Novel heme-containing lyase, phenylacetaldoxime dehydratase from Bacillus sp. strain OxB-1: purification, characterization, and molecular cloning of the gene

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.

Immobilization of aldoxime dehydratases on metal affinity resins and use of the immobilized catalysts for the synthesis of nitriles important in fragrance industry

Nitriles have a wide range of uses as building blocks, solvents, and alternative fuels, but also as intermediates and components of flavors and fragrances. The enzymatic synthesis of nitriles by aldoxime dehydratase (Oxd) is an emerging process with significant advantages over conventional approaches. Here we focus on the immobilization of His-tagged Oxds on metal affinity resins, an approach that has not been used previously for these enzymes. The potential of the immobilized Oxd was demonstrated for the synthesis of phenylacetonitrile (PAN) and E-cinnamonitrile, compounds applicable in the fragrance industry. A comparison of Talon and Ni-NTA resins showed that Ni-NTA with its higher binding capacity was more suitable for the immobilization of Oxd. Immobilized Oxds were prepared from purified enzymes (OxdFv from Fusarium vanettenii and OxdBr1 from Bradyrhizobium sp.) or the corresponding cell-free extracts. The immobilization of cell-free extracts reduced time and cost of the catalyst production. The immobilized OxdBr1 was superior in terms of recyclability (22 cycles) in the synthesis of PAN from 15 mM E/Z-phenylacetaldoxime at pH 7.0 and 30 °C (100% conversion, 61% isolated yield after product purification). The volumetric and catalyst productivity was 10.5 g/L/h and 48.3 g/g of immobilized protein, respectively.

Nitrile-synthesizing enzymes and biocatalytic synthesis of volatile nitrile compounds: A review

Nitriles (R-CN) comprise a broad group of chemicals industrially produced and used in fine chemicals, pharmaceuticals, and bulk applications, polymer chemistry, solvents, etc. Nitriles are important starting materials for producing carboxylic acids, amides, amines, and several other compounds. In addition, some volatile nitriles have been evaluated for their potential as ingredients in fragrance and flavor formulations. However, many nitrile synthesis methods have drawbacks, such as drastic reaction conditions, limited substrate scope, lack of readily available reagents, poor yields, and long reaction times. In contrast to chemical synthesis, biocatalytic approaches using enzymes can produce nitriles without harsh conditions, such as high temperatures and pressures, or toxic compounds. In this review, we summarize the nitrile-synthesizing enzymes from microorganisms, plants, and animals. Furthermore, we introduce several examples of biocatalytic synthesis of volatile nitrile compounds, particularly those using aldoxime dehydratase.

Enzymatic properties of a non-classical aldoxime dehydratase capable of producing alkyl and arylalkyl nitriles

Nitriles are of significant interest in the flavor and fragrance industries with potential application in cosmetics due to their higher stability than analogous aldehydes. However, the traditional methods to prepare nitriles need toxic reagents and hash conditions. This work aimed to develop a chemoenzymatic strategy to synthesize nitriles from natural aldehydes with aldoxime as the intermediate. A non-classical aldoxime dehydratase (Oxd) was discovered from the fungus Aspergillus ibericus (OxdAsp) to catalyze the dehydration of aldoximes to corresponding nitriles under mild conditions. The amino acid sequence of OxdAsp exhibits an approximately 20% identity with bacterial Oxds. OxdAsp contains a heme prosthetic group bound with the axial H287 in the catalytic pocket. The structure models of OxdAsp with substrates suggest that its catalytic triad is Y138-R141-E192, which is different from the classically bacterial Oxds of His-Arg-Ser/Thr. The catalytic mechanism of OxdAsp was proposed based on the mutagenesis of key residues. The hydroxyl group of the substrate is fixed by E192 to increase its basicity. Y138 acts as a general acid-based catalyst, and its phenolic proton is polarized by the adjacent R141. The protonated Y138 would donate a proton to the hydroxyl group of the substrate and eliminate a water molecule from aldoxime to produce nitrile. The recombinant OxdAsp can efficiently dehydrate citronellal oxime and cinnamaldoxime to citronellyl nitrile and cinnamonitrile in aqueous media, which are applied as fragrance ingredients in the food and cosmetic fields. KEY POINTS: • A novel aldoxime dehydratase from the Aspergillus genus was first characterized as a heme-binding protein. • The catalytic mechanism was predicted based on the molecular interactions of the catalytic pocket with the substrate. • A chemoenzymatic strategy was developed to synthesize nitriles from natural aldehydes with aldoxime as the intermediate.

Interactions of arylhydroxylamines and alkylaldoximes with a rhodium porphyrin

Heme enzymes are involved in the binding and metabolism of hydroxylamine (RNHOH) and aldoxime (RCH=NOH) compounds (R = H, alkyl, aryl). We report the synthesis and X-ray crystal structure of a metalloporphyrin in complex with an arylhydroxylamine, namely that of (TPP)Rh(PhNHOH)(C6H4Cl) (TPP = tetraphenylpophryinato dianion). The crystal structure reveals, in addition to N-binding of PhNHOH to Rh, the presence of an intramolecular H-bond between the hydroxylamine -OH proton and a porphyrin N-atom. Results from density functional theory (DFT) calculations support the presence of this intramolecular H-bond in this global minimum structure, and a natural bond order (NBO) analysis reveals that this H-bond comprises a donor π N=C (porphyrin) to acceptor σ* O-H (hydroxylamine) interaction of 2.32 kcal/mol. While DFT calculations predict the presence of similar intramolecular H-bond interactions in the related aldoxime complexes (TPP)Rh(RCH=NOH)(C6H4Cl) in their global minima structures, the X-ray crystal structure obtained for the (TPP)Rh(CH3(CH2)2CH=NOH)(C6H4Cl) complex is consistent with the local (non-global) minima conformation that does not have this intramolecular H-bond interaction.

