RegulonDB RegulonDB 10.9: Gene Form
   

rybB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybjL rcdA rybB DksA DksA-ppGpp DksA-ppGpp TSS_997 (cluster) TSS_997 (cluster) TSS_996 TSS_996 TSS_995 TSS_995 TSS_994 (cluster) TSS_994 (cluster) TSS_993 TSS_993 TSS_992 TSS_992 rybBp rybBp

Gene      
Name: rybB    Texpresso search in the literature
Synonym(s): ECK0837, G0-8880, b4417, p25
Genome position(nucleotides): 887979 <-- 888057 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.1
External database links:  
ASAP:
ABE-0047241
ECHOBASE:
EB4506
ECOLIHUB:
rybB
COLOMBOS: rybB


Product      
Name: small regulatory RNA RybB
Synonym(s): P25, RybB
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related
Gene Ontology Terms (GO)  
molecular_function GO:0061980 - regulatory RNA binding
GO:0005515 - protein binding
GO:0003729 - mRNA binding
GO:0048027 - mRNA 5'-UTR binding
biological_process GO:0006950 - response to stress
GO:0043488 - regulation of mRNA stability
GO:0070928 - regulation of mRNA stability, ncRNA-mediated
GO:1900191 - negative regulation of single-species biofilm formation
Note(s): Note(s): ...[more].
Evidence: [IEP] Inferred from expression pattern
[IMP] Inferred from mutant phenotype
Reference(s): [1] El-Mowafi SA., et al., 2014
[2] Gogol EB., et al., 2011
[3] Guo MS., et al., 2014
[4] Johansen J., et al., 2006
[5] Lalaouna D., et al., 2015
[6] Leiser OP., et al., 2012
[7] Malecka EM., et al., 2015
[8] Mihailovic MK., et al., 2018
[9] Serra DO., et al., 2016
[10] Thompson KM., et al., 2007
[11] Wassarman KM., et al., 2001
External database links:  
ECOCYC:
RYBB-RNA
ECOLIWIKI:
b4417


Operon      
Name: rybB         
Operon arrangement:
Transcription unit        Promoter
rybB


Transcriptional Regulation      
Display Regulation             
Repressed by: NsrR


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_992 888924 reverse nd [RS-EPT-CBR] [12]
  promoter TSS_993 888928 reverse nd [RS-EPT-CBR] [12]
  promoter TSS_994 (cluster) 888947 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [12]
  promoter TSS_995 888953 reverse nd [RS-EPT-CBR] [12]
  promoter TSS_996 889468 reverse nd [RS-EPT-CBR] [12]
  promoter TSS_997 (cluster) 889475 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [12]


Evidence    

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



Reference(s)    

 [1] El-Mowafi SA., Alumasa JN., Ades SE., Keiler KC., 2014, Cell-based assay to identify inhibitors of the Hfq-sRNA regulatory pathway., Antimicrob Agents Chemother 58(9):5500-9

 [2] Gogol EB., Rhodius VA., Papenfort K., Vogel J., Gross CA., 2011, Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon., Proc Natl Acad Sci U S A 108(31):12875-80

 [3] Guo MS., Updegrove TB., Gogol EB., Shabalina SA., Gross CA., Storz G., 2014, MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein., Genes Dev 28(14):1620-34

 [4] Johansen J., Rasmussen AA., Overgaard M., Valentin-Hansen P., 2006, Conserved small non-coding RNAs that belong to the sigmaE regulon: role in down-regulation of outer membrane proteins., J Mol Biol 364(1):1-8

 [5] Lalaouna D., Masse E., 2015, Identification of sRNA interacting with a transcript of interest using MS2-affinity purification coupled with RNA sequencing (MAPS) technology., Genom Data 5:136-8

 [6] Leiser OP., Charlson ES., Gerken H., Misra R., 2012, Reversal of the ΔdegP phenotypes by a novel rpoE allele of Escherichia coli., PLoS One 7(3):e33979

 [7] Malecka EM., Strozecka J., Sobanska D., Olejniczak M., 2015, Structure of bacterial regulatory RNAs determines their performance in competition for the chaperone protein Hfq., Biochemistry 54(5):1157-70

 [8] Mihailovic MK., Vazquez-Anderson J., Li Y., Fry V., Vimalathas P., Herrera D., Lease RA., Powell WB., Contreras LM., 2018, High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites., Nat Commun 9(1):4084

 [9] Serra DO., Mika F., Richter AM., Hengge R., 2016, The green tea polyphenol EGCG inhibits E. coli biofilm formation by impairing amyloid curli fibre assembly and downregulating the biofilm regulator CsgD via the σ(E) -dependent sRNA RybB., Mol Microbiol 101(1):136-51

 [10] Thompson KM., Rhodius VA., Gottesman S., 2007, {sigma}E Regulates and Is Regulated by a Small RNA in Escherichia coli., J Bacteriol 189(11):4243-56

 [11] Wassarman KM., Repoila F., Rosenow C., Storz G., Gottesman S., 2001, Identification of novel small RNAs using comparative genomics and microarrays., Genes Dev 15(13):1637-51

 [12] 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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