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

Table S1. Genes up-regulated inL. monocytogenes EGDe biofilm cells compared with its free-living cells

Functional category a / Gene ID / Gene name / Fold changes for EGDe (B/F) b / Descriptionc
Cell wall / lmo1694 / 3.02 / Similar to CDP-abequose synthase
Transport/binding proteins and lipoproteins / lmo0021 / 2.03 / Similar to PTS system, fructose-specific IIA component
lmo0154 / 2.98 / Similar to high-affinity zinc ABC transporter (ATP-binding protein)
lmo0155 / 3.48 / Similar to high-affinity zinc ABC transporter (membrane protein)
lmo0179 / 3.97 / Similar to sugar ABC transporters, permease proteins
lmo0180 / 3.76 / Similar to sugar ABC transporter, permease protein
lmo0181 / 4.22 / Similar to sugar ABC transporter, sugar-binding protein
lmo0278 / 3.84 / Similar to sugar ABC transporter, ATP-binding protein
lmo0366 / 2.86 / Conserved hypothetical protein, putative lipoprotein
lmo0373 / 4.52 / Similar to PTS betaglucoside-specific enzyme IIC component
lmo0427 / 2.68 / Similar to PTS fructose-specific enzyme IIB component
lmo0798 / 2.57 / Similar to lysine-specific permease
lmo0807 / 2.78 / Similar to spermidine/putrescine ABC transporter, ATP-binding protein
lmo0808 / 3.14 / Similar to spermidine/putrescine ABC transporter, permease protein
lmo0809 / 3.91 / Similar to spermidine/putrescine ABC transporter, permease protein
lmo0810 / 3.65 / Similar to spermidine/putrescine-binding protein
lmo0818 / 3.96 / Similar to cation transporting ATPase
lmo0897 / 2.97 / Similar to transport proteins
lmo1651 / 2.58 / Similar to ABC transporter (ATP-binding protein)
lmo1652 / 3.04 / Similar to ABC transporter (ATP-binding protein)
lmo1839 / pyrP / 4.66 / Highly similar to uracil permease
lmo1972 / 3.98 / Similar to pentitol PTS system enzyme II B component
lmo1997 / 2.75 / Similar to PTS mannose-specific enzyme IIA component
lmo2000 / 11.57 / Similar to PTS mannose-specific enzyme IID component
lmo2001 / 16.37 / Similar to PTS mannose-specific enzyme IIC component
lmo2002 / 17.27 / Similar to PTS mannose-specific enzyme IIB component
lmo2183 / 3.87 / Similar to ferrichrome ABC transporter (permease)
lmo2227 / 2.39 / Similar to ABC transporter (ATP-binding protein)
lmo2335 / fruA / 2.61 / Highly similar to phosphotransferase system (PTS) fructose-specific enzyme IIABC component
lmo2463 / 2.47 / Similar to transport protein
lmo2588 / 5.06 / Similar to drug-export proteins
lmo2689 / 2.52 / Highly similar to Mg2+ transport ATPase
lmo2751 / 2.4 / Similar to ABC transporter, ATP-binding protein
lmo2760 / 5.16 / Similar to ABC transporter (ATP-binding protein)
Membrane bioenergetics / lmo0103 / 2.83 / Similar to NADH oxidase
lmo1233 / trxA / 2.18 / Thioredoxin
lmo1609 / 2.66 / Similar to thioredoxin
lmo2478 / trxB / 3.48 / Thioredoxin reductase
lmo2830 / 2.28 / Similar to thioredoxin
Cell division / lmo0421 / 6.02 / Similar to rod shape-determining protein RodA
Cell surface proteins / lmo2085 / 3.81 / Putative peptidoglycan bound protein (LPXTG motif)
lmo0610 / 3.14 / Similar to internalin proteins, putative peptidoglycan bound protein (LPXTG motif)
lmo0601 / 2.88 / Similar to cell surface protein
lmo0821 / 2.70 / Lmo0821
Specific pathways / lmo0182 / 2.21 / Similar to alpha-xylosidase and alpha-glucosidase
lmo0191 / 2.56 / Similar to a putative phospho-beta-glucosidase
lmo0261 / 2.64 / Similar to phospho-beta-glucosidase
