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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bacteria: insight into novel genes involved in silver, gallium and copper resistance and toxicity in Escherichia coli (Unpublished doctoral thesis).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 Gene Names GO terms (biological process) Score aaeA aaeA // "yhcQ"carboxylic // "b3241" acid // transport "ECK3230" // "transmembrane transport" -0.0487841 aaeB aaeB // "yhcP"transmembrane // "b3240" // "ECK3229"transport // "carboxylic acid transport" 0.10667059 aaeR aaeR // "yhcS"positive // "qseA" regulation // "b3243" of transcription, // "ECK3232" DNA-templated // "DNA-templated0.18076241 transcription, initiation" // "regulation of transcription, DNA-templated" // "transcription, DNA-templated" aaeX aaeX // "yhcR" // "b3242" // "ECK3231" 0.06718923 aas aas // "b2836"phospholipid // "ECK2832" biosynthetic process // "metabolic process" // "fatty0.30458777 acid metabolic process" aat aat // "ycaA"protein // "b0885" catabolic // "ECK0876" process -0.0732 abgA abgA // "ydaJ"proteolysis // "b1338" // //"folic "ECK1334" acid catabolic process" 0.08978529 abgB abgB // "ydaI"proteolysis // "b1337" // // "folic "ECK1333" acid catabolic process" 0.22717458 abgR abgR // "b1339"regulation // "ECK1335" of transcription, DNA-templated // "transcription, DNA-templated"0.06734757 abgT abgT // "ydaH"p-aminobenzoyl-glutamate // "b1336" // "ECK1332" transmembrane transport // "amino-0.1126479 acid transport" // "p-aminobenzoyl-glutamate transport" abrB abrB // "ybgN"regulation // "b0715" of gene// "ECK0704" expression -0.0573451 aceA aceA // "icl" //carboxylic "b4015" acid // "ECK4007" metabolic process // "tricarboxylic acid cycle" // "glyoxylate0.2981715 cycle" aceB aceB // "mas"tricarboxylic // "b4014" acid // "ECK4006" cycle // "glyoxylate cycle" -0.0520439 aceE aceE // "b0114"oxidation-reduction // "ECK0113" process // "glycolytic process" 0.08209107 aceF aceF // "b0115"pyruvate // "ECK0114" metabolic process // "acetyl-CoA biosynthetic process -0.0435432from pyruvate" // "glycolytic process" aceK aceK // "b4016"peptidyl-serine // "ECK4008" dephosphorylation // "phosphorylation" // "glucose-0.018376 metabolic process" // "peptidyl-serine phosphorylation" // "regulation of catalytic activity" // "tricarboxylic acid cycle" // "glyoxylate cycle" ackA ackA // "b2296"single-species // "ECK2290" biofilm formation on inanimate substrate // "acetate0.11404148 metabolic process" // "organic acid metabolic process" // "propionate biosynthetic process" // "acetate biosynthetic process" // "acetyl-CoA biosynthetic process" // "phosphorylation" acnA acnA // "acn"citrate // "b1276" metabolic // "ECK1271" process // "glyoxylate cycle" // "anaerobic respiration"-0.2655182 // "response to oxidative stress" // "tricarboxylic acid cycle" acnB acnB // "yacJ"regulation // "yacI" of// translation"b0118" // //"ECK0117" "glyoxylate cycle" // "propionate catabolic0.03648468 process, 2-methylcitrate cycle" // "tricarboxylic acid cycle" acpT acpT // "yhhU"lysine // "b3475" biosynthetic // "ECK3459" process via aminoadipic acid // "peptidyl-serine0.03735872 phosphopantetheinylation" // "fatty acid biosynthetic process" acrA acrA // "sipB"drug // "Mb" transmembrane // "lir" // "mbl" transport // "mtcA" // "response // "nbsA" to //toxic "b0463" substance" // "ECK0457"-0.0131383 // "alkane transport" // "fatty acid transport" // "response to drug" // "drug transmembrane export" // "bile acid and bile salt transport" // "transmembrane transport" // "response to antibiotic" acrB acrB // "acrE"transmembrane // "b0462" // "ECK0456" transport // "drug transmembrane transport" 0.27424717// "response to antibiotic" // "alkane transport" // "fatty acid transport" // "enterobactin transport" // "response to toxic substance" // "bile acid and bile salt transport" // "drug transmembrane export" // "drug export" // "response to drug" acrD acrD // "yffA"response // "b2470" to antibiotic// "ECK2465" // "response to toxic substance" // "bile acid-0.0236443 and bile salt transport" // "drug transmembrane export" // "transmembrane transport" // "drug export" // "drug transmembrane transport" acrE acrE // "envC"response // "b3265" to drug // "ECK3252" // "drug transmembrane transport" // "response0.0937572 to antibiotic" // "transmembrane transport" acrF acrF // "envD"transmembrane // "b3266" // "ECK3253" transport // "drug transmembrane