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["E.coli Dynamical Backbone"]
["TF (from RegulonDB 6.0)","Dynamical Modules","EcoCyc protein description"]
["acrR","\"acrR\""," AcrR is a repressor that participates in controlling the acrAB operon involved in the susceptibility of Escherichia coli to dephalothin and cephaloridine. This repressor is negatively autoregulated [ Ma96  , Ma95  ]."]
["ada","\"ada\""," O6-methylguanine and O4-methylthymine are the major mutagenic lesions resulting from exposure of DNA to simple alkylating agents such as N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), N-methyl-N-nitrosourea (MNU) and, to a lesser degree, methane methanesulfonate (MMS). The O6-methylguanine and O4-methylthymine alkylation products constitute potentially mutagenic lesions due to their tendency to mispair with thymine and with guanine, respectively, forming transition mutations.\n\nIn Escherichia coli there are two separate direct repair mechanisms for the reversal of these types of alkylating lesions through the involvement of two methyltransferases, Ada and Ogt. The Ada (short for adaptive response to alkylation damage) protein, or O6-methylguanine-DNA-methyltransferase I, removes methyl (as well as larger) groups from the guanine and thymine substrates and transfers them to its own cysteine residue (Cys-321). The Ada protein also transfers methyl groups to a second cysteine residue (Cys-69) from alkylphosphotriesters in DNA. This reaction converts the Ada protein into a strong transcriptional activator of several genes including alkA--the gene for 3-methyladenine-DNA-glycosylase II, alkB, aidB and the ada gene itself [ Samson92 , Lindahl88 ]. "]
["agaR","\"agaR\"","AgaR is the transcriptional repressor of the agaZVWA and agaSYBCDI  operons. It responds to N-acetylgalactosamine (GalNAc) and D-galactosamine (GalN) in the medium [ Ray04  ]."]
["allR","“allR”"," AllR (for \"allantoin repressor\") regulates several genes involved in the anaerobic utilization of allantoin as a nitrogen source [ Cusa99  , Rintoul02  ].\nAt very low concentrations of glyoxylate, AllR represses transcription from allAp, allSp, and gclp. A highly conserved region featuring an almost perfect palindromic sequence has been identified in gclp and in the intergenic region between the divergent promoters allAp and allSp. It has been proven that AllR binds to this region, and it has been proposed that it may interfere with RNA polymerase by steric hindrance or contact inhibition, thus repressing transcription. In the presence of glyoxylate (the coeffector molecule of this regulator), DNA binding by AllR is inhibited and transcription of the allantoin regulon is derepressed [ Rintoul02 , Walker06 ].\nAllR belongs to the IclR family. Members of this family of regulators feature a conserved domain architecture, with a DNA-binding motif in the N-terminal domain and a ligand-binding motif in the C-terminal domain. This regulator adopts a tetrameric conformation [ Rintoul02 , Walker06 ].\nThe allR gene is expressed under both aerobic and anaerobic conditions, and it is autoregulated [ Walker06 ]"]
["alsR","\"alsR\"","This protein belongs to the RpiR/YebK/YfhH family and it controls the expression of several genes involved in ribose catabolism. AlsR is also known as RpiR and it is involved in rpiB gene and als operon repression [ Sorensen96  , Kim97  ]. RpiR was shown to be a regulator by [ Sorensen96  ]."]
["araC","\"araC\""," The AraC (arabinose regulator) transcriptional dual regulator, which belongs to the AraC/XylS family [ Gallegos97  , Tobes02  ], occurs as both a monomer (33.384 Kda) and a homodimer. It is composed of two domains: the carboxy-terminal domain that contains the DNA-binding region and the amino-terminal domain that is responsible for dimerization and L-arabinose binding [ Gallegos97  ].\nThe three-dimensional structure of AraC has been reported in the presence and absence of L-arabinose. This transcriptional regulator is encoded by the araC gene, which is negatively autoregulated and positively regulated by CRP [ Lobell91 , Stoltzfus89 ].\n\nAraC regulates, bound or unbound to L-arabinose, five operons involved in the transport and in the catabolism of L-arabinose (araE, araFGH, araJ, araBAD, araC). In addition, AraC co-regulates with another transcriptional regulator, CRP [ Gallegos97 , Reeder91 , Stoner83 , Hendrickso92 , Seabold98 ].\nThe arabinose regulator activates transcription by binding in a position overlapping the -35 box of sigma70 promoters and binding in tandem to direct repeat sequences at the same strand along the upstream region of promoters. The consensus 17 bp site sequence of this regulator is NAGCN7TCCATA [ Gallegos97 ]. "]
["arcA","E"," This is a dual transcriptional regulator of aerobic respiration control. It functions as a transcriptional repressor for the sdh, gltA lld, cyoABCDE, and sodA genes. It is an activator for the cydAB, pfl, and traY genes in order to sustain anaerobic growth. It belongs to the two-component (ArcB-ArcA) signal-transduction systems family.\n\nIn particular, ArcA works during microaerobic conditions to induce the expression of gene products that allow the activity of central metabolism enzymes that are sensitive to low oxygen levels [ Alexeeva03 ]. "]
["argP","A","ArgP is a protein that belongs to the LysR family [ Schell93  ]. This regulator participates in controlling several genes involved in the arginine transport system. It is an inhibitor of replication initiation when bound to three 13-mers located in the origin of replication (OriC). It activates the transcription of the dnaAN-recF and nrdAB operons. IciA has similarity to an Edwardsiella ictaluri protein that provokes an immune response in catfish [ Moore02  ]."]
["argR","\"argR\"","ArgR is a protein that negatively controls the expression of arginine biosynthesis in addition to the carAB operon. ArgR is also essential in the resolution of plasmid ColE1 multimers during replication through cer-mediated site-specific recombination. It belongs to the ArgR family."]
["asnC","\"asnC\""," AsnC is a transcriptional repressor that belongs to the AsnC family of regulatory proteins [ PerezRueda01  ]. It controls the expression of asnA, the gene encoding aspartate-ammonia ligase, dependent on the level of exogenous asparagine [ Kolling85  , deWind85  ].\n\nA crystal structure of AsnC complexed with the ligand L-asparagine has been solved at 2.4 Å resolution. The crystal structure shows an octamer with L-asparagine bound in a cleft at the interface between dimers [ Thaw06 ].\n\nAsnC autoregulates its own expression independently of the concentration of asparagine. Transcription of asnC traverses the origin of replication, oriC, and continues into gidA, possibly explaining the effect on gidA expression [ Kolling88 , Gielow88 , Schaefer88 ].\n\nExpression of asnC is regulated by nitrogen availability; under nitrogen-limiting conditions, Nac represses asnC [ Poggio02 ]. "]
["baeR","\"baeR\"","The transcriptional regulatory protein BaeR is part of the two-component BaeS/BaeR signal transduction system [ Nagasawa93  ]. BaeR is a positive response regulator of RNA synthesis. Overproduction of BaeR increases resistance to novobiocin, deoxycholate, bile salts, SDS, and a number of β-lactam antibiotics by stimulating expression of the mdtABCD and acrDmultidrug transporter genes [ Nagakubo02  , Baranova02  , Hirakawa03a  , Hirakawa03  ]. BaeR was also shown to regulate gene clusters involved in flagellar biosynthesis, chemotaxis, multidrug transport, maltose transport, signal transduction, and unknown functions [ Baranova02  , Raffa02  , Nishino05  ]. Expression of a number of these genes is induced by indole via BaeSR and CpxAR signal transduction systems [ Hirakawa05  ]. The BaeSR, PhoBR, and CreBC two-component systems have been shown to interact in the regulation of gene expression [ Nishino05  ]. BaeR suppresses envZ and phoR/creC mutations [ Nagasawa93  ]."]
["betI","\"betI\""," BetI belongs to the TetR/AcrR family of transcriptional regulators [ Rkenes96  , Lamark91  ]. It is a repressor of the glycine betaine synthesis from choline that controls the cellular response to osmotic stress and oxygen [ Lamark96  ]. This protein is conformed by two domains, an amino-terminal domain that contains a potential helix-turn-helix DNA-binding motif and a carboxy-terminal domain involved in co-inducer recognition and dimerization [ Lamark91  ].\n\nBetI represses the transcription of the betT gene (choline transporter) which is encoded divergently with respect to the betIBA operon, that is also repressed by BetI [ Rkenes96 ]. The betIBA operon comprises the regulatory gene (betI) and two structural genes, betB (betaine aldehyde dehydrogenase) and betA (choline dehydrogenase) [ Rkenes96 , Lamark96 ]. The position of the repressor gene within the operon is unusual, as regulatory genes tend to be positioned at the end of operons.\n\nBetI complexes with DNA in the presence of choline, binding to a 20 bp sequence with dyad symmetry (TATTGAACGTCCAATGAATA) that overlaps the betTp and betIp promoters simultaneously [ Rkenes96 ]. "]
["cadC","\"cadC\"","CadC regulates expression of the cadBA operon under conditions of low external pH and abundant lysine [ Watson92  , Neely94  ]. Although it is similar to ToxR in its amino-terminal domain and predicted inner membrane localization, it apparently does not require a ToxS-like component for its activity [ Watson92  ]."]
["chbR","\"chbR\"","ChbR belongs to the AraC/XylS family and negatively controls the expression of the celABCDF-ydjC (chbBCARFG) carbon uptake operon. chbBCARFG is induced by N,N'-diacetylchitobiose and encodes its own specific regulator, ChbR, which binds to two 19 bp direct repeats located between the two NagC sites. ChbR is necessary for transcription activation in the presence of chitobiose in vivo. In the absence of chitobiose, ChbR acts as a repressor [ Plumbridge04  ]."]
["cpxR","A"," CpxR is the response regulator that mediates a response by activating the transcription of stress-combative genes (csgBA, csgDEFG, degP, and cpxP). It senses a variety of envelope stresses, including misfolded proteins and degrading factors. It is a member of the two-component regulatory system CpxA/CpxR.\n\nOverproduction causes a drug resistance phenotype and affects transcription of genes involved in drug efflux [ Hirakawa03a ].\n\nCopper-inducible promoters regulated by CpxA-CpxR were characterized by [ Yamamoto06 "]
["crp","A","Crp is a dual transcriptional regulator that belongs to the CRP family. It is the major global regulator of catabolite-sensitive operons and it controls its own synthesis. This regulator induces a severe bend in the DNA and is capable of regulating the expression of more than 200 genes."]
["csgD","\"csgD\""," The CsgD protein belongs to the FixJ/LuxR/UhpA family and the sets of genes regulated by it constitute the regulon involved in biofilm formation [ Brombacher03  ]. CsgD activates the transcription of the csgBA operon, which encodes the curli structural subunits as well as the csgDEFG operon [ Hammar95  ]. CsgD may stimulate biofilm formation by activating both curli and YaiC expression and repressing negative determinants of biofilm formation such as yagS and pepD. Furthermore, it may have the capability to respond to starvation and high cell density [ Brombacher03  ].\n\nSince the csgD gene is induced in mid-exponential phase of growth and the CsgD dependent activation of the csgBAC and yaiC genes is detected in stationary phase, it has been suggested that the CsgD protein is post-transcriptionally activated in stationary phase [ Brombacher03 ].\n\nThe CsgD might activate the transcription through two different mechanisms because the localization of its binding sites to activate differs in the regulatory regions of the genes it activates. Besides, in one regulatory region the protein is bound to just one site, and in another it is bound to two sites, which are forming an inverted repeat. The conserved sequence of 11 bp that CsgD binds is CGGGT/GGAT/GNT/GA [ Brombacher03 ]. "]
["cspA","\"cspA\""," CspA is an RNA chaperone that prevents secondary structure formation in RNA at low temperatures [ Jiang97  ].\n\nCspA is detected only during early log phase growth at 37° C and during log phase after a shift from 37° C to 10° C [ Jones87 ]. cspA was also shown to be induced by addition of chloramphenicol and was induced even in the absence of protein synthesis [ Jiang93 , Etchegaray99 ]. cspA mRNA is very unstable at 37° C and rapidly disappears as cell density and RNase activity increase [ Tanabe92 , Brandi99 ]. The lability of cspA mRNA at high temperatures is mediated by cleavage toward its 3' end; this cleavage is partially dependent on Rne [ Hankins07 ]. The long 5' untranslated region of cspA mRNA contains a feature within the first 25 bases responsible for derepression of cspA expression and inhibition of synthesis of cellular proteins other than cold shock proteins following cold shock [ Jiang96 ].\n\nCspA acts as a positive transcription factor for hns following cold shock [ La91 ]. CspA also activates gyrA [ Brandi94 ]. CspA has been shown to negatively regulate its own expression [ Bae97 ].\n\ncspA is positively regulated by Fis and negatively regulated by H-NS during growth at 37° C [ Bae99 ].\n\nThe structure of CspA has been determined by NMR spectroscopy [ Newkirk94 , Feng98 ]. Its crystal structure has also been determined to a resolution of 2.0 Å [ Schindelin94 ]. "]
["cspE","“cspE”"," CspE belongs to the cold shock family of proteins and was shown to be involved in a variety of cellular processes both in vitro and by studying mutants and overexpressing strains. CspE is involved in resistance to camphor-induced chromosome decondensation [ Hu96  , Sand03  ], and a model of how its ssDNA binding activity might affect chromosome condensation has been proposed [ Johnston06  ].\n\nAlthough initially CspE did not appear to interact with free RNA [ Hanna98 ], it was later shown to interact with both RNA and DNA; a consensus sequence for selective RNA binding has been determined using an in vitro selection approach [ Phadtare99 ]. CspE was later shown to display the highest affinity towards ssDNA containing six contiguous dT residues [ Johnston06 ].\n\nCspE interacts with nascent RNA in an initial transcribing complex and inhibits Q-mediated transcription antitermination at the λ PR' promoter [ Hanna98 ]. In contrast, it was later found that CspE acts as a transcription antiterminator at ρ-independent terminators both in vitro and in vivo [ Bae00 ]. The nucleic acid melting activity of CspE is required for its transcription antitermination activity [ Phadtare02 , Phadtare02a ], and its melting activity on DNA substrates has been studied [ Phadtare05 ]. Purified CspE protein binds to poly(A) RNA tails and impedes poly(A)-mediated mRNA decay and internal mRNA cleavage by polynucleotide phosphorylase and RNase E [ Feng01 ]. CspE inhibits the expression of cspA in vitro by increasing pause recognition by RNA polymerase at the cspA \"cold box\" [ Bae99 ].\nPublished evidence disagrees on whether the protein behaves like a monomer [ Hanna98 ] or a dimer [ Johnston06 ] in solution.\nExpression of cspE is not cold-shock inducible [ Etchegaray96 ]; rather, its expression is constitutive at 37 °C [ Bae99 ].\nA cspE deletion strain has no growth defect, but shows a longer lag period than wild type after dilution into fresh medium [ Bae99 ]. A cspE insertion mutant is highly sensitive to UV and gamma radiation [ Mangoli01 ]. Overexpression of CspE leads to higher levels of rpoS mRNA [ Phadtare01 ]. Global gene expression changes in response to cold shock in a quadruple cspABGE deletion strain [ Phadtare04 ] and in response to a cspCE deletion and CspE overexpression [ Phadtare06 ] have been measured. A pagP (crcA) cspE crcB triple null mutant exhibits greater than wild-type sensitivity to camphor, which causes chromosome decondensation, and it enhances the nucleoid morphology phenotype of a topoisomerase IV mutant [ Sand03 ]. Overexpression of pagP, cspE, and crcB together results in resistance to camphor [ Hu96 ], increased DNA supercoiling and increased expression of rcsA [ Sand03 ], and suppresses phenotypes of a mukB mutant [ Yamanaka94 , Hu96 ], a gyrase mutant and a topoisomerase IV mutant [ Sand03 ].\nMsmC: \"multicopy suppressor of mukB106\" [ Yamanaka94 ]\nCspE: \"cold shock protein\" "]
["cusR","\"cusR\""," CusR is a positive DNA-binding transcriptional regulator of the copper efflux system as the response regulator in a two-component regulatory system with CusS.\n\nThe cusABFCRS gene cluster has similarity to a gene cluster contained on a silver resistance plasmid from a clinical Salmonella isolate [ Silver03 ].\n\nAgr: \"Ag(I) resistance\" [ Silver03 "]
["cynR","\"cynR\"","CynR is a dual transcriptional regulator that belongs to the LysR family. This protein controls the expression of the cynTSX operon involved in degrading and using cyanate as a sole nitrogen source. It also controls its own synthesis. (also detoxification)"]
["cysB","\"cysB\"","This protein controls the expression of the cysteine regulon (cysB, cysDNC, cysJIH, cysPUWAM, and cysK) that is a system of 10 or more loci involved in the biosynthesis of L-cysteine. It also controls its own synthesis. It belongs to the LysR family of transcriptional regulators."]
