Dipesh Kumar Trivedi

A critical review on fungi mediated plant responses with special emphasis to Piriformospora indica on improved production and protection of crops

The beneficial fungi are potentially useful in agriculture sector to avail several services to crop plants such as water status, nutrient enrichment, stress tolerance, protection, weed control and bio-control. Natural agro-ecosystem relies on fungi because of it takes part in soil organic matter decomposition, nutrient acquisition, organic matter recycling, nutrient recycling, antagonism against plant pests, and crop management. The crucial role of fungi in normalizing the toxic effects of phenols, HCN and ROS by β-CAS, ACC demainase and antioxidant enzymes in plants is well documented. Fungi also play a part in various physiological processes such as water uptake, stomatal movement, mineral uptake, photosynthesis and biosynthesis of lignan, auxins and ethylene to improve growth and enhance plant fitness to cope heat, cold, salinity, drought and heavy metal stress. Here, we highlighted the ethylene- and cyclophilin A (CypA)-mediated response of Piriformospora indica for sustainable crop production under adverse environmental conditions.

Genome wide analysis of Cyclophilin gene family from rice and Arabidopsis and its comparison with yeast

Cyclophilin proteins are the members of immunophillin group of proteins, known for their property of binding to the immune-suppressant drug cyclosporin A, hence named as cyclophilins. These proteins are characterized by the presence of peptidyl prolyl isomerase (PPIase) domain which catalyzes the cis-trans isomerisation process of proline residues. In the present study, an in-silico based approach was followed to identify and characterize the cyclophilin family from rice, Arabidopsis and yeast. We were able to identify 28 rice, 35 Arabidopsis and 8 yeast cyclophilin genes from their respective genomes on the basis of their annotation as well as the presence of highly conserved PPIase domain. The evolutionary relationship of the cyclophilin genes from the three genomes was analyzed using the phylogenetic tree. We have also classified the rice cyclophilin genes on the basis of localization of the protein in cell. The structural similarity of the cyclophilins was also analyzed on the basis of their homology model. The expression analysis performed using Genevestigator revealed a very strong stress responsive behavior of the gene family which was more prominent in later stages of stress. The study indicates the importance of the gene family in stress response as well as several developmental stages thus opening up many avenues for future study on the cyclophilin proteins.

Sequence-specific 1H, 13C and 15N NMR assignments of Cyclophilin A like protein from Piriformospora indica involved in salt stress tolerance

Cyclophilins are omnipresent proteins found in eukaryotes and prokaryotes, with presence in cytoplasm as well as in nucleus. Primary role of Cyclophilins is of peptidyl-prolyl cis–trans isomerase, a molecular chaperon action. Here, we report sequence-specific 1H, 13C and 15N resonance assignments for a Cyclophilin A like protein from Piriformospora indica. This protein is up-regulated during salt stress conditions.

Structure of RNA-interacting Cyclophilin A-like protein from Piriformospora indica that provides salinity-stress tolerance in plants

Soil salinity problems are widespread around the globe with increased risk of spreading over the years. The fungus Piriformospora indica, identified in Indian Thar desert, colonizes the roots of monocotyledon plants and provides resistance towards biotic as well as abiotic stress conditions. We have identified a cyclophilin A-like protein from P. indica (PiCypA), which shows higher expression levels during salinity stress. The transgenic tobacco plants overexpressing PiCypA develop osmotic tolerance and exhibit normal growth under osmotic stress conditions. The crystal structure and NMR spectroscopy of PiCypA show a canonical cyclophilin like fold exhibiting a novel RNA binding activity. The RNA binding activity of the protein and identification of the key residues involved in the RNA recognition is unique for this class of protein. Here, we demonstrate for the first time a direct evidence of countering osmotic stress tolerance in plant by genetic modification using a P. indica gene.

Genome-wide analysis of plant-type II Ca2+ATPases gene family from rice and Arabidopsis: Potential role in abiotic stresses

The Plant Ca(2+)ATPases are members of the P-type ATPase superfamily and play essential roles in pollen tube growth, vegetative development, inflorescence architecture, stomatal opening or closing as well as transport of Ca(2+), Mn(2+) and Zn(2+). Their role in abiotic stress adaptation by activation of different signaling pathways is emerging. In Arabidopsis, the P-type Ca(2+)ATPases can be classified in two distinct groups: type IIA (ECA) and type IIB (ACA). The availability of rice genome sequence allowed performing a genome-wide search for P-type Ca(2+)ATPases proteins, and the comparison of the identified proteins with their homologs in Arabidopsis model plant. In the present study, we identified the P-type II Ca(2+)ATPases from rice by analyzing their phylogenetic relationship, multiple alignment, cis-regulatory elements, protein domains, motifs and homology percentage. The phylogenetic analysis revealed that rice type IIA Ca(2+)ATPases clustered with Arabidopsis type IIA Ca(2+)ATPases and showed high sequence similarity within the group, whereas rice type IIB Ca(2+)ATPases presented variable sequence similarities with Arabidopsis type IIB members. The protein homology modeling, identification of putative transmembrane domains and conserved motifs of rice P-type II Ca(2+)ATPases provided information on their functions and structural architecture. The analysis of P-type II Ca(2+)ATPases promoter regions in rice showed multiple stress-induced cis-acting elements. The expression profile analysis indicated vital roles of P-type II Ca(2+)ATPases in stress signaling, plant development and abiotic stress responses. The comprehensive analysis and expression profiling provided a critical platform for functional characterization of P-type II Ca(2+)ATPase genes that could be applied in engineering crop plants with modified calcium signaling and homeostatic pathways.

