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Ana Maria Benko-iseppon - One of the best experts on this subject based on the ideXlab platform.

  • Osmoprotectant-Related Genes in Plants Under Abiotic Stress: Expression Dynamics, In Silico Genome Mapping, and Biotechnology
    Osmoprotectant-Mediated Abiotic Stress Tolerance in Plants, 2019
    Co-Authors: Ederson A Kido, Manassés D Silva, José Ribamar Costa Ferreira-neto, Vanessa Emanuelle Pereira Santos, Jorge Luís Bandeira Da Silva Filho, Ana Maria Benko-iseppon
    Abstract:

    Osmoprotectants are categorized as osmolytes, also known as compatible solutes, considering that they are small organic molecules that share characteristics, like low molecular weight, neutral charge, and low toxicity, even at high concentrations in cells. They are identified in different chemical classes, including polyamines (e.g., putrescine, spermidine, spermine), sugars (e.g., sucrose, trehalose, raffinose), sugar alcohols (e.g., myo-inositols), betaines (e.g., glycine betaine), and amino acids (e.g., proline). In plants exposed to abiotic stresses (salinity/drought), Osmoprotectants help cellular turgor preservation and drive the water uptake gradient. Some Osmoprotectants shield plants from damage through chaperone-like activities, helping in the conservation of membrane structures and protein functions, or scavenging for reactive oxygen species (ROS) generated by the stresses. Therefore, it is advantageous to understand how plants respond to abiotic stresses by regulating the expression of osmoprotectant-related genes. This chapter presents data on plant Osmoprotectants, including their regulating genes, associated pathways, and transcriptional regulations in plants under abiotic stresses. There is also an overview of their in silico mapping (model plants/crops) and their biotechnological potential as transgenes. Furthermore, these approaches are new perspectives for the analysis and introgression of these related genes into cultivated plant species, improving advances in plant breeding and crop production.

  • Expression dynamics and genome distribution of Osmoprotectants in soybean: identifying important components to face abiotic stress
    BMC Bioinformatics, 2013
    Co-Authors: Ederson A Kido, Luis C Belarmino, Nina M Soares-cavalcanti, Valesca Pandolfi, Manassés D Silva, Alexandre L Nepomuceno, José Ribamar Costa Ferreira Neto, Roberta Lane De Oliveira Silva, João Pacífico Bezerra Neto, Ana Maria Benko-iseppon
    Abstract:

    Despite the importance of Osmoprotectants, no previous in silico evaluation of high throughput data is available for higher plants. The present approach aimed at the identification and annotation of osmoprotectant-related sequences applied to short transcripts from a soybean HT-SuperSAGE (High Throughput Super Serial Analysis of Gene Expression; 26-bp tags) database, and also its comparison with other transcriptomic and genomic data available from different sources. A curated set of Osmoprotectants related sequences was generated using text mining and selected seed sequences for identification of the respective transcripts and proteins in higher plants. To test the efficiency of the seed sequences, these were aligned against four HT-SuperSAGE contrasting libraries generated by our group using soybean tolerant and sensible plants against water deficit, considering only differentially expressed transcripts (p ≤ 0.05). Identified transcripts from soybean and their respective tags were aligned and anchored against the soybean virtual genome. The workflow applied resulted in a set including 1,996 seed sequences that allowed the identification of 36 differentially expressed genes related to the biosynthesis of Osmoprotectants [Proline (P5CS: 4, P5CR: 2), Trehalose (TPS1: 9, TPPB: 1), Glycine betaine (BADH: 4) and Myo- inositol (MIPS: 7, INPS1: 8)], also mapped in silico in the soybean genome (25 loci). Another approach considered matches using Arabidopsis full length sequences as seed sequences, and allowed the identification of 124 osmoprotectant-related sequences, matching ~10.500 tags anchored in the soybean virtual chromosomes. Osmoprotectant-related genes appeared clustered in all soybean chromosomes, with higher density in some subterminal regions and synteny among some chromosome pairs. Soybean presents all searched osmoprotectant categories with some important members differentially expressed among the comparisons considered (drought tolerant or sensible vs. control; tolerant vs. sensible), allowing the identification of interesting candidates for biotechnological inferences. The identified tags aligned to corresponding genes that matched 19 soybean chromosomes. Osmoprotectant-related genes are not regularly distributed in the soybean genome, but clustered in some regions near the chromosome terminals, with some redundant clusters in different chromosomes indicating their involvement in previous duplication and rearrangements events. The seed sequences, transcripts and map represent the first transversal evaluation for osmoprotectant-related genes and may be easily applied to other plants of interest.