Scanning aldoxime dehydratase sequence space and characterization of a new aldoxime dehydratase from Fusarium vanettenii

The aim of this work was to map the sequence space of aldoxime dehydratases (Oxds) as enzymes with great potential for nitrile synthesis. Microbes contain an abundance of putative Oxds but fewer than ten Oxds were characterized in total and only two in fungi. In this work, we prepared and characterized a new Oxd (protein gb|EEU37245.1 named OxdFv) from Fusarium vanettenii 77-13-4. OxdFv is distant from the characterized Oxds with a maximum of 36% identity. Moreover, the canonical Oxd catalytic triad RSH is replaced by R141-E187-E303 in OxdFv. R141A and E187A mutants did not show significant activities, but mutant E303A showed a comparable activity as the wild-type enzyme. According to native mass spectrometry, OxdFv contained almost 1 mol of heme per 1 mol of protein, and was composed of approximately 88% monomer (41.8 kDa) and 12% dimer. A major advantage of this enzyme is its considerable activity under aerobic conditions (25.0 ± 4.3 U/mg for E,Z-phenylacetaldoxime at pH 9.0 and 55 °C). Addition of sodium dithionite (reducing agent) and Fe²⁺ was required for this activity. OxdFv favored (aryl)aliphatic aldoximes over aromatic aldoximes. Substrate docking in the homology model of OxdFv showed a similar substrate specificity. We conclude that OxdFv is the first characterized Oxd of the REE type.

Bioinspired Iron-Catalyzed Dehydration of Aldoximes to Nitriles: A General N-O Redox-Cleavage Method

Inspired by OxdA that operates biocatalytic aldoxime dehydration, we have developed an efficient iron catalyst, Cp*Fe(1,2-Cy₂PC₆H₄O) (1), which rapidly converts various aliphatic and aromatic aldoximes to nitriles with release of H₂O at room temperature. The catalysis involves redox activation of the N-O bond by a 1e^- transfer from the iron catalyst to the oxime. Such redox-mediated N-O cleavage was demonstrated by the isolation of a ferrous iminato intermediate from the reaction of the ketoxime substrate. This iron-catalyzed acceptorless dehydration approach represents a general method for the preparation of nitriles, and it also delivers salicylonitriles by catalyzing the Kemp elimination reaction.

Metabolism of Aldoximes and Nitriles in Plant-Associated Bacteria and Its Potential in Plant-Bacteria Interactions

In plants, aldoximes per se act as defense compounds and are precursors of complex defense compounds such as cyanogenic glucosides and glucosinolates. Bacteria rarely produce aldoximes, but some are able to transform them by aldoxime dehydratase (Oxd), followed by nitrilase (NLase) or nitrile hydratase (NHase) catalyzed transformations. Oxds are often encoded together with NLases or NHases in a single operon, forming the aldoxime-nitrile pathway. Previous reviews have largely focused on the use of Oxds and NLases or NHases in organic synthesis. In contrast, the focus of this review is on the contribution of these enzymes to plant-bacteria interactions. Therefore, we summarize the substrate specificities of the enzymes for plant compounds. We also analyze the taxonomic and ecological distribution of the enzymes. In addition, we discuss their importance in selected plant symbionts. The data show that Oxds, NLases, and NHases are abundant in Actinobacteria and Proteobacteria. The enzymes seem to be important for breaking through plant defenses and utilizing oximes or nitriles as nutrients. They may also contribute, e.g., to the synthesis of the phytohormone indole-3-acetic acid. We conclude that the bacterial and plant metabolism of aldoximes and nitriles may interfere in several ways. However, further in vitro and in vivo studies are needed to better understand this underexplored aspect of plant-bacteria interactions.

Rossellomorea arthrocnemi sp. nov., a novel plant growth-promoting bacterium used in heavy metal polluted soils as a phytoremediation tool

Strain EAR8^T is a root endophyte isolated from Arthrocnemum macrostachyum plants collected from the Odiel marshes, Huelva (Spain). It presented in vitro plant growth-promoting properties and improved the plant growth and heavy metal accumulation in polluted soils playing an important role in phytoremediation strategies. Phenotypically, strain EAR8^T cells were Gram-positive, aerobic and non-motile rods with terminal oval endospores and non-swollen sporangia which form beige, opaque, butyrous, raised and irregular colonies with undulate margins. The strain was able to grow between 15–45 °C, at pH 6.0–9.0 and tolerated 0–25 % NaCl (w/v) showing optimal growth conditions on trypticase soy agar plates supplemented with 2.5 % NaCl (w/v) at pH 7.0 and 37 °C for 24 h. Chemotaxonomic analyses showed that the isolate has meso-diaminopimelic acid as the peptidoglycan in the cell wall and MK-7 as the major respiratory quinone. The predominant fatty acids were anteiso-C_15 : 0 and iso-C_15 : 0 and the polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analyses based on the whole proteomes of closest sequenced relatives confirmed that strain EAR8^T is affiliated to the genus Rossellomorea and forms a clade with Rossellomorea vietnamensis 15-1^T with maximum support. Genome analyses showed that EAR8^T has indole-3-acetic acid and siderophore biosynthesis and transporters genes and genes related to resistance against heavy metals. Phenotypic and phylogenomic comparative studies suggested that strain EAR8^T is a new representative of the genus Rossellomorea and the name Rossellomorea arthrocnemi sp. nov. is proposed. Type strain is EAR8^T (=CECT 9072^T=DSM 103900^T).