["cytR","A","his protein negatively controls the expression of the transcription units that encode the proteins and enzymes required for the transport (nupC, nupG, and tsx) and the utilization of nucleosides (deoCABD, udp, and cdd). It activates the transcription of the txt gene involved in pore-forming. Moreover, it is a transcriptional repressor in the complex with CRP and his co-activator, inducer = cytidine. It belongs to the GalR/LacI family of transcriptional regulators."]
["dhaR","\"dhaR\"","DhaR is a transcriptional regulator that activates expression of the dhaKLM  operon and represses its own transcription. ADP-bound DhaL is the coactivator of DhaR, and DhaL is an antagonist of DhaL::ADP; both are able to form complexes with the sensing domain of DhaR. DhaL and DhaR are catalytic subunits of the PTS-dependent DHA kinase [ Bachler05  ]."]
["dnaA","A"," DnaA plays an important role in initiating chromosomal replication to bind sequences in the chromosomal origin. It belongs to the DnaA family of transcriptional regulators.\n\nDnaA also binds to sites at the datA locus and this binding serves to limit excess DnaA activity, but other DnaA-binding sites are shown not to share this function [ Ogawa02 ].\n\nRegulation has been described [ Kato01 , Katayama98 , Riber05 ]. IdaB is a member of the AAA chaperone-like family of ATPases [ Kato01 ] that is required for the inhibition of the initiation of DNA synthesis via antagonism of DnaA activity by the DNA polymerase III beta subunit (sliding clamp) [ Katayama98 , Kato01 ]. IdaB and the sliding clamp stimulate ATP hydrolysis within the DnaA-ATP complex, which renders it inactive, and DNA replication activity also contributes to this downregulation [ Katayama98 ].\n\nDnaA also can inhibit the gene expression of other genes such as guaA, dam, rpoH, ftsA, and mioC. "]
["dsdC","\"dsdC\"","DsdC belongs to the LysR family of bacterial transcriptional regulators. Moreover, it is absolutely required for the expression of D-serine deaminase. It auto-regulates the synthesis and positively controls the expression of dsdXA operon and dadA gene. "]
["emrR","“emrR”"," EmrR negatively autoregulates the transcription of the emrRAB operon, which encodes subunits of a multidrug resistance pump [ Lomovskaya95  ]. The purified protein binds 2,4-dinitrophenol, carbonyl cyanide m-chlorophenylhydrazone, and carbonyl cyanide p-(trifluoro-methoxy)phenylhydrazone, predicted ligands of the EmrAB pump, with micromolar affinity [ Brooun99  ]. Binding of these agents interferes with the ability of EmrR to bind DNA [ Xiong00  ].\n\nOverproduction of EmrR from a multicopy plasmid causes a mutator phenotype, including an increase inframeshift and base substitution mutations [ Yang04 ].\n\nEmrR, which is also known as MprA, was shown to be a repressor of microcin biosynthesis [ delCastill90 , delCastill91 ]. It acts as a repressor of the mcb operon contained on a conjugative plasmid isolated from clinical strains of E. coli [ Mao98 ].\n\nExpression of emrRAB is induced by antimicrobial agents such as CCCP and nalidixic acid; induction requires EmrR [ Lomovskaya95 ]. Expression of emrR is not osmoregulated [ delCastill91 ].\n\nReviews: [ Lewis01 , Grkovic02]"]
["evgA","\"evgA\"","from uniprot: Member of the two-component regulatory system evgS/evgA. Regulates the expression of emrKY operon and yfdX. Seems also to control expression of at least one other multidrug efflux operon."]
["exuR","\"exuR\"","ExuR is a protein that negatively controls the transcription initiation of genes involved in hexuronate utilization such as exuT, uxaCA, and uxuAB operons. It belongs to the GntR family of transcriptional regulators."]
["fadR","\"fadR\"","FadR is a dual DNA-binding transcriptional regulator for fatty acid metabolism. This protein controls the expression of several genes involved in fatty acid transport and beta-oxidation (fadBA, fadD, fadL, and fadE). It activates the transcription of at least three genes required for unsaturated fatty acid biosynthesis (fabA, fabB, and iclR). It belongs to the GntR family of transcriptional regulators."]
["fecI","“fecI”"," FecI (sigma19) was first described as a protein that regulated the expression of genes involved in the transport of ferric citrate [ Pressler88  , Van90  , Ochs95  ]; later, it was determined as sigma factor based on similarities to a subgroup of sigma70 factors, and it binds to the fec transport gene promoter upstream fecA [ Ochs95  , Enz95  ].\nFecI is a minor sigma factor that initiates transcription of ferric citrate transport genes in response to the presence of periplasmic iron(III) dictrate [ Harle95 , Ochs95 ] and it only leads to initiation of transcription by RNA polymerase, core enzyme at the citrate-transport promoters [ Angerer95 , Maeda00a ]. This limited role is typical of the minor sigma factors.\nThree proteins participate in the induction of the citrate transport genes of Escherichia coli K-12, which involve a signaling cascade that starts at the cell surface and proceeds to the cytoplasm: FecA in the outer membrane, FecR in the cytoplasmic membrane, and FecI in the cytoplasm [ Braun03 ].\nThe interaction of ferric citrate with the outer membrane receptor protein FecA induces transcription of the fec transport gene operon consisting of the fecIRABCDE genes [ Pressler88 , Van90 ]. A signal from FecA occupied with ferric citrate is transmitted across the outer membrane into the periplasm [ Wagegg81 ] with the help of the electrochemical potential of the cytoplasmic membrane and the Ton system. FecA interacts with FecR in the periplasm and then the signal is transmitted across the cytoplasmic membrane, which in turn activates the FecI sigma factor that directs the RNA polymerase core enzyme to the fec transport gene promoter [ Van90 , Ochs95 ]. The periplasmic amino-terminus of FecA binds to the carboxy-terminus of FecR, and the cytoplasmic amino-terminus of FecR binds FecI [ Enz00 , Braun05 ]. Mutations in FecR can be compensated by the putative RNA polymerase-binding region 2.1 of FecI, although actual FecI-FecR interaction appears to depend on region 4 of FecI [ Stiefel01 , Mahren02 ]. FecI in turn interacts with RNA polymerase, β' subunit ; the cytoplasmic domain of FecR stimulates this interaction [ Mahren03 ].\n\nThe promoter of the regulatory genes, fecI and fecR, is not controlled by ferric citrate but is regulated by iron via the Fur repressor [ Enz95 , Braun97 , Braun03 , Braun05a , Harle95 ].\nfecIR and fecABCDE are repressed by Fur protein loaded with Fe(2+) [ Staudenmai89 , Van90 , Braun03 ]. Under iron-limiting conditions, Fur is not loaded with Fe(2+), so the fecI and fecR genes are transcribed and the FecI and the FecR proteins are synthesized and are able to respond to the presence of ferric citrate in the medium when ferric citrate binds to the FecA protein [ Enz95 , Braun97 , Braun05 ].\nFecR could be considered as an antisigma because it would be the first instance in the ECF (extracytoplasmic function sigma factor) subfamily in which an antisigma factor is shown to be essential [ Hughes98 ].\nFecI, called the iron-starvation sigma, causes expression of genes for uptake of ferric citrate [ Visca02 ]. FecI sigma factors are widespread among bacteria [ Braun03 , Braun05a ]. FecI belongs to the polyamine modulon since its expression is enhanced by polyamines at the level of translation [ Igarashi06 ].\nReviews: [ Braun03 , Braun05 , Braun06 , Braun05a , Visca02 , Braun97 ]. "]
["fhlA","\"fhlA\"","from uniprot: Required for induction of expression of the formate dehydrogenase H and hydrogenase-3 structural genes."]
["fis","\"fis\""," Fis is a DNA-bending protein that is required for efficient initiation of chromosome replication and for activation of stable RNA (rRNA and tRNA) genes. It represses the gyrA and gyrB promoters and reduces DNA gyrase activity. Fis is involved in coupling the cellular physiology of the topology of the bacterial chromosome. It belongs to the EBP family of transcriptional regulators.\n\nFis actively inhibits transposition by the IS2 transposon, both by inhibiting transcription of IS2 genes and by directly blocking the transposase binding site [ Lei07 ]. "]
["flhCflhD","“flhCflhD”","FlhDC is a transcriptional activator of the flagellar regulon. FlhC and FlhD combine to act as a compound sigma factor, activating class II flagellar genes [ Liu94  ]. FlhDC can activate transcription of fliA, flhB, fliL, napF, nrfA, and dmsA. flhDC mutants have been shown to have improved growth on sugars as the sole carbon source, and could better colonize in the mouse intestine [ Leatham05  ]. The crystal structure of FlhDC has been solved to 3 Å resolution. FlhDC is hexameric, with each of its two FlhC monomers binding to an FlhD dimer [ Wang06  ]. Binding of FlhDC to a promoter region results in substantial bending of the DNA at the binding site [ Wang06  ]."]
["fliA","“fliA”"," Sigma 28 is a minor sigma factor responsible for initiation of transcription at a number of genes involved in motility. Most notable among its targets are many genes required for flagellar synthesis.\nSigma 28 initiates transcription at a number of genes required for motility. It activates transcription of both flagellar and chemotaxis genes, including tar, tsr and the flaA operon [ Komeda86 , Arnosti89 , Liu95 ]. Though the fliA and fliL operons can also be transcribed by Sigma 70, the flhB operon, tar and tsr can only be transcribed by Sigma 28 [ Liu96 , Kundu97 ]. Sigma 28 competes with Sigma 70 for RNA polymerase, core enzyme , binding to it more tightly than Sigma 70 [ Kundu97 ].\nThe dependence of Sigma 28 on promoter sequence has been tested using the Chlamydia trachomatis hctB promoter [ Yu06 ].\nSigma 28 is required for flagellin production [ Komeda80 , Komeda84 ]. The structural consequences of fliA mutation have been examined via electron microscopy [ Suzuki81 ].\nSigma 28 is half as abundant as Sigma 70 under most growth conditions, but drops in abundance following heat shock [ Jishage96 ].\nBiofilm formation depends on the level of fliA expression [ Barrios06 , Wood06]"]
["fnr","E"," FNR is a dual DNA-binding transcriptional regulator which stimulates the transcription of many genes that are required for fermentation and anaerobic respiration. Moreover, it represses the transcription of some genes that function only during aerobic growth. This system is active only during anaerobic growth. FNR belongs to the CRP family of transcriptional regulators.\nThe concentration of FNR is similar under both anaerobic and aerobic conditions [ ShalelLeva05 ], but its activity is regulated by oxygen. Under anaerobiosis FNR is active and displays a [4Fe-4S] cluster. Diffusion of O2 into the cytoplasm rapidly results in inactivation via oxidation of this [4Fe-4S] cluster and the protein may be reversibly reactivated by glutathione-mediated reduction in vivo [ Unden02 ]. The intact [4Fe-4S] cluster is involved in FNR dimerization, which in turn, appears to be involved in site-specific DNA binding activity [ Kiley98 ]\nFNR shares structural similarity with a group of DNA-binding transcriptional regulators that includes CRP, and the specificity of individual family members is conferred by differences in the sensory/regulatory, DNA binding, and RNA polymerase binding regions of these proteins [ Green01 ]\nSeveral reviews discuss FNR activity and function [ Unden91 , Unden02 , Kiley98 , Green01 , Unden97 , Unden97a , Rouault96 , Unden95 , Spiro94 , Iuchi93 , Spiro91 , Spiro90 , Unden91 ].FNR was named for the mutant defect in \"fumarate and nitrate reduction\" [ Lambden76 ]. The original mutant name of \"frdB\" was later changed to \"fnr\" [ Lambden76 ]. "]
["fruR","\"fruR\""," FruR is a dual transcriptional regulator that is implicated in the regulation of a large number of operons that encode enzymes, which comprise central pathways of carbon metabolism. It represses some operons (nirBDC-cysG, fruBKA, ptsHI-crr, and edd-eda) but activates others (aceBAK, icdA, pckA, and ppsA). It belongs to the GalR/LacI family of transcriptional regulators.\n\nCra was formerly known as FruR. Protein Complex FruR site length 14.\n\nThe wild-type Cra (FruR) protein binds to DNA as a homotetramer. "]
["fucR","\"fucR\"","FucR is a transcriptional activator that belongs to the DeoR family of transcriptional regulators. This protein regulates the expression of fuculose-1-phosphate aldolase (fucAO), fucose permease, fucose isomerase, and fuculose kinase (fucPIKUR). It is involved in L-fucose utilization."]
["fur","\"fur\""," Fur is a negative transcriptional regulator, which is implicated in the regulation of a large number of operons that encode enzymes involved in iron transport (fecABCDE, fecIR, and fhuACDB), including several outer-membrane proteins [ Hantke81  ]. It is activated by Mn2+ and belongs to the Fur family of transcriptional regulators.\n\nSynthesis of Fur is translationally coupled to that of Uof. Translation of uof is downregulated by the small RNA RyhB, which therefore indirectly regulates translation of fur [ Vecerek07 ]. "]
["gadE","B","GadE is involved in the resistance to low pH observed upon overexpression of evgA or ydeO [ Masuda03  ]. GadE overproduction causes resistance to low pH [ Masuda03  ]. Purified GadE protein binds to the promoter regions of target genes [ Hommais04  ]."]
