Developments in nitrile and amide biotransformation processes

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

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

Highly Efficient Biosynthesis of Nicotinic Acid by Immobilized Whole Cells of E. coli Expressing Nitrilase in Semi-Continuous Packed-Bed Bioreactor

A recombinant E. coli, expressing nitrilase from Acidovorax facilis 72W with dual-site expression plasmid pRSFduet (E. coli pRSF-AfNit2), was constructed. It showed higher soluble expression of nitrilase than that in the pET21a plasmid. The recombinant nitrilase can efficiently catalyze the hydrolysis of 3-cyanopyridine to nicotinic acid. The whole cells of E. coli pRSF-AfNit2 were immobilized by using sodium alginate/glutaraldehyde/polyethylene imine as the best immobilized reagents. The immobilized cells showed 95% activity recovery and excellent mechanical strength, with improved thermal stability and pH stability. They also retained 82% of initial activity after nearly two months of storage at 4 °C. A semi-continuous packed-bed bioreactor (sPBR) filled with the immobilized cells was studied for efficient production of nicotinic acid. After optimization, the highest space–time yield of 1576 g/(L·d) was obtained on 0.8 M substrate concentration at 2 mL/min of flow rate. The sPBR was repeatedly operated for 41 batches, keeping 100% conversion in the presence of 30 mM CaCl2. Finally, 95 g of nicotinic acid were obtained at 90% yield after separation and purification. The developed technology has potential application value.

Biotransformation of 3-cyanopyridine to nicotinic acid using whole-cell nitrilase of Gordonia terrae mutant MN12

In the present study, the Gordonia terrae was subjected to chemical mutagenesis using ethyl methane sulfonate (EMS) and methyl methane sulfonate (MMS), N-methyl-N-nitro-N-nitrosoguanidine (MNNG), 5-bromouracil (5-BU) and hydroxylamine with the aim of improving the catalytic efficiency of its nitrilase for conversion of 3-cyanopyridine to nicotinic acid. A mutant MN12 generated with MNNG exhibited increase in nitrilase activity from 0.5 U/mg dcw (dry cell weight) (in the wild G. terrae) to 1.33 U/mg dcw. Further optimizations of culture conditions using response surface methodology enhanced the enzyme production to 1.2-fold. Whole-cell catalysis was adopted for bench-scale synthesis of nicotinic acid, and 100% conversion of 100 mM 3-cyanopyridine was achieved in potassium phosphate buffer (0.1 M, pH 8.0) at 40 °C in 15 min. The whole-cell nitrilase of the mutant MN12 exhibited higher rate of product formation and volumetric productivity, i.e., 24.56 g/h/g dcw and 221 g/L as compared to 8.95 g/h/g dcw and 196.8 g/L of the wild G. terrae. The recovered product was confirmed by HPLC, FTIR and NMR analysis with high purity (> 99.9%). These results indicated that the mutant MN12 of G. terrae as whole-cell nitrilase is a very promising biocatalyst for the large-scale synthesis of nicotinic acid.

Evaluation of acrylamide production by Rhodococcus rhodochrous (RS-6) cells immobilized in agar matrix

AIMS

The efficiency of acrylamide production was examined with immobilized cells of Rhodococcus rhodochrous (RS-6) containing NHase.

METHODS AND RESULTS

Different entrapment matrices such as agar, alginate and polyacrylamide were used. Various immobilization parameters like agar concentration, cell concentration and reaction conditions affecting the bioconversion process using suitable matrices were determined. The cells immobilized with agar matrix were found to be most effective for acrylonitrile conversion. The bioconversion was more efficient in beads prepared with 2% agar and 5% (v/v) cell concentration. The entire conversion of acrylonitrile to acrylamide with agar entrapped cells was achieved in 120 min at 15°C. The agar entrapped R. rhodochrous (RS-6) cells exhibited 8% (w/v) tolerance to acrylonitrile and 35% tolerance to acrylamide. The immobilized cells also retained 50% of its conversion ability up to seven cycles. The laboratory-scale (1 L) production resulted in 466 g L^-1 accumulation of acrylamide in 16 h.

CONCLUSIONS

The cells immobilized in agar showed better stability and biocatalytic properties and increased reusability potential.

