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.

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.

Comprehensive Insight into the Protein-Surface Biomolecular Interactions on a Smart Material: Complex Formation between Poly(N-vinyl Caprolactam) and Heme Protein.

Proteins are naturally occurring biopolymers that exhibit a wide range of functional applications. Meticulous knowledge about biomolecular interactions between polymeric biomaterials and body fluids or proteins is essential for designing biospecific surfaces and understanding protein-polymer interactions beyond existing limitations. In this regard, we studied the comparative effect of heme proteins such as cytochrome c, myoglobin, and hemoglobin on the phase behavior of poly(N-vinyl caprolactam) (PVCL) aqueous solution and demonstrated various biomolecular interactions in the polymer-protein complex with the aid of various biophysical techniques. Absorption spectroscopy, steady-state fluorescence spectroscopy, Fourier transform infrared spectroscopy, dynamic light scattering studies, laser Raman spectroscopy, field emission scanning electron microscopy, and transmission electron microscopy were carried out at room temperature to examine the changes in absorbance, fluorescence intensity, molecular interactions, particle size, agglomeration behavior, and surface morphologies. Furthermore, differential scanning calorimetry studies were also performed to analyze conformational changes, coil to globule transition, and phase behavior in the presence of proteins. With the addition of heme proteins, the lower critical solution temperature of PVCL increases toward higher temperature. The present study may help in designing smart biomaterials and stimulate more novel concepts in polymer-protein interactions. It also helps in the development of a biomimetic polymer for "smart" applications such as pulsatile drug release systems and controlled bioadhesion by temperature-mediated hydrophilic/hydrophobic switching.

Biochemical properties of a Pseudomonas aminotransferase involved in caprolactam metabolism.

The biodegradation of the nylon-6 precursor caprolactam by a strain of Pseudomonas jessenii proceeds via ATP-dependent hydrolytic ring opening to 6-aminohexanoate. This non-natural ω-amino acid is converted to 6-oxohexanoic acid by an aminotransferase (PjAT) belonging to the fold type I pyridoxal 5'-phosphate (PLP) enzymes. To understand the structural basis of 6-aminohexanoatate conversion, we solved different crystal structures and determined the substrate scope with a range of aliphatic and aromatic amines. Comparison with the homologous aminotransferases from Chromobacterium violaceum (CvAT) and Vibrio fluvialis (VfAT) showed that the PjAT enzyme has the lowest KM values (highest affinity) and highest specificity constant (kcat /KM ) with the caprolactam degradation intermediates 6-aminohexanoate and 6-oxohexanoic acid, in accordance with its proposed in vivo function. Five distinct three-dimensional structures of PjAT were solved by protein crystallography. The structure of the aldimine intermediate formed from 6-aminohexanoate and the PLP cofactor revealed the presence of a narrow hydrophobic substrate-binding tunnel leading to the cofactor and covered by a flexible arginine, which explains the high activity and selectivity of the PjAT with 6-aminohexanoate. The results suggest that the degradation pathway for caprolactam has recruited an aminotransferase that is well adapted to 6-aminohexanoate degradation. DATABASE: The atomic coordinates and structure factors P. jessenii 6-aminohexanoate aminotransferase have been deposited in the PDB as entries 6G4B (E∙succinate complex), 6G4C (E∙phosphate complex), 6G4D (E∙PLP complex), 6G4E (E∙PLP-6-aminohexanoate intermediate), and 6G4F (E∙PMP complex).

Artificial Caprolactam-Specific Riboswitch as an Intracellular Metabolite Sensor.

Caprolactam is a monomer used for the synthesis of nylon-6, and a recombinant microbial strain for biobased production of nylon-6 was recently developed. An intracellular biosensor for caprolactam can facilitate high-throughput metabolic engineering of recombinant microbial strains. Because of the mixed production of caprolactam and valerolactam in the recombinant strain, a caprolactam biosensor should be highly specific for caprolactam. However, a highly specific caprolactam sensor has not been reported. Here, we developed an artificial riboswitch that specifically responds to caprolactam. This riboswitch was prepared using a coupled in vitro- in vivo selection strategy with a heterogeneous pool of RNA aptamers obtained from in vitro selection to construct a riboswitch library used in in vivo selection. The caprolactam riboswitch successfully discriminated caprolactam from valerolactam. Moreover, the riboswitch was activated by 3.36-fold in the presence of 50 mM caprolactam. This riboswitch enabled caprolactam-dependent control of cell growth, which will be useful for improving caprolactam production and is a valuable tool for metabolic engineering.

