Nitrile-converting enzymes: an eco-friendly tool for industrial biocatalysis

Magnetic nanoparticle-mediated enrichment technology combined with microfluidic single cell separation technology: A technology for efficient separation and degradation of functional bacteria in single cell liquid phase

Although there are many microorganisms in nature, the limitations of isolation and cultivation conditions have restricted the development of artificial enhanced remediation technology using functional microbial communities. In this study, an integrated technology of Magnetic Nanoparticle-mediated Enrichment (MME) and Microfluidic Single Cell separation (MSC) that breaks through the bottleneck of traditional separation and cultivation techniques and can efficiently obtain more in situ functional microorganisms from the environment was developed. MME technology was first used to enrich rapidly growing active bacteria in the environment. Subsequently, MSC technology was applied to isolate and incubate functional bacterial communities in situ and validate the degradation ability of individual bacteria. As a result, this study has changed the order of traditional pure culture methods, which are first selected and then cultured, and provided a new method for obtaining non-culturable functional microorganisms.

Isolation and characterization of novel 3,3'-iminodipropionitrile biodegrading Paracoccus communis, from an industrial wastewater treatment bioreactor

Until now, bacteria able to degrade, 3,3'-iminodipropionitrile (IDPN), a neurotoxin that destroys vestibular hair cells, causing ototoxicity, culminating in irreversible movement disorders, had never been isolated. The aim of this study was to isolate a novel IDPN-biodegrading microorganism and characterize its metabolic pathway. Enrichment was performed by inoculating activated sludge from a wastewater treatment bioreactor that treated IDPN-contaminated wastewater in M9 salt medium, with IDPN as the sole carbon source. A bacterial strain with a spherical morphology that could grow at high concentrations was isolated on a solid medium. Growth of the isolated strain followed the Monod kinetic model. Based on the 16S rRNA gene, the isolate was Paracoccus communis. Whole-genome sequencing revealed that the isolated P. communis possessed the expected full metabolic pathway for IDPN biodegradation. Transcriptome analyses confirmed the overexpression of the gene encoding hydantoinase/oxoprolinase during the exponential growth phase under IDPN-fed conditions, suggesting that the enzyme involved in cleaving the imine bond of IDPN may promote IDPN biodegradation. Additionally, the newly discovered P. communis isolate seems to metabolize IDPN through cleavage of the imine bond in IDPN via nitrilase, nitrile hydratase, and amidase reactions. Overall, this study lays the foundation for the application of IDPN-metabolizing bacteria in the remediation of IDPN-contaminated environments.

Metabolism of toxic benzonitrile and hydroxybenzonitrile isomers via several distinct central pathway intermediates in a catabolically robust Burkholderia sp

Aromatic nitriles are of considerable environmental concern, because of their hazardous impacts on the health of both humans and wildlife. In the present study, Burkholderia sp. strain BC1 was observed to be capable of utilizing toxic benzonitrile and hydroxybenzonitrile isomers singly, as sole carbon and energy sources. The results of chromatographic and spectrometric analyses in combination with oxygen uptake and enzyme activity studies, revealed the metabolism of benzonitrile as well as 2-, 3-, and 4-hydroxybenzonitriles by nitrile hydratase-amidase to the corresponding carboxylates. These carboxylates were further metabolized via central pathways, namely benzoate-catechol, salicylate-catechol, 3-hydroxybenzoate-gentisate and 4-hydroxybenzoate-protocatechute pathways in strain BC1, ultimately leading to the TCA cycle intermediates. Studies also evaluated substrate specificity profiles of both nitrile hydratase and amidase(s) involved in the denitrification of the nitriles. In addition, a few metabolic crosstalk events due to the induction of multiple operons by central metabolites were appraised in strain BC1. The present study illustrates the broad degradative potential of strain BC1, harboring diverse catabolic machinery of biotechnological importance, elucidating pathways for the assimilation of benzonitrile and that of hydroxybenzonitrile isomers for the first time.

Arylacetonitrilases: Potential Biocatalysts for Green Chemistry

Nitrilases are the enzymes that catalyze the hydrolysis of nitriles to corresponding carboxylic acid and ammonia. They are broadly categorized into aromatic, aliphatic, and arylacetonitrilases based on their substrate specificity. Most of the studies pertaining to these enzymes in the literature have focused on aromatic and aliphatic nitrilases. However, arylacetonitrilases have attracted the attention of academia and industry in the last several years due to their aryl specificity and enantioselectivity. They have emerged as interesting biocatalytic tools in green chemistry to synthesize useful aryl acids such as mandelic acid and derivatives of phenylacetic acid. The aim of the present review is to collate information on the arylacetonitrilases and their catalytic properties including enantioselectivity and potential applications in organic synthesis.

