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

Abstract

BackgroundGDSL 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.ResultsIn 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.ConclusionsOur 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.

Requirement of Catalytic-Triad and Related Amino Acids for the Acyltransferase Activity ofTanacetum cinerariifoliumGDSL Lipase/Esterase TcGLIP for Ester-Bond Formation in Pyrethrin Biosynthesis

“…4) This family consists of many members with such diverse functions as ceramidase, 5) sinapine esterase, 6) transesterification, 7) cutin synthesis 8) and cutinase activities 9) in plants. 10) We confirmed that the recombinant enzyme expressed in Escherichia coli as a fusion with maltosebinding protein (MBP) showed acyltransferase activity for pyrethrin synthesis. The enzyme displayed high substrate specificity for the acid and alcohol moieties, recognizing the absolute configuration of the three asymmetric carbons in the substrates.…”

“…4) GDSL lipases/esterases generally contain serine in Block I, glycine in Block II and asparagine in Block III, as well as aspartate and histidine in Block V as the amino acids involved in hydrolase activity. 10,11) Histidine in Block V deprotonates serine in Block I with the assistance of aspartate in Block V, and activated serine attacks the carbonyl carbon of substrates in the ''catay To whom correspondence should be addressed. Tel: +81-742-43-7153; Fax: +81-742-43-1445; E-mail: kmatsuda@nara.kindai.ac.jp Abbreviations: TcGLIP, Tanacetum cinerariifolium GDSL lipase/esterase; MBP, maltose-binding protein; SDS-PAGE, sodium dodecyl sulfatepolyacrylamide gel electrophoresis lytic triad.''…”

Arabidopsis DELLA and Two HD-ZIP Transcription Factors Regulate GA Signaling in the Epidermis through the L1 Box cis-Element

“…GDSL lipases represent a subfamily of lipolytic enzymes that show very broad substrate specificity (Chepyshko et al, 2012).…”

Hydroxycinnamoyltransferases in plant metabolism

“…GDSL lipases/esterases are known for their broad regio-and substrate specificity. More than 100 members of this enzyme group have been identified in the Oryza sativa genome (Chepyshko et al 2012). The native CGT from tomato was purified to near homogeneity and used for protein sequencing.…”