RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit       
Name: trpCBA
Gene(s): trpA, trpB, trpC   Genome Browser M3D Gene expression COLOMBOS
Note(s): FNR represses trpB gene expression under anaerobiosis, but it is still not known which of the two promoters (trpCp or trpLp) is affected, or even if this regulation is direct or indirect Salmon K,2003.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[PM] Polar mutation
Reference(s): [1] Imamoto F., et al., 1966
[2] Imamoto F., et al., 1965
[3] Yanofsky C., et al., 1966
[4] Yanofsky C., et al., 1981
Promoter
Name: trpCp
+1: 1319944
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 156
Sequence: gcaggcggaacaccggaagaaaaccgtgacattttaacacgtttgttacaaggtaaaggcGacgccgcccatgaagcagcc
                          -35                  -10          +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [5] Horowitz H., et al., 1983
[6] Horowitz H., et al., 1982


Transcription unit          
Name: trpL
Gene(s): trpL   Genome Browser M3D Gene expression COLOMBOS
Note(s): The RNA produced by the trpL gene has been observed mainly in the poles of the cell 31540875.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [7] Squires C., et al., 1976
[4] Yanofsky C., et al., 1981
Promoter
Name: trpLp
+1: 1323108
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 26
Sequence: tggcaaatattctgaaatgagctgttgacaattaatcatcgaactagttaactagtacgcAagttcacgtaaaaagggtat
                         -35                     -10        +1                   
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [8] Gunsalus RP., et al., 1980
[9] Salgado H, et al., 2012
[7] Squires C., et al., 1976
Terminator(s)
Type: rho-independent
Sequence: ttcaaaaaaaAGCCCGCTCATTAGGCGGGCTgggtatctga
Reference(s): [4] Yanofsky C., et al., 1981
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal TrpR-tryptophan repressor trpLp 1323103 1323120 -3.5 tcgaactagtTAACTAGTACGCAAGTTCacgtaaaaag nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [10], [11], [12], [13], [14]
proximal TrpR-tryptophan repressor trpLp 1323111 1323128 -11.5 attaatcatcGAACTAGTTAACTAGTACgcaagttcac nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [10], [11], [12], [13], [14]
proximal TrpR-tryptophan repressor trpLp 1323119 1323136 -19.5 tgttgacaatTAATCATCGAACTAGTTAactagtacgc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [10], [11], [12], [13], [14]


Transcription unit          
Name: trpLEDCBA
Synonym(s): OP00094, trp
Gene(s): trpA, trpB, trpC, trpD, trpE, trpL   Genome Browser M3D Gene expression COLOMBOS
Note(s): The trpLEDCBA (trp) operon codes for the enzymes of the tryptophan biosynthesis pathway. It is subject to several layers of regulation, including regulation of transcriptional initiation and ribosome-mediated transcriptional attenuation.
The expression of the trp operon is repressed 300-fold by TrpR. TrpR binds at the trpLp promoter, possibly directly blocking binding by RNA polymerase Klig LS,1988. The genes within the trp operon also appear to be targeted for repression during anaerobiosis by the global regulator FNR, although it is still unknown which trp promoter (trpCp or trpLp) is affected and whether the effect is direct or indirect Salmon K,2003.
WrbA initially appeared to influence the interaction betweenTrpR and the trp operator 8516330. However, other research indicates that this is a nonspecific effect, with both WrbA and BSA generating an equivalent gel shift result 9694845.
The Trp attenuator regulates transcription through the trp operon in response to the abundance of charged tRNA-Trp in the cell. When charged tRNA-Trp is abundant, mRNA transcription terminates within the leader sequence of the operon. Alternately, when charged tRNA-Trp is not abundant, transcription continues through the length of the operon 4578102. 4872441. 4586412. 340702. 781269. 781270. Squires C,1976. The physical mechanism of transcriptional attenuation involves the close coupling of transcription and translation. In the case of the trp attenuator, the ribosome begins translating the leader peptide, TrpL, as RNA polymerase continues to transcribe the rest of the trp operon 781274. This leader peptide contains a key pair of tryptophan codons. When charged tRNA-Trp is scarce, the ribosome stalls at these codons and RNA polymerase proceeds with transcription. Alternately, when charged tRNA-Trp is abundant, the ribosome quickly reads through these codons and RNA transcription terminates in the leader sequence 6159477. 366606.
Trp attenuation and the required close linking of translation and transcription all depend on the formation of alternate RNA secondary structures. When the ribosome proceeds quickly through the trpL leader sequence, a hairpin forms in the mRNA that acts as a transcriptional terminator. When the ribosome stalls due to lack of charged tRNA-Trp, an alternate RNA hairpin forms that prevents formation of the transcriptional terminator, allowing transcription of the RNA to continue 781274. 6159477. 366606. 118451. 368800. The close coupling of transcription and translation is achieved through yet another RNA secondary structure. The trpL leader region has a third alternative hairpin that forms in the absence of the ribosome. This prevents formation of the antiterminator, in turn allowing the terminator to form and stall RNA polymerase. Thus, transcription cannot proceed unless the ribosome is present and charged tRNA-Trp is scarce 2409288. 6168281. 2991886.
The trpLEDCBA, aroH, and trpR operons are coordinately regulated by the TrpR transcriptional repressor in response to intracellular levels of L-tryptophan (Kumamoto AA,1987 and references therein). TrpR acts differently at each operator and binds to multiple helically stacked sites Kumamoto AA,1987.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[PM] Polar mutation
Reference(s): [1] Imamoto F., et al., 1966
[2] Imamoto F., et al., 1965
[3] Yanofsky C., et al., 1966
Promoter
Name: trpLp
+1: 1323108
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 26
Sequence: tggcaaatattctgaaatgagctgttgacaattaatcatcgaactagttaactagtacgcAagttcacgtaaaaagggtat
                         -35                     -10        +1                   
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [8] Gunsalus RP., et al., 1980
[9] Salgado H, et al., 2012
[7] Squires C., et al., 1976
Terminator(s)
Type: rho-independent
Sequence: aaagaaagttAAAATGCCGCCAGCGGAACTGGCGGCtgtgggatta
Reference(s): [15] Stoltzfus A., et al., 1988
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal TrpR-tryptophan repressor trpLp 1323103 1323120 -3.5 tcgaactagtTAACTAGTACGCAAGTTCacgtaaaaag nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [10], [11], [12], [13], [14]
proximal TrpR-tryptophan repressor trpLp 1323111 1323128 -11.5 attaatcatcGAACTAGTTAACTAGTACgcaagttcac nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [10], [11], [12], [13], [14]
proximal TrpR-tryptophan repressor trpLp 1323119 1323136 -19.5 tgttgacaatTAATCATCGAACTAGTTAactagtacgc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [10], [11], [12], [13], [14]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -12.5 1322967 1322995 tcagatacccAGCCCGCCTAATGAGCGGGCTTTTTTTTgaacaaaatt
  anti-terminator -11.7 1322991 1323034 ttcctgaaacGGGCAGTGTATTCACCATGCGTAAAGCAATCAGATACCCAGCCcgcctaatga
  anti-anti-terminator -15.9 1323018 1323055 actgaaaggtTGGTGGCGCACTTCCTGAAACGGGCAGTGTATTCACCatgcgtaaag
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)
  Tryptophan operon leader 90.4 1322968 1323061 uuucguacugAAAGGUUGGUGGCGCACUUCCUGAAACGGGCAGUGUAUUCACCAUGCGUAAAGCAAUCAGAUACCCAGCCCGCCUAAUGAGCGGGCUUUUUUUUgaacaaaauu
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)    

