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Table S1 Table S1. Differential expression analysis of N. moscoviensis grown under nitrite-deplete and nitrite-replete conditions in air. Also shown are global proteomic spectral counts and normalized spectral abundance (riBAQ) values. MS/MS spectral counts Normalised spectral abundance (riBAQ) Nitrite- Nitrite- Nitrite- Nitrite- Nitrite- Nitrite- Nitrite- Nitrite- Nitrite- Nitrite- Nitrite- Nitrite- Protein Mol. weight Log2 fold Fold adjusted p number of Gene Name Annotation Length (aa) p value significant imputed deplete in air deplete in air deplete in air replete in air replete in air replete in air deplete in air deplete in air deplete in air replete in air replete in air replete in air UniProtKB IDs [kDa] change change value NAs 1 2 3 1 2 3 1 2 3 1 2 3 NITMOv2_3655 A0A0K2GHF5 Uncharacterized protein 28.679 265 0.213 1.16 2.55E-02 3.92E-02 no no 0 541 645 592 527 527 525 3.977774854 3.984598421 3.789033185 3.12511338 3.29147352 3.346303807 NITMOv2_4425 A0A0K2GIM6 Alginate_exp domain-containing protein 62.347 568 0.278 1.21 1.16E-02 2.03E-02 no no 0 537 584 571 419 420 477 2.896644696 2.929247895 3.094993812 2.342983606 2.413177565 2.682437409 groEL A0A0K2G9S5 60 kDa chaperonin 58.328 545 0.135 1.10 5.35E-02 7.47E-02 no no 0 1093 1145 1253 1592 1558 1438 2.489824417 2.401083772 2.393860667 2.30892646 2.425451646 2.38412908 hupB.1 A0A0K2GIF8 DNA-binding protein HU-beta 10.363 96 0.0835 1.06 3.24E-01 3.66E-01 no no 0 113 170 155 143 126 118 2.255639273 2.199673536 2.262530012 2.230002725 1.601379163 1.592721936 IDH A0A0K2GFJ5 Isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial 37.011 337 1.06 2.08 1.22E-06 3.15E-05 yes no 0 419 451 432 255 251 253 1.916207825 1.834319279 1.870321076 0.883901412 0.908592738 0.929359013 NITMOv2_4557 A0A0K2GJ23 Orotate phosphoribosyltransferase (Modular protein) 17.343 169 0.346 1.27 1.87E-01 2.24E-01 no no 0 39 68 45 13 16 20 1.81494541 1.709092954 1.65353922 1.2993986 1.310716493 1.312035195 rbr.1 A0A0K2GJA4 Rubrerythrin 15.609 141 0.491 1.41 9.63E-04 2.73E-03 no no 0 82 88 92 92 88 86 1.701014653 1.597261387 1.599377308 1.377670807 1.343079672 1.30469886 bcp2 A0A0K2GIB3 Peroxiredoxin 17.592 156 0.459 1.37 2.44E-04 1.01E-03 no no 0 103 104 101 96 94 90 1.586072116 1.5169515 1.563965962 1.202039583 1.201694687 1.189978719 groS A0A0K2GAU8 10 kDa chaperonin 10.935 99 0.297 1.23 1.17E-02 2.04E-02 no no 0 81 88 81 62 65 59 1.536579161 1.459754904 1.408554825 1.23009971 1.220090272 1.269150001 bcp3 A0A0K2GCR5 Peroxiredoxin 23.587 211 0.577 1.49 2.52E-04 1.03E-03 no no 0 175 175 150 141 123 116 1.371363755 1.369296287 1.266142547 0.932306982 0.937662112 0.907080289 NITMOv2_4533 A0A0K2GJX9 Putative Nitrite oxidoreductase, beta subunit 49.888 429 -1.03 -2.04 3.32E-05 2.66E-04 yes no 0 325 351 344 545 520 606 1.158615721 1.153024714 1.176645978 2.132125447 2.125435816 2.513234192 NITMOv2_4538 A0A0K2GJY5 Putative Nitrite oxidoreductase, alpha subunit 131.83 1145 -1.03 -2.04 4.93E-05 3.48E-04 yes no 0 782 833 823 1417 1359 1566 1.058512638 1.07339923 1.051776408 1.964653131 1.921126744 2.317418778 NITMOv2_3685 A0A0K2GHH6 Putative Monoheme cytochrome c 15.99 149 0.428 1.35 4.92E-03 9.81E-03 no no 0 88 87 92 74 87 78 