Publications

Tetrahydrofolate levels influence 2-aminoacrylate stress in Salmonella enterica.

Shen W, Downs DM.

Functional characterization of the dbu locus for D-branched-chain amino acid catabolism in Pseudomonas putida.

Fulton RL, Downs DM.

Modulators of a robust and efficient metabolism: Perspective and insights from the Rid superfamily of proteins.

Fulton RL, Downs DM.

DadY (PA5303) is required for fitness of Pseudomonas aeruginosa when growth is dependent on alanine catabolism.

Fulton RL, Downs DM.

The Cysteine Desulfurase IscS Is a Significant Target of 2-Aminoacrylate Damage in Pseudomonas aeruginosa

Fulton RL , Irons J, Downs DM.

2-Aminoacrylate stress damages diverse PLP-dependent enzymes in vivo

Shen W, Borchert AJ, Downs DM.

Serendipity Reveals the Function and Physiological Role of a Large Family of Proteins

Downs DM.

Genetic analysis using vitamin B6 antagonist 4-deoxypyridoxine uncovers a connection between pyridoxal 5'-phosphate and coenzyme A metabolism in Salmonella enterica.

Vu HN, Downs DM.

Pyridoxal and ?-Ketoglutarate Independently Improve Function of Saccharomyces cerevisiae Thi5 in the Metabolic Network of Salmonella enterica

Paxhia MD, Downs DM.

Absence of MMF1 disrupts heme biosynthesis by targeting Hem1pin Saccharomyces cerevisiae

Whitaker GH, Ernst DC, Downs DM.

Loss of YggS (COG0325) impacts aspartate metabolism in Salmonella enterica.

Vu HN, Downs DM.

The Rid family member RutC of Escherichia coli is a 3-aminoacrylate deaminase.

Buckner BA, Lato AM, Campagna SR, Downs DM.

An Unexpected Role for the Periplasmic Phosphatase PhoN in the Salvage of B6 Vitamers in Salmonella enterica.

Vu HN, Downs DM.

Functional characterization of the HMP-P synthase of Legionella pneumophila (Lpg1565).

Paxhia MD, Swanson MS, Downs DM.

The role of YggS in vitamin B6 homeostasis in Salmonella enterica is informed by heterologous expression of yeast SNZ3.

Vu HN, Ito T, Downs DM..

RidA Proteins Protect against Metabolic Damage by Reactive Intermediates

Irons JL, Hodge-Hanson K, Downs DM..

Pyridoxal Reductase, PdxI, Is Critical for Salvage of Pyridoxal in Escherichia coli.

Ito T, Downs DM..

Proton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a ridA Mutant of Salmonella enterica.

Borchert AJ, Gouveia GJ, Edison AS, Downs DM..

Integrated Metabolomics and Transcriptomics Suggest the Global Metabolic Response to 2-Aminoacrylate Stress in Salmonella enterica.

Borchert AJ, Walejko JM, Guennec AL, Ernst DC, Edison AS, Downs DM.

Reactive Enamines and Imines In Vivo: Lessons from the RidA Paradigm.

Borchert AJ, Ernst DC, Downs DM.

Cj1388 Is a RidA Homolog and Is Required for Flagella Biosynthesis and/or Function in Campylobacter jejuni.

Irons J, Sacher JC, Szymanski CM, Downs DM.

SNZ3 Encodes a PLP Synthase Involved in Thiamine Synthesis in Saccharomyces cerevisiae.

Paxhia MD, Downs DM.

Analyses of variants of the Ser/Thr dehydratase IlvA provide insight into 2-aminoacrylate metabolism in Salmonella enterica.

Borchert AJ, Downs DM.

PA5339, a RidA Homolog, Is Required for Full Growth in Pseudomonas aeruginosa.

Irons J, Hodge-Hanson KM, Downs DM.

Perturbation of the metabolic network in Salmonella enterica reveals cross-talk between coenzyme A and thiamine pathways.

Ernst DC, Borchert AJ, Downs DM.

Increased Activity of Cystathionine ?-Lyase Suppresses 2-Aminoacrylate Stress in Salmonella enterica.

Ernst DC, Christopherson MR, Downs DM.

