Informatics Publishing Limited

Hanchipura Mallesh Mahadevaswamy ¹, Ramasamy Asokan ¹, Riaz Mahmood ²

Affiliations
1 Division of Biotechnology, Indian Institute of Horticultural Research (IIHR), Hessarghatta Lake Post, Bangalore 560089, Karnataka., IN
2 Post-Graduate Department of Studies and Research in Biotechnology and Bioinformatics, Kuvempu University, Jnanasahayadri, Shankaraghatta, Shimoga 577451, Karnataka., IN

Abstract

The Cry3 class of Bacillus thuringiensis Cry proteins is known for toxicity to coleopteran larvae. Homology modelling is used to determine the three-dimensional (3D) structure of Coleopteran active Bt CRY3A toxin from native isolate of B. thuringiensis. The structure is made up of three domains, I, a seven-helix bundle (residues 64-294), II, a three-sheet domain (residues 295-502) and III, a beta-sandwich domain (residues 503-652). The main variations observed in domain I is at the position of α4 (P105-I152), α5 (Q163-A185), β1A(E190-L192), α6 (F193-Y217), Domain II is not consevered and main variations were observed at β2 (E292-L295), β3(V299-L308), β4(I340-F347), β5(D356-P368), β6(I375-T377), β7(V389-F394), β8(K398- N405), β9(Y416-Y427), β10 (T436-Y439), β12(G476-H495), β12A (M503-I504) where as in domain III main variations observed at positions of β18 (P583-I593), β19(F604-S610), β20(P611-L615), β21(N619-G626). Knowledge of the structure of CRY3A δ-endotoxin combined with information on the function of certain structures within the molecule is expected to lead to the design of crystal proteins with improved or new activities. Therefore, homology-based structures would be reliable 3D models for investigating their structure-function analysis and mode of action.

Keywords

Cry3 Class, 3D Structure, Homology Modelling, Structure-function Analysis

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H.M. Mahadeva Swamy ¹, R. Asokan ², Riaz Mahmood ³

Affiliations
1 Bio-Pesticide Laboratory, Division of Biotechnology, Indian Institute of Horticultural Research (IIHR), Hessarghatta Lake Post, Bangalore 560 089, IN
2 Bio-Pesticide laboratory (BPL), Division of Biotechnology, Indian Institute of Horticultural Research (IIHR), Hessarghatta lake post, Bangalore 560 089, IN
3 2Post-Graduate Department of Studies and Research in Biotechnology and Bioinformatics, Kuvempu University, Jnanasahayadri, Shankaraghatta, Shimoga 577451, Karnataka, IN

Abstract

Cry1I toxins are particularly interesting from an agricultural perspective because of their wide host range. We presented 3D structural model of the novel Coleopteran active Cry1Ib8 δ-endotoxin obtained from native Bt strain using homology modeling. Cry1Ib8 share a common structure contains three flexible domains that participate in the formation of a pore and determine the receptor binding specificity. The pore-forming domain I is composed of residues 60-282. It consists of 10α-helices and two small β-strands. The identified helices and strands are as follows: α1 (E33-K35); α2a (N39-S46); α2b (S56-I60); α3 (Q61-T73); α4 (F78-L93); α5 (K98- V146); α6 (T152-F177); α7a (L185-W210); α7b (A214-L246); α8a (T280-V282); β0 (Q10-L12) and β1a (E182-P184). Domain II comprised of residues 287-487, two helix (α9 F322-A328; α10 P333- L339) and 10 β-strands (β2 T292-T297; β3 V342-S346; β4 M359- P369; β5- L374-N375; β6 T390-Q393; β7 V398-W404; β9 E453- N454; β10 S470-I479 and β11 A486-H493). Domain III is comprised of residues 507-644, has a three antiparallel-sheet sandwich structure present at downstream sites (α11a K655-F664; α13 E678-S690; α14 L697-R718 and α12a is absent) and shows highly conserved β residues. Understanding the mode of action of coleopteran-specific B. thuringiensis toxins through 3-D homology models will aid in the development of novel B. thuringiensis biopesticide with increased efficacy as well as in the development of resistance detection and management strategies.

Keywords

3D Structure, Domains, Homology Modeling, Native Bt Strains

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Reena Rosy Thomas ¹, M. K. Chandra Prakash ¹, M. Krishna Reddy ², Sukhada Mohandas ³, Riaz Mahmood ⁴

Affiliations
1 Section of Economics and Statistics, Indian Institute of Horticultural Research, Hessaraghatta, Bangalore -560089, IN
2 Division of Plant Pathology, Indian Institute of Horticultural Research, Bangalore - 560 089, IN
3 Division of Biotechnology, Indian Institute of Horticultural Research, Bangalore - 560 089, IN
4 Dept. of Biotechnology, Kuvempu University, Shimoga - 577 451, IN

Abstract

Abiotic stress often causes a series of morphological, physiological, biochemical and molecular changes that affect plant growth, development and productivity. To cope with abiotic stresses, it is necessary to understand plant responses to stresses that disturb homeostatic equilibrium at the cellular and molecular level. Genomic information on Capsicum annuum has been explored to identify microsatellite markers associated with abiotic stress tolerance and assign them to cognate functional groups related to specific stress responses. Several in silico methods have been used to identify simple sequence repeats associated with stress responsive gene candidates in Capsicum annuum. In this study, a microsatellite marker has been identified in Capsicum annuum associated with Nucleoside Diphosphate Kinase (NDK) having multiple environmental stress tolerance (oxidative, high temperature and salt stress) and which is also highly conserved in crops of Solanaceae. These are house-keeping enzymes that maintain intracellular levels of all nucleoside triphosphates (NTP) with the exception of adenosine triphosphate (ATP). These are also involved in phytochrome A response, UV-B signaling, auxin responses and oxidative stress signaling.

Keywords

Nucleoside Diphosphate Kinase (NDK), Microsatellite, Abiotic Stress, Solanaceae.

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Vageeshbabu S. Hanur ¹, D. P. Prakash ¹, B. S. Deepali ¹, R. Asokan ¹, Y. L. Ramachandra ², Riaz Mahmood ², Lalitha Anand ¹

Affiliations
1 Division of Biotechnology, Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bangalore 560 089, IN
2 Department of Biotechnology, Kuvempu University, Shankaraghatta, Shimoga, IN

Abstract

Poor regeneration is one of the limiting factors in the development of transgenic crops since Agrobacterium as a plant pathogen can disturb the fragile in vitro conditions with wounding and infection regimes. We have tried to optimize the transformation system in two important varieties of brinjal after Agrobacterium infection to the explants. The effect of explant was studied and hypocotyls were found to be better than cotyledonary leaves. High BAP during the preconditioning period was found to further enhance the regeneration rate. Therefore, use of hypocotyls and high BAP during preconditioning can improve the regeneration of transformed cells and recovery of transformants in vegetables especially brinjal.

Keywords

Solanum melongena, Transformation, Hypocotyl, BAP, Preconditioning.

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