["gadW","\"gadW\"","GadW is a protein that belongs to the AraC/XylS family. This regulator participates in controlling several genes of the acid resistance system. GadW represses the transcription of the gadAX and gadBC operons."]
["gadX","B"," The GadX (glutamate decarboxylase regulator) transcriptional activator, which belongs to the AraC/XylS family [ Gallegos97  ], is a monomer of 31KDa that can conform a homodimer in vivo [12446650].\n\nThe gadX gene can be transcribed alone [ Tramonti02 , Ma02 ], or along with the upstream gene gadA [ Tramonti02 ], or along with the downstream gene gadW [ Tucker03 ]. Its transcription is regulated by HNS, GadW, GadE, and FNR; and its promoter is a sigma54 type.\nGadX is one of the responsible regulators of the glutamate-dependent acid-resistance (AR) system of E. coli (for AR information: [ CastanieCo99 , De99a ]); it regulates eleven operons (*1) in response to acid pH and/or during stationary phase [ Tramonti02 , Ma02 ]. The regulated operons can be regulated by other 10 transcription factors (*2). Initially, GadX was characterized as a dual regulator [ Shin01 ]; later, GadX was characterized as an activator [ Tramonti02 ]; and more recently, it has been proposed that it regulates along with GadW (another member of the AraC/XylS family) [ Ma02 , Tucker03 ].\n\nCurrently, the way GadX and GadW regulate and interact is under discussion and s"]
["galR","\"galR\"","GalR functions as a repressor of the gal operon in the absence of galactose. Furthermore, it negatively controls the transcription initiation of the galETKM operon and galS gene. GalR belongs to the GalR/LacI family of transcriptional regulators."]
["galS","\"galS\"","It is a negative DNA-binding transcriptional regulator for galactose utilization. This protein negatively controls transcription initiation of the mglBAC operon and controls its own expression. GalS belongs to the GalR/LacI family of transcriptional regulators."]
["gcvA","\"gcvA\""," The GcvA (glycine cleavage) transcriptional dual regulator, which belongs to the LysR-family [ Wilson94  ], has two domains: the amino-terminal, which appears to be involved in transcription activation and DNA binding through its helix-turn-helix subdomain; and the carboxy-terminal, involved in interaction with the GcvR protein [ Jourdan98  , Ghrist01  ].\n\nGcvA both autoregulates its own expression from the gcvA gene and regulates the expression its divergently transcribed neighbor, the gene gcvB [ Wilson95 ].\n\nGcvA regulates a small RNA gene and genes involved in the glycine cleavage system [ Wilson95 , Urbanowski00 ]. In the presence of glycine, the GcvA regulator activates transcription via interaction with the alpha (at the gcv operon) or sigma (at the gcvB gene) subunits of RNA polymerase [ Stauffer05 ]. In the absence of glycine and the presence of GcvR protein, GcvA represses the operons [ Ghrist01 ].\n\nGcvR is an accesory protein that binds directly to GcvA forming a repression complex (GcvA/GcvR) at the regulatory region of the gcvT operon[ Ghrist01 ]. Glycine binds directly to the GcvR protein to disrupt or block the association of the GcvA/GcvR complex, while purines appear to promote the formation of the repression complex through an unknown mechanism [ Heil02 , Ghrist01 ].\n\nThe GcvA binding sites do not show a clear conservation in their sequences except for a short 5'-CTAAT-3' sequence [ Wilson95 "]
["glcC","\"glcC\"","Activator for the glycolate oxidation locus. (from expasy)"]
["glnG","\"glnG\""," NtrC is a member of the sigma54-dependent activator family and belongs to the two-component system NtrB/NtrC [ Reitzer03  ]. Both the genes, glnG encoding the response regulator (NtrC) and glnL encoding the sensor kinase (NtrB), are organized in an operon in the E. coli chromosome [ MirandaRio87  ]. NtrB functions as a membrane-associated protein kinase that phosphorylates NtrC in response to limitation of nitrogen- and carbon-limited growth [ Reitzer85  ]. NtrC-P is autoregulated in a dual form and controls the transcriptional expression of several genes involved in the assimilation of nitrogen: it regulates dually the glnALG and glnHPQ operons, represses the glnLG operon, and activates a great variety of genes. In the phosphorylated state, the NtrC protein (NtrC-P) forms a tetramer that increases the affinity for its specific DNA binding sites and activates sigma54 promoters. The NtrC-P binds to a 17 bp long inverted repeat sequence (TGCACCn5GGTGCA) [ Reitzer01  ].\n\nIn the phosphorylated state the NRI-P protein forms a tetramer. It is the tetramer form of NRI-P that is the actual transcription activator [ Weiss92 ]. "]
["gntR","\"gntR\"","GntR belongs to the GalR-LacI family of transcriptional regulators. This regulator represses the gntI, gntKU, and gntT genes involved in the gluconate utilization system."]
["gutM","D","This protein is a positive DNA-binding transcriptional regulator for glucitol utilization. There is no protein family associated to this transcription factor. Citations: [ Yamada88 "]
["hcaR","\"hcaR\""," The HcaR transcriptional dual regulator, which belongs to the LysR-family, has a helix-turn-helix domain. This transcriptional regulator, which is negatively autoregulated, is encoded by the hcaR gene that is transcribed divergently from an operon that HcaR regulates [ Turlin05  , Diaz98  ].\n\nIn the presence of 3-phenylpropionate, HcaR regulates directly genes involved in the 3-phenylpropionic acid catabolism. Besides, using proteome analysis, it was shown that HcaR regulates the production of 30 proteins involved in several processes in E. coli; however, it is not known if this regulation is direct or indirect [ Turlin05 ].\n\nThe putative HcaR binding site sequence TAG-N7-CTA has been identified. This sequence matches the binding motif of LysR-type regulators [ Diaz98 ].\n\n"]
["hns","B"," Heat-stable nucleoid-structuring protein (H-NS) is a nucleoid-associated protein that acts as a transcriptional repressor and may serve to generally suppress horizontally acquired genes.\n\nH-NS binds plays an important role in the regulation of many genes in response to environmental change and adaptation to stress. It binds curved DNA, with a strong preference for horizontally acquired genes among the 250 loci to which it binds [ Yamada90 , Oshima06 ]. H-NS functions almost exclusively as a transcriptional repressor.\n\nBased on deletion studies, H-NS appears to inhibit the phase-variation inversion switching of the fim switch regulating type 1 fimbrial biogenesis [ Kawula91 ].\n\nThe initiating methionine of H-NS is cleaved [ Wasinger98 ].\n\nH-NS is belongs to the histone-like family of transcriptional regulators.\n\nRegulation of H-NS has been described [ Repoila03 ]. It is subject to post-transcriptional regulation by the sRNA DsrA [ Repoila03 ].\n\nReviews: [ Repoila03 , Dorman04 ] "]
["hyfR","\"hyfR\"","HyfR belongs to the EBP family; it is a transcriptional activator, which shows a potential helix-turn-helix motif DNA-binding domain and controls the expression of genes responsible for the proton-translocating formate hydrogenase system [ Skibinski02  , Andrews97  ]. The HyfR is positively autoregulated through the promoter of the hyfABCDEFGHIJR-focB operon. Its transcription is also strongly inhibited by oxygen, is sensitive to low pH, and weakly stimulated by formate [ Skibinski02  , Andrews97  ]."]
["iclR","\"iclR\""," IclR belongs to the IclR family. This regulator participates in controlling several genes involved in glyoxylate bypass. It represses the aceBAK operon, which encodes isocitrate lyase, malate synthase, and isocitrate dehydrogenase kinase/phosphorylase.\n\nIclR represses aceBAK by binding to the proximal site, overlapping the -35 promoter box, and preventing RNA polymerase binding, and by binding to the distal site after the RNA polymerase has bound to the promoter and formed the open complex, thus preventing promoter clearance through its interaction with the RNA polymerase alpha subunits [ Yamamoto03 ]. IclR binding at both sites may form an intermolecular bridge that leads to a DNA loop structure and thus enhances aceBAK repression [ Yamamoto03 ].\n\nGlyoxylate and pyruvate were identified as effectors of IclR and showed antagonistic effects. While glyoxylate favors the inactive dimeric state of IclR, pyruvate increases the binding of IclR to the aceBp promoter by stabilizing the active tetrameric form of the protein [ Lorca07 ]. "]
["idnR","\"idnR\"","IdnR (idonate regulator) is a transcriptional regulator that exhibits identity of transcriptional repressors of the LacI/GalR family. It was identified in the operon idnDOTR, which, besides transcribing together with idnDOT, is also transcribed as an independent transcription unit [ Bausch04  ]. IdnR is autoregulated positively and participates in the control of several genes involved in L-idonate metabolism, which are organized in two coordinately regulated transcription units (idnK and idnDOTR) [ Bausch04  ]. The synthesis of Idn proteins is induced in the presence of L-idonate/5KG and in the absence of glucose and gluconate. In addition, this regulator represses the transcription of the genes related with the gluconate metabolism [ Bausch98  ]. IdnR binds to the 16bp-long inverted repeat sequence, which shows homology with consensus binding sequence of GntR [ Bausch04  , Rodionov00  ]. "]
["ihfAihfB","\"ihfAihfB\"","(informacion de ihfa)The protein family is HI-HN-S. buscar del B http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=PD00348"]
["ilvY","\"ilvY\"","The protein belongs to the LysR family. This regulator participates in controlling several genes involved in isoleucine and valine biosynthesis. It activates the transcription of the ilvC gene in presence of acetolactate or acetohydroxibutyrate. IlvY is negatively auto-regulated."]
["iscR","\"iscR\""," IscR is a member of the Mar/Sox/Rob family of transcriptional regulators. The IscR protein has been shown to function as a negative regulator of expression of the iscRSUA operon both in vivo and in vitro; thus, it regulates its own synthesis [ Schwartz01  ].\n\nAnaerobically purified IscR protein contains a [2Fe-2S]1+ cluster. When the Fe-S cluster assembly genes iscS or hscA are mutated, IscR activity is decreased [ Schwartz01 ].\n\nTogether, the data suggests a novel feedback regulation mechanism for iron-sulfur cluster biogenesis. Under conditions when Fe-S cluster assembly becomes rate-limiting, levels of [2Fe-2S]- containing IscR may decrease due to a lower rate of its synthesis; thus, relieving repression of the iscRSUA operon [ Schwartz01 , Frazzon01 ]. "]
["lctR","“lctR”"," LldR is a protein that belongs to the GntR family. This regulator participates in controlling several genes involved in L-lactate utilization. It represses the lctPRD operon.\n\nTranscription of lctR is induced upon biofilm formation compared to planktonic growth in both exponential and stationary phases. Induction of expression was found to be dependent on the presence of the F plasmid [ Beloin04 ].\n\nA lctR mutant is impaired in biofilm formation [ Beloin04 ]. "]
["lexA","A","LexA is a protein that belongs to the LexA family [ Lamerichs89  , Madan03  ]. This regulator participates in controlling several genes involved in the SOS response [ Cole83  , Easton83  , Sedgwick85  ]. The recA protein interacts with LexA causing an autocatalytic cleavage, which disrupts the DNA-binding capacity of LexA [ Horii81  , Little80  , Markham81  ]."]
["lrhA","\"lrhA\"","LrhA is a protein that belongs to the LysR family [ Bongaerts95  ]. This regulator participates in controlling the proton translocating NADH dehydrogenase genes and in modulating the activity of SprE (Hnr) [ Gibson99  ]. LrhA is negatively autoregulated and represses the flhDC operon [ Lehnen02  ]."]
["lrp","\"lrp\"","The protein belongs to the AsnC family. This regulator participates in controlling several genes involved in the high-affinity branched-chain amino acid transport system. It is a mediator of the leucine response. Lrp affects several operons."]
["lysR","\"lysR\"","The protein belongs to the LysR family. This regulator participates in controlling several genes involved in lysine biosynthesis. LysR is negatively auto-regulated and activates the transcription of lysA."]
["malI","\"malI\""," MalI, a gene that encodes for a protein that exhibits identity to transcriptional repressors of the LacI/GalR family, was identified 174 nucleotides upstream and in the direction opposite the malXYoperon [ Reidl89  , Reidl91  ]. This repressor, involved in the transport of maltose-glucose, is autoregulated negatively and represses coordinately the transcription of the malXYdivergent operon, which comprises a maltose-glucose PTS permease (MalX) and a bifunctional protein that interacts directly with the MalT transcriptional activator (MalY) [ Reidl89  , Reidl91  ].\n\nMalI shows a high identity to GalR (28%), CytR (21%), and LacI (24%) as well as a homology with a fragment of 30 amino acids of MalT. Additionally, the N-terminal region represents a helix-turn-helix DNA-binding domain [ Reidl89 ].\n\nMalI binds to two directed repeat nucleotide sequences in tandem (12 bp long) that simultaneously overlap the promoters, malXp and malIp. Its consensus sequence is TAAAACGTTTTA [ Reidl89 , Reidl91 ]. "]
["marA","C"," The MarA protein belongs to the AraC/XylS family. This regulator participates in controlling several genes involved in the response to multiple antibiotics (acts as monomer, does not have a dimerization domain). It also activates the genes sodA, zwf, and micF.\n\nThe MarA protein is unstable due to proteolytic degradation; the protein is stable in a lon mutant. The instability provides a mechanism for rapid shut-off of the transcriptional response once the inducing conditions have subsided [ Griffith04 ].\n\nMar: multiple antibiotic resistance "]
["marR","C","The protein belongs to the MarR family. This regulator participates in controlling several genes involved in antibiotic resistance and oxidative stress. It is auto-regulated through the repression of the marRAB operon."]
["melR","\"melR\""," The melR gene is located upstream of and in the opposite direction of operon melAB [ Webster87  ]. It encodes MelR (melibiose regulator), a transcriptional activator, which is a member of the AraC family of activators. MelR subunits consist of two domains: a C-terminal DNA-binding domain, which contain two helix-turn-helix motive (HTH), and an N-terminal melibiose-binding domain involved in effector recognition [ Webster89  , Caswell92  , Michan95  , Bourgerie97  ]. This transcription factor is negatively autoregulated and sensitive to catabolite control [ Webster88  , Wade00  , Wade01  , Belyaeva00  , Kahramanog06  ]. It activates the transcription of the melAB operon in response to melibiose [ Tamai00  , Williams94  , Caswell92a  ], melA encodes an alpha-galactosidase protein [ Hanatani84  , Liljestrom87  ], whereas melB encodes the melibiose transporter [ Hanatani84  , Yazyu84  ].\n\nIn the presence of melibiose, MelR binds in tandem to five inverted repeated sequences along the melAB/melR intergenic region and activates the transcription overlapping the -35 box of promoter melAp [ Howard02 , Wade00 , Tamai00 , Caswell92a , Belyaeva00 ]. The binding targets for MelR consist of inverted repeated sequences 18 nucleotides long that possess conserved motifs; each monomer binds to one of these conserved sequences [ Wade00 , Belyaeva00 , Wade01 , Howard02 ]. The consensus sequence of this regulator is NAGCN7TCCATA [ Wade00 , Belyaeva00 ]. "]
["metJ","\"metJ\"","from uniprot: This regulatory protein, when combined with SAM (S-adenosylmethionine) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated."]
