Alicja B. Veselá

Heterologous expression, purification and characterization of nitrilase from Aspergillus niger K10

BackgroundNitrilases attract increasing attention due to their utility in the mild hydrolysis of nitriles. According to activity and gene screening, filamentous fungi are a rich source of nitrilases distinct in evolution from their widely examined bacterial counterparts. However, fungal nitrilases have been less explored than the bacterial ones. Nitrilases are typically heterogeneous in their quaternary structures, forming short spirals and extended filaments, these features making their structural studies difficult.ResultsA nitrilase gene was amplified by PCR from the cDNA library of Aspergillus niger K10. The PCR product was ligated into expression vectors pET-30(+) and pRSET B to construct plasmids pOK101 and pOK102, respectively. The recombinant nitrilase (Nit-ANigRec) expressed in Escherichia coli BL21-Gold(DE3)(pOK101/pTf16) was purified with an about 2-fold increase in specific activity and 35% yield. The apparent subunit size was 42.7 kDa, which is approx. 4 kDa higher than that of the enzyme isolated from the native organism (Nit-ANigWT), indicating post-translational cleavage in the enzymes native environment. Mass spectrometry analysis showed that a C-terminal peptide (Val327 - Asn356) was present in Nit-ANigRec but missing in Nit-ANigWT and Asp298-Val313 peptide was shortened to Asp298-Arg310 in Nit-ANigWT. The latter enzyme was thus truncated by 46 amino acids. Enzymes Nit-ANigRec and Nit-ANigWT differed in substrate specificity, acid/amide ratio, reaction optima and stability. Refolded recombinant enzyme stored for one month at 4°C was fractionated by gel filtration, and fractions were examined by electron microscopy. The late fractions were further analyzed by analytical centrifugation and dynamic light scattering, and shown to consist of a rather homogeneous protein species composed of 12-16 subunits. This hypothesis was consistent with electron microscopy and our modelling of the multimeric nitrilase, which supports an arrangement of dimers into helical segments as a plausible structural solution.ConclusionsThe nitrilase from Aspergillus niger K10 is highly homologous (≥86%) with proteins deduced from gene sequencing in Aspergillus and Penicillium genera. As the first of these proteins, it was shown to exhibit nitrilase activity towards organic nitriles. The comparison of the Nit-ANigRec and Nit-ANigWT suggested that the catalytic properties of nitrilases may be changed due to missing posttranslational cleavage of the former enzyme. Nit-ANigRec exhibits a lower tendency to form filaments and, moreover, the sample homogeneity can be further improved by in vitro protein refolding. The homogeneous protein species consisting of short spirals is expected to be more suitable for structural studies.

Biotransformation of benzonitrile herbicides via the nitrile hydratase–amidase pathway in rhodococci

The aim of this work was to determine the ability of rhodococci to transform 3,5-dichloro-4-hydroxybenzonitrile (chloroxynil), 3,5-dibromo-4-hydroxybenzonitrile (bromoxynil), 3,5-diiodo-4-hydroxybenzonitrile (ioxynil) and 2,6-dichlorobenzonitrile (dichlobenil); to identify the products and determine their acute toxicities. Rhodococcus erythropolis A4 and Rhodococcus rhodochrous PA-34 converted benzonitrile herbicides into amides, but only the former strain was able to hydrolyze 2,6-dichlorobenzamide into 2,6-dichlorobenzoic acid, and produced also more of the carboxylic acids from the other herbicides compared to strain PA-34. Transformation of nitriles into amides decreased acute toxicities for chloroxynil and dichlobenil, but increased them for bromoxynil and ioxynil. The amides inhibited root growth in Lactuca sativa less than the nitriles but more than the acids. The conversion of the nitrile group may be the first step in the mineralization of benzonitrile herbicides but cannot be itself considered to be a detoxification.

A Comparative Study of Nitrilases Identified by Genome Mining

Escherichia coli strains expressing different nitrilases transformed nitriles or KCN. Six nitrilases (from Aspergillus niger (2), A. oryzae, Neurospora crassa, Arthroderma benhamiae, and Nectria haematococca) were arylacetonitrilases, two enzymes (from A. niger and Penicillium chrysogenum) were cyanide hydratases and the others (from P. chrysogenum, P. marneffei, Gibberella moniliformis, Meyerozyma guilliermondi, Rhodococcus rhodochrous, and R. ruber) preferred (hetero)aromatic nitriles as substrates. Promising nitrilases for the transformation of industrially important substrates were found: the nitrilase from R. ruber for 3-cyanopyridine, 4-cyanopyridine and bromoxynil, the nitrilases from N. crassa and A. niger for (R,S)-mandelonitrile, and the cyanide hydratase from A. niger for KCN and 2-cyanopyridine.

