RegulonDB RegulonDB 10.9: Gene Form
   

rsd gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

thiC nudC rsd Cis-reg; riboswitch rsdp1 rsdp1 rsdp2 rsdp2 nudCp2 nudCp2 nudCp5 nudCp5 TSS_4819 TSS_4819 TSS_4818 (cluster) TSS_4818 (cluster) TSS_4817 TSS_4817

Gene      
Name: rsd    Texpresso search in the literature
Synonym(s): ECK3987, EG11738, b3995, yjaE
Genome position(nucleotides): 4196332 <-- 4196808 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
49.06
External database links:  
ASAP:
ABE-0013059
ECHOBASE:
EB1689
ECOLIHUB:
rsd
OU-MICROARRAY:
b3995
STRING:
511145.b3995
COLOMBOS: rsd


Product      
Name: regulator of sigma D
Synonym(s): Rsd, YjaE, regulator of sigma;70 (sigma;D), stationary phase protein
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 18.243
Isoelectric point: 5.931
Motif(s):
 
Type Positions Sequence
1 -> 147 MLNQLDNLTERVRGSNKLVDRWLHVRKHLLVAYYNLVGIKPGKESYMRLNEKALDDFCQSLVDYLSAGHFSIYERILHKLEGNGQLARAAKIWPQLEANTQQIMDYYDSSLETAIDHDNYLEFQQVLSDIGEALEARFVLEDKLILL
59 -> 71 QSLVDYLSAGHFS
101 -> 108 QQIMDYYD

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.1 - sigma factors, anti-sigmafactors
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.3 - stimulon
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0016989 - sigma factor antagonist activity
GO:0001000 - bacterial-type RNA polymerase core enzyme binding
biological_process GO:0030813 - positive regulation of nucleotide catabolic process
GO:0010922 - positive regulation of phosphatase activity
GO:0006355 - regulation of transcription, DNA-templated
GO:0010468 - regulation of gene expression
GO:0015968 - stringent response
GO:1903507 - negative regulation of nucleic acid-templated transcription
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[IGI] Inferred from genetic interaction
Reference(s): [1] Azam TA., et al., 2000
[2] Hofmann N., et al., 2011
[3] Jishage M., et al., 1998
[4] Jishage M., et al., 2002
[5] Lee JW., et al., 2018
[6] Neira JL., et al., 2018
External database links:  
DIP:
DIP-10800N
ECOCYC:
EG11738-MONOMER
ECOLIWIKI:
b3995
INTERPRO:
IPR038309
INTERPRO:
IPR023785
INTERPRO:
IPR007448
PDB:
4XWJ
PDB:
2P7V
PFAM:
PF04353
PRIDE:
P0AFX4
PRODB:
PRO_000023876
REFSEQ:
NP_418423
SMR:
P0AFX4
UNIPROT:
P0AFX4


Operon      
Name: rsd         
Operon arrangement:
Transcription unit        Promoter
rsd
rsd


Transcriptional Regulation      
Display Regulation             
Activated by: SlyA, McbR, RcdA, SdiA
Repressed by: ArcA
Growth Conditions:

[1] 

C: Escherichia coli| rpoS knockout mutant| LB medium| 37.0 C| exponential phase
E: Escherichia coli| rpoS knockout mutant| LB medium| 37.0 C| stationary phase

[2] 

C: Escherichia coli| LB medium| 37.0 C| exponential phase
E: Escherichia coli| LB medium| 37.0 C| stationary phase

[3] 

C: Escherichia coli| LB medium| 37.0 C| OD600 from 0.4 to 0.5
E: Escherichia coli| M9 minimal medium| casamino acids 0.4%; glycerol 0.4%| 37.0 C| OD600 from 0.4 to 0.5

[4] 

C: Escherichia coli| LB medium| 37.0 C| early stationary phase
E: Escherichia coli| rpoS knockout mutant| LB medium| 37.0 C| early stationary phase

[5] 

C: Escherichia coli| LB medium| 37.0 C| OD600 from 0.4 to 0.5
E: Escherichia coli| M9 minimal medium| glycerol 0.4%| 37.0 C| OD600 from 0.4 to 0.5

[6] 

C: Escherichia coli| 37.0 C| exponential phase
E: Escherichia coli| 37.0 C| stationary phase

[7] 

C: Escherichia coli| 37.0 C| stationary phase
E: Escherichia coli| rpoS knockout mutant| 37.0 C| stationary phase

[8] 

C: Escherichia coli| LB medium| 37.0 C| OD600 from 0.4 to 0.5
E: Escherichia coli| M9 minimal medium| casamino acids 0.4%; glucose 0.4%| 37.0 C| OD600 from 0.4 to 0.5

[9] 

C: Escherichia coli| LB medium| 37.0 C| OD600 from 0.4 to 0.5
E: Escherichia coli| M9 minimal medium| acetate 0.4%| 37.0 C| OD600 from 0.4 to 0.5



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_4817 4196300 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_4818 (cluster) 4196683 forward For this promoter, there
Read more >
[RS-EPT-CBR] [7]
  promoter TSS_4819 4196698 forward nd [RS-EPT-CBR] [7]
  promoter nudCp5 4196714 forward Similarity to the consensus
Read more >
[ICWHO] [8]
  promoter nudCp2 4196719 forward Similarity to the consensus
Read more >
[ICWHO] [8]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Azam TA., Hiraga S., Ishihama A., 2000, Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid., Genes Cells 5(8):613-26

 [2] Hofmann N., Wurm R., Wagner R., 2011, The E. coli anti-sigma factor Rsd: studies on the specificity and regulation of its expression., PLoS One 6(5):e19235

 [3] Jishage M., Ishihama A., 1998, A stationary phase protein in Escherichia coli with binding activity to the major sigma subunit of RNA polymerase., Proc Natl Acad Sci U S A 95(9):4953-8

 [4] Jishage M., Kvint K., Shingler V., Nystrom T., 2002, Regulation of sigma factor competition by the alarmone ppGpp., Genes Dev 16(10):1260-70

 [5] Lee JW., Park YH., Seok YJ., 2018, Rsd balances (p)ppGpp level by stimulating the hydrolase activity of SpoT during carbon source downshift in Escherichia coli., Proc Natl Acad Sci U S A 115(29):E6845-E6854

 [6] Neira JL., Hornos F., Cozza C., Camara-Artigas A., Abian O., Velazquez-Campoy A., 2018, The histidine phosphocarrier protein, HPr, binds to the highly thermostable regulator of sigma D protein, Rsd, and its isolated helical fragments., Arch Biochem Biophys 639:26-37

 [7] 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.

 [8] 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


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