Institute for Integrative Genome Biology


Natasha RaikhelNatasha Raikhel

Distinguished Professor of Plant Cell Biology, Emerita;
Ernst and Helen Leibacher Endowed Chair 

Mailing Address:

Botany and Plant Sciences
Genomics Building /4119C
University of California
Riverside, CA 92521

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

UCR Living the Promise Profile (2010) 


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:

Endosomal and Vacuolar Trafficking in Plant Cells

Awards / Honors:

2013  ASPB Adolph E. Gude, Jr., Award (American Society of Plant Biologists)
2012  Elected Member, National Academy of Sciences
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
1996  The Guggenheim Fellowship

Research Summary:

We are studying endosomal and vesicular trafficking to the vacuoles. Our focus is on the model plant Arabidopsis thaliana. These 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.

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.

Trafficking to the Vacuole
A functional vacuole and intact protein trafficking system are necessary for plant cell viability and function. Perturbations of the trafficking machinery often affect vital cell processes, such as plant hormone responses, cytokinesis and the development of tissue specificity. In the classical view, many soluble plant vacuolar proteins are sorted away from proteins destined for secretion at the trans-Golgi network (TGN), a process that requires the presence of positive sorting signals in the primary sequence of vacuolar proteins. Two of these sorting signals, an N-terminal propeptide (NTPP) and a C-terminal propeptide (CTPP), are directed to the vacuole by distinct pathways. The NTPP pathway is believed to be common to plant and yeast, and several components of the machinery involved in the sorting of NTPP-type cargo have been characterized. The CTPP pathway is believed to be unique to plants, and different genetic approaches, have been used to identify components that are specific for that pathway. To isolate new components of the plant-specific CTPP sorting machinery in Arabidopsis, we used a T-DNA mutagenized population in the Vac2 background (Vac2 T-DNA).

 Figure 1
Screening strategy: The Arabidopsis CLV3 protein (green) is synthesized in the shoot apical meristem and secreted to the apoplasm. There, it activates the CLV1/2 LRR kinase receptor (black). Plants lacking CLV3 protein (clv3-2) have uncontrolled growth at the SAM. The Vac2 reporter line targets the CLV3:CTPPBL fusion protein to the vacuole (V) in the clv3-2 background. T-DNA plants mutated in components of the vacuolar trafficking machinery shunt CLV3:T7:CTPPBL to the default secretion pathway, thereby complementing the clv3-2 phenotype.
The Vac2 line contains a genetically engineered CLV3 fused to the barley lectin C-terminal vacuolar sorting signal (CLV3:CTPPBL) in the clv3-2 mutant background. Previous studies using genetic crosses and EMS mutagenesis of the Vac2 line have been successfully used for the identification of components involved in the specific sorting of CTPP-proteins.  For example, a screen of EMS-mutagenized Vac2 plants and subsequent map-based cloning of one mutant line, mtv5, identified the shoor meristem identity gene TERMINAL FLOWER 1 (TFL1) as a component of vacuolar CTPP trafficking machinery. Recently, we  used   the Vac2 T-DNA screen that allowed us to identify a novel component of the vacuolar CTPP sorting machinery, the cytosolic ribosomal protein (r-protein) L4/L1 (RPL4A). Our  analysis of the two transcriptionally active members of the RPL4 family in Arabidopsis, suggests that the RPL4A and RPL4D proteins are equivalent. Mutations in both RPL4 genes cause similar developmental defects and both proteins are involved in the sorting of CTPP containing proteins to the vacuole. Moreover, our results suggest that the sorting defects in rpl4 mutants are due to the inability of a subset of ribosomal complexes, lacking RPL4 proteins in their structures, to properly interact with the nascent CTPP peptides. Thus, we propose that the interactions between RPL4 and the CTPP nascent peptides may be the first sorting checkpoint for CTPP vacuolar targeted proteins.

Several proteomic studies in Arabidopsis have shown the presence of heterogeneous ribosomal populations in different tissues. However, the phenotypic consequences of the imbalance of those ribosomal populations, and the regulatory mechanisms activated to control specific ratios between them, have yet to be evaluated. Our phenotypic characterization of the Arabidopsis ribosomal L4 (RPL4) family suggests that the maintenance of proper auxin-regulated developmental responses requires the simultaneous presence of RPL4A- and RPL4D-containing ribosomes. Based on the analysis of the compensatory mechanisms within the RPL4 family proteins in the rpl4a and rpl4d backgrounds, we propose the Gene Dosage Balance Hypothesis (GDBH) as a regulatory mechanism for ribosomal complexes in Arabidopsis. By using the concepts of dosage compensation and hierarchy, GDBH is able to explain the severity and specificity of different ribosomal mutant phenotypes associated with the same ribosomal complex.

