Paxhia MD, Downs DM. Pyridoxal and α-Ketoglutarate Independently Improve Function of Saccharomyces cerevisiae Thi5 in the Metabolic Network of Salmonella enterica J Bacteriol 2022. 201(1),
Vu HN, Downs DM. Genetic analysis using vitamin B6 antagonist 4-deoxypyridoxine uncovers a connection between pyridoxal 5'-phosphate and coenzyme A metabolism in Salmonella enterica. J Bacteriol. 2022. (),
Downs DM. Serendipity Reveals the Function and Physiological Role of a Large Family of Proteins J. Bacteriol 2022. (),
Shen W, Borchert AJ, Downs DM. 2-Aminoacrylate stress damages diverse PLP-dependent enzymes in vivo J. Biol Chem. 2022. (),
Fulton RL , Irons J, Downs DM. The Cysteine Desulfurase IscS Is a Significant Target of 2-Aminoacrylate Damage in Pseudomonas aeruginosa mBio 2022. (),
Fulton RL, Downs DM. DadY (PA5303) is required for fitness of Pseudomonas aeruginosa when growth is dependent on alanine catabolism. Microb Cell. 2022. (),
Vu HN, Downs DM. Loss of YggS (COG0325) impacts aspartate metabolism in Salmonella enterica. Mol Microbiol. 2021. (),
Whitaker GH, Ernst DC, Downs DM. Absence of MMF1 disrupts heme biosynthesis by targeting Hem1pin Saccharomyces cerevisiae Yeast 2021. 38(12), 615-624
Borchert AJ, Gouveia GJ, Edison AS, Downs DM.. Proton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a ridA Mutant of Salmonella enterica. mSystems. 2020. 5(2), e00843-19
Ito T, Downs DM.. Pyridoxal Reductase, PdxI, Is Critical for Salvage of Pyridoxal in Escherichia coli. J Bacteriol. 2020. 202(12), e00056-20
Irons JL, Hodge-Hanson K, Downs DM.. RidA Proteins Protect against Metabolic Damage by Reactive Intermediates Microbiol Mol Biol Rev. 2020. 84(3), e00024-20.
Vu HN, Ito T, Downs DM.. The role of YggS in vitamin B6 homeostasis in Salmonella enterica is informed by heterologous expression of yeast SNZ3. J Bacteriol. 2020. (), JB.00383-20
Paxhia MD, Swanson MS, Downs DM. Functional characterization of the HMP-P synthase of Legionella pneumophila (Lpg1565). Mol Microbiol. 2020. (),
Vu HN, Downs DM. An Unexpected Role for the Periplasmic Phosphatase PhoN in the Salvage of B6 Vitamers in Salmonella enterica. Appl Environ Microbiol. 2020. (),
Paxhia MD, Downs DM. SNZ3 Encodes a PLP Synthase Involved in Thiamine Synthesis in Saccharomyces cerevisiae. G3 (Bethesda) 2019. 9(2), 335-344
Irons J, Sacher JC, Szymanski CM, Downs DM. Cj1388 Is a RidA Homolog and Is Required for Flagella Biosynthesis and/or Function in Campylobacter jejuni. Front Microbiol. 2019. 10(), 2058
Borchert AJ, Ernst DC, Downs DM. Reactive Enamines and Imines In Vivo: Lessons from the RidA Paradigm. Trends Biochem Sci. 2019. 44(10), 849-860
Bazurto JV, Dearth SP, Tague ED, Campagna SR, Downs DM. Untargeted metabolomics confirms and extends the understanding of the impact of aminoimidazole carboxamide ribotide (AICAR) in the metabolic network of Salmonella enterica. Microb Cell. 2018. 5(2), 74-87
Ernst DC, Downs DM. Mmf1p Couples Amino Acid Metabolism to Mitochondrial DNA Maintenance in Saccharomyces cerevisiae. mBio. 2018. 9(1), e00084-18
Ernst DC, Christopherson MR, Downs DM. Increased Activity of Cystathionine β-Lyase Suppresses 2-Aminoacrylate Stress in Salmonella enterica. J Bacteriol. 2018. 200(9), e00040-18
Hodge-Hanson KM, Zoino A, Downs DM. Expression of Pyridoxal 5'-Phosphate-Independent Racemases Can Reduce 2-Aminoacrylate Stress in Salmonella enterica J Bacteriol. 2018. 200(9), e00751-17
