Nitrile Hydratase of Rhodococcus: Optimization of Synthesis in Cells and Industrial Applications for Acrylamide Production

A new concept of biocatalytic synthesis of acrylic monomers for obtaining water-soluble acrylic heteropolymers

Rhodococcus strains were designed as model biocatalysts (BCs) for the production of acrylic acid and mixtures of acrylic monomers consisting of acrylamide, acrylic acid, and N-alkylacrylamide (N-isopropylacrylamide). To obtain BC strains, we used, among other approaches, adaptive laboratory evolution (ALE), based on the use of the metabolic pathway of amide utilization. Whole genome sequencing of the strains obtained after ALE, as well as subsequent targeted gene disruption, identified candidate genes for three new amidases that are promising for the development of BCs for the production of acrylic acid from acrylamide. New BCs had two types of amidase activities, acrylamide-hydrolyzing and acrylamide-transferring, and by varying the ratio of these activities in BCs, it is possible to influence the ratio of monomers in the resulting mixtures. Based on these strains, a prototype of a new technological concept for the biocatalytic synthesis of acrylic monomers was developed for the production of water-soluble acrylic heteropolymers containing valuable N-alkylacrylamide units. In addition to the possibility of obtaining mixtures of different compositions, the advantages of the concept are a single starting reagent (acrylamide), more unification of processes (all processes are based on the same type of biocatalyst), and potentially greater safety for personnel and the environment compared to existing chemical technologies.

Draft Genome Sequence of Rhodococcus qingshengii (Formerly erythropolis) TA37, a First-Generation Biocatalyst for Synthesis of Functionalized Acrylamides

We describe here the 7.0-Mb draft genome sequence of Rhodococcus qingshengii strain TA37, which was obtained from samples of nitrile-contaminated soil collected in the Saratov Region (Russian Federation). This genomic resource will support the further development of biocatalysts for the inexpensive and green production of acrylic monomers.

Nitrile Hydratases: From Industrial Application to Acetamiprid and Thiacloprid Degradation

The widespread application of neonicotinoid insecticides (NEOs) in agriculture causes a series of environmental and ecological problems. Microbial remediation is a popular approach to relieve these negative impacts, but the associated molecular mechanisms are rarely explored. Nitrile hydratase (NHase), an enzyme commonly used in industry for amide production, was discovered to be responsible for the degradation of acetamiprid (ACE) and thiacloprid (THI) by microbes. Since then, research into NHases in NEO degradation has attracted increasing attention. In this review, microbial degradation of ACE and THI is briefly described. We then focus on NHase evolution, gene composition, maturation mechanisms, expression, and biochemical properties with regard to application of NHases in NEO degradation for bioremediation.

Copper stimulates neonicotinoid insecticide thiacloprid degradation by Ensifer adhaerens TMX-23

AIMS

Aims of this study are to elucidate the molecular mechanism of copper-improved thiacloprid (THI) degradation by Ensifer adhaerens TMX-23 and characterize copper resistance of this strain.

METHODS AND RESULTS

Resting cells of E. adhaerens TMX-23 were used to degrade THI, with formation of THI amide and 98·31% of 0·59 mmol l^-1 THI was degraded in 100 min. The addition of copper improved the degradation of THI and showed little inhibitory effects on the growth of E. adhaerens TMX-23. E. adhaerens TMX-23 degraded THI to THI amide by nitrile hydratases (NhcA and NhpA). QPCR analysis indicated that the expression of nhpA was up-regulated in the presence of copper. E. adhaerens TMX-23 nitrile hydratases were purified, and enzyme assay of NhpA exhibited the highest NHase activity toward THI. The addition of copper activated the activity of NhcA. Soil degradation experiment indicated that E. adhaerens TMX-23 could quickly eliminate THI residual in copper-added soil.

CONCLUSIONS

Copper improved THI degradation by E. adhaerens TMX-23 was attributed to the induced expression of nhpA and activated NhcA.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study broadens the investigation of regulatory mechanism of NHase expression and provided theoretical basis for using metal-resistant microbes to degrade pesticide in heavy metal co-contaminated environments.

