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Eduardo Blumwald

Publications and source records attributed to Eduardo Blumwald.

14 recordsLinked to original sources
PubMed2006

Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution.

BACKGROUND: DNA microarrays are a powerful technology that can provide a wealth of gene expression data for disease studies, drug development, and a wide scope of other investigations. Because of the large volume and inherent variability of DNA microarray data, many new statistical methods have been developed for evaluating the significance of the observed differences in gene expression. However, until now little attention has been given to the characterization of dispersion of DNA microarray data. RESULTS: Here we examine the expression data obtained from 682 Affymetrix GeneChips with 22 different types and we demonstrate that the Gaussian (normal) frequency distribution is characteristic for the variability of gene expression values. However, typically 5 to 15% of the samples deviate from normality. Furthermore, it is shown that the frequency distributions of the difference of expression in subsets of ordered, consecutive pairs of genes (consecutive samples) in pair-wise comparisons of replicate experiments are also normal. We describe a consecutive sampling method, which is employed to calculate the characteristic function approximating standard deviation and show that the standard deviation derived from the consecutive samples is equivalent to the standard deviation obtained from individual genes. Finally, we determine the boundaries of probability intervals and demonstrate that the coefficients defining the intervals are independent of sample characteristics, variability of data, laboratory conditions and type of chips. These coefficients are very closely correlated with Student's t-distribution. CONCLUSION: In this study we ascertained that the non-systematic variations possess Gaussian distribution, determined the probability intervals and demonstrated that the K(alpha) coefficients defining these intervals are invariant; these coefficients offer a convenient universal measure of dispersion of data. The fact that the K(alpha) distributions are so close to t-distribution and independent of conditions and type of arrays suggests that the quantitative data provided by Affymetrix technology give "true" representation of physical processes, involved in measurement of RNA abundance. REVIEWERS: This article was reviewed by Yoav Gilad (nominated by Doron Lancet), Sach Mukherjee (nominated by Sandrine Dudoit) and Amir Niknejad and Shmuel Friedland (nominated by Neil Smalheiser).

Journal Article↗
PubMed2006

Salt stress response in rice: genetics, molecular biology, and comparative genomics.

Significant progress has been made in unraveling the molecular biology of rice in the past two decades. Today, rice stands as a forerunner amongst the cereals in terms of details known on its genetics. Evidence show that salt tolerance in plants is a quantitative trait. Several traditional cultivars, landraces, and wild types of rice like Pokkali, CSR types, and Porteresia coarctata appear as promising materials for donation of requisite salt tolerance genes. A large number of quantitative trait loci (QTL) have been identified for salt tolerance in rice through generation of recombinant inbred lines and are being mapped using different types of DNA markers. Salt-tolerant transgenic rice plants have been produced using a host of different genes and transcript profiling by micro- and macroarray-based methods has opened the gates for the discovery of novel salt stress mechanisms in rice, and comparative genomics is turning out to be a critical input in this respect. In this paper, we present a comprehensive review of the genetic, molecular biology, and comparative genomics effort towards the generation of salt-tolerant rice. From the data on comprehensive transcript expression profiling of clones representing salt-stress-associated genes of rice, it is shown that transcriptional and translational machineries are important determinants in controlling salt stress response, and gene expression response in tolerant and susceptible rice plants differs mainly in quantitative terms.

Acclimatization↗
PubMed2006

Vacuolar citrate/H+ symporter of citrus juice cells.

We have isolated a cDNA, designated Citrus sinensis citrate transporter 1 CsCit1 encoding a novel vacuolar citrate/symporter. Immunoblots using antibodies raised against CsCit1 showed that the protein is localized to the juice sac cell vacuoles. The highest expression of CsCit1 and the amount of protein in the juice sac cell vacuoles coincided with the developmental stage at which the vacuolar citrate content began declining with the concomitant increase in vacuolar pH. Vacuoles from Sacharomyces cereviseae expressing CsCit1 displayed a citrate-dependent H(+) efflux, and our results clearly demonstrate that CsCit1 is able to mediate the electroneutral co-transport of H(+) and citrate ions, since the citrate-dependent H(+) fluxes are not affected by changing the electrical potential difference across the tonoplast. The roles of CsCit1 in mediating citrate efflux from the vacuole and on citric acid homoestasis in Citrus juice sac cells are discussed.