  • Transcriptomics of Sugarcane Osmoprotectants Under Drought
    Plants and Environment, 2011
    Co-Authors: Rlo Silva, Ana Maria Benko-iseppon, Valesca Pandolfi, Jrc Ferreira Neto, Sabrina Moutinho Chabregas, William Lee Burnquist, Ederson A Kido
    Abstract:

    Sugarcane (Saccharum spp.) is an alogamous plant from the Poaceae family and the Andropogoneae tribe (Daniels & Roach, 1987). This crop covers more than 23 million hectares worldwide, representing about 0.5 % of the total global area used for agriculture, with a production of 1.6 billion metric tons of crushable stems (FAOSTAT, 2009). Brazil is the world’s largest producer, contributing with two-thirds of total sugar production about 31 million tons per year of which 19.5 million tons are exported (UNICA, 2009). Sugarcane, its derivatives and by products have received great attention, due to their multiple uses, with emphasis on the ethanol production, representing an important renewable biofuel source. It has been estimated that sugarcane ethanol fuel may replace up to 10.0 % of the world’s refined petroleum products consumption in the next 15 to 20 years (Goldemberg, 2007). Despite its importance and similarity to other important agronomic crops, the sugarcane production has been adversely influenced by many environmental factors such as harsh climate and soil conditions. Abiotic stresses are among the main causes of losses in the productivity of the major crops worldwide (Bray et al., 2000), a scenario where drought figures as the most significant stress, causing negative impacts on crop adaptation and productivity. Besides, this condition can exacerbate the effect of other stresses (biotic or abiotic) to which the plants may be submitted. Although breeding activities have provided significant progress for the understanding of the physiological and molecular responses of plants to water deficit, there is still a large gap between yields in optimal and stressful conditions (Cattivelli et al., 2008). Essays regarding plant responses to drought stress have been published applying technologies of functional genomics (Wang et al., 2011). These evaluations provided important insights into molecular and biochemical mechanisms in the study of drought tolerance in various crops and model species. Plants are able to ‘‘perceive’’ the external stimuli by multiple sensors, recognizing adverse situations and invoking signal transduction cascades and consequently secondary messengers, activating stress responsive genes (Grennan, 2006), resulting in both molecular and physiological responses. Among the mechanisms developed by plants to face the adverse conditions generated under drought, the accumulation of Osmoprotectants compounds are often recognized as a mitigation mechanism of the negative consequences of water deficit (Choluj et al., 2008).

  • Osmoprotectants in the sugarcane (saccharum spp.) transcriptome revealed by in silico evaluation
    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2011
    Co-Authors: Petra Barros Dos Santos, Nina Da Mota Soares-cavalcanti, Gabriela S. Vieira-de-melo, Ana Maria Benko-iseppon
    Abstract:

    Environmental stresses such as drought and salinity limit crop productivity in worldwide level. These stresses often lead to the accumulation of Osmoprotectants in most organisms, including plants. In the present work, a search of known Osmoprotectants ( P5CS , P5CR , INPS1 , BADH , CMO , TPS , TPP , OASTL and SAT ) was carried out in the sugarcane transcriptome (237,954 expressed sequence tags) using in silico procedures. Alignments revealed that sugarcane presents a high number of osmoprotectant candidate genes, with 56 clusters found. In silico expression revealed higher expression in stressed callus tissues and those infected by Herbaspirilum rubrisubalbicans (HR), confirming the multi-function character of the Osmoprotectants. As expected, the phylogenetic analysis revealed distinct groups among angiosperms, algae, animals, fungi and bacteria, in almost all dendrograms, with high degree of sequence conservation among angiosperms. As observed in comparative analysis between the ORFs of sugarcane and other organisms, the genic structure of these plants was relatively conserved suggesting that the accumulation of compatible solutes is an ancient metabolic adaptation.

