Dynamic upregulation of the rate-limiting enzyme for valerolactam biosynthesis in Corynebacterium glutamicum.

Valerolactam is a monomer used to manufacture high-value nylon-5 and nylon-6,5. However, the biological production of valerolactam has been limited by the inadequate efficiency of enzymes to cyclize 5-aminovaleric acid to produce valerolactam. In this study, we engineered Corynebacterium glutamicum with a valerolactam biosynthetic pathway consisting of DavAB from Pseudomonas putida to convert L-lysine to 5-aminovaleric acid and ß-alanine CoA transferase (Act) from Clostridium propionicum to produce valerolactam from 5-aminovaleric acid. Most of the L-lysine was converted into 5-aminovaleric acid, but promoter optimization and increasing the copy number of Act were insufficient to significantly improve the titer of valerolactam. To eliminate the bottleneck at Act, we designed a dynamic upregulation system (a positive feedback loop based on the valerolactam biosensor ChnR/Pb). We used laboratory evolution to engineer ChnR/Pb to have higher sensitivity and a higher dynamic output range, and the engineered ChnR-B1/Pb-E1 system was used to overexpress the rate-limiting enzymes (Act/ORF26/CaiC) that cyclize 5-aminovaleric acid into valerolactam. In glucose fed-batch culture, we obtained 12.33 g/L valerolactam from the dynamic upregulation of Act, 11.88 g/L using ORF26, and 12.15 g/L using CaiC. Our engineered biosensor (ChnR-B1/Pb-E1 system) was also sensitive to 0.01-100 mM caprolactam, which suggests that this dynamic upregulation system can be used to enhance caprolactam biosynthesis in the future.

Catalytic and structural properties of ATP-dependent caprolactamase from Pseudomonas jessenii.

Caprolactamase is the first enzyme in the caprolactam degradation pathway of Pseudomonas jessenii. It is composed of two subunits (CapA and CapB) and sequence-related to other ATP-dependent enzymes involved in lactam hydrolysis, like 5-oxoprolinases and hydantoinases. Low sequence similarity also exists with ATP-dependent acetone- and acetophenone carboxylases. The caprolactamase was produced in Escherichia coli, isolated by His-tag affinity chromatography, and subjected to functional and structural studies. Activity toward caprolactam required ATP and was dependent on the presence of bicarbonate in the assay buffer. The hydrolysis product was identified as 6-aminocaproic acid. Quantum mechanical modeling indicated that the hydrolysis of caprolactam was highly disfavored (ΔG0 '= 23 kJ/mol), which explained the ATP dependence. A crystal structure showed that the enzyme exists as an (αß)2 tetramer and revealed an ATP-binding site in CapA and a Zn-coordinating site in CapB. Mutations in the ATP-binding site of CapA (D11A and D295A) significantly reduced product formation. Mutants with substitutions in the metal binding site of CapB (D41A, H99A, D101A, and H124A) were inactive and less thermostable than the wild-type enzyme. These residues proved to be essential for activity and on basis of the experimental findings we propose possible mechanisms for ATP-dependent lactam hydrolysis.

Glucose and Maltose Surface-Functionalized Thermoresponsive Poly(N-Vinylcaprolactam) Nanogels.

Soft nanoparticles are interesting materials due to their size, deformability, and ability to host guest molecules. Surface properties play an essential role in determining the fate of the particles in biological medium, and coating of the nanoparticles (and polymers) with carbohydrates has been found to be an efficient strategy for increasing their biocompatibility and fine-tuning other important properties such as aqueous solubility. In this work, soft nanogels of poly(N-vinylcaprolactam), PNVCL, were surface-functionalized with different glucose and maltose ligands, and the colloidal properties of the gels were analyzed. The PNVCL nanogels were first prepared via semibatch precipitation polymerization, where a comonomer, propargyl acrylate (PA), was added after preparticle formation. The aim was to synthesize "clickable" nanogels with alkyne groups on their surfaces. The nanogels were then functionalized with two separate azido-glucosides and azido-maltosides (containing different linkers) through a copper-catalyzed azide-alkyne cycloaddition (CuAAc) click reaction. The glucose and maltose bearing nanogels were thermoresponsive and shrank upon heating. Compared to the PNVCL-PA nanogel, the carbohydrate bearing ones were larger, more hydrophilic, had volume phase transitions at higher temperatures, and were more stable against salt-induced precipitation. In addition to investigating the colloidal properties of the nanogels, the carbohydrate recognition was addressed by studying the interactions with a model lectin, concanavalin A (Con A). The binding efficiency was not affected by the temperature, which indicates that the carbohydrate moieties are located on the gel surfaces, and are capable of interacting with other biomolecules independent of temperature. Thus, the synthesis produces nanogels, which have surface functions capable of biorelevant interactions and a thermoresponsive structure. These types of particles can be used for drug delivery.

