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Mobilization of Iron Stored in Bacterioferritin Is Required for Metabolic Homeostasis in Pseudomonas Aeruginosa

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SUPPORTING INFORMATION Mobilization of Iron Stored in Bacterioferritin is Required for Metabolic Homeostasis in Pseudomonas aeruginosa Achala N. D. Punchi Hewage 1, Leo Fontenot 2, Jessie Guidry 3, Thomas Weldeghiorghis 2, Anil K. Mehta 4, Fabrizio Donnarumma 2, and Mario Rivera 2,* 1 Department of Chemistry, University of Kansas, 2030 Becker Dr., Lawrence, KS, 66047, USA; [email protected] 2 Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA, 70803, USA; [email protected] (L.F); [email protected] (T.W); [email protected] (F.D) 3 Department of Biochemistry and Molecular Biology, Louisiana State University Health Science Center, 1901 Perdido Street, New Orleans, LA, 70112, USA; [email protected] 4 National High Magnetic Field Laboratory, University of Florida, 1149 Newell Drive, Gainesville, FL, 32610, USA; [email protected]. *Corresponding author. E-mail: [email protected] ORCID: 0000-0002-5692-5497 Figure S1. Growth curves and levels of pyoverdine secreted by wt and Δbfd P. aeruginosa cells. (A) P. aeruginosa cells (wt and Δbfd) were cultured in PI media supplemented with 10 µM Fe at 37 °C and shaking at 220 rpm. For the purpose of all the analyses reported in this work, the cells were harvested by centrifugation 30 h post inoculation. (B) Pyoverdine secreted by the cells was measured in the cell-free supernatants by acquiring fluorescence emission spectra (430-550 nm) with excitation at 400 nm (10 nm slit width) and emission at 460 nm (10 nm slit width). Fluorescence intensity normalized to viable cell count (CFU/mL) shows that the Δbfd cells secrete approximately sixfold more pyoverdine than the wt cells. p < 0.01 denoted by ** relative to wt. S2 Table S1: Proteins exhibiting significant abundance differences between wt and Δbfd cells. FC = Protein Metal Name Function Δbfd/wt p value ID binding log2FC Pyoverdine biosynthesis PA2385 PvdQ Acyl-homoserine lactone acylase 3.14 3.9E-10 PA2386 PvdA L-ornithine N(5)-monooxygenase 3.02 1.2E-15 PA2388 FpvR -2.18 1.7E-03 PA2389 PvdR 2.81 2.8E-06 PA2390 PvdT Macrolide export ATP-binding/permease protein 2.73 2.0E-10 PA2391 OpmQ Probable outer membrane protein 2.00 1.5E-04 PA2392 PvdP 4.11 5.2E-10 PA2393 PvdM Probable dipeptidase 3.22 1.3E-13 PA2394 PvdN 3.61 2.3E-11 PA2395 PvdO 3.48 7.9E-16 PA2396 PvdF Pyoverdine synthetase F 3.25 1.1E-10 PA2397 PvdE Pyoverdine biosynthesis protein 3.16 1.6E-12 PA2398 FpvA Ferripyoverdine receptor 1.72 3.3E-07 PA2399 PvdD Pyoverdine synthetase D 2.75 1.8E-13 PA2400 PvdJ Probable non-ribosomal peptide synthetase 2.87 1.4E-12 PA2402 PvdI Pyoverdine peptide synthetase 2.87 4.6E-18 PA2403 FpvG Uncharacterized protein 2.90 6.8E-12 PA2404 