Alexander J. Ninfa - Publications

Affiliations: 
University of Michigan, Ann Arbor, Ann Arbor, MI 
Area:
Biochemistry, Molecular Biology, Microbiology Biology

82 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2012 Jiang P, Ventura AC, Ninfa AJ. Characterization of the reconstituted UTase/UR-PII-NRII-NRI bicyclic signal transduction system that controls the transcription of nitrogen-regulated (Ntr) genes in Escherichia coli. Biochemistry. 51: 9045-57. PMID 23088566 DOI: 10.1021/bi300575j  1
2012 Jiang P, Zhang Y, Atkinson MR, Ninfa AJ. The robustness of the Escherichia coli signal-transducing UTase/UR-PII covalent modification cycle to variation in the PII concentration requires very strong inhibition of the UTase activity of UTase/UR by glutamine. Biochemistry. 51: 9032-44. PMID 23088522 DOI: 10.1021/bi3005736  1
2012 Perry N, Ninfa AJ. Synthetic networks: oscillators and toggle switches for Escherichia coli. Methods in Molecular Biology (Clifton, N.J.). 813: 287-300. PMID 22083749 DOI: 10.1007/978-1-61779-412-4_17  1
2012 Jiang P, Ventura AC, Sontag ED, Merajver SD, Ninfa AJ, Del Vecchio D. Theoretical biology: Response to comment on "'Load-induced modulation of signal transduction networks': Reconciling ultrasensitivity with bifunctionality?" Science Signaling. 5. DOI: 10.1126/scisignal.2002716  1
2011 Jiang P, Ninfa AJ. A source of ultrasensitivity in the glutamine response of the bicyclic cascade system controlling glutamine synthetase adenylylation state and activity in Escherichia coli. Biochemistry. 50: 10929-40. PMID 22085244 DOI: 10.1021/bi201410x  1
2011 Jiang P, Ventura AC, Sontag ED, Merajver SD, Ninfa AJ, Del Vecchio D. Load-induced modulation of signal transduction networks. Science Signaling. 4: ra67. PMID 21990429 DOI: 10.1126/scisignal.2002152  1
2011 Ninfa AJ. Unnecessary signaling: poorly named? Journal of Bacteriology. 193: 4571-3. PMID 21742895 DOI: 10.1128/JB.05682-11  1
2010 Ventura AC, Jiang P, Van Wassenhove L, Del Vecchio D, Merajver SD, Ninfa AJ. Signaling properties of a covalent modification cycle are altered by a downstream target. Proceedings of the National Academy of Sciences of the United States of America. 107: 10032-7. PMID 20479260 DOI: 10.1073/pnas.0913815107  1
2010 Ninfa AJ. Use of two-component signal transduction systems in the construction of synthetic genetic networks. Current Opinion in Microbiology. 13: 240-5. PMID 20149718 DOI: 10.1016/j.mib.2010.01.003  1
2010 Chang DE, Leung S, Atkinson MR, Reifler A, Forger D, Ninfa AJ. Building biological memory by linking positive feedback loops. Proceedings of the National Academy of Sciences of the United States of America. 107: 175-80. PMID 20018658 DOI: 10.1073/pnas.0908314107  1
2010 Ventura AC, Jiang P, Ninfa AJ, Van Wassenhove L, Merajver SD, Del Vecchio D. The impact of retroactivity on the input/output static characteristics of a signaling component Asme 2010 Dynamic Systems and Control Conference, Dscc2010. 1: 313-320. DOI: 10.1115/DSCC2010-4061  1
2009 Jiang P, Ninfa AJ. 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. Biochemistry. 48: 11522-31. PMID 19877670 DOI: 10.1021/bi9011594  1
2009 Jiang P, Ninfa AJ. 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. Biochemistry. 48: 11514-21. PMID 19877669 DOI: 10.1021/bi901158h  1
