arnab ganguli | TCG Life Sciences Pvt Ltd (original) (raw)
Papers by arnab ganguli
Planta, 2010
The gene coding for rice chloroplastic l-myo-inositol-1-phosphate synthase (MIPS; EC 5.5.1.4) has... more The gene coding for rice chloroplastic l-myo-inositol-1-phosphate synthase (MIPS; EC 5.5.1.4) has been identified by matrix-assisted laser desorption time-of-flight mass spectrometry analysis of the purified and immunologically cross-reactive ~60 kDa chloroplastic protein following two-dimensional polyacrylamide gel electrophoresis, which exhibited sequence identity with the cytosolic MIPS coded by OsINO1-1 gene. A possible chloroplastic transit peptide sequence was identified upstream of the OsINO1-1 gene upon analysis of rice genome. RT-PCR and confocal microscope studies confirmed transcription, effective translation and its functioning as a chloroplast transit peptide. Bioinformatic analysis mapped the chloroplastic MIPS (OsINO1-1) gene on chromosome 3, and a second MIPS gene (OsINO1-2) on chromosome 10 which lacks conventional chloroplast transit peptide sequence as in OsINO1-1. Two new PcINO1 genes, with characteristic promoter activity and upstream cis-elements were identified and cloned, but whether these proteins can be translocated to the chloroplast or not is yet to be ascertained. Electrophoretic mobility shift assay carried out with nuclear extract of Porteresia coarctata leaves grown under both control and stressed condition shows binding of nuclear proteins with the upstream elements. Nucleotide divergence among the different Oryza and Porteresia INO1 genes were calculated and compared.
Planta, 2010
The gene coding for rice chloroplastic l-myo-inositol-1-phosphate synthase (MIPS; EC 5.5.1.4) has... more The gene coding for rice chloroplastic l-myo-inositol-1-phosphate synthase (MIPS; EC 5.5.1.4) has been identified by matrix-assisted laser desorption time-of-flight mass spectrometry analysis of the purified and immunologically cross-reactive ~60 kDa chloroplastic protein following two-dimensional polyacrylamide gel electrophoresis, which exhibited sequence identity with the cytosolic MIPS coded by OsINO1-1 gene. A possible chloroplastic transit peptide sequence was identified upstream of the OsINO1-1 gene upon analysis of rice genome. RT-PCR and confocal microscope studies confirmed transcription, effective translation and its functioning as a chloroplast transit peptide. Bioinformatic analysis mapped the chloroplastic MIPS (OsINO1-1) gene on chromosome 3, and a second MIPS gene (OsINO1-2) on chromosome 10 which lacks conventional chloroplast transit peptide sequence as in OsINO1-1. Two new PcINO1 genes, with characteristic promoter activity and upstream cis-elements were identified and cloned, but whether these proteins can be translocated to the chloroplast or not is yet to be ascertained. Electrophoretic mobility shift assay carried out with nuclear extract of Porteresia coarctata leaves grown under both control and stressed condition shows binding of nuclear proteins with the upstream elements. Nucleotide divergence among the different Oryza and Porteresia INO1 genes were calculated and compared.
Planta, 2010
The gene coding for rice chloroplastic l-myo-inositol-1-phosphate synthase (MIPS; EC 5.5.1.4) has... more The gene coding for rice chloroplastic l-myo-inositol-1-phosphate synthase (MIPS; EC 5.5.1.4) has been identified by matrix-assisted laser desorption time-of-flight mass spectrometry analysis of the purified and immunologically cross-reactive ~60 kDa chloroplastic protein following two-dimensional polyacrylamide gel electrophoresis, which exhibited sequence identity with the cytosolic MIPS coded by OsINO1-1 gene. A possible chloroplastic transit peptide sequence was identified upstream of the OsINO1-1 gene upon analysis of rice genome. RT-PCR and confocal microscope studies confirmed transcription, effective translation and its functioning as a chloroplast transit peptide. Bioinformatic analysis mapped the chloroplastic MIPS (OsINO1-1) gene on chromosome 3, and a second MIPS gene (OsINO1-2) on chromosome 10 which lacks conventional chloroplast transit peptide sequence as in OsINO1-1. Two new PcINO1 genes, with characteristic promoter activity and upstream cis-elements were identified and cloned, but whether these proteins can be translocated to the chloroplast or not is yet to be ascertained. Electrophoretic mobility shift assay carried out with nuclear extract of Porteresia coarctata leaves grown under both control and stressed condition shows binding of nuclear proteins with the upstream elements. Nucleotide divergence among the different Oryza and Porteresia INO1 genes were calculated and compared.
