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| Operon |  |
|---|---|
| Name: | pcnB-folK |
| This page displays every known transcription unit of this operon and their known regulation. | |
| Name: | pcnB-folK |
| Gene(s): | folK, pcnB Genome Browser M3D Gene expression COLOMBOS |
| Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified |
| Reference(s): | [1] Talarico TL., et al., 1992 |
| Promoter | |
| Name: | pcnBp1 |
| +1: | 159151 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 25 |
| Sequence: |
caacattctcaaatgcgtcatgctgagctatgattagccgctatttttttgtcctgaatgAtgtttgacactaccgaggtg -35 -10 +1 |
| Note(s): | pcnBp1 and pcnBp2 may have minor roles in the pcnB-folK operon Nadratowska-Wesolowska B,2010 |
| Evidence: |
[COMP-AINF] [COMP-HINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
| Reference(s): |
[2] Huerta AM., et al., 2003 [3] Jasiecki J., et al., 2006 [4] Nadratowska-Wesolowska B., et al., 2010 |
| Name: | pcnB-folK |
| Gene(s): | folK, pcnB Genome Browser M3D Gene expression COLOMBOS |
| Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified |
| Reference(s): |
[5] Cao GJ., et al., 1996 [6] Liu JD., et al., 1989 [7] Podkovyrov SM., et al., 1995 [1] Talarico TL., et al., 1992 |
| Promoter | |
| Name: | pcnBp |
| +1: | 159171 |
| Sigma Factor: | Sigma38 Sigmulon |
| Distance from start of the gene: | 45 |
| Sequence: |
cgagtcggcaattgtaaattcaacattctcaaatgcgtcatgctgagctatgattagccgCtatttttttgtcctgaatga -35 -10 +1 |
| Note(s): | pcnBp3 (pB) activity is drastically impaired at the stationary phase of growth, and it is the major promoter of the pcnB-folK operon under various growth conditions Nadratowska-Wesolowska B,2010 pcnBp3 (pB) can also be weakly recognized by EσS Nadratowska-Wesolowska B,2010 |
| Evidence: |
[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP] |
| Reference(s): |
[8] Binns N., et al., 2002 [2] Huerta AM., et al., 2003 [3] Jasiecki J., et al., 2006 [4] Nadratowska-Wesolowska B., et al., 2010 |
| Allosteric regulation of RNA-polymerase |
| Regulator | Function | Promoter target of RNApol | Growth Conditions | Note | Evidence | Reference | |
|---|---|---|---|---|---|---|---|
| DksA-ppGpp | inhibition | pcnBp | nd |
[EXP-IDA-PURIFIED-PROTEIN] [EXP-IEP-GENE-EXPRESSION-ANALYSIS] |
[4] | ||
| ppGpp | inhibition | pcnBp | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | [4] |
| Evidence: |
[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis |
| Reference(s): | [4] Nadratowska-Wesolowska B., et al., 2010 |
| Name: | pcnB-folK |
| Gene(s): | folK, pcnB Genome Browser M3D Gene expression COLOMBOS |
| Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified |
| Reference(s): |
[5] Cao GJ., et al., 1996 [6] Liu JD., et al., 1989 [7] Podkovyrov SM., et al., 1995 [1] Talarico TL., et al., 1992 |
| Promoter | |
| Name: | pcnBp3 |
| +1: | 159171 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 45 |
| Sequence: |
cgagtcggcaattgtaaattcaacattctcaaatgcgtcatgctgagctatgattagccgCtatttttttgtcctgaatga -35 -10 +1 |
| Note(s): | pcnBp3 (pB) activity is drastically impaired at the stationary phase of growth, and it is the major promoter of the pcnB-folK operon under various growth conditions Nadratowska-Wesolowska B,2010 pcnBp3 (pB) can also be weakly recognized by EσS Nadratowska-Wesolowska B,2010 |
| Evidence: |
[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP] |
| Reference(s): |
[8] Binns N., et al., 2002 [2] Huerta AM., et al., 2003 [3] Jasiecki J., et al., 2006 [4] Nadratowska-Wesolowska B., et al., 2010 |
| Name: | pcnB-folK |
| Gene(s): | folK, pcnB Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | pcnBp1 and pcnBp2 may have minor roles in the pcnB-folK operon Nadratowska-Wesolowska B,2010 |
| Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified |
| Reference(s): | [1] Talarico TL., et al., 1992 |
| Promoter | |
| Name: | pcnBp2 |
| +1: | 159195 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 69 |
| Sequence: |
aaactggcggcttaccgccgtgcccgagtcggcaattgtaaattcaacattctcaaatgcGtcatgctgagctatgattag -35 -10 +1 |
| Evidence: |
[COMP-AINF] [COMP-HINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
| Reference(s): |
[2] Huerta AM., et al., 2003 [3] Jasiecki J., et al., 2006 [4] Nadratowska-Wesolowska B., et al., 2010 |
| Name: | pcnB-folk |
| Gene(s): | folK, pcnB Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | A promoter designated as pS1 was identified using primer extension by Nadratowska-Wesolowska et al. (2010); this promoter was also identified by Liu and Parkinson (1989) Nadratowska-Wesolowska B,2010. Liu JD,1989 This promoter is recognized more effectively by EσS than Eσ70; however, its transcriptional start site is 10 bp downstream of the translational start site of the pcnB gene Nadratowska-Wesolowska B,2010 The pS1 sequence bears the C residue in the -10 box, which is crucial for selective recognition of the promoter dependent on EσS Nadratowska-Wesolowska B,2010. Lacour S,2003 The pS1 promoter is active in vivo (under specific conditions) and in vitro, since there is a translation start codon, AUU, downstream of its transcriptional start site Nadratowska-Wesolowska B,2010. It is possible that there are two functional variants of PAP I, but this remains to be verified Liu JD,1989 |
| Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified |
| Reference(s): | [1] Talarico TL., et al., 1992 |
| Promoter | |
| Name: | pcnBp4 |
| +1: | 159391 |
| Sigma Factor: | Sigma38 Sigmulon |
| Distance from start of the gene: | 265 |
| Sequence: |
aagtgccagattacattcatctgccgctggcgcttaatccacaaggcgctaaactttccaAgcagaatcatgcgcctgcgt -35 -10 +1 |
| Note(s): | pcnBp4 (pS2) has at least two alternatives start sites, located in the region between positions -263 and -265 relative to the translation start codon, ATT Nadratowska-Wesolowska B,2010 The pS2 sequence bears the C residue in the -10 box, which is crucial for selective recognition of the promoter dependent on EσS Nadratowska-Wesolowska B,2010. Lacour S,2003 For the first time, activities have been reported for a σS-dependent promoter (pcnBp4) that is inhibited by the stringent response factors ppGpp and DksA; these findings are based on both passive and active models Nadratowska-Wesolowska B,2010 |
| Evidence: |
[COMP-AINF] [COMP-HINF] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP] |
| Reference(s): |
[2] Huerta AM., et al., 2003 [4] Nadratowska-Wesolowska B., et al., 2010 |
| Allosteric regulation of RNA-polymerase |
| Regulator | Function | Promoter target of RNApol | Growth Conditions | Note | Evidence | Reference | |
|---|---|---|---|---|---|---|---|
| DksA-ppGpp | inhibition | pcnBp4 | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | [4] | ||
| ppGpp | inhibition | pcnBp4 | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | [4] |
| Evidence: | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis |
| Reference(s): | [4] Nadratowska-Wesolowska B., et al., 2010 |
| Reference(s) |
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|---|---|
[COMP-AINF] Inferred computationally without human oversight