Some histone deacetylases are hydrolases, some are transferases

[pgaudet]

Protein deacetylases were classified as hydrolases. However, as pointed out by @kaxelsen in #22833, not all protein deacetylases are hydrolases; the NAD-dependent are transferases.

This is a nice review that explains the catalytic mechanism of histone deacetylases:

https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC3970420/

Class I, II and IV are zinc-dependent (hydrolase), while class III is NAD-dependent (ie transferases)

[pgaudet]

• [x] GO:0042903 'tubulin deacetylase activity': Add missing xref RHEA:21548

[pgaudet]

• [x] GO:0019213 deacetylase activity : change parent from 'hydrolase activity' to 'catalytic activity'. Most children are also classified as hydrolases; a couple need to be reviewed
• [x] protein lysine acetlyase activity: change def from "Catalysis of the reaction: H2O + N6-acetyl-L-lysyl-[protein] = acetate + L-lysyl-[protein]." to "Catalysis of the removal of an acetyl group from a lysine residue in a protein."
• [x] GO:0004407 'histone deacetylase activity': remove parent ''hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides''(since children are both hydrolases and transferases)

[pgaudet]

• [ ] GO:0033558 protein deacetylase activity should be obsoleted: it is used to mostly to annotate HDACs, both hydrolases (Class I, II, IV) and transferases (class III) (or made 'do not annotate')

[pgaudet]

If we are to represent the mechanisms of the HDACs, we would need to obsolete all 'grouping' classes:

• GO:0031078 histone deacetylase activity (H3-K14 specific)
• GO:1990162 histone deacetylase activity (H3-K4 specific)
• GO:0032129 histone deacetylase activity (H3-K9 specific)
• GO:0034739 histone deacetylase activity (H4-K16 specific) and create 'zinc-specific hydrolases'. The problem is that the grouping terms mix both hydrolases and transferases.

Alternatively, we can drop the mechanism and merge for example GO:0032041 NAD-dependent histone deacetylase activity (H3-K14 specific) into GO:0031078 histone deacetylase activity (H3-K14 specific), and keep these under 'protein deacetylase activity', that would just be a 'catalytic activity, acting on proteins', and not have and enzyme class.

@cmungall @hdrabkin @ValWood @sjm41 @colinlog do you have preferences one way or the other?

Thanks, Pascale

[hdrabkin]

I would be in favor of making two parents one specifying hydrolysis, the other specifying NAD perhaps naming like histone deacetylase (hydrolytic) activity histone deacetylase (transfer) activity

I see RHEA has the hydrolysis one for EC: 3.5.1.98;

[ValWood]

Generally, I am not interested in mechanism so much, but I guess if they are totally different enzyme classes, then it is useful. Naive question, how can a histone deacetylase be a transferase? (and specifically which ones fall into this class). Currently histone deacetylase is under hydrolase.

(I think there are two mechanisms for histone demethylation, but neither of those is. a transferase)

[ValWood]

right it's class 3 above (i'm new to this ticket!)

[hdrabkin]

Yes in this case the mechanisms are quite different; in both cases, the acetyl group is removed from the protein (hence the name). The 'transferase' isn't using water to hydrolyze the bond between the acetyl group and the lysine on the protein I believe. (see fig 5 in the article).

[sjm41]

I agree with @hdrabkin, having two separate parent terms to group the two mechanisms.

But maybe we don't need to make new terms - do these existing terms map to the hydrolytic and transferase mechanisms?:

id: GO:0017136 name: NAD-dependent histone deacetylase activity def: "Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from a histone." [PMID:28450737] synonym: "SIR2" RELATED []

id: GO:0045129 name: NAD-independent histone deacetylase activity def: "Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction does not require the presence of NAD, and represents the removal of an acetyl group from a histone." [PMID:28450737] synonym: "AcuC" RELATED []

Both could be children of "catalytic activity -> deacetylase activity -> protein deacetylase activity (if kept) -> histone deacetylase activity". And each would also have the appropriate parentage to 'transferase activity' and 'hydrolase activity'.

[colinlog]

Yes, that sounds right @sjm41 and if the EC classes are associated with each then we are done here with the catalytic MF parts once we make an overarching MF 'do-not-annotate-to' parent that is histone deacylases''' with these two terms as its MF children with the respective EC numbers.

