rename "carbon catabolite repression of transcription"

[gocentral]

Could the GO term carbon catabolite repression of transcription be switched for consistency with parents and children to be the exact synonym negative regulation of trasncription by carbon catabolites?

val

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/9928

[gocentral]

• assigned_to: nobody --> tairtb

Original comment by: tberardini

[gocentral]

It depends which parent you want to match. 'carbon catabolite repression of transcription' is an is_a child of both

carbon catabolite regulation of transcription (consistent naming)

and

negative regulation of transcription, DNA-dependent (not consistent naming)

If we change the primary term name as you suggest, the new term string will be inconsistent with former parent, instead of being inconsistent with the latter parent. Since there are several terms that are under 'carbon catabolite regulation of transcription' (GO:0045990) that share this same term composition, I am inclined to leave things as they are with the alternative names as synonyms (which currently exist).

Does it make sense to rename that entire branch (GO:0045990 and children)?

Original comment by: tberardini

[gocentral]

Hi Tanya,

In this case maybe the problem is bigger.

The childen like "regulation of transcription by glucose" do not mention the differentia "extent of transcription of specific genes involved in the metabolism of other carbon sources"

It might be useful if all the terms used consistent names so the ones which include "transcription of specific genes involved in the metabolism of other carbon sources" would be something like

negative regulation of transcription by carbon catabolites involved in carbohydrate metabolism or however these terms are usually worded.

This came up from our curator meeting today, so I'll check with Antonia and Midori, but I think we all thought that the differences in naming convention was potentially confusing....

Original comment by: ValWood

[gocentral]

I'm going to reassign this to Jane (sorry!) as she worked on the last iteration of changes on this set of terms and may have some memory of the decisions between them being named as they are now.

https://sourceforge.net/tracker/?func=detail&aid=3408498&group\_id=36855&atid=440764

Original comment by: tberardini

[gocentral]

• assigned_to: tairtb --> jl242

Original comment by: tberardini

[gocentral]

I have to admit, I don't have a lot to offer. I've done very little work on any of the transcription regulation terms, and I have no strong preference in this case. I suspect the "carbon catabolite" term names come from the widespread usage of the phrase "carbon catabolite repression" in the literature.

m

Original comment by: mah11

[gocentral]

So I think we probably need a new genus term, something like:

regulation of DNA-dependent transcription by chemical substance ; GO:new

with a child:

regulation of DNA-dependent transcription by catabolite ; GO:new

then we could make the following:

regulation of transcription, DNA-dependent ; GO:0006355 ---[i] regulation of DNA-dependent transcription by chemical substance ; GO:new ---[i] regulation of DNA-dependent transcription by catabolite ; GO:new ------[i] regulation of DNA-dependent transcription by carbon catabolite ; GO:0045990 ------[i] etc

Note the name change for GO:0045990 and its ilk. I'll make all the Pol II subtypes too.

"regulation of transcription by glucose" will be moved up under 'regulation of DNA-dependent transcription by chemical substance ; GO:new' - it's current placement is too specific as Val points out.

That sound okay?

Original comment by: jl242

[gocentral]

I'm sure there are some gotchas in this "carbon catabolite bit" but for this part, this sounds correct, and more consistent than the existing. (note that the glucose term should lgo UNDER the carbon catabolite parent)

val

Original comment by: ValWood

[gocentral]

But the glucose term is more general:

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

it doesn't mention anything about it being a catabolite or anything. What about I make subtypes:

regulation of transcription by glucose catabolite

?

Original comment by: jl242

[gocentral]

Yes the glucose term has some mammalian annotation, so probably shouldn't change the definition.

Original comment by: jl242

[gocentral]

Isn't glucose a "carbon catabolite"?

In fission yeast when people refer to carbon catabolite repression they are usually talking about "negative regulation of transcription by glucose"

i.e. "The catabolite repression was first shown to be initiated by glucose and therefore sometimes referred to as the glucose effect"

val

Original comment by: ValWood

[gocentral]

I guess this is difficult ontologically because glucose is not aalways a catabolite?

That is part of the reason these terms need to be explicit regulation of x by y etc with the phrases like "carbon catabolite repression of transcription" etc as related synonyms rather than term names

For this reason, probably shouldn't use "catabolite" in the term names at all but stick with things like "monosaccharide" and "carbohydrate"

val

Original comment by: ValWood

[gocentral]

Hi Val

The difficulty I'm having is with the definition of '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."

