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Lipase Gene Family in Rice (Oryza Sativa L. Japonica) Genome

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Lipase Gene Family in Rice (Oryza Sativa L. Japonica) Genome Chepyshko et al. BMC Genomics 2012, 13:309 http://www.biomedcentral.com/1471-2164/13/309 REASERCH ARTICLE Open Access 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 Shaw1,5,6,7* 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. * Correspondence: [email protected]; [email protected] 2Department of Food and Beverage Management, Far East University, Tainan, Taiwan 74448, ROC Full list of author information is available at the end of the article © 2012 Chepyshko et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Chepyshko et al. BMC Genomics 2012, 13:309 Page 2 of 19 http://www.biomedcentral.com/1471-2164/13/309 Background mature enzymes display expansive hydrolytic activity with The GDSL motif enzyme is a relatively newly discovered different types of substrates, including acyl-CoAs, a variety lipase, with many characteristics that have not yet been of esters, and amino acid derivatives. fully, clearly, and precisely described [1,2]. Since 1995, All the structures of the GDSL esterase/lipase that when Upton and Buckley first reported the new GDS[L]- have been described to date belong to the α/β hydrolase motif-like subfamily of lipases (pfam PF00657), new fold superfamily of proteins. The main difference in fold- questions have arisen about the specific functions of ing from classical α/β hydrolase fold is a distinct location these fascinating lipolytic enzymes. of the residues involved in active site formation, which The number of lipases (EC 3.1.1.3) and esterases (EC direct to a different analogous orientation of the catalytic 3.1.1.1) that have been studied tremendously increased triad with regard to the central parallel β-sheet [4,25]. over the last decades. The lipase and esterase families be- Recently, the structure of the GDSL esterase/lipase pro- long to hydrolases—a class of enzymes that shows very teins from several species of bacteria has been deter- broad substrate specificity. All enzymes in these families mined [21,23,25-28], but no structure from plants has contained a catalytic triad composed of serine (Ser), aspar- been resolved yet. tic (or glutamic), and histidine (His) residues. The role of The GDSL esterases/lipases have been also found in the nucleophile in lipases is played by a Ser residue, which plant species and have become very attractive subjects is a part of the highly conserved motif Gly-X-Ser-X-Gly (X because of their newly discovered properties and func- being any amino acid), positioned in the middle of the tions. Recently, in the plant kingdom, the novel family of amino acid sequence. In contrast, enzymes that belong to the GDSL esterases/lipases is represented by more than the GDSL family of esterases/lipases share five blocks of 1100 members from the twelve different fully sequenced highly conserved homology, which are important for their plant genomes. It was reported that GDSL family from classification. The active-site Ser is located close to the N- Arabidopsis thaliana consists of 108 members [29], and terminus. The GDSL family is further classified as SGNH Vitis vinifera, Sorghum bicolour, Populus trichocarpa, hydrolase because of the presence of the strictly conserved and Physcomitrella patens contain 96, 130, 126 and 57 residues Ser-Gly-Asn-His in the conserved blocks I, II, III, members, respectively [30]. Search across multiple data- and V [1-3]. Two other proton donors to the oxidation bases revealed 114 members from Oryza sativa,53 hole are the glycine (Gly) residue in block II and the as- members from Zea mays, 90 members from Selaginella paragine (Asn) in block III. The His amino acid in block V moellendorffii, 88 members from Medicago truncatula, serves as a base that makes the Ser in block I more nu- 102 members from Chlamydomonas reinhardtii,59 cleophilic by deprotonating the hydroxyl group. Add- members from Ostreococcus tauri, and 75 members itional characteristic for block V is the presence of from Phaeodactylum tricornutum [31,32]. Several plant aspartate (Asp) three amino acids ahead of His (i.e., DxxH GDSL esterases/lipases have been isolated, cloned, and sustain as the third member of the catalytic triad). Unlike characterized. Physiologically, the GDSL esterases/ other lipases, GDSL hydrolases have a flexible active site lipases that have been described so far are mainly and they change conformation in the presence of different involved in the regulation of plant development, mor- substrates; hence, some GDSL enzymes have broadly di- phogenesis, synthesis of secondary metabolites, and de- verse enzymatic activities, including esterase and protease fence response [33-55]. activity in the same enzyme [4,5]. Rice has become a model plant for genomic research The GDSL esterases/lipases are found throughout all of monocotyledonous species because of its small gen- kingdoms of life. Due to their broad substrate specificity, omic size and economic importance, but our knowledge these highly promising enzymes can be potentially used of the GDSL esterases/lipases gene family in rice is ra- for biotechnological application in a wide range of indus- ther limited. Although there are more than 100 mem- tries (e.g. food, fragrance, cosmetics, textile, pharmaceut- bers of the GDSL esterase/lipase family in the rice ical, and detergent industry) [3]. They have been genome, only a few GDSL esterases/lipases genes have previously identified in a wide range of organisms, and been studied and the functions and properties of the ma- several GDSL Ser esterases/lipases have been cloned and jority of members remain unknown. Currently, only two characterized. Many GDSL esterases/lipases have been rice GDSL esterases/lipases genes have been reported. found in bacteria, and advancement has been made to- GDSL-containing enzyme rice 1 (GER1) and wilted dwarf ward uncovering their structures, functions, and physio- and lethal 1 (WDL1) were cloned from the rice genome, logic roles [6-20]. The enzymes of GDSL esterases/lipases and their physiologic functions were suggested as regula- have been cloned and characterized, and at present, the tory in coleoptile elongation and plant growth in the crystal structures from Streptomyces scabies, Escherichia seedling stage, respectively [56,57]. coli, Pseudomonas fluorescens, Mycobacterium smegmatis, In the present study, 114 OsGELP genes were identi- and Pseudomonas aeruginosa are available [21-28]. Their fied in rice. This is the first bioinformatics genome-wide Chepyshko et al. BMC Genomics 2012, 13:309 Page 3 of 19 http://www.biomedcentral.com/1471-2164/13/309 survey of the OsGELP gene family with description of: Up to 24.5% (28 of 114) of the OsGELP genes were pre- the genomic distribution, gene structure of the OsGELP dicted to be alternatively spliced by the Rice Genome An- genes, phylogenetic analysis, as well as motif analysis, notation Project (RGAP) database (release 6.1). The and structure modelling for the OsGELP proteins. More OsGELP genes are present in two to four alternatively than 30 additional, clade-common and -specific peptide spliced forms, giving rise to a total of 68 transcripts (Add- motifs outside the GDSL domain were uncovered, itional file 1). This number is slightly higher than that pre- described, and their putative functionality based on the dicted for rice genes overall [59].
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