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

Abstract

BackgroundPhospholipase 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 FindingsA 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/SignificanceThe comprehensive analysis and expression profiling would provide a critical platform for the functional characterization of the candidate PLA genes in crop plants.

A Small Phospholipase A2-α from Castor Catalyzes the Removal of Hydroxy Fatty Acids from Phosphatidylcholine in Transgenic Arabidopsis Seeds

“…The rice sPLA 2 a protein fused to GFP was shown to colocalize with an ER marker (Singh et al, 2012). This result is consistent with our finding that recombinant RcsPLA 2 a produced in yeast showed high activity in the microsomal fraction of cell homogenates (Supplemental Fig.…”

“…This gene encodes an enzyme of the small PLA 2 family, RcsPLA 2 a. sPLA 2 a homologs have been identified in Arabidopsis, rice, and several other plant species (Ståhl et al, 1999;Lee et al, 2005;Singh et al, 2012). The rice sPLA 2 a is strongly expressed in seeds and other tissues (Singh et al, 2012), while the Arabidopsis homolog is not highly expressed in developing seeds (Supplemental Table S1). AtPLA 2 a is expressed in vegetative tissues, and the encoded enzyme likely acts in lipid signaling .…”

“…S1), but the activity in the highspeed supernatant also was high. The RcsPLA 2 a protein has a C-terminal sequence, -LHKP, that is identical to the sequence in the rice protein (Singh et al, 2012), and this may constitute the ER retention signal. Alternatively, protein acylation has been suggested as a potential mechanism for localization to the ER (Ståhl et al, 1999).…”

“…2). In relation to subcellular localization, both Arabidopsis homologs AtsPLA 2 a and AtsPLA 2 b and the rice homolog OssPLA 2 a possess signal sequences as predicted by PSORT (http://psort.hgc.jp) and have been localized previously to the endoplasmic reticulum (ER) or Golgi (Seo et al, 2008;Matos and Pham-Thi, 2009;Lee et al, 2010;Singh et al, 2012). A common motif (-LHKP) is found at the C terminus of both the rice and castor sPLA 2 a sequences, constituting a putative ER retention signal (Singh et al, 2012).…”

“…In relation to subcellular localization, both Arabidopsis homologs AtsPLA 2 a and AtsPLA 2 b and the rice homolog OssPLA 2 a possess signal sequences as predicted by PSORT (http://psort.hgc.jp) and have been localized previously to the endoplasmic reticulum (ER) or Golgi (Seo et al, 2008;Matos and Pham-Thi, 2009;Lee et al, 2010;Singh et al, 2012). A common motif (-LHKP) is found at the C terminus of both the rice and castor sPLA 2 a sequences, constituting a putative ER retention signal (Singh et al, 2012). RcsPLA 2 a and RcsPLA 2 b were cloned from a castor endosperm complementary DNA (cDNA) library, introduced into the expression vector pGate-DsRed-Phas (Lu et al, 2006), and expressed under the control of the seed-specific phaseolin promoter (Slightom et al, 1983) in the Arabidopsis CL37 line.…”