Amino Acid Sequence↗
PubMed2005

Developing salt-tolerant crop plants: challenges and opportunities.

Soil salinity, one of the major abiotic stresses reducing agricultural productivity, affects large terrestrial areas of the world; the need to produce salt-tolerant crops is evident. Two main approaches are being used to improve salt tolerance: (i) the exploitation of natural genetic variations, either through direct selection in stressful environments or through mapping quantitative trait loci and subsequent marker-assisted selection; and (ii) the generation of transgenic plants to introduce novel genes or to alter expression levels of the existing genes to affect the degree of salt stress tolerance. Here, we discuss the challenges and opportunities provided by recently developed functional tools for the development of salt-tolerant crops.

Adaptation, Physiological↗
PubMed2005

Vacuolar Na+/H+ antiporter cation selectivity is regulated by calmodulin from within the vacuole in a Ca2+- and pH-dependent manner.

The selective movement of ions between intracellular compartments is fundamental for eukaryotes. Arabidopsis thaliana Na(+)/H(+) exchanger 1 (AtNHX1), the most abundant vacuolar Na(+)/H(+) antiporter in A. thaliana, has important roles affecting the maintenance of cellular pH, ion homeostasis, and the regulation of protein trafficking. Previously, we have shown that the AtNHX1 C-terminal hydrophilic region localized in the vacuolar lumen plays an important role in regulating the antiporter's activity. Here, we have identified A. thaliana calmodulin-like protein 15 (AtCaM15), which interacts with the AtNHX1 C terminus. When expressed in yeast, AtCaM15 is localized in the vacuolar lumen. The transient expression of AtCaM15 in Arabidopsis leaf protoplasts showed that AtCaM15 is present in the central vacuole. The binding of AtCaM15 to AtNHX1 was Ca(2+)- and pH-dependent and decreased with increasing pH values. Our results also show that the binding of AtCaM15 to AtNHX1 modified the Na(+)/K(+) selectivity of the antiporter, decreasing its Na(+)/H(+) exchange activity. Taken together, the presence of a vacuolar calmodulin-like protein acting on the vacuolar-localized AtNHX1 C terminus in a Ca(2+)- pH-dependent manner suggests the presence of signaling entities acting within the vacuole.

Arabidopsis Proteins↗
PubMed2005

Expression of an Arabidopsis vacuolar sodium/proton antiporter gene in cotton improves photosynthetic performance under salt conditions and increases fiber yield in the field.

Drought and salinity are two major limiting factors in crop productivity. One way to reduce crop loss caused by drought and salinity is to increase the solute concentration in the vacuoles of plant cells. The accumulation of sodium ions inside the vacuoles provides a 2-fold advantage: (i) reducing the toxic levels of sodium in cytosol; and (ii) increasing the vacuolar osmotic potential with the concomitant generation of a more negative water potential that favors water uptake by the cell and better tissue water retention under high soil salinity. The success of this approach was demonstrated in several plants, where the overexpression of the Arabidopsis gene AtNHX1 that encodes a vacuolar sodium/proton antiporter resulted in higher plant salt tolerance. Overexpression of AtNHX1 increases sodium uptake in vacuoles, which leads to increased vacuolar solute concentration and therefore higher salt tolerance in transgenic plants. In an effort to engineer cotton for higher drought and salt tolerance, we created transgenic cotton plants expressing AtNHX1. These AtNHX1-expressing cotton plants generated more biomass and produced more fibers when grown in the presence of 200 mM NaCl in greenhouse conditions. The increased fiber yield was probably due to better photosynthetic performance and higher nitrogen assimilation rates observed in the AtNHX1-expressing cotton plants as compared with wild-type cotton plants under saline conditions. Furthermore, the field-grown AtNHX1-expressing cotton plants produced more fibers with better quality, indicating that AtNHX1 can indeed be used for improving salt stress tolerance in cotton.

