Zhongyao Shen

Production of poly-β-hydroxybutyrate on molasses by recombinant Escherichia coli

Beet molasses successfully replaced glucose as sole carbon source to produce poly-β-hydroxybutyrate by a recombinant Escherichia coli strain (HMS174/pTZ18u-PHB). The fermentation with molasses was cheaper than with glucose. The final dry cell weight, PHB content and PHB productivity were 39.5 g/L, 80% (w/w) and 1 g/Lh, respectively, in a 5 L stirred tank fermenter after 31.5 h fed-batch fermentation with constant pH and dissolved O2 content.

Insights into thermal stability of thermophilic nitrile hydratases by molecular dynamics simulation.

Thermal stability is of great importance for industrial enzymes. Here we explored the thermal-stable mechanism of thermophilic nitrile hydratases (NHases) utilizing a molecular dynamic simulation. At a nanosecond timescale, profiles of root mean square fluctuation (RMSF) of two thermophilic NHases, 1UGQ and 1V29, under enhancing thermal stress were carried out at 300 K, 320 K, 350 K and 370 K, respectively. Results showed that the region A1 (211-231 aa) and A2 (305-316 aa) in 1UGQ, region B1 (186-192 aa) in 1V29, and most of terminal ends in both enzymes are hyper-sensitive. Salt-bridge analyses revealed that in one hand, salt-bridges contributed to maintaining the rigid structure and stable performance of the thermophilic 1UGQ and 1V29; in the other hand, salt-bridges involved in thermal sensitive regions are relatively weak and prone to be broken at elevated temperature, thereby cannot hold the stable conformation of the spatial neighborhood. In 1V29, region A1 was stabilized by a well-organized hook-hook like cluster with multiple salt-bridge interactions, region A2 was stabilized by two strong salt-bridge interactions of GLU52-ARG332 and GLU334-ARG332. In 1UGQ, the absence of a charged residue decreased its thermal sensitivity of region B1, and the formation of a small beta-sheet containing a stable salt-bridge in C-beta-terminal significantly enhanced its thermal stability. By radius of gyration calculation containing or eliminating the thermal sensitive regions, we quantified the contribution of thermal sensitive regions for thermal sensitivity of 1UGQ and 1V29. Consequently, we presented strategies to improve thermal stability of the industrialized mesophilic NHase by introducing stable salt-bridge interactions into its thermal sensitive regions.

Improving stability of nitrile hydratase by bridging the salt-bridges in specific thermal-sensitive regions.

The regions and types suitable mutations for bridging salt-bridges to intensify enzyme stability are identified in this study. Using nitrile hydratase (NHase) as the model enzyme, three deformation-prone thermal-sensitive regions (A1, A2 and A3 in β-subunit), identified by RMSF calculations of the thermophilic NHase 1V29 from Bacillus SC-105-1 and 1UGQ from Pseudonocardia thermophila JCM3095, were determined and the stabilized salt-bridge interactions were transferred into the corresponding region of industrialized mesophilic NHase-TH from Rhodococcus ruber TH. Three types of salt bridges-active-center-adjacent (in A1), internal neighboring-residue-bridged (in A2) and C-terminal-residue-bridged (A3)-were constructed in NHase-TH. The engineered NHase-TH-A1 showed reduced expression of β-subunit, reduced activity and irregular stability. NHase-TH-A2 exhibited a enhanced expression of β-subunit but complete loss of activity; while NHase-TH-A3 exhibited not only a slightly enhanced expression of β-subunit and enzyme activity, but also a 160% increase in thermal stability, a 7% enhanced product tolerance and a 75% enhanced resistance to cell-disruption by ultrasonication. The molecular dynamic (MD) simulation revealed that NHase-TH-A3, with a moderate RMSD value, generates 10 new salt bridges in both internal-subunit and interfacial-subunit, confirming that a C-terminal salt-bridge strategy is powerful for enzyme stability intensification through triggering global changes of the salt bridge networks.

Identification of lipopeptide isoforms by MALDI-TOF-MS/MS based on the simultaneous purification of iturin, fengycin, and surfactin by RP-HPLC.

