Judy Callis

Judy Callis

Position Title
Professor

Unit
Department of Molecular and Cellular Biology

103A Briggs Hall
Bio

Research Interests

My laboratory studies two processes. The first is the ubiquitin pathway, which is a protein modification pathway, whereby the protein ubiquitin is covalently attached to other proteins. This alters the longevity, activity or localization of the ubiquitinated protein. We are interested in understanding the specificity and regulation of the ubiquitin pathway. We try to understand how proteins are recruited to the ubiquitinating enzymes. There are are large number of ubiquitinating enzymes whose functions are not known. We are taking a reverse genetics approach to understand the function of RING E3 ligases which interact with substrate proteins and catalyze ubiquitin transfer. We use a variety of techniques- biochemistry, molecular biology and genetics.

We also study a family of proteins called pfkB proteins, proteins related to E. coli phosphofructokinase, but which have diverse and uncharacterized roles. We are focusing on a subset of pfkB proteins localized to the plant plastid. Some of these are important for chloroplast transcription and we are determining their functions.

Grad Group Affiliations

  • Biochemistry, Molecular, Cellular and Developmental Biology
  • Integrative Genetics and Genomics
  • Plant Biology

Specialties / Focus

  • Cell and Developmental Biology
  • Genomics, Proteomics and Metabolomics
  • Model Plants
  • Molecular Biology, Biochemistry and Genomics

Courses

  • BIS 103 Energetics and Metabolism, Winter,Spring
  • MCB 138 Undergraduate Seminar, Winter
  • MCB 126 Plant Biochemistry, Winter,Spring

Labs

Honors and Awards

  • NIH Predoctoral Trainee, 1981-1983.
  • NSF Postdoctoral Fellowship in Plant Biology, 1987-1989.
  • National Science Foundation Presidential Young Investigator Faculty Award, 1991-1996.
  • Paul K. and Ruth R. Stumpf Endowed Chair in Plant Biochemistry  2005-2011
  • Davis Division of Academic Senate Distinguished Undergraduate Teaching Award 2008-2009
  • Fellow, American Association for the Advancement of Science (AAAS) 2002
  • Fellow, American Society for Plant Biologists (ASPB), 2012
  • UC-Davis NSF-ADVANCE scholar award for mentorship, 2015-2016
  • UC Davis Prize for Undergraduate Teaching and Scholarly Achievement, 2018

Professional Societies

  • American Society for Biochemistry and Molecular Biology
  • American Society of Plant Biologists
  • Genetics Society of America
  • International Society for Plant Molecular Biologists
  • International Proteolysis Society
  • Association for the Advancement of Science (AAAS)
  • Phytochemical Society of North America

Degrees

  • 1977 BA Biology Washington University
  • 1981 MA Botany University of Illinois, Champaign-Urbana
  • 1987 PhD Biology Stanford University

Publications

Riggs JW, and Callis J. 2017 Arabidopsis fructokinase-like protein associations are regulated by ATP. Biochemical J, 474 (11) 1789-1801; DOI: 10.1042/BCJ20161077

J.W. Riggs, P.C. Cavales, S.M. Chapiro, J. Callis 2017 Identification and biochemical characterization of the fructokinase gene family in Arabidopsis thaliana. BMC Plant Biol., 17 (2017), p. 83. https://doi.org/10.1186/s12870-017-1031-5

Guerra D, Pratelli R, Jia W, Leary J, Chapiro, S, Pilot, G, Callis J  2017 Control of Amino Acid Homeostasis by a Ubiquitin Ligase-Coactivator Protein Complex. J. Biol. Chem. 292: 3827-3840. doi:10.1074/jbc.M116.766469

Riggs JW, Rockwell NC, Cavales PC, Callis J. 2016 Identification of the Plant Ribokinase and Discovery of a Role for Arabidopsis Ribokinase in Nucleoside Metabolism. J Biol Chem. 2016;291(43):22572–82. doi:10.1074/jbc.M116.754689

Pauwels, L., et al. 2015. The RING E3 ligase KEEP ON GOING modulates JASMONATE ZIM-DOMAIN12 stability. Plant Physiol. 169: 1405–1417. DOI: https://doi.org/10.1104/pp.15.00479

Gilkerson J, Kelley DR, Tam R, Estelle M, Callis J. 2015 Lysine residues are not required for proteasome-mediated proteolysis of the auxin/IAA protein IAA1. Plant Physiol., 168: 708-720.

Callis, J, Browning, K, Spremulli L 2015, Chapter 10: Protein Synthesis, Assembly, and Degradation  B. Buchanan, W. Gruissem, and R. Jones, eds. John Wiley & Sons, Inc. Somerset NJ, Biochemistry and Molecular Biology of Plants, 2nd edition.

Callis J.  2014 The Ubiquitination Machinery of the Ubiquitin System, The Arabidopsis Book, invited book chapter, 12: e0174.