lmo0271 / 2.13 / Highly similar to phospho-beta-glucosidase
lmo0372 / 3.23 / Similar to beta-glucosidase
lmo0415 / 2.19 / Similar to endo-1,4-beta-xylanase
lmo0574 / 3.03 / Similar to beta-glucosidase
lmo0613 / 4.12 / Similar to oxidoreductase
lmo0669 / 2.85 / Similar to oxidoreductase
lmo0722 / 2.79 / Similar to pyruvate oxidase
lmo0811 / 2.39 / similar to carbonic anhydrase
lmo1000 / 2.06 / Similar to phytoene dehydrogenase
lmo1057 / 2.29 / Similar to L-lactate dehydrogenase
lmo1293 / glpD / 4.21 / Similar to glycerol 3 phosphate dehydrogenase
lmo1684 / 2.72 / Similar to glycerate dehydrogenases
lmo1737 / 2.25 / Similar to glycerol dehydrogenase
lmo1969 / 2.69 / Similar to 2-keto-3-deoxygluconate-6-phosphate aldolase
lmo1998 / 3.64 / Similar to opine catabolism protein
lmo1999 / 4.40 / Weakly similar to glucosamine-fructose-6-phosphate aminotransferase
lmo2005 / 2.51 / Similar to oxidoreductase
lmo2336 / fruB / 4.88 / Fructose-1-phosphate kinase
lmo2573 / 3.09 / Similar to zinc-binding dehydrogenase
lmo2660 / 2.16 / Similar to transketolase
lmo2695 / 2.75 / Similar to dihydroxyacetone kinase
lmo2696 / 3.71 / Similar to hypothetical dihydroxyacetone kinase
Main glycolytic pathways / lmo1305 / tkt / 3.48 / Highly similar to transketolase
TCA cycle / lmo1641 / citB / 2.16 / Highly similar to aconitate hydratases
Metabolism of amino acids and related molecules / lmo0009 / 2.44 / Similar to spermidine N1-acetyltransferase
lmo0203 / mpl / 2.24 / Zinc metalloproteinase precursor
lmo0458 / 6.58 / Similar to hydantoinase
lmo0560 / 8.72 / Similar to NADP-specific glutamate dehydrogenase
lmo0561 / hisE / 2.53 / Similar to phosphorybosil-AMP-cyclohydrolase (HisI2 protein)
lmo0562 / hisI / 2.84 / Similar to phosphoribosyl-AMP cyclohydrolase (HisI1 protein)
lmo0563 / hisF / 2.76 / Highly similar to cyclase HisF
lmo0564 / hisA / 3.20 / Highly similar to phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase
lmo0565 / hisH / 2.57 / Similar to amidotransferases
lmo0566 / hisB / 2.62 / Imidazoleglycerol-phosphate dehydratase
lmo0567 / hisD / 3.22 / Highly similar to histidinol dehydrogenases
lmo0568 / hisG / 3.48 / Similar to ATP phosphoribosyltransferase
lmo0595 / 3.12 / Similar to O-acetylhomoserine sulfhydrylase
lmo0820 / 3.39 / Some similarity to acatyltransferases
lmo1375 / pyrP / 4.66 / Similar to aminotripeptidase
lmo1393 / 2.36 / Similar to putative protease
lmo1600 / aroA / 2.51 / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase
lmo1679 / 3.37 / Similar to cystathionine beta-lyase
lmo1680 / 2.06 / Similar to cystathionine gamma-synthase
lmo1733 / 3.76 / Similar to glutamate synthase (small subunit)
lmo1734 / 3.58 / Similar to glutamate synthase (large subunit)
lmo1907 / dapB / 2.53 / Similar to dihydrodipicolinate reductase
lmo1924 / tyrA / 2.15 / Similar to prephenate dehydrogenase
lmo1925 / hisC / 2.50 / Similar to histidinol-phosphate aminotransferase and tyrosine/phenylalanine aminotransferase
lmo1927 / aroB / 2.32 / Similar to 3-dehydroquinate synthase
lmo1928 / aroF / 4.03 / Similar to chorismate synthase
Metabolism of nucleotides and nucleic acids / lmo1523 / relA / 2.65 / Similar to (p)ppGpp synthetase
lmo1836 / pyrAa / 2.14 / Highly similar to carbamoyl-phosphate synthetase (glutaminase subunit)
lmo1837 / pyrC / 2.62 / Highly similar to dihydroorotase
lmo1838 / pyrB / 3.34 / Highly similar to aspartate carbamoyltransferase