  • CIBB - Osmoprotectants in the sugarcane (Saccharum spp.) transcriptome revealed by in silico evaluation
    Computational Intelligence Methods for Bioinformatics and Biostatistics, 2011
    Co-Authors: Petra Barros Dos Santos, Gabriela S. Vieira-de-melo, Nina M Soares-cavalcanti, Ana Maria Benko-iseppon
    Abstract:

    Environmental stresses such as drought and salinity limit crop productivity in worldwide level. These stresses often lead to the accumulation of Osmoprotectants in most organisms, including plants. In the present work, a search of known Osmoprotectants (P5CS, P5CR, INPS1, BADH, CMO, TPS, TPP, OASTL and SAT) was carried out in the sugarcane transcriptome (237,954 expressed sequence tags) using in silico procedures. Alignments revealed that sugarcane presents a high number of osmoprotectant candidate genes, with 56 clusters found. In silico expression revealed higher expression in stressed callus tissues and those infected by Herbaspirilum rubrisubalbicans (HR), confirming the multi-function character of the Osmoprotectants. As expected, the phylogenetic analysis revealed distinct groups among angiosperms, algae, animals, fungi and bacteria, in almost all dendrograms, with high degree of sequence conservation among angiosperms. As observed in comparative analysis between the ORFs of sugarcane and other organisms, the genic structure of these plants was relatively conserved suggesting that the accumulation of compatible solutes is an ancient metabolic adaptation.

Ederson A Kido - One of the best experts on this subject based on the ideXlab platform.

  • Osmoprotectant-Related Genes in Plants Under Abiotic Stress: Expression Dynamics, In Silico Genome Mapping, and Biotechnology
    Osmoprotectant-Mediated Abiotic Stress Tolerance in Plants, 2019
    Co-Authors: Ederson A Kido, Manassés D Silva, José Ribamar Costa Ferreira-neto, Vanessa Emanuelle Pereira Santos, Jorge Luís Bandeira Da Silva Filho, Ana Maria Benko-iseppon
    Abstract:

    Osmoprotectants are categorized as osmolytes, also known as compatible solutes, considering that they are small organic molecules that share characteristics, like low molecular weight, neutral charge, and low toxicity, even at high concentrations in cells. They are identified in different chemical classes, including polyamines (e.g., putrescine, spermidine, spermine), sugars (e.g., sucrose, trehalose, raffinose), sugar alcohols (e.g., myo-inositols), betaines (e.g., glycine betaine), and amino acids (e.g., proline). In plants exposed to abiotic stresses (salinity/drought), Osmoprotectants help cellular turgor preservation and drive the water uptake gradient. Some Osmoprotectants shield plants from damage through chaperone-like activities, helping in the conservation of membrane structures and protein functions, or scavenging for reactive oxygen species (ROS) generated by the stresses. Therefore, it is advantageous to understand how plants respond to abiotic stresses by regulating the expression of osmoprotectant-related genes. This chapter presents data on plant Osmoprotectants, including their regulating genes, associated pathways, and transcriptional regulations in plants under abiotic stresses. There is also an overview of their in silico mapping (model plants/crops) and their biotechnological potential as transgenes. Furthermore, these approaches are new perspectives for the analysis and introgression of these related genes into cultivated plant species, improving advances in plant breeding and crop production.

  • Expression dynamics and genome distribution of Osmoprotectants in soybean: identifying important components to face abiotic stress
    BMC Bioinformatics, 2013
    Co-Authors: Ederson A Kido, José Rc Ferreira Neto, Roberta Lo Silva, Luis C Belarmino, João P Bezerra Neto, Nina M Soares-cavalcanti, Valesca Pandolfi, Manassés D Silva, Alexandre L Nepomuceno, Ana M Benko-iseppon
    Abstract:

