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{"sheet":"TableS1","index":0,"n_rows":244,"n_cols":4,"rows_kept":244,"cut":false,"hidden":false,"merged":[],"flags":["formulas_cached_only"]}
["Supplementary Information Table S1. Up-regulated ORFs in IrrE-expressing "]
[" strain, as revealed by microarray analysis a"]
["Gene","Locus","Function","MER b"]
["Amino acid transport and metabolism"]
["asnB","b0674","Asparagine synthase (glutamine-hydrolyzing)",2.985096928619823]
["evgS","b2370","hybrid sensory histidine kinase in two-component regulatory system with EvgA",1.7955731701307385]
["gadA","b3517","Glutamate decarboxylase and related PLP-dependent proteins",2.9394689845511977]
["gadB","b1493","Glutamate decarboxylase and related PLP-dependent proteins",3.84889534757658]
["gadc","b1492","Amino acid transporters",3.938859011737724]
["gltD","b3213","NADPH-dependent glutamate synthase beta chain and related oxidoreductases",2.1435469250725863]
["glyA","b2551","Glycine/serine hydroxymethyltransferase",2.2622804336741864]
["ldcC","b0186","Arginine/lysine/ornithine decarboxylases",2.0310450250085497]
["pheA","b2599","Prephenate dehydratase",4.962651381456478]
["pheL","b2598","pheA gene leader peptide",3.646889954232867]
["poxB","b0871","pyruvate oxidase monomer ",2.2277009183138743]
["sufS","b1680","Selenocysteine lyase",2.2277009183138743]
["ybaS","b0485","Glutaminase",5.078647858864285]
["ybaT","b0486","Amino acid transporters",4.524560867348372]
["ydcT","b1441","ABC-type spermidine/putrescine transport systems, ATPase components",2.424652133627089]
["yjhG","b4297","Dihydroxyacid dehydratase/phosphogluconate dehydratase",2.0625719468059907]
["yjhH","b4298","Dihydrodipicolinate synthase/N-acetylneuraminate lyase",2.6390158215457884]
["Nucleotide transport and metabolism"]
["purC","b2476","Phosphoribosylaminoimidazolesuccinocarboxamide (SAICAR) synthase",3.5091244444926626]
["purD","b4005","Phosphoribosylamine-glycine ligase",6.062866266041592]
["purE","b0523","Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase",4.77518145343308]
["purF","b2312","Glutamine phosphoribosylpyrophosphate amidotransferase",3.102289523667469]
["purH","b4006","AICAR transformylase/IMP cyclohydrolase PurH (only IMP cyclohydrolase domain in Aful)",4.12514389361198]
["purK","b0522","Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase)",4.48984819323749]
["purL","b2557","Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain",3.675085406963363]
["purM","b2499","Phosphoribosylaminoimidazole (AIR) synthetase",4.5947934199881395]
["purN","b2500","Folate-dependent phosphoribosylglycinamide formyltransferase PurN",2.578740616879158]
["purT","b1849","Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase)",3.7609864563446473]
["pyrB","b4245","Aspartate carbamoyltransferase, catalytic chain",1.895032015629677]
["pyrD","b0945","Dihydroorotate dehydrogenase",2.244924096618746]
["pyrI","b4244","Aspartate carbamoyltransferase, regulatory subunit",1.7545622222463313]
["pyrL","b4246","pyrBI operon leader peptide",2.4060500721642333]
["yicE","b3654","Xanthine/uracil permeases",4.254203035751053]
["Carbohydrate transport and metabolism"]
["amyA","b1927","Glycosidases",2.2106098771584803]
["dhaK","b1200","Dihydroxyacetone kinase",1.8660659830736148]
["dhaL","b1199","Dihydroxyacetone kinase",2.1435469250725863]
["dhaM","b1198","Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria)",1.7817974362806785]
["fbaB","b2097","DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes",3.054870261829286]
["garL","b3126","2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase",1.8950320156296772]
["kdgK","b3526","Sugar kinases, ribokinase family",4.030925476868606]
["kdgT","b3909","2-keto-3-deoxygluconate permease",10.970486160741862]
["kduI","b2843","5-keto 4-deoxyuronate isomerase",16]
["otsA","b1896","Trehalose-6-phosphate synthase",3.402668643803423]
["otsB","b1897","Trehalose-6-phosphatase",4.738546004718146]
["proP","b4111","proline/glycine betaine transporter ",2.1435469250725863]
["ptsG","b1101","PTS IIC components, glucose/maltose/N-acetylglucosamine-specific",3.249009585424942]
["srlA","b2702","Phosphotransferase system sorbitol-specific component IIC",2.0310450250085497]
["srlB","b2704","Phosphotransferase system sorbitol-specific component IIA",3.790064031259354]
["srlE","b2703","Phosphotransferase system sorbitol-specific component IIB",2.2]
["talA","b2464","Transaldolase",3.536254781201968]
["tktB","b2465","Transketolase",3.646889954232867]
["ydhC","b1660","inner membrane transport protein YdhC",2.82842712474619]
["yjgK","b4252","Beta-galactosidase, beta subunit",5.2375383006998915]
["Energy production and conversion"]
["appB","b0979","Cytochrome bd-type quinol oxidase, subunit 2",3.402668643803423]
["appC","b0978","Cytochrome bd-type quinol oxidase, subunit 1",3.1748021039363987]
["hyaA","b0972","Ni,Fe-hydrogenase I small subunit",5.656854249492381]
["hyaB","b0973","Ni,Fe-hydrogenase I large subunit",4.387299918778504]
["hyaC","b0974","Ni,Fe-hydrogenase I cytochrome b subunit",4.666116158304465]
["hyaD","b0975","Ni,Fe-hydrogenase maturation factor",4.189176491282506]
["leuB","b0073","Isocitrate/isopropylmalate dehydrogenase",2.985096928619822]
["yccX","b0968","Acylphosphatases",1.7955731701307387]
["yeaU","b1800","Isocitrate/isopropylmalate dehydrogenase",3.4822022531844965]
["Coenzyme transport and metabolism"]
["menC","b2261","O-succinylbenzoate synthase",1.9393262892934358]
["serA","b2913","Phosphoglycerate dehydrogenase and related dehydrogenases",2.3330580791522326]
["ymfD","b1137","e14 prophage; predicted SAM-dependent methyltransferase",195.51169675707433]
["Cell cycle control, cell division, chromosome partitioning"]
["fic","b3361","Protein involved in cell division",2.539323929432143]
["Cell motility"]
["fimA","b4314","P pilus assembly protein, pilin FimA",2.3692730023590736]
["Cell wall/membrane/envelope biogenesis"]
["blc","b4149","Bacterial lipocalin",3.1504448515904784]
["dacC","b0839","D-alanyl-D-alanine carboxypeptidase",2.03104502500855]
["glf","b2036","UDP-galactopyranose mutase",2.3510958125672174]
["mscS","b2924","Small-conductance mechanosensitive channel",2.21060987715848]
["ompT","b0565","Outer membrane protease",1.8804932281723237]
["osmF","b2131","Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system ",2.279770958979659]
["rfbA","b2039","dTDP-glucose pyrophosphorylase",2.279770958979659]
["rfbC","b2038","dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes",2.29739670999407]
["slp","b3506","Starvation-inducible outer membrane lipoprotein",6.59888475468242]
["wbbK","b2032","Glycosyltransferase",2.1768201590205254]
["Defense mechanisms"]
["mcrA","b1159","Restriction endonuclease",758.3219467707218]
["mdtK","b1663","Na+-driven multidrug efflux pump",1.9393262892934358]
["Inorganic ion transport and metabolism"]
["bfr","b3336","Bacterioferritin (cytochrome b1)",2.7426215401854654]
["katE","b1732","Catalase",2.481325690728238]
["sugE","b4148","Membrane transporters of cations and cationic drugs",1.984655892525887]
["yecI","b1902","Ferritin-like protein",2.279770958979659]
["Intracellular trafficking, secretion, and vesicular transport"]
["exbB","b3006","Biopolymer transport proteins",2]
["Lipid transport and metabolism"]
["aidB","b4187","Acyl-CoA dehydrogenases",2.3330580791522335]
["cls","b1249","Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthases and related enzymes",1.8804932281723237]
["kduD","b2842","2-deoxy-D-gluconate 3-dehydrogenase ",13.821946441499058]
["srlD","b2705","Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)",4.962651381456478]
["yohF","b2137","acetoin dehydrogenase ",2]
["Replication, recombination and repair"]
["intE","b1140","e14 prophage; predicted integrase",713.0096428383966]
["phrB","b0708","Deoxyribodipyrimidine photolyase",2.0945882456412535]
["pin","b1158","e14 prophage; site-specific DNA recombinase",13.402632051602499]
["ygiV","b3023","DNA gyrase inhibitor",2.078518452063687]
["Secondary metabolites biosynthesis, transport and catabolism"]
["ycaC","b0897","Amidases related to nicotinamidase",3.402668643803423]
["Signal transduction mechanisms"]
["bolA","b0435","Stress-induced morphogen (activity unknown)",3.536254781201967]
["evgA","b2369","Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain",2.5393239294321432]
["uspD","b3923","Universal stress protein UspA and related nucleotide-binding proteins",1.895032015629677]
["ybiI","b0803","DnaK suppressor protein",2.659419027232063]
["ydiV","b1707","FOG: EAL domain",3.1262744693934432]
["yeaG","b1783","Putative Ser protein kinase",4.093495567987099]
["small RNA "]
["gadY","b4452","GadY small RNA",2.850294739151409]
["isrB","b4434","IsrB small RNA",2.618769150349947]
["ryjA","b4459","RyjA small RNA",3.2240830092933495]
["sokC","b4413","antisense RNA blocking mokC and hokC translation ",3.1748021039363996]
["Transcription"]
["appY","b0564","AraC-type DNA-binding domain-containing proteins",3.1748021039363996]
["asnC","b3743","Transcriptional regulators",4.320238955569224]
["gadE","b3512","DNA-binding HTH domain-containing proteins",5.744662840314986]
["gadW","b3515","putative ARAC-type regulatory protein ",2.4813256907282386]
["gadX","b3516","DNA-binding transcriptional regulator GadX",4.88679602899063]
["pspA","b1304","Phage shock protein A (IM30), suppresses sigma54-dependent transcription",2.985096928619822]
["yeeY","b2015","putative transcriptional regulator LYSR-type",2]
["yhcO","b3239","Barstar, RNAse (barnase) inhibitor",3.1262744693934437]
["yhiF","b3507","DNA-binding HTH domain-containing proteins",2.4060500721642333]
["yiaG","b3555","Predicted transcriptional regulator",2.9621951045731283]
["yjhI","b4299","KpLE2 phage-like element; predicted transcriptional regulator",2.0945882456412535]
["ymgK","b1145","e14 prophage; predicted repressor protein",320.0652461812816]
["Translation, ribosomal structure and biogenesis"]
["osmE","b1739","DNA-binding transcriptional activator OsmE ",2.939468984551197]
["pheS","b1714","Phenylalanyl-tRNA synthetase alpha subunit",2.82842712474619]
