Biochemistry and Molecular Biology
Penn State Science
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B. Tracy Nixon

B. Tracy Nixon

Main Content

  • Professor of Biochemistry and Molecular Biology
332 South Frear Laboratory
University Park, PA 16802
Phone: (814) 863-4904

Research Interests

1. Functional bases of signal transduction and gene regulation by AAA+ATPases in bacteria.

2. Degradation of lignocellulose by cellulases.

3. Synthesis of cellulose.

Graduate Programs


Graduate Course: Computers in Molecular Biology

Molecular biologists and biochemists need to process data and create figures to help others quickly grasp the results. Increased processing capacity in computers has dramatically affected how one accomplishes these tasks. This course is designed to help graduate students in the BMMB and related programs to understand and apply modern quantitative analysis of data.

Please visit the course website to learn more:

Computers for Biochemists and Molecular Biologists

Research Summary

As postdoc I discovered the bacterial two-component signal transduction paradigm. This method of information processing is the predominant form used by bacteria, and it is also present in fungi and plants. Learning how these signals are processed will help us defend against bacterial pathogens and manipulate beneficial processes such as biological nitrogen fixation, chemotaxis, cell cycle regulation, fruiting body formation, sporulation, osmoregulation and fruit ripening. Using genetics, molecular biology, biochemistry and structural biology (crystallography, small-angle X-ray scattering, electron microscopy) my lab has discovered unexpected diversity in the mechanism of how a phosphorylated second component can regulate assembly of a AAA+ ATPase motor. We are now developing a model for how ATP binding and hydrolysis are harnessed by a AAA+ ATPase motor to perform mechanical work on bacterial RNA polymerase. Our collaborative studies (David Wemmer and Eva Nogales, UC Berkeley; S. De Carlo, CUNY, Haw Yang, Princeton) have resulted in the journal covers shown below, and helped establish the BioCAT (Director – Tom Irving; Advanced Photon Source and Illinois Institute of Technology) as a world premier site for small-angle X-ray scattering. Current cryoEM studies on this system include a collaboration with Seth Darst (Rockefeller University), and combination of bioinformatics and molecular dynamic simulations with Andrew Neuwald. In the latter study we apply Dr. Neuwald’s ‘Deep Analysis of Residue Correlations (DARC)’ with microsec molecular dynamic simulations (MDS) to identify correlated motions and allosteric pathways between functionally critical residues in this class of biological motors.

In addition to that major theme of research, I participate in two collaborations in the field of energy biosciences. The plant cell wall is composed of a primary cell wall and when the cell ages, a secondary wall is formed of which a large percentage is made of cellulose. If made accessible, such cellulose is a potentially rich source of reduced carbon for microbial fermentations yielding ethanol as a future combustible energy source. In 2007 the United States embarked on a federal mandate to produce about 20 billion gallons of cellulosic ethanol by the year 2017. Despite such intense interest, our ability to access this carbon is economically hampered because the cellulose is sequestered from water in crystalline fibers and amongst lignin and other polysaccharide polymers.  These barriers make it difficult to depolymerize cellulose into glucose. Efforts to bring the process to economic feasibility thus focus on enhancing access by altering the pretreatment processes and properties of depolymerizing cellulases.


The first of these two bioenergy projects arose from the fact that only enzymes produced by fungi and some bacteria are capable of breaking down the lignin barrier to gain full access to the energy-rich cellulose component of lignocellulose. Harnessing that efficiency has thus far eluded us, hindering our efforts to economically produce liquid fuels from plant biomass. This obstacle arises from our lack of understanding the cellular and molecular mechanisms that underlie the fungus-enzyme-lignocellulose gestalt. Working with Haw Yang (Princeton University), Chemistry Department; and Ming Tien, Biochemistry and Molecular Biology, Penn State), we administered DOE-funded research program to address this challenging problem.

The second and current bioenergy projects emerges from the observation that despite the overwhelming ecology and economical significance of cellulose synthesis, relatively little is known about the biochemistry of this process. Much knowledge would be gained if a 3-dimensional structure were available to guide research of cellulose synthesis. I collaborate closely with Manish Kumar and with several other members of the DOE's Center for Lignocellulose Structure and Formation to study structure / function questions about the enzymes that make cellulose. In bacteria these function as a single cellulose synthase that makes non-crystalline cellulose, or as an ordered array of synthases that make crystalline cellulose. In plants, they function as a complex of many CesA proteins called the Cellulose Synthase Complex. We have applied modern particle classification techniques to freeze-fracture images of the complex to establish that it likely contains 16 CesA molecules per complex, arranged in a set of six trimers. We seek high resolution structure via cryoTEM of a trimer of the catalytic domain of one such CesA. Recently we have worked with the Zimmer lab to establish that single isoforms of CesA can be overexpressed in Pichia, partially purified, reconstituted into proteoliposomes, and synthesize not only beta-glucan cellulose chains, but organized microfibrils of cellulose.

Working with Zimmer and Kumar, we are now adapting the systems to provide material for high resolution cryoTEM studies of CesAs and of the in vitro produced cellulose microfibrils. In a related project, I work with Hui Yang of the CLSF and Natarajan Kannan (University of Georgia) to apply Deep Analysis of Residue Correlations (DARC) and Molecular Dynamic Simulations to identify correlated motions and allosteric pathways between functionally critical residues in cellulose synthases.



Molecular genetics, general biochemistry, structural biology (gene cloning, expression, protein purification, enzyme assay, analytical ultracentrifugation, solution X-ray and neutron scattering, crystallography, and 3D reconstruction from single particles in electron micrographs).


