Dr. Huazhong Shi
Ph.D., Wuhan University, China, 1995; Research Associate, University of Arizona, 1999-2001, University of California, 2001-2003, Purdue University, 2003-2004
Interested in graduate study on molecular biology and biochemistry? Join the Shi lab! Applicants with strong Biology background are highly encouraged to apply. For more information, click here or contact Dr. Huazhong Shi.
Principal Research Interests
- Gene regulation in response to environmental stresses in plants
- Molecular mechanisms of plant salt tolerance
- Sulfonation of small molecules and plant stress response
Plants frequently encounter unfavorable conditions that adversely affect their growth, development, and productivity. How plants sense, transduce and respond to abiotic stresses is a fundamental question that is of tremendous significance for the future of agriculture. The research in the Shi lab focuses on understanding how plants cope with environmental stresses at molecular, cellular and organismal levels by employing genetic, molecular and biochemical research tools.
Gene regulation in plant stress response
Fine regulation of gene expression is required for normal growth, development and adaptation to environmental stress conditions in plants. Many genes are repressed at normal growth conditions while activated by stresses. In order to identify regulator proteins mediating gene repression and activation, the Shi lab established a forward genetic screening for mutations affecting gene expression in response to stress conditions. The forward genetic approach utilized a stress-inducible promoter fused with the firefly luciferase reporter gene and a highly sensitive CCD camera to detect bioluminescence generated in small plant seedlings expressing the luciferase gene (Figure 1). By using this high throughput mutant screening system, the Shi lab has identified a number of mutants, designated shiny (shi in short) mutants, showing elevated expression of luciferase gene in response to abiotic stresses. Eight SHI genes have been cloned using map-based cloning. Two of the SHI genes encode proteins forming a complex to regulate stress-inducible gene expression through modulating RNA polymerase II CTD phosphorylation. Another three SHI proteins are mRNA splicing factors that are presumably components of repressor complex modulating stress-inducible gene transcription. Two of the eight SHI genes encode proteins functioning in vesicle trafficking. The Shi lab is employing all available means to study the functions of these SHI genes in order to gain deep understanding of stress-inducible gene repression and activation. In addition, the Shi lab initiated a forward genetic screening for mutations altering heat stress responsive gene expression. Positional cloning of the mutant genes is currently underway.
Na+ transport and plant salt tolerance
Plants possess three cellular mechanisms to reduce Na+ toxicity, i.e. restricted Na+ entry, Na+ exclusion, and Na+ compartmentation into the vacuole. These three cellular mechanisms are executed by three membrane transporters named AtHKT1, SOS1 and AtNHX1 in Arabidopsis (Figure 2). Through a genetic screening for suppressors of Na+ hypersensitive mutant sos1, the Shi lab identified loss-of-function mutations in AtHKT1 and gain-of-function mutations in AtNHX1 that can suppress the salt sensitivity of sos1 mutant. Single, double and triple mutants with mutations in these three important salt tolerance determinants have been created. The functions of these transporters and their coordination in Na+ uptake, long-distance transport, and redistribution in plants have been studied. Structure-function analysis of the dominant gain-of-function mutations in AtNHX1 and molecular design of superactive AtNHX1 transporters based on such analysis will be our future focus. The ultimate goal of this project is to create salt tolerant crops capable of growing in marginal lands with high salinity to maximize land usage and to secure world food supply.
Sulfonation of small molecules and its function in plant stress response
Sulfonation of small molecules is an enzymatic process in living organisms catalyzed by sulfotransferases to transfer a sulfonate group from the universal donor 3’-phosphoadenosine 5’-phosphosulfate (PAPS) to the hydroxyl group of various molecules (Figure 3). Sulfonation changes the physiochemical properties and the biological activity of molecules, thus influencing the physiology of organisms. In human, sulfonation of small molecules plays important roles in detoxification of toxic compounds and modulation of steroid hormones. In Arabidopsis, 18 cytosolic sulfotransferases (SOTs) have been identified based on sequence similarity. The Shi lab carried out a genetic and biochemical analysis of the SOT12 and found that SOT12 can sulfonate the plant hormone salicylic acid (Figure 3) and xenobiotic compounds. The role of SOT12 in both biotic and abiotic stress response and tolerance is being studied. The Shi lab is also interested in the functions of other SOTs, in particular, their roles in stress response.
