Project titles for:
Project titles for: 2007-09
- Comparison of software for Analysis of Molecular Marker Data
- In silico Prediction of miRNA in Rice Genome
- Web Tools for Bioinformatics
- In silico Structure Prediction of enzyme Arsenite methyltransferase
- Comparison of various software for QTL Analysis
- QSAR studies of Tuberculosis Inhibitors
- Determination of common transcription factor binding site in promoter region of abiotic stress resistance gene in rice
- SNP Mining in Rice Genome
- Protein Modelling of Betaine Aldehyde Dehydrogenase-2 in Rice
- Data Mining of Chemical Substructures for Biological Efficacy
- Plant Disease Database mined from PubMed
- Comparison of Protein Structure Prediction Methods
- Virtual High Throughput Screening for Influenza Virus Inhibitors
- Combinatorial Libraries for Screening against Tuberculosis Inhibitors
Basmati rice constitute a small but special group, with superior aroma and grain quality. Fragrance is an important constitutent for high-quality rice varieties (Chen et al., 2006). Rice (Oryza sativa) possesses two genes encoding betaine aldehyde dehydrogenase (BADH, EC 1.2.1.8) isozymes (BADH1) and (BADH2) despite not accumulating glycine betaine. A mutant BADH2 allele (badh2) which codes for a substantially truncated BADH2 enzyme is responsible for the elevated level of 2-acetyl-1-pyrroline (2AP) which gives fragrant rice varieties their characteristics aroma. Bradbury et al. (2005) determined that the gene responsible for fragrance in rice is a mutant betaine aldehyde dehydrogenase (BADH) encoding gene homolog badh2. The gene for BADH1 is located on chromosome four whilst the gene for BADH2 is located on chromosome eight. Recently, an eight base pair deletion and three SNPs in exon 7 of the gene encoding betaine aldehyde dehydrogenase 2 (BADH2) on chromosome 8 resulting in a frame shift that generate a premature stop codon that presumably disables the BADH2 enzyme (Bradbury et al., 2005) of Oryza sativa was identified as the likely cause of fragrance in Jasmine and Basmati rice (Bradbury et al., 2005). To date, however, the biosynthetic pathway of 2AP has not been demonstrated clearly. Therefore, identification and characterization of the fragrance related genes would provide valuable insight regarding the mechanism of 2AP- biosynthesis. In this project, the work has been carried out to model 3D structures of these three BADH proteins in silico using homology modelling. In the current investigation two domains were found for each BADH2 and BADH1 and only single domain was predicted for truncated BADH2. This single domain may be due to 8-bp deletion and 3 SNPs in its exon 7 and make this BADH2 non functional in fragrant rice and may also be responsible for the elevated level of 2- acetyl-1-pyrroline(2AP) as shown in pathway (figure 1) which gives fragrant rice varieties their characteristic aroma (Fitzgerald et al., 2008). The completely different roles of BADH1 and BADH2 in rice may be because of structural dissimilarity. The production of 2AP and fragrance in rice varieties even in presence of BADH1 where BADH2 is nonfunctional may be because of different functional roles of BADH1 and BADH2, even though with high level of sequence similarity.