Jayita Saha

Polyamines as redox homeostasis regulators during salt stress in plants

The balance between accumulation of stress-induced polyamines and reactive oxygen species (ROS) is arguably a critical factor in plant tolerance to salt stress. Polyamines are compounds, which accumulate in plants under salt stress and help maintain cellular ROS homeostasis. In this review we first outline the role of polyamines in mediating salt stress responses through their modulation of redox homeostasis. The two proposed roles of polyamines in regulating ROS – as antioxidative molecules and source of ROS synthesis – are discussed and exemplified with recent studies. Second, the proposed function of polyamines as modulators of ion transport is discussed in the context of plant salt stress. Finally, we highlight the apparent connection between polyamine accumulation and programmed cell death induction during stress. Thus polyamines have a complex functional role in regulating cellular signaling and metabolism during stress. By focusing future efforts on how polyamine accumulation and turnover is regulated, research in this area may provide novel targets for developing stress tolerance.

Genome-wide analysis and evolutionary study of sucrose non-fermenting 1-related protein kinase 2 (SnRK2) gene family members in Arabidopsis and Oryza.

The over-expression of plant specific SnRK2 gene family members by hyperosmotic stress and some by abscisic acid is well established. In this report, we have analyzed the evolution of SnRK2 gene family in different plant lineages including green algae, moss, lycophyte, dicot and monocot. Our results provide some evidences to indicate that the natural selection pressure had considerable influence on cis-regulatory promoter region and coding region of SnRK2 members in Arabidopsis and Oryza independently through time. Observed degree of sequence/motif conservation amongst SnRK2 homolog in all the analyzed plant lineages strongly supported their inclusion as members of this family. The chromosomal distributions of duplicated SnRK2 members have also been analyzed in Arabidopsis and Oryza. Massively Parallel Signature Sequencing (MPSS) database derived expression data and the presence of abiotic stress related promoter elements within the 1 kb upstream promoter region of these SnRK2 family members further strengthen the observations of previous workers. Additionally, the phylogenetic relationships of SnRK2 have been studied in all plant lineages along with their respective exon-intron structural patterns. Our results indicate that the ancestral SnRK2 gene of land plants gradually evolved by duplication and diversification and modified itself through exon-intron loss events to survive under environmental stress conditions.

Human GMDS gene fragment hypermethylation in chronic high level of arsenic exposure with and without arsenic induced cancer.

Arsenic, though a poor mutagen, is an accepted environmental carcinogen. Perturbation of DNA methylation pattern leading to aberrant gene expression has been hypothesized as the mechanism for arsenic induced carcinogenesis. We had earlier demonstrated the hypermethylation of promoter region of p53 and p16 genes in persons exposed to different doses of arsenic. Till now no genomic hot spot has been identified which is frequently hypermethylated or hypomethylated in persons chronically exposed to environmental arsenic. In the present work, we have identified one hypermethylated sequence by methyl-sensitive arbitrarily primed polymerase chain reaction in the peripheral blood leukocyte DNA of chronically arsenic exposed persons with and without arsenic induced skin cancer. The sequence is from GMDS gene responsible for fucose metabolism. Southern hybridization of the sequence to the amplification products of methyl sensitive restriction enzyme digested genome of persons exposed to different doses of arsenic indicated that methylation increased in a dose dependent manner.

In silico characterization and evolutionary analyses of CCAAT binding proteins in the lycophyte plant Selaginella moellendorffii genome: A growing comparative genomics resource

NF-Y transcription factors encoded by HAP gene family, composed of three subunits (HAP2/NF-YA, HAP3/NF-YB and HAP5/NF-YC), are capable of transcriptional regulation of target genes with high specificity by binding to the CCAAT-containing promoter sequences. Here, we have characterized duplicated HAP genes in Selaginella moellendorffii and explored some features that might be involved in the regulation of gene expression and their function. Subsequently, the evolutionary relationships of LEC1-type of HAP3 genes have been studied starting from lycophytes to angiosperm to reveal the details of conservation and diversification of these genes during plant evolution. Computational analyses demonstrated the variation in length of cis-regulatory region of HAP3 duplicates in S. moellendorffii containing three thermodynamically stable and evolutionarily conserved RNA secondary structures. The homology modeling of NF-Y proteins, secondary structural details, DNA binding large positive patches, binding affinity of H2A-H2B interactive residues of NF-YC subunits on the duplicated NF-YB subunits, conserved domain analyses and protein structural alignments indicated that gene duplication process of HAP genes in S. moellendorffii, followed by structural diversification, provide specific hints about their functional specificity under various circumstances for the survival of this lycophytic plant. We have identified several conserved motifs in LEC1 proteins among all plant lineages during evolution.

The Attributes of RNA Interference in Relation to Plant Abiotic Stress Tolerance

Micro RNAs are small non coding RNA molecule that plays a vital role in post transcriptional gene regulation by either translational repression or by inducing mRNA cleavage. These small non coding RNAs have emerged as one of the master regulators of plant growth and development. Recent studies have revealed their role in abiotic stress responses. Expression level of several miRNA changes when exposed to drought, salinity, temperature variations and oxidative environment resulting in modulation of the expression of target genes that are associated with stress response. This review aims to focus on the regulatory role of plant micro RNAs during abiotic stress.

