Areas of Interest
Research in my laboratory is focused in two areas, each of which takes advantage of extensive collaborations with other University of Michigan investigators.
One project [Genetic Systems Bioengineering for Escherichia coli, GM063642, NIGMS] is to develop synthetic genetic circuitry that performs various computations, such as oscillators, toggle switches, and logic gates. One goal of these synthetic biology approaches is to provide a quantitative understanding of complex genetic regulatory processes through comparison of experimental data and mathematical models. Another goal is to develop the components and knowledge base to allow the engineering of synthetic biology devices with useful applications ranging from protein expression systems to computers that contain a living processor.
Another project is to study the design principles of signal transduction systems that employ reversible covalent modification. [Funded in part by Characterization of the Escherichia coli NRI/NRII Signal Transduction System, GM059637, NIGMS]. Current efforts are focused on understanding the two bicyclic signal transduction systems controlling glutamine synthetase and nitrogen-regulated gene expression. These bicyclic signaling systems have been studied for over 20 years in our lab, and we have reconstituted the entire system from purified components as well as assembled a substantial collection of mutant proteins with alterations in almost all of the known activities. We are using these reconstituted systems as model experimental systems to study signal transduction system design principles that are generally applicable to all covalent modification cycles. One current approach investigates sources of ultrasensitivity in the systems (zero order, inhibitor, multi-site). Another current approach examines how sequestration of an enzyme by competing receptors alters the sensory capabilities of a covalent modification cycle. Another approach investigates retroactivity, or the "backwards" flow of information in signaling systems.
Honors & Awards
1999 Henry Russel Award
A Source of Ultrasensitivity in the Glutamine Response of the Bicyclic Cascade System Controlling Glutamine Synthetase Adenylylation State and Activity in Escherichia coli. Jiang P, Ninfa AJ. Biochemistry. 2011 Dec 20;50(50):10929-40. Epub 2011 Nov 22. PMID: 22085244
Synthetic Networks: Oscillators and Toggle Switches for Escherichia coli. Perry N, Ninfa AJ. Methods Mol Biol. 2012;813:287-300. PMID: 22083749
Load-induced modulation of signal transduction networks. Jiang P, Ventura AC, Sontag ED, Merajver SD, Ninfa AJ, Del Vecchio D. Sci Signal. 2011 Oct 11;4(194):ra67. doi: 10.1126/scisignal.2002152. PMID: 21990429
Unnecessary signaling: poorly named? Ninfa AJ. J Bacteriol. 2011 Sep;193(18):4571-3. Epub 2011 Jul 8. PMID: 21742895
Signaling properties of a covalent modification cycle are altered by a downstream target. Ventura AC, Jiang P, Van Wassenhove L, Del Vecchio D, Merajver SD, Ninfa AJ. Proc Natl Acad Sci U S A. 2010 Jun 1;107(22):10032-7. Epub 2010 May 17.PMID: 20479260
Use of two-component signal transduction systems in the construction of synthetic genetic networks. Ninfa AJ. Curr Opin Microbiol. 2010 Apr;13(2):240-5. Epub 2010 Feb 9. Review. PMID: 20149718
Building biological memory by linking positive feedback loops. Chang DE, Leung S, Atkinson MR, Reifler A, Forger D, Ninfa AJ. Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):175-80. Epub 2009 Dec 14.PMID: 20018658
Sensation and signaling of alpha-ketoglutarate and adenylylate energy charge by the Escherichia coli PII signal transduction protein require cooperation of the three ligand-binding sites within the PII trimer. Jiang P, Ninfa AJ. Biochemistry. 2009 Dec 8;48(48):11522-31.PMID: 19877670
Alpha-ketoglutarate controls the ability of the Escherichia coli PII signal transduction protein to regulate the activities of NRII (NrB but does not control the binding of PII to NRII. Jiang P, Ninfa AJ. Biochemistry. 2009 Dec 8;48(48):11514-21.