["pheT","b1713","Phenylalanyl-tRNA synthetase beta subunit",2.679979977634712]
["Posttranslational modification, protein turnover, chaperones"]
["cbpA","b1000","DnaJ-class molecular chaperone",2.7006998923363796]
["lon","b0439","ATP-dependent Lon protease, bacterial type",3.5635948725613567]
["osmC","b1482","Predicted redox protein, regulator of disulfide bond formation",3.2994423773412103]
["sufB","b1683","ABC-type transport system involved in Fe-S cluster assembly, permease component",3.376563187118766]
["sufC","b1682","ABC-type transport system involved in Fe-S cluster assembly, ATPase component",2.91691722054331]
["sufD","b1681","ABC-type transport system involved in Fe-S cluster assembly, permease component",2.29739670999407]
["yqjG","b3102","Predicted glutathione S-transferase",2.1435469250725863]
["Function unknown"]
["ecnB","b4411","entericidin B membrane lipoprotein ",3.7034988491491614]
["elaB","b2266","Uncharacterized conserved protein",2.7851939173374882]
["erfK","b1990","Uncharacterized protein conserved in bacteria",2.8945384748807563]
["phnB","b4107","Uncharacterized protein conserved in bacteria",2.315158732197303]
["sufA","b1684","Uncharacterized conserved protein",4]
["ybaY","b0453","Uncharacterized protein conserved in bacteria",2.7851939173374882]
["ybgA","b0707","Uncharacterized conserved protein",3.2741288781199263]
["ycgB","b1188","Uncharacterized conserved protein",3.878652578586872]
["ydeI","b1536","Uncharacterized conserved protein",2.519842099789746]
["ydgA","b1614","Uncharacterized protein conserved in bacteria",2.424652133627089]
["yeaQ","b1795","Predicted membrane protein",4.254203035751054]
["yegP","b2080","Uncharacterized conserved protein",3.7609864563446473]
["ygaM","b2672","Uncharacterized conserved protein",6.204579047334939]
["ygaU","b2665","Uncharacterized protein containing LysM domain",3.0784885917339846]
["ygiW","b3024","Uncharacterized conserved protein",2.0154627384343033]
["yhaH","b3103","Predicted membrane protein",2.4622888266898326]
["yhiD","b3508","Uncharacterized membrane protein",2.244924096618746]
["yhjD","b3522","Predicted membrane protein",2.519842099789746]
["yiiS","b3922","Uncharacterized protein conserved in bacteria",2.1435469250725863]
["yjbJ","b4045","Uncharacterized protein conserved in bacteria",2.6799799776347126]
["yjdI","b4126","Uncharacterized conserved protein",3.536254781201967]
["ymfO","b1151","e14 prophage; conserved protein",77.58886827606679]
["ymfQ","b1153","e14 prophage; conserved protein",27.012505496950126]
["ymgE","b1195","Predicted membrane protein",3.22408300929335]
["ymgP","b1152","e14 prophage; conserved protein",10.475076601399788]
["ynhG","b1678","Uncharacterized protein conserved in bacteria",4.702191625134434]
["yobD","b1820","Predicted membrane protein",1.8804932281723237]
["yodC","b1957","Uncharacterized small protein",3.1748021039363987]
["yqaE","b2666","Uncharacterized homolog of Blt101",2.110782280726212]
["yqjD","b3098","Uncharacterized conserved protein",2.6390158215457884]
["yqjE","b3099","Predicted membrane protein",3.1262744693934437]
["General function prediction only"]
["chaB","b1217","Putative cation transport regulator",2.500509735791262]
["cvpA","b2313","Uncharacterized membrane protein, required for colicin V production",4.254203035751053]
["hyaE","b0976","hydrogenase-1 operon protein HyaE ",3.8193664156416665]
["osmY","b4376","Predicted periplasmic or secreted lipoprotein",2.6187691503499466]
["rfbX","b2037","Membrane protein involved in the export of O-antigen and teichoic acid",2.3875907267165406]
["sufE","b1679","SufE protein probably involved in Fe-S center assembly",2.4813256907282386]
["wbbJ","b2033","Acetyltransferase (isoleucine patch superfamily)",2.315158732197303]
["wrbA","b1004","Multimeric flavodoxin WrbA",2.558956380292532]
["ybhP","b0790","Metal-dependent hydrolase",2.0945882456412535]
["yedP","b1955","Predicted hydrolase (HAD superfamily)",3.1993476711933213]
["yedU","b1967","Putative intracellular protease/amidase",3.428975931412291]
["yhbO","b3153","Putative intracellular protease/amidase",1.9393262892934358]
["yjdJ","b4127","Predicted acetyltransferase",3.2994423773412103]
["ymfN","b1149","e14 prophage; predicted DNA-binding transcriptional regulator",93.34135105738588]
["Not in COGs"]
["cbpM","b0999","modulator of CbpA co-chaperone ",3.150444851590479]
["cnu","b1625","H-NS- and StpA-binding protein",2.04674778399355]
["gnsB","b1550","Qin prophage; predicted protein",3.4554866103747655]
["hlyE","b1182","hemolysin E",4.254203035751054]
["hyaF","b0977","hydrogenase-1 operon protein HyaF ",2.5393239294321424]
["lit","b1139","e14 prophage;cell death peptidase; phage exclusion; ",307.97440923702163]
["msyB","b1051","hypothetical protein",3.22408300929335]
["osmB","b1283","osmotically inducible lipoprotein",4.962651381456478]
["psiF","b0384","hypothetical protein ",3.1504448515904784]
["rfc","b2035","O-antigen polySLRase",2.4060500721642333]
