RegulonDB RegulonDB 11.1: Gene Form
   

rpoS gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ygbN nlpD rpoS MqsA ArcA CRP ArcA CRP DksA-ppGpp DksA-ppGpp ppGpp terminator TSS_3034 TSS_3034 rpoSp rpoSp rpoSp4 rpoSp4 rpoSp3 rpoSp3 TSS_3032 TSS_3032 rpoSp2 rpoSp2 TSS_3031 TSS_3031 rpoSp1 rpoSp1 TSS_3030 TSS_3030 TSS_3029 TSS_3029 TSS_3028 TSS_3028 TSS_3027 TSS_3027 TSS_3026 TSS_3026

Gene      
Name: rpoS    Texpresso search in the literature
Synonym(s): ECK2736, EG10510, abrD, appR, b2741, csi2, dpeB, katF, nur, otsX, sigS
Genome position(nucleotides): 2866559 <-- 2867551
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.06
External database links:  
ASAP:
 ABE-0009001
CGSC:
 18208
ECHOBASE:
 EB0505
ECOLIHUB:
 rpoS
OU-MICROARRAY:
 b2741
STRING:
 511145.b2741
COLOMBOS: rpoS


Shine dalgarno      
Sequence: ggatcacgggTAGGAGccacctTAT


Product      
Name: RNA polymerase sigma factor RpoS
Synonym(s): sigma;S, AbrD, AppR, DpeB, KatF, Nur, OtsX, RNA polymerase, sigma S (sigma 38) factor, RpoS, SigS, sigma 38 factor, sigma S factor
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 37.972
Isoelectric point: 4.584
Motif(s):
 
Type Positions Sequence Comment
25 -> 25 F UniProt: In Ref. 3; CAA78692..
29 -> 29 A UniProt: In Ref. 1; CAA34435..
33 -> 33 Q UniProt: In Ref. 2; BAA02747 and 6; BAA21003..
56 -> 89 DATQLYLGEIGYSPLLTAEEEVYFARRALRGDVA UniProt: Sigma-70 factor domain-1; Sequence Annotation Type: region of interest.
94 -> 164 MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT UniProt: Sigma-70 factor domain-2; Sequence Annotation Type: region of interest.

 
Classification:
Multifun Terms (GenProtEC)  
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.1 - sigma factors, anti-sigmafactors
Gene Ontology Terms (GO)  
cellular_component GO:1903865 - sigma factor antagonist complex
GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0016987 - sigma factor activity
GO:0003700 - DNA-binding transcription factor activity
GO:0001000 - bacterial-type RNA polymerase core enzyme binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0006950 - response to stress
GO:0006352 - DNA-templated transcription, initiation
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0010468 - regulation of gene expression
GO:2000142 - regulation of DNA-templated transcription, initiation
Note(s): Note(s): ...[more].
Evidence: [EXP] Inferred from experiment
Reference(s): [1] Frohlich KS., et al., 2018
[2] Van den Bergh B., et al., 2022
External database links:  
ALPHAFOLD:
 P13445
DIP:
 DIP-10777N
ECOCYC:
 RPOS-MONOMER
ECOLIWIKI:
 b2741
INTERPRO:
 IPR036388
INTERPRO:
 IPR007627
INTERPRO:
 IPR007624
INTERPRO:
 IPR000943
INTERPRO:
 IPR007630
INTERPRO:
 IPR009042
INTERPRO:
 IPR012761
INTERPRO:
 IPR013324
INTERPRO:
 IPR013325
INTERPRO:
 IPR014284
MODBASE:
 P13445
PDB:
 6UU5
PDB:
 6UU6
PDB:
 6UU7
PDB:
 6UUA
PDB:
 6UUB
PDB:
 6UUC
PDB:
 6UU4
PDB:
 6UU3
PDB:
 6UU2
PDB:
 6UU1
PDB:
 6UU0
PDB:
 6UTZ
PDB:
 6UTY
PDB:
 6UTX
PDB:
 6UTW
PDB:
 6UTV
PDB:
 6KJ6
PDB:
 6IDO
PDB:
 6FI7
PDB:
 5IPN
PDB:
 5IPL
PDB:
 5IPM
PFAM:
 PF04539
PFAM:
 PF04542
PFAM:
 PF04545
PFAM:
 PF00140
PRIDE:
 P13445
PRINTS:
 PR00046
PRODB:
 PRO_000023851
PROSITE:
 PS00716
PROSITE:
 PS00715
REFSEQ:
 NP_417221
SMR:
 P13445
SWISSMODEL:
 P13445
UNIPROT:
 P13445


Operon      
Name: nlpD-rpoS         
Operon arrangement:
Transcription unit        Promoter
rpoS
rpoS
rpoS
rpoS
rpoS
nlpD-rpoS
nlpD-rpoS


Transcriptional Regulation      
Display Regulation             
Activated by: GadX
Repressed by: CRP, MqsA, Fur, ArcA


RNA cis-regulatory element    
Attenuation: Translational


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_3026 2866797 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3027 2867113 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3028 2867456 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3029 2867493 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3030 2867551 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3031 2867572 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3032 2867645 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3034 2868128 reverse nd [RS-EPT-CBR] [3]


Evidence    

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


Reference(s)    

 [1] Frohlich KS., Gottesman S., 2018, Small Regulatory RNAs in the Enterobacterial Response to Envelope Damage and Oxidative Stress., Microbiol Spectr 6(4)

 [2] Van den Bergh B., Schramke H., Michiels JE., Kimkes TEP., Radzikowski JL., Schimpf J., Vedelaar SR., Burschel S., Dewachter L., Loncar N., Schmidt A., Meijer T., Fauvart M., Friedrich T., Michiels J., Heinemann M., 2022, Mutations in respiratory complex I promote antibiotic persistence through alterations in intracellular acidity and protein synthesis., Nat Commun 13(1):546

 [3] 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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