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Table 1 Chromosomal genes differentially expressed in response to anaerobic conditions not previously published in E. coli and S. flexneri microarray analysis

From: RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri

ORF IDab Gene Description RNA-seqclog2FC RNA-seqclog2FC FRT-seqclog2FC
    WT no O2/O2 Δfnr/WT no O2 Δfnr/WT no O2
Metabolism      
Energy production and conversion
SF5M90T_1519   putative oxidoreductase, major subunit 3.80 -4.97 -3.30
SF5M90T_3856 yiaY putative oxidoreductase 3.18 -2.73 -2.67
SF5M90T_1560   putative oxidoreductase, major subunit 3.06   -3.87
SF5M90T_3333 pckA phosphoenolpyruvate carboxykinase 1.99   0.62
SF5M90T_3877 yiaK putative dehydrogenase 1.93 1.22 0.93
SF5M90T_3374 ugpQ glycerophosphodiester phosphodiesterase, cytosolic 1.89   
SF5M90T_2534 hmpA dihydropteridine reductase, ferrisiderophore reductase activity 1.47 5.38 5.85
SF5M90T_33 caiB l-carnitine dehydratase 1.32   
SF5M90T_3679 atpF membrane-bound ATP synthase, F0 sector, subunit b 1.04   
SF5M90T_3680 atpE membrane-bound ATP synthase, F0 sector, subunit c 1.04   
SF5M90T_3937 ppc phosphoenolpyruvate carboxylase 0.91   0.64
SF5M90T_579 galT galactose-1-phosphate uridylyltransferase 0.77   
SF5M90T_1419 ydjA predicted oxidoreductase -1.17 1.69 1.52
SF5M90T_2771 ygaF hydroxyglutarate oxidase -1.31 4.12 2.99
SF5M90T_4044 gltP glutamate-aspartate symport protein -1.32   
SF5M90T_1603 rnfB electron transport complex protein -1.46   
SF5M90T_2869 fldB flavodoxin 2 -1.56   
SF5M90T_1602 rnfA Na + -translocating NADH-quinone reductase subunit E -1.75   
SF5M90T_1011 rutA pyrimidine monooxygenase -3.07   
Carbohydrate transport and metabolism
SF4250 treB PTS system trehalose(maltose)-specific transporter subunits IIBC 3.66   
SF5M90T_4160 treC trehalase 6-P hydrolase 3.56   
SF5M90T_1379 manX PTS enzyme IIAB, mannose-specific 3.36   
SF5M90T_1378 manY PTS enzyme IIC, mannose-specific 3.11   
SF5M90T_1377 manZ PTS enzyme IID, mannose-specific 2.89   
SF5M90T_3670 rbsD high affinity ribose transport protein 2.71   
SF5M90T_1101 ptsG PTS system, glucose-specific IIBC component 2.27   
SF5M90T_3491 treF cytoplasmic trehalase 2.12   
SF5M90T_2419 murP PTS system N-acetylmuramic acid transporter subunits EIIBC 2.09   -0.71
SF5M90T_3499 pfkA 6-phosphofructokinase I 2.08   
SF5M90T_2096   fructose-bisphosphate aldolase 2.02 2.08 1.86
SF5M90T_1001 agp periplasmic glucose-1-phosphatase 2.00 1.40 1.57
SF5M90T_2887 rpiA ribosephosphate isomerase, constitutive 1.84   
SF5M90T_2898 pgk phosphoglycerate kinase 1.84   
SF5M90T_1403 gapA glyceraldehyde-3-phosphate dehydrogenase A 1.83   
SF5M90T_2097 yegT putative nucleoside permease protein 1.74   
SF5M90T_2897 fba fructose-bisphosphate aldolase, class II 1.56   
SF5M90T_2404 ptsH PTS system protein HPr 1.56   
SF5M90T_3850 mtlA PTS system, mannitol-specific enzyme IIABC components 1.52   
SF5M90T_1640 ydhC putative transport protein 1.51   0.69
