RegulonDB RegulonDB 10.8: Operon Form
   

rrsH-ileV-alaV-rrlH-rrfH operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: rrsH-ileV-alaV-rrlH-rrfH
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
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
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
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]
[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-NS1 repressor rrsHp1 nd nd nd nd nd [GEA] [1], [9]
[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-leucine1 repressor rrsHp1 nd nd nd nd nd [GEA] [8]
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


Transcription unit       
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


Transcription unit       
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


Evidence    

 [HIPP] Human inference of promoter position

 [HTIM] High-throughput transcription initiation mapping

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IEP] Inferred from expression pattern


Reference(s)    

 [1] Gralla JD., 2005, Escherichia coli ribosomal RNA transcription: regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein., Mol Microbiol 55(4):973-7

 [2] Paul BJ., Ross W., Gaal T., Gourse RL., 2004, rRNA transcription in Escherichia coli., Annu Rev Genet 38:749-70

 [3] Schneider DA., Gourse RL., 2003, Changes in Escherichia coli rRNA promoter activity correlate with changes in initiating nucleoside triphosphate and guanosine 5' diphosphate 3'-diphosphate concentrations after induction of feedback control of ribosome synthesis., J Bacteriol 185(20):6185-91

 [4] Zhang X., Dennis P., Ehrenberg M., Bremer H., 2002, Kinetic properties of rrn promoters in Escherichia coli., Biochimie 84(10):981-96

 [5] 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

 [6] Newlands JT., Gaal T., Mecsas J., Gourse RL., 1993, Transcription of the Escherichia coli rrnB P1 promoter by the heat shock RNA polymerase (E sigma 32) in vitro., J Bacteriol 175(3):661-8

 [7] Hirvonen CA., Ross W., Wozniak CE., Marasco E., Anthony JR., Aiyar SE., Newburn VH., Gourse RL., 2001, Contributions of UP elements and the transcription factor FIS to expression from the seven rrn P1 promoters in Escherichia coli., J Bacteriol 183(21):6305-14

 [8] Pul U., Wurm R., Lux B., Meltzer M., Menzel A., Wagner R., 2005, LRP and H-NS--cooperative partners for transcription regulation at Escherichia coli rRNA promoters., Mol Microbiol 58(3):864-76

 [9] Afflerbach H., Schroder O., Wagner R., 1998, Effects of the Escherichia coli DNA-binding protein H-NS on rRNA synthesis in vivo., Mol Microbiol 28(3):641-53

 [10] Paul BJ., Barker MM., Ross W., Schneider DA., Webb C., Foster JW., Gourse RL., 2004, DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP., Cell 118(3):311-22

 [11] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

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