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Open Access Highly Accessed Research article

Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis

Hanna Chepyshko1, Chia-Ping Lai2*, Li-Ming Huang3, Jyung-Hurng Liu4 and Jei-Fu Shaw1567*

Author Affiliations

1 Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, Taiwan, 402, ROC

2 Department of Food and Beverage Management, Far East University, Tainan, Taiwan, 74448, ROC

3 Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan, 701, ROC

4 Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan, 40227, ROC

5 Department of Biological Science and Technology, I-Shou University, Kaohsiung, Taiwan, 84001, ROC

6 Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, 40227, ROC

7 Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taiwan, 115, ROC

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BMC Genomics 2012, 13:309  doi:10.1186/1471-2164-13-309

Published: 15 July 2012

Additional files

Additional file 1:

Characteristics of the rice GDSL esterase/lipase gene family. The gene name, locus ID MSU Osa1 RGAP Release 6.1, open reading frame length, protein length, FL-cDNA, genomic sequences and CDS accession numbers, and isoelectric points of all 114 OsGELP genes are given.

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Additional file 2:

Expression evidence for the OsGELP rice genes. The OsGELP gene names, locus ID, MPSS signature sequences, FL-cDNA number, total quantity of mapped ESTs, and the presence of microarray data from Genevestigator for each of 153 transcripts (including alternative spliced models) of the 114 OsGELP genes are given.

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Additional file 3:

Pattern of the OsGELP gene clusters on rice chromosomes. (A) The order and clusters’ structures of 54 OsGELP genes on rice chromosomes. (B) The pattern of the OsGELP gene clusters on rice chromosomes, which are interrupted by unrelated genes.

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Additional file 4:

The OsGELP genes present on duplicated chromosomal segments of rice O. sativa L. ssp. japonica. The segmental duplicated of the OsGELP genes, with their BLASTP E-value, locus ID, and chromosome coordinates, are present according to the RGAP Segmental Genome Duplication of Rice, with the maximal length distance permitted between collinear gene pairs of 500 kb.

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Additional file 5:

The OsGELP genes resulting from duplications after the eudicots-monocots split, and preceding the sorghum and rice speciation. Such OsGELP genes with their gene names and chromosome locations are presented.

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Additional file 6:

Gene structure of the OsGELP genes. The exon/intron structures of a total of 153 transcripts (including alternative spliced models) of the 114 OsGELP genes are presented. Green and blue boxes represent exon and UTR regions, respectively, and solid lines indicate intron regions. The length of the boxes and lines are scaled based on the length of genes.

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Additional file 7:

Chromosomal location and exon/intron number for the OsGELP rice genes. The OsGELP gene names, locus ID, chromosomal location, open reading frame and genomic sequence length, and numbers of exons/introns for each 114 GDSL esterase/lipase genes are given.

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Additional file 8:

Identification of the repetitive DNA sequences within the OsGELP rice gene family. Diverse types of repetitive sequences with names, length (bp), and their positions and numbers for the 71 OsGELP genes are shown. The list of the repetitive DNA sequences present in the OsGELP genes is displayed in the order of their appearance from 5′- to 3′-end.

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Additional file 9:

The 18 OsGELP proteins that were excluded from phylogenetic analysis. The GDSL esterase/lipase gene names, protein length, and the presence of five strictly conserved residues Ser-Gly-Asn-Asp-His in conserved blocks I, II, III, and V for 18 excluded genes are given. The presence of the consensus GDSL blocks is indicated by filled coloured boxes, and blank boxes display the absence of consensus alignment between them and other OsGELP proteins.

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Additional file 10:

Physiological role, properties, and putative functions of plant GDSL esterases/lipases . The name, accession number, properties, and putative functions, as well as general biological roles of 24 plant GDSL esterases/lipases, whose putative functions have been elucidated recently and were adjoined into the original rice OsGELP family NJ tree, are listed. The coloured table divides 24 plant GDSL esterase/lipase proteins into three parts according to their major biological roles: secondary metabolism, plant development and morphogenesis, and defence and are shaded in blue, green, and light pink, respectively. In total, 50 OsGELP proteins with their names and percentage of similarity to every plant homolog or ortholog protein, whose function was revealed recently, along with phylogenetic subclade specificity to the tree from Figure 4, are given.

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Additional file 11:

Putative conserved motifs predicted in the OsGELP and known plant GDSL esterase/lipase proteins. The consensus sequence, regular expression, amino acid length, number of the OsGELP proteins containing the motif, and E-value of each 45 predicted motifs are given. The overall height of each column in the motif LOGO indicates sequence conservation at that position, whereas the height of symbols within each column presents relative frequency of the corresponding amino acid. GDSL lipase consensus block distribution is as follows: block I is located in motif 3, block II in motif 5, block III in motif 6, and block V in motif 2. Four strictly conserved catalytic residues Ser-Gly-Asn-HisxxAsp from conserved blocks I, II, III, and V are coloured red in regular expression of corresponding motifs. Regular expression pattern sequences that are coloured in blue and green represent possible sequences for secondary structure elements like helix or sheet, respectively.

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Additional file 12:

Differential expression of rice OsGELP genes in response to plant hormone cytokinin. A. Comparison of the fold expression difference for the 17 representative genes under cytokinin (tZ, BAP, and KT) treatment for results from the real-time PCR, and the microarray data obtained from Genevestigator database are given. B. Real-time PCR analysis of representative OsGELP genes and their differential expression during cytokinin (tZ, BAP, and KT) treatment are shown. The mRNA levels for each gene in different tissue samples were calculated relative to its expression in control seedlings. The error bars represent standard deviation.

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Additional file 13:

The rice GDSL esterase/lipase genes excluded from the general list of the OsGELP candidates. The locus ID, ORF length, predicted protein length, the presence of GDSL-lipase domain with confidence (E-value), description, and cDNA support of all 19 excluded genes are given.

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Additional file 14:

Motifs represent 13 highly conserved OsGELP protein alignment blocks used for phylogenetic analysis. The consensus sequence, regular expression, length (amino acids), number of the OsGELP proteins containing the motif, and E-value of each of predicted motifs are given. The overall height of each column in the motif LOGO indicates sequence conservation at that position, whereas the height of symbols within each column presents relative frequency of the corresponding amino acid. GDSL lipase consensus block distribution is as follows: motif 3 is located in block I, motif 5 is in block II, motif 6 is in block III, and motif 2 is in block V. Four strictly conserved catalytic residues Ser-Gly-Asn-HisxxAsp from conserved blocks I, II, III, and V are coloured red in the regular expression of representative motif. Regular expression pattern sequences that are coloured in blue and green represent possible sequences for secondary structure elements like helix or sheet, respectively.

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Additional file 15:

Primer sequences used for real-time PCR analysis. The OsGELP gene names and sequences of PCR primers used in the quantitative RT PCRs to verify gene expression levels are listed.

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