RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: aslB
Gene(s): aslB   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: aslBp
+1: 3982781
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 177
Sequence: aaaaagcagtatttcggcgagtagcgcagcttggtagcgcaactggtttgggaccagtggGtcggaggttcgaatcctctc
                                -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: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF]
[EXP-IEP]
Reference(s): [1] Huerta AM., et al., 2003
[2] Zhao K., et al., 2010
TF binding sites (TFBSs)
[GadE-RcsB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadE-RcsB activator aslBp nd nd nd nd nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]
[Rob,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Rob activator aslBp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [3]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -19.0 3982810 3982848 ctcgccgaccAATTTTGAACCCCGCTTCGGCGGGGTTTTTTGTTTTCTgtgcatttcg
  anti-terminator -13.8 3982780 3982826 ggaccagtggGTCGGAGGTTCGAATCCTCTCTCGCCGACCAATTTTGAACCCCGCTtcggcggggt
  anti-anti-terminator -5.8 3982779 3982803 gggaccagtgGGTCGGAGGTTCGAATCCTCTCTCgccgaccaat
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IEP] Inferred from expression pattern

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis


Reference(s)    

 [1] 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

 [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] Bennik MH., Pomposiello PJ., Thorne DF., Demple B., 2000, Defining a rob regulon in Escherichia coli by using transposon mutagenesis., J Bacteriol 182(13):3794-801

 [4] Krin E., Danchin A., Soutourina O., 2010, Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli., BMC Microbiol 10:273

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