Flavonols are structurally and functionally diverse molecules playing roles in plant biotic and a... more Flavonols are structurally and functionally diverse molecules playing roles in plant biotic and abiotic stress tolerance, auxin transport inhibition, pollen development, etc. Despite their ubiquitous occurrence in land plants and multifunctionality, the effect of perturbation of flavonol biosynthesis over global gene expression and pathways other than flavonoid biosynthesis has not been studied in detail. To understand the signaling role of different flavonol metabolites, herein, we used the flavonol deficient Arabidopsis thaliana loss-of-function mutant flavonol synthase1 (fls1-3) as object of study. Comparative transcriptome and metabolic profiling were used to study the effects of genetic flavonol deficiency and exogenous supplementation with flavonol derivatives (kaempferol, quercetin and rutin) on different cellular processes in the seedling. Various flavonol biosynthesis-related regulatory and structural genes were found to be up-regulated in the fls1-3 mutant which could be r...
Abstract Wheat being an important crop is the major source of food throughout the world. The cult... more Abstract Wheat being an important crop is the major source of food throughout the world. The cultivated wheat includes Triticum aestivum and T. turgidum, an allohexaploid and allotetraploid, respectively. However, the wild relatives of wheat such as Aegilops tauschii and T. urartu are diploid and grown at a limited scale. The hybridization events among wild relatives have resulted in the formation of modern wheat with improved traits and genome complexity. However, the changing environmental conditions and interactions with new pathogens affect their growth and development. An in-depth analysis of transcriptional complexities is necessary for understanding the regulation of several biological pathways. In recent years, the studies have revealed the regulatory role of long noncoding RNAs (lncRNAs) in growth and development and stress-responsive pathways. A large set of lncRNAs have been reported in wheat and its wild relatives. Various lncRNAs showed tissue-specific expression patterns which indicate their role in developmental processes. However, during stress conditions, the differential expression of certain lncRNAs suggested their role in plant defense response. LncRNAs act directly or indirectly in regulating the myriad biological processes such as grain yield, vernalization, growth, and adaptation to climatic change. The co-expression analysis also revealed their regulatory role in development, stress responses, and other biological processes. In this chapter, numerous aspects of lncRNAs, including their conserveness among the wheat and its relative, expression profiling, regulatory mechanisms, co-expression, and miRNA interaction networks study, will be discussed.
Grapes (Vitis vinifera L.) are a very popular fruit and are produced around the world. They are c... more Grapes (Vitis vinifera L.) are a very popular fruit and are produced around the world. They are consumed as a fresh ripe fruit, dried fruit, juice, and processed product such as wine and are a good...
Various biotic and abiotic environmental stresses negatively affect the diverse aspects of plant ... more Various biotic and abiotic environmental stresses negatively affect the diverse aspects of plant growth and development, and crop productivity. Plants being sessile organisms have developed effective strategies to avoid, tolerate, or acclimatized to various kinds of stress conditions. Several stress factors of plants activate cellular responses and signaling pathways such as secretion of stress proteins. Receptor-like kinases (RLKs) is a class of defense-related proteins comprising more than a thousand members. The RLKs mostly consisted of an extracellular domain for signal perception, a transmembrane domain to anchor the protein into membrane and a cytoplasmic serine/threonine kinase domain for stimulating the immunity of plants. They are known to play a diverse range of functions in plants, ranging from growth and development to responses against various environmental stresses. RLK signaling is arbitrated by phosphorylation events which take place amid proteins present in receptor complexes. Several RLKs such as BR1, CLAVATA1, S-locus receptor kinase, Flagellin Insensitive 2, etc. provide fruitful information on the roles arbitrated by the members of RLK gene family. Plants recognize numerous number of RLKs as pattern recognition receptors (PRRs) which detect host and microbe-derived molecular patterns as the first layer of inducible defense. The studies have revealed the mechanism of PRR activation and signaling and their ligands. In this chapter, the systematic analyses of plant RLKs responses to different stresses have been explained in detail.
