RegulonDB RegulonDB 10.8: Operon Form
   

aroL-yaiA-aroM operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: aroL-yaiA-aroM
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: aroL-yaiA-aroM
Synonym(s): OP00013, aroLM
Gene(s): aroL, yaiA, aroM   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the aroL-yiaA-aroM operon seems to be repressed by the interaction of two proteins, TyrR and TrpR, because the effect of TrpR cannot be seen in the absence of TyrR and the effect of TyrR is enhanced in the presence of TrpR. This suggests that a putative physical interaction between TyrR and TrpR or a conformational change in the DNA caused by TyrR facilitates the binding of TrpR. Moreover, TrpR can stabilize TyrR binding Lawley B,1994
In the presence of tyrosine plus ATP, tryptophan, and to a lesser extent phenylalanine, the TyrR protein binds to three TyrR boxes located at positions bp -45, +12, and +31 from the transcriptional start site (TSS) of the aroLp promoter. The -45 and +31 sites are essential to the repression, and the TyrR dimers bound to them seem to interact through the formation of the DNA loop structure that would sequester the RNA polymerase-binding region Lawley B,1994 The +12 site, which is a weak TyrR box, may not be essential for repression Lawley B,1994
A putative IHF site was identified around the +31 TyrR box. This site seems to have a negative effect on the repression mediated by tyrosine Lawley B,1994
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] DeFeyter RC., et al., 1986
Promoter
Name: aroLp
+1: 406280
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 125
Sequence: taaatgtaatttattatttacacttcattcttgaatatttattggtatagtaaggggtgtAttgagattttcactttaagt
                        -35                   -10           +1                   
Note(s): aroLp was validated experimentally in anaerobic conditions Chung D,2013.
Evidence: [TIM]
Reference(s): [2] Chung D., et al., 2013
[3] Millar G., et al., 1986
TF binding sites (TFBSs)
[TrpR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote TrpR-tryptophan repressor aroLp 406319 406336 48.5 ttctttacaaTCGAAATTGTACTAGTTTgatggtatga nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [4], [5], [6], [7]
remote TrpR-tryptophan repressor aroLp 406327 406344 56.5 aatcgaaattGTACTAGTTTGATGGTATgatcgctatt nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [4], [5], [6], [7]
[TyrR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal TyrR-tyrosine repressor aroLp 406226 406243 -45.0 tggctaaatgTAATTTATTATTTACACTtcattcttga nd [BPP], [CV(SM)], [GEA], [SM] [1], [4], [5]
proximal TyrR-tyrosine repressor aroLp 406282 406299 12.0 aggggtgtatTGAGATTTTCACTTTAAGtggaattttt nd [BPP], [CV(SM)], [GEA], [SM] [1], [4], [5]
remote TyrR-tyrosine repressor aroLp 406301 406318 31.0 cactttaagtGGAATTTTTTCTTTACAAtcgaaattgt nd [BPP], [CV(SM)], [GEA], [SM] [1], [4], [5]


Transcription unit       
Name: aroL-yaiA-aroM
Gene(s): aroL, yaiA, aroM   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] DeFeyter RC., et al., 1986
Promoter
Name: aroLp2
+1: 406355
Distance from start of the gene: 50
Sequence: ttaagtggaattttttctttacaatcgaaattgtactagtttgatggtatgatcgctattCtcatgacaccggctttcgcc
Note(s): aroLp2 was validated experimentally in anaerobic conditions Chung D,2013.
Evidence: [TIM]
Reference(s): [2] Chung D., et al., 2013


Transcription unit       
Name: aroM
Gene(s): aroM   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
Reference(s): [8] Li Z., et al., 2019
Promoter
Name: aroMp
+1: 407400
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 28
Sequence: tgtcatttgtagcacaagtaagtgtcagcagtggtgcttcacacttgcccggtaattaacGacgaaagaaaagtaaggtgg
                         -35                       -10      +1                   
Evidence: [RE]
[TIM]
Reference(s): [8] Li Z., et al., 2019


Transcription unit       
Name: yaiA-aroM
Gene(s): yaiA, aroM   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: yaiAp
+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: [IEP]
Reference(s): [9] Zaslaver A., et al., 2006


Evidence    

 [TIM] Transcription initiation mapping

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

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [CV(GEA/SM)] cross validation(GEA/SM)

 [CV(SM)] cross validation(SM)

 [GEA] Gene expression analysis

 [SM] Site mutation

 [RE] RNA-seq evidence

 [IEP] Inferred from expression pattern


Reference(s)    

 [1] DeFeyter RC., Davidson BE., Pittard J., 1986, Nucleotide sequence of the transcription unit containing the aroL and aroM genes from Escherichia coli K-12., J Bacteriol 165(1):233-9

 [2] Chung D., Park D., Myers K., Grass J., Kiley P., Landick R., Keles S., 2013, dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data., PLoS Comput Biol 9(10):e1003246

 [3] Millar G., Lewendon A., Hunter MG., Coggins JR., 1986, The cloning and expression of the aroL gene from Escherichia coli K12. Purification and complete amino acid sequence of shikimate kinase II, the aroL-gene product., Biochem J 237(2):427-37

 [4] Heatwole VM., Somerville RL., 1992, Synergism between the Trp repressor and Tyr repressor in repression of the aroL promoter of Escherichia coli K-12., J Bacteriol 174(1):331-5

 [5] Lawley B., Pittard AJ., 1994, Regulation of aroL expression by TyrR protein and Trp repressor in Escherichia coli K-12., J Bacteriol 176(22):6921-30

 [6] Jeeves M., Evans PD., Parslow RA., Jaseja M., Hyde EI., 1999, Studies of the Escherichia coli Trp repressor binding to its five operators and to variant operator sequences., Eur J Biochem 265(3):919-28

 [7] Yang J., Gunasekera A., Lavoie TA., Jin L., Lewis DE., Carey J., 1996, In vivo and in vitro studies of TrpR-DNA interactions., J Mol Biol 258(1):37-52

 [8] Li Z., Pan Q., Xiao Y., Fang X., Shi R., Fu C., Danchin A., You C., 2019, Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation., Microb Biotechnol 12(2):360-376

 [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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