transport" -0.2791022 acrR acrR // "ybaH"negative // "b0464" regulation // "ECK0458" of transcription, DNA-templated // "response0.16977651 to drug" // "transcription, DNA-templated" acs acs // "yfaC" chemotaxis// "acsA" // // "b4069" "protein // deacetylation" "ECK4062" // "post-translational protein-0.0652781 acetylation" // "peptidyl-lysine acetylation" // "acetyl-CoA biosynthetic process from acetate" // "acetate catabolic process" actP actP // "yjcG"tellurite // "b4067" transport // "ECK4060" // "glycolate transmembrane transport" // "transmembrane-0.1122096 transport" // "ion transport" // "plasma membrane acetate transport" // "sodium ion transport" ada ada // "b2213"peptidyl-cysteine // "ECK2205" methylation // "positive regulation of transcription,0.25814502 DNA-templated" // "negative regulation of transcription, DNA-templated" // "metabolic process" // "DNA demethylation" // "regulation of transcription, DNA-templated" // "DNA dealkylation involved in DNA repair" // "methylation" // "cellular response to DNA damage stimulus" // "DNA repair" add add // "b1623"inosine // "ECK1618" biosynthetic process // "hypoxanthine biosynthetic process"-0.3914476 // "hypoxanthine salvage" // "purine nucleotide salvage" // "purine nucleotide interconversion" // "adenosine catabolic process" // "purine ribonucleoside monophosphate biosynthetic process" // "nucleotide metabolic process" // "cellular response to DNA damage stimulus" ade -0.0436342 adhE adhE // "adhC"metabolic // "ana" process // "b1241" // "alcohol // "ECK1235" metabolic process" // "carbon utilization"0.09847238 // "ethanol biosynthetic process" // "oxidation-reduction process" adhP adhP // "yddN"acetaldehyde // "b1478" catabolic// "ECK1472" process // "response to ethanol" // "cellular0.1536338 response to DNA damage stimulus" // "oxidation-reduction process" adiA adiA // "adi" cellular// "b4117" amino // "ECK4110"acid metabolic process // "arginine catabolic process"0.01161927 // "intracellular pH elevation" adiC adiC // "yjdD"transmembrane // "yjdE" // "b4115" transport // "ECK4108" // "arginine transmembrane transport"-0.0074044 // "amino acid transport" // "amino acid transmembrane transport" // "intracellular pH elevation" adiY adiY // "b4116"regulation // "ECK4109" of transcription, DNA-templated // "positive regulation0.12767056 of transcription, DNA-templated" aegA aegA // "yffG"glutamate // "b2468" biosynthetic // "ECK2463" process // "oxidation-reduction process"-0.0233589 aer aer // "yqjJ" //chemotaxis "air" // "b3072" // "positive // "ECK3062" aerotaxis" // "signal transduction" 0.08846473 aes aes // "ybaC"negative // "b0476" regulation // "ECK0470" of DNA-binding transcription factor activity 0.05525018// "negative regulation of hydrolase activity" afuB afuB // "fbpB" // "b0263" // "ECK0265" 0.02257587 afuC afuC // "fbpC"iron // "yagC"import //into "b0262" cell // "iron// "ECK0264" ion transport" // "ATP hydrolysis coupled-0.0307568 cation transmembrane transport" // "transmembrane transport" // "iron ion homeostasis" // "ion transport" agaA agaA // "yraA" // "b3135" // "ECK3123" -0.0206907 agaB agaB // "yraD"carbohydrate // "b3138" transmembrane// "ECK3126" transport // "phosphorylation" //0.00297853 "carbohydrate transport" // "phosphoenolpyruvate-dependent sugar phosphotransferase system" agaC agaC // "yraE"carbohydrate // "b3139" //transport "ECK3127" // "phosphoenolpyruvate-dependent sugar0.12460596 phosphotransferase system" agaD agaD // "yraF"phosphoenolpyruvate-dependent // "b3140" // "ECK3128" sugar phosphotransferase system0.19496 // "carbohydrate transport" agaI agaI // "yraG"N-acetylneuraminate // "b3141" // "ECK3129" catabolic process // "UDP-N-acetylglucosamine-0.0087468 biosynthetic process" // "N-acetylglucosamine catabolic process" // "glucosamine catabolic process" // "N-acetylglucosamine metabolic process" // "carbohydrate metabolic process" agaR agaR // "yhaW"regulation // "b3131" of transcription, // "ECK3119" DNA-templated -0.3003171 agaS agaS // "yraB"carbohydrate // "b3136" //derivative "ECK3124" metabolic process // "phosphoenolpyruvate-dependent0.28130805 sugar phosphotransferase system" agaV agaV // "yhaY"carbohydrate // "b3133" transmembrane// "ECK3121" transport // "phosphorylation" //0.14020971 "phosphoenolpyruvate-dependent sugar phosphotransferase system" // "carbohydrate transport" agaW agaW // "yhaZ" // "b3134" // "ECK3122" -0.0899568
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