B. Tracy Nixon

About Me

Professsor B. Tracy Nixon earned his PhD in Cell Biology at MIT with Howard Green (1977-1982) followed by two postdoctoral appointments with Howard Green in Physiology (Harvard Medical School, 1982-1983) and with Frederick M. Ausubel in Molecular Biology (Mass General Hospital/Harvard Medical School, 1983-1986). In 1987 he joined the BMB Department at Penn State and was a Visiting Scholar with Sydney Kustu and David Wemmer at the University of California – Berkeley (2002-2003), Haw Yang and Sacha DeCarlo at Princeton and the City College of New York (2010-2011), and a Member of Seth Darst’s Laboratory of Molecular Biophysics at Rockefeller University (2016-2018). 

Department or University Committees

• Peer Teaching Evaluation Committee: current Chair, past member and Chair.
   
• Graduate Program Steering Committee: current member.
   
• Steering Committee for the CSL Behring Fermentation Facility, Penn State: current member.
   
• RPO2 Investigative Committee, Penn State Office of Research Integrity: current member.  
   
• Neutron Scattering Science Committee for ORNL’s BioSANS Beam Allocation: current member, past co-Chair.

Program or Departmental Affiliations

Research Interests

• Genetic, Bioinformatic, Biochemical, and Structural studies of bacterial signal transduction and gene regulation by AAA+ ATPase and cellulose synthesis in bacteria and plants. 

Research Summary

Dr. Nixon’s research interests include study of the two-component signal transduction mechanism in bacteria that activates gene expression by the sigma54-form of bacterial RNA polymerase. He also studies the synthesis of cellulose in bacteria and plants, attempting to decipher the role oligomerization of the synthase enzyme plays in determining the physical nature of the cellulose produced for formation of bacterial and plant cell walls and how allosteric communication regulates function. He and his lab members use various approaches ranging from bioinformatics, molecular genetics and biochemistry to biophysical methods such as crystallography, cryo-electron microscopy and molecular dynamic simulations.

At various times since 1987 Dr. Nixon has taught graduate students and postdoctoral researchers to apply nonlinear regression and global analysis to model data from a variety of biochemical and structural studies in a course he developed called ‘Computers for Biochemists’, the Microbiology portion of Core Concepts required of BMMB graduate students, Microbiology.

Honors and Awards

• Ten at Ten Scientific Ideas Award, US Department of Energy Office of Science, 2019.  “For elucidating the structure of plant cellulose synthase and cellulose synthesis complex”, issued to Candace Haigler, James Kubicki, B. Tracy Nixon, Hugh O’Neill, Alison Roberts, Ming Tien, Yaroslava Yingling, Jochen Zimmer.  

Selected Publications

• Cho SH, Purushotham P, Fang C, Maranas C, Díaz-Moreno SM, Bulone V, Zimmer J, Kumar M, Nixon B.T. 2017. Synthesis and Self-Assembly of Cellulose Microfibrils from Reconstituted Cellulose Synthase. Plant Physiol. 175:146-156. doi: 10.1104/pp.17.00619. PMID:28768815
   
• Purushotham P., Cho S.H., Díaz-Moreno S.M., Kumar M., Nixon B.T., Bulone V., Zimmer J. A single heterologously expressed plant cellulose synthase isoform is sufficient for cellulose microfibril formation in vitro. Proc Natl Acad Sci U S A. 2016 Sep 19. pii: 201606210. [Epub ahead of print] PubMed PMID: 27647898
   
• Nixon, B.T., Mansouri, K., Singh, A., Du, J., Davis, J.K., Lee, J.-G., Slabaugh, E., Vandavasi, V.G., O’Neill, H., Roberts, E.M., Roberts, A.W., Yingling, Y.G., Haigler, C.H. 2016.  Comparative Structural and Computational Analysis Supports Eighteen Cellulose Synthases in the Plant Cellulose Synthesis Complex. Sci. Rep. 6:28696. doi: 10.1038/srep28696.
   
• Cho, S.H., Du, J., Sines, I., Poosarla, V.G., Vepachedu, V., Kafle, K., Park, Y.B., Kim, S.H., Kumar, M., Nixon, B.T. 2015. In vitro synthesis of cellulose microfibrils by a membrane protein from protoplasts of the non-vascular plant Physcomitrella patens. Biochem J. 470, 195-205. doi: 10.1042/BJ20141391. 
   
