Microbial Synthesis of the Energetic Material Precursor 1,2,4-Butanetriol

The lack of a route to precursor 1,2,4-butanetriol that is amenable to large-scale synthesis has impeded substitution of 1,2,4-butanetriol trinitrate for nitroglycerin. To identify an alternative to the current commercial synthesis of racemic d,l-1,2,4-butanetriol involving NaBH4 reduction of esterified d,l-malic acid, microbial syntheses of d- and l-1,2,4-butanetriol have been established. These microbial syntheses rely on the creation of biosynthetic pathways that do not exist in nature. Oxidation of d-xylose by Pseudomonas fragi provides d-xylonic acid in 70% yield. Escherichia coli DH5alpha/pWN6.186A then catalyzes the conversion of d-xylonic acid into d-1,2,4-butanetriol in 25% yield. P. fragi is also used to oxidize l-arabinose to a mixture of l-arabino-1,4-lactone and l-arabinonic acid in 54% overall yield. After hydrolysis of the lactone, l-arabinonic acid is converted to l-1,2,4-butanetriol in 35% yield using E. coli BL21(DE3)/pWN6.222A. As a catalytic route to 1,2,4-butanetriol, microbial synthesis avoids the high H2 pressures and elevated temperatures required by catalytic hydrogenation of malic acid.

Mutations in the “lid” region affect chain length specificity and thermostability of aPseudomonas fragilipase

The cold-adapted Pseudomonas fragi lipase (PFL) displays highest activity on short-chain triglyceride substrates and is rapidly inactivated at moderate temperature. Sequence and structure comparison with homologous lipases endowed with different substrate specificity and stability, pointed to three polar residues in the lid region, that were replaced with the amino acids conserved at equivalent positions in the reference lipases. Substitutions at residues T137 and T138 modified the lipase chain-length preference profile, increasing the relative activity towards C8 substrates. Moreover, mutations conferred to PFL higher temperature stability. On the other hand, replacement of the serine at position 141 by glycine destabilized the protein.

D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi: molecular cloning of the enzyme gene and crystal structure of the enzyme

The gene coding for d-3-hydroxybutyrate dehydrogenase (HBDH) was cloned from Pseudomonas fragi. The nucleotide sequence contained a 780 bp open reading frame encoding a 260 amino acid residue protein. The recombinant enzyme was efficiently expressed in Escherichia coli cells harboring pHBDH11 and was purified to homogeneity as judged by SDS-PAGE. The enzyme showed a strict stereospecificity to the D-enantiomer (3R-configuration) of 3-hydroxybutyrate as a substrate. Crystals of the ligand-free HBDH and of the enzyme-NAD+ complex were obtained using the hanging-drop, vapor-diffusion method. The crystal structure of the HBDH was solved by the multiwavelength anomalous diffraction method using the SeMet-substituted enzyme and was refined to 2.0 A resolution. The overall structure of P.fragi HBDH, including the catalytic tetrad of Asn114, Ser142, Tyr155, and Lys159, shows obvious relationships with other members of the short-chain dehydrogenase/reductase (SDR) family. A cacodylate anion was observed in both the ligand-free enzyme and the enzyme-NAD+ complex, and was located near the catalytic tetrad. It was shown that the cacodylate inhibited the NAD+-dependent D-3-hydroxybutyrate dehydrogenation competitively, with a Ki value of 5.6 mM. From the interactions between cacodylate and the enzyme, it is predicted that substrate specificity is achieved through the recognition of the 3-methyl and carboxyl groups of the substrate.

Unscrambling thermal stability and temperature adaptation in evolved variants of a cold-active lipase

Directed evolution by error-prone PCR was applied to stabilize the cold-active lipase from Pseudomonas fragi (PFL). PFL displays high activity at 10 degrees C, but it is highly unstable even at moderate temperatures. After two rounds of evolution, a variant was generated with a 5-fold increase in half-life at 42 degrees C and a shift of 10 degrees C in the temperature optimum, nevertheless retaining cold-activity. The evolved lipase displayed specific activity higher than the wild type enzyme in the temperature range 29-42 degrees C. Biophysical measurements did not indicate any obvious difference between the improved variant and the wild type enzyme in terms of loss of secondary structure upon heat treatment, nor a shift in the apparent melting temperature.

Adaptation response of Pseudomonas fragi on refrigerated solid matrix to a moderate electric field

BACKGROUND

Moderate electric field (MEF) technology is a promising food preservation strategy since it relies on physical properties-rather than chemical additives-to preserve solid cellular foods during storage. However, the effectiveness of long-term MEF exposure on the psychrotrophic microorganisms responsible for the food spoilage at cool temperatures remains unclear.

