Appendix C. List of gene up-regulated in cells grown as biofilms. Protein category GENE_NAME function FoldChange AveExpr t raw.P.val FDR.P.val Cell membrane function lmo1934 similar to non-specific DNA-binding protein HU 7.88455731 12.20228 13.74284 5.14E-16 7.69E-13 lmo2016 similar to major cold-shock protein 4.46054486 12.92885 12.4972 9.16E-15 5.06E-12 lmo1847 similar to adhesion binding proteins and lipoproteins with multiple5.10387178 specificity13.71246 for metal 11.18586cations (ABC2.32E-13 transporter)3.31E-11 lmo1548 similar to cell-shape determining protein MreB 3.12698287 13.84029 10.14071 3.58E-12 3.14E-10 lmo1364 similar to cold shock protein 3.21172011 12.68556 10.03885 4.71E-12 3.63E-10 lmo1547 similar to cell-shape determining protein MreC 3.25276936 13.32978 10.03399 4.77E-12 3.63E-10 lmo0971 DltD protein for D-alanine esterification of lipoteichoic acid and3.42366229 wall teichoic13.88932 acid 9.280949 3.77E-11 2.29E-09 lmo0973 DltB protein for D-alanine esterification of lipoteichoic acid and3.07776803 wall teichoic14.47105 acid 8.732509 1.78E-10 8.18E-09 lmo1546 similar to cell-shape determining protein MreD 3.22349266 12.61449 8.053721 1.28E-09 4.49E-08 lmo0045 highly similar to single-strand binding protein (SSB) 3.27406859 14.06565 7.792284 2.78E-09 8.59E-08 lmo1527 similar to protein-export membrane protein SecDF 2.46823503 13.93627 6.263443 2.90E-07 4.75E-06 lmo2637 conserved lipoprotein 3.67182434 14.17184 6.07871 5.14E-07 7.35E-06 lmo0927 hypothetical transmembrane protein 2.09623116 13.21212 5.573679 2.46E-06 2.63E-05 lmo0433 Internalin A 2.56964009 13.47947 5.227844 7.18E-06 6.25E-05 lmo0514 similar to internalin protein, putative peptidoglycan bound protein-2.4281866 (LPXTG motif)13.10804 -5.11582 1.01E-05 8.18E-05 lmo2007 weakly similar to putative sugar-binding lipoproteins -2.0438021 12.94108 -5.03773 1.29E-05 9.98E-05 Cell metabolic pathways/Biosynthesis lmo2459 glyceraldehyde-3-phosphate dehydrogenase 5.85859635 13.6642 12.4485 1.03E-14 5.06E-12 lmo2533 highly similar to H+transporting ATP synthase chain b 3.99411918 13.78088 12.43334 1.07E-14 5.06E-12 lmo2536 highly similar to ATP synthase subunit i 4.7226599 12.99497 12.07353 2.54E-14 7.24E-12 lmo1083 similar to dTDP-D-glucose 4,6-dehydratase 3.59784501 13.27281 11.94048 3.52E-14 9.11E-12 lmo2456 highly similar to phosphoglycerate mutase; catalyzes the interconversion4.65083394 of 14.234642-phosphoglycerate11.55326 and9.19E-14 3-phosphoglycerate2.01E-11 lmo1806 highly similar to acyl carrier proteins 4.76899981 12.94787 11.35056 1.53E-13 2.72E-11 lmo1634 similar to Alcohol-acetaldehyde dehydrogenase 3.89056269 14.33498 11.22769 2.09E-13 3.27E-11 lmo2535 ATP synthase subunit A 3.84039768 13.96756 10.05301 4.53E-12 3.63E-10 lmo2458 phosphoglycerate kinase 3.91310805 14.30025 9.842171 8.02E-12 5.71E-10 lmo0783 similar to mannose-specific phosphotransferase system (PTS) 3.49454099component IIB13.49287 9.493188 2.09E-11 1.35E-09 lmo1003 PTS enzyme I 3.33203576 13.42775 9.248565 4.13E-11 2.40E-09 lmo1673 naphthoate synthase 3.19751732 13.53146 9.189956 4.87E-11 2.67E-09 lmo1663 similar to asparagine synthetase 2.5480617 13.43093 9.070581 6.82E-11 3.59E-09 lmo2457 