A Functional Category Is Classed According to (Glaser Et Al., 2001)

Table S3. Genes up-regulated in biofilm in the comparison the prfA deletion mutant (DprfA) versus the wild strain EGDe

Functional category a / Gene ID / Gene name / Fold changes for biofilms in EGDeDprfA/EGDe / Description b
Cell wall / lmo0971 / dltD / 2.05 / DltD protein for D-alanine esterification of lipoteichoic acid and wall teichoic acid
lmo0972 / 2.38 / D-alanyl carrier protein
lmo0973 / dltB / 2.48 / DltB protein for D-alanine esterification of lipoteichoic acid and wall teichoic acid
lmo0974 / dltA / 2.18 / D-alanine-activating enzyme (dae), D-alanine-D-alanyl carrier protein ligase (dcl)
lmo1076 / 2.09 / Similar to autolysin (EC 3.5.1.28) (N-acetylmuramoyl-L-alanine amidase)
lmo1080 / 2.65 / Similar to B. subtilis minor teichoic acids biosynthesis protein GgaB
lmo1081 / 2.84 / Similar to glucose-1-phosphate thymidyl transferase
lmo1082 / 2.99 / Similar to dTDP-sugar epimerase
lmo1083 / 2.91 / Similar to dTDP-D-glucose 4,6-dehydratase
lmo1084 / 2.3 / Similar to DTDP-L-rhamnose synthetase
lmo1085 / 2.42 / Similar to teichoic acid biosynthesis protein B
lmo1090 / 3.1 / Similar to glycosyltransferases
lmo1546 / mreD / 2.49 / Similar to cell-shape determining protein MreD
lmo1547 / mreC / 2.04 / Similar to cell-shape determining protein MreC
lmo1548 / mreB / 2.02 / Similar to cell-shape determining protein MreB
lmo1694 / 2.28 / Similar to CDP-abequose synthase
lmo1855 / 2.02 / Similar to similar to D-alanyl-D-alanine carboxypeptidases
lmo2035 / murG / 2.3 / Similar to peptidoglycan synthesis enzymes, putative phospho-N-acetylmuramoyl-pentapeptide-transferase
lmo2036 / murD / 2.08 / Similar to UDP-N-acetylmuramoylalanine D-glutamate ligase
lmo2037 / mraY / 2.36 / Similar to phospho-N-acetylmuramoyl-pentapeptide transferase
lmo2038 / murE / 2.95 / Similar to UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase
lmo2549 / gtcA / 2.2 / Wall teichoic acid glycosylation protein GtcA
lmo2550 / 2.51 / Similar to glycosyl transferases
Transport/binding proteins and lipoproteins / lmo0096 / 4.33 / Similar to PTS system mannose-specific, factor IIAB
lmo0097 / 4.66 / Similar to PTS system mannose-specific, factor IIC
lmo0098 / 4.05 / Similar to PTS system mannose-specific, factor IID
lmo0135 / 2.71 / Similar to oligopeptide ABC transport system substrate-binding proteins
lmo0136 / 2.55 / Similar to oligopeptide ABC transporter, permease protein
lmo0278 / 2.8 / Similar to sugar ABC transporter, ATP-binding protein
lmo0400 / 2.08 / Similar to fructose-specific phosphotransferase enzyme IIC
lmo0607 / 2.4 / Similar to ABC transporter, ATP-binding protein
lmo0608 / 2.02 / Similar to ABC transporter, ATP-binding protein
lmo0641 / 2.36 / Similar to heavy metal-transporting ATPase
lmo0914 / 6.62 / Similar to PTS system, IIB component
lmo0915 / 4.18 / Similar to phosphotransferase system enzyme IIC
lmo0916 / 3.56 / Similar to phosphotransferase system enzyme IIA
lmo0979 / 3.47 / Similar to daunorubicin resistance ATP-binding proteins
lmo0980 / 2.66 / Similar to ABC transporter transmembrane component
lmo1023 / 2.36 / Similar to a bacterial K(+)-uptake system
lmo1064 / 2.03 / Similar to membrane and transport proteins
lmo1388 / tcsA / 5.94 / CD4+ T cell-stimulating antigen, lipoprotein
lmo1505 / 4.8 / Similar to ABC transporter, ATP-binding protein
lmo1506 / 3.47 / Similar to transporter
lmo1617 / 2.63 / Similar to multidrug-efflux transporter
lmo1720 / 2.99 / Similar to phosphotransferase system (PTS) lichenan-specific enzyme IIB component