SF5M90T_2359   beta-fructosidase 1.49   0.72
SF5M90T_3496 tpiA triosephosphate isomerase 1.45   
SF5M90T_2405 ptsI PEP-protein phosphotransferase system enzyme I 1.42   
SF5M90T_2808 fucI L-fucose isomerase 1.41   
SF5M90T_2875 bglA 6-phospho-beta-glucosidase A 1.27   
SF5M90T_3348 malP maltodextrin phosphorylase 1.16   0.78
SF5M90T_1107 ycfO beta-hexosaminidase 1.13   
SF5M90T_8 talB transaldolase B 1.10   
SF5M90T_2033 gnd gluconate-6-phosphate dehydrogenase 1.01   
SF5M90T_581 galM galactose-1-epimerase 1.01 1.41 1.00
SF5M90T_1805 eda keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase 0.97   
SF5M90T_580 galK galactokinase 0.95   0.62
SF5M90T_2913 tktA transketolase 1 isozyme 0.80   
SF5M90T_2187 fruB PTS system fructose-specific transporter subunit IIA/HPr protein -1.33   
SF5M90T_2186 fruK fructose-1-phosphate kinase -1.75   
SF5M90T_3161 ptsO phosphocarrier protein NPr -1.76   
SF5M90T_1637   putative transport protein -1.93 1.58  
SF5M90T_2185 fruA PTS system, fructose-specific transport protein -1.99   
Aminoacid transport and metabolism
SF5M90T_2823 argA N-acetylglutamate synthase 1.94   
SF5M90T_1910 fliY putative periplasmic binding transport protein 1.80   
SF5M90T_625 ybgH peptide transporter 1.64 -1.60 -1.21
SF5M90T_292 pepD aminoacyl-histidine dipeptidase (peptidase D) 1.54 1.78 1.75
SF5M90T_2879 gcvT aminomethyltransferase 1.53   1.44
SF5M90T_284 proA gamma-glutamylphosphate reductase 1.48   
SF5M90T_1121 potD spermidine/putrescine periplasmic transport protein 1.44   -0.69
SF5M90T_2674 cysD ATP:sulfurylase (ATP:sulfate adenylyltransferase), subunit 2 1.39 -2.30 -2.21
SF5M90T_1514 dcp dipeptidyl carboxypeptidase II 1.35   0.63
SF5M90T_285 proB gamma-glutamate kinase 1.26   -0.58
SF5M90T_2533 glyA serine hydroxymethyltransferase 1.16   
SF5M90T_2967 gsp glutathionylspermidine synthetase/amidase 1.16   0.70
SF5M90T_1806 edd 6-phosphogluconate dehydratase 1.15   -0.72
SF5M90T_807   glutathione transporter ATP-binding protein 1.08   
SF5M90T_2317 hisJ histidine-binding periplasmic protein of high-affinity histidine transport system 1.05   
SF5M90T_806 ybiK putative asparaginase 1.02   
SF5M90T_1122 potC spermidine/putrescine transport system permease 0.97 -1.09 -0.92
SF5M90T_2882 pepP proline aminopeptidase P II 0.94   
SF5M90T_2877 gcvP glycine decarboxylase 0.90 2.13 1.69
SF5M90T_3687 asnA asparagine synthetase A -1.23   -1.61
SF5M90T_4099 lysC aspartokinase III, lysine sensitive -1.33 1.37 1.14
SF5M90T_1253 trpE anthranilate synthase component I -1.57   
SF5M90T_4187 cycA transport of D-alanine, D-serine, and glycine -1.69   
SF5M90T_1946 yedA putative transmembrane subunit -1.79   
SF5M90T_3626 yifK putative amino acid/amine transport protein -1.94   
SF5M90T_3385 livJ Leu/Ile/Val-binding protein precursor -1.95   
SF5M90T_2843 lysA diaminopimelate decarboxylase -2.11 2.44  
SF5M90T_4029 proP low-affinity transport system; proline permease II -2.65 1.05 0.75
SF5M90T_4185 ytfF putative transmembrane subunit -3.70 2.71  