    Background Despite the importance of Osmoprotectants, no previous in silico evaluation of high throughput data is available for higher plants. The present approach aimed at the identification and annotation of osmoprotectant-related sequences applied to short transcripts from a soybean HT-SuperSAGE (High Throughput Super Serial Analysis of Gene Expression; 26-bp tags) database, and also its comparison with other transcriptomic and genomic data available from different sources. Methods A curated set of Osmoprotectants related sequences was generated using text mining and selected seed sequences for identification of the respective transcripts and proteins in higher plants. To test the efficiency of the seed sequences, these were aligned against four HT-SuperSAGE contrasting libraries generated by our group using soybean tolerant and sensible plants against water deficit, considering only differentially expressed transcripts (p ≤ 0.05). Identified transcripts from soybean and their respective tags were aligned and anchored against the soybean virtual genome. Results The workflow applied resulted in a set including 1,996 seed sequences that allowed the identification of 36 differentially expressed genes related to the biosynthesis of Osmoprotectants [Proline ( P5CS : 4, P5CR : 2), Trehalose ( TPS1 : 9, TPPB : 1), Glycine betaine ( BADH : 4) and Myo- inositol ( MIPS : 7, INPS1 : 8)], also mapped in silico in the soybean genome (25 loci). Another approach considered matches using Arabidopsis full length sequences as seed sequences, and allowed the identification of 124 osmoprotectant-related sequences, matching ~10.500 tags anchored in the soybean virtual chromosomes. Osmoprotectant-related genes appeared clustered in all soybean chromosomes, with higher density in some subterminal regions and synteny among some chromosome pairs. Conclusions Soybean presents all searched osmoprotectant categories with some important members differentially expressed among the comparisons considered (drought tolerant or sensible vs . control; tolerant vs . sensible), allowing the identification of interesting candidates for biotechnological inferences. The identified tags aligned to corresponding genes that matched 19 soybean chromosomes. Osmoprotectant-related genes are not regularly distributed in the soybean genome, but clustered in some regions near the chromosome terminals, with some redundant clusters in different chromosomes indicating their involvement in previous duplication and rearrangements events. The seed sequences, transcripts and map represent the first transversal evaluation for osmoprotectant-related genes and may be easily applied to other plants of interest.

  • Expression dynamics and genome distribution of Osmoprotectants in soybean: identifying important components to face abiotic stress
    BMC Bioinformatics, 2013
    Co-Authors: Ederson A Kido, Luis C Belarmino, Nina M Soares-cavalcanti, Valesca Pandolfi, Manassés D Silva, Alexandre L Nepomuceno, José Ribamar Costa Ferreira Neto, Roberta Lane De Oliveira Silva, João Pacífico Bezerra Neto, Ana Maria Benko-iseppon
    Abstract:

    Despite the importance of Osmoprotectants, no previous in silico evaluation of high throughput data is available for higher plants. The present approach aimed at the identification and annotation of osmoprotectant-related sequences applied to short transcripts from a soybean HT-SuperSAGE (High Throughput Super Serial Analysis of Gene Expression; 26-bp tags) database, and also its comparison with other transcriptomic and genomic data available from different sources. A curated set of Osmoprotectants related sequences was generated using text mining and selected seed sequences for identification of the respective transcripts and proteins in higher plants. To test the efficiency of the seed sequences, these were aligned against four HT-SuperSAGE contrasting libraries generated by our group using soybean tolerant and sensible plants against water deficit, considering only differentially expressed transcripts (p ≤ 0.05). Identified transcripts from soybean and their respective tags were aligned and anchored against the soybean virtual genome. The workflow applied resulted in a set including 1,996 seed sequences that allowed the identification of 36 differentially expressed genes related to the biosynthesis of Osmoprotectants [Proline (P5CS: 4, P5CR: 2), Trehalose (TPS1: 9, TPPB: 1), Glycine betaine (BADH: 4) and Myo- inositol (MIPS: 7, INPS1: 8)], also mapped in silico in the soybean genome (25 loci). Another approach considered matches using Arabidopsis full length sequences as seed sequences, and allowed the identification of 124 osmoprotectant-related sequences, matching ~10.500 tags anchored in the soybean virtual chromosomes. Osmoprotectant-related genes appeared clustered in all soybean chromosomes, with higher density in some subterminal regions and synteny among some chromosome pairs. Soybean presents all searched osmoprotectant categories with some important members differentially expressed among the comparisons considered (drought tolerant or sensible vs. control; tolerant vs. sensible), allowing the identification of interesting candidates for biotechnological inferences. The identified tags aligned to corresponding genes that matched 19 soybean chromosomes. Osmoprotectant-related genes are not regularly distributed in the soybean genome, but clustered in some regions near the chromosome terminals, with some redundant clusters in different chromosomes indicating their involvement in previous duplication and rearrangements events. The seed sequences, transcripts and map represent the first transversal evaluation for osmoprotectant-related genes and may be easily applied to other plants of interest.