RESULTS

The spoilage-associated psychrotroph Pseudomonas fragi MC16 was obtained from pork samples stored at 7 °C. Continuous MEF treatment attenuated growth and resulted in subsequent adaptation of M16 cultured on nutrient agar plates at 7 °C, compared to the control cultures, as determined by biomass analysis and plating procedures. Moreover, intracellular dehydrogenase activity and ATP levels also indicated an initial effect of MEF treatment followed by cellular recovery, and extracellular β-galactosidase activity assays indicated no obvious changes in cell membrane permeability. Furthermore, microscopic observations using scanning and transmission electron microscopy revealed that MEF induced sublethal cellular injury during early treatment stages, but no notable changes in morphology or cytology on subsequent days.

CONCLUSION

Our study provides direct evidence that psychrotrophic P. fragi MC16 cultured on nutrient agar plates at 7 °C are capable of adapting to MEF treatment.

RNA-binding domain of the key structural protein P7 for the Rice dwarf virus particle assembly

The Rice dwarf virus (RDV) P7 structural protein is the key protein in the RDV particle assembly. The P7 protein was digested partially or completely by Staphylococcus aureus V8 protease and/or Pseudomonas fragi Asp-N protease. The molecular mass and the N-terminal amino acid sequence of the polypeptide fragments of the P7 protein were determined by SDS-PAGE and the Edman degradation method, respectively. Then the polypeptides were located in the deduced amino acid sequence of the RDV P7 protein based on the nucleotide sequence information, with the knowledge of the specific cleavage sites of the Staphylococcus aureus V8 and Pseudomonas fragi Asp-N protease, and the two RNA-binding domains in the P7 protein were identified. Domain 1 was located in the residue 128-249 containing 122 amino acids and domain 2 was located in the residue 325-355 containing 31 amino acids. Thus, these two domains may play an important role in the virus particle assembly by contributing to the packaging of viral dsRNAs inside the particles. The two domains may be novel RNA-binding domains, because no amino acid sequences highly similar to the conservative sequences of known dsRNA-binding domains reported so far. The similarity between the motif of domain 1 and the motif of the DNA-binding protein suggests that the DNA-binding activity of the RDV P7 protein may be due to this sequence. The similarity between the motif of domain 1 and the motif of the RNA polymerase domain suggests that the P7 protein may also play a role in RNA synthesis, besides its function in the assembly and subsequent packaging of viral dsRNA into core particles.

Crystallization and preliminary X-ray characterization of D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi

A recombinant form of D-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) from Pseudomonas fragi has been crystallized by the hanging-drop method using PEG 3000 as a precipitating agent. The crystals belong to the orthorhombic group P2(1)2(1)2, with unit-cell parameters a = 64.3, b = 99.0, c = 110.2 A. The crystals are most likely to contain two tetrameric subunits in the asymmetric unit, with a VM value of 3.29 A3 Da(-1). Diffraction data were collected to a 2.0 A resolution using synchrotron radiation at the BL6A station of the Photon Factory.

Hydrolysis of myofibrillar proteins by protease AprA secreted from Pseudomonas fragi: Preference for degrading Ala-linked peptide bonds

Extracellular proteases of bacteria have attracted attention in recent years. Alkaline protease AprA secreted from Pseudomonas fragi has been shown to cause spoilage in chilled meat and to degrade myofibrillar proteins (MPs), but the spoilage mechanism was unknown. AprA possessed a high affinity for substrate proteins (Km = 1.40 mg/mL, Vmax = 11.20 mg/mL/min) and was controlled by metal ions and inhibitors. AprA exhibited strong hydrolytic activity on MPs, with alterations in secondary structure, tertiary structure and sulfhydryl content. Molecular docking and molecular dynamics revealed that AprA bound to actin and myosin heavy chain (MHC) through hydrogen bonds, hydrophobic interaction and salt bridges, respectively. AprA exhibited a broad spectrum of cleavage, with a relative preference for Ala-linked peptide bonds, according to peptide release kinetics. The above results reveal the mechanism of bacterial spoilage of chilled meat at low temperatures. Of course, this provides a theoretical basis for targeted control of the meat spoilage caused by AprA.

Discovery of a temperature-dependent protease spoiling meat from Pseudomonas fragi: Target to myofibrillar and sarcoplasmic proteins rather than collagen

Chilled meat frequently suffered microbial spoilage because bacteria can secrete various proteases that break down the proteins. In this study, Pseudomonas fragi NMC 206 exhibited a temperature-dependent secretion pattern, with the ability to release the specific protease only below 25 °C. It was identified as alkaline protease AprA by LC-MS/MS, with the molecular weight of 50.4 kDa, belonging to the Serralysin family metalloprotease. Its significant potential for meat spoilage in situ resulted in alterations in meat color and sensory evaluation, as well as elevated pH, total volatile basic nitrogen (TVB-N) and the formation of volatile organic compounds (VOCs). The hydrolysis of meat proteins in vitro showed that AprA possessed a considerable proteolysis activity and degradation preferences on meat proteins, especially its ability to degrade myofibrillar and sarcoplasmic proteins, rather than collagen. These observations demonstrated temperatures regulated the secretion of AprA, which was closely related to chilled chicken spoilage caused by bacteria. These will provide a new basis for the preservation of meat products at low temperatures.