Preparation of highly efficient electrocompetent Escherichia coli using glycerol/mannitol density step centrifugation

Traditional protocols for preparing Escherichia coli for electroporation are laborious and often deliver highly variable transformation efficiencies. Many laboratories resort to purchasing expensive commercially prepared cells. This article describes a simple method for producing electrocompetent E. coli by centrifuging bacteria through a glycerol/mannitol density cushion. The method is rapid and replaces tedious multistep procedures with two 15-min centrifugations. Standard cloning strains consistently produce more than 8 × 10⁹ transformants/μg pUC18, whereas the strains TG1 and LE392 display efficiencies of more than 3 × 10¹⁰/μg DNA.     

Evaluation of Ochrobactrum anthropi TRS-2 and its talc based formulation for enhancement of growth of tea plants and management of brown root rot disease

Aim: To evaluate Ochrobactrum anthropi TRS‐2 isolated from tea rhizosphere and its talc based formulation for growth promotion and management of brown root rot disease of tea. Methods and Results: Ochrobactrum anthropi TRS‐2, isolated from tea rhizosphere could solubilize phosphate, produce siderophore and IAA in vitro and also exhibited antifungal activity against six test pathogens. Application of an aqueous suspension of O. anthropi to the rhizosphere of nursery grown tea seedlings of five varieties of tea (TV‐18, T‐17, HV‐39, S‐449, UP‐3 and) led to enhanced growth of the treated plants, as evidenced by increase in height, in the number of shoots and number of leaves per shoot. Treatment with O. anthropi also decreased brown root rot of tea, caused by Phellinus noxius. Multifold increase in activities of chitinase, β‐1,3‐glucanase, peroxidase and phenylalanine ammonia lyase in tea plants was observed on application of O. anthropi to soil followed by inoculation with P. noxius. A concomitant increase in accumulation of phenolics was also obtained. Further, talc based formulation of O. anthropi was prepared and its survival determined every month up to a period of 12 months. Ochrobactrum anthropi could survive in the formulation up to a period of 9 months with a concentration of 7·0 log₁₀ CFU g^?1, after which there was a decline. Talc formulation was as effective as aqueous suspensions in both plant growth promotion and disease suppression. Conclusion: Ochrobactrum anthropi, either in aqueous suspension or as talc formulation induced growth of tea plants and suppressed brown root rot disease. It induced defense responses in tea plants. Significance and Impact of the Study: Ochrobactrum anthropi and its talc based formulation can be considered as an addition to available plant growth promoting rhizobacteria (PGPR) currently being used for field application. The present study offers a scope of utilizing this bacterium for growth promotion and disease management which would help in reduction of the use of chemicals in tea plantations.     

Tightly Regulated Expression Vectors for Ochrobactrum anthropi

Genetic studies of Ochrobactrum anthropi, a bacterial species important in bioremediation and biopesticide degradation, are hindered by the lack of suitably regulated gene expression system. A tightly regulated gene-expression system was developed for O. anthropi using the lacI^q gene and a re-engineered coliphage T5 promoter containing completely symmetrical DNA segment that binds more efficiently to the lactose repressor. The β-galactosidase activity was increased 57-fold when the expression of the re-engineered T5 promoter was induced. The degree of induction was controllable by varying the concentration of inducer isopropyl-β-d-thiogalactopyranoside.     

Rapid Protocol for Preparation of Electrocompetent Escherichia coli and Vibrio cholerae

Electroporation has become a widely used method for rapidly and efficiently introducing foreign DNA into a wide range of cells. Electrotransformation has become the method of choice for introducing DNA into prokaryotes that are not naturally competent. Electroporation is a rapid, efficient, and streamlined transformation method that, in addition to purified DNA and competent bacteria, requires commercially available gene pulse controller and cuvettes. In contrast to the pulsing step, preparation of electrocompetent cells is time consuming and labor intensive involving repeated rounds of centrifugation and washes in decreasing volumes of sterile, cold water, or non-ionic buffers of large volumes of cultures grown to mid-logarithmic phase of growth. Time and effort can be saved by purchasing electrocompetent cells from commercial sources, but the selection is limited to commonly employed E. coli laboratory strains. We are hereby disseminating a rapid and efficient method for preparing electrocompetent E. coli, which has been in use by bacteriology laboratories for some time, can be adapted to V. cholerae and other prokaryotes. While we cannot ascertain whom to credit for developing the original technique, we are hereby making it available to the scientific community.     