["stfE","b1157","e14 prophage; predicted side tail fiber protein fragment",137.1870032046455]
["tfaE","b1156","e14 prophage; predicted tail fiber assembly protein",59.255981586386554]
["uspB","b3494","universal stress protein UspB ",3.7034988491491614]
["wbbI","b2034","conserved protein,  β-1,6-galactofuranosyltransferase",2.015462738434303]
["yaiA","b0389","predicted protein",2.0625719468059907]
["ybcc","b0539","putative exonuclease encoded by prophage ",3.6750854069633614]
["ybjM","b0848","predicted inner membrane protein",2.0310450250085497]
["ybjP","b0865","predicted lipoprotein",2.424652133627089]
["yccJ","b1003","hypothetical protein ",3.402668643803423]
["ycfK","b1154","e14 prophage; predicted protein",38.794434138033445]
["ydcY","b1446","hypothetical protein",1.7411011265922482]
["ydiZ","b1724","hypothetical protein ",2.4813256907282386]
["yebF","b1847","predicted protein",1.8094554092654305]
["yebV","b1836","hypothetical protein ",3.878652578586871]
["yebW","b1837","hypothetical protein ",3.646889954232867]
["yfdY","b2377","predicted inner membrane protein ",2.5198420997897464]
["ygaW","b2670","predicted inner membrane protein ",1.9244476737882903]
["yhfG","b3362","hypothetical protein ",2.519842099789746]
["yhhA","b3448","hypothetical protein ",2.3692730023590736]
["ylaC","b0458","predicted inner membrane protein",2.1435469250725863]
["ymfE","b1138","e14 prophage; predicted inner membrane protein",114.91668288836732]
["ymfG","b1141","e14 prophage; predicted excisionase",226.32030599692595]
["ymfH","b1142","e14 prophage;hypothetical protein",88.44242431793766]
["ymfI","b1143","e14 prophage; predicted protein",373.36540422954357]
["ymfJ","b1144","e14 prophage; predicted protein",191.04620343166866]
["ymfL","b1147","e14 prophage; predicted DNA-binding transcriptional regulator",32]
["ymfM","b1148","e14 prophage; predicted protein",39.39662122703731]
["ymfR","b1150","e14 prophage; predicted protein",25.594781369546567]
["ymfS","b1155","e14 prophage; predicted protein",137.1870032046455]
["ymfT","b1146","e14 prophage; predicted DNA-binding transcriptional regulator",130.99185817558688]
["yniB","b1726","predicted inner membrane protein ",2.4060500721642333]
["yoaC","b1810","predicted protein",2.015462738434303]
["yodD","b1953","hypothetical protein ",5.485243080370929]
["yohC","b2135","predicted inner membrane protein",2.5393239294321432]
["yqjC","b3097","hypothetical protein ",3.274128878119927]
["yqjK","b3100","hypothetical protein ",3.150444851590479]
[]
["a Up-regulated represent genes whose expression is at least 1.8-fold higher in IrrE-expressing strain"]
["b Changes in gene expression were represented by mean expression ratios (MER)"]

{"sheet":"TableS2","index":1,"n_rows":174,"n_cols":4,"rows_kept":174,"cut":false,"hidden":false,"merged":[],"flags":["formulas_cached_only"]}
["Supplementary Information Table S2. Down-regulated ORFs "]
[" in IrrE-expressing strain, as revealed by microarray analysis a"]
["Gene","Locus","Function","MER b"]
["Amino acid transport and metabolism"]
["afuC","b0262","ABC-type spermidine/putrescine transport systems, ATPase components",-72.9526706873491]
["argF","b0273","Ornithine carbamoyltransferase",-170.20281774285206]
["betA","b0311","Choline dehydrogenase and related flavoproteins",-44.56310267739982]
["mmuM","b0261","Homocysteine/selenocysteine methylase (S-methylmethionine-dependent)",-157.58648490814926]
["mmuP","b0260","Amino acid transporters",-81.25836574182863]
["nikA","b3476","ABC-type dipeptide transport system, periplasmic component",-3.5091244444926626]
["oppA","b1243","ABC-type oligopeptide transport system, periplasmic component",-5.9243902091462575]
["oppB","b1244","ABC-type dipeptide/oligopeptide/nickel transport systems, permease components",-3.008175815123967]
["oppC","b1245","ABC-type dipeptide/oligopeptide/nickel transport systems, permease components",-2.539323929432143]
["oppD","b1246","ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component",-2.3692730023590736]
["oppF","b1247","ABC-type oligopeptide transport system, ATPase component",-2.4433980144953145]
["tdcB","b3117","Threonine dehydratase",-20.629924935033262]
["tdcC","b3116","Amino acid permeases",-23.88077542895859]
["tdcG1","b3111","L-serine deaminase",-20.004077886330094]
["tdcG2","b3112","L-serine deaminase",-22.802357913211267]
["yagE","b0268","Dihydrodipicolinate synthase/N-acetylneuraminate lyase",-456.140143687854]
["yagF","b0269","Dihydroxyacid dehydratase/phosphogluconate dehydratase",-28.95128654824689]
["yahI","b0323","Carbamate kinase",-57.01751796098168]
["yahN","b0328","Putative threonine efflux protein",-356.50482141919895]
["ygeX","b2871","Threonine dehydratase",-1.8660659830736148]
["ygfK","b2878","NADPH-dependent glutamate synthase beta chain and related oxidoreductases",-2.3875907267165406]
["yhaO","b3110","Amino acid permeases",-2.06257194680599]
["yjiM","b4335","Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB",-2.850294739151409]
["Nucleotide transport and metabolism"]
["ade","b3665","Adenine deaminase",-2.4060500721642333]
