Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis
© Chepyshko et al.; licensee BioMed Central Ltd. 2012
Received: 9 July 2011
Accepted: 15 July 2012
Published: 15 July 2012
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.
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.
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.
The GDSL motif enzyme is a relatively newly discovered lipase, with many characteristics that have not yet been fully, clearly, and precisely described [1, 2]. Since 1995, when Upton and Buckley first reported the new GDS[L]-motif-like subfamily of lipases (pfam PF00657), new questions have arisen about the specific functions of these fascinating lipolytic enzymes.
The number of lipases (EC 184.108.40.206) and esterases (EC 220.127.116.11) that have been studied tremendously increased over the last decades. The lipase and esterase families belong to hydrolases—a class of enzymes that shows very broad substrate specificity. All enzymes in these families contained a catalytic triad composed of serine (Ser), aspartic (or glutamic), and histidine (His) residues. The role of the nucleophile in lipases is played by a Ser residue, which is a part of the highly conserved motif Gly-X-Ser-X-Gly (X being any amino acid), positioned in the middle of the amino acid sequence. In contrast, enzymes that belong to the GDSL family of esterases/lipases share five blocks of highly conserved homology, which are important for their classification. The active-site Ser is located close to the N-terminus. The GDSL family is further classified as SGNH hydrolase because of the presence of the strictly conserved residues Ser-Gly-Asn-His in the conserved blocks I, II, III, and V [1–3]. Two other proton donors to the oxidation hole are the glycine (Gly) residue in block II and the asparagine (Asn) in block III. The His amino acid in block V serves as a base that makes the Ser in block I more nucleophilic by deprotonating the hydroxyl group. Additional characteristic for block V is the presence of aspartate (Asp) three amino acids ahead of His (i.e., DxxH sustain as the third member of the catalytic triad). Unlike other lipases, GDSL hydrolases have a flexible active site and they change conformation in the presence of different substrates; hence, some GDSL enzymes have broadly diverse enzymatic activities, including esterase and protease activity in the same enzyme [4, 5].
The GDSL esterases/lipases are found throughout all kingdoms of life. Due to their broad substrate specificity, these highly promising enzymes can be potentially used for biotechnological application in a wide range of industries (e.g. food, fragrance, cosmetics, textile, pharmaceutical, and detergent industry) . They have been previously identified in a wide range of organisms, and several GDSL Ser esterases/lipases have been cloned and characterized. Many GDSL esterases/lipases have been found in bacteria, and advancement has been made toward uncovering their structures, functions, and physiologic roles [6–20]. The enzymes of GDSL esterases/lipases have been cloned and characterized, and at present, the crystal structures from Streptomyces scabies Escherichia coli Pseudomonas fluorescens Mycobacterium smegmatis, and Pseudomonas aeruginosa are available [21–28]. Their mature enzymes display expansive hydrolytic activity with different types of substrates, including acyl-CoAs, a variety of esters, and amino acid derivatives.
All the structures of the GDSL esterase/lipase that have been described to date belong to the α/β hydrolase fold superfamily of proteins. The main difference in folding from classical α/β hydrolase fold is a distinct location of the residues involved in active site formation, which direct to a different analogous orientation of the catalytic triad with regard to the central parallel β-sheet [4, 25]. Recently, the structure of the GDSL esterase/lipase proteins from several species of bacteria has been determined [21, 23, 25–28], but no structure from plants has been resolved yet.
The GDSL esterases/lipases have been also found in plant species and have become very attractive subjects because of their newly discovered properties and functions. Recently, in the plant kingdom, the novel family of the GDSL esterases/lipases is represented by more than 1100 members from the twelve different fully sequenced plant genomes. It was reported that GDSL family from Arabidopsis thaliana consists of 108 members , and Vitis vinifera, Sorghum bicolour Populus trichocarpa, and Physcomitrella patens contain 96, 130, 126 and 57 members, respectively . Search across multiple databases revealed 114 members from Oryza sativa, 53 members from Zea mays, 90 members from Selaginella moellendorffii, 88 members from Medicago truncatula, 102 members from Chlamydomonas reinhardtii, 59 members from Ostreococcus tauri, and 75 members from Phaeodactylum tricornutum[31, 32]. Several plant GDSL esterases/lipases have been isolated, cloned, and characterized. Physiologically, the GDSL esterases/lipases that have been described so far are mainly involved in the regulation of plant development, morphogenesis, synthesis of secondary metabolites, and defence response [33–55].
Rice has become a model plant for genomic research of monocotyledonous species because of its small genomic size and economic importance, but our knowledge of the GDSL esterases/lipases gene family in rice is rather limited. Although there are more than 100 members of the GDSL esterase/lipase family in the rice genome, only a few GDSL esterases/lipases genes have been studied and the functions and properties of the majority of members remain unknown. Currently, only two rice GDSL esterases/lipases genes have been reported. GDSL-containing enzyme rice 1 (GER1) and wilted dwarf and lethal 1 (WDL1) were cloned from the rice genome, and their physiologic functions were suggested as regulatory in coleoptile elongation and plant growth in the seedling stage, respectively [56, 57].