FpvH Uncharacterized protein 2.52 1.8E-04 PA2405 FpvJ Probable adhesion protein 2.94 1.6E-11 PA2407 FpvC Probable ATP-binding component of ABC transporter 2.97 1.6E-09 PA2408 FpvD Uncharacterized protein 1.20 1.1E-03 PA2410 FpvF Probable thioesterase 2.44 1.9E-09 PA2411 MbtH domain-containing protein 2.73 6.3E-10 PA2412 L-2,4-diaminobutyrate:2-ketoglutarate 4-aminotransferase 1.20 4.5E-03 PA2413 PvdH L-sorbosone dehydrogenase 3.10 6.2E-19 PA2424 PvdL 2.76 6.2E-20 PA2425 PvdG 1.75 6.3E-05 PA2426 PvdS Sigma factor 0.91 4.8E-03 PA4168 FpvB Second ferric pyoverdine receptor FpvB 0.67 2.9E-01 Pyochelin biosynthesis PA4218 FptX Probable transporter 3.14 2.1E-08 PA4219 YfpB Uncharacterized protein 2.83 9.1E-11 PA4221 FptA Fe(3+)-pyochelin receptor (Fe(III)-pyochelin receptor) 2.50 2.9E-10 PA4222 PchI Probable ATP-binding component of ABC transporter 3.36 8.1E-19 PA4223 PchH Probable ATP-binding component of ABC transporter 3.32 1.8E-11 PA4224 PchG Pyochelin biosynthetic protein 2.74 3.2E-21 PA4225 PchF Pyochelin synthetase 2.38 9.0E-23 PA4226 PchE Dihydroaeruginoic acid synthetase 2.79 9.9E-17 PA4227 PchR Regulatory protein 1.19 4.1E-06 S3 PA4228 PchD Pyochelin biosynthesis protein 2.84 3.4E-17 PA4229 PchC Pyochelin biosynthetic protein 1.14 1.0E-07 PA4230 PchB Isochorismate pyruvate lyase 3.10 6.1E-18 PA4231 PchA Salicylate biosynthesis isochorismate synthase 1.93 1.2E-05 Heme iron acquisition PA0672 HemO Heme oxygenase 1.49 6.9E-13 PA4708 PhuT Heme-transport protein 1.42 2.3E-04 PA4709 PhuS 1.23 3.6E-04 PA4710 PhuR Heme/Hemoglobin uptake outer membrane receptor 2.59 1.5E-14 Other iron acquisition and transport related proteins PA0471 FiuR Probable transmembrane sensor 0.66 5.0E-02 PA2466 FoxA Ferrioxamine receptor FoxA 0.56 7.5E-04 PA3901 FecA Fe(III) dicitrate transport protein FecA Fe 0.81 1.2E-01 PA4514 PiuA Probable outer membrane receptor for iron transport 1.02 1.6E-04 PA4675 OptH Probable TonB-dependent receptor 0.53 4.8E-01 Quorum sensing PA0996 PqsA Anthranilate--CoA ligase 1.71 1.4E-03 PA0997 PqsB Hypothetical protein 2.06 1.6E-06 PA0998 PqsC Hypothetical protein 2.28 1.1E-04 PA0999 PqsD 3-oxoacyl-ACP synthase 2.39 7.2E-11 PA1000 PqsE Thioesterase PqsE 2.08 9.6E-03 PA1871 LasA Protease LasA (Staphylolytic protease) 0.55 8.2E-02 PA2569 Uncharacterized protein 0.78 4.3E-02 PA2570 LecA PA-I galactophilic lectin (PA-IL) (Galactose-binding lectin) 1.53 1.3E-02 PA3476 RhlI Acyl-homoserine-lactone synthase -0.54 9.5E-02 PA3478 RhlB Rhamnosyltransferase chain B 0.71 1.8E-12 PA3479 RhlA 3-(3-hydroxydecanoyloxy)decanoate synthase 0.70 2.3E-08 PA3724 LasB Elastase (Neutral metalloproteinase) (PAE) (Pseudolysin) -0.80 1.1E-01 Phenazine biosynthesis PA1899 PhzA2 Phenazine biosynthesis protein PhzA 1.94 1.2E-03 PA1900 PhzB2 Phenazine biosynthesis protein PhzB 0.99 7.2E-03 PA1904 PhzF2 Probable phenazine biosynthesis protein 0.61 2.2E-01 