two-component sensor molecule activity

[gocentral]

GO:0000155 two-component sensor molecule activity

no def

GO:0000156 two-component response regulator activity

no def

What is the difference between these two terms?

histidine kinases are response regulators so is the transcriptional regulator parentage for this term correct?

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/2717":https://sourceforge.net/p/geneontology/ontology-requests/2717

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I see (I think) are these the activities attributed to i) the two componets of the phosphorelay system?

are they always 'trascriptional regulator activity' (i.e binding to DNA or a transcription factor)....(I don't know)

Original comment by: ValWood

[gocentral]

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Hi Val,

Yes, the two function terms represent the separate functions of the two components. In prokaryotes, most of the time the two functions are on separate molecules but they do occur sometimes together on one.

The sensor molecule detects the presence of a particular signal substance outside the cell and then it phosphorylates the regulator which in turn regulates transcription. So, only the regulator activity can be child of "transcriptional regulator activity". The sensor molecule does not have transcriptional regulator activity (unless it is one of those cases where the sensor and regulator are together in one protein.)

I think the tree is correct as is. (These do need definitions though.)

Michelle

Original comment by: mlgwinn

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Thanks Michelle that makes sense.

My only other question is whether a molecule which phosphorylates a transcriptional regulator should be annotated to the function term 'transcription regulator activity' (rather than the process term transcriptional regulation)

The def of transcriptional regulator says Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor.

Does this phosphorylate the transcription factor directly or is it an upstream regulator?

and does it matter.....

cheers

Val

Original comment by: ValWood

[gocentral]

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Hi Val,

I would have initially said no, I wouldn't annotate the sensor to "transcription regulator acitivy", but then when I read the def you provided, it seems that the sensors (which phosphorylate the regulator directly) would fall into that category.

Michelle

Original comment by: mlgwinn

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Hi Michelle,

I agree that I wouldn't add this annotation, but I am picking this up from an Interpro mapping.

I wonder if we really mean:

may bind a promoter or enhancer DNA sequence or interact with a *DNA bound DNA-binding transcription factor

(this is certainly how I have used this term...., anything else I would annotate to a 'transcriptional regulation process term' but not to this activity? what do you think?

Original comment by: ValWood

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Hi Val,

Yes, I agree with your assessment - that's what I think too.

Michelle

Original comment by: mlgwinn

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....so maybe a tweak to the definition, ( or a clarification of its use?) is required.

Original comment by: ValWood

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Yes, I think so.

Michelle

Original comment by: mlgwinn

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Two things ...

1) 'transcription regulator activity' (GO:0030528) is used in about a zillion annotations, so tweaking its def is a big enough deal to put to the mailing list. I'll write ...

2) These aren't my best efforts, but would they do?

GO:0000155 two-component sensor molecule activity def: Catalysis of the phosphorylation of a specific transcription regulator in response to the presence of a particular signal substance outside the cell.

GO:0000156 two-component response regulator activity def: Alters the level of transcription of target genes when phosphorylated by a sensor that detects the presence of a particular signal substance outside the cell.

m

Original comment by: mah11

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OK, the mailing list has spoken, and it's not often that it's as unanimous as on this topic: we should NOT change the definition of transcription regulator activity. (For gory details, see the list archives; subject line is 'def of transcription regulator activity'.)

This means that the use of 'transcription regulator activity' is a matter for curator discretion.

The only other thing for this item, then, is whether anyone can improve on the defs I suggested for the two-component function terms. Any thoughts?

m

Original comment by: mah11

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should the def of two-component response regulator activity need to mention that this activity includes transcription factor binding ?

Original comment by: ValWood

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OK, I've put defs in. For the regulator I've used

Alters the level of transcription of target genes, usually by binding to a transcription factor, when phosphorylated by a sensor that detects the presence of a particular signal substance outside the cell.

I think that's everything for this one.

m

Original comment by: mah11

[gocentral]

• labels: --> Other term-related request
• milestone: --> TermGenie
• assigned_to: nobody --> gomidori
• status: open --> closed-fixed

Original comment by: mah11