In the present study, 114 OsGELP genes were identified in rice. This is the first bioinformatics genome-wide survey of the OsGELP gene family with description of: the genomic distribution, gene structure of the OsGELP genes, phylogenetic analysis, as well as motif analysis, and structure modelling for the OsGELP proteins. More than 30 additional, clade-common and -specific peptide motifs outside the GDSL domain were uncovered, described, and their putative functionality based on the GDSL-lipase protein tertiary structure was proposed. Potentially important regions for substrate specificity and binding, as well as functional grouping according to the phylogenetic relations are discussed. The expression patterns of some representative genes analysed by quantitative real-time PCR in response to cytokinin hormone treatment matched with the digital expression results. The results of the microarray expression profiling under the different treatment conditions, and the phylogenetic relatedness of the genes were analyzed in order to predict their functions in rice.
Considering the fact that a very limited number of the OsGELP genes have been characterized to date, results reported in this study is the first step towards the understanding of the roles of the GDSL esterases/lipases in rice, which provide a solid foundation for function predictions of possible roles of the GDSL enzymes in rice. Our work introduces a fundamental framework for selection of appropriate candidate genes for the subsequent functional analysis of the OsGELP family members.
Identification of the GDSL esterase/lipase family genes in rice
A total of 114 putative OsGELP genes were identified and designated as OsGELP1 to OsGELP114 based on their order and position in corresponding chromosomes 1–12 from top to bottom. Their gene name, locus ID, the accession numbers for coding sequences (CDSs), genomic DNA, cDNA, and predicted isoelectric points of all the 114 OsGELP genes are listed in Additional file 1. The open reading frame (ORF) sizes of the OsGELP genes vary from 570 bp (OsGELP76) to 1,362 bp (OsGELP30), with an average sequence length of 1,097 bp.
Up to 24.5% (28 of 114) of the OsGELP genes were predicted to be alternatively spliced by the Rice Genome Annotation Project (RGAP) database (release 6.1). The OsGELP genes are present in two to four alternatively spliced forms, giving rise to a total of 68 transcripts ( Additional file 1). This number is slightly higher than that predicted for rice genes overall . The expression of 33 of the 68 transcripts was confirmed by FL-cDNA evidence (Figure 1Additional file 2). Several annotation errors were observed in the automated annotation of the rice genome, including intron/exon numbers/positions that were corrected according to the rice FL-cDNA sequences from the Knowledge-based Oryza Molecular Biological Encyclopedia database (KOME) . For example, the annotation of two OsGELP (OsGELP79 and 113) genes were corrected. Their structure annotations were changed from 2 exon/1 intron into 3 exon/2 intron, and 4 exon/3 intron to 5 exon/4 intron patterns. Also, the predicted ORF sizes were modified according to the availability of FL-cDNA (AK066113 and AK063071), from 1,107 and 1,272 bp to 1,026 and 846 bp, respectively.
Chromosomal distribution, gene structure and evolutionary expansion of the OsGELP genes
The chromosomal regions where the candidate genes reside vary in their size. Their genomic sequence lengths range from 1009 to 24,799 bp due to the large introns ( Additional file 7). The intron sizes of 45.6% of the OsGELP genes appear to exceed 1,000 bp. The OsGELP21 and OsGELP97 genes contain over 10-fold longer introns than the other genes in the family. The two huge introns from these genes, 12,861, and 11,743 bp, are consistent through all alternative splicing forms. Within these long introns, a total of 13 and 12 repetitive elements were detected. These elements are represented by different types of miniature inverted-repeat transposable elements, transposons, and retrotransposons. In general, the diverse repetitive sequences, from several superclasses with a variety of sizes, were discovered within introns, exons, and 5′ or 3′ untranslated regions (UTRs) of 71 OsGELP genes ( Additional file 8).
Phylogenetic analysis and evolution of the OsGELP genes
To study the evolutionary relationship of the members of the OsGELP gene family, as well the phylogenetic relationship among the rice OsGELP genes and other plant GDSL genes, whose putative functions were elucidated recently, the unrooted phylogenetic trees based on the multiple sequence alignment of their protein sequences were constructed by the neighbour-joining (NJ) method and displayed using the Molecular Evolutionary Genetics Analysis (MEGA4) program.
For the rice OsGELP phylogenetic tree, a dataset of 96 protein sequences containing 13 conserved alignment regions were collected, including the special features of the GDSL esterase/lipase such as blocks I, II, III, and V. Other 18 OsGELP genes contain gap-rich regions. During evolution, they probably lost some common GDSL enzyme blocks, as well as other shared regions. For this reason, they were eliminated from further phylogenetic analyses ( Additional file 9).