Characterization of the caprolactam degradation pathway in Pseudomonas jessenii using mass spectrometry-based proteomics.

Some bacterial cultures are capable of growth on caprolactam as sole carbon and nitrogen source, but the enzymes of the catabolic pathway have not been described. We isolated a caprolactam-degrading strain of Pseudomonas jessenii from soil and identified proteins and genes putatively involved in caprolactam metabolism using quantitative mass spectrometry-based proteomics. This led to the discovery of a caprolactamase and an aminotransferase that are involved in the initial steps of caprolactam conversion. Additionally, various proteins were identified that likely are involved in later steps of the pathway. The caprolactamase consists of two subunits and demonstrated high sequence identity to the 5-oxoprolinases. Escherichia coli cells expressing this caprolactamase did not convert 5-oxoproline but were able to hydrolyze caprolactam to form 6-aminocaproic acid in an ATP-dependent manner. Characterization of the aminotransferase revealed that the enzyme deaminates 6-aminocaproic acid to produce 6-oxohexanoate with pyruvate as amino acceptor. The amino acid sequence of the aminotransferase showed high similarity to subgroup II ω-aminotransferases of the PLP-fold type I proteins. Finally, analyses of the genome sequence revealed the presence of a caprolactam catabolism gene cluster comprising a set of genes involved in the conversion of caprolactam to adipate.

Isolation and characterization of racemase from Ensifer sp. 23-3 that acts on α-aminolactams and α-amino acid amides.

Limited information is available on α-amino-ε-caprolactam (ACL) racemase (ACLR), a pyridoxal 5'-phosphate-dependent enzyme that acts on ACL and α-amino acid amides. In the present study, eight bacterial strains with the ability to racemize α-amino-ε-caprolactam were isolated and one of them was identified as Ensifer sp. strain 23-3. The gene for ACLR from Ensifer sp. 23-3 was cloned and expressed in Escherichia coli. The recombinant ACLR was then purified to homogeneity from the E. coli transformant harboring the ACLR gene from Ensifer sp. 23-3, and its properties were characterized. This enzyme acted not only on ACL but also on α-amino-δ-valerolactam, α-amino-ω-octalactam, α-aminobutyric acid amide, and alanine amide.

Characterization of an α-amino-ɛ-caprolactam racemase with broad substrate specificity from Citreicella sp. SE45.

α-Amino-ε-caprolactam (ACL) racemizing activity was detected in a putative dialkylglycine decarboxylase (EC 4.1.1.64) from Citreicella sp. SE45. The encoding gene of the enzyme was cloned and transformed in Escherichia coli BL21 (DE3). The molecular mass of the enzyme was shown to be 47.4 kDa on SDS-polyacrylamide gel electrophoresis. The enzymatic properties including pH and thermal optimum and stabilities were determined. This enzyme acted on a broad range of amino acid amides, particularly unbranched amino acid amides including L-alanine amide and L-serine amide with a specific activity of 17.5 and 21.6 U/mg, respectively. The K m and V max values for D- and L-ACL were 5.3 and 2.17 mM, and 769 and 558 µmol/min.mg protein, respectively. Moreover, the turn over number (K cat) and catalytic efficiency (K cat/K m ) of purified ACL racemase from Citreicella sp. SE45 using L-ACL as a substrate were 465 S-1 and 214 S-1mM-1, respectively. The new ACL racemase from Citreicella sp. SE45 has a potential to be used as the biocatalytic application.

