detection of glucose

[ValWood]

We have a term "detection of glucose" 13 EXP for 11 proteins

This is used to annotate "glucose receptors"

These should probably all be G-protein coupled glucose receptor activity (or some other receptor term)

My preference would be to obsolete as it is an activity, but if this is not possible for any reason F-P link needs adding from G-protein coupled glucose receptor activity

[ValWood]

curation.pombase.org/pombe/curs/ffbebba84aad52e5/ro

[pgaudet]

Hi @ValWood

How about merging with 'glucose mediated signaling pathway', 'The process in which a change in the level of mono- and disaccharide glucose trigger the expression of genes controlling metabolic and developmental processes. '

(I propose to do the same with the parent 'GO:0009732 detection of hexose stimulus' )

The children can probably also be merged into regulation glucose signaling: GO:2000970 | regulation of detection of glucose GO:2000971 | negative regulation of detection of glucose (single annotation by BHF - @RLovering do you want to comment?) GO:2000972 | positive regulation of detection of glucose

What do you think ?

Thanks, Pascale

[ValWood]

Well the annotations wouldn't be incorrect from this merge, but maybe a heads up to the annotating groups as they could definitely improve the annotation by changing to MF.

[pgaudet]

TO MOVE TO ANNOTATION TRACKER:

Some of the 'detection of glucose' could also have a 'glucose receptor activity' annotation:

ID | Symbol | Evidence | Reference | With | Taxon | Date | Source | Comment O94744 | git3 | IMP | PMID:24297439 | - | 284812 | 20140805 | PomBase | glucose receptor ? P10870 | SNF3 | IGI | PMID:8901598 | SGD:S000002297 | 559292 | 20100104 | SGD | glucose transporter ? P10870 | SNF3 | IMP | PMID:8901598 | - | 559292 | 20100104 | SGD | glucose transporter ? P17712 | Gck | IDA | PMID:17470517 | - | 10116 | 20100929 | BHF-UCL | glucokinase P17712 | Gck | IMP | PMID:16443775 | - | 10116 | 20081107 | RGD | glucokinase P35557 | GCK | IMP | PMID:12941786 | - | 9606 | 20061219 | UniProt | glucokinase P52947 | Pdx1 | IDA | PMID:21108535 | - | 10116 | 20110228 | BHF-UCL | homeobox protein P83293 | Gr64a | IMP | PMID:17715294 | - | 7227 | 20081113 | FlyBase | Gustatory receptor for sugar taste 64a Q04665 | gpa2 | IMP | PMID:24297439 | - | 284812 | 20140805 | PomBase | Guanine nucleotide-binding protein alpha-2 subunit Q12300 | RGT2 | IMP | PMID:8901598 | - | 559292 | 20100104 | SGD | glucose transporter Q12361 | GPR1 | IMP | PMID:15494315 | - | 559292 | 20071130 | SGD | G protein-coupled receptor Q60554 | NKX6-1 | IDA | PMID:21108535 | - | 10036 | 20110228 | BHF-UCL | Homeobox protein Q6FNU3 | SNF3 | IMP | PMID:26648919 | - | 284593 | 20160330 | CGD | glucose transporter ?

P35583 | Foxa2 |   | GO:2000971 | negative regulation of detection of glucose -> certainly does not have MF G-protein coupled glucose receptor activity

[pgaudet]

note: another set of similar terms: GO:0046015 regulation of transcription by glucose (and + and - children) Annotations are a mix of signalling in response to glucose and glucose-responsive transcription factors.

[ValWood]

proposed action (quick fix) how about obsolete GO:0051594 detection of glucose with consider

GO:1990576 G-protein coupled glucose receptor activity or GO:0010255 glucose mediated signaling pathway (or a descendant)

and open a new ticket for anything left over.

[pgaudet]

Dear all,

The proposal has been made to obsolete GO:0051594 detection of glucose and its regulation children, GO:2000970 regulation of detection of glucose GO:2000971 negative regulation of detection of glucose GO:2000972 positive regulation of detection of glucose

The reason for obsoletion is that this term is redundant with other terms in the ontology: GO:1990576 G-protein coupled glucose receptor activity and GO:0010255 glucose mediated signaling pathway.

There are 12 annotations to these terms, by BHF-UCL, CGD, FlyBase, RGD and SGD, see https://github.com/geneontology/go-annotation/issues/4404. There are no mappings to these terms, these terms are not present in any subsets.

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/13909

Thanks, Pascale

[pgaudet]

We'd like to proceed with the obsoletion on January 18th, 2023.

