RegulonDB RegulonDB 10.9: Sigmulon Form
   

Sigma28 Sigmulon in Escherichia coli K-12 genome




Sigma28 Signal transduction, see details.




Sigma Factor      
Name: Sigma28      Signal transduction
Synonyms: FliA
Gene name: fliA
Sigmulon regulators:
Sigmulon Genes:


Transcribed promoters    
  Promoter Name TSS Position Transcribed Gene(s) Distance from TSS
to gene		 Promoter Sequence Box
(-10) 		Box
(-35) 		Evidence Code(s) Reference(s)
  aerp 3219120 aer 44 aattgcgatctaaatcaaattaatcggttaaagataaccgcagcggggccgacataaactCtgacaagaagttaacaacca
                             -35                -10         +1                    		GCCGACAT TAAAG [HIPP]
[ICWHO]
[TIM] 		[1]
[2]
[3]
[4]
  flgKp 1138351 flgK, flgL 27 gaacattgataatctgttctgaataactcaagtccggcgggtcgctgccgataatactctGtaattgaaggcttataagga
                            -35                -10          +1                    		GCCGATAA TCAAG [HIPP]
[ICWHO] 		[1]
[3]
[5]
[6]
[7]
[4]
  flgMp 1130165 flgN, flgM 37 gaatattcttataaacctgtaagctgttaaagattacccgtcccttgccgataaataagcAacacatgataaaagcgccct
                            -35                -10          +1                    		GCCGATAA TAAAG [HIPP]
[ICWHO] 		[1]
[3]
[5]
[6]
[4]
  fliAp2 2001808 tcyJ, fliZ, fliA 19 acccactaatcgtccgattaaaaaccctgcagaaacggataatcatgccgataactcataTaacgcagggctgtttatcgt
                            -35                -10          +1                    		GCCGATAA TGCAG [HIPP]
[ICWHO]
[TIM] 		[3]
[5]
[8]
[9]
[4]
  fliCp 2003676 fliC 70 aaaaatggctgtttttgaaaaaaattctaaaggttgttttacgacagacgataacagggtTgacggcgattgagccgacgg
                            -35                -10          +1                    		GACGATAA TAAAG [HIPP]
[ICWHO]
[RPF] 		[1]
[10]
[11]
[3]
[5]
[7]
[4]
  fliDp1 null fliD, fliS, fliT       [HIPP]
[RPF] 		[1]
[11]
[5]
[6]
[7]
[4]
  fliEp 2013093 fliE 79 gaaaaattgacgctcccattatttgtgctttcgtttttttctatccgccaataaacccgtTtttttgttgctatttagcgc
                          -35                  -10          +1                    		GCCAATAA TGCTT [HIPP]
[ICWHO] 		[3]
[12]
  fliFp 2013205 fliF, fliG, fliH, fliI, fliJ, fliK 24 caatttttcgagtttgctgacccgggagtgagtcttgttccactttgccaataacgccgtCcataatcagccacgaggtgc
                          -35                  -10          +1                    		GCCAATAA GAGTG [HIPP]
[ICWHO] 		[3]
[12]
  fliLp2 2019595 fliL, fliM, fliN, fliO, fliP, fliQ, fliR 23 ccgcgtcttttccccgctttgttgcgctcaagacgcaggataattagccgataagcagtaGcgacacaggaagaccgcaac
                            -35                -10          +1                    		GCCGATAA TCAAG [HIPP]
[ICWHO]
[TIM] 		[13]
[1]
[11]
[3]
[5]
[8]
  flxAp 1646388 flxA 17 aacaattaatgacacaagaaatacgattaaagatttttttgtgcatgccgatagtgctttTttaaaaggagaaatctatgt
                            -35                -10          +1                    		GCCGATAG TAAAG [AIPP]
[HIPP]
[ICWHO] 		[3]
[14]
[4]
[15]
  hemLp 174921 hemL 39 gcaccagtacaagcagcctgatgtttgacgagtatttaacttgttatgaataacatagaaTagcagccattcactttttct
