The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

The physiological and molecular mechanisms of tolerance to osmotic and ionic components of salinity stress are reviewed at the cellular, organ, and whole-plant level. Plant growth responds to salinity in two phases: a rapid, osmotic phase that inhibits growth of young leaves, and a slower, ionic phase that accelerates senescence of mature leaves. Plant adaptations to salinity are of three distinct types: osmotic stress tolerance, Na + or Cl − exclusion, and the tolerance of tissue to accumulated Na + or Cl − . Our understanding of the role of the HKT gene family in Na + exclusion from leaves is increasing, as is the understanding of the molecular bases for many other transport processes at the cellular level. However, we have a limited molecular understanding of the overall control of Na + accumulation and of osmotic stress tolerance at the whole-plant level. Molecular genetics and functional genomics provide a new opportunity to synthesize molecular and physiological knowledge to improve the salinity tolerance of plants relevant to food production and environmental sustainability.

https://rodas5.us.es/file/c2a700e9-8b4a-1970-d343-4a269c302970/1/estres_salino_bibliografia_scorm.zip/files/estres_salino_bibliografia.pdf

Mechanisms of salinity tolerance

Several reactive oxygen species (ROS) are continuously produced in plants as byproducts of aerobic metabolism. Depending on the nature of the ROS species, some are highly toxic and rapidly detoxified by various cellular enzymatic and nonenzymatic mechanisms. Whereas plants are surfeited with mechanisms to combat increased ROS levels during abiotic stress conditions, in other circumstances plants appear to purposefully generate ROS as signaling molecules to control various processes including pathogen defense, programmed cell death, and stomatal behavior. This review describes the mechanisms of ROS generation and removal in plants during development and under biotic and abiotic stress conditions. New insights into the complexity and roles that ROS play in plants have come from genetic analyses of ROS detoxifying and signaling mutants. Considering recent ROS-induced genome-wide expression analyses, the possible functions and mechanisms for ROS sensing and signaling in plants are compared with those in animals and yeast.

REACTIVE OXYGEN SPECIES: Metabolism, Oxidative Stress, and Signal Transduction

Salt and drought stress signal transduction consists of ionic and osmotic homeostasis signaling pathways, detoxification (i.e., damage control and repair) response pathways, and pathways for growth regulation. The ionic aspect of salt stress is signaled via the SOS pathway where a calcium-responsive SOS3-SOS2 protein kinase complex controls the expression and activity of ion transporters such as SOS1. Osmotic stress activates several protein kinases including mitogen-activated kinases, which may mediate osmotic homeostasis and/or detoxification responses. A number of phospholipid systems are activated by osmotic stress, generating a diverse array of messenger molecules, some of which may function upstream of the osmotic stress-activated protein kinases. Abscisic acid biosynthesis is regulated by osmotic stress at multiple steps. Both ABA-dependent and -independent osmotic stress signaling first modify constitutively expressed transcription factors, leading to the expression of early response transcriptional activators, which then activate downstream stress tolerance effector genes.

/pdf/salt-and-drought-stress-signal-transduction-in-plants-4bj87ki2ww.pdf

Salt and drought stress signal transduction in plants

▪ Abstract Plant responses to salinity stress are reviewed with emphasis on molecular mechanisms of signal transduction and on the physiological consequences of altered gene expression that affect biochemical reactions downstream of stress sensing. We make extensive use of comparisons with model organisms, halophytic plants, and yeast, which provide a paradigm for many responses to salinity exhibited by stress-sensitive plants. Among biochemical responses, we emphasize osmolyte biosynthesis and function, water flux control, and membrane transport of ions for maintenance and re-establishment of homeostasis. The advances in understanding the effectiveness of stress responses, and distinctions between pathology and adaptive advantage, are increasingly based on transgenic plant and mutant analyses, in particular the analysis of Arabidopsis mutants defective in elements of stress signal transduction pathways. We summarize evidence for plant stress signaling systems, some of which have components analogous to t...

Plant cellular and molecular responses to high salinity.

This study is concerned with the characterization of the ionic currents in the vacuolar membrane (tonoplast) of plant cells. Voltage patch-clamp experiments at the whole vacuole and single channel levels were employed to study the effects of cytoplasmic chloride on the tonoplast inward rectifying currents of sugar beet cultured cells. Whole vacuole experiments showed that removal of cytoplasmic chloride induced a decrease in the level of the inward currents, an effect that was reversed upon returning to control levels of cytoplasmic chloride. Substitution of cytoplasmic chloride by any other anion (organic or inorganic) resulted in a reduction in the level of the inward currents. At a given negative tonoplast potential, the inward currents showed a linear relationship with the concentration of cytoplasmic chloride between 10 and 100 mM, with the slope of these relationships increasing as the potential was made more negative. Single channel experiments showed that reduction of cytoplasmic chloride changed the gating mechanism of the channels without affecting the single channel conductance. Reduction of cytoplasmic chloride caused a decrease in the open probability of the tonoplast cation channels by reducing their mean open time and by inducing the appearance of an additional closed state.

Cytoplasmic chloride regulates cation channels in the vacuolar membrane of plant cells.