2009 Jiang P, Ninfa AJ. Reconstitution of Escherichia coli glutamine synthetase adenylyltransferase from N-terminal and C-terminal fragments of the enzyme. Biochemistry. 48: 415-23. PMID 19105634 DOI: 10.1021/bi801775b  1
2009 Ninfa AJ, Atkinson MR, Forger D, Atkins S, Arps D, Selinsky S, Court D, Perry N, Mayo AE. A synthetic biology approach to understanding biological oscillations: Developing a genetic oscillator for Escherichia coli Bacterial Circadian Programs. 301-329. DOI: 10.1007/978-3-540-88431-6_17  1
2008 Conrad E, Mayo AE, Ninfa AJ, Forger DB. Rate constants rather than biochemical mechanism determine behaviour of genetic clocks. Journal of the Royal Society, Interface / the Royal Society. 5: S9-15. PMID 18426770 DOI: 10.1098/rsif.2008.0046.focus  1
2008 Del Vecchio D, Ninfa AJ, Sontag ED. Modular cell biology: retroactivity and insulation. Molecular Systems Biology. 4: 161. PMID 18277378 DOI: 10.1038/msb4100204  1
2008 Del Vecchio D, Ninfa AJ, Sontag ED. A systems theory with retroactivity: Application to transcriptional modules Proceedings of the American Control Conference. 1368-1373. DOI: 10.1109/ACC.2008.4586683  1
2007 Jiang P, Ninfa AJ. Escherichia coli PII signal transduction protein controlling nitrogen assimilation acts as a sensor of adenylate energy charge in vitro. Biochemistry. 46: 12979-96. PMID 17939683 DOI: 10.1021/bi701062t  1
2007 Ninfa AJ, Selinsky S, Perry N, Atkins S, Xiu Song Q, Mayo A, Arps D, Woolf P, Atkinson MR. Using two-component systems and other bacterial regulatory factors for the fabrication of synthetic genetic devices. Methods in Enzymology. 422: 488-512. PMID 17628156 DOI: 10.1016/S0076-6879(06)22025-1  1
2007 Ninfa AJ. Regulation of carbon and nitrogen metabolism: adding regulation of ion channels and another second messenger to the mix. Proceedings of the National Academy of Sciences of the United States of America. 104: 4243-4. PMID 17360507 DOI: 10.1073/pnas.0700325104  1
2007 Jiang P, Mayo AE, Ninfa AJ. Escherichia coli glutamine synthetase adenylyltransferase (ATase, EC 2.7.7.49): kinetic characterization of regulation by PII, PII-UMP, glutamine, and alpha-ketoglutarate. Biochemistry. 46: 4133-46. PMID 17355125 DOI: 10.1021/bi0620510  1
2007 Jiang P, Pioszak AA, Ninfa AJ. Structure-function analysis of glutamine synthetase adenylyltransferase (ATase, EC 2.7.7.49) of Escherichia coli. Biochemistry. 46: 4117-32. PMID 17355124 DOI: 10.1021/bi0620508  1
2005 Ninfa AJ, Jiang P. PII signal transduction proteins: sensors of alpha-ketoglutarate that regulate nitrogen metabolism. Current Opinion in Microbiology. 8: 168-73. PMID 15802248 DOI: 10.1016/j.mib.2005.02.011  1
2004 Pioszak AA, Ninfa AJ. Mutations altering the N-terminal receiver domain of NRI (NtrC) That prevent dephosphorylation by the NRII-PII complex in Escherichia coli. Journal of Bacteriology. 186: 5730-40. PMID 15317778 DOI: 10.1128/JB.186.17.5730-5740.2004  1
2004 Song Y, Peisach D, Pioszak AA, Xu Z, Ninfa AJ. Crystal structure of the C-terminal domain of the two-component system transmitter protein nitrogen regulator II (NRII; NtrB), regulator of nitrogen assimilation in Escherichia coli. Biochemistry. 43: 6670-8. PMID 15157101 DOI: 10.1021/bi049474r  1
