Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
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| MTBC0 PGAP re-annotation | toxin-antitoxin system toxin DarT |
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| Revised (this work) | DarT (DarT_Mtb), toxin of the DarTG toxin-antitoxin system: a DNA ADP-ribosyltransferase that sequence-specifically modifies thymidines on single-stranded DNA. Unchecked it blocks replication and is bactericidal; it is neutralised and reversed by the cognate antitoxin DarG (Rv0060). The toxin is dispensable for viability. |
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Curated reference (UniProt)
| UniProt |
O53604
SwissProt · reviewed
· Evidence at protein level
|
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| UniProt name | DNA ADP-ribosyl transferase |
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| EC (curated) |
EC 2.4.2.-
|
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| Curated function | Toxic component of the hybrid type II/IV toxin-antitoxin (TA) system DarTG, which plays a crucial role in controlling bacterial growth and bacteriophage infection. Its toxic effect is neutralized by cognate antitoxin DarG. ADP-ribosylates ssDNA, preferentially in the motif TTTW. In case of phage infection, DarT toxin ADP-ribosylates DNA, which inhibits both viral DNA and RNA synthesis and leads to abortive infection (By similarity). Uncontrolled expression of DarT leads to ADP-ribosylation of the origin of chromosomal replication DNA in cells (in vitro the most heavily modified motifs are TTTT. |
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Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
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| eggNOG description | Domain of unknown function (DUF4433) |
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| Orthologous group | COG4948 |
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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 |
0.397 · purifying
|
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| Polymorphic sites (≥ 0.1% of strains) |
4 synonymous, 5 missense, 0 nonsense, 1 frameshift
|
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| Disruption |
1 distinct premature-stop/frameshift site(s); most common in
0.19% of strains
(283) · clonal
|
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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 |
|---|
DarT | PF14487.13 |
6.6e-61 | 29–230 |
ssDNA thymidine ADP-ribosyltransferase, DarT |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner:
dnaB (replicative DNA helicase),
high confidence from genomic context alone
(score 857 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) |
|---|
Rv0060 darG hyp |
hypothetical protein |
989 |
947 ctx |
neighborhood:763 cooccurence:771 textmining:807 |
Rv0058 dnaB |
replicative DNA helicase |
856 |
857 ctx |
neighborhood:485 coexpression:733 |
Rv0355c PPE8 |
PPE family protein PPE8 |
624 |
625 ctx |
cooccurence:621 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 |
623 |
624 ctx |
cooccurence:623 |
Rv0341 iniB |
isoniazid inducible protein IniB |
622 |
623 ctx |
cooccurence:622 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 |
616 |
617 ctx |
cooccurence:616 |
Rv1525 wbbL2 |
rhamnosyl transferase WbbL |
615 |
615 ctx |
cooccurence:610 |
Rv3347c PPE55 |
PPE family protein PPE55 |
613 |
613 ctx |
cooccurence:611 |
Rv3350c PPE56 |
PPE family protein PPE56 |
610 |
610 ctx |
cooccurence:608 |
Rv1917c PPE34 |
PPE family protein PPE34 |
605 |
606 ctx |
cooccurence:600 |
Rv2209 |
integral membrane protein |
613 |
600 ctx |
cooccurence:598 |
Rv0304c PPE5 |
PPE family protein PPE5 |
589 |
589 ctx |
cooccurence:585 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK |
580 |
581 ctx |
cooccurence:580 |
Rv1004c |
membrane protein |
561 |
561 ctx |
cooccurence:561 |
Rv3343c PPE54 |
PPE family protein PPE54 |
561 |
561 ctx |
cooccurence:557 |
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 toxin DarT'
- Pfam (hmmscan --cut_ga): DarT PF14487 (E=6.6e-61), the DarT/DUF4433 ADP-ribosyltransferase domain
- Operon partner of Rv0060 (DarG, macrodomain) -- a complete DarTG module
ESM Atlas signal (exploratory)
Ancestral protein hash 7f8cb4b7850195d36c7a3c3b2e23ee1c ·
10 ESM-space neighbours (max similarity 0.957).
SAE features are orienting indices, not validated domains.
| # | Index | Activation | Interpretation |
|---|
| 1 | 1600 |
1.21 |
Active site-adjacent loops/hinges |
| 2 | 9906 |
1.03 |
ADP-ribosyltransferase/NADase catalytic core |
| 3 | 8638 |
0.97 |
ART/PARP NAD+-binding catalytic cleft |
| 4 | 12356 |
0.90 |
ADP-ribosyltransferase/NADase catalytic core |
| 5 | 12685 |
0.88 |
ADP-ribosyltransferase catalytic core |
| 6 | 13107 |
0.77 |
Noncatalytic loop-helix caps |
| 7 | 11478 |
0.71 |
Interfacial alpha-helical scaffold signature |
| 8 | 3297 |
0.66 |
ADP-ribose processing active sites |
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_214573.1)
- Domains: Pfam-A via hmmscan --cut_ga — DarT (PF14487.13)
- 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
COG4948
- Curated reference: UniProt
O53604
(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 —
74 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
Ancestral MTBC0 protein sequence
>mtbc0_000064|Rv0059|darT
MITRYKPESGFVARSGGPDRKRPHDWIVWHFTHADNLPGIITAGRLLADSAVTPTTEVAYNPVKELRRHKVVAPDSRYPASMASDHVPFYIAARSPMLYVVCKGHSGYSGGAGPLVHLGVALGDIIDADLTWCASDGNAAASYTKFSRQVDTLGTFVDFDLLCQRQWHNTDDDPNRQSRRAAEILVYGHVPFELVSYVCCYNTETMTRVRTLLDPVGGVRKYVIKPGMYY
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