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Table S1. Genes positively affected by LhrA. Gene lhrA/wt a Verification b, c sigB/wt d Description Amino acid biosynthesis lmo0490 glnA ilvN alsS lmo2524 thrB thrC -1.7 -2.2 -1.5 -2.1 -1.7 -1.9 -1.6 Up Up Up Up Up similar to shikimate 5-dehydrogenase highly similar to glutamine synthetases similar to acetolactate synthase (acetohydroxy-acid synthase) (small subunit) similar to alpha-acetolactate synthase protein, AlsS similar to hydroxymyristoyl-(acyl carrier protein) dehydratase highly similar to homoserine kinase highly similar to threonine synthase Biosynthesis of cofactors, prosthetic groups, and carriers folC lmo1592 lmo2101 hemH lmo2542 -1.5 -1.9 -2.3 -1.5 -1.5 Up Up Up similar to Folyl-polyglutamate synthetase similar to thiamin biosynthesis protein ThiI similar to a protein required for pyridoxine synthesis similar to ferrochelatase similar to protoporphyrinogen oxidase -1.5 -1.5 -1.9 -1.7 -2.2 -1.7 -2.9 -2.0 Up Up Up Up Up Up Up Up similar to penicillin-binding protein (D-alanyl-D-alanine carboxypeptidase) UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diamino pimelate-D-alanyl-D-alanyl ligase DltB protein for D-alanine esterification of lipoteichoic acid and wall teichoic acid D-alanyl carrier protein DltD protein for D-alanine esterification of lipoteichoic acid and wall teichoic acid similar to cell-shape determining protein MreD conserved lipoprotein similar to autolysin, N-acetylmuramidase Cell envelope lmo0441 murF dltB dltC dltD mreD lmo2637 lmo2691 Cellular processes lmo0252 ftsX -1.5 -1.5 similar to repressor (penicilinase repressor) highly similar to cell-division protein FtsX Central intermediary metabolism ackA lmo1736 lmo2540 lmo2638 lmo2761 lmo2800 -1.7 -1.5 -1.5 -2.3 -1.5 -1.6 Down Up highly similar to acetate kinase similar to unknown proteins similar to phosphatases similar to NADH dehydrogenase similar to beta-glucosidase similar to dehydrogenase DNA metabolism dnaA dnaN gyrA Ssb lmo2050 lmo2676 lmo2719 -1.5 -2.1 -1.6 -1.5 -1.5 -1.6 -1.5 Up Up Chromosomal replication initiation protein DnaA DNA polymerase III, beta chain DNA gyrase subunit A highly similar to single-strand binding protein (SSB) similar to excinuclease ABC (subunit A) similar to UV-damage repair protein conserved hypothetical proteins Energy metabolism lmo0031 lmo0096 lmo0097 lmo0098 Ldh lmo0734 lmo0735 lmo0736 lmo0737 lmo0738 lmo0739 glpD pflB lmo1634 -1.5 -1.5 -1.6 -1.5 -2.0 -1.7 -1.6 -1.8 -1.8 -2.2 -2.3 -7.1 -3.5 -2.2 Up Down Down 1.5 b Up Up transcriptional regulator LacI family similar to PTS system mannose-specific, factor IIAB similar to PTS system mannose-specific, factor IIC similar to PTS system mannose-specific, factor IID similar to L-lactate dehydrogenase similar to transcriptional regulator (LacI family) similar to Ribulose-5-Phosphate 3-Epimerase similar to ribose 5-phosphate isomerase unknown Phosphotransferase system (PTS) beta-glucoside-specific enzyme IIABC component similar to 6-phospho-beta-glucosidase similar to glycerol 3 phosphate dehydrogenase pyruvate formate-lyase similar to Alcohol-acetaldehyde dehydrogenase 1 pflA gpsA lmo1992 lmo2152 Gap atpE fbaA lmo2659 cydB cydA lmo2762 lmo2800 -4.8 -1.5 -2.9 -1.5 -1.8 -1.5 -2.0 -1.5 -2.2 -1.5 -1.5 -1.6 -1.2 b Up Up Down Up Down Up Up Up similar to pyruvate formate-lyase similar to NAD(P)H-dependent glycerol-3-phosphate dehydrogenase similar to alpha-acetolactate decarboxylase similar to thioredoxin highly similar to glyceraldehyde 3-phosphate dehydrogenase