Plant Sciences

Avi Levy, Head
The Gilbert de Botton Professorial Chair of Plant Sciences

The goal of the department of Plant Sciences is to better understand the biology of photosynthetic organisms, namely plants, algae, and several bacterial species. These organisms play a vital role to sustain life on Earth, through several unique features that we are studying. First is photosynthesis, the process that uses carbon dioxide, water and light energy to produce carbohydrates and oxygen. The global effect of photosynthetic organisms is to maintain the atmospheric levels of oxygen and CO2. In addition, photosynthetic organisms distinguish themselves from other organisms in many fascinating aspects. Plants and algae are extraordinary sun-powered chemical factories, producing primary metabolites: sugars, lipids and amino acids that constitute the bulk of their biomass and of our food and that can be used as biofuel. In addition, plants and algae produce hundreds of thousands of secondary metabolites: pigments, vitamins, volatiles, alkaloids and more, that we use as drugs, perfumes, dyes, detergents and many other uses and that they use for defense, signaling, light harvesting. Understanding how these metabolites are produced is a major challenge. Plants cannot move to escape stress and therefore they have developed highly sophisticated mechanisms for short and long-term adaptation to the changing environment. Plants do not have an established germline, and plant cells stick to their daughter through cell walls that prevent their mobility. In this, and other aspects, plant growth and development differ from that of other multicellular organisms in pattern and organ formation, cell-cell communication and reproduction. Plants are also champions in the evolutionary race, with hundreds of thousands of plant species compared to only a few thousands mammals. This makes plants excellent models to study speciation and evolution.

Ten research groups and emeritus professors, are studying the biology of: Higher plants such as the Arabidopsis model species and crop plants (Wheat, tomato, potato, etc..); Lower plants such as the moss Physcomitrella; Algae, such as Chlamydomonas (a model species) or diatoms that constitute most of the phytoplankton; and Cyanobacteria. We are involved in basic experimental research at the molecular, cellular, organism and population levels as well as in theoretical modeling approaches. Our fields of interest include: light harvesting, from biophysical aspects to gene expression regulation (Schertz, Noy, Danon, Edelman); Plant Development (Eshed) and Evolution (Levy, Feldman) using genetics, genomics and epigenetics approaches; Primary and Secondary Metabolism, including chemistry, gene regulation, designing and modeling of metabolic pathways (Galili, Aharoni, Milo, Vardi); Environmental studies on global aspects of carbon fixation (Milo) and marine biology (Vardi) and on sensing and responding to environmental insults from pathogens, weeds and parasites or from abiotic stresses such as drought, heat, nutrient starvation etc.. (Fluhr, Galili, Gressel, Scherz, Vardi). Finally, we are developing web-based tools for storing and handling complex genomic and biological data (Edelman, Milo).

The applications derived from our work are in the fields of Agriculture and Medicine, Biotechnology, Plant improvement, Alternative energies, human health, nutrition and environmental management. Our scientists have filed several patents in these fields and several biotech companies have emerged from our basic research. In addition, we have contributed to public efforts and our work had impact on securing more food, and food of better quality for the benefit of developed and developing countries. Finally, we are involved in education, at the national and international levels, from school children, to teachers, farmers, students and scientists in plant sciences. The highlights from our research are summarized below for each of our scientists.

Asaph Aharoni's group investigates how plants control their metabolism in the course of development and under stress conditions. The group research’s and achievements are: (i) Identification of regulatory networks coordinating activity of metabolic pathways during tomato fruit development and ripening. New mutants and genes in these pathways were identified. (ii) Deciphering the regulatory mechanisms that maintain the homeostasis between secondary metabolites and the biosynthesis of their precursors in primary/central metabolism (e.g. lipids, amino acids). (iii) Studies on the formation of the plant surface, i.e. the cuticular layer that mediates the plant interaction with the environment. The Aharoni group has made discoveries on the biosynthesis, transport and polymerization of cuticular components and the transcriptional networks that control cuticle-associated metabolic pathways. (iv) Studies on regulation through riboswitches, RNA elements that mediate gene control upon binding a small molecule. This is a newly identified mechanism for feedback regulation and gene control in metabolism. The group has discovered and characterized the activity of a Thiamine (Vitamin B1) riboswitch from plants through alternative splicing in the 3' untranslated region of genes. (v) Developing and applying new Metabolomics tools that allow extensive metabolic profiling of complex plant extracts and the integration of metabolic data with information derived from other levels of regulation such as the transcriptome. Finally, the knowledge acquired is translated into genetic tools for the production of plants with desired metabolic quality traits.