Plant Molecular Biology, 2006
Within the Arabidopsis family of 21 heat stress transcription factors (Hsfs) HsfA2 is the stronge... more Within the Arabidopsis family of 21 heat stress transcription factors (Hsfs) HsfA2 is the strongest expressed member under heat stress (hs) conditions. Irrespective of the tissue, HsfA2 accumulates under heat stress similarly to other heat stress proteins (Hsps). A SALK T-DNA insertion line with a complete HsfA2-knockout was analyzed with respect to the changes in the transcriptome under heat stress conditions. Ascorbate peroxidase 2 (APX2) was identified as the most affected transcript in addition to several sHsps, individual members of the Hsp70 and Hsp100 family, as well as many transcripts of genes with yet unknown functions. For functional validation, the transcription activation potential of HsfA2 on GUS reporter constructs containing 1 kb upstream promoter sequences of selected target genes were analyzed using transient reporter assays in mesophyll protoplasts. By deletion analysis the promoter region of the strongest affected target gene APX2 was functionally mapped in detail to verify potential HsfA2 binding sites. By electrophoretic mobility shift assays we identified TATA-Box proximal clusters of heat stress elements (HSE) in the promoters of selected target genes as potential HsfA2 binding sites. The results presented here demonstrate that the expression of HsfA2 in Arabidopsis is strictly heat stress-dependent and this transcription factor represents a regulator of a subset of stress response genes in Arabidopsis.
Plant Journal, 2008
The dehydration-responsive element binding protein (DREB)/C-repeat binding factor (CBF) family ar... more The dehydration-responsive element binding protein (DREB)/C-repeat binding factor (CBF) family are the classical transcriptional regulators involved in plant responses to drought, salt and cold stress. Recently it was demonstrated that DREB2A is induced by heat stress (hs) and is a regulator of the hs response of Arabidopsis. Here we provide molecular insights into the regulation and function of hs transcription factor HsfA3. Among the 21 members of the Arabidopsis Hsf family, HsfA3 is the only Hsf that is transcriptionally induced during hs by DREB2A, and HsfA3 in turn regulates the expression of Hsp-encoding genes. This transcription factor cascade was reconstructed in transient GUS reporter assays in mesophyll protoplasts by showing that DREB2A could activate the HsfA3 promoter, whereas HsfA3 in turn was shown to be a potent activator on the promoters of Hsp genes. Direct binding to the corresponding promoters was demonstrated by electrophoretic mobility shift assays, and the involvement of HsfA3 in the hs response in vivo was shown directly by observation of reduced thermotolerance in HsfA3 mutant lines. Altogether these data demonstrate that HsfA3 is transcriptionally controlled by DREB2A and important for the establishment of thermotolerance.
Cell Stress & Chaperones, 2001
Sequencing of the Arabidopsis genome revealed a unique complexity of the plant heat stress transc... more Sequencing of the Arabidopsis genome revealed a unique complexity of the plant heat stress transcription factor (Hsf) family. By structural characteristics and phylogenetic comparison, the 21 representatives are assigned to 3 classes and 14 groups. Particularly striking is the finding of a new class of Hsfs (AtHsfC1) closely related to Hsf1 from rice and to Hsfs identified from frequently found expressed sequence tags of tomato, potato, barley, and soybean. Evidently, this new type of Hsf is well expressed in different plant tissues. Besides the DNA binding and oligomerization domains (HR-A/B region), we identified other functional modules of Arabidopsis Hsfs by sequence comparison with the well-characterized tomato Hsfs. These are putative motifs for nuclear import and export and transcriptional activation (AHA motifs). There is intriguing flexibility of size and sequence in certain parts of the otherwise strongly conserved N-terminal half of these Hsfs. We have speculated about possible exon-intron borders in this region in the ancient precursor gene of plant Hsfs, similar to the exon-intron structure of the present mammalian Hsf-encoding genes.