Thespesia lampas mediated green synthesis of silver and gold nanoparticles for enhanced biological applications

The present study investigated the synthesis and biological applications of green, economical, and multifunctional silver and gold nanoparticles (TSAgNPs and TSAuNPs) using the ethnomedical important medicinal plant Thespesia lampas for biological activities. Relatively higher levels of antioxidant components were measured in T. lampas compared to the well-known Adhatoda vasica, and Diplocyclos palmatus suggested the potential of T. lampas for the study. Synthesized TSAgNPs and TSAuNPs were characterized through UV-Vis, XRD, SEM-EDS, HR-TEM, SAED, and FTIR techniques. SEM revealed that TSAgNPs and TSAuNPs were predominantly spherical in shape with 19 ± 7.3 and 43 ± 6.3 nm crystal sizes. The sizes of TSAgNPs and TSAuNPs were found to be12 ± 4.8 and 45 ± 2.9 nm, respectively, according to TEM measurements. The FTIR and phytochemical analyses revealed that the polyphenols and proteins present in T. lampas may act as bio-reducing and stabilizing agents for the synthesis. Synthesized NPs exhibited enhanced scavenging properties for ABTS and DPPH radicals. TSAgNPs and TSAuNPs were able to protect DNA nicking up to 13.48% and 15.38%, respectively, from oxidative stress. TSAgNPs possessed efficient antibacterial activities in a concentration-dependent manner against human pathogenic bacteria, such as E. coli, B. subtilis, P. vulgaris, and S. typhi. Furthermore, TSAgNPs and TSAuNPs showed significant cytotoxicity against FaDu HNSCC grown in 2D at 50 and 100 μg mL-1. Tumor inhibitory effects on FaDu-derived spheroid were significant for TSAgNPs > TSAuNPs at 100 μg mL-1 in 3D conditions. Dead cells were highest largely for TSAgNPs (76.65% ± 1.76%), while TSAuNPs were non-significant, and Saq was ineffectively compared with the control. However, the diameter of the spheroid drastically reduced for TSAgNPs (3.94 folds) followed by TSAuNPs (2.58 folds), Saq (1.94 folds), and cisplatin (1.83 folds) at 100 μg mL-1. The findings of the study suggested the bio-competence of TSAgNPs and TSAuNPs as multi-responsive agents for antioxidants, DNA protection, antibacterial, and anti-tumor activities to provide a better comprehension of the role of phytogenic nanoparticles in healthcare systems.

Streptomyces spp. as biocatalyst sources in pulp and paper and textile industries: Biodegradation, bioconversion and valorization of waste

Complex polymers represent a challenge for remediating environmental pollution and an opportunity for microbial-catalysed conversion to generate valorized chemicals. Members of the genus Streptomyces are of interest because of their potential use in biotechnological applications. Their versatility makes them excellent sources of biocatalysts for environmentally responsible bioconversion, as they have a broad substrate range and are active over a wide range of pH and temperature. Most Streptomyces studies have focused on the isolation of strains, recombinant work and enzyme characterization for evaluating their potential for biotechnological application. This review discusses reports of Streptomyces-based technologies for use in the textile and pulp-milling industry and describes the challenges and recent advances aimed at achieving better biodegradation methods featuring these microbial catalysts. The principal points to be discussed are (1) Streptomyces' enzymes for use in dye decolorization and lignocellulosic biodegradation, (2) biotechnological processes for textile and pulp and paper waste treatment and (3) challenges and advances for textile and pulp and paper effluent treatment.

