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| Operon |  |
|---|---|
| Name: | ymdAB-clsC |
| This page displays every known transcription unit of this operon and their known regulation. | |
| 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: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] 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: | [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
| Reference(s): | [1] Kim M., et al., 2017 |
| 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: | [COMP-AINF] Inferred computationally without human oversight [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] 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: | [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
| Reference(s): | [1] Kim M., et al., 2017 |
| 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: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] 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: | [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
| Reference(s): | [1] Kim M., et al., 2017 |
| 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: | [COMP-AINF] Inferred computationally without human oversight [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] 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: | [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
| Reference(s): | [1] Kim M., et al., 2017 |
| Name: | ymdB |
| Gene(s): | ymdB Genome Browser M3D Gene expression COLOMBOS |
| Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] 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: | [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
| Reference(s): | [1] Kim M., et al., 2017 |
| 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: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined [IC] Inferred by curator |
| Reference(s): | [1] Kim M., et al., 2017 |
| Promoter | |
| Name: | clsCp |
| +1: | 1106292 |
| Distance from start of the gene: | 63 |
| Sequence: |
taaaaaccgtttcagaatttattacccgtcacgctttacccgaacaggtatactttgtctGttatgatgaagaaaacgccc |
| Evidence: |
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
| 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 |
| 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" |
| Reference(s) |
|
|---|---|
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping