RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: glgAP
Gene(s): glgP, glgA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Montero M., et al., 2011
Promoter
Name: glgAp
+1: 3568392
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 359
Sequence: gtggtgccggaactggatatgtacgatcgcaattggccaattcgcacctacaatgaatcaTtaccgccagcgaaattcgtg
                               -35                    -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[1] Montero M., et al., 2011
Terminator(s)
Type: rho-independent
Sequence: ttttccgaaaTGATGGCGGAAAAAAACGGGACCCTTTGGCCCCGTTCTATTTATTGGTGAACTTAcaatctcacc
Reference(s): [3] Feng CQ., et al., 2019
[4] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[PhoP,+] 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 PhoP-phosphorylated activator glgAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]


Transcription unit          
Name: glgCAP
Synonym(s): OP00164, glgC, glgCAY
Gene(s): glgP, glgA, glgC   Genome Browser M3D Gene expression COLOMBOS
Note(s): In RegulonDB, the old name of this operon was glgBXCAP. With updated information, now there are two operons described, glgBX and glgCAP.
The glgCAP operon is positively regulated by the ppGpp stringent response regulator Romeo T,1989. Bridger WA, Paranchych W,1978. Traxler MF,2008 This operon is also under positive control of the PhoP-PhoQ regulatory system in the submillimolar Mg2+ concentration range Montero M, Eydallin G, Viale AM, Almagro G, Muñoz FJ, Rahimpour M, Sesma MT, Baroja-Fernández E, Pozueta-Romero J,2009
Based on gene expression analysis, it was shown that the glgCAP operon belongs to the RelA regulon Montero M, Eydallin G, Viale AM, Almagro G, Muñoz FJ, Rahimpour M, Sesma MT, Baroja-Fernández E, Pozueta-Romero J,2009
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [5] Romeo T., et al., 1988
[6] Romeo T., et al., 1989
[7] Yang H., et al., 1996
Promoter
Name: glgCp1
+1: 3569389
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 61
Sequence: ctggggagtggcacgccattcccccattcgctggagaggataacccagtgattacggctgTctggcagggacctgcacacg
                        -35                        -10      +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[6] Romeo T., et al., 1989
Terminator(s)
Type: rho-independent
Sequence: ttttccgaaaTGATGGCGGAAAAAAACGGGACCCTTTGGCCCCGTTCTATTTATTGGTGAACTTAcaatctcacc
Reference(s): [3] Feng CQ., et al., 2019
[4] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[CRP,+] 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 CRP-cyclic-AMP activator glgCp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation glgCp1 nd   [EXP-IMP] [6]
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [6] Romeo T., et al., 1989


Transcription unit       
Name: glgCAP
Synonym(s): glgC, glgCAY
Gene(s): glgP, glgA, glgC   Genome Browser M3D Gene expression COLOMBOS
Note(s): In RegulonDB, the old name of this operon was glgBXCAP. With updated information, now there are two operons described, glgBX and glgCAP.
The glgCAP operon is positively regulated by the ppGpp stringent response regulator Romeo T,1989. Bridger WA, Paranchych W,1978. Traxler MF,2008 This operon is also under positive control of the PhoP-PhoQ regulatory system in the submillimolar Mg2+ concentration range Montero M, Eydallin G, Viale AM, Almagro G, Muñoz FJ, Rahimpour M, Sesma MT, Baroja-Fernández E, Pozueta-Romero J,2009
Based on gene expression analysis, it was shown that the glgCAP operon belongs to the RelA regulon Montero M, Eydallin G, Viale AM, Almagro G, Muñoz FJ, Rahimpour M, Sesma MT, Baroja-Fernández E, Pozueta-Romero J,2009
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [5] Romeo T., et al., 1988
[6] Romeo T., et al., 1989
[7] Yang H., et al., 1996
Promoter
Name: glgCp2
+1: 3569455
Distance from start of the gene: 127
Sequence: tgctctcggatcgctttttgatcgcaattaacgccacgcttgaggtaacagagattgtttTacctgctggggagtggcacg
Evidence: [COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [6] Romeo T., et al., 1989
Terminator(s)
Type: rho-independent
Sequence: ttttccgaaaTGATGGCGGAAAAAAACGGGACCCTTTGGCCCCGTTCTATTTATTGGTGAACTTAcaatctcacc
Reference(s): [3] Feng CQ., et al., 2019
[4] Lesnik EA., et al., 2001
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation glgCp2 nd   [EXP-IMP] [6]
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [6] Romeo T., et al., 1989