1.050797808 1.031415951 0.93367468 0.759888976 0.843011856 0.729012333 NITMOv2_3003 A0A0K2GEN6 Nitrogen regulatory protein P-II 11.086 98 0.654 1.57 1.73E-04 7.93E-04 no no 0 90 96 75 47 41 43 1.043293765 1.019820197 1.009022049 0.665846829 0.65354044 0.586924785 NITMOv2_3763 A0A0K2GH25 Uncharacterized protein 22.251 210 0.574 1.49 1.88E-04 8.31E-04 no no 0 70 76 72 56 62 62 1.036422086 1.046805257 0.992744717 0.709928623 0.74368502 0.717720131 NITMOv2_3624 A0A0K2GGE5 Putative Nitrite oxidoreductase, membrane subunit 34.243 316 -1.11 -2.16 5.09E-05 3.55E-04 yes no 0 187 204 224 315 339 354 0.974071082 0.997665071 1.067114295 2.134938863 2.117978146 2.527079726 NITMOv2_1768 A0A0K2GB67 Uncharacterized protein 25.912 248 -1.18 -2.27 2.84E-05 2.37E-04 yes no 0 116 133 138 259 289 290 0.862985959 0.903530228 0.919487135 2.010852391 2.367654707 2.655465589 NITMOv2_3292 A0A0K2GFE6 Isocitrate dehydrogenase (NADP(+)) 13.507 117 1.3 2.46 1.51E-06 3.61E-05 yes no 0 64 67 85 68 73 77 0.8567888 0.802883774 0.826271129 0.356830051 0.342540084 0.345275259 NITMOv2_4492 A0A0K2GIV1 Uncharacterized protein 16.948 159 -1.2 -2.30 6.82E-05 4.34E-04 yes no 0 62 67 74 150 151 157 0.852889228 0.825469096 0.853150775 2.128867807 2.229221717 2.529776908 rbpA.1 A0A0K2GGK5 Putative RNA-binding protein RbpA 10.147 99 -0.393 -1.31 3.30E-02 4.90E-02 no no 0 65 94 104 85 85 85 0.786174918 0.925704909 1.058410044 1.168382238 1.134327072 1.177140133 NITMOv2_4475 A0A0K2GIZ3 Uncharacterized protein 23.354 218 -1 -2.00 8.68E-05 5.13E-04 yes no 0 181 181 162 261 272 283 0.728081825 0.705737555 0.689610558 1.520133331 1.459807737 1.691636591 NITMOv2_2966 A0A0K2GEJ0 Isocitrate dehydrogenase (NADP(+)) 13.296 116 0.997 2.00 5.91E-06 8.24E-05 no no 0 177 188 206 132 127 123 0.726985729 0.711154122 0.894448035 0.390709508 0.428241136 0.451346437 rbpF A0A0K2GHG7 Putative RNA-binding protein RbpF 11.195 110 -0.933 -1.91 1.06E-05 1.24E-04 no no 0 34 41 44 71 65 68 0.725130797 0.753469826 0.785664074 1.386881044 1.294278547 1.365277568 NITMOv2_4091 A0A0K2GHP0 Putative Response regulator, CheY-like 16.041 144 4.15 17.75 1.51E-08 3.40E-06 yes no 0 129 138 141 25 24 23 0.675363819 0.690563347 0.70425824 0.048149401 0.043994035 0.041033129 NITMOv2_4476 A0A0K2GIT2 Uncharacterized protein 17.752 169 -1.27 -2.41 6.56E-06 8.94E-05 yes no 0 42 43 53 96 89 104 0.625259581 0.613323499 0.637231675 1.484891589 1.410726949 1.689119221 tufB A0A0K2G9S8 Elongation factor Tu 43.714 401 -0.532 -1.45 1.61E-03 4.08E-03 no no 0 203 215 247 347 341 325 0.584956971 0.584813196 0.619765657 0.80798359 0.763743044 0.737193785 modA A0A0K2GAR7 Molybdate ABC transporter, periplasmic binding protein 27.524 257 0.985 1.98 3.76E-05 2.87E-04 no no 0 93 89 85 60 60 58 0.581731919 0.564085541 0.5381681 0.327303986 0.307007396 0.273889842 smbP A0A0K2GGB0 Metal-binding protein SmbP 11.803 115 1.1 2.14 2.16E-05 1.99E-04 yes no 0 59 56 58 51 48 40 0.526336909 0.529161397 0.463280868 0.310245797 0.342959577 0.323931559 NITMOv2_0132 A0A0K2G7I8 FGE-sulfatase domain-containing protein 35.065 321 0.486 1.40 5.06E-04 1.71E-03 no no 0 159 164 172 124 137 133 0.494381492 0.483990752 0.47516773 0.318019711 0.346362139 0.356675348 NITMOv2_0141 A0A0K2G6I2 PDZ domain-containing protein 15.155 150 