![]() ![]() ![]() |
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: 15590778. 8531889. 7517053. 2434021. 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: | Sigma32, Sigma70 |
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 16006239 |
Evidence: |
[HIPP] [HTIM] |
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 | [BPP], [GEA] | [7] |
remote | Fis | activator | rrsHp1 | 223344 | 223358 | -134.0 | gcggcggattGGGTGTTAAATAGCCtggcagacct | nd | [BPP], [GEA] | [7] |
proximal | Fis | activator | rrsHp1 | 223387 | 223401 | -91.0 | cgataaaaaaGCAGCAAAAACCGGCacaatgatta | nd | [BPP], [GEA] | [7] |
proximal | Fis | activator | rrsHp1 | 223407 | 223421 | -71.0 | ccggcacaatGATTAAAAGATGAGCggttgaaata | nd | [BPP], [GEA] | [7] |
Note(s): |
1Paradoxically, even though H-NS is an inhibitor it drives the bound RNA polymerase into open complexes Gralla JD.,2005. 1Based on studies of binding sites with gel shift and footprinting with Lrp and H-NS regulator proteins, it was demonstrated that both proteins interact with obvious synergism in the repression of all seven E. coli rrn P1 promoter upstream regions; as a result, they help the efficient shutdown of rRNA synthesis. Likewise, both proteins could be a transient heteromer via a protein-protein interaction that interferes with the RNA polymerase, and in this way it alters the DNA of the upstream regions of all seven ribosomal P1 promoters Pul U,2005. 5Based on studies of binding sites with gel shift and footprinting with Lrp and H-NS regulator proteins, it was demonstrated that both proteins interact with obvious synergism in the repression of all seven E. coli rrn P1 promoter upstream regions; as a result, they help the efficient shutdown of rRNA synthesis. Likewise, both proteins could be a transient heteromer via a protein-protein interaction that interferes with the RNA polymerase, and in this way it alters the DNA of the upstream regions of all seven ribosomal P1 promoters Pul U,2005. 6Paradoxically, even though H-NS is an inhibitor it drives the bound RNA polymerase into open complexes Gralla JD.,2005. |
Allosteric regulation of RNA-polymerase |
Regulator | Function | Promoter target of RNApol | Growth Conditions | Note | Evidence | Reference | |
---|---|---|---|---|---|---|---|
DksA | inhibition | rrsHp1 |
[APPH] [GEA] |
[10] | |||
DksA-ppGpp | inhibition | rrsHp1 | DskA amplifies the magnitude of inhibition effects of ppGpp from rrnBp1 and all rRNAP1 promoters Paul BJ,2004. Lemke JJ,2011 A model reflecting the contribution of DksA under regulation of rRNA expression has been developed Paul BJ,2004 |
[APPH] [GEA] [IMP] |
[10] | ||
ppGpp | inhibition | rrsHp1 | ppGpp binds RNA polymerase (RNAP) near the catalytic center in the secondary channel 15109491 Its binding is proposed to be stabilized by DskA. If the demand for rRNA is low, transcription can be inhibited by high levels of ppGpp or low levels of NTPs. RNAP is a direct target of ppGpp action. There are three proposed mechanisms through which ppGpp binding inhibits rRNA transcription: 1) ppGpp binds with the initiating NTP for the active site, 2) ppGpp pairs with a cytosine residue(s) just upstream of the transcription start site, 3) ppGpp decreases the lifetime of the open complex formed at all rRNA promoters 15109491 | [IMP] | [10] |
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: 15590778. 8531889. 7517053. 2434021. 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] [HTIM] |
Reference(s): | [5] Maciag A., et al., 2011 |
Name: | rrlH-rrfH |
Gene(s): | rrlH, rrfH Genome Browser M3D Gene expression COLOMBOS |
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) |
![]() |
---|---|