Institute for Integrative Genome Biology

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Natasha Raikhel

Director, Institute for Integrative Genome Biology;
Director, Center for Plant Cell Biology;
Distinguished Professor of Plant Cell Biology;
Ernst and Helen Leibacher Endowed Chair

Mailing Address:

Botany and Plant Sciences
Keen Hall /2024
University of California
Riverside, CA 92521

Phone: (951) 827-6370
Fax: (951) 827-2155
Email: nraikhel@ucr.edu
Website

Degree(s):

PhD 1975 Institute of Cytology in Leningrad
MS 1970 Leningrad State University, USSR

College/Division Affiliation:

College of Natural and Agricultural Sciences

Center/Inst Affiliation(s):

Center for Plant Cell Biology

Areas Of Expertise:

Vacuolar Trafficking through the Secretory System; Biosynthesis of Cell Wall Polysaccharides in Plants

Awards / Honors:

2007  Fellow of ASPB (American Society of Plant Biologists) Award
2007  UCR Faculty Research Lecturer Award
2004  2004 Stephen Hales Prize of ASPB
2003  AAAS Fellow (American Association for the Advancement of Science)
2002  Women in Cell Biology (WICB) Senior Achievement Award, American Society for Cell Biology
1996  The Japan Society for Promotion of Science Fellowship for Research in Japan
1996  The Guggenheim Fellowship

Research Summary:

Over the years my laboratory has been involved in studying vesicular trafficking to the vacuoles, vacuolar biogenesis and the genetic control of cell wall polysaccharide biosynthesis. Historically we have used a number of different plant systems, but over the last ten years we have focused on the model plant Arabidopsis thaliana. Our findings are important not only for a better understanding of the basic biology of endomembrane trafficking in Arabidopsis, but also because we can translate that knowledge to crops, trees, and grasses. This will result in better crop fitness and increased biomass production through the enhancement of nutritional reserves and the development of plants with improved cell walls.

Research in my laboratory utilizes all available approaches to address our scientific questions. Our multidisciplinary strategy uses a combination of cellular, molecular, genetic, proteomics, chemical genomics, bioinformatics and genomic technologies. Newer developments and initiatives undertaken by current members of my laboratory are summarized below.

Plant Vacuolar Biogenesis and Endomembrane Trafficking

There are at least two kinds of vacuoles in plants: lytic vacuoles (LV) that have an acidic pH and are the functional equivalent of yeast vacuoles and mammalian lysosomes, and protein storage vacuoles (PSVs) that are of neutral pH and store reserve proteins, minerals, and defense proteins such as lectins. Storage proteins can comprise up to 25% of the dry weight of leguminous seeds, and 15% of cereal grains; they are also found in root and shoot tubers. Thus, huge amounts of proteins are accumulated in the PSVs. Despite the demonstration that PSVs are present in tissues and organs other than seeds, their functions in vegetative tissues are not well understood. In particular, the mechanisms of sorting and trafficking of newly synthesized proteins to the PSV in any tissue remain unclear. My laboratory has begun to address this important question by developing tools for the experimental analysis of PSV protein transport pathways. We created an Arabidopsis screening line, Vac2, in a clv3-2 mutant background. CLV3 is an extracellular ligand that is a negative regulator of shoot stem cell proliferation, and clv3 mutants display increased growth at apical and floral meristems. When a vacuole targeting signal is fused to CLV3 (Vac2 construct) and expressed in a clv3-2 mutant background, the ligand is targeted to the PSV. Vac2 plants that have mutations in the PSV protein trafficking machinery secrete CLV3 to the extracellular space. These plants are complemented for the clv3-2 mutation and have reduced meristem phenotypes. Using this approach, we have identified the Q_b-SNARE protein VTI12 as a component of PSV, and not LV, trafficking (Sanmartín et al., 2007).

A screen of EMS-mutagenized Vac2 plants and subsequent map-based cloning of one mutant line, mtv5, identified the shoot meristem identity gene TERMINAL FLOWER 1 (TFL1) as a component of PSV trafficking, that is, PSV-localized proteins are secreted in this mutant, and trafficking of LV proteins is not affected. A combination of genetic, biochemical and cell biological evidence shows that TFL1 is involved in this process. We proposed a model in which protein storage vacuoles in meristematic tissues store factors important for flowering and meristem maintenance. The right combination of developmental and environmental cues triggers the release of these factors (Sohn et al., 2007). This is a surprising finding because, until now, many laboratories that study flower development have focused on how the genes involved in that process are regulated in the nucleus. Furthermore, many have considered the protein storage vacuole to be an inert reservoir for materials that the plant stores for future growth. Therefore, the finding that a regulator of flower development may also regulate transport to the protein storage vacuole suggests that there is interplay between transcriptional and trafficking events, and that the storage vacuole may have some heretofore-unforeseen roles in development.

