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Comparing the Mechanisms of Metal Action in Bacteria: Insight Into Novel Genes Involved in Silver, Gallium and Copper Resistance and Toxicity in Escherichia Coli

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Comparing the Mechanisms of Metal Action in Bacteria: Insight Into Novel Genes Involved in Silver, Gallium and Copper Resistance and Toxicity in Escherichia Coli University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2019-07-25 Comparing the mechanisms of metal action in bacteria: insight into novel genes involved in silver, gallium and copper resistance and toxicity in Escherichia coli Gugala, Natalie Gugala, N. (2019). Comparing the mechanisms of metal action in bacteria: insight into novel genes involved in silver, gallium and copper resistance and toxicity in Escherichia coli (Unpublished doctoral thesis). University of Calgary, Calgary, AB. http://hdl.handle.net/1880/110682 doctoral thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. 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Downloaded from PRISM: https://prism.ucalgary.ca ID Name Description Score P-value JW0001 thrA Bifunctional aspartokinase/homoserine0.0472 dehydrogenase0.4974 1 JW0002 thrB Homoserine kinase 0.4535 0.0103 JW0003 thrC L-threonine synthase 0.0791 0.0185 JW0004 yaaX DUF2502 family putative periplasmic0.0959 protein 0.0095 JW0005 yaaA Peroxide resistance protein, lowers0.0345 intracellular 0.4262iron JW0006 yaaJ Putative transporter 0.0623 0.1141 JW0008 mog Molybdochelatase incorporating0.0269 molybdenum into0.1935 molybdopterin JW0009 yaaH Succinate-acetate transporter 0.0876 0.0017 JW0010 yaaW UPF0174 family protein 0.0694 0.2053 JW0012 yaaI UPF0412 family protein -0.0435 0.1445 JW0018 nhaA Sodium-proton antiporter -0.0091 0.7726 JW0019 nhaR Transcriptional activator of nhaa-0.0725 0.0417 JW0022 rpsT 30S ribosomal subunit protein 0.002S20 0.9553 JW0024 ileS Isoleucyl-trna synthetase -0.1268 0.1086 JW0026 fkpB FKBP-type peptidyl-prolyl cis-trans0.0334 isomerase (rotamase)0.5347 JW0028 rihC Ribonucleoside hydrolase 3 0.0069 0.9094 JW0030 carA Carbamoyl phosphate synthetase0.0893 small subunit,0.1038 glutamine amidotransferase JW0031 carB Carbamoyl-phosphate synthase0.0651 large subunit 0.1219 JW0033 caiF Cai operon transcriptional activator0.114 0.0898 JW0035 caiD Carnitinyl-coa dehydratase 0.025 0.5492 JW0037 caiB Crotonobetainyl coa:carnitine 0.0036coa transferase 0.9101 JW0038 caiA Crotonobetaine reductase subunit-0.0047 II, FAD-binding0.9263 JW0039 caiT Putative transporter 0.4032 0.0002 JW0040 fixA Anaerobic carnitine reduction putative0.058 electron 0.1061transfer flavoprotein subunit JW0041 fixB Putative electron transfer flavoprotein,-0.0146 NAD/FAD-binding0.6336 domain and ETFP adenine nucleotide-binding domain-like protein JW0042 fixC Putative oxidoreductase -0.0065 0.8901 JW0043 fixX Putative 4Fe-4S ferredoxin-type0.0114 protein 0.6153 JW0044 yaaU Putative MFS sugar transporter;0.237 membrane protein0.004 JW0045 kefF Potassium-efflux system ancillary0.0365 protein for kefc,0.4077 glutathione-regulated; quinone oxidoreductase, FMN-dependent JW0046 kefC Potassium:proton antiporter 0.0821 0.1587 JW0048 apaH Diadenosine