The sclerostin-neutralizing antibody AbD09097 recognizes an epitope adjacent to sclerostin's binding site for the Wnt co-receptor LRP6.

The glycoprotein sclerostin has been identified as a negative regulator of bone growth. It exerts its function by interacting with the Wnt co-receptor LRP5/6, blocks the binding of Wnt factors and thereby inhibits Wnt signalling. Neutralizing anti-sclerostin antibodies are able to restore Wnt activity and enhance bone growth thereby presenting a new osteoanabolic therapy approach for diseases such as osteoporosis. We have generated various Fab antibodies against human and murine sclerostin using a phage display set-up. Biochemical analyses have identified one Fab developed against murine sclerostin, AbD09097 that efficiently neutralizes sclerostin's Wnt inhibitory activity. In vitro interaction analysis using sclerostin variants revealed that this neutralizing Fab binds to sclerostin's flexible second loop, which has been shown to harbour the LRP5/6 binding motif. Affinity maturation was then applied to AbD09097, providing a set of improved neutralizing Fab antibodies which particularly bind human sclerostin with enhanced affinity. Determining the crystal structure of AbD09097 provides first insights into how this antibody might recognize and neutralize sclerostin. Together with the structure-function relationship derived from affinity maturation these new data will foster the rational design of new and highly efficient anti-sclerostin antibodies for the therapy of bone loss diseases such as osteoporosis.

Application and Modification of Flavin-Dependent Halogenases.

The application of flavin-dependent halogenases is hampered by their lack of stability under reaction conditions. However, first attempts to improve halogenase stability by error-prone PCR have resulted in mutants with higher temperature stability. To facilitate the screening for mutants with higher activity, a high-throughput assay was developed. Formation of cross-linked enzyme aggregates (CLEAs) of halogenases has increased halogenase lifetime by a factor of about 10, and CLEAs have been used to produce halogenated tryptophan in gram scale. Analyses of the substrate specificity of tryptophan halogenases have shown that they accept a much broader range of substrates than previously thought. The introduction of tryptophan halogenase genes into bacteria and plants led to the in vivo formation of peptides containing halogenated tryptophan or novel tryptophan-derived alkaloids, respectively. The halogen atoms in these compounds could be chemically exchanged against other substituents by cross-coupling reactions leading to novel compounds. Site-directed mutageneses have been used to modify the substrate specificity and the regioselectivity of flavin-dependent tryptophan halogenases. Since many flavin-dependent halogenases only accept protein-bound substrates, enzymatic and chemoenzymatic syntheses for protein-tethered substrates were developed, and the synthesized substrates were used in enzymatic halogenation reactions.

Selecting highly structure-specific antibodies using structured synthetic mimics of the cystine knot protein sclerostin.

Antibodies directed against specific regions of a protein have traditionally been raised against full proteins, protein domains or simple unstructured peptides, containing contiguous stretches of primary sequence. We have used a new approach of selecting antibodies against restrained peptides mimicking defined epitopes of the bone modulator protein sclerostin, which has been identified as a negative regulator of the Wnt pathway. For a fast exploration of activity defining epitopes, we produced a set of synthetic peptide constructs mimicking native sclerostin, in which intervening loops from the cystine-knot protein sclerostin were truncated and whose sequences were optimized for fast and productive refolding. We found that the second loop within the cystine knot could be replaced by unnatural sequences, both speeding up folding, and increasing yield. Subsequently, we used these constructs to pan the HuCAL phage display library for antibodies capable of binding the native protein, thereby restricting recognition to the desired epitope regions. It is shown that the antibodies that were obtained recognize a complex epitope in the protein that cannot be mimicked with linear peptides. Antibodies selected against peptides show similar recognition specificity and potency as compared with antibodies obtained from full-length recombinant protein.

[Tryptophan 7-halogenase from Pseudomonas aureofaciens ACN strain: gene cloning and sequencing and the enzyme expression]. / Klonirovanie, sekvenirovanie i ékspressiia gena triptofan-7-galogenazy iz shtamma Pseudomonas aureofaciens ACN.

The gene of tryptophan 7-halogenase was isolated from the Pseudomonas aureofaciens ACN strain producing pyrrolnitrin, a chlorocontaining antibiotic, and sequenced. A high homology degree (over 95%) was established for the genes and the corresponding halogenases from P. aureofaciens ACN and P. fluorescens BL915. The tryptophan 7-halogenase gene was amplified by PCR, and the corresponding enzyme was expressed in Escherichia coli cells using the pBSII SK+ vector.

