RegulonDB RegulonDB 10.9: 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
ECOLIHUB:
rpoS
OU-MICROARRAY:
b2741
STRING:
511145.b2741
COLOMBOS: rpoS


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
288 -> 307 LEDVGREIGLTRERVRQIQV
173 -> 173 K
174 -> 249 ELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDT
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:
IPR009042
INTERPRO:
IPR007630
INTERPRO:
IPR007627
INTERPRO:
IPR007624
INTERPRO:
IPR013325
INTERPRO:
IPR036388
INTERPRO:
IPR014284
INTERPRO:
IPR000943
INTERPRO:
IPR012761
INTERPRO:
IPR013324
MODBASE:
P13445
PDB:
6KJ6
PDB:
6IDO
PDB:
6FI7
PDB:
5IPN
PDB:
5IPM
PDB:
5IPL
PFAM:
PF00140
PFAM:
PF04545
PFAM:
PF04542
PFAM:
PF04539
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: MqsA, CRP, 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


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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