Characterization of membrane-bound nitrate reductase from denitrifying bacteriaOchrobactrum anthropi SY509

In this study, we have purified and characterized the membrane bound nitrate reductase obtained from the denitrifying bacteria,Ochrobactrum anthropi SY509, which was isolated from soil samples.O. anthropi SY509 can grow in minimal medium using nitrate as a nitrogen source. We achieved an overall purification rate of 15-fold from the protein extracted from the membrane fraction, with a recovery of approximately 12% of activity. The enzyme exhibited its highest level of activity at pH 5.5, and the activity was increased up to 70°C. Periplasmic and cytochromic proteins, including nitrite and nitrous oxide reductase, were excluded during centrifugation and were verified using enzyme essay. Reduced methyl viologen was determined to be the most efficient electron donor among a variety of anionic and cationic dyestuffs, which could be also used as an electron donor with dimethyl dithionite. The effects of purification and storage conditions on the stability of enzyme were also investigated. The activity of the membrane-bound nitrate reductase was stably maintained for over 2 weeks in solution. To maintain the stability of enzyme, the cell was disrupted using sonication at low temperatures, and enzyme was extracted by hot water without any surfactant. The purified enzyme was stored in solution with no salt to prevent any significant losses in activity levels.     

A semi-quantitative GeLC-MS analysis of temporal proteome expression in the emerging nosocomial pathogen <Emphasis Type="Italic">Ochrobactrum anthropi</Emphasis>

Background  

The α-Proteobacteria are capable of interaction with eukaryotic cells, with some members, such as Ochrobactrum anthropi, capable of acting as human pathogens. O. anthropi has been the cause of a growing number of hospital-acquired infections; however, little is known about its growth, physiology and metabolism. We used proteomics to investigate how protein expression of this organism changes with time during growth.     

The influence of the growth phase of enteric bacteria on electrotransformation with plasmid DNA

Salmonella typhimurium LB5000 andEscherichia coli JM109 were transformed by electroporation. In accordance with the chemical transformation methods, the growth phase of these electrocompetent bacteria had a strong impact on transformation efficiency. Survival of bacteria, after the high-voltage electrical pulse was also influenced by the growth phase. Both bacterial species were most successfully electrotransformed when microbial cells were harvested at the late lag phase. The second optimum for transformation reachedE. coli cells in the mid-exponential andS. typhimurium cells in the late exponential phase. Transformation efficiencies ranged from 3.4×10⁴ to 2.7×10⁵ transformants per μg DNA in the case ofS. typhimurium and from 2.8 × 10² to 8.8×10⁵ transformants per μg DNA in the case ofE. coli. Survival of cells after the electrical pulse in late lag and late exponential phases was about 20% higher than during other phases of growth. Preparing electrocompetent cells from later phases of their growth is more useful for practice, because it provides more biomass with good yield of transformants.     

Temperature‐dependent regulation of the Ochrobactrum anthropi proteome

Ochrobactrum anthropi is a Gram‐negative rod belonging to the Brucellaceae family, able to colonize a variety of environments, and actually reported as a human opportunistic pathogen. Despite its low virulence, the bacterium causes a growing number of hospital‐acquired infections mainly, but not exclusively, in immunocompromised patients. The aim of this study was to obtain an overview of the global proteome changes occurring in O. anthropi in response to different growth temperatures, in order to achieve a major understanding of the mechanisms by which the bacterium adapts to different habitats and to identify some potential virulence factors. Combined quantitative mass spectrometry‐based proteomics and bioinformatics approaches were carried out on two O. anthropi strains grown at temperatures miming soil/plants habitat (25°C) and human host environment (37°C), respectively. Proteomic analysis led to the identification of over 150 differentially expressed proteins in both strains, out of over 1200 total protein identifications. Among them, proteins responsible for heat shock response (DnaK, GrpE), motility (FliC, FlgG, FlgE), and putative virulence factors (TolB) were identified. The study represents the first quantitative proteomic analysis of O. anthropi performed by high‐resolution quantitative mass spectrometry.     