Plant Journal, 2004
Heat stress transcription factors (Hsfs) are the major regulators of the plant heat stress (hs) r... more Heat stress transcription factors (Hsfs) are the major regulators of the plant heat stress (hs) response. Sequencing of the Arabidopsis genome revealed the existence of 21 open-reading frames (ORFs) encoding putative Hsfs assigned to classes A–C. Here we present results of a functional genomics approach to the Arabidopsis Hsf family focused on the analysis of their C-terminal domains (CTDs) harboring conserved modules for their function as transcription factors and their intracellular localization. Using reporter assays in tobacco protoplasts and yeast as well as glutathione-S-transferase (GST) pull-down assays, we demonstrate that short peptide motifs enriched with aromatic and large hydrophobic amino acid (aa) residues embedded in an acidic surrounding (AHA motifs) are essential for transcriptional activity of class A Hsfs. In contrast to this, class B and C Hsfs lack AHA motifs and have no activator function on their own. We also provide evidence for the function of a leucine (Leu)-rich region centered around a conserved QMGΦL motif at the very C-terminus as a nuclear export signal (NES) of class A Hsfs. Sequence comparison indicates that the combination of a C-terminal AHA motif with the consensus sequence FWxxF/L,F/I/L as well as the adjacent NES represents a signature domain for plant class A Hsfs, which allowed to identify more than 60 new Hsfs from the expressed sequence tag (EST) database.
Journal of Biosciences, 2004
Compared to the overall multiplicity of more than 20 plant Hsfs, detailed analyses are mainly res... more Compared to the overall multiplicity of more than 20 plant Hsfs, detailed analyses are mainly restricted to tomato and Arabidopsis and to three important representatives of the family (Hsfs A1, A2 and B1). The three Hsfs represent examples of striking functional diversification specialized for the three phases of the heat stress (hs) response (triggering, maintenance and recovery). This is best illustrated for the tomato Hsf system: (i) HsfA1a is the master regulator responsible for hs-induced gene expression including synthesis of HsfA2 and HsfB1. It is indispensible for the development of thermotolerance. (ii) Although functionally equivalent to HsfA1a, HsfA2 is exclusively found after hs induction and represents the dominant Hsf, the “working horse” of the hs response in plants subjected to repeated cycles of hs and recovery in a hot summer period. Tomato HsfA2 is tightly integrated into a network of interacting proteins (HsfA1a, Hsp17-CII, Hsp17-CI) influencing its activity and intracellular distribution. (iii) Because of structural peculiarities, HsfB1 acts as coregulator enhancing the activity of HsfA1a and/or HsfA2. But in addition, it cooperates with yet to be identified other transcription factors in maintaining and/or restoring housekeeping gene expression.
The present study was to formulate and study the release of niacinamide (vitamin B 3 ) and caffei... more The present study was to formulate and study the release of niacinamide (vitamin B 3 ) and caffeine from three different cream bases, vanishing cream, hydrophilic emulsion and cold cream. The releases of active components were evaluated using Franz-type diffusion cells with artificial membrane. Both vanishing cream and hydrophilic emulsion are the same in o/w type with difference in emulsifying agent and oil components. The vanishing cream is more liquid than hydrophilic emulsion where as the cold cream is w/o type with the most inflexible. In vitro releases of niacinamide and caffeine from three cream bases showed the similar kinetics. Both niacinamide and caffeine showed the highest release amounts and the fastest rates in vanishing cream. The lowest release amounts and release rates were found in cold cream. The results of the study suggest that the components and types of cream bases strongly affect the release of the actives from the formulations.
