RegulonDB RegulonDB 9.4: Operon Form
   

rpsU-dnaG-rpoD operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: rpsU-dnaG-rpoD
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: rpsU
Gene(s): rpsU   Genome Browser M3D Gene expression COLOMBOS
Note(s): The rpsU-dnaG-rpoD operon has several promoters which are activated under different conditions. This operon contains two terminators, an internal terminator (T1) at the intergenic region between the rpsU gene and dnaG gene and a rho-independent terminator at the end of the operon (T2). The internal terminator might respond to antitermination by the lambda phage N gene product.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Burton ZF., et al., 1983
[2] Lupski JR., et al., 1984
[3] Lupski JR., et al., 1983
[4] Yajnik V., et al., 1993
Promoter
Name: rpsUp1
+1: 3210646
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 135
Sequence: atgcgggttgatgtaaaactttgttcgcccctggagaaagcctcgtgtatactcctcaccCttataaaagtccctttcaaa
                     -35                        -10         +1                   
Note(s): There is a putative promoter, Px, which partially overlaps rpsp1. It promotes transcription in a direction opposite to that of the rpsU-dnaG-rpoD operon. rpsUp1 occludes downstream promoters.
Evidence: [HIPP]
[HTTIM]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Burton ZF., et al., 1983
[5] Maciag A., et al., 2011
[6] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: tgtagttgtaAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTattttcgttt
Reference(s): [1] Burton ZF., et al., 1983


Transcription unit       
Name: rpsU-dnaG-rpoD
Gene(s): rpsU, dnaG, rpoD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The unusual rpsU-dnaG-rpoD operon, conserved in different gram-negative bacteria, participates in macromolecular synthesis |CITS:[8316085]|. The rpsU gene encodes the S21 protein, which is a component of the 30S subunit of the ribosome, the dnaG gene encodes a DNA primase that catalyzes the synthesis of RNA primers on single-stranded template DNA, and the rpoD gene encodes the primary σ factor that plays the most important role in promoter regulation during exponential growth (σ70). As it can be seen, this operon comprises three essential genes, whose products represent each of the three different main cellular molecules (RNA, DNA, and protein). In this way, this operon comprises three existing information fluxes of the central dogma of molecular biology, and its products participate in indispensable functions: in the initiation of protein synthesis (S21) and RNA synthesis from different templates (DNA primase, single strand; σ70, double strand) |CITS:[8316085] [6186393]|.
The coordinated expression of this operon is dependent on three tandem promoters, P1, P2, and P3, which are activated under different conditions |CITS:[6206376] [2848013]|. However, the expression of individual rpsU and rpoD genes can be independently regulated by their own promoters. About the end of the operon, there are two terminators, an internal terminator (T1) in the intergenic region between the rpsU gene and dnaG gene and a rho-independent terminator at the end of the operon (T2). The internal terminator might respond to antitermination by the lambda phage N gene product.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Burton ZF., et al., 1983
[2] Lupski JR., et al., 1984
[3] Lupski JR., et al., 1983
[4] Yajnik V., et al., 1993
Promoter
Name: rpsUp1
+1: 3210646
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 135
Sequence: atgcgggttgatgtaaaactttgttcgcccctggagaaagcctcgtgtatactcctcaccCttataaaagtccctttcaaa
                     -35                        -10         +1                   
Note(s): There is a putative promoter, Px, which partially overlaps rpsp1. It promotes transcription in a direction opposite to that of the rpsU-dnaG-rpoD operon. rpsUp1 occludes downstream promoters.
Evidence: [HIPP]
[HTTIM]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Burton ZF., et al., 1983
[5] Maciag A., et al., 2011
[6] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: ctctgcacaaACGCCACCTTTTCGGTGGCGttttttatcg
Reference(s): [7] Burton Z., et al., 1981
[1] Burton ZF., et al., 1983
[3] Lupski JR., et al., 1983