Of the four clades of the original rice OsGELP phylogenetic tree, a new clade of the plant GDSL genes appeared. The emerging clade (II) is well supported by the bootstrap value (98%) and consists of six members of the GDSL esterase/lipase genes from A. thaliana Brassica rapa, and Carica papaya, which have been shown to be correlated with different kinds of biotic stress responses, except one CpEst gene (Figure 4) [33–38, 63]. The specific nature of clade II in the tree can be explained by the association of the clade members with the myrosinase–glucosinolate system. This system is almost exclusive to the order Capparales, which includes the Brassicaceae plants . This fact can account for separation of the group of genes in clade II from the other clades in the phylogenetic tree, and every member shows relatively low similarity (below 35%) to the OsGELP genes (Figure 4Additional file 10).
Relationship between protein motifs and phylogenetic classification
A total of 45 motifs with statistical significance (E-value) from 1.3e-966 to 9.1e-002 were found among the OsGELPs and the known plant GDSL esterase/lipase proteins ( Additional file 11). Motifs 3, 5, 6, and 2 represent GDSL esterase/lipase conserved blocks I, II, III, and V, respectively (Figure 4, Additional file 11). As expected, the presence of the common GDSL domain proteins, represented by the four blocks, affirms its major functional role. Other well-conserved motifs outside the GDSL domain were also detected. Significantly, 12 conserved motifs (1–12 with E-values around e-100) with more than 10 but less than 15 amino acids in length are present in almost all proteins ( Additional file 11). The other 33 motifs were found to be specific to the different subclades of the GDSL esterase/lipase phylogenetic tree. We found that the GDSL proteins that cluster in clade I in the phylogenetic tree share a similar motif pattern (motifs 14, 16, 20, and 21), whereas there were no specific motifs for clade III. At the same time, the subclades of clade III demonstrate high diversity in specific motifs (Figure 4). Most of the OsGELP proteins that clustered together with homologs and/or orthologs in the same subclade share more than one additional conserved motifs outside the GDSL domain. Motifs 13, 19, 22, and 27 are specific to subclades Ia, Ib, Ic, and Id, whereas motifs 33, 34, 38, 43, and 45 exclusively appear in subclade Ie (Figure 4). Subclades IIIa, IIIb, and IIId, IIIe, IIIf contain specific motifs 28, 31, 39, and 15, 25, respectively (Figure 4, Additional file 11). Subclades Ia and Ib exclusively contain motifs 23 and 32, respectively. Motif 24 is specific to subclade IIIb. Subclade IIIe appears to have distinct motifs 26 and 35. Finally, five particular motifs (28, 29, 37, 40, and 44) belong to subclade IIIf (Figure 4).
The newly found additional, subclade-specific motifs were considered as novel, because there were no any statistically significant sequence similarities of our motifs with known motifs or possible function assignments within the Prosite and UniProtKB/Swiss-Prot databases [64, 65].
Distribution of the conserved motifs and their locations on the three-dimensional structure
We consider the possibility that the consensus regions outside of the motifs encoding GDSL esterase/lipase conserved blocks I, II, III, and V may contain functionally important motifs involved in substrate specificity, protein structure ordering and arrangement, protein–protein interaction, etc. Such “supplemental” functional motifs often remain conserved among members of a subgroup in large families in plants [66, 67]. Thus, the proteins within the subgroups that share these motifs likely display similar functions. To find the three-dimensional orientation of these additional motifs, in order to support our functional prediction, the structure prediction were conducted on the OsGELP proteins using the Protein Homology/analogY Recognition Engine (PHYRE) server .
The predicted basic structural model consists of six α-helices and a central β-sheet core containing six parallel β-strands (Figure 5). The active Ser residue is located in the loop region (L1) right after the first β-strand; meanwhile, in the bacterial structural model, Ser appears in a short helical segment following the first β-strand. The aspartic acid and His residues, which together with Ser form the catalytic triad, seems to hold the same location in plants and bacteria, and reside in the turn structure preceding the C-terminal α-helix (Figure 5B). Blocks II and III with their representative Gly and Asn residues, which act as proton donors to the oxyanion hole, are located in the unstructured regions following the second β-sheet and right after the third β-sheet, respectively, and designated in Figure 5B as L3 and L5.
Moreover, many predicted putative motifs within the unstructured loop regions were observed to be specific to the members of phylogenetic clades I or III and/or the subclades of these clades (Figure 5B). Three loops (L1, L3, and L9) can be specified as the most divergent in terms of motifs for the different OsGELP phylogenetic groups that deviate in biological functions. These particular loops possibly play a role in differentiation of substrate-binding specificity for the different subclades and thus bring their broad functional divergence.