Heterologous expression, purification and characterization of arylacetonitrilases from Nectria haematococca and Arthroderma benhamiae

Abstract Two novel arylacetonitrilases were purified from Escherichia coli BL21-Gold (DE3) expressing nit genes from Nectria haematococca mpVI 77-13-4 (EEU45207; NitNh) and Arthroderma benhamiae CBS 112371 (EFE30690; NitAb). The nitrilases formed holoenzymes of 360 and 336 kDa through gel filtration, while their apparent subunit size in SDS-PAGE was approximately 36 and 37 kDa, respectively. The preferred substrates of the purified enzymes were phenylacetonitrile, (R,S)-mandelonitrile, and 3-indolylacetonitrile. Both enzymes hydrolyzed (R)-mandelonitrile preferentially but with different degrees of selectivity, the e.e.s of the product (R)-mandelic acid being 63 and 89% in NitAb and NitNh, respectively, at pH 8.0. NitAb exhibited a higher temperature and pH stability than NitNh. Significant amounts of amide (> 5% of total product) were produced only by NitNh (from 2-cyanopyridine, (R,S)-mandelonitrile and phenylacetonitrile).

Bringing nitrilase sequences from databases to life: the search for novel substrate specificities with a focus on dinitriles.

The aim of this study was to discover new nitrilases with useful activities, especially towards dinitriles that are precursors of high-value cyano acids. Genes coding for putative nitrilases of different origins (fungal, plant, or bacterial) with moderate similarities to known nitrilases were selected by mining the GenBank database, synthesized artificially and expressed in Escherichia coli. The enzymes were purified, examined for their substrate specificities, and classified into subtypes (aromatic nitrilase, arylacetonitrilase, aliphatic nitrilase, cyanide hydratase) which were largely in accordance with those predicted from bioinformatic analysis. The catalytic potential of the nitrilases for dinitriles was examined with cyanophenyl acetonitriles, phenylenediacetonitriles, and fumaronitrile. The nitrilase activities and selectivities for dinitriles and the reaction products (cyano acid, cyano amide, diacid) depended on the enzyme subtype. At a preparative scale, all the examined dinitriles were hydrolyzed into cyano acids and fumaronitrile was converted to cyano amide using E. coli cells producing arylacetonitrilases and an aromatic nitrilase, respectively.

Catabolism of Nitriles in Rhodococcus

The enzymes of nitrile catabolism in Rhodococcus include nitrilases and nitrile hydratases/amidase systems. According to their cofactor, nitrile hydratases are classified into Fe-type and Co-type subfamilies, which are typically produced by Rhodococcus erythropolis and Rhodococcus rhodochrous, respectively. The latter species is also the typical source of nitrilases, most of which strongly prefer aromatic substrates. The organization of the nitrilase, nitrile hydratase, amidase and relevant regulatory genes, and mechanisms of their expression control are shown. The unique structural and physico-chemical properties of these enzymes (subunit aggregation; Fe-type nitrile hydratase photoreactivity) are described. The overview of nitrile-converting enzyme applications emphasizes their use in the biodegradation of aliphatic nitriles and benzonitrile herbicides. The significant potential of these enzymes as biocatalysts for the production of bulk and fine chemicals is also presented. The suitability of different preparation methods for whole cells and enzymes is discussed. Finally, analytical methods for monitoring nitrile biotransformations are summarized.

Erratum to: Hydrolysis of benzonitrile herbicides by soil actinobacteria and metabolite toxicity

M. Mackova, P. Lovecka and P. Janů wish to correct a typographical error in Table 3 which reports the results of acute toxicity determination implemented by them. The units of EC50 ± SD were not properly given and should have appeared in lM. The correct representation of Table 3 is herewith re-published and should be treated as definitive by the reader. Table 3 Determination of acute toxicity of chloroxynil, bromoxynil, ioxynil, dichlobenil and standards of their biodegradation products using the luminescent bacterium Vibrio fischeri