Planta, 2010
The gene coding for rice chloroplastic l-myo-inositol-1-phosphate synthase (MIPS; EC 5.5.1.4) has... more The gene coding for rice chloroplastic l-myo-inositol-1-phosphate synthase (MIPS; EC 5.5.1.4) has been identified by matrix-assisted laser desorption time-of-flight mass spectrometry analysis of the purified and immunologically cross-reactive ~60 kDa chloroplastic protein following two-dimensional polyacrylamide gel electrophoresis, which exhibited sequence identity with the cytosolic MIPS coded by OsINO1-1 gene. A possible chloroplastic transit peptide sequence was identified upstream of the OsINO1-1 gene upon analysis of rice genome. RT-PCR and confocal microscope studies confirmed transcription, effective translation and its functioning as a chloroplast transit peptide. Bioinformatic analysis mapped the chloroplastic MIPS (OsINO1-1) gene on chromosome 3, and a second MIPS gene (OsINO1-2) on chromosome 10 which lacks conventional chloroplast transit peptide sequence as in OsINO1-1. Two new PcINO1 genes, with characteristic promoter activity and upstream cis-elements were identified and cloned, but whether these proteins can be translocated to the chloroplast or not is yet to be ascertained. Electrophoretic mobility shift assay carried out with nuclear extract of Porteresia coarctata leaves grown under both control and stressed condition shows binding of nuclear proteins with the upstream elements. Nucleotide divergence among the different Oryza and Porteresia INO1 genes were calculated and compared.
Planta, 2010
The gene coding for rice chloroplastic l-myo-inositol-1-phosphate synthase (MIPS; EC 5.5.1.4) has... more The gene coding for rice chloroplastic l-myo-inositol-1-phosphate synthase (MIPS; EC 5.5.1.4) has been identified by matrix-assisted laser desorption time-of-flight mass spectrometry analysis of the purified and immunologically cross-reactive ~60 kDa chloroplastic protein following two-dimensional polyacrylamide gel electrophoresis, which exhibited sequence identity with the cytosolic MIPS coded by OsINO1-1 gene. A possible chloroplastic transit peptide sequence was identified upstream of the OsINO1-1 gene upon analysis of rice genome. RT-PCR and confocal microscope studies confirmed transcription, effective translation and its functioning as a chloroplast transit peptide. Bioinformatic analysis mapped the chloroplastic MIPS (OsINO1-1) gene on chromosome 3, and a second MIPS gene (OsINO1-2) on chromosome 10 which lacks conventional chloroplast transit peptide sequence as in OsINO1-1. Two new PcINO1 genes, with characteristic promoter activity and upstream cis-elements were identified and cloned, but whether these proteins can be translocated to the chloroplast or not is yet to be ascertained. Electrophoretic mobility shift assay carried out with nuclear extract of Porteresia coarctata leaves grown under both control and stressed condition shows binding of nuclear proteins with the upstream elements. Nucleotide divergence among the different Oryza and Porteresia INO1 genes were calculated and compared.
Planta, 2010
The gene coding for rice chloroplastic l-myo-inositol-1-phosphate synthase (MIPS; EC 5.5.1.4) has... more The gene coding for rice chloroplastic l-myo-inositol-1-phosphate synthase (MIPS; EC 5.5.1.4) has been identified by matrix-assisted laser desorption time-of-flight mass spectrometry analysis of the purified and immunologically cross-reactive ~60 kDa chloroplastic protein following two-dimensional polyacrylamide gel electrophoresis, which exhibited sequence identity with the cytosolic MIPS coded by OsINO1-1 gene. A possible chloroplastic transit peptide sequence was identified upstream of the OsINO1-1 gene upon analysis of rice genome. RT-PCR and confocal microscope studies confirmed transcription, effective translation and its functioning as a chloroplast transit peptide. Bioinformatic analysis mapped the chloroplastic MIPS (OsINO1-1) gene on chromosome 3, and a second MIPS gene (OsINO1-2) on chromosome 10 which lacks conventional chloroplast transit peptide sequence as in OsINO1-1. Two new PcINO1 genes, with characteristic promoter activity and upstream cis-elements were identified and cloned, but whether these proteins can be translocated to the chloroplast or not is yet to be ascertained. Electrophoretic mobility shift assay carried out with nuclear extract of Porteresia coarctata leaves grown under both control and stressed condition shows binding of nuclear proteins with the upstream elements. Nucleotide divergence among the different Oryza and Porteresia INO1 genes were calculated and compared.
