Comprehensive Genomic Analysis and Expression Profiling of Phospholipase C Gene Family during Abiotic Stresses and Development in Rice Amarjeet Singh 1 , Poonam Kanwar 1 , Amita Pandey 1 , Akhilesh K. Tyagi 1,2 , Sudhir K. Sopory 3 , Sanjay Kapoor 1 , Girdhar K. Pandey 1 * 1 Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India, 2 National Institute of Plant Genome Research, New Delhi, India, 3 Jawaharlal Nehru University, New Delhi, India Abstract Background: Phospholipase C (PLC) is one of the major lipid hydrolysing enzymes, implicated in lipid mediated signaling. PLCs have been found to play a significant role in abiotic stress triggered signaling and developmental processes in various plant species. Genome wide identification and expression analysis have been carried out for this gene family in Arabidopsis, yet not much has been accomplished in crop plant rice. Methodology/Principal Findings: An exhaustive in-silico exploration of rice genome using various online databases and tools resulted in the identification of nine PLC encoding genes. Based on sequence, motif and phylogenetic analysis rice PLC gene family could be divided into phosphatidylinositol-specific PLCs (PI-PLCs) and phosphatidylcholine- PLCs (PC-PLC or NPC) classes with four and five members, respectively. A comparative analysis revealed that PLCs are conserved in Arabidopsis (dicots) and rice (monocot) at gene structure and protein level but they might have evolved through a separate evolutionary path. Transcript profiling using gene chip microarray and quantitative RT-PCR showed that most of the PLC members expressed significantly and differentially under abiotic stresses (salt, cold and drought) and during various developmental stages with condition/stage specific and overlapping expression. This finding suggested an important role of different rice PLC members in abiotic stress triggered signaling and plant development, which was also supported by the presence of relevant cis-regulatory elements in their promoters. Sub-cellular localization of few selected PLC members in Nicotiana benthamiana and onion epidermal cells has provided a clue about their site of action and functional behaviour. Conclusion/Significance: The genome wide identification, structural and expression analysis and knowledge of sub-cellular localization of PLC gene family envisage the functional characterization of these genes in crop plants in near future. Citation: Singh A, Kanwar P, Pandey A, Tyagi AK, Sopory SK, et al. (2013) Comprehensive Genomic Analysis and Expression Profiling of Phospholipase C Gene Family during Abiotic Stresses and Development in Rice. PLoS ONE 8(4): e62494. doi:10.1371/journal.pone.0062494 Editor: Miguel A. Andrade-Navarro, Max Delbru ¨ ck Center for Molecular Medicine, Germany Received November 5, 2012; Accepted March 22, 2013; Published April 30, 2013 Copyright: ß 2013 Singh et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The authors acknowledge Department of Biotechnology (DBT), Department of Science and Technology (DST) and Council for Scientific and Industrial Research (CSIR), INDIA for funding the research in GKP’s lab. AS and PK acknowledge senior research fellowship from CSIR, 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. * E-mail: gkpandey@south.du.ac.in Introduction Lipid signaling is one of the major signaling networks triggered in plants as an adaptive response upon exposure to various environmental cues and stress stimuli. Initial impact of a stress stimulus usually happens on the cell membrane and it leads to the hydrolysis of membrane lipids. This process is mediated by phospholipases as various stress stimuli activate phospholipase enzymes, which then catalyse the initial step of phospholipid breakdown and leads to generation of multiple lipid-derived second messengers [1–3]. Phospholipase C (PLC) constitutes an important group of lipid hydrolysing enzymes in animals and plants. Two major categories of PLCs have been identified in the plants based on their affinities to different substrates. A well- studied group of phosphatidylinositol-specific PLCs (PI-PLCs), which specifically act upon phosphatidylinositides (PIP 2 ) at the membrane and results in the generation of second messengers such as diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP 3 ). In animals, DAG remains attached to the membrane and it activates protein kinase C (PKC) and IP 3 is released into the cytoplasm where it bind to the ligand gated Ca 2+ channel (IP 3 receptors) in the intracellular membranes and leads to the release of Ca 2+ from the intracellular reservoirs [4]. However, plant cell lack the equivalents of animal PKC and IP 3 receptors, therefore the exact function of PLC reaction products DAG and IP 3 remains enigmatic in plants. Rather, it has been postulated that the phosphorylated products of DAG i.e. phosphatidic acid (PA) and diacylglycerol pyrophosphate (DGPP), and hexakisphosphate (IP 6 ), which is the phosphorylated product of IP 3 may function as second messengers in plants [5–10]. Another recently identified class of PLCs in plants is phosphatidylcholine-PLC (PC-PLC), which preferentially hydrolyse phosphatidylcholine (PC) but can also act upon other lipids such as phosphatidylethanolamine (PE) and PLOS ONE | www.plosone.org 1 April 2013 | Volume 8 | Issue 4 | e62494