- "RNA-Seq Analysis for Transcriptome Assembly, Gene Identification and SSR Mining in Ginkgo (Ginkgo biloba L.)". Han S, Wu Z, Jin Y, Yang W, Shi H. Tree Genet Genomes, 2015, 11:37, doi: 10.1007/s11295-015-0868-8.
- "Detoxification function of the Arabidopsis sulfotransferase AtSOT12 by sulfonation of xenobiotics", Chen J, Gao L, Baek DW, Liu C, Ruan Y, Shi H. Plant Cell Environ, 2015, 38: 1673-1682, doi: 10.1111/pce.12525.
- "Bacillus crassostreae sp. nov., isolated from an oyster (Crassostrea hongkongensis)", Chen J, Tian X, Ruan Y, Yang Y, He Z, Tang S, Li W, Shi H, Chen Y. Int J Syst Evol Microbiol, 2015, 65: 1561-1566, doi:10.1099/ijs.0.000139.
- "GmFLD, a soybean homolog of the autonomous pathway gene FLOWERING LOCUS D, promotes flowering in Arabidopsis thaliana", Hu Q, Jin Y, Shi H, Yang W. BMC Plant Biol, 2014, 14:263.
- "The Arabidopsis RNA Binding Protein with K Homology Motifs, SHINY1, Interacts with the C-terminal Domain Phosphatase-like 1 (CPL1) to Repress Stress-Inducible Gene Expression", Jiang, J.; Wang, B.; Shen, Y.; Wang, H.; Feng, Q.; Shi, H. PLoS Genet, 2013, 9(7): e1003625. doi:10.1371/journal.pgen.1003625.
- "Physiological and molecular mechanisms of plant salt tolerance", Zhang, J.; Shi, H. Photosynth Res, 2013, 115:1-22.
- “A novel HSI2 mutation in Arabidopsis affects the PHD-like domain and leads to derepression of seed-specific gene expression”Veerappan, V; Wang, J; Kang, M; Lee, J; Tang, Y; Jha, AK; Shi, H; Palanivelu, R; Allen, RDPlanta2012, 236,1-17.
- “Regulated AtHKT1 gene expression by a distal enhancer element and DNA methylation in the promoter plays an important role in salt tolerance”Baek, DW; Jiang, J; Chung, JS; Wang, B; Chen, J; Xin, Z; Shi, H.Plant Cell Physiol.2011, 52, 149-161.
- “A Stress-inducible Sulfotransferase Sulfonates Salicylic Acid and Confers Pathogen Resistance in Arabidopsis”Baek, DW; Pathange, P; Chung, JS; Jiang, J; Gao, L; Oikawa, A; Hirai, MY; Saito, K; Pare, PW; Shi, H. Plant Cell Environ.2010, 33,1383-1392.
- “HOS3, an ELO-like gene, inhibits effects of ABA and implicates a S-1-P/ceramide control system for abiotic stress response in Arabidopsis thaliana”Quist, TM; Sokolchik, I; Shi, H; Joly, RJ; Bressan, RA; Maggio, A; Narsimhan, M; Li, X. Mol. Plant2009, 2,138-151.
- "Signaling control of SOS1 mRNA stability". Jiang, J; Shi, H. Plant Signaling and Behavior2008, 3, 687-688.
- "Soil bacteria confer plant salt tolerance by tissue-specific regulation of the sodium transporter HKT1". Zhang, H; Kim, M-S; Sun, Y; Dowd, SE; Shi, H; Pare, PW. Molecular Plant-Microbe Interaction2008, 21, 737-744.
- "Involvement of Arabidopsis HOS15 in histone deacetylation and cold tolerance". Zhu, J; Jeong, JC; Zhu, Y; Sokolchik, I; Miyazaki, S; Zhu, J-K; Hasegawa, PM; Bohnert, HJ; Shi, H; Yun, D-J; Bressan, RA. Proc Natl Acad Sci USA2008, 105, 4945-4950
- "Reactive oxygen species mediate Na+-induced SOS1 mRNA stability in Arabidopsis". Chung, JS; Zhu, JK; Bressan, RA; Hasegawa, PM; Shi, H. Plant J.2008,53, 554-565.
- "Integration of Ca2+ in plant drought and salt stress signal transduction pathways". Shi, H. In Advances in molecular breeding towards salinity and drought tolerant (eds. Jenks MA, Hasegawa PM, Jain SM).Springer 2007, pp. 141-182.
