RegulonDB RegulonDB 10.8: Gene Form
   

glmY gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

purL glrK glmY GlrR GlrR IHF GlrR IHF TSS_2850 TSS_2850 glmYp2 glmYp2 glmYp1 glmYp1 glrKp glrKp TSS_2847 TSS_2847 TSS_2846 TSS_2846

Gene      
Name: glmY    Texpresso search in the literature
Synonym(s): ECK2554, G0-8910, b4441, sroF, tke1
Genome position(nucleotides): 2691157 <-- 2691340 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.0
External database links:  
ASAP:
ABE-0047261
ECHOBASE:
EB4527
PortEco:
glmY
COLOMBOS: glmY


Product      
Name: GlmY
Synonym(s): SroF, Tke1, glmY, small regulatory RNA GlmY, sroF, tke1
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional
Gene Ontology Terms (GO)  
molecular_function GO:0005515 - protein binding
GO:0003729 - mRNA binding
biological_process GO:0048519 - negative regulation of biological process
GO:1902201 - negative regulation of bacterial-type flagellum-dependent cell motility
GO:0036460 - cellular response to cell envelope stress
Note(s): Note(s): ...[more].
Evidence: [IDA] Inferred from direct assay
[IMP] Inferred from mutant phenotype
Reference(s): [1] Andrade JM., et al., 2012
[2] Gonzalez GM., et al., 2017
[3] Gopel Y., et al., 2018
[4] Gopel Y., et al., 2016
[5] Hobbs EC., et al., 2010
[6] Rivas E., et al., 2001
[7] Salim NN., et al., 2012
[8] Urban JH., et al., 2007
[9] Vogel J., et al., 2003
External database links:  
ECOCYC:
TKE1-RNA
ECOLIWIKI:
b4441


Operon      
Name: glmY         
Operon arrangement:
Transcription unit        Promoter
glmY
glmY


Transcriptional Regulation      
Display Regulation             
Activated by: IHF, GlrR


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_2846 2690181 reverse nd [RS-EPT-CBR] [10]
  promoter TSS_2847 2690186 reverse nd [RS-EPT-CBR] [10]
  promoter TSS_2850 2694924 reverse nd [RS-EPT-CBR] [10]


Evidence    

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



Reference(s)    

 [1] Andrade JM., Pobre V., Matos AM., Arraiano CM., 2012, The crucial role of PNPase in the degradation of small RNAs that are not associated with Hfq., RNA 18(4):844-55

 [2] Gonzalez GM., Durica-Mitic S., Hardwick SW., Moncrieffe MC., Resch M., Neumann P., Ficner R., Gorke B., Luisi BF., 2017, Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism., Nucleic Acids Res 45(18):10845-10860

 [3] Gopel Y., Gorke B., 2018, Interaction of lipoprotein QseG with sensor kinase QseE in the periplasm controls the phosphorylation state of the two-component system QseE/QseF in Escherichia coli., PLoS Genet 14(7):e1007547

 [4] Gopel Y., Khan MA., Gorke B., 2016, Domain swapping between homologous bacterial small RNAs dissects processing and Hfq binding determinants and uncovers an aptamer for conditional RNase E cleavage., Nucleic Acids Res 44(2):824-37

 [5] Hobbs EC., Astarita JL., Storz G., 2010, Small RNAs and small proteins involved in resistance to cell envelope stress and acid shock in Escherichia coli: analysis of a bar-coded mutant collection., J Bacteriol 192(1):59-67

 [6] Rivas E., Klein RJ., Jones TA., Eddy SR., 2001, Computational identification of noncoding RNAs in E. coli by comparative genomics., Curr Biol 11(17):1369-73

 [7] Salim NN., Faner MA., Philip JA., Feig AL., 2012, Requirement of upstream Hfq-binding (ARN)x elements in glmS and the Hfq C-terminal region for GlmS upregulation by sRNAs GlmZ and GlmY., Nucleic Acids Res 40(16):8021-32

 [8] Urban JH., Papenfort K., Thomsen J., Schmitz RA., Vogel J., 2007, A Conserved Small RNA Promotes Discoordinate Expression of the glmUS Operon mRNA to Activate GlmS Synthesis., J Mol Biol 373(3):521-8

 [9] 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

 [10] 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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