Shiru Jia

ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria

ICEberg (http://db-mml.sjtu.edu.cn/ICEberg/) is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. We propose that ICEberg will facilitate efficient, multi-disciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community.

Surfactant-activated lipase hybrid nanoflowers with enhanced enzymatic performance

Increasing numbers of materials have been extensively used as platforms for enzyme immobilization to improve catalytic performance. However, activity of the most of the enzymes was declined after immobilization. Here, we develop a surfactant-activated lipase-inorganic flowerlike hybrid nanomaterials with rational design based on interfacial activation and self-assembly. The resulting surfactant-activated lipase-inorganic hybird nanoflower (activated hNF-lipase) exhibited 460% and 200% higher activity than native lipase and conventional lipase-inorganic hybird nanoflower (hNF-lipase). Furthermore, the activated hNF-lipase displayed good reusability due to its monodispersity and mechanical properties, and had excellent long-time stability. The superior catalytic performances were attributed to both the conformational modulation of surfactants and hierarchical structure of nanoflowers, which not only anchored lipases in an active form, but also decreased the enzyme-support negative interaction and mass-transfer limitations. This new biocatalytic system is promising to find widespread use in applications related to biomedicine, biosensor, and biodiesel.

Metabolomic analysis of antimicrobial mechanisms of ε-poly-L-lysine on Saccharomyces cerevisiae.

ε-Poly-L-lysine (ε-PL), a naturally occurring amino acid homopolymer, has been widely used as a food preservative. However, its antimicrobial mechanism has not been fully understood. This study investigated the antimicrobial mode of action of ε-PL on a yeast, Saccharomyces cerevisiae. When treated with ε-PL at the concentration of 500 μg/mL, cell mortality was close to 100% and the phospholipid bilayer curvature, pores, and micelles on the surface of S. cerevisiae were clearly observed by scanning electron microscopy (SEM). At the level of 200 μg/mL, ε-PL significantly inhibited the cell growth of S. cerevisiae. When treated with 50 μg/mL ε-PL, the yeast cell was able to grow but the cell cycle was prolonged. A significant increase in cell membrane permeability was induced by ε-PL at higher concentrations. Metabolomics analysis revealed that the ε-PL stress led to the inhibition of primary metabolic pathways through the suppression of the tricarboxylic acid cycle and glycolysis. It is therefore proposed that the microbiostatic effect of ε-PL at lower levels on S. cerevisiae is achieved by inducing intracellular metabolic imbalance via disruption of cell membrane functions. Moreover, the results suggested that the antimicrobial mechanism of ε-PL on S. cerevisiae can in fact change from microbiostatic to microbicidal when the concentration of ε-PL increased, and the mechanisms of these two modes of action were completely different.

Characterization and antioxidant activities of extracellular and intracellular polysaccharides from Fomitopsis pinicola

Fomitopsis pinicola (F. pinicola) is a kind of medicinal fungi, and few studies has been carried out on F. pinicola polysaccharides from liquid submerged cultivation. The characterization and antioxidant activities of extracellular polysaccharide (EPS) and intracellular polysaccharide (IPS) isolated from F. pinicola were investigated. The results showed that the molecular weight of EPS was 2.30×10(4)Da, and EPS was composed of mannose, rhamnose, xylose and galactose with the molar ratio of 0.1:1.0:0.3:0.5. The molecular weight of IPS was 4.07×10(5)Da, and the monosaccharide compositions included glucose, mannose, rhamnose, xylose and galactose with the molar ratio of 1.0:0.9:0.9:0.8:1.1. Antioxidant activities of both EPS and IPS including in vitro scavenging activities on 1-diphenyl-2-picrylhydrazyl (DPPH) and hydroxyl radicals, cellular protective effects on yeast cells from ultraviolet (UV) radiation and H2O2 oxidative damage were tested. Both EPS and IPS showed antioxidant activities in a dose dependent manner, and IPS had higher antioxidant activity than EPS. So EPS and IPS could be potential novel antioxidants for functional food.

The Role of Lactic Acid Adsorption by Ion Exchange Chromatography

Background The polyacrylic resin Amberlite IRA-67 is a promising adsorbent for lactic acid extraction from aqueous solution, but little systematic research has been devoted to the separation efficiency of lactic acid under different operating conditions. Methodology/Principal Findings In this paper, we investigated the effects of temperature, resin dose and lactic acid loading concentration on the adsorption of lactic acid by Amberlite IRA-67 in batch kinetic experiments. The obtained kinetic data followed the pseudo-second order model well and both the equilibrium and ultimate adsorption slightly decreased with the increase of the temperature at 293–323K and 42.5 g/liter lactic acid loading concentration. The adsorption was a chemically heterogeneous process with a mean free energy value of 12.18 kJ/mol. According to the Boyd_plot, the lactic acid uptake process was primarily found to be an intraparticle diffusion at a lower concentration (<50 g/liter) but a film diffusion at a higher concentration (>70 g/liter). The values of effective diffusion coefficient Di increased with temperature. By using our Equation (21), the negative values of ΔG° and ΔH° revealed that the adsorption process was spontaneous and exothermic. Moreover, the negative value of ΔS° reflected the decrease of solid-liquid interface randomness at the solid-liquid interface when adsorbing lactic acid on IRA-67. Conclusions/Significance With the weakly basic resin IRA-67, in situ product removal of lactic acid can be accomplished especially from an open and thermophilic fermentation system without sterilization.

