RegulonDB RegulonDB 10.8: 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): 887977 <-- 888057 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.15
External database links:  
ASAP:
ABE-0047241
ECHOBASE:
EB4506
PortEco:
rybB
COLOMBOS: rybB


Product      
Name: RybB
Synonym(s): P25, small regulatory RNA RybB
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related
Gene Ontology Terms (GO)  
molecular_function 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: [IDA] Inferred from direct assay
[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] Thompson KM., et al., 2007
[10] Vogel J., et al., 2003
[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] 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

 [10] Vogel J., Bartels V., Tang TH., Churakov G., Slagter-Jager JG., Huttenhofer A., Wagner EG., 2003, RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria., Nucleic Acids Res 31(22):6435-43

 [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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