Photolysis and photo-enhanced toxicity of three novel designed neonicotinoids: Impact of novel modifying groups

Three novel neonicotinoids (cycloxaprid, flupyradifurone and sulfoxaflor) were designed to reduce the biotoxicity for non-target organisms. These neonicotinoids were photolyzed under light radiation, but it was unclear for the photo-enhanced toxicity and influences of the novel modifying group of the three neonicotinoids. The photolysis and photo-enhanced toxicity experiments were performed for the three neonicotinoids, coupled with quantum chemistry calculation, the mechanisms of photolysis, photo-enhanced toxicity and the influences of novel modifying groups were analyzed. The results showed the photolysis pathways were enriched as compared with previous neonicotinoids due to the composition of modifying groups, singlet oxygen and hydroxyl participated the photolysis of cycloxaprid and flupyradifurone. All tested neonicotinoids exhibited photo-enhanced toxicity to Vibrio fischeri. Due to the difference of photolysis mechanism and toxicity to V. fischeri, the photo-enhanced toxicity curves showed diverse variation when histidine, tert-butanol or dissolved organic matters was in presence of the test solutions. The impact of novel modifying groups over photolysis and photo-enhanced toxicity were analyzed based on the comparison with previous neonicotinoids, theoretically predicted UV-Vis spectra and photo-physical/chemical property descriptors. The data showed the composition of novel modifying group increased the light absorption and photo-chemical activities for the three neonicotinoids.

Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics

The terrestrial subsurface microbiome contains vastly underexplored phylogenetic diversity and metabolic novelty, with critical implications for global biogeochemical cycling. Among the key microbial inhabitants of subsurface soils and sediments are Thaumarchaeota, an archaeal phylum that encompasses ammonia-oxidizing archaea (AOA) as well as non-ammonia-oxidizing basal lineages. Thaumarchaeal ecology in terrestrial systems has been extensively characterized, particularly in the case of AOA. However, there is little knowledge on the diversity and ecophysiology of Thaumarchaeota in deeper soils, as most lineages, particularly basal groups, remain uncultivated and underexplored. Here we use genome-resolved metagenomics to examine the phylogenetic and metabolic diversity of Thaumarchaeota along a 234 cm depth profile of hydrologically variable riparian floodplain sediments in the Wind River Basin near Riverton, Wyoming. Phylogenomic analysis of the metagenome-assembled genomes (MAGs) indicates a shift in AOA population structure from the dominance of the terrestrial Nitrososphaerales lineage in the well-drained top ~100 cm of the profile to the typically marine Nitrosopumilales in deeper, moister, more energy-limited sediment layers. We also describe two deeply rooting non-AOA MAGs with numerous unexpected metabolic features, including the reductive acetyl-CoA (Wood-Ljungdahl) pathway, tetrathionate respiration, a form III RuBisCO, and the potential for extracellular electron transfer. These MAGs also harbor tungsten-containing aldehyde:ferredoxin oxidoreductase, group 4f [NiFe]-hydrogenases and a canonical heme catalase, typically not found in Thaumarchaeota. Our results suggest that hydrological variables, particularly proximity to the water table, impart a strong control on the ecophysiology of Thaumarchaeota in alluvial sediments.

In silico analysis of nitrilase-3 protein from Corynebacterium glutamicum for bioremediation of nitrile herbicides

Background

The nitrile compounds are produced either naturally or synthetically and are highly used in many manufacturing industries such as pharmaceuticals, pesticides, chemicals, and polymers. However, the extensive use and accumulation of these nitrile compounds have caused severe environmental pollution. Nitrilated herbicides are one such toxic substance that will persist in the soil for a long time. Therefore, effective measures must be taken to avoid its pollution to the environment. A variety of nitrile-converting bacterial species have the ability to convert these toxic substances into less toxic ones by using enzymatic processes. Among the bacterial groups, actinobacteria family members show good degradation capacity on these pollutants. The soil-dwelling Gram-positive industrial microbe Corynebacterium glutamicum is one such family member and its nitrile-degradation pathway is not well studied yet. In order to understand the effectiveness of using C. glutamicum for the degradation of such nitrile herbicides, an in silico approach has been done. In this perspective, this work focus on the structural analysis and molecular docking studies of C. glutamicum with nitrilated herbicides such as dichlobenil, bromoxynil, and chloroxynil.

Results

The bioinformatics analysis using different tools and software helped to confirm that the genome of C. glutamicum ATCC 13032 species have genes (cg 3093) codes for carbon-nitrogen hydrolase enzyme, which specifically act on non-peptide bond present in the nitrile compounds. The conserved domain analysis indicated that this protein sequence was nitrilase-3 and comes under the nitrilase superfamily. The multiple sequence alignment analysis confirmed that the conserved catalytic triad residues were 40E, 115K, and 151C, and the existence of nitrilase-3 protein in the genome of Corynebacterium sp. was evaluated by a phylogenetic tree. The analysis of physico-chemical properties revealed that alanine is the most abounded amino acid (10.20%) in the nitrilase-3 protein, and these properties influence the substrate specificity of aliphatic and aromatic nitrile compounds. The homology modelled protein showed better affinity towards nitrile herbicides such as 2,6-dichlorobenzamide (BAM) and 3,5-dichloro-4-hydroxy-benzamide (CIAM) with the affinity value of − 5.8 and − 5.7 kcal/mol respectively.