• Sysoeva, T.A., Chowdhury, S. and Nixon, B.T. 2014. Breaking symmetry in multimeric ATPase motors. Invited feature editorial in Cell Cycle 13, 509-510.
   
• Sysoeva, T.A., Chowdhury, S., Guo, L., and Nixon, B.T. 2013. Nucleotide-induced asymmetry within ATPase activator ring drives sigma54-RNAP interaction and ATP hydrolysis. Genes & Dev 27, 2500-2511. 
   
• Chakraborty, A., Wang, D., Ebright, Y.W., Korlann, Y., Korthonjia, E., Kim, T., Chowdhury, S., Wigneshweraraj, S., Irschik, H., Jansen, R., Nixon, B.T., Knight, J., Weiss, S., Ebright, R.H. 2012. Opening and closing of the bacterial RNA polymerase clamp. Science 337, 591-595. 
   
• Li, P., Banjade, S., Cheng, H-C., Kim, S., Chen, S., Guo, L., Llaguno, M., Hollingsworth,  J.V., King, D.S., Banani, S.F., Russo, P.S., Jiang, Q-X., Nixon, B.T., and Rosen, M.K. 2012. Phase transitions in the assembly of multi-valent signaling proteins. Nature 483, 336-340.
   
• Chen, B., T.A. Sysoeva, S. Chowdhury, L. Guo, S. De Carlo, J.A. Hanson, H. Yang, and Nixon, B.T. 2010. Engagement of arginine finger to ATP triggers large conformational changes in NtrC1 AAA+ ATPase for remodeling bacterial RNA polymerase. Structure, 18, 1420-1430. This article was chosen by the editors to be the subject of a commentary written by Martin Buck and Timothy R. Hoover, and used for the cover illustration.
   
• Doucleff, M., Pelton, J.G., Lee, P.S., Nixon, B.T. and Wemmer, D.E. 2007. Structural basis of DNA recognition by the alternative sigma-factor, sigma54. J. Mol. Biol. 369, 1070-1078.  Summary figure of my contribution used for cover of J. Mol. Biol. 369 (2007).   
   
• Chen, B., Doucleff, M., Wemmer, D.E., De Carlo, S., Huang, H.H., Nogales, E., Hoover, T.R., Kondrashkina, E., Guo, L. and Nixon, B.T. 2007. ATP ground- and transition states of bacterial enhancer binding AAA+ ATPases support complex formation with their target protein, 54. Structure 15, 429-440. Summary figure used for cover of Structure 15 (2007).
   
• De Carlo, S., Chen, B., Hoover, T.R., Kondrashkina, E., Nogales, E. and Nixon, B.T. 2006. The structural basis for assembly and function of the transcriptional activator NtrC. Genes & Dev 20, 1485-1495. Summary figure used for cover of Genes & Dev 20 (2006).
   
• Lee, S.-Y., De La Torre, A., Yan, D., Kustu, S., Nixon, B.T. and Wemmer, D.E. 2003. Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains. Genes & Dev. 17, 2552-2563. Summary figure used for cover of Genes & Dev. 17 (2003).
   
• Park, S., Meyer, M., Jones, A.D., Yennawar, H.P., Yennawar, N.H. and Nixon, B.T. 2002. Two-component signaling in the AAA+ ATPase DctD: binding Mg²⁺ and BeF₃^- selects between alternate dimeric states of the receiver domain. The FASEB Journal express article 10.1096/fj.02-0395fje. Published online October 4, 2002. Figure selected by editors for the journal cover, 12/2002. 
   
• Ronson*, C.W., Nixon*, B.T. and Ausubel, F.M. 1987. Conserved domains in bacterial regulatory proteins that respond to environmental stimuli.  Cell 49:579-581. 
   
• Nixon, B.T., Ronson, C.W. and Ausubel, F.M. 1986. Two-component regulatory systems responsive to environmental stimuli share strongly conserved domains with the nitrogen assimilation regulatory genes ntrB and ntrC.  Proc. Natl. Acad. Sci. USA 83:7850-7854.
   
• Green, H., Morikawa, M. and Nixon, T. 1985. A dual effector theory of growth-hormone action.  Differentiation 29:195-198.
   
• Wang, R.J. and Nixon, B.T. 1978. Identification of hydrogen peroxide as a photoproduct toxic to human cells in tissue-culture medium irradiated with daylight fluorescent light.  In Vitro 14:715-722.