RegulonDB RegulonDB 11.1: Operon Form
   

asnC-mioC-mnmG-rsmG operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: asnC-mioC-mnmG-rsmG
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: mnmG-rsmG
Gene(s): rsmG, mnmG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Benitez-Paez A., et al., 2012
Promoter
Name: mnmGp2
+1: 3925674
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 41
Sequence: atacccaggatcccaggtctttctcaagccgacaaagttgagtagaatccacggcccgggCttcaatccattttcataccg
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Kolling R., et al., 1988
[3] Lelong C., et al., 2007
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition mnmGp2 nd   [EXP-IEP] [4]
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s): [4] Ogawa T., et al., 1991


Transcription unit       
Name: mnmG-rsmG
Gene(s): rsmG, mnmG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Benitez-Paez A., et al., 2012
Promoter
Name: mnmGp
+1: 3925674
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 41
Sequence: atacccaggatcccaggtctttctcaagccgacaaagttgagtagaatccacggcccgggCttcaatccattttcataccg
                          -35                   -10         +1                   
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Kolling R., et al., 1988


Transcription unit          
Name: mioC
Gene(s): mioC   Genome Browser M3D Gene expression COLOMBOS
Note(s): The mioC promoter is stringently regulated Rokeach LA, Zyskind JW,1986 The sequence close to its transcription start point is GC-rich, and there is a poor fit to the consensus sequence in the -35 region of the gid promoter; these two conserved features are shared by promoters under stringent control Lamond AI, Travers AA,1985
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: mioCp
+1: 3926475
Distance from start of the gene: 20
Sequence: ttaatcccatacttttccacaggtagatcccaacgcgttcacagcgtacaatacgccactCttaataaaggtggcggttta
Evidence: [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [5] Mendoza-Vargas A., et al., 2009
TF binding sites (TFBSs)
[MraZ,-] 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 MraZ repressor mioCp 3926504 3926508 -31.0 cacaggtagaTCCCAacgcgttcac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
proximal MraZ repressor mioCp 3926517 3926521 -44.0 tcccatacttTTCCAcaggtagatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
proximal MraZ repressor mioCp 3926527 3926531 -54.0 gcttttttaaTCCCAtacttttcca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition mioCp nd   [EXP-IEP] [4]
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s): [4] Ogawa T., et al., 1991


Transcription unit          
Name: asnC
Synonym(s): OP00153
Gene(s): asnC   Genome Browser M3D Gene expression COLOMBOS
Note(s): About 20 % of the transcription initiated at the asnCp promoter reaches the end of the asnC gene. Under nitrogen-limiting growth conditions, the transcription of the asnC gene is repressed by the Nac protein Poggio S,2002.
In contrast to the effect of asparagine on the regulation of asnA by AsnC, this amino acid does not affect the autoregulation of AsnCKolling R,1985.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [7] Gielow A., et al., 1988
Promoter
Name: asnCp
+1: 3927031
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 28
Sequence: tcattcaataaaaagcctaactcacttttgattcattaaaaaagaaggctaaaatagaatGaatcatcaatccgcataaga
                                 -35                   -10  +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [8] Huerta AM., et al., 2003
[9] Kolling R., et al., 1985
TF binding sites (TFBSs)
[AsnC,-] 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 AsnC repressor asnCp 3927013 3927026 12.5 agaatgaatcATCAATCCGCATAAgaaaatccta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
proximal AsnC repressor asnCp 3927047 3927060 -22.5 tcacttttgaTTCATTAAAAAAGAaggctaaaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
proximal AsnC repressor asnCp 3927079 3927092 -54.5 acatgcaataATCATTCAATAAAAagcctaactc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
proximal AsnC repressor asnCp 3927110 3927123 -85.5 ttgcttatgaTTAAGCAACAAAAAccgacacaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
[Nac,-] 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 Nac repressor asnCp 3927009 3927023 16.0 atgaatcatcAATCCGCATAAGAAAatcctatgga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [10], [11]
proximal Nac repressor asnCp 3927031 3927045 -7.0 taaaaaagaaGGCTAAAATAGAATGaatcatcaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]
proximal Nac repressor asnCp 3927088 3927102 -64.0 aaaccgacacACATGCAATAATCATtcaataaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]


