Evolution of the RNA-dependent RNA polymerase (RdRP) genes: Duplications and possible losses before and after the divergence of major eukaryotic groups

Eukaryotic RNA-dependent RNA polymerases (RdRPs, encoded by RDR genes) play critical roles in developmental regulation, maintenance of genome integrity, and defense against foreign nucleic acids. However, the phylogenetic relationship of RDRs remains unclear. From available genome sequences, we identified 161 putative RDR genes from 56 eukaryotes, ranging from protists to multicellular organisms, including plants, fungi and invertebrate animals, such as nematodes, lancelet and sea anemone. On the other hand, we did not detect RDR homologs in vertebrates and insects, even though RNA interference functions in these organisms. Our phylogenetic analysis of the RDR genes suggests that the eukaryotic ancestor might have had three copies, i.e. RDRα, RDRβ and RDRγ. These three ancient copies were also supported by the patterns of protein sequence motifs. Further duplication events after the divergence of major eukaryotic groups were supported by the phylogenetic analyses, including some that likely occurred before the separation of subgroups within each kingdom. We present a model for a possible evolutionary history of RDR genes in eukaryotes.     

Characterization of mitogen activated protein kinases (MAPKs) in the Curcuma longa expressed sequence tag database

Mitogen activated protein kinase (MAPK) cascades are universal signal transduction modules that play crucial role in plant growth and development as well as biotic and abiotic stress responses. 20 and 17 MAPKs have been characterized in Arabidopsis and rice respectively, which are used for identification of the putative MAPKs in other higher plants. However, no MAPK gene sequences have yet been characterized for asexually reproducing plants. We describe the analysis of MAPK EST sequences from Curcuma longa (an asexually reproducible plant of great medicinal and economic significance). The four Curcuma MAPKs contains all 11 MAPK conserved domains and phosphorylation-activation motif, TEY. Phylogenetic analysis grouped them in the subgroup A and C as identified earlier for Arabidopsis. The Curcuma MAPKs identified showed high sequence homology to rice OsMPK3, OsMPK4 and OsMPK5 suggesting the presence of similar key element in signaling biotic and abiotic stress responses. Although further in vivo and in vitro analysis are required to establish the physiological role of Curcuma MAPKs, this study provides the base for future research on diverse signaling pathways mediated by MAPKs in Curcuma longa as well as other asexually reproducing plants.     

Survey and characterization of NBS-LRR (R) genes in Curcuma longa transcriptome

Resistance genes are among the most important gene classes for plant breeding purposes being responsible for activation of plant defense mechanisms. Among them, the nucleotide binding site-leucine rich repeat (NBS-LRR) class R-genes are the most abundant and actively found in all types of plants. Insilico characterization of EST database resulted in the detection of 28 NBS types R-gene sequences in Curcuma longa. All the 28 sequences represented the NB-ARC domain, 21 of which were found to have highly conserved motif characteristics and categorized as regular NBS genes. The Open Reading Frames varied from 361 (CL.CON.3566) to 112 (CL.CON.1267) with an average of 279 amino acids. Most alignment occurred with monocots (67.8%) with emphasis on Oryza sativa and Zingiber sequences. All best alignments with dicots occurred with Arabidopsis thaliana, Populus trichocarpa and Medicago sativa. These detected NBS type Rgenes from Curcuma longa can be used as a valuable resource for molecular marker development, molecular mapping of R-genes, and identification of resistance gene analogs and functional and evolutionary characterization of NBS-LRR-encoding resistance genes in asexually reproducing plants.     

Classification and comparative analysis of Curcuma longa L. expressed sequences tags (ESTs) encoding glycine-rich proteins (GRPs)

Glycine-rich proteins (GRPs) are a group of proteins characterized by their high content of glycine residues often occurring in repetitive blocs. The diverse expression pattern and sub cellular localization of various GRPs suggest their implication in different physiological processes. Several GRPs has been isolated and characterized from different monocots and dicots. However, little or no information is available about the structure and function of GRPs in asexually reproducing plants. In this study, in-silico analysis of expressed sequence tag database resulted in the isolation of fifty-one GRPs from Curcuma longa L., an asexually reproducible plant of great medicinal and economic significance. Phylogenetic analysis grouped the GRPs into four distinct classes based on conserved motifs and nature of glycine-rich repeats. Majority of the isolated GRPs exhibited high homology with known GRPs from other plants that are expressed in response to various stresses. The presence of high structural diversity and signal peptide in some GRPs suggest their diverse physiological role and tissue specific localization. The isolated sequences can be used as a framework for cloning, characterization and expressional analysis of GRPs in response to various biotic and abiotic stresses in Curcuma longa as well as other asexually reproducing plants.