The plants get exposed to different abiotic stresses and pathogen attack due to their sessile nat... more The plants get exposed to different abiotic stresses and pathogen attack due to their sessile nature. These stresses result in the overproduction of reactive oxygen species (ROS) such as superoxide radical (O2·−), hydrogen peroxide (H2O2), singlet oxygen (ˡO2) etc. To overcome the effect of these ROS, different classes of antioxidants are involved in providing tolerance to plants. The superoxide dismutase (SOD) consists of one such major class of antioxidant proteins, which provide primary defense against different stress conditions. These are ubiquitous metalloenzymes, which carry out the dismutation of superoxide radicals (O 2 ·− ) into molecular oxygen and hydrogen peroxide (H2O2). In plants, a total of three classes of SODs are reported i.e., Cu-ZnSODs, FeSODs, and MnSODs, which have cytoplasmic or apoplastic or nuclear, chloroplastic and mitochondrial subcellular localization, respectively. SODs are well known for their role in plant growth and development and in providing tole...
Catalases are crucial antioxidant enzymes that reduce the excessive level of H2O2 caused by vario... more Catalases are crucial antioxidant enzymes that reduce the excessive level of H2O2 caused by various environmental stresses and metal toxicity and hence protect the plant cells. In this study, a total of ten TaCAT genes, forming three homeologous groups, were identified in the genome of bread wheat (Triticum aestivum L.) and named as per the wheat gene symbolization guidelines. The identified catalases were characterized for various structural and physicochemical features. The proximal active-site (F(D/A)RERIPERVVHAKGASA) and heme-ligand (R(I/V)F(S/A)Y(A/S)DTQ) signature motifs, catalytic residues and peroxisomal targeting peptides were found conserved. Phylogenetic analysis clustered TaCATs into three classes, which showed conserved functional specialization based on their tissue specific expression. Modulated spatio-temporal expression of various TaCAT genes and alteration in total catalase enzyme activity during heat, drought, salt and arsenic (AsIII and AsV) treatment suggested their roles in abiotic stress response and arsenic tolerance. Molecular cloning and overexpression of TaCAT3-B gene in Escherichia coli showed tolerance against heat, drought, salt and varied concentrations of AsIII and AsV treatments. The results further confirmed their role in stress tolerance and recommended that these genes can be used in future stress management strategies for the development of abiotic and arsenic stress resistant transgenic crops.
KEY MESSAGE A total of seven glutathione reductase (GR) genes were identified in Triticum aestivu... more KEY MESSAGE A total of seven glutathione reductase (GR) genes were identified in Triticum aestivum, which were used for comparative structural characterization, phylogenetic analysis and expression profiling with the GR genes of other cereal plants. The modulated gene expression and enzyme activity revealed the role of GRs in abiotic stress response in T. aestivum. Glutathione reductase (GR) is an enzymatic antioxidant that converts oxidized glutathione (GSSG) into reduced glutathione (GSH) through the ascorbate-glutathione cycle. In this study, a total of seven GR genes forming two homeologous groups were identified in the allohexaploid genome of bread wheat (Triticum aestivum). Besides, we identified three GR genes in each Aegilops tauschii, Brachypodium distachyon, Triticum urartu and Sorghum bicolor, which were used for comparative characterization. Phylogenetic analysis revealed the clustering of GR proteins into two groups; class I and class II, which were predicted to be localized in cytoplasm and chloroplast, respectively. The exon-intron and conserved motif patterns were almost conserved in each group, in which a maximum of 10 and 17 exons were present in chloroplastic and cytoplasmic GRs, respectively. The protein structure analysis confirmed the occurrence of conserved pyridine nucleotide disulfide oxidoreductase (Pyr_redox) and pyridine nucleotide disulfide oxidoreductase dimerization (Pyr_redox_dim) domains in each GR. The active site of GR proteins consisted of two conserved cysteine residues separated by four amino acid residues. Promoter analysis revealed the occurrence of growth and stress-related cis-active elements. Tissue-specific expression profiling suggested the involvement of GRs in both vegetative and reproductive tissue development in various plants. The differential expression of TaGR genes and enhanced GR enzyme activity suggested their roles under drought, heat, salt and arsenic stress. Interaction of GRs with other proteins and chemical compounds of the ascorbate-glutathione cycle revealed their coordinated functioning. The current study will provide a foundation for the validation of the precise role of each GR gene in future studies.
