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Xing Liu

Biochemistry 

  • Assistant Professor
765.494.1793
765.494.7897
BCHM Room 29

Research:

The covalent attachment of ubiquitin, a small conserved protein of 76 amino acid residues, to cellular proteins plays significant roles in eukaryotic cells and organisms. Monoubiquitination serves as a signal in intracellular trafficking, DNA repair and signal transduction pathways, while assembly of a chain of ≥4 ubiquitins usually targets substrate proteins for degradation by the 26S proteasome. Polyubiquitination is achieved by a cascade of enzymes comprising ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin-ligating enzyme (E3). Ubiquitin is thio-esterified to E1 and is then transferred to E2 also through a thioester linkage (E2~Ub). The ubiquitin can finally be conjugated to substrate proteins when an E3 binds to both the substrate protein and E2~Ub, bringing them into proximity and thus enabling substrate ubiquitination. The pairing of E2~Ub and substrates by E3s determines the substrate specificity in ubiquitination reactions. One of the major types of E3s is the large family of cullin-RING ubiquitin ligases (CRLs).

Due to their ability of specifying the half-lives of many key regulatory proteins that control a broad spectrum of biological events, CRLs have shown great impacts on human health as well as almost every aspect of plant growth and development. CRLs are modular multi-subunit complexes composed of a cullin scaffold, a RING domain protein that recruits E2~Ub, and an interchangeable substrate adaptor that determines the specificity of the complex. Skp1•Cul1•F-box protein (SCF), the founding member of the CRL family, consists of the cullin Cul1, the RING domain protein Rbx1, the adapter protein Skp1, and an F-box protein that binds Skp1 (and Skp1•F-box protein forms the substrate receptor module). As the eukaryotic genome can encode multiple F-box proteins (e.g. 20 in yeast, 69 in human, ~900 in Arabidopsis thaliana), there are pools of diverse SCF ubiquitin ligases with distinct substrate specificities within a single eukaryotic cell. Additional cullins (e.g. Cul3, Cul4) also exist, each of which interacts with different sets of adaptor proteins and substrate receptors, forming a large number of CRLs.

The activity of CRLs is regulated by three master regulators: Nedd8, CSN, and Cand1. A CRL is activated by covalent modification of the cullin with the ubiquitin-like protein Nedd8, a process called neddylation. Neddylation is reversed by the COP9 signalosome complex (CSN), which removes Nedd8 from the cullin and allows its binding to Cand1. Cand1 serves as an exchange factor for substrate receptor proteins: it binds un-neddylated Cul1 in an extended manner and therefore disrupts both the association of Skp1 with Cul1 and Nedd8 conjugation of Cul1; in turn, the F-box•Skp1 module can remove Cand1 from Cul1, forming an SCF complex that can then be activated by neddylation. Thus, Nedd8, CSN, and Cand1 together enable dynamic cycling of Cul1, which optimizes the use of the Cul1 scaffold protein and ensures timely ubiquitination of target proteins in complicated cellular environment under varying external conditions.

My lab is interested in exploring the mechanisms governing the dynamics of CRLs, using approaches including biochemistry, biophysics, proteomics, mathematical modeling, and molecular genetics, in both human cells and plants.


Selected Publications:


Liu X, Reitsma JM, Mamrosh JL, Zhang Y, Straube R, Deshaies RJ (2018) Cand1-mediated adaptive exchange mechanism enables variation in F-box protein expression. Mol Cell 69: 773-786 (Featured article)

Reitsma JM, Liu X, Reichermeier KM, Moradian A, Sweredoski MJ, Hess S, Deshaies RJ (2017) Composition and Regulation of the Cellular Repertoire of SCF Ubiquitin Ligases. Cell 171: 1326-1339

Zhou Y, Liu X, Engstrom EM, Nimchuk ZL, Pruneda-Paz JL, Tarr PT, Yan A, Kay SA, Meyerowitz EM (2015) Control of plant stem cell function by conserved interacting transcriptional regulators. Nature 517: 377-380

