RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: glmUS
Gene(s): glmS, glmU   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for glmU . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Plumbridge J. 1995
Promoter
Name: glmUp1
+1: 3915223
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 23
Sequence: ctgtccatttcacgatgaaaaaaatgtagttttttcaaggtgaagcggtttaaattcgttCtcaaattacagtcaggacgc
                                   -35                  -10 +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[1] Plumbridge J. 1995
Terminator(s)
Type: rho-independent
Sequence: aggaagaaaaATGCCCCGCTTACGCAGGGCAtccatttatt
Reference(s): [5] Walker JE., et al., 1984
TF binding sites (TFBSs)
[NagC,+] 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 NagC activator glmUp1 3915258 3915280 -46.0 ttatcctctgTCCATTTCACGATGAAAAAAATGtagttttttc nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
remote NagC activator glmUp1 3915411 3915433 -199.0 ctgttttcctGTTTATTCATTGATCGAAATAAGagcaaaaaca nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA GlmZ glmUS activator 3913690 3913708 UCGUUGUCGGUCAACCUGU TRANSLATION-BLOCKING, MRNA-DEGRADATION [EXP] [3], [4]


Transcription unit          
Name: glmUS
Gene(s): glmS, glmU   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Plumbridge J. 1995
Promoter
Name: glmUp2
+1: 3915326
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 126
Sequence: aaattaaggtactgccttaattttctgcagacaaaaggcgtgacgatggtcgaaaatggcGctttcgtcagcggggataat
                              -35                        -10+1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[1] Plumbridge J. 1995
[6] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: aggaagaaaaATGCCCCGCTTACGCAGGGCAtccatttatt
Reference(s): [5] Walker JE., et al., 1984
TF binding sites (TFBSs)
[NagC,-] 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
remote NagC repressor glmUp2 3915258 3915280 58.0 ttatcctctgTCCATTTCACGATGAAAAAAATGtagttttttc nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
remote NagC repressor glmUp2 3915411 3915433 -96.0 ctgttttcctGTTTATTCATTGATCGAAATAAGagcaaaaaca nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA GlmZ glmUS activator 3913690 3913708 UCGUUGUCGGUCAACCUGU TRANSLATION-BLOCKING, MRNA-DEGRADATION [EXP-IDA], [EXP-IMP] [3], [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP] Inferred from experiment

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

 [EXP-IDA] Inferred from direct assay

 [EXP-IMP] Inferred from mutant phenotype


Reference(s)    

 [1] Plumbridge J., 1995, Co-ordinated regulation of amino sugar biosynthesis and degradation: the NagC repressor acts as both an activator and a repressor for the transcription of the glmUS operon and requires two separated NagC binding sites., EMBO J 14(16):3958-65

 [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., Maes A., Kalamorz F., Hajnsdorf E., Gorke B., 2008, The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli., Nucleic Acids Res 36(8):2570-80

 [4] Urban JH., Vogel J., 2008, Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation., PLoS Biol 6(3):e64

 [5] Walker JE., Saraste M., Gay NJ., 1984, The unc operon. Nucleotide sequence, regulation and structure of ATP-synthase., Biochim Biophys Acta 768(2):164-200

 [6] 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.

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