RegulonDB RegulonDB 10.10: 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: [BTEI] Boundaries of transcription experimentally identified
[CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] 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: [TIM]
Reference(s): [1] Hagewood BT., et al., 1994
[3] Sawers G. 2001
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 CRP-cyclic-AMP activator tdcAp 3267126 3267147 -43.5 ttgaaagttaATTTGTGAGTGGTCGCACATATcctgttcatt nd [GEA], [APIORCISFBSCS], [BCE], [BPP], [SM] [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR activator tdcAp 3267192 3267205 -105.5 actttaacttGTTGATATTTAAAGgtatttaatt nd [GEA], [AIBSCS] [4]
remote FNR activator tdcAp 3267235 3267248 -148.5 gtcattttttTTGACAAAAATCAGggtttatgct nd [GEA], [AIBSCS] [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF activator tdcAp 3267190 3267202 -103.0 ttaacttgttGATATTTAAAGGTatttaattgt nd [APIORCISFBSCS], [BCE], [BPP], [SM] nd
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote TdcA activator tdcAp 3267263 3267277 -177.0 tgttatcgccATAAAATATGGTTATccccgtcatt nd [GEA], [BCE], [SM] nd
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote TdcR activator tdcAp 3267282 3267293 -195.0 accacataacGAATGATGTTATcgccataaaa nd [BCE], [SM] nd


Transcription unit       
Name: tdcBCDEFG
Gene(s): tdcG, tdcF, tdcE, tdcD, tdcC, tdcB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [PAGTSBP] 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: [IEP]
Reference(s): [5] Zaslaver A., et al., 2006





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