Natasha V Raikhel

University of California, Riverside, Riverside, California, United States

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Publications (205)1526.55 Total impact

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    Chunhua Zhang · Glenn R Hicks · Natasha V Raikhel ·
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    ABSTRACT: The vacuole is an essential organelle for plant growth and development. It is the location for the storage of nutrients; such as sugars and proteins; and other metabolic products. Understanding the mechanisms of vacuolar trafficking and molecule transport across the vacuolar membrane is of great importance in understanding basic plant development and cell biology and for crop quality improvement. Proteins play important roles in vacuolar trafficking; such proteins include Rab GTPase signaling proteins; cargo recognition receptors; and SNAREs (Soluble NSF Attachment Protein Receptors) that are involved in membrane fusion. Some vacuole membrane proteins also serve as the transporters or channels for transport across the tonoplast. Less understood but critical are the roles of lipids in vacuolar trafficking. In this review, we will first summarize molecular composition of plant vacuoles and we will then discuss our latest understanding on the role of lipids in plant vacuolar trafficking and a surprising connection to ribosome function through the study of ribosomal mutants.
    06/2015; 4(2):320-333. DOI:10.3390/plants4020320
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    ABSTRACT: Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF–defective mutants gnom-like1 (gnl1-1) and gnom (van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER)–Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development.
    Proceedings of the National Academy of Sciences 02/2015; 112(7):E806–E815. DOI:10.1073/pnas.1424856112 · 9.67 Impact Factor
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    Natasha Raikhel ·

    Current Biology 02/2015; 25(3):R97-R99. DOI:10.1016/j.cub.2014.10.060 · 9.57 Impact Factor
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    Ruixi Li · Ruobai Sun · Glenn R Hicks · Natasha V Raikhel ·
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    ABSTRACT: The vacuole is the most prominent compartment in plant cells and is important for ion and protein storage. In our effort to search for key regulators in the plant vacuole sorting pathway, ribosomal large subunit 4 (rpl4d) was identified as a translational mutant defective in both vacuole trafficking and normal development. Polysome profiling of the rpl4d mutant showed reduction in polysome-bound mRNA compared with wild-type, but no significant change in the general mRNA distribution pattern. Ribsomal profiling data indicated that genes in the lipid metabolism pathways were translationally down-regulated in the rpl4d mutant. Live imaging studies by Nile red staining suggested that both polar and nonpolar lipid accumulation was reduced in meristem tissues of rpl4d mutants. Pharmacological evidence showed that sterol and sphingolipid biosynthetic inhibitors can phenocopy the defects of the rpl4d mutant, including an altered vacuole trafficking pattern. Genetic evidence from lipid biosynthetic mutants indicates that alteration in the metabolism of either sterol or sphingolipid biosynthesis resulted in vacuole trafficking defects, similar to the rpl4d mutant. Tissue-specific complementation with key enzymes from lipid biosynthesis pathways can partially rescue both vacuole trafficking and auxin-related developmental defects in the rpl4d mutant. These results indicate that lipid metabolism modulates auxin-mediated tissue differentiation and endomembrane trafficking pathways downstream of ribosomal protein function.
    Proceedings of the National Academy of Sciences 12/2014; 112(1). DOI:10.1073/pnas.1422656112 · 9.67 Impact Factor
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    ABSTRACT: Background: A highly regulated trafficking of cargo vesicles in eukaryotes performs protein delivery to a variety of cellular compartments of endomembrane system. The two main routes, the secretory and the endocytic pathways have pivotal functions in uni- and multi-cellular organisms. Protein delivery and targeting includes cargo recognition, vesicle formation and fusion. Developing new tools to modulate protein trafficking allows better understanding the endomembrane system mechanisms and their regulation. The compound Sortin2 has been described as a protein trafficking modulator affecting targeting of the vacuolar protein carboxypeptidase Y (CPY), triggering its secretion in Saccharomyces cerevisiae. Results: A reverse chemical-genetics approach was used to identify key proteins for Sortin2 bioactivity. A genome-wide Sortin2 resistance screen revealed six yeast deletion mutants that do not secrete CPY when grown at Sortin2 condition where the parental strain does: met18, sla1, clc1, dfg10, dpl1 and yjl175w. Integrating mutant phenotype and gene ontology annotation of the corresponding genes and their interactome pointed towards a high representation of genes involved in the endocytic process. In wild type yeast endocytosis towards the vacuole was faster in presence of Sortin2, which further validates the data of the genome-wide screen. This effect of Sortin2 depends on structural features of the molecule, suggesting compound specificity. Sortin2 did not affect endocytic trafficking in Sortin2-resistant mutants, strongly suggesting that the Sortin2 effects on the secretory and endocytic pathways are linked. Conclusions: Overall, the results reveal that Sortin2 enhances the endocytic transport pathway in Saccharomyces cerevisiae. This cellular effect is most likely at the level where secretory and endocytic pathways are merged. Them Sortin2 specificity over the endomembrane system places it as a powerful biological modulator for cell biology.