Chen Y-T, Liu H, Stone S, Callis J. 2013 ABA and the ubiquitin E3 ligase KEEP ON GOING affect proteolysis of the Arabidopsis thaliana transcription factors ABF1 and ABF3. Plant J. 75: 965–976.

Guerra D, Pratelli R, Kraft E, Callis J, Pilot G. 2013 Functional conservation between mammalian MGRN1 and plant LOG2 ubiquitin ligases. FEBS Letters, 587: 3400-3405.

Shin L-J, Lo J, Chen G-H, Callis J, Fu H-Y, Yeh, K-C. 2013 IRT1 DEGRADATION FACTOR 1, a RING E3 ubiquitin ligase, regulates the degradation of IRON REGULATED TRANSPORTER 1 in Arabidopsis. Plant Cell 2013 25: 3039-3051.

Réjane Pratelli, Damian D. Guerra, Shi Yu, Mark Wogulis, Edward Kraft, Wolf B. Frommer, Judy Callis and Guillaume Pilot 2012 The Ubiquitin E3 Ligase LOSS OF GDU2 Is Required for GLUTAMINE DUMPER1-Induced Amino Acid Secretion in Arabidopsi. Plant Physiology 158:1628-1642.

Guerra D, Callis J. 2012 Ubiquitin on the Move: the ubiquitn modification pathway plays diverse roles in the regulation of ER-and membrane-localized proteins Plant Physiol. 160: 56-64.

Hotton SK, Castro MF, Eigenheer RA, Callis J. 2012 Recovery of DDB1a (DAMAGED DNA BINDING PROTEIN1a) in a Screen to Identify Novel RUB-Modified Proteins in Arabidopsis thaliana. Molecular Plant 5: 1163-1166.

Gilkerson J, Perez-Ruiz JM, Chory J, Callis J. 2012 The plastid-localized pfkB-type carbohydrate kinases FRUCTOKINASE-LIKE 1 and 2 are essential for growth and development of Arabidopsis thaliana. BMC Plant Biology 12.

Hotton, SK., Eigenheer, RA., Castro, MF., Bostick M., and Callis, J. 2011 AXR1-ECR1 and AXL1-ECR1 heterodimeric RUB-activating enzymes diverge in function in Arabidopsis thaliana Plant Mol. Biology, 75: 515-526

Hsia, MM. and Callis, J. 2010 BRIZ1 and BRIZ2 proteins form a heteromeric E3 ligase complex required for seed germination and post-germination growth in Arabidopsis thaliana. J. Biol. Chem., 285:37070-37081

Berrocal-Lobo, M, Stone, S, Yang, X, Antico, J, Callis, J, Ramonell, KM, Somerville, S. 2010 ATL9, a RING Zinc Finger Protein with E3 Ubiquitin Ligase Activity Implicated in Chitin- and NADPH Oxidase-Mediated Defense Responses. Plos One vol 5, issue 12. 10.1371/journal.pone.0014426

Gilkerson, J. Hu, J. Brown, J. Jones, J. Sun, T-P. and Callis J. 2009 Isolation and Characterization of cul1-7, a Recessive Allele of CULLIN1 that Disrupts SCF Function at the C-terminus of CUL1 in Arabidopsis thaliana Genetics, 181:945-963

Jowett, J., Ramos, J. and Callis, J. 2008 Degradation of auxin response factor ARF1 Plant J. 54: 118-128

Hotton, S. and Callis, J 2008 Regulation of Cullin-based E3 ligases Ann. Rev. Plant Biol. 59: 469-489

Kraft, E., Bostick, M., Jacobsen, S., and Callis, J. 2008 ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases. Plant J. 56: 704-715

Dreher, K.A. and Callis, J. 2007 Ubiquitin, Hormones and Biotic Stress in Plants. Annals of Bot. 9: 787 - 822.

Stone SL, Callis J. 2007 Ubiquitin ligases mediate growth and development by promoting protein death. Curr Opin Plant Biol.  Sep 10; PMID: 17851112

Doelling JH, Phillips AR, Soyler-Ogretim G, Wise J, Chandler J, Callis J, Otegui MS, Vierstra RD 2007  The Ubiquitin-Specific Protease Subfamily UBP3/UBP4 Is Essential for Pollen Development and Transmission in Arabidopsis. Plant Physiol. PMID: 17905865

Scherer GF, Zahn M, Callis J, Jones AM. A role for phospholipase A in auxin-regulated gene expression. FEBS Lett. 2007 581:4205-11

Johnson, L.M., Bostick, M. Zhang, X, Kraft, E., Henderson, I., Callis, J. and Jacobsen, S.E. 2007 The SRA Methyl-Cytosine-Binding Domain Links DNA and Histone Methylation. Current Biology 17, 1-6

Stone, S.L., Williams, L.A., Farmer, L.M., Vierstra, R.D. and Callis, J. 2006 KEEP ON GOING, a RING E3 ligase essential for Arabidopsis growth and development, is involved in abscisic acid signaling. Plant Cell 18, 3415-3428

Dreher, K., Brown, J. Saw, R. and Callis, J. 2006 The Arabidopsis Aux/IAA Protein Family Has Diversified in Degradation and Auxin Responsiveness. The Plant Cell, 18, 699-714.

