RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: accD
Gene(s): accD   Genome Browser M3D Gene expression COLOMBOS
Note(s): accD is located at min 50, in a complex gene cluster. The length of the accD-specific mRNA suggested that the accD mRNA is monocistronic and terminates at the factor-independent terminator sequence predicted by Bognar et al. It should be noted that the messages observed may not be primary transcription products (the presence of 5' -triphosphates was not demostrated). However, each of the 5' ends lies dowstream of a reasonable -10 promoter element, strongly suggesting that np processing of the 5' ends ocurred.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Li SJ., et al., 1993
Promoter
Name: accDp
+1: 2434015
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 89
Sequence: actccgcggttcgaccacttttttatccaaagtttcgggctgttatgttttaatgtgcaaCattcatggtctgttgggggc
                    -35                     -10             +1                   
Evidence: [HIPP]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[1] Li SJ., et al., 1993
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: gattcgttacGGTGAGAATAGCAAAAGGGCAGAGCCAGTGGCCCTGCCCTTATCAGTTATCAGGCctcaggttcc
Reference(s): [4] Feng CQ., et al., 2019
[5] Lesnik EA., et al., 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 FadR activator accDp 2434056 2434072 -49.0 aaaaagtaacTCCGCGGTTCGACCACTTttttatccaa nd [AIBSCS], [BPP], [GEA] [6]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -11.4 2434025 2434070 aagtaactccGCGGTTCGACCACTTTTTTATCCAAAGTTTCGGGCTGTTATGTTTtaatgtgcaa
  anti-terminator -8.47 2434060 2434100 aacgcgctgcGGCACGCGCCGCAAAATAAAAAGTAACTCCGCGGTTCGACcactttttta
  anti-anti-terminator -13.32 2434085 2434143 gtggtttctaTTTTGCCGGGCGTCATCGAAATAATCCGTCACAAACGCGCTGCGGCACGCGCCGCAAAataaaaagta
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"




Reference(s)    

 [1] Li SJ., Cronan JE., 1993, Growth rate regulation of Escherichia coli acetyl coenzyme A carboxylase, which catalyzes the first committed step of lipid biosynthesis., J Bacteriol 175(2):332-40

 [2] 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

 [3] 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.

 [4] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477

 [5] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94

 [6] My L., Ghandour Achkar N., Viala JP., Bouveret E., 2015, Reassessment of the Genetic Regulation of Fatty Acid Synthesis in Escherichia coli: Global Positive Control by the Dual Functional Regulator FadR., J Bacteriol 197(11):1862-72


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