International Journal of Biological Macromolecules, 2019
Cysteine-rich receptor-like kinases (CRK) constitute one of the largest subfamily of receptor-lik... more Cysteine-rich receptor-like kinases (CRK) constitute one of the largest subfamily of receptor-like kinases, which play crucial roles in plant development and stress response. In total, 43, 37, 36, 38 and 170 CRK genes including duplicated genes were identified in the genome of Brachypodium distachyon, Hordeum vulgare, Oryza sativa, Sorghum bicolor and Triticum aestivum, respectively. These CRK proteins were tightly clustered into four phylogenetic groups and exhibited close syntenic relationship among orthologous genes. Majority of CRK proteins contain a transmembrane domain for plasma membrane localization. The organization of exon/intron, domains and motifs were variably conserved. Tissue-specific expression suggested the involvement of certain CRK genes in plant development. Modulated expression revealed their specific stress-responsive functions. Co-expression and interaction analysis indicated their role in signaling. Ks value and divergence time analysis suggested duplication of TaCRK genes before the hybridization of T. aestivum sub-genomes. Expression comparison of duplicated TaCRK genes revealed functional retention, neofunctionalization or pseudo-functionalization. Recombinant expression of a stress-responsive gene TaCRK68-A in Escherichia coli and Saccharomyces cerevisiae displayed enhanced tolerance against heat, drought, cold and salinity stresses. The study suggested vital functions of CRKs during development and stresses, and provides the basis for functional characterization of each gene in future studies.
Reactive oxygen species (ROS) induce oxidative stress at high concentrations and act as signaling... more Reactive oxygen species (ROS) induce oxidative stress at high concentrations and act as signaling molecules at low concentrations. Superoxide dismutases (SOD) are defence-related proteins, which are involved in detoxifying ROS. SODs have been characterized in various plants, but their comprehensive characterization has not been performed in Triticum aestivum. Herein, a total of 23 TaSOD genes were identified, which were classified into fourteen TaCu-ZnSOD and nine TaFe-MnSOD genes based on their domain organization. These genes were located on various homeologous chromosomes of each A, B and D-subgenome. Higher number of genes on each subgenome than their progenitor genome indicated the role of duplication events during the evolution of TaSODs. The phylogenetic analysis indicated evolutionary conservation in SODs from various plant species. Gene structure in terms of exon/intron organization and intron-phase, and physico-chemical properties like molecular weight and pI was variably conserved in homeologous TaSODs. Most of the Cu-ZnSODs were predicted as cytoplasmic, while Fe-MnSODs were chloroplastic and mitochondrial. Both TaCu-ZnSODs and TaFe-MnSODs were found structurally conserved in terms of various metal binding and active sites, and secondary and tertiary structures as well. They showed putative interaction with each other and other ROS detoxifying enzymes like catalases and peroxidases. Specifically high expression of a few TaSODs in certain tissue developmental stages suggested their precise role in those tissues. TaFe-MnSOD1 group genes were highly expressed during development of grain. Constitutive expression of certain genes indicated their role during all developmental stages. The modulated expression of a few genes during biotic (TaCu-ZnSOD3-A, TaFe-MnSOD2-A) and abiotic stresses (heat; TaCu-ZnSOD3-B, TaFe-MnSOD1-B, drought; TaFe-MnSOD1-A, salt; TaFe-MnSOD2-A) suggested their function in a stress response. The present study provided inclusive characterization of SOD proteins in T. aestivum, which extends the opportunity for future functional characterization of each individual protein.
Long non-coding RNAs (lncRNAs) are a family of regulatory RNAs that play essential role in the va... more Long non-coding RNAs (lncRNAs) are a family of regulatory RNAs that play essential role in the various developmental processes and stress responses. Recent advances in sequencing technology and computational methods enabled identification and characterization of lncRNAs in certain plant species, but they are less known in Triticum aestivum (bread wheat). Herein, we analyzed 52 RNA seq data (>30 billion reads) and identified 44,698 lncRNAs in T. aestivum genome, which were characterized in comparison to the coding sequences (mRNAs). Similar to the mRNAs, lncRNAs were also derived from each sub-genome and chromosome, and showed tissue developmental stage specific and differential expression, as well. The modulated expression of lncRNAs during abiotic stresses like heat, drought, and salt indicated their putative role in stress response. The co-expression of lncRNAs with vital mRNAs including various transcription factors and enzymes involved in Abscisic acid (ABA) biosynthesis, and...
Flavonols are structurally and functionally diverse molecules playing roles in plant biotic and a... more Flavonols are structurally and functionally diverse molecules playing roles in plant biotic and abiotic stress tolerance, auxin transport inhibition, pollen development, etc. Despite their ubiquitous occurrence in land plants and multifunctionality, the effect of perturbation of flavonol biosynthesis over global gene expression and pathways other than flavonoid biosynthesis has not been studied in detail. To understand the signaling role of different flavonol metabolites, herein, we used the flavonol deficient Arabidopsis thaliana loss-of-function mutant flavonol synthase1 (fls1-3) as object of study. Comparative transcriptome and metabolic profiling were used to study the effects of genetic flavonol deficiency and exogenous supplementation with flavonol derivatives (kaempferol, quercetin and rutin) on different cellular processes in the seedling. Various flavonol biosynthesis-related regulatory and structural genes were found to be up-regulated in the fls1-3 mutant which could be r...
Abstract Wheat being an important crop is the major source of food throughout the world. The cult... more Abstract Wheat being an important crop is the major source of food throughout the world. The cultivated wheat includes Triticum aestivum and T. turgidum, an allohexaploid and allotetraploid, respectively. However, the wild relatives of wheat such as Aegilops tauschii and T. urartu are diploid and grown at a limited scale. The hybridization events among wild relatives have resulted in the formation of modern wheat with improved traits and genome complexity. However, the changing environmental conditions and interactions with new pathogens affect their growth and development. An in-depth analysis of transcriptional complexities is necessary for understanding the regulation of several biological pathways. In recent years, the studies have revealed the regulatory role of long noncoding RNAs (lncRNAs) in growth and development and stress-responsive pathways. A large set of lncRNAs have been reported in wheat and its wild relatives. Various lncRNAs showed tissue-specific expression patterns which indicate their role in developmental processes. However, during stress conditions, the differential expression of certain lncRNAs suggested their role in plant defense response. LncRNAs act directly or indirectly in regulating the myriad biological processes such as grain yield, vernalization, growth, and adaptation to climatic change. The co-expression analysis also revealed their regulatory role in development, stress responses, and other biological processes. In this chapter, numerous aspects of lncRNAs, including their conserveness among the wheat and its relative, expression profiling, regulatory mechanisms, co-expression, and miRNA interaction networks study, will be discussed.
Grapes (Vitis vinifera L.) are a very popular fruit and are produced around the world. They are c... more Grapes (Vitis vinifera L.) are a very popular fruit and are produced around the world. They are consumed as a fresh ripe fruit, dried fruit, juice, and processed product such as wine and are a good...
Various biotic and abiotic environmental stresses negatively affect the diverse aspects of plant ... more Various biotic and abiotic environmental stresses negatively affect the diverse aspects of plant growth and development, and crop productivity. Plants being sessile organisms have developed effective strategies to avoid, tolerate, or acclimatized to various kinds of stress conditions. Several stress factors of plants activate cellular responses and signaling pathways such as secretion of stress proteins. Receptor-like kinases (RLKs) is a class of defense-related proteins comprising more than a thousand members. The RLKs mostly consisted of an extracellular domain for signal perception, a transmembrane domain to anchor the protein into membrane and a cytoplasmic serine/threonine kinase domain for stimulating the immunity of plants. They are known to play a diverse range of functions in plants, ranging from growth and development to responses against various environmental stresses. RLK signaling is arbitrated by phosphorylation events which take place amid proteins present in receptor complexes. Several RLKs such as BR1, CLAVATA1, S-locus receptor kinase, Flagellin Insensitive 2, etc. provide fruitful information on the roles arbitrated by the members of RLK gene family. Plants recognize numerous number of RLKs as pattern recognition receptors (PRRs) which detect host and microbe-derived molecular patterns as the first layer of inducible defense. The studies have revealed the mechanism of PRR activation and signaling and their ligands. In this chapter, the systematic analyses of plant RLKs responses to different stresses have been explained in detail.
The plants get exposed to different abiotic stresses and pathogen attack due to their sessile nat... more The plants get exposed to different abiotic stresses and pathogen attack due to their sessile nature. These stresses result in the overproduction of reactive oxygen species (ROS) such as superoxide radical (O2·−), hydrogen peroxide (H2O2), singlet oxygen (ˡO2) etc. To overcome the effect of these ROS, different classes of antioxidants are involved in providing tolerance to plants. The superoxide dismutase (SOD) consists of one such major class of antioxidant proteins, which provide primary defense against different stress conditions. These are ubiquitous metalloenzymes, which carry out the dismutation of superoxide radicals (O 2 ·− ) into molecular oxygen and hydrogen peroxide (H2O2). In plants, a total of three classes of SODs are reported i.e., Cu-ZnSODs, FeSODs, and MnSODs, which have cytoplasmic or apoplastic or nuclear, chloroplastic and mitochondrial subcellular localization, respectively. SODs are well known for their role in plant growth and development and in providing tole...
Catalases are crucial antioxidant enzymes that reduce the excessive level of H2O2 caused by vario... more Catalases are crucial antioxidant enzymes that reduce the excessive level of H2O2 caused by various environmental stresses and metal toxicity and hence protect the plant cells. In this study, a total of ten TaCAT genes, forming three homeologous groups, were identified in the genome of bread wheat (Triticum aestivum L.) and named as per the wheat gene symbolization guidelines. The identified catalases were characterized for various structural and physicochemical features. The proximal active-site (F(D/A)RERIPERVVHAKGASA) and heme-ligand (R(I/V)F(S/A)Y(A/S)DTQ) signature motifs, catalytic residues and peroxisomal targeting peptides were found conserved. Phylogenetic analysis clustered TaCATs into three classes, which showed conserved functional specialization based on their tissue specific expression. Modulated spatio-temporal expression of various TaCAT genes and alteration in total catalase enzyme activity during heat, drought, salt and arsenic (AsIII and AsV) treatment suggested their roles in abiotic stress response and arsenic tolerance. Molecular cloning and overexpression of TaCAT3-B gene in Escherichia coli showed tolerance against heat, drought, salt and varied concentrations of AsIII and AsV treatments. The results further confirmed their role in stress tolerance and recommended that these genes can be used in future stress management strategies for the development of abiotic and arsenic stress resistant transgenic crops.
KEY MESSAGE A total of seven glutathione reductase (GR) genes were identified in Triticum aestivu... more KEY MESSAGE A total of seven glutathione reductase (GR) genes were identified in Triticum aestivum, which were used for comparative structural characterization, phylogenetic analysis and expression profiling with the GR genes of other cereal plants. The modulated gene expression and enzyme activity revealed the role of GRs in abiotic stress response in T. aestivum. Glutathione reductase (GR) is an enzymatic antioxidant that converts oxidized glutathione (GSSG) into reduced glutathione (GSH) through the ascorbate-glutathione cycle. In this study, a total of seven GR genes forming two homeologous groups were identified in the allohexaploid genome of bread wheat (Triticum aestivum). Besides, we identified three GR genes in each Aegilops tauschii, Brachypodium distachyon, Triticum urartu and Sorghum bicolor, which were used for comparative characterization. Phylogenetic analysis revealed the clustering of GR proteins into two groups; class I and class II, which were predicted to be localized in cytoplasm and chloroplast, respectively. The exon-intron and conserved motif patterns were almost conserved in each group, in which a maximum of 10 and 17 exons were present in chloroplastic and cytoplasmic GRs, respectively. The protein structure analysis confirmed the occurrence of conserved pyridine nucleotide disulfide oxidoreductase (Pyr_redox) and pyridine nucleotide disulfide oxidoreductase dimerization (Pyr_redox_dim) domains in each GR. The active site of GR proteins consisted of two conserved cysteine residues separated by four amino acid residues. Promoter analysis revealed the occurrence of growth and stress-related cis-active elements. Tissue-specific expression profiling suggested the involvement of GRs in both vegetative and reproductive tissue development in various plants. The differential expression of TaGR genes and enhanced GR enzyme activity suggested their roles under drought, heat, salt and arsenic stress. Interaction of GRs with other proteins and chemical compounds of the ascorbate-glutathione cycle revealed their coordinated functioning. The current study will provide a foundation for the validation of the precise role of each GR gene in future studies.