[jlewsmith]

CGD done

[RLovering]

Hi The enzyme Glucokinase (GK) appears to be a glucose sensing. See https://pubmed.ncbi.nlm.nih.gov/32229720/ and https://pubmed.ncbi.nlm.nih.gov/17179917/ and many other refs

can I keep this with the detection of glucose term? Thanks Ruth

[deustp01]

The outcome is sensing, but the mechanism, at least in humans and mice, is that an enzyme with textbook glucokinase activity has evolved to have a Km higher than fasting blood glucose levels and a bit lower than postprandial levels, so pancreatic beta cells and hepatocytes, where the enzyme is expressed, are enabled to take up glucose and retain it as glucose 6-phosphate particularly efficiently in the postprandial state. The elevated glucose 6-phosphate levels feed into a mechanism for insulin granule release in the beta cells and provide substrate by mass action for glucose utilization pathways in hepatocytes. Is "detection" the best word to describe this? (That's a question, not an opinion.)

[pgaudet]

Thanks @deustp01

This was also how I understood the issue - ie we end up describing the same pathway using two different aspects.

PMID:17179917 GLUT-2, and glucose phosphorylating enzyme, glucokinase, are key for glucose sensing of the pancreatic beta-cell, the initial event in the pathway for glucose-stimulated insulin secretion.

This can also be read as GO:0010255 glucose mediated signaling pathway

GK in the PVN acts as part of a glucose-sensing mechanism within the PVN that regulates glucose homeostasis by controlling glucagon-like peptide 1 (GLP-1) release

So, GK seems to activate signal transduction that leads to insulin and glucagon secretion (I dont know whether these are describing the same pathway).

[pgaudet]

@RLovering 'detection of glucose', which is_a 'response to glucose', fails to describe that this really is signaling.

I could create 'glucose sensor activity' as a child of 'GO:0140299 small molecule sensor activity' - would that address the issue?

[RLovering]

I guess it depends whether scientists would expect Glucokinase and its regulator GK and GKRP to be associated with this term and would find it useful in their analysis. I think the systems might be more complex - see statements in https://pubmed.ncbi.nlm.nih.gov/34325016/ : Glucokinase (GCK) is critical for glucosensing. https://pubmed.ncbi.nlm.nih.gov/35870707/ : A glucokinase-linked sensor in the taste system contributes to glucose appetite https://link.springer.com/article/10.1007/s00592-021-01814-7: Maturity onset diabetes of the young (MODY ).....MODY 2 and MODY 3 are caused by heterozygous inactivating variants in glucokinase (GCK) and hepatocyte nuclear factor 1A (HNF1A), respectively.....Glucokinase also functions as the pancreatic β-cell glucose sensor regulating glucose-induced insulin secretion, I would suggest keeping Glucokinase with detecting glucose term Plus also considering including the Glucokinase regulator - https://pubmed.ncbi.nlm.nih.gov/30983961/ : Hepatocytes, β-cells and hypothalamic tanycytes are part of the glucosensor cell types, which express several proteins involved in the glucose sensing mechanism such as GLUT2, Glucokinase (GK) and Glucokinase regulatory protein (GKRP). GK catalyzes the phosphorylation of glucose to glucose-6-phosphate (G-6P), and its activity and subcellular localization are regulated by GKRP. In liver, when glucose concentration is low, GKRP binds to GK holding it in the nucleus, while the rise in glucose concentration induces a rapid export of GK from the nucleus to the cytoplasm. In contrast, hypothalamic tanycytes display inverse compartmentalization dynamic in response to glucose: a rise in the glucose concentration drives nuclear compartmentalization of GK.

[RLovering]

Sorry my github ticket hadn't updated with Pascale's comments. 'glucose sensor activity' is a good idea. and you would like the term GO:0010255 glucose mediated signaling pathway added to perhaps both Glucokinase and its regulator? and are you also suggesting keeping the detection term with Glucokinase or not?

[ValWood]

GO:0051594 detection of glucose has no annotations. I will proceed with the obsoletion.

[ValWood]

Also GO:0034287 detection of monosaccharide stimulus GO:0009732 detection of hexose stimulus GO:0009730 detection of carbohydrate stimulus (3 EXP)

but then we get to "detection of chemical stimulus" has 545,012 annotations 647 EXP. Presumable all should be "sensors" @hattrill any thoughts, 307 are drosophila

[hattrill]

So, most to these are receptors of some type, but there are also co-receptors and other partners. Some are gustatory, some are olfactory, not always able to classifiy them.

Because of the nature of the experiments - generally signaling in groups of neurones we cannot often say give a MF (as no binding data) - but can say that it is needed to detect that chemical class.

[ValWood]

Maybe we keep detection of stimulus and remove the specific children where is is known what is being sensed? @pgaudet ?

[pgaudet]

Maybe we can leave this for now? Seems low priority. We can revisit later. What do you think ?

[ValWood]

OK I'll close, but of we get predictions to these terms from the function prediction brigade, I'll open a new ticket. I'm also happy to process the unannotated children now...

[ValWood]

For the future