In addition to the EMS-mutagenized Vac2 seed collection, we have prepared a T-DNA collection of Vac2 plants. Our preliminary analysis of this collection identified several genes that may be involved in trafficking to the PSV. All these results demonstrate that the Vac2 system is extremely powerful for the genetic dissection of PSVs. Importantly, the assay allows us to specifically identify genes involved in trafficking to the PSV, distinguishing them from those that are important for traffic to the LV. Furthermore, because this assay is not restricted to seed tissues, it will be possible to identify genes for PSV trafficking components potentially specific to the vegetative tissues. We will continue analysis of this collection of mutants to analyze the biology of gene products involved in PSV in seed and non-seed tissues.

We also have taken a chemical genomics approach to study trafficking in plants. From the previous work in my lab it became clear that many genes that are involved in the endomembrane trafficking are either indispensable for the plant or redundant. There are several approaches that can be used to study essential or redundant genes and chemical genomics is one of them. Small molecules can be used to modify or disrupt the function of specific proteins, but at concentrations at which the plants are still alive. My lab was one of the first to use this approach in plants (Zouhar et al., 2004; Surpin et al., 2005). Recently, we identified a target of one of the gravitropic/vacuolar effectors in plants, which we called Gravacin (Rojas-Pierce et al., 2007). When Gravacin was applied to Arabidopsis, the plant shoots did not respond to the gravity vector. That is, the plants grew in all directions, even downwards and/or horizontally. We identified the target of Gravacin as P-glycoprotein19, which was previously identified as having an important role in gravitropism. Our work is one of the first identifications of a drug target from chemical genomics screens in plants; it highlights Gravacin as a novel inhibitor of P-glycoproteins and as a new tool for cell biology studies. Since P-glycoproteins are highly conserved, it is possible that inhibitors of these proteins in plants may have similar activity in other organisms, including humans, where inhibition of P-glycoprotein is an important component of the treatment of certain tumors.

We have also identified several other very exciting small molecules that affect vesicular trafficking and we are in the process of identifying their respective targets and pathways. We are also developing biochemical approaches for target isolation. Our chemical genomics approach has allowed my students and postdocs to become very familiar and "fluent” in chemistry.

My lab has also started work on the biochemical isolation of pure fractions of specific vesicles in order to analyze their cargo. It is our aim to define the cargoes of specific pathways, so that we may precisely understand the role of endomembrane trafficking in signaling and development. We will accomplish this goal using a combination of molecular, biochemical, and proteomics methods. This project is relevant to both our vesicular trafficking and cell wall biosynthesis projects.

Hemicellulose Biosynthesis

Xyloglucan (XyG), the principal hemicellulose of dicotyledonous plants, binds tightly but noncovalently to cellulose microfibrils, cross-linking them into a complex network. In collaboration with Dr. Ken Keegsrta’s laboratory at MSU, we have identified several genes whose products are involved in xyloglucan biosynthesis and developed a testable hypothesis regarding their biochemical function. Our first efforts were focused on fucosyltransferase, an enzyme that adds fucose as the terminal sugar on a xyloglucan side-chain. We purified the enzyme, isolated the cDNA clone, expressed it in the heterologous system and showed its activity (Perrin et al., 1999). This was the first Golgi glycosyltransferase to be isolated and cloned from plants. We have also identified an Arabidopsis gene that encodes an -xylosyltransferase activity involved in xyloglucan biosynthesis (Faik et al., 2002) and later provided a compelling case that the CSLC gene family encodes proteins that synthesize the XyG backbone (Cocuron et al., 2007).

We are now using a combination of genomic, bioinformatic, and biochemical approaches to identify and characterize additional genes required for the biosynthesis of xyloglucan. One line of investigation in my lab is the functional analysis of genes in the CAZy GT34 family. The analysis of several double and triple mutants between several genes from the GT3 family is currently in progress.

Selected Publications:

Lab Personnel: +

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