RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: phnCDEEFGHIJKLMNOP
Synonym(s): OP00283, phnCDE-b4103-phnFGHIJKLMNOP, phnCDE-w4011-phnFGHIJKLMNOP, phnCDE-w4011-phnFGHIJKLMNOPQ
Gene(s): phnP, phnO, phnN, phnM, phnL, phnK, phnJ, phnI, phnH, phnG, phnF, phnE, phnD, phnC   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene phnC is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression appears to be caused by the transcription factor PhoB Marzan LW,2013
Reference(s): [1] Metcalf WW., et al., 1991
[2] Metcalf WW., et al., 1993
[3] Wanner BL., et al., 1992
Promoter
Name: phnCp
+1: 4325206
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 41
Sequence: atcgaattcccgttaactcttcatctgttagtcacttttaattaaccaaatcgtcacaatAatccgccacgatggagccac
                                 -35                        +10                  
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Huerta AM., et al., 2003
[5] Jiang W., et al., 1995
[6] Makino K., et al., 1991
[2] Metcalf WW., et al., 1993
TF binding sites (TFBSs)
[PhoB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd PhoB-phosphorylated activator phnCp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6], [7], [8]


Transcription unit       
Name: phnLMNOP
Gene(s): phnP, phnO, phnN, phnM, phnL   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: phnLp
+1: Unknown
Note(s): Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Based on this, a putative promoter was suggested, but the +1 site of the transcription initiation has not been determined, although there exists promoter activity.
Evidence: [EXP-IEP]
Reference(s): [9] Zaslaver A., et al., 2006


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IEP] Inferred from expression pattern


Reference(s)    

 [1] Metcalf WW., Wanner BL., 1991, Involvement of the Escherichia coli phn (psiD) gene cluster in assimilation of phosphorus in the form of phosphonates, phosphite, Pi esters, and Pi., J Bacteriol 173(2):587-600

 [2] Metcalf WW., Wanner BL., 1993, Mutational analysis of an Escherichia coli fourteen-gene operon for phosphonate degradation, using TnphoA' elements., J Bacteriol 175(11):3430-42

 [3] Wanner BL., Metcalf WW., 1992, Molecular genetic studies of a 10.9-kb operon in Escherichia coli for phosphonate uptake and biodegradation., FEMS Microbiol Lett 79(1-3):133-9

 [4] 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

 [5] Jiang W., Metcalf WW., Lee KS., Wanner BL., 1995, Molecular cloning, mapping, and regulation of Pho regulon genes for phosphonate breakdown by the phosphonatase pathway of Salmonella typhimurium LT2., J Bacteriol 177(22):6411-21

 [6] Makino K., Kim SK., Shinagawa H., Amemura M., Nakata A., 1991, Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12., J Bacteriol 173(8):2665-72

 [7] Marzan LW., Hasan CM., Shimizu K., 2013, Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant., Arch Microbiol 195(3):161-71

 [8] Wanner BL., Boline JA., 1990, Mapping and molecular cloning of the phn (psiD) locus for phosphonate utilization in Escherichia coli., J Bacteriol 172(3):1186-96

 [9] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

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