RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit       
Name: htpG
Gene(s): htpG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Bardwell JC., et al., 1987
Promoter
Name: htpGp3
+1: 494817
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 303
Sequence: tcggtccggatgatatcgggcttgatcgtctggaacagcgtctggcagaggaaaaaatcaCtgaagtgatcctcgccacca
                               -24          -12             +1                   
Note(s): This promoter was identified by microarray assays with a mutant σ54 strain and a σ54-overexpressing strain, and by σ54-related promoter element identification Zhao K,2010
We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ54-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999.
Evidence: [HIPP]
[IEP]
Reference(s): [2] Zhao K., et al., 2010


Transcription unit          
Name: htpG
Gene(s): htpG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Bardwell JC., et al., 1987
Promoter
Name: htpGp1
+1: 495075
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 45
Sequence: acgagagcaggatcacctgctctcgcttgaaattattctcccttgtccccatctctcccaCatcctgtttttaaccttaaa
                           -35                 -10          +1                   
Evidence: [AIPP]
[CV(TIM)]
[HIPP]
[IDA]
[IEP]
[TIM]
Reference(s): [1] Bardwell JC., et al., 1987
[3] Cowing DW., et al., 1985
[4] Nonaka G., et al., 2006
[5] Wade JT., et al., 2006
[6] Zhou YN., et al., 1988
Terminator(s)
Type: rho-independent
Sequence: ttcctgatgtAATGCCGGATGACCTTCGTGTCATCCGGCATTtttcttttca
Reference(s): [1] Bardwell JC., et al., 1987
TF binding sites (TFBSs)
[AscG,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote AscG repressor htpGp1 495157 495171 89.5 cagtcagaagTGAAACAGCTTCTGCacctgatgat nd [AIBSCS], [BPP] [7]


Transcription unit       
Name: htpG
Gene(s): htpG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Bardwell JC., et al., 1987
Promoter
Name: htpGp2
+1: 495084
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 36
Sequence: ggatcacctgctctcgcttgaaattattctcccttgtccccatctctcccacatcctgttTttaaccttaaaatggcatta
                                 -35             -10        +1                   
Evidence: [AIPP]
[CV(TIM)]
[HIPP]
[IDA]
[IEP]
[TIM]
Reference(s): [3] Cowing DW., et al., 1985
[4] Nonaka G., et al., 2006
[5] Wade JT., et al., 2006
[6] Zhou YN., et al., 1988
Terminator(s)
Type: rho-independent
Sequence: ttcctgatgtAATGCCGGATGACCTTCGTGTCATCCGGCATTtttcttttca
Reference(s): [1] Bardwell JC., et al., 1987


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  gcvB unknown unknown activator       [IMP] [8]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


Evidence    

 [HIPP] Human inference of promoter position

 [IEP] Inferred from expression pattern

 [AIPP] Automated inference of promoter position

 [CV(TIM)] cross validation(TIM)

 [IDA] Inferred from direct assay

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins


Reference(s)    

 [1] Bardwell JC., Craig EA., 1987, Eukaryotic Mr 83,000 heat shock protein has a homologue in Escherichia coli., Proc Natl Acad Sci U S A 84(15):5177-81

 [2] Zhao K., Liu M., Burgess RR., 2010, Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis., Nucleic Acids Res 38(4):1273-83

 [3] Cowing DW., Bardwell JC., Craig EA., Woolford C., Hendrix RW., Gross CA., 1985, Consensus sequence for Escherichia coli heat shock gene promoters., Proc Natl Acad Sci U S A 82(9):2679-83

 [4] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89

 [5] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

 [6] Zhou YN., Kusukawa N., Erickson JW., Gross CA., Yura T., 1988, Isolation and characterization of Escherichia coli mutants that lack the heat shock sigma factor sigma 32., J Bacteriol 170(8):3640-9

 [7] Ishida Y., Kori A., Ishihama A., 2009, Participation of regulator AscG of the beta-glucoside utilization operon in regulation of the propionate catabolism operon., J Bacteriol 191(19):6136-44

 [8] Pulvermacher SC., Stauffer LT., Stauffer GV., 2009, Role of the sRNA GcvB in regulation of cycA in Escherichia coli., Microbiology 155(Pt 1):106-14

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