Cyanide-free synthesis of aromatic nitriles from aldoximes: Discovery and application of a novel heme-containing aldoxime dehydratase

Aromatic nitriles are important structural motifs that frequently existed in pharmaceutical drugs. Due to the convenient synthesis of aldoximes from aldehydes, the dehydration of aldoximes to corresponding nitriles by aldoxime dehydratases (Oxds) is considered as a safe and robust enzymatic production route. Although the Oxd genes are widely distributed in microbial kingdom, so far less than ten Oxds were expressed and further characterized. In this study, we found 26 predicted putative Oxd genes from the GenBank database using a genome mining strategy. The Oxd gene from Pseudomonas putida F1 was cloned and functionally expressed in Escherichia coli BL21 (DE3). The amino acid sequence of OxdF1 shows high identities of 33∼85 % to other characterized Oxds, and contained a ferrous heme as the catalytic site. The optimum reaction pH and temperature of recombinant OxdF1 were 7.0 and 35 °C, respectively. OxdF1 was stable in pH 7.0 potassium phosphate buffer at 30 °C, and its half-life was approximately 3.8 h. OxdF1 can efficiently dehydrate aromatic and heterocyclic aldoximes to nitriles, such as 2-bromobenzaldoxime, 2-chloro-6-fluorobenzaldoxime, thiophene-2-carboxaldoxime, and pyridine-3-aldoxime. Therefore, the recombinant OxdF1 shows a potential application in the cyanide-free synthesis of aromatic nitriles.

Rationalizing the Unprecedented Stereochemistry of an Enzymatic Nitrile Synthesis through a Combined Computational and Experimental Approach

In this contribution, the unique and unprecedented stereochemical phenomenon of an aldoxime dehydratase‐catalyzed enantioselective dehydration of racemic E‐ and Z‐aldoximes with selective formation of both enantiomeric forms of a chiral nitrile is rationalized by means of molecular modelling, comprising in silico mutations and docking studies. This theoretical investigation gave detailed insight into why with the same enzyme the use of racemic E‐ and Z‐aldoximes leads to opposite forms of the chiral nitrile. The calculated mutants with a larger or smaller cavity in the active site were then prepared and used in biotransformations, showing the theoretically predicted decrease and increase of the enantioselectivities in these nitrile syntheses. This validated model also enabled the rational design of mutants with a smaller cavity, which gave superior enantioselectivities compared to the known wild‐type enzyme, with excellent E‐values of up to E>200 when the mutant OxdRE‐Leu145Phe was utilized.

Segmented Flow Processes to Overcome Hurdles of Whole-Cell Biocatalysis in the Presence of Organic Solvents

In modern process development, it is imperative to consider biocatalysis, and whole-cell catalysts often represent a favored form of such catalysts. However, the application of whole-cell catalysis in typical organic batch two-phase synthesis often struggles due to mass transfer limitations, emulsion formation, tedious work-up and, thus, low yields. Herein, we demonstrate that utilizing segmented flow tools enables the conduction of whole-cell biocatalysis efficiently in biphasic media. Exemplified for three different biotransformations, the power of such segmented flow processes is shown. For example, a 3-fold increase of conversion from 34 % to >99 % and a dramatic simplified work-up leading to a 1.5-fold higher yield from 44 % to 65 % compared to the analogous batch process was achieved in such a flow process.

Protein engineering of the aldoxime dehydratase from Bacillus sp. OxB-1 based on a rational sequence alignment approach

Recently, the program INTMSAlign_HiSol for identifying aggregation hotspots in proteins only requiring secondary structure data was introduced. We explored the utility of this program further and applied it for engineering of the aldoxime dehydratase from Bacillus sp. OxB-1. Towards this end, the effect of inverting the hydropathy at selected positions of the amino acid sequence on the enzymatic activity was studied leading to 60% of our constructed variants, which showed improved activity. In part, this activity increase can be rationalised by an improved heme incorporation of the variants. For example, a single mutation gave a 1.8 fold increased enzymatic activity and 30% improved absolute heme incorporation.

