Journal Article

Genome-wide identification, characterization and expression profiling of purple acid phosphatases under variable phosphorus regimes in lentil (Lens culinaris Medik.)

Banerjee, Joydeep, Chakraborty, Ankita, Das, Arpita

2025

Overview

Background Purple acid phosphatases, an important sub-class of metallo-phosphoesterase, play a key role in the uptake and homeostasis of phosphorus in plants, especially under phosphorus limited conditions. Phosphorus deficiency in legumes leads to an impaired growth, poor nodulation and a significant decline in yield potential. Results In this study, 22 putative purple acid phosphatase genes in Lens culinaris ( LcPAP s) were identified, distributed across seven chromosomes with chromosome 4 harbouring the highest number. In-silico analysis revealed their gene structures, physico-chemical properties, structures of the PAP proteins, and predicted sub-cellular localization. Most of the LcPAPs were found to possess a signal peptide suggesting their involvement in the secretory pathway, whereas LcPAP3 lacking any signal peptide was uniquely localized in the nucleus. Considering molecular weights, the LcPAPs clustered into three groups and were classified in five out of six clades in a phylogenetic tree constructed with PAPs from soyabean, rice and Arabidopsis . Synteny analysis of LcPAPs revealed the highest conservation with soyabean followed by Arabidopsis and least with rice, consistent with the lineage divergence of dicots and monocots that occurred million years ago. Promoter analysis of the LcPAP s revealed the presence of multiple cis elements associated with stress responsive transcription factors, including PHR1, a key regulator of phosphorus starvation response. Docking studies of the protein with ligands like para-nitrophenyl phosphate (pNPP) and phytic acid revealed the involvement of the conserved motifs and different covalent bonds in protein–ligand interaction. Gene expression analysis under differential phosphorus regimes revealed root specific upregulation of LcPAP20 , while constitutive upregulation in both root and shoot tissues of LcPAP4 annotated with oxidoreductase and phosphatase enzyme activity under low as well as high phosphorus conditions as compared to control. In contrast, LcPAP9 predicted to possess dual phosphatase-phytase activity was highly upregulated in the shoots under phosphorus deficient condition as compared to phosphorus sufficiency. Conclusions These findings provide foundational insights into the functional diversification of LcPAPs on an intricate molecular level, and might pave the way of identifying key regulatory genes of lentil involved in phosphorus homeostasis. Further in-depth bioinformatics study on LcPAPs with their two potential interactors has unravelled their potential role and binding efficacies.

• Publisher: BioMed Central,BioMed Central Ltd,BMC
• Subject: Acid Phosphatase - chemistry / Acid Phosphatase - genetics / Acid Phosphatase - metabolism / Agriculture / Analysis / Biomedical and Life Sciences / Diseases and pests / DNA binding proteins / Gene expression / Gene Expression Profiling / Gene Expression Regulation, Plant / Genetic aspects / Genome, Plant / Glycoproteins - chemistry / Glycoproteins - genetics / Glycoproteins - metabolism / Growth / Lens culinaris / Lens Plant - enzymology / Lens Plant - genetics / Lens Plant - metabolism / Lentils / Life Sciences / Metallo-phosphoesterase / Molecular docking / Phosphorus - metabolism / Phylogeny / Plant Proteins - genetics / Plant Proteins - metabolism / Plant Sciences / Purple acid phosphatases / Tree Biology