                          -35                 -10           +1                    		ATGAATAA TGACG [ICWHO]
[TIM] 		[3]
[16]
  hemLp1 174902 hemL 20 gatgtttgacgagtatttaacttgttatgaataacatagaatagcagccattcactttttCtacgaatcaggaaccctcca
                            -35                -10          +1                    		GCCATTCA TGAAT [HIPP]
[ICWHO]
[IEP] 		[3]
[15]
  hemLp2 174941 hemL 59 tactctaagaaatcaggattgcaccagtacaagcagcctgatgtttgacgagtatttaacTtgttatgaataacatagaat
                            -35                -10          +1                    		GACGAGTA TACAA [HIPP]
[ICWHO] 		[3]
[15]
  lolBp 1263556 prs, ispE, lolB 56 ttgccgaaagccgttagattctggcaattaagacaacttgaacatagacgatagcggacgGtaacgctagcattaagggtt
                            -35                -10          +1                    		GACGATAG TTAAG [HIPP]
[ICWHO] 		[17]
[3]
[18]
  modAp1 794995 modA, modB, modC 94 ccgcttagtcgggcattttctttttctcaacttcctgcttttcctgccgatattttttctTatctacctcacaaaggttag
                           -35                -10           +1                    		GCCGATAT TCAAC [AIPP]
[HIPP]
[ICWHO] 		[3]
[19]
[15]
  motAp 1977302 cheW, cheA, motB, motA 163 accgccatcccgggcagtaaaaagacgtaaactttcccagaatcctgccgatattatcccAcaactgctggatgaacagag
                            -35                -10          +1                    		GCCGATAT TAAAC [HIPP]
[ICWHO] 		[3]
[5]
[6]
[4]
  oppAp 1301085 oppA, oppB, oppC, oppD, oppF 97 atcgtctgaatcaccagaataaataaagtcggtgatagtaatacgtaacgataaagtaacCtgacagcagaaagtctccga
                           -35                 -10          +1                    		AACGATAA AGTCG [AIPP]
[ICWHO]
[NTAS] 		[20]
[21]
[17]
[3]
  ppdAp 2964220 recC, ppdC, ygdB, ppdB, ppdA 43 gaaattttgcaacgtcctgcaacggcgtaaatagtccggaagatgcgccgaagaaatagaAactggccctcgtcttttttt
                            -35                -10          +1                    		GCCGAAGA TAAAT [HIPP]
[ICWHO] 		[3]
[4]
  rdcAp1 4327079 rdcA, rdcB 56 aaacaacacactaaatataaaattatttcttgcagtaattataaaagccgaaaacagaacTcaaaaacaatctggctaaat
                            -35                -10          +1                    		GCCGAAAA TCTTG [HIPP]
[ICWHO] 		[3]
[15]
  rdcAp2 4327064 rdcA, rdcB 71 atttattctgataaaaaacaacacactaaatataaaattatttcttgcagtaattataaaAgccgaaaacagaactcaaaa
                           -35                 -10          +1                    		GCAGTAAT TAAAT [HIPP]
[ICWHO] 		[3]
[15]
  tarp 1972716 cheZ, cheY, cheB, cheR, tap, tar 25 caatttcgcggcgggtggcatcagcaataaagtttcccccctccttgccgataacgagatCaacttgttttcaggaaggtg
                            -35                -10          +1                    		GCCGATAA TAAAG [HIPP]
[ICWHO]
[TIM] 		[13]
[11]
[3]
[5]
[6]
[7]
[22]
  trgp1 1492439 trg 31 tgtgacgcaaagaggtttttggtcataagtaattaccgtcaagtgccgatgactttctatCaggagtaaacctggacgaga
                          -35                -10            +1                    		GCCGATGA TAAGTAAT [HIPP]
[HTTIM] 		[11]