Plant Molecular Biology, 2006
Within the Arabidopsis family of 21 heat stress transcription factors (Hsfs) HsfA2 is the stronge... more Within the Arabidopsis family of 21 heat stress transcription factors (Hsfs) HsfA2 is the strongest expressed member under heat stress (hs) conditions. Irrespective of the tissue, HsfA2 accumulates under heat stress similarly to other heat stress proteins (Hsps). A SALK T-DNA insertion line with a complete HsfA2-knockout was analyzed with respect to the changes in the transcriptome under heat stress conditions. Ascorbate peroxidase 2 (APX2) was identified as the most affected transcript in addition to several sHsps, individual members of the Hsp70 and Hsp100 family, as well as many transcripts of genes with yet unknown functions. For functional validation, the transcription activation potential of HsfA2 on GUS reporter constructs containing 1 kb upstream promoter sequences of selected target genes were analyzed using transient reporter assays in mesophyll protoplasts. By deletion analysis the promoter region of the strongest affected target gene APX2 was functionally mapped in detail to verify potential HsfA2 binding sites. By electrophoretic mobility shift assays we identified TATA-Box proximal clusters of heat stress elements (HSE) in the promoters of selected target genes as potential HsfA2 binding sites. The results presented here demonstrate that the expression of HsfA2 in Arabidopsis is strictly heat stress-dependent and this transcription factor represents a regulator of a subset of stress response genes in Arabidopsis.
Plant Journal, 2008
The dehydration-responsive element binding protein (DREB)/C-repeat binding factor (CBF) family ar... more The dehydration-responsive element binding protein (DREB)/C-repeat binding factor (CBF) family are the classical transcriptional regulators involved in plant responses to drought, salt and cold stress. Recently it was demonstrated that DREB2A is induced by heat stress (hs) and is a regulator of the hs response of Arabidopsis. Here we provide molecular insights into the regulation and function of hs transcription factor HsfA3. Among the 21 members of the Arabidopsis Hsf family, HsfA3 is the only Hsf that is transcriptionally induced during hs by DREB2A, and HsfA3 in turn regulates the expression of Hsp-encoding genes. This transcription factor cascade was reconstructed in transient GUS reporter assays in mesophyll protoplasts by showing that DREB2A could activate the HsfA3 promoter, whereas HsfA3 in turn was shown to be a potent activator on the promoters of Hsp genes. Direct binding to the corresponding promoters was demonstrated by electrophoretic mobility shift assays, and the involvement of HsfA3 in the hs response in vivo was shown directly by observation of reduced thermotolerance in HsfA3 mutant lines. Altogether these data demonstrate that HsfA3 is transcriptionally controlled by DREB2A and important for the establishment of thermotolerance.
Cell Stress & Chaperones, 2001
Sequencing of the Arabidopsis genome revealed a unique complexity of the plant heat stress transc... more Sequencing of the Arabidopsis genome revealed a unique complexity of the plant heat stress transcription factor (Hsf) family. By structural characteristics and phylogenetic comparison, the 21 representatives are assigned to 3 classes and 14 groups. Particularly striking is the finding of a new class of Hsfs (AtHsfC1) closely related to Hsf1 from rice and to Hsfs identified from frequently found expressed sequence tags of tomato, potato, barley, and soybean. Evidently, this new type of Hsf is well expressed in different plant tissues. Besides the DNA binding and oligomerization domains (HR-A/B region), we identified other functional modules of Arabidopsis Hsfs by sequence comparison with the well-characterized tomato Hsfs. These are putative motifs for nuclear import and export and transcriptional activation (AHA motifs). There is intriguing flexibility of size and sequence in certain parts of the otherwise strongly conserved N-terminal half of these Hsfs. We have speculated about possible exon-intron borders in this region in the ancient precursor gene of plant Hsfs, similar to the exon-intron structure of the present mammalian Hsf-encoding genes.
