RegulonDB RegulonDB 11.1: Operon Form
   

rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF
Synonym(s): rrnD
Gene(s): rrfF, thrV, rrfD, rrlD, alaU, ileU, rrsD   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 to 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., Escherichia 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: rrsDp2
+1: 3428940
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 178
Sequence: agagaaaaaaatcctgaaattcagggttgactctgaaagaggaaagcgtaatatacgccaCctcgcgacagtgagctgaaa
                                -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
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Huerta AM., et al., 2003
[6] Liebig B., et al., 1995
[7] Sander P., et al., 1993
Terminator(s)
Type: rho-independent
Sequence: accgacaaacAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGtctggcagtt
Reference(s): [8] Feng CQ., et al., 2019
[9] Lesnik EA., et al., 2001


Transcription unit          
Name: rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF
Synonym(s): rrnD
Gene(s): rrfF, thrV, rrfD, rrlD, alaU, ileU, rrsD   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 to 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., Escherichia 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: rrsDp
+1: 3429047
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 285
Sequence: cagaaaaaaagatcaaaaaaatacttgtgcaaaaaattgggatccctataatgcgcctccGttgagacgacaacgtgaaac
                                -35              -10        +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Huerta AM., et al., 2003
[6] Liebig B., et al., 1995
[10] Newlands JT., et al., 1993
[7] Sander P., et al., 1993
Terminator(s)
Type: rho-independent
Sequence: accgacaaacAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGtctggcagtt
Reference(s): [8] Feng CQ., et al., 2019
[9] 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
proximal Fis activator rrsDp 3429111 3429125 -71.0 gcagcaaaaaGGGTGAAAAAACAACaaacagaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11]
proximal Fis activator rrsDp 3429131 3429145 -91.0 gcaccgttttGTGTGCGATTGCAGCaaaaagggtg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11]
remote Fis activator rrsDp 3429166 3429180 -126.0 attggccttgTGCAAGTCTTTTAGTatgcaaaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11]
remote Fis activator rrsDp 3429184 3429198 -144.0 aatgactttgGGGGCATTATTGGCCttgtgcaagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [11]
remote Fis activator rrsDp 3429214 3429228 -174.0 catacttaccTCAGCAATAAATGATttactaatga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11]
[H-NS,-] 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 H-NS repressor rrsDp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1], [12]
[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 rrsDp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [13]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA inhibition rrsDp nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] 		[14]
  DksA-ppGpp inhibition rrsDp nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[14]
  ppGpp inhibition rrsDp nd   [EXP-IMP] [14]
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): [14] Paul BJ., et al., 2004


Transcription unit          
Name: rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF
Synonym(s): rrnD
Gene(s): rrfF, thrV, rrfD, rrlD, alaU, ileU, rrsD   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 to 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., Escherichia 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: rrsDp1
+1: 3429047
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 285
Sequence: cagaaaaaaagatcaaaaaaatacttgtgcaaaaaattgggatccctataatgcgcctccGttgagacgacaacgtgaaac
                              -35                   -10     +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Huerta AM., et al., 2003
[6] Liebig B., et al., 1995
[10] Newlands JT., et al., 1993
[7] Sander P., et al., 1993
Terminator(s)
Type: rho-independent
Sequence: accgacaaacAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGtctggcagtt
Reference(s): [8] Feng CQ., et al., 2019
[9] 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
proximal Fis activator rrsDp1 3429111 3429125 -71.0 gcagcaaaaaGGGTGAAAAAACAACaaacagaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11]
proximal Fis activator rrsDp1 3429131 3429145 -91.0 gcaccgttttGTGTGCGATTGCAGCaaaaagggtg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11]
remote Fis activator rrsDp1 3429166 3429180 -126.0 attggccttgTGCAAGTCTTTTAGTatgcaaaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11]
remote Fis activator rrsDp1 3429184 3429198 -144.0 aatgactttgGGGGCATTATTGGCCttgtgcaagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [11]
remote Fis activator rrsDp1 3429214 3429228 -174.0 catacttaccTCAGCAATAAATGATttactaatga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11]
[H-NS,-] 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 H-NS repressor rrsDp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1], [12]
[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 rrsDp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [13]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA inhibition rrsDp1 nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] 		[14]
  DksA-ppGpp inhibition rrsDp1 nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[14]
  ppGpp inhibition rrsDp1 nd   [EXP-IMP] [14]
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): [14] Paul BJ., et al., 2004


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

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


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] 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

 [7] Sander P., Langert W., Mueller K., 1993, Mechanisms of upstream activation of the rrnD promoter P1 of Escherichia coli., J Biol Chem 268(23):16907-16

 [8] 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

 [9] 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

 [10] 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

 [11] 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

 [12] 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

 [13] 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

 [14] 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

RegulonDB