Recent News
Education
Ph.D. in Plant Physiology, Pennsylvania State University, 2008
Research
- Ubiquitylation
- Cross talk of gene expression regulatory pathways
- Superfamily evolution and computational biology
Ubiquitylation is a eukaryotic post-translational modification process that adds a 76-amino acid peptide, called ubiquitin (Ub), on to a myriad of proteins to determine their functions. Most of the time, ubiquitylated proteins are recognized and degraded by the 26S proteasome, a 2.5 MDa proteolytic complex, in all eukaryotes. Given the wide range and important regulatory roles of ubiquitylation, the finding of Ub won the Nobel Prize for chemistry in 2004.
Compared to other eukaryotic organisms, ubiquitylation is particularly important for plants in protein functional regulation, which is in part impliedfrom the dramatic expansionof theubiquitin-26S proteasome system (UPS) in plants. For example, in Arabidopsis thalian a, one of the most important model organisms for biological sciences, ~12% of its proteome (encoded by >3,000 genes) has been predicted to be either directly involved in the ubiquitylation process or regulated by ubiquitylation.
Our lab is interested in the roles of ubiquitylaiton in plant developmental and physiological processes. Taking advantage of high throughput sequencing technologies, we are tackling these roles in A. thaliana and rice, through the integration of evolutionary and computational biology, plant omics, genetics, biochemistry, and molecular biology . Our ultimate goal is to develop systems approaches for improving crop production through predictable manipulation of the UPS.
Hua Lab, Plant Ubiquitylation Laboratory
Publications
Publications from the Work at Ohio University
(*: Corresponding author; (g): graduate student; (u): undergraduate student; (v): visiting scholar; bold:Hua Lab members)
Yu, P.(g), Gao, Z.(v), and Hua, Z.* (2024). Overexpression of ubiquitin influences plant growth and development by changing proteasome and autophagy activities . Plants 13, 1485.
Tang, Q., Xu, D., Lenzen, B., Brachmann, A., Yapa, M.M. (g), Doroodian, D. (g), Schmitz-Linneweber, C., Masuda, T., Hua, Z., Leister, D., Kleine, T. (2024). Arabidopsis GENOMES UNCOUPLED PROTEIN1 binds to plastid RNAs and promotes their maturation . Plant Comm (pending revision)
Hua, Z.*(2023). Deciphering the protein ubiquitylation system in plants . J Exp Bot74, 6487-6504
Hua, Z.*(2023). The ubiquitin-26S proteasome system – a versatile player worthy of close attention in plants. Int J Mol Sci24, 8185
Yapa, M.M.(g), Doroodian, P.(g), Gao, Z.(v), Yu, P.(g)and Hua, Z.*(2023). MORF2 is a key effector in plastid retrograde signaling for stress response and plant morphogenesis beyond RNA editing. Front Plant Sci14, 1146922
Yu, P.(g)and Hua, Z.*(2023). To kill or to be killed: how the battle of two large protein degradation systems maintains the intracellular homeostasis in eukaryotes? Int J Mol Sci24, 2221
Yu, P.(g)and Hua, Z.*(2022). The ubituitin-26s proteasome system and autophagy relay proteome homeostasis regulation during silique development. Plant J111, 1324–1339
Li, Y.(g), Yapa, M.M.(g), and Hua, Z.*(2021). A machine learning approach to prioritizing functionally active F-box members in Arabidopsis thaliana . Front Plant Sci, 12, 639253.
Doroodian, P.(g)and Hua, Z.*(2021). The ubiquitin switch in plant stress response . Plants10, 246
Hua, Z.* (2021). Diverse evolution in 111 plant genomes reveals purifying and dosage balancing selection models for F-box genes . Int J Mol Sci22, 871.
Chen, J., Jiang, J., Liu, J., Qian, S., Song, J., Kabara, R., Delo, I., Serino, G., Liu, F., Hua, Z., Zhong, X. (2020). F-box protein CFK1 interacts with and degrades de novo DNA methyltransferase in Arabidopsis. New Phytol, (Early View: https://doi.org/10.1111/nph.17103)
Yapa, M.M.(g), Yu, P.(g), Liao, F.(v), Moore, A.G.(u), and Hua, Z.* (2020). Generation of a fertile ask1 mutant uncovers a comprehensive set of SCF-mediated intracellular functions . Plant J104, 493–509
Hua, Z.*, and Yu, P.(g)(2019). Diversifying evolution of the ubiquitin-26s proteasome system in Brassicaceae and Poaceae . Int J Mol Sci, 20, 3226.
Hua, Z.*, and Early, M.J.(u)(2019). Closing Target Trimming and CTTdocker programs for discovering hidden superfamily loci in genomes . PLoS ONE, 14, e0209468.
Hua, Z.*(2019). Using CTT for comprehensive superfamily gene annotations . Protocols.io. 2019.
Marshall, R.S., Hua, Z., Mali, S., McLoughlin, F., and Vierstra, R.D. (2019). ATG8-Binding UIM proteins define a new class of autophagy adaptors and receptors . Cell177, 766-781.
Hua, Z.*, and Gao, Z.(v)(2019). Adaptive and degenerative evolution of the S-Phase Kinase-Associated Protein 1-Like family in Arabidopsis thaliana . PeerJ7, e6740.