Bioremediation of glyphosate-contaminated soils

Based on the results of laboratory and field experiments, we performed a comprehensive assessment of the bioremediation efficiency of glyphosate-contaminated soddy-podzol soil. The selected bacterial strains Achromobacter sp. Kg 16 (VKM B-2534D) and Ochrobactrum anthropi GPK 3 (VKM B-2554D) were used for the aerobic degradation of glyphosate. They demonstrated high viability in soil with the tenfold higher content of glyphosate than the recommended dose for the single in situ treatment of weeds. The strains provided a two- to threefold higher rate of glyphosate degradation as compared to indigenous soil microbial community. Within 1–2 weeks after the strain introduction, the glyphosate content of the treated soil decreased and integral toxicity and phytotoxicity diminished to values of non-contaminated soil. The decrease in the glyphosate content restored soil biological activity, as is evident from a more than twofold increase in the dehydrogenase activity of indigenous soil microorganisms and their biomass (1.2-fold and 1.6-fold for saprotrophic bacteria and fungi, respectively). The glyphosate-degrading strains used in this study are not pathogenic for mammals and do not exhibit integral toxicity and phytotoxicity. Therefore, these strains are suitable for the efficient, ecologically safe, and rapid bioremediation of glyphosate-contaminated soils.     

Permeabilization of<Emphasis Type="Italic">Ochrobactrum anthropi</Emphasis> SY509 cells with organic solvents for whole cell biocatalyst

Permeabilization is known to overcome cell membrane barriers of whole cell biocatalysts. The use of organic solvents is advantageous in terms of cost, simplicity, and efficiency. In this study,Ochrobactrum anthropi SY509 was permeabilized with various organic solvents. Treatment with organic solvents resulted in lower permeability barriers due to falling out lipids of the cell membrane. Therefore, permeabilized cells showed higher enzyme activity with no cell viability. Among various organic solvents, 0.5% (v/v) chloroform was selected as the most efficient permeabilizing reagent. Changes in the cell membrane structure were observed and the residual amounts of phospholipids of the cell membrane were measured to investigate the mechanism of the improved permeability.     

A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: application for DNA fragment transfer between chromosomes and plasmid transformation

A rapid microcentrifuge-based method is described for preparation of Pseudomonas aeruginosa electrocompetent cells with up to 10,000-fold increased transformation efficiencies over existing procedures. This increased efficiency now enables the use of transformation for all applications requiring DNA transfer. These include transfer of chromosomal mutations marked with antibiotic resistance genes between P. aeruginosa strains, which solves the riddle of not having an efficient and reliable transduction procedure for this bacterium. Not surprisingly, the method also allows for very efficient transformation with replicative plasmids, with transformation efficiencies ranging from 10(7) to >10(11) transformants per microgram of DNA. Lastly, with efficiencies of up to >10(3) transformants per microgram of DNA the method replaces in most instances conjugation for the transfer of non-replicative plasmids used in gene replacement, site-specific gene integration and transposon mutagenesis experiments.     

