Natural nitriles and their metabolism

Catalytic and post-translational maturation roles of a conserved active site serine residue in nitrile hydratases

A highly conserved second-sphere active site αSer residue in nitrile hydratase (NHase), that forms a hydrogen bond with the axial metal-bound water molecule, was mutated to Ala, Asp, and Thr, in the Co-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) and to Ala and Thr in the Fe-type NHase from Rhodococcus equi TG328-2 (ReNHase). All five mutants were successfully purified; metal analysis via ICP-AES indicated that all three Co-type PtNHase mutants were in their apo-form while the Fe-type αSer117Ala and αSer117Thr mutants contained 85 and 50 % of their active site Fe(III) ions, respectively. The kcat values obtained for the PtNHase mutant enzymes were between 0.03 ± 0.01 and 0.2 ± 0.02 s-1 amounting to <0.8 % of the kcat value observed for WT PtNHase. The Fe-type ReNHase mutants retained some detectable activity with kcat values of 93 ± 3 and 40 ± 2 s-1 for the αSer117Ala and αSer117Thr mutants, respectively, which is ∼5 % of WT ReNHase activity towards acrylonitrile. UV-Vis spectra coupled with EPR data obtained on the ReNHase mutant enzymes showed subtle changes in the electronic environment around the active site Fe(III) ions, consistent with altering the hydrogen bonding interaction with the axial water ligand. X-ray crystal structures of the three PtNHase mutant enzymes confirmed the mutation and the lack of active site metal, while also providing insight into the active site hydrogen bonding network. Taken together, these data confirm that the conserved active site αSer residue plays an important catalytic role but is not essential for catalysis. They also confirm the necessity of the conserved second-sphere αSer residue for the metalation process and subsequent post-translational modification of the α-subunit in Co-type NHases but not Fe-type NHases, suggesting different mechanisms for the two types of NHases. SYNOPSIS: A strictly conserved active site αSer residue in both Co- and Fe-type nitrile hydratases was mutated. This αSer residue was found to play an important catalytic function, but is not essential. In Co-type NHases, it appears to be essential for active site maturation, but not in Fe-type NHases.

A single diiron enzyme catalyses the oxidative rearrangement of tryptophan to indole nitrile

Nitriles are uncommon in nature and are typically constructed from oximes through the oxidative decarboxylation of amino acid substrates or from the derivatization of carboxylic acids. Here we report a third nitrile biosynthesis strategy featuring the cyanobacterial nitrile synthase AetD. During the biosynthesis of the eagle-killing neurotoxin, aetokthonotoxin, AetD transforms the 2-aminopropionate portion of 5,7-dibromo-L-tryptophan to a nitrile. Employing a combination of structural, biochemical and biophysical techniques, we characterized AetD as a non-haem diiron enzyme that belongs to the emerging haem-oxygenase-like dimetal oxidase superfamily. High-resolution crystal structures of AetD together with the identification of catalytically relevant products provide mechanistic insights into how AetD affords this unique transformation, which we propose proceeds via an aziridine intermediate. Our work presents a unique template for nitrile biogenesis and portrays a substrate binding and metallocofactor assembly mechanism that may be shared among other haem-oxygenase-like dimetal oxidase enzymes.

Nitrile hydratase as a promising biocatalyst: recent advances and future prospects

Amides are an important type of synthetic intermediate used in the chemical, agrochemical, pharmaceutical, and nutraceutical industries. The traditional chemical process of converting nitriles into the corresponding amides is feasible but is restricted because of the harsh conditions required. In recent decades, nitrile hydratase (NHase, EC 4.2.1.84) has attracted considerable attention because of its application in nitrile transformation as a prominent biocatalyst. In this review, we provide a comprehensive survey of recent advances in NHase research in terms of natural distribution, enzyme screening, and molecular modification on the basis of its characteristics and catalytic mechanism. Additionally, industrial applications and recent significant biotechnology advances in NHase bioengineering and immobilization techniques are systematically summarized. Moreover, the current challenges and future perspectives for its further development in industrial applications for green chemistry were also discussed. This study contributes to the current state-of-the-art, providing important technical information for new NHase applications in manufacturing industries.

Molecular Modification Strategies of Nitrilase for Its Potential Application in Agriculture

Some feed source plants will produce secondary metabolites such as cyanogenic glycosides during metabolism, which will produce some poisonous nitrile compounds after hydrolysis and remain in plant tissues. The consumption of feed-source plants without proper treatment affect the health of the animals' bodies. Nitrilases can convert nitriles and have been used in industry as green biocatalysts. However, due to their bottleneck problems, their application in agriculture is still facing challenges. Acid-resistant nitrilase preparations, high-temperature resistance, antiprotease activity, strong activity, and strict reaction specificity urgently need to be developed. In this paper, the application potential of nitrilase in agriculture, especially in feed processing industry was explored, the source properties and catalytic mechanism of nitrilase were reviewed, and modification strategies for nitrilase application in agriculture were proposed to provide references for future research and application of nitrilase in agricultural and especially in the biological feed scene.

Nitrile biosynthesis in nature: how and why?

Covering: up to the end of 2023Natural nitriles comprise a small set of secondary metabolites which however show intriguing chemical and functional diversity. Various patterns of nitrile biosynthesis can be seen in animals, plants, and microorganisms with the characteristics of both evolutionary divergence and convergence. These specialized compounds play important roles in nitrogen metabolism, chemical defense against herbivores, predators and pathogens, and inter- and/or intraspecies communications. Here we review the naturally occurring nitrile-forming pathways from a biochemical perspective and discuss the biological and ecological functions conferred by diversified nitrile biosyntheses in different organisms. Elucidation of the mechanisms and evolutionary trajectories of nitrile biosynthesis underpins better understandings of nitrile-related biology, chemistry, and ecology and will ultimately benefit the development of desirable nitrile-forming biocatalysts for practical applications.

