RegulonDB RegulonDB 10.8: Operon Form
   

ackA-pta operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: ackA
Gene(s): ackA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene ackA is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013
Reference(s): [1] Pruss BM., et al., 1994
Promoter
Name: ackAp
+1: 2413459
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 11
Sequence: ggtgtcatcatgcgctacgctctatggctccctgacgtttttttagccacgtatcaattaTaggtacttccatgtcgagta
                         -35                 -10            +1                   
Note(s): This paper mentions the ackA promoter. There is no mapping of the promoter and no clear reference to find the previous work of its identification.
Evidence: [AIPP]
Reference(s): [2] Gama-Castro S., et al., 2008
[1] Pruss BM., et al., 1994
TF binding sites (TFBSs)
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ArcA-Phosphorylated1 activator ackAp nd nd nd nd nd [GEA] [3]
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR1 activator ackAp nd nd nd nd nd [GEA] [3]
Note(s): 1ArcA has a slightly positive effect on ackA expression Shalel-Levanon S,20051The positive effect of ArcA and FNR on ackA expression is independent Shalel-Levanon S,20051The positive effect of ArcA and FNR on ackA expression is independent Shalel-Levanon S,2005
2ArcA has a slightly positive effect on ackA expression Shalel-Levanon S,2005


Transcription unit       
Name: pta
Gene(s): pta   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene pta is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [4] De Mets F., et al., 2019
[5] Kakuda H., et al., 1994
Promoter
Name: ptap
+1: 2414486
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 261
Sequence: gctgatggatggtcgtctggacgctgttgtattcactggtggtatcggtgaaaatgccgcAatggttcgtgaactgtctct
                           -35                    -10       +1                   
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[RS-EPT-CBR]
[TIM]
Reference(s): [4] De Mets F., et al., 2019
[6] Salgado H, et al., 2012


Transcription unit       
Name: ackA-pta
Gene(s): ackA, pta   Genome Browser M3D Gene expression COLOMBOS
Note(s): There is a RNase processing sequence in the ackA-pta intergenic region De Mets F,2019.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [4] De Mets F., et al., 2019
[5] Kakuda H., et al., 1994


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -19.1 2414676 2414709 gcctgatttcACACCGCCAGCTCAGCTGGCGGTGCTGTTTTGTaacccgccaa
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    

 [AIPP] Automated inference of promoter position

 [GEA] Gene expression analysis

 [CV(RS-EPT-CBR)] cross validation(RS-EPT-CBR)

 [CV(TIM)] cross validation(TIM)

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

 [TIM] Transcription initiation mapping


Reference(s)    

 [1] Pruss BM., Wolfe AJ., 1994, Regulation of acetyl phosphate synthesis and degradation, and the control of flagellar expression in Escherichia coli., Mol Microbiol 12(6):973-84

 [2] Gama-Castro S., Jimenez-Jacinto V., Peralta-Gil M., Santos-Zavaleta A., Penaloza-Spinola MI., Contreras-Moreira B., Segura-Salazar J., Muniz-Rascado L., Martinez-Flores I., Salgado H., Bonavides-Martinez C., Abreu-Goodger C., Rodriguez-Penagos C., Miranda-Rios J., Morett E., Merino E., Huerta AM., Trevino-Quintanilla L., Collado-Vides J., 2008, RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation., Nucleic Acids Res 36(Database issue):D120-4

 [3] Shalel-Levanon S., San KY., Bennett GN., 2005, Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions., Biotechnol Bioeng 92(2):147-59

 [4] De Mets F., Van Melderen L., Gottesman S., 2019, Regulation of acetate metabolism and coordination with the TCA cycle via a processed small RNA., Proc Natl Acad Sci U S A 116(3):1043-1052

 [5] Kakuda H., Hosono K., Shiroishi K., Ichihara S., 1994, Identification and characterization of the ackA (acetate kinase A)-pta (phosphotransacetylase) operon and complementation analysis of acetate utilization by an ackA-pta deletion mutant of Escherichia coli., J Biochem 116(4):916-22

 [6] 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.

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