Pierce NW, Lee JE, Liu X, Sweredoski MJ, Graham RLJ, Larimore EA, Rome M, Zheng N, Clurman BE, Hess S, Shan SO, Deshaies RJ (2013) Cand1 promotes assembly of new SCF complexes through dynamic exchange of F-box proteins. Cell 153: 206-15

Li W, Zhou Y, Liu X, Yu P, Cohen JD, Meyerowitz EM (2013) LEAFY controls auxin response pathways in floral primordium formation. Science Signaling 6: ra23

Liu X, Wu J, Clark G, Lim M, Arnold D, Gardner G, Roux SJ (2012) Role for apyrases in polar auxin transport in Arabidopsis. Plant Physiology 160:1985-95

De Rybel B, Audenaert D, Xuan W, Overvoorde P, Strader LC, Kepinski S, Hoye R, Brisbois R, Parizot B, Vanneste S, Liu X, Gilday A, Graham IA, Nguyen L, Jansen L, Njo MF, Inzé D, Bartel B, Beeckman T (2012) A role for the root cap in root branching revealed by the non-auxin probe naxillin. Nature Chemical Biology 8:798–805

Liu X*, Hegeman AD, Gardner G, Cohen JD (2012) Protocol: High-throughput and quantitative assays of auxin and auxin precursors from minute tissue samples. Plant Methods 8:31 (* Denotes corresponding author)

Liu X*, Barkawi LS, Gardner G, Cohen JD (2012) Transport of indole-3-butyric acid and indole-3-acetic acid in Arabidopsis thaliana hypocotyls using stable isotope labeling. Plant Physiology 158:1988-2000 (* Denotes corresponding author)

Liu X*, Cohen JD, Gardner G (2011) Low fluence red light increases the transport and biosynthesis of auxin. Plant Physiology 157:891-904 (* Denotes corresponding author)

Cheng NH, Liu JZ, Liu X, Wu Q, Thompson SM, Lin J, Chang J, Whitham SA, Park S, Cohen JD, Hirschi KD (2011) Arabidopsis monothiol glutaredoxin, AtGRXS17, is critical for temperature-dependent postembryonic growth and development via modulating auxin response. Journal of Biological Chemistry 286:20398-406

Phillips KA, Skirpan AL, Liu X, Christensen A, Slewinski TL, Hudson C, Barazesh S, Cohen JD, Malcomber S, McSteen P (2011) vanishing tassel 2 encodes a grass-specific tryptophan aminotransferase required for vegetative and reproductive development in maize. Plant Cell 23:550-66

Selected Publications

Niyogi, D., Jacobs, E. M., Liu, X., Kumar, A., Biehl, L., & Rao, P. Suresh C. (2017). Assessment of a Long-Term High-Resolution Hydroclimatic Dataset for the US Midwest. EARTH INTERACTIONS, 21. doi:10.1175/EI-D-16-0022.1

Liu, X., Jacobs, E., Kumar, A., Biehl, L., Andresen, J., & Niyogi, D. (2017). The Purdue Agro-climatic (PAC) dataset for the U.S. Corn Belt: Development and initial results. CLIMATE RISK MANAGEMENT, 15, 61-72. doi:10.1016/j.crm.2016.10.005

Liu, X., Chen, F., Barlage, M., Zhou, G., & Niyogi, D. (2016). Noah-MP-Crop: Introducing dynamic crop growth in the Noah-MP land surface model. JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES, 121(23), 13953-13972. doi:10.1002/2016JD025597

Liu, X., Andresen, J., Yang, H., & Niyogi, D. (2015). Calibration and Validation of the Hybrid-Maize Crop Model for Regional Analysis and Application over the US Corn Belt. EARTH INTERACTIONS, 19. doi:10.1175/EI-D-15-0005.1

Niyogi, D., Liu, X., Andresen, J., Song, Y., Jain, A. K., Kellner, O., . . . Doering, O. C. (2015). Crop models capture the impacts of climate variability on corn yield. GEOPHYSICAL RESEARCH LETTERS, 42(9), 3356-3363. doi:10.1002/2015GL063841

Department of Biochemistry, 175 South University Street, West Lafayette, IN 47907-2063 USA, (765) 494-1600

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