Metabolism of lipids / lmo0008 / 2.65 / Similar to cardiolipin synthase
lmo1970 / 2.86 / Similar to putative phosphotriesterase related proteins
lmo2450 / 2.48 / Similar to carboxylesterase
lmo2452 / 2.14 / Similar to carboxylesterase
lmo2453 / 3.73 / Similar to lipolytic enzyme
Metabolism of coenzymes and prosthetic groups / lmo0224 / sul / 3.68 / Highly similar to dihydropteroate synthases
lmo0225 / folA / 3.92 / Highly similar to dihydroneopterin aldolase
lmo0226 / folK / 4.19 / Similar to 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase
lmo1901 / panC / 3.28 / Similar to panthotenate synthetases
lmo1902 / panB / 4.00 / Similar to ketopantoate hydroxymethyltransferases
lmo1904 / birA / 2.03 / Similar to transcriptional regulator and biotin acetyl-CoA-carboxylase synthetase
lmo2057 / ctaB / 3.27 / Highly similar to heme A farnesyltransferase
lmo2571 / 2.06 / Similar to nicotinamidase
lmo2572 / 2.37 / Similar to Chain A, Dihydrofolate Reductase
DNA replication / lmo2308 / 4.48 / Similar to single-stranded DNA-binding protein
lmo2704 / dnaX / 2.33 / Highly similar to DNA polymerase III (gamma and tau subunits)
DNA restriction/modification and repair / lmo0996 / 3.59 / Similar to methylated-DNA-protein-cystein methyltransferase
lmo1234 / uvrC / 2.74 / Highly similar to excinuclease ABC subunit C
lmo1689 / 2.79 / Similar to A/G-specific adenine glycosylase
lmo1975 / 5.01 / Similar to E. coli DNA-damage-inducible protein dinP
lmo2316 / 8.38 / Similar to site-specific DNA-methyltransferase
lmo2488 / uvrA / 2.52 / Excinuclease ABC (subunit A)
lmo2489 / uvrB / 3.75 / Excinuclease ABC (subunit B)
lmo2676 / 3.60 / Similar to UV-damage repair protein
DNA recombination / lmo0005 / recF / 2.59 / RecF protein
lmo1398 / recA / 2.19 / Recombination protein recA
lmo2268 / addB / 2.25 / Similar to ATP-dependent deoxyribonuclease (subunit B)
DNA packaging and segregation / lmo0006 / gyrB / 2.08 / DNA gyrase subunit B
Regulation / lmo0520 / 6.76 / Similar to transcription regulator
lmo0109 / 2.19 / Similar to transcriptional regulatory proteins, AraC family
lmo0192 / 2.67 / Similar to PurR, transcription repressor of purine operon of B. subtilis
lmo0229 / 3.43 / Highly similar to transcription repressor of class III stress genes (CtsR)
lmo0297 / 2.34 / Similar to transcriptional antiterminator (BglG family)
lmo0547 / 2.46 / Similar to B. subtilis DeoR transcriptional regulator
lmo0612 / 3.65 / Similar to transcription regulator MarR family
lmo0753 / 2.61 / Similar to transcription regulator Crp/Fnr family
lmo0770 / 2.10 / Similar to transcriptional regulator (LacI family)
lmo0806 / 2.48 / Similar to transcription regulator
lmo0948 / 2.30 / Similar to transcription regulator
lmo1475 / hrcA / 4.47 / Transcription repressor of class I heat-shock gene HrcA
lmo1735 / gltC / 3.13 / Transcription activator of glutamate synthase operon GltC
lmo1840 / pyrR / 3.09 / Highly similar to pyrimidine operon regulatory protein
lmo1974 / 2.02 / Similar to transcription regulators (GntR family)
lmo2003 / 22.95 / Similar to transcription regulator GntR family
lmo2004 / 27.94 / Similar to transcription regulator GntR family
lmo2200 / 2.33 / Similar to transcription regulator
lmo2324 / 5.58 / Similar to anti-repressor [Bacteriophage A118]
lmo2328 / 4.07 / Similar to transcription regulator
lmo2329 / 2.96 / Similar to a putative repressor protein [Bacteriophage A118]
lmo2337 / 6.64 / Similar to regulatory protein DeoR family
