Lab Publications

word cloud
  • Downs DM, Ernst DC. 2015. From microbiology to cancer biology: the Rid protein family prevents cellular damage caused by endogenously generated reactive nitrogen species. Mol. Microbiol. 96(2):211-9
  • Ernst DC, Downs DM. 2015. The STM4195 Gene Product (PanS) Transports Coenzyme A Precursors in Salmonella enterica. J. Bacteriol. 197(8):1368-77
  • Bazurto JV, Downs DM. 2014. Amino-4-imidazolecarboxamide ribotide directly inhibits coenzyme A biosynthesis in Salmonella enterica. J. Bacteriol. 4(196):772-9 PMC3911171
  • Ernst DC, Lambrecht JA, Schomer RA, Downs DM. 2014. Endogenous synthesis of 2-aminoacrylate contributes to cysteine sensitivity in Salmonella enterica. J. Bacteriol. 196(18):3335-42 PMC4135687
  • Niehaus TD, Nguyen TN, Gidda SK, ElBadawi-Sidhu M, Lambrecht JA, McCarty DR, Downs DM, Cooper AJ, Fiehn O, Mullen RT, Hanson AD. 2014. Arabidopsis and maize RidA proteins preempt reactive enamine/imine damage to branched-chain amino acid biosynthesis in plastids. Plant Cell 26(7):3010-22 PMC4145128
  • Palmer LD, Leung MH, Downs DM. 2014. The cysteine desulfhydrase CdsH is conditionally required for sulfur mobilization to the thiamine thiazole in Salmonella enterica J. Bacteriol. 196(22):3964-70 PMC4248823
  • Palmer LD, Downs DM. 2013. The Thiamine Biosynthetic Enzyme ThiC Catalyzes Multiple Turnovers and Is Inhibited by S-adenosylmethionine Metabolites. J. Biol. Chem. 288(42):30690-9
  • Flynn JM, Christopherson MR, Downs DM. 2013. Decreased coenzyme A levels in ridA mutant strains of Salmonella enterica result from inactivated serine hydroxymethyltransferase. Mol. Microbiol. 89(4):751-9
  • Flynn JM, Downs DM. 2013. In the absence of RidA, endogenous 2-aminoacrylate inactivates alanine racemases by modifying the pyridoxal 5'-phosphate cofactor. J. Bacteriol. 195(16):3603-9 PMC3754577 [Available on 02/01/14]
  • Lambrecht JA, Schmitz GE, Downs DM. 2013. RidA proteins prevent metabolic damage inflicted by PLP-dependent dehydratases in all domains of life. MBio 4(1):e00033-13 PMC3565831
  • Koenigsknecht MJ, Lambrecht JA, Fenlon LA, Downs DM. 2012. Perturbations in Histidine Biosynthesis Uncover Robustness in the Metabolic Network of Salmonella enterica. PLoS ONE 7(10):e48207 PMC3485032
  • Lambrecht JA, Downs DM. 2012. Anthranilate Phosphoribosyl Transferase (TrpD) Generates Phosphoribosylamine for Thiamine Synthesis from Enamines and Phosphoribosyl Pyrophosphate. ACS Chem. Biol. :
  • Palmer LD, Dougherty MJ, Downs DM. 2012. Analysis of ThiC variants in the context of the metabolic network of Salmonella enterica. J. Bacteriol. 194(22):6088-95 PMC3486400
  • Christopherson MR, Lambrecht JA, Downs D, Downs DM. 2012. Suppressor analyses identify threonine as a modulator of ridA mutant phenotypes in Salmonella enterica. PLoS ONE 7(8):e43082 PMC3416771
  • Boyd JM, Teoh WP, Downs DM. 2012. Decreased transport restores growth of a Salmonella enterica apbC mutant on tricarballylate. J. Bacteriol. 194(3):576-83 PMC3264071
  • Lambrecht JA, Flynn JM, Downs DM. 2012. Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions. J. Biol. Chem. 287(5):3454-61 PMC3270999 [Available on 01/27/13]
  • Martinez-Gomez NC, Palmer LD, Vivas E, Roach PL, Downs DM. 2011. The rhodanese domain of ThiI is both necessary and sufficient for synthesis of the thiazole moiety of thiamine in Salmonella enterica. J. Bacteriol. 193(18):4582-7 PMC3165671
  • Boyd JM, Endrizzi JA, Hamilton TL, Christopherson MR, Mulder DW, Downs DM, Peters JW. 2011. FAD binding by ApbE protein from Salmonella enterica: a new class of FAD-binding proteins. J. Bacteriol. 193(4):887-95 PMC3028670
  • Bazurto JV, Downs DM. 2011. Plasticity in the purine-thiamine metabolic network of Salmonella. Genetics 187(2):623-31 PMC3030501