Conclusions

The in silico studies manifested that C. glutamicum ATCC 13032 is one of the promising strains for the bioremediation of nitrilated herbicides contaminated soil.

The Application of Biocatalysis in the Preparation and Resolution of Morita-Baylis-Hillman Adducts and Their Derivatives

The Morita-Baylis-Hillman (MBH) reaction affords highly functionalised allylic alcohols containing a new stereogenic centre. These MBH adducts are very versatile and have been transformed into a large range of products, some of which have medicinal potential. Several examples of asymmetric syntheses of MBH adducts have been reported, although a generally applicable method remains to be developed. Biocatalytic approaches for the synthesis and enzymatic kinetic resolution of MBH adducts have been reported, and are discussed in detail in this review. Enzymes able to catalyse the asymmetric MBH reaction have been identified, but selectivity and efficiency have generally been low. Lipases, esterases and nitrile-converting enzymes have all been successfully applied in the resolution of MBH adducts, with excellent selectivity being realised in most cases.

Enzymatic and Chemical Approaches for Post-Polymerization Modifications of Diene Rubbers: Current state and Perspectives

Diene rubbers are polymeric materials which present elastic properties and have double bonds in the macromolecular backbone after the polymerization process. Post-polymerization modifications of rubbers can be conducted by enzymatic or chemical methods. Enzymes are environmentally friendly catalysts and with the increasing demand for rubber waste management, biodegradation and biomodifications have become hot topics of research. Some rubbers are renewable materials and are a source of organic molecules, and biodegradation can be conducted to obtain either oligomers or monomers. On the other hand, chemical modifications of rubbers by click-chemistry are important strategies for the creation and combination of new materials. In a way to expand the scope of uses to other non-traditional applications, several and effective modifications can be conducted with diene rubbers. Two groups of efficient tools, enzymatic, and chemical modifications in diene rubbers, are summarized in this review. By analyzing stereochemical and reactivity aspects, the authors also point to some applications perspectives for biodegradation products and to rational modifications of diene rubbers by combining both methodologies.

Characterization and genome functional analysis of an efficient nitrile-degrading bacterium, Rhodococcus rhodochrous BX2, to lay the foundation for potential bioaugmentation for remediation of nitrile-contaminated environments

Nitriles are a class of extremely toxic chemicals with extensive applications, and these compounds pose potential risks to humans and ecosystems. The activated sludge isolate Rhodococcus rhodochrous BX2 efficiently metabolizes aliphatic nitriles. However, the molecular underpinnings of the degradation mechanism of aliphatic nitriles by BX2 remain unknown, and the metabolic fate of aliphatic nitriles also has not been elucidated. Here, strain BX2 was capable of completely mineralizing three aliphatic nitriles. Bioinformatic analysis yielded a deeper insight into the genetic basis of BX2 for efficient degradation of aliphatic nitriles and adaptation to harsh environments. Transcriptional, enzyme activity and metabolite analyses confirmed that the intracellular inducible nitrile hydratase/amidase pathway is the preferred metabolic pathway. Our findings provide an in-depth understanding of the environmental fate of aliphatic nitriles and, most importantly, offer a new perspective on the potential applications of the genus Rhodococcus in bioremediation and the development of degradation enzyme resources.

