Genome-wide analysis of GDSL-type esterases/lipases in Arabidopsis.

KEY MESSAGE: In this present study, we introduce a fundamental framework and provide information regarding the possible roles of GDSL-type esterase/lipase gene family in Arabidopsis. GDSL-type esterases/lipases are hydrolytic enzymes with multifunctional properties such as broad substrate specificity, regiospecificity, and stereoselectivity. In this study, we identified 105 GDSL-type esterase/lipase genes in Arabidopsis thaliana by conducting a comprehensive computational analysis. Expression studies indicated that GDSL-type lipase proteins showed varied expression patterns. Phylogenetic tree analysis indicated that AtGELP (Arabidopsis thaliana GDSL-type esterase/lipase protein) gene family was divided into four clades. The phylogenetic analysis, combined with protein motif architectures, and expression profiling were used to predict the roles AtGELP genes. To investigate the physical roles of the AtGELP gene family, we successfully screened 88 AtGELP T-DNA knockout lines for 54 AtGELP genes from 199 putative SALK T-DNA mutants. Transgenic plants of AtGELP genes were used to elucidate the phenotypic characteristics in various developmental stages or stress conditions. Our results suggest that the AtGELP genes have diverse physical functions such as affecting the germination rate and early growth of seedlings subjected to high concentrations of glucose, or being involved in biotic stress responses.

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

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.

Multi-hop routing mechanism for reliable sensor computing.

Current research on routing in wireless sensor computing concentrates on increasing the service lifetime, enabling scalability for large number of sensors and supporting fault tolerance for battery exhaustion and broken nodes. A sensor node is naturally exposed to various sources of unreliable communication channels and node failures. Sensor nodes have many failure modes, and each failure degrades the network performance. This work develops a novel mechanism, called Reliable Routing Mechanism (RRM), based on a hybrid cluster-based routing protocol to specify the best reliable routing path for sensor computing. Table-driven intra-cluster routing and on-demand inter-cluster routing are combined by changing the relationship between clusters for sensor computing. Applying a reliable routing mechanism in sensor computing can improve routing reliability, maintain low packet loss, minimize management overhead and save energy consumption. Simulation results indicate that the reliability of the proposed RRM mechanism is around 25% higher than that of the Dynamic Source Routing (DSR) and ad hoc On-demand Distance Vector routing (AODV) mechanisms.

Arabidopsis SFAR4 is a novel GDSL-type esterase involved in fatty acid degradation and glucose tolerance.

BACKGROUND: SFARs (seed fatty acid reducers) belonging to the GDSL lipases/esterases family have been reported to reduce fatty acid storage and composition in mature Arabidopsis seeds. GDSL lipases/esterases are hydrolytic enzymes that possess multifunctional properties, such as broad substrate specificity, regiospecificity, and stereoselectivity. Studies on the physiological functions and biochemical characteristics of GDSL lipases/esterases in plants are limited, so it is important to elucidate the molecular functions of GDSL-type genes. RESULTS: We found that SFAR4 (At3g48460), a fatty acid reducer belonging to the Arabidopsis GDSL lipases/esterases family, was intensely expressed in embryo protrusion, early seedlings, and pollen. The characterization of recombinant SFAR4 protein indicated that it has short-length p-nitrophenyl esterase activity. In addition, SFAR4 enhanced the expression of genes involved in fatty acid metabolism during seed germination and seedling development. SFAR4 elevated the expression of COMATOSE, which transports fatty acids into peroxisomes, and of LACS6 and LACS7, which deliver long-chain acetyl-CoA for ß-oxidation. Furthermore, SFAR4 increased the transcription of PED1 and PNC1, which function in importing peroxisomal ATP required for fatty acid degradation. SFAR4 has another function on tolerance to high glucose concentrations but had no significant effects on the expression of the glucose sensor HXK1. CONCLUSIONS: The results demonstrated that SFAR4 is a GDSL-type esterase involved in fatty acid metabolism during post-germination and seedling development in Arabidopsis. We suggested that SFAR4 plays an important role in fatty acid degradation, thus reducing the fatty acid content.

Molecular analyses of the Arabidopsis TUBBY-like protein gene family.

In mammals, TUBBY-like proteins play an important role in maintenance and function of neuronal cells during postdifferentiation and development. We have identified a TUBBY-like protein gene family with 11 members in Arabidopsis, named AtTLP1-11. Although seven of the AtTLP genes are located on chromosome I, no local tandem repeats or gene clusters are identified. Except for AtTLP4, reverse transcription-PCR analysis indicates that all these genes are expressed in various organs in 6-week-old Arabidopsis. AtTLP1, 2, 3, 6, 7, 9, 10, and 11 are expressed ubiquitously in all the organs tested, but the expression of AtTLP5 and 8 shows dramatic organ specificity. These 11 family members share 30% to 80% amino acid similarities across their conserved C-terminal tubby domains. Unlike the highly diverse N-terminal region of animal TUBBY-like proteins, all AtTLP members except AtTLP8 contain a conserved F-box domain (51-57 residues). The interaction between AtTLP9 and ASK1 (Arabidopsis Skp1-like 1) is confirmed via yeast (Saccharomyces cerevisiae) two-hybrid assays. Abscisic acid (ABA)-insensitive phenotypes are observed for two independent AtTLP9 mutant lines, whereas transgenic plants overexpressing AtTLP9 are hypersensitive to ABA. These results suggest that AtTLP9 may participate in the ABA signaling pathway.