 [1] Imamoto F., Ito J., Yanofsky C., 1966, Polarity in the tryptophan operon of E. coli., Cold Spring Harb Symp Quant Biol 31:235-49

 [2] Imamoto F., Morikawa N., Sato K., 1965, On the transcription of the tryptophan operon in Escherichia coli. 3. Multicistronic messenger RNA and polarity for transcription., J Mol Biol 13(1):169-82

 [3] Yanofsky C., Ito J., 1966, Nonsense codons and polarity in the tryptophan operon., J Mol Biol 21(2):313-34

 [4] Yanofsky C., Platt T., Crawford IP., Nichols BP., Christie GE., Horowitz H., VanCleemput M., Wu AM., 1981, The complete nucleotide sequence of the tryptophan operon of Escherichia coli., Nucleic Acids Res 9(24):6647-68

 [5] Horowitz H., Platt T., 1983, Initiation in vivo at the internal trp p2 promoter of Escherichia coli., J Biol Chem 258(13):7890-3

 [6] Horowitz H., Platt T., 1982, Identification of trp-p2, an internal promoter in the tryptophan operon of Escherichia coli., J Mol Biol 156(2):257-67

 [7] Squires C., Lee F., Bertrand K., Squires CL., Bronson MJ., Yanofsky C., 1976, Nucleotide sequence of the 5' end of tryptophan messenger RNA of Escherichia coli., J Mol Biol 103(2):351-81

 [8] Gunsalus RP., Yanofsky C., 1980, Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor., Proc Natl Acad Sci U S A 77(12):7117-21

 [9] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [10] Bass S., Sugiono P., Arvidson DN., Gunsalus RP., Youderian P., 1987, DNA specificity determinants of Escherichia coli tryptophan repressor binding., Genes Dev 1(6):565-72

 [11] 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

 [12] Klig LS., Carey J., Yanofsky C., 1988, trp repressor interactions with the trp aroH and trpR operators. Comparison of repressor binding in vitro and repression in vivo., J Mol Biol 202(4):769-77

 [13] Kumamoto AA., Miller WG., Gunsalus RP., 1987, Escherichia coli tryptophan repressor binds multiple sites within the aroH and trp operators., Genes Dev 1(6):556-64

 [14] 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

 [15] Stoltzfus A., Leslie JF., Milkman R., 1988, Molecular evolution of the Escherichia coli chromosome. I. Analysis of structure and natural variation in a previously uncharacterized region between trp and tonB., Genetics 120(2):345-58


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