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Supplementary Information Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle. Grey filled shapes represent phosphorylated metabolites. Figure S5: Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-sensitivity are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle. Coloured shapes represent phosphorylated metabolites. Table S1. Synthetic Array Tools (version 1.0) was used to normalize and score the silver-resistant and -sensitive gene hits as a means of representing the growth differences in Escherichia coli K12 BW25113 in the presence of 100μM silver nitrate. Genes with a normalized score <0 are implied as silver-sensitive and those with a score of >0 are silver-resistant hits. ID Name Function1 Score2 P-value3 bifunctional aspartokinase/homoserine JW0001 thrA -0.0534 0.2569 dehydrogenase 1 JW0002 thrB homoserine kinase -0.0004 0.9944 JW0002 thrB homoserine kinase 0.2060 0.0897 JW0003 thrC L-threonine synthase 0.1294 0.0041 DUF2502 family putative periplasmic JW0004 yaaX 0.0001 0.9941 protein peroxide resistance protein, lowers JW0005 yaaA 0.0270 0.0685 intracellular iron JW0006 yaaJ putative transporter 0.0901 0.0002 JW0007 talB transaldolase B -0.1347 0.0009 molybdochelatase incorporating JW0008 mog -0.0590 0.0002 molybdenum into molybdopterin JW0009 yaaH succinate-acetate transporter 0.0493 0.1511 JW0010 yaaW UPF0174 family protein 0.0270 0.5107 JW0012 yaaI UPF0412 family protein 0.0007 0.6916 JW0013 dnaK chaperone Hsp70, with co-chaperone DnaJ 0.0990 0.0028 JW0014 dnaJ chaperone Hsp40, DnaK co-chaperone -0.1171 0.0037 JW0018 nhaA sodium-proton antiporter -0.0472 0.2963 JW0019 nhaR transcriptional activator of nhaA -0.0016 0.9484 JW0022 rpsT 30S ribosomal subunit protein S20 -0.0188 0.5675 JW0024 ileS isoleucyl-tRNA synthetase 0.0301 0.4161 FKBP-type peptidyl-prolyl cis-trans JW0026 fkpB -0.0763 0.4062 isomerase (rotamase) JW0028 rihC ribonucleoside hydrolase 3 0.0220 0.1171 carbamoyl phosphate synthetase small JW0030 carA -0.0749 0.0615 subunit, glutamine amidotransferase carbamoyl-phosphate synthase large JW0031 carB 0.0024 0.9649 subunit JW0033 caiF cai operon transcriptional activator 0.0552 0.2974 JW0035 caiD carnitinyl-CoA dehydratase 0.0320 0.1290 putative crotonobetaine/carnitine-CoA JW0036 caiC -0.2512 0.0002 ligase crotonobetainyl CoA:carnitine CoA JW0037 caiB -0.0480 0.1644 transferase crotonobetaine reductase subunit II, FAD- JW0038 caiA -0.0579 0.1935 binding JW0039 caiT putative transporter 0.0146 0.8119 anaerobic carnitine reduction putative JW0040 fixA 0.0458 0.0029 electron transfer flavoprotein subunit putative electron transfer flavoprotein, JW0041 fixB 0.0915 0.0037 NAD/FAD-binding domain and ETFP adenine nucleotide-binding domain-like protein JW0042 fixC putative oxidoreductase -0.0490 0.0303 JW0043 fixX putative 4Fe-4S ferredoxin-type protein 0.0065 0.8522 putative MFS sugar transporter; membrane JW0044 yaaU 0.1737 0.2868 protein potassium-efflux system ancillary protein JW0045 kefF for KefC, glutathione-regulated; quinone -0.0352 0.3635 oxidoreductase, FMN-dependent JW0046 kefC potassium:proton antiporter -0.0163 0.5461 JW0048 apaH diadenosine tetraphosphatase -0.1556 0.2481 protein associated with Co2+ and Mg2+ JW0049 apaG 0.0098 0.8831 efflux 16S rRNA m(6)A1518, m(6)A1519 JW0050 ksgA 0.0648 0.0128 dimethyltransferase, SAM-dependent 4-hydroxy-L-threonine phosphate JW0051 pdxA 0.2949 0.0557 dehydrogenase, NAD-dependent JW0052 surA peptidyl-prolyl cis-trans isomerase (PPIase) 0.0420 0.1053 membrane-anchored DnaK co-chaperone, JW0054 djlA 0.0149 0.3970 DNA-binding protein pseudogene, pentapeptide repeats- JW0055 yabP -0.0133 0.6481 containing dual specificity 23S rRNA pseudouridine(746), tRNA JW0057 rluA -0.0156 0.5632 pseudouridine(32) synthase, SAM- dependent