0.814 1.76 1.56E-04 7.54E-04 no no 0 45 42 35 28 36 28 0.475368441 0.477146715 0.440369899 0.29783715 0.282210644 0.259396984 NITMOv2_3174 A0A0K2GF39 Uncharacterized protein 9.9944 89 0.653 1.57 4.58E-05 3.28E-04 no no 0 29 28 27 24 23 24 0.474883629 0.485144461 0.479462338 0.351277255 0.348381925 0.319310387 idh A0A0K2G8E9 Isocitrate dehydrogenase [NADP] 81.549 743 0.221 1.17 1.45E-02 2.44E-02 no no 0 392 426 417 414 421 392 0.450390098 0.45205843 0.451662419 0.433103252 0.433461505 0.413657813 NITMOv2_0909 A0A0K2G8Q7 Uncharacterized protein 16.123 149 1.04 2.06 6.30E-05 4.12E-04 yes no 0 52 60 56 36 38 39 0.441789959 0.432582256 0.396043407 0.200981587 0.200145206 0.196211 NITMOv2_0731 A0A0K2G980 Putative Cytochrome c 19.55 182 0.454 1.37 5.04E-04 1.71E-03 no no 0 47 50 50 33 38 41 0.435803588 0.439308967 0.396100924 0.262669444 0.289497409 0.300178376 glnA A0A0K2G9R8 Glutamine synthetase 52.98 469 0.171 1.13 3.71E-02 5.42E-02 no no 0 150 150 196 228 213 196 0.434412389 0.433814183 0.43314192 0.406716367 0.385872251 0.36084699 NITMOv2_4530 A0A0K2GJ77 Copper-containing nitrite reductase 36.449 329 -1.57 -2.97 9.29E-07 2.93E-05 yes no 0 91 95 101 223 213 221 0.432810403 0.435593632 0.433122748 1.262143043 1.29538166 1.297308582 NITMOv2_2089 A0A0K2GC20 Heat shock protein, Hsp20 family 16.999 148 2.53 5.78 3.30E-07 1.46E-05 yes no 0 44 46 57 18 19 15 0.422755829 0.363359709 0.454384893 0.065881329 0.068675814 0.056667794 hupB A0A0K2G735 HU, DNA-binding transcriptional regulator, beta subunit 9.436 90 -0.997 -2.00 7.88E-06 1.01E-04 no no 0 32 34 32 46 43 52 0.419530777 0.430548599 0.443034857 0.875313088 0.880797382 0.917797092 NITMOv2_3764 A0A0K2GGR9 PepSY domain-containing protein 12.388 117 0.859 1.81 7.98E-05 4.85E-04 no no 0 18 21 20 18 13 12 0.41655867 0.425620892 0.408965576 0.214071377 0.203842967 0.185961709 icd A0A0K2GFQ1 Isocitrate dehydrogenase (NAD(+)) 37.189 338 1.08 2.11 1.75E-06 3.98E-05 yes no 0 83 78 83 44 48 44 0.415926307 0.394118767 0.361686541 0.176282752 0.187389484 0.178395214 fabI A0A0K2G6S1 Enoyl-[acyl-carrier-protein] reductase [NADH] 27.612 259 0.112 1.08 1.19E-01 1.50E-01 no no 0 40 45 45 49 49 45 0.403616305 0.406692241 0.367016456 0.263054438 0.275203542 0.294586218 NITMOv2_4244 A0A0K2GJ08 Isochorismatase family protein 29.246 268 0.772 1.71 9.51E-05 5.41E-04 no no 0 104 108 137 119 104 103 0.390252364 0.414865977 0.396024235 0.28957459 0.278233221 0.258012431 NITMOv2_2298 A0A0K2GCW8 LysM domain-containing protein 24.26 218 0.765 1.70 5.82E-05 3.90E-04 no no 0 87 87 78 58 70 68 0.35481895 0.347012237 0.332276143 0.166272912 0.20412263 0.222661365 htrA A0A0K2GGK4 Putative periplasmic serine endoprotease DegP-like 52.484 504 0.404 1.32 1.84E-03 4.50E-03 no no 0 138 130 144 132 126 123 0.354039036 0.327223193 0.436458738 0.382595023 0.367026099 0.365701917 NITMOv2_0430 A0A0K2G7B1 GYD family protein 11.313 101 1.06 2.08 4.43E-06 7.00E-05 yes no 0 21 20 24 19 17 17 0.342804051 0.351881281 0.321041141 0.174994503 0.171122442 0.172756305 aclA A0A0K2G940 ATP citrate lyase, alpha subunit 65.343 606 0.205 1.15 2.50E-02 3.87E-02 no no 0 216 222 216 210 206 200
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  • The Enzymatic Conversion of Phosphonates to Phosphate by Bacteria

