RegulonDB RegulonDB 11.1: Operon Form
   

acs-yjcH-actP operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: acs-yjcH-actP
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: actP
Gene(s): actP   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: actPp
+1: 4284935
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 33
Sequence: gatctcctttgttctcaccggtatctacatctggcgggcgaacggcgaattcgaccgtctTaataatgaagtcctgcatga
                                     -24        -12         +1                   
Note(s): This promoter was identified by microarray assays with a mutant σ54 strain and a σ54-overexpressing strain, and by σ54-related promoter element identification Zhao K,2010
We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ54-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IEP]
Reference(s): [1] Huerta AM., et al., 2003
[2] Zhao K., et al., 2010


Transcription unit          
Name: acs-yjcHG
Gene(s): actP, yjcH, acs   Genome Browser M3D Gene expression COLOMBOS
Note(s): Transcription of acs may be negatively regulated by IclR through an indirect effect Kumari S,2000Shin S, Song SG, Lee DS, Pan JG, Park C,1997. Fnr activates the transcription of acs by binding to two sites located close to the transcription start site. This has been demonstrated by gene expression analysis and protein binding to the region, but the specific sequences of the sites were not reported Kumari S,2000.
Based on arcA deletion experiments, it appears that ArcA-P represses the acs-yjcH-actP operon, resulting in a lower rate of acetate uptake and assimilation Veeravalli K, Schindler T, Dong E, Yamada M, Hamilton R, Laird MW,2018
The expression of the gene acs is diminished under oxygen limitation Kawaguchi H, Miyagawa H, Nakamura-Tsuruta S, Takaya N, Ogino C, Kondo A,2019, and it is highly increased in the presence of pyruvate El-Mansi M, Phue JN, Shiloach J,2021.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [3] Gimenez R., et al., 2003
[4] Kumari S., et al., 2000
Promoter
Name: acsp
+1: 4287391
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 20
Sequence: atactaaacaaaactgccaatacccctacatttaacgcttatgccacatattattaacatCctacaaggagaacaaaagca
                                       -35             -10  +1                   
Note(s): The effect of RpoS is likely indirect and may be mediated by competing with σ70 for core polymerase Kumari S,2000. Shin S, Song SG, Lee DS, Pan JG, Park C,1997
Evidence: [COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [5] Beatty CM., et al., 2003
[6] Kumari S., et al., 2000
[7] Olvera L., et al., 2009
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 acsp 4287450 4287471 -69.5 aattctacttTTGCGTGATCTGTCGCCCAAATactaaacaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [5], [11]
remote CRP-cyclic-AMP activator acsp 4287503 4287524 -122.5 ttaatcaactTTTGTTGCTGACCTTCAAAAATtaccctgccg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [5], [11]
[Fis,-] 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 Fis repressor acsp 4287443 4287457 -59.0 gtgatctgtcGCCCAAATACTAAACaaaactgcca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8]
remote Fis repressor acsp 4287482 4287496 -98.0 aaattaccctGCCGTTTATTTGCACaattctactt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8]
remote Fis repressor acsp 4287649 4287663 -265.0 tcgcccctatGTGTAACAAATAACCacactgtgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9], [10]
[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 repressor acsp 4287538 4287550 -153.0 tgcataactgCATGTTCCTCAAAgaattaatca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [11]
remote IHF repressor acsp 4287565 4287577 -180.0 tcagtatcttCCTCTTTTTCAACagcatgcata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8]
remote IHF repressor acsp 4287610 4287622 -225.0 ctttaatcaaTTGTAAGTGCATGtaaaatacca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9], [10]


Transcription unit          
Name: acs-yjcHG
Gene(s): actP, yjcH, acs   Genome Browser M3D Gene expression COLOMBOS
Note(s): Transcription of acs may be negatively regulated by IclR through an indirect effect Kumari S,2000. Shin S, Song SG, Lee DS, Pan JG, Park C,1997 Fnr activates the transcription of acs by binding to two sites located close to the transcription start site. This has been demonstrated by gene expression analysis and protein binding to the region, but the specific sequences of the sites were not reported Kumari S,2000.
Based on arcA deletion experiments, it appears that ArcA-P represses the acs-yjcH-actP operon, resulting in a lower rate of acetate uptake and assimilation Veeravalli K, Schindler T, Dong E, Yamada M, Hamilton R, Laird MW,2018.
The expression of the gene acs is diminished under oxygen limitation Kawaguchi H, Miyagawa H, Nakamura-Tsuruta S, Takaya N, Ogino C, Kondo A,2019, and it is highly increased in the presence of pyruvate El-Mansi M, Phue JN, Shiloach J,2021.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [3] Gimenez R., et al., 2003
[4] Kumari S., et al., 2000
Promoter
Name: acsp2
+1: 4287391
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 20
Sequence: atactaaacaaaactgccaatacccctacatttaacgcttatgccacatattattaacatCctacaaggagaacaaaagca
                                       -35             -10  +1                   
Note(s): The effect of RpoS is likely indirect and may be mediated by competing with σ70 for core polymerase Kumari S,2000. Shin S, Song SG, Lee DS, Pan JG, Park C,1997
Evidence: [COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [5] Beatty CM., et al., 2003
[6] Kumari S., et al., 2000
[7] Olvera L., et al., 2009
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 acsp2 4287450 4287471 -69.5 aattctacttTTGCGTGATCTGTCGCCCAAATactaaacaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [5], [11]
remote CRP-cyclic-AMP activator acsp2 4287503 4287524 -122.5 ttaatcaactTTTGTTGCTGACCTTCAAAAATtaccctgccg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [5], [11]
[Fis,-] 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 Fis repressor acsp2 4287443 4287457 -59.0 gtgatctgtcGCCCAAATACTAAACaaaactgcca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8]
remote Fis repressor acsp2 4287482 4287496 -98.0 aaattaccctGCCGTTTATTTGCACaattctactt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8]
remote Fis repressor acsp2 4287649 4287663 -265.0 tcgcccctatGTGTAACAAATAACCacactgtgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9], [10]
[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 repressor acsp2 4287538 4287550 -153.0 tgcataactgCATGTTCCTCAAAgaattaatca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [11]
remote IHF repressor acsp2 4287565 4287577 -180.0 tcagtatcttCCTCTTTTTCAACagcatgcata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8]
remote IHF repressor acsp2 4287610 4287622 -225.0 ctttaatcaaTTGTAAGTGCATGtaaaatacca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9], [10]