Nucleotide transport and metabolism    
SF5M90T_3587 udp uridine phosphorylase 3.12   0.59
SF5M90T_2387 nupC permease of transport system for 3 nucleosides 2.81   
SF5M90T_2949 nupG nucleoside permease 2.47   
SF5M90T_674 ybeK putative tRNA synthetase 1.60   
SF5M90T_444 adk adenylate kinase 1.51   -0.67
SF5M90T_2456 purC phosphoribosylaminoimidazole-succinocarboxamidesynthetase 1.35   
SF5M90T_4182 cpdB 2′:3′-cyclic-nucleotide 2′-phosphodiesterase 1.16   
SF5M90T_291 gpt guanine-hypoxanthine phosphoribosyltransferase 1.10   -0.89
SF5M90T_1598 add adenosine deaminase 0.95   
SF5M90T_478 purE phosphoribosylaminoimidazole carboxylase -1.41   
Coenzyme transport and metabolism
SF5M90T_2274 menB dihydroxynaphtoic acid synthetase 2.63 -1.75 -1.65
SF5M90T_2687   phenylacrylic acid decarboxylase-like protein 1.83   
SF5M90T_2276 menD 2-oxoglutarate decarboxylase 1.76 -1.63 -1.75
SF5M90T_2273 menC O-succinylbenzoate synthase 1.76 -1.72 -1.57
SF5M90T_3142 ispB octaprenyl diphosphate synthase 1.06   
SF5M90T_1613 pdxH pyridoxinephosphate oxidase 1.06   
SF5M90T_2880 visC putative FAD-dependent oxidoreductase 0.89   
SF5M90T_3011 ribB 3,4 dihydroxy-2-butanone-4-phosphate synthase -1.10   
SF5M90T_3577 yigC putative oxidoreductase -1.31   
SF5M90T_2885 ygfA putative ligase -1.59   
SF5M90T_3957 birA biotin--protein ligase -1.62   -0.51
SF5M90T_2103 thiM hydoxyethylthiazole kinase -1.95   
Lipid transport and metabolism
SF5M90T_1094 acpP acyl carrier protein 1.70 -3.04  
SF5M90T_2272 menE o-succinylbenzoate-CoA ligase 1.60 -1.54 -1.80
SF5M90T_2416 ucpA putative oxidoreductase 1.45   -0.56
SF5M90T_339 sbmA sensitivity to microcin B17, possibly envelope protein -1.64   
Inorganic ion transport and metabolism
SF5M90T_2903   hypothetical lipoprotein 3.41   
SF5M90T_929 ycbO alkanesulfonate transporter substrate-binding subunit 3.04   
SF5M90T_2415 cysP thiosulfate binding protein 2.81 -1.51 -1.88
SF5M90T_1636 sodB superoxide dismutase 2.52 2.13 1.67
SF5M90T_1187   putative ATP-binding protein of ABC transporter 2.14   
SF5M90T_454 copA copper exporting ATPase 1.95   
SF5M90T_1186   putative iron compound ABC transporter permease 1.69   
SF5M90T_1185   iron ABC transporter ATP-binding protein 1.52   
SF5M90T_4057 yjcE predicted cation/proton antiporter 1.49   
SF5M90T_2675 cysN ATP-sulfurylase (ATP:sulfate adenylyltransferase), subunit 1 1.08 -2.08 -2.05
SF5M90T_448 ybaL putative transport protein -1.01   -0.50
SF5M90T_2386 mntH divalent metal cation transporter -1.93 1.61 1.68
SF5M90T_330 tauC taurine transport system permease protein -2.09   
SF5M90T_3769 shiF putative membrane transport protein -2.16   
SF5M90T_3054 ygjT putative transport protein -2.41   
SF5M90T_1102 fhuE outer membrane receptor for ferric iron uptake -2.46   
SF5M90T_1483 ydiE hemin uptake protein -2.93 -2.20 -1.55
SF5M90T_1572 mdtI spermidine export protein -3.61   
Secondary metabolites biosynthesis, transport and catabolism
SF5M90T_1184   putative SAM-dependent methyltransferase 2.12   
