RegulonDB RegulonDB 10.10: Operon Form
   

pyrC operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: pyrC
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
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 Bsat N, Helmann JD,1999. 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]
[ICWHO]
[IHBCE]
[TIM]
Reference(s): [1] Huerta AM., et al., 2003
[2] Wilson HR., et al., 1992
[3] Wilson HR., et al., 1987
TF binding sites (TFBSs)
[Fur,-] Phrase
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 [GEA], [APIORCISFBSCS], [BPP] [4]
[PurR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PurR-hypoxanthine repressor pyrCp 1122659 1122674 -23.5 tttcgtgcaaAGGAAAACGTTTCCGCttatcctttg nd [GEA], [APIORCISFBSCS], [BPP], [SM] [5], [6]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [7] Merino E, et al., 2005
  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
Evidence: [ICA] Inferred by computational analysis
Reference(s): [8] null null
  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"


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [IHBCE] Inferred by a human based on computational evidence

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [SM] Site mutation


Reference(s)    

 [1] 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

 [2] Wilson HR., Archer CD., Liu JK., Turnbough CL., 1992, Translational control of pyrC expression mediated by nucleotide-sensitive selection of transcriptional start sites in Escherichia coli., J Bacteriol 174(2):514-24

 [3] Wilson HR., Chan PT., Turnbough CL., 1987, Nucleotide sequence and expression of the pyrC gene of Escherichia coli K-12., J Bacteriol 169(7):3051-8

 [4] Chai S., Song CK., Kim SK., Park JH., Wee S., 2007, Effect of fur on pyrC gene expression., J Microbiol 45(6):583-9

 [5] Choi KY., Zalkin H., 1990, Regulation of Escherichia coli pyrC by the purine regulon repressor protein., J Bacteriol 172(6):3201-7

 [6] Wilson HR., Turnbough CL., 1990, Role of the purine repressor in the regulation of pyrimidine gene expression in Escherichia coli K-12., J Bacteriol 172(6):3208-13

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

 [8] null, null, null, null


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