For plants, during the course of their evolution, gene families generally underwent either tandem and/or large-scale segmental duplication to maintain a high number of family members [69–71]. The phylogenetic tree (Figure 3) demonstrates that the genes from 7 gene clusters are sister genes, with high degrees of phylogenetic relatedness. Only 17 genes from gene clusters I, IV, VI, VIII, and XII probably emerged as a result of local duplication, as it was previously shown by the phylogenetic analysis by Volokita et al. . The phylogenetic study of plant GDSL esterases/lipases from bryophytes, gymnosperms, monocots, and eudicots suggested that duplication of more than 40% of rice GDSL genes predated the sorghum-oryza split . If this number is combined with the number of other instances of genes’ duplication events, such as segmental or tandem duplication, the high number (71%) of the OsGELP genes potentially arose from such mode of evolutionary novelty. Taken together, the data suggest that duplications in general played a major role in the multiplication of the OsGELP genes, in the course of evolution. These conclusions are in line with a previous examination of the evolutionary mechanisms of the GDSL esterase/lipase gene family in land plants . The fact that many OsGELP gene clusters are interrupted by a number of TE-related gene insertions implies that duplication events of the GDSL esterase/lipase protein family genes were followed by insertion of the TEs throughout the course of their evolution. The large number (62%) of the OsGELP genes with TEs can be also regarded as supporting evidence in favour of the theory that subsequent and important events for the expansion in size of the OsGELP gene family in the rice genome after duplication could be the amplification of the repetitive elements ( Additional file 8). This observation is consistent with the previous conclusion that one of the forces for amplification of the rice genome is the addition of TEs .
Several forms of gene regulation, positive and negative, that involve plant introns were found . Considering that the intron evolution in the rice genome is largely dominated by intron loss [74, 75], the large introns within the OsGELP genes that were left in the course of natural selection are likely due to their possible functionality. Recent studies have shown that some introns can function as alternative promoters or enhancer elements, and some introns promote mRNA accumulation through diverse processes called intron-mediated enhancement . In addition, in contrast to exon evolution, introns appear to be under a lower selection pressure; thus, they could frequently vary in size and sequence, and slowly diverge if their position in the genes that facilitate the evolution of new proteins through exon shuffling and alternative splicing increased the coding capacity of a genome [73, 76, 77]. Although the OsGELP genes with long introns contain repetitive elements, the majority of them (47 of 52) are expressed. For example, aforementioned OsGELP21 and OsGELP97 genes are expressed in various rice organs in three and two alternative splicing forms as supported by cDNA evidence (Figure 1Additional file 2). Stress conditions are one of the effectors of the alternative splicing of pre-mRNAs because stress regulation might enable plants to quickly regulate the splicing and gene expression of many unrelated genes . Many alternatively spliced transcripts that were expressed under stress conditions were found among long intron genes (Figure 1). For instance, the OsGELP21 gene that encodes three alternative spliced forms in the first and third forms is expressed in the shoots and calluses under the etiolation and heat treatments. These results suggest that subsequent studies should continue to investigate the advanced functions and transcriptome complexity of the OsGELP gene family.
To validate the results of the microarray data obtained from Genevestigator database, changes in the expression level of 17 representative OsGELP mRNAs from clades I and III, under cytokinins (tZ, KT, or BAP) treatments in rice seedling were examined by quantitative real-time RT-PCR. The treatment conditions were repeated according to the description of the experiments in the Genevestigator database. The expression patterns that were obtained via RT-qPCR for 8 and 2 selected genes which were treated with tZ and BAP, respectively, followed the same tendency and confirmed the microarray data ( Additional file 12). Results of the digital expression analysis for the OsGELP2, 17, 12, 61, 44, 77, 90, 100, and OsGELP9 2 genes were not coherent with the qPCR analysis, and did not show up-regulation during the tZ and KT treatments, respectively. Although, most of the genes from both clades showed up-regulation of their expression, only 3 genes (OsGELP15, 50, 88) from clade I were significantly up-regulated (>2-fold) after treatment with tZ or BAP hormones for 30 min or 3 h, respectively. At the same time, none of the genes from clade III demonstrated significant fold change under the cytokinins treatment ( Additional file 12), therefore suggesting functional differentiation of the two examined clades. Further experiments are needed to confirm the microarray validity in order to explore functional divergence of the OsGELP family.
Following the assumption that functional information of unknown GDSL esterases/lipases can be deduced from the orthologs of known functions , we attempted to extrapolate the functional characteristics of described plant GDSL onto the OsGELP rice genes. Using the functional descriptions of the potential orthologs and homologs, based on the phylogenetic grouping, the possible putative functions for a number of the OsGELP genes were predicted, and discussed further.
