Cloning and in vitro characterization of dTDP-6-deoxy-l-talose biosynthetic genes from Kitasatospora kifunensis featuring the dTDP-6-deoxy-l-lyxo-4-hexulose reductase that synthesizes dTDP-6-deoxy-l-talose

Kitasatospora kifunensis, the talosin producer, was used as a source for the dTDP-6-deoxy-l-talose (dTDP-6dTal) biosynthetic gene cluster, serving as a template for four recombinant proteins of RmlA_Kkf, RmlB_Kkf, RmlC_Kkf, and Tal, which complete the biosynthesis of dTDP-6dTal from dTTP, α-d-glucose-1-phosphate, and NAD(P)H. The identity of dTDP-6dTal was validated using ¹H and ¹³C NMR spectroscopy. K. kifunensistal and tll, the known dTDP-6dTal synthase gene of Actinobacillus actinomycetemcomitans origin, have low sequence similarity and are distantly related within the NDP-6-deoxy-4-ketohexose reductase family, providing an example of the genetic diversity within the dTDP-6dTal biosynthetic pathway.     

A translation-coupling DNA cassette for monitoring protein translation in Escherichia coli

A major challenge to using heterologous expression in metabolic engineering experiments is the inability to quickly dissect experiments that have failed at the stage of translating mRNA. While many methods of detecting proteins exist, methods that detect untagged proteins at low levels are limited. Here, we describe a method to quickly determine whether Escherichia coli is capable of expressing the product of any target gene by coupling translation of a target gene to a detectable response gene. A translational coupling cassette was designed to encode a mRNA sequence that forms a secondary structure in the absence of translation and contains the translational start sequence of a detectable response gene. The translational coupling method was successfully tested with fluorescent proteins and antibiotic resistance markers. Only when the target gene was fully translated was the response observed. Further characterization demonstrated that translational coupling functions at both low and high levels of expression and that the response signal is proportional to the amount of target gene product. The translational coupling system was used to determine that a large multi-domain enzyme was not actively translated in E. coli, to isolate the translation problems to the C-terminal domains, and to optimize conditions for expressing a codon-optimized sequence variant.     

Sorption of heavy metals from electroplating effluent using immobilized biomass Trichoderma viride in a continuous packed-bed column

The sorption of heavy metals ions by immobilized Trichoderma viride biomass in a packed-bed column was studied. Fungal biomass T. viride was immobilized to Ca-alginate used for removal of Cr(VI), Ni(II) and Zn(II) ions from synthetic solutions and electroplating effluent. The experiments were conducted to study the effect of important design parameters such as bed height, flow rate and initial concentration of metal ions. The maximum sorption capacity was observed at flow rate 5 ml/min, bed height 20 cm and metal ions concentration 50 mg/L with immobilized biomass. Whereas, breakthrough time and saturation time decreased with increase flow rate and metal ions concentration and an inverse condition was found in bed height. The bed depth service time (BDST) Adams-Bohart model was used to analyze the experimental data. The regeneration efficiency was observed 40.1%, 75% and 53% for Cr(VI), Ni(II) and Zn(II) without any significant alteration in sorption capacity after 5th sorption-desorption cycles.     

Fabrication of an amperometric d-amino acid biosensor based on nickel hexacyanoferrate polypyrrole hybrid film deposited on glassy carbon electrode

A nickel hexacyanoferrate polypyrrole film was synthesized through an electrochemical two-step methodology leading to a very stable and homogenous robust hybrid film. A highly sensitive, specific and rapid amperometric d-amino acid biosensor was constructed by immobilizing d-amino acid oxidase on this film deposited over the surface of a glassy carbon electrode. The modified electrode was characterized by scanning electron microscopy, electrochemical impedance spectroscopy and Fourier transform infrared spectrophotometry. The biosensor showed optimum response within 1 s, when operated at 50 mV s^?1 in 0.01 M Tris HCl buffer, pH 7.0 at 30 °C. The biosensor exhibited excellent sensitivity with a detection limit of 1.5 µM (S/N = 3) for d-amino acids and wider linear range, 20–500 µM. Analytical recovery of added d-alanine (5 and 10 mM) in serum samples was 98.00 and 98.80 %, respectively. Within-batch and between-batch coefficients of variation in serum samples were 1.36 and 2.77 %, respectively. The enzyme electrode was used more than 50 times over 2 months, when stored at 4 °C. The proposed modified electrode exhibited sufficient mechanical and electrochemical stability and high sensitivity compared to earlier electrochemical d-amino acid biosensors. Interference by ascorbic acid and uric acid, the main interfering species in the biological samples, was negligible.     

