Timothy Donohue

Research Description:
Our laboratory analyzes networks that microbes use to grow or produce bioproducts from renewable resources. To dissect this fundamentally important problem, we dissect genomic, metabolic and regulatory pathways of bacteria that convert renewable resources, such as non-edible lignocellulosic plant biomass, into products that are currently derived from fossil fuels. By mining genome sequence databases, coupling genomic (microarrays & RNAseq, proteomics, metabolomics), computational, molecular and synthetic biology techniques, we define how carbon and energy in nutrients is partitioned into cell growth or formation of bioproducts. The metabolic pathways, signal transduction networks, transcription factors, and signals that control these processes are identified, modelled or re-engineered using mutants, in vitro systems and in silico models. Our long range goals are to understand energy-conserving pathways of societal importance, and to combine computational and experimental systems to design microbial machines with increased capacity to utilize renewable resources, or enable a green production of fuels and chemicals.

Representative Publications:
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Linz AM, Ma Y, Scholz S, Noguera DR, Donohue TJ (2022) iNovo479: Metabolic Modeling Provides a Roadmap to Optimize Bioproduct Yield from Deconstructed Lignin Aromatics by Novosphingobium aromaticivorans . Metabolites 12((4)): PMC9028409 · Pubmed · DOI

Beach NK, Myers KS, Owen BR, Seib M, Donohue TJ, Noguera DR (2022) Correction for Beach et al., “Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome”. mSystems :e0021322 · Pubmed · DOI

Myers KS, Behari Lal P, Noguera DR, Donohue TJ (2021) Using Genome Scale Mutant Libraries to Identify Essential Genes. Methods in molecular biology (Clifton, N.J.) 2377:215-236 · Pubmed · DOI

Beach NK, Myers KS, Owen BR, Seib M, Donohue TJ, Noguera DR (2021) Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome. mSystems 6((5)):e0090621 PMC8510549 · Pubmed · DOI

Linz AM, Ma Y, Perez JM, Myers KS, Kontur WS, Noguera DR, Donohue TJ (2021) Aromatic Dimer Dehydrogenases from Novosphingobium aromaticivorans Reduce Monoaromatic Diketones. Applied and environmental microbiology 87((24)):e0174221 PMC8612281 · Pubmed · DOI

Ingle AT, Fortney NW, Walters KA, Donohue TJ, Noguera DR (2021) Mixed Acid Fermentation of Carbohydrate-Rich Dairy Manure Hydrolysate. Frontiers in bioengineering and biotechnology 9:724304 PMC8370043 · Pubmed · DOI

Fortney NW, Hanson NJ, Rosa PRF, Donohue TJ, Noguera DR (2021) Diverse Profile of Fermentation Byproducts From Thin Stillage. Frontiers in bioengineering and biotechnology 9:695306 PMC8320890 · Pubmed · DOI

Myers KS, Noguera DR, Donohue TJ (2021) Promoter Architecture Differences among Alphaproteobacteria and Other Bacterial Taxa. mSystems 6((4)):e0052621 PMC8407463 · Pubmed · DOI

Myers KS, Place M, Kominek J, Noguera DR, Donohue TJ (2021) Delila-PY, a Pipeline for Utilizing the Delila Suite of Software to Identify Potential DNA Binding Motifs. Microbiology resource announcements 10((15)): PMC8050967 · Pubmed · DOI

Ma Y, Donohue TJ, Noguera DR (2021) Kinetic modeling of anaerobic degradation of plant-derived aromatic mixtures by Rhodopseudomonas palustris. Biodegradation 32((2)):179-192 PMC7997838 · Pubmed · DOI

Perez JM, Kontur WS, Gehl C, Gille DM, Ma Y, Niles AV, Umana G, Donohue TJ, Noguera DR (2021) Redundancy in aromatic O-demethylation and ring opening reactions in Novosphingobium aromaticivorans and their impact in the metabolism of plant derived phenolics. Applied and environmental microbiology : PMC8091115 · Pubmed · DOI

Todor H, Osadnik H, Campbell EA, Myers KS, Li H, Donohue TJ, Gross CA (2020) Rewiring the specificity of extracytoplasmic function sigma factors. Proceedings of the National Academy of Sciences of the United States of America 117((52)):33496-33506 PMC7776599 · Pubmed · DOI

Henry KK, Ross W, Myers KS, Lemmer KC, Vera JM, Landick R, Donohue TJ, Gourse RL (2020) A majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation. Proceedings of the National Academy of Sciences of the United States of America 117((47)):29658-29668 PMC7703639 · Pubmed · DOI

Scarborough MJ, Hamilton JJ, Erb EA, Donohue TJ, Noguera DR (2020) Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models. mSystems 5((5)): PMC7527139 · Pubmed · DOI

Myers KS, Place M, Noguera DR, Donohue TJ (2020) COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database. Microbiology resource announcements 9((25)): PMC7303417 · Pubmed · DOI

Lemke RAS, Olson SM, Morse K, Karlen SD, Higbee A, Beebe ET, Ralph J, Coon JJ, Fox BG, Donohue TJ (2020) A bacterial biosynthetic pathway for methylated furan fatty acids. The Journal of biological chemistry 295((29)):9786-9801 PMC7380195 · Pubmed · DOI