peptidyl-tRNA hydrolase activity vs aminoacyl-tRNA hydrolase

[ValWood]

peptidyl-tRNA hydrolase activity
Is currently a related synonym of
GO:0004045 aminoacyl-tRNA hydrolase activity
Def: Catalysis of the reaction: N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA

but "peptidyl-tRNA hydrolase activity" is not equivalent to GO:0004045 aminoacyl-tRNA hydrolase activity

I can't find a term to use for "peptidyl-tRNA hydrolase activity"

Background

1. aminoacyl-tRNA hydrolases hydrolyses aminoacyl-tRNA molecules, which are tRNAs that have been charged with an amino acid, removing the amino acid from the tRNA when it is not properly charged or when the tRNA is no longer needed, ensuring that amino acids are not incorrectly incorporated into proteins.

so this also appears to be equivalent to a different GO term "aminoacyl-tRNA editing activity (GO:0002161) (The hydrolysis of an incorrectly aminoacylated tRNA.)

(Although note that there appear to be two main types of editing:
Pre-transfer editing – before the amino acid is transferred to tRNA, often catalysed by aminoacyl-tRNA synthetases.
Post-transfer editing – after the amino acid is attached to tRNA and can involve hydrolysis of misacylated tRNA.)

2. peptide-tRNA hydrolases work with tRNAs that are carrying incomplete or truncated peptides (polypeptides that are not fully synthesized). They hydrolyses the ester bond between a peptide and tRNA in peptidyl-tRNA molecules that have prematurely dissociated from the ribosome releasing the tRNA and the incomplete peptide. This activity helps prevent the accumulation of incomplete proteins that might have resulted from translation errors or premature termination of protein synthesis.
   i.e. Peptidyl-tRNA +H2O → Peptide + tRNA

I have genes described as Peptide-tRNA hydrolase but annotated as
aminoacyl-tRNA hydrolase, which seems a bit misleading.
Are these terms OK to lump?

CC @sjm41 could you advise if you think
a) peptidyl-tRNA hydrolase activity vs aminoacyl-tRNA hydrolase should be independent terms
b) GO:0051499 D-aminoacyl-tRNA deacylase activity should be a child of aminoacyl-tRNA hydrolase

[sjm41]

Hi @ValWood Your original post is a bit hard to follow (!) but I think I get your points.

1. aminoacyl-tRNA hydrolase activity

Here's the current GO term:

id: GO:0004045
name: aminoacyl-tRNA hydrolase activity
namespace: molecular_function
alt_id: GO:0019850
alt_id: GO:0019851
def: "Catalysis of the reaction: N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA." [EC:3.1.1.29]
synonym: "aminoacyl-transfer ribonucleate hydrolase activity" RELATED [EC:3.1.1.29]
synonym: "aminoacyl-tRNA aminoacylhydrolase activity" RELATED [EC:3.1.1.29]
synonym: "aminoacyl-tRNA hydrolase reaction" EXACT []
synonym: "D-tyrosyl-tRNA hydrolase activity" NARROW [PMID:15292242]
synonym: "N-substituted aminoacyl transfer RNA hydrolase activity" RELATED [EC:3.1.1.29]
synonym: "peptidyl-tRNA hydrolase activity" RELATED [EC:3.1.1.29]
xref: EC:3.1.1.29
xref: MetaCyc:AMINOCYL-TRNA-HYDROLASE-RXN
xref: RHEA:54448
is_a: GO:0052689 ! carboxylic ester hydrolase activity
is_a: GO:0140101 ! catalytic activity, acting on a tRNA

Looking at the EC:3.1.1.29 entry:

• accepted name is "peptidyl-tRNA hydrolase"
• def is "an N-acyl-L-alpha-aminoacyl-tRNA + H2O = an N-acyl-L-amino acid + a tRNA + H(+)"
• comment "The enzyme acts on premature protein synthesis products that dissociate from stalled ribosomes, cleaving the peptidyl chains and restoring functionality to the tRNA."
• human proteins with this EC are: PTRH1, PTRH2, PTRHD1, MRPL58

So, here I'd suggest:

• Change GO term name to match EC - "peptidyl-tRNA hydrolase activity"
• Update def to exactly match current EC/RHEA