The Role of a Nonribosomal Peptide Synthetase in l-Lysine Lactamization During Capuramycin Biosynthesis.

Capuramycins are one of several known classes of natural products that contain an l-Lys-derived l-α-amino-ɛ-caprolactam (l-ACL) unit. The α-amino group of l-ACL in a capuramycin is linked to an unsaturated hexuronic acid component through an amide bond that was previously shown to originate by an ATP-independent enzymatic route. With the aid of a combined in vivo and in vitro approach, a predicted tridomain nonribosomal peptide synthetase CapU is functionally characterized here as the ATP-dependent amide-bond-forming catalyst responsible for the biosynthesis of the remaining amide bond present in l-ACL. The results are consistent with the adenylation domain of CapU as the essential catalytic component for l-Lys activation and thioesterification of the adjacent thiolation domain. However, in contrast to expectations, lactamization does not require any additional domains or proteins and is likely a nonenzymatic event. The results set the stage for examining whether a similar NRPS-mediated mechanism is employed in the biosynthesis of other l-ACL-containing natural products and, just as intriguingly, how spontaneous lactamization is avoided in the numerous NRPS-derived peptides that contain an unmodified l-Lys residue.

Temperature-dependent control of Staphylococcus aureus biofilms and virulence by thermoresponsive oligo(N-vinylcaprolactam).

Bacterial biofilms are associated with persistent infections because they are highly tolerant of antimicrobial agents, and in the case of Staphylococcus aureus, which is a leading cause of nosocomial infections because of its resistance to diverse antibiotics, biofilm formation is a known mechanism of drug resistance. In the present study, we investigated the ability of thermoresponsive oligo (N-vinylcaprolactam) (OVCL) to control biofilm formation by and the virulence of S. aureus. One synthetic and four commercial OVCLs (MW ≤ 240,000) at 50 µg/mL were found to increase S. aureus biofilm formation 7-fold at 25 °C, but to markedly inhibit S. aureus biofilm formation at 37 °C. Confocal and scanning electron microscopy confirmed the temperature-dependent effect of OVCL on S. aureus biofilms. It was found that the addition of OVCL to S. aureus culture caused cells to become dramatically more hydrophilic at 37 °C, which partially supports the biofilm reduction. Also, transcriptional analysis showed that OVCL temperature-dependently regulated biofilm-related genes (aur, agrA, and icaA) in S. aureus. In addition, it was found surface coatings containing OVCL effectively controlled S. aureus biofilm formation on solid glass surfaces. Furthermore, OVCL inhibited the hemolysis of human red blood cells by S. aureus at 37 °C and attenuated S. aureus virulence in the nematode Caenorhabditis elegans. These results suggest that OVCL has potential use for controlling bacterial biofilm formation and virulence.

Tuning assembly and enzymatic degradation of silk/poly(N-vinylcaprolactam) multilayers via molecular weight and hydrophobicity.

We report on enzymatically degradable nanothin coatings obtained by layer-by-layer (LbL) assembly of silk fibroin with poly(N-vinylcaprolactam) (PVCL) via hydrogen bonding and hydrophobic interactions. We found that both silk ß-sheet content, controlled through dipping and spin-assisted LbL, and PVCL molecular weight regulate film thickness, microstructure, pH-stability, and biodegradability with a nanoscale precision. Thickness of (silk/PVCL) films increased with increase in PVCL molecular weight and decrease in deposition pH. The impact of assembly pH on film growth was more dramatic for dipped films. These systems show a significant rise in thickness with increase in PVCL molecular weight at pH < 5 but become independent on polymer chain length at pH ≥ 5. We also found that spin-assisted films exhibited a greater stability at elevated pH and against enzymatic degradation as compared to their dipped counterparts. For both film types, the pH and enzymatic stability was improved with increasing PVCL length and ß-sheet content, indicating enhanced hydrophobic and hydrogen-bonded interactions between PVCL and silk. Finally, we fabricated spherical and cubical (silk/PVCL) LbL capsules of regulated permeability and enzymatic degradation. Our approach gives a unique opportunity to tune thickness, morphology, structure, and biodegradability rate of silk films and capsules by varying silk secondary structure and PVCL length. Accounting for all-aqueous fabrication and the biocompatibility of both polymers these biodegradable materials provide novel platforms for delivery systems and medical devices.