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.

Sensitivity-Tunable Colorimetric Detection of Chloropicrin Vapor on Nylon-6 Nanofibrous Membrane Based on a Detoxification Reaction with Biological Thiols.

Detoxification reaction of chloropicrin in the human body with biological thiols was selected for detection of chloropicrin in the air. The consumption of free sulfhydryl group in biological thiols by chloropicrin is colorimetrically detectable with the addition of the Ellman's reagent. In this study, glutathione, N-acetyl-l-cysteine, l-homocysteine, cysteamine, and thioglycolic acid were tested as sensing agents for chloropicrin vapor detection in ppb concentration range. The reactivity of the selected biological thiols was investigated based on both their redox properties and the nucleophilic strength of the sulfhydryl groups. Nylon-6 nanofibrous membrane and an organic solvent were used as a sensor matrix and a vapor sorbent, respectively, to provide solid supports with ultrahigh surface area and enhanced adsorption to chloropicrin vapor. The tunable sensitivity and detection range by using different biological thiols was achieved on the sensors due to the different reactivity of thiols toward chloropicrin.

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.

Draft genome sequence of a caprolactam degrader bacterium: Pseudomonas taiwanensis strain SJ9

Abstract Pseudomonas taiwanensis strain SJ9 is a caprolactam degrader, isolated from industrial wastewater in South Korea and considered to have the potential for caprolactam bioremediation. The genome of this strain is approximately 6.2 Mb (G + C content, 61.75%) with 6,010 protein-coding sequences (CDS), of which 46% are assigned to recognized functional genes. This draft genome of strain SJ9 will provide insights into the genetic basis of its caprolactam-degradation ability.

Draft genome sequence of a caprolactam degrader bacterium: Pseudomonas taiwanensis strain SJ9.

Pseudomonas taiwanensis strain SJ9 is a caprolactam degrader, isolated from industrial wastewater in South Korea and considered to have the potential for caprolactam bioremediation. The genome of this strain is approximately 6.2 Mb (G+C content, 61.75%) with 6,010 protein-coding sequences (CDS), of which 46% are assigned to recognized functional genes. This draft genome of strain SJ9 will provide insights into the genetic basis of its caprolactam-degradation ability.

Development of a Transcription Factor-Based Lactam Biosensor.

Lactams are an important class of commodity chemicals used in the manufacture of nylons, with millions of tons produced every year. Biological production of lactams could be greatly improved by high-throughput sensors for lactam biosynthesis. To identify biosensors of lactams, we applied a chemoinformatic approach inspired by small molecule drug discovery. We define this approach as analogue generation toward catabolizable chemicals or AGTC. We discovered a lactam biosensor based on the ChnR/Pb transcription factor-promoter pair. The microbial biosensor is capable of sensing ε-caprolactam, δ-valerolactam, and butyrolactam in a dose-dependent manner. The biosensor has sufficient specificity to discriminate against lactam biosynthetic intermediates and therefore could potentially be applied for high-throughput metabolic engineering for industrially important high titer lactam biosynthesis.

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.

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.

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.

Protein adsorption on electrospun zinc doped hydroxyapatite containing nylon 6 membrane: kinetics and isotherm.

Surface modification of electrospun polymeric membrane surfaces is a critical step towards the separation process including protein adsorption. In this study, the electrospun Nylon fibers was incorporated with positively charged zinc doped hydroxyapatite (HAp) nanoparticles to study the adsorption of negatively charged proteins, namely bovine serum albumin (BSA). Effects of zinc amount within the atomic structure of HAp (nZH; n=0, 4, 8 At.%) was evaluated on produced scaffolds and consequently protein adsorption. The results showed that the ability of Nylon membrane to adsorb BSA increased with incorporation of nZH nanoparticles within the nylon structure. This phenomenon is appeared to be relate to different electrostatic charge and not to physical characteristic of scaffolds. The incorporated membrane (N-4ZH) by nanoparticles with highest zeta (ξ) potential adsorbed the maximum amount of protein. The adsorption of BSA was best fitted with pseudo-second order kinetic model. The experimental isotherm data were further analyzed by using Langmuir and Freundlich equations. By comparing the correlation coefficients obtained for each linear transformation of isotherm analysis, it was found that the Langmuir equation was the best fit equilibrium model that described the adsorption of BSA on these membranes.