Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|
| MTBC0 PGAP re-annotation | toxin-antitoxin system antitoxin DNA ADP-ribosyl glycohydrolase DarG |
|---|
| Revised (this work) | DarG (DarG_Mtb), antitoxin of the DarTG system: a macrodomain DNA ADP-ribosyl-glycohydrolase that removes the ADP-ribose mark deposited on DNA by the toxin DarT (Rv0059) and binds/neutralises it. In M. tuberculosis DarG is essential; its depletion triggers the DNA-damage response and cell death. |
|---|
Curated reference (UniProt)
| UniProt |
O53605
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | DNA ADP-ribosyl glycohydrolase |
|---|
| EC (curated) |
EC 3.2.2.-
|
|---|
| Curated function | Antitoxin component of the hybrid type II/IV toxin-antitoxin (TA) system DarTG, which plays a crucial role in controlling bacterial growth and bacteriophage infection. Keeps the toxin molecules in check under normal growth conditions. De-ADP-ribosylates DNA (probably) modified on thymidine by its cognate toxin DarT, which neutralizes the activity of DarT. Experiments in which DarG levels are depleted lead to cell death; expression of wild-type DarG protein from M.tuberculosis or T.aquaticus restores growth. Cells depleted of DarG are more sensitive to bedaquilline (targets respiration), DNA-da. |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|
| eggNOG description | Macro domain |
|---|
| Orthologous group | COG2110 |
|---|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are
computed annotations, not manual curation; cross-check against the primary literature
before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS |
0.165 · strong purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
4 synonymous, 2 missense, 0 nonsense, 0 frameshift
|
|---|
pN/pS from segregating SNPs (singletons removed) normalised by possible sites.
Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene).
A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic
variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A
clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a
convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|
Macro | PF01661.28 |
5.8e-26 | 18–130 |
Macro domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner:
dnaB (replicative DNA helicase),
medium confidence from genomic context alone
(score 531 excluding text-mining).
This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv0059 darT hyp |
hypothetical protein |
989 |
947 ctx |
neighborhood:763 cooccurence:771 textmining:807 |
Rv0058 dnaB |
replicative DNA helicase |
530 |
531 ctx |
neighborhood:463 |
Rv0056 rplI |
50S ribosomal protein L9 |
477 |
478 ctx |
neighborhood:408 |
Rv0057 hyp |
hypothetical protein |
463 |
464 ctx |
neighborhood:450 |
Rv2972c hyp |
hypothetical protein |
423 |
420 |
|
Rv1151c cobB |
NAD-dependent protein deacylase |
435 |
410 |
|
Rv1045 hyp |
hypothetical protein |
508 |
164 |
textmining:436 |
Rv2368c phoH1 |
phosphate starvation-inducible protein PhoH |
810 |
57 |
textmining:807 |
Rv0272c hyp |
hypothetical protein |
804 |
50 |
textmining:803 |
Rv0909 |
antitoxin |
532 |
47 |
textmining:529 |
Rv1546 hyp |
hypothetical protein |
527 |
47 |
textmining:525 |
Rv1545 hyp |
hypothetical protein |
515 |
47 |
textmining:512 |
Rv0836c hyp |
hypothetical protein |
436 |
45 |
textmining:434 |
Rv1989c mbcT hyp |
hypothetical protein |
660 |
44 |
textmining:659 |
Rv0837c hyp |
hypothetical protein |
516 |
44 |
textmining:515 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression,
experimental, database, text-mining) into a 0–1000 score. The ctx
badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion,
phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an
unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not
depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with
the operon context and the primary literature before assigning a function.
Evidence
- MTBC0 PGAP product: 'toxin-antitoxin system antitoxin DNA ADP-ribosyl glycohydrolase DarG'
- Pfam (hmmscan --cut_ga): Macro PF01661 (E=5.8e-26), an ADP-ribose-binding / hydrolase macrodomain
- Cognate antitoxin of Rv0059 (DarT); essential gene in M. tuberculosis
ESM Atlas signal (exploratory)
Ancestral protein hash c1dd089f1dcaf594f1fd0e9301281d44 ·
9 ESM-space neighbours (max similarity 0.859).
SAE features are orienting indices, not validated domains.
| # | Index | Activation | Interpretation |
|---|
| 1 | 1227 |
1.16 |
Macrodomain ADP-ribose recognition |
| 2 | 12615 |
1.06 |
Domain-edge interaction hotspots |
| 3 | 15026 |
0.90 |
Nucleotide phosphate cofactor recognition |
| 4 | 10450 |
0.90 |
Aromatic/Gly-rich core scaffold |
| 5 | 3068 |
0.86 |
Divalent-metal hydrolase and ADP-ribose folds |
| 6 | 15650 |
0.78 |
Mixed-charge amphipathic interaction helix |
| 7 | 4753 |
0.77 |
C-terminal region detector |
| 8 | 2443 |
0.61 |
Glycine aromatic clamp loops |
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024),
An imputed ancestral reference genome for the MTBC,
doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_214574.1)
- Domains: Pfam-A via hmmscan --cut_ga — Macro (PF01661.28)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG2110
- Curated reference: UniProt
O53605
(SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of
145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
23 functional partner(s); context anchor
dnaB
- Primary literature: Jankevicius G, Ariza A, Ahel M, Ahel I (2016). The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA Molecular Cell.
doi:10.1016/j.molcel.2016.11.014 PMID:27939941
- Primary literature: (2020). Depletion of the DarG antitoxin in Mycobacterium tuberculosis triggers the DNA-damage response and leads to cell death Molecular Microbiology.
doi:10.1111/mmi.14571 PMID:32634279
Ancestral MTBC0 protein sequence
>mtbc0_000065|Rv0060|darG
MITYGSGDLLRADTEALVNTVNCVGVMGKGIALQFKRRYPEMFTAYEKACKRGEVTIGKMFVVDTGQLDGPKHIINFPTKKHWRAPSKLAYIDAGLIDLIRVIRELNIASVAVPPLGVGNGGLDWEDVEQRLVSAFQQLPDVDAVIYPPSGGSRAIEGVEGLRMTWGRAVILEAMRRYLQQRRAMEPWEDPAGISHLEIQKLMYFANEADPDLALDFTPGRYGPYSERVRHLLQGMEGAFTVGLGDGTARVLANQPISLTTKGTDAITDYLATDAAADRVSAAVDTVLRVIEGFEGPYGVELLASTHWVATREGAKEPATAAAAVRKWTKRKGRIYSDDRIGVALDRILMTA
Spot an error? Suggest an improvement