RegulonDB

Gene
Name:	rybB
Synonym(s):	ECK0837, G0-8880, b4417, p25
Genome position(nucleotides):	887979 <-- 888057
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)
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:

[EXP-IEP] Inferred from expression pattern
[EXP-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	rybBp

Transcriptional Regulation
	Display Regulation
Repressed by:	NsrR

Elements in the selected gene context region unrelated to any object in RegulonDB

Type	Name	Post Left	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	nd	[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	nd	[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.