["codA","b0337","Cytosine deaminase and related metal-dependent hydrolases",-379.1609733853602]
["codB","b0336","Purine-cytosine permease and related proteins",-382.09240686333703]
["gpt","b0238","Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins",-1.8660659830736148]
["rihC","b0030","Inosine-uridine nucleoside N-ribohydrolase",-2.29739670999407]
["ssnA","b2879","predicted chlorohydrolase/aminohydrolase",-1.8660659830736148]
["yahJ","b0324","Cytosine deaminase and related metal-dependent hydrolases",-134.05364772104022]
["Carbohydrate transport and metabolism"]
["glpT","b2240","Sugar phosphate permease",-2.659419027232063]
["lamB","b4036","Maltoporin (phage lambda and maltose receptor)",-4.489848193237491]
["malE","b4034","Maltose-binding periplasmic proteins/domains",-2.7851939173374882]
["malF","b4033","ABC-type sugar transport systems, permease components",-3.274128878119927]
["malG","b4032","ABC-type maltose transport systems, permease component",-2.29739670999407]
["malK","b4035","ABC-type sugar transport systems, ATPase components",-4.221564561452422]
["mglB","b2150","ABC-type sugar transport system, periplasmic component",-2.3692730023590736]
["nupG","b2964","transport of nucleosides, permease protein",-2.91691722054331]
["prpB","b0331","PEP phosphonomutase and related enzymes",-13.506252748475067]
["treB","b4240","PTS IIC components, glucose/maltose/N-acetylglucosamine-specific",-5.401399784672761]
["treC","b4239","Glycosidases",-5.237538300699895]
["yadI","b0129","PTS, mannose/fructose-specific component IIA",-1.909683207820833]
["yagG","b0270","Na+/melibiose symporter and related transporters",-528.0184183823335]
["yagH","b0271","Beta-xylosidase",-85.75935928431073]
["yeaD","b1780","Uncharacterized enzymes related to aldose 1-epimerase",-1.7817974362806785]
["Energy production and conversion"]
["aceE","b0114","Pyruvate dehydrogenase complex, dehydrogenase (E1) component",-2.82842712474619]
["betB","b0312","NAD-dependent aldehyde dehydrogenases",-320.0652461812816]
["glpQ","b2239","Glycerophosphoryl diester phosphodiesterase",-1.8804932281723234]
["nfnB","b0578","Nitroreductase",-2.8723314201574928]
["nfsA","b0851","Nitroreductase",-4.353640318041051]
["prpC","b0333","Citrate synthase",-14.145019124807867]
["tdcD","b3115","Acetate kinase",-22.45381823883031]
["tdcE","b3114","Pyruvate-formate lyase",-26.193031024959417]
["xdhA","b2866","Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs",-2.0154627384343033]
["xdhB","b2867","Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs",-1.8660659830736148]
["yagR","b0284","Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs",-34.033624286008425]
["yagS","b0285","Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs",-135.09006596647757]
["yagT","b0286","Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs",-98.51163493548742]
["yahF","b0320","Succinyl-CoA synthetase, alpha subunit",-123.16465112245052]
["ydhT","b1671","Fe-S-cluster-containing hydrogenase components 1",-1.9846558925258866]
["ydhV","b1673","Aldehyde:ferredoxin oxidoreductase",-2]
["ygmF","b2880","Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs",-2.2106098771584795]
["yhbW","b3160","Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase",-3.6750854069633614]
["yiaI","b3573","Fe-S-cluster-containing hydrogenase components 2",-2.279770958979659]
["ykgC","b0304","pyridine nucleotide-disulfide oxidoreductase ",-75.81673607549031]
["ykgE","b0306","Fe-S oxidoreductase",-37.328929266435715]
["ykgF","b0307","Uncharacterized conserved protein containing a ferredoxin-like domain",-337.79402515786086]
["Cell cycle control, cell division, chromosome partitioning"]
["ykgK","b0294","putative regulator",-1185.3612708850196]
["Cell motility"]
["yagX","b0291","putative enzyme",-353.7696972717507]
["Cell wall/membrane/envelope biogenesis"]
["betT","b0314","Choline-glycine betaine transporter",-348.36224004464106]
["yebA","b1856","Membrane proteins related to metalloendopeptidases",-1.7817974362806785]
["Coenzyme transport and metabolism"]
["btuB","b3966","Outer membrane cobalamin receptor protein",-1.7545622222463315]
["hemB","b0369","Delta-aminolevulinic acid dehydratase",-2.3875907267165406]
["rimK","b0852","ribosomal protein S6 modification protein",-3.031433133020796]
["yqeC","b2876","hypothetical protein",-3.675085406963363]
["Inorganic ion transport and metabolism"]
["afuB","b0263","ABC-type Fe3+ transport system, permease component",-191.0462034316687]
["cynS","b0340","Cyanate lyase",-1.9694295058688625]
["cynT","b0339","Carbonic anhydrase",-171.51871856862147]
["Lipid transport and metabolism"]
["idi","b2889","Isopentenyldiphosphate isomerase",-2.1435469250725863]
["prpE","b0335","Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases",-45.60471582642252]
["yjiL","b4334","Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain)",-2.110782280726212]
["Replication, recombination and repair"]
["insF","b0299","putative transposase",-2.1768201590205263]
["intF","b0281","putative phage integrase",-512]
