RegulonDB RegulonDB 10.9: Gene Form
   

csrB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

syd csrB yqcC UvrY IHF TSS_3110 TSS_3110 csrBp csrBp TSS_3108 (cluster) TSS_3108 (cluster) TSS_3107 TSS_3107 TSS_3106 TSS_3106 TSS_3105 TSS_3105 TSS_3104 TSS_3104 TSS_3103 (cluster) TSS_3103 (cluster) TSS_3102 (cluster) TSS_3102 (cluster) TSS_3101 TSS_3101 TSS_3100 TSS_3100 TSS_3099 TSS_3099 TSS_3098 (cluster) TSS_3098 (cluster) TSS_3097 TSS_3097 TSS_3096 (cluster) TSS_3096 (cluster) TSS_3095 TSS_3095 TSS_3094 TSS_3094 TSS_3093 TSS_3093 TSS_3092 TSS_3092 TSS_3091 TSS_3091 TSS_3090 TSS_3090

Gene      
Name: csrB    Texpresso search in the literature
Synonym(s): ECK2787, G0-8785, b4408
Genome position(nucleotides): 2924156 <-- 2924524 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.49
External database links:  
ASAP:
ABE-0047213
ECHOBASE:
EB4282
ECOLIHUB:
csrB
COLOMBOS: csrB


Product      
Name: small regulatory RNA CsrB
Synonym(s): CsrB
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.4 - RNA degradation
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional
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
Reference(s): [1] Chavez RG., et al., 2010
[2] Cui Y., et al., 2001
[3] Cui YY., et al., 2014
[4] Hayes ET., et al., 2006
[5] Jackson DW., et al., 2002
[6] Jiang GR., et al., 2001
[7] Jonas K., et al., 2006
[8] Krol JE. 2018
[9] Kulkarni PR., et al., 2006
[10] Leistra AN., et al., 2017
[11] Liu MY., et al., 1997
[12] Vakulskas CA., et al., 2014
[13] Yakandawala N., et al., 2008
External database links:  
ECOCYC:
CSRB-RNA
ECOLIWIKI:
b4408


Operon      
Name: csrB         
Operon arrangement:
Transcription unit        Promoter
csrB


Transcriptional Regulation      
Display Regulation             
Activated by: UvrY, IHF


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_3090 2924137 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3091 2924349 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3092 2924385 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3093 2924391 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3094 2924394 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3095 2924415 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3096 (cluster) 2924424 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [14]
  promoter TSS_3097 2924436 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3098 (cluster) 2924452 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [14]
  promoter TSS_3099 2924464 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3100 2924466 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3101 2924468 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3102 (cluster) 2924473 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [14]
  promoter TSS_3103 (cluster) 2924477 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [14]
  promoter TSS_3104 2924484 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3105 2924496 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3106 2924507 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3107 2924509 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3108 (cluster) 2924522 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [14]
  promoter TSS_3110 2924528 reverse nd [RS-EPT-CBR] [14]


Evidence    

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



Reference(s)    

 [1] Chavez RG., Alvarez AF., Romeo T., Georgellis D., 2010, The physiological stimulus for the BarA sensor kinase., J Bacteriol 192(7):2009-12

 [2] Cui Y., Chatterjee A., Chatterjee AK., 2001, Effects of the two-component system comprising GacA and GacS of Erwinia carotovora subsp. carotovora on the production of global regulatory rsmB RNA, extracellular enzymes, and harpinEcc., Mol Plant Microbe Interact 14(4):516-26

 [3] Cui YY., Ling C., Zhang YY., Huang J., Liu JZ., 2014, Production of shikimic acid from Escherichia coli through chemically inducible chromosomal evolution and cofactor metabolic engineering., Microb Cell Fact 13:21

 [4] Hayes ET., Wilks JC., Sanfilippo P., Yohannes E., Tate DP., Jones BD., Radmacher MD., BonDurant SS., Slonczewski JL., 2006, Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12., BMC Microbiol 6:89

 [5] Jackson DW., Suzuki K., Oakford L., Simecka JW., Hart ME., Romeo T., 2002, Biofilm formation and dispersal under the influence of the global regulator CsrA of Escherichia coli., J Bacteriol 184(1):290-301

 [6] Jiang GR., Nikolova S., Clark DP., 2001, Regulation of the ldhA gene, encoding the fermentative lactate dehydrogenase of Escherichia coli., Microbiology 147(Pt 9):2437-46

 [7] 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

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

 [9] Kulkarni PR., Cui X., Williams JW., Stevens AM., Kulkarni RV., 2006, Prediction of CsrA-regulating small RNAs in bacteria and their experimental verification in Vibrio fischeri., Nucleic Acids Res 34(11):3361-9

 [10] Leistra AN., Amador P., Buvanendiran A., Moon-Walker A., Contreras LM., 2017, Rational Modular RNA Engineering Based on In Vivo Profiling of Structural Accessibility., ACS Synth Biol 6(12):2228-2240

 [11] Liu MY., Gui G., Wei B., Preston JF., Oakford L., Yuksel U., Giedroc DP., Romeo T., 1997, The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli., J Biol Chem 272(28):17502-10

 [12] 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

 [13] Yakandawala N., Romeo T., Friesen AD., Madhyastha S., 2008, Metabolic engineering of Escherichia coli to enhance phenylalanine production., Appl Microbiol Biotechnol 78(2):283-91

 [14] 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.


RegulonDB