Rice University
BioSciences at Rice

Bonnie Bartel

Ralph and Dorothy Looney Professor of BioSciences

Our laboratory uses genetic, cell biological, and biochemical approaches in Arabidopsis thaliana to elucidate fundamentals aspects of plant biology, including auxin regulation and the roles and biogenesis of peroxisomes.

Bartel's Research

The phytohormone auxin promotes cell expansion, division, and differentiation, thereby regulating a plethora of developmental events and environmental responses.  We use Arabidopsis mutants to identify genes providing inputs to the auxin pool, to distinguish precursors from active auxin, and to disentangle contributions of different auxin biosynthetic pathways to development.  We have identified enzymes that release auxin from precursors, discovered that the ER and peroxisomes compartmentalize auxin production pathways, and revealed the importance of different auxin sources for various aspects of plant development. We also have isolated novel auxin-signaling mutants and exploited these mutants to illuminate the interactions of auxin signaling with other phytohormone pathways and novel facets of auxin signaling.

Our finding that conversion of the auxin precursor indole-3-butryic acid (IBA) to the active auxin indole-3-acetic acid (IAA) occurs in peroxisomes motivated our study of the biogenesis, function, and dynamics this vital organelle.  Peroxisomes compartmentalize certain metabolic reactions, thereby protecting the cytosol from oxidative damage.  We employ IBA-response screens to isolate mutants defective in enzymes catalyzing IBA-to-IAA conversion and mutants defective in biogenesis of peroxisomes, which house these enzymes.  Our analysis of these mutants is revealing new matrix protein import components, unanticipated interdependencies among peroxisome biogenesis factors, and pathways for degrading peroxisome matrix proteins during developmentally controlled organelle remodeling.  We have uncovered multiple intriguing examples in which Arabidopsis peroxisomes closely resemble mammalian peroxisomes, suggesting that our studies can provide unique insights into human peroxisome biogenesis disorders.

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Kao, Y.T., Fleming, W.A., Ventura, M.J., and Bartel, B. Genetic interactions between PEROXIN12 and other peroxisome-associated ubiquitination components.  Plant Physiology, 172 2016: 1643-1656

Young, P.G. and Bartel, B. Pexophagy and peroxisomal protein turnover in plants.  Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 1863 2016: 999-1005

Reumann, S. and Bartel, B. Plant peroxisomes: Recent discoveries in organelle homeostasis, morphology dynamics, and functional complexity.  Current Opinion in Plant Biology, 33 2016: 17-26

McDonnell, M.M., Burkhart, S.E., Stoddard, J.M., Wright, Z.J., Strader, L.C., and Bartel, B. The early-acting peroxin PEX19 is redundantly encoded, farnesylated, and essential for viability in Arabidopsis thaliana.  PLoS ONE, 11 2016: e0148335

Rinaldi, M.A., Patel, A.B., Park, J., Lee, K., Strader, L.C., and Bartel, B. The roles of β-oxidation and cofactor homeostasis in peroxisome distribution and function in Arabidopsis thaliana.  Genetics, 204 2016: 1089-1115

Kao, Y.T. and Bartel, B. Elevated growth temperature decreases levels of the PEX5 peroxisome-targeting signal receptor and ameliorates defects of Arabidopsis mutants with an impaired PEX4 ubiquitin-conjugating enzyme.  BMC Plant Biology, 15 2015: 224

Bartel, B. Proteaphagy – selective autophagy of inactive proteasomes.  Molecular Cell, 58 2015: 970-971

Woodward, A.W., Fleming, W.A., Burkhart, S.E., Ratzel, S.E., Bjornson, M., and Bartel B. A viable Arabidopsis pex13 missense allele confers severe peroxisomal defects and decreases PEX5 association with peroxisomes.  Plant Molecular Biology, 86 2014: 201-214

Bartel, B., Farmer, L.M., Rinaldi, M.A., Young, P.G., Danan, C.H., and Burkhart, S.E. Mutation of the Arabidopsis LON2 peroxisomal protease enhances pexophagy.  Autophagy, 10 2014: 518-519