["yafM","b0228","Transposase and inactivated derivatives",-2.3151587321973035]
["yagA","b0267","hypothetical protein",-67.54503298323878]
["yagL","b0278","Site-specific recombinases, DNA invertase Pin homologs",-110.57557153199254]
["ybcK","b0544","Site-specific recombinases, DNA invertase Pin homologs",-3.274128878119926]
["insE-1","b0298","Transposase and inactivated derivatives",-2.03104502500855]
["Secondary metabolites biosynthesis, transport and catabolism"]
["mhpD","b0350","2-keto-4-pentenoate hydratase",-14.145019124807867]
["Signal transduction mechanisms"]
["yahA","b0315","FOG: EAL domain",-819.0330038254898]
["yehU","b2126","Putative regulator of cell autolysis",-1.9694295058688625]
["small RNA "]
["ryeA","b4432","small RNA that interacts with Hfq",-3.0784885917339846]
["Transcription"]
["betI","b0313","Transcriptional regulator",-101.59366732596486]
["cynR","b0338","Transcriptional regulator",-130.9918581755871]
["mhpR","b0346","Transcriptional regulator",-3.5091244444926626]
["prpR","b0330","Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain",-35.09839935022802]
["pspF","b1303","Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain",-3.3765631871187654]
["tdcA","b3118","transcriptional activator of tdc operon",-7.938623570103545]
["yagI","b0272","Transcriptional regulator",-212.79690141255375]
["yahB","b0316","putative transcriptional regulator LYSR-type",-335.20245124479277]
["ygeV","b2869","Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains",-2.193649959389252]
["ykgD","b0305","putative ARAC-type regulatory protein",-127.01797712165668]
["kdgR","b1827","Transcriptional regulator",-2.82842712474619]
["Translation, ribosomal structure and biogenesis"]
["tdcF","b3113","Putative translation initiation inhibitor, yjgF family",-15.277465662566659]
["ykgM","b0296","Ribosomal protein L31",-2048]
["Posttranslational modification, protein turnover, chaperones"]
["yagQ","b0283","Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family",-670.4049024895862]
["yedF","b1930","Predicted redox protein, regulator of disulfide bond formation",-1.9244476737882903]
["yqeB","b2875","Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family",-2.9394689845511977]
["Function unknown"]
["yagU","b0287","Predicted periplasmic/secreted protein",-806.5138820071634]
["yaiL","b0354","Uncharacterized protein conserved in bacteria",-2.127101517875527]
["yggJ","b2946","Uncharacterized protein conserved in bacteria",-1.781797436280678]
["ykgB","b0301","Predicted membrane protein",-388.0234410266619]
["ykgG","b0308","Uncharacterized conserved protein",-66.51259046603796]
["General function prediction only"]
["murQ","b2428","Predicted sugar phosphate isomerase",-1.9694295058688625]
["prpD","b0334","Uncharacterized protein involved in propionate catabolism",-35.64321469302197]
["yahD","b0318","FOG: Ankyrin repeat",-144.7859477551478]
["yahK","b0325","Zn-dependent alcohol dehydrogenases",-100.04078302059024]
["yeiR","b2173","Putative GTPases (G3E family)",-2.4813256907282386]
["yhjW","b3546","Predicted membrane-associated, metal-dependent hydrolase",-1.8375427034816811]
["ykgJ","b0288","Predicted Fe-S-cluster oxidoreductase",-47.761550857917136]
["Not in COGs"]
["b0309","b0309","hypothetical protein",-409.5165019127448]
["eaeH","b0297","attaching and effacing protein, pathogenesis factor",-345.6895862190565]
["malM","b4037","periplasmic protein of mal regulon",-3.4289759314122916]
["yagB","b0266","hypothetical protein",-204.7582509563724]
["yagJ","b0276","hypothetical protein",-89.12620535479964]
["yagK","b0277","hypothetical protein",-54.86361490259661]
["yagM","b0279","hypothetical protein",-256]
["yagN","b0280","hypothetical protein",-452.64061199385196]
["yagP","b0282","putative transcriptional regulator LYSR-type",-532.1007237283029]
["yagV","b0289","hypothetical protein",-185.2504623923683]
["yagW","b0290","putative receptor",-206.34131259477414]
["yagY","b0292","hypothetical protein",-33.51341193026005]
["yagZ","b0293","cryptic Mat fimbrillin gene",-97.75584837853715]
["yahC","b0317","predicted inner membrane protein",-548.7480128185821]
["yahE","b0319","hypothetical protein",-101.59366732596476]
["yahG","b0321","hypothetical protein",-23.15630779904603]
["yahL","b0326","hypothetical protein",-170.2028177428519]
["yahM","b0327","hypothetical protein",-233.40095707090333]
["ybjC","b0850","hypothetical protein",-4.254203035751054]
["ycgZ","b1164","connector protein for RcsB regulation of biofilm and acid-resistance",-3.7609864563446487]
["ydhW","b1672","hypothetical protein",-1.8094554092654305]
["ykgA","b0300","putative ARAC-type regulatory protein",-544.5379885761348]
["ykgH","b0310","hypothetical protein",-231.61029238597484]
["ykgI","b0303","predicted protein",-1176.2671155169628]
["ykgL","b0295","hypothetical protein",-206.34131259477434]
["ymgA","b1165","connector protein for RcsB regulation of biofilm",-3.675085406963363]
["ymgB","b1166","connector protein for RcsB regulation of biofilm and acid-resistance",-3.5911463402614756]