Expression of Pyridoxal 5'-Phosphate-Independent Racemases Can Reduce 2-Aminoacrylate Stress in Salmonella enterica

Hodge-Hanson KM, Zoino A, Downs DM.

Mmf1p Couples Amino Acid Metabolism to Mitochondrial DNA Maintenance in Saccharomyces cerevisiae.

Ernst DC, Downs DM.

Untargeted metabolomics confirms and extends the understanding of the impact of aminoimidazole carboxamide ribotide (AICAR) in the metabolic network of Salmonella enterica.

Bazurto JV, Dearth SP, Tague ED, Campagna SR, Downs DM.

Endogenously generated 2-aminoacrylate inhibits motility in Salmonella enterica.

Borchert AJ, Downs DM.

Members of the Rid protein family have broad imine deaminase activity and can accelerate the Pseudomonas aeruginosa D-arginine dehydrogenase (DauA) reaction in vitro

Hodge-Hanson KM, Downs DM.

L-2,3-diaminopropionate generates diverse metabolic stresses in Salmonella enterica.

Ernst DC, Anderson ME, Downs DM..

Metabolic network structure and function in bacteria goes beyond conserved enzyme components.

Bazurto JV, Downs DM.

2-Aminoacrylate Stress Induces a Context-Dependent Glycine Requirement in ridA Strains of Salmonella Enterica.

Ernst DC, Downs DM.

An Unexpected Route to an Essential Cofactor: Escherichia Coli Relies on Threonine for Thiamine Biosynthesis.

Bazurto JV, Farley KR, Downs DM.

Aminoimidazole Carboxamide Ribotide Exerts Opposing Effects on Thiamine Synthesis in Salmonella Enterica.

Bazurto JV, Heitman NJ, Downs DM.

Induction of the Sugar-Phosphate Stress Response Allows Saccharomyces cerevisiae 2-Methyl-4-Amino-5-Hydroxymethylpyrimidine Phosphate Synthase To Function in Salmonella enterica.

Palmer LD, Paxhia MD, Downs DM.

From microbiology to cancer biology: the Rid protein family prevents cellular damage caused by endogenously generated reactive nitrogen species.

Downs DM, Ernst DC.

The STM4195 Gene Product (PanS) Transports Coenzyme A Precursors in Salmonella enterica.

Ernst DC, Downs DM.

Endogenous synthesis of 2-aminoacrylate contributes to cysteine sensitivity in Salmonella enterica.

Ernst DC, Lambrecht JA, Schomer RA, Downs DM.

Arabidopsis and maize RidA proteins preempt reactive enamine/imine damage to branched-chain amino acid biosynthesis in plastids.

Niehaus TD, Nguyen TN, Gidda SK, ElBadawi-Sidhu M, Lambrecht JA, McCarty DR, Downs DM, Cooper AJ, Fiehn O, Mullen RT, Hanson AD.

Amino-4-imidazolecarboxamide ribotide directly inhibits coenzyme A biosynthesis in Salmonella enterica.

Bazurto JV, Downs DM.

The cysteine desulfhydrase CdsH is conditionally required for sulfur mobilization to the thiamine thiazole in Salmonella enterica.

Palmer LD, Leung MH, Downs DM.

The Thiamine Biosynthetic Enzyme ThiC Catalyzes Multiple Turnovers and Is Inhibited by S-adenosylmethionine Metabolites.

Palmer LD, Downs DM.

Decreased coenzyme A levels in ridA mutant strains of Salmonella enterica result from inactivated serine hydroxymethyltransferase.

Flynn JM, Christopherson MR, Downs DM.

In the absence of RidA, endogenous 2-aminoacrylate inactivates alanine racemases by modifying the pyridoxal 5'-phosphate cofactor.

Flynn JM, Downs DM.

RidA proteins prevent metabolic damage inflicted by PLP-dependent dehydratases in all domains of life.

Lambrecht JA, Schmitz GE, Downs DM.

Perturbations in Histidine Biosynthesis Uncover Robustness in the Metabolic Network of Salmonella enterica.

Koenigsknecht MJ, Lambrecht JA, Fenlon LA, Downs DM.