The rice GDSL esterase/lipase family members OsGELP4 5, and 12 from subclade Ia share high similarity with AmGDSH1 (Alopecurus myosuroides hydrolase) that demonstrates acetylajamaline hydrolase activity and it is involved in alkaloid metabolism . Subclade Ib (OsGELP2 3 63 77 84, and 85) is expected to be involved in plant development and morphogenesis at the seedling stage according to the function of their close homologue GER1 (OsGELP33) . These genes are not only expressed in many rice organs and development stages, as well as share analogous gene structure and special protein motif 32, but also change their expression dramatically under stress conditions during early plant development (Figures. 14, and 6). Two genes from clade Ib have received attention in recent literature. The OsGELP63 gene is induced by both red and far-red light and by jasmonic acid, and acts in response to drought and cold stresses . The study of OsGELP33 (GER1) has demonstrated the role of this gene in the rice plant development at the seedling and coleoptile elongation stages . OsGELP33, together with its sister genes OsGELP84 and OsGELP3, arose from the segmental duplication event (Figure 2). Their close phylogenetic relationship is confirmed by the high node number and the high protein similarity score (Figure 4Additional file 10). Therefore, the functions of these genes might be similar to that of the OsGELP33 (GER1). Subclade Ie, mentioned previously, is a good example of the group of genes with possibly related functions. The genes in subclade Ie appear to belong to the cell wall-associated proteins with carbohydrate substrate specificity (Figure 4Additional file 10). Together with the cell wall-associated GDSL esterase/lipase orthologs (e.g., AtFXG1 LAE Enod8, maize AChE, and Hevb13) [46, 50, 51, 53, 54, 80], rice OsGELP14 15 16 60 61 66 80 91, and 92 genes form a distinctive group in clade I (Figure 4). The α-fucosidase 1 (AtFXG1) from A. thaliana, lanatoside 15′-O-acetylesterase (LAE) from Digitalis lanata Ehrh. Woolly, and their homologue Early nodulin protein (Enod8) from Medicago sativa are reportedly active on oligo- or polysaccharide substrates [46, 50, 51]. LAE acts as deacetylators on cardenolide glycosides (cardenolides that contain structural groups derived from sugars) . AtFXG1 modifies xyloglucan oligosaccharides through the hydrolysis of t-fucosyl residues . The representatives of the acetylcholinesterase (AChE) gene family have been characterized and cloned recently in several plants, including Z. mays L., Macroptilium atropurpureum, and Salicornia europaea L. [52–55]. Although the definite physiologic role of the AChE gene family has not been elucidated yet, AChEs are suggested to play a role in the gravity response of plants. According to the motif analysis, this group of the cell wall-associated proteins shares several special motifs in the subclade Ie, such as motifs 38, 33, 34, 43, and 45 (Figure 4). A total of 29 rice OsGELP genes from clades I and III putatively can be important to the plant defence response against biotic infections, as evident from their microarray expression data (Figure 6) and relatively high similarity to the number of defensive GDSL esterases/lipases (e.g., CaGLIP1 CaGL1 AtLTL1 GLIP1 GLIP2 Br-SIL1 ESM1, and MVP1) ( Additional file 10) [33–41]. As potentially appealing subjects for future analyses of the OsGELP gene family, subclade IIIf can be specifically studied. It not only contains five different exclusive motifs (28, 29, 37, 40, and 44), but also some of its members show expression in all rice organs and share similar gene structure patterns within a particular subclade (Figures. 1 and 4Additional file 6).
Based on the protein sequence analysis, a diversity of the consensus regions outside of motifs that encoded the GDSL esterase/lipase conserved blocks I, II, III, and V was found. These consensus motifs are specific to different phylogenetic clades and/or subclades from conjoint tree that differed in biological functions (Figure 4). The GDSL esterases/lipases are active on a wide range of substrates. This multienzymatic activity can be explained by the flexible substrate-binding pocket in the active site, which facilitates the binding of different substrates . Considering that many motifs can be functionally important and play a role in enzyme specificity and biochemical activity, the long loop regions extending from the protein core in the plant GDSL esterases/lipases might be involved in the diversification of molecular multifunctionality, as this was found in bacterial species [25, 27]. For example, aryl esterase from M. smegmatis and thioesterase I from E. coli share a common structural fold, but differs in the additional insertions—unstructured loop regions in the aryl esterase proteins. It was suggested that such insertions might determine the type of enzymatic mechanism, contribute to the oligomerization, and greatly restrict the shape of the enzyme active site . Many of the predicted motifs within the loop regions were found to be specific to the members of particular phylogenetic subclades that unite the GDSL enzymes with similar biological functions (Figures. 4 and 5). Based on these findings, we would like to specifically highlight L1, L3, and L9. The peptide regions of these loops are specific to different subclades from clades I and III. Based on the functional prediction, these subclades represent the proteins with different molecular functions and reaction types. As shown in the 3D protein structure prediction model (Figure 5A), loops L1, L3, and L9 are hypothetically oriented around the enzyme active site and function in the flexibility of the substrate-binding pocket. Therefore, these loops should be studied further to determine their role in molecular functional diversification of the plant GDSL enzymes. Experiments using reverse genetics would be required to establish contribution of these motifs. The close homologs or orthologs from plant species with known putative functions, which cluster together with the OsGELP proteins in the same subclades, share one or more additional conserved motifs (Figure 4). Although the functions of these specific motifs outside the GDSL esterase/lipase domain are still unknown, the presence of the conserved motifs certainly reflects the functional similarities among the OsGELP proteins that share these common motifs with other plant homologue proteins of known function.