From sequence to function: a new workflow for nitrilase identification

Abstract

Nitrilases are industrially important biocatalysts due to their ability to degrade nitriles to carboxylic acids and ammonia. In this study, a workflow for simple and fast recovery of nitrilase candidates from metagenomes is presented. For identification of active enzymes, a NADH-coupled high-throughput assay was established. Purification of enzymes could be omitted as the assay is based on crude extract containing the expressed putative nitrilases. In addition, long incubation times were avoided by combining nitrile and NADH conversion in a single reaction. This allowed the direct measurement of nitrile degradation and provided not only insights into substrate spectrum and specificity but also in degradation efficiency. The novel assay was used for investigation of candidate nitrilase-encoding genes. Seventy putative nitrilase-encoding gene and the corresponding deduced protein sequences identified during sequence-based screens of metagenomes derived from nitrile-treated microbial communities were analyzed. Subsequently, the assay was applied to 13 selected candidate genes and proteins. Six of the generated corresponding Escherichia coli clones produced nitrilases that showed activity and one unusual nitrilase was purified and analyzed. The activity of the novel arylacetonitrilase Nit09 exhibited a broad pH range and a high long-term stability. The enzyme showed high activity for arylacetonitriles with a K_M of 1.29 mM and a V_max of 13.85 U/mg protein for phenylacetonitrile. In conclusion, we provided a setup for simple and rapid analysis of putative nitrilase-encoding genes from sequence to function. The suitability was demonstrated by identification, isolation, and characterization of the arylacetonitrilase.

Key points

• A simple and fast high-throughput nitrilase screening was developed.

• A set of putative nitrilases was successfully screened with the assay.

• A novel arylacetonitrilase was identified, purified, and characterized in detail.

Electronic supplementary material

The online version of this article (10.1007/s00253-020-10544-9) contains supplementary material, which is available to authorized users.

A simple, efficient and rapid screening technique for differentiating nitrile hydratase and nitrilase producing bacteria

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A rapid dye based plate screening method for nitrile hydrolyzing enzymes.

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Method identifies the end products of nitrile hydrolyzing enzymes.

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The method differentiates between nitrile hydratase and nitrilase producing bacteria.

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A potential NHase producing bacterial strain was identified as Rhodococcus rhodochrous.

Nitrile hydrolyzing enzymes catalyze the hydration of nitrile compounds to corresponding amides and acids. Bacteria, isolated from soil samples were screened for nitrile hydrolyzing enzymes by simple dye based 96 well plate and nesslerization method. Bromothymol blue was used as an indicator for the detection of amides and acids based on colour change of the indicator dye from blue to dark green or yellow. The screening assay also differentiates between nitrile hydratase (NHase) and nitrilase producing bacteria. Among the 108 bacterial strains screened for enzyme activity, six strains were positive for NHase activity and eleven strains were positive for nitrilase activity based on their ability to degrade acrylonitrile into products. The strain showing maximum NHase activity in quantitative assay was identified as Rhodococcus rhodochrous. The modified method developed by us would be useful for rapid screening of nitrile degrading bacteria potent for acrylamide/acrylic acid production when acrylonitrile is supplied as substrate.

Whole Cell Actinobacteria as Biocatalysts

Production of fuels, therapeutic drugs, chemicals, and biomaterials using sustainable biological processes have received renewed attention due to increasing environmental concerns. Despite having high industrial output, most of the current chemical processes are associated with environmentally undesirable by-products which escalate the cost of downstream processing. Compared to chemical processes, whole cell biocatalysts offer several advantages including high selectivity, catalytic efficiency, milder operational conditions and low impact on the environment, making this approach the current choice for synthesis and manufacturing of different industrial products. In this review, we present the application of whole cell actinobacteria for the synthesis of biologically active compounds, biofuel production and conversion of harmful compounds to less toxic by-products. Actinobacteria alone are responsible for the production of nearly half of the documented biologically active metabolites and many enzymes; with the involvement of various species of whole cell actinobacteria such as Rhodococcus, Streptomyces, Nocardia and Corynebacterium for the production of useful industrial commodities.

Interplay of nucleophilic catalysis with proton transfer in the nitrile reductase QueF from Escherichia coli

Proton relay through an active-site network of hydrogen bonds promotes enzymatic nitrile reduction to amine via a covalent thioimidate enzyme intermediate.

Hydrolytic denitrification and decynidation of acrylonitrile in wastewater with Arthrobacter nitroguajacolicus ZJUTB06-99

Acrylonitrile (C₃H₃N) widely used in chemical raw materials has biological toxicity with -CN bond, so it is the key to removal of cyanide from acrylonitrile wastewater. In our previous research and investigation, a strain was identified as Arthrobacter nitroguajacolicus named ZJUTB06-99 and was proved to be capable of degrading acrylonitrile. In this paper, the strain ZJUTB06-99 was domesticated with acrylonitrile-containing medium and its decyanidation and denitrification in simulated acrylonitrile wastewater were studied. The intermediate product of acrylonitrile in degradation process was identified through gas chromatography-mass spectrometer, as well as the biodegradation pathway of acrylonitrile in wastewater was deduced tentatively. The kinetics equation of biodegradation of acrylonitrile was lnC = - 0.1784t + 5.3349, with the degradation half-life of acrylonitrile in wastewater by 3.885 h. The results of this study showed that the optimum levels of temperature, pH and bacteria concentration to attain the maximum biodegradation were obtained as 30 °C, 6 and 100 g/L, respectively. The disadvantages of the biodegradation with this strain and its possible enhanced method to degrade acrylonitrile in wastewater were also discussed.

