RegulonDB RegulonDB 10.8: Operon Form
   

rrsB-gltT-rrlB-rrfB operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: rrsB-gltT-rrlB-rrfB
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: rrsB-gltT-rrlB-rrfB
Synonym(s): rrnB
Gene(s): rrsB, gltT, rrlB, rrfB   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; 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 to 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; 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 contain genes whose products interact with the RNA polymerase and participate in the translation elongation and in the replication apparatus.
Under alkylation stress, the protein AidB binds upstream of the rrnBp1 promoter, increasing the activity of this promoter 21788159 The roles of AidB, in the regulatory region of the rrnBp1 promoter and in other promoters also containing a UP element, are to prevent and to repair the DNA damage caused by alkylating agents and counteract the block to transcription that results upon exposure to the mentioned agents 21788159
The secondary channel factors (SCFs) GreB and DksA both selectively repress ribosomal RNA (rRNA) transcription by a similar mechanism, because their short-lived RNAP complexes do not allow sufficient time for SCFs to dissociate. Using GreB as a model to investigate the mechanism(s) of SCF-RNAP binding and action at rrsBp1, it was revealed that GreB functions by a delayed inhibition mechanism, and the results implied that DksA functions by the same mechanism 30720429
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., Escherichia 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] Fange D., et al., 2014
[2] Gralla JD. 2005
[3] Paul BJ., et al., 2004
[4] Schneider DA., et al., 2003
[5] Zhang X., et al., 2002
Promoter
Name: rrsBp1
+1: 4166367
Sigma Factor: Sigma32, Sigma70
Distance from start of the gene: 292
Sequence: cagaaaattattttaaatttcctcttgtcaggccggaataactccctataatgcgccaccActgacacggaacaacggcaa
                         -35                   -10          +1                   
Note(s): The σ32 holoenzyme can also recognize rrnBp1, at least in vitro Newlands JT,1993 but it has not been shown yet that this occurs in vivo.
The transcription of the rrnBp1 promoter is reduced by guanosine tetraphosphate (ppGpp), which modifies the RNA polymerase. Perhaps this RNA polymerase forms an inactive promoter complex, as happens with the argTp promoter Maitra A,2005
The presence of eight amino acids (alanine, glutamine, glutamic acid, isoleucine, leucine, methionine, serine, and valine) in the growth medium enhances the activity of the rrnBp1 promoter. 16675089suggested that it is a result of the slow synthesis of one of the enzymes that produces ppGpp (the spoT gene product).
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
Based 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 interfering with the RNA polymerase, and this way it may alter the DNA of the upstream regions of all seven ribosomal P1 promoters Pul U,2005.
Many Lrp and H-NS sites were observed through a DNase I footprinting analysis in the rrnBp upstream region. Although no specific central positions were determined, the Lrp clusters between positions -20 and -90. It is important to note that the same sequence is strongly protected by an H-NS-DNA complex Pul U,2005.
The rrsBp1 promoter is also recognized by σ32, which shows a -35 box, spacer, and -10 box, CGGAAT-14-CGCCAC, based on similarity to the consensus sequence of the set of known functional promoters for this σ factor, for which there is strong experimental evidence: high homology; score, 7.24; P-value, 2.35e05.
Conserved region 3.2 of the primary σ70 factor (σ finger) negatively affects interactions of the σ70 RNAP holoenzyme with rrsBp1, by decreasing promoter complex stability and making it a target for repression by the stringent response factors DksA and ppGpp Pupov D,2018 σ fingers play an important role in promoter complex formation, and this region is involved in the control of the activity of unstable promoters under changing growth conditions Pupov D,2018
Evidence: [HIPP]
[TIM]
Reference(s): [6] Bartlett MS., et al., 2000
[7] Bartlett MS., et al., 1994
[2] Gralla JD. 2005
[8] Liebig B., et al., 1995
[9] Newlands JT., et al., 1993
[3] Paul BJ., et al., 2004
[10] Pupov D., et al., 2018
[11] Ross W., et al., 1990
Terminator(s)
Type: rho-independent
Sequence: caggcatcaaATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATctgttgtttg
Reference(s): [12] Brosius J., et al., 1981
Type: rho-independent
Sequence: caaattaagcAGAAGGCCATCCTGACGGATGGCCTTTTtgcgtttcta
Reference(s): [12] Brosius J., et al., 1981
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis1 activator rrsBp1 4166217 4166231 -143.0 gccaggagctGAACAATTATTGCCCgttttacagc nd [BPP], [GEA] [6], [8], [11], [13], [14], [15], [16]
remote Fis2 activator rrsBp1 4166258 4166272 -102.0 gcttcgaaacGCTCGAAAAACTGGCagttttaggc nd [BPP], [GEA] [6], [8], [11], [13], [14], [15], [16]
proximal Fis3 activator rrsBp1 4166289 4166303 -71.0 aggctgatttGGTTGAATGTTGCGCggtcagaaaa nd [BPP], [GEA] [6], [8], [11], [13], [14], [15], [16]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal H-NS1 repressor rrsBp1 4166277 4166291 -83.0 actggcagttTTAGGCTGATTTGGTtgaatgttgc nd [BPP] [17]
proximal H-NS2 repressor rrsBp1 4166310 4166324 -50.0 gcgcggtcagAAAATTATTTTAAATttcctcttgt nd [BPP] [17]
proximal H-NS3 repressor rrsBp1 4166334 4166348 -26.0 tttcctcttgTCAGGCCGGAATAACtccctataat nd [BPP] [17]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Lrp-leucine repressor rrsBp1 4166308 4166319 -53.0 ttgcgcggtcAGAAAATTATTTtaaatttcct nd [BPP], [GEA] [18]
remote Lrp-leucine repressor rrsBp1 4166435 4166446 75.0 cggcagagaaAGCAAAAATAAAtgcttgactc nd [BPP], [IEP] [18]
remote Lrp-leucine repressor rrsBp1 4166629 4166640 269.0 aattcattacGAAGTTTAATTCtttgagcgtc nd [BPP], [IEP] [18]
Note(s): 1Fis appears to have little or no effect on rrsBp1 as a result of the addition of amino acids to the growth medium 16675089
2Fis appears to have little or no effect on rrsBp1 as a result of the addition of amino acids to the growth medium 16675089
3Fis appears to have little or no effect on rrsBp1 as a result of the addition of amino acids to the growth medium 166750891H-NS antagonizes the Fis-mediated activation of the P1 promoter through conformational changes in the DNA Tippner D,1994.
2H-NS antagonizes the Fis-mediated activation of the P1 promoter through conformational changes in the DNA Tippner D,1994.
3H-NS antagonizes the Fis-mediated activation of the P1 promoter through conformational changes in the DNA Tippner D,1994.1Fis appears to have little or no effect on rrsBp1 as a result of the addition of amino acids to the growth medium 16675089
2Fis appears to have little or no effect on rrsBp1 as a result of the addition of amino acids to the growth medium 16675089
3H-NS antagonizes the Fis-mediated activation of the P1 promoter through conformational changes in the DNA Tippner D,1994.
4Fis appears to have little or no effect on rrsBp1 as a result of the addition of amino acids to the growth medium 16675089
6H-NS antagonizes the Fis-mediated activation of the P1 promoter through conformational changes in the DNA Tippner D,1994.
7H-NS antagonizes the Fis-mediated activation of the P1 promoter through conformational changes in the DNA Tippner D,1994.
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA inhibition rrsBp1   [APPH]
[GEA]
[19]
  DksA-ppGpp inhibition rrsBp1 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]
[IEP]
[IMP]
[IPI]
[20]
[19]
[10]
  ppGpp inhibition rrsBp1 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
The regulatory effects on transcription initiation and properties between (p)ppApp with (p)ppGpp were assessed using the well-studied E. coli rrnBP1 promoter. Different from (p)ppGpp, (p)ppApp activates transcription at this promoter, and DksA hinders this effect; in contrast, pppApp exerts a stronger effect than ppApp. The X-ray crystal structure of the RNAP-(p)ppApp complex was determined and which shows that the analogs bind near the active site and switch regions of RNAP Klitgaard RN,2018
[IMP] [19]
Evidence: [APPH] Assay of protein purified to homogeneity
[GEA] Gene expression analysis
[IEP] Inferred from expression pattern
[IMP] Inferred from mutant phenotype
[IPI] Inferred from physical interaction
Reference(s): [19] Paul BJ., et al., 2004
[20] Mechold U., et al., 2013
[10] Pupov D., et al., 2018