Ernst DC, Borchert AJ, Downs DM. Perturbation of the metabolic network in Salmonella enterica reveals cross-talk between coenzyme A and thiamine pathways. PLoS One. 2018. 13(5), e0197703
Irons J, Hodge-Hanson KM, Downs DM. PA5339, a RidA Homolog, Is Required for Full Growth in Pseudomonas aeruginosa. J Bacteriol. 2018. 200(22), e00434-18
Borchert AJ, Downs DM. Analyses of variants of the Ser/Thr dehydratase IlvA provide insight into 2-aminoacrylate metabolism in Salmonella enterica. J Biol Chem. 2018. 293(50), 19240-19249
Hodge-Hanson KM, 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 PLoS One. 2017. 12(9), e0185544
Bazurto JV, Farley KR, Downs DM. An Unexpected Route to an Essential Cofactor: Escherichia Coli Relies on Threonine for Thiamine Biosynthesis. mBio 2016. 7(1), e01840-15
Ernst DC, Downs DM. 2-Aminoacrylate Stress Induces a Context-Dependent Glycine Requirement in ridA Strains of Salmonella Enterica. J Bacteriol. 2016. 198(3), 536-43
Bazurto JV, Downs DM. Metabolic network structure and function in bacteria goes beyond conserved enzyme components. Microb Cell. 2016. 3(6), 260–262
Ernst DC, Anderson ME, Downs DM.. L-2,3-diaminopropionate generates diverse metabolic stresses in Salmonella enterica. Mol Microbiol. 2016. 101(2), 210-23
Downs DM, Ernst DC. From microbiology to cancer biology: the Rid protein family prevents cellular damage caused by endogenously generated reactive nitrogen species. Mol. Microbiol. 2015. 96(2), 211-9
Ernst DC, Downs DM. The STM4195 Gene Product (PanS) Transports Coenzyme A Precursors in Salmonella enterica. J. Bacteriol. 2015. 197(8), 1368-77
Palmer LD, Paxhia MD, 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. J Bacteriol. 2015. 197(22), 3554-62
Bazurto JV, Downs DM. Amino-4-imidazolecarboxamide ribotide directly inhibits coenzyme A biosynthesis in Salmonella enterica. J. Bacteriol. 2014. 4(196), 772-9
Ernst DC, Lambrecht JA, Schomer RA, Downs DM. Endogenous synthesis of 2-aminoacrylate contributes to cysteine sensitivity in Salmonella enterica. J. Bacteriol. 2014. 196(18), 3335-42
Palmer LD, Leung MH, Downs DM. The cysteine desulfhydrase CdsH is conditionally required for sulfur mobilization to the thiamine thiazole in Salmonella enterica. J. Bacteriol. 2014. 196(22), 3964-70
Palmer LD, Downs DM. The Thiamine Biosynthetic Enzyme ThiC Catalyzes Multiple Turnovers and Is Inhibited by S-adenosylmethionine Metabolites. J. Biol. Chem. 2013. 288(42), 30690-9
Flynn JM, Christopherson MR, Downs DM. Decreased coenzyme A levels in ridA mutant strains of Salmonella enterica result from inactivated serine hydroxymethyltransferase. Mol. Microbiol. 2013. 89(4), 751-9
Flynn JM, Downs DM. In the absence of RidA, endogenous 2-aminoacrylate inactivates alanine racemases by modifying the pyridoxal 5'-phosphate cofactor. J. Bacteriol. 2013. 195(16), 3603-9
Lambrecht JA, Schmitz GE, Downs DM. RidA proteins prevent metabolic damage inflicted by PLP-dependent dehydratases in all domains of life. MBio 2013. 4(1), e00033-13
Lambrecht JA, Downs DM. Anthranilate Phosphoribosyl Transferase (TrpD) Generates Phosphoribosylamine for Thiamine Synthesis from Enamines and Phosphoribosyl Pyrophosphate. ACS Chem. Biol. 2012. (),
Palmer LD, Dougherty MJ, Downs DM. Analysis of ThiC variants in the context of the metabolic network of Salmonella enterica. J. Bacteriol. 2012. 194(22), 6088-95
Boyd JM, Teoh WP, Downs DM. Decreased transport restores growth of a Salmonella enterica apbC mutant on tricarballylate. J. Bacteriol. 2012. 194(3), 576-83
