RegulonDB RegulonDB 10.6.3: Operon Form
   

ssrS-fau operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: ssrS-fau
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: ssrS
Gene(s): ssrS   Genome Browser M3D Gene expression COLOMBOS
Note(s): Transcription from the ssrS promoters extends to sibC in vitro. However, in vivo studies showed that transcription from the ssrS promoters resulted in very low levels of ygfA expression |CITS:[21036909]|. Several Rho-dependent terminators are located ~90 bases downstream of the 3'-end of ssrS, which is generated via exoribonucleolytic trimming after termination |CITS:[21036909]|.
Rho factor binds to the precursor 6S RNA, not mature 6S RNA, suggesting that Rho factor terminates ssrS operon transcription through its binding to RNA. The ssrS transcription termination occurs at multiples sites around the major termination, which is at -279 downstream of the ssrS gene. The region from -193 to -265 downstream of ssrS is rich in C residues that could interact with Rho factor to terminate transcription |CITS:[21036909]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Chae H., et al., 2011
Promoter
Name: ssrSp2
+1: 3055759
Sigma Factor: Sigma38, Sigma70
Distance from start of the gene: 224
Sequence: gcagcggacgatctgaaccaacggttgcaagatctgaaagaacgcactagagtcacaaatActgaacagttggtcttcatt
                         -35                    -10         +1                   
Note(s): Transcription from the ssrSp1 and ssrSp2 promoters is regulated in a growth-phase-dependent manner Lee JY, Park H, Bak G, Kim KS, Lee Y,2013. In addition, transcription of ssrSp1 and ssrSp2 is feedback activated and feedback inhibited, respectively, and this feedback regulation is Fis dependent Lee JY, Park H, Bak G, Kim KS, Lee Y,2013. The differential feedback regulation could serve to integrate sigma factors, as well as providing a means for maintaining appropriate cellular concentrations of 6S RNA in response to environmental changes Lee JY, Park H, Bak G, Kim KS, Lee Y,2013.
Evidence: [AIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Hsu LM., et al., 1985
[3] Kim KS., et al., 2004
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-dependent
Sequence: acaagaaatcCGCAAAATGATTCGGCAACGTCGTCGTGCGTTAACGCCGGAACAACAGCaggaaatggg
Reference(s): [1] Chae H., et al., 2011
TF binding sites (TFBSs)
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fis repressor ssrSp2 nd nd nd nd nd [BPP], [GEA] [5]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor ssrSp2 nd nd nd nd nd [BPP], [GEA] [5]
[Lrp,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Lrp repressor ssrSp2 nd nd nd nd nd [BPP], [GEA] [5]
[StpA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd StpA repressor ssrSp2 nd nd nd nd nd [BPP], [GEA] [5]


Transcription unit          
Name: ssrS-ygfA
Gene(s): ssrS, fau   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [2] Hsu LM., et al., 1985
[3] Kim KS., et al., 2004
Promoter
Name: ssrSp2
+1: 3055759
Sigma Factor: Sigma38, Sigma70
Distance from start of the gene: 224
Sequence: gcagcggacgatctgaaccaacggttgcaagatctgaaagaacgcactagagtcacaaatActgaacagttggtcttcatt
                         -35                    -10         +1                   
Note(s): Transcription from the ssrSp1 and ssrSp2 promoters is regulated in a growth-phase-dependent manner Lee JY, Park H, Bak G, Kim KS, Lee Y,2013. In addition, transcription of ssrSp1 and ssrSp2 is feedback activated and feedback inhibited, respectively, and this feedback regulation is Fis dependent Lee JY, Park H, Bak G, Kim KS, Lee Y,2013. The differential feedback regulation could serve to integrate sigma factors, as well as providing a means for maintaining appropriate cellular concentrations of 6S RNA in response to environmental changes Lee JY, Park H, Bak G, Kim KS, Lee Y,2013.
Evidence: [AIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Hsu LM., et al., 1985
[3] Kim KS., et al., 2004
[4] Salgado H, et al., 2012
TF binding sites (TFBSs)
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fis repressor ssrSp2 nd nd nd nd nd [BPP], [GEA] [5]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor ssrSp2 nd nd nd nd nd [BPP], [GEA] [5]
[Lrp,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Lrp repressor ssrSp2 nd nd nd nd nd [BPP], [GEA] [5]
[StpA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd StpA repressor ssrSp2 nd nd nd nd nd [BPP], [GEA] [5]


