carbon catabolite confusion and NTR

[gocentral]

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

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

3. 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/8789

[gocentral]

Question: how completely taxon-agnostic should these terms become? As far as I know while mammals have systems to regulate the relative rates of consumption of different energy-rich molecules they work by quite different mechanisms so they probably shouldn't be grouped with catabolite repression as it operates in bacteria and yeasts.

Original comment by: deustp01

[gocentral]

Hi Peter, The problem at the moment is that the position in the ontology (parents/chidren) is not completely in synch with the definitions. It's fine to mention the organism specific processes if this is really the differentia.

GO:0045014 negative regulation of transcription by glucose is a general term which specifically mentions bacteria in the def, although it could be formally very simply defined. If there is something special about the bacterial process, it should be a child term of this term

It is possible the current terms are "missing" something , or we need

xxx involved in negative regulation of transcription by carbohydrate mediated signaling to describe the different mechanisms in the different taxa, if required

v.

Original comment by: ValWood

[gocentral]

I don't think of catabolite repression as being only about transcription. In E. coli, glucose uptake regulates transcription of lac by inhibiting adenyl cyclase (reducing cAMP and CAP-cAMP). However, although CAP-cAMP is what is emphasized in textbooks, the majority of the catabolite repression with lactose is due to inducer exclusion: glucose uptake inhibits lactose transport. Glucose also has catabolite effects on glycerol metabolism, but it is not via transcription. Glucose uptake inhibits glycerol kinase enzyme activity.

Original comment by: jimhu

[gocentral]

Assigned to you Karen, just to get your transcription-take on Val's request: thanks.

Val- do you have any reviews or other papers describing the signaling processes, so I can look into how GO:0045014 fits in with signaling? Is all glucose-control of transcription achieved by signaling?

Becky

Original comment by: rebeccafoulger

[gocentral]

• assigned_to: nobody --> kchris

Original comment by: rebeccafoulger

[gocentral]

It's okay, I'm working on something related Karen, so I'll take this one.

Original comment by: jl242

[gocentral]

• assigned_to: kchris --> jl242

Original comment by: jl242

[gocentral]

• status: open --> pending

Original comment by: jl242

[gocentral]

Hi Jane,

There are true path violations in here too.

The term carbon catabolite regulation of transcription A transcription regulation process in which the presence of one carbon source leads to the modulation of the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources.

has children Any process involving glucose that modulates the frequency, rate or extent or transcription.

which do not specify that the genes regulated are specifically involved in the metabolism of other carbon sources.

It all seems a bit messy, but formal definitions should help here.

Val

Original comment by: ValWood

[gocentral]

• status: pending --> open

Original comment by: ValWood

[gocentral]

From a recent PomBase curation discussion there are the terms we identified as being required to represent the events being regulated by the glucose-signalling pathway in fission yeast.

1. glucose-mediated signal transduction involved in negative regulation of gluconeogensis via negative regulation of transcription from RNA polymerase II promoter and 2. glucose-mediated signal transduction involved in negative regulation of conjugation with cellular fusion via negative regulation of transcription from RNA polymerase II promoter

with parents to signal transduction/ transcriptional regulation and regulation of conjugation OR gluconeogenesis as appropriate

Becky, from your previous question, I don't think we know enough to say whether all of glucose control of transcription is via signalling (although what we know is).

negative regulation of transcription by glucose would be a parent of the 2 requested terms above.

Antonia suggested a paper which may be useful for the fission yeast perspective http://genesdev.cshlp.org/content/5/4/561.long

VAl

Original comment by: ValWood

[gocentral]

Superseded by:

https://sourceforge.net/tracker/index.php?func=detail&aid=3599796&group\_id=36855&atid=440764

Original comment by: jl242

[gocentral]

• status: open --> closed-out-of-date

Original comment by: jl242