RegulonDB RegulonDB 10.8: Operon Form
   

gyrA operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: gyrA
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: gyrA
Synonym(s): OP00191
Gene(s): gyrA   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Neumann S., et al., 1997
Promoter
Name: gyrAp
+1: 2339457
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 37
Sequence: ggatgtgaataaagcgtataggtttacctcaaactgcgcggctgtgttataatttgcgacCtttgaatccgggatacagta
                        -35                     -10         +1                   
Note(s): A total of 554 promoter regions from Escherichia coli were aligned in order to analyze their sequence similarities. Mitchell et al. (2003) Mitchell JE,2003focused on conservation, patterns, similarities, and differences between promoters with or without an extended -10 5'-TG-3' element and other conserved elements. They experimentally show that, for several naturally occurring extended -10 promoters, the 5'-TRTG-3' motif is an important determinant for promoter activity. Eleven promoters were selected for further experimental study. Of those, the seven most active (aroF > ompF > envA > purFp1 > purEF > purMN > gyrA) were investigated for the contribution of the extended -10 motif by changing the 5'-TG-3' motif. Promoters with poor matches to the -10 and -35 consensus hexamers are more dependent on the 5'-TG-3' motif, and this plays a similar role on different promoters. The dinucleotide at -17 and -16 in aroFp results in similar patterns of activity, suggesting that these bases play a similar role for different promoters Mitchell JE,2003
Evidence: [CV(RS-EPT-CBR/TA)]
[CV(TA/TIM)]
[IMP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Mitchell JE., et al., 2003
[3] Salgado H, et al., 2012
[4] Swanberg SL., et al., 1987
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd CRP-cAMP activator gyrAp nd nd nd nd nd [GEA] [8]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CspA1 activator gyrAp 2339514 2339520 -60.0 tatatcaggcATTGGATgtgaataaag nd [APIORCISFBSCS] [5]
proximal CspA2 activator gyrAp 2339542 2339548 -88.0 ctactccgtaATTGGCAagacaaacga nd [APIORCISFBSCS] [5]
remote CspA3 activator gyrAp 2339562 2339568 -108.0 ttcggcattcATTGGCActtctactcc nd [APIORCISFBSCS] [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis repressor gyrAp 2339492 2339506 -42.5 gatgtgaataAAGCGTATAGGTTTAcctcaaactg nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [6], [7]
Note(s): 1CspA has been called CS7.4
2CspA has been called CS7.4
3CspA has been called CS7.41CspA has been called CS7.4
2CspA has been called CS7.4
3CspA has been called CS7.4




Reference(s)    

 [1] Neumann S., Quinones A., 1997, Discoordinate gene expression of gyrA and gyrB in response to DNA gyrase inhibition in Escherichia coli., J Basic Microbiol 37(1):53-69

 [2] Mitchell JE., Zheng D., Busby SJ., Minchin SD., 2003, Identification and analysis of 'extended -10' promoters in Escherichia coli., Nucleic Acids Res 31(16):4689-95

 [3] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [4] Swanberg SL., Wang JC., 1987, Cloning and sequencing of the Escherichia coli gyrA gene coding for the A subunit of DNA gyrase., J Mol Biol 197(4):729-36

 [5] Jones PG., Krah R., Tafuri SR., Wolffe AP., 1992, DNA gyrase, CS7.4, and the cold shock response in Escherichia coli., J Bacteriol 174(18):5798-802

 [6] Cameron AD., Stoebel DM., Dorman CJ., 2011, DNA supercoiling is differentially regulated by environmental factors and FIS in Escherichia coli and Salmonella enterica., Mol Microbiol 80(1):85-101

 [7] Schneider R., Travers A., Kutateladze T., Muskhelishvili G., 1999, A DNA architectural protein couples cellular physiology and DNA topology in Escherichia coli., Mol Microbiol 34(5):953-64

 [8] Gomez-Gomez JM., Baquero F., Blazquez J., 1996, Cyclic AMP receptor protein positively controls gyrA transcription and alters DNA topology after nutritional upshift in Escherichia coli., J Bacteriol 178(11):3331-4


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