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College of Arts & Sciences

Zhihua Hua

Zhihua Hua

Assistant Professor

Environmental & Plant Biology
Porter Hall

Recent News


Ph.D. in Plant Physiology, Pennsylvania State University, 2008


  • 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


Hua, Z.*, and Gao, Z. (2019). Adaptive and degenerative evolution of the S-Phase Kinase-Associated Protein 1-Like family in Arabidopsis thaliana. PeerJ 7:e6740. (*Corresponding author)

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.

Hua, Z.* (2019) Data Oriented Genomics Techniques (Book). figshare, (*Corresponding author)

Ruan, B.^, Hua, Z.^, Zhao, J.^, 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., Gao, Z. (2018) OsACL-A2 negatively regulates cell death and disease resistance in rice. Plant Biotechnology Journal,^Co-first authors)

Hua, Z.* and Early, M.J. (u) (2018) Closing Target Trimming: a Perl package for discovering hidden superfamily loci in genomes. bioRxiv, 490490. (*Corresponding author)

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 J 95, 296-311. (*Corresponding author)

Zhang, G. and Hua, Z.* (2018) Genome comparison implies the role of Wsm2 in membrane trafficking and protein degradation. PeerJ 6:e4678. (*Corresponding author)

Grene, R., Perrella, G., Ivanov, R., Hua, Z., Li, S., Fukao, T., and Haak, D.C. (2017) Multilevel regulation of abiotic stress responses in plants (Review Article). Frontiers in Plant Science 8:1564. (All authors contributed equally)

Hua, Z.* and Vierstra, R.D.* (2016). Ubiquitin goes green (Review Article). Trends in Cell Biology 26, 3-5. (*Corresponding author)

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 genonomic 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., and Vierstra, R.D. (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. (Recommended by the F1000 Faculty)

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 S-RNase-based self-incompatibility mechanism. AoB PLANTS 2011 plr016 doi:10.1093/aobpla/plr016.

Hua, Z., and Vierstra, R.D. (2011). The cullin-RING ubiquitin-protein ligases (Review Article). Ann Rev Plant Biol 62, 299-234.

Hua, Z., Zou, C., Shiu, S.H., and Vierstra, R.D. (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.

Kubo, K., Entani1, 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. (Science Feature Article) (Recommended by the F1000 Faculty)

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. (Recommended by the F1000 Faculty)

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.

"The 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. (Recommended by the F1000 Faculty)

Meng, X.*, Hua, Z.*, Wang, N., Fields, A.M., Dowd, P., and Kao, T.-h. (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).

Hua, Z., Fields, A.M., and Kao, T.-h. (2008). Biochemical models for S-RNase-based self-incompatibility (Review Article). Mol Plant 1, 575-585.

Hua, Z., and Kao, T.-h. (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.

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. (Recommended by the F1000 Faculty)

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 Genet Genomics (formerly Acta Genet. Sin. 遗传学报) 28, 1012-1018 (in Chinese with English abstract).

Hua, Z., and Huang, D. (1999) Genetic mode of exogenes in transgenic plants (Review Article). J Integr Plant Biol (formerly Acta Bot. Sin. 植物学报) 41, 1-5 (in Chinese with Engilish abstract).

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 (科学通报) 43, 784-787 (in English), 43: 67-70 (in Chinese).

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