Matrix: amino acid metabolism/ chromatin remodelling 4

[ValWood]

I'm not convinced that it should be annotated to chromatin remodelling, but I tried to get this one fixed last time and it seemed controversial...

these are all downstream of Catalysis of the reaction: 5-methyltetrahydrofolate + NAD(P)+ = 5,10-methylenetetrahydrofolate + NAD(P)H + H+. S

Wikipedia page says Natural variation in this gene is common in otherwise healthy people. Although some variants have been reported to influence susceptibility to occlusive vascular disease, neural tube defects, Alzheimer's disease and other forms of dementia, colon cancer, and acute leukemia, findings from small early studies have not been reproduced. Some mutations in this gene are associated with methylenetetrahydrofolate reductase deficiency.[6][7][8] Complex I deficiency with recessive spastic paraparesis has also been linked to MTHFR variants. In addition, the aberrant promoter hypermethylation of this gene is associated with male infertility and recurrent spontaneous abortion.[9][10]

So even if these variants do increas suceptibility they proably shouldn't be annotated?

The processes should relate to In the rate-limiting step of the methyl cycle, MTHFR irreversibly reduces 5,10-methylenetetrahydrofolate (substrate) to 5-methyltetrahydrofolate (product).

5,10-methylene tetrahydrofolate is used to convert dUMP to dTMP for de novo thymidine synthesis. 5-Methyltetrahydrofolate is used to convert homocysteine (a potentially toxic amino acid) to methionine by the enzyme methionine synthase. (Note that homocysteine can also be converted to methionine by the folate-independent enzyme betaine-homocysteine methyltransferase (BHMT))

but clearly processes which involve methylation to any degree will be impacted downstream?

the annotation causing the violation is this one

Methylenetetrahydrofolate reductase |   | regulation of histone methylation |   | BHF-UCL | Homo sapiens | IDA |   | family not named pthr45754 | protein |   | PMID:24769206 | 20150205

which seems very downstream to me because anything involved in the methylation cycle is going to affect/perturb but not regulate methylation.

You couldn't really regulate methylation processes from this point because you would be controlling pretty much everything?

[ValWood]

@pgaudet we might as well delete

• [x] MTHFR | Methylenetetrahydrofolate reductase |   | cellular amino acid metabolic process |   | PINC | Homo sapiens | TAS

since this is covered by BHF annotation

and

• [x] MTHFR | Methylenetetrahydrofolate reductase |   | blood circulation |   | PINC | Homo sapiens | TAS

which is a bit random

[pgaudet]

MTHFR | Methylenetetrahydrofolate reductase | | cellular amino acid metabolic process | | PINC | Homo sapiens | TAS

Removed (and other annotations from that paper PMID:7647779)

[pgaudet]

WRT GO:0031060 regulation of histone methylation

The abstract states "Methylenetetrahydrofolate reductase (MTHFR), a key enzyme in the folate cycle, catalyzes the reduction of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, a co-substrate for homocysteine remethylation to methionine. Methionine serves as the precursor of the active methyl donor S-adenosylmethionine, which provides methyl groups for many biological methylations. " (PMID:24769206)

This is a case where we can either delete the annotation OR use 'acts upstream of' histone methylation (and NOT regulation) if you want to capture the information.

@RLovering Would that work for you ? If so, please edit the annotation.

Thanks, Pascale

[ValWood]

CDK1/cyclin B phosphorylates and represses MTHFR

The argument here is that MTHFR is inhibited when phosphorylated. phosphorylation peaks in mitosis.

They say: Inhibition of MTHFR expression resulted in a decrease of H3K9me3 levels, and an increase of transcription of the centromeric heterochromatin markers

So , in a separate knock down experiment, if they mimic reduced activity they increase transcription.

But the centromeric DNA is constitutively heterochromatic at mitosis. This is an absolute necessity for the kinetochore to form over the centromeric heterochromatin.

we would expect MTHFR to be repressed in mitosis because methylation it isn't needed much during mitosis. The heterochromatin is already formed and the cell is preparing to divide.

To me the interesting point would be
"CDK1/cyclin B phosphorylates and represses MTHFR during mitotic M-phase".

Then If you knock down MTHFR you stuff up methylation. Assayed by expression of centromeric heterochromatin transcripts. This is an expected phenotype.

They also say "decrease of trimethylation of H3K9 (H3K9me3) levels, but not monomethylation of H3K9 (H3K9me1) or dimethylation ofH3K9 (H3K9me2"

However, this is no surprise because H3K9me3 necessarily occurs after H3K9me1 and H3K9me1 methylation, so because H3K9me3 happens last is likely to be the process most affected if you artifically deplete the producer of the substrate (remember its the same substrate for all 3 reactions?).

MAybe MTHFR doe have some specific role in the regulation of H3K9me3 but that isn't adequately demonstrated by this data.

Re "acts upstream of" I don't have an objection to the correctness of the annotation acts_upstream_of histone methylation- but this is a given, so I question its usefulness.

I also don't object to the relationship in principle - I think there are times when it can be useful if we had good guidelines when to use it. I see the value for "acts upstream of" if a connection isn't obvious, for example, if a specific metabolic process provides a substrate for a specific transport pathway, or transport provides a substrate for a specific metabolic pathway in a particular situation.

This example isn't a specific situation though it's a "generalization". My objection in annotating generalizations to "acts upstream of" are related to annotation consistency.

So,

MTHFR is upstream of methylation, and DNA synthesis and pyrimidine synthesis. This isn't a regulation point for methylation (otherwise you would regulate nearly all methylation events occurring in a cell simultaneously). The "purpose" of MTHFR isn't to regulate remodeling chromatin, it is just "required upstream" (if methionine from any other source is absent). Essentially you need methionine to do any methylation. The observations here are a pathological consequence of perturbation. For me, the annotation is more misleading than useful because it implies that MTHFR is somehow regulating chromatin remodelling rather than stuffing it up . If we annotate this, to be consistent we would also need to annotatate THF, methionine synthase etc, etc?

So "acts upsteam of" would be correct but it seems strange to connect these by annotating a single upstream gene product.

Making this annotation would be equivalent to annotating a gene product involved in "DNA replication to "chromosome segregation" with "acts upsteam of" . We don't do that because it's a given. To do this consistently we would be annotating every gene product involved in "DNA replication" acts_upstream_of' "chromosome segregation".

I still believe that the GO annotation isn't a useful place to make these general assertions about relationships between processes. This is because "acts upsteam of" will bring the same problems that we have been dealing with for years with qualifiers. Users will ignore them. Tools will ignore them. Annotation transfer procedures will ignore them. Curators will be unclear how to use them. Usage will never be consistent unless we annotate every upstream gene for a process to a term (I think consistency is my major objection). We could make these connections much more efficiently by connecting processes rather than connecting gene products.

Question: When will we finish annotation "acts upsteam of" everything would be annotated to everything eventually ;)

[ValWood]

so, I would only curate a subset of these as acts upstream of:

I think I would use if it was an immediately upstream process to the one I was annotating, but I haven't yet come across a case where it would be useful, or at least would not cause a headache, for the reasons above. I can imagine it causing bigger problems than the ones it was introduced to solve....

[RLovering]

ok done