Synthetic Processes toward Nitriles without the Use of Cyanide: A Biocatalytic Concept Based on Dehydration of Aldoximes in Water

While belonging to the most fundamental functional groups, nitriles represent a class of compound that still raises challenges in terms of an efficient, cost‐effective, general and, at the same time, sustainable way for their synthesis. Complementing existing chemical routes, recently a cyanide‐free enzymatic process technology based on the use of an aldoxime dehydratase (Oxd) as a biocatalyst component has been developed and successfully applied for the synthesis of a range of nitrile products. In these biotransformations, the Oxd enzymes catalyze the dehydration of aldoximes as readily available substrates to the nitrile products. Herein, these developments with such enzymes are summarized, with a strong focus on synthetic applications. It is demonstrated that this biocatalytic technology has the potential to “cross the bridge” between the production of fine chemicals and pharmaceuticals, on one hand, and bulk and commodity chemicals, on the other.

Complete Genomes of the Anaerobic Degradation Specialists Aromatoleum petrolei ToN1T and Aromatoleum bremense PbN1T

The betaproteobacterial genus Aromatoleum comprises facultative denitrifiers specialized in the anaerobic degradation of recalcitrant organic compounds (aromatic and terpenoid). This study reports on the complete and manually annotated genomes of Ar. petrolei ToN1T (5.41 Mbp) and Ar. bremense PbN1T (4.38 Mbp), which cover the phylogenetic breadth of the genus Aromatoleum together with previously genome sequenced Ar. aromaticum EbN1T [Rabus et al., Arch Microbiol. 2005 Jan;183(1):27-36]. The gene clusters for the anaerobic degradation of aromatic and terpenoid (strain ToN1T only) compounds are scattered across the genomes of strains ToN1T and PbN1T. The richness in mobile genetic elements is shared with other Aromatoleum spp., substantiating that horizontal gene transfer should have been a major driver in shaping the genomes of this genus. The composite catabolic network of strains ToN1T and PbN1T comprises 88 proteins, the coding genes of which occupy 86.1 and 76.4 kbp (1.59 and 1.75%) of the respective genome. The strain-specific gene clusters for anaerobic degradation of ethyl-/propylbenzene (strain PbN1T) and toluene/monoterpenes (strain ToN1T) share high similarity with their counterparts in Ar. aromaticum strains EbN1T and pCyN1, respectively. Glucose is degraded via the ED-pathway in strain ToN1T, while gluconeogenesis proceeds via the reverse EMP-pathway in strains ToN1T, PbN1T, and EbN1T. The diazotrophic, endophytic lifestyle of closest related genus Azoarcus is known to be associated with nitrogenase and type-6 secretion system (T6SS). By contrast, strains ToN1T, PbN1T, and EbN1T lack nif genes for nitrogenase (including cofactor synthesis and enzyme maturation). Moreover, strains PbN1T and EbN1T do not possess tss genes for T6SS, while strain ToN1T does and facultative endophytic "Aromatoleum" sp. CIB is known to even have both. These findings underpin the functional heterogeneity among Aromatoleum members, correlating with the high plasticity of their genomes.

Understanding molecular enzymology of porphyrin-binding α + β barrel proteins - One fold, multiple functions

There is a high functional diversity within the structural superfamily of porphyrin-binding dimeric α + β barrel proteins. In this review we aim to analyze structural constraints of chlorite dismutases, dye-decolorizing peroxidases and coproheme decarboxylases in detail. We identify regions of structural variations within the highly conserved fold, which are most likely crucial for functional specificities. The loop linking the two ferredoxin-like domains within one subunit can be of different sequence lengths and can adopt various structural conformations, consequently defining the shape of the substrate channels and the respective active site architectures. The redox cofactor, heme b or coproheme, is oriented differently in either of the analyzed enzymes. By thoroughly dissecting available structures and discussing all available results in the context of the respective functional mechanisms of each of these redox-active enzymes, we highlight unsolved mechanistic questions in order to spark future research in this field.

Indole-3-acetic acid biosynthesis and its regulation in plant-associated bacteria

Numerous studies have reported the stimulation of plant growth following inoculation with an IAA-producing PGPB. However, the specific mode of IAA production by the PGPB is rarely elucidated. In part, this is due to the overwhelming complexity of IAA biosynthesis and regulation. The promiscuity of the enzymes implicated in IAA biosynthesis adds another element of complexity when attempting to decipher their role in IAA biosynthesis. To date, the majority of research on IAA biosynthesis describes three separate pathways classified in terms of their intermediates-indole acetonitrile (IAN), indole acetamide (IAM), and indole pyruvic acid (IPA). Each of these pathways is mediated by a set of enzymes, many of which are traditionally assumed to exist for that specific catalytic role. This lends the possibility of missing other, novel, enzymes that may also incidentally serve that function. Some of these pathways are constitutively expressed, while others are inducible. Some enzymes involved in IAA biosynthesis are known to be regulated by IAA or by IAA precursors, as well as by a multitude of environmental cues. This review aims to provide an update to our current understanding of the biosynthesis and regulation of IAA in bacteria. KEY POINTS: • IAA produced by PGPB improves bacterial stress tolerance and promotes plant growth. • Bacterial IAA biosynthesis is convoluted; multiple interdependent pathways. • Biosynthesis of IAA is regulated by IAA, IAA-precursors, and environmental factors.

