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

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.

Figure 1

The riceOsGELPgene expression anatomy viewer. The expression patterns of 121 transcripts of 114 OsGELP genes in different rice tissues are shown. The evidence of gene expression for the genes is based on EST, FL-cDNA, MPSS, and Genevestigator data. A positive signal is indicated by a coloured box as follows: light blue for seed, light green for shoot, orange for mixed tissue, dirty green for callus, dark blue for panicle, light pink for pistil, green for leaf, black for root, red for flower, light yellow for whole plant, dark pink for anther, purple for immature seed, blue for endosperm, and lime for seedling. The white box indicates that no expression was observed. The colour in the cDNA column designates tissue library from where cDNA support was obtained. The black points display availability of expression data.

Figure 2

Genomic distribution of theOsGELPgenes in rice chromosomes. The OsGELP genes are numbered 1–114. The white rectangles on the chromosomes (vertical bars) indicate the positions of the centromeres. Chromosome numbers are indicated at the top of each bar, and the number in parentheses corresponds to the number of the OsGELP genes present on that chromosome. The OsGELP genes present on duplicated chromosomal segments are connected by coloured lines (one colour per chromosome). The tandemly duplicated genes present in the same colour box. The roman numerals and vertical black solid lines show the number and specify groups of the closely linked genes identified as clusters. The blue and red triangles indicate the upward and downward directions of transcription, respectively.

Figure 3

The phylogenetic relationship of theOsGELPgene family. The unrooted tree was constructed based on multiple sequence alignment of the rice OsGELP protein sequences using ClustalW program by NJ method with 1,000 bootstrap replicates. Subclades are numbered at the right part of the tree and marked with different alternating tones of a background to make subclade identification easier. OsGELP genes that are in the same coloured boxes are segmental duplicated genes. Coloured dots indicate genes in tandem duplication. Vertical dashed black lines point out genes from genomic clusters. The node numbers lower than 50 are not shown.

Figure 4

An analytical view of the phylogenetic relationship among the rice OsGELP and plant homologues of known function. Protein NJ tree: The unrooted tree, constructed using ClustalW, summarizes the evolutionary relationship among 120 members of the GDSL esterase/lipase plant family. The NJ tree was constructed using the alignment of only the highly conserved amino acid sequence regions. The tree shows 13 major phylogenetic groups. Left column identifies subclades and is marked with different alternating tones of background to make subclade identification easier. The numbers beside the branches represent bootstrap values based on 1,000 replications. The node numbers lower than 50 are not shown. Protein motif structure and location: the OsGELP and plant GDSL esterase/lipase proteins are in the order of their appearance in the phylogenetic tree. Each coloured box represents particular motif. Their consensus sequence, length (amino acids), number of the GDSL esterase/lipase proteins containing the motif, and E-value are given in Additional file 11. The GDSL motif blocks I, II, III, and V are indicated in pink boxes above the motif distribution pattern. The length of proteins (amino acids) can be estimated using the scale at the bottom. Motifs enclosed in red, blue, or green frames are highlighted motifs that exclusively appear in proteins from one, two, or three subclades, respectively. The number of highlighted motifs specific for one or several subclades is given at the right. The secondary element assignment, below the motif distribution scheme, corresponds to the general structure of the OsGELPs.

Figure 5

Schematic diagrams of the structure prediction for the rice OsGELP esterase/lipase proteins.A. The stereoview of the ribbon diagram for general structure prediction model of the OsGELP proteins is given. The six-stranded β-sheet is labelled. The catalytic triad Ser, Asp, and His are shown as sticks. B. Common schematic view of the OsGELP protein secondary structure. The folds showing six parallel β-strands are labelled β1–β6 and helices are labelled α1–α6. The loop regions are labelled L1–L10. The location of the GDSL consensus blocks is coloured magenta and catalytic residues are shown. Highly variable motif composition loops (L1, L3, and L9) are pointed out. The phylogenetic subclade in Figure 4, which contains specific motif(s) within the mentioned loops, is enclosed in shaded coloured boxes next to the motif’ numbers.

Figure 6

Expression pattern of theOsGELPgenes with predicted functions in response to different treatment conditions. The microarray data-based expression profiles under various conditions are presented using the meta-profile analysis tool at Genevestigator for 50 OsGELP genes. The transcript levels are depicted by numbers indicating relative fold values. The OsGELP genes are in the order of their appearance in the phylogenetic tree. The number of clades and subclades are presented in the left side of the diagram. The subclades are highlighted in the same alternating tones as they were shadowed in the phylogenetic tree in Figure 4.