Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks

Epistasis refers to the interaction between genes. Although high-throughput epistasis data from model organisms are being generated and used to construct genetic networks(1-3), the extent to which genetic epistasis reflects biologically meaningful interactions remains unclear(4-6). We have addressed this question through in silico mapping of positive and negative epistatic interactions amongst biochemical reactions within the metabolic networks of Escherichia coli and Saccharomyces cerevisiae using flux balance analysis. We found that negative epistasis occurs mainly between nonessential reactions with overlapping functions, whereas positive epistasis usually involves essential reactions, is highly abundant and, unexpectedly, often occurs between reactions without overlapping functions. We offer mechanistic explanations of these findings and experimentally validate them for 61 S. cerevisiae gene pairs.

Growth and antioxidant system of Escherichia coli in response to microcystin-RR

Microcystins are a kind of cyclic hepatoxins produced by many species of cyanobacteria. The toxic effects of microcystins on animals and plants have been well studied. However, the reports about the effects of microcystins on microbial cells are very limited. In present paper, Escherichia coli was undertaken to determine the effect of microcystin-RR. These results suggested that microcystin-RR could prolong the growth of E. coli when exposed to high concentrations of microcystin-RR and cause the accumulation of ROS and induce the oxidant stress for a short time. The antioxidant system protects E. coli from oxidative damage.

Cloning, expression and characterization of aerolysin from Aeromonas hydrophila in Escherichia coli

Aerolysin is a toxin (protein in nature) secreted by the strains of Aeromonas spp. and plays all important role in the virulence of Aeromonas strains. It has also found several applications such as for detection of glycosylphosphatidylinositol (GPI)-anchored proteins etc. A. hydrophila is a ubiquitous Gram-negative bacterium which causes frequent harm to the aquaculture. To obtain a significant amount of recombinant aerolysin in the active form, in this study, we expressed the aerolysin in E. Coli Under the control of T7 RNase promoter. The coding region (AerA-W) of the aerA gene of A. hydrophila XS91-4-1. excluding partial coding region of the signal peptide was cloned into the vector pET32a and then transformed into E. coli b121. After optimizing the expression conditions, the recombinant protein AerA-W was expressed in a soluble form and purified using His-Bind resin affinity chromatography. Recombinant aerolysin showed hemolytic activity in the agar diffusive hemolysis test. Western blot analysis demonstrated good antigenicity of the recombinant protein.

Gene structure of goose-type lysozyme in the mandarin fish Siniperca chuatsi with analysis on the lytic activity of its recombinant in Escherichia coli

A goose-type lysozyme (g-lysozyme) gene has been cloned from the mandarin fish (Siniperca chuatsi), with its recombinant protein expressed in Escherichia coli. From the first transcription initiation site, the mandarin fish g-lysozyme gene extends 1307 nucleotides to the end of the 3' untranslated region, and it contains 5 exons and 4 introns. The open reading frame of the glysozyme transcript has 582 nucleotides which encode a 194 amino acid peptide. The 5' flanking region of mandarin fish glysozyme gene shows several common transcriptional factor binding sites when compared with that from Japanese flounder (Paralichthys olivaceus). The recombinant mandarin fish g-lysozyme was expressed in E. coli by using pET-32a vector, and the purified recombinant g-lysozyme shows lytic activity against Micrococcus lysodeikticus. (c) 2005 Elsevier B.V All rights reserved.

Biosynthesis of gold nanoparticles assisted by Escherichia coli DH5 alpha and its application on direct electrochemistry of hemoglobin

In this communication, biosynthesis of gold nanoparticles assisted by Escherichia coli DH5 alpha and its application on direct electrochemistry of hemoglobin are reported. The gold nanoparticles formed on the bacteria surface are mostly spherical. The direct electrochemistry of hemoglobin can be achieved by incorporated into the bio-nanocomposite films on a glassy carbon electrode.