Lambrecht JA, Flynn JM, Downs DM. Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions. J. Biol. Chem. 2012. 287(5), 3454-61
Bazurto JV, Downs DM. Plasticity in the purine-thiamine metabolic network of Salmonella. Genetics 2011. 187(2), 623-31
Lambrecht JA, Browne BA, Downs DM. Members of the YjgF/YER057c/UK114 family of proteins inhibit phosphoribosylamine synthesis in vitro. J. Biol. Chem. 2010. 285(45), 34401-7
Koenigsknecht MJ, Downs DM. Thiamine biosynthesis can be used to dissect metabolic integration. Trends Microbiol. 2010. 18(6), 240-7
Koenigsknecht MJ, Fenlon LA, Downs DM. Phosphoribosylpyrophosphate synthetase (PrsA) variants alter cellular pools of ribose 5-phosphate and influence thiamine synthesis in Salmonella enterica. Microbiology (Reading, Engl.) 2010. 156(Pt 3), 950-9
Downs DM. MMBR to highlight microbial evolution, diversity, and ecology in 2009. Microbiol. Mol. Biol. Rev. 2009. 73(1), 13
Lewis JA, Boyd JM, Downs DM, Escalante-Semerena JC. Involvement of the Cra global regulatory protein in the expression of the iscRSUA operon, revealed during studies of tricarballylate catabolism in Salmonella enterica. J. Bacteriol. 2009. 191(7), 2069-76
Thorgersen MP, Downs DM. Oxidative stress and disruption of labile iron generate specific auxotrophic requirements in Salmonella enterica. Microbiology (Reading, Engl.) 2009. 155(Pt 1), 295-304
Boyd JM, Sondelski JL, Downs DM. Bacterial ApbC protein has two biochemical activities that are required for in vivo function. J. Biol. Chem. 2008. 284(1), 110-8
Thorgersen MP, Downs DM. Analysis of yggX and gshA mutants provides insights into the labile iron pool in Salmonella enterica. J. Bacteriol. 2008. 190(23), 7608-13
Martinez-Gomez NC, 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. Biochemistry 2008. 47(35), 9054-6
Boyd JM, Lewis JA, Escalante-Semerena JC, Downs DM. Salmonella enterica requires ApbC function for growth on tricarballylate: evidence of functional redundancy between ApbC and IscU. J. Bacteriol. 2008. 190(13), 4596-602
Christopherson MR, Schmitz GE, Downs DM. YjgF is required for isoleucine biosynthesis when Salmonella enterica is grown on pyruvate medium. J. Bacteriol. 2008. 190(8), 3057-62
Ramos I, Vivas EI, Downs DM. Mutations in the tryptophan operon allow PurF-independent thiamine synthesis by altering flux in vivo. J. Bacteriol. 2008. 190(3), 815-22
Thorgersen MP, Downs DM. Cobalt targets multiple metabolic processes in Salmonella enterica. J. Bacteriol. 2007. 189(21), 7774-81
Koenigsknecht MJ, Ramos I, Downs DM. Glutamine phosphoribosylpyrophosphate amidotransferase-independent phosphoribosyl amine synthesis from ribose 5-phosphate and glutamine or asparagine. J. Biol. Chem. 2007. 282(39), 28379-84
Dougherty MJ, Boyd JM, Downs DM. Inhibition of fructose-1,6-bisphosphatase by aminoimidazole carboxamide ribotide prevents growth of Salmonella enterica purH mutants on glycerol. J. Biol. Chem. 2006. 281(45), 33892-9
Browne BA, Ramos AI, Downs DM. PurF-independent phosphoribosyl amine formation in yjgF mutants of Salmonella enterica utilizes the tryptophan biosynthetic enzyme complex anthranilate synthase-phosphoribosyltransferase. J. Bacteriol. 2006. 188(19), 6786-92
Dougherty MJ, Downs DM. A connection between iron-sulfur cluster metabolism and the biosynthesis of 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate in Salmonella enterica. Microbiology (Reading, Engl.) 2006. 152(Pt 8), 2345-53