Gut Glucosinolate Metabolism and Isothiocyanate Production

The glucosinolate-myrosinase system in plants has been well studied over the years while relatively little research has been undertaken on the bacterial metabolism of glucosinolates. The products of myrosinase-based glucosinolate hydrolysis in the human gut are important to health, particularly the isothiocyanates, as they are shown to have anticancer properties as well as other beneficial roles in human health. This review is concerned with the bacterial metabolism of glucosinolates but is not restricted to the human gut. Isothiocyanate production and nitrile formation are discussed together with the mechanisms of the formation of these compounds. Side chain modification of the methylsulfinylalkyl glucosinolates is reviewed and the implications for bioactivity of the resultant products are also discussed.

Combination of a recombinant bacterium with organonitrile-degrading and biofilm-forming capability and a positively charged carrier for organonitriles removal

The immobilization of organonitrile-degrading bacteria via the addition of biofilm-forming bacteria represents a promising technology for the treatment of organonitrile-containing wastewater, but biofilm-forming bacteria simply mixed with degrading bacteria may reduce the biodegradation efficiency. Nitrile hydratase and amidase genes, which play critical roles in organonitriles degradation, were cloned and transformed into the biofilm-forming bacterium Bacillus subtilis N4 to construct a recombinant bacterium B. subtilis N4/pHTnha-ami. Modified polyethylene carriers with positive charge was applied to promote bacterial adherence and biofilm formation. The immobilized B. subtilis N4/pHTnha-ami was resistant to organonitriles loading shocks and could remove organic cyanide ion with a initial concentration of 392.6 mg/L for 24 h in a moving bed biofilm reactor. The imputed quorum-sensing signal and the high-throughput sequencing analysis of the biofilm indicated that B. subtilis N4/pHTnha-ami was successfully immobilized and became dominant. The successful application of the immobilized recombinant bacterium offers a novel strategy for the biodegradation of recalcitrant compounds.

Treating organic cyanide-containing groundwater by immobilization of a nitrile-degrading bacterium with a biofilm-forming bacterium using fluidized bed reactors

Organic cyanide are widely used as an ingredient in the production of plastics, synthetic rubbers, polymers, pharmaceuticals and pesticides or used in laboratories and industries as solvents. Although nitrile-containing wastewater is subjected to primary and secondary treatments, residual nitriles may slowly seep and further migrate through groundwater, resulting in the micropollution of groundwater by organic pollutants. In this study, water samples were collected from different study areas in North China during a period of 3y (from 2013 to 2015) and analyzed to evaluate organic cyanide (CN^-) contamination in groundwater. Three parallel lab-scale fluidized bed reactors (FBRs) were tested for their ability to remove organic cyanide from groundwater. The organic cyanide concentration in groundwater increased significantly (P < 0.05) from 2013 to 2015. With an optimal hydraulic residence time (HRT) of 54 min, reactor R3 (inoculated with a nitrile-degrading bacterium, BX2, and a biofilm-forming bacterium, M1) effectively removed 99.8% of CN^- under steady operation, which was better than that of other reactors. Short-term shutdowns of FBRs had no serious effects on the efficiency of treating organic cyanide. This work demonstrated that the biofilm-forming bacterium could facilitate the fixation of nitrile-degrading bacterium and enhance the efficiency of removing organic cyanide from groundwater.

