Differential phosphoproteomics of fragmenting yeast vacuoles

Many organelles exist in an equilibrium of fragmentation into smaller units and fusion into larger structures, which is coordinated with cell division, the increase in cell mass, and envi¬ronmental conditions. In yeast cells, organelle homeostasis can be studied using the yeast vacuole (lysosome) as a model system. Yeast vacuoles are the main compartment for degrada¬tion of cellular proteins and storage of nutrients, ions and metabolites. Fission and fusion of vacuoles can be induced by hyper- and hypotonic shock in vivo, respectively, and have also been reconstituted in vitro using isolated vacuoles. The conserved serine/threonine kinase TOR (target of rapamycin) is a central nutrient sensor and regulates cell growth and metabolism. In yeast, there are two TOR proteins, Torlp and Tor2p, which are part of larger protein complexes, TORCI and TORC2. Only TORCI is rapamycin-sensitive. Disregulation of TOR signaling is linked to a multitude of diseases in humans, e.g. cancer, neurodegenerative diseases and metabolic syndrome. It has been shown that TORCI localizes to the vacuole membrane, and recent findings of our laboratory demonstrated that TORCI positively regulates vacuole fragmentation. This suggests that the fragmentation machinery should contain target proteins phosphorylated by TORCI. I explored the rapamycin-and fission-dependent vacuolar phosphoproteome during frag¬mentation, using a label-free mass-spectrometry approach. I identified many vacuolar factors whose phosphorylation was downregulated in a TORCI- and fission-dependent manner. Among them were known protein complexes that are functionally linked to fission or fusion, like the HOPS, VTC and FAB1 complexes. Hence, TORCI-dependent phosphorylations might positively regulate vacuole fission. Several candidates were chosen for detailed microscopic analysis of in vivo vacuole frag-mentation, using deletion mutants. I was able to identify novel factors not previously linked to fission phenotypes, e.g. the SEA complex, Pib2, and several vacuolar amino acid transporters. Transport of neutral and basic amino acids across the membrane seems to control vacuole fission, possibly via TORCI. I analyzed vacuolar fluxes of amino acids in wildtype yeast cells and found evidence for a selective vacuolar export of basic amino acids upon hyperosmotic stress. This leads me to propose a model where vacuolar export of amino acids is necessary to reshape the organelle under salt stress. - Le nombre et la taille de certaines organelles peut être déterminé par un équilibre entre la fragmentation qui produit des unités plus petites et la fusion qui génère des structures plus larges. Cet équilibre est coordonné avec la division cellulaire, l'augmentation de la masse cellulaire, et les conditions environnementales. Dans des cellules de levure, l'homéostasie des organelles peut être étudié à l'aide d'un système modèle, la vacuole de levure (lysosome). Les vacuoles constituent le principal compartiment de la dégradation des protéines et de stockage des nutriments, des ions et des métabolites. La fragmentation et la fusion des vacuoles peuvent être respectivement induites par un traitement hyper- ou hypo-tonique dans les cellules vivantes. Ces processus ont également été reconstitués in vitro en utilisant des vacuoles isolées. La sérine/thréonine kinase conservée TOR (target of rapamycin/cible de la rapamycine) est un senseur de nutriments majeur qui régule la croissance cellulaire et le métabolisme. Chez la levure, il existe deux protéines TOR, Torlp et Tor2p, qui sont les constituants de plus grands complexes de protéines, TORCI et TORC2. TORCI est spécifiquement inhibé par la rapamycine. Une dysrégulation de la signalisation de TOR est liée à une multitude de maladies chez l'homme comme le cancer, les maladies neurodégénératives et le syndrome métabolique. Il a été montré que TORCI se localise à la membrane vacuolaire et les découvertes récentes de notre laboratoire ont montré que TORCI régule positivement la fragmentation de la vacuole. Ceci suggère que le mécanisme de fragmentation doit être contrôlé par la phosphorylation de certaines protéines cibles de TORCI. J'ai exploré le phosphoprotéome vacuolaire lors de la fragmentation, en présence ou absence de rapamycine et dans des conditions provoquant la fragmentation des organelles. La méthode choisie pour réaliser la première partie de ce projet a été la spectrométrie de masse différentielle sans marquage. J'ai ainsi identifié plusieurs facteurs vacuolaires dont la phosphorylation est régulée d'une manière dépendante de TORCI et de la fragmentation. Parmi ces facteurs, des complexes protéiques connus qui sont fonctionnellement liées à fragmentation ou la fusion, comme les complexes HOPS, VTC et FAB1 ont été mis en évidence. Par conséquent, la phosphorylation dépendante de TORCI peut réguler positivement la fragmentation des vacuoles. Plusieurs candidats ont été choisis pour une analyse microscopique détaillée de la fragmentation vacuolaire in vivo en utilisant des mutants de délétion. J'ai été en mesure d'identifier de nouveaux facteurs qui n'avaient pas été encore associés à des phénotypes de fragmentation tels que les complexes SEA, Pib2p, ainsi que plusieurs transporteurs vacuolaires d'acides aminés. Le transport des acides aminés à travers la membrane semble contrôler la fragmentation de la vacuole. Puisque ces transporteurs sont phosphorylés par TORCI, ces résultats semblent confirmer la

