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Seq205-17

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    Seq205 Annotation Main

    Amino acid sequence for Seq 205-17 was analyzed with InterProScan, in which a lipase (class 3) motif and an alpha/beta hydrolase fold were found as shown below:

    205-17.jpg

     

    Triacylglyercol lipase

    According to KEGG, triacylglycerol lipase in Z. mays (zma:100281750; top BLAST match in Z. mays in KEGG) also included lipase (class 3) motif and an alpha/beta hydrolase fold. In addition, a ribose 5-phosphate isomerase A motif was listed as well (http://ssdb.genome.jp/ssdb-bin/ssdb_motif?kid=zma:100281750). It appears that lipases in plants have been poorly documented, but recent work has suggested similar roles in plants as is mammals or microorganisms. cDNA has been collected in Alexandrov et al., 2009 to where this gene was identified. In general, triacylglycerol lipases hydrolyze long chain fatty acid molecules. This includes triacylglycerides, diacylglycerides, and monoacylglycerides. It also appears that alpha/beta hydrolase fold in this protein is highly conserved (Karim et al., 2005). This enzyme plays an important role in fatty acid metabolism as a lipid breakdown through the glycerolipid metabolism as shown in the KEGG Pathway figure below (highlighted in red).

    Untitled.jpg

     

    ClustalW2 alignment with BLASTn of triacylglyercerol lipase. KEGG BLAST of "zma-FGENESH" nucleotide base sequence against these plant species revealed top matched genes. Five plant species were analyzed: sbi= S. bicolor, zma= Z. mays, ath= A. thaliana, rcu= R. communis, vvi= V. vinifera, and osa= O. sativa japonica. "zma-FGENESH" is the sequence derived from the FGENESH analysis and "zma-KEGG" is the best BLASTed result analyzed through KEGG's BLAST tool.

    tacylglyc blastn.jpg

    ClustalW2 alignment with BLASTx of triacylglycerol lipase. KEGG BLAST of "zma-FGENESH" AA sequence against these plant species revealed top matched genes. Five plant species were analyzed: sbi= S. bicolor, zma= Z. mays, ath= A. thaliana, rcu= R. communis, vvi= V. vinifera, and osa= O. sativa japonica. "zma-FGENESH" is the sequence derived from the FGENESH analysis and "zma-KEGG" is the best BLASTed result analyzed through KEGG's BLAST tool.

    tacylglyc blastx.jpg


    MEGA 4.0 Neighbor-Joining, 1000 replicate bootstrap test of phylogeny. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Maximum Composite Likelihood method and are in the units of the number of base substitutions per site. KEGG BLASTn of "zma-FGENESH"  sequence against these plant species revealed top matched genes. Five plant species were analyzed: sbi= S. bicolor, zma= Z. mays, ath= A. thaliana, rcu= R. communis, vvi= V. vinifera, and osa= O. sativa japonica. "zma-FGENESH" is the sequence derived from the FGENESH analysis and "zma-KEGG" is the best BLASTed result analyzed through KEGG's BLAST tool.

    triacygly NJ.jpg

     

    It appears that Z. mays triacylglycerol lipase is more similar to Sorghum bicolor than to O. sativa japonica in whole nucleotide base and amino acid sequences. But rcu, ath, and vvi don't match up as well with zma as do both sbi and osa. Both the BLASTn and BLASTx show a high much higher score with zma and sbi and osa than with any other plant species shown. The phylogenetic tree analysis concurs that indeed sbi and osa are more similar to zma than the other three plant species. However, in future work it would be interesting to take the sequences coding for the particular structures in the protein and compare those amongst plant species. Please note, that zma's BLAST result was a hypothetical protein and needs much more annotation and bioinformatic work.

     

    The amino acid sequence from 205-17 was submitted to I-TASSER to obtain the putative tertiary structure of the protein.  A total of five models were produced by I-TASSER with C-Scores ranging from -3.51 to -4.27 as shown below:

    205-17 C-Score Comparisons

    Model C-Score
    205-17 Model 1 -3.51
    205-17 Model 2 -4.09
    205-17 Model 3 -4.21
    205-17 Model 4 -4.22
    205-17 Model 5 -4.27

     

    These putative proteins were loaded into Pymol and edited to highlight the main structural components such as the alpha helices (teal) and beta sheets (red).  Hydrogens and side chains were masked  to produce a clearer image of the protein. 205-17 Model is shown as Image 2.  Other putative models are located in Supplemental Data, Images 6 to 10.

     

    Image 1: 205-17 Model 1

    lipase model1.png

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