Mining of Microbial Genomes for the Novel Sources of Nitrilases

Next-generation DNA sequencing (NGS) has made it feasible to sequence large number of microbial genomes and advancements in computational biology have opened enormous opportunities to mine genome sequence data for novel genes and enzymes or their sources. In the present communication in silico mining of microbial genomes has been carried out to find novel sources of nitrilases. The sequences selected were analyzed for homology and considered for designing motifs. The manually designed motifs based on amino acid sequences of nitrilases were used to screen 2000 microbial genomes (translated to proteomes). This resulted in identification of one hundred thirty-eight putative/hypothetical sequences which could potentially code for nitrilase activity. In vitro validation of nine predicted sources of nitrilases was done for nitrile/cyanide hydrolyzing activity. Out of nine predicted nitrilases, Gluconacetobacter diazotrophicus, Sphingopyxis alaskensis, Saccharomonospora viridis, and Shimwellia blattae were specific for aliphatic nitriles, whereas nitrilases from Geodermatophilus obscurus, Nocardiopsis dassonvillei, Runella slithyformis, and Streptomyces albus possessed activity for aromatic nitriles. Flavobacterium indicum was specific towards potassium cyanide (KCN) which revealed the presence of nitrilase homolog, that is, cyanide dihydratase with no activity for either aliphatic, aromatic, or aryl nitriles. The present study reports the novel sources of nitrilases and cyanide dihydratase which were not reported hitherto by in silico or in vitro studies.

Hydrolysis of nitriles by soil bacteria: variation with soil origin

AIMS

The aim of this study was to explore bacterial soil diversity for nitrile biocatalysts, in particular, those for hydrolysis of β-substituted nitriles, to the corresponding carboxamides and acids that may be incorporated into peptidomimetics. To achieve this, we needed to compare the efficiency of isolation methods and determine the influence of land use and geographical origin of the soil sample.

METHODS AND RESULTS

Nitrile-utilizing bacteria were isolated from various soil environments across a 1000 km long transect of South Africa, including agricultural soil, a gold mine tailing dam and uncultivated soil. The substrate profile of these isolates was determined through element-limited growth studies on seven different aliphatic or aromatic nitriles. A subset of these organisms expressing broad substrate ranges was evaluated for their ability to hydrolyse β-substituted nitriles (3-amino-3-phenylpropionitrile and 3-hydroxy-4-phenoxybutyronitrile) and the active organisms were found to be Rhodococcus erythropolis from uncultivated soil and Rhodococcus rhodochrous from agricultural soils.

CONCLUSIONS

The capacity for hydrolysis of β-substituted nitriles appears to reside almost exclusively in Rhodococci. Land use has a much greater effect on the biocatalysis substrate profile than geographical location.

SIGNIFICANCE AND IMPACT OF THE STUDY

Enzymes are typically substrate specific in their catalytic reactions, and this means that a wide diversity of enzymes is required to provide a comprehensive biocatalysis toolbox. This paper shows that the microbial diversity of nitrile hydrolysis activity can be targeted according to land utilization. Nitrile biocatalysis is a green chemical method for the enzymatic production of amides and carboxylic acids that has industrial applications, such as in the synthesis of acrylamide and nicotinamide. The biocatalysts discovered in this study may be applied to the synthesis of peptidomimetics which are an important class of therapeutic compounds.

The Important Role of Halogen Bond in Substrate Selectivity of Enzymatic Catalysis

The use of halogen bond is widespread in drug discovery, design, and clinical trials, but is overlooked in drug biosynthesis. Here, the role of halogen bond in the nitrilase-catalyzed synthesis of ortho-, meta-, and para-chlorophenylacetic acid was investigated. Different distributions of halogen bond induced changes of substrate binding conformation and affected substrate selectivity. By engineering the halogen interaction, the substrate selectivity of the enzyme changed, with the implication that halogen bond plays an important role in biosynthesis and should be used as an efficient and reliable tool in enzymatic drug synthesis.

Unmasking the Action of Phosphinous Acid Ligands in Nitrile Hydration Reactions Catalyzed by Arene-Ruthenium(II) Complexes

The catalytic hydration of benzonitrile and acetonitrile has been studied by employing different arene-ruthenium(II) complexes with phosphinous (PR2OH) and phosphorous acid (P(OR)2OH) ligands as catalysts. Marked differences in activity were found, depending on the nature of both the P-donor and η(6)-coordinated arene ligand. Faster transformations were always observed with the phosphinous acids. DFT computations unveiled the intriguing mechanism of acetonitrile hydration catalyzed by these arene-ruthenium(II) complexes. The process starts with attack on the nitrile carbon atom of the hydroxyl group of the P-donor ligand instead of on a solvent water molecule, as previously suggested. The experimental results presented herein for acetonitrile and benzonitrile hydration catalyzed by different arene-ruthenium(II) complexes could be rationalized in terms of such a mechanism.