Improved method for high-efficiency electrotransformation of Escherichia coli with the large BAC plasmids

High transformation competency of Escherichia coli is one of the critical factors in the bacterial artificial chromosome (BAC)-based DNA library construction. Many electroporation protocols have been published until now, but the majority of them was optimized for transformation of small plasmids. Large plasmids with a size above 50 kbp display reduced transformation efficiency and thereby require specific conditions in the preparation and electroporation of electrocompetent cells. In the present work, we have optimized the parameters critical to the application of BAC DNA electrotransformation into E. coli. Systematic evaluation of electroporation variables has revealed several key factors like temperature of growth, media supplements, washing buffer, and cell concentration. Improvements made in the transformation protocol have led to electrocompetent cells with transformation efficiency up to 7?×?10⁸ transformants per microgram of 120 kbp BAC plasmid DNA. We have successfully used in-house prepared competent cells, the quality of which is comparable with those produced by different companies, in the construction of metagenomic libraries from the soil. Our protocol can also be beneficial for other application with limited DNA source.     

Cloning of Escherichia coli lacZ and lacY Genes and Their Expression in Gluconobacter oxydans and Acetobacter liquefaciens

An efficient transformation protocol for Gluconobacter oxydans and Acetobacter liquefaciens strains was developed by preparation of electrocompetent cells grown on yeast extract-ethanol medium. Plasmid pBBR122 was used as broad-host-range vector to clone the Escherichia coli lacZY genes in G. oxydans and A. liquefaciens. Although both lac genes were functionally expressed in both acetic acid bacteria, only a few transformants were able to grow on lactose. However, this ability strictly depended on the presence of a plasmid expressing both lac genes. Mutations in the plasmids and/or in the chromosome were excluded as the cause of growth ability on lactose.     

High-frequency transformation ofStaphylococcus aureus by electroporation

Plasmids carrying resistances for a variety of antibiotics were successfully transformed intoStaphylococcus aureus by electroporation. When frozen cell preparations were used, the procedure could be carried out in as little as 30 min. Frequencies as high as 7.6 × 10⁵ transformants/µg of DNA were obtained with DNA isolated from both large-scale plasmid preparations and from minilysate preparations. A procedure was also developed for preparation and freezing (–70°C) of electrocompetent cells. These preparations have remained electrotransformable for 2 months without loss of activity.     

Biodegradation of glyphosate by soil bacteria: Optimization of cultivation and the method for active biomass storage

Conditions for obtaining the active biomass of Ochrobactrum anthropi GPK 3 and Achromobacter sp. Kg 16, bacteria which are able to degrade the herbicide glyphosate (N-phosphonomethylglycine), were investigated. In the batch culture, degradation was most effective in the medium with pH 6.0–7.0 and aeration at 10–60% of air saturation supplemented with glutamate and ammonium chloride as sources of carbon and nitrogen, respectively. Due to the adaptation of the cells and induction of the relevant enzymatic systems, the inoculum grown in the presence of glyphosate exhibited 1.5–2-fold higher efficiency of xenobiotic degradation than that grown with other sources of phosphorus (orthophosphate and methylphosphonic acid). The efficiency of the toxicant decomposition increased with an increase in a specific load of glyphosate, which the cells were subjected to during the initial stage of growth. The specific load was regulated both by the initial cell concentration and the concentration of the phosphorus source, and the effect was probably determined by its availability to microorganisms. Storage of the liquid biopreparation as a paste with stabilizers (ascorbate, thiourea, and glutamate) at room temperature for 50 days resulted in high level of bacteria viability and a degrading activity approximately equal to that obtained when the bacteria were maintained on the agar medium containing glyphosate at 4°C with monthly transfers to the fresh culture medium.     

Degradation of ribonucleic acid in Candida lipolytica: extraction of ribonucleic acid degrading enzymes

We developed an efficient and simple method for RNase extraction from Candida lipolytica cells which consists of predrying the cells with solvents and incubating them for 8 to 15 hr at 37 to 45°C in a slightly acid buffer which contains EDTA or salts. This method is called Solvent Dehydration Buffer Extraction (SDBE) procedure. Predrying with acetone or ethanol, or by lyophilization, followed by washing with acetone or ethylacetate gives the most efficient RNase extraction. The yield and specific activity obtained by this extraction procedure are higher than by any other method examined. An apparent 1.5- to 2.0-fold activation of RNase occurred during the SDBE process. Activation of RNase in homogenates obtained by grinding fresh cells is also observed with EDTA or acetate buffer. The SDBE procedure works efficiently regardless of growth phase for Candida lipolytica, and works also with other Candida yeasts.     