highly similar to triose phosphate isomerase 3.69843203 14.64773 9.034993 7.54E-11 3.90E-09 lmo1082 similar to dTDP-sugar epimerase 3.37195644 13.7902 9.025468 7.74E-11 3.93E-09 lmo2455 highly similar to enolase 3.32466943 14.29139 8.746222 1.71E-10 8.13E-09 lmo2532 highly similar to H+transporting ATP synthase chain delta 3.18207364 14.13089 8.603506 2.58E-10 1.15E-08 lmo1084 similar to DTDP-L-rhamnose synthetase 3.17640938 13.25135 8.38256 4.89E-10 2.05E-08 lmo1464 similar to diacylglycerol kinase 2.62456951 13.0846 8.368846 5.09E-10 2.08E-08 lmo1002 PTS phosphocarrier protein Hpr (histidine containing protein) 3.36360858 13.92372 8.233748 7.55E-10 2.87E-08 lmo2530 highly similar to H+transporting ATP synthase chain gamma 3.51851988 14.46209 8.10579 1.10E-09 3.96E-08 lmo2534 ATP synthase subunit C 2.86002223 14.48747 7.933152 1.83E-09 6.05E-08 lmo1052 highly similar to pyruvate dehydrogenase (E1 alpha subunit) 2.68088614 14.05514 7.713303 3.51E-09 1.05E-07 lmo1571 6-phosphofructokinase 2.64472869 13.55894 7.511142 6.43E-09 1.78E-07 lmo1807 similar to 3-ketoacyl-acyl carrier protein reductase 2.58085367 13.78651 7.452592 7.67E-09 2.08E-07 lmo1917 similar to pyruvate formate-lyase 2.82421701 13.76796 7.313418 1.17E-08 3.02E-07 lmo1766 highly similar to phosphoribosylglycinamide formyltransferases4.73956737 10.91891 7.20597 1.61E-08 4.00E-07 lmo1676 menaquinone-specific isochorismate synthase 2.82903464 13.14482 7.161329 1.85E-08 4.46E-07 lmo0974 D-alanine--D-alanyl carrier protein ligase 3.04882149 14.38519 6.903874 4.05E-08 8.93E-07 lmo1406 pyruvate formate-lyase 3.6846588 13.82027 6.596606 1.04E-07 1.98E-06 lmo2635 1,4-dihydroxy-2-naphthoate octaprenyltransferase 2.4811628 12.81699 6.21985 3.32E-07 5.28E-06 lmo1773 adenylosuccinate lyase 3.34172348 12.82735 6.507699 1.37E-07 2.54E-06 lmo1081 similar to glucose-1-phosphate thymidyl transferase 2.55920438 14.08477 6.471138 1.53E-07 2.79E-06 lmo0539 tagatose 1,6-diphosphate aldolase 3.21911471 13.08826 6.390089 1.96E-07 3.47E-06 lmo0096 similar to PTS system mannose-specific, factor IIAB 2.55747356 13.56833 6.348359 2.23E-07 3.83E-06 lmo1675 2-oxoglutarate decarboxylase 2.33356608 13.70316 6.325768 2.39E-07 4.05E-06 lmo1435 dihydrodipicolinate synthase 2.306845 13.73059 6.247713 3.05E-07 4.93E-06 lmo2556 similar to fructose-1,6-bisphosphate aldolase 3.157626 14.48131 6.135191 4.31E-07 6.50E-06 lmo1086 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2.70051147 12.94498 6.101307 4.79E-07 6.99E-06 lmo1521 similar to N-acetylmuramoyl-L-alanine amidase 2.31743329 13.8367 6.07858 5.14E-07 7.35E-06 lmo2559 CTP synthetase 2.46589693 13.94196 6.024906 6.07E-07 8.51E-06 lmo1490 similar to shikimate 5-dehydrogenase (AroD) 2.12582712 13.51149 5.912444 8.60E-07 1.12E-05 lmo1764 phosphoribosylglycinamide synthetase 3.92189369 11.75212 5.884944 9.37E-07 1.19E-05 lmo1313 highly similar to uridylate kinases 2.37160977 13.87908 5.775736 1.31E-06 1.58E-05 lmo1572 highly similar to acetyl CoA carboxylase (alpha subunit); Catalyzes3.23449367 the carboxylation11.63607 of acetyl-CoA5.728176 to1.52E-06 malonyl-CoA1.77E-05 lmo2528 highly similar to H+transporting ATP synthase chain epsilon 1.96740641 13.48736 