RegulonDB RegulonDB 11.1: Operon Form
   

ycjY-ymjDC-mpaA operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: ycjY-ymjDC-mpaA
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: ycjY
Gene(s): ycjY   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: ycjYp6
+1: 1392072
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 219
Sequence: atcccaatcgttcttctatacgacgcactatctggcttaaagctgactgcgccatgctcaGgcgggctgctgcacgagtga
Evidence: [COMP-AINF]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[PgrR,-] 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 PgrR repressor ycjYp6 1391953 1391967 113.5 gcaatctattAATCATTTAAATGATaggtctaatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IGI], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [3]


Transcription unit          
Name: ycjY-ymjDC-mpaA
Gene(s): mpaA, ymjC, ymjD, ycjY   Genome Browser M3D Gene expression COLOMBOS
Note(s): The ycjY-ymjD-ymjC-mpaA operon is derepressed under nutrient starvation for self-generation of amino acids, but it is repressed under high osmotic conditions for maintenance of the rigidity of the peptidoglycan (PG) sacculus, which provides mechanical strength to resist osmotic challenges Shimada T,2013
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [3] Shimada T., et al., 2013
Promoter
Name: ycjYp6
+1: 1392072
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 219
Sequence: atcccaatcgttcttctatacgacgcactatctggcttaaagctgactgcgccatgctcaGgcgggctgctgcacgagtga
Evidence: [COMP-AINF]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[PgrR,-] 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 PgrR repressor ycjYp6 1391953 1391967 113.5 gcaatctattAATCATTTAAATGATaggtctaatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IGI], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [3]


Transcription unit       
Name: mpaA
Gene(s): mpaA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[IC] Inferred by curator
Reference(s): [3] Shimada T., et al., 2013


Transcription unit       
Name: ymjC-mpaA
Gene(s): mpaA, ymjC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IGI] Inferred from genetic interaction

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


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] Choi U., Park YH., Kim YR., Seok YJ., Lee CR., 2016, Increased expression of genes involved in uptake and degradation of murein tripeptide under nitrogen starvation in Escherichia coli., FEMS Microbiol Lett 363(14)

 [3] Shimada T., Yamazaki K., Ishihama A., 2013, Novel regulator PgrR for switch control of peptidoglycan recycling in Escherichia coli., Genes Cells 18(2):123-34

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