Callis, J. 2005 Plant biology: Auxin action (Invited commentary) Nature 435, 436-437

Kraft, E., Stone, S., Ma, L., Su, N., Gao, Y., Lau, O., Deng, X-W, and Callis, J. 2005 Genome Analysis and Functional Characterization of the E2 and RING domain E3 Ligase Ubiquitination Enzymes of Arabidopsis thaliana Plant Physiol., 139, 1597-1611.

Callis, J and Ling, R 2005 Preparation, Characterization, and Use of Tagged Ubiquitins. Methods in Enzymol. 399, 51-64

Figueroa, P., Gusmaroli, G., Serino, G., Habashi, J., Ma, L., Shen, Y., Feng, S., Bostick, M., Callis, J., Hellmann, H., and Deng, X-W. 2005 Arabidopsis Has Two Redundant Cullin3 Proteins That Are Essential for Embryo Development and that Interact with RBX1 and BTB Proteins to Form Multisubunit E3 Ubiquitin Ligase Complexes in Vivo. Plant Cell 17, 1180-1195

Stone, S., Hauksdottir, H., Troy, A., Herschleb, J., Kraft, E., and Callis, J. 2005 Functional analysis of the RING type ubiquitin ligase family of Arabidopsis thaliana L. Plant Physiol., 137: 13-30.

Laplaza JM+, Bostick M+, Scholes DT, Curcio, MJ and Callis, J. 2004 Saccharomyces cerevisiae ubiquitin-like protein Rub1p conjugates to cullin family members Rtt101p and Cul3p in vivo. Biochemical Journal 377:459-467. +these authors contributed equally to the work.

Magnolia Bostick, Stephanie R. Lochhead, Adria Honda, Scott Palmer, and Judy Callis 2004 RUB1 and RUB2 (Related to Ubiquitin) are redundant, essential, and regulate vegetative growth, auxin signaling, and ethylene production in Arabidopsis, Plant Cell 16, 2418-2432

Zenser, N., Dreher, K.A. Edwards, S.R., and Callis, J. 2003. Acceleration of Aux/IAA proteolysis is specific for auxin and independent of AXR1 Plant J. 35: 285-294.

Yoshida, S., Ito, M., Callis, J., Nishida, I. and Watanabe, A. 2002. A delayed leaf senescence mutant is defective in arginyl-tRNA : protein arginyltransferase, a component of the N-end rule pathway in Arabidopsis. Plant J. 32:129-137.

Linghu, B., Callis, J., and Goebl, M. 2002 Rub1p processing by Yuh1p is required for wild-type levels of Rub1p conjugation to Cdc53p. Eukaryotic Cell, 1: 491-494.

Ramos, JA, Zenser, N, Leyser, O, and Callis, J 2001 Rapid Degradation of Auxin/Indoleacetic Acid Proteins Requires Conserved Amino Acids of Domain II and Is Proteasome Dependent Plant Cell 13: 2349-2360.

Schwechheimer C, Serino G, Callis J, Crosby WL, Lyapina S, Deshaies R, Gray WL, Estelle M and X-W Deng. 2001. Interactions of the COP9 Signalosome with the E3 Ubiquitin Ligase SCFTIR in Mediating Auxin Response. Science 292:1379-1382.

Zenser N, Ellsmore A, Leasure C, and J Callis. 2001. Auxin modulates the degradation rate of Aux/IAA proteins. Proceedings of the National Academy of Sciences USA. 98:11795-11800

McClinton, R. S.; Chandler, J. S.; Callis, J. 2001 cDNA isolation, characterization, and protein intracellular localization of a katanin-like p60 subunit from Arabidopsis thaliana. Protoplasma . 216 (3-4): 181-190.

Callis, J; Vierstra, RD. 2000 Protein degradation in signaling. Current Opinion in Plant Biology 3: 381-6.

Worley, CK; Zenser, N; Ramos, J; Rouse, D; Leyser, O; Theologis, A; Callis, J. 2000 Degradation of Aux/IAA proteins is essential for normal auxin signalling. Plant Journal 21: 553-62.

Ling, R; Colon, E; Dahmus, ME; Callis, J. 2000 Histidine-tagged ubiquitin substitutes for wild-type ubiquitin in Saccharomyces cerevisiae and facilitates isolation and identification of in vivo substrates of the ubiquitin pathway. Analytical Biochemistry 282: 54-64.

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