---

2. aminoacyl-tRNA editing activity & D-aminoacyl-tRNA deacylase activity

Here are the GO terms:

id: GO:0002161 (33 direct EXP annotations)
name: aminoacyl-tRNA editing activity
def: "The hydrolysis of an incorrectly aminoacylated tRNA." [GOC:hjd, PMID:14663147, PMID:16087889]
synonym: "aminoacyl-tRNA hydrolysis activity" RELATED []
is_a: GO:0052689 ! carboxylic ester hydrolase activity
is_a: GO:0140101 ! catalytic activity, acting on a tRNA

id: GO:0051499 (8 EXP annotations to dtd/DTD1 and Dtd2 genes)
name: D-aminoacyl-tRNA deacylase activity
def: "Catalysis of the reaction: a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H+. Removal of a D-amino acid from a charged tRNA." [PMID:14527667, RHEA:13953]
xref: EC:3.1.1.96
xref: MetaCyc:RXN-15041
xref: RHEA:13953 {source="skos:exactMatch"}
is_a: GO:0002161 ! aminoacyl-tRNA editing activity
is_a: GO:0052689 ! carboxylic ester hydrolase activity
is_a: GO:0160215 ! deacylase activity

And the EC:3.1.1.96 entry is:

• accepted name: D-aminoacyl-tRNA deacylase
• def: a D-aminoacyl-tRNA + H2O = a tRNA + a D-alpha-amino acid + H(+) AND glycyl-tRNA(Ala) + H2O = tRNA(Ala) + glycine + H(+) (so it's used for the general case, and the specific glycyl-tRNA(Ala) case)
• comment: The enzyme, found in all domains of life, can cleave mischarged glycyl-tRNA(Ala).

So, as described, I'd say these two terms describe the same thing, except that GO:0051499 is specifying the D-stereoisomer. So, current relations here are OK?

• But maybe 'aminoacyl-tRNA editing activity' would be better named 'aminoacyl-tRNA deacylase activity'?

• Also, remove redundant 'is_a: GO:0052689 ! carboxylic ester hydrolase activity' on GO:0051499

---

3. Looking at the 5 other current children of 'aminoacyl-tRNA editing activity/D-aminoacyl-tRNA deacylase activity'

From a brief review, I'm not sure if we need these specific terms or not - there's some overlap in the annotated genes, but I haven't checked if enzymes are really specific to certain amino acids. (Though I do see that RHEA has a bunch of additional specific reactions that aren't in GO - see 'related reactions on https://www.rhea-db.org/rhea/13953)
If we do keep the specific terms, then there's some xref and naming tasks to do:

id: GO:0043907 (1 EXP annotation to E.coli ybaK)
name: Cys-tRNA(Pro) hydrolase activity
def: "Catalysis of the hydrolysis of misacylated Cys-tRNA(Pro)." [GOC:jl, PMID:15886196]
synonym: "Cys-tRNA(Pro) deacetylase activity" EXACT []
is_a: GO:0002161 ! aminoacyl-tRNA editing activity
property_value: term_tracker_item "#21843" xsd:anyURI

=> this is RHEA:25351/EC:3.6.1.n2: L-cysteinyl-tRNA(Pro) + H2O = tRNA(Pro) + L-cysteine + H(+)

• Add RHEA and EC xrefs, update def to match RHEA, update name to match EC "Cys-tRNA(Pro) deacylase activity"

id: GO:0106105 (5 EXP annotations to 'DTD2' genes)
name: Ala-tRNA(Thr) hydrolase activity
def: "Catalysis of the hydrolysis of misacylated ala-tRNA(thr)." [PMID:29410408]
synonym: "L-alanyl-tRNA(Thr) deacylase" EXACT []
is_a: GO:0002161 ! aminoacyl-tRNA editing activity

=> this is RHEA:17793: L-alanyl-tRNA(Thr) + H2O = tRNA(Thr) + L-alanine + H(+)

• Add RHEA (exact) xrefs, update def to match RHEA, update name to match EC style "Ala-tRNA(Thr) deacylase activity"

id: GO:0106026 (6 EXP annotations to 'DTD/dtd1' genes)
name: Gly-tRNA(Ala) hydrolase activity
def: "Catalysis of the hydrolysis of misacylated Gly-tRNA(Ala)." [PMID:28362257]
is_a: GO:0002161 ! aminoacyl-tRNA editing activity

=> this is RHEA:53744/EC:3.1.1.96: glycyl-tRNA(Ala) + H2O = tRNA(Ala) + glycine + H(+)