["metR","\"metR\"","Control of the last step in methionine biosynthesis; metR is a positive activator of the metA, metE and metH genes. metR is also a negative regulator of its own expression. Binds homocysteine as an inducer."]
["mlc","“mlc”"," DgsA, better known as Mlc, \"makes large colonies,\" [ Hosono95  ] is a transcriptional dual regulator that controls the expression of a number of genes encoding enzymes of the Escherichia coli phosphotransferase (PTS) and phosphoenolpyruvate (PEP) systems [ Plumbridge02  , Pradhanang05  ]. It also regulates genes involved in the uptake of glucose [ Plumbridge01  ]. It is considered a global regulator of carbohydrate metabolism [ Decker98  , Kimata98  ]. In addition, Mlc regulates expression of the MalT transcriptional regulator, the activator of the maltose regulon [ Decker98  ].\n\nMlc repressor function is disabled by binding of Mlc to an actively-transported and dephosphorylated form of PtsG (EIICBGlc) [ Lee00 , Nam01 ]. The membrane-bound part of EIICBGlc is essential for Mlc inactivation [ Nam01 , Seitz03 ]. Analysis of the crystal structures of the tetrameric Mlc/EIIB complex shows a molecular mechanism of Mlc inactivation by membrane sequestration, in which Mlc loss its DNA binding ability in vivo due to the conformational obstruction by EIIB molecules [ Nam08 ].\nIts crystal structure has been determined [ Gerber05 , Schiefner05 ]. Mlc forms stable dimers and binds to palindromic operator sites. The N-terminal region has a helix-turn-helix domain, and a C-terminal helix is implicated in EIICBGlc binding [ Seitz03 ]. Mlc forms tetramers in solution [ Gerber05 , Seitz03 , Nam01 ]. The Mlc monomer is composed of three domains: a DNA-binding motif (D-domain), an EIICBGlc-binding motif (E-domain), and an oligomerization domain (O-domain) [ Nam08 ].\nMlc is autoregulated [ Decker98 , Shin01 ], but it is also repressed and activated by CRP [ Shin01 ]. Mlc binds to sites with a length of 23 bp. Its consensus sequence has been determined [ Plumbridge01 ].\nThe intracellular concentration of Mlc is very limited [ Nam01 ]. Zinc mediates the Mlc repressor function [ Schiefner05 ]. Mlc has a high homology with the NagC transcriptional dual regulator (40% identity and 80% similarity) [ Hosono95 , Cho05 ]. At the post-transcriptional level, Mlc interacts with MtfA, which is involved in the regulation of the ptsG [ Becker06 ].\nMlc is a member of the ROK (repressor, ORFs, kinases) (NagC/XylR) family of proteins, which contains at least two distinct classes of proteins: xylose repressor (XylR) and a series of glucose/fructose kinases [ Titgemeyer94 , Hansen02 ]. "]
["mngR","\"mngR\"","MngR (FarR) belongs to the GntR family of transcriptional regulators. 2-O-α-Mannosyl-D-glycerate utilization is controlled by the divergently transcribed mngR gene and mngAB operon. MngR acts as a repressor of the expression both mngR and mngAB [ Sampaio04  ]. MngR is a negative DNA-binding transcriptional regulator for the TCA cycle. This regulator negatively auto-regulates its own synthesis in response to a long-chain fatty acid deficiency. As well, it exhibits weak binding to the citrate synthase, succinyl-CoA synthase, and lipoamide dehydratase promoters. The MngR binding-site consensus is a tandem repeat of TGTATTA(A/T)TT [ Quail94a  ]."]
["modE","\"modE\"","from uniprot: The modE-Mo complex acts as a repressor of the modABC operon, involved in the transport of molybdate. Upon binding molybdate, the conformation of the protein changes, promoting dimerization of ModE-Mo. The protein dimer is then competent to bind a DNA region, upstream of the modABC operon, which contains an 8-base inverted repeat 5'-TAACGTTA-3' flanked by two CAT boxes. Acts also as an enhancer of the expression of genes coding for molybdoenzymes, both directly and indirectly. ModE also interacts with tungstate."]
["mtlR","\"mtlR\"","This regulator participates in controlling several genes involved in mannitol utilization. MtlR is auto-regulated through the repression of the promoter upstream of the mtlADR operon. There is no protein family associated to this transcription factor. "]
["nac","\"nac\""," The Nac (nitrogen [N] assimilation control) transcriptional dual regulator, which belongs to the LysR family [ Muse98  ], has a helix-turn-helix motif located close to the N terminus [ Muse99  ]. This transcriptional regulator, which is negatively autoregulated [ Muse98  ], is encoded by the nac gene that is expressed in N-limiting conditions [ Camarena98  ]. In contrast with most LysR family members that are transcribed divergently from the gene that they regulate, nac is distant on the genome from its regulated gene [ Muse98  ].\n\nUnder N-limiting conditions, Nac without a coeffector regulates genes involved in N metabolism [ Muse98 ] through binding to a consensus sequence of 15 base pairs (ATA-N9-TAT) in the regulatory region of these genes [ Poggio02 ]. Using DNA microarray analysis, it was shown that Nac could affect the expression of 25 genes [ Zimmer00 ].\n\nThe affected genes by Nac are transcribed in a sigma70-dependent way. These genes are coupled to the N regulatory (Ntr) system, which is sigma54-dependent, through the Nac protein whose transcription is activated by NtrC [ Muse98 ]. "]
["nagC","\"nagC\"","This regulator belongs to the NagC/XylR family and participates in controlling several genes coding for catabolic enzymes [ Plumbridge98  ]."]
["narL","\"narL\""," The protein belongs to the LuxR/UhpA family. This regulator participates in the two-component regulatory system and controls the expression of several genes involved in anaerobic respiration and fermentation. It activates/represses several operons in response to nitrate/nitrite induction signals which are transmitted by NarX or NarQ. In this activated state phospho-NarL can act as both an activator of nitrate and nitrite reductase transcription and as a repressor of fumarate reductase transcription. Both actions switch anaerobic respiration to utilization of either nitrate or nitrite as electron acceptors. In the presence of nitrite the NarL protein is phosphorylated only by phospho-NarQ. The sensor protein NarX acts as a phospho-NarL phosphatase under these conditions, countering the sensor protein NarQ phosphorylation to some extent. [ Hoch95  , Walker93  , Egan91  ]\n\nOverproduction causes a drug resistance phenotype [ Hirakawa03 ]. "]
["nikR","\"nikR\""," NikR is the nickel-responsive repressor of the nikABCDER operon, which encodes a nickel-specific transport system [ De99  , Leitch07  ]. It is a member of the ribbon-helix-helix family of transcription factors [ Chivers99  ].\n\nThe NikR dimer/tetramer contains both high-affinity and low-affinity nickel-binding sites [ Helmann02 , Leitch07 ]; saturation of the high-affinity binding sites may lead to substantial binding to the nik operator, while nickel-binding to the low-affinity sites leads to a large increase in operator binding and an increased footprint size of NikR [ Chivers02 ]. DNA binding regulates coordination of nickel in NikR [ Carrington03 ].\n\nThe NikR protein can bind to a variety of divalent metal ions in addition to nickel; however, nickel binding selectively stabilizes the metal-protein complex [ Wang04 ]. The enhanced DNA binding affinity of the NikR-metal complex is also selective for nickel [ Bloom04 ]. "]
["ompR","\"ompR\"","from uniprot:The N-terminus of this protein is required for the transcriptional expression of both major outer membrane protein genes ompF and ompC; its C-terminal moiety mediates the multimerization of the ompR protein. As a multimer, it turns on the expression of the ompC gene; as a monomer, it turns on the expression of the ompF gene."]
["oxyR","\"oxyR\"","The protein belongs to the LysR family. This regulator participates in controlling several genes involved in the response to oxidative stress and the production of surface proteins that control the colony morphology and auto-aggregation ability. It regulates intracellular hydrogen peroxide levels by activating genes such dps, fur, and katG. OxyR is negatively autoregulated."]
["pdhR","\"pdhR\""," The PdhR (pyruvate dehydrogenase complex repressor) transcriptional dual regulator belongs to the GntR family of transcriptional regulatory proteins sharing sequence similarities in their N-terminal DNA-binding domain [ Haydon91  , Dong93a  ].\n\nThis transcriptional regulator, which is negatively autoregulated, is encoded by the pdhR gene [ Buck89 ].\n\nPdhR regulates genes involved in the pyruvate dehydrogenase complex of Escherichia coli [ Quail95 , Urbanowski00 ]. In the absence of pyruvate, the PdhR regulator binds to pdh promoter (Ppdh), and this repression is antagonized by its co-effector, pyruvate [ Quail95 ]. PdhR is responsible for constitutive synthesis of the PDH complex in response to pyruvate-limitation [ Haydon93 ].\n\nThe PdhR operator sequence determined from the pdh promoter was AATTGGTaagACCAATT [ Quail95 ]. "]
["phoB","A","The protein belongs to the two-component family. Phosphate regulon transcriptional regulatory protein PhoB is a member of the two-component regulatory system PhoR/PhoB. The PhoR/PhoB system is involved in the regulation of the phosphate regulon gene expression. Under conditions of phosphate limitation the PhoB protein is phosphorylated by phospho-PhoR. In this phosphorylated state phospho-PhoB acts as a transcriptional activator of the Pho regulon. There are also two phosphate-independent signal transduction pathways that control the Pho regulon. These controls are regulated by the carbon and energy source. The catabolite sensor kinase-phosphotransferase CreC can phosphorylate PhoB in one pathway. In the other acetyl phosphate is required, as well as another sensor kinase. [ Hoch95  , Makino89  , Hiratsu95  , Wanner93  , Kim96  ]."]
["phoP","\"phoP\"","Transcriptional regulatory protein PhoP is a member of the two-component regulatory system PhoQ/PhoP. In E. coli this system is believed to play a role in Mg++, or other divalent cation, starvation response and stress. The gene(s) that may be regulated by the PhoP protein have not been identified. [ Groisman92  , Waldburger96  , Kasahara92  ]"]
["prpR","\"prpR\"","PrpR (propinate regulator) is a member of the sigma54-dependent activator family and participates in controlling several genes involved in propionate catabolism. It consists of two domains, an amino-terminal domain involved in effector recognition and a carboxy-terminal DNA-binding domain [ Palacios00  ]. PrpR is negatively autoregulated, sensitive to catabolite control, and activates the transcription of the prpBCDE operon [ Lee05  ]. PrpR binds to the palindromic sequence 5'-CGGGAAC-GTTCCCG-3' [ Lee05  ]."]
["purR","\"purR\"","PurR is a protein that belongs to the GalR/LacI family. This regulator participates in controlling several genes involved in de novo purine nucleotide biosynthesis. PurR necessarily binds hypoxanthine and guanine to become active. This protein represses the transcription of several operons and genes like codBA, cvpA-purF-ubiX, gcvTHP, glnB, guaBA, purC, purEK, purHD, purMN, ycfC-purB, and others."]
["putA","\"putA\"","The PutA protein is a bifunctional enzyme and a transcriptional repressor of the put (proline utilization) regulon, belonging to the PutA family. The proline dehydrogenase activity resides in the amino terminal 669 amino acids of PutA; a truncated protein retains proline dehydrogenase and DNA binding activity, but lacks membrane association and 1-pyrroline-5-carboxylate dehydrogenase activity [ Vinod02  ]. The amino-terminal 47 residues contain the dimerization domain and the specific DNA binding activity [ Gu04  ]."]
["qseB","\"qseB\"","from uniprot: Member of a two-component regulatory system qseB/qseC. Activates the flagella regulon by activating transcription of flhDC. Currently it is not known whether this effect is direct or not."]
["rbsR","\"rbsR\"","RbsR belongs to the GalR/LacI family. This regulator participates in controlling several genes involved in ribose metabolism. RbsR represses the transcription of the rbsDACBK operon. When D-ribose binds to RbsR, the protein becomes inactive."]
["rcsArcsB","\"rcsArcsB\"","from rcs:positive regulator of capsular polysaccharide synthesis.The binding site length comes from a single reference [ Ebel99  ]. The amount of RcsA protein is limited both by its rapid degradation by Lon, an ATP-dependent protease, and by its low level of synthesis. RcsA is degraded in a Lon-dependent fashion. RcsA belongs to the LuxR/UhpA protein family. RCSB: http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=RCSB-MONOMER  Regulator protein RcsB is a member of the two-component regulatory system RcsC/RcsB [ Stout94  , Jayaratne93  , Brill88  ]. It is involved in the activiation of colanic acid capsule synthesis (cps) and cell division (ftsZ) genes [ Wehland00  , Stout94  , Sledjeski96  , Brill88  , Carballes99  ]. Based on its homology to other regulator proteins in E. coli, it is believed that the RcsB protein is activated through phosphorylation,  probably by the sensor protein RcsC [ Gupte97  ]. However, direct phosphorylation of RcsB by RcsC has not been shown. The RcsF protein may also be capable of phosphorylating RcsB. Once activated, the RcsB protein is a positive regulator of capsule synthesis and cell division [ Wehland00  , Stout94  , Sledjeski96  , Brill88  , Carballes99  ]. Regulator protein RcsB complexes with the RcsA protein (forming a heterodimer) for capsule synthesis activation [ Wehland00  , Gottesman91  , Stout94  ]. RcsB activates the fts genes independently (in the form of a homodimer) [ Gervais92  ].  "]
["rhaR","\"rhaR\"","RhaR is a protein that belongs to the AraC/XylS family. This regulator participates in controlling several genes involved in L-rhamnose catabolism. It is autoregulated through activation of the promoter upstream the rhaSR operon."]
["rob","C","Rob is a protein that belongs to the AraC/XylS family. Rob forms a nucleoprotein structure at the E. coli replication origin for the initiation of the replication. Rob also participates in controlling several genes involved in resistance to antibiotics, organic solvents, and heavy metals. This protein activates the transcription of fumC, inaA, marRAB, nfo, sodA and zwf. A microarray analysis for Rob of Escherichia coli was done by [ Martin02  ]."]