Transcription unit       
Name: glgCAP
Synonym(s): glgC, glgCAY
Gene(s): glgP, glgA, glgC   Genome Browser M3D Gene expression COLOMBOS
Note(s): In RegulonDB, the old name of this operon was glgBXCAP. With updated information, now there are two operons described, glgBX and glgCAP.
The glgCAP operon is positively regulated by the ppGpp stringent response regulator Romeo T,1989. Bridger WA, Paranchych W,1978. Traxler MF,2008 This operon is also under positive control of the PhoP-PhoQ regulatory system in the submillimolar Mg2+ concentration range Montero M, Eydallin G, Viale AM, Almagro G, Muñoz FJ, Rahimpour M, Sesma MT, Baroja-Fernández E, Pozueta-Romero J,2009
Based on gene expression analysis, it was shown that the glgCAP operon belongs to the RelA regulon Montero M, Eydallin G, Viale AM, Almagro G, Muñoz FJ, Rahimpour M, Sesma MT, Baroja-Fernández E, Pozueta-Romero J,2009
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [5] Romeo T., et al., 1988
[6] Romeo T., et al., 1989
[7] Yang H., et al., 1996
Promoter
Name: glgCp3
+1: 3569571
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 243
Sequence: tttggtggagaatcgctggtgggaagaaggcgacggcaatgtccgttggctaaatcgataTgctcaacctttaagcacgga
                                -35                     -10 +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[8] Maciag A., et al., 2011
[6] Romeo T., et al., 1989
Terminator(s)
Type: rho-independent
Sequence: ttttccgaaaTGATGGCGGAAAAAAACGGGACCCTTTGGCCCCGTTCTATTTATTGGTGAACTTAcaatctcacc
Reference(s): [3] Feng CQ., et al., 2019
[4] Lesnik EA., et al., 2001


Transcription unit          
Name: glgBXCAP
Gene(s): glgP, glgA, glgC, glgX, glgB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of this transcription unit is induced during the exponential growth phase, reaching a plateau in the stationary phase Montero M,2011
Montero et al. Montero M,2011did not find experimentally the transcription start sites upstream of glgC that had been reported by T. Romeo and J. Preiss in 1989 Romeo T,1989 Montero et al. suggested that only the promoters glgBp and glgAp transcribe the genes of this operon and that glgBp is the main promoter directing the expression of the operon Montero M,2011
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Montero M., et al., 2011
Promoter
Name: glgBp
+1: 3573657
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 155
Sequence: taagcgcagatgtttcatgatttaccgggagttaaatagagcattggctattctttaaggGtggctgaatacatgagtatt
                           -35                        -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[1] Montero M., et al., 2011
Terminator(s)
Type: rho-independent
Sequence: ttttccgaaaTGATGGCGGAAAAAAACGGGACCCTTTGGCCCCGTTCTATTTATTGGTGAACTTAcaatctcacc
Reference(s): [3] Feng CQ., et al., 2019
[4] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[PhoP,+] 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
proximal PhoP-phosphorylated activator glgBp 3573683 3573699 -34.0 gatgtttcatGATTTACCGGGAGTTAAatagagcatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences


Reference(s)    

 [1] Montero M., Almagro G., Eydallin G., Viale AM., Munoz FJ., Bahaji A., Li J., Rahimpour M., Baroja-Fernandez E., Pozueta-Romero J., 2011, Escherichia coli glycogen genes are organized in a single glgBXCAP transcriptional unit possessing an alternative suboperonic promoter within glgC that directs glgAP expression., Biochem J 433(1):107-17

 [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] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477

 [4] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94

 [5] Romeo T., Kumar A., Preiss J., 1988, Analysis of the Escherichia coli glycogen gene cluster suggests that catabolic enzymes are encoded among the biosynthetic genes., Gene 70(2):363-76

 [6] Romeo T., Preiss J., 1989, Genetic regulation of glycogen biosynthesis in Escherichia coli: in vitro effects of cyclic AMP and guanosine 5'-diphosphate 3'-diphosphate and analysis of in vivo transcripts., J Bacteriol 171(5):2773-82

 [7] Yang H., Liu MY., Romeo T., 1996, Coordinate genetic regulation of glycogen catabolism and biosynthesis in Escherichia coli via the CsrA gene product., J Bacteriol 178(4):1012-7

 [8] 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

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