2004 Ninfa AJ, Mayo AE. Hysteresis vs. graded responses: the connections make all the difference. Science's Stke : Signal Transduction Knowledge Environment. 2004: pe20. PMID 15138328 DOI: 10.1126/ stke.2322004pe20  1
2003 Bondarenko V, Liu YV, Ninfa AJ, Studitsky VM. Assay of prokaryotic enhancer activity over a distance in vitro. Methods in Enzymology. 370: 324-37. PMID 14712657 DOI: 10.1016/S0076-6879(03)70029-9  1
2003 Pioszak AA, Ninfa AJ. Mechanism of the PII-activated phosphatase activity of Escherichia coli NRII (NtrB): how the different domains of NRII collaborate to act as a phosphatase. Biochemistry. 42: 8885-99. PMID 12873150 DOI: 10.1021/bi030065p  1
2003 Atkinson MR, Savageau MA, Myers JT, Ninfa AJ. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell. 113: 597-607. PMID 12787501 DOI: 10.1016/S0092-8674(03)00346-5  1
2003 Blauwkamp TA, Ninfa AJ. Antagonism of PII signalling by the AmtB protein of Escherichia coli. Molecular Microbiology. 48: 1017-28. PMID 12753193 DOI: 10.1046/j.1365-2958.2003.03479.x  1
2003 Pioszak AA, Ninfa AJ. Genetic and biochemical analysis of phosphatase activity of Escherichia coli NRII (NtrB) and its regulation by the PII signal transduction protein. Journal of Bacteriology. 185: 1299-315. PMID 12562801 DOI: 10.1128/JB.185.4.1299-1315.2003  1
2002 Atkinson MR, Pattaramanon N, Ninfa AJ. Governor of the glnAp2 promoter of Escherichia coli. Molecular Microbiology. 46: 1247-57. PMID 12453212 DOI: 10.1046/j.1365-2958.2002.03211.x  1
2002 Blauwkamp TA, Ninfa AJ. Physiological role of the GlnK signal transduction protein of Escherichia coli: survival of nitrogen starvation. Molecular Microbiology. 46: 203-14. PMID 12366843 DOI: 10.1046/j.1365-2958.2002.03153.x  1
2002 Atkinson MR, Blauwkamp TA, Ninfa AJ. Context-dependent functions of the PII and GlnK signal transduction proteins in Escherichia coli. Journal of Bacteriology. 184: 5364-75. PMID 12218023 DOI: 10.1128/JB.184.19.5364-5375.2002  1
2002 Atkinson MR, Blauwkamp TA, Bondarenko V, Studitsky V, Ninfa AJ. Activation of the glnA, glnK, and nac promoters as Escherichia coli undergoes the transition from nitrogen excess growth to nitrogen starvation. Journal of Bacteriology. 184: 5358-63. PMID 12218022 DOI: 10.1128/JB.184.19.5358-5363.2002  1
2002 Blauwkamp TA, Ninfa AJ. Nac-mediated repression of the serA promoter of Escherichia coli. Molecular Microbiology. 45: 351-63. PMID 12123449 DOI: 10.1046/j.1365-2958.2002.02994.x  1
2002 Bondarenko V, Liu Y, Ninfa A, Studitsky VM. Action of prokaryotic enhancer over a distance does not require continued presence of promoter-bound sigma54 subunit. Nucleic Acids Research. 30: 636-42. PMID 11809874 DOI: 10.1093/nar/30.3.636  1
2002 Jiang P, Pioszak A, Atkinson MR, Peliska JA, Ninfa AJ. New Insights into the Mechanism of the Kinase and Phosphatase Activities of Escherichia coli NRII (NtrB) and Their Regulation by the PII Protein Histidine Kinases in Signal Transduction. 143-164. DOI: 10.1016/B978-012372484-7/50008-4  1
2001 Ninfa AJ, Jiang P, Atkinson MR, Peliska JA. Integration of antagonistic signals in the regulation of nitrogen assimilation in Escherichia coli Current Topics in Cellular Regulation. 36. PMID 10842746 DOI: 10.1016/S0070-2137(01)80002-9  1