- "Isolation and characterization of shs1, a sugar-hypersensitive and ABA-insensitive mutant with multiple stress responses". Inan, G; Goto, F; Jin, JB; Rosado, A; Koiwa, H; Shi, H; Hasegawa, PM; Bressan, RA; Maggio, A; Li, X. Plant Mol Biol2007, 65, 295-309.
- "An enhancer mutant of Arabidopsis salt overly sensitive 3 mediates both ion homeostasis and the oxidative stress response". Zhu, J; Fu, X; Koo, YD; Zhu, JK; Jenney, FE Jr; Adams, MW; Zhu, Y; Shi, H; Yun, DJ; Hasegawa, PM; Bressan, RA. Mol Cell Biol2007,27, 5214-5224.
- "Salt stress affects cortical microtubule organization and helical growth in Arabidopsis". Shoji, T; Suzuki, K; Abe, T; Kaneko, Y; Shi, H; Zhu, JK; Rus, A; Hasegawa, PM; Hashimoto, T. Plant Cell Physiol.2006, 47, 1158-1168.
- "RNA Extraction". Shi, H; Bressan, R. In Methods in Molecular Biology, Vol. 323, Arabidopsis Protocols (2nd ed) (Eds Salinas J, Sanchez-Serrano J), Humana Press, New Jersey, 2006, pp 345-348.
- "Sodium", Shi, H.; Bressan, R.; Hasegawa, P.M.; Zhu, J.-K. In Plant Nutritional Genomics (Broadley. M; White, P., Eds), Blackwell Publishing, London 2004.
- "An Arabidopsis homeodomain transcription factor gene, HOS9, mediates cold tolerance through a CBF-independent pathway", Zhu, J.; Shi, H.; Lee, B.H.; Damsz, B.; Cheng, S.; Stirm, V.; Zhu, J.K.; Hasegawa, P.M.; Bressan, R.A. Proc Natl Acad Sci USA 2004, 101, 9873-9878.
- "Topological analysis of a plant vacuolar Na/H antiporter reveals a luminal C-terminus that regulates the antiporter activity", Yamaguchi, T.; Apse, M.P.; Shi, H.; Blumwald, E. Proc Natl Acad Sci USA 2003, 100, 12510-12515.
- "The Arabidopsis SOS5 locus encodes a putative cell surface adhesion protein and is required for normal cell expansion", Shi, H.; Kim, Y.-S.; Guo, Y.; Zhu, J.-K. Plant Cell 2003, 15, 19-32.
- "Overexpression of a plasma membrane Na+/H+ antiporter gene improves salt tolerance in Arabidopsis", Shi, H.; Lee, B.; Wu, S.-J.; Zhu, J.-K. Nat Biotechnol. 2003, 21, 81-85.
- "Regulation of the vacuolar Na+/H+ antiporter gene AtNHX1 expression by salt stress and abscisic acid", Shi, H.; Zhu, J.-K. Plant Mol Biol. 2002, 50, 543-550.
- "Reconstitution in yeast of the Arabidopsis SOS signaling pathway for Na+ homeostasis", Quintero, F.J.; Ohta, M.; Shi, H.; Zhu, J.K.; Pardo, J.M. Proc Natl Acad Sci USA 2002, 99, 9061-9066.
- "SOS4, a pyridoxal kinase gene, is required for root hair development in Arabidopsis", Shi, H.; Zhu, J.-K. Plant Physiol. 2002, 129, 585-593.
- "The Arabidopsis salt overly sensitive 4 mutants uncover a critical role for vitamin B6 in plant salt tolerance", Xiong, L.; Stevenson, B.; Lu, T.; Zhu, J.-K. Plant Cell 2002, 14, 575-588.
- "The putative plasma membrane Na+/H+ antiporter SOS1 controls long-distance Na+ transport in plants", Shi, H.; Quintero, F.J.; Pardo, J.M.; Zhu, J.-K. Plant Cell 2002, 14, 465-477.
- "The Arabidopsis thaliana salt tolerance gene SOS1 encodes a putative Na+/H+ antiporter", Shi, H.; Ishitani, M.; Kim, C.; Zhu, J. –K. Proc Natl Acad Sci USA 2000, 97, 6896-6901.