Avihai Danon studies the regulation of gene expression by redox signals. In particular, he is investigating post-transcriptional regulation in the adaptation of plants to changing environments. Redox reactions of two proteins involve the transfer of electron(s) from one protein (the donor) to the other (the acceptor). While there is accumulating evidence that changes in the redox state of particular proteins are used by plants as signals, very little is known about the nature of the signaling redox reactions. In plants, multiple redox signaling programs, such as in protection mechanisms against the accumulation of free radicals, in regulation of protein synthesis, or in controlling enzymes of carbon fixation, seem to take place in parallel. This raises questions about the identity of the signaling proteins and the principals of their redox reactions. Danon has found that regulatory proteins of the thioredoxin family exchange electrons along specific pathways in the soluble compartments of the cell. His studies suggest that the flow of electronic information in biology can take place also in solution by means of non-insulated routes.

Marvin Edelman and Vladimir Sobolev are using DNA sequence data to predict 3D metal binding sites in proteins. A new algorithm, SeqCHED, has been developed and added to their SPACE suite of tools for Structure Prediction & Analysis based on Complementarity & Environment (http://ligin.weizmann.ac.il/space/servers). Current work involves the association of metal binding sites with disease-related single nucleotide polymorphisms in humans, and a comprehensive identification of the metalloproteome of the model plant, Arabidopsis. Edelman is also collaborating with Autar K. Mattoo (ARS-USDA, Beltsville, USA) to study the relationship between Photosystem II reaction center proteins and phosphorylation. Currently, using nitric oxide donor-mediated inhibition of phosphorylation, they find that light-mediated degradation of the photosystem II D1 protein and phosphorylation are not tightly coupled. Edelman and Ron Vunsh are using polyploidization of Spirodela (duckweed) to produce stable clonal lines of modified plants in a non-genetically engineered manner. Currently, in collaboration with Asaph Aharoni’s group, they have identified a stable, fast growing, non-genetically engineered, vegetative line producing a significantly increased level of the anti-oxidant, caffeic acid. Edelman, in collaboration with Joel Sussman, has spearheaded a campaign to establish a UNESCO international training center in BIOmics (bioinformatics, proteomics & functional genomics) at the Weizmann Institute of Science. Currently, the program has received official endorsement by UNESCO and the Israeli Ministry of Science and Technology and is poised to take off. The first BIOmics international workshop was held in the summer of 2009 (http://www.weizmann.ac.il/ISPC/workshop/2009/biomics).

Yuval Eshed: To understand how variation between plants occurs through evolutionary processes, Yuval Eshed’s group studies the genetic and developmental mechanisms that shape plant organs of several unrelated species. These include the annual plant Arabidopsis and the perennial bush, tomato. In both plants, leaves are initiated by common mechanisms, however, Arabidopsis leaves turn small and simple whereas tomato leaves become large and compound. Indeed, in both species leaf initiation entails interaction between the two sides of the leaf primordia, the upper and the lower, which in turn, activate a growth program that generates the flat leaf lamina. However in the small leaves, this program is short lived whereas in large leaves in lasts longer. What are the mechanisms that time the leaf growth period? What are the instructions that halt growth when time arrives? While numerous mechanisms can impact the growth process via regulation of basic process such as cell division or cell expansion, the mechanism that guide timing of growth are elusive. Based on genetic and expression profiling studies, interactions between several groups of transcription regulators and micro RNAs that counteract their activities were identified. Minor modifications in the relations between these factors account for significant portion of the differences between the small Arabidopsis and large tomato leaves, allowing first entry to mechanisms that "measure" the size of organs. Through the study of plant development, several new tools were developed that can be used in a wide array of applications. Methods to down or up regulate multiple genes in specific time and place via tailored micro RNAs should allow precise manipulations of endogenous or introduced traits with minimal side effects.

