C-terminal hybrid mutant of Bacillus pumilus cyanide dihydratase dramatically enhances thermal stability and pH tolerance by reinforcing oligomerization

Design and development of spectrophotometric enzymatic cyanide assays

Determination of free cyanide (fCN) is required for various industrial, environmental, food, and clinical samples. Enzymatic methods are not widely used in this field despite their selectivity and mild conditions. Therefore, we present here a proof of concept for new spectrophotometric enzymatic assays of fCN. These are based on the hydrolysis of fCN affording the readily detectable NADH. fCN is hydrolyzed either in one step by cyanide dihydratase (CynD) or in two steps by cyanide hydratase (CynH) and formamidase (AmiF). An advantage of the latter route is the higher activity of CynH and AmiF compared to CynD. In both cases, the resulting formate is then transformed by an NAD-dependent formate dehydrogenase (FDH). The NADH thus formed is quantified colorimetrically using a known method based on a reduction of a tetrazolium salt (WST-8) with NADH. The developed assays of fCN are selective except for formic acid interference, proceed under mild conditions, and, moreover, fCN is detoxified during the reactions. The assays proceeded in a microtiter plate format. The limit of detection (LOD) and the limit of quantification (LOQ) were lower for the three-enzyme (CynH-AmiF-FDH) method (7.00 and 21.2 µmol/L, respectively) than for the two-enzyme (CynD-FDH) method (10.7 and 32.4 µmol/L, respectively). In conclusion, the new fCN assays presented in this work are selective, high-throughput, do not require harsh conditions, and use only small amounts of chemicals and enzymes.

Multidomain chimeric enzymes as a promising alternative for biocatalysts improvement: a minireview

Searching for new and better biocatalysts is an area of study in constant development. In nature, mechanisms generally occurring in evolution, such as genetic duplication, recombination, and natural selection processes, produce various enzymes with different architectures and properties. The recombination of genes that code proteins produces multidomain chimeric enzymes that contain two or more domains that sometimes enhance their catalytic properties. Protein engineering has mimicked this process to enhance catalytic activity and the global stability of enzymes, searching for new and better biocatalysts. Here, we present and discuss examples from both natural and synthetic multidomain chimeric enzymes and how additional domains heighten their stability and catalytic activity. Moreover, we also describe progress in developing new biocatalysts using synthetic fusion enzymes and revise some methodological strategies to improve their biological fitness.

Recent Progress in the Production of Cyanide-Converting Nitrilases—Comparison with Nitrile-Hydrolyzing Enzymes

Nitrilases have a high potential for application in organic chemistry, environmental technology, and analytics. However, their industrial uses require that they are produced in highly active and robust forms at a reasonable cost. Some organic syntheses catalyzed by nitrilases have already reached a high level of technological readiness. This has been enabled by the large-scale production of recombinant catalysts. Despite some promising small-scale methods being proposed, the production of cyanide-converting nitrilases (cyanide hydratase and cyanide dihydratase) is lagging in this regard. This review focuses on the prospects of cyanide(di)hydratase-based catalysts. The current knowledge of these enzymes is summarized and discussed in terms of the origin and distribution of their sequences, gene expression, structure, assays, purification, immobilization, and uses. Progresses in the production of other nitrilase catalysts are also tackled, as it may inspire the development of the preparation processes of cyanide(di)hydratases.

Genomic Characterization of Bacillus safensis Isolated from Mine Tailings in Peru and Evaluation of Its Cyanide-Degrading Enzyme CynD

Understanding the biochemistry and metabolic pathways of cyanide degradation is necessary to improve the efficacy of cyanide bioremediation processes and industrial requirements. We have isolated and sequenced the genome of a cyanide-degrading Bacillus strain from water in contact with mine tailings from Lima, Peru. This strain was classified as Bacillus safensis based on 16S rRNA gene sequencing and core genome analyses and named B. safensis PER-URP-08. We searched for possible cyanide-degradation enzymes in the genome of this strain and identified a putative cyanide dihydratase (CynD) gene similar to a previously characterized CynD from Bacillus pumilus C1. Sequence analysis of CynD from B. safensis and B. pumilus allow us to identify C-terminal residues that differentiate both CynDs. We then cloned, expressed in Escherichia coli, and purified recombinant CynD from B. safensis PER-URP-08 (CynD_PER-URP-08) and showed that in contrast to CynD from B. pumilus C1, this recombinant CynD remains active at up to pH 9. We also showed that oligomerization of CynD_PER-URP-08 decreases as a function of increased pH. Finally, we demonstrated that transcripts of CynD_PER-URP-08 in B. safensis PER-URP-08 are strongly induced in the presence of cyanide. Our results suggest that the use of B. safensis PER-URP-08 and CynD_PER-URP-08 as potential tool for cyanide bioremediation warrants further investigation. IMPORTANCE Despite being of environmental concern around the world due to its toxicity, cyanide continues to be used in many important industrial processes. Thus, searching for cyanide bioremediation methods is a matter of societal concern and must be present on the political agenda of all governments. Here, we report the isolation, genome sequencing and characterization of cyanide degradation capacity of a bacterial strain isolated from an industrial mining site in Peru. We characterize a cyanide dehydratase (CynD) homolog from one of these bacteria, Bacillus safensis PER-URP-08.

