Protein phosphatase complement in rice: genome-wide identification and transcriptional analysis under abiotic stress conditions and reproductive development

<p>Abstract</p> <p>Background</p> <p>Protein phosphatases are the key components of a number of signaling pathways where they modulate various cellular responses. In plants, protein phosphatases constitute a large gene family and are reportedly involved in the regulation of abiotic stress responses and plant development. Recently, the whole complement of protein phosphatases has been identified in <it>Arabidopsis </it>genome. While PP2C class of serine/threonine phosphatases has been explored in rice, the whole complement of this gene family is yet to be reported.</p> <p>Results</p> <p><it>In silico </it>investigation revealed the presence of 132-protein phosphatase-coding genes in rice genome. Domain analysis and phylogenetic studies of evolutionary relationship categorized these genes into PP2A, PP2C, PTP, DSP and LMWP classes. PP2C class represents a major proportion of this gene family with 90 members. Chromosomal localization revealed their distribution on all the 12 chromosomes, with 42 genes being present on segmentally duplicated regions and 10 genes on tandemly duplicated regions of chromosomes. The expression profiles of 128 genes under salinity, cold and drought stress conditions, 11 reproductive developmental (panicle and seed) stages along with three stages of vegetative development were analyzed using microarray expression data. 46 genes were found to be differentially expressing in 3 abiotic stresses out of which 31 were up-regulated and 15 exhibited down-regulation. A total of 82 genes were found to be differentially expressing in different developmental stages. An overlapping expression pattern was found for abiotic stresses and reproductive development, wherein 8 genes were up-regulated and 7 down-regulated. Expression pattern of the 13 selected genes was validated employing real time PCR, and it was found to be in accordance with the microarray expression data for most of the genes.</p> <p>Conclusions</p> <p>Exploration of protein phosphatase gene family in rice has resulted in the identification of 132 members, which can be further divided into different classes phylogenetically. Expression profiling and analysis indicate the involvement of this large gene family in a number of signaling pathways triggered by abiotic stresses and their possible role in plant development. Our study will provide the platform from where; the expression pattern information can be transformed into molecular, cellular and biochemical characterization of members belonging to this gene family.</p

Antisense expression of a gene encoding a calcium-binding protein in transgenic tobacco leads to altered morphology and enhanced chlorophyll

Entamoeba histolytica contains a novel calcium-binding protein like calmodulin, which was discovered earlier, and we have reported the presence of its homologue(s) and a dependent protein kinase in plants. To understand the functions of these in plants, a cDNA encoding a calcium-binding protein isolated from Entamoeba histolytica (EhCaBP) was cloned into vector pBI121 in antisense orientation and transgenic tobacco plants were raised. These plants showed variation in several phenotypic characters, of which two distinct features, more greenness and leaf thickness, were inherited in subsequent generations. The increase in the level of total chlorophyll in different plants ranged from 60% to 70%. There was no major change in chloroplast structure and in the protein level of D1, D2, LHCP and RuBP carboxylase. These morphological changes were not seen in antisense calmodulin transgenic tobacco plants, nor was the calmodulin level altered in EhCaBP antisense plants

CIFKAS A Measurer of Functional Disability Status in Knee Osteoarthritis

Knee osteoarthritis (OA) results in structural and functional abnormalities and reduced functional performance abilities. In developing countries majority of population lives in rural areas having limited resources and socio-cultural biodiversity. Their personal, socio-cultural and occupational habits vary and need to be addressed. So a culturally relevant and contextually appropriate, Composite Indian Functional Knee Assessment Scale (CIFKAS) for measuring the functional status in knee osteoarthritis was formulated. 128 participants from various geographical regions of India of age range 40 to 60 years using convenient sampling were included and informed consent signed by the participants. Each participant was assigned to one of the two groups. 39 participants in group A reported no episode of knee pain while 89 participants in group B reported at least one episode of knee pain in the last two months. Each participant was assessed on Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) and CIFKAS and statistical analysis was done. The Pearson correlation coefficient calculated for all 128 subjects for pain, physical functional abilities and total functional disability score were 0.878, 0.925 and 0.945 respectively. Between group analysis was done using Independent t test and p value was found to be not significant for pain (&le;178), highly significant for physical functional abilities (p&le;0001) and very significant for total functional disability status score (p&le;004). The results indicate that both WOMAC and CIFKAS are highly correlated and there is no difference between the two for measuring pain, but for functional ability and overall functional disability status within their functional context, CIFKAS is a better tool than WOMAC.KEYWORDS: Knee osteoarthritis; Functional disability; Socio-cultural biodiversities; Functional contextInternet Journal of Medical Update 2012 January;7(1):47-5

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

An Intergenic Region Shared by At4g35985 and At4g35987 in Arabidopsis Thaliana is a Tissue Specific and Stress Inducible Bidirectional Promoter Analyzed in Transgenic Arabidopsis and Tobacco Plants

