Welcome to the Callis lab at UC DAVIS

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Our over-arching goal is to better understand the role of the ubiquitin modification system in plant biology using the model plant Arabidopsis thaliana. We seek to uncover the molecular mechanisms by which specific proteins are targetted for vacuolar or proteasomal degradation, and how the various stages of this pathway are regulated. This includes identifying the cis-acting signals that mediate the recognition of protein substrates by E3 ubiquitin ligases and discovering trans-acting factors that facilitate or impede substrate ubiquitination. Our lab focuses on three major projects.
1. The PFKb project 2. The RING project 3. The Auxin Signaling Project
Sophia's beautiful diagram of the RING structure
Graph showing auxin-mediated acceleration of IAA1:LUC degradation
7-day old phenotype of fln mutants. Seeds segregating for fln alleles grown under a 16 h photoperiod at 18o C. Homozygous individuals are circled.
(Gilkerson et al., 2012)
General structure for a RING-HC domain showing spacing between metal-binding residues
(Stone et al, 2005)
Auxin accelerates the degradation of IAA1:LUC
in Arabidopsis seedlings
(Zenser et al, 2001)
We are studying the function of the family of phosphofructokinase-B (pfkB) type proteins in plants. The Callis lab has begun characterization of two of these members, fructokinase like protein 1 and 2 (FLN1, -2), in Arabidopsis and found both to be important during chloroplast development. These proteins were found by other groups to associate with the plastid encoded RNA polymerase (PEP) complex, which transcribes a subset of genes in the plastid mainly having to do with photosynthetic and translational machinery. One group has published data showing an association with FLN proteins and thioredoxin-Z (TRXZ), which is also a member of the PEP complex. Plants lacking either FLN or TRXZ have similar chlorotic phenotypes due to poor development of chloroplasts in these plants. Poor development of the chloroplasts is likely due, in part, to a lack of certain PEP encoded transcripts but the molecular mechanism of FLN protein involvement in the observed phenotype remains unknown. We are using tools from both molecular biology and biochemistry to study the molecular mechanisms that lead to the chlorotic phenotype seen in the absence of FLN proteins. A more general aim of this research project is to begin characterization of the other ~20 uncharacterized members of the pfkB family in A. thaliana. All of these proteins are part of the pfkB family and, as such, have been annotated as carbohydrate kinases. However, their carbohydrate specificity and the possible pathways they may operate in are still unknown. We are using a number of techniques to provide insights into the function of these proteins such as: fluorescent tagging and microscopy to determine their localization, comparative genomics and other bioinformatics tools to generate testable hypotheses about their possible functions, and finally both molecular and biochemical methods to test those hypotheses.
We are examining the activity of another family of proteins containing RING and variant RING domains. These domains have been implicated in the E3 ubiquitin ligase activity of many proteins. We seek to identify putative proteins containing these domains, verify their ligase activity using in vitro ubiquitination assays, identify interacting partners, and characterize their function in vivo by studying the phenotypes of plants with mutations in RING-domain-containing proteins.
Auxin signal transduction requires the ubiquitin/proteasome pathway. We are interested in studying the degradation of the AUX/IAA family of transcriptional repressors as well as other components of auxin signaling pathways. We hope to characterize the regions required for recognition of the proteolytic targets, and to learn more about the ways in which auxin affects the rate of proteolysis of specific substrates.
 
 
 
 
 
 
     
Graduate students from the BMCDB (Biochemistry, Molecular, Cellular, and Developmental Biology), PB (Plant Biology), and GGG (Genetics) programs, as well as undergraduate students from many disciplines, work in the Callis lab.

Judy Callis
University of California, Davis
Department of Molecular and Cellular Biology
One Shields Avenue
Davis, CA 95616
office: 103A Briggs Hall (530-752-1015)
lab: 103 Briggs Hall (530-752-1014)
departmental fax (530-752-3085)

jcallis@ucdavis.edu

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