RegulonDB

Gene
Name:	gcvB
Synonym(s):	ECK2804, G0-8867, IS145, b4443, psrA11
Genome position(nucleotides):	2942696 --> 2942900 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	42.93
Reference(s):	[1] Argaman L., et al., 2001
External database links:

ASAP:	ABE-0047263
ECHOBASE:	EB4291
PortEco:	gcvB
COLOMBOS:	gcvB

Product

Name:

GcvB

Synonym(s):

IS145, PsrA11, psrA11, small regulatory RNA GcvB

Type:

small RNA

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.2 - RNA related --> 2.2.7 - antisense RNA
		3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional
Gene Ontology Terms (GO)
	molecular_function	GO:0003729 - mRNA binding
	biological_process	GO:0040033 - negative regulation of translation, ncRNA-mediated GO:1900192 - positive regulation of single-species biofilm formation GO:1902201 - negative regulation of bacterial-type flagellum-dependent cell motility

Note(s):

Note(s): ...[more].

Evidence:

[IDA] Inferred from direct assay
[IEP] Inferred from expression pattern
[IGI] Inferred from genetic interaction
[IMP] Inferred from mutant phenotype

Reference(s):

[2] Andreassen PR., et al., 2018
[1] Argaman L., et al., 2001
[3] Baisa G., et al., 2013
[4] Busi F., et al., 2009
[5] Chen S., et al., 2002
[6] Harwani D., et al., 2012
[7] Kuryllo K., et al., 2014
[8] Lalaouna D., et al., 2019
[9] Melamed S., et al., 2016
[10] Pulvermacher SC., et al., 2008
[11] Pulvermacher SC., et al., 2009
[12] Urban JH., et al., 2007
[13] Urbanowski ML., et al., 2000
[14] Yang Q., et al., 2014

External database links:

ECOCYC:

GCVB-RNA

ECOLIWIKI:

b4443

Operon

Name:

gcvB

Operon arrangement:

Transcription unit	Promoter
gcvB	gcvBp

Transcriptional Regulation
	Display Regulation
Activated by:	GcvA

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	ygdDp2	2941721	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.103. P-value: 6.790e-6 Read more >	[ICWHO]	[15]
promoter	TSS_3118	2942729	forward	nd	[RS-EPT-CBR]	[16]
promoter	TSS_3119	2942760	forward	nd	[RS-EPT-CBR]	[16]

Evidence
[ICWHO] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Argaman L., Hershberg R., Vogel J., Bejerano G., Wagner EG., Margalit H., Altuvia S., 2001, Novel small RNA-encoding genes in the intergenic regions of Escherichia coli., Curr Biol 11(12):941-50
[2] Andreassen PR., Pettersen JS., Szczerba M., Valentin-Hansen P., Moller-Jensen J., Jorgensen MG., 2018, sRNA-dependent control of curli biosynthesis in Escherichia coli: McaS directs endonucleolytic cleavage of csgD mRNA., Nucleic Acids Res 46(13):6746-6760
[3] Baisa G., Stabo NJ., Welch RA., 2013, Characterization of Escherichia coli D-Cycloserine Transport and Resistant Mutants., J Bacteriol 195(7):1389-99
[4] Busi F., Cayrol B., Lavelle C., LeDerout J., Pietrement O., Le Cam E., Geinguenaud F., Lacoste J., Regnier P., Arluison V., 2009, Auto-assembly as a new regulatory mechanism of noncoding RNA., Cell Cycle 8(6):952-4
[5] Chen S., Lesnik EA., Hall TA., Sampath R., Griffey RH., Ecker DJ., Blyn LB., 2002, A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome., Biosystems 65(2-3):157-77
[6] Harwani D., Zangoui P., Mahadevan S., 2012, The β-Glucoside (bgl) Operon of Escherichia coli Is Involved in the Regulation of oppA, Encoding an Oligopeptide Transporter., J Bacteriol 194(1):90-9
[7] Kuryllo K., Jahanshahi S., Zhu W., Brown ED., Li Y., 2014, A dual reporter system for detecting RNA interactions in bacterial cells., Chembiochem 15(18):2703-9
[8] Lalaouna D., Eyraud A., Devinck A., Prevost K., Masse E., 2019, GcvB small RNA uses two distinct seed regions to regulate an extensive targetome., Mol Microbiol 111(2):473-486
[9] Melamed S., Peer A., Faigenbaum-Romm R., Gatt YE., Reiss N., Bar A., Altuvia Y., Argaman L., Margalit H., 2016, Global Mapping of Small RNA-Target Interactions in Bacteria., Mol Cell 63(5):884-97
[10] Pulvermacher SC., Stauffer LT., Stauffer GV., 2008, The role of the small regulatory RNA GcvB in GcvB/mRNA posttranscriptional regulation of oppA and dppA in Escherichia coli., FEMS Microbiol Lett 281(1):42-50
[11] Pulvermacher SC., Stauffer LT., Stauffer GV., 2009, Role of the sRNA GcvB in regulation of cycA in Escherichia coli., Microbiology 155(Pt 1):106-14
[12] Urban JH., Vogel J., 2007, Translational control and target recognition by Escherichia coli small RNAs in vivo., Nucleic Acids Res 35(3):1018-37
[13] Urbanowski ML., Stauffer LT., Stauffer GV., 2000, The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli., Mol Microbiol 37(4):856-68
[14] Yang Q., Figueroa-Bossi N., Bossi L., 2014, Translation enhancing ACA motifs and their silencing by a bacterial small regulatory RNA., PLoS Genet 10(1):e1004026
[15] 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
[16] 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.