search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
222 stars 40 forks source link

carbon catabolite repression #8999

Closed gocentral closed 9 years ago

gocentral commented 13 years ago

I know I asked a question about this recently but I can't find it. Anyway, I think this is a slightly different question

1. There are terms

carbon catabolite repression of transcription A transcription regulation process in which the presence of one carbon source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources. Carbon catabolite repression is a mechanism of genetic regulation which the accumulation of catabolites of one substance in the cell represses the formation of enzymes that contribute to the catabolism of other substances.

and GO:0045014 negative regulation of transcription by glucose Any process involving glucose that stops, prevents or reduces the rate of transcription. The presence of glucose in the growth medium inhibits the synthesis of certain enzymes in bacteria growing on the medium. For example, transcription of some catabolic operons is under negative control by specific repressors and glucose is an anti-inducer of xylose utilization and glycerol kinase.

I wonder if the term could be renamed more formally and "carbon catabolite repression" could be used as an exact synonym ?

(glucose repression is a synonym of the child term GO:0045014 negative regulation of transcription by glucose be defined more formally withough reference to "bacterial enzymes"

  1. From reading this definition it appears to be describing a signalling pathway where glucose is the ligand and the result is negative regulation of transcription. At least all of the fission yeast annotations are part of a signalling pathway which senses glucose and negatively activates transcription through tup co repressors. However this term does not have a parent to transcription,

so for the negative regulation of transcription from RNA pol II by glucose/carbon terms I would like a "signaling" child term which has a parent to "carbohydrate mediated signaling"

negative regulation of transcription from RNA pol II by carbohydrate mediated signaling

I know I asked a question about this recently but I can't find it. Anyway, I think this is a slightly different question

1. There are terms A) carbon catabolite repression of transcription A transcription regulation process in which the presence of one carbon source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources. Carbon catabolite repression is a mechanism of genetic regulation which the accumulation of catabolites of one substance in the cell represses the formation of enzymes that contribute to the catabolism of other substances. and b) GO:0045014 negative regulation of transcription by glucose Any process involving glucose that stops, prevents or reduces the rate of transcription. The presence of glucose in the growth medium inhibits the synthesis of certain enzymes in bacteria growing on the medium. For example, transcription of some catabolic operons is under negative control by specific repressors and glucose is an anti-inducer of xylose utilization and glycerol kinase.

I wonder if the A) could be renamed more formally and "carbon catabolite repression" could be used as an exact synonym ? -glucose repression is a synonym of the child term GO:0045014 negative regulation of transcription by glucose

  1. Could B be defined more formally without reference to "bacterial enzymes" And to match the parent term with some differentia

  2. This definition it appears to be describing a signalling pathway where glucose is the ligand and the result is negative regulation of transcription. At least all of the fission yeast annotations are part of a signalling pathway which senses glucose and negatively activates transcription through tup co repressors. However this term does not have a parent to signalling so maybe it is broader?

so for the negative regulation of transcription from RNA pol II by glucose/carbon terms I would like a "signaling" child term which has a parent to "carbohydrate mediated signaling"

the term I need is negative regulation of transcription from RNA pol II by carbohydrate mediated signaling

standard terms and defs

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/8788

gocentral commented 13 years ago

sorry confusing cut and paste error, will open again!

Original comment by: ValWood

gocentral commented 13 years ago

Original comment by: ValWood