[Bacteria that degrade low-molecular linear epsilon-caprolactam olygomers].

Five bacterial strains with the unique ability to utilize low-molecular linear caprolactam olygomers (nylon olygomers) were isolated from soil samples contaminated with industrial wastes of epsilon-caprolactam. Based on the properties studied and also on the analysis of 16S rRNA gene nucleotide sequences, the strains BS2,BS3, BS9, BS38, and BS57 were classified to the general Arthrobacter, Brevibacterium, Microbacteriun, Gulosibacter, and Achromobacter, respectively. All of the strains also utilized 6-aminohexanoic and adipic acids, which are intermidiates of the epsilon-caprolactam catabolism. This indirectly points to the fact that degradation of olygomers in these bacteria occurs via the monomer degradation pathway. The BS9 and BS57 strains utilized only olygomers of the epsilon-caprolactam, while BS2, BS3, and BS38 also degraded epsilon-caprolactam and its homologs, enantolactam and caprylolactam, which differentiates the latter from the previously known degraders of olygomers and suggests the presence in these strains of enzymes with lactam hydrolase activity, in addition to 6-aminohexanoate-dimer hydrolase.

Isolation and characterization of a novel ε-caprolactam-degrading microbe, Acinetobacter calcoaceticus, from industrial wastewater by chemostat-enrichment.

For the isolation of a ε-caprolactam-degrading microbe from wastewaters of a factory producing caprolactam, we applied a chemostat-enrichment technique with a selective medium containing caprolactam as sole source of carbon and nitrogen. This allowed for the isolation of a novel caprolactam-degrading microbe, identified as Acinetobacter calcoaceticus. The strain had a critical tolerance of 19 g caprolactam l(-1) in minimal medium, which is higher than any previously reported caprolactam-degrading microbe. A. calcoaceticus also decreased the caprolactam content in medium by 65 % within 72 h despite the high caprolactam content (10 g l(-1)). This study highlights the potential use of A. calcoaceticus strain for the bioremediation of recalcitrant synthetic polymers, such as caprolactam.

[scpA the new salicylate hydroxylase gene localized on salicylate/caprolactam degradation plasmids].

Both caprolactam and salicylate biodegradation by Pseudomonas salicylate/caprolactam degraders is controlled by large conjugative plasmids (SAL/CAP). Some of these plasmids determined to be the members of IncP-7 group. The new salicylate 1-hydroxylase gene (scpA) on SAL/CAP-plasmids has been detected and partially sequenced. Gene scpA was equally related to closest homologs nahG (NAH7), salA (P. reinekei MT1) and nahU (pND6-1), but identity of scpA to these genes did not exceed 72-74%. Synthesis of salicylate 1-hydroxylase ScpA was not induced by salicylate. This enzyme had wide substrate specificity and exhibited highest specific activity with 4-methylsalicylate and nonsubstituted salicylate. Besides pseudomonad's salicylate degradative conjugative plasmids without "classical" nah2-operon and harboring only salicylate 1-hydroxylase gene nahU have been firstly described.

[The new gene encoding TrfA-type replication initiator has been found on caprolactam/salicylate degradation plasmid pBS270].

The mini-replicon of pseudomonads' caprolactam/salicylate degradation plasmid pBS270 (105 kb, contains incompatibility determinants of P-7 group) has been obtained and its nucleotide sequence has been determined. The new gene encoding TrfA-like replication initiator has been found on this replicon. Poor homology of this replication initiator with known proteins of TrfA-family allows us to classify obtained replicon as IncP-1-like. The pBS270mini reveals chimeric nature.

[Selection of initiation replication mutants of IncP-9 plasmid pBS267].