    Biological research 12/2014; 48(1):1-11. DOI:10.1186/S40659-015-0032-9 · 1.48 Impact Factor
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    Chunhua Zhang · Glenn R Hicks · Natasha V Raikhel ·
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    ABSTRACT: Plant vacuoles are essential organelles for plant growth and development, and have multiple functions. Vacuoles are highly dynamic and pleiomorphic, and their size varies depending on the cell type and growth conditions. Vacuoles compartmentalize different cellular components such as proteins, sugars, ions and other secondary metabolites and play critical roles in plants response to different biotic/abiotic signaling pathways. In this review, we will summarize the patterns of changes in vacuole morphology in certain cell types, our understanding of the mechanisms of plant vacuole biogenesis, and the role of SNAREs and Rab GTPases in vacuolar trafficking.
    Frontiers in Plant Science 09/2014; 5:476. DOI:10.3389/fpls.2014.00476 · 3.95 Impact Factor
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    Glenn R Hicks · Natasha V Raikhel ·
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    ABSTRACT: As an early adopter of plant chemical genetics to the study of endomembrane trafficking, we have observed the growth of small molecule approaches.Within the field, we often describe the strengths of the approach in a broad, generic manner, such as the ability to address redundancy and lethality. But, we are now in a much better position to evaluate the demonstrated value of the approach based on examples. In this perspective, we offer an assessment of chemical genetics in plants and where its applications may be of particular utility from the perspective of the cell biologist. Beyond this, we suggest areas to be addressed to provide broader access and enhance the effectiveness of small molecule approaches in plant biology.
    Frontiers in Plant Science 09/2014; 5(455):1. DOI:10.3389/fpls.2014.00455 · 3.95 Impact Factor
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    Chunhua Zhang · Glenn R. Hicks · Natasha V. Raikhel ·
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    ABSTRACT: Chemical genomics is useful in studying essential cellular processes such as endomembrane trafficking pathways. This chapter describes a small molecule – Sortin1 – that connects plant vacuolar trafficking defects and flavonoid metabolism, both of which play important roles in plant growth and development. The compartmentalized endomembrane system ensures proper processing and trafficking of macromolecules to the sites of function. A normally functioning endomembrane trafficking machinery is essential for plant growth and development. Chemical genomics in combination with reverse genetics can identify and integrate different cellular pathways. In the case of Sortin1, chemical genomics connects three cellular processes: protein vacuolar trafficking, flavonoid vacuolar trafficking and metabolism, and vacuole biogenesis. Further identification of target proteins that directly interact with Sortin1 or its active decomposition product will reveal proteins that serve as a linker or hub of three different cellular processes.
    Concepts and Case Studies in Chemical Biology, 06/2014: pages 285-294; , ISBN: 9783527336111
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    ABSTRACT: Metabolomics and chemical genomics studies can each provide unique insights into plant biology. Although a variety of analytical techniques can be used for the interrogation of plant systems, nuclear magnetic resonance (NMR) provides unbiased characterization of abundant metabolites. An example methodology is provided for probing the metabolism of Arabidopsis thaliana in a chemical genomics experiment including methods for tissue treatment, tissue collection, metabolite extraction, and methods to minimize variance in biological and technical sample replicates. Additionally, considerations and methods for data analysis, including multivariate statistics, univariate statistics, and data interpretation are included. The process is illustrated by examining the metabolic effects of chemical treatment of Arabidopsis with Sortin 1, also known as vacuolar protein sorting inhibitor 1. Sortin 1 was applied to Arabidopsis seedlings to examine metabolic effects in a chemical genomics experiment and to demonstrate the utility of metabolomics in conjunction with other "omics" techniques.