SIGNIFICANCE AND IMPACT OF THE STUDY

The agar-immobilized Rhodococcus rhodochrous (RS-6) cells showed enhanced tolerance for both the substrate and product and is economical for the large-scale production of acrylamide.

The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870

BACKGROUND

Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The genome of the organism was sequenced and analysed in order to better understand this whole cell biocatalyst.

RESULTS

The genome of R. rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using Nanopore sequencing. The circular genome contains 5.9 megabase pairs (Mbp) and includes a 0.53 Mbp linear plasmid, that together encode 7548 predicted protein sequences according to BASys annotation, and 5535 predicted protein sequences according to RAST annotation. The genome contains numerous oxidoreductases, 15 identified antibiotic and secondary metabolite gene clusters, several terpene and nonribosomal peptide synthetase clusters, as well as 6 putative clusters of unknown type. The 0.53 Mbp plasmid encodes 677 predicted genes and contains the nitrile converting gene cluster, including a nitrilase, a low molecular weight nitrile hydratase, and an enantioselective amidase. Although there are fewer biotechnologically relevant enzymes compared to those found in rhodococci with larger genomes, such as the well-known Rhodococcus jostii RHA1, the abundance of transporters in combination with the myriad of enzymes found in strain BAA-870 might make it more suitable for use in industrially relevant processes than other rhodococci.

CONCLUSIONS

The sequence and comprehensive description of the R. rhodochrous ATCC BAA-870 genome will facilitate the additional exploitation of rhodococci for biotechnological applications, as well as enable further characterisation of this model organism. The genome encodes a wide range of enzymes, many with unknown substrate specificities supporting potential applications in biotechnology, including nitrilases, nitrile hydratase, monooxygenases, cytochrome P450s, reductases, proteases, lipases, and transaminases.

IrIII-Catalyzed direct syntheses of amides and esters using nitriles as acid equivalents: a photochemical pathway

An unprecedented Ir^III[df(CF₃)ppy]₂(dtbbpy)PF₆-catalyzed simple photochemical process for direct addition of amines and alcohols to the relatively less reactive nitrile triple bond is described herein.

N-terminal engineering of overlapping genes in the nitrile hydratase gene cluster improved its activity

Nitrile hydratase which catalyzes the hydration of nitriles to the corresponding amides is operon-encoded. However, when heterologously expressed, genes in the same operon are usually not equally expressed, and the ratio needs to be fine-tuned. A gene cluster of three genes (corresponding to α-subunit, β-subunit and activator) encoding the nitrile hydratase was cloned from Aurantimonas manganoxydans ATCC BAA-1229 and expressed in Escherichia coli. However, difficulty was encountered in heterologous expression of the activator and the expression level of β-subunit was lower than that of α-subunit, which together resulted in low catalytic efficiency. To improve the expression of activator, a set of SKIK tags were fused to the N-terminus of the activator. To elevate the expression level of β-subunit, a silent mutation strategy was applied in the overlapping sequence with α-subunit around its translation initial region. Finally, the expression of β-subunit and activator were improved and the maximum activity of NHase1229 was doubled, reaching 160 U/mL towards 3-cyanopyridine. These results indicate that N-terminal engineering is an efficient strategy for optimizing the expression of multiple genes in operons.

Bioconversion of acrylonitrile using nitrile hydratase activity of Bacillus sp. APB-6

Bacillus sp. APB-6 harboring nitrile hydratase was used in the production of acrylamide from acrylonitrile. Bacillus sp. APB-6, for maximum production of Co⁺⁺ containing nitrile hydratase, was cultured in the medium containing lactose (18.0 g l^-1), peptone (1.0 g l^-1), yeast extract (2.0 g l^-1), MgSO₄ (0. 5 g l^-1), K₂HPO₄ (0.6 g l^-1), urea (9.0 g l^-1), and CoCl₂ (0.01 g l^-1), pH 7.0, and incubated at 35 °C for 24 h in an incubator shaker (160 rpm). Nitrile hydratase exhibited relatively high specificity for aliphatic nitriles. Free cells were immobilized using 2% (w/v) agar solution to enhance enzyme stability and reusability in repetitive cycles of acrylamide production. Under optimized conditions, nearly complete bioconversion of acrylonitrile was achieved with a fair recovery of 85% using free and immobilized cells equivalent to 500 mg dcw l^-1. An efficient nitrile hydratase-mediated bioconversion of acrylonitrile to acrylamide at 1-l scale was achieved with time and space productivity of 426 g h^-1 g^-1 dcw using free cells.