Rutinosidase and other diglycosidases: Rising stars in biotechnology

Diglycosidases are a special class of glycosidases (EC 3.2.1) that catalyze the separation of intact disaccharide moieties from the aglycone part. The main diglycosidase representatives comprise rutinosidases that cleave rutinose (α-l-Rha-(1-6)-β-d-Glc) from rutin or other rutinosides, and (iso)primeverosidases processing (iso)primeverosides (d-Xyl-(1-6)-β-d-Glc), but other activities are known. Notably, some diglycosidases may be ranked as monoglucosidases with enlarged substrate specificity. Diglycosidases are found in various microorganisms and plants. Diglycosidases are used in the food industry for aroma enhancement and flavor modification. Besides their hydrolytic activity, they also possess pronounced synthetic (transglycosylating) capabilities. Recently, they have been demonstrated to glycosylate various substrates in a high yield, including peculiar species like inorganic azide or carboxylic acids, which is a unique feature in biocatalysis. Rhamnose-containing compounds such as rutinose are currently receiving increased attention due to their proven activity in anti-cancer and dermatological experimental studies. This review demonstrates the vast and yet underrated biotechnological potential of diglycosidases from various sources (plant, microbial), and reveals perspectives on the use of these catalysts as well as of their products in biotechnology.

Steroids Bearing Heteroatom as Potential Drugs for Medicine

Heteroatom steroids, a diverse class of organic compounds, have attracted significant attention in the field of medicinal chemistry and drug discovery. The biological profiles of heteroatom steroids are of considerable interest to chemists, biologists, pharmacologists, and the pharmaceutical industry. These compounds have shown promise as potential therapeutic agents in the treatment of various diseases, such as cancer, infectious diseases, cardiovascular disorders, and neurodegenerative conditions. Moreover, the incorporation of heteroatoms has led to the development of targeted drug delivery systems, prodrugs, and other innovative pharmaceutical approaches. Heteroatom steroids represent a fascinating area of research, bridging the fields of organic chemistry, medicinal chemistry, and pharmacology. The exploration of their chemical diversity and biological activities holds promise for the discovery of novel drug candidates and the development of more effective and targeted treatments.

Oxidative rearrangement of tryptophan to indole nitrile by a single diiron enzyme

Nitriles are uncommon in nature and are typically constructed from oximes via the oxidative decarboxylation of amino acid substrates or from the derivatization of carboxylic acids. Here we report a third strategy of nitrile biosynthesis featuring the cyanobacterial nitrile synthase AetD. During the biosynthesis of the 'eagle-killing' neurotoxin, aetokthonotoxin, AetD converts the alanyl side chain of 5,7-dibromo-L-tryptophan to a nitrile. Employing a combination of structural, biochemical, and biophysical techniques, we characterized AetD as a non-heme diiron enzyme that belongs to the emerging Heme Oxygenase-like Diiron Oxidase and Oxygenase (HDO) superfamily. High-resolution crystal structures of AetD together with the identification of catalytically relevant products provide mechanistic insights into how AetD affords this unique transformation that we propose proceeds via an aziridine intermediate. Our work presents a new paradigm for nitrile biogenesis and portrays a substrate binding and metallocofactor assembly mechanism that may be shared among other HDO enzymes.

Natural Products Containing the Nitrile Functional Group and Their Biological Activities

The importance of nitriles as a key class of chemicals with applications across the sciences is widely appreciated. The natural world is an underappreciated source of chemically diverse nitriles. With this in mind, this review describes novel nitrile-containing molecules isolated from natural sources from 1998 to 2021, as well as a discussion of the biological activity of these compounds. This study gathers 192 molecules from varied origins across the plant, animal, and microbial worlds. Their biological activity is extremely diverse, with many potential medicinal applications.

Alternative Pathway for 3-Cyanoalanine Assimilation in Pseudomonas pseudoalcaligenes CECT5344 under Noncyanotrophic Conditions

3-Cyanoalanine and cyanohydrins are intermediate nitriles produced in cyanide degradation pathways in plants and bacteria. 3-Cyanoalanine is generated from cyanide by the 3-cyanoalanine synthase, an enzyme mainly characterized in cyanogenic plants. NIT4-type nitrilases use 3-cyanoalanine as a substrate, forming ammonium and aspartate. In some organisms, this enzyme also generates asparagine through an additional nitrile hydratase activity. The alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 assimilates cyanide through an intermediate cyanohydrin, which is further converted into ammonium by the nitrilase NitC. This bacterium also contains three additional nitrilases, including Nit4. In this work, a proteomic analysis of P. pseudoalcaligenes CECT5344 cells grown with 3-cyanoalanine as the sole nitrogen source has revealed the overproduction of different proteins involved in nitrogen metabolism, including the nitrilase NitC. In contrast, the nitrilase Nit4 was not induced by 3-cyanoalanine, and it was only overproduced in cells grown with a cyanide-containing jewelry-manufacturing residue. Phenotypes of single and double mutant strains defective in nit4 or/and nitC revealed the implication of the nitrilase NitC in the assimilation of 3-cyanoalanine and suggest that the 3-cyanoalanine assimilation pathway in P. pseudoalcaligenes CECT5344 depends on the presence or absence of cyanide. When cyanide is present, 3-cyanoalanine is assimilated via Nit4, but in the absence of cyanide, a novel pathway for 3-cyanoalanine assimilation, in which the nitrilase NitC uses the nitrile generated after deamination of the α-amino group from 3-cyanoalanine, is proposed. IMPORTANCE Nitriles are organic cyanides with important industrial applications, but they are also found in nature. 3-Cyanoalanine is synthesized by plants and some bacteria to detoxify cyanide from endogenous or exogenous sources, but this nitrile may be also involved in other processes such as stress tolerance, nitrogen and sulfur metabolism, and signaling. The cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344 grows with 3-cyanoalanine as the sole nitrogen source, but it does not use this nitrile as an intermediate in the cyanide assimilation pathway. In this work, a quantitative proteomic analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to study, for the first time, the response to 3-cyanoalanine at the proteomic level. Proteomic data, together with phenotypes of different nitrilase-defective mutants of P. pseudoalcaligenes CECT5344, provide evidence that in the absence of cyanide, the nitrilase Nit4 is not involved in 3-cyanoalanine assimilation, and instead, the nitrilase NitC participates in a novel alternative 3-cyanoalanine assimilation pathway.