  • Transcriptomics of Sugarcane Osmoprotectants Under Drought
    Plants and Environment, 2011
    Co-Authors: Rlo Silva, Ana Maria Benko-iseppon, Valesca Pandolfi, Jrc Ferreira Neto, Sabrina Moutinho Chabregas, William Lee Burnquist, Ederson A Kido
    Abstract:

    Sugarcane (Saccharum spp.) is an alogamous plant from the Poaceae family and the Andropogoneae tribe (Daniels & Roach, 1987). This crop covers more than 23 million hectares worldwide, representing about 0.5 % of the total global area used for agriculture, with a production of 1.6 billion metric tons of crushable stems (FAOSTAT, 2009). Brazil is the world’s largest producer, contributing with two-thirds of total sugar production about 31 million tons per year of which 19.5 million tons are exported (UNICA, 2009). Sugarcane, its derivatives and by products have received great attention, due to their multiple uses, with emphasis on the ethanol production, representing an important renewable biofuel source. It has been estimated that sugarcane ethanol fuel may replace up to 10.0 % of the world’s refined petroleum products consumption in the next 15 to 20 years (Goldemberg, 2007). Despite its importance and similarity to other important agronomic crops, the sugarcane production has been adversely influenced by many environmental factors such as harsh climate and soil conditions. Abiotic stresses are among the main causes of losses in the productivity of the major crops worldwide (Bray et al., 2000), a scenario where drought figures as the most significant stress, causing negative impacts on crop adaptation and productivity. Besides, this condition can exacerbate the effect of other stresses (biotic or abiotic) to which the plants may be submitted. Although breeding activities have provided significant progress for the understanding of the physiological and molecular responses of plants to water deficit, there is still a large gap between yields in optimal and stressful conditions (Cattivelli et al., 2008). Essays regarding plant responses to drought stress have been published applying technologies of functional genomics (Wang et al., 2011). These evaluations provided important insights into molecular and biochemical mechanisms in the study of drought tolerance in various crops and model species. Plants are able to ‘‘perceive’’ the external stimuli by multiple sensors, recognizing adverse situations and invoking signal transduction cascades and consequently secondary messengers, activating stress responsive genes (Grennan, 2006), resulting in both molecular and physiological responses. Among the mechanisms developed by plants to face the adverse conditions generated under drought, the accumulation of Osmoprotectants compounds are often recognized as a mitigation mechanism of the negative consequences of water deficit (Choluj et al., 2008).

Teruhiro Takabe - One of the best experts on this subject based on the ideXlab platform.

  • Osmoprotectant and Sunscreen Molecules From Halophilic Algae and Cyanobacteria
    Algal Green Chemistry, 2017
    Co-Authors: Hakuto Kageyama, Rungaroon Waditee-sirisattha, Yoshito Tanaka, Teruhiro Takabe
    Abstract:

    Abstract To survive under halophilic environments, halophilic microorganisms must have developed the special systems such as synthesis of osmoprotectant and sunscreen molecules. Osmoprotectants are small molecules that act as osmolytes and help organisms survive under extreme saline conditions. Examples of compatible solutes include betaines, amino acids, dimethylsulfoniopropionate, and sugars. These molecules accumulate in cells and balance the osmotic difference between the cell's surroundings and the cytosol. Compatible solutes have also been shown to play a protective role by maintaining enzyme activity under abiotic stress conditions. Their specific action is unknown but is thought that they are preferentially excluded from the proteins interface due to their propensity to form water structures. Here, we summarize recent progress on the research of osmoprotectant and sunscreen molecules in halophilic algae/cyanobacteria. Their possible biotechnological application in the field of green energy, biomedical research, and various biochemical industries were described.

  • Osmoprotectant and Sunscreen Molecules From Halophilic Algae and Cyanobacteria
    Algal Green Chemistry, 2017
    Co-Authors: Hakuto Kageyama, Rungaroon Waditee-sirisattha, Yoshito Tanaka, Teruhiro Takabe
    Abstract:

    Abstract To survive under halophilic environments, halophilic microorganisms must have developed the special systems such as synthesis of osmoprotectant and sunscreen molecules. Osmoprotectants are small molecules that act as osmolytes and help organisms survive under extreme saline conditions. Examples of compatible solutes include betaines, amino acids, dimethylsulfoniopropionate, and sugars. These molecules accumulate in cells and balance the osmotic difference between the cell's surroundings and the cytosol. Compatible solutes have also been shown to play a protective role by maintaining enzyme activity under abiotic stress conditions. Their specific action is unknown but is thought that they are preferentially excluded from the proteins interface due to their propensity to form water structures. Here, we summarize recent progress on the research of osmoprotectant and sunscreen molecules in halophilic algae/cyanobacteria. Their possible biotechnological application in the field of green energy, biomedical research, and various biochemical industries were described.

