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| Operon |  |
|---|---|
| Name: | pyrC |
| This page displays every known transcription unit of this operon and their known regulation. | |
| Name: | pyrC |
| Synonym(s): | OP00083 |
| Gene(s): | pyrC Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | The primary mechanism of regulation of pyrC gene expression occurs in the translation-initiation level, when it is controlled by the formation of a hairpin at the 5' end of the transcript. Pyrimidine availability modulates the formation of this hairpin by influencing the site of transcription initiation. On the other hand, the pyrC gene is expressed, at least, from four start sites Wilson HR,1992. The Fur-DNA interaction is weak, and it is possible that Fur acts with an unknown cellular condition or DNA-binding antagonist, such as another protein, a low-molecular-weight ligand, or another metal ion 10400588. Chai S,2007. This effect of Fur on pyrC could occur indirectly via PurR, inasmuch as Fur controls purR expression negatively and PurR also represses pyrC Chai S,2007. |
| Promoter | |
| Name: | pyrCp |
| +1: | 1122643 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 36 |
| Sequence: |
cgcattcgcgccctttatttttcgtgcaaaggaaaacgtttccgcttatcctttgtgtccGgcaaaaacatcccttcagcc -35 -10 +1 |
| Note(s): | pyrCp is primarily expressed under conditions of pyrimidine limitation, in which the CTP and GTP levels are low Wilson HR,1992. On the other hand, under conditions of pyrimidine excess, in which the CTP level is high and similar to that of GTP, pyrC is also expressed from another transcriptional start site, at a position two bases downstream of pyrCp. Despite that, pyrC transcripts form a regulatory hairpin at their 5' end, which blocks its own translational initiation, hence preventing translation of the pyrC cistron. Finally, pyrC is also expressed in a small percentage from other transcriptional start sites, located one base upstream and one position downstream of the pyrCp promoter Wilson HR,1992. |
| Evidence: |
[HIPP] [TIM] |
| Reference(s): | [1] Wilson HR., et al., 1992 |
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | Fur-Fe2+ | repressor | pyrCp | 1122720 | 1122744 | -88.5 | gaagtgaagcCAGGCGAAATTGTCATTCCATTTACtgattaatca | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [2] |
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | PurR-hypoxanthine1 | repressor | pyrCp | 1122659 | 1122674 | -23.5 | tttcgtgcaaAGGAAAACGTTTCCGCttatcctttg | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] | [3], [4], [5] |
| Note(s): | 1When the CTP level within the cell is high relative to the level of GTP, the pyrC gene is transcribed from a start site that allows formation of a secondary structure within the 5' end of the mRNA. This hairpin structure is thought to obscure the Shine-Dalgarno sequence, and it results in poor translation efficiency. When the CTP level is low relative to the level of GTP, pyrC is transcribed from an alternate start site. This shorter mRNA is translated efficiently. The PurR protein, which represses the pyrC gene, is also regulated by the level of GTP, because this protein is active when GTP is present.2When the CTP level within the cell is high relative to the level of GTP, the pyrC gene is transcribed from a start site that allows formation of a secondary structure within the 5' end of the mRNA. This hairpin structure is thought to obscure the Shine-Dalgarno sequence, and it results in poor translation efficiency. When the CTP level is low relative to the level of GTP, pyrC is transcribed from an alternate start site. This shorter mRNA is translated efficiently. The PurR protein, which represses the pyrC gene, is also regulated by the level of GTP, because this protein is active when GTP is present. |
| RNA cis-regulatory element | |
|---|
| Regulation, transcriptional elongation | |
| Attenuator type: | Transcriptional |
| Strand: | reverse |
| Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
|---|---|---|---|---|---|
| terminator | -14.6 | 1122681 | 1122708 | gattaatcacGAGGGCGCATTCGCGCCCTTTATTTTTcgtgcaaagg | |
| anti-terminator | -6.2 | 1122703 | 1122746 | ttgaagtgaaGCCAGGCGAAATTGTCATTCCATTTACTGATTAATCACGAGGGcgcattcgcg | |
| anti-anti-terminator | -14.9 | 1122728 | 1122782 | agggcgaagcAATGGCGAAAAAACTGGCGAAAGGCATTGAAGTGAAGCCAGGCGAAATTGTCATtccatttact |
| 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" |
| REGULATION, RNA cis-regulatory element: | |
| Rfam type: | Cis-reg; leader |
| Strand: | reverse |
| Description | Rfam score | Left Pos | Right Pos | Sequence (RNA-strand) | |
|---|---|---|---|---|---|
| PyrC leader | 68.5 | 1122608 | 1122657 | cguuuccgcuUAUCCUUUGUGUCCGGCAAAAACAUCCCUUCAGCCGGAGCAUAGAGAUUAaugacugcac |
| Notes: "The provied "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appears as the reverse complement of the sequence delimited by LeftPos-RightPos" |
| Reference(s) |
|
|---|---|
[HIPP] Human inference of promoter position