|
|
| Operon |  |
|---|---|
| Name: | rrsH-ileV-alaV-rrlH-rrfH |
| This page displays every known transcription unit of this operon and their known regulation. | |
| Name: | rrsH-ileV-alaV-rrlH-rrfH | |||||||||
| Synonym(s): | rrnH | |||||||||
| Gene(s): | rrsH, ileV, alaV, rrlH, rrfH Genome Browser M3D Gene expression COLOMBOS | |||||||||
| Note(s): | The seven ribosomal operons of E. coli are complexly transcribed. Each operon has two σ70 promoters (p1 and p2); their transcription starts with a large precursor that contains rRNAs Gralla JD.,2005; and they are the target of regulation by the alarmone ppGpp, several triphosphate nucleotides (NTPs), and the transcriptional regulators FIS and HNS. FIS and HNS regulate at the p1; however, ppGpp and NTPs control both promoters in accordance with their concentration changes, even in the absence of the transcriptional regulators Paul BJ,2004. Schneider DA,2003. Zhang X,2002. In addition, these two small regulating metabolites (ppGpp and NTPs) require the help of the DskA coregulatory protein that binds to the RNA polymerase Paul BJ,2004. The net amount of rRNA transcription can be seen as a complex function of the ratio of inhibitors to activators. HNS/Fis and ppGpp/NTP ratios are the highest ones during slow growth and the lowest ones during rapid growth, and the ribosomal production is in accordance with the growth rate (higher in rapid growth and lower in slow growth) Gralla JD.,2005. Schneider DA,2003. It is important to note that the ribosomal gene-containing operons also encode genes whose products interact with the RNA polymerase and participate in the translation elongation and in the replication apparatus. Reviews: Dennis PP, Ehrenberg M, Bremer H,2004. Condon C, Squires C, Squires CL,1995. Zengel JM, Lindahl L,1994. Lindahl L, Zengel JM,1986. Gralla JD.,2005. Paul BJ,2004. Additional reference:Keener J. and Nomura M. (1996). Regulation of Ribosome Synthesis, in: Neidhardt, F. (Editor in Chief) et al., E. coli and Salmonella. Cellular and Molecular Biology. ASM Press, Washington, D.C., p. 1417-1431. |
|||||||||
| Evidence: | [BTEI] Boundaries of transcription experimentally identified | |||||||||
| Reference(s): |
[1] Gralla JD. 2005 [2] Paul BJ., et al., 2004 [3] Schneider DA., et al., 2003 [4] Zhang X., et al., 2002 |
|||||||||
| Promoter | ||||||||||
| Name: | rrsHp1 | |||||||||
| +1: | 223485 | |||||||||
| Sigma Factor: | Sigma70 Sigmulon | |||||||||
| Distance from start of the gene: | 286 | |||||||||
| Sequence: |
tgaaataaaaatgcatttttccgcttgtcttcctgagccgactccctataatgcgcctccAtcgacacggcggatgtgaat -10 +1 |
|||||||||
| Note(s): | Keener J. and Nomura M. (1996). Regulation of Ribosome Synthesis, in: Neidhardt, F. (Editor in Chief) et al., E. coli and Salmonella. Cellular and Molecular Biology. ASM Press, Washington, D.C., p. 1417-31. Although the organization and sequence of the seven major ribosomal RNA (rRNA) P1 promoters are highly conserved, the upstream region differs considerably in its regulation, with different transcription factor affinities for the individual upstream regions and strikingly different architectures of the resulting DNA-protein complexes that form with the individual rRNA operon upstream regions Hillebrand A, Wurm R, Menzel A, Wagner R,2005 |
|||||||||
| Evidence: |
[HIPP] [HTTIM] [IHBCE] |
|||||||||
| Reference(s): |
[5] Maciag A., et al., 2011 [6] Newlands JT., et al., 1993 |
|||||||||
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| remote | Fis | activator | rrsHp1 | 223297 | 223311 | -181.0 | aagtgctggtGCGTACGGGTAAACCtattacgcct | nd | [GEA], [BPP] | [7] |
| remote | Fis | activator | rrsHp1 | 223344 | 223358 | -134.0 | gcggcggattGGGTGTTAAATAGCCtggcagacct | nd | [GEA], [BPP] | [7] |