SF5M90T_331 tauD taurine dioxygenase, 2-oxoglutarate-dependent -2.97 1.94  
Cellular processes and signalling
Cell cycle control, cell division, chromosome partitioning
SF5M90T_1243 yciB probable intracellular septation protein A 0.93   -0.80
Defense mechanisms
SF5M90T_4215 ampC beta-lactamase; penicillin resistance 1.55   -1.69
SF5M90T_3751 emrD multidrug resistance protein D 1.41   
SF5M90T_4273   putative restriction modification enzyme R subunit 1.41 -0.94 -0.99
SF5M90T_3781 shiA virulence factor 1.30   
SF5M90T_101 ampD N-acetyl-anhydromuranmyl-L-alanine amidase 1.18   
SF5M90T_772 ybhF putative ABC-type multidrug transport system component 1.16   0.54
SF5M90T_771 ybhS putative ABC-type multidrug transport system component 1.15   
SF5M90T_770 ybhR putative ABC-type multidrug transport system component 0.90   
SF5M90T_418 mdlA ATP-binding component of a transport system -1.29   
Signal transduction mechanisms
SF5M90T_2126 yehU putative 2-component sensor protein 1.36   
SF5M90T_3428 uspA universal stress protein 0.86   
SF5M90T_2388 yfeA predicted diguanylate cyclase -1.20   -0.81
SF5M90T_4339 creC sensory histidine kinase -1.63 1.43  
Cell wall/membrane/envelope biogenesis
SF5M90T_1923 nmpC outer membrane porin protein 2.04 -1.34 -1.13
SF5M90T_1618 slyB putative outer membrane protein 1.82 -1.43 -0.92
SF5M90T_952 ompA outer membrane protein 3a 1.59   
SF5M90T_374 tsx outer membrane protein 1.53   
SF5M90T_256 gtrB bactoprenol glucosyl transferase 1.36 -2.59  
SF5M90T_2039 rfbC dTDP-4-dehydrorhamnose 3,5-epimerase 1.20 -2.64  
SF5M90T_4332 slt soluble lytic murein transglycosylase 0.96 1.54 1.46
SF5M90T_3951 murI glutamate racemase 0.93   -0.48
SF5M90T_3821 rfaD ADP-L-glycero-D-mannoheptose-6-epimerase 0.82   
SF5M90T_1241 tonB transport protein -1.72   
SF5M90T_3956 murB UDP-N-acetylenolpyruvoylglucosamine reductase -2.23   -0.60
Cell motility
SF5M90T_1938 fliQ flagellar biosynthetic protein 3.55   
Intracellular trafficking, secretion and vesicular transport    
SF5M90T_3964 secE preprotein translocase 0.87 -1.06 -0.76
SF5M90T_3580 tatC Sec-independent protein translocase 0.84   -0.57
SF5M90T_3501 yiiO uncharacterized periplasmic protein -4.72   2.64
Posttranslational modification, protein turnover, chaperones
SF5M90T_4204 mopB co-chaperonin GroES 1.41   
SF5M90T_3279 slyD FKBP-type peptidyl-prolyl cis-trans isomerase 1.31   
SF5M90T_462 ybbN putative thioredoxin-like protein 0.90   
SF5M90T_407 clpP ATP-dependent proteolytic subunit of clpA-clpP serine protease 0.84   
SF5M90T_3738 ibpA heat shock protein -1.17   
SF5M90T_2074 yegD putative heat shock protein -2.80   -1.11
Information storage and processing
Translation, ribosomal structure and biogenesis
SF5M90T_2801 yfiA translation inhibitor protein RaiA 2.70   
SF5M90T_2392 gltX glutamate tRNA synthetase, catalytic subunit 1.65   
SF5M90T_155 frr ribosome releasing factor 1.21   
SF5M90T_650 glnS glutamine tRNA synthetase 1.08   
