RegulonDB RegulonDB 10.7: Operon Form
   

lsrACDBFG-tam operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: lsrACDBFG-tam
Gene(s): lsrA, lsrC, lsrD, lsrB, lsrF, lsrG, tam   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IHBCE] Inferred by a human based on computational evidence
[ITC] Inferred through co-regulation
[LTED] Length of transcript experimentally determined
Reference(s): [1] Wang L., et al., 2005
[2] Wang L., et al., 2005
[3] Xavier KB., et al., 2005
Promoter
Name: lsrAp
+1: 1601460
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 30
Sequence: atatgtgcaatgtccacctaaggttatgaacaaattaaaagcagaaatacatttgttcaaAactcacctgcaaaactgaac
                          -35                 -10           +1                   
Evidence: [AIPP]
Reference(s): [4] Gama-Castro S., et al., 2008
[1] Wang L., et al., 2005
[3] Xavier KB., et al., 2005
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
remote CRP-cAMP activator lsrAp 1601307 1601328 -142.5 gctcatttatATCTGTGATGGCAACCACAGTTtgactctacg nd [APIORCISFBSCS], [GEA], [SM] [1], [2]
proximal CRP-cAMP activator lsrAp 1601378 1601399 -71.5 aaatagcataAATTGTGATCTATTCGTCGGAAatatgtgcaa nd [BPP], [GEA], [SM] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal LsrR repressor lsrAp 1601456 1601485 11.5 atacatttgtTCAAAACTCACCTGCAAAACTGAACGGGGGaaatatgcaa nd [BPP], [GEA], [SM] [1], [5]


Transcription unit       
Name: tam
Gene(s): tam   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[ICWHO] Inferred computationally without human oversight
[IEP] Inferred from expression pattern
Reference(s): [6] Maciag A., et al., 2011
[7] Zaslaver A., et al., 2006
Promoter
Name: tamp
+1: 1607221
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 125
Sequence: gcctataaagatgaagacgcagtggcgttccataaaaccacgccccactacaaaacctgtGtcgcgaaactggaatcttta
                                                -10         +1                   
Note(s): Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Based on this, a putative promoter was suggested, but the +1 site of the transcription initiation has not been determined, although there exists promoter activity.
Evidence: [HTIM]
[IEP]
Reference(s): [6] Maciag A., et al., 2011
[7] Zaslaver A., et al., 2006


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [8] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -8.6 1607274 1607309 tctgttcaatGGTTTGATGCCGTGAGGCGAATTTATCAATTTTATctacaattgg
  anti-terminator -3.3 1607273 1607287 gtctgttcaaTGGTTTGATGCCGTgaggcgaatt
  anti-anti-terminator -12.8 1607202 1607277 taaaaccacgCCCCACTACAAAACCTGTGTCGCGAAACTGGAATCTTTAATGACCGGGCCGCGTAAAAAACGTCTGTTCAATGGTttgatgccgt
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"




Reference(s)    

 [1] Wang L., Hashimoto Y., Tsao CY., Valdes JJ., Bentley WE., 2005, Cyclic AMP (cAMP) and cAMP receptor protein influence both synthesis and uptake of extracellular autoinducer 2 in Escherichia coli., J Bacteriol 187(6):2066-76

 [2] Wang L., Li J., March JC., Valdes JJ., Bentley WE., 2005, luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling., J Bacteriol 187(24):8350-60

 [3] Xavier KB., Bassler BL., 2005, Regulation of uptake and processing of the quorum-sensing autoinducer AI-2 in Escherichia coli., J Bacteriol 187(1):238-48

 [4] 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

 [5] Xue T., Zhao L., Sun H., Zhou X., Sun B., 2009, LsrR-binding site recognition and regulatory characteristics in Escherichia coli AI-2 quorum sensing., Cell Res 19(11):1258-68

 [6] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [7] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

 [8] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.


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