| proximal | Fis | activator | rrsHp1 | 223387 | 223401 | -91.0 | cgataaaaaaGCAGCAAAAACCGGCacaatgatta | nd | [GEA], [BPP] | [7] |
| proximal | Fis | activator | rrsHp1 | 223407 | 223421 | -71.0 | ccggcacaatGATTAAAAGATGAGCggttgaaata | nd | [GEA], [BPP] | [7] |
| Evidence: |
[APPH] Assay of protein purified to homogeneity [GEA] Gene expression analysis [IMP] Inferred from mutant phenotype |
| Reference(s): | [10] Paul BJ., et al., 2004 |
| Name: | rrsH-ileV-alaV-rrlH-rrfH | |||||||||
| Synonym(s): | rrnH | |||||||||
| Gene(s): | rrsH, ileV, alaV, rrlH, rrfH Genome Browser M3D Gene expression COLOMBOS | |||||||||
| Note(s): | The seven ribosomal operons of E. coli are complexly transcribed. Each operon has two σ70 promoters (p1 and p2); their transcription starts with a large precursor that contains rRNAs Gralla JD.,2005; and they are the target of regulation by the alarmone ppGpp, several triphosphate nucleotides (NTPs), and the transcriptional regulators FIS and HNS. FIS and HNS regulate at the p1; however, ppGpp and NTPs control both promoters in accordance with their concentration changes, even in the absence of the transcriptional regulators Paul BJ,2004. Schneider DA,2003. Zhang X,2002. In addition, these two small regulating metabolites (ppGpp and NTPs) require the help of the DskA coregulatory protein that binds to the RNA polymerase Paul BJ,2004. The net amount of rRNA transcription can be seen as a complex function of the ratio of inhibitors to activators. HNS/Fis and ppGpp/NTP ratios are the highest ones during slow growth and the lowest ones during rapid growth, and the ribosomal production is in accordance with the growth rate (higher in rapid growth and lower in slow growth) Gralla JD.,2005. Schneider DA,2003. It is important to note that the ribosomal gene-containing operons also encode genes whose products interact with the RNA polymerase and participate in the translation elongation and in the replication apparatus. Reviews: Dennis PP, Ehrenberg M, Bremer H,2004. Condon C, Squires C, Squires CL,1995. Zengel JM, Lindahl L,1994. Lindahl L, Zengel JM,1986. Gralla JD.,2005. Paul BJ,2004. Additional reference:Keener J. and Nomura M. (1996). Regulation of Ribosome Synthesis, in: Neidhardt, F. (Editor in Chief) et al., E. coli and Salmonella. Cellular and Molecular Biology. ASM Press, Washington, D.C., p. 1417-1431. |
|||||||||
| Evidence: | [BTEI] Boundaries of transcription experimentally identified | |||||||||
| Reference(s): |
[1] Gralla JD. 2005 [2] Paul BJ., et al., 2004 [3] Schneider DA., et al., 2003 [4] Zhang X., et al., 2002 |
|||||||||
| Promoter | ||||||||||
| Name: | rrsHp | |||||||||
| +1: | 223485 | |||||||||
| Sigma Factor: | Sigma32 Sigmulon | |||||||||
| Distance from start of the gene: | 286 | |||||||||
| Sequence: |
tgaaataaaaatgcatttttccgcttgtcttcctgagccgactccctataatgcgcctccAtcgacacggcggatgtgaat -10 +1 |
|||||||||
| Note(s): | Keener J. and Nomura M. (1996). Regulation of Ribosome Synthesis, in: Neidhardt, F. (Editor in Chief) et al., E. coli and Salmonella. Cellular and Molecular Biology. ASM Press, Washington, D.C., p. 1417-31. Although the organization and sequence of the seven major ribosomal RNA (rRNA) P1 promoters are highly conserved, the upstream region differs considerably in its regulation, with different transcription factor affinities for the individual upstream regions and strikingly different architectures of the resulting DNA-protein complexes that form with the individual rRNA operon upstream regions Hillebrand A, Wurm R, Menzel A, Wagner R,2005 |
|||||||||
| Evidence: |
[HIPP] [HTTIM] [IHBCE] |
|||||||||
| Reference(s): |
[5] Maciag A., et al., 2011 [6] Newlands JT., et al., 1993 |
|||||||||