["rpoD","A","Sigma 70 is the primary sigma factor during exponential growth, targeting RNA polymerase sigma 70 to a wide range of promoters that are essential for normal growth. \nSigma 70 is the predominant sigma factor during exponential growth [ Jishage96  ]. Changes away from typical growth conditions, such as heat shock or growth into stationary phase, lead to the replacement of sigma 70 with other sigma factors in the RNA polymerase holoenzyme complex [ Blaszczak95  , Ozaki91  , Wade04  ]. When this occurs, the holoenzyme no longer recognizes the same transcription targets, leading to a decline in many RNA and protein levels, including components of the protein synthesis machinery [ Osawa81  , Fujita87a  , Magnusson03  ]. \nSigma 70 has the strongest interaction with the RNA polymerase core complex of all the known sigma factors [ Maeda00  ]. This interaction may in fact be required for sigma 70 to bind DNA, as its amino-terminal portion normally blocks such binding in the absence of core complex [ Dombroski92  ]. When it does bind promoter DNA, sigma 70 contacts both the -10 and -35 regions simultaneously, with a binding affinity depending on the spacing between these points [ Dombroski96  ]. In promoters with a -35 site, sigma 70 is more effective when there is also a proximal half-site or a complete UP element, whereas the stationary phase sigma, RNA polymerase, sigma S (sigma 38) factor , has opposite selectivity [ Typas05  ]. Both sigma 70 and RNA polymerase, sigma S (sigma 38) factor compete for available core complex during stationary phase growth [ Farewell98  ]. Sigma 70 also competes with NusA for binding to RNA polymerase, core enzyme , though sigma 70's affinity for the core drops off dramatically during the change from transcriptional initiation to elongation [ Gill91  , Traviglia99  ]. Sigma 70 even competes with the nascent RNA strand for binding to RNA polymerase, core enzyme [ Daube99  ]. The majority of early elongation complexes do appear to retain sigma 70 for a while, with this retention being promoted by promoter-like sequences in the initial transcribed region [ Kapanidis05  ]. These sequences, bearing similarity to -10 promoters, can induce sigma 70-mediated pausing of RNA polymerase sigma 70 [ Mooney03  , Nickels04  ]. Notably, promoters recognized by sigma 70 occur in regions rife with such promoter-like sequences [ Huerta03  ]. \nSigma 70 function is blocked by the anti-sigma factor, stationary phase protein, binds sigma 70 RNA polymerase subunit . \nSigma 70 has undergone significant structural analysis. A crystal structure of sigma 70 has been determined to 2.6 Å resolution, revealing that residues that bind core polymerase are on one face, with DNA-binding residues on the other [ Malhotra96  ]. Most of sigma 70 must be present to allow promoter melting [ Young04  ]. Within sigma 70, there are conserved motifs responsible for binding to the -10 and -35 and other promoter regions [ Siegele89  , Gardella89  , Poznanski03  , Kumar93  , Sanderson03  ]. Region 1.2 of sigma 70 is responsible for recognition of the -10-like pause regions described above, as well as recognition of the fork junction and actual promoter-proximal pausing [ Zenkin07  ]. A region of sigma 70 that partially blocks the RNA exit channel in the holoenzyme is involved in binding the 3' initiating nucleotide in the active site and aids in promoter clearance [ Kulbachins06  ]. A crystal structure of RNA polymerase sigma 70 has been determined to 9.5 Å resolution [ Finn00  ]. Sigma 70 undergoes conformational change when it binds to the core complex, revealing the sigma factor's DNA-binding surfaces, then undergoes another change on promoter melting [ Callaci98  , McMahan99  , Gruber01  ]. RNA polymerase, α subunit interacts with sigma 70 at a subset of UP and activator-dependent promoters [ Chen03  ]. Interaction between RNA polymerase, β' subunit and sigma 70 promotes sigma 70 interaction with the nontemplate strand in the -10 region, while interaction between RNA polymerase, β subunit and sigma 70 acts to block extension of nascent RNA, and thus must be disrupted to allow elongation to occur [ Young01  , Nickels05  ]. The interaction of sigma 70 with activator proteins has also been addressed in detail [ Kumar94  ]."]
["rpoE","A"," Sigma E is a minor sigma factor, specializing in responses to the effects of heat shock and other stresses on membrane and periplasmic proteins. It is regulated by a multistep protease system that sense disruptions in those proteins. Its transcriptional initiation targets include another minor sigma factor, Sigma 32.Sigma E drives transcription of a number of genes whose functions revolve around heat shock and misfolded proteins. Notably, Sigma E is induced by heat shock and is required for heat-induced transcription of rpoH, which codes for the heat-shock factor Sigma 32 [ Ades03 , Erickson87 , Wang89 ]. Sigma E is also required for transcription of degP, which codes for a protease that degrades abnormal proteins in the periplasm [ Lipinska88 , Erickson89 , Hiratsu95 ]. Both rpoH and degP are induced at high temperature [ Erickson89 ]. Sigma E also initiates transcription of the peptidyl-prolyl cis-trans isomerase FkpA, which also acts as a chaperone in the periplasm [ Danese97 ]. In addition to these specific genes, a number of additional targets for Sigma E have been identified [ Dartigalon01 , Rezuchova03 , Rhodius05 ].A number of cellular stresses other than heat shock also induce Sigma E. Sigma E is induced in response to increased expression of as well as misfolding of outer membrane proteins (OMPs) [ Mecsas93 ]. Other inducers include hyperosmotic shock, metal ion exposure, and changes in outer membrane lipopolysaccharide structure [ Bianchi99 , Egler05 , Tam05 ]. Sigma E is also induced by the starvation signal ppGpp on entry into stationary phase [ Costanzo06 ].\nrpoE expression is regulated by a multistep system that allows increased transcription in response to unassembled or misfolded proteins, in addition to initiating its own transcription at at least one of its promoters [ Rouviere95 , Raina95 ]. Binding of unassembled OMPs to the protease DegS stimulate its cleavage of the regulatory protein RseA [ Walsh03 , Alba01 ]. The destabilized RseA is then degraded by YaeL [ Kanehara02 ]. As RseA normally tethers Sigma E to the membrane with the aid of RseB, its degradation releases Sigma E to allow it to interact with RNA polymerase, core enzyme and initiate transcription [ Tam02 , Ades03 , Collinet00 , Missiakas97 , De97 , Alba01 ].\nA structure of Sigme E complexed with RseA to 2 Å resolution shows that RseA sterically blocks surfaces required for binding to RNA polymerase, core enzyme [ Campbell03a ].\nSigma E is required for resistance to zinc, cadmium and copper, as well as for growth at high temperature [ Egler05 , Rouviere95 , Hiratsu95 ]. It is also required for growth at normal temperature, but an unlinked suppressor mutation almost always occurs to allow such growth when rpoE function is lost [ De97a ].\nOverexpression of Sigma E appears to prompt lysis of dead cells during stationary phase [ Nitta00 ]. Sigma E-dependent gene expression during stationary phase has been studied [ Kabir05 ]. "]
["rpoH","A"," Sigma 32 is the primary sigma factor controlling the heat shock response during log-phase growth. It is subject to tight control via a multivalent regulatory system that measures temperature and the abundance of misfolded proteins within the cell.\nSigma 32 is the sigma factor controlling the heat shock response. Its levels rise, plateau and then drop following a heat shock, causing a similar induction in expression in heat shock genes [ Zhao05 , Yamamori82 , Tobe84 , Zhou88 , Grossman84 , Yura84 ]. Large-scale identification of Sigma 32 transcriptional targets has been carried out [ Zhao05 , Nonaka06 ]. The consensus promoter for Sigma 32 initiation is TNtCNCcCTTGAA at -35 and CCCCATtTa at -10, where lowercase letters indicate a tendency toward, but not an absolute requirement for, a certain nucleotide at that location [ Cowing85 ]. Notably, recent work indicates that Sigma 32 may only be involved in heat shock that occurs during log-phase, aerobic growth, with entirely different systems accounting for heat shocks during stationary phase and anaerobic growth [ DiazAcosta06 ].\nSigma 32 is also responsible for genetic responses to other environmental insults. Ethanol, alkaline pH changes and hyperosmotic shock all induce the Sigma 32-dependent heat shock response [ VanBogelen87 , Taglicht87 , Bianchi99 ]. In addition, Sigma 32 is induced by carbon starvation [ Jenkins91 ].\nSigma 32 regulation is a multivalent process consisting of transcriptional, translational and postranslational controls.\nrpoH is transcribed from two constitutive Sigma 70-driven promoters, as well as at least one heat-shock responsive promoter and one Sigma 24-driven promoter [ Erickson87 , Fujita87 , Wang89 , Erickson89 ]. Three of the rpoH promoters are suppressed by DnaA binding [ Wang89a ]. rpoH transcription does not depend on Sigma 32 [ Tilly86 ].\nSigma 32 abundance is regulated at the translational level via mRNA secondary structure. Two sequences in the rpoH mRNA, one near the translation start site and one internal, form a secondary structure element that is disrupted by higher temperatures, allowing translation [ KamathLoeb91 , Nagai91 , Yuzawa93 , Morita99 , Morita99a ].\nSigma 32 is regulated post-translationally via degradation and by direct inhibition of its activity [ Grossman87 ]. Sigma 32 is very unstable, with a half life that drops as temperature rises, ranging from 1-4 minutes [ Grossman87 , Tilly89 , Morita00 ]. Sigma 32 is stabilized in the absence of the chaperone protein GroES and by the presence of abnormal proteins [ Kanemori94 , Kanemori94a ]. Degradation of Sigma 32 depends on HflB, integral membrane ATP-dependent zinc metallopeptidase and HslVU protease [ Kanemori97 ]. Sigma 32 has greater affinity for RNA polymerase, core enzyme than Sigma 70 at high temperatures due to unfolding of Sigma 70. The DnaJ/DnaK/GrpE complex assists Sigma 70 in refolding, which in turn displaces Sigma 32, effectively downregulating Sigma 32 activity [ Blaszczak95 ]. Sigma 32 activity is also directly controlled by the DnaJ/DnaK/GrpE complex as part of an ATP-driven binding and release cycle. When DnaJ/DnaK/GrpE is occupied by substrates such as misfolded proteins, it is not available to bind Sigma 32 and limit its activity [ Gamer96 , Tomoyasu98 , Tatsuta98 , Gamer92 ]. In this way, Sigma 32 activity is tied directly to the level of misfolded proteins in the cell. CbpA and the GroEL/S chaperone can also both limit Sigma 32 activity in the same manner [ Tatsuta98 , Guisbert04 ].\nSigma 32 activity can also be attenuated via phosphorylation [ Klein03 ].\nConserved region 2 of Sigma 32 is heavily involved in its activity and regulation. Region 2.2 is involved in interaction with the RNA polymerase, core enzyme , along with other portions of the protein [ Joo97 , Joo98 ]. Region 2 is important for FtsH-mediated degradation [ Bertani01 ]. Sigma 32 becomes more flexible as temperature rises, and in particular region 2 appears to undergo a reversible unfolding [ Rist03 ]. Region 2.1 is involved in Sigma 32 stability and its transcriptional efficacy [ Horikoshi04 , Obrist05 ].\nrpoH mutants suffer a number of ills in addition to failure of the heat shock response. They are deficient in cell division at higher temperatures and sensitive to oxidative stress at any temperature [ Tsuchido86 , Kogoma92 ]. Both F and mini-F plasmid replication depend on Sigma 32 and fail in its absence [ Wada86 , Wada87 ]. In rpoH mutants, newly synthesized protein aggregates readily even under normal growth conditions [ Gragerov91 ].\nSigma 32 has been evaluated via linker insertion mutational analysis [ Narberhaus03 ].\nWhereas Sigma 70-directed transcription is rifampicin sensitive, Sigma 32-directed transcription is partially rifampicin resistant [ Wegrzyn98 ]. "]
["rpoN","A"," Sigma 54 controls expression of nitrogen-related genes, directing RNA polymerase sigma 54  to the consensus nitrogen promoter.\nSigma 54 is the sigma factor controlling nitrogen-regulated and other nitrogen-related promoters [ Hunt85 , Reitzer87 ]. It copurifies with the RNA polymerase core enzyme and binds to the consensus nitrogen promoter [ Hirschman85 , Hunt85 ]. It is also involved in the nitric oxide stress response [ Gardner03 ]. During typical exponential and stationary phase growth, the amount of sigma 54 present in the cell is one tenth that of the amount of sigma 70 [ Jishage96 ]. The metabolic context of genes dependent on sigma54 for transcription is reviewed in [ Reitzer01 ].\nSigma 54 activity is activator dependent, requiring NtrC-Phosphorylated transcriptional dual regulator to initiate transcription.\nIn some sigma 54-dependent promoters, DNA bending occurs, allowing NtrC-Phosphorylated transcriptional dual regulator to reach the translational start site [ Carmona96 ]. It has been suggested, however, that DNA bending related to sigma 54 is not as extreme as originally reported [ Schulz98 ]. Sigma 54 has also been alternately reported to remain bound to the promoter after RNA polymerase departs during transcript elongation, or to separate from the promoter between each round of transcription [ Tintut95 , Bondarenko02 ].\nThe binding affinity of RNA polymerase sigma 54 for several target promoters has been evaluated [ Vogel02 ].\n\nSigma 54 has a number of structural features that affect its activity. It has a pair of leucine zipper motifs that are involved in promoter melting, as well as an acidic region that has a role in the same process and a carboxy-terminal helix-turn-helix motif that is required for promoter recognition [ SasseDwigh90 , Wong92 , Wong94 ]. A strongly acidic hydrophic repeat region is required for binding to RNA core polymerase [ Tintut94 , Hsieh94 ]. Four leucines in the amino-terminal region are required for NtrC-Phosphorylated transcriptional dual regulator regulation of sigma 54 activity [ Wang95a , Syed97 ]. Sigma 54 binds to the core polymerase via a region that is very similar to sigma70 [ Tintut95a , Oguiza97 ].\n\nThe structure of sigma 54 has been evaluated via scanning force microscopy [ Rippe97 ]. Additional examination via x-ray scattering microscopy shows that sigma 54 and sigma 70 share broad structural similarity [ Svergun00 ]. A 24 Å cryo-electron structure of sigma 54 holoenzyme reveals major conformational changes during DNA binding [ Ray05 ]. "]
