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Timothy J. Donohue

Email: tdonohue@bact.wisc.edu

Professor Director & Principal Investigator NIGMS Biotechnology pre-doctoral training program Degrees: B.S., 1975, Polytechnic Institute of Brooklyn M. S., 1977, Pennsylvania State University Ph. D, 1980, Pennsylvania State University Postdoctorial Research 1980-1986, Microbiology Deprtment, University of Illinois at Urbana-Champaign

Affiliations

Trainer, NIH Biotechnology, Genetics, Genomics, Medical Scientist, & Molecular BiosciencesPredoctoral Training Programs.
Community of Science profile: http://myprofile.cos.com/donohuet24

Research Focus

Our laboratory takes an integrative approach to analyze the pathways and regulatory networks that allow cells to generate energy. To dissect this fundamentally important problem, we are studying key metabolic and regulatory networks of the photosynthetic bacterium Rhodobacter sphaeroides.

In experiments made possible by completion of the R. sphaeroides genome sequence, whole genome microarrays and proteomics are being used to determine how environmental signals like oxygen, light, or nutrients dictate the pathways used to generate energy. High-resolution microscopy is being used to visualize the assembly of key energy-generating membrane enzymes. These experiments will define the metabolic pathways, genetic networks, and macromolecular machines that are critical to generating energy under different conditions.

The signals and alternative sigma factors controlling the expression of well-studied electron carriers (c-type cytochromes) that participate in respiration and photosynthesis are also being studied. To accomplish this, we are using mutants and in vitro systems to decipher what controls the function of these alternative sigma factors and global transcriptional regulatory circuits. Such interdisciplinary approaches are critical to understanding how the activity of these regulators is controlled at the molecular level.

Another goal is to determine how R. sphaeroides metabolizes formaldehyde. Specifically, we are identifying proteins that participate in formaldehyde oxidation, determining how cells sense formaldehyde, and dissecting the pathways that control expression of genes required for removal of this toxic compound.

The long range goals of these projects are to identify important metabolic and regulatory activities, to obtain a thorough understanding of energy-generating pathways of agricultural, environmental and medical importance, and to generate computational models to help design microbial machines with increased capacity to utilize solar energy, generate renewable sources of energy, remove toxic compounds, or synthesize biodegradable polymers.

Go to Dr. Donohue's Laboratory Page

Representative Publications:

1. MacGregor, B. J., R. K. Karls, and T. J. Donohue. 1998. Transcription of the Rhodobacter sphaeroides cycA P1 promoter by alternate RNA polymerase holoenzymes. J. Bacteriol. 180:1-9.

2. Karls, R. K., J. Brooks, P. Rossmeissl, J. Luedke, and T. J. Donohue. 1998. Metabolic roles of a Rhodobacter sphaeroides member of the sigma 32 family. J. Bacteriol. 180:10-19.

3. Barber, R. D. and T. J. Donohue. 1998. Function of a glutathione-dependent formaldehyde dehydrogenase in Rhodobacter sphaeroides formaldehyde oxidation and assimilation. Biochemistry 37:530-537.

4. Barber, R. D. and T. J. Donohue. 1998 Pathways for transcriptional activation of a glutathione-dependent formaldehyde dehydrogenase gene. J. Mol. Biol. 280:775-784.

5. Karls, R. K., Wolf, J. and T. J. Donohue. 1999. Activation of the cycA P2 promoter for the Rhodobacter sphaeroides cytochrome c₂ gene by the photosynthesis response regulator. Mol. Microbiol. 34:822-835.

6. Newman, J., Falkowski, M., Schilke, B. A., Anthony, L. and T. J. Donohue. 1999. The Rhodobacter sphaeroides ECF sigma factor, sigma E, and the target promoters cycA P3, and rpoE P1. J. Mol. Biol. 294:307-320.

7. Rios-Velazquez, C., Cox, R. and T. J. Donohue. 2001. Characterization of Rhodobacter sphaeroides cytochrome c₂ proteins with altered heme attachment sites. Arch. Biochem. Biophys. 389:234-244.

8. Cox, R. Patterson, C., and T. J. Donohue. 2001. Roles for the Rhodobacter sphaeroides CcmA and CcmG proteins. J. Bacteriol. 183:4643-4647.

9. Newman, J., Anthony, J. and T. J. Donohue. 2001 The importance of zinc coordination for ChrR function as an anti-sigma factor. J. Mol. Biol. 313:485-499.

10. MacKenzie, C., Choudhary, M., Larimer, F. W. Predki, P. F., Stilwagen, S., Armitage, J. P., Barber, R. D., Donohue, T. J., Hosler, J. P., Newman, J., Shapleigh, J. P., Sockett, R. E., Zeilstra-Ryalls, J. and S. Kaplan. 2001 The home stretch, a preliminary analysis of the nearly completed genome of Rhodobacter sphaeroides 2.4.1. Photosynthesis Research 70:19-41.

11. Comolli, J., Carl, A., Hall, C. and T. J. Donohue. 2002 Transcriptional activation of the Rhodobacter sphaeroides cycA P2 promoter by the response regulator PrrA. J. Bacteriol. 184:390-399.

12. Hickman, J., Barber, R. D., Skaar, E. and T. J. Donohue. 2002 A link between the membrane-bound pyridine nucleotide transhyrdogenase and glutathione-dependent processes. J. Bacteriol. 184:400-409.

13. Comolli, J. C., and T. J. Donohue. 2002 Pseudomonas aeruginosa RoxR, a response regulator related to Rhodobacter sphaeroides PrrA, activates expression of the cyanide-insensitive terminal oxidase, CioAB. Mol. Microbiol. 45:755-768.

14. Rios-Velazquez, C., Coller, R. and T. J. Donohue. 2003. Features of Rhodobacter sphaeroides CcmFH. J. Bacteriol. 185:422-431.

15. Zhou, S., Kvikstad, E. Kile, A., Severin, J., Forrest, D., Runnheim, R., Churas, C., Anantharaman, T. S., Hickman, J. W., Mackenzie, C., Donohue, T. J., Kaplan, S., and Schwartz, D. C. 2003. Whole-Genome Shotgun Optical Mapping of Rhodobacter sphaeroides strain 2.4.1 Genome Research 214:2142-2151.

16. Anthony, J., Green, H., and T. J. Donohue. 2003. Rhodobacter sphaeroides RNA polymerase and its sigma factors. In RNA Polymerase and Associated Factors, (S. Adhya and S. Garges eds). Meth. Enzymol. 370:54-65.

17. Comolli, J. C., and T. J. Donohue. 2004. Differences in two Pseudomonas aeruginosa cbb₃ oxidases. Mol. Microbiol. 51:1193-1203.

18. Tavano, C. L., Comolli, J. C. and T. J. Donohue. 2004 The role of dor gene products in controlling the P2 promoter of the Rhodobacter sphaeroides cytochrome c₂ gene, cycA. Microbiology (In press).

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