Computational characterization of substrate and product specificities,and functionality of S‐adenosylmethionine binding pocket in histone lysine methyltransferases from Arabidopsis,rice and maize

Histone lysine methylation by histone lysine methyltransferases (HKMTs) has been implicated in regulation of gene expression. While significant progress has been made to understand the roles and mechanisms of animal HKMT functions, only a few plant HKMTs are functionally characterized. To unravel histone substrate specificity, degree of methylation and catalytic activity, we analyzed Arabidopsis Trithorax‐like protein (ATX), Su (var)3‐9 h omologs protein (SUVH), Su(var)3‐9 related protein (SUVR), ATXR5, ATXR6, and E(Z) HKMTs of Arabidopsis, maize and rice through sequence and structure comparison. We show that ATXs may exhibit methyltransferase specificity toward histone 3 lysine 4 (H3K4) and might catalyse the trimethylation. Our analyses also indicate that most SUVH proteins of Arabidopsis may bind histone H3 lysine 9 (H3K9). We also predict that SUVH7, SUVH8, SUVR1, SUVR3, ZmSET20 and ZmSET22 catalyse monomethylation or dimethylation of H3K9. Except for SDG728, which may trimethylate H3K9, all SUVH paralogs in rice may catalyse monomethylation or dimethylation. ZmSET11, ZmSET31, SDG713, SDG715, and SDG726 proteins are predicted to be catalytically inactive because of an incomplete S‐adenosylmethionine (SAM) binding pocket and a post‐SET domain. E(Z) homologs can trimethylate H3K27 substrate, which is similar to the Enhancer of Zeste homolog 2 of humans. Our comparative sequence analyses reveal that ATXR5 and ATXR6 lack motifs/domains required for protein‐protein interaction and polycomb repressive complex 2 complex formation. We propose that subtle variations of key residues at substrate or SAM binding pocket, around the catalytic pocket, or presence of pre‐SET and post‐SET domains in HKMTs of the aforementioned plant species lead to variations in class‐specific HKMT functions and further determine their substrate specificity, the degree of methylation and catalytic activity.     

Development of a transformation system in the swainsonine producing, slow growing endophytic fungus, Undifilum oxytropis

Undifilum oxytropis (Phylum: Ascomycota; Family: Pleosporaceae) is a slow growing endophytic fungus that produces a toxic alkaloid, swainsonine. This endophyte resides in locoweeds, which are perennial flowering legumes. Consumption of this fungus by grazing animals induces a neurological disorder called locoism. The alkaloid swainsonine, an α-mannosidase inhibitor, is responsible for the field toxicity related to locoism. Little is known about the biosynthetic pathway of swainsonine in endophytic fungi. Genetic manipulation of endophytic fungi is important to better understand biochemical pathways involved in alkaloid synthesis, but no transformation system has been available for studying such enzymes in Undifilum. In this study we report the development of protoplast and transformation system for U. oxytropis. Fungal mycelia required for generating protoplasts were grown in liquid culture, then harvested and processed with various enzymes. Protoplasts were transformed with a fungal specific vector driving the expression of Enhanced Green Florescent Protein (EGFP). The quality of transformed protoplasts and transformation efficiency were monitored during the process. In all cases, resistance to antibiotic hygromycin B was maintained. Such manipulation will open avenues for future research to decipher fungal metabolic pathways.     

Changes in carbohydrates and lipids during embryonic development ofAntheraea mylitta (Lepidoptera)

Changes in carbohydrate and lipid metabolism during embryonic development inAntheraea mylitta were studied. While carbohydrates were metabolized during early embryogenesis, lipids were catabolised at the later stages. A significant increase in both total carbohydrates and glycogen on days 5 and 6 suggested the concurrent occurrence of both gluconeogenesis and glycogenesis. As the development of the embryo proceeds, both lipids and carbohydrates were utilised, resulting in the increase in the concentration of citrate, pyruvate and lactate.     

Isolation and characterization of biosurfactant producing <Emphasis Type="Italic">Bacillus</Emphasis> sp. from diesel fuel-contaminated site

Among hydrocarbon pollutants, diesel oil is a complex mixture of alkanes and aromatic compounds which are often encountered as soil contaminants leaking from storage tanks and pipelines or as result of accidental spillage. One of the best ecofriendly approaches is to restore contaminated soil by using microorganisms able to degrade those toxic compounds in a bioremediation process. In the present study, nineteen bacteria were isolated by enrichment culture technique from diesel spilled soil collected from electric generator shed of NBAIM, Mau. All the isolates were subjected to screening for lipase production and twelve isolates were found to be positive for lipase. When the isolates were screened for biosurfactant production using CTAB-methylene blue agar plates, only one isolate viz. 2NBDSH3 was found positive which was found to be phylogenetically closely related with Bacillus flexus. Despite having low emulsification index, the bacterium could degrade 88.6% of diesel oil in soil. Biosurfactant from the isolate was extracted and characterized through infra-red spectroscopy which indicated its possible lipopeptide nature which was further supported by strong absorption in UV range in the UV-Vis spectrum. The results of the present study indicated that the isolate either does not produce any bioemulsifier or produces very low amount of emulsifier rather it produces a lipopeptide biosurfactant which helps in degradation of diesel oil by lowering the surface tension. The bacterium thus isolated and characterized can serve as a promising solution for ecofriendly remediation of bacterium diesel contaminated soils.