I would argue that the specific histone residues connect to specific 'BPs' that will require the above MFs but only work under certain circumstances (eg; chromatin assembly involves H4K5 and H4K12 acetylation in the cytoplasm, followed by their deacetylation after nucleosome assembly in a replication-coupled chromatin maturation pathway, while H4K8 and K16 acetylation/deacetylation controls gene expression and higher order folding of polynucleosomal fibres).

I am not a fan of the 'independent' label , however, as this is in fact a negative definition. That class can be positively identified as being 'Zn-dependent' and corresponds to three of the 4 phylogenetic HDAC classes (I, II and IV -- the hydrolases).

Of note, some of these enzymes (for sure in classes I and III) may be involved in removing larger groups than acetates from histone lysines such as succinyl, crotonyl, malonyl and glutaryl modifications. (see PMID: 30940741 and 30391813). Furthermore, one of the Zn-dependent HDACs, HDAC3, appears to be stimulated by D-myo-inositol-(1,4,5,6)-tetrakisphosphate (Ins(1,4,5,6)P4).

The field is therefore moving towards calling both the NAD-dep and indep enzymes deacylases rather than deacetylases...

Last thing: the histones are not their unique targets, tubulin as noted by pascale (for HDAC6?) and many dbTFs and coTF are ac(et)ylated and deac(et)ylated. However the classifications based on their activity on the histone types and residues is very likely to be leading for the other substrate classifications and associated BPs.

[pgaudet]

@sjm41

do these existing terms map to the hydrolytic and transferase mechanisms?:

Not really, since the NAD is a child of the non-NAD, and more importantly, the non-NAD has annotations for proteins that belong in both groups.

[pgaudet]

According to wikipedia https://en.wiktionary.org/wiki/deacylase removes an acyl group by hydrolysis

But we can decide that we define it differently...

[pgaudet]

@ValWood

Naive question, how can a histone deacetylase be a transferase?

The acyl group is transferred, rather than just removed, so products are [protein]-L-lysine + 2''-O-acetyl-ADP-D-ribose + nicotinamide rather than acetate + L-lysyl-[histone] for hydrolases

[colinlog]

Absolutely let's do it right. Wikipedia follows the literature and GO knowledge, not the opposite, even though it is a fantastic and immensely broad encyclopedic community-generated knowledge resource.

It has been known for > 20 years that there are sirtuin-type (NAD-dependent) histone deacetylases; eg1 H3K56ac is deacetylated by Hst3 and Hst4 sirtuins in S.c,, eg2 H3K9ac is deacetylated by Sir2 at the S.c subtelomeric regions to enable Sir3+Sir4 - mediated heterochromatin formation and there are the Zn-dependent deacetylases that can remove also H3K9ac (but not H3K56ac).

Enzymatically, the NAD-dependent mechanism is different (transferase). But still functionally they are protein lysine deacetylases, as Val just pointed- out.

[kaxelsen]

The reaction in this GO term is wrong!

id: GO:0017136 name: NAD-dependent histone deacetylase activity def: "Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from a histone." [PMID:28450737] synonym: "SIR2" RELATED []

It should be: "Catalysis of the reaction: N6-acetyl-L-lysyl-[protein] + NAD+ + H2O = 2''-O-acetyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide" (RHEA:43636).

The old reaction above IS a hydrolylsis reaction. The new reaction I have just added is the transfer reaction. The lysyl group is transferred to half of a NAD+ molecule (ADP-D-ribose). The rest of the NAD+ molecule is liberated as nicotinamide. That the reaction is NAD-dependent does in this case mean that NAD+ is part of the reaction.

[ValWood]

Aligning GO with Rhea is the best thing ever!

I think we should definitely have both the histone acetyltransferase grouping and then the transferase/acetyltransferase grouping for the subtypes. Apart from being explicit and correct, if we do not do this we will spend the next decade trying to explain to function prediction pipelines why the sirtuins are not hydrolases.

[sjm41]

And RHEA:43636 = EC:2.3.1.286 (Protein acetyllysine N-acetyltransferase)

[sjm41]

We should try to finish this one.