Erhard Bremer - One of the best experts on this subject based on the ideXlab platform.

  • Ectoine functions as an osmoprotectant in Bacillus subtilis and is accumulated via the ABC-transport system OpuC
    FEMS Microbiology Letters, 2006
    Co-Authors: Mohamed Jebbar, Carsten Von Blohn, Erhard Bremer
    Abstract:

    We report here that the cyclic amino acid ectoine functions as an osmoprotectant for the soil bacterium Bacillus subtilis. Growth experiments with a set of B. subtilis strains that carry defined mutations in the glycine betaine transport systems OpuA, OpuC and OpuD and the choline transport system OpuB revealed that ectoine was specifically accumulated via the ABC-transport system OpuC. Competition experiments employing unlabeled ectoine and radiolabeled glycine betaine showed that the OpuC transport system has a low affinity for ectoine with a Ki value of approximately 1.5 mM. Ectoine was identified by 1H NMR spectroscopy in the solute pool of cells grown in the presence of ectoine. Ectoine could not be used by B. subtilis as sole carbon or nitrogen source. Our data thus characterise ectoine as a metabolically inert stress compound for B. subtilis and establish a crucial role for the ABC-transport system OpuC for the acquisition of the osmoprotectant ectoine from the environment.

  • Stress responses ofBacillus subtilis to high osmolarity environments: Uptake and synthesis of Osmoprotectants
    Journal of Biosciences, 1998
    Co-Authors: Bettina Kempf, Erhard Bremer
    Abstract:

    A decrease in the water content of the soil imposes a considerable stress on the voil-living bacteriumBacillus subtilis: water exits from the cells, resulting in decreased turgor and cessation of growth. Under these adverse circumstances,B. subtilis actively modulates the osmolarity of its cytoplasm to maintain turgor within acceptable boundaries. A rapid uptake of potassium ions via turgor-responsive transport systems is the primary stress response to a sudden increase in the external osmolarity. This is followed by the massive accumulation of the so-called compatible solutes, i.e., organic osmolytes that are highly congruous with cellular functions and hence can be accumulated by bacterial cells up to molar concentrations. Initially, the compatible solute proline is accumulated viade novo synthesis, butB. subtilis can also acquire proline from the environment by an osmoregulated transport system, OpuE. The preferred compatible solute ofB. subtilis is the potent osmoprotectant glycine betaine. This trimethylammonium compound can be taken up by the cell through three high-affinity transport systems: the multicomponent ABC transporters OpuA and OpuC, and the single-component transporter OpuD. The OpuC systems also mediates the accumulation of a variety of naturally occurring betaines, each of which can confer a considerable degree of osmotic tolerance. In addition to the uptake of glycine betaine from the environment,B. subtilis can also synthesize this osmoprotectant but it requires exogenously provided choline as its precursor. Two evolutionarily closely related ABC transport systems, OpuB and OpuC, mediate the uptake of choline which is then converted by the GbsA and GbsB enzymes in a two-step oxidation process into glycine betaine. Our data show that the intracellular accumulation of Osmoprotectants is of central importance for the cellular defence ofB. subtilis against high osmolarity stress.

  • The osmoprotectant proline betaine is a major substrate for the binding-protein-dependent transport system ProU of Escherichia coli K-12
    Molecular & general genetics : MGG, 1995
    Co-Authors: Martin Haardt, Bettina Kempf, Elke Faatz, Erhard Bremer
    Abstract:

    The ProP and ProU transport systems of Escherichia coli mediate the uptake of several Osmoprotectants including glycine betaine. Here we report that both ProP and ProU are involved in the transport of the potent osmoprotectant proline betaine. A set of isogenic E. coli strains carrying deletions in either the proP or proU loci was constructed. The growth properties of these mutants in high osmolarity minimal media containing 1 mM proline betaine demonstrated that the osmoprotective effect of this compound was dependent on either an intact ProP or ProU uptake system. Proline betaine competes with glycine betaine for binding to the proU-encoded periplasmic substrate binding protein (ProX) and we estimate a KD of 5.2 μM for proline betaine binding. This value is similar to the binding constant of the ProX protein determined previously for the binding of glycine betaine (KD of 1.4 μM). Our results thus demonstrate that the binding-protein-dependent ProU transport system of E. coli mediates the efficient uptake of the Osmoprotectants glycine betaine and proline betaine.