Cloning and sequencing of the gene of tryptophan-7-halogenase from Pseudomonas fluorescens strain CHA0.

The gene of tryptophan-7-halogenase from the Pseudomonas fluorescens strain CHA0, a producer of the halogenated antibiotic pyrrolnitrin, has been cloned and sequenced.

Halogenating enzymes in the biosynthesis of antibiotics.

Using blot hybridization, it has been shown that microorganisms producing halogen-containing antibiotics--Pseudomonas pyrrocinia, P. aureofaciens ACN, P. aureofaciens Pa1, P. fluorescens CHA0, Actinoplanes sp., Kitasatasporia sp., Sacharothrix aerocolonigenes, Actinomadura melliaura, and Streptomyces albogriseolus--contain the genes of the halogenating enzymes related to tryptophan-7-halogenase and monodechloroaminopyrrolnitrin halogenase from P. fluorescens BL 915.

Evaluation of peracid formation as the basis for resistance to infection in plants transformed with haloperoxidase.

Nonheme haloperoxidase (HPO-P) isolated from Pseudomonas pyrrocinia catalyzed the peroxidation of alkyl acids to peracids. Among acids tested as substrates, acetic acid was most readily peroxidized. The reaction product peracetate possessed potent antifungal activity: 50% death (LD(50)) of Aspergillus flavus occurred at 25 microM peracetate. Viability of A. flavus was inhibited by up to 80% by leaf extracts of tobacco plants transformed with the HPO-P gene from P. pyrrocinia compared to viability of fungi exposed to extracts from controls. To elucidate if peracid formation by HPO-P was the basis for antifungal activity in transgenic leaf tissues, lethalities of hydrogen peroxide-acetate-HPO-P combinations against A. flavus were examined in vitro. LD(50) of A. flavus exposed to the combinations occurred at 30 mM acetate when concentrations of hydrogen peroxide and HPO-P were held constant. This value was identical to the LD(50) produced by 30 mM acetate in the absence of hydrogen peroxide-HPO-P and therefore did not account for enhanced antifungal activity in transgenic plants. For clarification, kinetics of the enzymic reaction were examined. According to the concentration of acetate needed for enzyme saturation (K(m) = 250 mM), acetate was lethal prior to its oxidation to peracetate. Results indicate that peracid generation by HPO-P was not the basis for enhanced antifungal activity in transgenic plants expressing the HPO-P gene.

Isolation and characterization of a thermostable intracellular enzyme with peroxidase activity from Bacillus sphaericus.

During a screening for bacteria producing enzymes with peroxidase activity, a Bacillus sphaericus strain was isolated. This strain was found to contain an intracellular enzyme with peroxidase activity. The native enzyme had a molecular mass of above 300 kDa and precipitated at a salt concentration higher than 0.1 M. Proteolytic digestion with trypsin reduced the molecular mass of the active enzyme to 13 kDa (dimer) or 26 kDa (tetramer) and increased its solubility, allowing purification to homogeneity. Spectroscopic investigations showed the enzyme to be a hemoenzyme containing heme c as the covalently bound prosthetic group. The enzyme was stable up to 90 degrees C and at alkaline conditions up to pH 11, with a pH optimum at pH 8.5. It could be visualized by activity staining after SDS-PAGE and showed activity with a number of typical substrates for peroxidases, e.g., 2,2'-azino-bis(3-ethylbenz-thiazoline-6-sulfonic acid) diammonium salt, guaiacol and 2,4-dichlorophenol; however the enzyme had no catalase and cytochrome c peroxidase activity.

[Oxidation of indole and its derivatives by heme-independent chloroperoxidases]. / Okislenie indola i ego proizvodnykh gem-nezavisimymi khlorperoksidazami.

Indole, indolylacetic acid, and tryptophan were oxidized by cloroperoxidases isolated from strains of Streptomyces lividans and Pseudomonas pyrrocinia. Indigo (indoxyl), isatin, and anthranilic acid (intermediate products of oxidative degradation of indole and indole derivatives) were extracted from the reaction medium.

Microbial biosynthesis of halometabolites.

