RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: tnaCAB
Synonym(s): OP00116, tna, tnaAB
Gene(s): tnaC, tnaA, tnaB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The tnaCAB operon codes for two key enzymes in tryptophan metabolism, including tryptophanase. It is regulated by attenuation within its leader region in response to tryptophan abundance. When tryptophan is present, transcription continues through a Rho-dependent terminator and tnaA and tnaB are transcribed Stewart V,1985. In addition, tnaCAB is also subject to regulation at the level of transcriptional initiation via CRP, although this is not the main regulatory control on the operon Stewart V,1985.
Attenuation of tnaCAB occurs via ribosomal pausing at the tail end of the tnaC leader sequence. As translation of the leader peptide nears completion, it halts with the terminal proline of TnaC still attached to its tRNA and stuck within the ribosome. In the absence of tryptophan, peptide chain release factor RF1 and peptide chain release factor RF2 cleave TnaC from the tRNA and free the ribosome. This, in turn, allows access by Rho to a Rho-dependent terminator that then prematurely terminates transcription of tnaCAB. In the presence of tryptophan, release by RF1 and RF2 is prevented, and the ribosome remains in place, blocking access by Rho to the terminator and allowing continued transcription of the operon Stewart V,1985. Yanofsky C,1996. Konan KV, Yanofsky C,2000. Gong F, Yanofsky C,2001. Gong F, Ito K, Nakamura Y, Yanofsky C,2001. Gong F, Yanofsky C,2002. Eventually, the stalled ribosome is cleared away by ribosome recycling factor and peptide chain release factor RF3 Gong M,2007. As a natural consequence of this mechanism, attenuation at tnaCAB depends on both translation of the leader peptide and the presence of Rho Yanofsky C, Horn V,1995. Gish K, Yanofsky C,1995. Gollnick P,1990.
This close coupling of transcription and translation is achieved via an RNA polymerase-pausing mechanism. There is a pause site toward the latter end of the tnaC sequence. The RNA polymerase pauses there, allowing time for the ribosome to attach to the nascent RNA and begin translation. When the ribosome reaches the paused RNA polymerase, transcription continues. This pausing mechanism ensures that the ribosome is in the proper position to regulate the Rho-dependent terminator in response to tryptophan abundance Gong F, Yanofsky C,2003.
Rho-dependent termination within the tnaC sequence depends on both a rut- and a boxA-like sequence within the leader region of the operon Konan KV, Yanofsky C,2000. The role of the boxA-like sequence in promoting termination is peculiar, as the actual boxA sequence normally acts as an antiterminator Gong F, Yanofsky C,2002.
Stalling of the ribosome during translation of TnaC depends on a complex interaction between the leader peptide and the ribosome. Attenuation is completely dependent on the sole tryptophan within the leader peptide sequence. Mutations at this position make tryptophan induction of tnaCAB impossible Gollnick P,1990. Specific residues within TnaC, most notably Asp-16 and Pro-24, are essential for inhibiting clearing of the TnaC-tRNA complex from the peptidyl transferase center within the ribosome and for altering the conformation of the 23S RNA in a manner that may help generate a tryptophan-binding site on the ribosome Cruz-Vera LR, Yanofsky C,2008.
Both YdgT and HolE appear to influence expression of tnaA by enhancing transcription termination at the leader DNA sequence Dietrich M, Pedró L, García J, Pons M, Hüttener M, Paytubi S, Madrid C, Juárez A,2014.
Based on work with mutant strains, it was determined that FNR, NarL, and NarP negatively regulate the tnaCAB operon in the exponential growth phase during anaerobic respiration of nitrate Lai Y, Xu Z, Yan A,2017
ZraR represses tnaAB operon transcription. This operon is among the most strongly regulated, and its genes are repressed by ZraR with a 20-fold and a 50-fold drop in expression, respectively, compared to the wild type or a zraR strain, reducing the amount of indole by downregulating the tnaAB operon Rome K,2018
The tnaA gene is upregulated by the antibiotic...
Evidence: [COMP-HINF] Inferred by a human based on computational evidence
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Deeley MC., et al., 1981
[2] Deeley MC., et al., 1982
[3] Edwards RM., et al., 1982
[4] Gish K., et al., 1993
[5] Stewart V., et al., 1985
Promoter
Name: tnaCp
+1: 3888411
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 24
Sequence: cgattcacatttaaacaatttcagaatagacaaaaactctgagtgtaataatgtagcctcGtgtcttgcgaggataagtgc
                    -35                        -10          +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Deeley MC., et al., 1982
[6] Huerta AM., et al., 2003
[7] Salgado H, et al., 2012
Terminator(s)
Type: rho-dependent
Sequence: atgtgtgaccTCAAAATGGTTCAATATTGACAACAAAATTGTCGATCACCGCCCTTGAtttgcccttc
Reference(s): [8] Konan KV., et al., 1997
TF binding sites (TFBSs)
[CRP,+] 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
proximal CRP-cyclic-AMP activator tnaCp 3888341 3888362 -59.5 ctccccgaacGATTGTGATTCGATTCACATTTaaacaatttc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [5], [10]
[TorR,+] 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
remote TorR-phosphorylated activator tnaCp 3888304 3888313 -102.5 cgtaatttatAATCTTTAAAaaaagcattt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
proximal TorR-phosphorylated activator tnaCp 3888351 3888360 -55.5 gattgtgattCGATTCACATttaaacaatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]