tetraphosphatase0.0322 0.4279 JW0049 apaG Protein associated with Co2+ and0.0018 Mg2+ efflux 0.9319 JW0050 ksgA 16S rrna m(6)A1518, m(6)A15190.0183 dimethyltransferase,0.4308 SAM-dependent JW0051 pdxA 4-hydroxy-L-threonine phosphate-0.0399 dehydrogenase,0.2976 NAD-dependent JW0052 surA Peptidyl-prolyl cis-trans isomerase0.0615 (ppiase) 0.076 JW0054 djlA Membrane-anchored dnak co-chaperone,-0.0886 DNA-binding0.0213 protein JW0055 yabP Pseudogene, pentapeptide repeats-containing-0.011 0.7437 JW0057 rluA Dual specificity 23S rrna pseudouridine(746),-0.0337 trna0.3005 pseudouridine(32) synthase, SAM-dependent JW0058 hepA RNA polymerase remodeling/recycling-0.035 factor atpase;0.0106 RNA polymerase-associated, ATP-dependent RNA translocase JW0059 polB DNA polymerase II -0.1108 0.0259 JW0063 araC Ara regulon transcriptional activator;-0.0071 autorepressor0.6309 JW0065 thiQ Thiamine/thiamine pyrophosphate-0.0016 ABC transporter0.9684 atpase JW0066 thiP Thiamine/thiamine pyrophosphate-0.0074 ABC transporter0.7744 permease JW0067 tbpA Thiamine/thiamine pyrophosphate/thiamine-0.0807 monophosphate0.0846 ABC transporter periplasmic binding protein JW0068 sgrR Transcriptional DNA-binding transcriptional0.0142 activator0.5347 of sgrs srna JW0069 setA Broad specificity sugar efflux system0.1591 0.0062 JW0070 leuD 3-isopropylmalate dehydratase0.1276 small subunit 0.0071 JW0071 leuC 3-isopropylmalate dehydratase0.2046 large subunit 0.0029 JW0073 leuA 2-isopropylmalate synthase 0.3018 0.0007 JW0074 leuL Leu operon leader peptide 0.1839 0.0154 JW0075 leuO Global transcription factor -0.0954 0.0058 JW0076 ilvI Acetolactate synthase 3 large -0.0369subunit 0.371 JW0077 ilvH Acetolactate synthase 3, small-0.0466 subunit, valine-sensitive0.266 JW0079 mraZ Rsmh methytransferase inhibitor0.0949 0.0169 JW0080 mraW 16S rrna m(4)C1402 methyltransferase,-0.0108 SAM-dependent0.7186 JW0090 ddlB D-alanine:D-alanine ligase 0.0217 0.6523 JW0097 mutT Dgtp-preferring nucleoside triphosphate0.0637 pyrophosphohydrolase0.0378 JW0099 yacF Ftsz stabilizer 0.0369 0.3961 JW0100 coaE Dephospho-coa kinase -0.0713 0.2217 JW0101 guaC GMP reductase -0.0906 0.0906 JW0102 hofC Assembly protein in type IV pilin0.0423 biogenesis, transmembrane0.2413 protein JW0103 hofB T2SE secretion family protein; P-loop0.1302 atpase superfamily0.2282 protein JW0104 ppdD Putative prepilin peptidase-dependent0.0307 pilin 0.2973 JW0105 nadC Quinolinate phosphoribosyltransferase0.0531 0.2658 JW0106 ampD 1,6-anhydro-N-acetylmuramyl-L-alanine-0.0325 amidase,0.2875 Zn-dependent; murein amidase JW0107 ampE Ampicillin resistance inner membrane0.0507 protein; putative0.149 signaling protein in beta-lactamase regulation JW0108 aroP Aromatic amino acid transporter-0.004 0.9494 JW0109 pdhR Pyruvate dehydrogenase complex0.3527 repressor; autorepressor0.0006 JW0110 aceE Pyruvate dehydrogenase, decarboxylase0.0231 component0.6135 E1, thiamine triphosphate-binding JW0111 aceF Pyruvate dehydrogenase, dihydrolipoyltransacetylase-0.0074 0.9198 component E2 JW0112 lpd Dihydrolipoyl dehydrogenase;0.0169 E3 component of0.6226 pyruvate and 2-oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase JW0114 acnB Aconitate hydratase 2; aconitase0.0773 B; 2-methyl-cis-aconitate0.0493 