Halometabolites are compounds that are commonly found in nature and they are produced by many different organisms. Whereas bromometabolites can mainly be found in the marine environment, chlorometabolites are predominately produced by terrestrial organisms; iodo- and fluorocompounds are only produced infrequently. The halogen atoms are incorporated into organic compounds by enzyme-catalyzed reactions with halide ions as the halogen source. For over 40 years haloperoxidases were thought to be responsible for the incorporation of halogen atoms into organic molecules. However, haloperoxidases lack substrate specificity and regioselectivity, and the connection of haloperoxidases with the in vivo formation of halometabolites has never been demonstrated. Recently, molecular genetic investigations showed that, at least in bacteria, a different class of halogenases is involved in halometabolite formation. These halogenases were found to require FADH2, which can be produced from FAD and NADH by unspecific flavin reductases. In addition to FADH2, oxygen and halide ions (chloride and bromide) are necessary for the halogenation reaction. The FADH2-dependent halogenases show substrate specificity and regioselectivity, and their genes have been detected in many halometabolite-producing bacteria, suggesting that this type of halogenating enzymes constitutes the major source for halometabolite formation in bacteria and possibly also in other organisms.

Antifungal and peroxidative activities of nonheme chloroperoxidase in relation to transgenic plant protection.

Nonheme chloroperoxidase (CPO-P) of Pseudomonas pyrrocinia catalyzes the oxidation of alkyl acids to peracids by hydrogen peroxide. Alkyl peracids possess potent antifungal activity as found with peracetate: 50% killing (LD(50)) of Aspergillus flavus occurred at 25 microM compared to 3.0 mM for the hydrogen peroxide substrate. To evaluate whether CPO-P could protect plants from fungal infection, tobacco was transformed with a gene for CPO-P from P. pyrrocinia and assayed for antifungal activity. Leaf extracts from transformed plants inhibited growth of A. flavus by up to 100%, and levels of inhibition were quantitatively correlated to the amounts of CPO-P activity expressed in leaves. To clarify if the peroxidative activity of CPO-P could be the basis for the increased resistance, the antifungal activity of the purified enzyme was investigated. The LD(50) of hydrogen peroxide combined with CPO-P occurred at 2.0 mM against A. flavus. Because this value was too small to account for the enhanced antifungal activity of transgenic plants, the kinetics of the enzyme reaction was examined and it was found that the concentration of hydrogen peroxide needed for enzyme saturation (K(m) = 5.9 mM) was already lethal. Thus, the peroxidative activity of CPO-P is not the basis for antifungal activity or enhanced resistance in transgenic plants expressing the gene.

Enzymatic halogenation catalyzed via a catalytic triad and by oxidoreductases.

During the search for haloperoxidases in bacteria we detected a type of enzymes that catalyzed the peroxide-dependent halogenation of organic substrates. However, in contrast to already known haloperoxidases, these enzymes do not contain a prosthetic group or metal ions nor any other cofactor. Biochemical and molecular genetic studies revealed that they contain a catalytic triad consisting of a serine, a histidine, and an aspartate. The reaction they catalyze is actually the perhydrolysis of an acetic acid serine ester leading to the formation of peracetic acid. As a strong oxidizing agent the enzymatically formed peracetic acid can oxidize halide ions, resulting in the formation of hypohalous acid which then acts as the actual halogenating agent. Since hypohalous acid is also formed by the heme- and vanadium-containing haloperoxidases, enzymatic halogenation catalyzed by haloperoxidases and perhydrolases in general lacks substrate specificity and regioselectivity. However, detailed studies on the biosynthesis of several halometabolites led to the detection of a novel type of halogenases. These enzymes consist of a two-component system and require NADH and FAD for activity. Whereas the gene for one of the components is part of the biosynthetic cluster of the halometabolite, the second component is an enzyme which is also present in bacteria from which no halometabolites have ever been isolated, like Escherichia coli. In contrast to haloperoxidases and perhydrolases the newly detected NADH/FAD-dependent halogenases are substrate-specific and regioselective and might provide ideal tools for specific halogenation reactions.

Conservation of the pyrrolnitrin biosynthetic gene cluster among six pyrrolnitrin-producing strains.

The prnABCD gene cluster from Pseudomonas fluorescens encodes the biosynthetic pathway for pyrrolnitrin, a secondary metabolite derived from tryptophan which has strong anti-fungal activity. We used the prn genes from P. fluorescens strain BL915 as a probe to clone and sequence homologous genes from three other Pseudomonas strains, Burkholderia cepacia and Myxococcus fulvus. With the exception of the prnA gene from M. fulvus59% similar among the strains, indicating that the biochemical pathway for pyrrolnitrin biosynthesis is highly conserved. The prnA gene from M. fulvus is about 45% similar to prnA from the other strains and contains regions which are highly conserved among all six strains.

Specific enzymatic chlorination of tryptophan and tryptophan derivatives.