  • Lambrecht JA, Browne BA, Downs DM. 2010. Members of the YjgF/YER057c/UK114 family of proteins inhibit phosphoribosylamine synthesis in vitro. J. Biol. Chem. 285(45):34401-7 PMC2966054
  • Koenigsknecht MJ, Downs DM. 2010. Thiamine biosynthesis can be used to dissect metabolic integration. Trends Microbiol. 18(6):240-7 PMC2906612
  • Koenigsknecht MJ, Fenlon LA, Downs DM. 2010. Phosphoribosylpyrophosphate synthetase (PrsA) variants alter cellular pools of ribose 5-phosphate and influence thiamine synthesis in Salmonella enterica. Microbiology (Reading, Engl.) 156(Pt 3):950-9 PMC2889433
  • Downs DM. 2009. MMBR to highlight microbial evolution, diversity, and ecology in 2009. Microbiol. Mol. Biol. Rev. 73(1):13 PMC2650884
  • Lewis JA, Boyd JM, Downs DM, Escalante-Semerena JC. 2009. 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. 191(7):2069-76 PMC2655522
  • Thorgersen MP, Downs DM. 2009. Oxidative stress and disruption of labile iron generate specific auxotrophic requirements in Salmonella enterica. Microbiology (Reading, Engl.) 155(Pt 1):295-304
  • Boyd JM, Drevland RM, Downs DM, Graham DE. 2009. Archaeal ApbC/Nbp35 homologs function as iron-sulfur cluster carrier proteins. J. Bacteriol. 191(5):1490-7 PMC2648223
  • Martinez-Gomez NC, Poyner RR, Mansoorabadi SO, Reed GH, Downs DM. 2009. Reaction of AdoMet with ThiC generates a backbone free radical. Biochemistry 48(2):217-9 PMC2654281
  • Boyd JM, Sondelski JL, Downs DM. 2008. Bacterial ApbC protein has two biochemical activities that are required for in vivo function. J. Biol. Chem. 284(1):110-8 PMC2610507
  • Thorgersen MP, Downs DM. 2008. Analysis of yggX and gshA mutants provides insights into the labile iron pool in Salmonella enterica. J. Bacteriol. 190(23):7608-13 PMC2583615
  • Martinez-Gomez NC, Downs DM. 2008. ThiC is an [Fe-S] cluster protein that requires AdoMet to generate the 4-amino-5-hydroxymethyl-2-methylpyrimidine moiety in thiamin synthesis. Biochemistry 47(35):9054-6 PMC2538623
  • Boyd JM, Pierik AJ, Netz DJ, Lill R, Downs DM. 2008. Bacterial ApbC can bind and effectively transfer iron-sulfur clusters. Biochemistry 47(31):8195-202 PMC2562686
  • Boyd JM, Lewis JA, Escalante-Semerena JC, Downs DM. 2008. Salmonella enterica requires ApbC function for growth on tricarballylate: evidence of functional redundancy between ApbC and IscU. J. Bacteriol. 190(13):4596-602 PMC2446783
  • Christopherson MR, Schmitz GE, Downs DM. 2008. YjgF is required for isoleucine biosynthesis when Salmonella enterica is grown on pyruvate medium. J. Bacteriol. 190(8):3057-62 PMC2293226
  • Ramos I, Vivas EI, Downs DM. 2008. Mutations in the tryptophan operon allow PurF-independent thiamine synthesis by altering flux in vivo. J. Bacteriol. 190(3):815-22 PMC2223571
  • Thorgersen MP, Downs DM. 2007. Cobalt targets multiple metabolic processes in Salmonella enterica. J. Bacteriol. 189(21):7774-81 PMC2168735
  • Koenigsknecht MJ, Ramos I, Downs DM. 2007. Glutamine phosphoribosylpyrophosphate amidotransferase-independent phosphoribosyl amine synthesis from ribose 5-phosphate and glutamine or asparagine. J. Biol. Chem. 282(39):28379-84
  • Dougherty MJ, Boyd JM, Downs DM. 2006. Inhibition of fructose-1,6-bisphosphatase by aminoimidazole carboxamide ribotide prevents growth of Salmonella enterica purH mutants on glycerol. J. Biol. Chem. 281(45):33892-9
  • Browne BA, Ramos AI, Downs DM. 2006. PurF-independent phosphoribosyl amine formation in yjgF mutants of Salmonella enterica utilizes the tryptophan biosynthetic enzyme complex anthranilate synthase-phosphoribosyltransferase. J. Bacteriol. 188(19):6786-92 PMC1595518
  • Dougherty MJ, Downs DM. 2006. A connection between iron-sulfur cluster metabolism and the biosynthesis of 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate in Salmonella enterica. Microbiology (Reading, Engl.) 152(Pt 8):2345-53