Rapid and sensitive hormonal profiling of complex plant samples by liquid chromatography coupled to electrospray ionization tandem mass spectrometry

Background Plant hormones play a pivotal role in several physiological processes during a plant's life cycle, from germination to senescence, and the determination of endogenous concentrations of hormones is essential to elucidate the role of a particular hormone in any physiological process. Availability of a sensitive and rapid method to quantify multiple classes of hormones simultaneously will greatly facilitate the investigation of signaling networks in controlling specific developmental pathways and physiological responses. Due to the presence of hormones at very low concentrations in plant tissues (10-9 M to 10-6 M) and their different chemistries, the development of a high-throughput and comprehensive method for the determination of hormones is challenging. Results The present work reports a rapid, specific and sensitive method using ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UPLC/ESI-MS/MS) to analyze quantitatively the major hormones found in plant tissues within six minutes, including auxins, cytokinins, gibberellins, abscisic acid, 1-amino-cyclopropane-1-carboxyic acid (the ethylene precursor), jasmonic acid and salicylic acid. Sample preparation, extraction procedures and UPLC-MS/MS conditions were optimized for the determination of all plant hormones and are summarized in a schematic extraction diagram for the analysis of small amounts of plant material without time-consuming additional steps such as purification, sample drying or re-suspension. Conclusions This new method is applicable to the analysis of dynamic changes in endogenous concentrations of hormones to study plant developmental processes or plant responses to biotic and abiotic stresses in complex tissues. An example is shown in which a hormone profiling is obtained from leaves of plants exposed to salt stress in the aromatic plant, Rosmarinus officinalis.

RpoN (sigma54) controls production of antifungal compounds and biocontrol activity in Pseudomonas fluorescens CHA0.

Pseudomonas fluorescens CHA0 is an effective biocontrol agent of root diseases caused by fungal pathogens. The strain produces the antibiotics 2,4-diacetylphloroglucinol (DAPG) and pyoluteorin (PLT) that make essential contributions to pathogen suppression. This study focused on the role of the sigma factor RpoN (sigma54) in regulation of antibiotic production and biocontrol activity in P. fluorescens. An rpoN in-frame-deletion mutant of CHAO had a delayed growth, was impaired in the utilization of several carbon and nitrogen sources, and was more sensitive to salt stress. The rpoN mutant was defective for flagella and displayed drastically reduced swimming and swarming motilities. Interestingly, the rpoN mutant showed a severalfold enhanced production of DAPG and expression of the biosynthetic gene phlA compared with the wild type and the mutant complemented with monocopy rpoN+. By contrast, loss of RpoN function resulted in markedly lowered PLT production and plt gene expression, suggesting that RpoN controls the balance of the two antibiotics in strain CHA0. In natural soil microcosms, the rpoN mutant was less effective in protecting cucumber from a root rot caused by Pythium ultimum. Remarkably, the mutant was not significantly impaired in its root colonization capacity, even at early stages of root infection by Pythium spp. Taken together, our results establish RpoN for the first time as a major regulator of biocontrol activity in Pseudomonas fluorescens.