Transcription unit       
Name: rpsU-dnaG-rpoD
Gene(s): rpsU, dnaG, rpoD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The unusual rpsU-dnaG-rpoD operon, conserved in different gram-negative bacteria, participates in macromolecular synthesis |CITS:[8316085]|. The rpsU gene encodes the S21 protein, which is a component of the 30S subunit of the ribosome, the dnaG gene encodes a DNA primase that catalyzes the synthesis of RNA primers on single-stranded template DNA, and the rpoD gene encodes the primary σ factor that plays the most important role in promoter regulation during exponential growth (σ70). As it can be seen, this operon comprises three essential genes, whose products represent each of the three different main cellular molecules (RNA, DNA, and protein). In this way, this operon comprises three existing information fluxes of the central dogma of molecular biology, and its products participate in indispensable functions: in the initiation of protein synthesis (S21) and RNA synthesis from different templates (DNA primase, single strand; σ70, double strand) |CITS:[8316085] [6186393]|.
The coordinated expression of this operon is dependent on three tandem promoters, P1, P2, and P3, which are activated under different conditions |CITS:[6206376] [2848013]|. However, the expression of individual rpsU and rpoD genes can be independently regulated by their own promoters. About the end of the operon, there are two terminators, an internal terminator (T1) in the intergenic region between the rpsU gene and dnaG gene and a rho-independent terminator at the end of the operon (T2). The internal terminator might respond to antitermination by the lambda phage N gene product.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Burton ZF., et al., 1983
[2] Lupski JR., et al., 1984
[3] Lupski JR., et al., 1983
Promoter
Name: rpsUp2
+1: 3210712
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 69
Sequence: aaagtccctttcaaaaaaggccgcggtgctttacaaagcagcagcaattgcagtaaaattCcgcaccattttgaaataagc
                              -35                     -10   +1                   
Note(s): rpsUp2 has a sequence similar to that of a number of promoters under stringent control. Transcription initiation from rpsUDp2 and rpsUDp3 allows for greater readthrough at the internal terminator T2, thus increasing the relative ratio of dnaG and rpoD. rpsUp2 overlaps rpsUp3.
Evidence: [HIPP]
[HTTIM]
[IMP]
[TIM]
Reference(s): [1] Burton ZF., et al., 1983
[3] Lupski JR., et al., 1983
[5] Maciag A., et al., 2011
Terminator(s)
Type: rho-independent
Sequence: ctctgcacaaACGCCACCTTTTCGGTGGCGttttttatcg
Reference(s): [7] Burton Z., et al., 1981
[1] Burton ZF., et al., 1983
[3] Lupski JR., et al., 1983
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition rpsUp2 Amino acid starvation, Stationary phase Together ppGpp and DksA can inhibit more strongly the transcription initiation from the ribosomal protein promoter in vitro and in vivo |CITS:[21402902]|.    


Transcription unit          
Name: rpsU-dnaG-rpoD
Gene(s): rpsU, dnaG, rpoD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The unusual rpsU-dnaG-rpoD operon, conserved in different gram-negative bacteria, participates in macromolecular synthesis |CITS:[8316085]|. The rpsU gene encodes the S21 protein, which is a component of the 30S subunit of the ribosome, the dnaG gene encodes a DNA primase that catalyzes the synthesis of RNA primers on single-stranded template DNA, and the rpoD gene encodes the primary σ factor that plays the most important role in promoter regulation during exponential growth (σ70). As it can be seen, this operon comprises three essential genes, whose products represent each of the three different main cellular molecules (RNA, DNA, and protein). In this way, this operon comprises three existing information fluxes of the central dogma of molecular biology, and its products participate in indispensable functions: in the initiation of protein synthesis (S21) and RNA synthesis from different templates (DNA primase, single strand; σ70, double strand) |CITS:[8316085] [6186393]|.
The coordinated expression of this operon is dependent on three tandem promoters, P1, P2, and P3, which are activated under different conditions |CITS:[6206376] [2848013]|. However, the expression of individual rpsU and rpoD genes can be independently regulated by their own promoters. About the end of the operon, there are two terminators, an internal terminator (T1) in the intergenic region between the rpsU gene and dnaG gene and a rho-independent terminator at the end of the operon (T2). The internal terminator might respond to antitermination by the lambda phage N gene product.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Burton ZF., et al., 1983
[2] Lupski JR., et al., 1984
[3] Lupski JR., et al., 1983
Promoter
Name: rpsUp3
+1: 3210735
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 46
Sequence: cggtgctttacaaagcagcagcaattgcagtaaaattccgcaccattttgaaataagctgGcgttgatgccagcggcaaac
                               -35               -10        +1                   
Note(s): Transcription initiation from rpsUp2 and rpsUp3 allows for greater readthrough at the internal terminator, thus increasing the relative ratio of dnaG and rpoD. rpsUp2 overlaps rpsUp3. The rpsUp3 promoter is SOS inducible.
Evidence: [HIPP]
[HTTIM]
[IMP]
Reference(s): [3] Lupski JR., et al., 1983
[5] Maciag A., et al., 2011
Terminator(s)
Type: rho-independent
Sequence: ctctgcacaaACGCCACCTTTTCGGTGGCGttttttatcg
Reference(s): [7] Burton Z., et al., 1981
[1] Burton ZF., et al., 1983
[3] Lupski JR., et al., 1983
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
proximal LexA repressor rpsUp3 3210729 3210748 4.5 attttgaaatAAGCTGGCGTTGATGCCAGCggcaaaccga nd [BCE], [SM] [2], [3]