highly similar to H+-transporting ATP synthase chain c similar to fructose-1,6-bisphosphate aldolase similar to ribulose-phosphate 3-epimerase highly similar to cytochrome D ubiquinol oxidase subunit II highly similar to cytochrome D ubiquinol oxidase subunit I similar to PTS cellobiose-specific enzyme IIB similar to dehydrogenase Fatty acid and phospholipid metabolism lmo0786 -1.9 Up similar to acyl-carrier protein phosphodiesterase and to NAD(P)H dehydrogenase Up Up conserved hypothetical protein similar to B. subtilis YlxP protein similar to B. subtilis YqzC protein similar to hypothetical proteins similar to unknown protein similar to unknown proteins similar to unknown proteins similar to unknown proteins similar to unknown proteins unknown unknown unknown unknown Hypothetical proteins lmo1326 lmo1333 lmo1717 lmo1750 lmo2048 lmo2113 lmo2149 lmo2151 lmo2187 lmo2669 lmo2675 lmo2767 -1.6 -1.5 -1.5 -1.9 -1.5 -1.5 -1.7 -1.5 -1.6 -1.5 -1.6 -1.9 Up Down Up Mobile and extrachromosomal element functions lmo0152 lmo1097 lmo2569 lmo0049 lmo0104 lmo0412 lmo0451 lmo0471 lmo1188 lmo1257 lmo1306 rpmG lmo1649 lmo2129 lmo2156 lmo2642 lmo2828 -2.0 -1.6 -1.8 -1.8 -1.5 -1.8 -1.5 -1.5 -1.5 -2.9 -1.5 -1.5 -1.5 -1.6 -1.5 -1.6 -1.8 Up Up Up -2.1 c Up similar to oligopeptide ABC transporter-binding protein similar to integrases similar to dipeptide ABC transporter (dipeptide-binding protein) unknown unknown unknown unknown unknown unknown unknown highly similar to B. subtilis YneF protein ribosomal protein L33 unknown unknown unknown unknown unknown Protein fate lmo0960 lmo0961 tig pflC lmo1603 clpP gtcA -1.6 -1.7 -1.5 -3.1 -1.5 -1.6 -1.6 Up Up Up -1.1 similar to proteases similar to proteases trigger factor (prolyl isomerase) pyruvate-formate lyase activating enzyme similar to aminopeptidase ATP-dependent Clp protease proteolytic subunit wall teichoic acid glycosylation protein GtcA Protein synthesis rpsR lysS rplK rplA rplJ rplL rpsT valS -1.5 -1.5 -1.6 -1.6 -2.6 -2.7 -1.8 -1.5 Up Up Up -1.7 c Up Up Up ribosomal protein S18 lysyl-tRNA synthetase ribosomal protein L11 ribosomal protein L1 ribosomal protein L10 ribosomal protein L12 ribosomal protein S20 valyl-tRNA synthetase 2 rpsD gatB rplT rpmI rplS rpsP rpmF lmo2448 rpmE rpsI rplM rplQ rpsE rplR rplF rpsH rpsN rplE rplX rplN rpsQ rpmC rplP rpsC rplV rpsS rplB rplW rplC -1.5 -1.6 -1.8 -1.5 -1.9 -1.6 -2.3 -1.5 -1.9 -1.9 -1.5 -1.7 -1.5 -1.6 -1.7 -1.8 -1.9 -1.7 -1.8 -1.8 -2.1 -1.9 -2.2 -2.0 -2.1 -2.0 -1.7 -1.8 -1.7 Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up Up ribosomal protein S4 glutamyl-tRNA(Gln) amidotransferase (subunit B) ribosomal protein L20 ribosomal protein L35 ribosomal protein L19 ribosomal protein S16 ribosomal protein L32 conserved hypothetical protein ribosomal protein L31 ribosomal protein S9 ribosomal protein L13 ribosomal protein L17 ribosomal protein S5 ribosomal protein L18 ribosomal protein L6 ribosomal protein S8 ribosomal protein S14 ribosomal protein L5 ribosomal protein L24 ribosomal protein L14 ribosomal protein S17 ribosomal protein L29 ribosomal protein L16 ribosomal protein S3 ribosomal protein L22 ribosomal protein S19 ribosomal protein L2 ribosomal protein L23 ribosomal protein L3 Purines, pyrimidines, nucleosides, and nucleotides prs lmo0280 lmo1827 pnp pdp pyrG -1.6 -1.7 -1.5 -1.6 -1.7 -1.6 Up Up Up phosphoribosyl pyrophosphate synthetase highly similar to anaerobic ribonucleotide reductase activator protein similar to guanylate kinases similar to purine-nucleoside phosphorylase similar to