Pioszak, A. A. and A. J. Ninfa. Genetic and Biochemical analysis of the PII-dependant phosphatase activity of Escherichia coli NRII. J. Bacteriol. 185:1299-315 (2003)
Blauwkamp, T. A., and A. J. Ninfa. Antagonism of PII signalling by the AmtB protein of Escherichia coli. Mol. Microbiol. 48:1017-1028 (2003)
Atkinson, M. R., M. A. Savageau, J. Meyers, and A. J. Ninfa. Development of a genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113:597-607 (2003).
Pioszak, A. A., and A. J. Ninfa. How the domains of NRII collaborate in the PII-activated phosphatase activity of Escherichia coli NRII (NtrB). Biochemistry 42:8885-8899. (2003).
Song, Y., D. Peisach, A. Pioszak, Z. Xu, and A. J. Ninfa. Crystal structure of the C-terminal domain of the two-component systems transmitter protein NRII (NtrB), regulator of nitrogen assimilation in Escherichia coli. Biochemistry 43: 6670-6678 (2004).
Pioszak, A. A., and A. J. Ninfa. Mutations altering the N-terminal receiver domain of NRI (NtrC) that prevent dephosphorylation by the NRII::PII complex in Escherichia coli. J. Bacteriol. 186: 5730-5740 (2004).
Ninfa, A. J. and A. Mayo. Hysteresis vs graded outputs: the connections make all the difference. Science STKE Perspective 2004:PE20
Ninfa, A. J., and P. Jiang. PII signal transduction proteins: sensors of a-ketoglutarate that regulate nitrogen metabolism. Curr Opinion Microbiol. 8: 168-173 (2005).
Ninfa, A. J., S. Selinsky, N. Perry, S. Atkins, Q. X. Song, A. Mayo, D. Arps, P. Woolf, and M. R. Atkinson. Using two component systems and other bacterial regulatory factors for the fabrication of synthetic genetic devices. Methods in Enzymology 422: 488-512 (2007).doi:10.1016/S0076-6879(06)22025-1
Jiang, P., A. A. Pioszak, and A. J. Ninfa. Structure/function analysis of glutamine synthetase adenylyltransferase (ATase, E.C. 188.8.131.52) of Escherichia coli. Biochemistry 46: 4117-4132 (2007). http://pubs.acs.org/doi/abs/10.1021/bi0620508
Jiang, P., A. E. Mayo, and A. J. Ninfa. Escherichia coli glutamine synthetase adenylyltransferase (ATase, E.C. 184.108.40.206): Kinetic characterization of regulation by PII, PII-UMP, glutamine, and Î±-ketoglutarate. Biochemistry 46: 4133-4146 (2007). http://pubs.acs.org/doi/abs/10.1021/bi0620510
Jiang, P., and A. J. Ninfa. Escherichia coli PII signal transduction protein controlling nitrogen assimilation acts as a sensor of adenylate energy charge in vitro. Biochemistry46: 12979-12996 (2007).http://pubs.acs.org/doi/abs/10.1021/bi701062t
Del Vecchio D, A. J. Ninfa, and E. D. Sontag. Modular cell biology: retroactivity and insulation. Mol Syst Biol. 4:161 (2008).http://www.nature.com/msb/journal/v4/n1/full/msb4100204.html
Conrad E, A. E. Mayo, A. J. Ninfa, and D. B. Forger. Rate constants rather than biochemical mechanism determine behaviour of genetic clocks. J R Soc Interface.5 Suppl 1:S9-15 (2008).http://journals.royalsociety.org/content/86rv1u8807121pt6/
Jiang P, and A. J. Ninfa. Reconstitution of Escherichia coli Glutamine Synthetase Adenylyltransferase from N-Terminal and C-Terminal Fragments of the Enzyme Biochemistry Dec 23. [Epub ahead of print] (2008).http://pubs.acs.org/doi/abs/10.1021/bi801775b
Ninfa, A. , and Ballou, D. P. Fundamental Laboratory Approaches for Biochemistry and Biotechnology