PA1905 PhzG2 Pyridoxamine 5'-phosphate oxidase 1.22 2.1E-03 PA4213 PhzD1 Phenazine biosynthesis protein PhzD 1.47 1.2E-10 PA4214 PhzE1 Phenazine biosynthesis protein PhzE 0.95 1.3E-10 Carbon metabolism and amino acid metabolism PA0400 MetB Probable cystathionine gamma-lyase 0.57 7.2E-07 PA0792 PrpD Propionate catabolic protein Fe 0.95 1.1E-13 PA0794 Probable aconitate hydratase -0.65 3.9E-08 PA0865 Hpd 4-hydroxyphenylpyruvate dioxygenase (4HPPD) 0.56 2.4E-03 S4 PA1254 LhpC Probable dihydrodipicolinate synthetase -0.74 4.6E-04 PA1255 LhpK Probable trans-3-hydroxy-L-proline dehydratase (T3LHyp -0.90 2.6E-02 dehydratase) PA1260 LhpP Amino acid ABC transporter periplasmic binding protein -0.52 6.9E-02 PA1261 LhpR Probable transcriptional regulator 0.68 3.9E-01 PA1311 PhnX Phosphonoacetaldehyde hydrolase (Phosphonatase) -0.54 4.6E-01 PA1422 GbuR GbuR 0.87 1.2E-01 PA1562 AcnA Aconitate hydratase 1 Fe -0.98 6.2E-15 PA2015 LiuA Putative isovaleryl-CoA dehydrogenase -0.78 2.1E-02 PA2152 Probable trehalose synthase 0.54 2.0E-01 PA2300 ChiC Chitinase 0.76 1.6E-05 PA2416 TreA Periplasmic trehalase 0.81 4.2E-02 PA3120 LeuD 3-isopropylmalate dehydratase small subunit -0.76 3.3E-03 PA3121 LeuC 3-isopropylmalate dehydratase large subunit Fe -0.83 2.1E-07 PA3236 BetX Probable glycine betaine-binding protein -0.68 5.0E-03 PA3374 PhnM Amidohydro_3 domain-containing protein -0.94 9.0E-05 PA3375 PhnL Probable ATP-binding component of ABC transporter -0.56 1.2E-01 PA3376 PhnK Probable ATP-binding component of ABC transporter -0.60 4.2E-03 PA3377 PhnJ Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase -0.76 6.4E-02 PA3378 PhnI Uncharacterized protein -0.97 4.9E-03 PA3379 PhnH Uncharacterized protein -0.80 6.3E-04 PA3380 PhnG Uncharacterized protein -1.09 4.6E-03 PA3417 PdhA Pyruvate dehydrogenase E1 component subunit alpha -0.54 9.5E-02 PA3430 Putative aldolase class 2 protein PA3430 -0.86 3.5E-02 PA3459 Probable glutamine amidotransferase -0.66 2.7E-06 PA3506 Probable decarboxylase Mn -0.62 3.3E-01 PA3524 GloA1 Lactoylglutathione lyase Zn, Ni -0.67 1.2E-02 PA3896 Probable 2-hydroxyacid dehydrogenase 0.49 3.5E-01 PA4150 AcoA Probable dehydrogenase E1 component -0.53 4.0E-01 PA4151 AcoB Acetoin catabolism protein -0.72 2.5E-04 PA4152 AcoC Probable hydrolase -0.67 5.0E-02 PA4333 FumA Probable fumarase Fe -2.08 8.5E-13 PA4470 FumC1 Fumarate hydratase Mn 3.11 8.0E-16 PA4628 LysP Lysine-specific permease 0.65 2.1E-01 PA5354 GlcE Glycolate oxidase subunit GlcE -0.61 2.2E-01 PA5376 CbcV -0.53 4.7E-01 PA5398 DgcA Dimethylglycine catabolism -1.40 9.0E-05 PA5410 GbcA Glycine betaine catabolism protein Fe -1.41 1.3E-07 PA5415 GlyA1 Serine hydroxymethyltransferase -0.79 2.3E-06 PA5416 SoxB Sarcosine oxidase beta subunit -0.69 2.7E-01 PA5417 SoxD Sarcosine oxidase delta subunit -0.66 2.0E-02 PA5418 SoxA Sarcosine oxidase alpha subunit Fe -0.60 5.7E-03 