Bright Side of Fusarium oxysporum: Secondary Metabolites Bioactivities and Industrial Relevance in Biotechnology and Nanotechnology

Fungi have been assured to be one of the wealthiest pools of bio-metabolites with remarkable potential for discovering new drugs. The pathogenic fungi, Fusarium oxysporum affects many valuable trees and crops all over the world, producing wilt. This fungus is a source of different enzymes that have variable industrial and biotechnological applications. Additionally, it is widely employed for the synthesis of different types of metal nanoparticles with various biotechnological, pharmaceutical, industrial, and medicinal applications. Moreover, it possesses a mysterious capacity to produce a wide array of metabolites with a broad spectrum of bioactivities such as alkaloids, jasmonates, anthranilates, cyclic peptides, cyclic depsipeptides, xanthones, quinones, and terpenoids. Therefore, this review will cover the previously reported data on F. oxysporum, especially its metabolites and their bioactivities, as well as industrial relevance in biotechnology and nanotechnology in the period from 1967 to 2021. In this work, 180 metabolites have been listed and 203 references have been cited.

Ni2 P Nanoalloy as an Air-Stable and Versatile Hydrogenation Catalyst in Water: P-Alloying Strategy for Designing Smart Catalysts

Non-noble metal-based hydrogenation catalysts have limited practical applications because they exhibit low activity, require harsh reaction conditions, and are unstable in air. To overcome these limitations, herein we propose the alloying of non-noble metal nanoparticles with phosphorus as a promising strategy for developing smart catalysts that exhibit both excellent activity and air stability. We synthesized a novel nickel phosphide nanoalloy (nano-Ni₂ P) with coordinatively unsaturated Ni active sites. Unlike conventional air-unstable non-noble metal catalysts, nano-Ni₂ P retained its metallic nature in air, and exhibited a high activity for the hydrogenation of various substrates with polar functional groups, such as aldehydes, ketones, nitriles, and nitroarenes to the desired products in excellent yields in water. Furthermore, the used nano-Ni₂ P catalyst was easy to handle in air and could be reused without pretreatment, providing a simple and clean catalyst system for general hydrogenation reactions.

A cobalt phosphide catalyst for the hydrogenation of nitriles

A well-defined nano-cobalt phosphide serves as an air-stable, highly active and reusable heterogeneous catalyst for the selective hydrogenation of nitriles to primary amines under mild reaction conditions.

The study of metal phosphide catalysts for organic synthesis is rare. We present, for the first time, a well-defined nano-cobalt phosphide (nano-Co₂P) that can serve as a new class of catalysts for the hydrogenation of nitriles to primary amines. While earth-abundant metal catalysts for nitrile hydrogenation generally suffer from air-instability (pyrophoricity), low activity and the need for harsh reaction conditions, nano-Co₂P shows both air-stability and remarkably high activity for the hydrogenation of valeronitrile with an excellent turnover number exceeding 58000, which is over 20- to 500-fold greater than that of those previously reported. Moreover, nano-Co₂P efficiently promotes the hydrogenation of a wide range of nitriles, which include di- and tetra-nitriles, to the corresponding primary amines even under just 1 bar of H₂ pressure, far milder than the conventional reaction conditions. Detailed spectroscopic studies reveal that the high performance of nano-Co₂P is attributed to its air-stable metallic nature and the increase of the d-electron density of Co near the Fermi level by the phosphidation of Co, which thus leads to the accelerated activation of both nitrile and H₂. Such a phosphidation provides a promising method for the design of an advanced catalyst with high activity and stability in highly efficient and environmentally benign hydrogenations.

Recent Advances and Promises in Nitrile Hydratase: From Mechanism to Industrial Applications

Nitrile hydratase (NHase, EC 4.2.1.84) is one type of metalloenzyme participating in the biotransformation of nitriles into amides. Given its catalytic specificity in amide production and eco-friendliness, NHase has overwhelmed its chemical counterpart during the past few decades. However, unclear catalytic mechanism, low thermostablity, and narrow substrate specificity limit the further application of NHase. During the past few years, numerous studies on the theoretical and industrial aspects of NHase have advanced the development of this green catalyst. This review critically focuses on NHase research from recent years, including the natural distribution, gene types, posttranslational modifications, expression, proposed catalytic mechanism, biochemical properties, and potential applications of NHase. The developments of NHase described here are not only useful for further application of NHase, but also beneficial for the development of the fields of biocatalysis and biotransformation.

Genetic and Functional Diversity of Nitrilases in Agaricomycotina

Nitrilases participate in the nitrile metabolism in microbes and plants. They are widely used to produce carboxylic acids from nitriles. Nitrilases were described in bacteria, Ascomycota and plants. However, they remain unexplored in Basidiomycota. Yet more than 200 putative nitrilases are found in this division via GenBank. The majority of them occur in the subdivision Agaricomycotina. In this work, we analyzed their sequences and classified them into phylogenetic clades. Members of clade 1 (61 proteins) and 2 (25 proteins) are similar to plant nitrilases and nitrilases from Ascomycota, respectively, with sequence identities of around 50%. The searches also identified five putative cyanide hydratases (CynHs). Representatives of clade 1 and 2 (NitTv1 from Trametes versicolor and NitAg from Armillaria gallica, respectively) and a putative CynH (NitSh from Stereum hirsutum) were overproduced in Escherichia coli. The substrates of NitTv1 were fumaronitrile, 3-phenylpropionitrile, β-cyano-l-alanine and 4-cyanopyridine, and those of NitSh were hydrogen cyanide (HCN), 2-cyanopyridine, fumaronitrile and benzonitrile. NitAg only exhibited activities for HCN and fumaronitrile. The substrate specificities of these nitrilases were largely in accordance with substrate docking in their homology models. The phylogenetic distribution of each type of nitrilase was determined for the first time.

Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans

Background

Burkholderia cenocepacia is a human opportunistic pathogen causing devastating symptoms in patients suffering from immunodeficiency and cystic fibrosis. Out of the 303 B. cenocepacia strains with available genomes, the large majority were isolated from a clinical context. However, several isolates originate from other environmental sources ranging from aerosols to plant endosphere. Plants can represent reservoirs for human infections as some pathogens can survive and sometimes proliferate in the rhizosphere. We therefore investigated if B. cenocepacia had the same potential.

Results

We selected genome sequences from 31 different strains, representative of the diversity of ecological niches of B. cenocepacia, and conducted comparative genomic analyses in the aim of finding specific niche or host-related genetic determinants. Phylogenetic analyses and whole genome average nucleotide identity suggest that strains, registered as B. cenocepacia, belong to at least two different species. Core-genome analyses show that the clade enriched in environmental isolates lacks multiple key virulence factors, which are conserved in the sister clade where most clinical isolates fall, including the highly virulent ET12 lineage. Similarly, several plant associated genes display an opposite distribution between the two clades. Finally, we suggest that B. cenocepacia underwent a host jump from plants/environment to animals, as supported by the phylogenetic analysis. We eventually propose a name for the new species that lacks several genetic traits involved in human virulence.

Conclusion

Regardless of the method used, our studies resulted in a disunited perspective of the B. cenocepacia species. Strains currently affiliated to this taxon belong to at least two distinct species, one having lost several determining animal virulence factors.

Study of Iron Gall Inks, Ingredients and Paper Composition Using Non-Destructive Techniques

Old manuscripts are among the most important elements of the cultural and historical heritage of ancient knowledge. Unfortunately, many of them suffer from degradation, mostly those written with iron gall inks. In the present work, a study using non-destructive techniques was designed with the aim of analyzing the elemental composition and structural characteristics of iron gall inks, reproduced in laboratory, paper and their interaction when the ink is deposited on paper, inducing the paper degradation. Proton induced X-ray emission, X-ray diffraction and Fourier-transform infrared spectroscopy provided the elemental and structural information, and photography under infrared (IR) and ultraviolet (UV) light allowed the differentiation between manufactured inks. Results show that the first step of inked paper deterioration is due to acid-hydrolysis of the cellulose and the presence of reactive Fe(II) species by reducing the crystallinity index of the paper, which is affected depending on the ink recipe and the starting raw materials. These results will be useful to future studies on ancient documents written with iron gall inks, which suffer deterioration due to ink corrosion, and to differentiate between the different paper degradation mechanisms.

Combined Markers to Assess Meat Intake-Human Metabolomic Studies of Discovery and Validation

SCOPE

Biomarkers of red meat may clarify the relationship between meat intake and health. This paper explores the discovery of biomarkers of intake for three types of meat with varying heme iron content. Candidate biomarkers for red and general meat are further evaluated based on defined validation criteria.

METHODS AND RESULTS

In a randomized cross-over meal study, healthy volunteers consume a randomized sequence of four test meals: chicken, pork, beef, and a control made of egg white and pea. Fasting and postprandial urine samples are collected to cover 48 h and profiled by untargeted LC-ESI-qTOF-MS metabolomics. The profiles following the meal challenges are explored by univariate and multivariate analyses. Nine red, four white, and eight general meat biomarkers are selected as putative biomarkers, originating from collagen degradation, flavour compounds, and amino acid metabolism. Heme-related metabolites are masked by the chlorophyll content of the control meal. The candidate biomarkers are confirmed in an independent meal study and validated for plausibility, robustness, time-response, and prediction performance. Combinations of biomarkers are more efficient than single markers in predicting meat intake.

CONCLUSION

New combinations of partially validated biomarkers are proposed to assess terrestrial meat intake and thus help disentangle the effects of meat consumption on human health.

In vivo metal selectivity of metal-dependent biosynthesis of cobalt-type nitrile hydratase in Rhodococcus bacteria: a new look at the nitrile hydratase maturation mechanism?

Metal-dependent cblA-mediated mechanism of transcription regulation of NHase could not discriminate Ni and Co, but mechanism of NHase enzyme maturation could do this.

Conversion of aliphatic nitriles by the arylacetonitrilase from Pseudomonas fluorescens EBC191

The conversion of aliphatic nitriles by the arylacetonitrilase from Pseudomonas fluorescens EBC191 (NitA) was analyzed. The nitrilase hydrolysed a wide range of aliphatic mono- and dinitriles and showed a preference for unsaturated aliphatic substrates containing 5-6 carbon atoms. In addition, increased reaction rates were also found for aliphatic nitriles carrying electron withdrawing substituents (e.g. chloro- or hydroxy-groups) close to the nitrile group. Aliphatic dinitriles were attacked only at one of the nitrile groups and with most of the tested dinitriles the monocarboxylates were detected as major products. In contrast, fumarodinitrile was converted to the monocarboxylate and the monocarboxamide in a ratio of about 65:35. Significantly different relative amounts of the two products were observed with two nitrilase variants with altered reaction specifities. NitA converted some aliphatic substrates with higher rates than 2-phenylpropionitrile, which is one of the standard substrates for arylacetonitrilases. This indicated that the traditional classification of nitrilases as "arylacetonitrilases", "aromatic" or "aliphatic" nitrilases might require some corrections. This was also suggested by the construction of some variants of NitA which were modified in an amino acid residue which was previously suggested to be essential for the conversion of aliphatic substrates by a homologous nitrilase.