Robert Fluhr’s laboratory investigates the response of plants to biotic and abiotic stresses. Cultivated plants are prone to disease and environmental insults but also have inbuilt mechanisms to sense the type of damage and mount a defense. These are part of a complex system called innate immunity. It is innate in the sense that the plant is genetically pre-programmed to respond in a particular manner. Clearly the response should be particular to each insult. For example, biotrophic pathogens that exist on living cells are met with a response that hastens the death of those cells. In contrast, chewing insects are met with a battery of rapidly synthesized, anti-herbivory proteins and chemicals that are produced by living tissue. As the environment is complex and herbivory and microbial pathogens are likely to be simultaneous events it is also essential to understanding the molecular architecture of their signal transduction and the interaction between these events. Robert Fluhr's group used molecular genetic techniques to uncover the genes that are central for resistance to plant vascular diseases. Many other plant resistance genes and even innate human resistance genes can be shown to have common molecular features. Importantly, a conserved TIR domain appearing in different molecular context appears to play a dual role in signaling pathogen and herbivory defense and contributing to the balance between them. In another project, the rapid adaptive responses of plants to the biotic and abiotic environment necessitates whole plant signaling and was shown by us to include rapid activation of reactive oxygen species produced by NADPH oxidases and the participation of a special class of aldehyde oxidases (in collaboration with Moshe Sagi; Ben-Gurion University of the Negev). Stress-related responses are multi-tiered and in another project the effect of stress on alternative splicing is examined. A LAMMER-type kinase conserved in humans and plants originally isolated in the lab as a kinase whose activity is modulated by the stress hormone ethylene was shown to localize to the nucleus and regulate the alternative splicing of a particular subset of transcripts. Based on that result, important parallels but major differences between plant and human alternative splicing were discovered. Our challenge is to understand the biological importance of stress motivated alternative splicing.

Gad Galili: Breeders of higher yielding crops have traditionally relied on assembling the best of what is available in nature into crop plants. But with the help of fundamental understanding of plant metabolism, particularly amino acid synthesis, Gad Galili's group has shown that biosynthetic and catabolic pathways can be manipulated for enhanced production of essential amino acids as well as various health associated compounds that are produced by plants. The production can be directed to special cells in the seeds. Research is directed into genomics-based elucidation of complex regulatory networks linking between amino acids metabolism and other metabolic networks and regulatory processes that control seed development and germination. In addition, a new research has been initiated to elucidate how metabolism in plant seeds interacts with and regulated by metabolic networks in vegetative tissues.

Plants are essential elements for human health, serving both as food sources as well as bioreactors for modern therapeutic drugs. Improving the quality of plants for human health requires the modulation of metabolic networks in plant cells, and research activity in Gad Galili's group is targeted at these issues.

Plant growth requires continuous remodeling of its metabolic networks in response to various stresses imposed by the changing environment. This remodeling is regulated by a number of different intra-cellular processes, one of which, called autophagy, has been implicated to protect plants against nutrient stresses. Yet, Gad Galili's group has recently shown that the autophagy process operates not only under nutrient stress, but also under normal plant growth, implying a broader function of this pathway. In an attempt to elucidate new functions of autophagy in plants, Gad Galili's group has also identified novel plant proteins that interact with the core proteins of autophagy. The functions of these proteins in plant growth and response to environmental stresses as well as the significance of their interaction with the autophagy machinery are being elucidated.

