Chromosome evolution of Escherichia coli Nissle 1917 for high-level production of heparosan

Heparosan is a crucial-polysaccharide precursor for the chemoenzymatic synthesis of heparin, a widely used anticoagulant drug. Presently, heparosan is mainly extracted with the potential risk of contamination from Escherichia coli strain K5, a pathogenic bacterium causing urinary tract infection. Here, a nonpathogenic probiotic, E. coli strain Nissle 1917 (EcN), was metabolically engineered to carry multiple copies of the 19-kb kps locus and produce heparosan to 9.1 g/L in fed-batch fermentation. Chromosome evolution driven by antibiotics was employed to amplify the kps locus, which governed the synthesis and export of heparosan from EcN at 21 mg L⁻¹ OD⁻¹. The average copy number of kps locus increased from 1 to 24 copies per cell, which produced up to 104 mg L^-1 OD⁻¹ of heparosan in the shaking flask cultures of engineered strains. The following in-frame deletion of recA stabilized the recombinant duplicates of chromosomal kps locus and the productivity of heparosan in continuous culture for at least 56 generations. Fed-batch fermentation of the engineered strain EcN8 was carried out to bring the yield of heparosan up to 9.1 g/L. Heparosan from the fermentation culture was further purified at a 75% overall recovery. The structure of purified heparosan was characterized and further modified by N-sulfotransferase with 3′-phosphoadenosine-5′-phosphosulfate as the sulfo-donor. The analysis of element composition showed that heparosan was N-sulfated by over 80%. These results indicated that duplicating large DNA cassettes up to 19-kb, followed by high-cell-density fermentation, was promising in the large-scale preparation of chemicals and could be adapted to engineer other industrial-interest bacteria metabolically.     

Uptake of Yolk Very Low Density Lipoprotein by Chicken and Quail Embryos Is Not Mediated by a Homologue of the Oocyte Vitellogenesis Receptor

In chicken (Gallus domesticus) embryos, a limited amount of yolk engulfment occurs via coated invaginations at the yolk sac membrane apical surface. Because the presence of these so-called “coated pits” is associated with receptor-mediated endocytosis, the purpose of the present study was to demonstrate the existence on the yolk sac membrane of receptor sites for the interaction with very low density lipoprotein (VLDL), the major component of egg yolk. Ligand blotting experiments revealed the presence of a VLDL-binding protein (M_r ∼95 kDa) in yolk sac membranes of both chicken and Japanese quail (Coturnix coturnix japonica) embryos 8 days of age and older. However, these VLDL-binding proteins were present in very low abundance relative to that of another apolipoprotein B receptor that is found in the plasma membrane of chicken and quail oocytes (the so-called oocyte vitellogenesis receptor [OVR]; M_r 95 kDa). Furthermore, no signals were detected when chicken and quail yolk sac membrane proteins were probed with a rabbit polyclonal antibody raised against the 14 C-terminal amino acids of the chicken OVR. It was concluded that chicken and quail yolk sac membrane VLDL-binding proteins were structurally different from the chicken OVR and that receptor-mediated endocytosis plays a minor role in the uptake of yolk VLDL by developing avian embryos.     

Comparative studies of the interaction of human and bovine platelet factor 4 with heparin using histidine NMR resonances as spectroscopic probes

ThepK _a values of His-38 and His-50 of the heparin-binding protein, bovine platelet factor 4, are 5.6 and 6.5, respectively, as determined by¹H NMR spectroscopy. The¹H NMR resonance of His-38 of bovine platelet factor 4 which exhibits the lowerpK _a value is perturbed upon heparin binding to a greater degree than the resonance of His-50. Human platelet factor 4 contains the homologous residues His-23 and His-35. ThepK _a values of the two histidine residues of human platelet factor 4 are 5.3 and 6.4. The¹H NMR resonance of the histidine of human platelet factor 4 exhibiting the lowerpK _a value also is perturbed upon heparin binding to a greater degree than the histidine resonance exhibiting the higherpK _a , thereby suggesting comparable heparin-protein interactions in bovine and human platelet factor 4.     

Techniques for RNA extraction from cells cultured in starPEG–heparin hydrogels

Three-dimensional (3D) cell culture models that provide a biologically relevant microenvironment are imperative to investigate cell–cell and cell–matrix interactions in vitro. Semi-synthetic star-shaped poly(ethylene glycol) (starPEG)–heparin hydrogels are widely used for 3D cell culture due to their highly tuneable biochemical and biomechanical properties. Changes in gene expression levels are commonly used as a measure of cellular responses. However, the isolation of high-quality RNA presents a challenge as contamination of the RNA with hydrogel residue, such as polymer or glycosaminoglycan fragments, can impact template quality and quantity, limiting effective gene expression analyses. Here, we compare two protocols for the extraction of high-quality RNA from starPEG–heparin hydrogels and assess three subsequent purification techniques. Removal of hydrogel residue by centrifugation was found to be essential for obtaining high-quality RNA in both isolation methods. However, purification of the RNA did not result in further improvements in RNA quality. Furthermore, we show the suitability of the extracted RNA for cDNA synthesis of three endogenous control genes confirmed via quantitative polymerase chain reaction (qPCR). The methods and techniques shown can be tailored for other hydrogel models based on natural or semi-synthetic materials to provide robust templates for all gene expression analyses.     