A three-stage linear gradient strategy using reverse-phase high-performance liquid chromatography (HPLC) was optimized for rapid, high-quality, and simultaneous purification of the lipopeptide isoforms of iturin, fengycin, and surfactin, which may differ in composition by only a single amino acid and/or the fatty acid residue. Matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry (MALDI-TOF-MS/MS) was applied to detect the lipopeptides harvested from each reversed-phase HPLC peak. Amino acid analysis based on phenyl isothiocyanate derivatization was further used for confirmation of the amino acid species and molar ratio in a certain HPLC fraction. By this MALDI-TOF-MS/MS coupled with amino acid analysis, it was revealed that iturin at m/z 1,043 consists of a circular Asn-Tyr-Asn-Gln-Pro-Asn-Ser peptide and C14 β-OH fatty acid. Surfactin homologs from Bacillus subtilis THY-7 at m/z 1,030, 1,044, 1,058, and 1,072 possess a circular Glu-Leu-Leu-Val-Asp-Leu-Leu peptide and the β-OH fatty acid with a different length (C13–C16). Fengycin species at m/z 1,463 and 1,477 are homologs possessing the circular peptide Glu-Orn-Tyr-Thr-Glu-Ala-Pro-Gln-Tyr-Ile linked to a C16 or C17 γ-OH fatty acid, whereas fengycin at m/z 1,505 contains a Glu-Orn-Tyr-Thr-Glu-Val-Pro-Gln-Tyr-Ile sequence with a Val instead of Ala at position 6. The method developed in this work provided an efficient approach for characterization of diverse lipopeptide isoforms from the iturin, fengycin, and surfactin families.

Identification of nitrile hydratase-producing Rhodococcus ruber TH and characterization of an amiE-negative mutant.

Microbial transformation of acrylonitrile to acrylamide by nitrile hydratase is of great interest to green chemistry. During the transformation, acrylic acid is generally accumulated as a by-product through biocatalysis of amidase. A novel strain with high nitrile hydratase activity was isolated from soil and identified as Rhodococcus ruber TH by morphology and 16S rRNA gene analysis. An amidase-negative recombinant, R. ruber TH3 was constructed. Its nitrile hydratase activity was 25% higher than that of the wild type, reaching 490+/-29.2U/mg dry cell weight, while the amidase activity was 60% lower. After 6 h hydration of acrylonitrile using free cells as biocatalysts at 18 degrees C, acrylamide production by TH3 was 23% higher and the production of the by-product, acrylic acid, was 87% lower than that of the wild type. This result demonstrates that the strain TH3 could be valuable for industrial applications.

Construction and selection of the novel recombinant Escherichia coli strain for poly(β-hydroxybutyrate) production

Heterogeneous cloning of Vitreoscilla hemoglobin gene (vgb), lytic genes of phage lambda with S amber mutation (S(-)RRz) and PHB biosynthetic genes (phbCAB) in the same host strain E. coli JM105 was carried out for production of poly(beta-hydroxybutyrate) (PHB). A superior novel strain, VG1 (pTU14), was constructed and selected, which contained the vgb gene in the chromosomal DNA and the plasmid pTU14 containing S(-)RRz and phbCAB genes. When cultured in 100 ml of LBG medium in a 300-ml flask, all of the exogenous genes in VG1 (pTU14) were expressed. The cell concentration of VG1 (pTU14) grown by batch culture in a flask reached 10.2 gl(-1); PHB concentration, PHB content and PHB yield, which is the ratio of the PHB accumulation to the glucose consumption, were 8.54 gl(-1), 84% and 0.43 gg(-1), respectively. When cultured by batch-feeding of glucose in a 300-ml shaking flask, the cell concentration and PHB content reached 26 gl(-1) and over 96%, respectively.

Overexpression of synthesized cephalosporin C acylase containing mutations in the substrate transport tunnel.

Cephalosporin C (CPC) acylase converts CPC into 7-aminocephalosporanic acid (7-ACA) by single-step enzymatic catalysis. An optimized CPC acylase gene with substituted codons and a reduced GC content was artificially designed, synthesized and overexpressed in recombinant Escherichia coli. The synthetic CPC acylase (sCPCAcy) exhibited 2.3 times more CPC specific deacylation activity with substrate CPC than with substrate glutaryl-7-ACA (GL-7-ACA). Site-directed mutagenesis of the residues around the active center showed that not only the residues that were adjacent to the CPC D-α-aminoadipyl moiety, but also the residues that were in the substrate transport tunnel (Leu666, Ala675, Leu677), played crucial roles in catalysis as the ones locating in active center. Mutant sCPCAcy(Leu666Phe) and sCPCAcy(Leu677Ala) exhibited significantly reduced specific enzymatic activity, while mutant sCPCAcy(Ala675Gly) demonstrated enhanced activity. The specific activity of purified sCPCAcy and sCPCAcy(Ala675Gly) was 10.0 U/mg and 11.3 U/mg, respectively. The optimal CPC acylase productivity of mutant sCPCAcy(Ala675Gly) reached 5349 U/l after 24h in culture, which was a 35% increase over the activity of sCPCAcy.