Transcription unit          
Name: acs-yjcHG
Gene(s): actP, yjcH, acs   Genome Browser M3D Gene expression COLOMBOS
Note(s): Transcription of acs may be negatively regulated by IclR through an indirect effect Kumari S,2000Shin S, Song SG, Lee DS, Pan JG, Park C,1997. Fnr activates the transcription of acs by binding to two sites located close to the transcription start site. This has been demonstrated by gene expression analysis and protein binding to the region, but the specific sequences of the sites were not reported Kumari S,2000.
The expression of the gene acs is diminished under oxygen limitation Kawaguchi H, Miyagawa H, Nakamura-Tsuruta S, Takaya N, Ogino C, Kondo A,2019, and it is highly increased in the presence of pyruvate El-Mansi M, Phue JN, Shiloach J,2021.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [3] Gimenez R., et al., 2003
[4] Kumari S., et al., 2000
Promoter
Name: acsp1
+1: 4287595
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 224
Sequence: aataaccacactgtgaatgttgtctttaatcaattgtaagtgcatgtaaaataccactttAgagttagtcagtatcttcct
                         -35                        -10     +1                   
Note(s): The effect by RpoS is likely indirect and might be mediated by competing with σ70 for core polymerase Kumari S,2000. Shin S, Song SG, Lee DS, Pan JG, Park C,1997
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
Reference(s): [9] Browning DF., et al., 2002
[1] Huerta AM., et al., 2003
[6] Kumari S., et al., 2000
TF binding sites (TFBSs)
[Fis,-] 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 Fis repressor acsp1 4287649 4287663 -61.0 tcgcccctatGTGTAACAAATAACCacactgtgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9]
[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
proximal IHF repressor acsp1 4287610 4287622 -21.0 ctttaatcaaTTGTAAGTGCATGtaaaatacca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [9]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IEP] Inferred from expression pattern

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

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

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] 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

 [2] Zhao K., Liu M., Burgess RR., 2010, Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis., Nucleic Acids Res 38(4):1273-83

 [3] Gimenez R., Nunez MF., Badia J., Aguilar J., Baldoma L., 2003, The gene yjcG, cotranscribed with the gene acs, encodes an acetate permease in Escherichia coli., J Bacteriol 185(21):6448-55

 [4] Kumari S., Beatty CM., Browning DF., Busby SJ., Simel EJ., Hovel-Miner G., Wolfe AJ., 2000, Regulation of acetyl coenzyme A synthetase in Escherichia coli., J Bacteriol 182(15):4173-9

 [5] Beatty CM., Browning DF., Busby SJ., Wolfe AJ., 2003, Cyclic AMP receptor protein-dependent activation of the Escherichia coli acsP2 promoter by a synergistic class III mechanism., J Bacteriol 185(17):5148-57

 [6] Kumari S., Simel EJ., Wolfe AJ., 2000, sigma(70) is the principal sigma factor responsible for transcription of acs, which encodes acetyl coenzyme A synthetase in Escherichia coli., J Bacteriol 182(2):551-4

 [7] Olvera L., Mendoza-Vargas A., Flores N., Olvera M., Sigala JC., Gosset G., Morett E., Bolivar F., 2009, Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation., PLoS One 4(10):e7466

 [8] Browning DF., Beatty CM., Sanstad EA., Gunn KE., Busby SJ., Wolfe AJ., 2004, Modulation of CRP-dependent transcription at the Escherichia coli acsP2 promoter by nucleoprotein complexes: anti-activation by the nucleoid proteins FIS and IHF., Mol Microbiol 51(1):241-54

 [9] Browning DF., Beatty CM., Wolfe AJ., Cole JA., Busby SJ., 2002, Independent regulation of the divergent Escherichia coli nrfA and acsP1 promoters by a nucleoprotein assembly at a shared regulatory region., Mol Microbiol 43(3):687-701

 [10] Browning DF., Grainger DC., Beatty CM., Wolfe AJ., Cole JA., Busby SJ., 2005, Integration of three signals at the Escherichia coli nrf promoter: a role for Fis protein in catabolite repression., Mol Microbiol 57(2):496-510

 [11] Sclavi B., Beatty CM., Thach DS., Fredericks CE., Buckle M., Wolfe AJ., 2007, The multiple roles of CRP at the complex acs promoter depend on activation region 2 and IHF., Mol Microbiol 65(2):425-40

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