The psbE-F-L-J operon from chloroplast genome of Populus deltoides: Cloning, nucleotide sequence and transcript analysis

A 5-5-kbp HindIII fragment carrying psbE-F-L-J operon from the chloroplast DNA of Populus deltoides was cloned and nucleotide sequence was determined for a 1672-bp region. The coding regions showed more than 90% homology at nucleotide sequence level with plastid-encoded psbE, psbF, psbL and psbJ genes of higher plants. Pairwise alignments of psbE, psbF, psbL and psbJ coding regions of poplar with published sequences from other plants were carried out to analyse the nature of nucleotide substitutions. The 5' and 3' untranslated regions of the genes revealed high variability among different organisms both in terms of homology and the number of nucleotides. Northern hybridization data indicated that all four genes of psbE-F-L-J operon were transcribed as a single tetracistronic message which was not subjected to further processing into smaller transcripts. The transcript showed quantitative increase in mature leaves

Transcriptomic and metabolomic shifts in rice roots in response to Cr (VI) stress

<p>Abstract</p> <p>Background</p> <p>Widespread use of chromium (Cr) contaminated fields due to careless and inappropriate management practices of effluent discharge, mostly from industries related to metallurgy, electroplating, production of paints and pigments, tanning, and wood preservation elevates its concentration in surface soil and eventually into rice plants and grains. In spite of many previous studies having been conducted on the effects of chromium stress, the precise molecular mechanisms related to both the effects of chromium phytotoxicity, the defense reactions of plants against chromium exposure as well as translocation and accumulation in rice remain poorly understood.</p> <p>Results</p> <p>Detailed analysis of genome-wide transcriptome profiling in rice root is reported here, following Cr-plant interaction. Such studies are important for the identification of genes responsible for tolerance, accumulation and defense response in plants with respect to Cr stress. Rice root metabolome analysis was also carried out to relate differential transcriptome data to biological processes affected by Cr (VI) stress in rice. To check whether the Cr-specific motifs were indeed significantly over represented in the promoter regions of Cr-responsive genes, occurrence of these motifs in whole genome sequence was carried out. In the background of whole genome, the lift value for these 14 and 13 motifs was significantly high in the test dataset. Though no functional role has been assigned to any of the motifs, but all of these are present as promoter motifs in the Database of orthologus promoters.</p> <p>Conclusion</p> <p>These findings clearly suggest that a complex network of regulatory pathways modulates Cr-response of rice. The integrated matrix of both transcriptome and metabolome data after suitable normalization and initial calculations provided us a visual picture of the correlations between components. Predominance of different motifs in the subsets of genes suggests the involvement of motif-specific transcription modulating proteins in Cr stress response of rice.</p

Glutathione S-Transferases: Role in Combating Abiotic Stresses Including Arsenic Detoxification in Plants

Arsenic (As), naturally occurring metalloid and a potential hazardous material, is found in low concentrations in the environment and emerges from natural sources and anthropogenic activities. The presence of As in ground water, which is used for irrigation, is a matter of great concern since it affects crop productivity and contaminates food chain. In plants, As alters various metabolic pathways in cells including the interaction of substrates/enzymes with the sulfhydryl groups of proteins and the replacement of phosphate in ATP for energy. In addition, As stimulates the generation of free radicals and reactive oxygen species (ROS), resulting in oxidative stress. Glutathione S-transferases (GSTs) quench reactive molecules with the addition of glutathione (GSH) and protect the cell from oxidative damage. GSTs are a multigene family of isozymes, known to catalyze the conjugation of GSH to miscellany of electrophilic and hydrophobic substrates. GSTs have been reported to be associated with plant developmental processes and are responsive to multitude of stressors. In past, several studies suggested involvement of plant GST gene family in As response due to the requirement of sulfur and GSH in the detoxification of this toxic metalloid. This review provides updated information about the role of GSTs in abiotic and biotic stresses with an emphasis on As uptake, metabolism, and detoxification in plants. Further, the genetic manipulations that helped in enhancing the understanding of the function of GSTs in abiotic stress response and heavy metal detoxification has been reviewed

Plastid gene expression is not associated with midday depression in CO<SUB>2</SUB> assimilation and electron transport

To investigate the effect of diurnal variations on chloroplastic electron transport as well as accumulation of gene products associated with it, studies were carried out on Populus deltoides, a tree species. Electron transport studies showed two peak responses as a large diurnal change with pronounced midday depression in whole chain (H<SUB>2</SUB>O&#8594; MV) as well as partial reactions for PSII (H<SUB>2</SUB>O&#8594; PBQ) and PSI (DCPIP&#8594; MV). The electron transport rates first increased from 05:00 h to a maximum at around 09:00 h and then showed a decrease at 13:00 h followed by recovery and further decrease. The pigments associated with electron transport chain did not show any change during the day. Surprisingly midday depression in the accumulation of transcripts and polypeptides related to electron transport was not observed. This suggests that chloroplastic gene expression is not associated with the midday depression observed for both CO<SUB>2</SUB> assimilation and electron transport. Studies on the transcripts of psbD/C operon during the day showed that there were differences in the processing pattern although the steady state levels of the processed transcripts of this operon did not show any variation