Transcription unit          
Name: asnC-mioC-mnmG
Synonym(s): asnC-mioC-gidA
Gene(s): mnmG, mioC, asnC   Genome Browser M3D Gene expression COLOMBOS
Note(s): About 20 % of the transcription initiated at the asnCp promoter reaches the end of the gidA gene.
In contrast to the effect of asparagine on the regulation of asnA by AsnC, this amino acid does not affect the autoregulation of AsnCKolling R,1985.
It has been observed that the transcriptional regulator IHF binds in the intergenic region of the genes mnmG and mioC, which corresponds to the oriC region Kasho K,2021.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [7] Gielow A., et al., 1988
Promoter
Name: asnCp
+1: 3927031
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 28
Sequence: tcattcaataaaaagcctaactcacttttgattcattaaaaaagaaggctaaaatagaatGaatcatcaatccgcataaga
                                 -35                   -10  +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [8] Huerta AM., et al., 2003
[9] Kolling R., et al., 1985
Terminator(s)
Type: rho-independent
Sequence: cttgatgcgtTGCCTGGTAAGCGGGTGCTTACCAGGCAtttttaatgc
Reference(s): [1] Benitez-Paez A., et al., 2012
TF binding sites (TFBSs)
[AsnC,-] 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 AsnC repressor asnCp 3927013 3927026 12.5 agaatgaatcATCAATCCGCATAAgaaaatccta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
proximal AsnC repressor asnCp 3927047 3927060 -22.5 tcacttttgaTTCATTAAAAAAGAaggctaaaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
proximal AsnC repressor asnCp 3927079 3927092 -54.5 acatgcaataATCATTCAATAAAAagcctaactc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
proximal AsnC repressor asnCp 3927110 3927123 -85.5 ttgcttatgaTTAAGCAACAAAAAccgacacaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
[Nac,-] 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 Nac repressor asnCp 3927009 3927023 16.0 atgaatcatcAATCCGCATAAGAAAatcctatgga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [10], [11]
proximal Nac repressor asnCp 3927031 3927045 -7.0 taaaaaagaaGGCTAAAATAGAATGaatcatcaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]
proximal Nac repressor asnCp 3927088 3927102 -64.0 aaaccgacacACATGCAATAATCATtcaataaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]


Transcription unit          
Name: asnC-mioC
Gene(s): mioC, asnC   Genome Browser M3D Gene expression COLOMBOS
Note(s): About 50 % of the transcription initiated at the asnCp promoter reaches the end of the mioC gene Gielow A,1988.
In contrast to the effect of asparagine on the regulation of asnA by AsnC, this amino acid does not affect the autoregulation of AsnCKolling R,1985.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [7] Gielow A., et al., 1988
Promoter
Name: asnCp
+1: 3927031
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 28
Sequence: tcattcaataaaaagcctaactcacttttgattcattaaaaaagaaggctaaaatagaatGaatcatcaatccgcataaga
                                 -35                   -10  +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [8] Huerta AM., et al., 2003
[9] Kolling R., et al., 1985
TF binding sites (TFBSs)
[AsnC,-] 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 AsnC repressor asnCp 3927013 3927026 12.5 agaatgaatcATCAATCCGCATAAgaaaatccta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
proximal AsnC repressor asnCp 3927047 3927060 -22.5 tcacttttgaTTCATTAAAAAAGAaggctaaaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
proximal AsnC repressor asnCp 3927079 3927092 -54.5 acatgcaataATCATTCAATAAAAagcctaactc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
proximal AsnC repressor asnCp 3927110 3927123 -85.5 ttgcttatgaTTAAGCAACAAAAAccgacacaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
[Nac,-] 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 Nac repressor asnCp 3927009 3927023 16.0 atgaatcatcAATCCGCATAAGAAAatcctatgga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [10], [11]
proximal Nac repressor asnCp 3927031 3927045 -7.0 taaaaaagaaGGCTAAAATAGAATGaatcatcaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]
proximal Nac repressor asnCp 3927088 3927102 -64.0 aaaccgacacACATGCAATAATCATtcaataaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]