2000 Pioszak AA, Jiang P, Ninfa AJ. The Escherichia coli PII signal transduction protein regulates the activities of the two-component system transmitter protein NRII by direct interaction with the kinase domain of the transmitter module. Biochemistry. 39: 13450-61. PMID 11063581 DOI: 10.1021/bi000795m  1
2000 Jiang P, Atkinson MR, Srisawat C, Sun Q, Ninfa AJ. Functional dissection of the dimerization and enzymatic activities of Escherichia coli nitrogen regulator II and their regulation by the PII protein Biochemistry. 39: 13433-13449. PMID 11063580 DOI: 10.1021/bi000794u  1
2000 Jiang P, Peliska JA, Ninfa AJ. Asymmetry in the autophosphorylation of the two-component regulatory system transmitter protein nitrogen regulator II of Escherichia coli Biochemistry. 39: 5057-5065. PMID 10819971 DOI: 10.1021/bi992921w  1
1999 Atkinson MR, Ninfa AJ. Characterization of the GlnK protein of Escherichia coli Molecular Microbiology. 32: 301-313. PMID 10231487 DOI: 10.1046/j.1365-2958.1999.01349.x  1
1999 Jiang P, Ninfa AJ. Regulation of autophosphorylation of Escherichia coli nitrogen regulator II by the PII signal transduction protein Journal of Bacteriology. 181: 1906-1911. PMID 10074086  1
1998 Jiang P, Peliska JA, Ninfa AJ. The regulation of escherichia coli glutamine synthetase revisited: Role of 2-ketoglutarate in the regulation of glutamine synthetase adenylylation state Biochemistry. 37: 12802-12810. PMID 9737857 DOI: 10.1021/bi980666u  1
1998 Jiang P, Peliska JA, Ninfa AJ. Reconstitution of the signal-transduction bicyclic cascade responsible for the regulation of Ntr gene transcription in Escherichia coli Biochemistry. 37: 12795-12801. PMID 9737856 DOI: 10.1021/bi9802420  1
1998 Jiang P, Peliska JA, Ninfa AJ. Enzymological characterization of the signal-transducing uridylyltransferase/uridylyl-removing enzyme (EC 2.7.7.59) of Escherichia coli and its interaction with the PII protein Biochemistry. 37: 12782-12794. PMID 9737855 DOI: 10.1021/bi980667m  1
1998 Atkinson MR, Ninfa AJ. Role of the GlnK signal transduction protein in the regulation of nitrogen assimilation in Escherichia coli Molecular Microbiology. 29: 431-447. PMID 9720863 DOI: 10.1046/j.1365-2958.1998.00932.x  1
1998 Dworkin J, Ninfa AJ, Model P. A protein-induced DNA bend increases the specificity of a prokaryotic enhancer-binding protein Genes and Development. 12: 894-900. PMID 9512522  1
1997 Wu J, Ohta N, Benson AK, Ninfa AJ, Newton A. Purification, characterization, and reconstitution of DNA-dependent RNA polymerases from Caulobacter crescentus Journal of Biological Chemistry. 272: 21558-21564. PMID 9261176 DOI: 10.1074/jbc.272.34.21558  1
1997 Jiang P, Zucker P, Ninfa AJ. Probing interactions of the homotrimeric PII signal transduction protein with its receptors by use of PII heterotrimers formed in vitro from wild-type and mutant subunits. Journal of Bacteriology. 179: 4354-60. PMID 9209054  1
1997 Jiang P, Zucker P, Atkinson MR, Kamberov ES, Tirasophon W, Chandran P, Schefke BR, Ninfa AJ. Structure/function analysis of the PII signal transduction protein of Escherichia coli: genetic separation of interactions with protein receptors. Journal of Bacteriology. 179: 4342-53. PMID 9209053  1