Click to view MyBibliography




Selected Publications

  • Synthesis and Self-Assembly of Cellulose Microfibrils from Reconstituted Cellulose Synthase.
    Cho SH, Purushotham P, Fang C, Maranas C, Díaz-Moreno SM, Bulone V, Zimmer J, Kumar M, Nixon BT. Plant physiology. 2017; 175(1):146-156. PubMed PMID: 28768815
  • Abdallah, Q.A.,, Nixon, B.T. and Fortwendel, J.R. 2016. The enzymatic conversion of major algal and cyanobacterial carbohydrates to bioethanol. Front. Energy Res. 4:36. doi: 10.3389/fenrg.2016.00036
  • Purushotham P, Cho SH, Díaz-Moreno SM, Kumar M, Nixon BT, 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. and Haigler, C.H. 2016. Comparative structural and computational analysis supports eighteen cellulose synthases in the plant cellulose synthase complex. Sci. Rep. 6:28696. doi: 10.1038/srep28696.
  • Du, J., Vepachedu, V., Cho, S.H., Kumar, M. and Nixon, B.T. 2016. Structure of the cellulose synthase complex of Gluconacetobacter hansenii at 23.4 A resolution. PLoS One 11:e0155886. doi: 10.1371/journal.pone.0155886.eCollection2016.
  • Vandavasi, V.G., Pulman, D.K., Zhang, Q., Petridis, L., Heller, W.T., Nixon, B.T., Haigler, C.H., Kalluri, U., Coates, L., Langan, P., Smith, J.C., Meiler, J., O'Neill, H. 2016. A structural studyu of CESA1 catalytic domain of Arabidopsis cellulose synthase complex: evidence for CESA trimers. Plant Physiol. 170:123-135. doi: 10.1104/pp.15.01356.Epub2015Nov10.
  • Cho, S.H., Du, J., Sines, I., Poosarla, V.G., Vepechadu, V., Kafle, K., Park, Y.B., Kim, S.H., Kumar, M. and Nixon, B.T. 2015. In vitro synthesis of cellulose microfibrils by a membrane protein from protoplases of the non-vascular plant Physcomitrella patens. Biochem. J. 470:195-205. doi: 10.1042/BJ20141391.Epub2015.Jun30.
  • Erbakan, M., Curtis, B.S., Nixon, B.T., Kumar, M. and Curtis, W.R. 2015. Advancing Rhodobacter sphaeroides as a platform for expression of functional membrane proteins. Protein Expr. Purif. 115:109-117. doi: 10.106/j.pep.2015.05.012.Epub2015May22.

  • 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., Yennawar, N., Allaire, M., and Nixon, B.T. 2013. Crystallization and preliminary X-ray analysis of the ATPase domain of the sigma54-dependent transcription activator NtrC1 from Aquifex aeolicus bound to ATP analog ADP-BeFxActa Crystallogr Sect F Struct Biol Cryst Commun69, 1384-1388.
  • Sysoeva, T.A., Chowdhury, S., Guo, L., and Nixon, B.T. 2013. Nucleotide-induced asymmetry within ATPase activator ring drives s54-RNAP interaction and ATP hydrolysis. Genes & Dev 15, 2500-2511.

  • Chakraborty, A., Wang, D., Ebright, Y.W., Korlann, Y., Kortkhonjia, E., Kim, T., Chowdhury, S., Wigneshweraraj, S., Irschik, H., Jansen, R., Nixon, B.T., Knight, J., Weiss, S., Ebright, R.H. Science. 2012 Aug 3;337(6094:591-5 (Click here to access the article on Pub Med - opens in new window.)
  • Li, P., Banjade, S., Cheng, H.-C., Kim, S., Chen, B., 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 multivalent signalling proteins. Nature 483, 336-340.
  • Baoyu Chen, Tatyana A. Sysoeva, Saikat Chowdhury, Liang Guo, Sacha De Carlo, Jeffrey A. Hanson, Haw Yang, and B. Tracy Nixon. 2010. Engagement of Arginine Finger to ATP Triggers Large Conformational Changes in NtrC1 AAA+ ATPase For Remodeling Bacterial RNA Polymerase. Structure. 2010 Nov 10;18(11):1420-30.
  • Burrows, P.C., Joly, N., Cannon, W.V., Camara, B.P., Rappas, M., Zhang, X.,  Dawes, K., Nixon, B.T., Wigneshweraraj, S.R., and Buck, M. 2009. Coupling sigma factor conformation to RNA polymerase reorganisation for DNA melting. J. Mol. Biol. 387, 306-319.
  • Burrows, P.C., Schumacher, J., Amartey, S., Ghos, T., Burgis, T.A., Zhang, X., Nixon, B.T. and Buck, M. (2009) Functional roles of the pre-sensor I insertion sequence in an AAA+ bacterial enhancer binding protein. Mol. Micro. doi:10.1111/j.1365-2958.2009.06744.x.
  • Burrows, P. C., Joly, N., Nixon, B.T. and Buck, M. (2009) Comparative Analysis of Activator-E?54 Complexes formed with Nucleotide-Metal Fluoride Analogues. Nuc. Acids Res. 37: 5138-5150.
  • Chen, B., Sysoeva, T.A., Chowdhury, S., Guo, L., and Nixon, B.T. 2009. ADPase activity of recombinantly expressed thermotolerant ATPases may be caused by co-purification of adenylate kinase of Escherichia coli. FEBS J 276: 807-815.
  • Chen, B., Sysoeva, T.A., Chowdhury, S., and Nixon, B.T. 2008. Regulation and action of the bacterial enhancer binding AAA+ ATPases. Biochem. Soc. Transact. 36, 89-93.
  • 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 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 the 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).