Avraham Levy’s laboratory is interested in understanding how species are formed and evolve. Levy’s research focuses on the molecular mechanisms responsible for the plasticity and biodiversity seen in the plant kingdom. Mechanisms, such as hybridization and polyploidization are studied for their contribution to rapid and successful speciation. In addition we study mechanistic aspects of genome maintenance that preserve the genome’s integrity as well as its ability to evolve through a fine regulation of homologous recombination, DNA repair, and transposons. Homologous recombination contributes to genomic diversity through the exchange of chromosomal homologous segments. It is also the mechanism that enables precise genetic modifications via gene targeting. Levy’s group studies the process of homology search, with some emphasis on the role and function of the homologs of RAD51, RAD52 and of the chromatin remodeling RAD54 genes. We test how chromatin structure and cytosine methylation can affect meiotic recombination and gene targeting. Wheat species have evolved through hybridization between related species followed by whole genome doubling (polyploidy). Levy’s group, in collaboration with Prof. Moshe Feldman, studies how these speciation events have affected genome structure and function. They showed, that a new, non-additive variation, not previously present in the diploid progenitors, is induced immediately upon hybridization and polyploidization rather than on an evolutionary scale. The basis for that is both genetic and epigenetic, involving sequence elimination, activation of transposons, alterations in gene expression, cytosine methylation and fluctuations in the profile of small RNAs. These events promote the generation of new traits necessary for rapid speciation, but on the other hand, they may have deleterious effects, establishing a barrier between species (e.g. mutator effects or genetic incompatibilitie). Levy’s lab also studies, in collaboration with Prof. Naama Barkai, hybridization and polyploidization in budding yeast, as a model for similar mechanisms in plants, as it provides a much simpler system to investigate the origin of new traits that contribute to fitness and speciation, and the genetic basis for the heterosis (Hybrid vigor) frequently observed in hybrids.

Ron Milo’s group brings the tools of systems biology to bear on the grand challenges of sustainability. It studies the efficiency of photosynthesis: the engine that drives our biosphere, the source of our food, and the dominant process determining atmospheric CO2. One aim of the research is to find the bottlenecks and limiting factors in the process of converting photons of sunlight into molecules of stored sugars that are used for food and fuel. Milo’s group wants to understand the constraints that shape photosynthesis properties and the limitations on the maximal productivity of plants and other photosynthetic organisms. Specifically, Milo’s research explores the possibilities, limits and optimality of carbon metabolism, trying to understand the fundamentals of its design principles with the goal of improving our ability to produce food and fuel more efficiently; and to conserve water and nitrogen usage. A major approach is to computationally design and experimentally implement novel synthetic carbon fixation cycles. In addition, Milo’s group develops BioNumbers, a cooperative, community resource of useful biological numbers for both researchers and the public. This resource can help biologist in quantitative assessment of biological phenomena. Another interest of the laboratory is to develop optimality models that help us test our ideas about the tradeoffs and dominant forces of evolution. Here is an ontology of examples: Optimality in biology collection

Dror Noy’s laboratory studies the fundamental processes involved in photosynthetic solar energy conversion. These provide plants and other evolutionary older photosynthetic organisms the energy for all their metabolic needs. As such they are a source of inspiration for designing artificial devices for solar energy conversion and storage. Dror Noy’s group focuses on the flow of energy and electrons to and from the catalytic sites of photosynthetic enzyme complexes. In contrast to the highly elaborate and very specific arrangement of cofactors and protein residues at catalytic centers, the relays of energy and electrons favor universal pigments, and redox cofactors, most of which are embedded and immobilized within simple and resilient redox proteins, and the rest are diffusible. By applying state of the art computational and empirical tools of protein de novo design, the Noy lab constructs novel protein-cofactor complexes that serve as minimal functional analogs of the natural energy- and electron-transfer proteins. In the next stage, an interface is designed to couple the artificial proteins with their natural redox and/or catalytic partners. New designs are tested by a variety of analytical and spectroscopic methods, and the results are used for optimizing the previous designs in an iterative process. This learning by design approach provides substantial insights into folding and assembly of protein-cofactor complexes, and the critical parameters affecting their function as energy- and electron-transfer relays. Most importantly, it can teach us important lessons on how Nature achieves functional diversity by combining only a few basic modules into a variety of elaborate networks of long-distance inter- and intra-protein energy- and electron-transfer reactions. In the future, these lessons may be used for designing and constructing custom-built networks of enzyme complexes to carry out chemical transformations of our choice either in a non-biological context, or in a biological setting.