5.643083 1.98E-06 2.21E-05 lmo2696 similar to hypothetical dihydroxyacetone kinase 2.30080604 13.16061 5.624803 2.10E-06 2.29E-05 lmo1820 similar to putative serine/threonine-specific protein kinase 2.1229096 13.76891 5.607514 2.22E-06 2.40E-05 lmo2529 ATP synthase subunit B 2.15304487 14.81267 5.594445 2.31E-06 2.48E-05 lmo2137 similar to PTS system, fructose-specific enzyme IIA component-2.2812563 12.82015 -5.67064 1.82E-06 2.05E-05 lmo0298 similar to PTS beta-glucoside-specific enzyme IIC component -2.3619881 14.00698 -5.63729 2.02E-06 2.22E-05 lmo0345 similar to sugar-phosphate isomerase -2.5400987 13.61374 -5.59696 2.29E-06 2.47E-05 lmo2134 similar to fructose-1,6-biphosphate aldolase type II -2.2568445 13.50064 -5.5458 2.68E-06 2.82E-05 lmo2717 highly similar to cytochrome D ubiquinol oxidase subunit II 2.1427138 14.31347 5.540592 2.73E-06 2.84E-05 lmo1407 pyruvate-formate lyase activating enzyme 2.20920501 13.47548 5.533843 2.78E-06 2.88E-05 lmo2847 highly similar to rhamnulose-1-phosphate aldolase -2.7161691 14.2083 -5.49977 3.09E-06 3.14E-05 lmo0543 similar to PTS system, glucitol/sorbitol-specific enzyme IIBC component-2.0095442 13.48649 -5.48877 3.20E-06 3.23E-05 lmo1856 purine nucleoside phosphorylase 1.87192731 13.82264 5.472569 3.37E-06 3.37E-05 lmo2135 similar to PTS system, fructose-specific enzyme IIC component-2.4878185 13.83088 -5.44131 3.71E-06 3.64E-05 lmo1034 similar to glycerol kinase -2.2386655 13.35672 -5.43442 3.79E-06 3.71E-05 lmo2683 similar to cellobiose phosphotransferase enzyme IIB component1.98808642 12.25486 5.373264 4.58E-06 4.31E-05 lmo1581 highly similar to acetate kinase; AckA; TdcD; acetate/propionate2.13631679 kinase; TdcD13.68868 has both and5.322325 functions5.36E-06 in anerobic4.86E-05 threonine catabolism; AckA utilizes acetate and can acetylate CheY which increases signal strength during flagellar rotation; utilizes magnesium and ATP; also involved in conver lmo0210 similar to L-lactate dehydrogenase; catalyzes the conversion of2.76230255 lactate to pyruvate14.44002 5.314529 5.49E-06 4.96E-05 lmo1570 highly similar to pyruvate kinases; catalyzes the formation of phosphoenolpyruvate3.24540277 13.92711 from5.278943 pyruvate 6.13E-06 5.45E-05 lmo1373 similar to branched-chain alpha-keto acid dehydrogenase E1 subunit2.1079549 (2-oxoisovalerate14.39781 dehydrogenase5.187341 8.14E-06 beta subunit)6.77E-05 lmo2531 ATP synthase subunit A 2.62888309 14.64755 5.174596 8.46E-06 7.00E-05 lmo0913 similar to succinate semialdehyde dehydrogenase 2.69510884 13.47991 5.143012 9.33E-06 7.63E-05 lmo1720 similar to PTS lichenan-specific enzyme IIB component 1.98180914 13.49185 5.095068 1.08E-05 8.67E-05 lmo0355 similar to Flavocytochrome C Fumarate Reductase chain A; Reduces2.66433441 fumarate14.45225 to succinate5.064265 in anaerobic1.19E-05 bacterial9.32E-05 respiration lmo2787 beta-glucoside-specific PTS enzyme II ABC component -2.0871064 13.37121 -5.05981 1.21E-05 9.43E-05 lmo0567 highly similar to histidinol dehydrogenases; catalyzes the oxidation-2.02803 of L-histidinol13.68141 to L-histidinaldehyde-5.02384 1.35E-05 and then0.000102 to L-histidine in histidine biosynthesis lmo2336 fructose-1-phosphate kinase -2.0266083