Rujin Chen, Ph.D. Assistant Scientist email: rchen@noble.org

Ph.D., Biochemistry, 1996, Michigan State University Postdoctoral Fellow, University of Wisconsin-Madison Joined the Noble Foundation in 2002

Research Video: Functional Genomics and Bioinformatics Flash Player is required

600kb 2.8mb

Research Emphasis: Functional genomics of legume root development; molecular mechanisms of polar auxin transport; auxin efflux carriers; ATP-binding cassette (ABC) multidrug resistance transporters; Arabidopsis thaliana; Medicago truncatula

Two long-term projects in my laboratory center on developing functional genomics tools for the study of legume root development and elucidating molecular mechanisms of polar auxin transport that plays regulatory roles in many plant growth and developmental processes.

Auxins are a class of plant hormones that regulate cell division, elongation and differentiation, and therefore diverse growth and developmental processes including tropic responses to light and gravity, pattern formation during embryogenesis, vasculature differentiation, and lateral organ formation. At the molecular level, auxins regulate the expression of auxin responsive genes, i.e. SAURs, Aux/IAA and ARF genes. In developing plants, indole-3-acetic acid, the major endogenous auxin is synthesized in young tissues including apical meristems and young leaves and transported to other cells/tissues to regulate plant growth and development. The transport process is unilateral and conventionally referred to polar auxin transport.

Using a map-based cloning strategy, we have independently cloned the Arabidopsis AGRAVITROPIC 1 (AtAGR1) gene (also named as EIR1 or PIN2 by other groups) that our data suggest encodes a component of the auxin efflux carrier complex, and belongs to the AGR/EIR/PIN gene family. Our molecular genetics analyses indicated that one of the biological functions of the AGR1 is to regulate gravitropic response at the distal elongation zone in roots and transiently in etiolated hypocotyls.

Previous physiological analyses suggested that polar auxin transport occurs in a cell-to-cell fashion and is mediated by plasma membrane-localized auxin influx and efflux carrier proteins. Recent experimental evidence supports the hypothesis that an asymmetric cellular localization of the auxin efflux carriers within transport-competent cells determines the direction of polar auxin transport, which can be either basipetal or acropetal in plants. Additional experimental data suggest that the candidate auxin influx carrier AtAUX1 also undergoes asymmetric cellular localization in some cells and therefore may contribute to regulate the direction or the rate of auxin transport in these cells (Swarup et al., Genes & Dev. 15:2648-53).

Earlier physiological and biochemical studies using chemical inhibitors of polar auxin transport, such as NPA and TIBA suggest that the auxin efflux carrier is in a complex consisting of three biochemically distinctive components, auxin efflux carrier, NPA-binding protein and a third labile component (Lomax, et al., 1995, in Plant Hormones: Physiology, biochemistry, and molecular biology). While our data suggest that the AGR1/PIN2 protein is the candidate for the auxin efflux carrier, several ATP-binding cassette (ABC) multidrug resistance transporter proteins that bind to NPA were identified by biochemical means (Murphy et al., Plant Physiol. 128:935-50). Mutants in the corresponding genes displayed phenotypes consistent with their roles in auxin transport or response process (Noh et al., Plant Cell 13:2441-54). However, their in vitro as well as in vivo association with the auxin efflux carrier complex has not been demonstrated so far.

We are taking biochemical, molecular genetics and cell biology approaches to identify and characterize the complex structure of the auxin efflux carriers. We are interested in addressing the following questions. (1) What are the cellular components that interact with AGR1/PIN2 proteins? (2) What are the mechanisms that underlie and regulate the asymmetric distribution of the auxin efflux carrier proteins and their redistribution upon environmental cues such as gravistimulation? (3) If the polar auxin transport process closely linked to auxin-regulated gene expression (auxin response), what is the signaling process involved? (4) What are the biological functions of the AGR1/PIN2-like proteins and how their functions are regulated? (5) Are there any interactions between auxin efflux carrier proteins and NPA-binding ABC transporters and how these interactions regulate auxin transport? And (6) what are the cellular and genetic networks involved in regulating the process of auxin transport and how these networks are regulated by or responsive to developmental and environmental cues?

To facilitate our research, we are using model organisms Arabidopsis thaliana and Medicago truncatula so that the involvement of polar auxin transport in mediating plant growth and development can be broadly examined and specific processes such as symbiotic interactions between legume and nitrogen-fixing bacteria leading to nodule formation can also be evaluated.

Selected publications:
Peer, W.A., Bandyopadhyay, A., Blakeslee, J.J., Makam, S.N., Chen, R., Masson, P.H. and Murphy, A.S. (2004) Variation in expression and protein localization of the PIN family of auxin efflux facilitator proteins in flavonoid mutants with altered auxin transport in Arabidopsis thaliana. Plant Cell 16:1898-911.

Hou, G., Kramer, V.L., Wang, Y-S., Chen, R., Perbal, G., Gilroy, S. and Blancaflor, E.B. (2004) The promotion of gravitropism in Arabidopsis roots upon actin disruption is coupled with the extended alkalinization of the columella cytoplasm and a persistent lateral auxin gradient. Plant J. 39:113-25.

Boonsirichai, K., Sedbrook, J., Chen, R., Gilroy, S. and Masson, P.H. (2003) ALTERED RESPONSE TO GRAVITY Is a Peripheral Membrane Protein That Modulates Gravity-Induced Cytoplasmic Alkalinization and Lateral Auxin Transport in Plant Statocytes. Plant Cell 15: 2612-25.

Chen, R., Changhui, G., Boonsirichai, K., and Masson, P.H. (2002) Complex physiological and molecular processes underlying root gravitropism. Plant Mol. Biol. 49:305-17.

Boonsirichai, K., Guan, C., Chen, R., and Masson, P.H. (2002) Root Gravitropism: An Experimental Tool to Investigate Basic Cellular and Molecular Processes Underlying Mechanosensing and Signal Transmission in Plants. Annu. Rev. Plant Biol. 53:421-447.

Chen, R., Rosen, E. and Masson, P.H. (1999) Gravitropism in higher plants. Plant Physiol. 120: 343-350.

Sedbrook, J., Chen, R. and Masson, P.H. (1999) ARG1 (altered response to gravity) encodes a novel DnaJ-like protein which potentially interacts with the cytoskeleton. Proc. Natl. Acad. Sci. USA 96: 1140-1145.

Chen, R., Hilson, P., Sedbrook, J., Rosen, E., Caspar, T. and Masson, P.H. (1998) The Arabidopsis thaliana AGRAVITROPIC 1 (AGR1) gene encodes a component of the polar-auxin-transport efflux carrier. Proc. Natl. Acad. Sci. USA 95:15112-15117.

Chen, R., Silver, D. and de Bruijn, F.J. (1998) Nodule parenchyma specific expression of the Sesbania rostrata early nodulin SrEnod2 gene is mediated by cis-acting sequences located in its 3?UTR region. Plant Cell 10: 1585-1602.

Silver, D., Pinaev, A., Chen, R., and de Bruijn, F.J. (1996) Post-transcriptional regulation of the Sesbania rostrata early nodulin SrEnod2 gene by cytokinin. Plant Physiol. 112: 559-567.