1997 Ohta N, Ninfa AJ, Allaire A, Kulick L, Newton A. Identification, characterization, and chromosomal organization of cell division cycle genes in Caulobacter crescentus Journal of Bacteriology. 179: 2169-2180. PMID 9079901  1
1995 Kamberov ES, Atkinson MR, Ninfa AJ. The Escherichia coli PII signal transduction protein is activated upon binding 2-ketoglutarate and ATP Journal of Biological Chemistry. 270: 17797-17807. PMID 7629080 DOI: 10.1074/jbc.270.30.17797  1
1995 Feng J, Goss TJ, Bender RA, Ninfa AJ. Repression of the Klebsiella aerogenes nac promoter Journal of Bacteriology. 177: 5535-5538. PMID 7559339  1
1995 Feng J, Goss TJ, Bender RA, Ninfa AJ. Activation of transcription initiation from the nac promoter of Klebsiella aerogenes Journal of Bacteriology. 177: 5523-5534. PMID 7559338  1
1994 Benson AK, Ramakrishnan G, Ohta N, Feng J, Ninfa AJ, Newton A. The Caulobacter crescentus FlbD protein acts at ftr sequence elements both to activate and to repress transcription of cell cycle-regulated flagellar genes Proceedings of the National Academy of Sciences of the United States of America. 91: 4989-4993. PMID 8197169 DOI: 10.1073/pnas.91.11.4989  1
1994 de Mel VSJ, Kamberov ES, Martin PD, Zhang J, Ninfa AJ, Edwards BFP. Preliminary X-ray diffraction analysis of crystals of the PII protein from Escherichia coli Journal of Molecular Biology. 243: 796-798. PMID 7966297 DOI: 10.1016/0022-2836(94)90049-3  1
1994 Kamberov ES, Atkinson MR, Chandran P, Ninfa AJ. Effect of mutations in Escherichia coli glnL (ntrB), encoding nitrogen regulator II (NRII or NtrB), on the phosphatase activity involved in bacterial nitrogen regulation Journal of Biological Chemistry. 269: 28294-28299. PMID 7961767  1
1994 Atkinson MR, Kamberov ES, Weiss RL, Ninfa AJ. Reversible uridylylation of the Escherichia coli PII signal transduction protein regulates its ability to stimulate the dephosphorylation of the transcription factor nitrogen regulator I (NRI or NtrC). The Journal of Biological Chemistry. 269: 28288-93. PMID 7961766  1
1994 Kamberov ES, Atkinson MR, Feng J, Chandran P, Ninfa AJ. Sensory components controlling bacterial nitrogen assimilation Cellular and Molecular Biology Research. 40: 175-191. PMID 7874194  1
1993 McCleary WR, Stock JB, Ninfa AJ. Is acetyl phosphate a global signal in Escherichia coli? Journal of Bacteriology. 175: 2793-8. PMID 8491699  1
1993 Roychoudhury S, Zielinski NA, Ninfa AJ, Allen NE, Jungheim LN, Nicas TI, Chakrabarty AM. Inhibitors of two-component signal transduction systems: Inhibition of alginate gene activation in Pseudomonas aeruginosa Proceedings of the National Academy of Sciences of the United States of America. 90: 965-969. PMID 8381538 DOI: 10.1073/pnas.90.3.965  1
1993 Ninfa EG, Atkinson MR, Kamberov ES, Ninfa AJ. Mechanism of autophosphorylation of Escherichia coli nitrogen regulator II (NR(II) or NtrB): trans-Phosphorylation between subunits Journal of Bacteriology. 175: 7024-7032. PMID 8226644  1
1993 Atkinson MR, Ninfa AJ. Mutational analysis of the bacterial signal-transducing protein kinase/phosphatase nitrogen regulator II (NR(II) or NtrB) Journal of Bacteriology. 175: 7016-7023. PMID 7901195  1
1992 Feng J, Atkinson MR, McCleary W, Stock JB, Wanner BL, Ninfa AJ. Role of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli. Journal of Bacteriology. 174: 6061-70. PMID 1356964  1