Schmitz GE, Downs DM. An allele of gyrA prevents Salmonella enterica serovar Typhimurium from using succinate as a carbon source. J. Bacteriol. 2006. 188(8), 3126-9
Vivas E, Skovran E, Downs DM. Salmonella enterica strains lacking the frataxin homolog CyaY show defects in Fe-S cluster metabolism in vivo. J. Bacteriol. 2006. 188(3), 1175-9
Downs DM, Schmitz GE, Skovran E. Probing the complex system of metabolic integration. Prog. Nucleic Acid Res. Mol. Biol. 2005. 80(), 43-94
Zhang Y, Dougherty M, Downs DM, Ealick SE. Crystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily. Structure 2004. 12(10), 1809-21
Martinez-Gomez NC, Robers M, Downs DM. Mutational analysis of ThiH, a member of the radical S-adenosylmethionine (AdoMet) protein superfamily. J. Biol. Chem. 2004. 279(39), 40505-10
Dougherty MJ, Downs DM. A mutant allele of rpoD results in increased conversion of aminoimidazole ribotide to hydroxymethyl pyrimidine in Salmonella enterica. J. Bacteriol. 2004. 186(12), 4034-7
Lauhon CT, Skovran E, Urbina HD, Downs DM, Vickery LE. Substitutions in an active site loop of Escherichia coli IscS result in specific defects in Fe-S cluster and thionucleoside biosynthesis in vivo. J. Biol. Chem. 2004. 279(19), 19551-8
Schmitz G, Downs DM. 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. J. Bacteriol. 2004. 186(3), 803-10
Skovran E, Lauhon CT, Downs DM. Lack of YggX results in chronic oxidative stress and uncovers subtle defects in Fe-S cluster metabolism in Salmonella enterica. J. Bacteriol. 2004. 186(22), 7626-34
Ramos I, Downs DM. Anthranilate synthase can generate sufficient phosphoribosyl amine for thiamine synthesis in Salmonella enterica. J. Bacteriol. 2003. 185(17), 5125-32
Gralnick JA, 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. J. Biol. Chem. 2003. 278(23), 20708-15
Beck BJ, Huelsmeyer M, Paul S, Downs DM. A mutation in the essential gene gmk (encoding guanlyate kinase) generates a requirement for adenine at low temperature in Salmonella enterica. J. Bacteriol. 2003. 185(22), 6732-5
Dougherty M, 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. J. Bacteriol. 2002. 185(1), 332-9
Skovran E, Downs DM. Lack of the ApbC or ApbE protein results in a defect in Fe-S cluster metabolism in Salmonella enterica serovar Typhimurium. J. Bacteriol. 2002. 185(1), 98-106
Allen S, Zilles JL, 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. J. Bacteriol. 2002. 184(22), 6130-7
Rubio A, Downs DM. Elevated levels of ketopantoate hydroxymethyltransferase (PanB) lead to a physiologically significant coenzyme A elevation in Salmonella enterica serovar Typhimurium. J. Bacteriol. 2002. 184(10), 2827-32
Zilles JL, Kappock TJ, Stubbe J, Downs DM. Altered pathway routing in a class of Salmonella enterica serovar Typhimurium mutants defective in aminoimidazole ribonucleotide synthetase. J. Bacteriol. 2001. 183(7), 2234-40
Frodyma M, Rubio A, Downs DM. Reduced flux through the purine biosynthetic pathway results in an increased requirement for coenzyme A in thiamine synthesis in Salmonella enterica serovar typhimurium. J. Bacteriol. 2000. 182(1), 236-40
Claas K, Weber S, 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. J. Bacteriol. 2000. 182(1), 228-32
Skovran E, Downs DM. Metabolic defects caused by mutations in the isc gene cluster in Salmonella enterica serovar typhimurium: implications for thiamine synthesis. J. Bacteriol. 2000. 182(14), 3896-903
