Publications from the Callis Lab

Linden, KJ and Callis J. 2020. The ubiquitin system affect agronomic plant traits. J. Biol. Chem. 295: 13940-13955.   doi:10.1074/jbc.REV120.011303

Vain T, Raggi S, Ferro N, Barange DK, Keiffer M, Ma Q, Doyle SM, Thelander M, Pařízková B, Novák O, Ismail A, Enquist P-A, Rigal A, Łangowska M, Harborough SR, Zhang Y, Ljung K, Callis J, Amqvist F, Kepinski S, Estelle M, Pauwels L and Robert S.   2019. Selective auxin agonists induce specific AUX/IAA protein degradation to modulate plant development. Proc. Natl. Acad, Sci. USA 116: 6463-6472.

Riggs JW, Callis J. 2017. Arabidopsis fructokinase-like protein associations are regulated by ATP. Biochemical Journal 474:1789-1801

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

Guerra DD and Callis J.  2012 Ubiquitin on the move: the ubiquitin modification pathway plays diverse roles in the regulation of ER- and membrane-localized proteins. Plant Physiology 160: 56-64.

Riggs JW, Cavales PC, Chapiro SM, Callis J. 2017. Identification and biochemical characterization of the fructokinase gene. family in Arabidopsis thaliana.  BMC Plant Biology 17:83 DOI: 10.1186/s12870-017-1031-5

Gilkerson J, Tam R, Zhang A, Dreher K and Callis J. 2016. Cycloheximide Assays to Measure Protein Degradation in vivo in Plants. Bio-protocol, 6: e1919.

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. 291: 22572-22582. doi:10.1074/jbc.M116.754689

Pauwels L, Ritter A, Goossens J, Durand AN, Liu H, Gu Y, Geerinck J, Boter M, Vanden Bossche R, De Clercq R, Van Leene J, Gevaert K, De Jaeger G, Solano R, Stone S, Innes RW, Callis J, Goossens A. 2015. The RING E3 Ligase KEEP ON GOING Modulates JASMONATE ZIM-DOMAIN12 Stability. Plant Physiol. 169:1405-1417

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.

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. Mol Plant. 5:1163-6.

Gilkerson J, Callis J 2014. A genetic screen for mutants defective in IAA1-LUC degradation in Arabidopsis thaliana reveals an important requirement for TOPOISOMERASE6B in auxin physiology. Plant Signal. Behav. 9: e972207

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 Journal. 75: 965–976.

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 25: 3039-3051.

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.

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 Biol. 12:102.

Pratelli R, Guerra DD, Yu S, Wogulis M, Kraft E, Frommer WB, Callis J, and Pilot G (2012) The ubiquitin E3 ligase LOSS OF GDU2 is required for GLUTAMINE DUMPER1-induced amino acid secretion in Arabidopsis. Plant Physiology 158: 1628-1642. (1): Authors contributed equally to this work.

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

SK Hotton, RA Eigenheer, MF Castro, M Bostick, and J Callis (2011) AXR1-ECR1 and AXL1-ECR1 heterodimeric RUB-activating enzymes diverge in function in Arabidopsis thaliana. Plant Molecular Biology, Mar 2011; 75: 515-26.

Hsia M-M 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. Journal of Biological Chemistry, Nov 2010; 285: 37070-37081.

Gilkerson J, Hu J, Brown J, Jones A, Sun T, 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, Mar 2009; 181: 945 – 963.

Salmon J, Ramos J, and Callis J. Degradation of the auxin response factor ARF1. The Plant Journal 2008. 54(1): 118-28.

Kraft E, Bostick M, Jacobsen SE, and Callis J. ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases. The Plant Journal 2008 56: 704-15.

Stone, S.L., Williams, L.A., Farmer, L.M., Vierstra, R.D., and Callis J. KEEP ON GOING, a RING E3 Ligase Essential for Arabidopsis Growth and Development, Is Involved in Abscisic Acid Signaling.
The Plant Cell 2006 18: 3415-3428. [Full Text] [Supplemental Data]

Dreher, K.A., Brown, J., Saw, R.E., and Callis J. The Arabidopsis Aux/IAA Protein Family Has Diversified in Degradation and Auxin Responsiveness. The Plant Cell 2006 18: 699-714. [Full Text] [Supplemental Data]

Callis J, and Ling R. Preparation, Characterization, and Use of Tagged Ubiquitins. Methods in Enzymology 2005 399:51-64. [Full Text]

Kraft, E, Stone, SL, Ma, L, Su,N, Gao,Y, Lau, O-S, Deng,X-W, and Callis, J. Genome Analysis and Functional Characterization of the E2 and RING-Type E3 Ligase Ubiquitination Enzymes of Arabidopsis Plant Physiolgy 2005 139: 1597-1611. [Full Text] [Supplemental Data]