lmo1852 / 2.52 / Similar to putative mercuric ion binding proteins
lmo1853 / 2.04 / Similar to heavy metal-transporting ATPases
lmo1884 / 2.57 / Similar to xanthine permeases
lmo2001 / 2.07 / Similar to PTS mannose-specific enzyme IIC component
lmo2002 / 2.25 / Similar to PTS mannose-specific enzyme IIB component
lmo2575 / 3.36 / Similar to cation transport protein (efflux)
lmo2683 / 2.9 / Similar to cellobiose phosphotransferase enzyme IIB component
lmo2684 / 2.71 / Similar to cellobiose phosphotransferase enzyme IIC component
Sensors (signal transduction) / lmo1021 / 2.36 / Similar to two-component sensor histidine kinase in particular B. subtilis YvqE protein
lmo1508 / 2.47 / Similar to two-component sensor histidine kinase
Membrane bioenergetics / lmo2152 / 3.84 / Similar to thioredoxin
lmo2153 / 4.48 / Similar to flavodoxin
lmo2528 / atpC / 2.34 / Highly similar to H+-transporting ATP synthase chain epsilon
lmo2530 / atpG / 2.23 / Highly similar to H+-transporting ATP synthase chain gamma
lmo2531 / atpA / 2.29 / Highly similar to H+-transporting ATP synthase chain alpha
lmo2532 / atpH / 2.31 / Highly similar to H+-transporting ATP synthase chain delta
lmo2534 / atpE / 3.45 / Highly similar to H+-transporting ATP synthase chain c
lmo2535 / atpB / 2.16 / Highly similar to H+-transporting ATP synthase chain a
lmo2536 / atpI / 2.72 / Highly similar to ATP synthase subunit i
Mobility and chemotaxis / lmo0697 / 2.02 / Similar to flagellar hook protein FlgE
lmo0699 / 2.01 / Similar to flagellar switch protein FliM
Protein secretion / lmo1269 / 2.36 / Similar to type-I signal peptidase
lmo1270 / 2.51 / Similar to signal peptidase I
lmo1444 / 2.21 / Similar to protein secretion PrsA (post-translocation molecular chaperone)
Cell division
/ lmo2032 / ftsZ / 2.02 / Highly similar to cell-division initiation protein FtsZ
lmo2033 / ftsA / 2.41 / Highly similar to cell-division protein FtsA
lmo2034 / divIB / 2.50 / Similar to cell-division initiation protein divIB
Cell surface proteins / lmo2714 / 2.00 / Peptidoglycan anchored protein (LPXTG motif)
Metabolism of carbohydrates and related molecules / lmo1086 / 2.38 / Similar to CDP-ribitol pyrophosphorylase
lmo1087 / 2.07 / Similar to glucitol dehydrogenase
Specific pathways / lmo0347 / 7.58 / Similar to dihydroxyacetone kinase
lmo0539 / 2.13 / Similar to tagatose-1,6-diphosphate aldolase
lmo0727 / 2.68 / Similar to L-glutamine-D-fructose-6-phosphate amidotransferase
lmo0823 / 3.22 / Similar to oxydoreductases
lmo0917 / 3.88 / Similar to beta-glucosidase
lmo1293 / glpD / 2.39 / Similar to glycerol 3 phosphate dehydrogenase
lmo1634 / 4.16 / Similar to Alcohol-acetaldehyde dehydrogenase
lmo2564 / 2.1 / Similar to 4-oxalocrotonate isomerase
Main glycolytic pathways / lmo0830 / fbp / 3.98 / Highly similar to fructose-1,6-bisphosphatase
lmo1072 / pycA / 2.13 / Highly similar to pyruvate carboxylase
lmo2455 / eno / 2.26 / Highly similar to enolase
Metabolism of amino acids and related molecules / lmo0043 / 2.08 / Similar to arginine deiminase
lmo0886 / dal / 2.23 / Similar to alanine racemase
lmo0961 / 2.5 / Similar to proteases
lmo1299 / glnA / 2.25 / Highly similar to glutamine synthetases
lmo1387 / 2.05 / Similar to pyrroline-5-carboxylate reductase
lmo1579 / 2.65 / Similar to alanine dehydrogenase
lmo1886 / 3 / Similar to probable thermostable carboxypeptidases
lmo2188 / 2.1 / Similar to oligoendopeptidase
Metabolism of nucleotides and nucleic acids / lmo0279 / 3.05 / Highly similar to anaerobic ribonucleoside-triphosphate reductase