Genome-wide analysis of glutathione reductase (GR) genes from rice and Arabidopsis

Plant cells and tissues remain always on risk under abiotic and biotic stresses due to increased production of reactive oxygen species (ROS). Plants protect themselves against ROS induced oxidative damage by the upregulation of antioxidant machinery. Out of many components of antioxidant machinery, glutathione reductase (GR, EC 1.6.4.2) and glutathione (GSH, γ-Glu-Cys-Gly) play important role in the protection of cell against oxidative damage. In stress condition, the GR helps in maintaining the reduced glutathione pool for strengthening the antioxidative processes in plants. Present study investigates genome wide analysis of GR from rice and Arabidopsis. We were able to identify 3 rice GR genes (LOC_Os02 g56850, LOC_Os03 g06740, LOC_Os10 g28000) and 2 Arabidopsis GR genes (AT3G54660, AT3G24170) from their respective genomes on the basis of their annotation as well as the presence of pyridine nucleotide-disulphide oxidoreductases class-I active site. The evolutionary relationship of the GR genes from rice and Arabidopsis genomes was analyzed using the multiple sequence alignment and phylogenetic tree. This revealed evolutionary conserved pyridine nucleotide-disulphide oxidoreductases class-I active site among the GR protein in rice and Arabidopsis. This study should make an important contribution to our better understanding of the GR under normal and stress condition in plants.

Multiple abiotic stress responsive rice cyclophilin: (OsCYP-25) mediates a wide range of cellular responses

Cyclophilins (CYP), a member of immunophillin group of proteins, are more often conserved in all genera including plants. Here, we report on the identification of a new cyclophilin gene OsCYP-25 (LOC_Os09 g39780) from rice which found to be upregulated in response to various abiotic stresses viz., salinity, cold, heat and drought. It has an ORF of 540 bp, encoding a protein of 179 amino acids, consisting of PPIase domain, which is highly conserved. The OsCYP-25 promoter analysis revealed that different cis-regulatory elements (e.g., MYBCORE, MYC, CBFHV, GT1GMSCAM4, DRECRTCOREAT, CCAATBOX1, WRKY71OS and WBOXATNPR1) are involved to mediate OsCYP-25 response under stress. We have also predicted interacting partners by STRING software. In interactome, protein partners includes WD domain containing protein, the 60S ribosome subunit biogenesis protein, the ribosomal protein L10, the DEAD-box helicase, the EIF-2α, YT521-B protein, the 60S ribosomal protein and the PPR repeat domain containing protein. The in silico analysis showed that OsCYP-25 interacts with different proteins involved in cell growth, differentiation, ribosome biogenesis, RNA metabolism, RNA editing, gene expression, signal transduction or stress response. These findings suggest that OsCYP-25 might perform an important function in mediating wide range of cellular response under multiple abiotic stresses.

Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of a cyclophilin A-like protein from Piriformospora indica.

Cyclophilins are widely distributed both in eukaryotes and prokaryotes and have a primary role as peptidyl-prolyl cis-trans isomerases (PPIases). This study focuses on the cloning, expression, purification and crystallization of a salinity-stress-induced cyclophilin A (CypA) homologue from the symbiotic fungus Piriformospora indica. Crystallization experiments in the presence of 56 mM sodium phosphate monobasic monohydrate, 1.34 M potassium phosphate dibasic pH 8.2 yielded crystals that were suitable for X-ray diffraction analysis. The crystals belonged to the orthorhombic space group C222(1), with unit-cell parameters a = 121.15, b = 144.12, c = 110.63 Å. The crystals diffracted to a resolution limit of 2.0 Å. Analysis of the diffraction data indicated the presence of three molecules of the protein per asymmetric unit (V(M) = 4.48 Å(3) Da(-1), 72.6% solvent content).

Response of PiCypA tobacco T2 transgenic matured plant to potential tolerance to salinity stress.

Cyclophilins are molecular chaperone act as peptidyl prolyl cis-trans isomerase responsible for protein folding and assembly in many normal cellular processes, stabilize proteins and membranes under stress conditions. Recently, we report on the role cyclophilin A-like gene from Piriformospora indica (PiCypA) in salinity stress tolerance in T1 transgenic and up to seedling stage of T2 transgenic of tobacco plants. Here, PiCypA T2 generation matured tobacco plants were evaluated under salt (200 mM NaCl) up to flowering and seed set stages. We found that PiCypA T2 tobacco lines showed comparatively better survival and exhibited higher root growth and fresh weight as compared with wild type and vector control. This study provides further direct evidence that PiCypA transgene maintained the sustainability in providing salinity stress tolerance in T2 generation of transgenic tobacco plants.

Cyclophilin: A Versatile Chaperone of Biological System

Tel: 01262393596 The functional cellular proteome machinery depends on the protein folding and unfolding within the cell. The primary amino acid sequence and the chaperone activity play a significant role in proper protein folding [1]. Chaperone interacts with nascent polypeptide and helps in proper folding and formation of stable protein complexes [2]. Molecular chaperone prevents inappropriate interand intra-molecular interactions among polypeptides. Immunophilins are the receptors for immunosuppressant drug consist of two large groups of proteins called ‘cyclophilins’ (receptors for cyclosporine A, CYPs) and FK506binding proteins (FKBPs). Cyclophilins are ubiquitous proteins found to be present in all organisms ranging from bacteria to mammals [3]. Cyclophilins are involved in a wide range of cellular processes like protein folding, protein complex stabilization, cell division, protein trafficking, cell signalling, transcriptional regulation, pre-mRNA splicing and stress tolerance [4,5].