SF5M90T_3893 glyQ glycine tRNA synthetase, alpha subunit 1.06   -0.50
SF5M90T_4220 yjeA putative lysyl-tRNA synthetase 0.95 -1.75 -1.72
SF5M90T_3894 glyS glycine tRNA synthetase, beta subunit 0.81   
Transcription
SF5M90T_3025 ygiP putative transcriptional regulator/nucleoid-associated protein 3.04 -4.57 -2.45
SF5M90T_2417 murR HTH-type transcriptional regulator 2.35   
SF5M90T_3510 rhaR positive regulator for rhaRS operon 2.33   
SF5M90T_1595 malI repressor of malX and Y genes 1.98   
SF5M90T_2125 yehT putative two-component response regulator 1.80   
SF5M90T_1373 cspC cold shock protein 1.59 -1.38  
SF5M90T_3349 malT positive regulator of mal regulon 1.58   0.58
SF5M90T_3335 ompR osmolarity response regulator 1.42   
SF5M90T_3453 yiaG putative transcriptional regulator 1.38   3.65
SF5M90T_2089 gatR galactitol utilization operon repressor 1.33   
SF5M90T_71 cra transcriptional repressor of fru operon and others 1.16   
SF5M90T_4197 yjdC putative transcriptional regulator 1.15   1.37
SF5M90T_1370   putative regulator 1.09   
SF5M90T_3578 rfaH transcriptional activator -1.57   -0.96
SF5M90T_4242 yjeB HTH-type transcriptional repressor -1.95   
SF5M90T_984 cspH cold shock-like protein -3.35   
Replication, recombination and repair
SF5M90T_2925 endA DNA-specific endonuclease I 1.42 -3.26 -2.74
SF5M90T_3034 ygjF G/U mismatch-specific DNA glycosylase 1.23   1.10
SF5M90T_410 hupB DNA-binding protein HU-beta 1.08   
SF5M90T_775 rhlE putative ATP-dependent RNA helicase -1.16   
SF5M90T_3117 deaD inducible ATP-independent RNA helicase -1.20   
SF5M90T_1769 dbpA ATP-dependent RNA helicase -1.86   
Poorly characterized
General function prediction only
SF5M90T_2762 stpA DNA-binding protein 3.51 -3.00 -2.60
SF5M90T_275   putative crossover junction endodeoxyribonuclease 2.84   
SF5M90T_2418 muQ N-acetylmuramic acid 6-phosphate etherase 2.77   -0.93
SF5M90T_1724   putative acetyltransferase 2.06 -2.41  
SF5M90T_2435   putative amino acid antiporter 2.03 1.90 1.58
SF5M90T_2301 yfbT putative phosphatase 2.00   
SF5M90T_773 ybhG putative membrane protein 1.78 1.02  
SF5M90T_1227 hns DNA-binding protein 1.69 -1.24  
SF5M90T_2275 yfbB putative enzyme 1.62 -1.90 -1.85
SF5M90T_3225 yrdA putative transferase 1.51   
SF5M90T_4236 hfq RNA-binding protein 1.45 -2.10  
SF5M90T_3315 gph phosphoglycolate phosphatase 1.25   
SF5M90T_2192 yeiR putative GTPases 1.03   
SF5M90T_1919 yedE putative transport system permease protein 1.03 -1.83 -1.96
SF5M90T_3295 yhfC putative transport 0.97 -1.30 -1.25
SF5M90T_2205 yejK nucleoid-associated protein 0.95   
SF5M90T_2066 yegH putative transport protein 0.84   
SF5M90T_3344 yhgH putative gluconate periplasmic binding protein 0.81   
SF5M90T_3102 yraM putative glycosylase 0.73   
SF5M90T_794 ybiP putative enzyme -1.14   
SF5M90T_2207 yejM putative sulfatase -1.36   
SF5M90T_3139 yhbE putative permeases of drug/metabolite transporter superfamily -1.36   -0.90
SF5M90T_966 yccA putative carrier/transport protein -1.38   -1.18