Transcription unit       
Name: rpoD
Gene(s): rpoD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The rpsU-dnaG-rpoD operon has several promoters which are activated under different conditions. This operon contains two terminators, an internal terminator (T1) at the intergenic region between the rpsU and dnaG genes and a rho-independent terminator at the end of the operon (T2). The internal terminator might respond to antitermination by the lambda phage N gene product.
The expression of the gene rpoD is increased under acidic growth conditions |CITS:[23274360]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Burton ZF., et al., 1983
[2] Lupski JR., et al., 1984
[3] Lupski JR., et al., 1983
Promoter
Name: rpoDp1
+1: 3212473
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 574
Sequence: agagcggcgtttctcgccctgttccgcagctaaaacgcacgaccatgcgtatacttatagGgttgctggtgcaaaatccag
                            -35                   -10       +1                   
Note(s): The rpoDp1 promoter is an internal promoter to the rpsU-dnaG-rpoD operon, and it is located in the C terminus of the dnaG gene.
Evidence: [HIPP]
[IMP]
[TIM]
Reference(s): [8] Taylor WE., et al., 1984
Terminator(s)
Type: rho-independent
Sequence: ctctgcacaaACGCCACCTTTTCGGTGGCGttttttatcg
Reference(s): [7] Burton Z., et al., 1981
[1] Burton ZF., et al., 1983
[3] Lupski JR., et al., 1983


Transcription unit       
Name: rpoD
Gene(s): rpoD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The rpsU-dnaG-rpoD operon has several promoters which are activated under different conditions. This operon contains two terminators, an internal terminator (T1) at the intergenic region between the rpsU and dnaG genes and a rho-independent terminator at the end of the operon (T2). The internal terminator might respond to antitermination by the lambda phage N gene product.

The expression of the gene rpoD is increased under acidic growth conditions |CITS:[23274360]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Burton ZF., et al., 1983
[2] Lupski JR., et al., 1984
[3] Lupski JR., et al., 1983
Promoter
Name: rpoDp2
+1: 3212637
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 410
Sequence: acttgtctctcccagccaggtctgaccaccgggcaacttttagagcactatcgtggtacaAataatgctgccacccttgaa
                      -35                        -10        +1                   
Note(s): The rpoDp2 promoter is an internal promoter to the rpsU-dnaG-rpoD operon, and it is located in the C terminus of dnaG gene.
Evidence: [HIPP]
[IMP]
[TIM]
Reference(s): [8] Taylor WE., et al., 1984
Terminator(s)
Type: rho-independent
Sequence: ctctgcacaaACGCCACCTTTTCGGTGGCGttttttatcg
Reference(s): [7] Burton Z., et al., 1981
[1] Burton ZF., et al., 1983
[3] Lupski JR., et al., 1983


Transcription unit       
Name: rpoD
Gene(s): rpoD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The rpsU-dnaG-rpoD operon has several promoters which are activated under different conditions. This operon contains two terminators, an internal terminator (T1) at the intergenic region between the rpsU and dnaG genes and a rho-independent terminator at the end of the operon (T2). The internal terminator might respond to antitermination by the lambda phage N gene product.

