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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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Citation and License

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

Published: 15 July 2012

Abstract

Background

GDSL esterases/lipases are a newly discovered subclass of lipolytic enzymes that are very important and attractive research subjects because of their multifunctional properties, such as broad substrate specificity and regiospecificity. Compared with the current knowledge regarding these enzymes in bacteria, our understanding of the plant GDSL enzymes is very limited, although the GDSL gene family in plant species include numerous members in many fully sequenced plant genomes. Only two genes from a large rice GDSL esterase/lipase gene family were previously characterised, and the majority of the members remain unknown. In the present study, we describe the rice OsGELP (Oryza sativa GDSL esterase/lipase protein) gene family at the genomic and proteomic levels, and use this knowledge to provide insights into the multifunctionality of the rice OsGELP enzymes.

Results

In this study, an extensive bioinformatics analysis identified 114 genes in the rice OsGELP gene family. A complete overview of this family in rice is presented, including the chromosome locations, gene structures, phylogeny, and protein motifs. Among the OsGELPs and the plant GDSL esterase/lipase proteins of known functions, 41 motifs were found that represent the core secondary structure elements or appear specifically in different phylogenetic subclades. The specification and distribution of identified putative conserved clade-common and -specific peptide motifs, and their location on the predicted protein three dimensional structure may possibly signify their functional roles. Potentially important regions for substrate specificity are highlighted, in accordance with protein three-dimensional model and location of the phylogenetic specific conserved motifs. The differential expression of some representative genes were confirmed by quantitative real-time PCR. The phylogenetic analysis, together with protein motif architectures, and the expression profiling were analysed to predict the possible biological functions of the rice OsGELP genes.

Conclusions

Our current genomic analysis, for the first time, presents fundamental information on the organization of the rice OsGELP gene family. With combination of the genomic, phylogenetic, microarray expression, protein motif distribution, and protein structure analyses, we were able to create supported basis for the functional prediction of many members in the rice GDSL esterase/lipase family. The present study provides a platform for the selection of candidate genes for further detailed functional study.