["rpoS","B","rpoS encodes the alternative sigma factor σS, a subunit of RNA polymerase that acts as the master regulator of the general stress response in E. coli.\n\nσS is homologous to the housekeeping sigma factor σ70 and recognizes similar consensus promoter sequences [ Gaal01 , Checroun04 ]. Discrimination between σS and σ70 promoters may be achieved by tolerating different levels of deviation from the consensus [ Gaal01 ] and non-optimal spacing between the -35 and -10 elements [ Typas06 ]. The presence and location of UP-elements [ Typas05 ] and-35 region elements [ Rosenthal06 ] may also influence usage of a subset of promoters. Genome-wide analyses of RpoS-dependent gene expression showed that up to 10% of the genes in E. coli are under direct or indirect control of σS [ Patten04 , Weber05 ]. The effect of σS on E. coli metabolism has been investigated [ Rahman06 ].\n\nPolymorphisms in rpoS that affect fitness across different environments are commonly found in E. coli [ NotleyMcRo02 , Zinser04 , King06 ].\n\nσS is itself subject to complex regulation at all levels (transcription, translation, activity, and protein degradation), thereby allowing integration of multiple stress signals in the cell. The regulatory mechanisms and signals are summarized below.\n\nTranscription: Transcription of rpoS is repressed by the phosphorylated response regulator ArcA [ Mika05 ]. During entry into stationary phase in complex medium, transcription of rpoS increases 5-10 fold [ Mulvey90 , Lange94 , Takayanagi94 ], but this effect is limited in defined medium [ Mandel05 ]. cAMP-CRP negatively controls rpoS transcription [ Lange94 ]. The BarA regulator is required for exponential phase induction of rpoS transcription [ Mukhopadhy00a ], and ppGpp has a positive effect on the basal level of σS synthesis [ Gentry93 , Hirsch02 ], affecting transcription elongation, but not initiation [ Lange95 ].\n\nmRNA stability and translation: The rpoS mRNA contains a long untranslated 5' region which plays an important role in the regulation of its stability and translation [ Cunning98 ]; a review by Majdalani et al. ([ Majdalani05 ]) summarizes the current knowledge with respect to small RNA regulators. Many factors have been shown to influence formation of secondary structures, translation and degradation of rpoS mRNA: H-NS binds to rpoS mRNA and enhances its cleavage [ Brescia04 ], while the DsrA small RNA stabilizes it [ Lease00 ]. rpoS mRNA stability during glucose starvation is diminished in the absence of RNase III function [ Freire06 ]. Hfq is required for translation of the rpoS mRNA [ Muffler96 ], whereas the OxyS small RNA represses translation of rpoS, possibly by altering Hfq activity [ Zhang98a ]. HU [ Balandina01 ] and the RprA small RNA [ Majdalani02 ] each stimulate translation of rpoS. Starvation for phosphorus leads to accumulation of σS due to increased translation of rpoS mRNA. The upregulation is dependent on Hfq and may therefore involve an as yet unidentified small RNA [ Ruiz03 ]. LrhA represses translation of rpoS in an Hfq-dependent manner, which may also involve an unidentified small RNA [ Peterson06 ]. 24 nucleotides of the ribosome binding site were shown to be necessary and sufficient for a 10-fold increase in rpoS translation [ Hirsch05 ].\nProtein activity: 6S RNA activates transcription from several σS-dependent promoters while not affecting the levels of rpoS transcription or σS protein [ Trotochaud04 ]. The alarmone ppGpp enhances the ability of σS to compete with σ70 for binding to core RNA polymerase [ Jishage02 ]; the Rsd protein appears to serve a similar function [ Jishage99 ]. Nitrogen starvation induces σS-dependent gene expression [ Gyaneshwar05 ], although levels of σS are only increased approximately twofold [ Mandel05 ], suggesting that nitrogen starvation acts at the level of σS activity [ Peterson05 ]. Crl transcriptional regulator enhances σS actvity by increasing its ability to compete for RNA polymerase, core enzyme [ Typas07 ].\nProtein degradation: In exponentially growing cells, the energy-dependent ClpXP protease degrades σS rapidly [ Schweder96 ]. The RssB protein is required for rapid proteolysis of σS; it acts as a direct recognition factor, facilitating degradation of σS by the ClpXP protease [ Becker99 ]. poly(A) polymerase I [ Santos06 ] as well as IraP [ Bougdour06 ], Crl transcriptional regulator [ Typas07 ], and H-NS [ Zhou06 ] modulate the effect of RssB. rssB transcription is itself controlled by σS [ Ruiz01 ]. Acetyl phosphate is able to transfer a phosphate group to the Asp-58 residue of RssB and activate it [ Bouche98 ], although the phosphorylation level of RssB does not appear to play a role in signalling carbon starvation [ Peterson04 ]. Carbon starvation leads to accumulation of σS due to stabilization of the protein [ Zgurskaya97 , Mandel05 ]; the molecular signal has not yet been determined [ Peterson05 ].\nSelected reviews: [ HenggeAron02 , Repoila03 , Venturi03 , Majdalani05 , Magnusson05 , Ferenci05 , Peterson05 , Klauck07 ].\nCrl is a new thermosensor identified in Escherichia coli RpoS regulon, which interacts directly with σS promoting the binding of the EσS to the csgBp promoter [ Bougdour04 ].\nFlores, N et al. (2007) identified a new role for RpoS as controller of almost all the glycolytic genes in Escherichia coli strains lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system. In addition, they were able to identify genes whose products participate in the ppGpp metabolism, which were also controlled by RpoS. On the other hand, relA is not transcribed by this factor. Finally, an additional factor to RpoS was involved in the spot and gpp gene expression [ Flores07 ].\n\n"]
["sdaR","“sdaR”"," The SdaR (sugar diacid regulator) or CdaR (carbohydrate diacid regulator) positive regulator, which is a member of the XylR family, is a monomer (43.68 KDa) constituted by two domains: Diac_rec and HTH [Monterrubi00]. This transcriptional regulator is encoded by the sdaR operon, which is positively autoregulated [Monterrubi00].\n\nAlthough the exact position and sequence to which SdaR binds to regulate has not been determined, its regulatory effect has been characterized as the carbohydrate diacid regulon. SdaR responds to D-galactarate, D-glucarate, and even better to D-glycerate, to activate the operons that encode the enzymes that process these types of diacid carbohydrates (sdaR, gudPXD, garPLRK-rnpB, and garD) [Monterrubi00]. In addition, SdaR coregulates with FNR. In another publication, it was found that the 2-O-a-mannosyl-D-glycerate (MG) can induce the SdaR regulon [Sampaio04]. MG has been recognized as an osmolyte in hyperthermophylic prokaryotes and as a carbon source for E. coli K12 [Sampaio04]. "]
["soxR","\"soxR\""," SoxR belongs to the MerR family of transcriptional regulators. Each SoxR polypeptide contains a [2Fe-2S] cluster that senses the redox state of the cell. Both Fe-bound and apo-SoxR bind to the promoter region, but only Fe-SoxR activates soxS transcription [ Hidalgo94  ]. The redox state of the iron-sulfur cluster regulates SoxR activity [ Hidalgo97  , Gaudu97  ]. Proteins that may be involved in returning SoxR to the reduced state have been identified [ Koo03  ].\n\nSoxR acts at a single binding site to simultaneously activate transcription of soxS and repress transcription of the soxR gene [ Hidalgo98 ]. The SoxS protein in turn regulates several other genes involved in the response to oxidative stress.\n\nThe active form of SoxR is a homodimer [ Wu95a ].\n\nReviews: [ Demple99 , Zheng00 , Touati00 , Kiley03 ] "]
["soxS","\"soxS\""," The SoxS protein belongs to the AraC/XylS family. This regulator participates in controlling several genes involved in the response to oxidative stress. SoxS facilitates the binding of RNA polymerase to some promoters. It activates the transcription of the following genes/operons: acrAB, fldA-fur, fpr, fumC, fur, inaA, marRAB, nfo, sodA and zwf. Transcription is induced upon biofilm formation [ Ren04  ].\n\nThe SoxS protein is unstable due to proteolytic degradation; the protein is stable in a lon ftsH double mutant. The instability provides a mechanism for rapid shut-off of the transcriptional response once the inducing conditions have subsided [ Griffith04 ]. "]
["srlR","D","It is a transcriptional repressor for the glucitol utilization. It belongs to the DeoR family of transcriptional regulators. GutR is required for the repression of the expression of the srlAEBD-gutM-srlR-gutQ genes."]
["tdcA","\"tdcA\"","TdcA belongs to the LysR family. This regulator participates in controlling several genes involved in amino acid degradation. TdcA activates the operon tdcABCDEFG."]
["tdcR","\"tdcR\"","TdcR is a regulator that participates in controlling the expression of several structural genes for the enzyme threonine dehydratase. TdcR activates the tdcABCDEFG operon."]
["torR","\"torR\"","from uniprot: Member of the two-component regulatory system torS/torR involved in the anaerobic utilization of trimethylamine-N-oxide (TMAO). Phosphorylated torR activates the transcription of the torCAD operon by binding to four decameric boxes located in the torCAD promoter. Box1, 2 and 4 contain the DNA sequence 5'-CTGTTCATAT-3' and box3 contains the DNA sequence 5'-CCGTTCATCC-3'. Phosphorylated as well as unphosphorylated torR negatively regulates its own expression by binding to box1 and 2."]
["trpR","\"trpR\"","from uniprot: This protein is an aporepressor. When complexed with L-tryptophan it binds the operator region of the trp operon (5'-ACTAGT-'3') and prevents the initiation of transcription. The complex also regulates trp repressor biosynthesis by binding to its regulatory region."]
["tyrR","\"tyrR\"","The protein belongs to the EBP family. This regulator participates in controlling several genes involved in the biosynthesis and transport of aromatic amino acids. The amino acids phenylalanine, tyrosine, and tryptophan are TyrR effectors. This protein regulates negatively the following genes and operons: aroP, aroL-yaiA-aroM, aroG, tyrR, aroF-tyrA and tyrB. TyrR also regulates positively the mtr gene and dually the tyrP gene."]
["uidR","\"uidR\""," UidR is a transcriptional repressor that contains one helix-turn-helix tetR-type DNA-binding domain and controls the expression of genes responsible for the utilization of glucuronides. This protein is encoded by the uidR gene, which is located upstream of the uidABC operon. UidR is negatively autoregulated, sensitive to catabolite control [ Blanco85  ], and represses the transcription of the uidABC  operon [ Blanco86  , Ritzenthal83  , Blanco87  ], which codes for a beta-glucuronidase protein (UidA), a proton-dependent transporter specific for alpha- and beta-glucuronides (UidB), and a protein that improves the efficiency of transport by UidB (UidC).\n\nAlthough little is known about the mechanism of regulation of UidR, it has been shown to act as a repressor and bind to a putative inverted repeat sequence in a cooperative process with UxuR [ Blanco86 , Ritzenthal83 ]. "]
["uxuR","\"uxuR\"","UxuR is a protein that belongs to the GntR family and participates as a regulator in controlling several genes involved in carbon uptake. UxuR negatively controls the expression of the uxuBA operon [ Blanco86a  ]."]
["xylR","\"xylR\"","XylR is a protein that belongs to the AraC/XylS family. This regulator participates in controlling several genes involved in xylose utilization. XylR activates the xylAB and xylFGHR operons."]
["ydeO","\"ydeO\""," YdeO belongs to the AraC/XylS family of transcriptional regulators [ Masuda02  , Masuda03  ]. This protein consists of two domains, an amino-terminal domain involved in coinducer recognition and dimerization, and a carboxy-terminal domain that contain a potential helix-turn-helix DNA-binding motif [ Gallegos97  ].\n\nAnalysis of microarrays showed that YdeO is a regulator involved in the cellular response to acid resistance [ Masuda02 , Masuda03 , Ma04 ]. In addition this regulator activates the transcription of the gadE gene, which comprises an essential activator of the gadA and gadBC genes [ Ma04 ]. "]
["yeiL","\"yeiL\"","YeiL is the third member of CRP/FNR family in Escherichia coli and is a positive DNA-binding transcriptional regulator of nucleoside metabolism. The transcription-regulatory activity of YeiL was suggested by analogy with FNR and it might be modulated by a sensory iron-sulfur cluster and/or by reversible disulfide bond formation. YeiL expression increases during stationary phase, is RpoS-dependent and is positively autoregulated, positively activated by Lrp (and IHF in the absence of FNR), and negatively regulated by FNR [ Anjum00  ]."]
["zraR","\"zraR\"","ZraR is a protein that belongs to the EBP family. This regulator is a member of the two-component regulatory system ZraS/ZraR to control the expression of genes related with the activity of the enzyme hydrogenase 3. ZraR activates the zraP gene and the zraSR operon, and acts in conjunction with sigma54 as a transcriptional activator [ Leonhartsb01  , Stoker89  , Bairoch  ]."]

{"sheet":"B subtilis DB","index":1,"n_rows":73,"n_cols":3,"rows_kept":73,"cut":false,"hidden":false,"merged":[],"flags":["formulas_cached_only"]}
["B subtilis DB"]
["Dynamical module","gene name","DESCRIPTION IN DBTBS AND/OR SWISPROT AND/OR BACILIST"]
["E","comk","Positive autoregulatory gene occupying a central position in the competence-signal-transduction network; CTF = competence transcription factor. Typically, more than one ComK binding site is found in each promoter, with distances of 8, 18, or 31 basepairs between them."]
["E","rok","repressor of comK (FROM SWISSPROT:034857) repressor of comK "]
["D","sigh","RNA Polymerase Sigma-30 Factor (Sigma-H). Non-essential sigma factor involved in expression of vegetative and early stationary-phase genes"]
["D","spo0a","a key bi-functional regulator to control developmental transcription activities. Increases its affinity after phosphorylation (phosphorelay system). Spo0F is required for the phosphorylation. Two-domain structure. Binding consensus is called 0A box and can be located downstream of the initiation site. Often, two adjacent boxes are found. These listed sites might be viewed in its complementary strand."]
["D","abrb","Bi-functional; expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation; acts as the Spo0A-AbrB circuit; also involved in catabolite repression."]
["C","resd","resD seems to form a two-component signal transduction system with resE and plays a regulatory role in respiration. Interactions with resABCDE operon and ctaA may be indirect"]
["C","phop","PhoP is phosphorylated by PhoR sensor kinase. PhoP~P binds to DNA only(?) under phosphate starvation condition. A consensus core PhoP-binding region composed of four TT(A/T)ACA direct repeats each separated by 5+-2 non-conserved nucleotides was identified."]
["B","spovt","a bi-functional factor which acts both positively and negatively in controlling sigma G-dependent gene expression. Homologous to AbrB (FROM SWISSPROT P37554) Positive and negative transcriptional regulator of sigma G-dependent genes. May provide a mechanism of feedback control that is important for forespore development."]
["B","sigg","RNA polymerase sporulation-specific sigma factor (Sigma G). Control of transcription in the forespore at late stages of sporulation. Null mutations prevent activation of Sigma K. Inactive in a spoIIIA mutant."]
["A","sigd","RNA polymerase Sigma-28 factor (Sigma D). Autolytic enzymes; defect in flagellar synthesis.(FROM SWISSPROT P10726)Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This alternative sigma factor is required for the transcription of the flagellin and motility genes as well as for wild-type chemotaxis."]
["A","siga","RNA polymerase major Sigma-43 factor (Sigma A). Essential gene."]
["--","yvrh","As the sequence data of the yvrGH genes was corrected, the former gene yvrH was divided into two genes, yvrHa and yvrHb. The latter functions as a response regulator of a two-component system, with yvrG acting as the Class IIIA sensor kinase."]
["--","sigb","RNA Polymerase Sigma-37 Factor (Sigma-B). General stress factor sigma."]
["--","adaa","adaptative response to DNA alkylation; positive regulation of the adaAB operon"]
["--","sigf","RNA polymerase sporulation-specific sigma factor. Synthesized shortly after the onset of sporulation but do not become active until after polar division; transcription reduced, and probably activation impeded, in hyperosmotic conditions; moving this gene in the 30% region of the chromosome trapped in the forespore during a short interval is sufficient to produce spores in the absence of SpoIIA and SpoIIE."]
["--","sige","RNA polymerase sporulation-specific sigma-29 factor. Inactive precursor, processed by SpoIIGA after Tyr-27; synthesized shortly after the start of sporulation but do not become active until after polar division; expression negatively regulated by sigma-K; disappears in the forespore shortly after septation through a SpoIIIE-dependent process, probably by selective degradation of both SigE and SpoIIGA; pro-sigma-E associated with the cytoplasmic membrane in the predivisional sporangium, then accumulated at the mother cell side of the sporulation septum, and mature sigma-E distributed throughout the mother cell cytoplasm; transcription reduced, and probably processing impeded, in hyperosmotic conditions."]
