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|
| Operon |  |
|---|---|
| Name: | ssrS-fau |
| This page displays every known transcription unit of this operon and their known regulation. | |
| Name: | ssrS-ygfA |
| Gene(s): | ssrS, fau Genome Browser M3D Gene expression COLOMBOS |
| Evidence: | [LTED] Length of transcript experimentally determined |
| Reference(s): |
[1] Hsu LM., et al., 1985 [2] Kim KS., et al., 2004 |
| Promoter | |
| Name: | ssrSp2 |
| +1: | 3055759 |
| Sigma Factor: | Sigma70 Sigmulon |
| 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] [ICWHO] [RS-EPT-CBR] [TIM] |
| Reference(s): |
[1] Hsu LM., et al., 1985 [3] Huerta AM., et al., 2003 [2] Kim KS., et al., 2004 [4] Salgado H, et al., 2012 |
| 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 Chae H,2011 Several Rho-dependent terminators are located ~90 bases downstream of the 3'-end of ssrS, which is generated via exoribonucleolytic trimming after termination Chae H,2011 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 Chae H,2011 |
| Evidence: | [BTEI] Boundaries of transcription experimentally identified [LTED] Length of transcript experimentally determined |
| Reference(s): | [6] Chae H., et al., 2011 |
| Promoter | |
| Name: | ssrSp2 |
| +1: | 3055759 |
| Sigma Factor: | Sigma70 Sigmulon |
| 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] [ICWHO] [RS-EPT-CBR] [TIM] |
| Reference(s): |
[1] Hsu LM., et al., 1985 [3] Huerta AM., et al., 2003 [2] Kim KS., et al., 2004 [4] Salgado H, et al., 2012 |
| Terminator(s) | |
| Type: | rho-dependent |
| Sequence: | acaagaaatcCGCAAAATGATTCGGCAACGTCGTCGTGCGTTAACGCCGGAACAACAGCaggaaatggg |
| Reference(s): | [6] Chae H., et al., 2011 |
| 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 Chae H,2011 Several Rho-dependent terminators are located ~90 bases downstream of the 3'-end of ssrS, which is generated via exoribonucleolytic trimming after termination Chae H,2011 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 Chae H,2011 |
| Evidence: | [BTEI] Boundaries of transcription experimentally identified [LTED] Length of transcript experimentally determined |
| Reference(s): | [6] Chae H., et al., 2011 |
| Promoter | |
| Name: | ssrSp |
| +1: | 3055759 |
| Sigma Factor: | Sigma38 Sigmulon |
| 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] [ICWHO] [RS-EPT-CBR] [TIM] |
| Reference(s): |
[1] Hsu LM., et al., 1985 [3] Huerta AM., et al., 2003 [2] Kim KS., et al., 2004 [4] Salgado H, et al., 2012 |
| Terminator(s) | |
| Type: | rho-dependent |
| Sequence: | acaagaaatcCGCAAAATGATTCGGCAACGTCGTCGTGCGTTAACGCCGGAACAACAGCaggaaatggg |
| Reference(s): | [6] Chae H., et al., 2011 |
| Name: | ssrS-ygfA |
| Gene(s): | ssrS, fau Genome Browser M3D Gene expression COLOMBOS |
| Evidence: | [LTED] Length of transcript experimentally determined |
| Reference(s): |
[1] Hsu LM., et al., 1985 [2] Kim KS., et al., 2004 |
| Promoter | |
| Name: | ssrSp |
| +1: | 3055759 |
| Sigma Factor: | Sigma38 Sigmulon |
| 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] [ICWHO] [RS-EPT-CBR] [TIM] |
| Reference(s): |
[1] Hsu LM., et al., 1985 [3] Huerta AM., et al., 2003 [2] Kim KS., et al., 2004 [4] Salgado H, et al., 2012 |
| 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 Chae H,2011 Several Rho-dependent terminators are located ~90 bases downstream of the 3'-end of ssrS, which is generated via exoribonucleolytic trimming after termination Chae H,2011 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 Chae H,2011 |
| Evidence: | [BTEI] Boundaries of transcription experimentally identified |
| Reference(s): | [6] 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): | The activity of this promoter appears to be decreased in the presence of σE. It is repressed during the first 5 minutes following σE induction and decreased from 5 to 10 minutes and from 10 to 20 minutes after induction of the σ factor Lacoux C,2020. 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] [ICWHO] [IE] [IHBCE] [RS-EPT-CBR] [TIM] |
| Reference(s): |
[3] Huerta AM., et al., 2003 [2] Kim KS., et al., 2004 [7] Maciag A., et al., 2011 [4] Salgado H, et al., 2012 |
| Terminator(s) | |
| Type: | rho-dependent |
| Sequence: | acaagaaatcCGCAAAATGATTCGGCAACGTCGTCGTGCGTTAACGCCGGAACAACAGCaggaaatggg |
| Reference(s): | [6] Chae H., et al., 2011 |
| Name: | ssrS-ygfA |
| Gene(s): | ssrS, fau Genome Browser M3D Gene expression COLOMBOS |
| Evidence: | [LTED] Length of transcript experimentally determined |
| Reference(s): |
[1] Hsu LM., et al., 1985 [2] 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): | The activity of this promoter appears to be decreased in the presence of σE. It is repressed during the first 5 minutes following σE induction and decreased from 5 to 10 minutes and from 10 to 20 minutes after induction of the σ factor Lacoux C,2020. 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] [ICWHO] [IE] [IHBCE] [RS-EPT-CBR] [TIM] |
| Reference(s): |
[3] Huerta AM., et al., 2003 [2] Kim KS., et al., 2004 [7] Maciag A., et al., 2011 [4] Salgado H, et al., 2012 |
| Reference(s) |
|
|---|---|
[AIPP] Automated inference of promoter position