Judy Callis

image of Judy Callis

Professor

Departments

Molecular & Cellular Biology

Offices and Labs

103A Briggs Hall
752-1015
752-1014

Degrees

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

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.

Awards

Elected Fellow, American Association for the Advancement of Science 2002
National Science Foundation Presidential Young Investigator Faculty Award, 1991-1996.
NSF Postdoctoral Fellowship in Plant Biology, 1987-1989.
NIH Predoctoral Trainee, 1981-1983.
Paul K. and Ruth R. Stumpf Endowed Chair in Plant Biochemistry
Davis Division of Academic Senate Distinguished Undergraduate Teaching Award 2008-2009
ASUCD Excellence in Education Award, 2004

Department and Center Affiliations

Department of Molecular and Cellular Biology
Secondary Member, Department of Plant Biology

ProfessionalSocieties

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

CBS Grad Group Affiliations

Biochemistry, Molecular, Cellular and Developmental Biology
Integrated Genetics and Genomics
Plant Biology

Specialties / Focus

Plant Biology
  • Cell and Developmental Biology
  • Molecular Biology, Biochemistry, and Genomics
Integrated Genetics and Genomics
  • Model Plants
Biochemistry, Molecular, Cellular and Developmental Biology
  • Genomics, Proteomics and Metabolomics

Labs

Briggs Hall Room 103 website
  • see our web page for current and past members!

Teaching Interests

Biochemistry- I teach BIS103, called Bioenergetics and metabolism. I co-teach Plant Biochemistry. I also teach an undergraduate seminar in Biochemistry/Molecular Biology.
website

Courses

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

Publications

11/18/2013 1:26:26 PM
  • 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.  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.