University of Wisconsin–Madison
College of Agriculture and Life Sciences | School of Medicine and Public Health

Timothy Donohue


608-262-4663; 608-265-5224

Microbial approaches to produce alternative fuels and chemicals

5166 Wisconsin Energy Institute
Ph.D., Pennsylvania State University (1980), Postdoctoral Research: University of Illinois at Urbana-Champaign
Research Interests
Our laboratory analyzes pathways and networks that microbes use to grow, generate biomass, or produce alternative fuels from sunlight or other renewable sources of energy.
Research Fields
Computational, Systems & Synthetic Biology, Gene Expression, Genomics & Proteomics, Bacteria

Research Description:
Our laboratory analyzes pathways and networks that microbes use to grow, generate biomass, or produce alternative fuels from sunlight or other renewable sources of energy. To dissect this fundamentally important problem, we are studying metabolic and regulatory pathways of the photosynthetic bacterium Rhodobacter sphaeroides. By taking advantage of the R. sphaeroides genome sequence, microarrays, proteomics and molecular techniques we are defining how the energy in sunlight or renewable nutrients is partitioned into processes like cell growth or formation of biofuels. The metabolic pathways, global signal transduction networks, alternative sigma factors, and signals that control expression of well-studied components of the respiratory and photosynthetic electron transport chains are being defined or modelled using mutants, in vitro systems and computational techniques.

The long range goals are to identify metabolic and regulatory activities that are critical to bioenergy formation, to obtain a thorough understanding of energy-conserving pathways of agricultural, environmental and medical importance, and to use 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.

Representative Publications:
Search PubMed for more publications by Timothy Donohue

Burger BT, Imam S, Scarborough MJ, Noguera DR, Donohue TJ (2017) Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides. mSystems 2(3): (PMC5513736)

Gall DL, Ralph J, Donohue TJ, Noguera DR (2017) Biochemical transformation of lignin for deriving valued commodities from lignocellulose. Curr. Opin. Biotechnol. 45:120-126

Lemmer KC, Zhang W, Langer SJ, Dohnalkova AC, Hu D, Lemke RA, Piotrowski JS, Orr G, Noguera DR, Donohue TJ (2017) Mutations That Alter the Bacterial Cell Envelope Increase Lipid Production. MBio 8(3): (PMC5442454)

Warwick Anderson, Rolf Apweiler, Alex Bateman, Guntram A Bauer, Helen Berman, Judith A Blake, Niklas Blomberg, Stephen K Burley, Guy Cochrane, Valentina Di Francesco, Tim Donohue, Christine Durinx, Alfred Game, Eric Green, Takashi Gojobori, Peter Goodhand, Ada Hamosh, Henning Hermjakob, Minoru Kanehisa, Robert Kiley, Johanna McEntyre, Rowan McKibbin, Satoru Miyano, Barbara Pauly, Norbert Perrimon, Mark A Ragan, Geoffrey Richards, Yik-Ying Teo, Monte Westerfield, Eric Westhof, Paul F Lasko (2017) Towards Coordinated International Support Of Core Data Resources For The Life Sciences BioRxiv : 10.1101/110825

Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams PD (2016) Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6. J. Biol. Chem. 291(19):10228-38 (PMC4858972)

Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL (2016) Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges. MBio 7(3): (PMC4895116)

Spero MA, Brickner JR, Mollet JT, Pisithkul T, Amador-Noguez D, Donohue TJ (2016) Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes. J. Bacteriol. 198(8):1268-80 (PMC4859585)

Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP, Bingman C, Deng K, Holland KC, Noguera DR, Simmons BA, Sale KL, Ralph J, Donohue TJ, Adams PD, Phillips GN (2016) Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin. J. Biol. Chem. 291(10):5234-46 (PMC4777856)

Lin TY, Santos TM, Kontur WS, Donohue TJ, Weibel DB (2015) A Cardiolipin-Deficient Mutant of Rhodobacter sphaeroides Has an Altered Cell Shape and Is Impaired in Biofilm Formation. J. Bacteriol. 197(21):3446-55 (PMC4621061)

Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, Ruby EG, Taha SA, Alivisatos AP, Balskus EP, Biteen JS, Blaser MJ, Brodie EL, Browning ND, Cardon ZG, Cavanaugh CM, Chun M, Cliffel DE, Colwell RR, Dangl JL, Donohue TJ, Dorrestein PC, Fraser SE, Friesen ML, Gilbert JA, Gilbert SF, Green JL, Harwood CS, Henriksen JR, Highlander SK, Huang Y, Jansson JK, Johnson AT, Kasper DL, Knight R, Kujawinski EB, Martin CL, Maxon ME, McFall-Ngai MJ, Miller JF, Moran MA, Nelson KE, Orphan VJ, Ozcan A, Paša-Tolić L, Pollard KS, Regev A, Rubin EM, Ruby EG, Segre JA, Silver PA, Taha SA, Vivanco JM, Weinstock GM, Weiss PS, Yan

Austin S, Kontur WS, Ulbrich A, Oshlag JZ, Zhang W, Higbee A, Zhang Y, Coon JJ, Hodge DB, Donohue TJ, Noguera DR (2015) Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris. Environ. Sci. Technol. 49(14):8914-22 (PMC5031247)

Lemmer KC, Dohnalkova AC, Noguera DR, Donohue TJ (2015) Oxygen-dependent regulation of bacterial lipid production. J. Bacteriol. 197(9):1649-58 (PMC4403652)

Spero MA, Aylward FO, Currie CR, Donohue TJ (2015) Phylogenomic analysis and predicted physiological role of the proton-translocating NADH:quinone oxidoreductase (complex I) across bacteria. MBio 6(2): (PMC4453560)

Imam S, Fitzgerald CM, Cook EM, Donohue TJ, Noguera DR (2015) Quantifying the effects of light intensity on bioproduction and maintenance energy during photosynthetic growth of Rhodobacter sphaeroides. Photosyn. Res. 123(2):167-82

Imam S, Noguera DR, Donohue TJ (2015) CceR and AkgR regulate central carbon and energy metabolism in alphaproteobacteria. MBio 6(1): (PMC4323418)

Imam S, Noguera DR, Donohue TJ (2015) An integrated approach to reconstructing genome-scale transcriptional regulatory networks. PLoS Comput. Biol. 11(2):e1004103 (PMC4344238)

Imam S, Noguera DR, Donohue TJ (2014) Global analysis of photosynthesis transcriptional regulatory networks. PLoS Genet. 10(12):e1004837 (PMC4263372)

Peterson AC, Hauschild JP, Quarmby ST, Krumwiede D, Lange O, Lemke RA, Grosse-Coosmann F, Horning S, Donohue TJ, Westphall MS, Coon JJ, Griep-Raming J (2014) Development of a GC/Quadrupole-Orbitrap mass spectrometer, part I: design and characterization. Anal. Chem. 86(20):10036-43 (PMC4204906)

Gall DL, Ralph J, Donohue TJ, Noguera DR (2014) A group of sequence-related sphingomonad enzymes catalyzes cleavage of β-aryl ether linkages in lignin β-guaiacyl and β-syringyl ether dimers. Environ. Sci. Technol. 48(20):12454-63 (PMC4207535)

Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, Ma J, Markowitz V, Moore ER, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP (2014) Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol. 12(8):e1001920 (PMC4122341)

Lemke RA, Peterson AC, Ziegelhoffer EC, Westphall MS, Tjellström H, Coon JJ, Donohue TJ (2014) Synthesis and scavenging role of furan fatty acids. Proc. Natl. Acad. Sci. U.S.A. 111(33):E3450-7 (PMC4143029)

Lennon CW, Lemmer KC, Irons JL, Sellman MI, Donohue TJ, Gourse RL, Ross W (2014) A Rhodobacter sphaeroides protein mechanistically similar to Escherichia coli DksA regulates photosynthetic growth. MBio 5(3):e01105-14 (PMC4010833)

Gall DL, Kim H, Lu F, Donohue TJ, Noguera DR, Ralph J (2014) Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway. J. Biol. Chem. 289(12):8656-67 (PMC3961688)