Enzymatic degradation of aliphatic nitriles by Rhodococcus rhodochrous BX2, a versatile nitrile-degrading bacterium

Nitriles are common environmental pollutants, and their removal has attracted increasing attention. Microbial degradation is considered to be the most acceptable method for removal. In this work, we investigated the biodegradation of three aliphatic nitriles (acetonitrile, acrylonitrile and crotononitrile) by Rhodococcus rhodochrous BX2 and the expression of their corresponding metabolic enzymes. This organism can utilize all three aliphatic nitriles as sole carbon and nitrogen sources, resulting in the complete degradation of these compounds. The degradation kinetics were described using a first-order model. The degradation efficiency was ranked according to t1/2 as follows: acetonitrile>trans-crotononitrile>acrylonitrile>cis-crotononitrile. Only ammonia accumulated following the three nitriles degradation, while amides and carboxylic acids were transient and disappeared by the end of the assay. mRNA expression and enzyme activity indicated that the tested aliphatic nitriles were degraded via both the inducible NHase/amidase and the constitutive nitrilase pathways, with the former most likely preferred.

Enantioselective biotransformations of nitriles in organic synthesis

The hydration and hydrolysis of nitriles are valuable synthetic methods used to prepare carboxamides and carboxylic acids. However, chemical hydration and hydrolysis of nitriles involve harsh reaction conditions, have low selectivity, and generate large amounts of waste. Therefore, researchers have confined the scope of these reactions to simple nitrile substrates. However, biological transformations of nitriles are highly efficient, chemoselective, and environmentally benign, which has led synthetic organic chemists and biotechologists to study these reactions in detail over the last two decades. In nature, biological systems degrade nitriles via two distinct pathways: nitrilases catalyze the direct hydrolysis of nitriles to afford carboxylic acids with release of ammonia, and nitrile hydratases catalyze the conversion of nitriles into carboxamides, which then furnish carboxylic acids via hydrolysis in the presence of amidases. Researchers have subsequently developed biocatalytic methods into useful industrial processes for the manufacture of commodity chemicals, including acrylamide. Since the late 1990s, research by my group and others has led to enormous progress in the understanding and application of enantioselective biotransformations of nitriles in organic synthesis. In this Account, I summarize the important advances in enantioselective biotransformations of nitriles and amides, with a primary focus on research from my laboratory. I describe microbial whole-cell-catalyzed kinetic resolution of various functionalized nitriles, amino- and hydroxynitriles, and nitriles that contain small rings and the desymmetrization of prochiral and meso dinitriles and diamides. I also demonstrate how we can apply the biocatalytic protocol to synthesize natural products and bioactive compounds. These nitrile biotransformations offer an attractive and unique protocol for the enantioselective synthesis of polyfunctionalized organic compounds that are not readily obtainable by other methods. Nitrile substrates are readily available, and the mild reaction conditions are specific toward cyano and amido functional groups without interfering with other reactive functional groups. I anticipate that further advances in this field will lead to new and engineered nitrile-hydrolyzing enzymes or catalytic systems with improved activity and altered selectivity. These advances will broaden the scope of these transformations and their applications in organic synthesis.

Synthesis of quaternary-carbon-containing and functionalized enantiopure pentanecarboxylic acids from biocatalytic desymmetrization of meso-cyclopentane-1,3-dicarboxamides

Catalyzed by Rhodococcus erythropolis AJ270, a nitrile hydratase-amidase containing microbial whole-cell catalyst under mild conditions, enantioselective desymmetrizations of meso-cyclopentane-1,3-dicarbonitriles and cyclopentane-1,3-dicarboxamides were studied. Although the nitrile hydratase was found to exhibit high enzymatic activity, but low 1R enantioselectivity toward dinitriles, a number of 2,2-unsymmetrically substituted meso-cyclopentane-1,3-dicarboxamide substrates were converted by the 1S enantioselective amidase into quaternary carbon-bearing enantiopure (1S,2R,3R)-3-carbamoylcyclopentanecarboxylic acids in yields up to 94 %. The application of the method was demonstrated by convenient and practical transformations of the resulting (1S,2R,3R)-2-allyl-3-carbamoylcyclopentanecarboxylic acid derivatives into functionalized cyclopentane-fused δ-lactam and δ-lactone compounds.

Nitrile reductase as a biocatalyst: opportunities and challenges

The review highlights the recent progress and challenges in developing a family of nitrile reductases as biocatalysts for nitrile-to-amine transformation.