Burkhart, S.E., Kao, Y.T, and Bartel, B. Peroxisomal ubiquitin-protein ligases Peroxin2 and Peroxin10 have distinct but synergistic roles in matrix protein import and Peroxin5 retrotranslocation in Arabidopsis.  Plant Physiology, 166 2014: 1329-1344

Bartel, B., Burkhart, S.E., and Fleming, W. Protein transport in and out of plant peroxisomes.  Molecular Machines Involved in Peroxisomes Maintenance 2014: 325-345

Rampey, R.A., Baldridge, M.T., Farrow, D.C., Bay, S.N., and Bartel, B. Compensatory mutations in predicted metal transporters modulate auxin conjugate responsiveness in Arabidopsis.  G3: Genes, Genomes, Genetics, 3 2013: 131-141

Farmer, L.M., Rinaldi, M.A., Young, P.G., Danan, C.H., Burkhart, S.E., and Bartel, B. Disrupting autophagy restores peroxisome function to an Arabidopsis lon2 mutant and reveals a role for the LON2 peroxisomal protease in matrix protein degradation.  The Plant Cell, 25 2013: 4085-4100

Burkhart, S.E., Lingard, M.J., and Bartel, B. Genetic dissection of peroxisome-associated matrix protein degradation in Arabidopsis thaliana.  Genetics, 193 2013: 125-141

Rinaldi, M.A., Liu, J., Enders, T.A., Bartel, B., and Strader, L.C. A gain-of-function mutation in IAA16 confers reduced responses to auxin and abscisic acid and impedes plant growth and fertility.  Plant Molecular Biology, 79 2012: 359-373

De Rybel, B., Audenaert, D., Xuan, W. Overvoorde, P., Strader, L.C., Kepinksi, S., Hoye, R., Brisbois, R., Parizot, B., Vanneste, S., Liu, X., Gilday, A., Graham, I.A., Nguyen, L., Jansen, L., Njo, M.F., Inzé, D., Bartel, B., and Beeckman, T. A role for the root cap in root branching revealed by the non-auxin probe naxillin.  Nature Chemical Biology, 8 2012: 798-805

Hu, J., Baker, A., Bartel, B., Linka, N., Mullen, R.T., Reumann, S., Zolman, B.K. Plant peroxisomes: biogenesis and function.  The Plant Cell, 24 2012: 2279-2303

Monroe-Augustus, M., Ramón, N.M., Ratzel, S.E., Lingard, M.J., Christensen, S.E., Murali, C., and Bartel, B. Matrix proteins are inefficiently imported into Arabidopsis peroxisomes lacking the receptor-docking peroxin PEX14.  Plant Molecular Biology, 77 2011: 1-15

Strader, L.C., Wheeler, D.L., Christensen, S.E., Berens, J., Cohen, J.D., Rampey, R.A., and Bartel, B. Multiple facets of Arabidopsis seedling development require indole-3-butyric acid-derived auxin.  The Plant Cell, 23 2011: 984-999

Ratzel, S.E., Lingard, M.J., Woodward, A.W., and Bartel, B. Reducing PEX13 expression ameliorates physiological defects of late-acting peroxin mutants.  Traffic, 12 2011: 121-134

Strader, L.C. and Bartel, B. Transport and metabolism of the endogenous auxin precursor indole-3-butyric acid.  Molecular Plant, 4 2011: 477-486

Ruzicka, K., Strader, L.C., Bailly, A., Yang, H., Blakeslee, J., Langowski, L., Nejedlá, E., Fujita, H., Itoh, H., Syono, K., Hejátko, J., Gray, W.M., Martinoia, E., Geisler, M., Bartel, B., Murphy, A.S., and Friml, J. Arabidopsis PIS1 encodes the ABCG37 transporter of auxinic compounds including the auxin precursor indole-3-butyric acid.  Proc. Natl. Acad. Sci. USA, 107 2010: 10749-10753

Strader, L.C., Culler, A.H., Cohen, J.D., and Bartel, B. Conversion of endogenous indole-3-butyric acid to indole-3-acetic acid drives cell expansion in Arabidopsis thaliana seedlings.  Plant Physiology, 153 2010: 1577-1586

Strader, L.C., Chen, G.L., and Bartel, B. Ethylene directs auxin to control root cell expansion.  The Plant Journal, 64 2010: 874-884