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| remote | Fis | activator | rrsHp | 223297 | 223311 | -181.0 | aagtgctggtGCGTACGGGTAAACCtattacgcct | nd | [GEA], [BPP] | [7] |
| remote | Fis | activator | rrsHp | 223344 | 223358 | -134.0 | gcggcggattGGGTGTTAAATAGCCtggcagacct | nd | [GEA], [BPP] | [7] |
| proximal | Fis | activator | rrsHp | 223387 | 223401 | -91.0 | cgataaaaaaGCAGCAAAAACCGGCacaatgatta | nd | [GEA], [BPP] | [7] |
| proximal | Fis | activator | rrsHp | 223407 | 223421 | -71.0 | ccggcacaatGATTAAAAGATGAGCggttgaaata | nd | [GEA], [BPP] | [7] |
| Evidence: |
[APPH] Assay of protein purified to homogeneity [GEA] Gene expression analysis [IMP] Inferred from mutant phenotype |
| Reference(s): | [10] Paul BJ., et al., 2004 |
| Name: | rrsH-ileV-alaV-rrlH-rrfH |
| Synonym(s): | rrsH |
| Gene(s): | rrsH, ileV, alaV, rrlH, rrfH Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | The seven ribosomal operons of E. coli are complexly transcribed. Each operon has two σ70 promoters (p1 and p2); their transcription starts with a large precursor that contains rRNAs Gralla JD.,2005; and they are the target of regulation by the alarmone ppGpp, several triphosphate nucleotides (NTPs), and the transcriptional regulators FIS and HNS. FIS and HNS regulate at the p1; however, ppGpp and NTPs control both promoters in accordance with their concentration changes, even in the absence of the transcriptional regulators Paul BJ,2004. Schneider DA,2003. Zhang X,2002. In addition, these two small regulating metabolites (ppGpp and NTPs) require the help of the DskA coregulatory protein that binds to the RNA polymerase Paul BJ,2004. The net amount of rRNA transcription can be seen as a complex function of the ratio of inhibitors to activators. HNS/Fis and ppGpp/NTP ratios are the highest ones during slow growth and the lowest ones during rapid growth, and the ribosomal production is in accordance with the growth rate (higher in rapid growth and lower in slow growth) Gralla JD.,2005. Schneider DA,2003. It is important to note that the ribosomal gene-containing operons also encode genes whose products interact with the RNA polymerase and participate in the translation elongation and in the replication apparatus. Reviews: Dennis PP, Ehrenberg M, Bremer H,2004. Condon C, Squires C, Squires CL,1995. Zengel JM, Lindahl L,1994. Lindahl L, Zengel JM,1986. Gralla JD.,2005. Paul BJ,2004. Additional reference:Keener J. and Nomura M. (1996). Regulation of Ribosome Synthesis, in: Neidhardt, F. (Editor in Chief) et al., E. coli and Salmonella. Cellular and Molecular Biology. ASM Press, Washington, D.C., p. 1417-1431. |
| Evidence: | [BTEI] Boundaries of transcription experimentally identified |
| Reference(s): |
[1] Gralla JD. 2005 [2] Paul BJ., et al., 2004 [3] Schneider DA., et al., 2003 [4] Zhang X., et al., 2002 |
| Promoter | |
| Name: | rrsHp2 |
| +1: | 223593 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 178 |
| Sequence: |
gaagagaaaaatcctgaaattcagggttgactctgaaagaggaaagcgtaatatacgccaCctcgcgacagtgagctgaaa -10 +1 |
| Evidence: |
[HIPP] [HTTIM] [IHBCE] |
| Reference(s): | [5] Maciag A., et al., 2011 |
| Name: | rrlH-rrfH |
| Gene(s): | rrlH, rrfH Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for rrlH. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020. |
| Evidence: | [PAGTSBP] Products of adjacent genes in the same biological process |
| Promoter | |
| Name: | rrlHp |
| +1: | Unknown |
| Note(s): | Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Based on this, a putative promoter was suggested, but the +1 site of the transcription initiation has not been determined, although there exists promoter activity. |
| Evidence: | [IEP] |
| Reference(s): | [11] Zaslaver A., et al., 2006 |
| Reference(s) |
|
|---|---|
[HIPP] Human inference of promoter position