Genetic and epigenetic factors affecting transient and lasting adaptation
(a) The impact of life history on plant acclimation to stress. A short exposure to mild stress (conditioning) can dramatically enhance the plant ability to cope with extreme stress. Our working hypothesis is that epigenetic modifications underlie at least part of this “memory” system. In the framework of this center two major types of activities will be coordinated – Identification of genes required for the conditioning process, and organization of a know-how center on the characterization of genome-wide epigenetic modifications.
(b) Trans-generational transmission of drought tolerance: Common Mendelian factors have a major impact on plant performance in normal and stressed conditions. In addition, hints for non-Mendelian inheritance, and especially, changes in genome content in response to stress are sparsely reported in the scientific literature. Tomato germplasm representing cultivated lines, wild species, and introgression lines established by D. Zamir, will be used to characterize the role of the two types of inheritance modes in adaptation to stress.
(c) Exploiting Arabidopsis natural variation for elucidating mechanisms underlying drought tolerance. Over one thousand natural accessions of Arabidopsis are publicly available, and the genome sequences of several hundred of them is already determined (http://1001genomes.org/index.html). This natural accession collection exhibits highly variable phenotypes including diverse responses to abiotic stress. These lines will be evaluated under normal and drought conditions in the I-CORE phenotyping platforms.
Phytohormones in local and long-distance signaling of stress
(a) How plants sense and track water: Tropic responses have major effects on root architecture and whole plant performance under stress. To elucidate the molecular – genetic basis of water sensing and tracking and its effect on root architecture, high throughput screening of mutants and natural accessions will be performed combined with Next Generation Sequencing to identify the genes underlying plant – water responses.
(b) Phytohormones, root architecture and stomata regulation under stress: Factors affecting root architecture in response to osmotic stress will be studies in two directions (i) ABA, cytokinin, auxin and ethylene signaling pathway(s) upstream and downstream to ABI4 (ii) Investigation of the ubiquitin-proteasome system, which plays a critical role in cellular responses to environmental changes by facilitating a rapid turnover of proteins important for various cellular functions. (
(c) Whole-plant and cell-specific hormonal balance. Exposure to drought changes the root-to-shoot ratio due to the rapid inhibition of shoot growth and sustained root growth. These changes involve long-distance communication between plant organs, with hormones playing a major role. In the proposed research, the growth-promoting and growth-suppressing regulatory networks will be elucidated in different plant organs and cell types in response to moderate (short) and prolonged osmotic stress (drought and salinity) in tomato and Arabidopsis .
(d) Auxin transport machinery and phenotypic plasticity – membrane interaction dynamics. Asymmetric auxin distribution and auxin signaling are integrators of internal and external signals underlying phenotypic plasticity. The localization of polar auxin transporter PIN proteins depends on vesicle trafficking, cytoskeleton, plasma membrane and cell wall composition. These will be studied using a confocal microscope equipped with a tandem scanner for both high resolution real-time imaging to determine the precise membrane microdomains occupied by PINs and interaction with various membrane-associated proteins including ROPs and Ca2+-binding proteins, and the interactions of ROP with the ABA signaling components under stress.
This part of the research investigates key metabolic pathways, their regulatory mechanisms, and their effect on metabolite remobilization.
(a) Carbon – nitrogen balance
(b) Dehydration responsive proteases as molecular set-points of cellular survival.
(c) Ca2+ and ROS signaling networks under stress: The two important stress-response signaling systems Ca2+ and ROS, which mediate plant responses to a plethora of environmental cues, including drought and salinity, and which link environmental stimuli with intrinsic growth and development programs, will be investigated under different severity, duration, periodicity (stress / recovery cycles) and combination of stresses (drought, salinity, heat and nutrient starvation) at the levels of the transcriptome, metabolome, proteome, hormonal signaling and cell polarity.
Dynamics of cell structures and their role in signaling in stress responses
the plant cell wall is a complex extracellular matrix composed of cellulose microfibrils, acting as the major load bearing component, cross-linked by hemicelluloses and embedded in a matrix of pectins. Despite their importance, very little is known about the mechanisms operating in cell wall polysaccharide biosynthesis, transport and assembly. This part of the research addresses the dynamics of cell structures and their functions under stress and upon recovery from stress.
(a) Linking plant surface patterning to drought stress response:
(b) Dynamics of plant cell wall biosynthesis and modulation under stress:
(c) Roles of cell surface bio-mineralization in tolerance to drought and salt stresses. Plant cell structures include calcium and silicon mineralization. Silicon is thought to improve plant fitness by reducing the porosity of the cell wall and increasing its stiffness and by removing poisonous metals through co-deposition. In the proposed research, bio-mineralization processes will be studied in cultured plant cells with focus on molecular mechanisms underlying the basis of silicon – cell interactions.
Systems approach – linking experimental data with network analysis, modeling and predictability
Topological, logical and constraint-based models (CBM) are being used and further developed to model plant behavior under stress and upon recovery from stress. These include genome-scale, sub-cellular compartmentalized metabolic network models for multiple Arabidopsis tissues and cell cultures. Computational frameworks are being used for inferring pathways describing a process of interest and learning their underlying logic given context-dependent omics data. These methods lay a solid foundation for providing a computational perspective to the various ‘omic’ studies that are undertaken in this I-CORE. The resulting network models will generate novel insights and predictions (e.g. of key regulatory factors) to be further tested experimentally.