|
|
| Operon |  |
|---|---|
| Name: | rpsU-dnaG-rpoD |
| This page displays every known transcription unit of this operon and their known regulation. | |
| 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 |
| 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 |
| 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]|. |
| 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 |
| 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 |
| 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 |
| 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 |
| 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) |
|
|---|---|
[HIPP] Human inference of promoter position