lmo2494 / 2.20 / Similar to negative regulator of phosphate regulon
lmo2589 / 2.02 / Similar to transcription regulator TetR/AcrR family
lmo2672 / 3.28 / Weakly similar to transcription regulator
lmo2690 / 3.54 / Similar to transcription regulator, TetR family
lmo2722 / 2.18 / Similar to merR-family transcriptional regulator
RNA modification / lmo0637 / 2.51 / Weakly similar to methyltransferase
lmo1751 / 2.05 / Similar to hypothetical RNA methyltransferase
lmo1905 / cca / 2.51 / Similar to tRNA CCA-adding enzyme
lmo2449 / 2.39 / Similar to exoribonuclease RNase-R
Ribosomal proteins / lmo0250 / rplJ / 2.55 / Ribosomal protein L10
lmo0251 / rpIL / 2.16 / Ribosomal protein L12
lmo1882 / 3.01 / Similar to ribosomal protein S14
Aminoacyl-tRNA synthetases / lmo0569 / hisZ / 2.80 / Histidyl-tRNA synthetase
lmo1221 / pheS / 2.78 / Phenylalany-tRNA synthetase alpha subunit
Initiation / lmo0423 / 6.89 / Similar to RNA polymerase ECF-type sigma factor
Protein folding / lmo1473 / dnaK / 3.50 / Class I heat-shock protein (molecular chaperone) DnaK
Adaptation to atypical conditions / lmo0942 / 2.27 / Similar to heat shock protein HtpG
lmo0997 / clpE / 5.35 / ATP-dependent protease
lmo1138 / 2.44 / Similar to ATP-dependent Clp protease proteolytic component
lmo1278 / clpQ / 2.49 / Highly similar to beta-type subunit of the 20S proteasome
lmo1472 / dnaJ / 3.32 / Heat shock protein DnaJ
lmo1474 / grpE / 4.73 / Heat shock protein GrpE
lmo1601 / 2.95 / Similar to general stress protein
lmo2206 / clpB / 3.58 / Similar to endopeptidase Clp ATP-binding chain B (ClpB)
Detoxification / lmo2067 / 2.55 / Similar to conjugated bile acid hydrolase
lmo2230 / 2.00 / Similar to arsenate reductase
Phage-related functions / lmo2273 / 3.93 / Protein gp30 [Bacteriophage A118]
lmo2274 / 4.74 / Protein gp29 [Bacteriophage A118]
lmo2275 / 5.38 / Protein gp28 [Bacteriophage A118]
lmo2276 / 3.44 / Similar to an unknown bacteriophage protein
lmo2303 / 3.90 / Protein gp66 [Bacteriophage A118]
lmo2304 / 3.90 / Bacteriophage A118 gp65 protein
lmo2306 / 4.84 / Similar to phage protein
lmo2313 / 5.46 / Similar to a bacteriophage protein
lmo2315 / 6.02 / Similar to protein gp51 [Bacteriophage A118]
lmo2317 / 4.75 / Similar to protein gp49 [Bacteriophage A118]
lmo2319 / 3.76 / Similar to bacteriophage proteins
lmo2322 / 5.45 / Gp44 [Bacteriophage A118]
lmo2323 / 6.49 / Gp43 [Bacteriophage A118]
lmo2326 / 7.18 / Similar to protein gp41 [Bacteriophage A118]
Miscellaneous / lmo0439 / 2.29 / Weakly similar to a module of peptide synthetase
Similar to unknown proteins from Listeria / lmo2132 / 4.02 / Lmo2132
Similar to unknown proteins from other organisms / lmo0004 / 2.42 / Similar to B. subtilis YaaA protein
lmo0019 / 2.34 / Lmo0019
lmo0102 / 2.25 / Lmo0102
lmo0134 / 2.32 / Similar to E. coli YjdJ protein
lmo0163 / 2.09 / Lmo0163
lmo0165 / 2.60 / Conserved hypothetical protein
lmo0166 / 2.07 / Similar to B. subtilis YazA protein
lmo0190 / 2.13 / Similar to B. subtilis YabH protein
lmo0227 / 2.88 / Conserved hypothetical protein
lmo0230 / 2.62 / Similar to B. subtilis YacH protein
lmo0260 / 3.26 / Similar to unknown proteins
lmo0422 / 7.37 / Similar to unknown proteins
lmo0457 / 9.12 / Similar to unknown proteins
lmo0485 / 2.20 / Lmo0485
lmo0496 / 7.78 / Similar to B. subtilis YnzC protein
lmo0589 / 2.70 / Lmo0589
lmo0590 / 2.46 / Similar to a fusion of two types of conserved hypothetical proteinconserved hypothetical