Overproduction and characterization of the first enzyme of a new aldoxime dehydratase family in Bradyrhizobium sp

Almost 100 genes within the genus Bradyrhizobium are known to potentially encode aldoxime dehydratases (Oxds), but none of the corresponding proteins have been characterized yet. Aldoximes are natural substances involved in plant defense and auxin synthesis, and Oxds are components of enzymatic cascades enabling bacteria to transform, utilize and detoxify them. The aim of this work was to characterize a representative of the highly conserved Oxds in Bradyrhizobium spp. which include both plant symbionts and members of the soil communities. The selected oxd gene from Bradyrhizobium sp. LTSPM299 was expressed in Escherichia coli, and the corresponding gene product (OxdBr1; GenBank: WP_044589203) was obtained as an N-His₆-tagged protein (monomer, 40.7 kDa) with 30-47% identity to Oxds characterized previously. OxdBr1 was most stable at pH ca. 7.0-8.0 and at up to 30 °C. As substrates, the enzyme acted on (aryl)aliphatic aldoximes such as E/Z-phenylacetaldoxime, E/Z-2-phenylpropionaldoxime, E/Z-3-phenylpropionaldoxime, E/Z-indole-3-acetaldoxime, E/Z-propionaldoxime, E/Z-butyraldoxime, E/Z-valeraldoxime and E/Z-isovaleraldoxime. Some of the reaction products of OxdBr1 are substrates of nitrilases occurring in the same genus. Regions upstream of the oxd gene contained genes encoding a putative aliphatic nitrilase and its transcriptional activator, indicating the participation of OxdBr1 in the metabolic route from aldoximes to carboxylic acids.

Determination of the Absolute Configuration of (-)-Hydroxynitrilaphos and Related Biosynthetic Questions

The ongoing search for bioactive natural products has led to the development of new genome-based screening approaches to identify possible phosphonate producing microorganisms. From the identified phosphonate producers, several until now unknown phosphonic acid natural products were isolated, including (hydroxy)nitrilaphos (4 and 5) and (hydroxy)phosphonocystoximate (7 and 6). We present the synthesis of phosphonocystoximate via an aldoxime intermediate. Chlorination and coupling with methyl N-acetylcysteinate furnished 6 after global deprotection. The obtained experimental data confirm the previously assigned structure of the natural product. We were also able to determine the absolute configuration of (-)-hydroxynitrilaphos. Chiral resolution of diethyl cyanohydroxymethylphosphonate (24) with Noe's lactol furnished both enantiomers of 4. Conversion of (+)-24 to (R)-2-amino-1-hydroxyethylphosphonic acid by reduction of the cyano-group showed (-)-hydroxynitrilaphos ultimately to be S-configured. Further, we present a ¹³ C-isotope labeling strategy for 4 and 5 that will possibly solve the question of whether hydroxynitrilaphos is a biosynthetic intermediate or a downstream product of hydroxyphosphonocystoximate biosynthesis.

Biodegradation of butyronitrile and demonstration of its mineralization by Rhodococcus sp. MTB5

A nitrile utilizing bacterium Rhodococcus sp. MTB5 was previously isolated in our laboratory by the enrichment culture technique. It is able to utilize butyronitrile as sole carbon, nitrogen, and energy source. Maximum butyronitrile degrading property of this strain has been investigated. Results reveal that 100, 98, and 88 % degradation was achieved for 2, 2.5, and 3 % butyronitrile, respectively. The strain is capable of growing in as high as 5 % butyronitrile concentration. A two-step pathway involving nitrile hydratase (NHase) and amidase was observed for the biodegradation of butyronitrile. Complete degradation (mineralization) of butyronitrile with the help of metabolite feeding experiment was reported. The significance of this investigation was the capability of the strain to completely degrade and its ability to grow on higher concentrations of butyronitrile. These potential features make it a suitable candidate for practical field application for effective in situ bioremediation of butyronitrile contaminated sites.

Traceability of Satsuma Mandarin (Citrus unshiu Marc.) Honey through Nectar/Honey-Sac/Honey Pathways of the Headspace, Volatiles, and Semi-Volatiles: Chemical Markers

Headspace solid-phase microextraction (HS-SPME) and ultrasonic solvent extraction (USE), followed by GC-MS/FID, were applied for monitoring the nectar (NE)/honey-sac (HoS)/honey (HO) pathways of the headspace, volatiles, and semi-volatiles. The major NE (4 varieties of Citrus unshiu) headspace compounds were linalool, α-terpineol, 1H-indole, methyl anthranilate, and phenylacetonitrile. Corresponding extracts contained, among others, 1H-indole, methyl anthranilate, 1,3-dihydro-2H-indol-2-one and caffeine. The major HoS headspace compounds were linalool, α-terpineol, 1,8-cineole, 1H-indole, methyl anthranilate, and cis-jasmone. Characteristic compounds from HoS extract were caffeine, 1H-indole, 1,3-dihydro-2H-indol-2-one, methyl anthranilate, and phenylacetonitrile. However, HO headspace composition was significantly different in comparison to NE and HoS with respect to phenylacetaldehyde and linalool derivatives abundance that appeared as the consequence of the hive conditions and the bee enzyme activity. C. unshiu honey traceability is determined by chemical markers: phenylacetaldehyde, phenylacetonitrile, linalool and its derivatives, as well as 1H-indole, 1,3-dihydro-2H-indol-2-one, and caffeine.

Diversity of nitrogen assimilation pathways among microbial photosynthetic eukaryotes

In an effort to better understand the diversity of genes coding for nitrogen (N) uptake and assimilation pathways among microalgae, we analyzed the transcriptomes of five phylogenetically diverse single celled algae originally isolated from the same high arctic marine region. The five photosynthetic flagellates (a pelagophyte, dictyochophyte, chrysoph-yte, cryptophyte and haptophyte) were grown on standard media and media with only urea or nitrate as a nitrogen source; cells were harvested during late exponential growth. Based on homolog protein sequences, transcriptomes of each alga were interrogated to retrieve genes potentially associated with nitrogen uptake and utilization pathways. We further investigated the phylogeny of poorly characterized genes and gene families that were identified. While the phylogeny of the active urea transporter (DUR3) was taxonomically coherent, those for the urea transporter superfamily, putative nitrilases and amidases indicated complex evolutionary histories, and preliminary evidence for horizontal gene transfers. All five algae expressed genes for ammonium assimilation and all but the chrysophyte expressed genes involved in nitrate utilization and the urea cycle. Among the four algae with nitrate transporter transcripts, we detected lower expression levels in three of these (the dictyochophyte, pelagophyte, and cryptophyte) grown in the urea only medium compared with cultures from the nitrate only media. The diversity of N pathway genes in the five algae, and their ability to grow using urea as a nitrogen source, suggest that these flagellates are able to use a variety of organic nitrogen sources, which would be an advantage in an inorganic nitrogen - limited environment, such as the Arctic Ocean.

