RegulonDB RegulonDB 10.9: Operon Form
   

gcl-hyi-glxR-ybbW-allB-ybbY-glxK operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: gcl-hyi-glxR-ybbW-allB-ybbY-glxK
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: gcl-hyi-glxR-ybbVW-allB-ybbY-glxK
Gene(s): gcl, hyi, glxR, ybbW, allB, ybbY, glxK   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ITCR] Inferred through co-regulation
Reference(s): [1] Cusa E., et al., 1999
Promoter
Name: gclp
+1: 533907
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 9
Sequence: gcggagcgggtttttttgacaaaatttgaaagttggaaaaattttccaataaatagaggtAggaataaaatggcaaaaatg
                          -35                     -10       +1                   
Note(s): The gclp promoter is activated in the presence of glyoxylate and repressed in the presence of allantoin 20964794 Single-cell assays show that this promoter is heterogeneously activated by glyoxylate in the cells within the same culture. In some cells the promoter is activated to a greater extent than in others; in approximately 30% of the cells in a given culture the promoter is not activated 20964794
Evidence: [AIPP]
[ICWHO]
Reference(s): [2] Huerta AM., et al., 2003
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
proximal AllR-allantoin repressor gclp 533879 533895 -20.0 aatttgaaagTTGGAAAAATTTTCCAATaaatagaggt nd [BCE], [BPP], [GEA], [SM] [3], [4]


Transcription unit       
Name: allB
Gene(s): allB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of the allB gene is induced during the first 24 h after the induction of nitrogen starvation 32571968.
Evidence: [IEP] Inferred from expression pattern
Reference(s): [5] Li Z., et al., 2019
Promoter
Name: allBp3
+1: 538944
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 203
Sequence: tacgataacggttttaacctcactgcgttttcagtaactctggtggccgttattttatctCttggcggtaagtttattcac
                            -35                    -10      +1                   
Evidence: [ICWHO]
[RSE]
[TIM]
Reference(s): [5] Li Z., et al., 2019


Transcription unit       
Name: allB
Gene(s): allB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of the allB gene is induced during the first 24 h after the induction of nitrogen starvation 32571968.
Evidence: [IEP] Inferred from expression pattern
Reference(s): [5] Li Z., et al., 2019
Promoter
Name: allBp2
+1: 538986
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 161
Sequence: gtggccgttattttatctcttggcggtaagtttattcactttatggaaccgttatcgcgtGtttcatggtttgtcggcgtc
                                                  -10       +1                   
Evidence: [ICWHO]
[RSE]
[TIM]
Reference(s): [5] Li Z., et al., 2019


Transcription unit       
Name: allB
Gene(s): allB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of the allB gene is induced during the first 24 h after the induction of nitrogen starvation 32571968.
Evidence: [IEP] Inferred from expression pattern
Reference(s): [5] Li Z., et al., 2019
Promoter
Name: allBp1
+1: 539041
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 106
Sequence: cgcgtgtttcatggtttgtcggcgtcatcgtcgcctttgcggcctacgccttattaaagaAacgtacaacagcagaaaaaa
                                                    -10     +1                   
Evidence: [ICWHO]
[RSE]
[TIM]
Reference(s): [5] Li Z., et al., 2019


Transcription unit       
Name: ybbY-glxK
Gene(s): ybbY, glxK   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC] Inferred by curator
Promoter
Name: ybbYp
+1: 540359
Distance from start of the gene: 206
Sequence: gatgccgacttcgtcttcattcagccgaatagcagctatgttcttaccaatgacgatctgGaatatcgccacaaagtcagc
Evidence: [HTTIM]
Reference(s): [6] Mendoza-Vargas A., et al., 2009


Transcription unit       
Name: glxK
Gene(s): glxK   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [7] Zaslaver A., et al., 2006
Promoter
Name: glxKp
+1: Unknown
Evidence: [IEP]
Reference(s): [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 -13.1 533839 533864 ctgtcgcatcCCGCTCTGCGGAGCGGGTTTTTTTGacaaaatttg
  terminator -7.5 536539 536566 ggcaggggatCGTGTTGTCTGAATTCAGGAAAAGCGAaatttaaaag
  anti-terminator -10.2 533800 533848 atcagcacggCGTTGGGACTGAAAGCACATCCATAATGTCTGTCGCATCCCGCTCTGCggagcgggtt
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] Cusa E., Obradors N., Baldoma L., Badia J., Aguilar J., 1999, Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli., J Bacteriol 181(24):7479-84

 [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] Hasegawa A., Ogasawara H., Kori A., Teramoto J., Ishihama A., 2008, The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and reutilization of purines., Microbiology 154(Pt 11):3366-78

 [4] Rintoul MR., Cusa E., Baldoma L., Badia J., Reitzer L., Aguilar J., 2002, Regulation of the Escherichia coli allantoin regulon: coordinated function of the repressor AllR and the activator AllS., J Mol Biol 324(4):599-610

 [5] Li Z., Pan Q., Xiao Y., Fang X., Shi R., Fu C., Danchin A., You C., 2019, Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation., Microb Biotechnol 12(2):360-376

 [6] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [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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