SSToSS - sequence-structural templates of single-member superfamilies

The presence of sequence homologues and the availability of structural information of proteins enable better understanding of the biological function of a protein family. A majority of entries in protein structural databank are single member superfamilies for which it is hard to derive motifs due to the paucity of structural homologues. Important conserved segments for these superfamilies have been identified and compiled into a database, SSToSS (Sequence Structural Templates of Single member Superfamily). Conserved regions, recognized by permitted amino acid exchanges, are mapped on the structure and various structural features (solvent accessibility, secondary structure content, hydrogen bonding and residue packing) are examined. These conserved segments with high structural feature content are projected as sequence-structural templates for the particular superfamily member. Interactive three-dimensional displays of the templates in three-dimensional structure (in Chime® and RASMOL) are provided for better understanding and visualization. In SSToSS database, we also provide the application of sequence-structural templates in three different areas: multiple-motif based sequence search, multiple sequence alignment and homology modeling. In each case, the inclusion of the sequence-structural templates can give rise to sensitive and accurate results. This enables the inclusion of singletons to provide added value to the recognition of additional members, comparative modeling and in designing experiments

Stress Responses in Alfalfa (Medicago sativa L.): X. Molecular Cloning and Expression of S-Adenosyl-l-Methionine:Caffeic Acid 3-O-Methyltransferase, a Key Enzyme of Lignin Biosynthesis

S-Adenosyl-l-methionine:caffeic acid 3-O-methyltransferase (COMT, EC 2.1.1.6) catalyzes the conversion of caffeic acid to ferulic acid, a key step in the biosynthesis of lignin monomers. We have isolated a functionally active cDNA clone (pCOMT1) encoding alfalfa (Medicago sativa L.) COMT by immunoscreening a λZAPII cDNA expression library with anti-(aspen COMT) antibodies. The derived amino acid sequence of pCOMT1 is 86% identical to that of COMT from aspen. Southern blot analysis indicates that COMT in alfalfa is encoded by at least two genes. Addition of an elicitor preparation from bakers' yeast to alfalfa cell suspension cultures resulted in a rapid accumulation of COMT transcripts, which reached a maximum level around 19 hours postelicitation. Northern blot analysis of total RNA from different organs of alfalfa plants at various developmental stages showed that COMT transcripts are most abundant in roots and stems. Transcripts encoding ATP: i-methionine-S-adenosyl transferase (AdoMet synthetase, EC 2.5.1.6), the enzyme responsible for the synthesis of the methyl donor for the COMT reaction, were coinduced with COMT transcripts in elicitor-treated cells and exhibited a similar pattern of expression to that of COMT in different organs of alfalfa plants at various stages of development

Exploitation of natural variability in maize for β - carotene content using HPLC and gene specific markers

Vitamin A deficiency is a major world health problem, affecting up to 127 million pre-school children and 7 millionpregnant women worldwide (West, 2003). Human selection for yellow endosperm has led to diversification of graincarotenoid content and composition. This variation has remained largely untapped in modern breeding programs thathave focused nearly exclusively on yield gains. Maize displays considerable natural variation for carotenoidcomposition, including vitamin A precursors α-carotene, β-carotene, and β -cryptoxanthin. Sixty four maize inbred linesof India were grown and evaluated for whole kernel carotenoids and beta carotene content using high performanceliquid chromatography (HPLC). The lines averaged 14 :g/g for total carotenoids (5.58 to 63.9 :g/g) and 1.69 :g/g for β-carotene (0.122 to 4.74 :g/g). High level of β - carotene was observed in UMI 946, UMI 176, UMI 79, UMI 34 andUMI 12 and these would be used in the breeding programs to enhance the β – carotene contents. Previous study showedfour natural lcyE polymorphisms explained 58% of the variation in these two branches and a threefold difference in provitaminA compounds. In screening for polymorphisms in key haplotypes, four regions were selected and scored acrossthe entire panel of favourable haplotype using SNP and SSR markers. The polymorphs were obtained for all primer usedand the presence of the amplification of for particular marker showed the increase in β - carotene content across theinbreds. Development of LCYE based breeding markers for maize alone will not be effective unless hydroxylation isalso controlled, for non pro vitamin A xanthophylls compounds will predominate. So in our future study, we should beaiming at breeding for high β - carotene in maize by emphasizing on characterization of β - carotene hydroxylase genesfor enhancing the relative levels of seed β - carotene