Soil salinization and maize and cowpea yield in the crop rotation system using saline waters

The use of saline water and the reuse of drainage water for irrigation depend on long-term strategies that ensure the sustainability of socio-economic and environmental impacts of agricultural systems. In this study, it was evaluated the effects of irrigation with saline water in the dry season and fresh water in the rainy season on the soil salt accumulation yield of maize and cowpea, in a crop rotation system. The experiment was conducted in the field, using a randomized complete block design, with five replications. The first crop was installed during the dry season of 2007, with maize irrigated with water of different salinities (0.8, 2.2, 3.6 and 5.0 dS m-1). The maize plants were harvested at 90 days after sowing (DAS), and vegetative growth, dry mass of 1000 seeds and grain yield were evaluated. The same plots were utilized for the cultivation of cowpea, during the rainy season of 2008. At the end of the crop, cycle plants of this species were harvested, being evaluated the vegetative growth and plant yield. Soil samples were collected before and after maize and cowpea cultivation. The salinity of irrigation water above 2.2 dS m-1 reduced the yield of maize during the dry season. The high total rainfall during the rainy season resulted in leaching of salts accumulated during cultivation in the dry season, and eliminated the possible negative effects of salinity on cowpea plants. However, this crop showed atypical behavior with a significant proportion of vegetative mass and low pod production, which reduced the efficiency of this strategy of crop rotation under the conditions of this study.

Physiological response of vicia faba to prohexadione-calcium under saline conditions

Changes in the activities of oxidative enzymes (indole acetic acid oxidase, peroxidase and catalase), endogenous hormones (gibberellic acid (GA3), indole acetic acid (IAA), abscisic acid (ABA) and cytokinins (AsZeatin), photosynthetic pigments (chlorophyll a, chlorophyll b and carotenoids), total carbohydrates, total soluble sugars, amino acid proline and vegetative growth parameters were used as indicators to explain the physiological role of the growth retardant prohexadione-calcium on Vicia faba seedlings 40 days after sowing under salinity stress for 30 days. The obtained results show that soaking faba bean seeds prior to sowing at different concentrations of prohexadione-calcium (0, 10, 20 and 30 ppm) significantly increased the activities of indole acetic acid oxidase (IAA-oxidase) and peroxidase enzymes, but decreased the catalase enzyme activity as compared with their respective control. Application of prohexadione-Ca caused markedly decreases in the endogenous contents of gibberellins and indole acetic acid (IAA) but increased the levels of natural growth inhibitor abscisic acid (ABA) and cytokinins in the shoots of faba bean seedlings. All the prohexadione-Ca concentrations increased the contents of amino acid proline, photosynthetic pigments (chlorophyll a, chlorophyll b and carotenoids), total carbohydrates and total soluble sugars in faba bean seedlings grown under salt stress. Application of prohexadione-Ca decreased significantly seedling height and shoot fresh weight but significantly increased shoot dry weight.

Effect of ecological factors on germination of horse purslane (Trianthema portulacastrum)

Trianthema portulacastrum is a very problematic summer crop weed and a complete crop failure has been observed because of this weed at high density. The effect of different ecological factors on germination of T. portulacastrum seeds collected in two different years (2009 and 2005) was studied in laboratory experiments. An increase in temperature from 25 to 35 ºC increased germination percentage of T. portulacastrum from 65 to 85%, after which germination started to decrease, reducing to 71.25% at 45 ºC. Trianthema portulacastrum had maximum germination with distilled water compared with different salt solutions and drought stress levels. Germination was significantly minimum at salinity and drought stress level of 250 mM and -0.8 MPa, respectively. Emergence of T. portulacastrum was maximum (86.25%) at 100% field capacity level but decreased sharply as field capacity decreased thereafter, and minimum emergence (30%) was recorded at field capacity level of 25%. Germination of T. portulacastrum was lowest at pH 5 and any increase in pH resulted in increased germination. A pH range of 8 to 10 had statistically similar germination. Sowing depth of 6 cm reduced the emergence of T. portulacastrum to zero. Reduction in emergence was recorded with depth increase from zero to 5 cm. Maximum emergence was recorded from soil surface (0 cm). An increase in temperature, salinity, drought, sowing depth (up to 4 cm) and a decrease in field capacity increased time to start germination/emergence, time to 50% germination/emergence and mean germination/emergence time but decreased germination/emergence index. Seeds collected during 2009 gave higher germination than old seeds collected in 2005. This information might contribute to development of effective control of T. portulacastrum.