Ramón, N.M. and Bartel, B. Interdependence of the peroxisome-targeting receptors in Arabidopsis thaliana: PEX7 facilitates PEX5 accumulation and import of PTS1 cargo into peroxisomes.  Molecular Biology of the Cell, 21 2010: 1263-1271

Lingard, M.J. and Bartel, B. Arabidopsis LON2 is necessary for peroxisomal function and sustained matrix protein import.  Plant Physiology, 151 2009: 1354-1365

Dong, C.-H., Zolman, B.K., Bartel, B., Lee, B., Stevenson, B., Agarwal, M., and Zhu, J.-K. Disruption of Arabidopsis CHY1 reveals an important role of metabolic status in plant cold stress signaling.  Molecular Plant, 2 2009: 59-72

Lingard, M.J., Monroe-Augustus, M., and Bartel, B. Peroxisome-associated matrix protein degradation in Arabidopsis.  Proc. Natl. Acad. Sci. USA, 106 2009: 4561-4566

Strader, L.C., Beisner, E.R., and Bartel, B. Silver ions increase auxin efflux independently of effects on ethylene response.  The Plant Cell, 21 2009: 3585-3590

Strader, L.C. and Bartel, B. The Arabidopsis PLEIOTROPIC DRUG RESISTANCE8 ATP binding cassette transporter modulates sensitivity to the auxin precursor indole-3-butyric acid.  The Plant Cell, 21 2009: 1992-2007

Strader, L.C. and Bartel, B. A new path to auxin.  Nature Chemical Biology, 4 2008: 337-339

Strader, L.C., Monroe-Augustus, M., Rogers, K.C., Lin, G.L., and Bartel, B. Arabidopsis iba response5 (ibr5) suppressors separate responses to various hormones.  Genetics, 180 2008: 2019-2031

Meyers, B.C, Axtell, M.J., Bartel, B., Bartel, D.P., Baulcombe, D., Bowman, J.L., Cao, X., Carrington, J.C., Chen, X., Green, P.J., Griffiths-Jones, S., Jacobsen, S.E., Mallory, A.C., Martienssen, R.A., Poethig, R.S., Qi, Y., Vaucheret, H., Voinnet, O., Watanabe, Y., Wiegel, D., Zhu, J.K. Criteria for annotation of plant microRNAs.  The Plant Cell, 20 2008: 3186-3190

Zolman, B.K., Martinez, N., Millius, A., Adham, A.R., and Bartel, B. Identification and characterization of Arabidopsis indole-3-butyric acid response mutants defective in novel peroxisomal enzymes.  Genetics, 180 2008: 237-251

Dugas, D.V. and Bartel, B. Sucrose induction of Arabidopsis miR398 represses two Cu/Zn superoxide dismutases.  Plant Molecular Biology, 67 2008: 403-417

Strader, L.C., Monroe-Augustus, M., Bartel, B. The IBR5 phosphatase promotes Arabidopsis auxin responses through a novel mechanism distinct from TIR1-mediated repressor degradation.  BMC Plant Biology, 8 2008: 41

Shan, H., Wilson, W.K., Phillips, D.R., Bartel, B., and Matsuda, S.P.T. Trinorlupeol: a major nonsterol triterpenoid in Arabidopsis.  Organic Letters, 10 2008: 1897-1900

Rasbery, J.M., Shan, H., LeClair, R.J., Norman, M., Matsuda, S.P.T., and Bartel, B. Arabidopsis thaliana Squalene Epoxidase 1 is Essential for Root and Seed Development.  Journal of Biological Chemistry, 282 2007: 17002-17013

Zolman, B.K., Nyberg, M., and Bartel, B. IBR3, a Novel Peroxisomal Acyl-CoA Dehydrogenase-Like Protein Required for Indole-3-Butyric Acid Response.  Plant Molecular Biology, 64 2007: 59-72

Woodward, A.W., Ratzel, S.E., Woodward, E.E., Shamoo, Y., and Bartel, B. Mutation of E1-CONJUGATING ENZYME-RELATED1 Decreases RELATED TO UBIQUITIN Conjugation and Alters Auxin Response and Development.  Plant Physiology, 144 2007: 976-987

