RegulonDB RegulonDB 10.9: Operon Form
   

ymdAB-clsC operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: ymdAB-clsC
Gene(s): ymdA, ymdB, clsC   Genome Browser M3D Gene expression COLOMBOS
Note(s): The ymdAB-clsC operon participates in the regulation of biofilm formation and in the control of apramycin susceptibility via a sucA-mediated pathway, and the promoters are sensitive to cold shock in the following order: ymdAp > clsCp > ymdBp Kim M,2017
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Kim M., et al., 2017
Promoter
Name: ymdAp
+1: 1105201
Distance from start of the gene: 213
Sequence: accctttcattgcctgctaatcaacccattgctttgacgaagttgagtttaaatatttccCcggacgatcgggtgaaaata
Note(s): ymdA is expressed only during the exponential phase Kim M,2017. It seems that activation of ymdA is necessary when bacteria are recovering from cold-induced damage Kim M,2017. Two TSS were identified at -213C and -211G upstream of the ymdA translation star site Kim M,2017.
Evidence: [TIM]
Reference(s): [1] Kim M., et al., 2017


Transcription unit       
Name: ymdAB
Gene(s): ymdA, ymdB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The ymdAB operon is transcribed during the exponential growth phase Kim M,2017The ymdAB operon is transcribed during the exponential growth phase Kim M,2017
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Kim M., et al., 2017
Promoter
Name: ymdAp
+1: 1105201
Distance from start of the gene: 213
Sequence: accctttcattgcctgctaatcaacccattgctttgacgaagttgagtttaaatatttccCcggacgatcgggtgaaaata
Note(s): ymdA is expressed only during the exponential phase Kim M,2017. It seems that activation of ymdA is necessary when bacteria are recovering from cold-induced damage Kim M,2017. Two TSS were identified at -213C and -211G upstream of the ymdA translation star site Kim M,2017.
Evidence: [TIM]
Reference(s): [1] Kim M., et al., 2017


Transcription unit       
Name: ymdA
Gene(s): ymdA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The activity of the ymdA promoter was increased after cold shock exposure Kim M,2017
The ymdA transcript is present during the exponential growth phase Kim M,2017
The probable ymdAB-clsC polycistronic transcript was detected only after cold shock exposure Kim M,2017
Overexpression of ymdA inhibited biofilm formation and increased the susceptibility to apramycin. These effects were dependent on the presence of the sucA gene. On the other hand, biofilm formation increased in ymdA knockout cells compared with wild-type cells. This effect was even greater in ymdA-ymdB-clsC triple knockout cells Kim M,2017
Evidence: [BTEI] Boundaries of transcription experimentally identified
[ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
Reference(s): [1] Kim M., et al., 2017
Promoter
Name: ymdAp
+1: 1105201
Distance from start of the gene: 213
Sequence: accctttcattgcctgctaatcaacccattgctttgacgaagttgagtttaaatatttccCcggacgatcgggtgaaaata
Note(s): ymdA is expressed only during the exponential phase Kim M,2017. It seems that activation of ymdA is necessary when bacteria are recovering from cold-induced damage Kim M,2017. Two TSS were identified at -213C and -211G upstream of the ymdA translation star site Kim M,2017.
Evidence: [TIM]
Reference(s): [1] Kim M., et al., 2017


Transcription unit       
Name: ymdB
Gene(s): ymdB   Genome Browser M3D Gene expression COLOMBOS
Note(s): ymdB is more abundant during the stationary phase than during the exponential phase.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Kim M., et al., 2017
Promoter
Name: ymdBp
+1: 1105803
Distance from start of the gene: 17
Sequence: gttgctgagcagaaaaatgcgatttaaccaaaaagcctgctgtacacttaagaaacaagaAggtgtaaggaggcgttatga
Evidence: [TIM]
Reference(s): [1] Kim M., et al., 2017


Transcription unit       
Name: ymdB-clsC
Gene(s): ymdB, clsC   Genome Browser M3D Gene expression COLOMBOS
Note(s): ymdB and clsC are transcribed together, and YmdB and ClsC may function in the same biological pathway Kim M,2017 Both genes are induced during the stationary phase Kim M,2017
Evidence: [BTEI] Boundaries of transcription experimentally identified
[ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
Reference(s): [1] Kim M., et al., 2017
Promoter
Name: ymdBp
+1: 1105803
Distance from start of the gene: 17
Sequence: gttgctgagcagaaaaatgcgatttaaccaaaaagcctgctgtacacttaagaaacaagaAggtgtaaggaggcgttatga
Evidence: [TIM]
Reference(s): [1] Kim M., et al., 2017


Transcription unit       
Name: clsC
Gene(s): clsC   Genome Browser M3D Gene expression COLOMBOS
Note(s):
The promoter activity for clsC was increased after cold shock exposure Kim M,2017
The clsC transcript is present during the exponential and stationary growth phases Kim M,2017
Overexpression of clsC enhanced biofilm formation and promoted apramycin resistance; this effect was dependent on the absence of the sucA gene. On the other hand, the biofilm formation and the resistance to apramycin were increased in single clsC knockout cells compared with wild-type cells. These effects were greater in a ymdA-ymdB-clsC triple knockout Kim M,2017
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IC] Inferred by curator
[LTED] Length of transcript experimentally determined
Reference(s): [1] Kim M., et al., 2017
Promoter
Name: clsCp
+1: 1106292
Distance from start of the gene: 63
Sequence: taaaaaccgtttcagaatttattacccgtcacgctttacccgaacaggtatactttgtctGttatgatgaagaaaacgccc
Evidence: [HTTIM]    
[TIM]
Reference(s): [1] Kim M., et al., 2017
[2] Mendoza-Vargas A., et al., 2009


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [3] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -9.0 1105378 1105402 taacacaaccCTCAAGGATGACTAATCATTGAGGaaatagaata
  terminator -13.4 1105777 1105816 aaccaaaaagCCTGCTGTACACTTAAGAAACAAGAAGGTGTAAGGAGGCgttatgaaaa
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"





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