    The Enzymatic Conversion of Phosphonates to Phosphate by Bacteria

    Available online at www.sciencedirect.com The enzymatic conversion of phosphonates to phosphate by bacteria 1 Siddhesh S Kamat and Frank M Raushel Phosphonates are ubiquitous organophosphorus compounds annually into the environment in the form of herbicides that contain a characteristic C–P bond which is chemically inert and detergent wastes. With such large quantities of and hydrolytically stable. Bacteria have evolved pathways to phosphonates being released into the environment, there metabolize these phosphonate compounds and utilize the is a significant interest in understanding the mechanisms products of these pathways as nutrient sources. This review by which phosphonates are degraded or metabolized by aims to present all of the known bacterial enzymes capable of bacterial species [1]. The abundance and universal preva- transforming phosphonates to phosphates. There are three lence of phosphonates in the environment has led to the major classes of enzymes known to date performing such evolution of several bacterial species that are able to transformations: phosphonatases, the C-P lyase complex and metabolize and utilize phosphonates as carbon and phos- an oxidative pathway for C–P bond cleavage. A brief phorus sources [2–4]. There are three known classes of description of each class is presented. enzymes or enzymatic systems that have been mechan- istically characterized which are capable of breaking the Addresses C–P bonds of phosphonate compounds. These include Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, TX 77843, United States phosphonate hydrolases, the C-P lyase complex, and an oxidative pathway. Corresponding author: Raushel, Frank M ([email protected]) 1 Present address: The Skaggs Institute for Chemical Biology and Phosphonate hydrolases Department of Chemical Physiology, The Scripps Research Institute, La Phosphonate hydrolases have been generically referred to Jolla, CA 92037, United States.
  • Letters to Nature