[pgaudet]

Dear all,

The proposal has been made to obsolete GO:0045129 NAD-independent histone deacetylase activity. The reason for obsoletion is that this represents the same activity as GO:0004407 histone deacetylase activity (now renamed: GO:0004407 histone deacetylase activity, hydrolytic mechanism). There are 7 annotations: 1 ComplexPortal, 1 SGD, 5 FlyBase, see https://github.com/geneontology/go-annotation/issues/5453

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/22836

Thanks, Pascale

[pgaudet]

@sjm41 I changed the label of

GO:0004407 'histone deacetylase activity' to 'histone deacetylase activity, hydrolytic mechanism', and added comment:

+comment: Histone deacytylase (HDAC) enzymes are divided into four classes: the Class I Rpd3-like proteins (in human: HDAC1, HDAC2, HDAC3, and HDAC8); the Class II Hda1-like proteins (in human: HDAC4, HDAC5, HDAC6, HDAC7, HDAC9, and HDAC10); the Class III Sir2-like proteins (in human: SIRT1, SIRT2, SIRT3, SIRT4, SIRT5, SIRT6, and SIRT7); and the Class IV protein (HDAC11 in human). Except for Class III enzymes, the mechanism is a metal-dependent hydrolysis of the acetylated substrate. The Class III HDACs use NAD+ as a reactant to deacetylate acetyl lysine residues of protein substrates forming nicotinamide, the deacetylated product, and the metabolite 2′-O-acetyl-ADP-ribose. Therefore, Class III are classified as transferases (EC:2) and others are hydrolases (EC:3).

to this term and the other general grouping term NAD-dependent histone lysine deacetylase activity

Current structure is:

but I think I need to add 'hydrolytic mechanism' to the terms highlighted below

and create a mechanism-neutral parent for H3K deacetylase activity and H4K deacetylase activity.

What do you think ?

[pgaudet]

Created new grouping term: +[Term] +id: GO:0141221 +name: histone deacetylase activity, hydrolytic mechanism +namespace: molecular_function +def: "Catalysis of the reaction: H2O + N6-acetyl-L-lysyl-[histone] = acetate + L-lysyl-[histone]." [PMID:24691964, PMID:28450737] +comment: Histone deacytylase (HDAC) enzymes are divided into four classes: the Class I Rpd3-like proteins (in human: HDAC1, HDAC2, HDAC3, and HDAC8); the Class II Hda1-like proteins (in human: HDAC4, HDAC5, HDAC6, HDAC7, HDAC9, and HDAC10); the Class III Sir2-like proteins (in human: SIRT1, SIRT2, SIRT3, SIRT4, SIRT5, SIRT6, and SIRT7); and the Class IV protein (HDAC11 in human). Except for Class III enzymes, the mechanism is a metal-dependent hydrolysis of the acetylated substrate. The Class III HDACs use NAD+ as a reactant to deacetylate acetyl lysine residues of protein substrates forming nicotinamide, the deacetylated product, and the metabolite 2′-O-acetyl-ADP-ribose. Therefore, Class III are classified as transferases (EC:2) and others are hydrolases (EC:3). +synonym: "histone deacetylase activity" BROAD [] +synonym: "histone deacetylase activity, NAD-independent" EXACT [] +xref: EC:3.5.1.98 {source="skos:exactMatch"} +is_a: GO:0004407 ! histone deacetylase activity

[pgaudet]

So it now looks like this:

and unfolded view:

[sjm41]

Hi, I'll take a look at the changes now and get back to you

Though I noticed an issue with RHEA:43636/EC:2.3.1.286 on these two terms:

id: GO:0034979 name: NAD-dependent protein lysine deacetylase activity namespace: molecular_function def: "Catalysis of the reaction: N(6)-acetyl-L-lysyl-[protein] + NAD+ + H2O = L-lysyl-[protein] + 2''-O-acetyl-ADP-D-ribose + nicotinamide." [GOC:BHF, GOC:mah, RHEA:43636] synonym: "NAD(+)-dependent protein deacetylase" BROAD [] synonym: "NAD-dependent protein deacetylase activity" BROAD [] synonym: "protein acetyllysine N-acetyltransferase" BROAD [] synonym: "protein lysine deacetylase" BROAD [] xref: RHEA:43636 is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups is_a: GO:0033558 ! protein lysine deacetylase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22295" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27528" xsd:anyURI

id: GO:0017136 name: NAD-dependent histone deacetylase activity namespace: molecular_function def: "Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from a histone." [PMID:28450737] synonym: "SIR2" RELATED [] xref: EC:2.3.1.286 is_a: GO:0004407 ! histone deacetylase activity is_a: GO:0034979 ! NAD-dependent protein lysine deacetylase activity

RHEA:43636/EC:2.3.1.286 refer to the same reaction, so both should be xrefs on GO:0034979 only? (maybe you've already fixed this)

[pgaudet]

@sjm41 EC:2.3.1.286 is a broad xref on GO:0017136; (and all its childre) otherwise that term has no dbxref.