Mannose-Escherichia coli interaction in the presence of metal cations studied in vitro by colorimetric polydiacetylene/glycolipid liposomes

Supramolecular assemblies of liposomes (vesicles) made of diacetylenic lipids and synthetic mannoside derivative glycolipid receptors were successfully used to mimic the molecular recognition occurring between mannose and Escherichia coli. This specific molecular recognition was translated into visible blue-to-red color transition (biochromism) of the polymerized liposomes, readily quantified by UV-visible spectroscopy. Some transition metal cations (Cd2+, Ag+, Cu2+, Fe3+, Zn2+ and Ni2+) and alkali earth metal cations (Ca2+, Mg2+ and Ba2+) were introduced into the system to analyze their effects on specific biochromism. Results showed that the presence of Cd2+, Ag+, Ca2+, Mg2+ and Ba2+ enhanced biochromisin. A possible enhancement mechanism was proposed in the process of bacterial adhesion to host cells. However, Cu2+, Fe3+, Zn2+ and Ni2+ exhibited inhibitory effects that cooperated with diacetylene lipid with a carboxylic group and increased the rigidity of the liposomal outer leaflet, blocking changes in the side chain conformation and electrical structure of polydiacetylene polymer during biochromism.

Electrochemical and Raman studies of the biointeraction between Escherichia coli and mannose in polydiacetylene derivative supported on the self-assembled monolayers of octadecanethiol on a gold electrode

Here, we describe a new method to study the biointeraction between Escherichia coli and mannose by using supramolecular assemblies composed of polydiacetylene supported on the self-assembled monolayer of octadecanethiol on a gold electrode. These prepared bilayer materials simply are an excellent protosystem to study a range of important sensor-related issues. The experimental results from UV-vis spectroscopy, resonance Raman spectroscopy, and electrochemistry confirm that the specific interactions between E. coli and mannose can cause conformational changes of the polydiacetylene backbone rather than simple nonspecific adsorption. Moreover, the direct electrochemical detection by polydiacetylene supramolecular assemblies not only opens a new path for the use of these membranes in the area of biosensor development but also offers new possibilities for diagnostic applications and screening for binding ligands.

Functional biosynthesis of an allophycocyan beta subunit in Escherichia coli

Allophycocyanin is a phycobiliprotein with various biological and pharmacological properties. An expression vector was constructed using CpeS as the bilin lyase for the allophycocyanin beta subunit, resulting in overexpression of a fluorescent allophycocyanin beta-subunit in Escherichia coli. A high-density cell culture was developed using a continuous feeding strategy. After 16 h of culture, the dry cell density reached 21.4 g 1(-1), the expression of the allophycocyanin beta-subunit was 0.86 g l(-1) broth, and the relative chromoprotein yield was 81.4%. The recombinant protein showed spectral features similar to native allophycocyanin, which provide an efficient methodology for large-scale production of this valuable fluorescent protein. (C) 2008, The Society for Biotechnology, Japan. All rights reserved.

Highly soluble and stable recombinant holo-phycocyanin alpha subunit expressed in Escherichia coli

C-phycocyanin (Cpc) is one of the phycobiliproteins with highly fluorescent and various pharmacological activities Holo-Cpc-alpha Subunit (holo-CpcA) expressed in Escherichia colt resulted in low yield and tended to aggregate after purification in this Study, we constructed a new plasmid coding holo-CpcA fused with hexahistidine and maltose-binding protein tag, which designated as HMCpcA. to Improve Its Solubility and stability without the Impairment of its spectra anti fluorescent properties HMCpcA was significantly more stable over time and a wider range of pH as compared to holo-CpcA. In addition. both the solubility and yields of HMCpcA increase significantly We here provided an example to demonstrate that MBP could also Improve the stability of the protein it fused while it has been reported as a soluble fusion partner before. This novel fluorescent protein will facilitate the large-scale production and be potentially applicable for the development Of fluorescent probes, as well as antioxidant agents (C) 2009 Elsevier B V. All rights reserved