Germination ecology of wild onion: a rainfed crop weed

Asphodelus tenuifolius is becoming a more common weed in rain-fed area in Pakistan. Laboratory and greenhouse experiments were conducted to determine the effect of different environmental factors on germination and emergence of A.tenuifolius. Results showed that A.tenuifolius can tolerate a wide range of varying environmental factors. Greatest percentage of germination (80%) was recorded at 15 ºC constant temperature; however, considerable germination occurred at 20 and 25 ºC. Light for 10 h photoperiod stimulate germination of Asphodelus tenuifolius compared with complete darkness. Germination was totally inhibited at osmotic stress higher than -0.8 MPa. There was no significant difference in germination at pH 6 to 8; however, there was a slightly decrease at pH 9, compared with distilled water. Asphodelus tenuifolius was very sensitive to salinity; however, a few seeds of A.tenuifolius were able to germinate even at 150 mM NaCl concentration. Greatest emergence occurred with seed placed at soil surface and emergence decreased with increase in burial depth. No emergence occurred from 4 cm or greater. This information may aid in developing tools and strategies for management.

The role of Stl1p in glycerol accumulation in osmotically stressed icewine yeast Saccharomyces cerevisiae K1 V1116

The high sugar concentration in Icewine juice exerts hyperosmotic stress in the wine yeast causing water loss and cell shrinkage. To counteract the dehydration, yeast synthesize and accumulate glycerol as an internal osmolyte. In a laboratory strain of S. cerevisiae, STLl encodes for Stllp, an H+ /glycerol symporter that is glucose inactivated, but induced upon hyperosmotic stress. STLl, was found to be a highly upregulated gene in Icewine fermenting cells and its expression was 25-fold greater than in yeast cells fermenting diluted Icewine juice, making it one of the most differentially expressed genes between the two fermentation conditions. In addition, Icewine fermenting cells showed a two-fold higher glycerol production in the wine compared to yeast fermenting diluted Icewine juice. We proposed that Stllp is (1) active during Icewine fermentation and is not glucose inactivated and (2) its activity contributes to the limited cell growth observed during Icewine fermentation as a result of the dissipation of the plasma membrane proton gradient. To measure the contribution ofStl1p in active glycerol transport (energy dependent) during Icewine fermentation, we first developed an Stllp-dependent (14C]glycerol uptake assay using a laboratory strain of S. cerevisiae (BY 4742 and LiSTLl) that was dependent on the plasma membrane proton gradient and therefore energy-dependent. Wine yeast K1-Vll16 was also shown to have this energy dependent glycerol uptake induced under salt stress. The expression of STLl and Stllp activity were compared between yeast cells harvested from Icewine and diluted Icewine fermentations. Northern blot analysis revealed that STLl was expressed in cells fermenting Icewine juice but not expressed under the diluted juice conditions. Glycerol uptake by cells fermenting Icewine juice was not significantly different than cells fermenting diluted Icewine juice on day 4 and day 7 of Vidal and Riesling fermentations respectively, despite encountering greater hyperosmotic stress. Furthermore, energy- dependent glycerol uptake was not detected under either fermentation conditions. Because our findings show that active glycerol uptake was not detected in yeast cells harvested from Icewine fermentation, it is likely that Stllp was glucose inactivated despite the hyperosmotic stress induced by the Icewine juice and therefore did not play a role in active glycerol uptake during Icewine fermentation.

Influence of sodium chloride on seed germination and seedling root growth of cotton (Gossypium hirsutum L.)