[23]
  tsrp 4591633 tsr 24 ctcggcgtaatctccgcgggatattcataaagtttttcctttccaggccgaaaatcttgcAtcggtccacaggaaagagaa
                            -35                -10          +1                    		GCCGAAAA TAAAG [HIPP]
[ICWHO]
[TIM] 		[13]
[1]
[11]
[3]
[5]
[6]
[7]
[4]
  vesp 1824984 ves 47 agttgtaaaaaaagcctgatcaccactaacgtaaatcacccgagttgccgataaccatccAcggttacctgaacgataaca
                           -35                 -10          +1                    		GCCGATAA TAACG [ICWHO]
[TIM] 		[3]
[24]
[15]
  ycgRp 1244556 ycgR 29 catgtaaaaaatattcacgcatttgtattaagttttgttaactgtgaccgataaaccaaaGacagtttgtcagtcaggagt
                            -35                -10          +1                    		ACCGATAA TTAAG [AIPP]
[HIPP]
[ICWHO] 		[3]
[6]
[15]
  yecFp 1995717 yecF 101 gataaaaatatttattggtcattatattaacgtattttatagcactgccgatatcacgctCaaaaaacaaccactgctatt
                            -35                -10          +1                    		GCCGATAT TAACG [HIPP]
[ICWHO] 		[3]
[19]
  ygbKp 2862197 ygbK 138 cccgcattcagccgtcgatatttttgttaaggatcttggtctggttgccgatacagccaaAgccctgcacttcccgctgcc
                           -35                 -10          +1                    		GCCGATAC TTAAG [HIPP]
[ICWHO] 		[3]
[4]
  yhiLp null yhiL       [HIPP] [19]
  yhjHp 3679229 pdeH 42 gtgaggaaatttaccccggccaggcggtaaagttctgcccttacgcgccgataatctttgTcgagtccgggcagcatcact
                            -35                -10          +1                    		GCCGATAA TAAAG [AIPP]
[HIPP]
[ICWHO] 		[3]
[6]
[15]
  yjcSp null yjcS       [HIPP] [19]
  ykfBp1 266158 ykfI, yafW, ykfH, ykfG, yafX, ykfF, ykfB 71 ccaggaggtgacggacccgtataccaaagaaaaatactttgagtacgcccatgacggcaaActgatggggcagctactgat
                            -35                -10          +1                    		GCCCATGA AGAAA [HIPP]
[ICWHO] 		[3]
[15]
  ykfBp2 266227 ykfI, yafW, ykfH, ykfG, yafX, ykfF, ykfB 140 tatgcaggaaaaaaccgtccagccactgatgaatgcgctgtgtattgccgataacatcaaActggaataccaggaggtgac
                           -35                 -10          +1                    		GCCGATAA TGATG [HIPP]
[ICWHO] 		[3]
[15]
  ynjHp 1842163 ynjH 28 ataaccaaatgcgataactcagacgctaaagttttgccacccggctaccgttatcagtagCagagacaataacgttaagga
                           -35                 -10          +1                    		ACCGTTAT TAAAG [AIPP]
[HIPP]
[ICWHO] 		[3]
[19]
[15]
  ynjHp2 1842188 ynjH 53 gcaaattaataacgagagtaatctcataaccaaatgcgataactcagacgctaaagttttGccacccggctaccgttatca
                           -35                 -10          +1                    		GACGCTAA TAACC [HIPP]
[ICWHO] 		[3]
[15]
Evidence: [HIPP] Human inference of promoter position
[ICWHO] Inferred computationally without human oversight
[TIM] Transcription initiation mapping
[RPF] RNA polymerase footprinting
[AIPP] Automated inference of promoter position
[IEP] Inferred from expression pattern
[NTAS] Non-traceable author statement
[HTTIM] High-throughput transcription initiation mapping