    Methods in molecular biology (Clifton, N.J.) 01/2014; 1056:225-39. DOI:10.1007/978-1-62703-592-7_21 · 1.29 Impact Factor
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    Michelle Q Brown · Nolan Ung · Natasha V Raikhel · Glenn R Hicks ·
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    ABSTRACT: Endomembrane cycling processes in plants remain mostly intractable through classical genetic interrogation. Chemical disruption of these processes provides an opportunity to slow or inhibit these processes for study. Tobacco pollen, which is dependent upon endomembrane cycling for tube growth, provides a plant system that is amenable to high-throughput screening of chemical disruptors. We describe here the process that allowed the identification of over 360 endomembrane cycling disruptors.
    Methods in molecular biology (Clifton, N.J.) 01/2014; 1056:111-4. DOI:10.1007/978-1-62703-592-7_11 · 1.29 Impact Factor
  • Michelle Q. Brown · Abel Rosado · Natasha V. Raikhel ·
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    ABSTRACT: Chemical biology is a highly interdisciplinary field of research defined by the use of low-molecular-mass molecules as probes to modify biological processes. The discipline itself is as old as the period in which natural products and bioactive metabolites were purified from plants and used as medicines in a systematic manner. From the early attempts to methodically collect information on medicinal plants and the development of herbal pharmacopoeias in the ancient world to the latest attempts in the postgenomic era to systematize the application of small molecules to biology through the development of diversity-oriented synthesis (DOS) and in silico chemical genetics, the use of small molecules has been inextricably intertwined with the development of modern disciplines including pharmacology, physiology, and cell biology. In this historical review, we explore the foundations of plant chemical biology in medicine and how this groundwork led to new insights and applications in plant biology.
    Plant Chemical Biology, Edited by eds D. Audenaert and P. Overvoorde, 11/2013: chapter 1; John Wiley & Sons, Inc, Hoboken, NJ.., ISBN: 978-0-470-94669-5
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    ABSTRACT: Translation inhibition is a major but poorly understood mode of action of microRNAs (miRNAs) in plants and animals. In particular, the subcellular location where this process takes place is unknown. Here, we show that the translation inhibition, but not the mRNA cleavage activity, of Arabidopsis miRNAs requires ALTERED MERISTEM PROGRAM1 (AMP1). AMP1 encodes an integral membrane protein associated with endoplasmic reticulum (ER) and ARGONAUTE1, the miRNA effector and a peripheral ER membrane protein. Large differences in polysome association of miRNA target RNAs are found between wild-type and the amp1 mutant for membrane-bound, but not total, polysomes. This, together with AMP1-independent recruitment of miRNA target transcripts to membrane fractions, shows that miRNAs inhibit the translation of target RNAs on the ER. This study demonstrates that translation inhibition is an important activity of plant miRNAs, reveals the subcellular location of this activity, and uncovers a previously unknown function of the ER. PAPERCLIP:
    Cell 04/2013; 153(3):562-74. DOI:10.1016/j.cell.2013.04.005 · 32.24 Impact Factor
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    Chunhua Zhang · Natasha V Raikhel · Glenn R Hicks ·
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    ABSTRACT: The role, if any, of microtubules in auxin transport is poorly understood in plant biology. In this issue of Developmental Cell, Ambrose et al. (2013) show that the microtubule binding protein CLASP regulates PIN2 auxin transporter trafficking and stability via Sorting Nexin1, a component of the retromer complex.
