Yao Xu , Ph.D.
Research Associate Professor of Biological Sciences

Lab Url: N/A

Phone Number: 615-343-1350

Email Address: yao.xu@vanderbilt.edu

Xu, Yao's picture

Office Address   Mailing Address

U8215, Medical Research Building III (MRB III)

Department of Biological Sciences Vanderbilt University 37235

Research Keywords
Biological Clocks; Molecular Chronobiology; Circadian Rhythms; BRET assay; Protein-protein interaction; ,Gene regulation,Knockout,Mutation,Post-transcriptional modification,Recombination

Research Specialty
Molecular Mechanisms of Circadian Clocks

Pattanayek R, Xu Y, Lamichhane A, Johnson CH, Egli M. An arginine tetrad as mediator of input-dependent and input-independent ATPases in the clock protein KaiC. Acta Crystallogr D Biol Crystallogr, 70(Pt 5), 1375-1390, 2014.

Egli, M, Pattanayek, R, Sheehan, JH, Xu, Y, Mori, T, Smith, JA, Johnson, CH. Loop-Loop Interactions Regulate KaiA-Stimulated KaiC Phosphorylation in the Cyanobacterial KaiABC Circadian Clock. Biochemistry, 52(7), 1208-20, 2013.

Xu, Y, Ma, P, Shah, P, Rokas, A, Liu, Y, Johnson, CH. Non-optimal codon usage is a mechanism to achieve circadian clock conditionality. Nature, 495(7439), 116-120, 2013.

Xu, Y, Weyman, PD, Umetani, M, Xiong, J, Qin, X, Xu, Q, Iwasaki, H, Johnson, CH. Circadian yin-yang regulation and its manipulation to globally reprogram gene expression. Curr Biol, 23(23), 2365-74, 2013.

Edgar RS, Green EW, Zhao Y, van Ooijen G, Olmedo M, Qin X, Xu Y, Pan M, Valekunja UK, Feeney KA, Maywood ES, Hastings MH, Baliga NS, Merrow M, Millar AJ, Johnson CH, Kyriacou CP, O'Neill JS, Reddy AB. Peroxiredoxins are conserved markers of circadian rhythms. Nature, 485(7399), 459-464, 2012.

Egli, M, Mori, T, Pattanayek, R, Xu, Y, Qin, X, Johnson, CH. Dephosphorylation of the core clock protein KaiC in the cyanobacterial KaiABC circadian oscillator proceeds via an ATP synthase mechanism. Biochemistry, 51(8), 1547-58, 2012.

Zhang, LJ, Jia, JF, Xu, Y, Wang, YL, Hao, JG, Li, TK. Production of transgenic Nicotiana sylvestris plants expressing melatonin synthetase genes and their effect on UV-B-induced DNA damage. In Vitro Cellular & Developmental Biology - Plant, 48(3), 275-282, 2012.

Qin, X, Byrne, M, Xu, Y, Mori, T, Johnson, CH. Coupling of a core post-translational pacemaker to a slave transcription/translation feedback loop in a circadian system. PLoS Biol, 8(6), e1000394, 2010.

Johnson, CH, Xu, Y. A decade of discovery: how Synechococcus elongatus became a model circadian system. In: Bacterial Circadian Clock and Rhythms (J. L. Ditty, S. R. Mackey, and C.H. Johnson, eds), Springer, Verlag Berlin Heidelberg, 63-86, 2009.

Pattanayek, R, Mori, T, Xu, Y, Pattanayek, S, Johnson, CH, Egli, M. Structures of KaiC circadian clock mutant proteins: a new phosphorylation site at T426 and mechanisms of kinase, ATPase and phosphatase. PLoS One, 4(11), e7529, 2009.

Wang Y, Jia J, Bu H, Zhao Y, Xu Y, Johnson CH, Kol??r J.. Genetic transformation of Nicotiana tabacum L. by Agrobacterium tumefaciens carrying genes in the melatonin synthesis pathway and the enhancement of antioxidative capability in transgenic plants. Chinese J. Biotech., 25(7), 1014-1021, 2009.

