Rice Phospholipase A Superfamily: Organization, Phylogenetic and Expression Analysis during Abiotic Stresses and Development

Phylogenetic and Expression Analysis during Abiotic Stresses and Development. PLoS ONE 7(2): e30947. doi:10.1371/journal.pone.0030947 Rice Phospholipase A Superfamily: Organization, Phylogenetic and Expression Analysis during Abiotic Stresses and Development Amarjeet Singh 0 Vinay Baranwal 0 Alka Shankar 0 Poonam Kanwar 0 Rajeev Ranjan 0 Sandeep Yadav 0 Amita Pandey 0 Sanjay Kapoor 0 Girdhar K. Pandey 0 Maria Gasset, Consejo Superior de Investigaciones Cientificas, Spain 0 Department of Plant Molecular Biology, University of Delhi South Campus , New Delhi , India Background: Phospholipase A (PLA) is an important group of enzymes responsible for phospholipid hydrolysis in lipid signaling. PLAs have been implicated in abiotic stress signaling and developmental events in various plants species. Genome-wide analysis of PLA superfamily has been carried out in dicot plant Arabidopsis. A comprehensive genome-wide analysis of PLAs has not been presented yet in crop plant rice. Methodology/Principal Findings: A comprehensive bioinformatics analysis identified a total of 31 PLA encoding genes in the rice genome, which are divided into three classes; phospholipase A1 (PLA1), patatin like phospholipases (pPLA) and low molecular weight secretory phospholipase A2 (sPLA2) based on their sequences and phylogeny. A subset of 10 rice PLAs exhibited chromosomal duplication, emphasizing the role of duplication in the expansion of this gene family in rice. Microarray expression profiling revealed a number of PLA members expressing differentially and significantly under abiotic stresses and reproductive development. Comparative expression analysis with Arabidopsis PLAs revealed a high degree of functional conservation between the orthologs in two plant species, which also indicated the vital role of PLAs in stress signaling and plant development across different plant species. Moreover, sub-cellular localization of a few candidates suggests their differential localization and functional role in the lipid signaling. Conclusion/Significance: The comprehensive analysis and expression profiling would provide a critical platform for the functional characterization of the candidate PLA genes in crop plants. - Funding: This work was supported by the Department of Biotechnology, Council of Scientific and Industrial Research, University Grant Commission, Government of India. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Plants often encounter abiotic stresses such as high salinity, dehydration and low temperature during their life span. These abiotic stresses impose adverse growth conditions, which affect the plant development, longevity and productivity. The adaptive mechanism involves the activation of numerous signal transduction pathways, which lead to various molecular, cellular and physiological changes [14]. Recent findings propose an integral place for lipid signaling in complex regulatory network in response to abiotic stresses in plants [58]. Various environmental cues have been identified to trigger the hydrolysis of membrane phospholipids, which results in the generation of different classes of lipid and lipid-derived signal messengers such as phosphatidic acid (PA), diacylglycerol (DAG), DAG-pyrophosphate (DGPP), lysophospholipids, free fatty acids (FFAs), phosphoinositides and inositol polyphosphates [911]. Phospholipases are of utmost importance in lipid signaling as they are the essential enzymes for the catalysis of the initial step of phospholipids hydrolysis. Phospholipases have been broadly categorized as phospholipase A (PLA), phospholipase C (PLC) and phospholipase D (PLD) based on the action of respective enzyme at different sites on a glycerophospholipid molecule [12]. PLAs form an important group of lipid hydrolysing enzymes in plants. Based on their catalytic activity at the specific positions on a membrane glycerophospholipid, PLA superfamily has been divided into PLA1 and PLA2 subtypes. PLA1 catalyses the hydrolysis at sn-1 position of a phospholipid whereas PLA2 acts on sn-2 position. Products generated in the reaction such as FFA and lysophospholipids such as lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE) are biologically active compounds, which are involved in several cellular signaling pathways [13]. PLA1 specifically hydrolyses phosphatidylcholine (PC) and PApreferring PLA1 acts on PA. Depending on the particular sequences at N-terminal and similarity in the catalytic region, PC-hydrolysing PLA1s have been divided into groups I, II and III; and members of respective groups are predicted to be localized to chloroplast, cytosol and mitochondria, respectively [1314]. Plant PLA1 members are characterised by the presence of a highly conserved GXSXG motif, a triad of three amino acids; Ser, Asp and His in the catalytic centre and a molecular weight of 45 50 kDa [1517]. Sequence analysis also suggests three major groups of PLA2; calcium-dependent cytosolic phospholipase A2 (cPLA2), patatin like phospholipase A, which are homologous to animal calcium-independent phospholipase A2 (iPLA2) and low molecular weight secreted phospholipase A2 (sPLA2) [1821]. However, cPLA2s are yet to be identified in plants [13]. Plant sPLA2s are characterised by the molecular weight of 1318 kDa, PA2c domain, which comprises of a highly conserved Ca2+ binding loop (YGKYCGxxxxGC) and a catalytic site motif (DACCxxHDxC) with enzymatically active His/Asp residues [18,2224]. pPLAs are a group of vacuolar nonspecific lipid acyl hydrolases in solanaceae plants, possessing a combined PLA1 and PLA2 activity [13,17,2526]. Based on the sequence analysis, plant pPLAs have been majorly categorised into three groups (I, II and III) [27] and recognized by the presence of a catalytic centre containing the esterase box (GTSTG) and the anion binding (DGGGXRG) motif. Arabidopsis genome exploration have resulted in the finding of twelve PC-hydrolysing PLA1 [14], one PApreferring PLA1 [28], four sPLA2 [2930] and ten pPLA members [20]. Moreover, two sPLA2 genes have also been reported in the rice genome [22]. In plants, different PLA members have been characterized and reported to be involved in seed development [31], root development [32], wounding and pathogen attack [33], hyperosmotic stress [1], cold and high salinity [34]. As evident by the survey of phospholipases in plants, most of the work has been carried out on dicot model plant Arabidopsis and some other species, but knowledge related to phospholipases A is minuscule in crop plant rice. Several individual reports proposed the involvement of these enzymes in numerous signaling networks and regulation of cellular processes such as stress signaling and tolerance, and development in dicot plant, especially Arabidopsis. It is quite obvious that these enzymes might als (...truncated)