1992 Atkinson MR, Ninfa AJ. Characterization of Escherichia coli glnL mutations affecting nitrogen regulation Journal of Bacteriology. 174: 4538-4548. PMID 1352516  1
1992 Ernsting BR, Atkinson MR, Ninfa AJ, Matthews RG. Characterization of the regulon controlled by the leucine-responsive regulatory protein in Escherichia coli. Journal of Bacteriology. 174: 1109-18. PMID 1346534  1
1991 Ninfa AJ, Bennett RL. Identification of the site of autophosphorylation of the bacterial protein kinase/phosphatase NRII. The Journal of Biological Chemistry. 266: 6888-93. PMID 2016302  1
1991 Ninfa AJ. Protein phosphorylation and the regulation of cellular processes by the homologous two-component regulatory systems of bacteria Genetic Engineering. 13: 39-72. PMID 1369339  1
1991 Stock JB, Ninfa AJ, Stock AM. Microbiology Scientist. 5.  1
1989 Weglenski P, Ninfa AJ, Ueno-Nishio S, Magasanik B. Mutations in the glnG gene of Escherichia coli that result in increased activity of nitrogen regulator I. Journal of Bacteriology. 171: 4479-85. PMID 2666403  1
1989 Igo MM, Ninfa AJ, Silhavy TJ. A bacterial environmental sensor that functions as a protein kinase and stimulates transcriptional activation Genes & Development. 3: 598-605. PMID 2663643  1
1989 Ninfa AJ, Mullin DA, Ramakrishnan G, Newton A. Escherichia coli σ54 RNA polymerase recognizes Caulobacter crescentus flbG and flaN flagellar gene promoters in vitro Journal of Bacteriology. 171: 383-391. PMID 2644197  1
1989 Igo MM, Ninfa AJ, Stock JB, Silhavy TJ. Phosphorylation and dephosphorylation of a bacterial transcriptional activator by a transmembrane receptor. Genes & Development. 3: 1725-34. PMID 2558046  1
1989 Stock JB, Ninfa AJ, Stock AM. Protein phosphorylation and regulation of adaptive responses in bacteria. Microbiological Reviews. 53: 450-90. PMID 2556636  1
1988 Stock AM, Wylie DC, Mottonen JM, Lupas AN, Ninfa EG, Ninfa AJ, Schutt CE, Stock JB. Phosphoproteins involved in bacterial signal transduction. Cold Spring Harbor Symposia On Quantitative Biology. 53: 49-57. PMID 3076087  1
1988 Ninfa AJ, Ninfa EG, Lupas AN, Stock A, Magasanik B, Stock J. Crosstalk between bacterial chemotaxis signal transduction proteins and regulators of transcription of the Ntr regulon: evidence that nitrogen assimilation and chemotaxis are controlled by a common phosphotransfer mechanism. Proceedings of the National Academy of Sciences of the United States of America. 85: 5492-6. PMID 3041412  1
1987 Ninfa AJ, Reitzer LJ, Magasanik B. Initiation of transcription at the bacterial glnAp2 promoter by purified E. coli components is facilitated by enhancers. Cell. 50: 1039-46. PMID 3304660 DOI: 10.1016/0092-8674(87)90170-X  1
1986 Ninfa AJ, Ueno-Nishio S, Hunt TP, Robustell B, Magasanik B. Purification of nitrogen regulator II, the product of the glnL (ntrB) gene of Escherichia coli. Journal of Bacteriology. 168: 1002-4. PMID 3536843  1
1986 Ninfa AJ, Magasanik B. Covalent modification of the glnG product, NRI, by the glnL product, NRII, regulates the transcription of the glnALG operon in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 83: 5909-13. PMID 2874557  1
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