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

Timothy Donohue

Professor

tdonohue@bact.wisc.edu

608-262-4663; 608-265-5224

Bacteriology
Unlocking the secrets of microbes to benefit society

Address
Wisconsin Energy Institute 1552 University Avenue Madison WI 53726
Education
Ph.D., Pennsylvania State University (1980), Postdoctoral Research: University of Illinois at Urbana-Champaign
Department
Bacteriology
Research Interests
Unlocking the secrets of microbes to benefit society
Research Fields
Metabolism, Genomics, Genetics, Systems & Synthetic Biology

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

Gall DL, Ralph J, Donohue TJ, Noguera DR. Biochemical transformation of lignin for deriving valued commodities from lignocellulose. Curr Opin Biotechnol. 2017 Jun;45:120-126. doi: 10.1016/j.copbio.2017.02.015. Epub 2017 Mar 24. Review. PubMed PMID: 28346893.

Lemmer KC, Zhang W, Langer SJ, Dohnalkova AC, Hu D, Lemke RA, Piotrowski JS, Orr G, Noguera DR, Donohue TJ. Mutations That Alter the Bacterial Cell Envelope Increase Lipid Production. MBio. 2017 May 23;8(3). pii: e00513-17. doi: 10.1128/mBio.00513-17. PubMed PMID: 28536286; PubMed Central PMCID: PMC5442454.

Burger BT, Imam S, Scarborough MJ, Noguera DR, Donohue TJ. Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides. mSystems. 2017 Jun 6;2(3). pii: e00015-17. doi: 10.1128/mSystems.00015-17. eCollection 2017 May-Jun. PubMed PMID: 28744485; PubMed Central PMCID: PMC5513736.

Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL. Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges. MBio. 2016 May 13;7(3). pii: e00714-16. doi: 10.1128/mBio.00714-16. PubMed PMID: 27178263; PubMed Central PMCID: PMC4895116.

Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams PD. 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. 2016 May 6;291(19):10228-38. doi: 10.1074/jbc.M115.700427. Epub 2016 Mar 3. PubMed PMID: 26940872; PubMed Central PMCID: PMC4858972.

Spero MA, Brickner JR, Mollet JT, Pisithkul T, Amador-Noguez D, Donohue TJ. Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes. J Bacteriol. 2016 Mar 31;198(8):1268-80. doi: 10.1128/JB.01025-15. Print 2016 Apr. PubMed PMID: 26833419; PubMed Central PMCID: 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 Jr. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin. J Biol Chem. 2016 Mar 4;291(10):5234-46. doi: 10.1074/jbc.M115.694307. Epub 2015 Dec 4. PubMed PMID: 26637355; PubMed Central PMCID: PMC4777856.

Lin TY, Santos TM, Kontur WS, Donohue TJ, Weibel DB. A Cardiolipin-Deficient Mutant of Rhodobacter sphaeroides Has an Altered Cell Shape and Is Impaired in Biofilm Formation. J Bacteriol. 2015 Nov;197(21):3446-55. doi: 10.1128/JB.00420-15. Epub 2015 Aug 17. PubMed PMID: 26283770; PubMed Central PMCID: 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; Unified Microbiome Initiative Consortium.. MICROBIOME. A unified initiative to harness Earth’s microbiomes. Science. 2015 Oct 30;350(6260):507-8. doi: 10.1126/science.aac8480. Epub 2015 Oct 28. PubMed PMID: 26511287.

Austin S, Kontur WS, Ulbrich A, Oshlag JZ, Zhang W, Higbee A, Zhang Y, Coon JJ, Hodge DB, Donohue TJ, Noguera DR. Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris. Environ Sci Technol. 2015 Jul 21;49(14):8914-22. doi: 10.1021/acs.est.5b02062. Epub 2015 Jul 9. PubMed PMID: 26121369; PubMed Central PMCID: PMC5031247.

Lemmer KC, Dohnalkova AC, Noguera DR, Donohue TJ. Oxygen-dependent regulation of bacterial lipid production. J Bacteriol. 2015 May;197(9):1649-58. doi: 10.1128/JB.02510-14. Epub 2015 Mar 2. PubMed PMID: 25733615; PubMed Central PMCID: PMC4403652.

Spero MA, Aylward FO, Currie CR, Donohue TJ. Phylogenomic analysis and predicted physiological role of the proton-translocating NADH:quinone oxidoreductase (complex I) across bacteria. MBio. 2015 Apr 14;6(2). pii: e00389-15. doi: 10.1128/mBio.00389-15. PubMed PMID: 25873378; PubMed Central PMCID: PMC4453560.

Imam S, Noguera DR, Donohue TJ. CceR and AkgR regulate central carbon and energy metabolism in alphaproteobacteria. MBio. 2015 Feb 3;6(1). pii: e02461-14. doi: 10.1128/mBio.02461-14. PubMed PMID: 25650399; PubMed Central PMCID: PMC4323418.

Imam S, Noguera DR, Donohue TJ. An integrated approach to reconstructing genome-scale transcriptional regulatory networks. PLoS Comput Biol. 2015 Feb 27;11(2):e1004103. doi: 10.1371/journal.pcbi.1004103. eCollection 2015 Feb. PubMed PMID: 25723545; PubMed Central PMCID: PMC4344238.

Imam S, Fitzgerald CM, Cook EM, Donohue TJ, Noguera DR. Quantifying the effects of light intensity on bioproduction and maintenance energy during photosynthetic growth of Rhodobacter sphaeroides. Photosynth Res. 2015 Feb;123(2):167-82. doi: 10.1007/s11120-014-0061-1. Epub 2014 Nov 27. PubMed PMID: 25428581.

Imam S, Noguera DR, Donohue TJ. Global analysis of photosynthesis transcriptional regulatory networks. PLoS Genet. 2014 Dec 11;10(12):e1004837. doi: 10.1371/journal.pgen.1004837. eCollection 2014 Dec. PubMed PMID: 25503406; PubMed Central PMCID: 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. Development of a GC/Quadrupole-Orbitrap mass spectrometer, part I: design and characterization. Anal Chem. 2014 Oct 21;86(20):10036-43. doi: 10.1021/ac5014767. Epub 2014 Sep 10. PubMed PMID: 25208235; PubMed Central PMCID: PMC4204906.

Gall DL, Ralph J, Donohue TJ, Noguera DR. 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. 2014 Oct 21;48(20):12454-63. doi: 10.1021/es503886d. Epub 2014 Oct 1. PubMed PMID: 25232892; PubMed Central PMCID: PMC4207535.

Lemke RA, Peterson AC, Ziegelhoffer EC, Westphall MS, Tjellström H, Coon JJ, Donohue TJ. Synthesis and scavenging role of furan fatty acids. Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3450-7. doi: 10.1073/pnas.1405520111. Epub 2014 Aug 4. PubMed PMID: 25092314; PubMed Central PMCID: PMC4143029.