Biosynthetic pathway for the cyanide-free production of phenylacetonitrile in Escherichia coli by utilizing plant cytochrome P450 79A2 and bacterial aldoxime dehydratase

The biosynthetic pathway for the production of phenylacetonitrile (PAN), which has a wide variety of uses in chemical and pharmaceutical industries, was constructed in Escherichia coli utilizing enzymes from the plant glucosinolate-biosynthetic and bacterial aldoxime-nitrile pathways. First, the single-step reaction to produce E,Z-phenylacetaldoxime (PAOx) from l-Phe was constructed in E. coli by introducing the genes encoding cytochrome P450 (CYP) 79A2 and CYP reductase from Arabidopsis thaliana, yielding the E,Z-PAOx-producing transformant. Second, this step was expanded to the production of PAN by further introducing the aldoxime dehydratase (Oxd) gene from Bacillus sp. strain OxB-1, yielding the PAN-producing transformant. The E,Z-PAOx-producing transformant also produced phenethyl alcohol and PAN as by-products, which were suggested to be the metabolites of E,Z-PAOx produced by E. coli enzymes, while the PAN-producing transformant accumulated only PAN in the culture broth, which suggested that the CYP79A2 reaction (the conversion of l-Phe to E,Z-PAOx) was a potential bottleneck in the PAN production pathway. Expression of active CYP79A2 and concentration of biomass were improved by the combination of the autoinduction method, coexpression of groE, encoding the heat shock protein GroEL/GroES, N-terminal truncation of CYP79A2, and optimization of the culture conditions, yielding a >60-fold concentration of E,Z-PAOx (up to 2.9 mM). The concentration of PAN was 4.9 mM under the optimized conditions. These achievements show the potential of this bioprocess to produce nitriles and nitrile derivatives in the absence of toxic chemicals.

Mild and selective hydrogenation of aromatic and aliphatic (di)nitriles with a well-defined iron pincer complex

The catalytic hydrogenation of carboxylic acid derivatives represents an atom-efficient and clean reduction methodology in organic chemistry. More specifically, the selective hydrogenation of nitriles offers the possibility for a green synthesis of valuable primary amines. So far, this transformation lacks of useful, broadly applicable non-noble metal-based catalyst systems. In the present study, we describe a molecular-defined iron complex, which allows for the hydrogenation of aryl, alkyl, heterocyclic nitriles and dinitriles. By using an iron PNP pincer complex, we achieve very good functional group tolerance. Ester, ether, acetamido as well as amino substituents are not reduced in the presence of nitriles. Moreover, nitriles including an α,β-unsaturated double bond and halogenated derivatives are well tolerated in this reaction. Notably, our complex constitutes the first example of an homogeneous catalyst, which permits the selective hydrogenation of industrially important adipodinitrile to 1,6-hexamethylenediamine.

Effect of physicochemical parameters on nitrile-hydrolyzing potentials of newly isolated nitrilase of Fusarium oxysporum f. sp. lycopercisi ED-3

In recent years, nitrilases from fungus have received increasing attention, and most of the studies are performed on nitrilases of bacterial origin. Frequently used methods are based on analytical methods such as high-performance liquid chromatography, liquid chromatography-mass spectrometry, and gas chromatography; therefore, an efficient, user friendly, and rapid method has been developed to screen nitrilase enzyme based on the principle of color change of a pH indicator. Phenol red amended with the minimal medium appears light yellow at neutral pH, which changes into pink with the formation of ammonia, indicating nitrilase activity in the reaction medium. A highly potent strain ED-3 identified as Fusarium oxysporum f. sp. lycopercisi (specific activity 17.5 µmol/Min/mg dcw) was isolated using this method. The nitrilase activity of F. oxysporum f. sp. lycopercisi ED-3 strain showed wide substrate specificity toward aliphatic nitriles, aromatic nitriles, and orthosubstituted heterocyclic nitriles. 4-Aminobenzonitrile was found to be a superior substrate among all the nitriles used in this study. This nitrilase was active within pH 5-10 and temperature ranging from 25 to 60 °C with optimal at pH 7.0 and temperature at 50 °C. The nitrilase activity was enhanced to several folds through optimization of culture and biotransformation conditions from 1,121 to 1,941 µmol/Min.

Cyanohydrin phosphonate natural product from Streptomyces regensis

Streptomyces regensis strain WC-3744 was identified as a potential phosphonic acid producer in a large-scale screen of microorganisms for the presence of the pepM gene, which encodes the key phosphonate biosynthetic enzyme phosphoenolpyruvate phosphonomutase. (31)P NMR revealed the presence of several unidentified phosphonates in spent medium after growth of S. regensis. These compounds were purified and structurally characterized via extensive 1D and 2D NMR spectroscopic and mass spectrometric analyses. Three new phosphonic acid metabolites, whose structures were confirmed by comparison to chemically synthesized standards, were observed: (2-acetamidoethyl)phosphonic acid (1), (2-acetamido-1-hydroxyethyl)phosphonic (3), and a novel cyanohydrin-containing phosphonate, (cyano(hydroxy)methyl)phosphonic acid (4). The gene cluster responsible for synthesis of these molecules was also identified from the draft genome sequence of S. regensis, laying the groundwork for future investigations into the metabolic pathway leading to this unusual natural product.