• Add RHEA (exact) and EC (broad) xrefs, update def to match RHEA, update name to match EC style "Gly-tRNA(Ala) deacylase activity"

id: GO:0002196 (11 EXP annotations to mouse Aars1, E.coli proXp-y & alaS, yeast YNL040W)
name: Ser-tRNA(Ala) hydrolase activity
def: "Catalysis of the hydrolysis of misacylated Ser-tRNA(Ala)." [GOC:hjd, PMID:21285375]
is_a: GO:0002161 ! aminoacyl-tRNA editing activity

=> I can't easily find a RHEA for this; unclear whether it refers to L/D-Ser, so leave relations alone

• rename to "Ser-tRNA(Ala) deacylase activity"

id: GO:0043906 (6 EXP annotations to to E.coli ybaK and other bacterial genes)
name: Ala-tRNA(Pro) hydrolase activity
def: "Catalysis of the hydrolysis of misacylated Ala-tRNA(Pro)." [GOC:jl, PMID:14663147]
is_a: GO:0002161 ! aminoacyl-tRNA editing activity
property_value: term_tracker_item "#21843" xsd:anyURI

=> I can't easily find a RHEA for this; unclear whether it refers to L/D-Ala, so leave relations alone

• rename to "Ala-tRNA(Pro) deacylase activity"

[pgaudet]

GO:0002196 (11 EXP annotations to mouse Aars1, E.coli proXp-y & alaS, yeast YNL040W)
name: Ser-tRNA(Ala) hydrolase activity

Could this be RHEA:74215 ? (from P64483 · PROXY_ECOLI)

More recent review: PMID:34995670 - could add to all the terms.

---

GO:0043906 (6 EXP annotations to to E.coli ybaK and other bacterial genes)
name: Ala-tRNA(Pro) hydrolase activity

Request a new RHEA?

[sjm41]

GO:0002196 (11 EXP annotations to mouse Aars1, E.coli proXp-y & alaS, yeast YNL040W)
name: Ser-tRNA(Ala) hydrolase activity

Could this be RHEA:74215 ? (from P64483 · PROXY_ECOLI

I fear not - RHEA:74215 is for L-seryl-tRNA(Lys) whereas GO:0002196 is for L-seryl-tRNA(Ala)

[ValWood]

I also see that some genes are annotated with both

This is fission yeast pth4 and it has these 2 PAINT mappings
GO:0004045 | aminoacyl-tRNA hydrolase activity | IBA with Q8IIJ1 , PTN008511941 , Q14197 , S000005474
and
GO:0016150 | translation release factor activity, codon nonspecific | IBA with Q14197 , PTN008511941

translation release factors are peptidyl tRNA hydrolases.

So the peptidyl tRNA hydrolases occur in 2 contexts
translation termination AND premature termination (which I guess is the translation fidelity).
In the final organization, the parentage for the peptidyl tRNA hydrolases should be general enough to cover both of these contexts.

[raymond91125]

@ValWood Not sure what to do. GO:0016150 | translation release factor activity, codon nonspecific has an ISBN source that I can't check. But the definition reads like the UniProt description for prfC https://www.uniprot.org/uniprotkb/P0A7I4/entry.
I'm not sure why MRPL58 is annotated here.
The two GO terms are quite far apart.

[ValWood]

So, 'translation factors' are a bit weird. They group many different functions, and because we do not have specific terms for every type of translation factor activity, we sometimes need to co-annotate. This is what we are seeing here.

If I understood correctly, aminoacyl-tRNA hydrolase will be renamed to peptidyl-tRNA hydrolase.
This comment was just a heads-up that the peptidyl-tRNA hydrolase definition will need to cover:

1. peptide-tRNA hydrolases work with tRNAs that are carrying incomplete or truncated peptides (polypeptides that are not fully synthesized). They hydrolyses the ester bond between a peptide and tRNA in peptidyl-tRNA molecules that have prematurely dissociated from the ribosome releasing the tRNA and the incomplete peptide. This activity helps prevent the accumulation of incomplete proteins that might have resulted from translation errors or premature termination of protein synthesis.
   AND
2. translation release factors.

This will affect the links that can be made to biological processes (i.e they will not all be "regulation of translational fidelity")

Note: "regulation of translational fidelity" is a terrible term, anyway. It shouldn't be a regulation term. It should be some sort of quality control probably