Transcription unit          
Name: ssrS
Gene(s): ssrS   Genome Browser M3D Gene expression COLOMBOS
Note(s): Transcription from the ssrS promoters extends to sibC in vitro. However, in vivo studies showed that transcription from the ssrS promoters resulted in very low levels of ygfA expression |CITS:[21036909]|. Several Rho-dependent terminators are located ~90 bases downstream of the 3'-end of ssrS, which is generated via exoribonucleolytic trimming after termination |CITS:[21036909]|.
Rho factor binds to the precursor 6S RNA, not mature 6S RNA, suggesting that Rho factor terminates ssrS operon transcription through its binding to RNA. The ssrS transcription termination occurs at multiples sites around the major termination, which is at -279 downstream of the ssrS gene. The region from -193 to -265 downstream of ssrS is rich in C residues that could interact with Rho factor to terminate transcription |CITS:[21036909]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Chae H., et al., 2011
Promoter
Name: ssrSp1
+1: 3055974
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 9
Sequence: cgaaaaaactaaccaaaactttgaatgacacttttcggtttactgtggtagagtaaccgtGaagacaaaatttctctgaga
                         -35                     -10        +1                   
Note(s): Transcription from the ssrSp1 and ssrSp2 promoters is regulated in a growth-phase-dependent manner Lee JY, Park H, Bak G, Kim KS, Lee Y,2013. In addition, transcription of ssrSp1 and ssrSp2 is feedback activated and feedback inhibited, respectively, and this feedback regulation is Fis dependent Lee JY, Park H, Bak G, Kim KS, Lee Y,2013. The differential feedback regulation could serve to integrate sigma factors, as well as providing a means for maintaining appropriate cellular concentrations of 6S RNA in response to environmental changes Lee JY, Park H, Bak G, Kim KS, Lee Y,2013.
Evidence: [HTTIM]
[RS-EPT-CBR]
[TIM]
Reference(s): [3] Kim KS., et al., 2004
[6] Maciag A., et al., 2011
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-dependent
Sequence: acaagaaatcCGCAAAATGATTCGGCAACGTCGTCGTGCGTTAACGCCGGAACAACAGCaggaaatggg
Reference(s): [1] Chae H., et al., 2011
TF binding sites (TFBSs)
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fis activator ssrSp1 nd nd nd nd nd [BPP], [GEA] [5]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor ssrSp1 nd nd nd nd nd [BPP], [GEA] [5]
[Lrp,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Lrp repressor ssrSp1 nd nd nd nd nd [BPP], [GEA] [5]
[StpA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd StpA repressor ssrSp1 nd nd nd nd nd [BPP], [GEA] [5]


Transcription unit          
Name: ssrS-ygfA
Gene(s): ssrS, fau   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [2] Hsu LM., et al., 1985
[3] Kim KS., et al., 2004
Promoter
Name: ssrSp1
+1: 3055974
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 9
Sequence: cgaaaaaactaaccaaaactttgaatgacacttttcggtttactgtggtagagtaaccgtGaagacaaaatttctctgaga
                         -35                     -10        +1                   
Note(s): Transcription from the ssrSp1 and ssrSp2 promoters is regulated in a growth-phase-dependent manner Lee JY, Park H, Bak G, Kim KS, Lee Y,2013. In addition, transcription of ssrSp1 and ssrSp2 is feedback activated and feedback inhibited, respectively, and this feedback regulation is Fis dependent Lee JY, Park H, Bak G, Kim KS, Lee Y,2013. The differential feedback regulation could serve to integrate sigma factors, as well as providing a means for maintaining appropriate cellular concentrations of 6S RNA in response to environmental changes Lee JY, Park H, Bak G, Kim KS, Lee Y,2013.
Evidence: [HTTIM]
[RS-EPT-CBR]
[TIM]
Reference(s): [3] Kim KS., et al., 2004
[6] Maciag A., et al., 2011
[4] Salgado H, et al., 2012
TF binding sites (TFBSs)
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fis activator ssrSp1 nd nd nd nd nd [BPP], [GEA] [5]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor ssrSp1 nd nd nd nd nd [BPP], [GEA] [5]
[Lrp,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Lrp repressor ssrSp1 nd nd nd nd nd [BPP], [GEA] [5]
[StpA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd StpA repressor ssrSp1 nd nd nd nd nd [BPP], [GEA] [5]


Evidence    

 [AIPP] Automated inference of promoter position

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

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [HTTIM] High-throughput transcription initiation mapping


Reference(s)    

 [1] Chae H., Han K., Kim KS., Park H., Lee J., Lee Y., 2011, Rho-dependent termination of ssrS (6S RNA) transcription in Escherichia coli: implication for 3' processing of 6S RNA and expression of downstream ygfA (putative 5-formyl-tetrahydrofolate cyclo-ligase)., J Biol Chem 286(1):114-22

 [2] Hsu LM., Zagorski J., Wang Z., Fournier MJ., 1985, Escherichia coli 6S RNA gene is part of a dual-function transcription unit., J Bacteriol 161(3):1162-70

 [3] Kim KS., Lee Y., 2004, Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases., Nucleic Acids Res 32(20):6057-68

 [4] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-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.

 [5] Neusser T., Gildehaus N., Wurm R., Wagner R., 2008, Studies on the expression of 6S RNA from E. coli: involvement of regulators important for stress and growth adaptation., Biol Chem 389(3):285-97

 [6] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

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