lmo1765 / purH / 2.17 / Bifunctional phosphoribosylaminoimidazole carboxy formyl formyltransferase and inosine-monophosphate cyclohydrolase
lmo1767 / 3.1 / Phosphoribosylaminoimidazole synthetase
lmo1773 / purB / 2.25 / Adenylosuccinate lyase
lmo1856 / deoD / 2.54 / Purine nucleoside phosphorylase
lmo1885 / 2.42 / Similar to xanthine phosphoribosyltransferase
lmo2154 / 3.37 / Similar to ribonucleoside-diphosphate reductase, subunit beta
lmo2155 / 3.77 / Similar to ribonucleoside-diphosphate reductase, subunit alpha
Metabolism of lipids / lmo0580 / 2.04 / Weakly similar to carboxylesterase
lmo0931 / 2.07 / Similar to lipoate protein ligase A
lmo1357 / 2.15 / Acetyl-CoA carboxylase subunit (biotin carboxylase subunit)
lmo1372 / 2.65 / Similar to branched-chain alpha-keto acid dehydrogenase E1 subunit (2-oxoisovalerate dehydrogenase alpha subunit)
lmo1373 / 3.85 / Similar to branched-chain alpha-keto acid dehydrogenase E1 subunit (2-oxoisovalerate dehydrogenase beta subunit)
lmo1374 / 2.66 / Similar to branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase)
Metabolism of coenzymes and prosthetic groups / lmo1093 / 2.26 / Similar to NH(3)-dependent NAD(+) synthetases, nitrogen regulatory protein
lmo1553 / hemL / 2.62 / Highly similar to glutamate-1-semialdehyde 2,1-aminotransferases
lmo1554 / hemB / 2.95 / Highly similar to delta-aminolevulinic acid dehydratases (porphobilinogen synthase)
lmo2023 / nadB / 2.36 / Similar to L-aspartate oxidase
lmo2024 / nadC / 2.32 / Similar to nicotinate-nucleotide pyrophosphorylase
lmo2025 / nadA / 2.31 / Similar to quinolinate synthetase
lmo2101 / 4.32 / Similar to a protein required for pyridoxine synthesis
DNA replication / lmo1320 / polC / 2.03 / Highly similar to DNA polymerase III (alpha subunit)
lmo1758 / 2.22 / Similar to DNA ligase
DNA restriction/modification and repair / lmo1782 / 2.40 / similar to 3'-exo-deoxyribonuclease exoA
DNA packaging and segregation / lmo1934 / hup / 3.19 / Similar to non-specific DNA-binding protein HU
Regulation / lmo0606 / 2.69 / Similar to transcription regulator MarR family
lmo0612 / 2.31 / Similar to transcription regulator MarR family
lmo0785 / 2.11 / Similar to transcriptional regulator (NifA/NtrC family)
lmo1022 / 2.34 / Similar to two-component response regulator, in particular B. subtilis YvqC protein
lmo1405 / 2.2 / Similar to putative anti-terminator regulatory protein
lmo1507 / 2.28 / Similar to two-component response regulators
lmo1618 / 2.96 / Similar to transcription regulator MarR family
lmo1850 / 2.06 / Similar to transcriptional regulator (MarR family)
lmo2003 / 2.62 / Similar to transcription regulator GntR family
lmo2004 / 2.05 / Similar to transcription regulator GntR family
lmo2165 / 2.23 / Similar to transcription regulator CRP/FNR family
RNA modification / lmo0935 / 2.07 / Similar to B. subtilis CspR protein, rRNA methylase homolog
lmo1530 / 2.44 / Similar to tRNA-guanine transglycosylase Tgt
lmo1822 / 2.02 / Similar to RNA-binding Sun protein
lmo2855 / rnpA / 2.11 / Ribonuclease P protein component
Ribosomal proteins / lmo1480 / rpsT / 2.04 / Ribosomal protein S20
Aminoacyl-tRNA synthetases / lmo1458 / glyS / 2.23 / Similar to glycyl-tRNA synthetase beta chain
lmo1755 / gatA / 2.49 / Glutamyl-tRNA(Gln) amidotransferase (subunit A)
lmo2561 / argS / 2.27 / Arginyl tRNA synthetase
lmo2747 / serS / 2.54 / Seryl-trna synthetase
Initiation / lmo0895 / sigB / 2.18 / RNA polymerase sigma-37 factor (sigma-B)
lmo1454 / 2.48 / RNA polymerase sigma factor RpoD