On-line monitoring of the denitrification process by measurement of NADH fluorescence

On-line monitoring method of the denitrification process was developed by NADH fluorescence measurements using the facultative microorganism, Ochrobactrum anthropi SY509. The NADH fluorescence signals showed a rapid drop and a rise at the initiation and termination points of the denitrification, respectively. This NADH fluorescence method could be applied successfully to the monitoring of the denitrification process in sequential batch and continuous operations while these rapid changes of fluorescence were not observed in a batch operation due to accumulation of some metabolites secreted from the microorganism.     

Effect of aeration on denitrification byOchrobactrum anthropi SY509

Aeration was found to affect the biological denitrification byOchrobactrum anthropi SY509. Although cell growth was vigorous under 1 vvm of aeration and an agitation speed of 400 rpm in a 3-L jar fermentor, almost no nitrate was removed. Yet under low agitation speeds (100, 200, and 300 rpm), denitrification occurred when the dissolved oxygen was exhausted shortly after the inoculation of the microorganism.Ochrobactrum anthropi SY509 was found to express highly active denitrifying enzymes under anaerobic conditions. The microorganism also synthesized denitrifying enzymes under aerobic conditions (1 vvm and 400 rpm), yet their activity was only 60% of the maximum level under anaerobic conditions and the nitrate removal efficiency was merely 15%. However, although the activities of the denitrifying enzymes were inhibited in the presence of oxygen, they were fully recovered when the conditions were switched to anaerobic conditions.     

Distribution of glyphosate and methylphosphonate catabolism systems in soil bacteria <Emphasis Type="Italic">Ochrobactrum anthropi</Emphasis> and <Emphasis Type="Italic">Achromobacter</Emphasis> sp

Bacterial strains capable of utilizing methylphosphonic acid (MP) or glyphosate (GP) as the sole sources of phosphorus were isolated from soils contaminated with these organophosphonates. The strains isolated from MP-contaminated soils grew on MP and failed to grow on GP. One group of the isolates from GP-contaminated soils grew only on MP, while the other one grew on MP and GP. Strains Achromobacter sp. MPS 12 (VKM B-2694), MP degraders group, and Ochrobactrum anthropi GPK 3 (VKM B-2554D), GP degraders group, demonstrated the best degradative capabilities towards MP and GP, respectively, and were studied for the distribution of their organophosphonate catabolism systems. In Achromobacter sp. MPS 12, degradation of MP was catalyzed by C–P lyase incapable of degrading GP (C–P lyase I). Adaptation to growth on GP yielded the strain Achromobacter sp. MPS 12A, which retained its ability to degrade MP via C–P lyase I and was capable of degrading GP with formation of sarcosine, thus suggesting the involvement of a GP-specific C–P lyase II. O. anthropi GPK 3 also degraded MP via C–P lyase I, but degradation of GP in it was initiated by glyphosate oxidoreductase, which was followed by product transformation via the phosphonatase pathway.     

Localization of glycoprotein glycosyltransferases in the Golgi apparatus of rat and mouse testis

Golgi fractions prepared from rat testis have been shown to be enriched in the following glycoprotein glycosyltransferases: N-acetylglucosaminyltransferase, 47-fold, galactosyltransferase, 33-fold, and N-acetylglucosaminide fucosyltransferase, 15-fold. Appreciably lower transferase levels were obtained in other subcellular fractions. In the mouse, Golgi fractions were prepared from testis homogenates, testis cell suspensions and partially purified testis germinal cells; these fractions were also enriched in the above glycoprotein glycosyltransferases. Electron microscopic analysis indicated that a major portion of the total transferase activity was located in the Golgi apparatus of both rat and mouse testis although these experiments could not rule out the possible presence of some transferase activity in other organelles.