pyrimidine-nucleoside phosphorylase highly similar to CTP synthases Regulatory functions lmo0048 lmo0051 lmo0161 lmo0402 lmo0725 lmo0788 lmo0797 lmo1172 lmo1173 glnR lmo2173 lmo2179 lmo2764 lmo2792 -1.5 -1.5 -1.5 -1.8 -1.5 -2.1 -1.5 -1.3 -1.8 -1.9 -2.1 -1.9 -1.8 -1.6 Down Up Down Up -1.8 b Up Up similar to Staphylococcus two-component sensor histidine kinase AgrB similar to 2-components response regulator protein (AgrA from Staphylococcus) unknown similar to transcriptional antiterminator (BglG family) putative peptidoglycan bound protein (LPXTG motif) unknown unknown similar to similar to two-component response regulator similar to two-component sensor histidine kinase similar to glutamine synthetase repressor similar to sigma-54-dependent transcriptional activator putative peptidoglycan bound protein (LPXTG motif) similar to xylose operon regulatory protein and to glucose kinase unknown Signal transduction lmo2763 -1.9 similar to PTS cellobiose-specific enzyme IIC Transport and binding proteins lmo0179 lmo0181 lmo0283 lmo0284 lmo0947 clpE lmo1003 lmo1224 lmo1389 -1.7 -1.5 -1.6 -1.6 -1.5 -1.9 -1.5 -1.5 -1.5 Up Up similar to sugar ABC transporters, permease proteins similar to sugar ABC transporter, sugar-binding protein similar to ABC transporter permease protein similar to ABC transporter (ATP-binding protein) hypothetical transport protein ATP-dependent protease phosphotransferase system enzyme I similar to different proteins similar to sugar ABC transporter, ATP-binding protein 3 lmo1390 lmo1391 lmo1746 lmo1997 lmo2192 cydD cydC lmo2765 lmo2799 -1.6 -1.8 -1.5 -1.5 -1.5 -1.6 -1.5 -1.5 -1.7 similar to ABC transporter (permease proteins) similar to sugar ABC transporter, permease protein similar to ABC transporter (permease) similar to PTS mannose-specific enzyme IIA component similar to oligopeptide ABC transporter (ATP-binding protein) ABC transporter (ATP-binding protein) required for expression of cytochrome BD highly similar to ABC transporter required for expression of cytochrome BD similar to PTS cellobiose-specific enzyme IIA similar to phosphotransferase system mannitol-specific enzyme IIBC Unclassified lmo0130 hly lmo0285 lmo0354 lmo0355 lmo0394 lmo0814 lmo0912 dltA lmo2029 lmo2102 lmo2142 lmo2269 lmo0624 lemA -1.7 -1.8 -1.6 -2.0 -2.5 -1.6 -1.6 -1.5 -1.6 -1.6 -2.2 -1.8 -2.7 -1.7 -1.6 -1.6 b Up -1.6 b Down Up similar to 5-nucleotidase, putative peptidoglycan bound protein (LPXTG motif) listeriolysin O precursor putative lipoprotein similar to fatty-acid--CoA ligase similar to Flavocytochrome C Fumarate Reductase chain A similar to L. monocytogenes extracellular P60 protein similar to oxidoreductases similar to transporters (formate) D-alanine-activating enzyme (dae), D-alanine-D-alanyl carrier protein ligase (dcl) similar to unknown proteins unknown unknown unknown similar to unknown proteins Listeria epitope LemA Viral functions lmo2504 spl -1.5 -1.7 similar to cell wall binding proteins peptidoglycan lytic protein P45 a Fold of change b Verified by quantitative RT-PCR c Verified by Northern blotting d Genes regulated by σB after NaCl stress or in stationary growth phase, as described by Raengpradub et al. [1] Reference List 1. Raengpradub S, Wiedmann M, Boor KJ (2008) Comparative analysis of the sigma B-dependent stress responses in Listeria monocytogenes and Listeria innocua strains exposed to selected stress conditions. Appl Environ Microbiol 74: 158-171. AEM.00951-07 [pii];10.1128/AEM.00951-07 [doi]. 4
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