Organization and post-transcriptional processing of the psb B operon from chloroplasts of Populus deltoides

Chloroplast genes are typically organized into polycistronic transcription units that give rise to complex sets of mono- and oligo-cistronic overlapping RNAs through a series of processing steps. The psbB operon contains genes for the PSII (psbB, psbT, psbH) and cytochrome b6f (petB and petD) complexes which are needed in different amounts during chloroplast biogenesis. The functional significance of gene organization in this polycistronic unit, containing information for two different complexes, is not known and is of interest. To determine the organization and expression of these complexes, studies have been carried out on crop plants by different groups, but not much information is known about trees. We present the nucleotide sequences of PSII genes and RNA profiles of the genes located in the psbB operon from Populus deltoides, a tree species. Although the gene organization of this operon in P. deltoides is similar to that in other species, a few variations have been observed in the processing scheme

Cloning and nucleotide sequence analysis ofpsbD/C operon from chloroplasts of Populus deltoides

We report the cloning and nucleotide sequence analysis of psbD/C operon from a dicotyledonous tree species,Populus deltoides (poplar). The coding regions of psbD and psbC and deduced amino acid sequences show very high homology with those from other higher plants. In pairwise alignment of the gene sequences,P. deltoides clustered with dicotyledonous annuals rather than with Pinus, the only other tree whose psbD/C nucleotide sequence is available. Comparison of several reported sequences showed that synonymous substitutions were distributed in both psbD and psbC uniformly, throughout the length of the genes. The frequency of nonsynonymous substitutions located in the amino-terminal end of psbD was distinctly higher, suggesting a lower degree of structural constraints in this region of the encoded D2 protein. The arrangement of reading frames and Northern analysis suggest that organization and expression of psbD/C operon in P. deltoides is similar to that in other higher plants

Plants and endophytes interaction: a “secret wedlock” for sustainable biosynthesis of pharmaceutically important secondary metabolites

Abstract Many plants possess immense pharmacological properties because of the presence of various therapeutic bioactive secondary metabolites that are of great importance in many pharmaceutical industries. Therefore, to strike a balance between meeting industry demands and conserving natural habitats, medicinal plants are being cultivated on a large scale. However, to enhance the yield and simultaneously manage the various pest infestations, agrochemicals are being routinely used that have a detrimental impact on the whole ecosystem, ranging from biodiversity loss to water pollution, soil degradation, nutrient imbalance and enormous health hazards to both consumers and agricultural workers. To address the challenges, biological eco-friendly alternatives are being looked upon with high hopes where endophytes pitch in as key players due to their tight association with the host plants. The intricate interplay between plants and endophytic microorganisms has emerged as a captivating subject of scientific investigation, with profound implications for the sustainable biosynthesis of pharmaceutically important secondary metabolites. This review delves into the hidden world of the "secret wedlock" between plants and endophytes, elucidating their multifaceted interactions that underpin the synthesis of bioactive compounds with medicinal significance in their plant hosts. Here, we briefly review endophytic diversity association with medicinal plants and highlight the potential role of core endomicrobiome. We also propose that successful implementation of in situ microbiome manipulation through high-end techniques can pave the way towards a more sustainable and pharmaceutically enriched future

Arsenomics: Omics of Arsenic Metabolism in Plants

AbstractArsenic (As) contamination of drinking water and groundwater used for irrigation can lead to contamination of the food chain and poses serious health risk to people worldwide. To reduce As intake through the consumption of contaminated food, identification of the mechanisms for As accumulation and detoxification in plant is a prerequisite to develop efficient phytoremediation methods and safer crops with reduced As levels. Transcriptome, proteome and metabolome analysis of any organism reflects the total biological activities at any given time which are responsible for the adaptation of the organism to the surrounding environmental conditions. As these approaches are very important in analyzing plant As transport and accumulation, we termed Arsenomics as approach which deals transcriptome, proteome and metabolome alterations during As exposure. Although, various studies have been performed to understand modulation in transcriptome in response to As, many important questions need to be addressed regarding the translated proteins of plants at proteomic and metabolomic level, resulting in various ecophysiological responses. In this review, the comprehensive knowledge generated in this area has been compiled and analyzed. There is a need to strengthen Arsenomics which will lead to develop of tools to develop As-free plants for safe consumption