The rice GDSL esterase/lipase family is notably one of the 11 largest families in the rice genome, with more than 100 members . In other fully sequenced plant genomes, the GDSL esterase/lipase family also consist of high number of family members [29, 30]. The remarkably high number of genes in the GDSL family in different plants can be explained by differences in enzyme function and activity on a wide range of substrates, as it was shown by Volokita et al. . This claim is supported by the existing data collected by investigations of the GDSL esterases/lipases, which have already undergone functional analysis, cloned, and characterized in different plant species, and whose physiologic role, properties, and functions have been elucidated ( Additional file 10). The multifunctionality of the OsGELP family in rice, as well as in other land plant species, their diverse roles in different aspects of plant growth and development can be explained by the complexity and diversity of the genes at the structural level. The large number of genes that comprise the GDSL esterase/lipase family in land plant species, with many distinct groups and subgroups arising in the course of evolution, further explains functional divergence. Hypothetically, plant GDSL esterase/lipase proteins are the evolutionary product of recombination of several proteins, and contain various domains/motifs with putative functions. Such an assumption provides a clue to further study the diverse functionality of this enzyme family. Motif search analysis, presented here, offers further evidence for such supposition. Our manuscript introduces, for the first time, a concrete rationale for further experimentation with the rice OsGELP family members, and presents unique opportunities, and articulates coherent basis for functional studies. Further analyses of the gene functions using RNAi and overexpression are currently under way to elucidate the mechanisms further.
The present bioinformatics analysis accommodates new insights into the genomic and proteomic diversity of the rice GDSL esterase/lipase gene family. The phylogenetic analysis divides the OsGELP gene family into the distinct groups that share similar protein motif structure. We found 41 additional motifs that represent the core secondary structure elements or appear specifically in different phylogenetic subclades. Members within the specified subclades can have common evolutionary origins, and obtain common unambiguous motifs that probably reflect their related molecular functions. Thus, our study support required basis, and should stimulate future full-fledged functional studies of these particular motifs, as understanding the structure-function relationship of the members of the OsGELP gene family is necessary.
Recently, only few rice OsGELP genes have been studied in order to determine their function. Here, we provide a rationally reasoned, well defined platform for more detailed functional, in-depth studies of the OsGELP genes based on combination of the phylogenetic, motif, and protein dimensional structure analyses. The findings presented in our manuscript can be utilized for selection of candidate genes for functional validation studies. It is of broad interest to the biological research community with wide and important practical applications in biotechnology and food science. The researchers from different domains, with different goals will find our analyses crucial for the initiation of their investigations.
Identification of genes coding the GDSL esterase/lipase in genome sequences of rice subsp. japonica cv. Nipponbare
A total of 132 genes were identified as possible candidates of the GDSL esterase/lipase proteins using primary bioinformatics analysis. First, the genes previously annotated as GDSL esterase/lipase were collected from several public online databases, such as MSU RGAP (release 6.1), Rice Protein Database in GRAMENE, and GenBank from the National Centre for Biotechnology Information [31, 32, 82]. Then, multiple BLAST algorithm analysis of the primary candidates, using the typical GDSL esterase/lipase protein sequence as our query, was done. The OsGELP candidates were tested against the Hidden Markov Model (HMM) profile (build 2.3.2) of GDSL domain, numbered PF00657 in the Pfam HMM library in the MyHits protein domains database . All sequences with an E-value below 0.1, gathering cut-off above −69.0, and length above 100 amino acids were selected for further analyses. Subsequently, five genes that possessed repetitive sequences and were defined as retrotransposon genes, such as LOC_Os01g12340, LOC_Os01g32630, LOC_ Os06g24420, LOC_Os10g09130, and LOC_Os11g19690, were excluded from our analyses. We also eliminated several putative OsGELP genes that were annotated as esterase, anther-specific proline-rich protein APG precursor, alpha-l-fucosidase 3 precursor, hypothetical protein, expressed protein, and carboxylic ester hydrolase, and had GDSL motif with Pham E-value less than 0.1 ( Additional file 13).