Adaptation, Physiological↗
PubMed2004

DNA array analyses of Arabidopsis thaliana lacking a vacuolar Na+/H+ antiporter: impact of AtNHX1 on gene expression.

AtNHX1, a vacuolar cation/proton antiporter of Arabidopsis, plays an important role in salt tolerance, ion homeostasis and development. We used the T-DNA insertional mutant of AtNHX1 (nhx1 plants) and Affymetrix ATH1 DNA arrays to assess differences in transcriptional profiles and further characterize the roles of a vacuolar cation/proton antiporter. Mature, soil-grown plants were used in this study to approximate typical physiological growing conditions. A comparison of plants grown in the absence of salt stress yielded many transcripts that were affected by the absence of the AtNHX1 vacuolar antiporter. Furthermore, changes in gene expression due to a non-lethal salt stress (100 mm NaCl) in the nhx1 plants were significantly different from the changes seen in wild-type plants. The nhx1 transcriptome was differentially affected when the plants were grown in the absence or presence of salt. In conclusion, in addition to the known role(s) of AtNHX1 on ion homeostasis, the vacuolar cation/proton antiporter plays a significant role in intracellular vesicular trafficking, protein targeting, and other cellular processes.

Arabidopsis↗
PubMed2003

Topological analysis of a plant vacuolar Na+/H+ antiporter reveals a luminal C terminus that regulates antiporter cation selectivity.

We conducted an analysis of the topology of AtNHX1, an Arabidopsis thaliana vacuolar Na+/H+ antiporter. Several hydrophilic regions of the antiporter were tagged with a hemagglutinin epitope, and protease protection assays were conducted to determine the membrane topology of the antiporter by using yeast as a heterologous expression system. The overall structure of AtNHX1 is distinct from the human Na+/H+ antiporter NHE1 or any known Na+/H+ antiporter. It is comprised of nine transmembrane domains and a hydrophilic C-terminal domain. Three hydrophobic regions do not appear to span the tonoplast membrane, yet appear to be membrane associated. Our results also indicate that, whereas the N terminus of AtNHX1 is facing the cytosol, almost the entire C-terminal hydrophilic region resides in the vacuolar lumen. Deletion of the hydrophilic C terminus resulted in a dramatic increase in the relative rate of Na+/H+ transport. The ratio of Na+/K+ transport was twice that of the unmodified AtNHX1. This altered ratio resulted from a relatively small decrease in K+/H+ transport with a large increase in Na+/H+ transport. The vacuolar localization of the C terminus of the AtNHX1, taken together with the regulation of the antiporter selectivity by its C terminus, demonstrates the existence of luminal vacuolar regulatory mechanisms of the antiporter activity.

Arabidopsis↗
PubMed2003

Vacuolar cation/H+ exchange, ion homeostasis, and leaf development are altered in a T-DNA insertional mutant of AtNHX1, the Arabidopsis vacuolar Na+/H+ antiporter.

The function of vacuolar Na+/H+ antiporter(s) in plants has been studied primarily in the context of salinity tolerance. By facilitating the accumulation of Na+ away from the cytosol, plant cells can avert ion toxicity and also utilize vacuolar Na+ as osmoticum to maintain turgor. As many genes encoding these antiporters have been cloned from salt-sensitive plants, it is likely that they function in some capacity other than salinity tolerance. The wide expression pattern of Arabidopsis thaliana sodium proton exchanger 1 (AtNHX1) in this study supports this hypothesis. Here, we report the isolation of a T-DNA insertional mutant of AtNHX1, a vacuolar Na+/H+ antiporter in Arabidopsis. Vacuoles isolated from leaves of the nhx1 plants had a much lower Na+/H+ and K+/H+ exchange activity. nhx1 plants also showed an altered leaf development, with reduction in the frequency of large epidermal cells and a reduction in overall leaf area compared to wild-type plants. The overexpression of AtNHX1 in the nhx1 background complemented these phenotypes. In the presence of NaCl, nhx1 seedling establishment was impaired. These results place AtNHX1 as the dominant K+ and Na+/H+ antiporter in leaf vacuoles in Arabidopsis and also suggest that its contribution to ion homeostasis is important for not only salinity tolerance but development as well.