Significantly enhanced substrate tolerance of Pseudomonas putida nitrilase via atmospheric and room temperature plasma and cell immobilization

The objective of the study was to enhance the substrate tolerance of Pseudomonas putida nitrilase via atmospheric and room temperature plasma (ARTP) and cell immobilization. The mutant library was constructed by ARTP and rapidly screened by an OPA-TCA microscale reaction. A mutant strain of mut-D3 was obtained and its optimum substrate concentration was improved to 150mM from 100mM. It could accumulate 189g/L nicotinic acid (NA) from 3-cyanopyridine (3-CP), which was increased by 42% compared with that of wild type (WT). Additionally, composite immobilization of mut-D3 was performed and SA-PVA immobilized cells could catalyze 250mM 3-CP each batch with finally accumulating 346g/L NA, while free cells accumulated 175g/L NA. These results indicated that the free or immobilized catalysts of mut-D3 could serve as a good choice for NA production. This is the first report on mutation breeding of nitrilase-producing microorganisms by ARTP.

Nitrilase-Activatable Noncanonical Amino Acid Precursors for Cell-Selective Metabolic Labeling of Proteomes

Cell-selective protein metabolic labeling is of great interest for studying cell-cell communications and tissue homeostasis. We herein describe a nitrilase-activatable noncanonical amino acid tagging (NANCAT) strategy that exploits an exogenous nitrilase to enzymatically convert the nitrile-substituted precursors to their corresponding noncanonical amino acids (ncAAs), l-azidohomoalanine (Aha) or homopropargylglycine (Hpg), in living cells. Only cells expressing the nitrilase can generate Aha or Hpg in cellulo and metabolically incorporate them into the nascent proteins. Subsequent click-labeling of the azide- or alkyne-incorporated proteins with fluorescent probes or with affinity tags enables visualization and proteomic profiling of nascent proteomes, respectively. We have demonstrated that NANCAT can serve as a versatile strategy for cell-selective labeling of proteomes in both bacterial and mammalian cells.

Amides in Nature and Biocatalysis

Amides are widespread in biologically active compounds with a broad range of applications in biotechnology, agriculture and medicine. Therefore, as alternative to chemical synthesis the biocatalytic amide synthesis is a very interesting field of research. As usual, Nature can serve as guide in the quest for novel biocatalysts. Several mechanisms for carboxylate activation involving mainly acyl-adenylate, acyl-phosphate or acyl-enzyme intermediates have been discovered, but also completely different pathways to amides are found. In addition to ribosomes, selected enzymes of almost all main enzyme classes are able to synthesize amides. In this review we give an overview about amide synthesis in Nature, as well as biotechnological applications of these enzymes. Moreover, several examples of biocatalytic amide synthesis are given.

Refining the Structural Model of a Heterohexameric Protein Complex: Surface Induced Dissociation and Ion Mobility Provide Key Connectivity and Topology Information