lmo0591 / 2.52 / Similar to unknown membrane proteins
lmo0599 / 3.62 / Conserved hypothetical protein
lmo0600 / 3.70 / Lmo0600
lmo0636 / 3.93 / Similar to unknown proteins
lmo0719 / 3.49 / Similar to unknown protein
lmo0794 / 2.55 / Similar to B. subtilis YwnB protein
lmo0795 / 3.34 / Conserved hypothetical protein
lmo0800 / 4.97 / Similar to B. subtilis YqkB protein
lmo0940 / 2.52 / Lmo0940
lmo0941 / 2.62 / Lmo0941
lmo0944 / 2.26 / Similar to B. subtilis YneR protein
lmo0977 / 2.06 / Similar to B. subtilis YjcH protein
lmo0991 / 2.25 / Conserved hypothetical protein
lmo0994 / 2.89 / Lmo0994
lmo0995 / 6.99 / Similar to B. subtilis YkrP protein
lmo1058 / 2.21 / Similar to B. subtilis YktA protein
lmo1140 / 2.12 / Lmo1140
lmo1220 / 2.13 / Similar to unknown protein
lmo1303 / 5.15 / Similar to B. subtilis YneA protein
lmo1304 / 5.44 / Similar to B. subtilis YnzC protein
lmo1416 / 2.70 / Lmo1416
lmo1470 / 2.07 / Similar to unknown proteins
lmo1575 / 2.14 / Similar to unknown proteins
lmo1576 / 2.08 / Similar to unknown proteins
lmo1602 / 3.52 / Similar to unknown proteins
lmo1608 / 2.41 / Similar to unknown proteins
lmo1613 / 2.13 / Similar to unknown proteins
lmo1650 / 2.18 / Similar to hypothetical proteins
lmo1736 / 2.40 / Similar to unknown proteins
lmo1781 / 2.06 / Lmo1781
lmo1795 / 2.09 / Similar to unknown proteins
lmo1830 / 3.00 / Similar to conserved hypotheticl proteins
lmo1945 / 2.67 / Similar to unknown protein
lmo1963 / 2.07 / Similar to unknown proteins
lmo2083 / 2.80 / Lmo2083
lmo2084 / 2.78 / Lmo2084
lmo2208 / 2.17 / Similar to unknown protein
lmo2209 / 3.27 / Lmo2209
lmo2226 / 2.81 / Similar to unknown proteins
lmo2318 / 5.53 / Lmo2318
lmo2360 / 4.44 / Transmembrane protein
lmo2361 / 3.84 / Conserved hypothetical protein
lmo2391 / 2.32 / Conserved hypothetical protein similar to B. subtilis YhfK protein
lmo2392 / 3.09 / Similar to B. subtilis YuzB protein
lmo2393 / 4.87 / Similar to B. subtilis YuzD protein
lmo2448 / 2.05 / Conserved hypothetical protein
lmo2511 / 2.60 / Similar to conserved hypothetical proteins like to B. subtilis YvyD protein
lmo2602 / 3.32 / Conserved hypothetical protein
lmo2603 / 2.54 / Lmo2603
lmo2670 / 2.39 / Conserved hypothetical protein
lmo2673 / 4.21 / Conserved hypothetical protein
lmo2697 / 2.79 / Lmo2697
lmo2703 / 2.01 / Highly similar to B. subtilis YaaK protein
lmo2748 / 3.49 / Similar to B. subtilis stress protein YdaG
lmo2759 / 7.26 / Similar to unknown protein
No similarity / lmo0254 / 2.77 / Lmo0254
lmo0647 / 2.56 / Lmo0647
lmo0819 / 3.51 / Lmo0819
lmo0881 / 2.13 / Lmo0881
lmo0939 / 2.33 / Lmo0939
lmo2269 / 5.45 / Lmo2269
lmo2302 / 4.09 / Lmo2302
lmo2305 / 4.15 / Lmo2305
lmo2309 / 4.94 / Lmo2309
lmo2310 / 3.90 / Lmo2310
lmo2311 / 5.15 / Lmo2311
lmo2312 / 5.28 / Lmo2312
lmo2314 / 6.25 / Lmo2314
lmo2320 / 6.23 / Lmo2320
lmo2327 / 5.12 / Lmo2327
lmo2675 / 3.12 / Lmo2675
lmo2828 / 7.87 / Lmo2828
Unknown d / lmo2321 / 5.38 / Lmo2321
lmo0368 / 2.45 / Similar to different proteins
lmo1279 / hslU / 2.36 / Highly similar to ATP-dependent Clp protease-like proteins

a Functional category is classed according to (Glaser et al., 2001).

b Bin bracketrepresents biofilm cells; F in bracketrepresents free-living cells (planktonic cells).

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

d Unknown means the function of protein encoded by the identified gene in this study was not found within any category in