PA5421 FdhA Glutathione-independent formaldehyde dehydrogenase (FALDH) Zn -0.61 7.3E-09 (FDH) PA5445 PsecoA Probable coenzyme A transferase -0.62 3.2E-01 S5 Sulfur assimilation PA0280 CysA Sulfate transport protein 1.17 1.2E-06 PA0282 CysT Sulfate transport protein 1.28 5.5E-06 PA0283 Sbp Sulfate-binding protein precursor 2.05 2.8E-19 PA0500 BioB Biotin synthase Fe 0.79 3.4E-02 PA0916 YliG Ribosomal protein S12 methylthiotransferase Fe -0.85 8.9E-02 PA1192 YdaO tRNA-cytidine(32) 2-sulfurtransferase Fe -0.78 1.8E-01 PA1505 MoaA2 Molybdenum cofactor biosynthesis protein A 2 Fe -0.61 3.7E-01 PA1838 CysI Sulfite reductase Fe 0.68 2.0E-14 PA2062 Probable pyridoxal-phosphate dependent enzyme Fe 3.05 3.9E-05 PA2566 Conserved hypothetical protein -0.75 1.7E-01 PA2594 Conserved hypothetical protein 1.54 4.0E-05 PA3445 Conserved hypothetical protein 2.87 9.1E-06 PA3938 TauA Probable periplasmic taurine-binding protein 2.47 4.1E-04 PA3980 MiaB tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase Fe -1.74 5.8E-06 PA3996 LipA Lipoate synthase (Sulfur insertion protein LipA) Fe -0.63 1.7E-01 PA4442 CysN ATP sulfurylase GTP-binding subunit/APS kinase 0.83 5.3E-10
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    Supplementary File 1

    Table S1. Prevalence of E. coli in meat samples sold at the Tamale Metropolis. Sample No. of samples examined aNo. samples positive bNo. E. coli Beef 45 39 39 Chevon 45 34 34 Mutton 45 40 40 Local chicken 45 36 36 Guinea fowl 45 40 40 Overall 225 189 189 aNumber of samples positive for E. coli. bOne E. Coli isolate was selected from each positive sample. Table S2. A table showing the eBURST (Based Upon Related Sequence Types) analyses of the study sequence types with global curated STs in Escherichia PubMLST database. MLST (Isolate) Type of clone Closet global ancestry Source sequence type (ST) ST69 (SG6) Similar a ST69 Animal (Food), Human ST155 (SLC2, Similar ST155 Animal (Food), Human, TLC13, CM4) Environment ST297 (TLC1) Similar ST297 Human ST1727 (NC3) Similar ST1727 Human ST44 (AC1) Single-Locus Variant ST10, ST752 Animal (Food), (SLV) b Human ST469 (CC6) Single-Locus Variant ST162 Food (SLV) ST540 (AB1, Single-Locus Variant ST4093 Human TG1) (SLV) ST1141 (NM11) Single-Locus Variant ST10, ST744 Animal (Food), (SLV) Human ST7473 (NB12) Single-Locus Variant ST10 Animal (Food), (SLV) Human ST6646 (CB1) Satellite c None - ST7483 (NB12) Satellite None - a Similar: study isolate was similar to a global curated known sequence type. b Single-Locus Variant (SLV): study isolate only shared similarity with global curated known sequence types that differed in one allelic gene. c Satellite: study isolate as a distantly related and did not shared any similarity with global curated known sequence types. Table S3. In silico identification and characterization of conserved stress response mechanisms in the E.