A Set of Active Promoters with Different Activity Profiles for Superexpressing Rhodococcus Strain

Rhodococcus bacteria are a promising platform for biodegradation, biocatalysis, and biosynthesis, but the use of rhodococci is hampered by the insufficient number of both platform strains for expression and promoters that are functional and thoroughly studied in these strains. To expand the list of such strains and promoters, we studied the expression capability of the Rhodococcus rhodochrous M33 strain, and the functioning of a set of recombinant promoters in it. We showed that the strain supports superexpression of the target enzyme (nitrile hydratase) using alternative inexpensive feedings-acetate and urea-without growth factor supplementation, thus being a suitable expression platform. The promoter set included P_tuf (elongation factor Tu) and P_sod (superoxide dismutase) from Corynebacterium glutamicum ATCC13032, P_cpi (isocitrate lyase) from Rhodococcus erythropolis PR4, and P_nh (nitrile hydratase) from R. rhodochrous M8. Activity levels, regulation possibilities, and growth-phase-dependent activity profiles of these promoters were studied in derivatives of the M33 strain. The activities of the promoters were significantly different (P_cpi < P_sod ≪ P_tuf < P_nh), covering 10³-fold range, and the most active P_nh and P_tuf produced up to a 30-50% portion of target protein in soluble intracellular proteins. On the basis of the mRNA quantification and amount of target protein, the production level of P_nh was positioned close to the theoretical upper limit of expression in a bacterial cell. A selection method for the laboratory evolution of such active promoters directly in Rhodococcus was also proposed. Concerning regulation, P_tuf could not be regulated (2-fold change), while others were tunable (6-fold for P_sod, 79-fold for P_nh, and 44-fold for P_cpi). The promoters possessed four different activity profiles, including three with peak of activity at different growth phases and one with constant activity throughout the growth phases. P_tuf and P_cpi did not change their activity profile under different growth conditions, whereas the P_sod and P_nh profiles changed depending on the growth media. The results allow flexible construction of Rhodococcus strains using the studied promoters, and demonstrate a valuable approach for complex characterization of promoters intended for biotechnological strain construction.

Complete Genome Sequence of Rhodococcus sp. Strain M8, a Platform Strain for Acrylic Monomer Production

We report a 6.27-Mbp complete genome of Rhodococcus sp. strain M8, an originally discovered strain that is now under investigation for production of acrylic monomers. The genome consists of a 6.1-Mbp circular chromosome and a 173.2-kbp plasmid.

We report a 6.27-Mbp complete genome of Rhodococcus sp. strain M8, an originally discovered strain that is now under investigation for production of acrylic monomers. The genome consists of a 6.1-Mbp circular chromosome and a 173.2-kbp plasmid.

Response surface methodology: An effective optimization strategy for enhanced production of nitrile hydratase (NHase) by Rhodococcus rhodochrous (RS-6)

Nitrile hydratase is an enzyme which catalyze the hydration of nitriles into amide and their role as catalysts for acrylamide production in industries are well known. The present study aims at statistically optimizing physiological and nutritional parameters for NHase production from Rhodococcus rhodochrous (RS-6). The effect of incubation period, temperature, pH, carbon and nitrogen sources on the production of NHase was investigated by one factor at a time strategy. Further optimization process was carried out by response surface methodology for studying the interactive effect of these variables using central composite design. The optimized levels of variables obtained by statistical analysis were: incubation period 48 h, temperature 33 °C, pH 7.0, glycerol 1% and urea 0.75%, which resulted in maximum NHase production. The results of ANOVA were significant with the F-value of the model being 296.78, value of R² is 0.9983 and the lack of fit test was not significant. The contour and response surface plots showed significant interaction between the variables. The NHase yield was enhanced up to 6.22 fold by statistical optimization using RSM. Thus, the developed experimental design is effective towards process optimization for NHase production from R. rhodochrous (RS-6).

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.

Draft Genome Sequence of Rhodococcus sp. Strain M8, Which Can Degrade a Broad Range of Nitriles

Rhodococcus sp. strain M8 is a nitrile-degrading bacterium isolated from acrylonitrile-contaminated sites. This strain produces the enzymes for sequential nitrile degradation, cobalt-type nitrile hydratase, and amidase in large amounts. Its draft genome sequence, announced here, has an estimated size of 6.3 Mbp.