Transcription unit       
Name: rrsB-gltT-rrlB-rrfB
Synonym(s): rrnB
Gene(s): rrsB, gltT, rrlB, rrfB   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; 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 to 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; 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 contain 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., Escherichia coli and Salmonella: Cellular and Molecular Biology. ASM Press, Washington, D.C., p. 1417-1431.
Reference(s): [2] Gralla JD. 2005
[3] Paul BJ., et al., 2004
[4] Schneider DA., et al., 2003
[5] Zhang X., et al., 2002
Promoter
Name: rrsBp2
+1: 4166484
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 175
Sequence: ccggcagagaaagcaaaaataaatgcttgactctgtagcgggaaggcgtattatgcacacCccgcgccgctgagaaaaagc
                           -35                   -10        +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the promoters, whose transcription start sites were determined experimentally, present a distance of 6 nucleotides between the transcription start site and the -10 box.
The rrsBp2 promoter appears not to be activated as part of the stringent response 16675089
Evidence: [AIPP]
[TIM]
Reference(s): [8] Liebig B., et al., 1995
[21] Murray HD., et al., 2003
[22] Murray HD., et al., 2004
Terminator(s)
Type: rho-independent
Sequence: caggcatcaaATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATctgttgtttg
Reference(s): [12] Brosius J., et al., 1981
Type: rho-independent
Sequence: caaattaagcAGAAGGCCATCCTGACGGATGGCCTTTTtgcgtttcta
Reference(s): [12] Brosius J., et al., 1981


Transcription unit       
Name: rrlB-rrfB
Gene(s): rrlB, rrfB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [PAGTSBP] Products of adjacent genes in the same biological process
Promoter
Name: rrlBp
+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): [23] Zaslaver A., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: caggcatcaaATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATctgttgtttg
Reference(s): [12] Brosius J., et al., 1981
Type: rho-independent
Sequence: caaattaagcAGAAGGCCATCCTGACGGATGGCCTTTTtgcgtttcta
Reference(s): [12] Brosius J., et al., 1981




Reference(s)    

 [1] Fange D., Mellenius H., Dennis PP., Ehrenberg M., 2014, Thermodynamic Modeling of Variations in the Rate of RNA Chain Elongation of E. coli rrn Operons., Biophys J 106(1):55-64

 [2] 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

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

 [4] 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

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

 [6] Bartlett MS., Gaal T., Ross W., Gourse RL., 2000, Regulation of rRNA transcription is remarkably robust: FIS compensates for altered nucleoside triphosphate sensing by mutant RNA polymerases at Escherichia coli rrn P1 promoters., J Bacteriol 182(7):1969-77

 [7] Bartlett MS., Gourse RL., 1994, Growth rate-dependent control of the rrnB P1 core promoter in Escherichia coli., J Bacteriol 176(17):5560-4

 [8] Liebig B., Wagner R., 1995, Effects of different growth conditions on the in vivo activity of the tandem Escherichia coli ribosomal RNA promoters P1 and P2., Mol Gen Genet 249(3):328-35

 [9] 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

 [10] Pupov D., Petushkov I., Esyunina D., Murakami KS., Kulbachinskiy A., 2018, Region 3.2 of the σ factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA., Nucleic Acids Res 46(21):11477-11487

 [11] Ross W., Thompson JF., Newlands JT., Gourse RL., 1990, E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo., EMBO J 9(11):3733-42

 [12] Brosius J., Dull TJ., Sleeter DD., Noller HF., 1981, Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli., J Mol Biol 148(2):107-27

 [13] 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

 [14] Appleman JA., Ross W., Salomon J., Gourse RL., 1998, Activation of Escherichia coli rRNA transcription by FIS during a growth cycle., J Bacteriol 180(6):1525-32

 [15] 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

 [16] Zhang X., Bremer H., 1996, Effects of Fis on ribosome synthesis and activity and on rRNA promoter activities in Escherichia coli., J Mol Biol 259(1):27-40

 [17] Tippner D., Afflerbach H., Bradaczek C., Wagner R., 1994, Evidence for a regulatory function of the histone-like Escherichia coli protein H-NS in ribosomal RNA synthesis., Mol Microbiol 11(3):589-604

 [18] 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

 [19] 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

 [20] Mechold U., Potrykus K., Murphy H., Murakami KS., Cashel M., 2013, Differential regulation by ppGpp versus pppGpp in Escherichia coli., Nucleic Acids Res 41(12):6175-89

 [21] Murray HD., Appleman JA., Gourse RL., 2003, Regulation of the Escherichia coli rrnB P2 promoter., J Bacteriol 185(1):28-34

 [22] Murray HD., Gourse RL., 2004, Unique roles of the rrn P2 rRNA promoters in Escherichia coli., Mol Microbiol 52(5):1375-87

 [23] 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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