  • Supplementary Information 2 to Accompany

    Supplementary Information 2 to Accompany

    1 Supplementary Information 2 to accompany 3 Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2 fixation 4 Brandon K. B. Seah*1,7, Chakkiath Paul Antony1,8, Bruno Huettel2, Jan Zarzycki3, Lennart 5 Schada von Borzyskowski3, Tobias J. Erb3, Angela Kouris4, Manuel Kleiner5, Manuel 6 Liebeke1, Nicole Dubilier1,6, Harald R. Gruber-Vodicka1 7 1 Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany 8 2 Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, 9 Carl-von-Linné-Weg 10, 50829 Cologne, Germany 10 3 Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, 11 Germany 12 4 Energy Bioengineering and Geomicrobiology Group, University of Calgary, 2500 13 University Drive Northwest, Calgary, Alberta T2N 1N4, Canada 14 5 Department of Plant and Microbial Biology, North Carolina State University, Raleigh 15 27695, North Carolina, United States of America 16 6 MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 17 Bremen, Germany 18 7 Current address: Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 19 72076 Tübingen, Germany 20 8 Current address: Red Sea Research Center, Biological and Environmental Sciences and 21 Engineering (BESE) Division, King Abdullah University of Science and Technology 22 (KAUST), Thuwal 23955, Kingdom of Saudi Arabia 23 * Corresponding author 1 24 Supplementary Materials and Methods 25 Metabolite extraction and identification 26 Kentrophoros sp. H was collected on Elba in 2014 for metabolomics (Supplementary Table 27 7). Samples were fixed in 1 mL cold methanol (HPLC-grade, Sigma-Aldrich) and stored at - 28 20°C until use.
  • NST110: Advanced Toxicology Lecture 4: Phase I Metabolism

    NST110: Advanced Toxicology Lecture 4: Phase I Metabolism

    Absorption, Distribution, Metabolism and Excretion (ADME): NST110: Advanced Toxicology Lecture 4: Phase I Metabolism NST110, Toxicology Department of Nutritional Sciences and Toxicology University of California, Berkeley Biotransformation The elimination of xenobiotics often depends on their conversion to water-soluble chemicals through biotransformation, catalyzed by multiple enzymes primarily in the liver with contributions from other tissues. Biotransformation changes the properties of a xenobiotic usually from a lipophilic form (that favors absorption) to a hydrophilic form (favoring excretion in the urine or bile). The main evolutionary goal of biotransformation is to increase the rate of excretion of xenobiotics or drugs. Biotransformation can detoxify or bioactivate xenobiotics to more toxic forms that can cause tumorigenicity or other toxicity. Phase I and Phase II Biotransformation Reactions catalyzed by xenobiotic biotransforming enzymes are generally divided into two groups: Phase I and phase II. 1. Phase I reactions involve hydrolysis, reduction and oxidation, exposing or introducing a functional group (-OH, -NH2, -SH or –COOH) to increase reactivity and slightly increase hydrophilicity. O R1 - O S O sulfation O R2 OH Phase II Phase I R1 R2 R1 R2 - hydroxylation COO R1 O O glucuronidation OH R2 HO excretion OH O COO- HN H -NH2 R R1 R1 S N 1 Phase I Phase II COO O O oxidation glutathione R2 OH R2 R2 conjugation 2. Phase II reactions include glucuronidation, sulfation, acetylation, methylation, conjugation with glutathione, and conjugation with amino acids (glycine, taurine and glutamic acid) that strongly increase hydrophilicity. Phase I and II Biotransformation • With the exception of lipid storage sites and the MDR transporter system, organisms have little anatomical defense against lipid soluble toxins.