Rampey, R.A., Woodward, A.W., Hobbs, B.N., Tierney, M.P., Lahner, B., Salt, D.E., and Bartel, B. An Arabidopsis Basic Helix-Loop-Helix Leucine Zipper Protein Modulates Metal Homeostasis and Auxin Conjugate Responsiveness.  Genetics, 174 2006: 1841-1857

Phillips, D.R., Rasbery, J.M., Bartel, B., and Matsuda, S.P.T. Biosynthetic Diversity in Plant Triterpene Cyclization.  Current Opinion in Plant Biology, 9 2006: 305-314

Jones-Rhoades, M.W., Bartel, D.P., and Bartel, B. MicroRNAs and Their Regulatory Roles in Plants.  Annual Review of Plant Biology, 57 2006: 19-53

Woodward, A.W., and Bartel, B. A Receptor for Auxin.  Plant Cell, 17 2005: 2425-2429

Lopez-Bucio, J., Hernandez-Abreu, E., Sanchez-Calderon, L., Perez-Torres, A., Rampey, R.A., Bartel, B., and Herrera-Estrella, L. An auxin transport independent pathway is involved in phosphate stress-induced root architectural alterations in Arabidopsis. Identification of BIG as a mediator of auxin in pericycle cell activation.  Plant Physiology, 137 2005: 681-691

Woodward, A.W., and Bartel, B. Auxin: Regulation, Action, and Interaction.  Annals of Botany, 95 2005: 707-735

Zolman, B.K., Monroe-Augustus, M., Silva, I.D., and Bartel, B. Identification and Functional Characterization of Arabidopsis PEROXIN4 and the Interacting Protein PEROXIN22.  Plant Cell, 17 2005: 3422-3435

Mallory, A.C., Bartel, D.P., and Bartel, B. MicroRNA-Directed Regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is Essential for Proper Development and Modulates Expression of Early Auxin Response Genes.  Plant Cell, 17 2005: 1360-1375

Bartel, B. MicroRNAs Directing siRNA Biogenesis.  Nature Structural & Molecular Biology, 12 2005: 569-571

Adham, A.R., Zolman, B.K., Millius, A., and Bartel, B. Mutations in Arabidopsis Acyl-CoA Oxidase Genes Reveal Overlapping and Distinct Roles in Beta-oxidation.  The Plant Journal, 41 2005: 859-874

Woodward, A.W. and Bartel, B. The Arabidopsis Peroxisomal Targeting Signal Type 2 Receptor PEX7 is Necessary for Peroxisome Function and Dependent on PEX5.  Molecular Biology of the Cell, 16 2005: 573-583

LeClere, S., Rampey, R.A., and Bartel, B. IAR4, a Gene Required for Auxin Conjugate Sensitivity in Arabidopsis, Encodes a Pyruvate Dehydrogenase E1a Homolog.  Plant Physiology, 135 2004: 989-999

Rampey, R.A., LeClere, S., Kowalczyk, M., Ljung, K., Sandberg, G., and Bartel, B. A Family of Auxin-Conjugate Hydrolases that Contributes to Free Indole-3-acetic Acid Levels During Arabidopsis Germination.  Plant Physiology, 135 2004: 978-988

Zolman, B.K., and Bartel. B. An Arabidopsis Indole-3-Butyric Acid-Response Mutant Defective in PEROXIN6, an Apparent ATPase Implicated in Peroxisomal Function.  Proc. Natl. Acad. Sci. USA, 101 2004: 1786-1791

Dugas, D.V. and Bartel, B. MicroRNA Regulation of Gene Expression in Plants.  Current Opinion in Plant Biology, 7 2004: 512-520

Mallory, A.C., Dugas, D.V., Bartel, D.P., and Bartel, B. MicroRNA Regulation of NAC-Domain Targets is Required for Proper Formation and Separation of Adjacent Embryonic, Vegetative, and Floral Organs.  Current Biology, 14 2004: 1035-1046

Magidin, M., Pittman, J.K., Hirschi, K.D., and Bartel, B. ILR2, a Novel Gene Involved in IAA Conjugate Sensitivity and Metal Transport in Arabidopsis thaliana.  The Plant Journal, 35 2003: 523-534