The nomenclature of the OsGELP genes is based on the arrangement of positions on rice chromosomes 1–12. In the present study, the LOC prefix from all RGAP locus IDs that represent the GDSL esterase/lipase genes were removed for convenience. Information regarding ORF length, amino acid number, molecular weight, and isoelectric point of protein was downloaded from RGAP. The full-length cDNAs of all predicted genes were searched in the KOME . Genomic sequences that were misannotated compared with available FL-cDNA sequences were corrected manually for the following analysis.
Distribution of the OsGELP genes on rice chromosomes and duplication events
The chromosomal distribution of the predicted OsGELP genes members was retrieved from the RGAP database. Information regarding their physical positions was derived from the RGAP database according to the location of the rice chromosome pseudomolecules . To identify the closely linked OsGELP genes, defined as gene cluster sets, in the rice chromosomes, the RGAP Rice Genome Browser was explored. Segmental duplication analysis was done with the RGAP rice segmental duplication database with the maximum length distance permitted between collinear gene pairs set to be 500 kb. The information on tandemly duplicated OsGELP genes, paralogs, and orthologs was obtained from the Rice Protein Database in Gramene , the Kyoto Encyclopedia of Genes and Genomes (KEGG) Database , the GreenPhyl Orthologs Search Tool (GOST) , and the Orthologous Groups Search page on RGAP. Outparalogs were determined from phylogenetic analyses of GDSL esterase-lipases from 7 plant species by Volokita et al. . Proteins designated as homologous to 24 plant GDSL esterase/lipase genes, whose putative functions were annotated recently, share 30%–80% similarity.
Exon/intron structure and sequence analysis
The exon/intron structures of the OsGELP genes were retrieved from the RGAP  and Gramene/Ensembl Genome Annotation for Rice . For genes whose cDNA sequences were available, their structure was checked manually, aligning genomic and cDNA sequences. The diagram of the exon/intron structures and information on intron distribution pattern were obtained using the online Gene Structure Display Server . The alternative splicing of the OsGELP genes was validated manually by alignment of rice FL-cDNA with genomic sequences or using RGAP Rice Genome Browser. The repetitive sequences were screened using RepeatMasker database .
Multiple sequence alignment, and phylogenetic analysis
The OsGELP genes nucleotide cDNA and CDS sequences were translated into protein sequences. The protein sequences were aligned using multiple sequence alignment via the ClustalW method and were then manually corrected and implemented in the MEGA4 software (version 4.0) . A total of 18 OsGELP genes were excluded from the final alignment because of the absence of some conserved GDSL blocks and poorly matched alignable regions with gaps. The culled protein set consisting of 96 OsGELP genes was used to construct trees. Second unrooted NJ phylogenetic tree combined 96 OsGELP genes and 24 plant GDSL orthologs or homologs whose putative functions were annotated recently following by procedure described by Volokita et al. .
A multiple-step strategy was used to construct the phylogenetic trees. Very large protein families commonly contain various domains and repeats that make them extremely difficult to analyze. The special feature of the GDSL esterases/lipases is the presence of the four strictly conserved residues Ser-Gly-Asn-His in conserved blocks I, II, III, and V. Consequently, our first consideration was to construct the phylogenetic tree based on the four blocks of the GDSL enzyme. Surprisingly, the node numbers were very low, and any kind of phylogenetic tree analysis would not help. The multiple alignments showed diversity of the strictly conserved areas that were consistent throughout the protein sequences of all GDSL candidates, along with the less conserved regions with gaps. To analyse those well-conserved regions, a motif identification search was conducted together with the protein structural prediction analysis. First, using Multiple Em for Motif Elicitation (MEME) program, the additional putative conserved motifs from a total of 120 plant GDSL esterase/lipase proteins (96 rice OsGELP proteins and 24 plant GDSL esterases/lipases whose putative functions were elucidated recently) were identified . Second, after the structural topology of the OsGELP was predicted, the multiple sequence alignment, motif search, and protein structure analysis were analytically combined. Thirteen aligned regions (including GDSL esterase/lipase blocks I, II, III, and V) were found to be consistent throughout all 120 proteins and, in most cases, they encode the core secondary structure elements such as α-helices and/or β-sheets. Assuming that these core structure regions are mainly ancient, less mutated, and, probably, in the course of evolution, were under the lowest selections pressure, the phylogenetic study was performed based on these well-conserved regions. As a result, the trees were based on 13 conserved alignment blocks, which are represented by 23 putative conserved motifs (motifs 1–7, 10–12, 17, 20, 22, 24, 27, 30, 36–38, 40, 42, and 44) that were identified through motif search analysis ( Additional file 14). The phylogenetic trees that were built based on that strict alignment blocks showed the highest node numbers compared with the other trees that were based on full-length or four GDSL block alignments. In parts of the sequences that were out of those well-conserved alignment regions, including the N- and C-terminus, rich gap parts were manually removed from the alignment and phylogenetic analysis of all 120 GDSL protein sequences. Finally, two unrooted phylogenetic trees were constructed using the NJ method and were displayed using the MEGA4 program. The bootstrap values of 1,000 replicates were placed at the nodes, and the scale bar corresponded to 0.1 estimated nucleic acid substitutions per site. The topologies of the eventual unrooted NJ trees were maintained in trees that were built using the distance or parsimony methods.