Isn't that what we agreed on ?

[pgaudet]

Note that I also added

+xref: EC:2.3.1.- {source="skos:broadMatch"} +xref: EC:3.5.1.- {source="skos:broadMatch"}

on

• GO:0004407 histone deacetylase activity
• GO:0141050 histone H3K deacetylase activity
• GO:0141051 histone H4K deacetylase activity

to make sure these terms have dbxrefs.

[sjm41]

EC:2.3.1.286 is a broad xref on GO:0017136; (and all its childre) otherwise that term has no dbxref.

Yes, that's fine. My main point was that both RHEA:43636/EC:2.3.1.286 should be (exactMatch) xrefs on GO:0034979, and I see from the latest go-edit-obo that that is now true, so that's all good!

Only issue I see with the new tree/terms is that "GO:0141221 histone deacetylase activity, hydrolytic mechanism" appears to lack parentage to 'hydrolase activity':

[pgaudet]

Thanks @sjm41 ! I've added the parent GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides

Pascale

[ValWood]

I'm a bit confused. Some of my annotations have changed in an unexpected way.

sirtuins, which are NAD dependent have become annotated as GO:1990162 histone H3K4 deacetylase activity, hydrolytic mechanism because histone deacetylase activity (H3-K4 specific) is now called GO:1990162 histone H3K4 deacetylase activity, hydrolytic mechanism

so sir2 now has a mixture of NAD-dependent and hydrolytic https://www.pombase.org/gene/SPBC16D10.07c but should these be mutually exclusive?

[pgaudet]

I see. The reason why I just renamed the term is because it fitted the definition:

Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 4) + H2O = histone H3 L-lysine (position 4) + acetate.

(still hasn't been changed in AmiGO, see below):

Should I have obsoleted? (I must say, since the meaning of the term didn't change, I thought I could just go ahead).

Thanks, Pascale

[ValWood]

Ah, so in that case, I must have used the wrong term based on the definition? I'm not completely sure why it was wrong so maybe obsoletion would be better. I wonder if other groups now have misannotations from using these terms?

[ValWood]

I think quite a lot of people must have used these incorrectly (because there was only one term for the particular modification, we used it as if it was a parent without requesting NAD-dependent term)

For example GO:0031078 JSON histone H3K14 deacetylase activity, hydrolytic mechanism

has the following intersections

(I didn't look at the other terms but I suspect they will be similar?) I think obsoletion would probably be cleaner here but if not it will be a lot of reannotation.

[ValWood]

fixed the link in the comment above.

I guess most people didn't realise that NAD-dependent and NAD-independent were different mechanisms (I didn't)

[pgaudet]

You're making it look very scary ;) If I limit for EXP, I get this: https://www.ebi.ac.uk/QuickGO/annotations?goUsage=descendants&goUsageRelationships=is_a,part_of,occurs_in&goId=GO:0031078&evidenceCode=ECO:0000269&evidenceCodeUsage=descendants There is only the one Sir2, all others are hydrolases

[ValWood]

OK! we can reannotate the sirtuins. @pcarme could you read the thread and update our Sirtuin annotations from the hydrolytic terms to the appropriate NAD-dependent term.

[PCarme]

HI all ! There is no existing NAD-dependent term for H3K4 deacetylase activity, only the hydrolytic equivalent, is it normal ?

[ValWood]

Hi @PCarme I think it is just an oversight. Can you request the ones we are missing in a new term ticket? tks v

[PCarme]

OK! we can reannotate the sirtuins. @PCarme could you read the thread and update our Sirtuin annotations from the hydrolytic terms to the appropriate NAD-dependent term.

That's done now.

[pgaudet]

Great ! Thanks both