Arabidopsis↗
PubMed2002

Engineering salt tolerance in plants.

Recent progress has been made in the identification and characterization of the mechanisms that allow plants to tolerate high salt concentrations. The understanding of metabolic fluxes and the main constraints for the production of compatible solutes (i.e. feedback inhibition and the limitation of substrate supply) open up the possibility of genetically engineering entire pathways that could lead to the production of osmoprotectants. This, together with the identification of the different sodium transporters (in particular vacuolar and plasma membrane Na(+)/H(+) antiporters) that could provide the needed ion homeostasis during salt stress, opens the possibility of engineering crop plants with improved salt tolerance.

Biological Transport↗
PubMed2002

Domains as functional building blocks of plant proteins.

Emerging evidence in eukaryotic systems suggests that many proteins of diverse cellular processes are made up of protein domains that are well defined in both sequence and structure. This article updates the identification of many 'classic' eukaryotic protein domains in various plant cellular processes, with particular emphasis on the non-catalytic categories. We discuss the importance of domains to plant-protein functions and cellular networking, and the emergence of plant-specific domains.

Amino Acid Sequence↗
PubMed2002

Identification and characterization of a NaCl-inducible vacuolar Na+/H+ antiporter in Beta vulgaris.

We have cloned, by RT-PCR and the use of degenerate oligonucleotide primers, a Na+/H+ antiporter from Beta vulgaris that is homologous to NHX1 of Arabidopsis thaliana and is a member of the family of recently cloned plant NHX-genes. This antiporter, BvNHX1, partially complements the salt-sensitive phenotype of a Deltaena1-4Deltanhx1 yeast strain. Antibodies were raised against a central portion of the BvNHX1 open reading frame that was predicted from the cloned cDNA. This antiporter was found to be highly enriched in tonoplast membranes isolated from plant tissues. BvNHX1 transcript abundance increased after salt treatments, in both suspension-cell cultures and whole plants. BvNHX1 protein abundance in the tonoplast-enriched membranes was also elevated after salt treatments. The vacuolar Na+/H+ antiporter activity increased up to 3-fold when the cell were exposed to 100 mM NaCl. The increase in protein abundance in response to the salt treatment, together with the salt-induced vacuolar Na+/H+ antiporter activity in B. vulgaris suggests that BvNHX1 plays an important role in salinity tolerance.

Journal Article↗
PubMed2002

Regulation of ADL6 activity by its associated molecular network.

Plant dynamin-like proteins consist of a group of high molecular weight GTPase with diverse structural arrangements and cellular localizations. In addition, unlike animal dynamins, there was no evidence for the involvement of any plant dynamin-like protein in clathrin-mediated vesicle trafficking. In this study we demonstrate that ADL6 (Arabidopsis dynamin-like protein 6), due to its domain arrangement, behaves similarly to the animal dynamins. The association of ADL6 with clathrin-coated vesicles was demonstrated by co-fractionation and immunocytochemical studies. ADL6 also interacted via its C-terminus with gamma-adaptin, an adaptor protein of clathrin-coated vesicles. Our results suggest that ADL6 participates in clathrin-mediated vesicle trafficking originating from the Golgi. In addition, our studies demonstrate that ADL6 intrinsic GTPase activity is regulated by its association with acidic phospholipids and an SH3 (Src homology 3)-containing protein.

Adaptor Protein Complex gamma Subunits↗