Response of cotton (Gossypium hirsutum L. cv. NIAB-78) to salinity, in terms of seed germination, seedling root growth and root Na+ and K+ content was determined in a laboratory experiment. Cotton seeds were exposed to increasing salinity levels using germination water with Sodium chloride concentrations of 0, 50, 100, 150 and 200 mM, to provide different degrees of salt stress. Germinated seeds were counted and roots were harvested at 24, 48, 72 and 96 h after the start of the experiment. It appeared that seed germination was only slightly affected by an increase in salinity (in most cases the differences between treatment were non-significant), whereas root length, root growth rate, root fresh and dry weights were severely affected, generally highly significant differences in these variables were found for comparisons involving most combinations of salinity levels, in particular with increased incubation period. K+ contents decreased with increasing salinity levels, although differences in K+ content were only significant when comparing the control and the 4 salinity levels. Na+ content of the roots increased with increasing levels of NaCl in the germination water, suggesting an exchange of K+ for Na+. The ratio K+/Na+ strongly decreased with rising levels of salinity from around 4.5 for the control to similar to 1 at 200 mM NaCl.

Germin, a protein marker of early plant development, is an oxalate oxidase

Germin is a homopentameric glycoprotein, the synthesis of which coincides with the onset of growth in germinating wheat embryos. There have been detailed studies of germin structure, biosynthesis, homology with other proteins, and of its value as a marker of wheat development. Germin isoforms associated with the apoplast have been speculated to have a role in embryo hydration during maturation and germination. Antigenically related isoforms of germin are present during germination in all of the economically important cereals studied, and the amounts of germin-like proteins and coding elements have been found to undergo conspicuous change when salt-tolerant higher plants are subjected to salt stress. In this report, we describe how circumstantial evidence arising from unrelated studies of barley oxalate oxidase and its coding elements have led to definitive evidence that the germin isoform made during wheat germination is an oxalate oxidase. Establishment of links between oxalate degradation, cereal germination, and salt tolerance has significant implications for a broad range of studies related to development and adaptation in higher plants. Roles for germin in cell wall biochemistry and tissue remodeling are discussed, with special emphasis on the generation of hydrogen peroxide during germin-induced oxidation of oxalate.

Análise metagenômica da microbiota de ambientes aquáticos do estado do Rio Grande do Norte - Brasil

The screening for genes in metagenomic libraries from soil creates opportunities to explore the enormous genetic and metabolic diversity of microorganisms. Rivers are ecosystems with high biological diversity, but few were examined using the metagenomic approach. With this objective, a metagenomic library was constructed from DNA soil samples collected at three different points along the Jundiaí-river (Rio Grande do Norte-Brazil). The points sampled are from open area, rough terrain and with the direct incidence of sunlight. This library was analyzed functionally and based in sequence. For functional analysis Luria-Bertani solid medium (LB) with NaCl concentration varied from 0.17M to 0.85M was used for functional analysis. Positives clones resistant to hypersaline medium were obtained. The recombinant DNAs were extracted and transformed into Escherichia coli strain DH10B and survival curves were obtained for quantification of abiotic stress resistance. The sequences of clones were obtained and submitted to the BLASTX tool. Some clones were found to hypothetical proteins of microorganisms from both Archaea and Bacteria division. One of the clones showed a complete ORF with high similarity to glucose-6-phosphate isomerase which participates in the synthesis of glycerol pathway and serves as a compatible solute to balance the osmotic pressure inside and outside of cells. Subsequently, in order to identify genes encoding osmolytes or enzymes related halotolerance, environmental DNA samples from the river soil, from the water column of the estuary and ocean were collected and pyrosequenced. Sequences of osmolytes and enzymes of different microorganisms were obtained from the UniProt and used as RefSeqs for homology identification (TBLASTN) in metagenomic databases. The sequences were submitted to HMMER for the functional domains identification. Some enzymes were identified: alpha-trehalose-phosphate synthase, L-ectoina synthase (EctC), transaminase L-2 ,4-diaminobutyric acid (EctB), L-2 ,4-diaminobutyric acetyltransferase (EctA), L-threonine 3 dehydrogenase (sorbitol pathway), glycerol-3-phosphate dehydrogenase, inositol 3-phosphate dehydrogenase, chaperones, L-proline, glycine betaine binding ABC transporter, myo-inositol-1-phosphate synthase protein of proline simportadora / PutP sodium-and trehalose-6-phosphate phosphatase These proteins are commonly related to saline environments, however the identification of them in river environment is justified by the high salt concentration in the soil during prolonged dry seasons this river. Regarding the richness of the microbiota the river substrate has an abundance of halobacteria similar to the sea and more than the estuary. These data confirm the existence of a specialized response against salt stress by microorganisms in the environment of the Jundiaí river