Ruan, B.^, Hua, Z.^, Zhao, J.^, Zhang, B., Ren, D., Liu, C., Yang, S., Zhang, A., Jiang, H., Yu, H., Hu, J., Zhu, L., Chen, G., Shen, L., Dong, G., Zhang, G., Zeng, D., Guo, L., Qian, Q., and Gao, Z. (2019). OsACL-A2 negatively regulates cell death and disease resistance in rice . Plant Biotechnology Journal17, 1344-1356 (^ Co-first author).
Hua, Z.*(2019). Data Oriented Genomics Techniques (Book). figshare
Zhang, G., and Hua, Z.*(2018). Genome comparison implies the role of Wsm2 in membrane trafficking and protein degradation . PeerJ6, e4678.
Hua, Z.*, and Early, M.J.(u)(2018). Closing Target Trimming: a Perl package for discovering hidden superfamily loci in genomes . biooRxiv 490490.
Hua, Z.*, Doroodian, P.(u), and Vu, W.(u)(2018). Contrasting duplication patterns reflect functional diversities of ubiquitin and ubiquitin-like protein modifiers in plants . Plant Journal95, 296-311.
Haak, D.C., Fukao, T., Grene, R., Hua, Z., Ivanov, R., Perrella, G., and Li, S. (2017). Multilevel Regulation of Abiotic Stress Responses in Plants . Frontiers in Plant Science8, 1564.
Hua, Z., and Vierstra, R.D. (2016). Ubiquitin Goes Green . Trends in Cell Biology26, 3-5.
Publications from the Work Prior to Ohio University
Hua, Z., Pool, J.E., Schmitz, R.J., Schultz, M.D., Shiu, S.H., Ecker, J.R., and Vierstra, R.D. (2013). Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis . Proc Natl Acad Sci USA110, 16927-16932.
Christians, M.J., Gingerich, D.J., Hua, Z., Lauer, T.D., and Vierstra, R.D. (2012). The light-response BTB1 and BTB2 proteins assemble nuclear ubiquitin ligases that modify phytochrome B and D signaling in Arabidopsis . Plant Physiol160, 118-134.
Hua, Z., Zou, C., Shiu, S.H., and Vierstra, R.D. (2011). Phylogenetic comparison of F-Box ( FBX ) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift . PLoS ONE6, e16219.
Hua, Z., and Vierstra, R.D. (2011). The cullin-RING ubiquitin-protein ligases . Annu Rev Plant Biol62, 299-334.
Miller, M.J., Barrett-Wilt, G.A., Hua, Z., and Vierstra, R.D. (2010). Proteomic analyses identify a diverse array of nuclear processes affected by small ubiquitin-like modifier conjugation in Arabidopsis . Proc Natl Acad Sci USA107, 16512-16517.
International Brachypodium Initiative (including Hua, Z. and Vierstra, R.D.) (2010). Genome sequencing and analysis of the model grass Brachypodium distachyon . Nature463, 763-768.
Meng, X., Hua, Z., Sun, P., and Kao, T.H. (2011). The amino terminal F-box domain of Petunia inflata S -locus F-box protein is involved in the S-RNase-based self-incompatibility mechanism . AoB Plants2011, plr016.
Kubo, K., Entani, T., Takara, A., Wang, N., Fields, A.M., Hua, Z., Toyoda, M., Kawashima, S., Ando, T., Isogai, A., Kao, T.H., and Takayama, S. (2010). Collaborative non-self recognition system in S-RNase-based self-incompatibility . Science330, 796-799.
Fields, A.M., Wang, N., Hua, Z., Meng, X., and Kao, T.H. (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 Biol74, 279-292.
Meng, X., Hua, Z., Wang, N., Fields, A.M., Dowd, P.E., and Kao, T.H. (2009). Ectopic expression of S-RNase of Petunia inflata in pollen results in its sequestration and non-cytotoxic function . Sex Plant Reprod22, 263-275.
Hua, Z., Fields, A., and Kao, T.H. (2008). Biochemical models for S-RNase-based self-incompatibility . Mol Plant1, 575-585.
Hua, Z., and Kao, T.H. (2008). Identification of major lysine residues of S(3)-RNase of Petunia inflata involved in ubiquitin-26S proteasome-mediated degradation in vitro . Plant J54, 1094-1104.
Hua, Z., Meng, X., and Kao, T.H. (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 Cell19, 3593-3609.
Hua, Z., and Kao, T.H. (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 Cell18, 2531-2553.
Hua, Z., Zhu, X., Lin, H., Gao, Z., Qian, Q., Yan, M., and Huang, D. (2001). [Studies of the integration and expression of exogenes in transgenic rice obtained via particle bombardment transformation]. J Genetics Genomics(formerly Acta Genetica Sinica) 28, 1012-1018.
Hua, Z., and Huang, D.N. (1999). Genetic mode of exogenes in transgenic plants. J Integr Plant Biol(formerly Acta Bot Sin) 41, 1-5.
Huang, D., Li, J., Zhang, S., Xue, R., Yang, W., Hua, Z., Xie, X., and Wang, X. (1998). New technology to examine and improve the purity of hybrid rice with herbicide resistant gene . Chin Sci Bull43, 784-787.
Computational Programs in Bioinformatics from the Work at Ohio University
Hua, Z.*, and Early, M.J.*(u)(2018). CTT Perl Package .
Hua, Z.* (2019) CTTdocker Package .