    Developmental Cell 03/2013; 24(6):569-71. DOI:10.1016/j.devcel.2013.03.008 · 9.71 Impact Factor
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    Abel Rosado · Ruixi Li · Wilhelmina van de Ven · Emily Hsu · Natasha V Raikhel ·
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    ABSTRACT: Upstream ORFs are elements found in the 5'-leader sequences of specific mRNAs that modulate the translation of downstream ORFs encoding major gene products. In Arabidopsis, the translational control of auxin response factors (ARFs) by upstream ORFs has been proposed as a regulatory mechanism required to respond properly to complex auxin-signaling inputs. In this study, we identify and characterize the aberrant auxin responses in specific ribosomal protein mutants in which multiple ARF transcription factors are simultaneously repressed at the translational level. This characteristic lends itself to the use of these mutants as genetic tools to bypass the genetic redundancy among members of the ARF family in Arabidopsis. Using this approach, we were able to assign unique functions for ARF2, ARF3, and ARF6 in plant development.
    Proceedings of the National Academy of Sciences 11/2012; 109(48). DOI:10.1073/pnas.1214774109 · 9.67 Impact Factor
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    Nolan Ung · Michelle Q Brown · Glenn R Hicks · Natasha V Raikhel ·
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    ABSTRACT: Tip growth of pollen tubes and root hairs occurs via rapid polar growth. These rapidly elongating cells require tip-focused endomembrane trafficking for the deposition and recycling of proteins, membranes, and cell wall materials. Most of the image-based data published to date are subjective and non-quantified. Quantitative and comparative descriptors of these highly dynamic processes have been a major challenge, but are highly desirable for genetic and chemical genomics approaches to dissect this biological network. To address this problem, we screened for small molecules that perturbed the localization of a marker for the Golgi Ras-like monomeric G-protein RAB2:GFP expressed in transgenic tobacco pollen. Semi-automated high-throughput imaging and image analysis resulted in the identification of novel compounds that altered pollen tube development and endomembrane trafficking. Six compounds that caused mislocalization and varying degrees of altered movement of RAB2:GFP-labeled endomembrane bodies were used to generate a training set of image data from which to quantify vesicle dynamics. The area, velocity, straightness, and intensity of each body were quantified using semi-automated image analysis tools revealing quantitative differences in the phenotype caused by each compound. A score was then given to each compound enabling quantitative comparisons between compounds. Our results demonstrate that image analysis can be used to quantitatively evaluate dynamic subcellular endomembrane phenotypes induced by bioactive chemicals, mutations, or other perturbing agents as part of a strategy to quantitatively dissect the endomembrane network.
    Molecular Plant 11/2012; 6(4). DOI:10.1093/mp/sss092 · 6.34 Impact Factor
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    Ruixi Li · Natasha V. Raikhel · Glenn R. Hicks ·

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    Ruixi Li · Natasha V. Raikhel · Glenn R. Hicks ·
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    ABSTRACT: Plant endocytosis and endomembrane trafficking relies on the coordination of a highly organized and dynamic network of intracellular organelles. Membrane trafficking and associated signal transduction pathways provide critical cellular regulation of plant development and response to environmental stimuli. However, the efficiency of studies on this complex network has been hampered due to the rapid and dynamic nature of endomembrane trafficking as well as gene redundancy and embryonic lethality in mutagenesis-based strategies. Chemical genomics emerged in recent years as a complementary approach to illuminate biological functions through the integration of organic chemistry, biology, and bioinformatics to overcome gene redundancy. The approach presents significant advantages in dosage dependence and reversibility, which offers the ideal ability to study dynamic endomembrane trafficking processes in real time. In this chapter, several successful examples of chemical screening focused on the endomembrane system is presented to illuminate the efficiency and power of chemical genomics in dissecting endomembrane trafficking and its regulation of plant development and environmental responses. Perspectives are also presented to suggest directions for future development of this field. © 2012 Springer-Verlag Berlin Heidelberg. All rights are reserved.
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    ABSTRACT: The use of small molecules to transiently modulate protein function can circumvent the limitations of classical genetic approaches caused by gene redundancy and lethality. Although chemical genomics and genetics screens facilitate the characterization of new biological components, they have infrequently led to the identification of target proteins involved in metabolism. The current state of metabolomics technologies permits the detection of thousands of molecules, allowing the exploration of yet uncharacterized metabolic pathways. The combination of these two approaches, termed here "ChemoMetabolomics", is a promising application of both technologies. This novel approach will facilitate the detection of metabolic modulators, the dissection of the crosstalk in the metabolic network, and the development of hypotheses on how changes in metabolism affect developmental or cellular responses. Furthermore, it will facilitate the elucidation of the linkage between metabolic and developmental programs and assist the gain of an elaborated view of biological processes at the system level.