Na+/H+ antiporters (NHXs) are integral membrane transporters that catalyze the electroneutral exchange of K+ or Na+ for H+ and are implicated in cell expansion, development, pH and ion homeostasis and salt tolerance. Arabidopsis contains four vacuolar NHX isoforms (NHX1–NHX4), but only the functional roles for NHX1 and NHX2 have been assessed thus far. Colocalization studies indicated that NHX3 and NHX4 colocalize to the tonoplast. To investigate the role of all vacuolar NHX isoforms, a quadruple knockout nhx1nhx2nhx3nhx4, lacking all vacuolar NHXs, was generated. Seedlings of nhx1nhx2nhx3nhx4 displayed significantly reduced growth, with markedly shorter hypocotyls. Under high K+, but not Na+, pronounced root skewing occurred in nhx1nhx2nhx3nhx4, suggesting that the organization of the cytoskeleton might be perturbed. Whole mount immunolabeling of cortical microtubules indicated that high K+ caused significant microtubule reorganization in nhx1nhx2nhx3nhx4 root cells of the elongation zone. Using microtubule stabilizing (Taxol) and destabilizing (propyzamide) drugs, we found that the effect of K+ on nhx1nhx2nhx3nhx4 root growth was antagonistic to that of Taxol, whereas elevated K+ exacerbated the endogenous effect of propyzamide on root skewing. Collectively, our results suggest that altered K+ homeostasis leads to an increase in the dynamics of cortical microtubule reorganization in nhx1nhx2nhx3nhx4 root epidermal cells of the elongation zone.

Vacuolar Na+/H+ NHX-Type Antiporters Are Required for Cellular K+ Homeostasis, Microtubule Organization and Directional Root Growth

We investigated sugar metabolism in leaves and fruits of two Japanese plum (Prunus salicina Lindl.) cultivars, the climacteric Santa Rosa and its bud sport mutant the non-climacteric Sweet Miriam, during development on the tree. We previously characterized differences between the two cultivars. Here, we identified key sugar metabolic pathways. Pearson coefficient correlations of metabolomics and transcriptomic data and weighted gene co-expression network analysis (WGCNA) of RNA sequencing (RNA-Seq) data allowed the identification of 11 key sugar metabolism-associated genes: sucrose synthase, sucrose phosphate synthase, cytosolic invertase, vacuolar invertase, invertase inhibitor, α-galactosidase, β-galactosidase, galactokinase, trehalase, galactinol synthase, and raffinose synthase. These pathways were further assessed and validated through the biochemical characterization of the gene products and with metabolite analysis. Our results demonstrated the reprogramming of sugar metabolism in both leaves and fruits in the non-climacteric plum, which displayed a shift towards increased sorbitol synthesis. Climacteric and non-climacteric fruits showed differences in their UDP-galactose metabolism towards the production of galactose and raffinose, respectively. The higher content of galactinol, myo-inositol, raffinose, and trehalose in the non-climacteric fruits could improve the ability of the fruits to cope with the oxidative processes associated with fruit ripening. Overall, our results support a relationship between sugar metabolism, ethylene, and ripening behavior.

/pdf/sugar-metabolism-reprogramming-in-a-non-climacteric-bud-1wlmvs53jj.pdf

Sugar metabolism reprogramming in a non-climacteric bud mutant of a climacteric plum fruit during development on the tree.

Patch-clamp techniques were employed to study the electrical properties of vacuoles from sugar beet (Beta vulgaris) cell suspensions at physiological concentrations of cytoplasmic Ca2+. Vacuoles exposed to K+ malate revealed the activation of instantaneous and time-dependent outward currents by positive membrane potentials. Negative potentials induced only instantaneous inward currents. The time-dependent outward currents were 10 times more selective for malate than for K+ and were completely blocked by zinc. Vacuoles exposed to KCl developed instantaneous currents when polarized to positive or negative membrane potentials. The time-dependent outward channels could serve as the route for the movement of malate into the vacuole, whereas K+ could move through the time-independent inward and outward channels.

Characterization of Vacuolar Malate and K+ Channels under Physiological Conditions

The gene-for-gene concept is central to most efforts to bioengineer plants for disease resistance. In the more than 50 years since Flor first proposed the gene-for-gene concept, it has served as an important focus for research on plant disease resistance. This presentation looks briefly at the "evolution" of our understanding of gene-for-gene resistance in relation to the prospects for bio-engineering. The Cladosporium fulvum-tomato interaction is used to illustrate how understanding the signal transduction pathway following interactions between the pathogen elicitor and a putative receptor may lead to new approaches to bioengineering disease resistant cultivars. In this context, recent data are reviewed, confirming that the oxidative burst seen in the defense response of tomato to C. fulvum has strong similarity to that of mammalian phagocytic neutrophil cells.

Eduardo Blumwald

Papers

Cytoplasmic chloride regulates cation channels in the vacuolar membrane of plant cells.

Vacuolar Na+/H+ NHX-Type Antiporters Are Required for Cellular K+ Homeostasis, Microtubule Organization and Directional Root Growth

Sugar metabolism reprogramming in a non-climacteric bud mutant of a climacteric plum fruit during development on the tree.

Characterization of Vacuolar Malate and K+ Channels under Physiological Conditions

The gene-for-gene concept and beyond: Interactions and signals