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Kashyap S.,National Bureau of Agriculturally Important Microorganisms ICAR | Singh B.D.,Banaras Hindu University | Amla D.V.,Indian National Institute of Engineering
Journal of Microbiology and Biotechnology | Year: 2012

We report the computational structural simulation of the Cry1Ab19 toxin molecule from B. thuringiensis BtX-2 based on the structure of Cry1Aa1 deduced by x-ray diffraction. Validation results showed that 93.5% of modeled residues are folded in a favorable orientation with a total energy Z-score of -8.32, and the constructed model has an RMSD of only 1.13Å. The major differences in the presented model are longer loop lengths and shortened sheet components. The overall result supports the hierarchical three-domain structural hypothesis of Cry toxins and will help in better understanding the structural variation within the Cry toxin family along with facilitating the design of domain-swapping experiments aimed at improving the toxicity of native toxins. © The Korean Society for Microbiology and Biotechnology. Source


Kashyap S.,National Bureau of Agriculturally Important Microorganisms ICAR | Dev Singh B.,Banaras Hindu University | Amla D.V.,Indian National Institute of Engineering
Biotechnologia | Year: 2012

Cry1Ab18 is an δ-endotoxin produced by Bacillus thuringiensis strain. Till date the detailed mechanism of this toxin action is unclear. Therefore, solution of the three-dimensional structure of all Cry1 family members would be desirable for a comprehensive understanding of the initial mechanisms that underlie the toxicity of this type of toxin. Here, we predict a theoretical structural model of the newly reported Cry1Ab18 δ-endotoxin, using a homology modeling technique with the structure of Cry1Aa toxin molecule (resolution 2.25Å). Cry1Ab18 resembles Cry1Aa toxin by sharing a common three-domain structure. Domain I is composed of nine α helixes and one small β strand, domain II is composed of nine β strands and two α helixes and domain III consists of two α helixes and eleven β strands. This model supports the existing hypotheses of receptor insertion and will further provide the initiation point for the domain swapping experiments aimed towards improving protein toxicity, and will help in the deeper understanding of the mechanism of action of common toxins. Source


Ramesh A.,Directorate of Soybean Research DSR ICAR | Sharma S.K.,National Bureau of Agriculturally Important Microorganisms ICAR | Sharma M.P.,Directorate of Soybean Research DSR ICAR | Yadav N.,Directorate of Soybean Research DSR ICAR | Joshi O.P.,Directorate of Soybean Research DSR ICAR
Applied Soil Ecology | Year: 2014

Zinc deficiency not only affects crop yields, but also nutritional quality and human health. Microbial transformation of unavailable forms of soil zinc to plant available zinc is an important approach contributing to plant zinc nutrition and growth promotion. Therefore, the objectives were to (a) assess in vitro zinc solubilization ability of Bacillus aryabhattai strains MDSR7, MDSR11 and MDSR14 in medium supplemented with three insoluble zinc salts (zinc oxide, zinc carbonate and zinc phosphate) and (b) to evaluate their response of inoculation on crop growth, soil biological properties, zinc mobilization from native zinc-pool of soil and acquisition by soybean and wheat under microcosm conditions. The microcosm experiment comprised of five treatments for each crop, viz., (1) un-inoculated control without crop (non-rhizosphere soil); (2) un-inoculated control with crop; (3) B. aryabhattai MDSR7; (4) B. aryabhattai MDSR11; and (5) B. aryabhattai MDSR14 in completely randomized block design with twelve replications. While testing under in vitro, all the three strains possessed IAA, siderophore and ammonia producing traits. The strains MDSR7 and MDSR14 produced substantially higher soluble zinc content with significant decline in pH and increase in total organic acid production in Tris-minimal broth supplemented with insoluble zinc compounds. Further on inoculation with MDSR7 and MDSR14 substantially decreased rhizosphere soil pH and increased dehydrogenase, β-glucosidase, auxin production, microbial respiration and microbial biomass-C in the rhizosphere soils of soybean and wheat. The operation of all these soil processes regulated by B. aryabhattai strains resulted in a depletion of organically complexed and calcium carbonate bound zinc and an increase in exchangeable and sesquioxide bound zinc in soil. Such enhanced microbial activities and redistribution among different zinc pools in rhizosphere might have paved way for increased plant available zinc resulting in increased growth promotion and zinc assimilation in seeds by soybean and wheat crops. This assumes significance as the increased zinc concentration found in this study has large implications in terms of overcoming zinc malnutrition. We conclude that the strains MDSR7 and MDSR14 substantially influenced mobilization of zinc and its concentration in edible portion, yield of soybean and wheat, and can be utilized as bio-inoculants for biofertilization and biofortification. © 2013 Elsevier B.V. Source


Kashyap S.,National Bureau of Agriculturally Important Microorganisms ICAR
BioMed Research International | Year: 2013

The theoretical homology based structural model of Cry1Ab15 δ-endotoxin produced by Bacillus thuringiensis BtB-Hm-16 was predicted using the Cry1Aa template (resolution 2.25 Å). The Cry1Ab15 resembles the template structure by sharing a common three-domain extending conformation structure responsible for pore-forming and specificity determination. The novel structural differences found are the presence of β0 and α3, and the absence of α7b, β1a, α10a, α10b, β12, and α11a while α9 is located spatially downstream. Validation by SUPERPOSE and with the use of PROCHECK program showed folding of 98% of modeled residues in a favourable and stable orientation with a total energy Z-score of -6.56; the constructed model has an RMSD of only 1.15 Å. These increments of 3D structure information will be helpful in the design of domain swapping experiments aimed at improving toxicity and will help in elucidating the common mechanism of toxin action. © 2013 Sudhanshu Kashyap. Source


Kashyap S.,National Bureau of Agriculturally Important Microorganisms ICAR
International Journal of Pharma and Bio Sciences | Year: 2012

The theoretical homology based structural model of Cry1Aa9 δ-endotoxin produced by Bacillus thuringiensis dendrolimus T84A1was predicted using the Cry1Aa template (Resolution 2.25Å). The Cry1Aa9 resembles the template structure by sharing a common three domains extending conformation structure responsible in pore-forming and specificity determination. The novel structural differences found are presence of β0 and β12b, absence of α7b, β1a, α9a, β9 and α11a. These increments of 3D structure information will be helpful in the design of domain swapping experiments aimed at improving toxicity, and will help in elucidation of the common mechanism of toxins action. Source

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