hydratase JW0115 yacL UPF0231 family protein -0.0274 0.5653 JW0116 speD S-adenosylmethionine decarboxylase0.0504 0.1356 JW0117 speE Spermidine synthase (putrescine-0.0934 aminopropyltransferase)0.0296 JW0118 yacC Puls_outs family protein 0.0396 0.0607 JW0119 cueO Multicopper oxidase (laccase)-0.0318 0.2142 JW0120 gcd Glucose dehydrogenase -0.0276 0.4399 JW0123 yadG Putative ABC transporter atpase-0.0423 0.1017 JW0124 yadH Putative ABC transporter permease-0.0854 0.0743 JW0125 yadI Putative PTS Enzyme IIA 0.0623 0.1383 JW0126 yadE Putative polysaccharide deacetylase0.0522 lipoprotein0.0587 JW0127 panD Aspartate 1-decarboxylase -0.054 0.3328 JW0129 panC Pantothenate synthetase 0.0956 0.0027 JW0130 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase-0.0001 0.9988 JW0131 yadC Putative fimbrial-like adhesin -0.0385protein 0.2861 JW0132 yadK Putative fimbrial-like adhesin protein0.0591 0.0284 JW0133 yadL Putative fimbrial-like adhesin -0.0544protein 0.3251 JW0134 yadM Putative fimbrial-like adhesin -0.0475protein 0.1698 JW0135 htrE Putative outer membrane usher0.0886 protein 0.025 JW0136 ecpD Putative periplasmic pilin chaperone0.0361 0.0565 JW0137 yadN Putative fimbrial-like adhesin protein0.0044 0.9023 JW0141 dksA Transcriptional regulator of rrna0.0751 transcription; dnak0.169 suppressor protein JW0142 sfsA Sugar fermentation stimulation0.0127 protein A 0.7298 JW0144 hrpB Putative ATP-dependent helicase-0.0254 0.2078 JW0145 mrcB Fused glycosyl transferase and0.2493 transpeptidase 0.0002 JW0147 fhuC Iron(3+)-hydroxamate import ABC0.011 transporter atpase0.7885 JW0148 fhuD Iron(3+)-hydroxamate import-0.0405 ABC transporter periplasmic0.6255 binding protein JW0149 fhuB Iron(3+)-hydroxamate import ABC0.0109 transporter permease0.8317 JW0153 yadS UPF0126 family inner membrane0.0828 protein 0.0008 JW0154 btuF Vitamin B12 ABC transporter periplasmic0.0151 binding0.5763 protein JW0155 pfs 5'-methylthioadenosine/S-adenosylhomocysteine-0.3293 0.0001 nucleosidase JW0156 dgt Deoxyguanosine triphosphate0.0022 triphosphohydrolase0.9574 JW0157 degP Serine endoprotease (protease0.0039 Do), membrane-associated0.9025 JW0159 yaeH UPF0325 family protein 0.0036 0.9317 JW0162 glnD Uridylyltransferase -0.0336 0.2002 JW0173 hlpA Periplasmic chaperone 0.09 0.0279 JW0178 rnhB Ribonuclease HII, degrades RNA0.0321 of DNA-RNA hybrids0.2498 JW0181 ldcC Lysine decarboxylase 2, constitutive-0.049 0.2259 JW0182 yaeR Putative lyase -0.0432 0.372 JW0185 yaeP UPF0253 family protein 0.0589 0.0006 JW0186 yaeQ PDDEXK superfamily protein 0.0076 0.8627 JW0187 yaeJ Alternative stalled-ribosome rescue0.0106 factor B; peptidyl-trna0.8532 hydrolase, ribosome-attached JW0188 nlpE Lipoprotein involved with copper-0.0371 homeostasis and0.3837 adhesion JW0191 yaeB Trna-Thr(GGU) m(6)t(6)A37 methyltransferase,-0.0365 0.3118SAM-dependent JW0192 rcsF Putative outer membrane protein0.0082 0.7331 JW0193 metQ DL-methionine transporter subunit0.0465 0.1112 JW0194 metI DL-methionine transporter subunit-0.0544 0.2145 JW0195 metN DL-methionine transporter subunit0.0282 0.4134 JW0196 gmhB D,D-heptose 1,7-bisphosphate-0.0387 phosphatase 0.2674 JW0197 dkgB 2,5-diketo-D-gluconate
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