SF5M90T_2742 yqaB putative phosphatase -1.51   
SF5M90T_3882 bax putative ATP-binding protein -1.70   -0.77
SF5M90T_3370 yhhX putative regulator -1.97   1.30
SF5M90T_3621 aslB putative arylsulfatase regulator -2.73   
SF5M90T_2516   putative enzyme -3.91   
Function unknown
SFxv_3833   conserved hypothetical protein 3.59 -4.23  
SF5M90T_2431   conserved hypothetical protein 2.89   
SF5M90T_2432   conserved hypothetical protein 2.69   
SF5M90T_11   uncharacterized protein 2.57   
SF5M90T_1402 yeaD conserved hypothetical protein 2.45   
SF5M90T_828 ybjO conserved hypothetical protein 2.23   -2.52
SF5M90T_1941 dsrB conserved hypothetical protein 2.03 -2.43  
SF5M90T_2302 yfbU conserved hypothetical protein 1.87   
SF5M90T_451 ybaK conserved hypothetical protein 1.86 -1.21 -1.10
SSJG_00311   conserved hypothetical protein 1.75   -1.60
SF5M90T_5 yaaA conserved hypothetical protein 1.54   
SF5M90T_1387   conserved hypothetical protein 1.51   
SF5M90T_3911 yiiU conserved hypothetical protein 1.45 -2.49  
SF5M90T_957   conserved hypothetical protein 1.37   
SF5M90T_4146 yjgD conserved hypothetical protein 1.28 -2.30  
SF5M90T_2622   conserved hypothetical protein 1.24 -1.46  
SF5M90T_3155 yhbN conserved hypothetical protein 0.81   
SF5M90T_479 ybbF conserved hypothetical protein -1.19   
SF5M90T_2195 rtn conserved hypothetical protein -1.50   
SF5M90T_438 ybaN conserved hypothetical protein -1.73   
SF5M90T_1853   conserved hypothetical protein -2.03 -2.58  
SF5M90T_1647   conserved hypothetical protein -2.11   
SF5M90T_983 ymcD conserved hypothetical protein -2.34   
SF5M90T_4094 yjbA P-starvation inducible protein PsiE -2.51 1.69  
SF5M90T_1110 ycfJ conserved hypothetical protein -2.52   0.99
SF2861   hypothetical protein remnant -2.64   
SF5M90T_2146 yohO membrane protein -2.96   
SF5M90T_1952   putative outer membrane pore protein -2.98   
SF5M90T_4307   putative inner membrane protein -3.40   
SF1231   conserved hypothetical protein -3.71   -1.60
SF5M90T_427 ybaA conserved hypothetical protein -3.88   
Phage related     
S1668 relF prophage maintenance protein 1.75   
SF5M90T_1793   putative phage integrase protein 1.45 -1.60  
SF5M90T_1056   hypothetical bacteriophage protein 1.14   
SF5M90T_740   putative bacteriophage protein -1.93   
  1. aGenomes used as reference are: S. flexneri 5a str. M90T, S. flexneri 2a str. 301, S. flexneri 2002017, Shigella sp. D9 and S. flexneri 2457 T with GenBank accession numbers AGNM00000000, NC_004337, NC_017328, NZ_GG657384 and NC_004741 respectively.
  2. bGenes are classified in functional categories based on the database of Clusters of Orthologous Groups (COGs). http://www.ncbi.nlm.nih.gov/COG/. Inside each subgroup, genes are arranged in descending order in relation to Log2 of Fold Change values of WT no O2/WT O2 comparison.
  3. cLog2 of Fold Change values of WT no O2/WT O2 and Δfnr no O2/WT no O2 comparisons are presented. Only values considered differentially expressed are shown (p adjust <0.05).