Biodegradation of cyanide using recombinant Escherichia coli expressing Bacillus pumilus cyanide dihydratase

Despite its high toxicity, cyanide is used in several industrial processes, and as a result, large volumes of cyanide wastewater need to be treated prior to discharge. Enzymatic degradation of industrial cyanide wastewater by cyanide dihydratase, which is capable of converting cyanide to ammonia and formate, is an attractive alternative to conventional chemical methods of cyanide decontamination. However, the main impediment to the use of this enzyme for the biodegradation of cyanide is the intolerance to the alkaline pH at which cyanide waste is kept and its low thermoresistance. In the present study, the catalytic properties of whole E. coli cells overexpressing a cyanide dihydratase gene from B. pumilus were compared to those of the purified enzyme under conditions similar to those found in industrial cyanide wastewater. In addition, the capacity of whole cells to degrade free cyanide in contaminated wastewater resulting from the gold mining process was also determined. The characteristics of intracellular enzyme, relative to purified enzyme, included increased thermostability, as well as greater tolerance to heavy metals and to a lesser extent pH. On the other hand, significant enzymatic degradation (70%) of free cyanide in the industrial sample was achieved only after dilution. Nevertheless, the increased thermostability observed for intracellular CynD suggest that whole cells of E. coli overexpressing CynD are suited for process that operate at elevated temperatures, a limitation observed for the purified enzyme.

Cryo-EM and directed evolution reveal how Arabidopsis nitrilase specificity is influenced by its quaternary structure

Nitrilases are helical enzymes that convert nitriles to acids and/or amides. All plants have a nitrilase 4 homolog specific for ß-cyanoalanine, while in some plants neofunctionalization has produced nitrilases with altered specificity. Plant nitrilase substrate size and specificity correlate with helical twist, but molecular details of this relationship are lacking. Here we determine, to our knowledge, the first close-to-atomic resolution (3.4 Å) cryo-EM structure of an active helical nitrilase, the nitrilase 4 from Arabidopsis thaliana. We apply site-saturation mutagenesis directed evolution to three residues (R95, S224, and L169) and generate a mutant with an altered helical twist that accepts substrates not catalyzed by known plant nitrilases. We reveal that a loop between α2 and α3 limits the length of the binding pocket and propose that it shifts position as a function of helical twist. These insights will allow us to start designing nitrilases for chemoenzymatic synthesis.

Immobilization of E. coli expressing Bacillus pumilus CynD in three organic polymer matrices

Cyanide is toxic to most living organisms. The toxicity of cyanide derives from its ability to inhibit the enzyme cytochrome C oxidase of the electronic transport chain. Despite its high toxicity, several industrial processes rely on the use of cyanide, and considerable amounts of industrial waste must be adequately treated before discharge. Biological treatments for the decontamination of cyanide waste include the use of microorganisms and enzymes. Regarding the use of enzymes, cyanide dihydratase (CynD), which catalyzes the conversion of cyanide into ammonia and formate, is an attractive candidate. Nevertheless, the main impediment to the effective use of this enzyme for the biodegradation of cyanide is the marked intolerance to the alkaline pH at which cyanide waste is kept. In this work, we explore the operational capabilities of whole E. coli cells overexpressing Bacillus pumilus CynD immobilized in three organic polymer matrices: chitosan, polyacrylamide, and agar. Remarkably, the immobilized cells on agar and polyacrylamide retained more than 80% activity even at pH 10 and displayed high reusability. Conversely, the cells immobilized on chitosan were not active. Finally, the suitability of the active complexes for the degradation of free cyanide from a solution derived from the gold processing industry was demonstrated.