Ambros, V., Bartel, B., Bartel, D.P., Burge, C.B., Carrington, J.C., Chen, X., Dreyfuss, G., Eddy, S.R., Griffiths-Jones, S., Marshall, M., Matzke, M., Ruvkun, G., and Tuschl, T. A Uniform System for MicroRNA Annotation.  RNA, 9 2003: 277-279

Monroe-Augustus, M., Zolman, B.K., and Bartel, B. IBR5, a Dual-Specificity Phosphatase-Like Protein Modulating Auxin and Abscisic Acid Responsiveness in Arabidopsis.  Plant Cell, 15 2003: 2979-2991

Bartel, B. and Bartel, D.P. MicroRNAs: At the Root of Plant Development?.  Plant Physiology, 132 2003: 709-717

Bartel, B. and Matsuda, S.P.T. Seeing Red.  Science, 299 2003: 352-353

LeClere, S., Tellez, R., Rampey, R.A., Matsuda, S.P.T., and Bartel, B. Characterization of a Family of IAA-Amino Acid Conjugate Hydrolases from Arabidopsis.  Journal of Biological Chemistry, 277 2002: 20446-20452

Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., and Bartel, D.P. MicroRNAs in Plants.  Genes and Development, 16 2002: 1616-1626

Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B., and Bartel, D.P. Prediction of Plant MicroRNA Targets.  Cell, 110 2002: 513-520

Zolman, B.K., Monroe-Augustus, M., Thompson, B., Hawes, J.W., Krukenberg, K.A., Matsuda, S.P.T., and Bartel, B. chy1, an Arabidopsis Mutant with Impaired beta-Oxidation, is Defective in a Peroxisomal beta-Hydroxyisobutyryl-CoA Hydrolase.  Journal of Biological Chemistry, 276 2001: 31037-31046

Rogg, L.E., Lasswell, J., and Bartel, B. A Gain-of-function Mutation in IAA28 Suppresses Lateral Root Development.  Plant Cell, 13 2001: 465-480

LeClere, S., and Bartel, B. A Library of Arabidopsis 35S-cDNA Lines for Identifying Novel Mutants.  Plant Molecular Biology, 46 2001: 695-703

Rogg, L.E. and Bartel, B. Auxin Signaling: Derepression Through Regulated Proteolysis.  Developmental Cell, 1 2001: 595-604

Bartel, B., LeClere, S., Magidin, M., and Zolman, B.K. Inputs to the Active Indole-3-Acetic Acid Pool: De novo Synthesis, Conjugate Hydrolysis, and Indole-3-Butyric acid beta-oxidation.  Journal of Plant Growth Regulation, 20 2001: 198-216

Zolman, B.K., Silva, I.D., and Bartel, B. The Arabidopsis pxa1 Mutant is Defective in an ATP-Binding Cassette Transporter-Like Protein Required for Peroxisomal Fatty Acid beta-oxidation.  Plant Physiology, 127 2001: 1266-1278

Nelson, D.C., Lasswell, J., Rogg, L.E., Cohen, M.A., and Bartel, B. FKF1, a Clock-controlled Gene that Regulates the Transition to Flowering in Arabidopsis.  Cell, 101 2000: 331-340

Lasswell, J., Rogg, L.E., Nelson, D.C., Rongey, C., and Bartel, B. Cloning and Characterization of IAR1, a Gene Involved in IAA Conjugate Sensitivity.  Plant Cell, 12 2000: 2395-2408

Zolman, B.K, Yoder, A., and Bartel, B. Genetic Analysis of Indole-3-butyric Acid Responses in Arabidopsis thaliana Reveals Four Mutant Classes.  Genetics, 156 2000: 1323-1337

HHMI Professor
Bartel Lab

  • B.A. Biology (1983) Bethel College
  • Ph.D. Biology (1990) Massachusetts Institute of Technology
  • Institute of Biosciences and Bioengineering
Research Areas
  • Genetics of peroxisome biogenesis, dynamics, and function and auxin regulation and responses in Arabidopsis development.
Professional Experience
  • Faculty member
    Rice University
  • American Cancer Society Postdoctoral Fellow
    Whitehead Institute for Biomedical Research
Contact Information
Email: bartel@rice.edu
Phone: 713-348-5602
Office: George R. Brown Hall, W300D