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Table S1 Page 1 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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