Plant Journal, 2004
Heat stress transcription factors (Hsfs) are the major regulators of the plant heat stress (hs) r... more Heat stress transcription factors (Hsfs) are the major regulators of the plant heat stress (hs) response. Sequencing of the Arabidopsis genome revealed the existence of 21 open-reading frames (ORFs) encoding putative Hsfs assigned to classes A–C. Here we present results of a functional genomics approach to the Arabidopsis Hsf family focused on the analysis of their C-terminal domains (CTDs) harboring conserved modules for their function as transcription factors and their intracellular localization. Using reporter assays in tobacco protoplasts and yeast as well as glutathione-S-transferase (GST) pull-down assays, we demonstrate that short peptide motifs enriched with aromatic and large hydrophobic amino acid (aa) residues embedded in an acidic surrounding (AHA motifs) are essential for transcriptional activity of class A Hsfs. In contrast to this, class B and C Hsfs lack AHA motifs and have no activator function on their own. We also provide evidence for the function of a leucine (Leu)-rich region centered around a conserved QMGΦL motif at the very C-terminus as a nuclear export signal (NES) of class A Hsfs. Sequence comparison indicates that the combination of a C-terminal AHA motif with the consensus sequence FWxxF/L,F/I/L as well as the adjacent NES represents a signature domain for plant class A Hsfs, which allowed to identify more than 60 new Hsfs from the expressed sequence tag (EST) database.
Journal of Biosciences, 2004
Compared to the overall multiplicity of more than 20 plant Hsfs, detailed analyses are mainly res... more Compared to the overall multiplicity of more than 20 plant Hsfs, detailed analyses are mainly restricted to tomato and Arabidopsis and to three important representatives of the family (Hsfs A1, A2 and B1). The three Hsfs represent examples of striking functional diversification specialized for the three phases of the heat stress (hs) response (triggering, maintenance and recovery). This is best illustrated for the tomato Hsf system: (i) HsfA1a is the master regulator responsible for hs-induced gene expression including synthesis of HsfA2 and HsfB1. It is indispensible for the development of thermotolerance. (ii) Although functionally equivalent to HsfA1a, HsfA2 is exclusively found after hs induction and represents the dominant Hsf, the “working horse” of the hs response in plants subjected to repeated cycles of hs and recovery in a hot summer period. Tomato HsfA2 is tightly integrated into a network of interacting proteins (HsfA1a, Hsp17-CII, Hsp17-CI) influencing its activity and intracellular distribution. (iii) Because of structural peculiarities, HsfB1 acts as coregulator enhancing the activity of HsfA1a and/or HsfA2. But in addition, it cooperates with yet to be identified other transcription factors in maintaining and/or restoring housekeeping gene expression.
The present study was to formulate and study the release of niacinamide (vitamin B 3 ) and caffei... more The present study was to formulate and study the release of niacinamide (vitamin B 3 ) and caffeine from three different cream bases, vanishing cream, hydrophilic emulsion and cold cream. The releases of active components were evaluated using Franz-type diffusion cells with artificial membrane. Both vanishing cream and hydrophilic emulsion are the same in o/w type with difference in emulsifying agent and oil components. The vanishing cream is more liquid than hydrophilic emulsion where as the cold cream is w/o type with the most inflexible. In vitro releases of niacinamide and caffeine from three cream bases showed the similar kinetics. Both niacinamide and caffeine showed the highest release amounts and the fastest rates in vanishing cream. The lowest release amounts and release rates were found in cold cream. The results of the study suggest that the components and types of cream bases strongly affect the release of the actives from the formulations.