Possible evolution of alliarinoside biosynthesis from the glucosinolate pathway in Alliaria petiolata

Nitrile formation in plants involves the activity of cytochrome P450s. Hydroxynitrile glucosides are widespread among plants but generally do not occur in glucosinolate producing species. Alliaria petiolata (garlic mustard, Brassicaceae) is the only species known to produce glucosinolates as well as a γ-hydroxynitrile glucoside. Furthermore, A. petiolata has been described to release diffusible cyanide, which indicates the presence of unidentified cyanogenic glucoside(s). Our research on A. petiolata addresses the molecular evolution of P450s. By integrating current knowledge about glucosinolate and hydroxynitrile glucoside biosynthesis in other species and new visions on recurrent evolution of hydroxynitrile glucoside biosynthesis, we propose a pathway for biosynthesis of the γ-hydroxynitrile glucoside, alliarinoside. Homomethionine and the corresponding oxime are suggested as shared intermediates in the biosynthesis of alliarinoside and 2-propenyl glucosinolate. The first committed step in the alliarinoside pathway is envisioned to be catalysed by a P450, which has been recruited to metabolize the oxime. Furthermore, alliarinoside biosynthesis is suggested to involve enzyme activities common to secondary modification of glucosinolates. Thus, we argue that biosynthesis of alliarinoside may be the first known case of a hydroxynitrile glucoside pathway having evolved from the glucosinolate pathway. An intriguing question is whether the proposed hydroxynitrile intermediate may also be converted to novel homomethionine-derived cyanogenic glucoside(s), which could release cyanide. Elucidation of the pathway for biosynthesis of alliarinoside and other putative hydroxynitrile glucosides in A. petiolata is envisioned to offer significant new knowledge on the emerging picture of P450 functional dynamics as a basis for recurrent evolution of pathways for bioactive natural product biosynthesis.

Nature and lability of northern Adriatic macroaggregates

The key organic constituents of marine macroaggregates (macrogels) of prevalently phytoplankton origin, periodically occurring in the northern Adriatic Sea, are proteins, lipids and especially polysaccharides. In this article, the reactivity of various macroaggregate fractions in relation to their composition in order to decode the potentially »bioavailable« fractions is summarized and discussed. The enzymatic hydrolysis of the macroaggregate matrix, using α-amylase, β-glucosidase, protease, proteinase and lipase, revealed the simultaneous degradation of polysaccharides and proteins, while lipids seem largely preserved. In the fresh surface macroaggregate samples, a pronounced degradation of the α-glycosidic bond compared to β-linkages. Degradation of the colloidal fraction proceeded faster in the higher molecular weight (MW) fractions. N-containing polysaccharides can be important constituents of the higher MW fraction while the lower MW constituents can mostly be composed of poly- and oligosaccharides. Since the polysaccharide component in the higher MW fraction is more degradable compared to N-containing polysaccharides, the higher MW fraction represents a possible path of organic nitrogen preservation. Enzymatic hydrolysis, using α-amylase and β-glucosidase, revealed the presence of α- and β-glycosidic linkages in all fractions with similar decomposition kinetics. Our results indicate that different fractions of macroaggregates are subjected to compositional selective reactivity with important implications for macroaggregate persistence in the seawater column and deposition.

Real-time PCR detection of Fe-type nitrile hydratase genes from environmental isolates suggests horizontal gene transfer between multiple genera

Nitriles are widespread in the environment as a result of biological and industrial activity. Nitrile hydratases catalyse the hydration of nitriles to the corresponding amide and are often associated with amidases, which catalyze the conversion of amides to the corresponding acids. Nitrile hydratases have potential as biocatalysts in bioremediation and biotransformation applications, and several successful examples demonstrate the advantages. In this work a real-time PCR assay was designed for the detection of Fe-type nitrile hydratase genes from environmental isolates purified from nitrile-enriched soils and seaweeds. Specific PCR primers were also designed for amplification and sequencing of the genes. Identical or highly homologous nitrile hydratase genes were detected from isolates of numerous genera from geographically diverse sites, as were numerous novel genes. The genes were also detected from isolates of genera not previously reported to harbour nitrile hydratases. The results provide further evidence that many bacteria have acquired the genes via horizontal gene transfer. The real-time PCR assay should prove useful in searching for nitrile hydratases that could have novel substrate specificities and therefore potential in industrial applications.

Nitrilase enzymes and their role in plant-microbe interactions

Nitrilase enzymes (nitrilases) catalyse the hydrolysis of nitrile compounds to the corresponding carboxylic acid and ammonia, and have a wide range of industrial and biotechnological applications, including the synthesis of industrially important carboxylic acids and bioremediation of cyanide and toxic nitriles. Nitrilases are produced by a wide range of organisms, including plants, bacteria and fungi, but despite their biotechnological importance, the role of these enzymes in living organisms is relatively underexplored. Current research suggests that nitrilases play important roles in a range of biological processes. In the context of plant-microbe interactions they may have roles in hormone synthesis, nutrient assimilation and detoxification of exogenous and endogenous nitriles. Nitrilases are produced by both plant pathogenic and plant growth-promoting microorganisms, and their activities may have a significant impact on the outcome of plant-microbe interactions. In this paper we review current knowledge of the role of nitriles and nitrilases in plants and plant-associated microorganisms, and discuss how greater understanding of the natural functions of nitrilases could be applied to benefit both industry and agriculture.

A conserved mechanism for nitrile metabolism in bacteria and plants

Pseudomonas fluorescens SBW25 is a plant growth-promoting bacterium that efficiently colonizes the leaf surfaces and rhizosphere of a range of plants. Previous studies have identified a putative plant-induced nitrilase gene (pinA) in P. fluorescens SBW25 that is expressed in the rhizosphere of sugar beet plants. Nitrilase enzymes have been characterised in plants, bacteria and fungi and are thought to be important in detoxification of nitriles, utilisation of nitrogen and synthesis of plant hormones. We reveal that pinA is a NIT4-type nitrilase that catalyses the hydrolysis of beta-cyano-L-alanine, a nitrile common in the plant environment and an intermediate in the cyanide detoxification pathway in plants. In plants cyanide is converted to beta-cyano-L-alanine, which is subsequently detoxified to aspartic acid and ammonia by NIT4. In P. fluorescens SBW25 pinA is induced in the presence of beta-cyano-L-alanine, and the beta-cyano-L-alanine precursors cyanide and cysteine. pinA allows P. fluorescens SBW25 to use beta-cyano-L-alanine as a nitrogen source and to tolerate toxic concentrations of this nitrile. In addition, pinA is shown to complement a NIT4 mutation in Arabidopsis thaliana, enabling plants to grow in concentrations of beta-cyano-L-alanine that would otherwise prove lethal. Interestingly, over-expression of pinA in wild-type A. thaliana not only resulted in increased growth in high concentrations of beta-cyano-L-alanine, but also resulted in increased root elongation in the absence of exogenous beta-cyano-L-alanine, demonstrating that beta-cyano-L-alanine nitrilase activity can have a significant effect on root physiology and root development.