["ymgC","b1167","hypothetical protein",-2.7215800003487534]
["ytfK","b4217","hypothetical protein",-2.659419027232063]
["a Down-regulated represent genes whose expression is at least 1.8-fold lower in IrrE-expressing strain"]
["b Changes in gene expression were represented by mean expression ratios (MER)"]

{"sheet":"TableS3","index":2,"n_rows":69,"n_cols":6,"rows_kept":69,"cut":false,"hidden":false,"merged":[],"flags":["formulas_cached_only"]}
["Supplementary Information Table S3. Up-regulated proteins of IrrE-expressing"]
[" E. coli strain versus empty plasmid strain, as revealed by proteome analysis"]
["Protein function a","Protein","ORF no.","Exp. ","Fold ","transcriptional "]
[null,null,null,"pI/Mr (kDa)","change b","ratios d"]
["Energy production and conversion"]
["Phosphoenolpyruvate carboxylase","Ppc","b3956","5.27/97.79",3.21,1.43]
["Amino acid transport and metabolism"]
["Glutamate synthase, small subunit","GltD","b3213","5.72/57.05",2.1,2.14]
["Selenophosphate synthase","SelD","b1764","5.52/38.51","Present c",1.16]
["oligopeptide transport; periplasmic binding protein","OppA","b1243","6.38/62.03","Present",-5.92]
["Chorismate mutase T/prephenate dehydrogenase","TyrA","b2600","5.97/39.94",4.37,1.57]
["Chorismate mutase-P/prephenate dehydratase","PheA","b2599","5.69/93.45","Present",4.96]
["Glycine dehydrogenase","GcvP","b2903","5.90/100.28",5.915,1.3]
["Aminomethyltransferase","GcvT","b2905","5.52/37.55",3.375,1.52]
["Serine hydroxymethyltransferase","GlyA","b2551","6.49/44.93",4.87,2.26]
["Nucleotide transport and metabolism"]
["Phosphoribosylformyl-glycineamide synthetase","PurL","b2557","5.37/118",18.62,3.67]
["Amidophosphoribosyltransferase","PurF","b2312","5.35/63.57","Present",3.1]
["AICAR transformylase/IMP cyclohydrolase","PurH","b4006","5.87/52.40",5.17,4.12]
["Phosphoribosylglycineamide synthetase","PurD","b4005","5.10/43.75","Present",6.06]
["Adenylosuccinate lyase","PurB","b1131","6.32/46.27","Present",1.75]
["Phosphoribosylaminoimidazole-succinocarboxamide synthase","PurC","b2476","5.02/29.04",8.51,3.5]
["Phosphoribosylaminoimidazole carboxylase catalytic subunit","PurE","b0523","6.68/17.31","Present",4.77]
["Phosphoribosylglycinamide formyltransferase 2","PurT","b1849","5.70/42.27",2.405,3.76]
["Aspartate carbamoyltransferase catalytic chain","PyrB","b4245","6.62/35.38","Present",1.89]
["Carbohydrate transport and metabolism"]
["dihydroxyacetone kinase subunit M","DhaM","b1198","4.61/49.06","Present",1.78]
["PTS, mannose/fructose/N-acetylgalactosamine-specific ","ManX","b1817","5.75/35.22",5.47,1.29]
["       component IIB"]
["Ketodeoxygluconokinase","KdgK","b3526","4.92/37.90",6.665,4.03]
["4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase","KduI","b2843","6.04/31.28","Present",16]
["KHG/KDPG aldolase","Eda","b1850","5.73/25.38",2.245,1.61]
["Coenzyme transport and metabolism"]
["Pantothenate synthetase","PanC","b0133","6.25/33.30",2.52,1.17]
["3-phosphoserine aminotransferase","SerC","b0907","5.51/39.03",2.94,1.7]
["D-3-phosphoglycerate dehydrogenase","SerA","b2913","6.36/44.49",2.395,2.33]
["Lipid transport and metabolism"]
["Enzyme involved in the deoxyxylulose pathway of ","IspG","b2515","6.22/41.64",5.5,1.17]
["       isoprenoid biosynthesis"]
["2-deoxy-D-gluconate 3-dehydrogenase","KduD","b2842","5.43/27.07",2.37,13.82]
["Translation, ribosomal structure and biogenesis"]
["Phenylalanine tRNA synthetase, beta subunit","PheT","b1713","5.27/97.79",11.35,2.68]
["Phenylalanine tRNA synthetase, alpha subunit","PheS","b1714","6.38/36.72",5.48,2.83]
["Translation elongation factor EF-Tu","TufA","b3339","5.47/47.51",2.74,1.08]
["30S ribosomal subunit protein S6","RpsF","b4200","5.43/15.14","Present",1.33]
["Transcription"]
["DNA-binding transcriptional regulator","AsnC","b3743","6.4514.10",2.375,4.32]
["Phage shock protein, putative inner membrane protein","PspA","b1304","5.50/29.00","Present",2.98]
["Cell wall/membrane/envelope biogenesis"]
["Outer membrane protein F precursor","OmpF","b0929","4.62/37.60",9.65,1.55]
["Naphthoate synthase","OmpT","b0565","5.52/37.55",2.41,1.88]
["Glucose-1-phosphate thymidylyltransferase","RfbA","b2039","5.69/31.90",2.655,2.28]
["Posttranslational modification, protein turnover, chaperones"]
["ATP-dependent protease La","Lon","b0439","6.40/97.53",7.005,3.56]
["Ppeptidyl-prolyl cis-trans isomerase B","PpiB","b0525","5.62/16.60","Present",1.1]
["Inorganic ion transport and metabolism"]
["hydroperoxidase HPII","KatE","b1732","5.80/95.30",3.91,2.48]
["Stress response DNA-binding protein","Dps","b0812","6.30/18.51",2.085,1.26]
["General function prediction only"]
["Predicted hydrolases of the HAD superfamily","YidA","b3697","5.18/29/67",2.305,1]
["Trp repressor binding protein","WrbA","b1004","5.91/24.40",3.295,2.56]
["Osmotically inducible protein Y precursor","OsmY","b4376","5.45/20.86",5.68,2.62]
[]
["a Protein names, accession numbers, and descriptions are from EcoCyc database. "]
["The data are grouped according to their biological function."]