Ammonium acrylate biomanufacturing by an engineered Rhodococcus ruber with nitrilase overexpression and double-knockout of nitrile hydratase and amidase

Rhodococcus ruber TH was selected as a parent strain to engineer for biomanufacturing of ammonium acrylate; the characteristics of this strain included accelerated growth rate, high cell tolerance and natively overexpressed nitrile hydratase (NHase). Transcriptome analysis revealed that the transcription levels of the native NHase, amidase and nitrilase were extremely high, moderate and extremely low, respectively. Through NHase-amidase double-knockout and amidase single-knockout, the engineered strains R. ruber THdAdN and R. ruber THdA were obtained for overexpression of a heterologous nitrilase from R. rhodochrous tg1-A6 using a urea-induced Pa2 promoter. The nitrilase activity toward substrate acrylonitrile in the engineered THdAdN(Nit) reached 187.0 U/mL at 42 h, threefold of that R. rhodochrous tg1-A6 and 2.3-fold of that of THdA(Nit). The optimal catalysis temperature and pH of the nitrilases in different cells exhibited no significant difference. Using the cells as catalysts, biomanufacturing of ammonium acrylate was performed under room temperature. When catalyzed by the engineered THdAdN(Nit), the titer and productivity of ammonium acrylate dramatically increased to 741.0 g/L and 344.9 g/L/h, which are the highest results reported to date.

Involvement of a putative cyclic amp receptor protein (CRP)-like binding sequence and a CRP-like protein in glucose-mediated catabolite repression of thn genes in Rhodococcus sp. strain TFB

Glucose catabolite repression of tetralin catabolic genes in Rhodococcus sp. strain TFB was shown to be exerted by a protein homologous to transcriptional regulators of the cyclic AMP receptor (CRP)-FNR family. The protein was detected bound to putative CRP-like boxes localized at the promoters of the thnA1 and thnS genes.

Generation of mutant of Rhodococcus rhodochrous PA-34 through chemical mutagenesis for hyperproduction of nitrile hydratase

Rhodococcus rhodochrous PA-34 has been reported to produce nitrile hydratase enzyme that converts 3-cyanopyridine to nicotinamide. A mutant of R. rhodochrous PA-34 was generated through chemical mutagenesis using N-methyl-N-nitro-N-nitrosoguanidine (MNNG) that exhibited 2 times higher nitrile hydratase activity as compared to wild strain. The reaction conditions using resting cells of this mutant strain for the conversion of nicotinamide were optimized. Under the optimized reaction conditions the mutant strain exhibited maximum nitrile hydratase activity [7.8 U/mgdcm (milligram dry cell mass)] at 55 degrees C in 0.3 M potassium phosphate buffer (pH 5.5).

Zinc(II)/ketoxime system as a simple and efficient catalyst for hydrolysis of organonitriles

The hydrolysis of sterically hindered and unhindered alkyl nitriles, and also of benzyl and phenyl nitriles RCN (R = Me, CH(2)Cl, Et, n-Pr, i-Pr, n-Bu, t-Bu, p-MeOC(6)H(4)CH(2), Ph), to carboxamides is catalyzed by a novel system of superior simplicity consisting of cheap, widely commercially available, and rather environmentally friendly compounds, that is, a ZnX(2)/ketoxime combination, but it does not proceed at all with either the zinc salt or the ketoxime taken alone. The nature of the anion X(-) in the zinc salt (X = NO(3), Cl, CF(3)SO(3)) or of the ketoxime (Me(2)C=NOH, C(4)H(8)C=NOH, C(5)H(10)C=NOH) does not affect strongly the catalytic properties of the system, but the best results were obtained so far with a Zn(NO(3))(2).6H(2)O/2-propanone oxime molar ratio of 1:4; turnover numbers are typically above ca. 100 but reach as high as 1000 for p-MeOC(6)H(4)CH(2)C(=O)NH(2). The previously unknown structures of the two carboxamide products n-BuC(=O)NH(2) and p-MeOC(6)H(4)CH(2)C(=O)NH(2) were determined by X-ray diffraction studies. The complexes [ZnX(2)(R(2)C=NOH)(2)] (X = Cl, R(2) = 2Me, C(4)H(8), C(5)H(10); X = NO(3), R = C(4)H(8)), prepared by heating the appropriate zinc salts with 2 equiv of the ketoxime in acetone and characterized by C, H, N analyses, FAB-MS, (1)H and (13)C[(1)H] NMR spectroscopies, and also X-ray crystallography (for X = Cl, R(2) = 2Me; X = NO(3), R = C(4)H(8)), proved to be catalyst precursors in the conversions because the activity of these species is high only in the presence of 2 equiv of the ketoxime.