International Journal of Biological Macromolecules, 2019
Cysteine-rich receptor-like kinases (CRK) constitute one of the largest subfamily of receptor-lik... more Cysteine-rich receptor-like kinases (CRK) constitute one of the largest subfamily of receptor-like kinases, which play crucial roles in plant development and stress response. In total, 43, 37, 36, 38 and 170 CRK genes including duplicated genes were identified in the genome of Brachypodium distachyon, Hordeum vulgare, Oryza sativa, Sorghum bicolor and Triticum aestivum, respectively. These CRK proteins were tightly clustered into four phylogenetic groups and exhibited close syntenic relationship among orthologous genes. Majority of CRK proteins contain a transmembrane domain for plasma membrane localization. The organization of exon/intron, domains and motifs were variably conserved. Tissue-specific expression suggested the involvement of certain CRK genes in plant development. Modulated expression revealed their specific stress-responsive functions. Co-expression and interaction analysis indicated their role in signaling. Ks value and divergence time analysis suggested duplication of TaCRK genes before the hybridization of T. aestivum sub-genomes. Expression comparison of duplicated TaCRK genes revealed functional retention, neofunctionalization or pseudo-functionalization. Recombinant expression of a stress-responsive gene TaCRK68-A in Escherichia coli and Saccharomyces cerevisiae displayed enhanced tolerance against heat, drought, cold and salinity stresses. The study suggested vital functions of CRKs during development and stresses, and provides the basis for functional characterization of each gene in future studies.
Reactive oxygen species (ROS) induce oxidative stress at high concentrations and act as signaling... more Reactive oxygen species (ROS) induce oxidative stress at high concentrations and act as signaling molecules at low concentrations. Superoxide dismutases (SOD) are defence-related proteins, which are involved in detoxifying ROS. SODs have been characterized in various plants, but their comprehensive characterization has not been performed in Triticum aestivum. Herein, a total of 23 TaSOD genes were identified, which were classified into fourteen TaCu-ZnSOD and nine TaFe-MnSOD genes based on their domain organization. These genes were located on various homeologous chromosomes of each A, B and D-subgenome. Higher number of genes on each subgenome than their progenitor genome indicated the role of duplication events during the evolution of TaSODs. The phylogenetic analysis indicated evolutionary conservation in SODs from various plant species. Gene structure in terms of exon/intron organization and intron-phase, and physico-chemical properties like molecular weight and pI was variably conserved in homeologous TaSODs. Most of the Cu-ZnSODs were predicted as cytoplasmic, while Fe-MnSODs were chloroplastic and mitochondrial. Both TaCu-ZnSODs and TaFe-MnSODs were found structurally conserved in terms of various metal binding and active sites, and secondary and tertiary structures as well. They showed putative interaction with each other and other ROS detoxifying enzymes like catalases and peroxidases. Specifically high expression of a few TaSODs in certain tissue developmental stages suggested their precise role in those tissues. TaFe-MnSOD1 group genes were highly expressed during development of grain. Constitutive expression of certain genes indicated their role during all developmental stages. The modulated expression of a few genes during biotic (TaCu-ZnSOD3-A, TaFe-MnSOD2-A) and abiotic stresses (heat; TaCu-ZnSOD3-B, TaFe-MnSOD1-B, drought; TaFe-MnSOD1-A, salt; TaFe-MnSOD2-A) suggested their function in a stress response. The present study provided inclusive characterization of SOD proteins in T. aestivum, which extends the opportunity for future functional characterization of each individual protein.
Long non-coding RNAs (lncRNAs) are a family of regulatory RNAs that play essential role in the va... more Long non-coding RNAs (lncRNAs) are a family of regulatory RNAs that play essential role in the various developmental processes and stress responses. Recent advances in sequencing technology and computational methods enabled identification and characterization of lncRNAs in certain plant species, but they are less known in Triticum aestivum (bread wheat). Herein, we analyzed 52 RNA seq data (>30 billion reads) and identified 44,698 lncRNAs in T. aestivum genome, which were characterized in comparison to the coding sequences (mRNAs). Similar to the mRNAs, lncRNAs were also derived from each sub-genome and chromosome, and showed tissue developmental stage specific and differential expression, as well. The modulated expression of lncRNAs during abiotic stresses like heat, drought, and salt indicated their putative role in stress response. The co-expression of lncRNAs with vital mRNAs including various transcription factors and enzymes involved in Abscisic acid (ABA) biosynthesis, and...
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