Xu, Y, Mori, T, Qin, X, Yan, H, Egli, M, Johnson, CH. Intramolecular regulation of phosphorylation status of the circadian clock protein KaiC. PLoS One, 4(11), e7509, 2009.

Johnson, CH, Mori, T, Xu, Y. A cyanobacterial circadian clockwork. Curr Biol, 18(17), R816-R825, 2008.

Woelfle, MA, Xu, Y, Qin, X, Johnson, CH. Circadian rhythms of superhelical status of DNA in cyanobacteria. Proc Natl Acad Sci U S A, 104(47), 18819-24, 2007.

Pattanayek, R, Williams, DR, Pattanayek, S, Xu, Y, Mori, T, Johnson, CH, Stewart, PL, Egli, M. Analysis of KaiA-KaiC protein interactions in the cyano-bacterial circadian clock using hybrid structural methods. EMBO J, 25(9), 2017-28, 2006.

Soutto, M., Xu, Y., Johnson, C.H. . Bioluminescence RET (BRET): Techniques and Potential. In: Molecular Imaging: FRET Microscopy and Spectroscopy. Editors, Ammasi Periasamy and Richard N. Day (Oxford University Press, NY), , pp. 260-271., 2005.

Pattanayek, R, Wang, J, Mori, T, Xu, Y, Johnson, CH, Egli, M. Visualizing a circadian clock protein: crystal structure of KaiC and functional insights. Mol Cell, 15(3), 375-88, 2004.

Subramanian, C, Xu, Y, Johnson, CH, von Arnim. AG. In vivo detection of protein-protein Interaction in plant cells using BRET. Methods Mol Biol., 284, 271-286, 2004.

Xu, Y, Mori, T, Pattanayek, R, Pattanayek, S, Egli, M, Johnson, CH. Identification of key phosphorylation sites in the circadian clock protein KaiC by crystallographic and mutagenetic analyses. Proc Natl Acad Sci U S A, 101(38), 13933-8, 2004.

Xu, Y, Kanauchi, A, von Arnim, AG, Piston, DW, Johnson, CH. Bioluminescence resonance energy transfer: monitoring protein-protein interactions in living cells. Methods Enzymol, 360, 289-301, 2003.

Xu, Y, Mori, T, Johnson, CH. Cyanobacterial circadian clockwork: roles of KaiA, KaiB and the kaiBC promoter in regulating KaiC. EMBO J, 22(9), 2117-26, 2003.

Mori, T, Saveliev, SV, Xu, Y, Stafford, WF, Cox, MM, Inman, RB, Johnson, CH. Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA. Proc Natl Acad Sci U S A, 99(26), 17203-8, 2002.

Xu, Y, Johnson, CH, Piston, D. Bioluminescence resonance energy transfer assays for protein-protein interactions in living cells. Methods Mol Biol, 183, 121-33, 2002.

Xu, Y, Kanauchi A, Piston DW, Johnson, CH.. Resonance energy transfer as an emerging technique for monitoring protein-protein interactions in vivo: BRET vs. FRET. In Luminescence Biotechnology: Instruments and Applications (K. V. Dyke, C. V. Dyke and K. Woodfork, eds), CRC Press, Boca Raton., pp. 529-538, 2002.

Xu, Y, Johnson, CH. A clock- and light-regulated gene that links the circadian oscillator to LHCB gene expression. Plant Cell, 13(6), 1411-25, 2001.

Xu, Y, Mori, T, Johnson, CH. Circadian clock-protein expression in cyanobacteria: rhythms and phase setting. EMBO J, 19(13), 3349-57, 2000.

Xu, Y, Piston, DW, Johnson, CH. A bioluminescence resonance energy transfer (BRET) system: application to interacting circadian clock proteins. Proc Natl Acad Sci U S A, 96(1), 151-6, 1999.

Xu, Y, Zhu, Q, Lamb, C. Regulation, expression and fuction of a new basic chitinase gene in rice (Oryza sativa L.). Plant Mol. Biol., 30, 30: 387-401., 1996.

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