On chromosome 4 in the Arabidopsis genome, two neighboring genes (calmodulin methyl transferase At4g35987 and senescence associated gene At4g35985) are located in a head-to-head divergent orientation sharing a putative bidirectional promoter. This 1258 bp intergenic region contains a number of environmental stress responsive and tissue specific cis-regulatory elements. Transcript analysis of At4g35985 and At4g35987 genes by quantitative real time PCR showed tissue specific and stress inducible expression profiles. We tested the bidirectional promoter-function of the intergenic region shared by the divergent genes At4g35985 and At4g35987 using two reporter genes (GFP and GUS) in both orientations in transient tobacco protoplast and Agro-infiltration assays, as well as in stably transformed transgenic Arabidopsis and tobacco plants. In transient assays with GFP and GUS reporter genes the At4g35985 promoter (P85) showed stronger expression (about 3.5 fold) compared to the At4g35987 promoter (P87). The tissue specific as well as stress responsive functional nature of the bidirectional promoter was evaluated in independent transgenic Arabidopsis and tobacco lines. Expression of P85 activity was detected in the midrib of leaves, leaf trichomes, apical meristemic regions, throughout the root, lateral roots and flowers. The expression of P87 was observed in leaf-tip, hydathodes, apical meristem, root tips, emerging lateral root tips, root stele region and in floral tissues. The bidirectional promoter in both orientations shows differential up-regulation (2.5 to 3 fold) under salt stress. Use of such regulatory elements of bidirectional promoters showing spatial and stress inducible promoter-functions in heterologous system might be an important tool for plant biotechnology and gene stacking applications

Abiotic Stress Signaling in Plants: Functional Genomic Intervention

Abiotic stresses such as high temperature, low-temperature, drought and salinity limit crop productivity worldwide. Understanding plant responses to these stresses is essential for rational engineering of crop plants. In Arabidopsis, the signal transduction pathways for abiotic stresses, light, several phytohormones and pathogenesis have been elucidated. A significant portion of plant genomes (Arabidopsis and rice were mostly studied) encodes for proteins involves in signaling such as receptor, sensors, kinases, phosphatases, transcription factors and transporters/channels. Despite decades of physiological and molecular effort, knowledge pertaining to how plants sense and transduce low and high temperature, low-water availability (drought), water-submergence, microgravity and salinity signals is still a major question for plant biologist. One major constraint hampering our understanding of these signal transduction processes in plants has been the lack or slow pace of application of molecular genomic and genetics knowledge in the form of gene function. In the post-genomic era, one of the major challenges is investigation and understanding of multiple genes and gene families regulating a particular physiological and developmental aspect of plant life cycle. One of the important physiological processes is regulation of stress response, which leads to adaptation or adjustment in response to adverse stimuli. With the holistic understanding of the signaling pathways involving not only one gene family but multiple genes or gene families, plant biologist can lay a foundation for designing and generating future crops, which can withstand the higher degree of environmental stresses (especially abiotic stresses, which are the major cause of crop loss throughout the world) without losing crop yield and productivity. Therefore, in this e-Book, we intend to incorporate the contribution from leading plant biologists to elucidate several aspects of stress signaling by functional genomics approaches

The UNC-53-mediated InteractomeAnalysis of its Role in the Generation of the C. elegans Connectome /

VI, 87 p. 15 illus., 14 illus. in color.online re

Calcium- and salt-stress signaling in plants: shedding light on SOS pathway

As salt stress imposes a major environmental threat to agriculture, understanding the basic physiology and genetics of cell under salt stress is crucial for developing any transgenic strategy. Salt Overly Sensitive (SOS) genes (SOS1-SOS3) were isolated through positional cloning. Since sos mutants are hypersensitive to salt, their characterization resulted in the discovery of a novel pathway, which has helped in our understanding the mechanism of salt-stress tolerance in plants. Genetic analysis confirmed that SOS1-SOS3 function in a common pathway of salt tolerance. This pathway also emphasizes the significance of Ca<SUP>2+</SUP> signal in reinstating cellular ion homeostasis. SOS3, a Ca<SUP>2+</SUP> sensor, transduces the signal downstream after activating and interacting with SOS2 protein kinase. This SOS3-SOS2 complex activates the Na<SUP>+</SUP>/H<SUP>+</SUP> antiporter activity of SOS1 thereby reestablish cellular ion homeostasis. Recently, SOS4 and SOS5 have also been characterized. SOS4 encodes a pyridoxal (PL) kinase that is involved in the biosynthesis of pyridoxal-5-phosphate (PLP), an active form of vitamin B6. SOS5 has been shown to be a putative cell surface adhesion protein that is required for normal cell expansion. Under salt stress, the normal growth and expansion of a plant cell becomes even more important and SOS5 helps in the maintenance of cell wall integrity and architecture. In this review we focus on the recent advances in salt stress and SOS signaling pathway. A broad coverage of the discovery of SOS mutants, structural aspect of these genes and the latest developments in the field of SOS1-SOS5 has been described