    Plant physiology 09/2012; 160(3). DOI:10.1104/pp.112.203919 · 6.84 Impact Factor
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    Patricio Pérez-Henríquez · Natasha V Raikhel · Lorena Norambuena ·
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    ABSTRACT: Plants' developmental plasticity plays a pivotal role in responding to environmental conditions. One of the most plastic plant organs is the root system. Different environmental stimuli such as nutrients and water deficiency may induce lateral root formation to compensate for a low level of water and/or nutrients. It has been shown that the hormone auxin tunes lateral root development and components for its signaling pathway have been identified. Using chemical biology, we discovered an Arabidopsis thaliana lateral root formation mechanism that is independent of the auxin receptor SCF(TIR). The bioactive compound Sortin2 increased lateral root occurrence by acting upstream from the morphological marker of lateral root primordium formation, the mitotic activity. The compound did not display auxin activity. At the cellular level, Sortin2 accelerated endosomal trafficking, resulting in increased trafficking of plasma membrane recycling proteins to the vacuole. Sortin2 affected Late endosome/PVC/MVB trafficking and morphology. Combining Sortin2 with well-known drugs showed that endocytic trafficking of Late E/PVC/MVB towards the vacuole is pivotal for Sortin2-induced SCF(TIR)-independent lateral root initiation. Our results revealed a distinctive role for endosomal trafficking in the promotion of lateral root formation via a process that does not rely on the auxin receptor complex SCF(TIR).
    Molecular Plant 07/2012; 5(6). DOI:10.1093/mp/sss066 · 6.34 Impact Factor
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    Glenn R Hicks · Natasha V Raikhel ·
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    ABSTRACT: Since the introduction of chemical genomics to plant biology as a tool for basic research, the field has advanced significantly. There are now examples of important basic discoveries that demonstrate the power and untapped potential of this approach. Given the combination of protein and small-molecule complexity, new phenotypes can be described through the perturbation of cellular functions that can be linked to growth and developmental phenotypes. There are now clear examples of overcoming functional redundancy in plants to dissect molecular mechanisms or critical pathways such as hormone signaling and dynamic intracellular processes. Owing to ongoing advances, including more sophisticated high-content screening and rapid approaches for target identification, the field is beginning to move forward. However, there are also challenges to improve automation, imaging, and analysis and provide chemical biology resources to the broader plant biology community.
    Annual Review of Plant Biology 01/2012; 63(1):261-82. DOI:10.1146/annurev-arplant-042811-105456 · 23.30 Impact Factor

Publication Stats

13k Citations
1,526.55 Total Impact Points


  • 2002-2015
    • University of California, Riverside
      • • Department of Botany and Plant Sciences
      • • Center for Plant Cell Biology
      Riverside, California, United States
    • University of Wisconsin, Madison
      • Department of Biochemistry
      Madison, MS, United States
  • 2009
    • University of Santiago, Chile
      • Departamento de Biología
      CiudadSantiago, Santiago, Chile
  • 1981-2006
    • University of Georgia
      Атина, Georgia, United States
  • 2005
    • Spanish National Research Council
      • Department of Plant Molecular Genetics
      Madrid, Madrid, Spain
  • 1987-2003
    • Michigan State University
      • MSU-DOE Plant Research Laboratory
      Ист-Лансинг, Michigan, United States
  • 1991-2000
    • University of California, San Diego
      San Diego, California, United States
  • 1999
    • University of Oregon
      • Institute of Molecular Biology
      Eugene, Oregon, United States
    • University of California, Davis
      • Department of Plant Pathology
      Davis, California, United States
  • 1996
    • State of Michigan
      Lansing, Michigan, United States
  • 1995
    • Nagoya University
      • Graduate School of Bio-Agricultural Sciences
      Nagoya, Aichi, Japan
  • 1993
    • Virginia Commonwealth University
      • Department of Biochemistry and Molecular Biology
      Richmond, VA, United States
  • 1990
    • The Rockefeller University
      New York, New York, United States