Anthranilate Phosphoribosyl Transferase (TrpD) Generates Phosphoribosylamine for Thiamine Synthesis from Enamines and Phosphoribosyl Pyrophosphate.

Lambrecht JA, Downs DM.

Analysis of ThiC variants in the context of the metabolic network of Salmonella enterica.

Palmer LD, Dougherty MJ, Downs DM.

Suppressor analyses identify threonine as a modulator of ridA mutant phenotypes in Salmonella enterica.

Christopherson MR, Lambrecht JA, Downs D, Downs DM.

Decreased transport restores growth of a Salmonella enterica apbC mutant on tricarballylate.

Boyd JM, Teoh WP, Downs DM.

Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions.

Lambrecht JA, Flynn JM, Downs DM.

The rhodanese domain of ThiI is both necessary and sufficient for synthesis of the thiazole moiety of thiamine in Salmonella enterica.

Martinez-Gomez NC, Palmer LD, Vivas E, Roach PL, Downs DM.

Plasticity in the purine-thiamine metabolic network of Salmonella.

Bazurto JV, Downs DM.

FAD binding by ApbE protein from Salmonella enterica: a new class of FAD-binding proteins.

Boyd JM, Endrizzi JA, Hamilton TL, Christopherson MR, Mulder DW, Downs DM, Peters JW.

Members of the YjgF/YER057c/UK114 family of proteins inhibit phosphoribosylamine synthesis in vitro.

Lambrecht JA, Browne BA, Downs DM.

Thiamine biosynthesis can be used to dissect metabolic integration.

Koenigsknecht MJ, Downs DM.

Phosphoribosylpyrophosphate synthetase (PrsA) variants alter cellular pools of ribose 5-phosphate and influence thiamine synthesis in Salmonella enterica.

Koenigsknecht MJ, Fenlon LA, Downs DM.

MMBR to highlight microbial evolution, diversity, and ecology in 2009.

Downs DM.

Involvement of the Cra global regulatory protein in the expression of the iscRSUA operon, revealed during studies of tricarballylate catabolism in Salmonella enterica.

Lewis JA, Boyd JM, Downs DM, Escalante-Semerena JC.

Archaeal ApbC/Nbp35 homologs function as iron-sulfur cluster carrier proteins.

Boyd JM, Drevland RM, Downs DM, Graham DE.

Oxidative stress and disruption of labile iron generate specific auxotrophic requirements in Salmonella enterica.

Thorgersen MP, Downs DM.

Reaction of AdoMet with ThiC generates a backbone free radical.

Martinez-Gomez NC, Poyner RR, Mansoorabadi SO, Reed GH, Downs DM.

Bacterial ApbC protein has two biochemical activities that are required for in vivo function.

Boyd JM, Sondelski JL, Downs DM.

Analysis of yggX and gshA mutants provides insights into the labile iron pool in Salmonella enterica.

Thorgersen MP, Downs DM.

ThiC is an [Fe-S] cluster protein that requires AdoMet to generate the 4-amino-5-hydroxymethyl-2-methylpyrimidine moiety in thiamin synthesis.

Martinez-Gomez NC, Downs DM.

Bacterial ApbC can bind and effectively transfer iron-sulfur clusters.

Boyd JM, Pierik AJ, Netz DJ, Lill R, Downs DM.

Salmonella enterica requires ApbC function for growth on tricarballylate: evidence of functional redundancy between ApbC and IscU.

Boyd JM, Lewis JA, Escalante-Semerena JC, Downs DM.

YjgF is required for isoleucine biosynthesis when Salmonella enterica is grown on pyruvate medium.

Christopherson MR, Schmitz GE, Downs DM.

Mutations in the tryptophan operon allow PurF-independent thiamine synthesis by altering flux in vivo.

Ramos I, Vivas EI, Downs DM.

Cobalt targets multiple metabolic processes in Salmonella enterica.

Thorgersen MP, Downs DM.

Glutamine phosphoribosylpyrophosphate amidotransferase-independent phosphoribosyl amine synthesis from ribose 5-phosphate and glutamine or asparagine.

Koenigsknecht MJ, Ramos I, Downs DM.