Determination of conserved motifs, and structure modelling
To identify the additional putative conserved motifs in the rice OsGELP gene family and in 24 plant GDSL esterases/lipases, whose putative functions were recently elucidated, the MEME motif search tool was used . During our motif distribution search, different sets of parameters for width, number, and occurrences were tried for a single motif. Our final motif search was based on the following criteria: number of repetitions, zero or one per sequence; maximum number of motifs, 45; optimum motif width, ≥6 and ≤15. The N and C-termini were removed from all protein sequences in the final motif search after we confirmed no additional motifs were present in those parts. To determine which of our motifs can be considered novel, all regular expressions of found motifs were compared against the Prosite database patterns . Functional annotation search was completed with UniProtKB/Swiss-Prot and Prosite databases [64, 65].
To gather information about the secondary and tertiary structure of the OsGELP proteins, 3D models were constructed using the automatic protein structure homology modelling server using the PHYRE software . Each submitted OsGELP sequence was scanned against the non-redundant sequence database structural classification of proteins and the PDB database. Aligned structures were displayed and analyzed within the PyMOL Molecular Graphics System . Topology map was created using the TopDraw program .
Expression analysis of the OsGELP genes
The evidence of expression of the rice OsGELP genes was obtained by several types of transcript data, such as FL-cDNA, EST, and/or MPSS from Expression Evidence Search page at RGAP , and the microarray data were available at the Genevestigator site . The locus name of the GDSL esterase/lipase genes was used to query the MPSS database containing the signature information of the genes .
Hormone treatment and quantitative real-time RT-PCR analysis
To confirm the differential expression of representative OsGELP genes under the hormone treatment identified by microarray data analysis, the tissue samples of seedling, from the rice (O. sativa L. cv Tainung 67, a japonica variety) were collected. The seeds that were sterilized with 70% ethanol for 15 min and then with 2% (w/v) sodium hypochlorite for 15 min, soaked in distilled water at 30°C for 1 day, and germinated seeds were grown for 7 days or 2 weeks with a photoperiod of 12 h light (30°C)/12 h dark (28°C). For hormone treatment with tZ, the whole roots were cut at the lamina joint in water from the 2-week-old seedlings and immediately dipped in distilled water containing either 5 μM trans-zeatin in dimethylsulfoxide [DMSO; 0.1% (v/v)] or an equal volume of DMSO as a control. Each excised organ was incubated at 30°C for 30 min, as it was described previously . For kinetin responsive study, rice seeds were germinated and grown hydroponically in nutrient solution . Seedling samples grown till the 3-leaves stage (two-week-old seedlings) and then treated with 100 μM kinetin for 60 min. For cytokinin treatment with benzyl aminopurine (BAP), rice seedlings that were grown hydroponically for 7 days, were transferred to a solution containing 50 μM benzyl aminopurine for 3 h. Seedlings mock-treated with dimethylsulfoxide (final concentration 0.1%) served as the control. All samples are harvested and stored at −80°C until the RNA was extracted.
Real-time PCR analysis was performed using gene-specific primers as described earlier . The primer sequences are listed in Additional file 15. There are at least three biological replicates of each treatment and duplicate QRT-PCR analyses for each sample. Total RNA was prepared using RNeasy plant Mini Kit (Qiagen) with RNase-free DNase I (Qiagen). Approximately 2 μg of total RNA was used as template for first-strand cDNA synthesis, which was performed by SuperScript III RT (Invitrogen, Carlsbad, CA, USA) with oligo(dT)15 primers in a reaction volume of 20 μl. The RT reaction was diluted 1:10 and 5 μl used in the amplification with the specific PCR primers. Quantitative RT-PCR analysis was performed using an ABI 7500 real-time detection system and SYBER Green Dye (ABI, Foster City, CA). PCR amplification was performed in duplicate. The RNA expressions were normalized with the internal control, ACTIN 1 (ACT1) or 18 s rRNA  to ensure the equal amount of cDNA. The mRNA levels for each candidate gene in different tissue samples were calculated using the ΔΔCT method.
This research was supported by a grant from the National Science Council of Taiwan (NSC 98-2313-B-005 -023 -MY3) and the research is partially supported by grant from the Ministry of Education, Taiwan, R.O.C. under the ATU plan to Jei-Fu Shaw.
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