  • Downs DM. 2006. Understanding microbial metabolism. Annu. Rev. Microbiol. 60:533-59
  • Schmitz GE, Downs DM. 2006. An allele of gyrA prevents Salmonella enterica serovar Typhimurium from using succinate as a carbon source. J. Bacteriol. 188(8):3126-9 PMC1446994
  • Cui Q, Thorgersen MP, Westler WM, Markley JL, Downs DM. 2006. Solution structure of YggX: a prokaryotic protein involved in Fe(II) trafficking. Proteins 62(3):578-86
  • Vivas E, Skovran E, Downs DM. 2006. Salmonella enterica strains lacking the frataxin homolog CyaY show defects in Fe-S cluster metabolism in vivo. J. Bacteriol. 188(3):1175-9 PMC1347345
  • Downs DM, Schmitz GE, Skovran E. 2005. Probing the complex system of metabolic integration. Prog. Nucleic Acid Res. Mol. Biol. 80:43-94
  • Zhang Y, Dougherty M, Downs DM, Ealick SE. 2004. Crystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily. Structure 12(10):1809-21
  • Martinez-Gomez NC, Robers M, Downs DM. 2004. Mutational analysis of ThiH, a member of the radical S-adenosylmethionine (AdoMet) protein superfamily. J. Biol. Chem. 279(39):40505-10
  • Dougherty MJ, Downs DM. 2004. A mutant allele of rpoD results in increased conversion of aminoimidazole ribotide to hydroxymethyl pyrimidine in Salmonella enterica. J. Bacteriol. 186(12):4034-7 PMC419934
  • Lauhon CT, Skovran E, Urbina HD, Downs DM, Vickery LE. 2004. 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. 279(19):19551-8
  • Schmitz G, Downs DM. 2004. 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. 186(3):803-10 PMC321505
  • Skovran E, Lauhon CT, Downs DM. 2004. Lack of YggX results in chronic oxidative stress and uncovers subtle defects in Fe-S cluster metabolism in Salmonella enterica. J. Bacteriol. 186(22):7626-34 PMC524902
  • Ramos I, Downs DM. 2003. Anthranilate synthase can generate sufficient phosphoribosyl amine for thiamine synthesis in Salmonella enterica. J. Bacteriol. 185(17):5125-32 PMC180985
  • Gralnick JA, Downs DM. 2003. 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. 278(23):20708-15
  • Downs DM. 2003. Genomics and bacterial metabolism. Curr Issues Mol Biol 5(1):17-25
  • Beck BJ, Huelsmeyer M, Paul S, Downs DM. 2003. A mutation in the essential gene gmk (encoding guanlyate kinase) generates a requirement for adenine at low temperature in Salmonella enterica. J. Bacteriol. 185(22):6732-5 PMC262127
  • Dougherty M, Downs DM. 2002. 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. 185(1):332-9 PMC141821
  • Skovran E, Downs DM. 2002. Lack of the ApbC or ApbE protein results in a defect in Fe-S cluster metabolism in Salmonella enterica serovar Typhimurium. J. Bacteriol. 185(1):98-106 PMC141979
  • Allen S, Zilles JL, Downs DM. 2002. 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. 184(22):6130-7 PMC151968
  • Rubio A, Downs DM. 2002. Elevated levels of ketopantoate hydroxymethyltransferase (PanB) lead to a physiologically significant coenzyme A elevation in Salmonella enterica serovar Typhimurium. J. Bacteriol. 184(10):2827-32 PMC135036
  • Zilles JL, Kappock TJ, Stubbe J, Downs DM. 2001. Altered pathway routing in a class of Salmonella enterica serovar Typhimurium mutants defective in aminoimidazole ribonucleotide synthetase. J. Bacteriol. 183(7):2234-40 PMC95129
  • Frodyma M, Rubio A, Downs DM. 2000. 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. 182(1):236-40 PMC94266
  • Claas K, Weber S, Downs DM. 2000. 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. 182(1):228-32 PMC94264
  • Skovran E, Downs DM. 2000. Metabolic defects caused by mutations in the isc gene cluster in Salmonella enterica serovar typhimurium: implications for thiamine synthesis. J. Bacteriol. 182(14):3896-903 PMC94571
  • Zilles JL, Croal LR, Downs DM. 2000. Action of the thiamine antagonist bacimethrin on thiamine biosynthesis. J. Bacteriol. 182(19):5606-10 PMC111009