Estresse salino associado à aplicação exógena de espermidina no acúmulo de glicina betaína em Guandu

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Influência do estresse hídrico e salino na germinação de urochloa decumbens e urochloa ruziziensis

Studies of the germination response of seeds subjected to artificial stresses are provided tools for better understanding of the survivability and adaptation of these species in natural stress conditions such as drought or saline soils, common in agricultural and forest regions, contributing significantly to the development of management strategies. Thus, the purpose of this study was to evaluate the possible effects of water and salt stress on germination of Urochloa decumbens and Urochloa ruziziensis. The test was conducted at the Faculty of Technology of São Paulo, campus of Capon Bonito. The seeds were sown with four replicates of 50 seeds in paper soaked in solutions with the potentials of 0.0, -0.2, -0.4 and -0.8 MPa, induced with polyethylene glycol (PEG 6000) and NaCl. The germination test was conducted at 25 degrees C in the presence of light, evaluating the first test score at seven days after sowing, and weekly germination (normal seedlings) until 35 days. We calculated the index of germination rate. The results allowed the conclusion that water stress causes a greater reduction in force, speed of germination and cumulative germination of seeds of U. decumbens and U. ruziziensis than salt stress. The species U. decumbens showed higher tolerance to water and salt stresses.

Estado nutricional e componentes da produção de plantas de pimentão conduzidas em sistema de fertirrigação durante indução de estresse salino em cultivo protegido

O uso das técnicas de fertirrigação em ambiente protegido vem aumentando no Brasil devido à praticidade de condução e redução dos custos de produção. Apesar dessas vantagens, salienta-se que esta prática também pode trazer riscos, principalmente pelo acúmulo de sais na superfície do solo e na região periférica do bulbo radicular. em caso de salinização do solo pelo manejo incorreto do sistema podem ocorrer alterações na disponibilidade de nutrientes, com conseqüências fisiológicas no desenvolvimento das plantas. Neste trabalho, utilizou-se o pimentão (Capsicum annuum L.) como planta-modelo para estudos da interferência da salinidade na nutrição das plantas, pela alteração da condutividade elétrica (CE) na solução do solo. Os resultados revelaram indícios de antagonismo entre nutrientes, notadamente entre as formas catiônicas em razão do aumento da concentração de KCl nos tratamentos com alta CE. A suplementação do solo com adubo orgânico não atenuou os efeitos do aumento da concentração salina e os valores extremos de CE interferiram drasticamente na produção.

Viabilidade da cultura Cnidoscolus quercifolius POHL para produção de Biodiesel no semiárido nordestino

The northeastern semiarid is a region that presents a serious picture stagnation or slowness of the economic growth, beyond the presence of social pointers below of the averages national and regional. The half-dryness conditions become the improper region for many agricultural cultures, what it affects the local populations directly, as well as the economy that is based mainly on agriculture. Cnidoscolus quercifolius Pohl, popularly know as favelone is a native species of the semiarid region that withholds great potential for the development of the region in virtue of its multiple uses. Being an oleaginous, its production in familiar farmings makes with that biodiesel either for the misery an important alternative eradication for the possibility of occupation of enormous contingents of people. The present study it aims at to evaluate the germination of the faveleira without thorns under conditions of water and saline stresses, main stresses which the vegetal species of the semiarid one are submitted; beyond verifying the acceptance of the species for agriculturists of a cooperative in the city of Apodi/RN. The methodology used for germination corresponds to using treatments with polyethylene glycol and sodium chloride to assess water and salt stress respectively, being held in rolo. O system approach used for the verification of acceptance of faveleira was the use of interview with farmers cooperative in the study area determined. In this direction it was verified that the faveleira is a resistant species the conditions of drought and salinity of the ground, factor of great relevance, since one is about a species with high added value, making possible the development for the semiarid region. It was verified that the agriculturists are favorable the introduction of the faveleira and reveal receptive the idea to cultivate a species with potential for production of biodiesel