Inhibition of fructose-1,6-bisphosphatase by aminoimidazole carboxamide ribotide prevents growth of Salmonella enterica purH mutants on glycerol.

Dougherty MJ, Boyd JM, Downs DM.

Understanding microbial metabolism.

Downs DM.

PurF-independent phosphoribosyl amine formation in yjgF mutants of Salmonella enterica utilizes the tryptophan biosynthetic enzyme complex anthranilate synthase-phosphoribosyltransferase.

Browne BA, Ramos AI, Downs DM.

A connection between iron-sulfur cluster metabolism and the biosynthesis of 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate in Salmonella enterica.

Dougherty MJ, Downs DM.

An allele of gyrA prevents Salmonella enterica serovar Typhimurium from using succinate as a carbon source.

Schmitz GE, Downs DM.

Solution structure of YggX: a prokaryotic protein involved in Fe(II) trafficking.

Cui Q, Thorgersen MP, Westler WM, Markley JL, Downs DM.

Salmonella enterica strains lacking the frataxin homolog CyaY show defects in Fe-S cluster metabolism in vivo.

Vivas E, Skovran E, Downs DM.

Probing the complex system of metabolic integration.

Downs DM, Schmitz GE, Skovran E.

Lack of YggX results in chronic oxidative stress and uncovers subtle defects in Fe-S cluster metabolism in Salmonella enterica.

Skovran E, Lauhon CT, Downs DM.

Crystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily.

Zhang Y, Dougherty M, Downs DM, Ealick SE.

Mutational analysis of ThiH, a member of the radical S-adenosylmethionine (AdoMet) protein superfamily.

Martinez-Gomez NC, Robers M, Downs DM.

A mutant allele of rpoD results in increased conversion of aminoimidazole ribotide to hydroxymethyl pyrimidine in Salmonella enterica.

Dougherty MJ, Downs DM.

Substitutions in an active site loop of Escherichia coli IscS result in specific defects in Fe-S cluster and thionucleoside biosynthesis in vivo.

Lauhon CT, Skovran E, Urbina HD, Downs DM, Vickery LE.

Reduced transaminase B (IlvE) activity caused by the lack of yjgF is dependent on the status of threonine deaminase (IlvA) in Salmonella enterica serovar Typhimurium.

Schmitz G, Downs DM.

A mutation in the essential gene gmk (encoding guanlyate kinase) generates a requirement for adenine at low temperature in Salmonella enterica.

Beck BJ, Huelsmeyer M, Paul S, Downs DM.

Anthranilate synthase can generate sufficient phosphoribosyl amine for thiamine synthesis in Salmonella enterica.

Ramos I, Downs DM.

The YggX protein of Salmonella enterica is involved in Fe(II) trafficking and minimizes the DNA damage caused by hydroxyl radicals: residue CYS-7 is essential for YggX function.

Gralnick JA, Downs DM.

Genomics and bacterial metabolism.

Downs DM.

The stm4066 gene product of Salmonella enterica serovar Typhimurium has aminoimidazole riboside (AIRs) kinase activity and allows AIRs to satisfy the thiamine requirement of pur mutant strains.

Dougherty M, Downs DM.

Lack of the ApbC or ApbE protein results in a defect in Fe-S cluster metabolism in Salmonella enterica serovar Typhimurium.

Skovran E, Downs DM.

Metabolic flux in both the purine mononucleotide and histidine biosynthetic pathways can influence synthesis of the hydroxymethyl pyrimidine moiety of thiamine in Salmonella enterica.

Allen S, Zilles JL, Downs DM.

Elevated levels of ketopantoate hydroxymethyltransferase (PanB) lead to a physiologically significant coenzyme A elevation in Salmonella enterica serovar Typhimurium.

Rubio A, Downs DM.

Altered pathway routing in a class of Salmonella enterica serovar Typhimurium mutants defective in aminoimidazole ribonucleotide synthetase.

Zilles JL, Kappock TJ, Stubbe J, Downs DM.

Action of the thiamine antagonist bacimethrin on thiamine biosynthesis.

Zilles JL, Croal LR, Downs DM.

