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

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 A 1 (PLA 1), 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 th

Chromosomal localization of PLA genes on 12 chromosomes of rice.

<p>Genes from different PLA classes have been mapped by their position on 12 chromosomes. Dashed red lines join the genes, lying on duplicated segments of the genome. Tandemly duplicated genes are joined with vertical green lines. Chromosomes are grouped randomly to show the duplication with clarity. No PLA gene was localized to chromosome 4. Respective chromosome numbers are mentioned at the bottom.</p

Features of PLAs in the rice genome.

<p>Features of PLAs in the rice genome.</p

Validation of microarray expression profiles for selected PLA candidate genes by quantitative RT-PCR.

<p>Real time PCR and microarray analysis was performed taking two and three biological replicates, respectively. Standard error bars have been shown for data obtained both from microarray and real time PCR. Y-axis represents raw expression values from microarray and normalized expression value from real time PCR and X-axis shows different experimental conditions; purple bars represent the expression from microarrays, while brown bars represent the real-time PCR values.</p

Phylogenetic relationship between rice and <i>Arabidopsis</i> PLA superfamily.

<p>An un-rooted neighbor-joining tree was made from the total protein sequences of rice and <i>Arabidopsis</i> PLAs (PLA₁, pPLA and sPLA₂). Multiple sequence alignment was done using clustalX 2.0.8 and tree was generated using MEGA5. PLAs from rice and <i>Arabidopsis</i> are grouped, based on the bootstrap support value ≥50%. Scale bar represents 0.1 amino acid substitutions per site.</p

Expression profiles of rice PLA superfamily.

<p>Different PLA class expression has been represented by a separate heat map. Reproductive development comprising six stages of panicle [P1 (0–3 cm), P2 (3–5 cm), P3 (5–10 cm), P4 (10–15 cm), P5 (15–22 cm), and P6 (22–30 cm)] and five stages of seed [S1 (0–2 DAP), S2 (3–4 DAP), S3 (4–10 DAP), S4 (11–20 DAP) and S5 (21–29 DAP)]. Clustering of the expression profile was done with log transformed average values taking mature leaf as base line. Three experimental stress conditions are denoted as C: Cold Stress, D: Drought Stress, S: Salt Stress and SL: control, seven day old unstressed seedling. A gene is considered differentially expressed during reproductive development if up- or down-regulated at least two-fold, with respect to the three vegetative controls (mature leaf, root and 7- day old seedling) and with respect to the seven day old unstressed seedling in case of abiotic stress. The color scale at the bottom of each heat map is given in log₂ intensity value.</p