RegulonDB RegulonDB 11.1: Operon Form
   

rrsE-gltV-rrlE-rrfE operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: rrsE-gltV-rrlE-rrfE
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: rrsE-gltV-rrlE-rrfE
Synonym(s): rrnE
Gene(s): rrsE, gltV, rrlE, rrfE   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 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 ribosome 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: [EXP-IDA-BOUNDARIES-DEFINED] 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: rrsEp3
+1: 4207863
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 284
Sequence: agtcatttttctgcaatttttctattgcggcctgcggagaactccctataatgcgcctccAtcgacacggcggatgtgaat
                         -35                -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. 1417-1431.
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
The rrsEp is also recognized by σ32, which shows a -35 box, spacer and -10 box, TTGCGG-13-CCCTAT, 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, 6.26; P-value, 7.26e05.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [5] Huerta AM., et al., 2003
[6] Newlands JT., et al., 1993
Terminator(s)
Type: rho-independent
Sequence: ggaactgccaGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATtatttgcatg
Reference(s): [7] Feng CQ., et al., 2019
[8] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis activator rrsEp3 4207686 4207700 -170.0 tttcaatggtGATCACAATTTTGACtgtggttacc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
remote Fis activator rrsEp3 4207713 4207727 -143.0 tggttaccgtGGGCAAAATACAGAAattacattga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
remote Fis activator rrsEp3 4207739 4207753 -117.0 ttacattgatGATTGTGGATAACTCtgtgcgtaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
remote Fis activator rrsEp3 4207755 4207769 -101.0 ggataactctGTGCGTAAAAAGGTAtaaagcgggc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
proximal Fis activator rrsEp3 4207784 4207798 -72.0 gcgggcttttGCTGGGGAATGCAGCagtcagtcat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
[Lrp,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Lrp-L-leucine repressor rrsEp3 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA inhibition rrsEp3 nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] 		[11]
  DksA-ppGpp inhibition rrsEp3 nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[11]
  ppGpp inhibition rrsEp3 nd   [EXP-IMP] [11]
Evidence: [EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [11] Paul BJ., et al., 2004


Transcription unit          
Name: rrsE-gltV-rrlE-rrfE
Synonym(s): rrnE
Gene(s): rrsE, gltV, rrlE, rrfE   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 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 ribosome 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: [EXP-IDA-BOUNDARIES-DEFINED] 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: rrsEp1
+1: 4207863
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 284
Sequence: agtcatttttctgcaatttttctattgcggcctgcggagaactccctataatgcgcctccAtcgacacggcggatgtgaat
                         -35                   -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. 1417-1431.
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
The rrsEp is also recognized by σ32, which shows a -35 box, spacer and -10 box, TTGCGG-13-CCCTAT, 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, 6.26; P-value, 7.26e05.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [5] Huerta AM., et al., 2003
[6] Newlands JT., et al., 1993
Terminator(s)
Type: rho-independent
Sequence: ggaactgccaGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATtatttgcatg
Reference(s): [7] Feng CQ., et al., 2019
[8] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis activator rrsEp1 4207686 4207700 -170.0 tttcaatggtGATCACAATTTTGACtgtggttacc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
remote Fis activator rrsEp1 4207713 4207727 -143.0 tggttaccgtGGGCAAAATACAGAAattacattga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
remote Fis activator rrsEp1 4207739 4207753 -117.0 ttacattgatGATTGTGGATAACTCtgtgcgtaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
remote Fis activator rrsEp1 4207755 4207769 -101.0 ggataactctGTGCGTAAAAAGGTAtaaagcgggc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
proximal Fis activator rrsEp1 4207784 4207798 -72.0 gcgggcttttGCTGGGGAATGCAGCagtcagtcat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
[Lrp,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Lrp-L-leucine repressor rrsEp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA inhibition rrsEp1 nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] 		[11]
  DksA-ppGpp inhibition rrsEp1 nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[11]
  ppGpp inhibition rrsEp1 nd   [EXP-IMP] [11]
Evidence: [EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [11] Paul BJ., et al., 2004


Transcription unit       
Name: rrsE-gltV-rrlE-rrfE
Gene(s): rrsE, gltV, rrlE, rrfE   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 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 ribosome 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.
Promoter
Name: rrsEp2
+1: 4207971
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 176
Sequence: gaagagaaaaatcctgaaattcagggttgactctgaaagaggaaagcgtaatatacgccaCctcgcgacagtgcgctaaag
                           -35                   -10        +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [5] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: ggaactgccaGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATtatttgcatg
Reference(s): [7] Feng CQ., et al., 2019
[8] Lesnik EA., et al., 2001


Transcription unit       
Name: rrlE-rrfE
Gene(s): rrlE, rrfE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Promoter
Name: rrlEp
+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: [EXP-IEP]
Reference(s): [12] Zaslaver A., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: ggaactgccaGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATtatttgcatg
Reference(s): [7] Feng CQ., et al., 2019
[8] Lesnik EA., et al., 2001


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-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] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [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] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477

 [8] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94

 [9] 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

 [10] 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

 [11] 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

 [12] 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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