Transcription unit       
Name: rsmG
Gene(s): rsmG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Benitez-Paez A., et al., 2012


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -9.8 3926533 3926571 cctgcaaaacCCGATCATGCGTACCATCAAGCCCTGATCGGCTTTTTTaatcccatac
  anti-terminator -4.2 3926565 3926588 accgagacatTGATCGTCCTGCAAAACCCGATCatgcgtacca
  anti-anti-terminator -4.8 3926581 3926613 ccaaacaattGATGAAATTCAGTCCACCGAGACATTGATCGTcctgcaaaac
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    

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP] Inferred from expression pattern

 [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

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IEP-RNA-SEQ] RNA-seq evidence

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-CHIP-SEQ] ChIP-seq evidence


Reference(s)    

 [1] Benitez-Paez A., Villarroya M., Armengod ME., 2012, Regulation of expression and catalytic activity of Escherichia coli RsmG methyltransferase., RNA 18(4):795-806

 [2] Kolling R., Gielow A., Seufert W., Kucherer C., Messer W., 1988, AsnC, a multifunctional regulator of genes located around the replication origin of Escherichia coli, oriC., Mol Gen Genet 212(1):99-104

 [3] Lelong C., Aguiluz K., Luche S., Kuhn L., Garin J., Rabilloud T., Geiselmann J., 2007, The Crl-RpoS regulon of Escherichia coli., Mol Cell Proteomics 6(4):648-59

 [4] Ogawa T., Okazaki T., 1991, Concurrent transcription from the gid and mioC promoters activates replication of an Escherichia coli minichromosome., Mol Gen Genet 230(1-2):193-200

 [5] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [6] Eraso JM., Markillie LM., Mitchell HD., Taylor RC., Orr G., Margolin W., 2014, The Highly Conserved MraZ Protein Is a Transcriptional Regulator in Escherichia coli., J Bacteriol 196(11):2053-66

 [7] Gielow A., Kucherer C., Kolling R., Messer W., 1988, Transcription in the region of the replication origin, oriC, of Escherichia coli: termination of asnC transcripts., Mol Gen Genet 214(3):474-81

 [8] 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

 [9] Kolling R., Lother H., 1985, AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli., J Bacteriol 164(1):310-5

 [10] Poggio S., Domeinzain C., Osorio A., Camarena L., 2002, The nitrogen assimilation control (Nac) protein represses asnC and asnA transcription in Escherichia coli., FEMS Microbiol Lett 206(2):151-6

 [11] Aquino P., Honda B., Jaini S., Lyubetskaya A., Hosur K., Chiu JG., Ekladious I., Hu D., Jin L., Sayeg MK., Stettner AI., Wang J., Wong BG., Wong WS., Alexander SL., Ba C., Bensussen SI., Bernstein DB., Braff D., Cha S., Cheng DI., Cho JH., Chou K., Chuang J., Gastler DE., Grasso DJ., Greifenberger JS., Guo C., Hawes AK., Israni DV., Jain SR., Kim J., Lei J., Li H., Li D., Li Q., Mancuso CP., Mao N., Masud SF., Meisel CL., Mi J., Nykyforchyn CS., Park M., Peterson HM., Ramirez AK., Reynolds DS., Rim NG., Saffie JC., Su H., Su WR., Su Y., Sun M., Thommes MM., Tu T., Varongchayakul N., Wagner TE., Weinberg BH., Yang R., Yaroslavsky A., Yoon C., Zhao Y., Zollinger AJ., Stringer AM., Foster JW., Wade J., Raman S., Broude N., Wong WW., Galagan JE., 2017, Coordinated regulation of acid resistance in Escherichia coli., BMC Syst Biol 11(1):1

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