Effect of poly(β-hydroxybutyrate) accumulation on the stability of a recombinant plasmid in Escherichia coli

Poly(beta-hydroxybutyrate) (PHB) production using a recombinant Escherichia coli VG1 (pTU14) was carried out. PHB granules were gradually biosynthesized in recombinant cells as inclusion bodies and the morphology of cells became linearly inflated with PHB accumulation from 6 h to 36 h of culture. The stability of plasmid pTU14 was inevitably affected by in-cell PHB accumulation. During repeated subcultures under both PHB-accumulating and non-PHB-accumulating conditions, plasmid DNAs of pTU14 were extracted and analyzed after more than 60 generations. The results showed that plasmid pTU14 is structurally stable but segregationally unstable, and that the segregational instability worsened with increasing accumulation of PHB granules. This is due to not only the serious metabolic burden of plasmid replication and gene expression on the host cell, but also the volume effects of PHB granules on the natural random distribution of plasmids during the binary fission of cells.

Modeling catalytic mechanism of nitrile hydratase by semi-empirical quantum mechanical calculation.

Nitrile hydratase (NHase) is an important industrial enzyme capable of converting nitriles to corresponding amides. Utilizing the method of semi-empirical quantum mechanical (QM) calculation by TRITON, the bioconversion process of acrylonitrile to acrylamide catalyzed by NHase was successfully performed on a computer. Crystal structure of a Co-type NHase from Pseudonocardia thermophila JCM 3095 (PDB code 1IRE) was selected as the target for acrylonitrile autodock. In silico calculations were performed on the NHase-acrylonitrile complex to simulate the enzyme catalysis mechanism by quantitatively comparing energy changes of each reaction pathway. Simulation results showed that active site activation is the first step of NHase catalysis, in which the Co2+ coordinated to a water molecule forms a Co-OH complex mediated by the oxidized alpha-CEA113. Then the oxygen atom in the Co-OH attacks the C atom in the -CN triple bond of acrylonitrile, forming a precursor of acrylamide. Consequently, proton rearrangement happens transforming the precursor into the final product of acrylamide, under the assistance of the hydrogen atom in the -OH group of alpha-SER112. Gibbs energy changes of three steps corresponding to the active center activation, nucleophilic attack and proton rearrangement are around -31, 23 and -12 kcal/mol, respectively.

Immobilization and stabilization of cephalosporin C acylase on aminated support by crosslinking with glutaraldehyde and further modifying with aminated macromolecules

In this work, cephalosporin C acylase (CA), a heterodimeric enzyme of industrial potential in direct hydrolysis of cephalosporin C (CPC) to 7‐aminocephalosporanic acid (7‐ACA), was covalently immobilized on the aminated support LX1000‐HA (HA) with two different protocols. The stability of CA adsorbed onto the HA support followed by crosslinking with glutaraldehyde (HA–CA–glut) was better than that of the CA covalently immobilized on the glutaraldehyde preactivated HA support (HA–glut–CA). The thermostabilization factors (compared with the free enzyme) of these two immobilized enzymes were 11.2‐fold and 2.2‐fold, respectively. In order to improve the stability of HA–CA–glut, a novel strategy based on postimmobilization modifying with aminated molecules was developed to take advantage of the glutaraldehyde moieties left on the enzyme and support. The macromolecules, such as polyethyleneimine (PEI) and chitosan, had larger effects than small molecules on the thermal stability of the immobilized enzyme perhaps due to crosslinking of the enzymes and support with each other. The quaternary structure of the CA could be much stabilized by this novel approach including physical adsorption on aminated support, glutaraldehyde treatment, and macromolecule modification. The HA–CA–glut–PEI20000 (the HA–CA–glut postmodified with PEI Mw = 20,000) had a thermostabilization factor of 20‐fold, and its substrate affinity (Km = 14.3 mM) was better than that of HA–CA–glut (Km = 33.4 mM). The half‐life of the immobilized enzymes HA–CA–glut–PEI20000 under the CPC‐catalyzing conditions could reach 28 cycles, a higher value than that of HA–CA–glut (21 cycles).