["--","pyrr","Involved in repression of the pyr operon by transcriptional attenuation in the presence of excess UTP. Tight binding to the pyr mRNA requires the (C)NGNGA sequence."]
["--","purr","a purine repressor which mediates adenine nucleotide-dependent regulation of pur operon. GAAC-N24-GTTC motif seems necessary for its binding but this motif was not required for its binding to purA"]
["--","ywfk","(FROM SUBTILIST BG10635) function unknown. similar to transcriptional regulator (LysR family). (FROM SWISPROT P39647) Contains 1 HTH lysR-type DNA-binding domain."]
["--","sens","shows partial homology with the N-terminal core binding domain of sigma factors and a helix-turn-helix motif. Stimulates the expression of several extracellular protein genes during the onset of stationary phase. The 9bp sequence TTTAGATAA might be the binding consensus"]
["--","rsfa","A bi-functional transcriptional regulator of genes dependent on SigF (and possibly SigG) in the prespore. Similar to regulatory leucine zipper proteins."]
["--","ansr","helix-turn-helix type repressor; regulates the immediately upstream ans operon.(FROM SWISPROT Q07683) Transcriptional repressor for the ans operon coding for L-asparaginase and L-aspartase. NH4(+) may influence this repression."]
["--","rocr","NtrC/NifA transcriptional activator (cf. LevR). Sigma 54-dependent activators generally bind two inverted repeat sequences called UAS, which are located approx. 100bp upstream from the -12/-24 promoters. DNA bending is used for activation (AhrC may be involved). Inducible by ornithine or citrulline? At least upstream UAS1 is the target of RocR"]
["--","xre","repressor of a phage-like bacteriocin, PBSX (phibacin damaged-prophage). Helix-turn-helix protein. Acts at the operator-promoter region."]
["--","tnra","Positively regulates many genes for degrading nitrogen-containing compounds but negatively regulates glnR. Binds to the same sequence with GlnR (repressor)"]
["--","yvba","(FROM SWISSPROT:O32242) Represses the transcription of the sdpIR operon and of several other operons that probably contribute to delaying commitment to sporulation.INDUCTION: By spo0A during nutrient starvation. Repressed by abrB during regular growth when nutrients are plentiful. Represses its own transcription."]
["--","sigw","ECF-type sigma factor. (FROM SWISSPROT:Q45585) Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. Sigma-W controls genes involved in transport processes and detoxification.By different stresses causing damage to the cell envelope, such as alkaline shock, salt shock, phage infection and certain antibiotics that affect cell wall biosynthesis."]
["--","ytra","GntR family. (FROM SWISSPROT O34712) Negatively regulates ABC transporter complex ytrBCDEF that plays a role in acetoin utilization during stationary phase and sporulation."]
["--","ysia","YsiA binding is inhibited by long-chain acyl-CoAs."]
["--","yrhi","(FROM SWISSPROT:O08335) Negatively regulates the transcription of the bscR-CYP102A3 operon."]
["--","yfhp","UNKNOWN FUNCTION"]
["--","sigm","Essential for growth and survival in high concentrations of salt; expression positively autoregulated through a sigma-M promoter; expression maximal during exponential growth and increased in high concentrations of salt; activity negatively regulated by YhdL and YhdK"]
["--","sigk","sigK is formed by a site-specific recombination event which joins the previously separated spoIVCB and spoIIIC genes into a single cistron."]
["--","sigi","temperature-sensitive growth in a null mutant; transcription induced by heat shock in rich medium but not in minimal medium; reduced amount of GsiB protein in a sigI mutant under heat shock conditions"]
["--","spla","TRAP-like protein"]
["--","sinr","dual-function regulator which is essential for the late-growth processes of competence and motility and is also a repressor of others, e.g., sporulation and subtilisin synthesis. Might be a leucine zipper protein. In aprE there are two binding sites and SinR binds more strongly to the distal site, which contains two dyad symmetry sites"]
["--","sigy","RNA polymerase ECF(extracytoplasmic function)-type sigma factor"]
["--","sigx","ECF-type sigma factor. (FROM SWISSPROT:P35165) Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. May be involved in the regulation of iron metabolism."]
["--","arfm","Fnr-dependent anaerobic transcription"]
["--","degu","pleiotropic regulator involved in various post-exponential phase responses; makes a two component system with DegS kinase"]
["--","dnaa","(FROM SWISSPROT P05648) Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. DnaA can inhibit its own gene expression as well as that of other genes."]
["--","cssr","(FROM SWISSPROT O32192) Member of the two-component regulatory system cssS/cssR required to control the cellular response to secretion stress."]
["--","ctsr","binding to a directly repeated heptanucleotide operator sequence (A/GGTCAAANANA/GGTCAAA); three functional domains: HTH DNA-binding, dimerization, and putative heat-sensing domains; active as a dimer; specifically degraded by ClpP and ClpX at 37 degrees C; labile and substrate of the ClpCP protease under stress conditions (autoregulation by controlled proteolysis); negatively regulates its own synthesis (FROM SWISPROT P37568) Negative regulator of class III stress genes (clpC, clpP)."]
["--","gabr","positive regulation of gabTD and negative autoregulation"]
["--","glnr","originally identified as a repressor of glnRA operon; binds to the same sequence with TnrA (activator)"]
["--","fnr","same binding consensus with E. coli CAP exists in the narK-fnr operon (FROM SWISSPROT P46908) It is involved in the activation of genes necessary for anaerobic respiration."]
["--","frur","repression of the hexuronate utilization operon (uxaC-yjmBCD-uxuA-yjmf-exuTR-uxaBA)"]
["--","ccpa","also called AlsA; common repressor in catabolite repression (CR) but may act as a positive regulator of genes involved in excretion of excess carbon; its binding site is called CRE; it binds to fructose-1,6-bisphosphate and Hpr (FROM SWISSPROT P25144)Transcriptional regulator involved in both the repression of carbohydrate utilization genes such as the alpha-amylase (amyE) and the acetyl-coenzyme A synthetase (acsA); and in the positive regulation of genes involved in excretion of excess carbon such as the acetate kinase (ackA). May play a role in regulation of citrate synthase gene expression."]
["--","ccpb","mediates catabolite repression by glucose, mannitol, and sucrose of gluconate (gnt) and xylose (xyl) operons, in parallel to CcpA"]
["--","arsr","(FROM SWISSPROT P45949) Transcriptional repressor for the ars operon."]
["--","azlb","first gene of the operon; its product represses the expression of the operon itself (FROM SWISSPROT O07920) Transcriptional repressor of the azlBCD operon involved in branched-chain amino acid transport."]
["--","cody","transcriptional regulator; negative regulation of srfA and comK genes (in the presence of casamino-acids), dpp operon"]
["--","arar","transcriptional regulator (LacI family); negative regulation of the L-arabinose metabolic operon (araABDLMNPQ); alternate gene name: araC, yvbS"]
["--","ccpc","carbon catabolite and anaerobic repression of citB and citZ"]
["--","cggr","repression of gapA expression"]
["--","lrpc","the first Lrp (Leucine responsive regulatory protein) detected in Gram-positive bacteria; can repress genes when expressed in E. coli"]
["--","lytr","(FROM SWISSPROT Q02115) Attenuator role for both its own and lytABC operon expression."]
["--","lexa","Negative regulator of DNA damage-inducible genes; SOS-like or SOS regulon; analogue of E. coli LexA"]
["--","lmra","a putative repressor of the lmr operon (lmrA and lmrB) (FROM SWISSPROT O34619) Acts as repressor of the lincomycin-resistance (ImrAB) and yxaGH operons."]
["--","nsrr","NsrR from Nitrosomonas europaea is a nitrite-sensitive transcription repressor of nirK encoding nitrite reductase. (see Beaumont HJ, et al., 2004 (PMID:15458412)"]
["--","perr","transcription induced by hydrogen peroxide, by general stress, or by entry into stationary phase under conditions of iron and manganese limitation (class III stress response); expression modulated by Ca2+; mutants lead to higher expression from all peroxide regulon promoters (mrgA, katA, hemAXCDBL, and ahpCF), but has no effect on spore resistance to alkyl hydroperoxides, heat or hydrogen peroxide"]
["--","med","disruption leads to significant decrease of comK, expression; function downstream from mecA in comK, activation; putative lipoprotein; no effect on competence"]
["--","mta","The N-terminal domain of Mta(MtaN) acts as a constitutive activator of the transcription of bmr and blt genes."]
["--","gntr","negatively autoregulates the expression of the gntRKPZ operon; inactivated by gluconate; suggested consensus of the gntR family is ACNNNTATANANNTAT"]
["--","hbs","non-specific DNA binding protein; acts as a repressor on its own expression (FROM SWISSPROT P08821) Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions."]
["--","gltc","Like many members of LysR family, GltC is encoded just upstream of and in the opposite orientation to its target genes (gltAB); it negatively autoregulates itself. The binding site for the autoregulation is the same with the box I of gltA (-71:-57) in its genome position. Box II of gltA overlaps with its -35 region. cf. GltR"]
["--","gltr","it activates the transcription of gltAB in the absense of the normal regulator, GltC. It also negatively regulates its own expression. cf. GltC"]
["--","iolr","a negative regulator (presumably a repressor) which exists immediately upstream of the iol operon in the opposite direction"]
["--","kdgr","preliminary data indicates that KdgR negatively autoregulates the kdgRKAT operon (P. Pujic)"]
["--","hrca","the promoters of class I heat-inducible genes are sigA-dependent and have an inverted repeat, called the CIRCE (controlling IR of chaperone expression) element, which is highly conserved among eubacteria; heat-shock and general stress responses are reviewed in Hecker, M. et al., 1996"]
["--","htra","(FROM SWISSPROT O34358) May be involved in processing, maturation, or secretion of extracellular enzymes."]

{"sheet":"Yeast DB","index":2,"n_rows":94,"n_cols":4,"rows_kept":94,"cut":false,"hidden":false,"merged":[],"flags":["formulas_cached_only"]}
["Yeast Dynamical backbone"]
["Systematic name (from Balaji et al)","Dynamical Module","Standard name","Description from Saccaromyces Genome Database"]
["\"YBR049C\"","A","  REB1","RNA polymerase I enhancer binding protein; DNA binding protein which binds to genes transcribed by both RNA polymerase I and RNA polymerase II; required for termination of RNA polymerase I transcription "]
["\"YDR146C\"","A","SWI5","Transcription factor that activates transcription of genes expressed at the M/G1 phase boundary and in G1 phase; localization to the nucleus occurs during G1 and appears to be regulated by phosphorylation by Cdc28p kinase"]
["\"YGL181W\"","A","GTS1","Protein that localizes to the nucleus and is involved in transcription regulation; also localizes to actin patches and plays a role in endocytosis; N-terminus contains an ARF-GAP domain and C-terminus contains a Gln-rich domain"]
["\"YNL216W\"","A","RAP1","DNA-binding protein involved in either activation or repression of transcription, depending on binding site context; also binds telomere sequences and plays a role in telomeric position effect (silencing) and telomere structure"]
["\"YBR083W\"","A","TEC1","Transcription factor required for full Ty1 epxression, Ty1-mediated gene activation, and haploid invasive and diploid pseudohyphal growth; TEA/ATTS DNA-binding domain family member"]
["\"YHR084W\"","A","STE12","Transcription factor that is activated by a MAP kinase signaling cascade, activates genes involved in mating or pseudohyphal/invasive growth pathways; cooperates with Tec1p transcription factor to regulate genes specific for invasive growth"]
["\"YBR182C\"","A","SMP1","Putative transcription factor involved in regulating the response to osmotic stress; member of the MADS-box family of transcription factors"]
["\"YHL027W\"","A","RIM101","Transcriptional repressor involved in response to pH and in cell wall construction; required for alkaline pH-stimulated haploid invasive growth and sporulation; activated by proteolytic processing; similar to A. nidulans PacC"]
["\"YKL185W\"","A","ASH1","Zinc-finger inhibitor of HO transcription; mRNA is localized and translated in the distal tip of anaphase cells, resulting in accumulation of Ash1p in daughter cell nuclei and inhibition of HO expression; potential Cdc28p substrate"]
["\"YDR259C\"","A","YAP6","Putative basic leucine zipper (bZIP) transcription factor; overexpression increases sodium and lithium tolerance"]
["\"YOL028C\"","A","YAP7","Putative basic leucine zipper (bZIP) transcription factor"]
["\"YOR028C\"","A","CIN5","Basic leucine zipper transcriptional factor of the yAP-1 family that mediates pleiotropic drug resistance and salt tolerance; localizes constitutively to the nucleus"]
["\"YIL101C\"","A","XBP1","Transcriptional repressor that binds to promoter sequences of the cyclin genes, CYS3, and SMF2; expression is induced by stress or starvation during mitosis, and late in meiosis; member of the Swi4p/Mbp1p family; potential Cdc28p substrate"]
["\"YKL043W\"","A","PHD1","Transcriptional activator that enhances pseudohyphal growth; regulates expression of FLO11, an adhesin required for pseudohyphal filament formation; similar to StuA, an A. nidulans developmental regulator; potential Cdc28p substrate"]
["\"YKL109W\"","A","HAP4","Subunit of the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex, a transcriptional activator and global regulator of respiratory gene expression; provides the principal activation function of the complex"]
["\"YLR013W\"","A","GAT3","Protein containing GATA family zinc finger motifs"]
["\"YMR016C\"","A","SOK2","Nuclear protein that plays a regulatory role in the cyclic AMP (cAMP)-dependent protein kinase (PKA) signal transduction pathway; negatively regulates pseudohyphal differentiation; homologous to several transcription factors"]
["\"YPR065W\"","A","ROX1","Heme-dependent repressor of hypoxic genes; contains an HMG domain that is responsible for DNA bending activity"]
["\"YEL009C\"","A","GCN4","Transcriptional activator of amino acid biosynthetic genes in response to amino acid starvation; expression is tightly regulated at both the transcriptional and translational levels"]
["\"YIR023W\"","A","DAL81","Positive regulator of genes in multiple nitrogen degradation pathways; contains DNA binding domain but does not appear to bind the dodecanucleotide sequence present in the promoter region of many genes involved in allantoin catabolism"]
["\"YCL067C\"","A","HMLALPHA2","Silenced copy of ALPHA2 at HML; homeobox-domain protein that associates with Mcm1p in haploid cells to repress a-specific gene expression and interacts with a1p in diploid cells to repress haploid-specific gene expression"]
["\"YER111C\"","A","SWI4","DNA binding component of the SBF complex (Swi4p-Swi6p), a transcriptional activator that in concert with MBF (Mbp1-Swi6p) regulates late G1-specific transcription of targets including cyclins and genes required for DNA synthesis and repair"]
["\"YLR256W\"","A","HAP1","Zinc finger transcription factor involved in the complex regulation of gene expression in response to levels of heme and oxygen; the S288C sequence differs from other strain backgrounds due to a Ty1 insertion in the carboxy terminus"]