Genomics meets Cell Biology: A Chemical, Genetic and Proteomic Approach to Dissecting Plant Endosomes
Although it is known that proteins are delivered to and recycled from the plasma membrane (PM) via endosomes, the nature of the endosomal compartments and the pathways responsible for cargo and vesicle sorting and cellular signaling is poorly understood. More specifically, the molecular mechanisms that regulate protein trafficking to and from the PM, via interconnected endocytosis and recycling pathways, or towards the vacuole remain ill-defined due to the transient nature of endosomal compartments and their cargoes. We have pioneered a novel approach to the study of this cell-biological problem that involves indentifying components and cargoes of this trafficking system using a combination of chemical genomics, proteomics and genetics The significance of dissecting these processes is broad-based in that these sorting mechanisms can control the distribution of cellular receptors, transporters and other proteins that are critical for plant development or responses to pathogens and environment.

Many cellular processes, especially endomembrane trafficking events such as endocytosis and recycling occur within minutes in vivo. Attempts to study such rapid processes using mutants is clearly valuable; however, unless the effects of the mutations are conditional, one has to accept that the state of the cell is at equilibrium with the mutation (Hicks and Raikhel, 2009). An additional limitation of classical genetics is that endomembrane-related mutations can be silent due to redundancy or lethality. To dissect these highly dynamic processes, a chemical genomics approach, we are using bioactive compounds that act specifically and reversibly within minutes to perturb endosome sorting and cycling. We started to address the biological functions uncovered by one these chemicals, endosidin 1 (ES1). ES1 arrests the endocytosis of specific PM proteins and results in the formation of endosome agglomerations known as “endosidin 1 bodies” that are tagged by the endosome/trans-Golgi network (TGN) markers SYP61 and VHA-a1. ES1 bodies also contain PM proteins that are detectable in SYP61 compartments only upon arrest of transit with ES1, providing an opportunity to identify transient cargoes and their transport pathways. The ability of ES1 to arrest transport of transitory cargoes in ES1 bodies resulted in the discovery of a previously unknown connection between the endocytosis of PIN2, BRI1 and AUX1(Robert et al., 2008). Thus, it became clear that chemical screens can uncover new specific reagents that can target transitory compartments in order to dissect their functions in a systematic manner. Initially, a limited chemical genomics screen was performed to test the hypothesis that reagents could be found that perturbed PM protein cycling at the PM and endosome sorting. This small-scale screen resulted in ES1. We subsequently used this high-throughput pollen-based screen to identify a library of compounds targeting the endomembrane system in Arabidopsis.Figure 2We screened nearly 47,000 compounds at the cellular level with a broad set of fluorescent protein markers resulting in the identification of small molecules (endosidins) that perturb specific pathways such as endocytosis, sorting to the vacuole, cell plate formation, polarity and other PM-networked processes. The approach has required the development of methodologies and informatic tools to present the complex interactions of compounds and intracellular phenotypes, but clear phenotypic classes of compounds have been found. By combining proteomics, genetics and cell biology, including in vivo imaging and EM immunocytochemistry, we are analyzing the cell biological effects of these endosidins in the cells and their targets.

Related Press Releases:

Selected Publications:

List of publications from PubMed

Lab Personnel:

Hicks, Glenn
Associate Research Plant Cell Biologist — Protein Targeting to the Plant Cell Vacuole; Chemical Genomics
Van de Ven, Wilhemina
Staff Research Associate — Plant Cell Wall Biosynthesis
Li, Ruixi
Postgraduate Researcher—  Protein Targeting to the Plant Cell Vacuole
Zhang, Chunhua
Postgraduate Researcher—  Protein Targeting to the Plant Cell Vacuole
Ung, Nolan
Graduate Student Researcher

More Information

General Campus Information

University of California, Riverside
900 University Ave.
Riverside, CA 92521
Tel: (951) 827-1012

Career OpportunitiesUCR Libraries
Campus StatusDirections to UCR

Genomics Information

Institute of Integrative Genome Biology
2150 Batchelor Hall

Tel: (951) 827-7177
E-mail: Aurelia Espinoza, Managing Director