Mesoporous Metal–Organic Framework with Well-Defined Cruciate Flower-Like Morphology for Enzyme Immobilization

Metal-organic frameworks (MOFs) have recently emerged as a promising candidates for the immobilization of enzymes due to their diversified structures and porosity. However, a lack of good size and morphological control over the as-prepared MOFs has limited their practical applications in some cases. Herein, instead of zeolitic imidazolate framework-8 (ZIF-8) with the standard rhombic dodecahedral morphology, we successfully synthesize a novel mesoporous catalase@ZIF composite with cruciate flower-like morphology by embedding catalase molecules into uniformly sized ZIF crystals. With extraordinarily large mesopore size and high protein loading capacity, the catalase@ZIF composites with cruciate flower-like morphology exhibit 400% higher activity than that of catalase@ZIF composites with conventional rhombic dodecahedral morphology, and show higher reusability than conventional rhombic dodecahedral morphology. More importantly, we demonstrate for the first time that the biomacromolecules (proteins) can not directly regulate the crystal size, morphology, and crystallinity of ZIF-8. Moreover, the crystal morphology of ZIF has primary dependence on concentrations of 2-methylimidazole and Zn2+ ions, and can be directly controlled by adjusting concentrations of Zn2+ ions while keeping the high concentration of 2-methylimidazole.

Improvement of antimicrobial activity of graphene oxide/bacterial cellulose nanocomposites through the electrostatic modification

Graphene oxide (GO) has an attracting and ever-growing interest in various research fields for its fascinating nanostructures. In this study, bacterial cellulose (BC) was used as a matrix to synthesize GO-based materials by a mechanical mixing method. The modification of GO with PEI significantly improved the bonding force between GO nanofillers and BC matrix. The morphology of the nanocomposites had a significant effect on the mechanical properties, hydrophilic properties as well as the antibacterial activity. After the modification, the GO-PEI/BC showed a strong antimicrobial effect on Saccharomyces cerevisiae due to the effective direct contacts between the nanofillers of the composites and the cell surfaces. This study demonstrates that the morphology of the nanocomposites has a great effect on physiochemical properties and the interactions between the microorganism and the nanocomposites.

Revealing Differences in Metabolic Flux Distributions between a Mutant Strain and Its Parent Strain Gluconacetobacter xylinus CGMCC 2955

A better understanding of metabolic fluxes is important for manipulating microbial metabolism toward desired end products, or away from undesirable by-products. A mutant strain, Gluconacetobacter xylinus AX2-16, was obtained by combined chemical mutation of the parent strain (G. xylinus CGMCC 2955) using DEC (diethyl sulfate) and LiCl. The highest bacterial cellulose production for this mutant was obtained at about 11.75 g/L, which was an increase of 62% compared with that by the parent strain. In contrast, gluconic acid (the main byproduct) concentration was only 5.71 g/L for mutant strain, which was 55.7% lower than that of parent strain. Metabolic flux analysis indicated that 40.1% of the carbon source was transformed to bacterial cellulose in mutant strain, compared with 24.2% for parent strain. Only 32.7% and 4.0% of the carbon source were converted into gluconic acid and acetic acid in mutant strain, compared with 58.5% and 9.5% of that in parent strain. In addition, a higher flux of tricarboxylic acid (TCA) cycle was obtained in mutant strain (57.0%) compared with parent strain (17.0%). It was also indicated from the flux analysis that more ATP was produced in mutant strain from pentose phosphate pathway (PPP) and TCA cycle. The enzymatic activity of succinate dehydrogenase (SDH), which is one of the key enzymes in TCA cycle, was 1.65-fold higher in mutant strain than that in parent strain at the end of culture. It was further validated by the measurement of ATPase that 3.53–6.41 fold higher enzymatic activity was obtained from mutant strain compared with parent strain.

Mesoporous CLEAs-silica composite microparticles with high activity and enhanced stability.

A novel enzyme immobilization approach was used to generate mesoporous enzymes-silica composite microparticles by co-entrapping gelatinized starch and cross-linked phenylalanine ammonia lyase (PAL) aggregates (CLEAs) containing gelatinized starch into biomemitic silica and subsequently removing the starch by α-amylase treatment. During the preparation process, the gelatinzed starch served as a pore-forming agent to create pores in CLEAs and biomimetic silica. The resulting mesoporous CLEAs-silica composite microparticles exhibited higher activity and stability than native PAL, conventional CLEAs, and PAL encapsulated in biomimetic silica. Furthermore, the mesoporous CLEAs-silica composite microparticles displayed good reusability due to its suitable size and mechanical properties, and had excellent stability for storage. The superior catalytic performances were attributed to the combinational unique structure from the intra-cross-linking among enzyme aggregates and hard mesoporous silica shell, which not only decreased the enzyme-support negative interaction and mass-transfer limitations, but also improved the mechanical properties and monodispersity. This approach will be highly beneficial for preparing various bioactive mesoporous composites with excellent catalytic performance.

Influence of amino acids, organic solvents and surfactants for phenylalanine ammonia lyase activity in recombinant Escherichia coli

Aim:  To improve phenylalanine ammonia lyase (E.C.4·3·1·5‐PAL) activity in recombinant Escherichia coli. Some methods for enrichment of PAL activity in recombinant E. coli JM109 were described. In an effort to create a rich enzyme source these methods would lead to improvements in the production of l‐phenylalanine.