["\"YBR112C\"","A","CYC8","General transcriptional co-repressor, acts together with Tup1p; also acts as part of a transcriptional co-activator complex that recruits the SWI/SNF and SAGA complexes to promoters"]
["\"YCR065W\"","A","HCM1","Forkhead transcription factor that drives S-phase specific expression of genes involved in chromosome segregation, spindle dynamics, and budding; suppressor of calmodulin mutants with specific SPB assembly defects; telomere maintenance role"]
["\"YDR451C\"","A","YHP1","One of two homeobox transcriptional repressors (see also Yox1p), that bind to Mcm1p and to early cell cycle box (ECB) elements of cell cycle regulated genes, thereby restricting ECB-mediated transcription to the M/G1 interval "]
["\"YDR501W\"","A","PLM2","Protein required for partitioning of the 2-micron plasmid GO: Transcription factor activity"]
["\"YML027W\"","A","YOX1","Homeodomain-containing transcriptional repressor, binds to Mcm1p and to early cell cycle boxes (ECBs) in the promoters of cell cycle-regulated genes expressed in M/G1 phase; expression is cell cycle-regulated; potential Cdc28p substrate"]
["\"YOR344C\"","A","TYE7","Serine-rich protein that contains a basic-helix-loop-helix (bHLH) DNA binding motif; binds E-boxes of glycolytic genes and contributes to their activation; may function as a transcriptional activator in Ty1-mediated gene expression"]
["\"YGL035C\"","A","MIG1","Transcription factor involved in glucose repression; sequence specific DNA binding protein containing two Cys2His2 zinc finger motifs; regulated by the SNF1 kinase and the GLC7 phosphatase"]
["\"YPL248C\"","A","GAL4","DNA-binding transcription factor required for the activation of the GAL genes in response to galactose; repressed by Gal80p and activated by Gal3p"]
["\"YGL071W\"","A","AFT1","Transcription factor involved in iron utilization and homeostasis; binds the consensus site PyPuCACCCPu and activates the expression of target genes in response to changes in iron availability"]
["\"YER040W\"","A","GLN3","Transcriptional activator of genes regulated by nitrogen catabolite repression (NCR), localization and activity regulated by quality of nitrogen source"]
["\"YGL162W\"","A","SUT1","Transcription factor of the Zn[II]2Cys6 family involved in sterol uptake; involved in induction of hypoxic gene expression"]
["\"YKL062W\"","A","MSN4","Transcriptional activator related to Msn2p; activated in stress conditions, which results in translocation from the cytoplasm to the nucleus; binds DNA at stress response elements of responsive genes, inducing gene expression"]
["\"YMR037C\"","A","MSN2","Transcriptional activator related to Msn4p; activated in stress conditions, which results in translocation from the cytoplasm to the nucleus; binds DNA at stress response elements of responsive genes, inducing gene expression"]
["\"YPL177C\"","A","CUP9","Homeodomain-containing transcriptional repressor of PTR2, which encodes a major peptide transporter; imported peptides activate ubiquitin-dependent proteolysis, resulting in degradation of Cup9p and de-repression of PTR2 transcription"]
["\"YJL110C\"","A","GZF3","GATA zinc finger protein and Dal80p homolog that negatively regulates nitrogen catabolic gene expression by competing with Gat1p for GATA site binding; function requires a repressive carbon source; dimerizes with Dal80p and binds to Tor1p"]
["\"YKR034W\"","A","DAL80","Negative regulator of genes in multiple nitrogen degradation pathways; expression is regulated by nitrogen levels and by Gln3p; member of the GATA-binding family, forms homodimers and heterodimers with Deh1p "]
["\"YJR060W\"","A","CBF1","Helix-loop-helix protein that binds the motif CACRTG, which is present at several sites including MET gene promoters and centromere DNA element I (CDEI); required for nucleosome positioning at this motif; targets Isw1p to DNA"]
["\"YDL020C\"","A","RPN4","Transcription factor that stimulates expression of proteasome genes; Rpn4p levels are in turn regulated by the 26S proteasome in a negative feedback control mechanism; RPN4 is transcriptionally regulated by various stress responses"]
["\"YKL015W\"","A","PUT3","Transcriptional activator of proline utilization genes, constitutively binds PUT1 and PUT2 promoter sequences and undergoes a conformational change to form the active state; has a Zn(2)-Cys(6) binuclear cluster domain"]
["\"YIR018W\"","A","YAP5","Basic leucine zipper (bZIP) transcription factor "]
["\"YKL112W\"","A","ABF1","DNA binding protein with possible chromatin-reorganizing activity involved in transcriptional activation, gene silencing, and DNA replication and repair"]
["\"YPR104C\"","A","FHL1","Transcriptional activator with similarity to DNA-binding domain of Drosophila forkhead but unable to bind DNA in vitro; required for rRNA processing; isolated as a suppressor of splicing factor prp4"]
["\"YFL021W\"","A","GAT1","Transcriptional activator of genes involved in nitrogen catabolite repression; contains a GATA-1-type zinc finger DNA-binding motif; activity and localization regulated by nitrogen limitation and Ure2p"]
["\"YML007W\"","A","YAP1","Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance; activated by H2O2 through the multistep formation of disulfide bonds and transit from the cytoplasm to the nucleus; mediates resistance to cadmium"]
["\"YML099C\"","A","ARG81","Zinc-finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type, involved in the regulation of arginine-responsive genes; acts with Arg80p and Arg82p"]
["\"YLR131C\"","A","ACE2","Transcription factor that activates expression of early G1-specific genes, localizes to daughter cell nuclei after cytokinesis and delays G1 progression in daughters, localization is regulated by phosphorylation; potential Cdc28p substrate"]
["\"YNL167C\"","A","SKO1","Basic leucine zipper (bZIP) transcription factor of the ATF/CREB family, forms a complex with Tup1p and Ssn6p to both activate and repress transcription; cytosolic and nuclear protein involved in osmotic and oxidative stress responses"]
["\"YGL209W\"","A","MIG2","Protein containing zinc fingers, involved in repression, along with Mig1p, of SUC2 (invertase) expression by high levels of glucose; binds to Mig1p-binding sites in SUC2 promoter"]
["\"YPL202C\"","A","AFT2","Iron-regulated transcriptional activator; activates genes involved in intracellular iron use and required for iron homeostasis and resistance to oxidative stress; similar to Aft1p"]
["\"YDR216W\"","A","ADR1","Carbon source-responsive zinc-finger transcription factor, required for transcription of the glucose-repressed gene ADH2, of peroxisomal protein genes, and of genes required for ethanol, glycerol, and fatty acid utilization"]
["\"YIL131C\"","A","FKH1","Forkhead family transcription factor with a minor role in the expression of G2/M phase genes; negatively regulates transcriptional elongation; positive role in chromatin silencing at HML and HMR; regulates donor preference during switching"]
["\"YGL096W\"","A","TOS8","Homeodomain-containing transcription factor; SBF regulated target gene that in turn regulates expression of genes involved in G1/S phase events such as bud site selection, bud emergence and cell cycle progression; similarity to Cup9p"]
["\"YLR451W\"","A","LEU3","Zinc-finger transcription factor that regulates genes involved in branched chain amino acid biosynthesis and ammonia assimilation; positively regulated by alpha-isopropylmalate, an intermediate in leucine biosynthesis"]
["\"YOL108C\"","A","INO4","Transcription factor required for derepression of inositol-choline-regulated genes involved in phospholipid synthesis; forms a complex, with Ino2p, that binds the inositol-choline-responsive element through a basic helix-loop-helix domain"]
["\"YLR183C\"","A","TOS4","Transcription factor that binds to a number of promoter regions, particularly promoters of some genes involved in pheromone response and cell cycle; potential Cdc28p substrate; expression is induced in G1 by bound SBF"]
["\"YNL068C\"","A","FKH2","Forkhead family transcription factor with a major role in the expression of G2/M phase genes; positively regulates transcriptional elongation; negative role in chromatin silencing at HML and HMR; substrate of the Cdc28p/Clb5p kinase"]
["\"YLR182W\"","A","SWI6","Transcription cofactor, forms complexes with DNA-binding proteins Swi4p and Mbp1p to regulate transcription at the G1/S transition; involved in meiotic gene expression; localization regulated by phosphorylation; potential Cdc28p substrate"]
["\"YCR106W\"","RDS1","RDS1","Zinc cluster transcription factor involved in conferring resistance to cycloheximide "]
["\"YDL106C\"","PHO2","PHO2","Homeobox transcription factor; regulatory targets include genes involved in phosphate metabolism; binds cooperatively with Pho4p to the PHO5 promoter; phosphorylation of Pho2p facilitates interaction with Pho4"]
["\"YDR310C\"","SUM1","SUM1","Transcriptional repressor required for mitotic repression of middle sporulation-specific genes; involved in telomere maintenance, regulated by the pachytene checkpoint"]
["\"YFR034C\"","PHO4","PHO4","Basic helix-loop-helix (bHLH) transcription factor of the myc-family; binds cooperatively with Pho2p to the PHO5 promoter; function is regulated by phosphorylation at multiple sites and by phosphate availability"]
["\"YGL013C\"","PDR1","PDR1","Zinc cluster protein that is a master regulator involved in recruiting other zinc cluster proteins to pleiotropic drug response elements (PDREs) to fine tune the regulation of multidrug resistance genes. Transcription activator activity (IDA, IMP)"]
["\"YHL009C\"","YAP3","YAP3","Basic leucine zipper (bZIP) transcription factor "]
["\"YJL089W\"","SIP4","SIP4","C6 zinc cluster transcriptional activator that binds to the carbon source-responsive element (CSRE) of gluconeogenic genes; involved in the positive regulation of gluconeogenesis; regulated by Snf1p protein kinase; localized to the nucleus"]
["\"YMR280C\"","CAT8","CAT8","Zinc cluster transcriptional activator necessary for derepression of a variety of genes under non-fermentative growth conditions, active after diauxic shift, binds carbon source responsive elements"]
["\"YAL051W\"","OAF1","OAF1","Oleate-activated transcription factor, acts alone and as a heterodimer with Pip2p; activates genes involved in beta-oxidation of fatty acids and peroxisome organization and biogenesis"]
["\"YDR207C\"","UME6  ","UME6  ","Key transcriptional regulator of early meiotic genes, binds URS1 upstream regulatory sequence, couples metabolic responses to nutritional cues with initiation and progression of meiosis, forms complex with Ime1p, and also with Sin3p-Rpd3p"]
["\"YMR043W\"","MCM1","MCM1","Transcription factor involved in cell-type-specific transcription and pheromone response; plays a central role in the formation of both repressor and activator complexes"]
["\"YBL005W\"","PDR3","PDR3","Transcriptional activator of the pleiotropic drug resistance network, regulates expression of ATP-binding cassette (ABC) transporters through binding to cis-acting sites known as PDREs (PDR responsive elements)"]
["\"YBR297W\"","MAL33","MAL33","MAL-activator protein, part of complex locus MAL3; nonfunctional in genomic reference strain S288C (1) transcription factor activity "]
["\"YDL056W\"","MBP1","MBP1","Transcription factor involved in regulation of cell cycle progression from G1 to S phase, forms a complex with Swi6p that binds to MluI cell cycle box regulatory element in promoters of DNA synthesis genes "]
["\"YNL027W\"","CRZ1","CRZ1","transcription factor that activates transcription of genes involved in stress response; nuclear localization is positively regulated by calcineurin-mediated dephosphorylation"]
["\"YDR043C\"","NRG1","NRG1","Transcriptional repressor that recruits the Cyc8p-Tup1p complex to promoters; mediates glucose repression and negatively regulates a variety of processes including filamentous growth and alkaline pH response"]
["\"YDR123C\"","INO2","INO2","Component of the heteromeric Ino2p/Ino4p basic helix-loop-helix transcription activator that binds inositol/choline-responsive elements (ICREs), required for derepression of phospholipid biosynthetic genes in response to inositol depletion"]
["\"YGL073W\"","HSF1","HSF1","Trimeric heat shock transcription factor, activates multiple genes in response to stresses that include hyperthermia; recognizes variable heat shock elements (HSEs) consisting of inverted NGAAN repeats; posttranslationally regulated"]
["\"YHR124W\"","NDT80","NDT80","Meiosis-specific transcription factor required for exit from pachytene and for full meiotic recombination; activates middle sporulation genes; competes with Sum1p for binding to promoters containing middle sporulation elements (MSE)"]
["\"YDR253C\"","MET32","MET32","Zinc-finger DNA-binding protein, involved in transcriptional regulation of the methionine biosynthetic genes, similar to Met31p"]
["\"YDR421W\"","ARO80","ARO80","Zinc finger transcriptional activator of the Zn2Cys6 family; activates transcription of aromatic amino acid catabolic genes in the presence of aromatic amino acids"]
["\"YHR178W\"","STB5","STB5","Activator of multidrug resistance genes, forms a heterodimer with Pdr1p; contains a Zn(II)2Cys6 zinc finger domain that interacts with a PDRE (pleotropic drug resistance element) in vitro; binds Sin3p in a two-hybrid assay"]
["\"YHR206W\"","SKN7","SKN7","Nuclear response regulator and transcription factor, part of a branched two-component signaling system; required for optimal induction of heat-shock genes in response to oxidative stress; involved in osmoregulation"]
["\"YJL056C\"","ZAP1","ZAP1","Zinc-regulated transcription factor, binds to zinc-responsive promoter elements to induce transcription of certain genes in the presence of zinc; regulates its own transcription; contains seven zinc-finger domains"]
["\"YKL032C\"","IXR1","IXR1","Protein that binds DNA containing intrastrand cross-links formed by cisplatin, contains two HMG (high mobility group box) domains, which confer the ability to bend cisplatin-modified DNA; mediates aerobic transcriptional repression of COX5b"]
["\"YLR098C\"","CHA4","CHA4","DNA binding transcriptional activator, mediates serine/threonine activation of the catabolic L-serine (L-threonine) deaminase (CHA1); Zinc-finger protein with Zn[2]-Cys[6] fungal-type binuclear cluster domain"]
["\"YMR021C\"","MAC","MAC","Copper-sensing transcription factor involved in regulation of genes required for high affinity copper transport"]
["\"YMR042W\"","ARG80","ARG80","Transcription factor involved in regulation of arginine-responsive genes; acts with Arg81p and Arg82p "]
["\"YOL089C\"","HAL9","HAL9","Putative transcription factor containing a zinc finger; overexpression increases salt tolerance through increased expression of the ENA1 (Na+/Li+ extrusion pump) gene while gene disruption decreases both salt tolerance and ENA1 expression"]
["\"YOR113W\"","AZF1","AZF1","Zinc-finger transcription factor, involved in induction of CLN3 transcription in response to glucose; genetic and physical interactions indicate a possible role in mitochondrial transcription or genome maintenance"]
["\"YOR363C\"","PIP2","PIP2","Autoregulatory oleate-specific transcriptional activator of peroxisome proliferation, contains Zn(2)-Cys(6) cluster domain, forms heterodimer with Oaf1p, binds oleate response elements (OREs), activates beta-oxidation genes"]
["\"YPL038W\"","MET31","MET31","Zinc-finger DNA-binding protein, involved in transcriptional regulation of the methionine biosynthetic genes, similar to Met32p"]