    Letters to Nature

    letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997).
  • The Reaction Mechanism of Phosphomannomutase in Plants

    The Reaction Mechanism of Phosphomannomutase in Plants

    CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector FEBS 18031 FEBS Letters 401 (1997) 35-37 The reaction mechanism of phosphomannomutase in plants Christine Oesterhelt, Claus Schnarrenberger, Wolfgang Gross* Institut für Pflanzenphysiologie und Mikrobiologie, Freie Universität Berlin, Königin-Luise-Str. 12-16a, D-14195 Berlin, Germany Received 11 November 1996 the presence of an excess of GIC-I.6-P2, purified PMM from G. sul- Abstract The enzyme phosphomannomutase catalyzes the phuraria, pig brain, and yeast was incubated with 1 mM GIC-I.6-P2 interconversion of mannose-1-phosphate (Man-l-P) and man- and 0.1 mM Man-l-P for 3 h at room temperature. The reaction nose-6-phosphate (Man-6-P). In mammalian cells the enzyme products were separated by TLC at pH 10 as described [8]. The has to be activated by transfer of a phosphate group from a corresponding regions for Man-l-P, Man-6-P, and Glc-6-P were sugar-1.6-P2 (Guha, S.K. and Rose, Z.B. (1985) Arch. Biochem. scraped off, the sugar phosphates eluted, and identified enzymatically. Biophys. 243, 168). In contrast, in the red alga Galdieria The concentration of Glc-6-P was determined by the addition of Glc- sulphuraria the co-substrate (Man-1.6-P2 or GIC-I.6-P2) is 6-P dehydrogenase and NADP. For Man-6-P determination PGI and PMI were included and for Man-l-P purified PMM from G. sulphu- converted to the corresponding sugar monophosphate while the raria was added.
  • Multi-Enzymatic Cascades in the Synthesis of Modified Nucleosides

    Multi-Enzymatic Cascades in the Synthesis of Modified Nucleosides

    biomolecules Article Multi-Enzymatic Cascades in the Synthesis of Modified Nucleosides: Comparison of the Thermophilic and Mesophilic Pathways Ilja V. Fateev , Maria A. Kostromina, Yuliya A. Abramchik, Barbara Z. Eletskaya , Olga O. Mikheeva, Dmitry D. Lukoshin, Evgeniy A. Zayats , Maria Ya. Berzina, Elena V. Dorofeeva, Alexander S. Paramonov , Alexey L. Kayushin, Irina D. Konstantinova * and Roman S. Esipov Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 GSP, B-437 Moscow, Russia; [email protected] (I.V.F.); [email protected] (M.A.K.); [email protected] (Y.A.A.); [email protected] (B.Z.E.); [email protected] (O.O.M.); [email protected] (D.D.L.); [email protected] (E.A.Z.); [email protected] (M.Y.B.); [email protected] (E.V.D.); [email protected] (A.S.P.); [email protected] (A.L.K.); [email protected] (R.S.E.) * Correspondence: [email protected]; Tel.: +7-905-791-1719 ! Abstract: A comparative study of the possibilities of using ribokinase phosphopentomutase ! nucleoside phosphorylase cascades in the synthesis of modified nucleosides was carried out. Citation: Fateev, I.V.; Kostromina, Recombinant phosphopentomutase from Thermus thermophilus HB27 was obtained for the first time: M.A.; Abramchik, Y.A.; Eletskaya, a strain producing a soluble form of the enzyme was created, and a method for its isolation and B.Z.; Mikheeva, O.O.; Lukoshin, D.D.; chromatographic purification was developed. It was shown that cascade syntheses of modified nu- Zayats, E.A.; Berzina, M.Y..; cleosides can be carried out both by the mesophilic and thermophilic routes from D-pentoses: ribose, Dorofeeva, E.V.; Paramonov, A.S.; 2-deoxyribose, arabinose, xylose, and 2-deoxy-2-fluoroarabinose.
  • The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose

    The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose

    Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota.