RegulonDB RegulonDB 11.0: Operon Form
   

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




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


Transcription unit          
Name: codBA
Synonym(s): OP00277
Gene(s): codB, codA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the codBA operon, whose genes overlap, is induced under nitrogen-limited growth conditions and repressed by purines or pyrimidines. This induction and repression are mediated by NAC and PurR proteins, respectively Muse WB,2003. Danielsen S,1992.
Evidence: [ITCR] Inferred through co-regulation
[PM] Polar mutation
Reference(s): [1] Danielsen S., et al., 1992
Promoter
Name: codBp
+1: 354884
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 38
Sequence: aaaaatatatttccccacgaaaacgattgctttttatcttcagatgaatagaatgcggcgGattttttgggtttcaaacag
                           -35                   -10        +1                   
Note(s): There are two codBA transcriptional start positions, G7 and A8, relative to the -10 box. A8 always leads to reiterative transcription and the synthesis of transcripts with sequence AUUUUn, which are not extended downstream to include the codBA structural gene sequences. The G7 does not engage in reiterative transcription, which permits them to be extended downstream to generate productive codBA mRNA Qi F,1995.
Evidence: [HIPP]
[ICWHO]
[IDA]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Imashimizu M., et al., 2020
[4] Qi F., et al., 1995
TF binding sites (TFBSs)
[Nac,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Nac activator codBp 354819 354833 -58.0 gcactcattcATATAAAAAATATATttccccacga nd [GEA], [RSE], [AIBSCS], [AIBSPD], [BPP], [CSE], [SM] [5], [6], [7]
[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 codBp 354840 354855 -36.5 atatttccccACGAAAACGATTGCTTtttatcttca nd [GEA], [AIBSCS], [APIORCISFBSCS] [1], [8], [9]


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [IDA] Inferred from direct assay

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [RSE] RNA-seq evidence

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [AIBSPD] Automated inference based on sequence pattern discovery

 [BPP] Binding of purified proteins

 [CSE] ChIP-seq evidence

 [SM] Site mutation

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


Reference(s)    

 [1] Danielsen S., Kilstrup M., Barilla K., Jochimsen B., Neuhard J., 1992, Characterization of the Escherichia coli codBA operon encoding cytosine permease and cytosine deaminase., Mol Microbiol 6(10):1335-44

 [2] 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

 [3] Imashimizu M., Tokunaga Y., Afek A., Takahashi H., Shimamoto N., Lukatsky DB., 2020, Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences., Biomolecules 10(9)

 [4] Qi F., Turnbough CL., 1995, Regulation of codBA operon expression in Escherichia coli by UTP-dependent reiterative transcription and UTP-sensitive transcriptional start site switching., J Mol Biol 254(4):552-65

 [5] Aquino P., Honda B., Jaini S., Lyubetskaya A., Hosur K., Chiu JG., Ekladious I., Hu D., Jin L., Sayeg MK., Stettner AI., Wang J., Wong BG., Wong WS., Alexander SL., Ba C., Bensussen SI., Bernstein DB., Braff D., Cha S., Cheng DI., Cho JH., Chou K., Chuang J., Gastler DE., Grasso DJ., Greifenberger JS., Guo C., Hawes AK., Israni DV., Jain SR., Kim J., Lei J., Li H., Li D., Li Q., Mancuso CP., Mao N., Masud SF., Meisel CL., Mi J., Nykyforchyn CS., Park M., Peterson HM., Ramirez AK., Reynolds DS., Rim NG., Saffie JC., Su H., Su WR., Su Y., Sun M., Thommes MM., Tu T., Varongchayakul N., Wagner TE., Weinberg BH., Yang R., Yaroslavsky A., Yoon C., Zhao Y., Zollinger AJ., Stringer AM., Foster JW., Wade J., Raman S., Broude N., Wong WW., Galagan JE., 2017, Coordinated regulation of acid resistance in Escherichia coli., BMC Syst Biol 11(1):1

 [6] Muse WB., Rosario CJ., Bender RA., 2003, Nitrogen regulation of the codBA (cytosine deaminase) operon from Escherichia coli by the nitrogen assimilation control protein, NAC., J Bacteriol 185(9):2920-6

 [7] Zimmer DP., Soupene E., Lee HL., Wendisch VF., Khodursky AB., Peter BJ., Bender RA., Kustu S., 2000, Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation., Proc Natl Acad Sci U S A 97(26):14674-9

 [8] Cho BK., Federowicz SA., Embree M., Park YS., Kim D., Palsson BO., 2011, The PurR regulon in Escherichia coli K-12 MG1655., Nucleic Acids Res 39(15):6456-64

 [9] Kilstrup M., Meng LM., Neuhard J., Nygaard P., 1989, Genetic evidence for a repressor of synthesis of cytosine deaminase and purine biosynthesis enzymes in Escherichia coli., J Bacteriol 171(4):2124-7

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