The expression of the gene rpoD is increased under acidic growth conditions |CITS:[23274360]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Burton ZF., et al., 1983
[2] Lupski JR., et al., 1984
[3] Lupski JR., et al., 1983
Promoter
Name: rpoDp3
+1: 3212688
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 359
Sequence: cgtggtacaaataatgctgccacccttgaaaaactgtcgatgtgggacgatatagcagatAagaatattgctgagcaaacc
                                     -35             -10    +1                   
Note(s): The rpoDp3 promoter is an internal promoter to the rpsU-dnaG-rpoD operon, and it is located in the C terminus of the dnaG gene. The activity of this rpoDp3 promoter is induced by heat shock.
Evidence: [HIPP]
[IDA]
[IEP]
[IMP]
[TIM]
Reference(s): [8] Taylor WE., et al., 1984
[9] Wade JT., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: ctctgcacaaACGCCACCTTTTCGGTGGCGttttttatcg
Reference(s): [7] Burton Z., et al., 1981
[1] Burton ZF., et al., 1983
[3] Lupski JR., et al., 1983


Transcription unit       
Name: rpoD
Gene(s): rpoD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The rpsU-dnaG-rpoD operon has several promoters which are activated under different conditions. This operon contains two terminators, an internal terminator (T1) at the intergenic region between the rpsU and dnaG genes and a rho-independent terminator at the end of the operon (T2). The internal terminator might respond to antitermination by the lambda phage N gene product.

The expression of the gene rpoD is increased under acidic growth conditions |CITS:[23274360]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Burton ZF., et al., 1983
[2] Lupski JR., et al., 1984
[3] Lupski JR., et al., 1983
Promoter
Name: rpoDp4
+1: 3212693
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 354
Sequence: tacaaataatgctgccacccttgaaaaactgtcgatgtgggacgatatagcagataagaaTattgctgagcaaaccttcac
                          -35                     -10       +1                   
Evidence: [AIPP]
[TIM]
Reference(s): [10] Dartigalongue C., et al., 2001


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [11] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -22.5 3211043 3211077 tagttgtaagGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTcgtttatgaa
  anti-terminator -16.42 3210980 3211050 acgcacgccgCACTCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCttccgaaagg
  anti-anti-terminator -6.36 3210979 3211009 aacgcacgccGCACTCGTCTGTACTAATTCCCCGAGAGCGttgctctccg
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"




Reference(s)    

 [1] Burton ZF., Gross CA., Watanabe KK., Burgess RR., 1983, The operon that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21 and DNA primase in E. coli K12., Cell. 32(2):335-49

 [2] Lupski JR., Ruiz AA., Godson GN., 1984, Promotion, termination, and anti-termination in the rpsU-dnaG-rpoD macromolecular synthesis operon of E. coli K-12., Mol Gen Genet. 195(3):391-401

 [3] Lupski JR., Smiley BL., Godson GN., 1983, Regulation of the rpsU-dnaG-rpoD macromolecular synthesis operon and the initiation of DNA replication in Escherichia coli K-12., Mol Gen Genet. 189(1):48-57

 [4] Yajnik V., Godson GN., 1993, Selective decay of Escherichia coli dnaG messenger RNA is initiated by RNase E., J Biol Chem. 268(18):13253-60

 [5] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements., Nucleic Acids Res. 39(13):5338-55

 [6] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [7] Burton Z., Burgess RR., Lin J., Moore D., Holder S., Gross CA., 1981, The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12., Nucleic Acids Res. 9(12):2889-903

 [8] Taylor WE., Straus DB., Grossman AD., Burton ZF., Gross CA., Burgess RR., 1984, Transcription from a heat-inducible promoter causes heat shock regulation of the sigma subunit of E. coli RNA polymerase., Cell. 38(2):371-81

 [9] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol. 13(9):806-14

 [10] Dartigalongue C., Missiakas D., Raina S., 2001, Characterization of the Escherichia coli sigma E regulon., J Biol Chem. 276(24):20866-75

 [11] Merino E, Yanofsky C,, 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet 21(5):260-4


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