RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: asr
Gene(s): asr   Genome Browser M3D Gene expression COLOMBOS
Note(s): The asr gene was significantly upregulated in bacterial cells associated with lettuce roots in a microarray analysis Hou Z,2012. The expression of asr is also increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013
The asr gene is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides 32385082.
Based on microarray and RT-qPCR analyses, it was determined that the asr, frc, oxc, ydeO, and yegR acid stress genes are significantly upregulated upon exposure to exogenous glutathione (GSH) Goswami M,2018
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Suziedeliene E., et al., 1999
Promoter
Name: asrp2
+1: 1671327
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 49
Sequence: gttacacgctgaaaccaaccactcacggaagtctgccattcccagggatatagttatttcAacggccccgcagtggggtta
                                 -35              -10       +1                   
Evidence: [ICWHO]
[IMP]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Seputiene V., et al., 2004
[1] Suziedeliene E., et al., 1999
Terminator(s)
Type: rho-independent
Sequence: cagtaatgctGGCGCGCCCCCTCGCGCCtgaaaattac
Reference(s): [1] Suziedeliene E., et al., 1999
TF binding sites (TFBSs)
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor asrp2 nd nd nd nd nd [BPP], [GEA], [IGI] [3]
[PhoB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PhoB-Phosphorylated activator asrp2 1671288 1671306 -30.0 aaaccaaccaCTCACGGAAGTCTGCCATTCccagggatat nd [APIORCISFBSCS], [BCE], [GEA] [1]
[RcdA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RcdA1 activator asrp2 1671254 1671264 -68.5 tttattcagcGTTTGTACATAtcgttacacg nd [BPP], [GEA], [IC] [4]
proximal RcdA2 activator asrp2 1671264 1671274 -58.5 gtttgtacatATCGTTACACGctgaaaccaa nd [BPP], [GEA], [IC] [4]
[RstA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RstA-Phosphorylated activator asrp2 1671257 1671273 -62.0 attcagcgttTGTACATATCGTTACACGctgaaaccaa nd [APIORCISFBSCS], [BPP], [GEA] [5]
Note(s): 1The curator assigned the possible central position of this binding site based on similarity to a consensus sequence (TTGTGTACA) identified by Shimada et al. in 2012 Shimada T,2012
2The curator assigned the possible central position of this binding site based on similarity to a consensus sequence (TTGTGTACA) identified by Shimada et al. in 2012 Shimada T,20121The curator assigned the possible central position of this binding site based on similarity to a consensus sequence (TTGTGTACA) identified by Shimada et al. in 2012 Shimada T,2012
3The curator assigned the possible central position of this binding site based on similarity to a consensus sequence (TTGTGTACA) identified by Shimada et al. in 2012 Shimada T,2012


Transcription unit          
Name: asr
Gene(s): asr   Genome Browser M3D Gene expression COLOMBOS
Note(s): The asr gene was significantly upregulated in bacterial cells associated with lettuce roots in a microarray analysis Hou Z,2012. The expression of asr is also increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013
The asr gene is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides 32385082.
Based on microarray and RT-qPCR analyses, it was determined that the asr, frc, oxc, ydeO, and yegR acid stress genes are significantly upregulated upon exposure to exogenous glutathione (GSH) Goswami M,2018
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Suziedeliene E., et al., 1999
Promoter
Name: asrp
+1: 1671327
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 49
Sequence: gttacacgctgaaaccaaccactcacggaagtctgccattcccagggatatagttatttcAacggccccgcagtggggtta
                      -35                        -10        +1                   
Evidence: [ICWHO]
[IMP]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Seputiene V., et al., 2004
[1] Suziedeliene E., et al., 1999
Terminator(s)
Type: rho-independent
Sequence: cagtaatgctGGCGCGCCCCCTCGCGCCtgaaaattac
Reference(s): [1] Suziedeliene E., et al., 1999
TF binding sites (TFBSs)
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor asrp nd nd nd nd nd [BPP], [GEA], [IGI] [3]
[PhoB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PhoB-Phosphorylated activator asrp 1671288 1671306 -30.0 aaaccaaccaCTCACGGAAGTCTGCCATTCccagggatat nd [APIORCISFBSCS], [BCE], [GEA] [1]
[RcdA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RcdA1 activator asrp 1671254 1671264 -68.5 tttattcagcGTTTGTACATAtcgttacacg nd [BPP], [GEA], [IC] [4]
proximal RcdA2 activator asrp 1671264 1671274 -58.5 gtttgtacatATCGTTACACGctgaaaccaa nd [BPP], [GEA], [IC] [4]
[RstA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RstA-Phosphorylated activator asrp 1671257 1671273 -62.0 attcagcgttTGTACATATCGTTACACGctgaaaccaa nd [APIORCISFBSCS], [BPP], [GEA] [5]
Note(s): 1The curator assigned the possible central position of this binding site based on similarity to a consensus sequence (TTGTGTACA) identified by Shimada et al. in 2012 Shimada T,2012
2The curator assigned the possible central position of this binding site based on similarity to a consensus sequence (TTGTGTACA) identified by Shimada et al. in 2012 Shimada T,20121The curator assigned the possible central position of this binding site based on similarity to a consensus sequence (TTGTGTACA) identified by Shimada et al. in 2012 Shimada T,2012
3The curator assigned the possible central position of this binding site based on similarity to a consensus sequence (TTGTGTACA) identified by Shimada et al. in 2012 Shimada T,2012


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -7.9 1671330 1671346 tatttcaacgGCCCCGCAGTGGGGTTaaatgaaaaa
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    

 [ICWHO] Inferred computationally without human oversight

 [IMP] Inferred from mutant phenotype

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IGI] Inferred from genetic interaction

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BCE] Binding of cellular extracts

 [IC] Inferred by curator


Reference(s)    

 [1] Suziedeliene E., Suziedelis K., Garbenciute V., Normark S., 1999, The acid-inducible asr gene in Escherichia coli: transcriptional control by the phoBR operon., J Bacteriol 181(7):2084-93

 [2] 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

 [3] Seputiene V., Suziedelis K., Normark S., Melefors O., Suziedeliene E., 2004, Transcriptional analysis of the acid-inducible asr gene in enterobacteria., Res Microbiol 155(7):535-42

 [4] Shimada T., Katayama Y., Kawakita S., Ogasawara H., Nakano M., Yamamoto K., Ishihama A., 2012, A novel regulator RcdA of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli., Microbiologyopen 1(4):381-94

 [5] Ogasawara H., Hasegawa A., Kanda E., Miki T., Yamamoto K., Ishihama A., 2007, Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade., J Bacteriol 189(13):4791-9

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