Biodegradation potential of the genus Rhodococcus

A large number of aromatic compounds and organic nitriles, the two groups of compounds covered in this review, are intermediates, products, by-products or waste products of the chemical and pharmaceutical industries, agriculture and the processing of fossil fuels. The majority of these synthetic substances (xenobiotics) are toxic and their release and accumulation in the environment pose a serious threat to living organisms. Bioremediation using various bacterial strains of the genus Rhodococcus has proved to be a promising option for the clean-up of polluted sites. The large genomes of rhodococci, their redundant and versatile catabolic pathways, their ability to uptake and metabolize hydrophobic compounds, to form biofilms, to persist in adverse conditions and the availability of recently developed tools for genetic engineering in rhodococci make them suitable industrial microorganisms for biotransformations and the biodegradation of many organic compounds. The peripheral and central catabolic pathways in rhodococci are characterized for each type of aromatics (hydrocarbons, phenols, halogenated, nitroaromatic, and heterocyclic compounds) in this review. Pathways involved in the hydrolysis of nitrile pollutants (aliphatic nitriles, benzonitrile analogues) and the corresponding enzymes (nitrilase, nitrile hydratase) are described in detail. Examples of regulatory mechanisms for the expression of the catabolic genes are given. The strains that efficiently degrade the compounds in question are highlighted and examples of their use in biodegradation processes are presented.

Discovery of a mandelonitrile hydrolase from Bradyrhizobium japonicum USDA110 by rational genome mining

A mandelonitrile hydrolase bll6402 from Bradyrhizobium japonicum USDA110 was predicted by rational genome mining, i.e. combining traditional genome mining with functional analysis of the genetic organization of the putative nitrilase gene within the chromosome of microorganisms. This putative gene was cloned and over-expressed in Escherichia coli, and the encoded protein was purified to give a nitrilase with a molecular mass of about 37kDa. The molecular weight of the holoenzyme was about 455kDa, suggesting that nitrilase bll6402 self-aggregated to the active form with native structure being 12 subunits of identical size. This nitrilase was most active toward mandelonitrile with V(max) and K(m) for mandelonitrile being 44.7U/mg and 0.26mM, respectively. The k(cat) and overall catalytic efficiency k(cat)/K(m) were 27.0s(-1) and 1.04x10(5)M(-1)s(-1), indicating that nitrilase bll6402 is very active for the hydrolysis of mandelonitrile to mandelic acid. Nitrilase bll6402 also effectively hydrolyzed several mandelonitrile derivatives.

Exploring nitrilase sequence space for enantioselective catalysis

Nitrilases are important in the biosphere as participants in synthesis and degradation pathways for naturally occurring, as well as xenobiotically derived, nitriles. Because of their inherent enantioselectivity, nitrilases are also attractive as mild, selective catalysts for setting chiral centers in fine chemical synthesis. Unfortunately, <20 nitrilases have been reported in the scientific and patent literature, and because of stability or specificity shortcomings, their utility has been largely unrealized. In this study, 137 unique nitrilases, discovered from screening of >600 biotope-specific environmental DNA (eDNA) libraries, were characterized. Using culture-independent means, phylogenetically diverse genomes were captured from entire biotopes, and their genes were expressed heterologously in a common cloning host. Nitrilase genes were targeted in a selection-based expression assay of clonal populations numbering 10(6) to 10(10) members per eDNA library. A phylogenetic analysis of the novel sequences discovered revealed the presence of at least five major sequence clades within the nitrilase subfamily. Using three nitrile substrates targeted for their potential in chiral pharmaceutical synthesis, the enzymes were characterized for substrate specificity and stereospecificity. A number of important correlations were found between sequence clades and the selective properties of these nitrilases. These enzymes, discovered using a high-throughput, culture-independent method, provide a catalytic toolbox for enantiospecific synthesis of a variety of carboxylic acid derivatives, as well as an intriguing library for evolutionary and structural analyses.

Characterization and synthetic applications of recombinant AtNIT1 from Arabidopsis thaliana

The nitrilase AtNIT1 from Arabidopsis thaliana was overexpressed in Escherichia coli with an N-terminal His6 tag and purified by zinc chelate affinity chromatography in a single step almost to homogeneity in a 68% yield with a specific activity of 34.1 U.mg-1. The native enzyme (approximately 450 kDa) consists of 11-13 subunits (38 kDa). The temperature optimum was determined to be 35 degrees C and a pH optimum of 9 was found. Thus, recombinant AtNIT1 resembles in its properties the native enzyme and the nitrilase from Brassica napus. The stability of AtNIT1 could be significantly improved by the addition of dithiothreitol and EDTA. The substrate range of AtNIT1 differs considerably from those of bacterial nitrilases. Aliphatic nitriles are the most effective substrates, showing increasing rates of hydrolysis with increasing size of the residues, as demonstrated in the series butyronitrile, octanenitrile, phenylpropionitrile. In comparison with 3-indolylacetonitrile, the rate of hydrolysis of 3-phenylpropionitrile is increased by a factor of 330, and the Km value is reduced by a factor of 23. With the exception of fluoro, substituents in the alpha position to the nitrile function completely inhibit the hydrolysis.