X-ray-induced photoreduction of heme metal centers rapidly induces active-site perturbations in a protein-independent manner

Since the advent of protein crystallography, atomic-level macromolecular structures have provided a basis to understand biological function. Enzymologists use detailed structural insights on ligand coordination, interatomic distances, and positioning of catalytic amino acids to rationalize the underlying electronic reaction mechanisms. Often the proteins in question catalyze redox reactions using metal cofactors that are explicitly intertwined with their function. In these cases, the exact nature of the coordination sphere and the oxidation state of the metal is of utmost importance. Unfortunately, the redox-active nature of metal cofactors makes them especially susceptible to photoreduction, meaning that information obtained by photoreducing X-ray sources about the environment of the cofactor is the least trustworthy part of the structure. In this work we directly compare the kinetics of photoreduction of six different heme protein crystal species by X-ray radiation. We show that a dose of ∼40 kilograys already yields 50% ferrous iron in a heme protein crystal. We also demonstrate that the kinetics of photoreduction are completely independent from variables unique to the different samples tested. The photoreduction-induced structural rearrangements around the metal cofactors have to be considered when biochemical data of ferric proteins are rationalized by constraints derived from crystal structures of reduced enzymes.

Cyanide-Free Enantioselective Catalytic Strategies for the Synthesis of Chiral Nitriles

The development of enantioselective syntheses of nitriles gained increasing interest due to, e.g., an increasing demand for chiral nitriles for drug synthesis. Complementing existing routes, recently catalytic processes enabling an enantioselective formation of the chiral nitrile moiety without the need to utilize cyanide were accomplished. It is noteworthy that these processes are complementary to each other as they are based on different types of substrates, catalytic methods (utilizing chemo- and biocatalysts), and stereochemical reaction concepts (asymmetric synthesis versus resolution).

Aldoxime Dehydratase Mutants as Improved Biocatalysts for a Sustainable Synthesis of Biorenewables-Based 2-Furonitrile

2-Furonitrile is an interesting nitrile product for the chemical industry due to its use as intermediate in the field of fine chemicals and pharmaceuticals or as a potential sweetener, as well as due to its access from biorenewables. As an alternative to current processes based on, e.g., the ammoxidation of furfural with ammonia as a gas phase reaction running at > 400 °C, we recently reported an enzymatic dehydration of 2-furfuryl aldoxime being obtained easily from furfural and hydroxylamine. However, improving the catalytic properties of the aldoxime dehydratase biocatalyst from Rhodococcus sp. YH3-3 (OxdYH3-3) in terms of activity and stability remained a challenge. In this contribution, the successful development of aldoxime dehydratase OxdYH3-3 mutants that were generated by directed evolution and its enhanced activity toward 2-furfuryl aldoxime is reported. The mutant OxdYH3-3 N266S showed an improved activity of up to six times higher than the wild type when utilizing a substrate concentration of 50–100 mM of 2-furfuryl aldoxime.

The Pathway Less Traveled: Engineering Biosynthesis of Nonstandard Functional Groups

The field of metabolic engineering has achieved biochemical routes for conversion of renewable inputs to structurally diverse chemicals, but these products contain a limited number of chemical functional groups. In this review, we provide an overview of the progression of uncommon or 'nonstandard' functional groups from the elucidation of their biosynthetic machinery to the pathway optimization framework of metabolic engineering. We highlight exemplary efforts from primarily the last 5 years for biosynthesis of aldehyde, ester, terminal alkyne, terminal alkene, fluoro, epoxide, nitro, nitroso, nitrile, and hydrazine functional groups. These representative nonstandard functional groups vary in development stage and showcase the pipeline of chemical diversity that could soon appear within customized, biologically produced molecules.

Rhodococcus as A Versatile Biocatalyst in Organic Synthesis

The application of purified enzymes as well as whole-cell biocatalysts in synthetic organic chemistry is becoming more and more popular, and both academia and industry are keen on finding and developing novel enzymes capable of performing otherwise impossible or challenging reactions. The diverse genus Rhodococcus offers a multitude of promising enzymes, which therefore makes it one of the key bacterial hosts in many areas of research. This review focused on the broad utilization potential of the genus Rhodococcus in organic chemistry, thereby particularly highlighting the specific enzyme classes exploited and the reactions they catalyze. Additionally, close attention was paid to the substrate scope that each enzyme class covers. Overall, a comprehensive overview of the applicability of the genus Rhodococcus is provided, which puts this versatile microorganism in the spotlight of further research.

Enzymatic Synthesis of Aliphatic Nitriles at a Substrate Loading of up to 1.4 kg/L: A Biocatalytic Record Achieved with a Heme Protein

A biocatalytic approach toward linear aliphatic nitriles being widely used as industrial bulk chemicals has been developed that runs at high substrate loadings of up to 1.4 kg/L as demonstrated for the synthesis of n-octanenitrile. This substrate loading is one of the highest ever reported in biocatalysis and to best of our knowledge the highest obtained for a water-immiscible product in aqueous medium. It is noteworthy that the biotransformation at such a high substrate loading was achieved by means of a metalloprotein bearing an iron-containing heme subunit in the active site. In detail, an aldoxime dehydratase from Bacillus sp. OxB-1 was used as a biocatalyst for a dehydration of aldoximes as readily available starting materials due to their easy preparation from aliphatic aldehydes through spontaneous condensation with hydroxylamine as bulk chemical. Excellent conversions toward the nitriles in the two-phase system were achieved and the products are easily separated from the reaction mixture without the need for further purification. Aliphatic nitriles are used in industry as solvents and intermediates for the production of surfactants and life sciences products.

