Zhihua Hua
Ph.D. in Plant Physiology, Penn State University 2008
Contact
My research interests fall into two primary fields, evolutionary and computational biology, and experimental biology, for studying the functions of F-box genes in plants. The first F-box gene was identified in yeast to encode the substrate receptor, named the F-box protein, in an SKP1-Cul1-F-box (SCF) complex. In eukaryotes, numerous SCF complexes form a large group of E3 ubiquitin ligases catalyzing protein ubiquitylation at the last step of a three-enzyme cascade reaction, which starts with ubiquitin activation by a ubiquitin-activating enzyme (E1) and ubiquitin conjugation by a ubiquitin-conjugating enzyme (E2). Most of the time, the ubiquitylated proteins are recognized by the 26S proteasome for degradation. This highly selective protein degradation pathway allows a eukaryotic cell to precisely maintain the homeostasis of its entire proteome.
In Arabidopsis thaliana nearly 900 F-box genes have been predicted, providing an excellent system for understanding genome function and the roles of the ubiquitylation in plants. Surprisingly, only ~5% of them have been functionally characterized to date although Arabidopsis has been developed as one of the best model organisms for functional genomic studies since its first genome draft was released in 2000. However, this small number of studies has demonstrated that the F-box genes play a wide range of functions in plants, including cell cycle control, circadian rhythms, floral development, plant pathogen defense, self-incompatibility, and phytohormone signaling. Exploring the functions of other F-box gene members and the dynamic roles of the ubiquitylation network are challenging due to both breadth and depth. Through the integration of evolutionary biology, bioinformatics, computational biology, genetics, and biochemistry, I am developing a systems approach to tackle this challenge.
Selected Publications
(2013) Epigenomic programming contributes to the genonomic drift evolution of the F-Box protein superfamily in Arabidopsis. Proc Natl Acad Sci USA 110, 16927–16932.
(2012) The light-response BTB 1 and 2 proteins assemble nuclear ubiquitin ligases that modify phytochrome B and D signaling in Arabidopsis. Plant Physiol 160,118-134.
(2011) The cullin-RING ubiquitin-protein ligases (Review Article). Ann Rev Plant Biol 62, 299-234.
(2011) Phylogenetic comparison of F-box (FBX) superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift. PLoS One 6(1), e16219.
(2011) The amino terminal F-box domain of Petunia inflata S-locus F-box protein is involved in S-RNase-based self-incompatibility mechanism. AoB PLANTS 2011 plr016 doi:10.1093/aobpla/plr016.
(2010) Proteomic analyses identify a diverse array of nuclear processes affected by small ubiquitin-like modifier conjugation in Arabidopsis. Proc Natl Acad Sci USA 107, 16512-16517. (FFa = 6 in Faculty of 1000,Link)
(2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463, 763-768. (FFa = 6 in Faculty of 1000, Link )
(2010) Collaborative non-self recognition system in S-RNase-based self-incompatibility. Science 330, 796-799. (Science Feature Article) (FFa = 10 in Faculty of 1000, Link )
(2010) Functional characterization of two chimeric proteins between a Petunia inflata S-locus F-box protein, PiSLF2, and a PiSLF-like protein, PiSLFLb-S2. Plant Mol Biol 74, 279-292.
(2009) Ectopic expression of S-RNase of Petunia inflata in pollen results in its sequestration and non-cytotoxic function in pollen tubes. Sex Plant Reprod 22, 263-275 (*Contributed equally to this study).
(2008) Biochemical models for S-RNase-based self-incompatibility (Review Article). Mol Plant 1, 575-585.
(2008) Identification of major lysine residues of S3-RNase of Petunia inflata involved in ubiquitin-26S proteasome mediated degradation in vitro. Plant J 54, 1094-1104.
(2007) Comparison of Petunia inflata S-locus F-box protein (Pi SLF) with Pi SLF-like proteins reveals its unique function in S-RNase-based self-incompatibility. Plant Cell 19, 3593-3609.
(2006) Identification and characterization of components of a putative Petunia S-locus F-box–containing E3 ligase complex involved in S-RNase-based self-incompatibility. Plant Cell 18, 2531-2553. (FFa = 6 in Faculty of 1000, Link )