RegulonDB RegulonDB 10.8: Gene Form
   

gcvB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

gcvA ygdI gcvB GcvA GcvA TSS_3119 TSS_3119 TSS_3118 TSS_3118 gcvBp gcvBp gcvAp gcvAp ygdDp2 ygdDp2

Gene      
Name: gcvB    Texpresso search in the literature
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


Transcriptional Regulation      
Display Regulation             
Activated by: GcvA


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 ygdDp2 2941721 reverse Similarity to the consensus
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.


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