Biocatalytic production of adiponitrile and related aliphatic linear α,ω-dinitriles

Linear α,ω-dinitriles are important precursors for the polymer industry. Most prominently, adiponitrile is produced on an annual scale of ca. 1 million tons. However, a drawback of today’s dominating process is the need for large amounts of highly toxic hydrogen cyanide. In this contribution, an alternative approach towards such linear dinitriles is presented based on dehydration of readily available α,ω-dialdoximes at ambient conditions by means of aldoxime dehydratases. In contrast to existing production routes this biocatalytic route enables a highly regio- and chemoselective approach towards dinitriles without the use of hydrogen cyanide or harsh reaction conditions. In addition, a selective synthesis of adiponitrile with substrate loadings of up to 100 g/L and high yields of up to 80% was achieved. Furthermore, a lab scale process on liter scale leading to > 99% conversion at 50 g/L underlines the potential and robustness of this method for technical applicability.

Typically, preparation of the polymer precursors α,ω-dinitriles requires hydrogen cyanide. Here, the authors use aldoxime hydratase to produce adiponitrile and related aliphatic linear dinitriles under ambient conditions starting from readily available substrates without needing hydrogen cyanide.

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.

Biocatalytic Synthesis of Nitriles through Dehydration of Aldoximes: The Substrate Scope of Aldoxime Dehydratases

Nitriles, which are mostly needed and produced by the chemical industry, play a major role in various industry segments, ranging from high-volume, low-price sectors, such as polymers, to low-volume, high-price sectors, such as chiral pharma drugs. A common industrial technology for nitrile production is ammoxidation as a gas-phase reaction at high temperature. Further popular approaches are substitution or addition reactions with hydrogen cyanide or derivatives thereof. A major drawback, however, is the very high toxicity of cyanide. Recently, as a synthetic alternative, a novel enzymatic approach towards nitriles has been developed with aldoxime dehydratases, which are capable of converting an aldoxime in one step through dehydration into nitriles. Because the aldoxime substrates are easily accessible, this route is of high interest for synthetic purposes. However, whenever a novel method is developed for organic synthesis, it raises the question of substrate scope as one of the key criteria for application as a "synthetic platform technology". Thus, the scope of this review is to give an overview of the current state of the substrate scope of this enzymatic method for synthesizing nitriles with aldoxime dehydratases. As a recently emerging enzyme class, a range of substrates has already been studied so far, comprising nonchiral and chiral aldoximes. This enzyme class of aldoxime dehydratases shows a broad substrate tolerance and accepts aliphatic and aromatic aldoximes, as well as arylaliphatic aldoximes. Furthermore, aldoximes with a stereogenic center are also recognized and high enantioselectivities are found for 2-arylpropylaldoximes, in particular. It is further noteworthy that the enantiopreference depends on the E and Z isomers. Thus, opposite enantiomers are accessible from the same racemic aldehyde and the same enzyme.

Oximes: Unrecognized Chameleons in General and Specialized Plant Metabolism

Oximes (R₁R₂C=NOH) are nitrogen-containing chemical constituents that are formed in species representing all kingdoms of life. In plants, oximes are positioned at important metabolic bifurcation points between general and specialized metabolism. The majority of plant oximes are amino acid-derived metabolites formed by the action of a cytochrome P450 from the CYP79 family. Auxin, cyanogenic glucosides, glucosinolates, and a number of other bioactive specialized metabolites including volatiles are produced from oximes. Oximes with the E configuration have high biological activity compared with Z-oximes. Oximes or their derivatives have been demonstrated or proposed to play roles in growth regulation, plant defense, pollinator attraction, and plant communication with the surrounding environment. In addition, oxime-derived products may serve as quenchers of reactive oxygen species and storage compounds for reduced nitrogen that may be released on demand by the activation of endogenous turnover pathways. As highly bioactive molecules, chemically synthesized oximes have found versatile uses in many sectors of society, especially in the agro- and medical sectors. This review provides an update on the structural diversity, occurrence, and biosynthesis of oximes in plants and discusses their role as key players in plant general and specialized metabolism.

Cyanide-Free and Broadly Applicable Enantioselective Synthetic Platform for Chiral Nitriles through a Biocatalytic Approach

A cyanide-free platform technology for the synthesis of chiral nitriles by biocatalytic enantioselective dehydration of a wide range of aldoximes is reported. The nitriles were obtained with high enantiomeric excess of >90 % ee (and up to 99 % ee) in many cases, and a "privileged substrate structure" with respect to high enantioselectivity was identified. Furthermore, a surprising phenomenon was observed for the enantiospecificity that is usually not observed in enzyme catalysis. Depending on whether the E or Z isomer of the racemic aldoxime substrate was employed, one or the other enantiomer of the corresponding nitrile was formed preferentially with the same enzyme.