Reference(s)    

 [1] Chilcott GS., Hughes KT., 2000, Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli., Microbiol Mol Biol Rev 64(4):694-708

 [2] Hollands K., Lee DJ., Lloyd GS., Busby SJ., 2010, Activation of sigma 28-dependent transcription in Escherichia coli by the cyclic AMP receptor protein requires an unusual promoter organization., Mol Microbiol 75(5):1098-111

 [3] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [4] Park K., Choi S., Ko M., Park C., 2001, Novel sigmaF-dependent genes of Escherichia coli found using a specified promoter consensus., FEMS Microbiol Lett 202(2):243-50

 [5] Ide N., Ikebe T., Kutsukake K., 1999, Reevaluation of the promoter structure of the class 3 flagellar operons of Escherichia coli and Salmonella., Genes Genet Syst 74(3):113-6

 [6] Ko M., Park C., 2000, Two novel flagellar components and H-NS are involved in the motor function of Escherichia coli., J Mol Biol 303(3):371-82

 [7] Kundu TK., Kusano S., Ishihama A., 1997, Promoter selectivity of Escherichia coli RNA polymerase sigmaF holoenzyme involved in transcription of flagellar and chemotaxis genes., J Bacteriol 179(13):4264-9

 [8] Liu X., Matsumura P., 1996, Differential regulation of multiple overlapping promoters in flagellar class II operons in Escherichia coli., Mol Microbiol 21(3):613-20

 [9] Mytelka DS., Chamberlin MJ., 1996, Escherichia coli fliAZY operon., J Bacteriol 178(1):24-34

 [10] Clarke MB., Sperandio V., 2005, Transcriptional regulation of flhDC by QseBC and sigma (FliA) in enterohaemorrhagic Escherichia coli., Mol Microbiol 57(6):1734-49

 [11] Helmann JD., Chamberlin MJ., 1987, DNA sequence analysis suggests that expression of flagellar and chemotaxis genes in Escherichia coli and Salmonella typhimurium is controlled by an alternative sigma factor., Proc Natl Acad Sci U S A 84(18):6422-4

 [12] Muller V., Jones CJ., Kawagishi I., Aizawa S., Macnab RM., 1992, Characterization of the fliE genes of Escherichia coli and Salmonella typhimurium and identification of the FliE protein as a component of the flagellar hook-basal body complex., J Bacteriol 174(7):2298-304

 [13] Arnosti DN., Chamberlin MJ., 1989, Secondary sigma factor controls transcription of flagellar and chemotaxis genes in Escherichia coli., Proc Natl Acad Sci U S A 86(3):830-4

 [14] Ide N., Kutsukake K., 1997, Identification of a novel Escherichia coli gene whose expression is dependent on the flagellum-specific sigma factor, FliA, but dispensable for motility development., Gene 199(1-2):19-23

 [15] Zhao K., Liu M., Burgess RR., 2007, Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli., Nucleic Acids Res 35(13):4441-52

 [16] Minagawa S., Ogasawara H., Kato A., Yamamoto K., Eguchi Y., Oshima T., Mori H., Ishihama A., Utsumi R., 2003, Identification and molecular characterization of the Mg2+ stimulon of Escherichia coli., J Bacteriol 185(13):3696-702

 [17] Gama-Castro S., Jimenez-Jacinto V., Peralta-Gil M., Santos-Zavaleta A., Penaloza-Spinola MI., Contreras-Moreira B., Segura-Salazar J., Muniz-Rascado L., Martinez-Flores I., Salgado H., Bonavides-Martinez C., Abreu-Goodger C., Rodriguez-Penagos C., Miranda-Rios J., Morett E., Merino E., Huerta AM., Trevino-Quintanilla L., Collado-Vides J., 2008, RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation., Nucleic Acids Res 36(Database issue):D120-4

 [18] Post DA., Hove-Jensen B., Switzer RL., 1993, Characterization of the hemA-prs region of the Escherichia coli and Salmonella typhimurium chromosomes: identification of two open reading frames and implications for prs expression., J Gen Microbiol 139(2):259-66

 [19] Yu HH., Kibler D., Tan M., 2006, In Silico Prediction and Functional Validation of {sigma}28-Regulated Genes in Chlamydia and Escherichia coli., J Bacteriol 188(23):8206-8212

 [20] Andrews JC., Short SA., 1986, opp-lac Operon fusions and transcriptional regulation of the Escherichia coli trp-linked oligopeptide permease., J Bacteriol 165(2):434-42

 [21] Fraenkel YM., Mandel Y., Friedberg D., Margalit H., 1995, Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon., Comput Appl Biosci 11(4):379-87

 [22] Liu X., Matsumura P., 1995, An alternative sigma factor controls transcription of flagellar class-III operons in Escherichia coli: gene sequence, overproduction, purification and characterization., Gene 164(1):81-4

 [23] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [24] Yamada M., Nagamitsu H., Izu H., Nakamura K., Talukder AA., 2002, Characterization of the ves gene, which is expressed at a low temperature in Escherichia coli., J Mol Microbiol Biotechnol 4(2):163-9

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