Biosynthesis of fluorescent allophycocyanin alpha-subunits by autocatalysis in Escherichia coli

APC (allophycocyanin) is widely used for fluorescence tagging and may be a promising antioxidant agent for use within the food and pharmaceutical industries. Chromophore attachment to apo-ApcA (apo-APC alpha-subunit without chromophore) can be auto-catalysed both in vitro and in vivo. In the present study, a plasmid containing genes of apo-ApcA and chromophore synthetases (HOI (ferredoxin-dependent haem oxygenase) and PcyA (phycocyanobilin:ferredoxin oxidoreductase)] was constructed and expressed in Escherichia coli. The results show that holo-ApcA (APC alpha-subunit with chromophore) can be synthesized by autocatalysis in E. coli. Recombinant holo-ApcA showed the same spectral and fluorescent properties as PC (phycocyanin) and could serve as a good substitute for native PC for fluorescent tagging. Moreover, recombinant ApcA can inhibit hydroxyl and peroxyl radicals more strongly than holo-ApcA and native APC. The EC50 values were 296.4 +/- 22.4 mu g/ml against hydroxyl radicals and 38.5 +/- 2.6 mu g/ml against peroxyl radicals.

Scale-up of fermentation and purification of recombinant allophycocyanin over-expressed in Escherichia coli

Phycobiliprotein is a photosynthetic antenna pigment found in cyanobacteria, rhodophytes, cryptophytes and certain dinoflagellates, which has been found to have anti-oxidative and anti-tumour activities. In this paper, a recombinant allophycocyanin (rAPC) had been expressed in Escherichia coli for anti-tumour effect. E. coli cells were cultured using glucose fed-batch method to achieve high cell densities. The biomass of rAPC was up to 3.52 g/L broth. The rAPC was purified from soluble E. coli cell lysate employing hydrophobic interaction chromatographic (HIC) method developed at the bench scale using 20 mL column. The process was performed at the pilot scale using 500 mL column for evaluation of scale-up. An amylose affinity column was used to improve the purity of final product in pilot scale purification. The purification process resulted in greater than 98% pure product and yielded up to 2.0 g/kg wet cells at the bench scale and 1.2 g/kg wet cells at the pilot scale. Peptide mapping was used to prove the identity of rAPC purified from bench scale and pilot scale process. Purified rAPC at the pilot scale was found to have remarkable inhibition on S-180 carcinoma in mice. (c) 2005 Elsevier Ltd. All rights reserved.

Pilot-scale fermentation and purification of the recombinant allophycocyanin over-expressed in Escherichia coli

A recombinant allophycocyanin (rAPC), used for treatment of tumors, has been expressed in E. coli which was grown in glucose fed-batch culture in a 30 l fermentor. Recombinant allophycocyanin was purified from soluble E. coli cell lysate using hydrophobic interaction chromatography followed by chromatography using amylose affinity column. The purity of product was greater than 98% and yielded an average of 5.5 g kg(-1) dry cells. Recombinant allophycocyanin significantly inhibited H-22 hepatoma (p (0.01) in mice with inhibition rates ranging from 36% to 62% with doses from 6.25 to 50 mg kg(-1) d(-1).

Combinational biosynthesis of a fluorescent cyanobacterial holo-alpha-allophycocyanin in Escherichia coli

Allophycocyanin ( APC) is a phycobiliprotein with various biological and pharmacological properties. An expression vector containing five essential genes in charge of biosynthesis of cyanobacterial APC holo-alpha subunit ( holo- ApcA) was constructed, resulting in over- expression of a fluorescent holo- ApcA in E. coli. After being cultured for 16 h, the dry cell density reached 22.5 gl(-1), and the expression of holo- HT- ApcA was up to 1 gl(-1) broth. The recombinant protein showed similar spectral features to native APC.