New function of aldoxime dehydratase: Redox catalysis and the formation of an unexpected product

In general, hemoproteins are capable of catalyzing redox reactions. Aldoxime dehydratase (OxdA), which is a unique heme-containing enzyme, catalyzes the dehydration of aldoximes to the corresponding nitriles. Its reaction is a rare example of heme directly activating an organic substrate, unlike the utilization of H₂O₂ or O₂ as a mediator of catalysis by other heme-containing enzymes. While it is unknown whether OxdA catalyzes redox reactions or not, we here for the first time detected catalase activity (which is one of the redox activities) of wild-type OxdA, OxdA(WT). Furthermore, we constructed a His320 → Asp mutant of OxdA [OxdA(H320D)], and found it exhibits catalase activity. Determination of the kinetic parameters of OxdA(WT) and OxdA(H320D) revealed that their K_m values for H₂O₂ were similar to each other, but the k_cat value of OxdA(H320D) was 30 times higher than that of OxdA(WT). Next, we examined another redox activity and found it was the peroxidase activity of OxdAs. While both OxdA(WT) and OxdA(H320D) showed the activity, the activity of OxdA(H320D) was dozens of times higher than that of OxdA(WT). These findings demonstrated that the H320D mutation enhances the peroxidase activity of OxdA. OxdAs (WT and H320D) were found to catalyze another redox reaction, a peroxygenase reaction. During this reaction of OxdA(H320D) with 1-methoxynaphthalene as a substrate, surprisingly, the reaction mixture changed to a color different from that with OxdA(WT), which was due to the known product, Russig’s blue. We purified and identified the new product as 1-methoxy-2-naphthalenol, which has never been reported as a product of the peroxygenase reaction, to the best of our knowledge. These findings indicated that the H320D mutation not only enhanced redox activities, but also significantly altered the hydroxylation site of the substrate.

Kemp Elimination Catalyzed by Naturally Occurring Aldoxime Dehydratases

Recently, the Kemp elimination reaction has been extensively studied in computational enzyme design of new catalysts, as no natural enzyme has evolved to catalyze this reaction. In contrast to in silico enzyme design, we were interested in searching for Kemp eliminase activity in natural enzymes with catalytic promiscuity. Based on similarities of substrate structures and reaction mechanisms, we assumed that the active sites of naturally abundant aldoxime dehydratases have the potential to catalyze the non-natural Kemp elimination reaction. We found several aldoxime dehydratases that are efficient catalysts of this reaction. Although a few natural enzymes have been identified with promiscuous Kemp eliminase activity, to the best of our knowledge, this is a rare example of Kemp elimination catalyzed by naturally occurring enzymes with high catalytic efficiency.

The molecular bases of floral scent evolution under artificial selection: insights from a transcriptome analysis in Brassica rapa

In an artificial selection experiment using fast-cycling Brassica rapa plants it was recently shown that floral VOCs respond rapidly to selection for increased amounts. Here we carried out transcriptome analysis in these plants to explore the molecular bases of the augmentation in the artificially selected scent compound, phenylacetaldehyde (PAA), as well as other compounds that increased through pleiotropy. In the transcriptome data, we found up-regulation of genes likely underlying PAA synthesis, but also several genes of the shikimate pathway and the related phenylalanine metabolism. As phenylalanine is the precursor of many aromatic volatiles that showed increased emission, this result could explain some of the pleiotropic evolutionary responses. In addition, we found that ribosomal protein genes were up-regulated in “high” (high PAA amount) selection line plants, a mechanism that might further augment the effect of elevated gene expression at the proteomic level. Our study shows that selection on an individual trait can impose changes in the expression of several different genes, which could explain pleiotropic responses in the biosynthetic network of floral volatiles.

The genome of newly classified Ochroconis mirabilis: Insights into fungal adaptation to different living conditions

BACKGROUND

Ochroconis mirabilis, a recently introduced water-borne dematiaceous fungus, is occasionally isolated from human skin lesions and nails. We identified an isolate of O. mirabilis from a skin scraping with morphological and molecular studies. Its genome was then sequenced and analysed for genetic features related to classification and biological characteristics.

RESULTS

UM 578 was identified as O. mirabilis based on morphology and internal transcribed spacer (ITS)-based phylogeny. The 34.61 Mb assembled genome with 13,435 predicted genes showed less efficiency of this isolate in plant cell wall degradation. Results from the peptidase comparison analysis with reported keratin-degrading peptidases from dermatophytes suggest that UM 578 is very unlikely to be utilising these peptidases to survive in the host. Nevertheless, we have identified peptidases from M10A, M12A and S33 families that may allow UM 578 to invade its host via extracellular matrix and collagen degradation. Furthermore, the lipases in UM 578 may have a role in supporting the fungus in host invasion. This fungus has the potential ability to synthesise melanin via the 1,8-dihydroxynaphthalene (DHN)-melanin pathway and to produce mycotoxins. The mating ability of this fungus was also inspected in this study and a mating type gene containing alpha domain was identified. This fungus is likely to produce taurine that is required in osmoregulation. The expanded gene family encoding the taurine catabolism dioxygenase TauD/TdfA domain suggests the utilisation of taurine under sulfate starvation. The expanded glutathione-S-transferase domains and RTA1-like protein families indicate the selection of genes in UM 578 towards adaptation in hostile environments.

CONCLUSIONS

The genomic analysis of O. mirabilis UM 578 provides a better understanding of fungal survival tactics in different habitats.

