RegulonDB RegulonDB 10.7: 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 DsrA RprA ArcZ 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 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.06
External database links:  
ASAP:
ABE-0009001
CGSC:
18208
ECHOBASE:
EB0505
OU-MICROARRAY:
b2741
PORTECO:
rpoS
REGULONDB:
b2741
STRING:
511145.b2741
M3D: rpoS
COLOMBOS: rpoS
PortEco: b2741


Shine dalgarno      
Sequence: ggatcacgggTAGGAGccacctTAT


Product      
Name: RNA polymerase, sigma S (sigma 38) factor
Synonym(s): sigma;S, AbrD, AppR, DpeB, KatF, Nur, OtsX, 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
174 -> 248 ELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPED
288 -> 307 LEDVGREIGLTRERVRQIQV
173 -> 173 K
178 -> 178 Y
29 -> 29 A

 

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: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:0010468 - regulation of gene expression
GO:2000142 - regulation of DNA-templated transcription, initiation
GO:0001123 - transcription initiation from bacterial-type RNA polymerase promoter
Note(s): Note(s): ...[more].
Evidence: [IE] Inferred from experiment
Reference(s): [1] Frohlich KS., et al., 2018
External database links:  
DIP:
DIP-10777N
ECOCYC:
RPOS-MONOMER
ECOLIWIKI:
b2741
INTERPRO:
IPR012761
INTERPRO:
IPR009042
INTERPRO:
IPR013325
INTERPRO:
IPR013324
INTERPRO:
IPR007630
INTERPRO:
IPR036388
INTERPRO:
IPR014284
INTERPRO:
IPR000943
INTERPRO:
IPR007624
INTERPRO:
IPR007627
MINT:
MINT-1228474
MODBASE:
P13445
PDB:
6FI7
PDB:
5IPN
PDB:
5IPM
PDB:
5IPL
PFAM:
PF00140
PFAM:
PF04545
PFAM:
PF04542
PFAM:
PF04539
PRIDE:
P13445
PRINTS:
PR00046
PRODB:
PRO_000023851
PROSITE:
PS00715
PROSITE:
PS00716
PROTEINMODELPORTAL:
P13445
REFSEQ:
NP_417221
SMR:
P13445
SWISSMODEL:
P13445
UNIPROT:
P13445


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


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

[1] 

C: Escherichia coli| LB medium
E: Escherichia coli| relA knockout mutant; spoT knockout mutant| LB medium

[2] 

C: Escherichia coli| plasmid pRL48 (from nt -1398 to nt +70 relative to rpoS translational start site) mutant| LB medium| exponential phase
E: Escherichia coli| plasmid pRL48 (from nt -1398 to nt +70 relative to rpoS translational start site) mutant| LB medium| stationary phase

[3] 

C: Escherichia coli| LB medium| 28.0 C| mid to late exponential phase
E: Escherichia coli| conditioned culture medium| 28.0 C| mid to late exponential phase



RNA cis-regulatory element    
Attenuation: Translational


Regulation by small RNA    
  Display Regulation
small RNA arcZ, rprA, dsrA, oxyS


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] [2]
  promoter TSS_3027 2867113 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3028 2867456 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3029 2867493 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3030 2867551 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3031 2867572 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3032 2867645 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3034 2868128 reverse nd [RS-EPT-CBR] [2]


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] 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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