Metabolic defects caused by mutations in the isc gene cluster in Salmonella enterica serovar typhimurium: implications for thiamine synthesis.

Skovran E, Downs DM.

Impact of genomics and genetics on the elucidation of bacterial metabolism.

Downs DM, Escalante-Semerena JC.

Reduced flux through the purine biosynthetic pathway results in an increased requirement for coenzyme A in thiamine synthesis in Salmonella enterica serovar typhimurium.

Frodyma M, Rubio A, Downs DM.

Lesions in the nuo operon, encoding NADH dehydrogenase complex I, prevent PurF-independent thiamine synthesis and reduce flux through the oxidative pentose phosphate pathway in Salmonella enterica serovar typhimurium.

Claas K, Weber S, Downs DM.

A periplasmic location is essential for the role of the ApbE lipoprotein in thiamine synthesis in Salmonella typhimurium.

Beck BJ, Downs DM.

Defects in pyruvate kinase cause a conditional increase of thiamine synthesis in Salmonella typhimurium.

Christian T, Downs DM.

Thiamin biosynthesis in prokaryotes.

Begley TP, Downs DM, Ealick SE, McLafferty FW, Van Loon AP, Taylor S, Campobasso N, Chiu HJ, Kinsland C, Reddick JJ, Xi J.

Biosynthesis of the pyrimidine moiety of thiamine independent of the PurF enzyme (Phosphoribosylpyrophosphate amidotransferase) in Salmonella typhimurium: incorporation of stable isotope-labeled glycine and formate.

Enos-Berlage JL, Downs DM.

Complex metabolic phenotypes caused by a mutation in yjgF, encoding a member of the highly conserved YER057c/YjgF family of proteins.

Enos-Berlage JL, Langendorf MJ, Downs DM.

The apbE gene encodes a lipoprotein involved in thiamine synthesis in Salmonella typhimurium.

Beck BJ, Downs DM.

Evidence that rseC, a gene in the rpoE cluster, has a role in thiamine synthesis in Salmonella typhimurium.

Beck BJ, Connolly LE, De Las Peñas A, Downs DM.

Identification and characterization of an operon in Salmonella typhimurium involved in thiamine biosynthesis.

Petersen LA, Downs DM.

Characterization of thiI, a new gene involved in thiazole biosynthesis in Salmonella typhimurium.

Webb E, Claas K, Downs DM.

Mutations in sdh (succinate dehydrogenase genes) alter the thiamine requirement of Salmonella typhimurium.

Enos-Berlage JL, Downs DM.

A novel involvement of the PurG and PurI proteins in thiamine synthesis via the alternative pyrimidine biosynthetic (APB) pathway in Salmonella typhimurium.

Zilles JL, Downs DM.

Mutations in apbC (mrp) prevent function of the alternative pyrimidine biosynthetic pathway in Salmonella typhimurium.

Petersen L, Downs DM.

Genetic analysis of metabolic crosstalk and its impact on thiamine synthesis in Salmonella typhimurium.

Petersen L, Enos-Berlage J, Downs DM.

Involvement of the oxidative pentose phosphate pathway in thiamine biosynthesis in Salmonella typhimurium.

Enos-Berlage JL, Downs DM.

Thiamine pyrophosphate (TPP) negatively regulates transcription of some thi genes of Salmonella typhimurium.

Webb E, Febres F, Downs DM.

apbA, a new genetic locus involved in thiamine biosynthesis in Salmonella typhimurium.

Downs DM, Petersen L.

Accumulation of factor F395 in nifNE mutants of Klebsiella pneumoniae.

Downs DM, Ludden PW, Shah VK.

Evidence for a new, oxygen-regulated biosynthetic pathway for the pyrimidine moiety of thiamine in Salmonella typhimurium.

Downs DM.

Synthesis of thiamine in Salmonella typhimurium independent of the purF function.

Downs DM, Roth JR.

Synthesis of the iron-molybdenum cofactor of nitrogenase is inhibited by a low-molecular-weight metabolite of Klebsiella pneumoniae.

Downs DM, Ludden PW, Shah VK.

A novel P22 prophage in Salmonella typhimurium.

Downs DM, Roth JR.