Termination / lmo1359 / 2.60 / Similar to transcription termination protein (NusB)
Protein modification / lmo0764 / 2.03 / Similar to lipoate-protein ligase
lmo1674 / 2.05 / Similar to prolyl aminopetidases
lmo1698 / 2.04 / Similar to ribosomal-protein-alanine N-acetyltransferase
lmo1820 / 2.39 / Similar to putative serine/threonine-specific protein kinase
lmo1821 / 2.49 / Similar to putative phosphoprotein phosphatase
Adaptation to atypical conditions / lmo0890 / rsbS / 2.74 / Highly similar to negative regulation of sigma-B activity
lmo0891 / rsbT / 2.45 / Highly similar to positive regulation of sigma-B activity
lmo0892 / rsbU / 2.6 / Highly similar to serine phosphatase RsbU
lmo0893 / rsbV / 2.66 / Anti-anti-sigma factor (antagonist of RsbW)
lmo0894 / rsbW / 2.36 / Sigma-B activity negative regulator RsbW
lmo0896 / rsbX / 2.6 / Indirect negative regulation of sigma B dependant gene expression (serine phosphatase)
Detoxification / lmo1400 / 2.5 / Similar to N-acetyltransferase
lmo1439 / sod / 2.44 / Superoxide dismutase
lmo1604 / 2.16 / Similar to 2-cys peroxiredoxin
lmo2168 / 2.79 / Similar to glyoxalase I
lmo2230 / 3.02 / Similar to arsenate reductase
Miscellaneous / lmo0762 / 2.38 / Similar to ATP/GTP-binding protein
Similar to unknown proteins from Listeria / lmo2166 / 2.35 / Lmo2166
Similar to unknown proteins from other organisms / lmo0099 / 2.02 / Lmo0099
lmo0471 / 2.46 / Lmo0471
lmo0515 / 2.61 / Conserved hypothetical protein
lmo0788 / 2.17 / Lmo0788
lmo0887 / 2.05 / Similar to B. subtilis YdcD protein
lmo0927 / 2.12 / Hypothetical transmembrane protein
lmo1065 / 2.08 / Similar to B. subtilis YktB protein
lmo1069 / 2.71 / Similar to B. subtilis YlaI protein
lmo1092 / 2.39 / Conserved hypothetical protein, similar to B. subtilis YueK protein
lmo1094 / 2.39 / Lmo1094
lmo1140 / 2.07 / Lmo1140
lmo1526 / 2.36 / Similar to unknown proteins
lmo1528 / 2.92 / Similar to unknown proteins
lmo1529 / 2.32 / Similar to unknown proteins
lmo1580 / 2.72 / Similar to unknown protein
lmo1718 / 2.03 / Similar to putative outer surface protein
lmo1757 / 2.33 / Similar to unknown protein
lmo1819 / 2.23 / Similar to unknown proteins
lmo1854 / 3.19 / Similar to conserved hypothetical proteins
lmo1857 / 3.99 / Similar to hypoyhetical protein
lmo1887 / 2 / Similar to conserved hypothetical proteins
lmo1945 / 2.08 / Similar to unknown protein
lmo2030 / 2.2 / Similar to unknown proteins
lmo2031 / 2.6 / Similar to unknown proteins
lmo2102 / 3.59 / Lmo2102
lmo2113 / 2.01 / Similar to unknown proteins
lmo2151 / 3 / Similar to unknown proteins
lmo2158 / 2.58 / Similar to B. subtilis YwmG protein
lmo2221 / 2.03 / Similar to unknown proteins
lmo2357 / 2.06 / Similar to unknown protein
lmo2437 / 2.57 / Lmo2437
lmo2570 / 2.2 / Lmo2570
No similarity / lmo0442 / 3.05 / Lmo0442
lmo0937 / 2.48 / Lmo0937
lmo1059 / 2.2 / Lmo1059
lmo1137 / 2.29 / Lmo1137
lmo1257 / 2.01 / Lmo1257
lmo1380 / 2.23 / Lmo1380
lmo1597 / 2.68 / Lmo1597
lmo1626 / 2.39 / Lmo1626
lmo2080 / 16.51 / Lmo2080
lmo2169 / 2.61 / Lmo2169
lmo2574 / 2.44 / Lmo2574
lmo2746 / 2.44 / Lmo2746
Unknown c / lmo1663 / ansB / 2.95 / Similar to asparagine synthetase
lmo1806 / acpP / 2.86 / Highly similar to acyl carrier proteins

a Functional category is classed according to http://genolist.pasteur.fr/ListiList/ (Glaser et al., 2001).

b Description for gene is obtained from NCBI (nr) Listeria monocytogenes EGD-e database

c Unknown means the function of protein encoded by the identified gene in this study was not found within any category in http://genolist.pasteur.fr/ListiList/.