Transcription unit          
Name: tnaC
Gene(s): tnaC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [2] Deeley MC., et al., 1982
[8] Konan KV., et al., 1997
Promoter
Name: tnaCp
+1: 3888411
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 24
Sequence: cgattcacatttaaacaatttcagaatagacaaaaactctgagtgtaataatgtagcctcGtgtcttgcgaggataagtgc
                    -35                        -10          +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Deeley MC., et al., 1982
[6] Huerta AM., et al., 2003
[7] Salgado H, et al., 2012
Terminator(s)
Type: rho-dependent
Sequence: atgtgtgaccTCAAAATGGTTCAATATTGACAACAAAATTGTCGATCACCGCCCTTGAtttgcccttc
Reference(s): [8] Konan KV., et al., 1997
TF binding sites (TFBSs)
[CRP,+] 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
proximal CRP-cyclic-AMP activator tnaCp 3888341 3888362 -59.5 ctccccgaacGATTGTGATTCGATTCACATTTaaacaatttc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [5], [10]
[TorR,+] 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
remote TorR-phosphorylated activator tnaCp 3888304 3888313 -102.5 cgtaatttatAATCTTTAAAaaaagcattt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
proximal TorR-phosphorylated activator tnaCp 3888351 3888360 -55.5 gattgtgattCGATTCACATttaaacaatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]


Transcription unit       
Name: tnaAB
Gene(s): tnaA, tnaB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [11] Rome K., et al., 2018


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -13.7 3888398 3888436 ctgagtgtaaTAATGTAGCCTCGTGTCTTGCGAGGATAAGTGCATTATgaatatctta
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"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [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-CELLULAR-EXTRACTS] Binding of cellular extracts

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


Reference(s)    

 [1] Deeley MC., Yanofsky C., 1981, Nucleotide sequence of the structural gene for tryptophanase of Escherichia coli K-12., J Bacteriol 147(3):787-96

 [2] Deeley MC., Yanofsky C., 1982, Transcription initiation at the tryptophanase promoter of Escherichia coli K-12., J Bacteriol 151(2):942-51

 [3] Edwards RM., Yudkin MD., 1982, Location of the gene for the low-affinity tryptophan-specific permease of Escherichia coli., Biochem J 204(2):617-9

 [4] Gish K., Yanofsky C., 1993, Inhibition of expression of the tryptophanase operon in Escherichia coli by extrachromosomal copies of the tna leader region., J Bacteriol 175(11):3380-7

 [5] Stewart V., Yanofsky C., 1985, Evidence for transcription antitermination control of tryptophanase operon expression in Escherichia coli K-12., J Bacteriol 164(2):731-40

 [6] 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

 [7] 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.

 [8] Konan KV., Yanofsky C., 1997, Regulation of the Escherichia coli tna operon: nascent leader peptide control at the tnaC stop codon., J Bacteriol 179(5):1774-9

 [9] Bordi C., Theraulaz L., Mejean V., Jourlin-Castelli C., 2003, Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli., Mol Microbiol 48(1):211-23

 [10] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [11] Rome K., Borde C., Taher R., Cayron J., Lesterlin C., Gueguen E., De Rosny E., Rodrigue A., 2018, The Two-Component System ZraPSR Is a Novel ESR that Contributes to Intrinsic Antibiotic Tolerance in Escherichia coli., J Mol Biol 430(24):4971-4985

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