Toyocamycin nitrile hydratase (TNH) is a protein hexamer that catalyzes the hydration of toyocamycin to produce sangivamycin. The structure of hexameric TNH and the arrangement of subunits within the complex, however, have not been solved by NMR or X-ray crystallography. Native mass spectrometry (MS) clearly shows that TNH is composed of two copies each of the α, β, and γ subunits. Previous surface induced dissociation (SID) tandem mass spectrometry on a quadrupole time-of-flight (QTOF) platform suggests that the TNH hexamer is a dimer composed of two αβγ trimers; furthermore, the results suggest that α-β interact most strongly (Blackwell et al. Anal. Chem. 2011, 83, 2862-2865). Here, multiple complementary MS based approaches and homology modeling have been applied to refine the structure of TNH. Solution-phase organic solvent disruption coupled with native MS agrees with the previous SID results. By coupling surface induced dissociation with ion mobility mass spectrometry (SID/IM), further information on the intersubunit contacts and relative interfacial strengths are obtained. The results show that TNH is a dimer of αβγ trimers, that within the trimer the α, β subunits bind most strongly, and that the primary contact between the two trimers is through a γ-γ interface. Collisional cross sections (CCSs) measured from IM experiments are used as constraints for postulating the arrangement of the subunits represented by coarse-grained spheres. Covalent labeling (surface mapping) together with protein complex homology modeling and docking of trimers to form hexamer are utilized with all the above information to propose the likely quaternary structure of TNH, with chemical cross-linking providing cross-links consistent with the proposed structure. The novel feature of this approach is the use of SID-MS with ion mobility to define complete connectivity and relative interfacial areas of a heterohexameric protein complex, providing much more information than is available from solution disruption. That information, when combined with CCS-guided coarse-grained modeling and covalent labeling restraints for homology modeling and trimer-trimer docking, provides atomic models of a previously uncharacterized heterohexameric protein complex.

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

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

Metagenomic technology and genome mining: emerging areas for exploring novel nitrilases

Nitrilase is one of the most important members in the nitrilase superfamily and it is widely used for bioproduction of commodity chemicals and pharmaceutical intermediates as well as bioremediation of nitrile-contaminated wastes. However, its application was hindered by several limitations. Searching for new nitrilases and improving their application performances are the driving force for researchers. Genetic data resources in various databases are quite rich in post-genomic era. Besides, more than 99 % of microbes in the environment are unculturable. Metagenomic technology and genome mining are thus becoming burgeoning areas and provide unprecedented opportunities for searching more useful novel nitrilases due to the abundance of already existing but unexplored gene resources, namely uncharacterized genome information in the database and unculturable microbes in the natural environment. These techniques seem to be innovative and highly efficient. This study reviews the current status and future directions of metagenomics and genome mining in nitrilase exploration. Moreover, it discussed their utilization in coping with the challenges for nitrilase application. In the next several years, with the rapid development of nitrile biocatalysis, these two techniques would be bound to attract increasing attentions and even become a dominant trend for finding more novel nitrilases. Also, this review would provide guidance for exploitation of other commercially important enzymes.

Nitrilases in nitrile biocatalysis: recent progress and forthcoming research

Over the past decades, nitrilases have drawn considerable attention because of their application in nitrile degradation as prominent biocatalysts. Nitrilases are derived from bacteria, filamentous fungi, yeasts, and plants. In-depth investigations on their natural sources function mechanisms, enzyme structure, screening pathways, and biocatalytic properties have been conducted. Moreover, the immobilization, purification, gene cloning and modifications of nitrilase have been dwelt upon. Some nitrilases are used commercially as biofactories for carboxylic acids production, waste treatment, and surface modification. This critical review summarizes the current status of nitrilase research, and discusses a number of challenges and significant attempts in its further development. Nitrilase is a significant and promising biocatalyst for catalytic applications.

Silica-carrageenan hybrids used for cell immobilization realizing high-temperature degradation of nitrile substrates

In this work the application of hybrid materials, containing TEOS as source of SiO2 and k-carrageenan in different percentage, synthesized by the sol-gel method at room temperature was studied. They were used as matrices for entrapment of whole Bacillus sp. UG-5B cells, producers of thermostable nitrilase. The effect of the surface area and size and quantity of pores in the synthesized materials on the enzyme activity was evaluated. The process of biodegradation of different concentrations of toxic, potentially carcinogenic and mutagenic substrates by the obtained biocatalysts was investigated. The enzyme reaction takes place by the nitrilase pathway, catalysing nitrile hydrolysis directly to the corresponding carboxylic acid, forming ammonia. At batch experiments the influence of the substrate concentration of different nitriles was tested and 20 mM concentration was found most suitable. A two-step biodegradation process in a laboratory-scale column bioreactor of o-, m- and p-tolunitrile as a mixture was followed. After operation of the system for nine hours for the mixture of substrates at a flow rate of 45 mL h−1 and at 60°C, the overall conversion realized was above 90%, showing a good efficiency of the investigated process.