  • Beck BJ, Downs DM. 2000. A periplasmic location is essential for the role of the ApbE lipoprotein in thiamine synthesis in Salmonella typhimurium. J. Bacteriol. 181(23):7285-90 PMC103691
  • Downs DM, Escalante-Semerena JC. 2000. Impact of genomics and genetics on the elucidation of bacterial metabolism. Methods 20(1):47-54
  • Enos-Berlage JL, Downs DM. 1999. 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. 181(3):841-8 PMC93450
  • Enos-Berlage JL, Langendorf MJ, Downs DM. 1999. Complex metabolic phenotypes caused by a mutation in yjgF, encoding a member of the highly conserved YER057c/YjgF family of proteins. J. Bacteriol. 180(24):6519-28 PMC107753
  • Begley TP, Downs DM, Ealick SE, McLafferty FW, Van Loon AP, Taylor S, Campobasso N, Chiu HJ, Kinsland C, Reddick JJ, Xi J. 1999. Thiamin biosynthesis in prokaryotes. Arch. Microbiol. 171(5):293-300
  • Christian T, Downs DM. 1999. Defects in pyruvate kinase cause a conditional increase of thiamine synthesis in Salmonella typhimurium. Can. J. Microbiol. 45(7):565-72
  • Beck BJ, Downs DM. 1998. The apbE gene encodes a lipoprotein involved in thiamine synthesis in Salmonella typhimurium. J. Bacteriol. 180(4):885-91 PMC106968
  • Petersen LA, Downs DM. 1997. Identification and characterization of an operon in Salmonella typhimurium involved in thiamine biosynthesis. J. Bacteriol. 179(15):4894-900 PMC179339
  • Beck BJ, Connolly LE, De Las PeƱas A, Downs DM. 1997. Evidence that rseC, a gene in the rpoE cluster, has a role in thiamine synthesis in Salmonella typhimurium. J. Bacteriol. 179(20):6504-8 PMC179570
  • Webb E, Claas K, Downs DM. 1997. Characterization of thiI, a new gene involved in thiazole biosynthesis in Salmonella typhimurium. J. Bacteriol. 179(13):4399-402 PMC179266
  • Enos-Berlage JL, Downs DM. 1997. Mutations in sdh (succinate dehydrogenase genes) alter the thiamine requirement of Salmonella typhimurium. J. Bacteriol. 179(12):3989-96 PMC179209
  • Zilles JL, Downs DM. 1997. A novel involvement of the PurG and PurI proteins in thiamine synthesis via the alternative pyrimidine biosynthetic (APB) pathway in Salmonella typhimurium. Genetics 144(3):883-92 PMC1207629
  • Webb E, Febres F, Downs DM. 1996. Thiamine pyrophosphate (TPP) negatively regulates transcription of some thi genes of Salmonella typhimurium. J. Bacteriol. 178(9):2533-8 PMC177976
  • Petersen L, Downs DM. 1996. Mutations in apbC (mrp) prevent function of the alternative pyrimidine biosynthetic pathway in Salmonella typhimurium. J. Bacteriol. 178(19):5676-82 PMC178406
  • Enos-Berlage JL, Downs DM. 1996. Involvement of the oxidative pentose phosphate pathway in thiamine biosynthesis in Salmonella typhimurium. J. Bacteriol. 178(5):1476-9 PMC177826
  • Petersen L, Enos-Berlage J, Downs DM. 1996. Genetic analysis of metabolic crosstalk and its impact on thiamine synthesis in Salmonella typhimurium. Genetics 143(1):37-44 PMC1207269
  • Downs DM, Petersen L. 1994. apbA, a new genetic locus involved in thiamine biosynthesis in Salmonella typhimurium. J. Bacteriol. 176(16):4858-64 PMC196320
  • Downs DM, Ludden PW, Shah VK. 1993. Accumulation of factor F395 in nifNE mutants of Klebsiella pneumoniae. Can. J. Microbiol. 39(3):351-4
  • Downs DM. 1992. Evidence for a new, oxygen-regulated biosynthetic pathway for the pyrimidine moiety of thiamine in Salmonella typhimurium. J. Bacteriol. 174(5):1515-21 PMC206546
  • Downs DM, Roth JR. 1991. Synthesis of thiamine in Salmonella typhimurium independent of the purF function. J. Bacteriol. 173(20):6597-604 PMC208997
  • Downs DM, Ludden PW, Shah VK. 1990. Synthesis of the iron-molybdenum cofactor of nitrogenase is inhibited by a low-molecular-weight metabolite of Klebsiella pneumoniae. J. Bacteriol. 172(10):6084-9 PMC526933
  • Downs DM, Roth JR. 1988. A novel P22 prophage in Salmonella typhimurium. Genetics 117(3):367-80 PMC1203213