RegulonDB RegulonDB 11.0: Operon Form
   

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




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


Transcription unit       
Name: glmY
Gene(s): glmY   Genome Browser M3D Gene expression COLOMBOS
Note(s): The glmY gene is transcribed from two overlapping promoters: one of them is σ70 (glmYp2) and the other is σ54 dependent (glmYp1) Reichenbach B,2009 Both promoters start transcription at the same nucleotide; however, they are active during different growth phases, as glmYp1 is mainly active during the transition to stationary phase and glmYp2 is active during exponential phase Reichenbach B,2009 The overlapping of promoters upstream of glmY is a conserved feature in other enterobacterial species Reichenbach B,2009
The glmY gene is located upstream of the gene cluster glrK-yfhG-glrR in the genome of all species of the Enterobacteriaceae family Gopel Y,2011
Evidence: [ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
Reference(s): [1] Vogel J., et al., 2003
Promoter
Name: glmYp2
+1: 2691340
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 0
Sequence: ataatcagtacgttaccaaactattttctttattggcacagttactgcataatagtaaccAgtggctcattcaccgactta
                        -35                     -10         +1                   
Evidence: [HIPP]
[ICWHO]
[IDA]
[IHBCE]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Reichenbach B., et al., 2009
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: gttcagatacAACAAAGCCGGGAATTACCCGGCTTTGTTatggaataag
Reference(s): [5] Urban JH., et al., 2007


Transcription unit          
Name: glmY
Synonym(s): sroF
Gene(s): glmY   Genome Browser M3D Gene expression COLOMBOS
Note(s): The glmY gene is transcribed from two overlapping promoters: one of them is σ70 (glmYp2) and the other is σ54 dependent (glmYp1) Reichenbach B,2009 Both promoters start transcription at the same nucleotide; however, they are active during different growth phases, as glmYp1 is mainly active during the transition to stationary phase and glmYp2 is active during exponential phase Reichenbach B,2009 The overlapping of promoters upstream of glmY is a conserved feature in other enterobacterial species Reichenbach B,2009
The activity of the glmYp1 promoter is dependent on the presence of the transcription factors GlrR and IHF. GlrR binds to three sites, designated ABS1, ABS2, and ABS3Reichenbach B,2009.They are located at -221.5, -188.5, and -125.5 upstream of the transcription start site, respectively Reichenbach B,2009|. While ABS2 and ABS3 are essential for the activity of glmYp1, ABS1 only contributes slightly in the transcription of glmY Reichenbach B,2009. IHF binds to two sites, located at -169 and -52 upstream of the transcription start site Gopel Y,2011
The glmY gene is located upstream of the gene cluster glrK-yfhG-glrR in the genome of all species of the Enterobacteriaceae family Gopel Y,2011
Evidence: [ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
Reference(s): [1] Vogel J., et al., 2003
Promoter
Name: glmYp1
+1: 2691340
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 0
Sequence: ataatcagtacgttaccaaactattttctttattggcacagttactgcataatagtaaccAgtggctcattcaccgactta
                                  -24         -12           +1                   
Evidence: [HIPP]
[ICWHO]
[IDA]
[IHBCE]
[IMP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Reichenbach B., et al., 2009
[4] Salgado H, et al., 2012
[5] Urban JH., et al., 2007
[1] Vogel J., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: gttcagatacAACAAAGCCGGGAATTACCCGGCTTTGTTatggaataag
Reference(s): [5] Urban JH., et al., 2007
TF binding sites (TFBSs)
[GlrR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote GlrR-phosphorylated activator glmYp1 2691457 2691474 -125.5 tatcttaagtTGTCTCTTTTTAGCGACAcagtggctga nd [GEA], [APIORCISFBSCS], [BPP], [SM] [3]
remote GlrR-phosphorylated activator glmYp1 2691520 2691537 -188.5 tggtttgccgTGTCGCTTTCTGGCGACActtaactcat nd [GEA], [APIORCISFBSCS], [BPP], [SM] [3]
remote GlrR-phosphorylated activator glmYp1 2691553 2691570 -221.5 agcttttttgTGTCTGTAAATCACGACAatgggtggtt nd [GEA], [APIORCISFBSCS], [BPP], [SM] [3]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF activator glmYp1 2691386 2691398 -52.0 agcaacgtatAATCAGTACGTTAccaaactatt nd [GEA], [APIORCISFBSCS], [BPP] [6]
remote IHF activator glmYp1 2691503 2691515 -169.0 gcgacacttaACTCATTGATTTTaatattatct nd [GEA], [APIORCISFBSCS], [BPP], [SM] [3], [6]


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [IDA] Inferred from direct assay

 [IHBCE] Inferred by a human based on computational evidence

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [TIM] Transcription initiation mapping

 [IMP] Inferred from mutant phenotype

 [GEA] Gene expression analysis

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

 [BPP] Binding of purified proteins

 [SM] Site mutation


Reference(s)    

 [1] Vogel J., Bartels V., Tang TH., Churakov G., Slagter-Jager JG., Huttenhofer A., Wagner EG., 2003, RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria., Nucleic Acids Res 31(22):6435-43

 [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] Reichenbach B., Gopel Y., Gorke B., 2009, Dual control by perfectly overlapping sigma 54- and sigma 70- promoters adjusts small RNA GlmY expression to different environmental signals., Mol Microbiol 74(5):1054-70

 [4] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [5] Urban JH., Papenfort K., Thomsen J., Schmitz RA., Vogel J., 2007, A Conserved Small RNA Promotes Discoordinate Expression of the glmUS Operon mRNA to Activate GlmS Synthesis., J Mol Biol 373(3):521-8

 [6] Gopel Y., Luttmann D., Heroven AK., Reichenbach B., Dersch P., Gorke B., 2011, Common and divergent features in transcriptional control of the homologous small RNAs GlmY and GlmZ in Enterobacteriaceae., Nucleic Acids Res 39(4):1294-309

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