RegulonDB RegulonDB 10.9: Gene Form
   

csrC gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yihA yihI csrC CRP UvrY CRP CRP terminator TSS_4543 TSS_4543 yihIp yihIp csrCp csrCp yihAp9 yihAp9 TSS_4540 (cluster) TSS_4540 (cluster)

Gene      
Name: csrC    Texpresso search in the literature
Synonym(s): ECK3858, G0-8874, IS198, b4457, psrA21, ryiB, sraK, tpk2
Genome position(nucleotides): 4051036 --> 4051281 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.37
External database links:  
ASAP:
ABE-0047275
ECHOBASE:
EB4540
ECOLIHUB:
csrC
COLOMBOS: csrC


Product      
Name: small regulatory RNA CsrC
Synonym(s): CsrC, IS198, PsrA21, RNA inhibitor of CsrA, RyiB, SraK, Tpk2
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related
Gene Ontology Terms (GO)  
molecular_function GO:0005515 - protein binding
biological_process GO:1900192 - positive regulation of single-species biofilm formation
GO:1902201 - negative regulation of bacterial-type flagellum-dependent cell motility
GO:1904572 - negative regulation of mRNA binding
Note(s): Note(s): ...[more].
Evidence: [IDA] Inferred from direct assay
[IMP] Inferred from mutant phenotype
Reference(s): [1] Friedman RC., et al., 2017
[2] Jonas K., et al., 2006
[3] Krol JE. 2018
[4] Mercante J., et al., 2009
[5] Vakulskas CA., et al., 2014
[6] Wang X., et al., 2005
[7] Weilbacher T., et al., 2003
External database links:  
ECOCYC:
CSRC-RNA
ECOLIWIKI:
b4457


Operon      
Name: csrC         
Operon arrangement:
Transcription unit        Promoter
csrC


Transcriptional Regulation      
Display Regulation             
Activated by: UvrY
Repressed by: CRP


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_4540 (cluster) 4050794 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [8]
  promoter yihAp9 4050985 reverse Similarity to the consensus
Read more >
[ICWHO] [9]
  promoter TSS_4543 4051320 forward nd [RS-EPT-CBR] [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] Friedman RC., Kalkhof S., Doppelt-Azeroual O., Mueller SA., Chovancova M., von Bergen M., Schwikowski B., 2017, Common and phylogenetically widespread coding for peptides by bacterial small RNAs., BMC Genomics 18(1):553

 [2] Jonas K., Tomenius H., Romling U., Georgellis D., Melefors O., 2006, Identification of YhdA as a regulator of the Escherichia coli carbon storage regulation system., FEMS Microbiol Lett 264(2):232-7

 [3] Krol JE., 2018, Regulatory loop between the CsrA system and NhaR, a high salt/high pH regulator., PLoS One 13(12):e0209554

 [4] Mercante J., Edwards AN., Dubey AK., Babitzke P., Romeo T., 2009, Molecular geometry of CsrA (RsmA) binding to RNA and its implications for regulated expression., J Mol Biol 392(2):511-28

 [5] Vakulskas CA., Pannuri A., Cortes-Selva D., Zere TR., Ahmer BM., Babitzke P., Romeo T., 2014, Global effects of the DEAD-box RNA helicase DeaD (CsdA) on gene expression over a broad range of temperatures., Mol Microbiol 92(5):945-58

 [6] Wang X., Dubey AK., Suzuki K., Baker CS., Babitzke P., Romeo T., 2005, CsrA post-transcriptionally represses pgaABCD, responsible for synthesis of a biofilm polysaccharide adhesin of Escherichia coli., Mol Microbiol 56(6):1648-63

 [7] Weilbacher T., Suzuki K., Dubey AK., Wang X., Gudapaty S., Morozov I., Baker CS., Georgellis D., Babitzke P., Romeo T., 2003, A novel sRNA component of the carbon storage regulatory system of Escherichia coli., Mol Microbiol 48(3):657-70

 [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.

 [9] 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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