Zhihua Hua

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 thaliana, 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 ofevolutionary 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 Bot 74, 6487-6504

Hua, Z.* (2023). The ubiquitin-26S proteasome system – a versatile player worthy of close attention in plants. Int J Mol Sci 24, 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 Sci 14, 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 Sci 24, 2221

Yu, P.(g) and Hua, Z.* (2022). The ubituitin-26s proteasome system and autophagy relay proteome homeostasis regulation during silique development. Plant J 111, 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. Plants 10, 246

Hua, Z.* (2021). Diverse evolution in 111 plant genomes reveals purifying and dosage balancing selection models for F-box genes. Int J Mol Sci 22, 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 J 104, 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. Cell 177, 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. PeerJ 7, 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 Journal 17, 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. PeerJ 6, 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 Journal 95, 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 Science 8, 1564.

Hua, Z., and Vierstra, R.D. (2016). Ubiquitin Goes Green. Trends in Cell Biology 26, 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 USA 110, 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 Physiol 160, 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 ONE 6, e16219.

Hua, Z., and Vierstra, R.D. (2011). The cullin-RING ubiquitin-protein ligases. Annu Rev Plant Biol 62, 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 USA 107, 16512-16517.

International Brachypodium Initiative (including Hua, Z. and Vierstra, R.D.) (2010). Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463, 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 Plants 2011, 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. Science 330, 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 Biol 74, 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 Reprod 22, 263-275.

Hua, Z., Fields, A., and Kao, T.H. (2008). Biochemical models for S-RNase-based self-incompatibility. Mol Plant 1, 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 J 54, 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 Cell 19, 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 Cell 18, 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 Bull 43, 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.