Molecular phylogenomic study and the role of exogenous spermidine in the metabolic adjustment of endogenous polyamine in two rice cultivars under salt stress

Compelling evidences anticipated the well acclamation of involvement of exogenous and endogenous polyamines (PAs) in conferring salt tolerance in plants. Intracellular PAs anabolism and catabolism should have contributed to maintain endogenous PAs homeostasis to induce stress signal networks. In this report, the evolutionary study has been conducted to reveal the phylogenetic relationship of genes encoding enzymes of the anabolic and catabolic pathway of PAs among the five plant lineages including green algae, moss, lycophyte, dicot and monocot along with their respective exon-intron structural patterns. Our results indicated that natural selection pressure had considerable influence on the ancestral PA metabolic pathway coding genes of land plants. PA metabolic genes have undergone gradual evolution by duplication and diversification process leading to subsequent structural modification through exon-intron gain and loss events to acquire specific function under environmental stress conditions. We have illuminated on the potential regulation of both the pathways by investigating the real-time expression analyses of PA metabolic pathway related enzyme coding genes at the transcriptional level in root and shoot tissues of two indica rice varieties, namely IR 36 (salt sensitive) and Nonabokra (salt-tolerant) in response to salinity in presence or absence of exogenous spermidine (Spd) treatment. Additionally, we have performed tissue specific quantification of the intracellular PAs and tried to draw probable connection between the PA metabolic pathway activation and endogenous PAs accumulation. Our results successfully enlighten the fact that how exogenous Spd in presence or absence of salt stress adjust the intracellular PA pathways to equilibrate the cellular PAs that would have been attributed to plant salt tolerance.

Polyamines: Osmoprotectants in Plant Abiotic Stress Adaptation

Environmental stress is one of the major threats affecting the living world. The most crucial function of plant is to induce different regulatory self-defence pathways in response to stress. Abiotic stresses such as drought, high temperature and salinity cause rapid depletion of cellular water leading to loss of crops and agricultural productivity worldwide. On exposure to these prevalent stresses, plant accumulates several polyhydroxylic compounds and zwitterionic alkylamines commonly known as osmolytes or compatible solutes. These are low molecular weight water soluble compounds providing stress tolerance when accumulated without hindering cellular mechanisms. Genes involved in the biosynthetic pathways of different osmolytes have been identified from various sources. Genetic engineering utilising these endogenous genes has resulted in development of transgenic varieties with better adaptability towards stress. Polyamines are ubiquitous biogenic amines that have been implicated in diverse cellular functions. The protective role of plant polyamines as osmolytes is still controversial and needs further investigation. However, there are some reports that suggest functional similarities between polyamines and other osmolytes commonly found in plant defence mechanism. Functions include protection of macromolecules, cellular pH maintenance, ROS scavenging, stabilisation of native protein structure, etc. Apart from these direct functions, exogenous application of polyamines results in the elevation of endogenous level of different osmolytes. Thus, polyamines play an indirect role in plant abiotic stress tolerance by participating in osmolyte synthesis in response to stress. In this review, we have dissected the role of polyamines as osmoprotectants.

In silico characterization and evolutionary analyses of CCAAT binding proteins in the lycophyte plant Selaginella moellendorffii genome

NF-Y transcription factors encoded by HAP gene family, composed of three subunits (HAP2/NF-YA, HAP3/NF-YB and HAP5/NF-YC), are capable of transcriptional regulation of target genes with high specificity by binding to the CCAAT-containing promoter sequences. Here, we have characterized duplicated HAP genes in Selaginella moellendorffii and explored some features that might be involved in the regulation of gene expression and their function. Subsequently, the evolutionary relationships of LEC1-type of HAP3 genes have been studied starting from lycophytes to angiosperm to reveal the details of conservation and diversification of these genes during plant evolution. Computational analyses demonstrated the variation in length of cis-regulatory region of HAP3 duplicates in S. moellendorffii containing three thermodynamically stable and evolutionarily conserved RNA secondary structures. The homology modeling of NF-Y proteins, secondary structural details, DNA binding large positive patches, binding affinity of H2A-H2B interactive residues of NF-YC subunits on the duplicated NF-YB subunits, conserved domain analyses and protein structural alignments indicated that gene duplication process of HAP genes in S. moellendorffii, followed by structural diversification, provide specific hints about their functional specificity under various circumstances for the survival of this lycophytic plant. We have identified several conserved motifs in LEC1 proteins among all plant lineages during evolution.

Brief communication: In silico characterization and evolutionary analyses of CCAAT binding proteins in the lycophyte plant Selaginella moellendorffii genome: A growing comparative genomics resource

NF-Y transcription factors encoded by HAP gene family, composed of three subunits (HAP2/NF-YA, HAP3/NF-YB and HAP5/NF-YC), are capable of transcriptional regulation of target genes with high specificity by binding to the CCAAT-containing promoter sequences. Here, we have characterized duplicated HAP genes in Selaginella moellendorffii and explored some features that might be involved in the regulation of gene expression and their function. Subsequently, the evolutionary relationships of LEC1-type of HAP3 genes have been studied starting from lycophytes to angiosperm to reveal the details of conservation and diversification of these genes during plant evolution. Computational analyses demonstrated the variation in length of cis-regulatory region of HAP3 duplicates in S. moellendorffii containing three thermodynamically stable and evolutionarily conserved RNA secondary structures. The homology modeling of NF-Y proteins, secondary structural details, DNA binding large positive patches, binding affinity of H2A-H2B interactive residues of NF-YC subunits on the duplicated NF-YB subunits, conserved domain analyses and protein structural alignments indicated that gene duplication process of HAP genes in S. moellendorffii, followed by structural diversification, provide specific hints about their functional specificity under various circumstances for the survival of this lycophytic plant. We have identified several conserved motifs in LEC1 proteins among all plant lineages during evolution.