RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: uspA
Gene(s): uspA   Genome Browser M3D Gene expression COLOMBOS
Note(s): uspA gene expression is upregulated upon L-valine addition (isoleucine starvation) in the cellular growth medium Gummesson B, Shah SA, Borum AS, Fessler M, Mitarai N, Sørensen MA, Svenningsen SL,2020.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for uspA. 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-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Nystrom T., et al., 1992
Promoter
Name: uspAp1
+1: 3639983
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 128
Sequence: tttatctaacgagtaagcaaggcggattgacggatcatccgggtcgctataaggtaaggaTggtcttaacactgaatcttt
                           -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] Nystrom T., et al., 1992
[3] Nystrom T., et al., 1994
Terminator(s)
Type: rho-independent
Sequence: cgtgttcctgAACGCCCGCATATGCGGGCGTTttgctttttg
Reference(s): [1] Nystrom T., et al., 1992
TF binding sites (TFBSs)
[FadR,-] 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 FadR repressor uspAp1 3639979 3639995 5.0 ctataaggtaAGGATGGTCTTAACACTgaatctttac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [6]
remote FadR repressor uspAp1 3640071 3640087 97.0 agaaacgctaGCTGGCCAGTCATCGACaactttatgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [6]
[IHF,+] 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 IHF activator uspAp1 3639896 3639908 -81.0 ggttaaccacTATCAATATATTCatgtcgaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4], [5]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation uspAp1 nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [6]
[7]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [6] Farewell A., et al., 1996
[7] Kvint K., et al., 2000


Transcription unit       
Name: uspA
Gene(s): uspA   Genome Browser M3D Gene expression COLOMBOS
Note(s): uspA gene expression is upregulated upon L-valine addition (isoleucine starvation) in the cellular growth medium Gummesson B, Shah SA, Borum AS, Fessler M, Mitarai N, Sørensen MA, Svenningsen SL,2020.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for uspA. 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-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Nystrom T., et al., 1992
Promoter
Name: uspAp2
+1: 3639998
Distance from start of the gene: 113
Sequence: agcaaggcggattgacggatcatccgggtcgctataaggtaaggatggtcttaacactgaAtctttacggctgggttagcc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Nystrom T., et al., 1992
[8] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: cgtgttcctgAACGCCCGCATATGCGGGCGTTttgctttttg
Reference(s): [1] Nystrom T., et al., 1992


Transcription unit       
Name: uspA
Gene(s): uspA   Genome Browser M3D Gene expression COLOMBOS
Note(s): uspA gene expression is upregulated upon L-valine addition (isoleucine starvation) in the cellular growth medium Gummesson B, Shah SA, Borum AS, Fessler M, Mitarai N, Sørensen MA, Svenningsen SL,2020.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for uspA. 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-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Nystrom T., et al., 1992
Promoter
Name: uspAp3
+1: 3640000
Distance from start of the gene: 111
Sequence: caaggcggattgacggatcatccgggtcgctataaggtaaggatggtcttaacactgaatCtttacggctgggttagcccc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Nystrom T., et al., 1992
Terminator(s)
Type: rho-independent
Sequence: cgtgttcctgAACGCCCGCATATGCGGGCGTTttgctttttg
Reference(s): [1] Nystrom T., et al., 1992


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

 [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-CELLULAR-EXTRACTS] Binding of cellular extracts

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

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


Reference(s)    

 [1] Nystrom T., Neidhardt FC., 1992, Cloning, mapping and nucleotide sequencing of a gene encoding a universal stress protein in Escherichia coli., Mol Microbiol 6(21):3187-98

 [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] Nystrom T., Neidhardt FC., 1994, Expression and role of the universal stress protein, UspA, of Escherichia coli during growth arrest., Mol Microbiol 11(3):537-44

 [4] Farewell A., Kvint K., Nystrom T., 1998, uspB, a new sigmaS-regulated gene in Escherichia coli which is required for stationary-phase resistance to ethanol., J Bacteriol 180(23):6140-7

 [5] Nystrom T., 1995, Glucose starvation stimulon of Escherichia coli: role of integration host factor in starvation survival and growth phase-dependent protein synthesis., J Bacteriol 177(19):5707-10

 [6] Farewell A., Diez AA., DiRusso CC., Nystrom T., 1996, Role of the Escherichia coli FadR regulator in stasis survival and growth phase-dependent expression of the uspA, fad, and fab genes., J Bacteriol 178(22):6443-50

 [7] Kvint K., Hosbond C., Farewell A., Nybroe O., Nystrom T., 2000, Emergency derepression: stringency allows RNA polymerase to override negative control by an active repressor., Mol Microbiol 35(2):435-43

 [8] 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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