RegulonDB RegulonDB 10.9: Operon Form
   

tff-rpsB-tsf operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: tff-rpsB-tsf
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: rpsB-tsf
Gene(s): tff, rpsB, tsf   Genome Browser M3D Gene expression COLOMBOS
Note(s): There is a typical rho-independent termination or attenuation site in the intergenic region of rpsB and tsf which is preceded by a very stable stem-loop structure that, in its RNA form, is reminiscent of an RNA polymerase III site An G,1981. However, neither an attenuator effect nor promoter activity was observed An G,1981.
Reference(s): [1] An G., et al., 1981
Promoter
Name: rpsBp
+1: 189712
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 0
Sequence: tgctgtacacagcgccaacaattattggtgtccacgacgtatttgtggtataaagcgcgcCggacttccgatccatttcgt
                         -35                     -10        +1                   
Note(s): The rpsB promoter belongs to the extended -10 promoter class Aseev LV,2008 It comprises a TGTG extension upstream of the -10 hexamer TATAAA, a suboptimal -35 box, TTGGTG, and a GC-rich discriminator, GCGCGC, that separates the -10 element from the transcription start site and is reminiscent of a GC-rich discriminator typical for promoters under growth rate and stringent control Aseev LV,2014. Aseev LV,2008and references therein|. The design of the rpsB promoter region is highly conserved in γ-proteobacteria Aseev LV,2008
Site-directed mutation on both the TGTG extension and the TTG element in the -35 region had effects on transcription, since they dramatically decreased the activity of the promoter Aseev LV,2014
Evidence: [HTTIM]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Aseev LV., et al., 2008
[3] Huerta AM., et al., 2003
[4] Mendoza-Vargas A., et al., 2009
[5] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: atcaaaaaggAGCCGCCTGAGGGCGGCTtctttttgtg
Reference(s): [1] An G., et al., 1981
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition rpsBp nd Upon amino acid starvation, rpsBp is negatively regulated by ppGpp due to the presence of the GC-rich discriminator, whose substitution for the AT-rich element abolished stringent control Aseev LV,2014 [GEA] [6]
Evidence: [GEA] Gene expression analysis
Reference(s): [6] Aseev LV., et al., 2014


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [7] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -18.9 190768 190808 gtacacgtttGGTTAGGGGGCCTGCATATGGCCCCCTTTTTCACTTTTATatctgtgcgg
  terminator -10.8 189676 189714 caacaattatTGGTGTCCACGACGTATTTGTGGTATAAAGCGCGCCGGacttccgatc
  anti-terminator -13.6 190738 190781 tgaagggggaGAGCCCTTATAGACCAGGTAGTACACGTTTGGTTAGGGGGCCTgcatatggcc
  anti-anti-terminator -7.62 190710 190760 gaagataacgCATCTGCGGCGCGAAATATGAAGGGGGAGAGCCCTTATAGACCAGGTAGTacacgtttgg
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [HTTIM] High-throughput transcription initiation mapping

 [ICWHO] Inferred computationally without human oversight

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

 [TIM] Transcription initiation mapping


Reference(s)    

 [1] An G., Bendiak DS., Mamelak LA., Friesen JD., 1981, Organization and nucleotide sequence of a new ribosomal operon in Escherichia coli containing the genes for ribosomal protein S2 and elongation factor Ts., Nucleic Acids Res 9(16):4163-72

 [2] Aseev LV., Levandovskaya AA., Tchufistova LS., Scaptsova NV., Boni IV., 2008, A new regulatory circuit in ribosomal protein operons: S2-mediated control of the rpsB-tsf expression in vivo., RNA 14(9):1882-94

 [3] 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

 [4] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [5] 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.

 [6] Aseev LV., Koledinskaya LS., Boni IV., 2014, Dissecting the extended "-10" Escherichia coli rpsB promoter activity and regulation in vivo., Biochemistry (Mosc) 79(8):776-84

 [7] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

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