The bifurcation of the cyanogenic glucoside and glucosinolate biosynthetic pathways

The biosynthetic pathway for the cyanogenic glucoside dhurrin in sorghum has previously been shown to involve the sequential production of (E)- and (Z)-p-hydroxyphenylacetaldoxime. In this study we used microsomes prepared from wild-type and mutant sorghum or transiently transformed Nicotiana benthamiana to demonstrate that CYP79A1 catalyzes conversion of tyrosine to (E)-p-hydroxyphenylacetaldoxime whereas CYP71E1 catalyzes conversion of (E)-p-hydroxyphenylacetaldoxime into the corresponding geometrical Z-isomer as required for its dehydration into a nitrile, the next intermediate in cyanogenic glucoside synthesis. Glucosinolate biosynthesis is also initiated by the action of a CYP79 family enzyme, but the next enzyme involved belongs to the CYP83 family. We demonstrate that CYP83B1 from Arabidopsis thaliana cannot convert the (E)-p-hydroxyphenylacetaldoxime to the (Z)-isomer, which blocks the route towards cyanogenic glucoside synthesis. Instead CYP83B1 catalyzes the conversion of the (E)-p-hydroxyphenylacetaldoxime into an S-alkyl-thiohydroximate with retention of the configuration of the E-oxime intermediate in the final glucosinolate core structure. Numerous microbial plant pathogens are able to detoxify Z-oximes but not E-oximes. The CYP79-derived E-oximes may play an important role in plant defense.

Characterization of a nitrilase from Arthrobacter aurescens CYC705 for synthesis of iminodiacetic acid

A nitrilase gene cyc705 from Arthrobacter aurescens CYC705 for synthesis of iminodiacetic acid (IDA) was cloned. This gene contained a 930 bp ORF, which encoded a polypeptide of 310 amino acids. A recombinant Escherichia coli BL21(DE3)/pET28a-cyc705 was constructed to achieve the heterologous expression of cyc705. This recombinant nitrilase was purified to homogeneity with a molecular weight of 36.7 kDa on SDS-PAGE and mass spectrometry, and characterized to be an oligomer of 14 subunits by gel permeation chromatography. Using iminodiacetonitrile (IDAN) as the substrate, the Vmax, Km, kcat and kcat/Km were 9.05 U mg(-1), 43.17 mM(-1), 94.1 min(-1) and 2.18×10(3) min(-1) M(-1), respectively. The optimum temperature and pH were 25°C and 5.8. The suitable substrates for the purified nitrilase were short-chain aliphatic dinitriles. High concentration of IDAN could be hydrolyzed to IDA in a shorter time.

Complete Genome Sequence of an Aldoxime Degrader, Bacillus sp. OxB-1

Bacillus sp. OxB-1 has been characterized as a strain that produces a new enzyme, aldoxime dehydratase, which catalyzes the dehydration of aldoxime to form nitrile. Here, its complete genome sequence (3,594,618 bp, with a GC content of 47.85%), comprising a circular chromosome, is announced.

Identification and characterization of CYP79D16 and CYP71AN24 catalyzing the first and second steps in L-phenylalanine-derived cyanogenic glycoside biosynthesis in the Japanese apricot, Prunus mume Sieb. et Zucc

Japanese apricot, Prunus mume Sieb. et Zucc., belonging to the Rosaceae family, produces as defensive agents the cyanogenic glycosides prunasin and amygdalin, which are presumably derived from L-phenylalanine. In this study, we identified and characterized cytochrome P450s catalyzing the conversion of L-phenylalanine into mandelonitrile via phenylacetaldoxime. Full-length cDNAs encoding CYP79D16, CYP79A68, CYP71AN24, CYP71AP13, CYP71AU50, and CYP736A117 were cloned from P. mume ‘Nanko’ using publicly available P. mume RNA-sequencing data, followed by 5′- and 3′-RACE. CYP79D16 was expressed in seedlings, whereas CYP71AN24 was expressed in seedlings and leaves. Enzyme activity of these cytochrome P450s expressed in Saccharomyces cerevisiae was evaluated by liquid and gas chromatography–mass spectrometry. CYP79D16, but not CYP79A68, catalyzed the conversion of L-phenylalanine into phenylacetaldoxime. CYP79D16 showed no activity toward other amino acids. CYP71AN24, but not CYP71AP13, CYP71AU50, and CYP736A117, catalyzed the conversion of phenylacetaldoxime into mandelonitrile. CYP71AN24 also showed lower conversions of various aromatic aldoximes and nitriles. The K m value and turnover rate of CYP71AN24 for phenylacetaldoxime were 3.9 µM and 46.3 min(−1), respectively. The K m value and turnover of CYP71AN24 may cause the efficient metabolism of phenylacetaldoxime, avoiding the release of the toxic intermediate to the cytosol. These results suggest that cyanogenic glycoside biosynthesis in P. mume is regulated in concert with catalysis by CYP79D16 in the parental and sequential reaction of CYP71AN24 in the seedling.

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.

Indole-3-acetic acid in plant-microbe interactions

Indole-3-acetic acid (IAA) is an important phytohormone with the capacity to control plant development in both beneficial and deleterious ways. The ability to synthesize IAA is an attribute that many bacteria including both plant growth-promoters and phytopathogens possess. There are three main pathways through which IAA is synthesized; the indole-3-pyruvic acid, indole-3-acetamide and indole-3-acetonitrile pathways. This chapter reviews the factors that effect the production of this phytohormone, the role of IAA in bacterial physiology and in plant-microbe interactions including phytostimulation and phytopathogenesis.