Zilles JL, Croal LR, Downs DM. Action of the thiamine antagonist bacimethrin on thiamine biosynthesis. J. Bacteriol. 2000. 182(19), 5606-10
Beck BJ, Downs DM. A periplasmic location is essential for the role of the ApbE lipoprotein in thiamine synthesis in Salmonella typhimurium. J. Bacteriol. 2000. 181(23), 7285-90
Downs DM, Escalante-Semerena JC. Impact of genomics and genetics on the elucidation of bacterial metabolism. Methods 2000. 20(1), 47-54
Enos-Berlage JL, Downs DM. 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. J. Bacteriol. 1999. 181(3), 841-8
Enos-Berlage JL, Langendorf MJ, Downs DM. Complex metabolic phenotypes caused by a mutation in yjgF, encoding a member of the highly conserved YER057c/YjgF family of proteins. J. Bacteriol. 1999. 180(24), 6519-28
Christian T, Downs DM. Defects in pyruvate kinase cause a conditional increase of thiamine synthesis in Salmonella typhimurium. Can. J. Microbiol. 1999. 45(7), 565-72
Beck BJ, Downs DM. The apbE gene encodes a lipoprotein involved in thiamine synthesis in Salmonella typhimurium. J. Bacteriol. 1998. 180(4), 885-91
Petersen LA, Downs DM. Identification and characterization of an operon in Salmonella typhimurium involved in thiamine biosynthesis. J. Bacteriol. 1997. 179(15), 4894-900
Beck BJ, Connolly LE, De Las Peñas A, Downs DM. Evidence that rseC, a gene in the rpoE cluster, has a role in thiamine synthesis in Salmonella typhimurium. J. Bacteriol. 1997. 179(20), 6504-8
Webb E, Claas K, Downs DM. Characterization of thiI, a new gene involved in thiazole biosynthesis in Salmonella typhimurium. J. Bacteriol. 1997. 179(13), 4399-402
Enos-Berlage JL, Downs DM. Mutations in sdh (succinate dehydrogenase genes) alter the thiamine requirement of Salmonella typhimurium. J. Bacteriol. 1997. 179(12), 3989-96
Zilles 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. Genetics 1997. 144(3), 883-92
Webb E, Febres F, Downs DM. Thiamine pyrophosphate (TPP) negatively regulates transcription of some thi genes of Salmonella typhimurium. J. Bacteriol. 1996. 178(9), 2533-8
Petersen L, Downs DM. Mutations in apbC (mrp) prevent function of the alternative pyrimidine biosynthetic pathway in Salmonella typhimurium. J. Bacteriol. 1996. 178(19), 5676-82
Enos-Berlage JL, Downs DM. Involvement of the oxidative pentose phosphate pathway in thiamine biosynthesis in Salmonella typhimurium. J. Bacteriol. 1996. 178(5), 1476-9
Petersen L, Enos-Berlage J, Downs DM. Genetic analysis of metabolic crosstalk and its impact on thiamine synthesis in Salmonella typhimurium. Genetics 1996. 143(1), 37-44
Downs DM, Petersen L. apbA, a new genetic locus involved in thiamine biosynthesis in Salmonella typhimurium. J. Bacteriol. 1994. 176(16), 4858-64
Downs DM, Ludden PW, Shah VK. Accumulation of factor F395 in nifNE mutants of Klebsiella pneumoniae. Can. J. Microbiol. 1993. 39(3), 351-4
Downs DM. Evidence for a new, oxygen-regulated biosynthetic pathway for the pyrimidine moiety of thiamine in Salmonella typhimurium. J. Bacteriol. 1992. 174(5), 1515-21
Downs DM, Roth JR. Synthesis of thiamine in Salmonella typhimurium independent of the purF function. J. Bacteriol. 1991. 173(20), 6597-604
Downs DM, Ludden PW, Shah VK. Synthesis of the iron-molybdenum cofactor of nitrogenase is inhibited by a low-molecular-weight metabolite of Klebsiella pneumoniae. J. Bacteriol. 1990. 172(10), 6084-9
Downs DM, Roth JR. A novel P22 prophage in Salmonella typhimurium. Genetics 1988. 117(3), 367-80
