 month without significant loss of sensitivity.

A disposable acetylcholinesterase-based electrode biosensor to detect anatoxin-a(s) in water

Anatoxin-a(s) is a hazardous toxin released by cyanobacteria during bacterial blooms. A simple and fast method to detect this hazardous compound using a biosensor based on the electrochemical detection of the activity of acetylcholinesterase was developed. Among several acetylcholinesterases, electric eel enzyme was found to be the most sensitive to anatoxin-a(s) and was thus used to build disposable amperometric sensors. The system displayed a detection limit of 1 microg/L anatoxin-a(s). No unspecific effect was noticed with real water samples but spiked toxin was accurately detected. Oxime reactivation was used to discriminate between the toxin and potential insecticides present in the sample.

Construction and characterization of bioelectrocatalytic sensors based on cytochromes P450

Semisynthetic flavocytochromes RfP450 1A2, RfP450 2B4 and RfP450scc--molecular conjugates of protein with riboflavin--could be reduced on rhodium-graphite screen-printed thick film electrodes as was confirmed by cyclic voltammograms of immobilized enzymes. Amperometric enzyme electrodes for direct measurement of organic pollutants were developed. The efficiency of controlled potential electrolysis for the reduction of flavocytochromes P450 was comparable with traditional reduction by pyridine nucleotides. The rate constants for substrates conversion obtained by electrochemical methods were close to those obtained using NAD(P)H as an electron source.

Monitoring of phosphorus bioavailability in water by an immobilized luminescent cyanobacterial reporter strain

Massive growth of cyanobacteria, known as "algal blooms", has become a major concern for water monitoring. It has been observed that environmental factors like temperature, light, and certain patterns of availability of nutrients such as P, N, Fe influence cyanobacterial proliferation and toxin production. In order to monitor nutrients in aquatic ecosystems, an assay for monitoring phosphorus bioavailability to cyanobacteria was developed. The test consists of an immobilized luminescent reporter strain of Synechococcus PCC 7942, designated APL. The reporter strain harbours the gene coding the reporter protein luciferase from Vibrio harveyi under control of the inducible alkaline phosphatase promoter from Synechococcus PCC 7942, and can be induced under phosphorus limitation. The resultant CyanoSensor detects PO(3-)(4)-P in a concentration range of 0.3-8 microM after a sample incubation time of 8 h under continuous illumination (50 microE m(-2) s(-1)). The sensor also responded to a variety of organic phosphorus sources and was storable for 3 weeks at 4 degrees C. It could be demonstrated that the CyanoSensor for bioavailability monitoring is an improvement to conventional phosphorus detection methods.

Engineering cytochrome P450 BM-3 for oxidation of polycyclic aromatic hydrocarbons

Cytochrome P450 BM-3, a self-sufficient P450 enzyme from Bacillus megaterium that catalyzes the subterminal hydroxylation of long-chain fatty acids, has been engineered into a catalyst for the oxidation of polycyclic aromatic hydrocarbons. The activities of a triplet mutant (A74G/F87V/L188Q) towards naphthalene, fluorene, acenaphthene, acenaphthylene, and 9-methylanthracene were 160, 53, 109, 287, and 22/min, respectively. Compared with the activities of the wild type towards these polycyclic aromatic hydrocarbons, those of the mutant were improved by up to 4 orders of magnitude. The coupling efficiencies of the mutant towards naphthalene, fluorene, acenaphthene, acenaphthylene, and 9-methylanthracene were 11, 26, 5.4, 15, and 3.2%, respectively, which were also improved several to hundreds fold. The high activities of the mutant towards polycyclic aromatic hydrocarbons indicate the potential of engineering P450 BM-3 for the biodegradation of these compounds in the environment.