Callis, J . Plant biology: Auxin action Nature 2005 May 26; 435:436-437. [Full Text]

Figueroa, P., Gusmaroli, G., Serino, G., Habashi, J., Ma, L., Shen, Y., Feng, S., Bostick, M., Callis J., Hellmann, H., and Deng, X.W. 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 2005 Apr;17(4):1180-95. [Full Text]

Stone SL, Hauksdottir H, Troy A, Herschleb J, Kraft E, Callis J. Functional Analysis of the RING-Type Ubiquitin Ligase Family of Arabidopsis. Plant Physiology 2005 137(1):13-30 [Full Text] [Supplemental Data]

Bostick M, Lochhead SR, Honda A, Palmer S, Callis J. Related to Ubiquitin 1 and 2 Are Redundant and Essential and Regulate Vegetative Growth, Auxin Signaling, and Ethylene Production in Arabidopsis. Plant Cell 2004 16:2418-2432 [Full Text]

*Laplaza, J.M., *Bostick, M., Scholes, D.T., Curcio, M.J., and Callis, J. Saccharomyces cerevisiae ubiquitin-like protein Rub1p conjugates to cullin family members Rtt101p and Cul3p in vivo.
Biochemical Journal 2004 377:459-467. [Full Text] *First two authors contributed equally to publication

Zenser, N., Dreher, K., Edwards, S.E., and Callis, J. Acceleration of Aux/IAA proteolysis is specific for auxin and independent of AXR1. The Plant Journal 2003 35(3): 284-295. [Full Text]

Linghu, B., Callis, J., and Goebl, M.G. Rub1p processing by Yuh1p is required for wild-type levels of Rub1p conjugation to Cdc53p. Eukaryotic Cell 2002 1(3): 491-494. [Full Text]

Yoshida, S., Ito, M., Callis, J., Nishida, I., and Watanabe, A. A delayed leaf senescence mutant is defective in arginyl-tRNA:protein arginyltransferase, a component of the N-end rule pathway in Arabidopsis. Plant Journal 2002 32(1): 129-137. [Full Text]

*Ramos, J. A., *Zenser, N., Leyser, O., and Callis, J. Rapid Degradation of Auxin/Indoleacetic Acid Proteins Requires Conserved Amino Acids of Domain II and Is Proteasome Dependent
Plant Cell 2001 13: 2349-2360. [Full Text] *First two authors contributed equally to publication

Zenser, N., Ellsmore, A., Leasure, C., and Callis, J. Auxin modulates the degradation rate of Aux/IAA proteins PNAS 2001 98: 11795-11800. [Full Text]

Schwechheimer, C., Serino, G., Callis, J., Crosby, W.L., Estelle, M., Lyapina, S., Deshaies, R.J., and Deng, X.-W. The COP9 signalosome interacts with the E3 ubiquitin ligase SCF-TIR1 and mediates auxin-response in Arabidopsis. Science 2001 292: 1379-1382. [Full Text]

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

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

Rao-Naik, C; Chandler, JS; McArdle, B; Callis, J. Ubiquitin-specific proteases from Arabidopsis thaliana: cloning of AtUBP5 and analysis of substrate specificity of AtUBP3, AtUBP4, and AtUBP5 using Escherichia coli in vivo and in vitro assays. Archives of Biochemistry and Biophysics 2000 379: 198-208. [Full Text]

Ling, R; Colón, E; Dahmus, ME; Callis, J. 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 2000 282: 54-64. [Full Text]

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

Vierstra, RD; Callis, J. Polypeptide tags, ubiquitous modifiers for plant protein regulation. Plant Molecular Biology 1999 41: 435-42. [Full Text]

Rao-Naik, C; Delacruz, W; Laplaza, JM; Tan, S; Callis, J; Fisher, AJ. The Rub family of ubiquitin-like proteins: Crystal structure of arabidopsis Rub1 and expression of multiple Rubs in Arabidopsis. Journal of Biological Chemistry 1998 273: 34976-34982. [Full Text]

del Pozo, JC; Timpte, C; Tan, S; Callis, J; Estelle, M. The ubiquitin-related protein RUB1 and auxin response in Arabidopsis. Science 1998 280: 1760-1763. [Full Text]

Worley, CK; Ling, R; Callis, J. Engineering in vivo instability of firefly luciferase and Escherichia coli beta-glucuronidase in higher plants using recognition elements from the ubiquitin pathway. Plant Molecular Biology 1998 37: 337-347. [Full Text]

Lammer, D; Mathias, N; Laplaza, JM; Jiang, W; Liu, Y; Callis, J; Goebl, M; Estelle, M.
Modification of yeast Cdc53p by the ubiquitin-related protein Rub1p affects function of the SCFCdc4 complex. Genes & Development 1998 12: 914-926. [Full Text]