Structure and dynamics analysis of a new member heparinase II/III of family 12 polysaccharide lyase from Pseudopedobacter saltans by computational modeling and small-angle X-ray scattering

Abstract

The structure of heparinase II/III belonging to family 12 polysaccharide lyase (PsPL12a) from Pseudopedobacter saltans was generated by homology modeling. Multiple sequence alignment showed conserved (Asn216, Tyr270 and His400) and semi-conserved active site amino acid residues. The modeled structure of PsPL12a displayed α/α toroid domain at N-terminal and antiparallel β sheets at C-terminal domain. The modeled structure was similar to those of heparinases from polysaccharide lyase 12 and 21 families. Validation of PsPL12a model by Ramachandran plot showed 94.6% of residues in the favored region, 5.2% of residues in the allowed region and only 0.2% of residues in the outlier region. The area and volume computed for PsPL12a displayed nearly a closed conformation of the active site, similar to HepIII from Bacteroides thetaiotaomicron. The charge calculation on the surface of the PsPL12a structure showed the higher distribution of positive charge in the active site cleft as compared with other homologous structures. Molecular docking study of MD-simulated PsPL12a structure with heparin oligosaccharide showed high binding affinity as compared with heparan sulfate oligosaccharides. Comparison of the active site of modeled PsPL12a with other homologous heparinases revealed putative catalytic triad involving the residues Asn216, His400 and Tyr270. Small-angle X-ray scattering analysis of PsPL12a displayed a fully folded and boxing glove-like envelop.

Communicated by Ramaswamy H. Sarma     

Detection of cell type and marker specificity of nuclear binding sites for anionic carbohydrate ligands

The emerging functionality of glycosaminoglycan chains engenders interest in localizing specific binding sites using cytochemical tools. We investigated nuclear binding of labeled heparin, heparan sulfate, a sulfated fucan, chondroitin sulfate, and hyaluronic acid in epidermal keratinocytes, bone marrow stromal cells, 3T3 fibroblasts and glioma cells using chemically prepared biotinylated probes. Binding of the markers was cell-type specific and influenced by extraction of histones, but was not markedly affected by degree of proliferation, differentiation or malignancy. Cell uptake of labeled heparin and other selected probes and their transport into the nucleus also was monitored. Differences between keratinocytes and bone marrow stromal cells were found. Preincubation of permeabilized bone marrow stromal cells with label-free heparin reduced the binding of carrier-immobilized hydrocortisone to its nuclear receptors. Thus, these tools enabled binding sites for glycosaminoglycans to be monitored in routine assays.     

低分子肝素对子痫前期大鼠炎症反应、肝功能及胎盘组织Bcl-2、Bax蛋白表达的影响

目的:研究低分子肝素对子痫前期大鼠炎症反应、肝功能及胎盘组织Bcl-2、Bax蛋白表达的影响.方法:将90只孕期大鼠以随机数表法分成正常孕组、子痫前期组、治疗组,每组30只.其中子痫前期组和治疗组大鼠于妊娠第13 d开始皮下注射左旋硝基精氨酸甲酯,建立子痫前期大鼠模型,注射剂量为200mg/(kg·d),正常孕组予以等...     

Polyanion binding accelerates the formation of stable and low‐toxic aggregates of ALS‐linked SOD1 mutant A4V

The toxic property thus far shared by both ALS‐linked SOD1 variants and wild‐type SOD1 is an increased propensity to aggregation. However, whether SOD1 oligomers or aggregates are toxic to cells remains to be well defined. Moreover, how the toxic SOD1 species are removed from intra‐ and extracellular environments also needs to be further explored. The DNA binding has been shown to be capable of accelerating the aggregatio\n of wild‐type and oxidized SOD1 forms under acidic and neutral conditions. In this study, we explore the binding of DNA and heparin, two types of essential life polyanions, to A4V, an ALS‐linked SOD1 mutant, under acidic conditions, and its consequences. The polyanion binding alters the A4V conformation, neutralizes its local positive charges, and increases its local concentrations along the polyanion chain, which are sufficient to lead to acceleration of the pH‐dependent A4V aggregation. The accelerated aggregation, which is ascribed to the polyanion binding‐mediated removal or shortening of the lag phase in aggregation, contributes to the formation of amorphous A4V nanoparticles. The prolonged incubation with polyanions not only results in the complete conversion of likely soluble toxic A4V oligomers into non‐ and low‐toxic SDS‐resistant aggregates, but also increases their stability. Although this is only an initial step toward reducing the toxicity of SOD1 mutants, the accelerating role of polyanions in protein aggregation might become one of the rapid pathways that remove toxic forms of SOD1 mutants from intra‐ and extracellular environments. Proteins 2014; 82:3356–3372. © 2014 Wiley Periodicals, Inc.