RNA polymerase remodeling/recycling JW0058 hepA factor ATPase; RNA polymerase-associated, -0.1693 0.0063 ATP-dependent RNA translocase JW0059 polB DNA polymerase II 0.0069 0.8212 ara regulon transcriptional activator; JW0063 araC -0.1094 0.0056 autorepressor thiamine/thiamine pyrophosphate ABC JW0065 thiQ -0.0575 0.0012 transporter ATPase thiamine/thiamine pyrophosphate ABC JW0066 thiP -0.0545 0.0856 transporter permease thiamine/thiamine pyrophosphate/thiamine JW0067 tbpA monophosphate ABC transporter -0.0160 0.5373 periplasmic binding protein transcriptional DNA-binding transcriptional JW0068 sgrR -0.0487 0.0562 activator of sgrS sRNA JW0069 setA broad specificity sugar efflux system -0.1094 0.3620 3-isopropylmalate dehydratase small JW0070 leuD 0.0129 0.8362 subunit 3-isopropylmalate dehydratase large JW0071 leuC 0.1346 0.0024 subunit JW0073 leuA 2-isopropylmalate synthase -0.0199 0.5889 JW0074 leuL leu operon leader peptide 0.0472 0.0718 JW0075 leuO global transcription factor -0.1227 0.0001 JW0076 ilvI acetolactate synthase 3 large subunit -0.0103 0.6806 acetolactate synthase 3, small subunit, JW0077 ilvH -0.0073 0.7893 valine-sensitive transcriptional repressor-activator for JW0078 fruR 0.0608 0.0029 carbon metabolism JW0079 mraZ RsmH methytransferase inhibitor -0.0571 0.0421 16S rRNA m(4)C1402 methyltransferase, JW0080 mraW 0.0118 0.5659 SAM-dependent JW0090 ddlB D-alanine:D-alanine ligase 0.1386 0.0002 dGTP-preferring nucleoside triphosphate JW0097 mutT -0.1218 0.3731 pyrophosphohydrolase JW0099 yacF FtsZ stabilizer 0.0615 0.0567 JW0100 coaE dephospho-CoA kinase -0.0409 0.0817 JW0101 guaC GMP reductase -0.1751 0.0434 assembly protein in type IV pilin biogenesis, JW0102 hofC -0.0395 0.1599 transmembrane protein T2SE secretion family protein; P-loop JW0103 hofB 0.0946 0.4871 ATPase superfamily protein JW0104 ppdD putative prepilin peptidase-dependent pilin 0.0023 0.9355 JW0105 nadC quinolinate phosphoribosyltransferase 0.4257 0.0000 1,6-anhydro-N-acetylmuramyl-L-alanine JW0106 ampD -0.0929 0.0752 amidase, Zn-dependent; murein amidase ampicillin resistance inner membrane JW0107 ampE protein; putative signaling protein in beta- 0.1436 0.0137 lactamase regulation JW0108 aroP aromatic amino acid transporter -0.3680 0.0491 pyruvate dehydrogenase complex repressor; JW0109 pdhR 0.0247 0.5738 autorepressor pyruvate dehydrogenase, decarboxylase JW0110 aceE component E1, thiamine triphosphate- 0.0364 0.2135 binding pyruvate dehydrogenase, JW0111 aceF -0.0775 0.0140 dihydrolipoyltransacetylase component E2 dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2-oxoglutarate JW0112 lpd dehydrogenases complexes; glycine 0.0103 0.5847 cleavage system L protein; dihydrolipoamide dehydrogenase JW0113 yacH DUF3300 family protein -0.0650 0.0010 aconitate hydratase 2; aconitase B; 2-methyl- JW0114 acnB 0.0361 0.0767 cis-aconitate hydratase JW0115 yacL UPF0231 family protein -0.0922 0.0144 JW0116 speD S-adenosylmethionine decarboxylase -0.1070 0.0060 spermidine synthase (putrescine JW0117 speE 0.2887 0.0469 aminopropyltransferase) JW0118 yacC PulS_OutS family protein 0.0084 0.6483 JW0119 cueO multicopper oxidase (laccase) 0.0047 0.9004 JW0120 gcd glucose dehydrogenase -0.0185 0.3599 JW0123 yadG putative ABC transporter ATPase -0.1331 0.0230 JW0124 yadH putative ABC transporter permease -0.1005 0.0054 JW0125 yadI putative PTS Enzyme IIA -0.0348 0.0541 putative polysaccharide deacetylase JW0126 yadE -0.0887 0.0027 lipoprotein JW0127 panD aspartate 1-decarboxylase -0.0101 0.6568 JW0129 panC pantothenate synthetase -0.0502 0.1273 3-methyl-2-oxobutanoate JW0130 panB 0.0583 0.3930 hydroxymethyltransferase JW0131 yadC putative fimbrial-like adhesin protein -0.0327 0.1033 JW0132 yadK putative fimbrial-like
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