A novel cysteine carbamoyl-switch is responsible for the inhibition of formamidase, a nitrilase superfamily member

Formamidases (EC 3.5.1.49) and amidases (EC 3.5.1.4) are paralogous cysteine-dependent enzymes which catalyze the conversion of amide substrates to ammonia and the corresponding carboxylic acid. Both enzymes have been suggested as an alternative pathway for ammonia production during urea shortage. Urea was proved key in the transcriptional regulation of formamidases/amidases, connecting urea level to amide metabolism. In addition, different amidases have also been shown to be inhibited by urea, pointing to urea-regulation at the enzymatic level. Although amidases have been widely studied due to its biotechnological application in the hydrolysis of aliphatic amides, up to date, only two formamidases have been extensively characterized, belonging to Helicobacter pylori (HpyAmiF) and Bacillus cereus (BceAmiF). In this work, we report the first structure of an acyl-intermediate of BceAmiF. We also report the inhibition of BceAmiF by urea, together with mass spectrometry studies confirming the S-carbamoylation of BceAmiF after urea treatment. X-ray studies of urea-soaked BceAmiF crystals showed short- and long-range rearrangements affecting oligomerization interfaces. Since cysteine-based switches are known to occur in the regulation of different metabolic and signaling pathways, our results suggest a novel S-carbamoylation-switch for the regulation of BceAmiF. This finding could relate to previous observations of unexplained modifications in the catalytic cysteine of different nitrilase superfamily members and therefore extending this regulation mechanism to the whole nitrilase superfamily.

Cyanide bioremediation: the potential of engineered nitrilases

The cyanide-degrading nitrilases are of notable interest for their potential to remediate cyanide contaminated waste streams, especially as generated in the gold mining, pharmaceutical, and electroplating industries. This review provides a brief overview of cyanide remediation in general but with a particular focus on the cyanide-degrading nitrilases. These are of special interest as the hydrolysis reaction does not require secondary substrates or cofactors, making these enzymes particularly good candidates for industrial remediation processes. The genetic approaches that have been used to date for engineering improved enzymes are described; however, recent structural insights provide a promising new approach.

Bacillus pumilus Cyanide Dihydratase Mutants with Higher Catalytic Activity

Cyanide degrading nitrilases are noted for their potential to detoxify industrial wastewater contaminated with cyanide. However, such application would benefit from an improvement to characteristics such as their catalytic activity and stability. Following error-prone PCR for random mutagenesis, several cyanide dihydratase mutants from Bacillus pumilus were isolated based on improved catalysis. Four point mutations, K93R, D172N, A202T, and E327K were characterized and their effects on kinetics, thermostability and pH tolerance were studied. K93R and D172N increased the enzyme’s thermostability whereas E327K mutation had a less pronounced effect on stability. The D172N mutation also increased the affinity of the enzyme for its substrate at pH 7.7 but lowered its k_cat. However, the A202T mutation, located in the dimerization or the A surface, destabilized the protein and abolished its activity. No significant effect on activity at alkaline pH was observed for any of the purified mutants. These mutations help confirm the model of CynD and are discussed in the context of the protein–protein interfaces leading to the protein quaternary structure.

Probing an Interfacial Surface in the Cyanide Dihydratase from Bacillus pumilus, A Spiral Forming Nitrilase

Nitrilases are of significant interest both due to their potential for industrial production of valuable products as well as degradation of hazardous nitrile-containing wastes. All known functional members of the nitrilase superfamily have an underlying dimer structure. The true nitrilases expand upon this basic dimer and form large spiral or helical homo-oligomers. The formation of this larger structure is linked to both the activity and substrate specificity of these nitrilases. The sequences of the spiral nitrilases differ from the non-spiral forming homologs by the presence of two insertion regions. Homology modeling suggests that these regions are responsible for associating the nitrilase dimers into the oligomer. Here we used cysteine scanning across these two regions, in the spiral forming nitrilase cyanide dihydratase from Bacillus pumilus (CynD), to identify residues altering the oligomeric state or activity of the nitrilase. Several mutations were found to cause changes to the size of the oligomer as well as reduction in activity. Additionally one mutation, R67C, caused a partial defect in oligomerization with the accumulation of smaller oligomer variants. These results support the hypothesis that these insertion regions contribute to the unique quaternary structure of the spiral microbial nitrilases.