To me that last bit makes it more specific than just general regulation of transcription by carbohydrate or whatever. I think it only makes sense to talk about using different carbon sources for unicellular orgs? Whereas the glucose term is defined more generally and used for annotating multicellular orgs e.g. http://europepmc.org/abstract/MED/9837962

Are you suggesting we broaden out the catabolite terms to remove the specific genes and carbon sources bits?

Jane

Original comment by: jl242

[gocentral]

There's also some overlap with the utilization terms e.g carbon utilization ; GO:0015976

Original comment by: jl242

[gocentral]

I think there are more problems with this.

The glucose does repress genes involved in the the expression of involved in carbon metabolism, but it isn't restricted to these genes. I suppose one fix could be

specific genes including those involved in the metabolism of other carbon sources ?

Original comment by: ValWood

[gocentral]

• Description has changed:

Diff:

--- old
+++ new
@@ -1,4 +1,3 @@
-

 Could the GO term 
 carbon catabolite repression of transcription be switched for consistency with parents and children to be the exact synonym

• assigned_to: Jane Lomax --> David Hill
• Group: --> None

Original comment by: paolaroncaglia

[gocentral]

Assigning to David H as transcription- and metabolism-related... thank you David.

Original comment by: paolaroncaglia

[ukemi]

@ValWood. I'm looking into this ticket again as part of the ontology developers' workshop. I think I agree with Jane that the general 'regulation of transcription of glucose' etc should be moved from being children of the carbon catabolite terms because they are less general. I think the catabolite terms reflect more the reason/result for the transcription regulation than the trigger. The general terms don't reflect this at all. I think these terms encompass the mechanism by which an organism controls the carbon source that it utilizes.

I propose that the general terms that don't state 'of specific genes involved in the metabolism of other carbon sources.' be moved out of this branch and the other terms be renamed to be consistent with the branch. For example: 'regulation of transcription from RNA polymerase II promoter by a nonfermentable carbon source' will be renamed 'carbon catabolite regulation of transcription from RNA polymerase II promoter by a nonfermetable carbon source'. This way it is clear that the term reflects aspects of both the trigger and the response.

[ukemi]

also see #10613. @jimhu-tamu any comments about this proposal as a start?

[jimhu-tamu]

Hi David,

I may have forgotten some earlier input related to this, but here are my initial thoughts on seeing this today:

I would want to look at the proposals for how this fits more globally into catabolite repression and related topics. From looking at the current structure of GO, it seems to me that the existing structure doesn't fully capture the biology in bacteria, which I suspect has analogous parts in eukaryotes.

General issues In bacteria, catabolite repression tends to be taught in terms of how glucose represses the transcription initiation at lac based on the synthesis or lack of synthesis of cyclic AMP from adenyl cyclase (cya) and activation of initiation by CAP-cAMP (crp). But it's more complex. IIRC, there is data that suggest that CAP-cAMP is a minor contributor to the effect of glucose on lac expression induced by lactose (as opposed to the membrane permeable lactose analog IPTG), and a larger contribution comes from a phenomenon known as inducer exclusion. In that, transport of glucose via the PTS system negatively regulates the activity of a number of other proteins, including sugar transporters and adenyl cyclase. When lac permease is inhibited, the lactose can't get into the cell to derepress lac independent of CAP-cAMP.

One could shoehorn this into regulation of transcription because the inducer exclusion does affect initiation. But in glycerol metabolism, the glucose effect on the PTS system acts by regulating the activity of glycerol kinase, the first step in metabolizing glycerol. Thus, I would argue for a more general umbrella term for catabolite regulation that is not specific to transcription.

The catabolite effects are not only seen with glucose. There is a hierarchy of C source preference in E. coli, and I think that's also true in S. cerevisiae. (http://mmbr.asm.org/content/62/2/334.full)

I'm also not sure that fermentable/nonfermentable is right here... glucose is fermentable.

[ukemi]

Thanks Jim. I think I will add the general catabolite repression term and then make the transcription regulatory terms children of it. But I think we are on the same page here that these terms are much more than just the regulation of transcription. The terms here really encompass a metabolic control system that controls the use of a carbon source. I'm not sure that I will add all of the detailed processes under catabolite repression until we need them for annotation, but at least the structure will be in place so that we can add them. I will sort out the transcription terms based on the new structure and the additional general catabolite repression parent. Hope all this makes sense.

-D

[jimhu-tamu]

sounds good!

[pgaudet]

I also think that these terms really try to capture some signaling event, which unfortunately is described as transcription in papers, since that's the last step. I am not sure it even makes sense to have this under transcription, especially if you think about how this groups when you do a slim (or any kind of enrichment analysis).

Pascale

[ukemi]

Closed via #15152