Avigdor Scherz’s group studies the role of proteins in regulating this mechanism. Using spectroscopy and theoretical calculations of metal substituted bacteriochlorophylls he follows and investigates charge flow between atoms, groups and whole molecules. These studies provide insight to mechanisms that underlay chemical reactivity in biological and non-biological systems. Other metal susbtituted Bchl that have been recently synthesized by Scherz are used for vascular targeting photodynamic therapy of tumors and other diseases. The first of theses novel compound is now in phase II clinical trials against prostate cancer. Studies of quantitative structure activity relations

Assaf Vardi's laboratory investigates Marine photosynthetic microorganisms (phytoplankton). These organisms are the basis of marine foodwebs and are responsible for nearly 50% of the global annual carbon-based primary production. Despite their importance, the molecular basis for their ecological success has been largely unexplored. During bloom succession phytoplankton populations are thought to utilize chemical signals (infochemicals) to enhance their defense capacities against viruses and grazers, and to outcompete other phytoplankton for available resources. Recent advances in algal genomics and genetic and cell biology tools provide an unprecedented opportunity to elucidate the cellular mechanisms that are employed by phytoplankton during acclimation to stress in the marine environment. In light of their unique evolutionary history, studying members of the three dominant bloom-forming algal taxa in contemporary oceans (diatoms, coccolithophores and dinoflagellates), will provide exciting insights into their unique biology and ecological success. We specifically explore the signal transduction pathways related to the origin of programmed cell death (PCD), cell-cell communication, host-virus interactions and chemical-based defense. As well as examining how these signaling pathways regulate cell fate and developmental changes as resting stage and biofilm formation.

http://www.weizmann.ac.il/Plant_Sciences/ 

Research Staff, Visitors and Students

Professors

Robert Fluhr, Ph.D., Weizmann Institute of Science, Rehovot, Israel
       The Sir Siegmund Warburg Professorial Chair of Agricultural Molecular Biology
Gad Galili, Ph.D., Weizmann Institute of Science, Rehovot, Israel
       The Bronfman Professorial Chair of Plant Science
Avraham Levy, Ph.D., Weizmann Institute of Science, Rehovot, Israel
       The Gilbert de Botton Professorial Chair of Plant Sciences
Avigdor Scherz, Ph.D., The Hebrew University of Jerusalem, Jerusalem, Israel
       The Robert and Yadelle Sklare Professorial Chair in Biochemistry

Professors Emeriti

Dan Atsmon, Ph.D., The Hebrew University of Jerusalem, Jerusalem, Israel
Marvin Edelman, Ph.D., Brandeis University, Waltham, United States
Moshe Feldman, Ph.D., The Hebrew University of Jerusalem, Jerusalem, Israel
Esra Galun, Ph.D., The Hebrew University of Jerusalem, Jerusalem, Israel
Jonathan Gressel, Ph.D., University of Wisconsin, Madison, United States

Associate Professors

Avihai Danon, Ph.D., University of Arizona, Tucson, United States
       The Henry and Bertha Benson Professorial Chair
Yuval Eshed, Ph.D., The Hebrew University of Jerusalem, Jerusalem, Israel
       The Jacques Mimran Professorial Chair

Senior Scientists

Asaph Aharoni, Ph.D., Wagenigen University, Wagenigen, Netherlands
       Incumbent of the Adolfo and Evelyn Blum Career Development Chair of Cancer Research
Ron Milo, Ph.D., Weizmann Institute of Science, Rehovot, Israel
       Yigal Allon Fellow
       Incumbent of the Anna and Maurice Boukstein Career Development Chair
Dror Noy, Ph.D., Weizmann Institute of Science, Rehovot, Israel
Assaf Vardi, Ph.D., The Hebrew University of Jerusaelm, Jerusalem, Israel
       Incumbent of the Edith and Nathan Goldenberg Career Development Chair

Senior Staff Scientists

Vlad Brumfeld, Ph.D., University of Bucharest, Romania
Vladimir Sobolev, Ph.D., Institute of Catalysis, Siberian Branch of the Academy of Sciences, Siberia, Russian Federation

Associate Staff Scientists

Cathy Bessudo, Ph.D., Weizmann Institute of Science, Rehovot, Israel
Olga Davydov, Ph.D., Rsearch Institute for Essential Oil Plants, Crimea, Ukraine

Assistant Staff Scientists

Avital Adato, Ph.D., Tel Aviv University, Tel-Aviv, Israel (left December 2010)
Ilana Rogachev, Ph.D., Weizmann Institute of Science, Rehovot, Israel
Hadas Zehavi, Ph.D., Weizmann Institute of Science, Rehovot, Israel

Senior Intern

Ilit Cohen Ofri, Ph.D., Weizmann Institute of Science, Rehovot, Israel

Engineers

Zohar Hagbi, B.A., The Hebrew University of Jerusalem, Jerusalem, Israel
Yair Ream, B.A., The Hebrew University of Jerusalem, Jerusalem, Israel

Consultants

Alexander Brandis, Steba Labs, Kiryat Ha'mada, Rehovot, Israel
Leonid Brodsky, Haifa University, Haifa, Israel
Leon Esterman
Esra Galun
Eran Goldberg, Panaxia Ltd., Bet-Dagan, Israel
Asael Herman
Ilan Samish

Visiting Scientists

Saul Buderman, Hebrew University , Givat Ram, Jerusalem, Israel
Pierre Goloubinoff, University of Lausanne, Switzerland
Theodore Muth, City University of New-York, U.S.A.

Postdoctoral Fellows

Noam Alkan, Agriculture Faculty, Israel
Ruthie Angelovici, Weizmann Institute of Science, Israel
Yuval Ben Abu, Ben-Gurion University, Israel
Samuel Bocobza, Ben-Gurion University, Israel
Revital Bronstein, Tel-Aviv University, Israel
Youlia Denisov, Hebrew University of Jerusalem, Israel
Jorge Gerardo Dinamarca Cerda, Universidad De La Frontera
Idan Efroni, Weizmann Institute of Science, Israel
Liron Even-Faitelson, Ph.D., Hebrew University of Jerusalem, Israel
Eiri Aulikki Heyno, Cea Saclay, Ibitec-S Sb2sm
Arie Honig, Tel-Aviv University, Israel
Maxim Itkin, Weizmann Institute of Science, Israel
Michal Kenan-Eichler, Weizmann Institute of Science, Israel
Frieda Kopnov, Ph.D., Weizmann Institute of Science, Israel
Nardy Lampl, Weizmann Institute of Science, Israel
Michal Lieberman-Lazarovich, Weizmann Institute of Science, Israel
Arieh Moussaieff, Hebrew University of Jerusalem, Israel
Moran Oliva, Tel-Aviv University, Israel
Shilo Rosenwasser, Agriculture Faculty, Israel
Jianxin Shi, Ph.D., Agriculture Faculty, Israel
Jebasingh Tennyson, Ph.D., Madurai Kamaraj University
Libbat Tirosh, Weizmann Institute of Science, Israel
Gal Wittenberg, Weizmann Institute of Science, Israel
Boris Zorin, Humboldt Univerity of Berlin

Research Students

Ran Afik Tamar Avin Wittenberg
Arren Bar-Even Dario A. Breitel
Louise Chappell Inbal Dangoor
Idan Efroni Ilan Feine
Ruth Goldschmidt Liat Goldshaid
Maxim Itkin Michal Kenan-Eichler
Ruth Khait Menny Kirma
Nardy Lampl-Saady Noam Leviatan
Ronen Levy Michal Lieberman-Lazarovich
Sergey Malitsky Dikla Malter
Arie Marcovich Iris Margalit
Shira Mintz Avishai Mor
Elad Noor Sharon Reikhav
Dadi Segal Anat Shperberg
Vered Tzin Gal Wittenberg
Tamar Yifhar

Administrator

Maanit Zibziner