In the search for an alternative to chemical halogenation reactions using the free halogens, a novel type of halogenating enzymes was detected. In contrast to haloperoxidases, these NADH-dependent halogenases are specific. Tryptophan halogenase which catalyses the regioselective chlorination of tryptophan to 7-chlorotryptophan can also chlorinate tryptamine, tryptophol, indole-3-acetonitrile, and 3-methylindole. However, indole-3-acetonitrile is not chlorinated in the 7-position, but in positions two and three of the indole ring. Chlorination in the 3-position is obviously stereospecific. In addition to tryptophan and indole derivatives, aminophenylpyrrole is also accepted as a substrate for regioselective chlorination. Since the new NADH-dependent halogenases have a fairly broad substrate specificity and catalyse regioselective chlorination reactions they could be a good alternative to chemical halogenation.

Regulation of activity of chloroperoxidase from Serratia marcescens.

The influence of various factors on the activity of chloroperoxidase from Serratia marcescens was investigated. The enzyme is active only in acetate-containing buffers within the pH range 4.2-5.8. F-, Cu2+, [Fe(CN)6]4+, and [Fe(CN)6]3+ inhibit the enzyme. The chloroperoxidase is thermostable and resistant to the effect of lower alcohols.

Structural investigation of the cofactor-free chloroperoxidases.

The structures of cofactor-free haloperoxidases from Streptomyces aureofaciens, Streptomyces lividans, and Pseudomonas fluorescens have been determined at resolutions between 1.9 A and 1.5 A. The structures of two enzymes complexed with benzoate or propionate identify the binding site for the organic acids which are required for the haloperoxidase activity. Based on these complexes and on the structure of an inactive variant, a reaction mechanism is proposed for the halogenation reaction with peroxoacid and hypohalous acid as reaction intermediates. Comparison of the structures suggests that a specific halide binding site is absent in the enzymes but that hydrophobic organic compounds may fit into the active site pocket for halogenation at preferential sites.

Functions encoded by pyrrolnitrin biosynthetic genes from Pseudomonas fluorescens.

Pyrrolnitrin is a secondary metabolite derived from tryptophan and has strong antifungal activity. Recently we described four genes, prnABCD, from Pseudomonas fluorescens that encode the biosynthesis of pyrrolnitrin. In the work presented here, we describe the function of each prn gene product. The four genes encode proteins identical in size and serology to proteins present in wild-type Pseudomonas fluorescens, but absent from a mutant from which the entire prn gene region had been deleted. The prnA gene product catalyzes the chlorination of L-tryptophan to form 7-chloro-L-tryptophan. The prnB gene product catalyzes a ring rearrangement and decarboxylation to convert 7-chloro-L-tryptophan to monodechloroaminopyrrolnitrin. The prnC gene product chlorinates monodechloroaminopyrrolnitrin at the 3 position to form aminopyrrolnitrin. The prnD gene product catalyzes the oxidation of the amino group of aminopyrrolnitrin to a nitro group to form pyrrolnitrin. The organization of the prn genes in the operon is identical to the order of the reactions in the biosynthetic pathway.

Four genes from Pseudomonas fluorescens that encode the biosynthesis of pyrrolnitrin.

Pyrrolnitrin is a secondary metabolite of Pseudomonas and Burkholderia sp. strains with strong antifungal activity. Production of pyrrolnitrin has been correlated with the ability of some bacteria to control plant diseases caused by fungal pathogens, including the damping-off pathogen Rhizoctonia solani. Pseudomonas fluorescens BL915 has been reported to produce pyrrolnitrin and to be an effective biocontrol agent for this pathogen. We have isolated a 32-kb genomic DNA fragment from this strain that contains genes involved in the biosynthesis of pyrrolnitrin. Marker-exchange mutagenesis of this DNA with Tn5 revealed the presence of a 6.2-kb region that contains genes required for the synthesis of pyrrolnitrin. The nucleotide sequence of the 6.2-kb region was determined and found to contain a cluster of four genes that are required for the production of pyrrolnitrin. Deletion mutations in any of the four genes resulted in a pyrrolnitrin-nonproducing phenotype. The putative coding sequences of the four individual genes were cloned by PCR and fused to the tac promoter from Escherichia coli. In each case, the appropriate tac promoter-pyrrolnitrin gene fusion was shown to complement the pyrrolnitrin-negative phenotype of the corresponding deletion mutant. Transfer of the four gene cluster to E. coli resulted in the production of pyrrolnitrin by this organism, thereby demonstrating that the four genes are sufficient for the production of this metabolite and represent all of the genes required to encode the pathway for pyrrolnitrin biosynthesis.