RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: tdcABCDEFG
Synonym(s): OP00167, tdcABC
Gene(s): tdcG, tdcF, tdcE, tdcD, tdcC, tdcB, tdcA   Genome Browser M3D Gene expression COLOMBOS
Note(s): tdcABCDEFG operon expression is regulated by TdcA and TdcR proteins Hagewood BT,1994. In addition, this operon is induced under anaerobiosis, but it is repressed by glucose Sawers G.,2001. On the other hand, the TcbC protein (from Clostridium butyricum), induces the expression of this operon, altering the topology of the DNA Sawers G.,2001.
In Salmonella enterica serovar Typhimurium, the tdc operon is induced mainly under anaerobic shock. However, in E. coli the operon is not induced under this shock unless the transcriptional activator TdcR is deleted, and coincidentally, TdcR is not present in Salmonella Kim M, Lim S, Ryu S,2011.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for tdcA, tdcC and tdcE . This structure could regulate the expression of the genes, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Hagewood BT., et al., 1994
[2] Hesslinger C., et al., 1998
[3] Sawers G. 2001
Promoter
Name: tdcAp
+1: 3267093
Distance from start of the gene: 28
Sequence: aagttaatttgtgagtggtcgcacatatcctgttcatttcattttgatacacttcatgccGtcaatgaggtaattaacgta
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Hagewood BT., et al., 1994
[3] Sawers G. 2001
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 tdcAp 3267126 3267147 -43.5 ttgaaagttaATTTGTGAGTGGTCGCACATATcctgttcatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3]
[FNR,+] 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 FNR activator tdcAp 3267192 3267205 -105.5 actttaacttGTTGATATTTAAAGgtatttaatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4]
remote FNR activator tdcAp 3267235 3267248 -148.5 gtcattttttTTGACAAAAATCAGggtttatgct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4]
[IHF,+] 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 IHF activator tdcAp 3267190 3267202 -103.0 ttaacttgttGATATTTAAAGGTatttaattgt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C nd
[TdcA,+] 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 TdcA activator tdcAp 3267263 3267277 -177.0 tgttatcgccATAAAATATGGTTATccccgtcatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] W nd
[TdcR,+] 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 TdcR activator tdcAp 3267282 3267293 -195.0 accacataacGAATGATGTTATcgccataaaa nd [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] nd nd


Transcription unit       
Name: tdcBCDEFG
Gene(s): tdcG, tdcF, tdcE, tdcD, tdcC, tdcB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Promoter
Name: tdcBp
+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): [5] Zaslaver A., et al., 2006


Evidence    

 [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-CELLULAR-EXTRACTS] Binding of cellular extracts

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

 [EXP-IMP-SITE-MUTATION] Site mutation

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

 [EXP-IEP] Inferred from expression pattern


Reference(s)    

 [1] Hagewood BT., Ganduri YL., Datta P., 1994, Functional analysis of the tdcABC promoter of Escherichia coli: roles of TdcA and TdcR., J Bacteriol 176(20):6214-20

 [2] Hesslinger C., Fairhurst SA., Sawers G., 1998, Novel keto acid formate-lyase and propionate kinase enzymes are components of an anaerobic pathway in Escherichia coli that degrades L-threonine to propionate., Mol Microbiol 27(2):477-92

 [3] Sawers G., 2001, A novel mechanism controls anaerobic and catabolite regulation of the Escherichia coli tdc operon., Mol Microbiol 39(5):1285-98

 [4] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

 [5] 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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