Nina M Soares-cavalcanti - One of the best experts on this subject based on the ideXlab platform.

  • Expression dynamics and genome distribution of Osmoprotectants in soybean: identifying important components to face abiotic stress
    BMC Bioinformatics, 2013
    Co-Authors: Ederson A Kido, José Rc Ferreira Neto, Roberta Lo Silva, Luis C Belarmino, João P Bezerra Neto, Nina M Soares-cavalcanti, Valesca Pandolfi, Manassés D Silva, Alexandre L Nepomuceno, Ana M Benko-iseppon
    Abstract:

    Background Despite the importance of Osmoprotectants, no previous in silico evaluation of high throughput data is available for higher plants. The present approach aimed at the identification and annotation of osmoprotectant-related sequences applied to short transcripts from a soybean HT-SuperSAGE (High Throughput Super Serial Analysis of Gene Expression; 26-bp tags) database, and also its comparison with other transcriptomic and genomic data available from different sources. Methods A curated set of Osmoprotectants related sequences was generated using text mining and selected seed sequences for identification of the respective transcripts and proteins in higher plants. To test the efficiency of the seed sequences, these were aligned against four HT-SuperSAGE contrasting libraries generated by our group using soybean tolerant and sensible plants against water deficit, considering only differentially expressed transcripts (p ≤ 0.05). Identified transcripts from soybean and their respective tags were aligned and anchored against the soybean virtual genome. Results The workflow applied resulted in a set including 1,996 seed sequences that allowed the identification of 36 differentially expressed genes related to the biosynthesis of Osmoprotectants [Proline ( P5CS : 4, P5CR : 2), Trehalose ( TPS1 : 9, TPPB : 1), Glycine betaine ( BADH : 4) and Myo- inositol ( MIPS : 7, INPS1 : 8)], also mapped in silico in the soybean genome (25 loci). Another approach considered matches using Arabidopsis full length sequences as seed sequences, and allowed the identification of 124 osmoprotectant-related sequences, matching ~10.500 tags anchored in the soybean virtual chromosomes. Osmoprotectant-related genes appeared clustered in all soybean chromosomes, with higher density in some subterminal regions and synteny among some chromosome pairs. Conclusions Soybean presents all searched osmoprotectant categories with some important members differentially expressed among the comparisons considered (drought tolerant or sensible vs . control; tolerant vs . sensible), allowing the identification of interesting candidates for biotechnological inferences. The identified tags aligned to corresponding genes that matched 19 soybean chromosomes. Osmoprotectant-related genes are not regularly distributed in the soybean genome, but clustered in some regions near the chromosome terminals, with some redundant clusters in different chromosomes indicating their involvement in previous duplication and rearrangements events. The seed sequences, transcripts and map represent the first transversal evaluation for osmoprotectant-related genes and may be easily applied to other plants of interest.

  • Expression dynamics and genome distribution of Osmoprotectants in soybean: identifying important components to face abiotic stress
    BMC Bioinformatics, 2013
    Co-Authors: Ederson A Kido, Luis C Belarmino, Nina M Soares-cavalcanti, Valesca Pandolfi, Manassés D Silva, Alexandre L Nepomuceno, José Ribamar Costa Ferreira Neto, Roberta Lane De Oliveira Silva, João Pacífico Bezerra Neto, Ana Maria Benko-iseppon
    Abstract:

    Despite the importance of Osmoprotectants, no previous in silico evaluation of high throughput data is available for higher plants. The present approach aimed at the identification and annotation of osmoprotectant-related sequences applied to short transcripts from a soybean HT-SuperSAGE (High Throughput Super Serial Analysis of Gene Expression; 26-bp tags) database, and also its comparison with other transcriptomic and genomic data available from different sources. A curated set of Osmoprotectants related sequences was generated using text mining and selected seed sequences for identification of the respective transcripts and proteins in higher plants. To test the efficiency of the seed sequences, these were aligned against four HT-SuperSAGE contrasting libraries generated by our group using soybean tolerant and sensible plants against water deficit, considering only differentially expressed transcripts (p ≤ 0.05). Identified transcripts from soybean and their respective tags were aligned and anchored against the soybean virtual genome. The workflow applied resulted in a set including 1,996 seed sequences that allowed the identification of 36 differentially expressed genes related to the biosynthesis of Osmoprotectants [Proline (P5CS: 4, P5CR: 2), Trehalose (TPS1: 9, TPPB: 1), Glycine betaine (BADH: 4) and Myo- inositol (MIPS: 7, INPS1: 8)], also mapped in silico in the soybean genome (25 loci). Another approach considered matches using Arabidopsis full length sequences as seed sequences, and allowed the identification of 124 osmoprotectant-related sequences, matching ~10.500 tags anchored in the soybean virtual chromosomes. Osmoprotectant-related genes appeared clustered in all soybean chromosomes, with higher density in some subterminal regions and synteny among some chromosome pairs. Soybean presents all searched osmoprotectant categories with some important members differentially expressed among the comparisons considered (drought tolerant or sensible vs. control; tolerant vs. sensible), allowing the identification of interesting candidates for biotechnological inferences. The identified tags aligned to corresponding genes that matched 19 soybean chromosomes. Osmoprotectant-related genes are not regularly distributed in the soybean genome, but clustered in some regions near the chromosome terminals, with some redundant clusters in different chromosomes indicating their involvement in previous duplication and rearrangements events. The seed sequences, transcripts and map represent the first transversal evaluation for osmoprotectant-related genes and may be easily applied to other plants of interest.

  • CIBB - Osmoprotectants in the sugarcane (Saccharum spp.) transcriptome revealed by in silico evaluation
    Computational Intelligence Methods for Bioinformatics and Biostatistics, 2011
    Co-Authors: Petra Barros Dos Santos, Gabriela S. Vieira-de-melo, Nina M Soares-cavalcanti, Ana Maria Benko-iseppon
    Abstract:

    Environmental stresses such as drought and salinity limit crop productivity in worldwide level. These stresses often lead to the accumulation of Osmoprotectants in most organisms, including plants. In the present work, a search of known Osmoprotectants (P5CS, P5CR, INPS1, BADH, CMO, TPS, TPP, OASTL and SAT) was carried out in the sugarcane transcriptome (237,954 expressed sequence tags) using in silico procedures. Alignments revealed that sugarcane presents a high number of osmoprotectant candidate genes, with 56 clusters found. In silico expression revealed higher expression in stressed callus tissues and those infected by Herbaspirilum rubrisubalbicans (HR), confirming the multi-function character of the Osmoprotectants. As expected, the phylogenetic analysis revealed distinct groups among angiosperms, algae, animals, fungi and bacteria, in almost all dendrograms, with high degree of sequence conservation among angiosperms. As observed in comparative analysis between the ORFs of sugarcane and other organisms, the genic structure of these plants was relatively conserved suggesting that the accumulation of compatible solutes is an ancient metabolic adaptation.

  • CIBB - In Silico Evaluation of Osmoprotectants in Eucalyptus Transcriptome
    Computational Intelligence Methods for Bioinformatics and Biostatistics, 2009
    Co-Authors: Petra Santos Barros, Nina M Soares-cavalcanti, Gabriela S. Vieira-mello, Ana Carolina Wanderley-nogueira, Tercílio Calsa-junior, Ana Maria Benko-iseppon
    Abstract:

    The synthesis of Osmoprotectants is one of the main mechanisms to dribble harmful effects caused by abiotic stresses. In the present work, osmoprotectant genes were selected and used in a search for orthologs in the FORESTs database using in silico procedures. The studied genes were here analyzed for the first time in Eucalyptus , including 51 identified orthologs from nine gene families (P5CS =3, P5CR =4, TPS1 =10, TPPB =8, SAT =6, OASTL =13, CMO =1, BADH =3 and INPS1 =3). In general, the most represented genes were those involved in the trehalose and cysteine synthesis, probably due to their vital importance in the maintenance of cellular homeostasis. Overall expression pattern revealed significant amounts of reads in most libraries. Dendrograms based on analysis of selected genes from other flowering plants revealed no clear separation between mono and dicots, since diversity regarding the evolution and diversity in gene signatures may be more related to fitness and adaptation, than evolutionary patterns.