["b Translation level ratios (cells expressing IrrE/cells carrying only vector pMG1)."]
["c Present: all of these proteins were detectable only in the IrrE-expressing strain, and they were absent in the control strain. "]
["d The transcriptional ratios obtained from DNA microarray experiment (see Materials and Methods) are indicated."]
["If the transcription data reflect the protein synthesis data, the protein symbol is given in boldface."]

{"sheet":"TableS4","index":3,"n_rows":38,"n_cols":6,"rows_kept":38,"cut":false,"hidden":false,"merged":[[33,0,33,5],[32,0,32,5]],"flags":["formulas_cached_only"]}
["Supplementary Information Table S4. Down-regulated proteins of IrrE-"]
["expressing E. coli strain versus empty plasmid strain, "]
["as revealed by proteome analysis"]
["Protein function a","Protein","ORF no.","Exp. ","Fold ","transcriptional "]
[null,null,null,"pI/Mr (kDa)","change b","ratios d"]
["Energy production and conversion"]
["Pyruvate formate-lyase 4/2-ketobutyrate formate-lyase","TdcE","b3114","5.79/83.06",-7.142857142857142,-34.03]
["Putative formate acetyltransferase 3","PflD","b3951","5.78/79.01",-7.4074074074074066,-1.03]
["Fumarate reductase, anaerobic, flavoprotein","FrdA","b4154","6.13/72.80",-2.0202020202020203,-1.25]
["Phosphoenolpyruvate carboxykinase","PckA","b3403","5.92/33.88",-2.1739130434782608,-1.28]
["Nitroreductase A, NADPH-dependent, FMN-dependent","MdaA","b0851","6.86/25.77",-2.941176470588235,-4.35]
["Carbohydrate transport and metabolism"]
["Trehalose-6-P hydrolase","TreC","b4239","5.73/62.32",-12.5,-5.24]
["Galactose ABC transporter","MglB","b2150","5.21/33.07",-8,-2.37]
["Tagatose-bisphosphate aldolase GatY","GatY","b2096","6.40/29.77",-2.4691358024691357,-1.01]
["D-ribose periplasmic binding protein","RbsB","b3751","6.35/28.74",-1.8867924528301885,-1.33]
["Coenzyme transport and metabolism"]
["Porphobilinogen synthase","HemB","b0369","5.38/38.73",-4.878048780487805,-2.39]
["Translation, ribosomal structure and biogenesis"]
["Polynucleotide phosphorilase","Pnp","b3164","5.26/53.83",-2.857142857142857,1.01]
["Transcription"]
["Transcriptional regulator KdgR","KdgR","b1827","5.73/30.76",-2.272727272727273,-2.83]
["Purine nucleotide synthesis repressor","PurR","b1658","6.76/37.85","absent c",1.6]
["Cell wall/membrane/envelope biogenesis"]
["Outer membrane proease P","OmpX","b0814","6.32/33.80","absent",1.05]
["Posttranslational modification, protein turnover, chaperones"]
["heat shock protein hslVU, ATPase subunit","HslU","b3931","5.32/51.26",-3.125,-1.34]
["Secondary metabolites biosynthesis, transport and catabolism"]
["Putative toluene transporter: ATP-binding component","YrbF","b3195","6.78/29.65",-2.380952380952381,-1.49]
["General function prediction only"]
["Modulator of drug activity B","MdaB","b3028","6.29/23.52",-2.4096385542168677,-1.92]
[]
["a Protein names, accession numbers, and descriptions are from EcoCyc database. "]
["    The data are grouped according to their biological function."]
["b Translation level ratios (Inverse value of cells carrying only vector pMG1/cells expressing IrrE)."]
["c Absent: all of these proteins were absent in the IrrE-expressing strain, and they were detectable only in the control strain. "]
["d The transcriptional ratios obtained from DNA microarray experiment (see Materials and Methods) are indicated."]
["If the transcription data reflect the protein synthesis data, the protein symbol is given in boldface."]