A minireplicon containing the rep gene and oriV site of the gamma subgroup of the IncP-9 caprolactam pBS267 biodegradation plasmid was cloned for the first time. It was established that a minimized variant of pBS267 plasmid cannot be sustained in E. coli and is inherited in an unstable way in bacteria Pseudomonas. Using in vitro mutagenesis, mutant variants of the minireplicon were produced, characterized by an increased number of copies in cells, the ability to replicate in E. coli, and relatively stable inheritance in P. putida cells. The obtained constructs are the basis for a study of the replication mechanisms of IncP-9 group plasmids, as well as use as vectors for molecular cloning in a wide range of gram-negative bacteria.

X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation.

We performed x-ray crystallographic analyses of the 6-aminohexanoate cyclic dimer (Acd) hydrolase (NylA) from Arthrobacter sp., an enzyme responsible for the degradation of the nylon-6 industry byproduct. The fold adopted by the 472-amino acid polypeptide generated a compact mixed alpha/beta fold, typically found in the amidase signature superfamily; this fold was especially similar to the fold of glutamyl-tRNA(Gln) amidotransferase subunit A (z score, 49.4) and malonamidase E2 (z score, 44.8). Irrespective of the high degree of structural similarity to the typical amidase signature superfamily enzymes, the specific activity of NylA for glutamine, malonamide, and indoleacetamide was found to be lower than 0.5% of that for Acd. However, NylA possessed carboxylesterase activity nearly equivalent to the Acd hydrolytic activity. Structural analysis of the inactive complex between the activity-deficient S174A mutant of NylA and Acd, performed at 1.8 A resolution, suggested the following enzyme/substrate interactions: a Ser(174)-cis-Ser(150)-Lys(72) triad constitutes the catalytic center; the backbone N in Ala(171) and Ala(172) are involved in oxyanion stabilization; Cys(316)-S(gamma) forms a hydrogen bond with nitrogen (Acd-N(7)) at the uncleaved amide bond in two equivalent amide bonds of Acd. A single S174A, S150A, or K72A substitution in NylA by site-directed mutagenesis decreased the Acd hydrolytic and esterolytic activities to undetectable levels, indicating that Ser(174)-cis-Ser(150)-Lys(72) is essential for catalysis. In contrast, substitutions at position 316 specifically affected Acd hydrolytic activity, suggesting that Cys(316) is responsible for Acd binding. On the basis of the structure and functional analysis, we discussed the catalytic mechanisms and evolution of NylA in comparison with other Ser-reactive hydrolases.

A limited LCA of bio-adipic acid: manufacturing the nylon-6,6 precursor adipic acid using the benzoic acid degradation pathway from different feedstocks.

A limited life cycle assessment (LCA) was performed on a combined biological and chemical process for the production of adipic acid, which was compared to the traditional petrochemical process. The LCA comprises the biological conversion of the aromatic feedstocks benzoic acid, impure aromatics, toluene, or phenol from lignin to cis, cis-muconic acid, which is subsequently converted to adipic acid through hydrogenation. Apart from the impact of usage of petrochemical and biomass-based feedstocks, the environmental impact of the final concentration of cis, cis-muconic acid in the fermentation broth was studied using 1.85% and 4.26% cis, cis-muconic acid. The LCA focused on the cumulative energy demand (CED), cumulative exergy demand (CExD), and the CO(2) equivalent (CO(2) eq) emission, with CO(2) and N(2) O measured separately. The highest calculated reduction potential of CED and CExD were achieved using phenol, which reduced the CED by 29% and 57% with 1.85% and 4.26% cis, cis-muconic acid, respectively. A decrease in the CO(2) eq emission was especially achieved when the N(2) O emission in the combined biological and chemical process was restricted. At 4.26% cis, cis-muconic acid, the different carbon backbone feedstocks contributed to an optimized reduction of CO(2) eq emissions ranging from 14.0 to 17.4 ton CO(2) eq/ton adipic acid. The bulk of the bioprocessing energy intensity is attributed to the hydrogenation reactor, which has a high environmental impact and a direct relationship with the product concentration in the broth.

Pestalactams A-C: novel caprolactams from the endophytic fungus Pestalotiopsis sp.

Chemical investigations of a fermentation culture from the endophytic fungus Pestalotiopsis sp. yielded three novel caprolactams, pestalactams A-C (). The structures of were determined by analysis of 1D and 2D-NMR, UV, IR, and MS data. The structure of pestalactam A was confirmed following single crystal X-ray diffraction analysis. Pestalactams A-C are the first C-7 alkylated caprolactam natural products to be reported. Pestalactams A () and B () were tested against two different strains of the malaria parasite Plasmodium falciparum (3D7 and Dd2), and the mammalian cell lines, MCF-7 and NFF, and showed modest in vitro activity in all assays.

Thermoresponsive poly(N-vinylcaprolactam) cryogels: synthesis and its biophysical evaluation for tissue engineering applications.

The thermoresponsive poly(N-vinylcaprolactam) (PVCl) based cryogel network were synthesized and characterized with respect to physical and biological properties. The PVCl cryogel crosslinked with polyethylene glycol-diacrylate (PEGda) was synthesized in 1% dimethyl sulfoxide containing aqueous medium at -12°C for 12-14 h. The cryogel synthesized in this manner were highly spongy in nature and can absorb water in its porous network. These polymeric cryogel networks have good physical morphology as confirmed by scanning electron microscopy. The estimated porosity of these cryogels was 90% as demonstrated by various methods based on absorption of water and cyclohexane. The median pore diameter and surface area was 30 µm and 2.0253 m(2)/g, respectively as confirmed by analysis on mercury porosimeter. These materials can interact with biological system without any cytotoxic effects. Change in temperature influenced the adsorption of fetal bovine serum (FBS) on PVCl scaffold which showed maximum protein adsorption at 37°C, as compared to that at 25°C. Furthermore, the fibroblast cell adhesion studies showed the potential of these PVCl based cryogels as tissue engineering scaffolds.

Identification, Characterization, and Application of a Highly Sensitive Lactam Biosensor from Pseudomonas putida.

Caprolactam is an important polymer precursor to nylon traditionally derived from petroleum and produced on a scale of 5 million tons per year. Current biological pathways for the production of caprolactam are inefficient with titers not exceeding 2 mg/L, necessitating novel pathways for its production. As development of novel metabolic routes often require thousands of designs and result in low product titers, a highly sensitive biosensor for the final product has the potential to rapidly speed up development times. Here we report a highly sensitive biosensor for valerolactam and caprolactam from Pseudomonas putida KT2440 which is >1000× more sensitive to an exogenous ligand than previously reported sensors. Manipulating the expression of the sensor oplR (PP_3516) substantially altered the sensing parameters, with various vectors showing Kd values ranging from 700 nM (79.1 µg/L) to 1.2 mM (135.6 mg/L). Our most sensitive construct was able to detect in vivo production of caprolactam above background at ∼6 µg/L. The high sensitivity and range of OplR is a powerful tool toward the development of novel routes to the biological synthesis of caprolactam.

A novel aryl acylamidase from Nocardia farcinica hydrolyses polyamide.

An alkali stable polyamidase was isolated from a new strain of Nocardia farcinica. The enzyme consists of four subunits with a total molecular weight of 190 kDa. The polyamidase cleaved amide and ester bonds of water insoluble model substrates like adipic acid bishexylamide and bis(benzoyloxyethyl)terephthalate and hydrolyzed different soluble amides to the corresponding acid. Treatment of polyamide 6 with this amidase led to an increased hydrophilicity based on rising height and tensiometry measurements and evidence of surface hydrolysis of polyamide 6 is shown. In addition to amidase activity, the enzyme showed activity on p-nitrophenylbutyrate. On hexanoamide the amidase exhibited a K(m) value of 5.5 mM compared to 0.07 mM for p-nitroacetanilide. The polyamidase belongs to the amidase signature family and is closely related to aryl acylamidases from different strains/species of Nocardia and to the 6-aminohexanoate-cyclic dimer hydrolase (EI) from Arthrobacter sp. KI72.